Methods for analysis of network metagene expression for cancer target discovery and prediction of drug resistance

Abstract

Compositions, methods, and kits are provided for detecting pre-malignant and cancerous cells having lineage plasticity and drug resistance. Also provided are methods of screening candidate agents for efficacy in switching pre-malignant or cancerous cells, identified as being in a cell state having lineage plasticity and drug resistance, to a non-drug resistant proliferative cell state that can be treated with anti-mitotic therapeutic agents.

Description

METHODS FOR ANALYSIS OF NETWORK METAGENE EXPRESSION FOR CANCER TARGET DISCOVERY AND PREDICTION OF DRUG RESISTANCECROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims benefit of U.S. Provisional Patent Application No. 63 / 654,829, filed May 31 , 2024, which application is incorporated herein by reference in its entirety.STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

[0002] This invention was made with government support under R01 CA184510, U01 CA176287, and R35 CA210018 awarded by the National Institutes of Health. The government has certain rights in the invention.BACKGROUND OF THE INVENTION

[0003] Human tumors arise as a consequence of exposure to environmental agents, including mutagens and tumor-promoting chemicals, but cancer incidence is also heavily influenced by complex genetic and lifestyle factors. The development of phenotypic plasticity is a common, and likely universal, feature of cancer development recently recognized as an emerging cancer hallmark (D. Hanahan, Hallmarks of Cancer: New Dimensions. Cancer Discov 12, 31 -46 (2022)). The mechanistic basis for this plasticity, defined as the redeployment of lineage-specific gene expression programs along alternative cell fate trajectories, is presently unclear (Feinberg, A. Levchenko, Epigenetics as a mediator of plasticity in cancer. Science 379, 1-11 (2023)). Elucidation of this process has major practical implications for understanding and treatment of cancer, since cell plasticity has been associated with invasion, metastasis, and resistance to chemotherapy or targeted drugs (A. K. Singh, R. K. Arya, S. Maheshwari, A. Singh, S. Meena, P. Pandey, O. Dormond, D. Datta, Tumor heterogeneity and cancer stem cell paradigm: Updates in concept, controversies and clinical relevance. Int J Cancer 13, 1991 -2000 (2015); T. Wang, S. Shigdar, M. P. Gantier, Y. Hou, L. Wang, Y. Li, H. Al Shamaileh, W. Yin, S. F. Zhou, X. Zhao, W. Duan, Cancer stem cell targeted therapy: Progress amid controversies. Oncotarget 6, 44191 (2015); L. T. H. Phi, I. N. Sari, Y. G. Yang, S. H. Lee, N. Jun, K. S. Kim, Y. K. Lee, H. Y. Kwon, Cancer stem cells (CSCs) in drug resistance and their therapeutic implications in cancer treatment. Stem Cells Int, doi: 10.1155 / 2018 / 5416923 (2018)). Tumor cell plasticity has been attributed to the existence of cancer stem cells (CSCs), but there is presently no consensus as to how CSCs relate to their normal tissue counterparts, to the cells of origin of tumors, or even whether they exist (C. T. Jordan, Cancer Stem Cells: Controversial or Just Misunderstood? Cell Stem Cell 4, 203-205 (2009); T. Reya, S. J. Morrison, M. F. Clarke, I. L. Weissman, Stem cells, cancer, and cancer stem cells. Nature 414, 105-111 (2001 )). Different models suggest that CSCsmay lie within a hierarchy of differentiation within tumors (J. Perez-Losada, A. Balmain, Stem-cell hierarchy in skin cancer. Nat Rev Cancer 3, 434-443 (2003); B. Beck, C. Blanpain, Unravelling cancer stem cell potential. Nat Rev Cancer 13, 727-738 (2013)) or they may show complete plasticity, being essentially interconvertible (M. Schober, E. Fuchs, Tumor-initiating stem cells of squamous cell carcinomas and their control by TGF-p and integrin / focal adhesion kinase (FAK) signaling. Proc Natl Acad Sci U S A 108, 10544-10549 (201 1 )).SUMMARY OF THE INVENTION

[0004] Compositions, methods, and kits are provided for detecting pre-malignant and cancerous cells having lineage plasticity and drug resistance. Also provided are methods of screening candidate agents for efficacy in switching pre-malignant or cancerous cells, identified as being in a cell state having lineage plasticity and drug resistance, to a non-drug resistant proliferative cell state that can be treated with anti-mitotic therapeutic agents.

[0005] In one aspect, a cell is provided, the cell comprising: a first lineage tracing reporter gene operably linked to a promoter of a first gene whose expression is positively correlated with a stem cell plasticity state, wherein expression of the first lineage tracing reporter gene coincides with the expression of the first gene; and a second lineage tracing reporter gene operably linked to a promoter of a second gene whose expression is positively correlated with a proliferative state, wherein expression of the second lineage tracing reporter gene coincides with the expression of the second gene.

[0006] In certain embodiments, the first gene is selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Prom1 metagene, and a Prom2 metagene; and the second gene is selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene.

[0007] In certain embodiments, the Sox2 metagene comprises genes selected from Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, Mtrnrl O, Esd, Sox13, Nfe2l2, Pls1 , Tom1 l2, Bink, Suox, Sid 6a11 , Xrcc5, Chst15, Krt12, Eval c, Nppc, Esd, Ddx59, Nop2, Krt13, Plekhh3, Osbpl6, Aldh5a1 , Cirhl a, Wnk4, Arntl2, Fam110c, Tmem180, Dili , Galnt12, Pitxl , Caleb, Ankrd9, Isl1 , Btc, Gss, Ociad2, Klra33, Aldh3a1 , Minkl , Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl , Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrl a, Pthlh, Usp6nl, Ufspl , Irgq, Nkiras2, Grtpl , Nqo1 , Krt20, Snord42b, Avpil , Ifrdl , Srd5a2, Cpn1 , Bail , Sprr3, Rap1gap2, Rassf7, Fetub, Ramp3, Arl4d, Tle1 , Krt76, Ptprzl , Pradd , Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl , G6pdx, Tsg101 , Nmrkl , Ralgapb, A430105119Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik.

[0008] In certain embodiments, the Foxal metagene comprises genes selected from Foxal, Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1, Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1, Tjp3, Plekhg6, Bspry, Ocln, Ceacaml, Marveld3, Cldn3, Mal2, Tmem30b, Sowahb, Spns2, Slc9a3r1, Kctdl, Cwh43, Cystml, Rab17, S100a2, Ppbp, Padil, Caleb, Gstol, S100a16, Spint2, Slc52a3, Sid 6a11 , Crispl, Mall, Aldh1a3, Entpd3, Tmprss11g, Anxal, Pgapl, Prss22, Kif21 a, Omp, Liph, Epb4.1l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, ArhgeflOl, Tmprss11d, Mxd1, Elf5, Acss2, Leprell, Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppf i bp2 , Mboatl , Zdhhd 3, Dgka, Ehf , Mst1 , St 14, Ap1 s3, Malt 1 , Spintl , Sprr3, Pllp, AA986860, Prss27, Tmprssl 1a, Serpinb11 , Hs3st1, StardlO, Arhgap40, lldrl, Ppi, Fbp2, Cnksrl, Map7, and 1700001 C19Rik, E330009J07Rik.

[0009] In certain embodiments, the Krt15 metagene comprises genes selected from Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrd , Zfp750, Lipm, Ocln, Paqr5, Grhll, Erbb3, PsapH , Aldh3b2, Ppi, RapgefH, Aldh3b2, Efna3, Mud 5, Liph, 2610528A11 Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1pr5, Klhl29, 4833423E24Rik, Nccrpl, Slc27a4, Barx2, Aimll, Wnt4, L1cam, Leprell, Rnf43, Ckmtl, Lipk, Mapk13, Il22ra1, Zfp185, Cds1, Arhgap40, Krt80, Dsc3, Prss8, Fgfr3, Hsd17b2, Padil, Ripk4, Prom2, Adtrp, Caszl, 1700055N04Rik, Scnnla, Ptprf, ArhgeflOl, Tmprssl 1e, Slc25a48, Mall, Mst1, Crnn, Celsrl , Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinb11, Vsnll, Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprss13, Sowahb, Celsr2, Ly6g6e, SytH, Tprg, AA986860, and Sptbn2.

[0010] In certain embodiments, the Krt19 metagene comprises genes selected from Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal , Mall, Slc37a1 , Cblc, Marveld3, Marveld2, Gstol, Ceacaml, Gm9573, Ocln, Slc9a3r1, Mal2, Tmprssl 1g, Spns2, Anxal, 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, ArhgeflOl, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, Upk3bl, Gsta4, Ppbp, Tmprssl 1d, Spintl, Tmem30b, S100a2, Pgapl, Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1, Kif21 a, Krt13, Padil, Tmprssl 1 bnl, Foxql, S100a16, L1cam, Seel, Ehf, SamdIO, Epb4.115, Rab27b, Plekha7, Llgl2, Erbb2, Stap2, Rab25, Hebp2, Cnksrl, 1117re, Pllp, Cystml, Tnk1, Mboatl, Tmprss11e, Tacstd2, Plekha6, Arg1, Ltf, Evpl, S100a14, Plekhhl , Slc25a48, Ap1s3, Zdhhd 3, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl, Ppfibp2, Nipal2, Rab27a, Rbm47, and StardlO.

[0011] In certain embodiments, the Pitxl metagene comprises genes selected from Pitxl , Cldn8, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1, Klf5, Cep170b,Llgl2, 1700001 C19Rik, Tmprssl 1d, Dsc2, Fam160a1, Erbb2, Gsta4, Shb, Duoxal, Rab27b, Barx2, Fhdd, Tmprssl 1 bnl, Krt13, Plekhg6, Fam57a, Gstol, Ppp1r13l, Dsg3, Epn3, Als2cl, Grhl3, Myo5b, Arhgef5, Tmem63b, Phldb3, Tmprssl 1a, Gstal, Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinb11, Foxql, Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhd 3, Tgm1, Gclm, Rhov, Gsta2, Samd12, Spns2,Proser2, Ehf, Sostdcl, Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl, Arhgap27, Lpar5, Duoxl, Sult2b1 , Jup, 2200002D01 Rik, Map3k9, Ppap2c, Anxal, Arhgap27, Foxql, Mir200a, Cnksrl, Tmprss11g, Dennd2c, Lztsl, S100a16, Arhgap32, Sox15, Spintl, Clic3, Crb3, and Rtkn.

[0012] In certain embodiments, the Klf5 metagene comprises genes selected from Klf5, Dsg3, Tmprssl 1 bnl, Grhl3, Dsp, Jup, Pkp1 , Ripk4, Esrpl , Tgm1 , Ehf, Aqp3, Cdh1 , Spintl , Tjp2, Foxql , 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll, Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1, Rab25, Duoxal, Plekhg6, Slc9a3r1, Pkp3, Tnk1, Krtcap3, Fam160a1, Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1r13l, Sult2b1 , Celsrl , Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1g, Col17a1 , Grb7, Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2, Llgl2, Anxa8, Krt5, Tmprssl 1e, Ppi, Dennd2c, Tacstd2, Sprrla, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl , Tmem63b, Grhl2, Cldn4, Krt14, TtlHO, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1 , and Itgb4.

[0013] In certain embodiments, the Psca metagene comprises genes selected from Psca, Mai, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1d, Cblc, Ceacaml, Gstol, Tmprssl 1g, Anxal, Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1 bnl, Krt13, Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, Upk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinb11, Rab25, Dsg3, Prss22, Tmprssl 1a, Calml3, Epn3, Slc6a20a, Tmprssl 1e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl , Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rab11fip1, Ocln, Crispl, Prss8, Pglyrp4, Kif21 a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1, Gstal, Gstal, Pvrl4, ArhgeflOl, Elf5, Mapk13, Ikzf2, Tjp3, Osginl , Gsta2, Cldn7, Epb4.1l5, Duoxa2, Zfp750, Zdhhc13, Gm10639, Klk11 , Arhgap40, Arg1, Ltf, Rnf223, and St14.

[0014] In certain embodiments, the Cd44 metagene comprises genes selected from Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Fam83h, Col17a1, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpzl2, Arhgef5, Spint2, 1810019J16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltUb, Grb7, Esrp2, Lsr, Itga3, Plekha7, Dsg3, Clca5, Ap1m2, Plch2, Arhgef5, Celsrl, Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5, Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgef16, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1, Lypd3, Trim29, Tmprssl 1g, Cnksrl, Tmprssl 1 bnl, Mir200b, Ptprf, Gm9908, Dlg1, Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, Il17re, Fat1, Nrg1, Mdfi, and Nipal2.

[0015] In certain embodiments, the Promt metagene comprises genes selected from Promt, Ceacaml, Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca, Tmprssl 1d, Cwh43, Slc37a1, Marveld2, ArhgeflOl, Gclm, Ocln, Mctp2,Lrrc26, Fxyd3, lldrl, Cblc, Spintl, Cldn4, Slc52a3, Tmprss11g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, Upk3bl, Slc9a3r1, Mall, Sostdcl, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2l1, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO, Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprss11bnl, Gpx2, Gstol, Spns2, Serpinb11, Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N1 ORik, Sh3yl1 , Slc5a9, SamdIO, Elf3, St14, Ikzf2, Kif21 a, and Erbb3.

[0016] In certain embodiments, the Prom2 metagene comprises genes selected from Prom2, Clic3, Tmem54, Evpl, Zfp750, GrhH, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8l1, Gltp, Llgl2, Ovol1, Tmprss13, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14, Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinb11, H22ra1, Erbb2, Dsc2, Rnf39, Tmprss11e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, ArhgeflOl, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl, Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1, Ttc39a, Spintl, Ppfia3, S100a7a, Dsp, Chitl, Pinlyp, Grb7, Tmem79, Barx2, Klk10, Perp, Efna3, CcbH, Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml , Slc6a20a, SytH , Rnf223, Ide, Calml3, Caszl , and Celsr2.

[0017] In certain embodiments, the Bmi1 metagene comprises genes selected from Bmi1, Klhdc2, Bbx, Tusc3, Glg1 , Blod s6, Wdr34, 5730455P16 Ri k, Hs2st1 , Terf2, Fut8, Zmym4, Pcm1 , Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajdO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301 B20Rik, Mib1, Tiam2, Cers2, Stk3, Hspa13, Txndc12, Dock7, Psmd5, Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1 , Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy1911 , Ilf3, Bbs4, Slc30a4, InppH , Inf2, Zmynd11, Atp8b2, Gludl, Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, KifapS, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7.

[0018] In certain embodiments, the Sox4 metagene comprises genes selected from Sox4, Abl1 , Rab34, Fgfrll , Ptovl, Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl, Tcf3, Tcf12, Clip2, Bbx, Nf1, Spats2, Farpl , Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl , Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl, MicalU, Ubxn7, Mvb12b, Trio, Stonl, Dok1, Fam65a, Fmnl3, Hsf2, Sestdl, Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1, Cep120, Rnf139, Dpy19l1, Dbn1, Ctps2, Magedl, Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbl , AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl , Staul , Mecp2, Phf20, Pex11 b, Ehmt2, Cep170, Fgf r1 , Txndc5, Zmym4, Samdl 4, Kansl2,Teadl , Zkscanl 7, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdm1 a, Loxl3, Acvrl , Wwtrl , AsxH , and Phf2.

[0019] In certain embodiments, the Lrigl metagene comprises genes selected from Lrig 1 , Rgmb, Zcchc24, Teadl, Lambi, Cep170, Evalb, Sept9, Farpl, Satb2, Maplb, Ccdc88a, Axl, Loxl3, Pdgfra, list, Lgalsl, KifapS, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamd, Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1, Stx2, Lbh, Wipfl, Igfbp4, Myo9a, Cul7, Abl1, Phf20, Xxyltl, Myo9a, Dok1, Dst, Gkapl, Tspan11, Phldbl , Sydel, Teadl, Rab34, Stxbpl, AI597468, St6gal1, Ilk, Zeb1, Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl, Ank, Displ, Fhl3, Fermt2, Cdr2, Dock5, Crabpl, S1pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl, Sdccag8, Gliprl, and Nnt.

[0020] In certain embodiments, the Lgr6 metagene comprises genes selected from Lgr6, Tnnt2, Cnnm4, Prss12, Sox9, Itga2, Shf, Igsf8, Itpr3, Nt5e, Bhlhe41, Fzd7, Krt18, Arid5a, Tgfbl, Tes, Raplgap, Add2, Sdc1, Jam2, Gpr39, B4galnt1, D8Ertd82e, Plekhg3, Lamc2, Socs2, Rampl, Etv6, Lamb3, Egr3, Dusp6, Foxpl, Dnaja4, Tnfrsf12a, Pip4k2c, Rnf181, Anol, A130010J15Rik, 1118r1, Chst2, Jag1, 1600029D21Rik, Tnfsf9, Src, Runxl, Rhbddl, Smad7, Itga6, Socs2, Slco2a1, Aplp2, Cd9, Rail 4, Smurfl, Nedd9, C1galt1, Pmepal, Padi3, Gpr25, Fermtl, Nav2, Arhgef3, Capnsl, Foxp4, Ubald2, Gm7367, Gm7367, Ctnnal, Cd80, Hivep2, Dyrk3, Rab6a, Runx2, Iqgapl, Ggct, Lrch4, Skil, Frrsl, Slc20a2, Ncmap, Reep3, Nadsynl, Bhlhe40, Gprc5a, Slc39a4, Hes6, Acsl3, Erc1, Lama5, Ephb4, Rmnd5b, Plekhal, Bcr, Zbtb18, Shq1, Scyl2, Padi4, Scin, Dhcr7, and AtplOd.

[0021] In certain embodiments, the Sox9 metagene comprises genes selected from Sox9, Lgr6, Shf, Cnnm4, Runxl, Ctnnal, Capnsl, Rail 4, Itpr3, Runx2, Iqgapl, Bhlhe41, Rnf181, Ccndl, Prss12, Tes, Aig1, Foxc2, Raplgap, Krt18, Rab6a, Etv6, Dusp6, Igsf8, Tubgcp2, Alcam, Sos2, Dusp4, Bzw2, Nck2, Add2, Foxpl, Ubald2, Tnnt2, Kcnn4, Fzd7, Reep3, Nav2, Cpe, Casp3, Cnot7, Cttn, Anol, Bcarl, Cyth2, Myof, Egr3, Nadsynl, Nt5e, Dnaja4, Plekhal, Capg, Phc2, I tga2, B4galnt1 , Smurfl , Gtf2i rd 1 , Pwwp2b, Phldal , Enppl , Nfat5, Cd151 , Hivep2, Ppmel , Tgif 1 , Gm7367, Gm7367, Zbtb18, Sdc4, D630045J12Rik, Smad7, Slc20a2, Igflr, Rsf1, Tnfrsf12a, Slc27a1, Chst2, 2810408A11Rik, Igfbp3, Kdelrl, Ern1 , Atxn2l,Dyrk3, Tgfbl, Bhlhe40, Phrfl, Tnfrsf22, Ddhdl, Traf4, A130010J15Rik, Papd7, Mast4, Skil, Pyroxdl, Fubp3, Nr1h2, Ctnnbl, Foxci, Tbc1d1, and 181001101 ORik.

[0022] In certain embodiments, a cell is provided, the cell comprising: a first lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf 5 , Psca, Cd44, Prom1 , and Prom2, wherein expression of the first lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Sox2, Foxal, Krt15, Krt19, Pitxl, Klf5, Psca, Cd44, Prom1, and Prom2; and asecond lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9, wherein expression of the second lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9.

[0023] In certain embodiments, the first lineage tracing reporter gene encodes a first fluorescent protein, and the second lineage tracing reporter gene encodes a second fluorescent protein. In some embodiments, the first fluorescent protein and the second fluorescent protein have different fluorescent emission wavelengths.

[0024] In certain embodiments, the cell is a cancerous cell or a pre-malignant cell.

[0025] In certain embodiments, the cell is a mammalian cell. In some embodiments, the mammalian cell is a rodent, non-human primate, or human cell.

[0026] In certain embodiments, the cell is derived from a cancerous cell that was previously treated with a chemotherapeutic agent.

[0027] In certain embodiments, the cell is derived from a pre-neoplasia lesion, optionally wherein the pre-neoplasia lesion is a papilloma.

[0028] In certain embodiments, the cell is a pre-malignant epithelial cell.

[0029] In certain embodiments, the first lineage tracing reporter gene is fused to a regulatory region of the first gene whose expression is positively correlated with a stem cell plasticity state such that the first lineage tracing reporter gene is under the control of the promoter of the first gene.

[0030] In certain embodiments, the second lineage tracing reporter gene is fused to a regulatory region of the second gene whose expression is positively correlated with a proliferative state such that the second lineage tracing reporter gene is under the control of the promoter of the second gene.

[0031] In certain embodiments, the first lineage tracing reporter gene is fused in frame to a coding region of the first gene whose expression is positively correlated with a stem cell plasticity state such that the first lineage tracing reporter gene and the first gene are transcribed into a single messenger RNA (mRNA), wherein the mRNA is translated into a fusion protein comprising a protein encoded by the first gene covalently linked to a reporter protein encoded by the first lineage tracing reporter gene. In some embodiments, the cell further comprises an insertion of a polynucleotide encoding a flexible linker region between the first lineage tracing reporter gene and the first gene such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the first gene.

[0032] In certain embodiments, the second lineage tracing reporter gene is fused in frame to a coding region of the second gene whose expression is positively correlated with a proliferative state such that the second lineage tracing reporter gene and the second gene are transcribedinto a single messenger RNA (mRNA), wherein the mRNA is translated into a fusion protein comprising a protein encoded by the second gene covalently linked to a reporter protein encoded by the second lineage tracing reporter gene.

[0033] In certain embodiments, the cell further comprises an insertion of a polynucleotide encoding a flexible linker region between the second lineage tracing reporter gene and the second gene such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the second gene.

[0034] In certain embodiments, the first lineage tracing reporter gene is fused to a regulatory region of the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 such that the first lineage tracing reporter gene is under the control of the promoter of the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2.

[0035] In certain embodiments, the second lineage tracing reporter gene is fused to a regulatory region of the gene selected from the group consisting of Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9 such that the second lineage tracing reporter gene is under the control of the promoter of the gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9.

[0036] In certain embodiments, the first lineage tracing reporter gene is fused in frame to a coding region of the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Proml , and Prom2 such that the first lineage tracing reporter gene and the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 are transcribed into a single messenger RNA (mRNA), wherein the mRNA is translated into a fusion protein comprising a protein encoded by the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 covalently linked to a reporter protein encoded by the first lineage tracing reporter gene.

[0037] In certain embodiments, the cell further comprises an insertion of a polynucleotide encoding a flexible linker region between the first lineage tracing reporter gene and the gene selected from the group consisting of Sox2, Foxal , Krtt 5, Krtt 9, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2.

[0038] In certain embodiments, the second lineage tracing reporter gene is fused in frame to a coding region of the gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 such that the second lineage tracing reporter gene and the gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 are transcribed into a single messenger RNA (mRNA), wherein the mRNA is translated into a fusion protein comprising a protein encoded bythe gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 covalently linked to a reporter protein encoded by the second lineage tracing reporter gene.

[0039] In certain embodiments, the cell further comprises an insertion of a polynucleotide encoding a flexible linker region between the second lineage tracing reporter gene and the gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9.

[0040] In another aspect, a method of detecting whether a cell is in a cell state having lineage plasticity and drug resistance or a proliferative cell state is provided, the method comprising: (a) providing a cell comprising: a first lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Sox2, Foxal , Krt 15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2, wherein expression of the first lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2; and a second lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9, wherein expression of the second lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9; (b) contacting the cell with a candidate agent; and (c) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the first lineage tracing reporter gene compared to the second lineage tracing reporter gene indicates that the cell is in the cell state having lineage plasticity and drug resistance, and wherein increased expression of the second lineage tracing reporter gene compared to the first lineage tracing reporter gene indicates that the cell is in the proliferative cell state.

[0041] In certain embodiments, the method further comprise screening for an agent that switches the cell identified as being in the cell state having lineage plasticity and drug resistance to the proliferative cell state, the method comprising: (a) contacting the cell with a candidate agent; and (b) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the second lineage tracing reporter gene compared to the first lineage tracing reporter gene indicates that the cell has switched to the proliferative cell state. In some embodiments, the candidate agent induces cell differentiation. In some embodiments, the candidate agent is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A. In some embodiments, the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.

[0042] In certain embodiments, the method further comprises screening for an agent that switches the cell identified as being in the proliferative cell state to the cell state having lineage plasticity and drug resistance, the method comprising: (a) contacting the cell with a candidateagent; and (b) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the first lineage tracing reporter gene compared to the second lineage tracing reporter gene indicates that the cell has switched to the cell state having lineage plasticity and drug resistance. In some embodiments, the candidate agent is an anti-mitotic agent such as, but not limited to, an alkylating agent, a taxane, or a vinca alkaloid. In some embodiments, the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.

[0043] In certain embodiments, the first lineage tracing reporter gene encodes a first fluorescent protein, and wherein the second lineage tracing reporter gene encodes a second fluorescent protein. In some embodiments, the first fluorescent protein and the second fluorescent protein have different fluorescent emission wavelengths.

[0044] In another aspect, a method of screening for an agent that switches cells between cell states is provided, the method comprising: (a) providing a first population of cells and a second population of cells, wherein the first population of cells has increased lineage plasticity, increased levels of expression of a gene selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Proml metagene, and a Prom2 metagene, and decreased levels of expression of a gene selected from a Bmi1 metagene, a Sox4 metagene, a Lrig 1 metagene, a Lgr6 metagene, and a Sox9 metagene compared to the second population of cells, and wherein the second population of cells has increased proliferation, increased levels of expression of a gene selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene, and decreased levels of expression of a gene selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Promt metagene, and a Prom2 metagene compared to the first population of cells; (b) contacting the first population of cells and the second population of cells with a candidate agent; (c) measuring levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krtt 9 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene, and one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the first population of cells and the second population of cells; and (d) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Promt metagene, and Prom2 metagene and increased levels of expression of the one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the first population of cells in presence of the candidate agent compared to referencevalue ranges for the levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein increased levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene and decreased levels of expression of the one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the second population of cells in the presence of the candidate agent compared to the reference value ranges for the levels of expression of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the candidate agent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.

[0045] In another aspect, a method of screening for an agent that switches cells between cell states is provided, the method comprising: (a) providing a first population of cells and a second population of cells, wherein the first population of cells has increased lineage plasticity, increased levels of expression of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2, and decreased levels of expression of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 compared to the second population of cells, and wherein the second population of cells has increased proliferation, increased levels of expression of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9, and decreased levels of expression of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 compared to the first population of cells; (b) contacting the first population of cells and the second population of cells with a candidate agent; (c) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the first population of cells and the second population of cells; and (d) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the first population of cells in presence of the candidate agent compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt 15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein increased levels of expression of the oneor more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the second population of cells in the presence of the candidate agent compared to the reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.

[0046] In certain embodiments, the method further comprises measuring proliferation of the first population of cells and the second population of cells, wherein an increased level of proliferation in combination with decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2, and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the first population of cells in the presence of the candidate agent compared to reference value ranges for the level of proliferation and the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein a decreased level of proliferation in combination with increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2, and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the second population of cells in the presence of the candidate agent compared to reference value ranges for the level of proliferation and the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.

[0047] In certain embodiments, the levels of expression are measured by reverse transcription polymerase chain reaction, RNA sequencing (e.g., single cell RNA sequencing or bulk RNA sequencing), global run-on sequencing, microarray analysis, or any combination thereof.

[0048] In certain embodiments, the candidate agent inhibits mitosis or induces cell differentiation.

[0049] In certain embodiments, the candidate agent inhibits KRAS4A or protein phosphatase 2A(PP2A). In some embodiments, the candidate agent selectively inhibits a PP2A subunit.

[0050] In certain embodiments, the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.

[0051] In certain embodiments, the first population of cells and the second population of cells are mammalian cells. In some embodiments, the mammalian cells are rodent, non-human primate, or human cells.

[0052] In certain embodiments, the first population of cells or the second population of cells are cancerous cells or pre-malignant cells.

[0053] In certain embodiments, the first population of cells or the second population of cells is derived from a cancerous cell that was previously treated with a chemotherapeutic agent.

[0054] In certain embodiments, the first population of cells or the second population of cells is derived from a pre-neoplasia lesion, optionally wherein the pre-neoplasia lesion is a papilloma.

[0055] In certain embodiments, the first population of cells and the second population of cells are pre-malignant epithelial cells.

[0056] In another aspect, a method of detecting cell type switching of a cancerous cell in response to treatment with a therapeutic agent is provided, the method comprising: (a) treating the cancerous cell with an effective amount of the therapeutic agent; (b) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in progeny of the cancerous cell; and (c) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the progeny of the cancerous cell after said treating the cancerous cell compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the progeny of the cancerous cell are in a proliferative cell state susceptible to treatment with an anti-mitotic agent, and wherein increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the progeny of the cancerous cell after said treating the cancerous cell compared to the reference value ranges for the levels of expression of the Sox2, Foxal , Krtt 5, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the progeny of the cancerous cell are in a cell state having lineage plasticity and drug resistance.

[0057] In certain embodiments, the method further comprises treating the cancerous cell and the progeny thereof with an anti-mitotic agent if the progeny of the cancerous cell are in the proliferative cell state susceptible to treatment with the anti-mitotic agent, or treating the cancerous cell with an inducer of differentiation if the progeny of the cancerous cell are in the cell state having lineage plasticity and drug resistance.

[0058] In certain embodiments, the method further comprises treating the cancerous cell and the progeny thereof with the anti-mitotic agent after said treating the cancerous cell with the inducerof differentiation if the progeny of the cancerous cell are in the cell state having lineage plasticity and drug resistance.

[0059] In certain embodiments, the inducer of differentiation is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A. In some embodiments, the inhibitor of PP2A is LB100.

[0060] In certain embodiments, the anti-mitotic agent is cisplatin, cyclophosphamide, chlorambucil, vinblastine, vincristine, vinorelbine, vinflunine, paclitaxel, docetaxel, or a combretastatin.

[0061] In certain embodiments, the cancer cell is a carcinoma cell. In some embodiments, the carcinoma cell is a squamous cell carcinoma cell such as, but not limited to a cutaneous squamous cell carcinoma cell.

[0062] In certain embodiments, the cancerous cell is in vivo or in vitro.

[0063] In certain embodiments, the cancerous cell comprises a reporter gene for lineage tracing of the progeny of the cancerous cell. In some embodiments, the reporter gene encodes a fluorescent protein.

[0064] In certain embodiments, the levels of expression are measured by reverse transcription polymerase chain reaction, RNA sequencing (e.g., single cell RNA sequencing or bulk RNA sequencing), global run-on sequencing, microarray analysis, or any combination thereof.In another aspect, a method of treating a cancerous or pre-malignant lesion in a patient is provided, the method comprising: (a) administering a therapeutically effective amount of an anti-mitotic therapeutic agent to the patient; (b) obtaining a biological sample comprising cancerous or pre-malignant cells from the cancerous or premalignant lesion of the patient; (c) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the biological sample, wherein increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the biological sample compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the cancerous or pre-malignant cells are in a drug resistant state, and wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt 15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the biological sample compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krtt 5, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the cancerous or pre-malignant cells are in non-drug resistant state; continuingtreatment of the patient with the anti-mitotic therapeutic agent if the patient is in the non-drug resistant state; and (d) continuing treatment of the patient with the anti-mitotic therapeutic agent if the patient is in the non-drug resistant state; or discontinuing treatment of the patient with the anti-mitotic therapeutic agent if the patient is in the drug resistant state, and administering a therapeutically effective amount of an agent that induces differentiation to the patient to switch the cell state of the cancerous or pre-malignant cells from the drug resistant state to the non-drug resistant state before subsequently administering another therapeutically effective amount of the anti-mitotic agent to the patient.

[0065] In certain embodiments, the inducer of differentiation is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A. In some embodiments, the inhibitor of PP2A is LB100. In some embodiments, the anti-mitotic agent is cisplatin, cyclophosphamide, chlorambucil, vinblastine, vincristine, vinorelbine, vinflunine, paclitaxel, docetaxel, or a combretastatin.

[0066] In another aspect, a composition comprising an RNA transcript of a gene selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Prom1 metagene, a Prom2 metagene, a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene for use in a method of diagnosing development of drug resistance of a cancer in response to treatment with a therapeutic agent is provided.

[0067] In another aspect, a composition comprising an RNA transcript of a gene selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 for use as a biomarker in a method of diagnosing development of drug resistance of a cancer in response to treatment with a therapeutic agent is provided.BRIEF DESCRIPTION OF THE DRAWINGS

[0068] FIGS. 1A-1 D. Bulk-tissue and single-cell expression data. (FIG. 1A) Experimental pipeline showing creation of an interspecific backcross mapping population segregating genetic variation in resistance to inflammation, infection, and cancer. Mice were randomly selected for subsequent matched normal skin and carcinoma expression analysis. Tumor initiation occurred by DMBA application to dorsal back skin and promotion by twice weekly TPA treatment for 20 weeks. Matched normal skin and tumors were co- sampled for bulk gene expression assays by microarray. Co-expression gene networks for genes of interest were inferred from bulk expression data. Several normal skin, papilloma, and carcinoma samples from inbred FVB mice were profiled using scRNAseq. Network expression inferred from bulk samples was overlaid onto the single-cell data as tissue-specific metagenes: a normal-skin metagene generated from normal skin bulk-tissue samples and a carcinoma metagene generated from carcinoma bulk-tissue samples. Spearman rank correlations of selected stem cell-related genes in (FIG. 1 B) 106 normal skin and (FIG. 1C) 157 carcinoma samples. (FIG. 1 D) Single-cell data from normal skin, papilloma, and carcinoma from FVB mice displayed on a UMAP with cells colored according to cell type; OuB is for outer bulge; Isth isthmus; UnF undifferentiated follicular; InB inner bulge; SG sebaceous gland; UHF upper hair follicle; Bas basal cells; tK terminal keratinocytes; IfE interfollicular epidermal cells; Inf infundibulum; mEp mitotic epithelial cells; Er erythrocytes; Mel melanocytes; T T-cells; nEp neoplastic epithelia of the papilloma; LS lower spike cells (defined hereafter); US upper spike cells (defined hereafter); Sp spindle cells of the carcinoma; Sq squamous cells of the carcinoma; Neut neutrophils; LC Langerhans cells; Mac macrophages; End endothelial cells; Myo myofibroblasts.

[0069] FIGS. 2A-2G. Single-cell expression of stem-cell seed genes and metagenes. (FIG. 2A) Expression of Lgr6 alone in the single-cell UMAP. (FIG. 2B) Expression of the Lgr6 normal skin metagene defined as the top 100 genes correlated with Lgr6 in normal skin (NSk) bulk-tissue samples. (FIG. 2C) Expression of the Lgr6 carcinoma metagene defined as the top 100 genes correlated with Lgr6 in carcinoma (Car) bulk-tissue samples. (FIG. 2D) Expression of Lgr5 alone in the single-cell manifold. (FIG. 2E) Expression of the Lgr5 carcinoma metagene defined as the top 100 genes correlated with Lgr5 in Car bulk-tissue samples. (FIG. 2F) A comparison of metagene expression during carcinogenesis for the Lgr5 and Lgr6 carcinoma metagenes. Y-axis is log metagene expression for each stage-specific parenchyma cell; box-and-whisker plots are median+IQR with outliers (Q1-1.5xlQR or Q3+1.5xlQR) not shown. All within-plot pairwise comparisons are significant at FDR<0.05. (FIG. 2G) Exemplar carcinoma metagenes that localize to the upper spike (US, upper panels) and lower spike (LS, lower panels) of the papilloma. The location of the spikes is colored red in the panels next to the metagenes and corresponds to unsupervised cell clusters 19 and 33. Purple is low expression and yellow is high expression.

[0070] FIGS. 3A-3C. Immunofluorescent single-cell lineage tracing of Lgr6+ cells and their progeny. Lgr6 lineage tracing in normal dorsal mouse skin, benign papilloma, and carcinoma tissue. Representative immunofluorescence images of LgrtTd riven lineage tracing for: (FIG. 3A) normal dorsal mouse skin; (FIG. 3B) benign papilloma tissue; (FIG. 3C) carcinoma, 10 days after topical 4-OH-tamoxifen treatment in vivo. Lgr6+ stem cells (green) are localized within (a) the hair follicle epithelium and epidermis of the normal dorsal skin; (b) predominantly the basal epithelium of the papilloma; (c) scattered throughout the carcinoma epithelium. These give rise to tdTomato+ (red) progeny within those tissues. Yellow boxes indicate the magnified region, dotted lines represent the epidermal-dermal border, and nuclei were counterstained with DAPI (blue), scale bar = 50 pm.

[0071] FIGS. 4A-4C. Lgr6-progeny cells form the papilloma lower spike and express high levels of a Spearman group 3 program. (FIG. 4A) Proportion of FACS-sorted Lgr6, progeny, andunsorted cells in each cell population. (FIG. 4B) Aggregated expression of top 100 DEGs by fold change from stem cell to progeny cells (tdTomato+ / Lgr6 GFP+) discovered for DEGs within normal skin parenchyma; papilloma parenchyma; and finally carcinoma parenchyma. (FIG. 4C) Carcinoma metagene expression means across individual cells of the Lgr6‘.GPP+ (L) and tdTomato+ Progeny (P) lineages taken from neoplastic parenchyma cells (pooled papilloma and carcinoma parenchyma); red and blue lines are significant differences at Bonferroni-adjusted p<0.01 by t-tests, and gray are non-significant; error bars are standard errors.

[0072] FIGS. 5A-5B. Recapitulation of lower spike signature genes in orthologous human prostate adenocarcinoma and vice versa. (FIG. 5A) Expression of lower spike (LS) markers in (left) mouse cells and (right) human prostate adenocarcinoma (PAD). (FIG. 5B) Expression of human prostate regenerative signature in (left) mouse cells and (right) PAD cells. Light gray arrows point to cells with peak expression. Black arrows show direction of orthologous transformation origin: LS signature was discovered in mouse SCC and was preserved in human PAD; the PAD regenerative signature was preserved in mouse SCC.

[0073] FIGS. 6A-6F. Cisplatin activates genes that localize to the lower spike, whereas Pp2a inhibition elevates expression of upper spike genes. (FIG. 6A) Differentially expressed genes in squamous cell carcinoma parenchyma cells treated with cisplatin in vivo. Data derived from scRNAseq of 2 control and 2 treated tumors. Positive values represent genes that are upregulated by cisplatin, and negative downregulated. Labelled genes are those mentioned in the main text. (FIG. 6B) Integrated expression of the top 100 genes significantly upregulated by cisplatin ordered by fold-change (p<0.05). (FIG. 6C) The intersection of 1 ) genes that define a cell cluster ordered from high to low marker score and 2) genes that are upregulated by cisplatin challenge ordered from high to low fold change. The x-axis refers to the number of genes concurrently tested for intersection size in each list. For example, 100 refers to the top 100 marker genes in a cluster and the top 100 positively upregulated genes, which are then tested for the number of overlaps (intersection size), which is displayed on the y-axis. The red line shows the results for lower-spike markers, the blue for upper-spike markers, and gray lines show 1000 randomly chosen sets of n = 100 genes to establish a null distribution of intersection curves between cisplatin DEGs and potential marker genes in the scRNAseq data. (FIG. 6D) Box and violin plots of integrated expression of the top 100 positively upregulated DEGs shown in panel B. nEp refers to all papilloma cells that are not in the spikes; US is for upper spike (cluster 19); and LS is for lower spike (cluster 33). All pairwise comparisons are significant at p<0.01. (FIG. 6E) Integrated expression of the top 100 genes significantly upregulated by Pp2a inhibition with LB100 ordered by fold- change (p<0.05). (FIG. 6F) Box and violin plots of integrated expression of the top 100 positively upregulated DEGs shown in panel E. nEp refers to all papilloma cellsthat are not in the spikes; US is for upper spike (cluster 19); and LS is for lower spike (cluster 33). LS cells are significantly different at FDR<0.01 .

[0074] FIGS. 7A-7F. Whole-chromosome aneuploidy and pseudotime imply the upper spike is transitional between normal skin and neoplasia. (FIG. 7A) Inferred trajectories and pseudotime of parenchyma cells and the papillomas. (FIG. 7B) UMAR showing cells with chromosome complements greater than regular diploid of any chromosome in parenchyma cells. (FIG. 7C) Gains (red) of chromosome 7 in the papilloma parenchyma; (FIG. 7D) chromosome 6; (FIG. 7E) chromosome 10; (FIG. 7F) chromosome 1 .

[0075] FIG. 8. Multistage chemical carcinogenesis model of initiation and promotion in single cells reveals simplified stem-cell paths to malignancy. The model for carcinoma development in single cells based on co-expression networks from bulk-tissue samples. DMBA initiates carcinogenesis by inducing oncogenic Hras mutations in cells, which then lie dormant until promoted by the inflammatory promoter TPA. A single initiated Lgr6+ papilloma cell or its early progenitor clonally expands and begins to divide rapidly, developing towards the upper-spike cell state characterized by cell cycle activation and genomic instability. This results in specific aneuploid gains and subsequent movement towards a critical transition point in the papilloma. At this transition point several cell fates become available to the pre-malignant cells: 1 ) a lower- spike cell state characterized by oxidative stress, reduced cell growth linked to elevated Cdkn2a / b expression, increased lineage plasticity, and immune activation; 2) a high-Lgr6+ state that shows similar metagene expression patterns to a carcinoma; 3) a maintained upper spike cell state with increasingly heavy aneuploid burden. Chemotherapy treatment of neoplasia increases stress, causing a reversion towards the lower-spike high plasticity cell state and away from the upperspike cell state; Pp2a inhibition causes the opposite patterns with movement away from the lower- spike cell state and towards the upper spike. This latter treatment renders upper-spike-like cells vulnerable to chemotherapeutic toxicity.

[0076] FIGS. 9A-9B. Bulk normal skin and carcinoma samples that generate metagenes contain mixtures of different cell types. Average cell type proportions of bulk samples deconvoluted based upon single-cell RNAseq using Bisque for (FIG. 9A) 157 carcinoma samples, and (FIG. 9B) 106 normal skin samples. Error bars represent standard errors. OuB is for outer bulge; Isth isthmus; UnF undifferentiated follicular; InB inner bulge; SG sebaceous gland; UHF upper hair follicle; Bas basal cells; tK terminal keratinocytes; IfE interfollicular epidermal cells; Inf infundibulum; mEp mitotic epithelial cells; Er erythrocytes; Mel melanocytes; T T-cells; nEp neoplastic epithelia of the papilloma; LS lower spike cells (defined hereafter); US upper spike cells (defined hereafter); Sp spindle cells of the carcinoma; Sq squamous cells of the carcinoma; Neut neutrophils; LC Langerhans cells; Mac macrophages; End endothelial cells; MyFi myofibroblasts.

[0077] FIGS. 10A-10E. Unsupervised clustering and high-resolution reanalysis of carcinoma and innate immune cells. (FIG. 10A) Unsupervised Leiden-based cell clusters at default ‘partition - level resolution (k=10, partition q-value=0.05). (FIG. 10B) Fraction of cells derived from each carcinogenic stage populating unsupervised cell clusters shown in A. (FIG. 10C) Carcinoma parenchyma cells projected within its own manifold overlain by vimentin expression, showing unsupervised disjunction between the squamous and spindle phases. (FIG. 10D) Langerhans (LC) and macrophage (Mac) cells projected within their own manifold, and analyzed by cell type, inflammatory markers, and M1 / M2 polarization. (FIG. 10E) T cells projected within their own manifolds.

[0078] FIGS. 11A-11 L. Canonical marker expression for cell types in normal skin single-cell parenchyma, including Krt14 (FIG. 11A), Mt2 (FIG. 11 B), Krt10 (FIG. 11 C), Fth1 (FIG. 11 D), Thbsl (FIG. 11 E), Krt5 (FIG. 11 F), Krt79 (FIG. 11 G), Mgstl (FIG. 11 H), Postn (FIG. 111), Cd34 (FIG. 11 J), Krt6a (FIG. 11 K), Krt75 and (FIG. 11 L). OuB is for outer bulge; Isth isthmus; UnF undifferentiated follicular; InB inner bulge; SG sebaceous gland; UHF upper hair follicle; Bas basal cells; tK terminal keratinocytes; IfE interfollicular epidermal cells; Inf infundibulum; mEp mitotic epithelial cells.

[0079] FIGS. 12A-12C. Lgr6 normal skin metagene is expressed most highly in terminal keratinocytes but also shows robust expression in hair follicle, isthmus, and sebaceous gland. Testing whether the Lgr6 normal skin metagene is expressed in follicular and interfollicular cells. (FIG. 12A) The normal skin metagene with all cells. (FIG. 12B) Normal skin metagene with the differentiated interfollicular cells removed. These upper hair follicle cells express this metagene at higher levels than any neoplastic or stromal cell. (FIG. 12C) Distribution of the Lgr6 normal skin metagene expression in normal skin interfollicular epithelium (IfE), isthmus (Isth), sebaceous gland (SG), and T cells (T). T cells are included as a negative control since Lgr6 is not known to have major function in uninflamed skin and thus is expected to show low expression under normal homeostatic conditions.

[0080] FIGS. 13A-13C. (FIG. 13A) The Lgr5 carcinoma metagene is more highly expressed in normal skin than in neoplastic cells. (FIGS. 13B-13C) This series shows the effect of sequentially removing rare cell populations (low-resolution cell clusters 13 (FIG. 13C) and 14 (FIG. 13B)) with high expression of the Lgr5 carcinoma metagene on its expression visualization in the UMAP. Cluster 13 consisted of 181 fibroblasts (0.31 % of all cells) and cluster 14 consisted of 151 cells (0.26%).

[0081] FIGS. 14A-14N. Individual seed genes show disparate expression patterns but their respective carcinoma metagenes show high expression in the same single-cell populations. Seed gene and carcinoma metagene expression UMAPs for 14 stem-associated genes not shown in the main text, including Bmi1 (FIG. 14A), Sox4 (FIG. 14B), Lrigl (FIG. 14C), Sox9 (FIG. 14D),Sox2 (FIG. 14E), Proml (FIG. 14F), Foxal (FIG. 14G), Krt15 (FIG. 14H), Krt19 (FIG. 191), Pitxl (FIG. 19J), Psca (FIG. 19K), Prom2 (FIG. 19L), Klf5 (FIG. 19M), and Cd44 (FIG. 19N). Dark gray shows low expression and light gray shows high expression. Color gradients are rescaled in each panel.

[0082] FIGS. 15A-15G. Metagenes related to cell cycle show highest expression in cells classified in the G2M phase. (FIG. 15A) Cell-cycle phasing using the Cyclone program to classify cells according to cell cycle phase with all cells belonging in (FIG. 15B) G1 only; (FIG. 15C) G2M1 only; and (FIG. 15D) S only. Violin and box-plots showing the single-cell expression for the carcinoma (red) and normal skin (blue) metagenes for (FIG. 15E) E2F1 , (FIG. 15F) Foxml , and (FIG. 15G) Mki67 across all cell-cycle-phased cells in the UMAP.

[0083] FIGS. 16A-16E. Parenchyma cells whose cell phase proportions are shown in Table S3. Dark red highlighted cells show cells that belong to (FIG. 16A) normal skin interfollicular epithelium; (FIG. 16B) normal skin proliferating epithelium; (FIG. 16C) neoplastic epithelium; (FIG. 16D) lower spike cells; (FIG. 16E) upper spike cells.

[0084] FIG. 17. Metagenes associated with cell cycle and genomic instability have high expression in the upper spike. Seed gene and carcinoma metagene expression UMAPs for cell cycle checkpoint genes (Cdkn2a / b), cell cycle progression genes (E2f1 and Foxml), and DNA damage / genomic instability genes (Atm and Atr). Purple shows low expression and yellow shows high expression. Color gradients are rescaled in each panel.

[0085] FIG. 18. Negative metagenes localize to the opposite spike population: upper spike negative metagenes localize to the lower spike. Exemplar positive (POS) and negative (NEG) carcinoma metagene patterns demonstrating that for a given seed gene, its positive metagene is more expressed in one spike and its negative metagene is expressed in the opposite spike of the papilloma parenchyma. A positive carcinoma metagene is defined as the 100 genes most correlated to a seed gene in the bulk-tissue carcinoma samples, and a negative carcinoma metagene is defined as the 100 genes most anticorrelated to a seed gene. For example, for Bmi1, its positive metagene is more highly expressed in the US than the LS; however, its negative eigengene is more highly expressed in the LS than the US.

[0086] FIG. 19. Lgr6 papilloma metagene shows robust expression in the lower spike but is rewired as the Lgr6 carcinoma metagene to show low expression in the lower spike. Independent and previously published bulk-expression papillomas (30) and carcinomas were used to generated papilloma- and carcinoma-specific metagenes. Purple is low expression and yellow is high expression.

[0087] FIGS. 20A-20D. Spike cells and metagenes recapitulate in independent samples. (FIG. 20A) UMAP of parenchyma cells from additional papilloma (Pap) and carcinoma (Car) samples.(FIG. 20B) Expression of a lower spike-specific carcinoma metagene, Pitxl, whose peak expression colocalizes with (FIG. 20C) lower spike cells. (FIG. 20D) Upper spike cells.

[0088] FIGS. 21A-21 F. Integration of parenchyma cells from 7 independent papillomas and 4 independent carcinomas with original data maintain the upper spike as a key transitional population between normal skin and neoplasia. Cells colored by cell-cycle phase called by Cyclone (FIG. 21 A) without and (FIG. 21 B) with cell cycle regression. Cells colored according to sample origin (FIG. 21 C) without and (FIG. 21 D) with cell cycle regression. “Original” refers to the initial set of normal skin, papilloma, and carcinoma samples presented in the paper and which generate the UMAPs show in all the main text figures except for FIG. 6. “Additional” refers to the 7 independent papillomas and 4 carcinomas gathered in order to test whether the LS and US cell states recapitulated in these additional data. Upper spike cells colored red, showing them to be intermediate between the normal skin and neoplastic parenchyma (FIG. 21 E) without and (FIG. 21 F) with cell cycle regression. Arrows show direction of global neoplastic development moving from normal skin to neoplasia.

[0089] FIG. 22 Seed gene and carcinoma metagene expression UMAPs for drug resistance- associated genes from basal cell carcinomas ( Tacstd2, Ly6d, and Lypd3), lung adenocarcinoma (Slc4a11 and Tigit), and prostate adenocarcinoma (Foxal). Purple shows low expression and yellow shows high expression. Color gradients are rescaled in each panel.

[0090] FIGS. 23A-23C. Pre-treatment with a PP2A inhibitor potentiates the effect of paclitaxel on CCK168 cell growth. (FIG. 23A) Schematic representation of the sequential treatment protocol: Cells were treated with LB100 for 24 h, then the compound was washed off and paclitaxel was added for 72 h. After the drug treatment, cells were replated at low densities in 6- well plates and allowed to grow for 10 days until distinct colonies were formed. (FIG. 23B) Representative images of cell colonies stained with crystal violet. LB100 was at 10 pM and paclitaxel was at 25 nM. All images were acquired using Keyance microscope at 4x magnification and stitched to produce a composite image of each well. (FIG. 23C) Quantitative analysis of each image was done using Imaged, and the total colony area was plotted for each treatment group relative to the control. Data are the mean ± SD of three independent experiments. *, p< 0.05; as compared with control and monotherapy groups. Unpaired T-test with Holm-Sidak's multiple comparisons test.

[0091] FIGS. 24A-24F. Force-directed layouts of parenchyma cells show upper spike to be transitional between normal skin and neoplastic cells. Fruchterman-Reingold layout displaying (FIG. 24A) parenchyma cell types with edges included as gray lines; (FIG. 24B) parenchyma cells types without edges drawn; (FIG. 24C) parenchyma tissue with edges. Distributed recursive layout displaying (FIG. 24D) parenchyma cell types with edges included as gray lines; (FIG. 24E)parenchyma cells types without edges drawn; (FIG. 24F) parenchyma tissue with edges. Pap refres to papilloma parenchyma and CA to carcinoma.

[0092] FIGS. 25A-25C. FACS gating strategy for isolating Lgr6GFP+ SCs and tdTomato+ derived progeny from normal skin, benign papilloma, and squamous cell carcinoma tissue for scRNA sequencing. (FIG. 25A) Representative flow cytometry gating strategy used to enrich and purify Lgr6GPP+ SCs and tdTomato+ progeny from normal dorsal mouse skin, benign papilloma, and squamous cell carcinoma tissue in vivo. (FIG. 25B) Bar chart displaying the percentage of Lg'rGGFP+SCs observed per sample. (FIG. 25C) Bar chart displaying the percentage of tdTomato+, Lgr6-6emeti progeny present per sample.

[0093] FIG. 26. UMAPs showing stage-specific FACS-sorted cells. Columns are carcinogenic stage and rows are FACS sorting status; gray dots are cells that do not fall into a stagexFACS factor, whereas colored cells do.

[0094] FIG. 27. Number of nodes versus edges from STRING for a particular seed gene. Panels are for separate tumor metagenes, seeded by the gene shown in the panel title; the x-axis is the number of genes included within a metagene in increments of 5 from the top 5 to top 500 most correlated genes to the seed gene; y-axis shows the Iog10 number of protein-protein network associations indexed by STRING among all of the genes included in an metagene of the size denoted by the x-axis; red vertical lines are for N=100 metagenes.

[0095] FIG. 28. Lgr6 network from STRING. Interactions (edges) among proteins encoded by the 97 genes mapping into the STRING database of the carcinoma metagene seeded by Lgr6. The black circle shows the seed gene Lgr6.

[0096] FIG. 29. Foxal carcinoma metagene expression for a range of metagene sizes. Metagene sizes range from N=10 to N=2000, where N is the number of constituent genes in the metagenes that are most correlated to the seed gene Foxal. Dark gray is low expression and light gray is high expression. Panel numbers show the number of genes in the network metagene.

[0097] FIG. 30. Sox2 carcinoma metagene expression for a range of metagene sizes. Metagene sizes range from N=10 to N=2000, where N is the number of constituent genes in the metagenes that are most correlated to the seed gene Sox2. Dark gray is low expression and light gray is high expression. Panel numbers show the number of genes in the network metagene.

[0098] FIG. 31 . Alternative stem cell states can be exploited to increase efficacy of combinatorial drug treatments.

[0099] FIG. 32. The Kras4A network is most highly expressed in the lower spike plasticity cell state that arises after cancer chemotherapy using known small molecule cancer drugs. Inhibition of this state activates the upper spike state corresponding to the Kras4B network. Transitions between these states can be accomplished by inhibition of Kras4A or Kras4B splice isoforms using shRNA specific for each isoform.DETAILED DESCRIPTION OF THE INVENTION

[0100] Compositions, methods, and kits are provided for detecting pre-malignant and cancerous cells having lineage plasticity and drug resistance. Also provided are methods of screening candidate agents for efficacy in switching pre-malignant or cancerous cells, identified as being in a cell state having lineage plasticity and drug resistance, to a non-drug resistant proliferative cell state that can be treated with anti-mitotic therapeutic agents.

[0101] Before the present compositions, methods, and kits are described, it is to be understood that this invention is not limited to particular methods or compositions described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.

[0102] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limits of that range is also specifically disclosed. Each smaller range between any stated value or intervening value in a stated range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included or excluded in the range, and each range where either, neither or both limits are included in the smaller ranges is also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

[0103] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, some potential and preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and / or materials in connection with which the publications are cited. It is understood that the present disclosure supersedes any disclosure of an incorporated publication to the extent there is a contradiction.

[0104] As will be apparent to those of skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present invention. Any recited method can be carried out in the order of events recited or in any other order which is logically possible.

[0105] It must be noted that as used herein and in the appended claims, the singular forms "a", "an", and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a biomarker" includes a plurality of such biomarkers and reference to "the mRNA" includes reference to one or more mRNAs and equivalents thereof, e.g., RNA transcripts known to those skilled in the art, and so forth.

[0106] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.Definitions

[0107] The term "about", particularly in reference to a given quantity, is meant to encompass deviations of plus or minus five percent.

[0108] Biomarkers. The term “biomarker” as used herein refers to a compound, such as a mRNA, a protein, a metabolite, or a metabolic byproduct which is differentially expressed or present at different concentrations, levels or frequencies in one cell type compared to another, such as a pre-malignant or cancerous cell in a cell state having lineage plasticity and drug resistance or a pre-malignant or cancerous cell in a non-drug resistant, proliferative cell state. Exemplary biomarkers include, but are not limited to, RNA transcripts of the genes of the Sox2 metagene, including Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, Mtrnrl O, Esd, Sox13, Nfe2l2, Pls1 , Tom1 l2, Bink, Suox, Slc16a11 , Xrcc5, Chst15, Krt12, Evalc, Nppc, Esd, Ddx59, Nop2, Krt13, Plekhh3, Osbpl6, Aldh5a1 , Cirhl a, Wnk4, Arntl2, Fam110c, Tmem180, Dili , Galnt12, Pitxl , Caleb, Ankrd9, Isl1 , Btc, Gss, Ociad2, Klra33, Aldh3a1 , Minkl , Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl , Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrl a, Pthlh, Usp6nl, Ufspl , Irgq, Nkiras2, Grtpl , Nqo1 , Krt20, Snord42b, Avpil , Ifrdl , Srd5a2, Cpn1 , Bail , Sprr3, Rap1 gap2, Rassf7, Fetub, Ramp3, Arl4d, Tle1 , Krt76, Ptprzl , Pradcl , Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl , G6pdx, Tsg101 , Nmrkl , Ralgapb, A430105119Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik; genes of the Foxal metagene, including Foxal , Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1 , Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1 , Tjp3, Plekhg6, Bspry, Ocln, Ceacaml , Marveld3, Cldn3, Mal2, Tmem30b, Sowahb, Spns2, Slc9a3r1 , Kctdl , Cwh43, Cystml , Rab17, S100a2, Ppbp, Padil , Caleb, Gstol , S100a16, Spint2, Slc52a3, Sid 6a11 , Crispl , Mall, Aldh1 a3, Entpd3, Tmprssl 1 g, Anxal , Pgapl , Prss22, Kif21 a, Omp, Liph, Epb4.1 l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, Arhgefl 01, Tmprssl 1 d, Mxd1 , Elf5, Acss2, LepreH , Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppfibp2, Mboatl , Zdhhc13, Dgka, Ehf, Mst1 , St14, Ap1 s3, Maltl , Spintl , Sprr3, Pllp,AA986860, Prss27, Tmprssl 1a, Serpinb11 , Hs3st1, StardlO, Arhgap40, lldrl , Ppi, Fbp2, Cnksrl, Map7, and 1700001 C19Rik, E330009J07Rik; genes of the Krt15 metagene, including Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrd , Zfp750, Lipm, Ocln, Paqr5, GrhH, Erbb3, PsapH , Aldh3b2, Ppi, RapgefH, Aldh3b2, Efna3, Muc15, Liph, 2610528A11 Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1pr5, Klhl29, 4833423E24Rik, Nccrpl, Slc27a4, Barx2, Aimll, Wnt4, L1cam, Leprell , Rnf43, Ckmtl, Lipk, Mapk13, Il22ra1, Zfp185, Cds1, Arhgap40, Krt80, Dsc3, Prss8, Fgfr3, Hsd17b2, Padil, Ripk4, Prom2, Adtrp, Caszl, 1700055N04Rik, Scnnla, Ptprf, ArhgeflOl, Tmprssl 1e, Slc25a48, Mall, Mst1, Crnn, Celsrl, Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinb11, Vsnll, Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprss13, Sowahb, Celsr2, Ly6g6e, SytH, Tprg, AA986860, and Sptbn2; genes of the Krt19 metagene, including Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal, Mall, Slc37a1, Cblc, Marveld3, Marveld2, Gstol, Ceacaml, Gm9573, Ocln, Slc9a3r1, Mal2, Tmprssl 1g, Spns2, Anxal, 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, ArhgeflOl, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, Upk3bl, Gsta4, Ppbp, Tmprss11d, Spintl, Tmem30b, S100a2, Pgapl, Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1, Kif21a, Krt13, Padil, Tmprss11bnl, Foxql, S100a16, L1cam, Seel, Ehf, Samd10, Epb4.1l5, Rab27b, Plekha7, Llgl2, Erbb2, Stap2, Rab25, Hebp2, Cnksrl, 1117re, Pllp, Cystml, Tnk1, Mboatl, Tmprss11e, Tacstd2, Plekha6, Arg1, Ltf, Evpl, S100a14, Plekhhl, Slc25a48, Ap1s3, Zdhhc13, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl, Ppfibp2, Nipal2, Rab27a, Rbm47, and StardlO; genes of the Pitxl metagene, including Pitxl, Cldn8, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1, Klf5, Cep170b,Llgl2, 1700001 C19Rik, Tmprssl 1d, Dsc2, Fam160a1, Erbb2, Gsta4, Shb, Duoxal, Rab27b, Barx2, Fhdd, Tmprssl 1bnl, Krt13, Plekhg6, Fam57a, Gstol, Ppp1r13l, Dsg3, Epn3, Als2cl, Grhl3, Myo5b, Arhgef5, Tmem63b, Phldb3, Tmprssl 1a, Gstal, Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinb11, Foxql, Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhc13, Tgm1, Gclm, Rhov, Gsta2, Samd12, Spns2, Proser2, Ehf, Sostdd, Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl, Arhgap27, Lpar5, Duoxl, Sult2b1, Jup, 2200002D01 Rik, Map3k9, Ppap2c, Anxal, Arhgap27, Foxql, Mir200a, Cnksrl, Tmprssl 1g, Dennd2c, Lztsl, S100a16, Arhgap32, Sox15, Spintl, Clic3, Crb3, and Rtkn; genes of the Klf5 metagene, including Klf5, Dsg3, Tmprssl 1 bnl, Grhl3, Dsp, Jup, Pkp1, Ripk4, Esrpl, Tgm1, Ehf, Aqp3, Cdh1, Spintl, Tjp2, Foxql, 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll, Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1, Rab25, Duoxal, Plekhg6, Slc9a3r1, Pkp3, Tnk1, Krtcap3, Fam160a1, Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1r13l, Sult2b1, Celsrl, Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1g, Col17a1 , Grb7, Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2,Llgl2, Anxa8, Krt5, Tmprssl 1e, Ppi, Dennd2c, Tacstd2, Sprrla, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl, Tmem63b, Grhl2, Cldn4, Krt14, TtlHO, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1, and Itgb4; genes of the Psca metagene including Psca, Mai, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1 d, Cblc, Ceacaml, Gstol, Tmprssl 1g, Anxal, Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1bnl, Krt13, Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, Upk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinbl 1 , Rab25, Dsg3, Prss22, Tmprssl 1a, Calml3, Epn3, Slc6a20a, Tmprss11e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl , Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rab11fip1, Ocln, Crispl, Prss8, Pglyrp4, Kif21 a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1 , Gstal , Gstal , Pvrl4, Arhgefl 01, Elf5, Mapk13, Ikzf2, Tjp3, Osginl , Gsta2, Cldn7, Epb4.115, Duoxa2, Zfp750, Zdhhc13, Gm10639, Klk11 , Arhgap40, Arg1, Ltf, Rnf223, and St14; genes of the Cd44 metagene, including Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Fam83h, Col17a1, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpzl2, Arhgef5, Spint2, 1810019J 16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltHb, Grb7, Esrp2, Lsr, Itga3, Plekha7, Dsg3, Clca5, Ap1m2, Plch2, Arhgef5, Celsrl , Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5,Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgefl 6, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1 , Lypd3, Trim29, Tmprssl 1g, Cnksrl, Tmprssl 1bnl, Mir200b, Ptprf, Gm9908, Dlg1 , Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, 1117re, Fat1, Nrg1, Mdfi, and Nipal2; genes of the Proml metagene, including Prom1, Ceacaml, Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca, Tmprssl 1d, Cwh43, Slc37a1, Marveld2, Arhgefl 01, Gclm, Ocln, Mctp2, Lrrc26, Fxyd3, lldrl, Cblc, Spintl, Cldn4, Slc52a3, Tmprssl 1g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, Upk3bl, Slc9a3r1, Mall, Sostdcl, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2H, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO, Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprssl 1bnl, Gpx2, Gstol, Spns2, Serpinbl 1, Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N1 ORik, Sh3yl1 , Slc5a9, SarndlO, Elf3, St14, Ikzf2, Kif21 a, and Erbb3; genes of the Prom2 metagene, including Prom2, Clic3, Tmem54, Evpl, Zfp750, GrhH, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8H, Gltp, Llgl2, Ovoll, Tmprssl 3, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14, Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinbl 1, H22ra1, Erbb2, Dsc2, Rnf39, Tmprssl 1e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, Arhgefl 01, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl,Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1, Ttc39a, Spintl , Ppfia3, S100a7a, Dsp, Chitl , Pinlyp, Grb7, Tmem79, Barx2, Klk10, Perp, Efna3, CcbH, Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml, Slc6a20a, SytH, Rnf223, Ide, Calml3, Caszl , and Celsr2; genes of the Bmi1 metagene comprises genes selected from Bmi1 , Klhdc2, Bbx, Tusc3, Gig 1 , Blocl s6, Wdr34, 5730455P16 Ri k, Hs2st1 , Terf2, Fut8, Zmym4, Pcm1 , Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajcIO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301 B20Rik, Mib1, Tiam2, Cers2, Stk3, Hspa13, Txndc12, Dock7, Psmd5, Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1, Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy19l1, Ilf3, Bbs4, Slc30a4, InppH, Inf2, Zmynd11, Atp8b2, Gludl, Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, Kifap3, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7; genes of the Sox4 metagene, including Sox4, Abl1, Rab34, Fgfrll, Ptovl, Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl, Tcf3, Tcf12, Clip2, Bbx, Nf1, Spats2, Farpl , Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl , Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl, MicalH, Ubxn7, Mvb12b, Trio, Stonl, Dok1, Fam65a, Fmnl3, Hsf2, Sestdl, Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1, Cep120, Rnf139, Dpy1911 , Dbn1, Ctps2, Magedl, Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbl , AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl , Staul , Mecp2, Phf20, Pex11 b, Ehmt2, Cep170, Fgf r1 , Txndc5, Zmym4, Samdl 4, Kansl2, Teadl , Zkscanl 7, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdm1 a, Loxl3, Acvrl , Wwtrl , AsxH , and Phf2; genes of the Lrigl metagene including Lrigl, Rgmb, Zcchc24, Teadl, Lambl, Cep170, Evalb, Sept9, Farpl, Satb2, Maplb, Ccdc88a, Axl, Loxl3, Pdgfra, Ust, Lgalsl, KifapS, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamd , Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1, Stx2, Lbh, Wipfl, Igfbp4, Myo9a, Cul7, Abl1, Phf20, Xxyltl, Myo9a, Dok1, Dst, Gkapl, Tspan11, Phldbl, Sydel, Teadl, Rab34, Stxbpl , AI597468, St6gal1, Ilk, Zeb1, Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl , Ank, Displ , Fhl3, Fermt2, Cdr2, Dock5, Crabpl, S1pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl, Sdccag8, Gliprl, and Nnt; genes of the Lgr6 metagene, including Lgr6, Tnnt2, Cnnm4, Prss12, Sox9, Itga2, Shf, Igsf8, Itpr3, Nt5e, Bhlhe41, Fzd7, Krt18, Arid5a, Tgfbl, Tes, Raplgap, Add2, Sdd, Jam2, Gpr39, B4galnt1, D8Ertd82e, Plekhg3, Lamc2, Socs2, Rampl, Etv6, Lamb3, Egr3, Dusp6, Foxpl, Dnaja4, Tnfrsf12a, Pip4k2c, Rnf181, Anol, A130010J15Rik, 1118r1, Chst2, Jag1, 1600029D21 Rik, Tnfsf9, Src, Runxl, Rhbddl, Smad7, Itga6, Socs2, Slco2a1, Aplp2, Cd9, Rail 4, Smurf 1, Nedd9, C1galt1, Pmepal, Padi3, Gpr25, Fermtl, Nav2, Arhgef3, Capnsl, Foxp4, Ubald2, Gm7367, Gm7367, Ctnnal, Cd80, Hivep2,Dyrk3, Rab6a, Runx2, Iqgapl , Ggct, Lrch4, Skil, Frrsl , Slc20a2, Ncmap, Reep3, Nadsynl , Bhlhe40, Gprc5a, Slc39a4, Hes6, Acsl3, Erc1 , Lama5, Ephb4, Rmnd5b, Plekhal , Bcr, Zbtb18, Shq1 , Scyl2, Padi4, Scin, Dhcr7, and Atpl Od; and genes of the Sox9 metagene, including Sox9, Lgr6, Shf, Cnnm4, Runxl , Ctnnal , Capnsl , Rail 4, Itpr3, Runx2, Iqgapl , Bhlhe41 , Rnf181 , Ccndl , Prss12, Tes, Aig1 , Foxc2, Raplgap, Krt18, Rab6a, Etv6, Dusp6, Igsf8, Tubgcp2, Alcam, Sos2, Dusp4, Bzw2, Nck2, Add2, Foxpl , Ubald2, Tnnt2, Kcnn4, Fzd7, Reep3, Nav2, Cpe, Casp3, Cnot7, Cttn, Anol , Bcarl , Cyth2, Myof, Egr3, Nadsynl , Nt5e, Dnaja4, Plekhal , Capg, Phc2, Itga2, B4galnt1 , Smurfl , Gtf2ird1 , Pwwp2b, Phldal , Enppl , Nfat5, Cd151 , Hivep2, Ppmel , Tgifl , Gm7367, Gm7367, Zbtb18, Sdc4, D630045J12Rik, Smad7, Slc20a2, Igfl r, Rsf1 , Tnfrsf12a, Slc27a1 , Chst2, 2810408A1 1 Rik, IgfbpS, Kdelrl , Ern1 , Atxn2l,Dyrk3, Tgfbl , Bhlhe40, Phrfl , Tnfrsf22, Ddhdl , Traf4, A130010J15Rik, Papd7, Mast4, Skil, Pyroxdl , Fubp3, Nr1 h2, Ctnnbl , Foxci , Tbc1 d1 , and 181001 101 ORik.

[0109] A "reference level" or "reference value" of a biomarker means a level of the biomarker that is indicative of a particular cell state or lack thereof. A "positive" reference level of a biomarker means a level that is indicative of a particular cell state. A "negative" reference level of a biomarker means a level that is indicative of a lack of a particular cell state. A "reference level" of a biomarker may be an absolute or relative amount or concentration of the biomarker, a presence or absence of the biomarker, a range of amount or concentration of the biomarker, a minimum and / or maximum amount or concentration of the biomarker, a mean amount or concentration of the biomarker, and / or a median amount or concentration of the biomarker; and, in addition, "reference levels" of combinations of biomarkers may also be ratios of absolute or relative amounts or concentrations of two or more biomarkers with respect to each other. Appropriate positive and negative reference levels of biomarkers for a particular cell state or lack thereof may be determined by measuring levels of desired biomarkers in one or more appropriate cells or tissue samples, and such reference levels may be tailored to specific cells or tissues (e.g., a reference level may be cell-type matched, tissue type-matched, cancer type-matched, age-matched, gender-matched) so that comparisons may be made between biomarker levels in samples from cells or tissue for a particular pre-malignant cell or cancerous cell of a particular tissue or tumor type from an individual of a certain age or gender group). Such reference levels may also be tailored to specific techniques that are used to measure levels of biomarkers in biological samples (e.g., reverse transcription polymerase chain reaction (RT-PCR), RNA sequencing (e.g., single cell RNA sequencing or bulk RNA sequencing), global run-on sequencing, microarray analysis, immunoassays (e.g., ELISA, electrochemiluminescence-based immunoassay, or immunofluorescent assay), aptamer-based proteomic assays, mass spectrometry (e.g., LC-MS, GC-MS, or tandem mass spectrometry), NMR, biochemical orenzymatic assays, etc.), where the levels of biomarkers may differ based on the specific technique that is used.

[0110] A "similarity value" is a number that represents the degree of similarity between two things being compared. For example, a similarity value may be a number that indicates the overall similarity between a biomarker profile using specific phenotype-related biomarkers and reference value ranges for the biomarkers in one or more control samples or a reference profile (e.g., the similarity to “an expression profile for a cell state having lineage plasticity and drug resistance” or “an expression profile for a proliferative cell state”). The similarity value may be expressed as a similarity metric, such as a correlation coefficient, or may simply be expressed as the expression level difference, or the aggregate of the expression level differences, between levels of biomarkers in a patient sample and a control sample or reference expression profile.

[0111] The terms "quantity", "amount", and "level" are used interchangeably herein and may refer to an absolute quantification of a molecule or an analyte in a sample, or to a relative quantification of a molecule or analyte in a sample, i.e., relative to another value such as relative to a reference value as taught herein, or to a range of values for the biomarker. These values or ranges can be obtained from a single cell or from multiple cells or obtained from normal, pre-malignant, or cancerous tissue from a single patient or a group of patients.

[0112] The term “biological sample” encompasses samples of fluids, cells, or tissue isolated from a subject, including but not limited to, samples of skin, organs, or tissue obtained by surgical resection or biopsy (e.g., tumor sample, papilloma sample), and also samples of in vitro cell culture constituents, including but not limited to, cells in culture, cell lysates, conditioned media resulting from the growth of cells and tissues in culture medium, recombinant cells, and cell components. The definition also includes samples that have been manipulated in any way after their procurement, such as by treatment with reagents, washed, or enriched for particular types of molecules, e.g., biomarker mRNA transcripts, proteins, peptides, etc.

[0113] The term “biological sample” encompasses a clinical sample, solid tissue samples such as a biopsy specimen or tissue cultures or cells derived or isolated therefrom, and the progeny thereof. A “biological sample” can include cells (e.g., tumor cells, cancerous cells, pre-malignant cells, normal cells, tissue cells etc.) can be suspected of comprising such cells, or can be devoid of cells. A biological sample can include biological fluids derived from cells (e.g., tumor cells, cancerous cells, pre-malignant cells, etc.), e.g., a sample comprising polynucleotides and / or polypeptides that is obtained from such cells (e.g., a cell lysate or other cell extract comprising polynucleotides and / or polypeptides).

[0114] Obtaining and assaying a sample. The term “assaying” is used herein to include the physical steps of manipulating a biological sample to generate data related to the biological sample. As will be readily understood by one of ordinary skill in the art, a biological sample mustbe “obtained” prior to assaying the sample. Thus, the term “assaying” implies that the sample has been obtained. The terms “obtained” or “obtaining” as used herein encompass the act of receiving an extracted or isolated biological sample. For example, a testing facility can “obtain” a biological sample in the mail (or via delivery, etc.) prior to assaying the sample. In some such cases, the biological sample was “extracted” or “isolated” from an individual by another party prior to mailing (i.e., delivery, transfer, etc.), and then “obtained” by the testing facility upon arrival of the sample. Thus, a testing facility can obtain the sample and then assay the sample, thereby producing data related to the sample.

[0115] The terms “obtained” or “obtaining” as used herein can also include the physical extraction or isolation of a biological sample from a subject. Accordingly, a biological sample can be isolated from a subject (and thus “obtained”) by the same person or same entity that subsequently assays the sample. When a biological sample is “extracted” or “isolated” from a first party or entity and then transferred (e.g., delivered, mailed, etc.) to a second party, the sample was “obtained” by the first party (and also “isolated” by the first party), and then subsequently “obtained” (but not “isolated”) by the second party. Accordingly, in some embodiments, the step of obtaining does not comprise the step of isolating a biological sample.

[0116] In some embodiments, the step of obtaining comprises the step of isolating a biological sample (e.g., a pre-treatment biological sample, a post-treatment biological sample, etc.). Methods and protocols for isolating various biological samples will be known to one of ordinary skill in the art and any convenient method may be used to isolate a biological sample.

[0117] It will be understood by one of ordinary skill in the art that in some cases, it is convenient to wait until multiple samples have been obtained prior to assaying the samples. Accordingly, in some cases an isolated biological sample is stored until all appropriate samples have been obtained. One of ordinary skill in the art will understand how to appropriately store a variety of different types of biological samples and any convenient method of storage may be used (e.g., refrigeration) that is appropriate for the particular biological sample. In some embodiments, a pretreatment biological sample is assayed prior to obtaining a post-treatment biological sample. In some cases, a pre-treatment biological sample and a post-treatment biological sample are assayed in parallel. In some cases, multiple different post-treatment biological samples and / or a pre-treatment biological sample are assayed in parallel. In some cases, biological samples are processed immediately or as soon as possible after they are obtained.

[0118] In the subject methods, the concentration (i.e., “level”), or expression level of a gene product, which may be an RNA, a protein, etc., in a biological sample is measured (i.e., “determined”). By “expression level” (or “level”) it is meant the level of a gene product (e.g. the absolute and / or normalized value determined for the RNA expression level or for the expression level of the encoded polypeptide, or the concentration of the protein in a biological sample). Theterm “gene product” or “expression product” are used herein to refer to the RNA transcription products (RNA transcripts, e.g., nascent RNA, mRNA, pre-mRNA, unspliced RNA, splice variant mRNA, and / or fragmented RNA) of the gene, including mRNA, and the polypeptide translation products of such RNA transcripts. A gene product can be, for example, a nascent RNA, an unspliced RNA, an mRNA, a pre-mRNA, a splice variant mRNA, a fragmented RNA, a polypeptide, a post-translationally modified polypeptide, a splice variant polypeptide, etc. Measuring a level of transcription of a gene may comprise measuring the absolute level and / or normalized value determined for the level of a nascent RNA, an unspliced RNA, an mRNA, a pre- mRNA, a splice variant mRNA, or a fragmented RNA in a biological sample.

[0119] The terms “determining”, “measuring”, “evaluating”, “assessing,” “assaying,” and “analyzing” are used interchangeably herein to refer to any form of measurement, and include determining if an element is present or not. These terms include both quantitative and / or qualitative determinations. Assaying may be relative or absolute. For example, “assaying” can be determining whether the expression level or transcription level is less than or “greater than or equal to” a particular threshold, (the threshold can be pre-determined or can be determined by assaying a control sample). On the other hand, “assaying” to determine the expression level or transcription level can mean determining a quantitative value (using any convenient metric) that represents the level of expression (i.e., expression level, e.g., the amount of protein and / or RNA, e.g., nascent RNA or mature mRNA) of a particular biomarker gene. The level of expression can be expressed in arbitrary units associated with a particular assay (e.g., fluorescence units, e.g., mean fluorescence intensity (MFI)), or can be expressed as an absolute value with defined units (e.g., number of nascent RNA or mature mRNA transcripts, number of RNA transcripts, concentration of RNA, etc.). Additionally, the level of expression of a biomarker gene can be compared to the expression level of one or more additional genes (e.g., nucleic acids and / or their encoded proteins) to derive a normalized value that represents a normalized expression level. The specific metric (or units) chosen is not crucial as long as the same units are used (or conversion to the same units is performed) when evaluating multiple biological samples from the same individual (e.g., biological samples taken at different points in time from the same individual). This is because the units cancel when calculating a fold-change (i.e., determining a ratio) in the expression level from one biological sample to the next (e.g., biological samples taken at different points in time from the same individual).

[0120] For measuring RNA levels, the amount or level of an RNA biomarker in the sample is determined. In some instances, the level of one or more additional RNAs may also be measured, and the level of an RNA biomarker compared to the level of the one or more additional RNAs to provide a normalized value for the RNA biomarker level. Any convenient protocol for evaluatingRNA levels may be employed wherein the level of one or more RNAs in the assayed sample is determined.

[0121] A number of exemplary methods for measuring RNA (e.g., nascent RNA or mRNA) levels in a sample are known by one of ordinary skill in the art, and any convenient method can be used. Exemplary methods include, but are not limited to: GRO-seq to measure levels of nascent RNA transcripts (see, e.g., Gardini et al. (2017) Methods Mol. Biol. 1468:1 11 -120, Tzerpos et al. (2021 ) Methods Mol. Biol. 2351 :25-39.Jordan-Pla et al. (2019) Methods 159-160:177-182, Cardiello et al. (2020) Transcription 11 (1 ):3-18; herein incorporated by reference in their entireties), RNA-seq to measure levels of RNA transcripts (see, e.g., Hrdlickova et al. (2017) Wiley Interdiscip Rev RNA 8(1 ):10.1002 / wrna.1364, Wang et al. (2009) Nat. Rev. Genet. 10(1 ):57-63; Withanage et al. (2022) Methods Mol. Biol. 2418:405-424; Owens et al. (2019) Cold Spring Harb Protoc. 2019(6); herein incorporated by reference in their entireties), hybridization-based methods such as Northern blotting, array hybridization (e.g., microarray); in situ hybridization; and in situ hybridization followed by FACS, and the like (see, e.g., Parker & Barnes (1999) Methods in Molecular Biology 106:247-283); RNAse protection assays (Hod (1992) Biotechniques 13:852- 854); PCR-based methods such as reverse transcription PCR (RT-PCR), quantitative RT-PCR (qRT-PCR), real-time RT-PCR, and the like (see, e.g., Weis et al. (1992) Trends in Genetics 8:263-264); and the like. See also, Robert E. Farrell Jr, RNA Methodologies: A Laboratory Guide for Isolation and Characterization (6thEdition, Academic Press, November 22, 2022; herein incorporated by reference in its entirety.

[0122] In some embodiments, the biological sample can be assayed directly. In some embodiments, nucleic acids of the biological sample are amplified (e.g., by PCR) prior to assaying. For example, techniques such as PCR (Polymerase Chain Reaction), RT-PCR (reverse transcriptase PCR), qRT-PCR (quantitative RT-PCR, real time RT-PCR), etc. can be used prior to the hybridization methods and / or the sequencing methods discussed above.

[0123] For measuring protein levels, the amount or level of a protein in the biological sample is determined. In some cases, the protein comprises a post-translational modification (e.g., phosphorylation, glycosylation) associated with regulation of activity of the protein such as by a signaling cascade, wherein the modified protein is the biomarker, and the amount of the modified protein is therefore measured. In some embodiments, an extracellular protein level is measured. For example, in some cases, the protein (i.e. , polypeptide) being measured is a secreted protein, and the concentration can be measured in blood or plasma. In some embodiments, concentration is a relative value measured by comparing the level of one protein relative to another protein. In other embodiments the concentration is an absolute measurement of weight / volume or weight / weight.

[0124] In some instances, the concentration of one or more additional proteins may also be measured, and biomarker concentration is compared to the level of the one or more additional proteins to provide a normalized value for the biomarker concentration. Any convenient protocol for evaluating protein levels may be employed wherein the level of one or more proteins in the assayed sample is determined.

[0125] While a variety of different methods of assaying protein levels are known to one of ordinary skill in the art, and any convenient method may be used, two representative and convenient techniques for assaying protein levels include antibody-based methods such as the enzyme-linked immunosorbent assay (ELISA) and electrochemiluminescence-based immunoassays.

[0126] In ELISA and ELISA-based assays, one or more antibodies specific for the proteins of interest may be immobilized onto a selected solid surface, preferably a surface exhibiting a protein affinity such as the wells of a polystyrene microtiter plate. After washing to remove incompletely adsorbed material, the assay plate wells are coated with a non-specific “blocking” protein that is known to be antigenically neutral with regard to the test sample such as bovine serum albumin (BSA), casein or solutions of powdered milk. This allows for blocking of nonspecific adsorption sites on the immobilizing surface, thereby reducing the background caused by non-specific binding of antigen onto the surface. After washing to remove unbound blocking protein, the immobilizing surface is contacted with the sample to be tested under conditions that are conducive to immune complex (antigen / antibody) formation. Following incubation, the antisera-contacted surface is washed so as to remove non-immunocomplexed material. The occurrence and amount of immunocomplex formation may then be determined by subjecting the bound immunocomplexes to a second antibody having specificity for the target that differs from the first antibody and detecting binding of the second antibody. In certain embodiments, the second antibody will have an associated enzyme, e.g. urease, peroxidase, or alkaline phosphatase, which will generate a color precipitate upon incubating with an appropriate chromogenic substrate. After such incubation with the second antibody and washing to remove unbound material, the amount of label is quantified, for example by incubation with a chromogenic substrate such as urea and bromocresol purple in the case of a urease label or 2,2'-azino-di-(3- ethyl-benzthiazoline)-6-sulfonic acid (ABTS) and H2O2, in the case of a peroxidase label. Quantitation is then achieved by measuring the degree of color generation, e.g., using a visible spectrum spectrophotometer.

[0127] The preceding format may be altered by first binding the sample to the assay plate. Then, primary antibody is incubated with the assay plate, followed by detecting of bound primary antibody using a labeled second antibody with specificity for the primary antibody. The solid substrate upon which the antibody or antibodies are immobilized can be made of a wide varietyof materials and in a wide variety of shapes, e.g., microtiter plate, microbead, dipstick, resin particle, etc. The substrate may be chosen to maximize signal to noise ratios, to minimize background binding, as well as for ease of separation and cost. Washes may be effected in a manner most appropriate for the substrate being used, for example, by removing a bead or dipstick from a reservoir, emptying or diluting a reservoir such as a microtiter plate well, or rinsing a bead, particle, chromatographic column or filter with a wash solution or solvent.

[0128] Electrochemiluminescence-based immunoassays utilize a biomarker-specific antibody tagged with an electrochemiluminescent luminophore that generates a high-energy species in an electron transfer reaction at an electrode. The species generated at the electrode is in an electronically excited state, which emits light upon relaxation to a lower-energy state. Photons generated by the electrochemiluminescent luminophore may be detected, for example, with photomultiplier tubes or silicon photodiode or gold coated fiber-optic sensors. In some embodiments, the electrochemiluminescent luminophore comprises a ruthenium complex (e.g., Ru(bpy)32+) or silicon nanoparticle. For a description of electrochemiluminescence-based immunoassays, see, e.g., Wang et al. (2023) Bioelectrochemistry 149:108281 , Muzyka et al. (2014) Biosens. Bioelectron. 54:393-407, Keustermans et al. (2013) Methods 61 (1 ):10-7, and Sornambigai et al. (2023) Anal. Bioanal. Chem. 415(24):5875-5898; herein incorporated by reference in their entireties.

[0129] Alternatively, other methods for measuring the levels of one or more proteins in a sample may be employed. Representative exemplary methods include but are not limited to antibodybased methods (e.g., immunofluorescence assay, radioimmunoassay, immunoprecipitation, Western blotting, proteomic arrays, xMAP microsphere technology (e.g., Luminex technology), immunohistochemistry, flow cytometry, and the like) as well as non-antibody-based methods (e.g., aptamer-based proteomic assays, nuclear magnetic resonance, mass spectrometry, liquid chromatography-mass spectrometry, or tandem mass spectrometry).Additional terms.

[0130] The terms "treatment", "treating", "treat" and the like are used herein to generally refer to obtaining a desired pharmacologic and / or physiologic effect. The effect can be prophylactic in terms of completely or partially preventing a disease or symptom(s) thereof and / or may be therapeutic in terms of a partial or complete stabilization or cure for a disease and / or adverse effect attributable to the disease. The term "treatment" encompasses any treatment of a disease in a mammal, particularly a human, and includes: (a) preventing the disease and / or symptom(s) from occurring in a subject who may be predisposed to the disease or symptom but has not yet been diagnosed as having it; (b) inhibiting the disease and / or symptom(s), i.e., arresting their development; or (c) relieving the disease symptom(s), i.e., causing regression of the diseaseand / or symptom(s). Those in need of treatment include those already inflicted (e.g., those with a drug resistant cancer or premalignant lesion) as well as those in which prevention is desired, those with a genetic predisposition to developing a drug resistant cancer or premalignant lesion, those with cancer susceptible to developing drug resistance (e.g., those undergoing chemotherapy, etc.).

[0131] A therapeutic treatment is one in which the subject is inflicted prior to administration and a prophylactic treatment is one in which the subject is not inflicted prior to administration. In some embodiments, the subject has an increased likelihood of becoming inflicted or is suspected of being inflicted prior to treatment. In some embodiments, the subject is suspected of having an increased likelihood of becoming inflicted.

[0132] The terms “individual”, “subject”, and “patient” are used interchangeably herein and refer to any mammalian subject for whom diagnosis, treatment, or therapy is desired, particularly humans. Mammals include human and non-human mammals such as non-human primates, including chimpanzees and other apes and monkey species; laboratory animals such as mice, rats, rabbits, hamsters, guinea pigs, and chinchillas; domestic animals such as dogs and cats; farm animals such as sheep, goats, pigs, horses and cows. In some cases, the methods of the invention find use in experimental animals, in veterinary application, and in the development of animal models for disease, including, but not limited to, rodents including mice, rats, and hamsters; primates, and transgenic animals.

[0133] “Isolated” refers to an entity of interest that is in an environment different from that in which it may naturally occur. “Isolated” is meant to include entities that are within samples that are substantially enriched for the entity of interest and / or in which the entity of interest is partially or substantially purified.

[0134] "Substantially purified" generally refers to isolation of a component such as a substance (compound, drug, inhibitor, metabolite, nucleic acid, polynucleotide, protein, or polypeptide) such that the substance comprises the majority percent of the sample in which it resides. Typically in a sample, a substantially purified component comprises 50%, preferably 80%-85%, more preferably 90-95% of the sample. Techniques for purifying polynucleotides and polypeptides of interest are well-known in the art and include, for example, ion-exchange chromatography, affinity chromatography, gel filtration, and sedimentation according to density.

[0135] The terms "pharmaceutically acceptable", "physiologically tolerable" and grammatical variations thereof, as they refer to compositions, carriers, diluents and reagents, are used interchangeably and represent that the materials are capable of administration to or upon a human without the production of undesirable physiological effects to a degree that would prohibit administration of the composition.

[0136] The terms "polypeptide," "peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. Both full-length proteins and fragments thereof are encompassed by the definition. The terms also include postexpression modifications of the polypeptide, for example, phosphorylation, glycosylation, acetylation, hydroxylation, oxidation, and the like.

[0137] The terms "polynucleotide," "oligonucleotide," "nucleic acid" and "nucleic acid molecule" are used herein to include a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, the term includes triple-, double- and single-stranded DNA, as well as triple-, double- and single-stranded RNA. It also includes modifications, such as by methylation and / or by capping, and unmodified forms of the polynucleotide. More particularly, the terms "polynucleotide," "oligonucleotide," "nucleic acid" and "nucleic acid molecule" include polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), and any other type of polynucleotide which is an N- or C-glycoside of a purine or pyrimidine base. There is no intended distinction in length between the terms "polynucleotide," "oligonucleotide," "nucleic acid" and "nucleic acid molecule," and these terms are used interchangeably.

[0138] By “test agent,” “candidate agent,” and grammatical equivalents herein, which terms are used interchangeably herein, is meant any molecule including macromolecules (e.g., proteins, antibodies, polynucleotides), small molecules (e.g., 5-1000 Da, 100-750 Da, 200-500 Da, or less than 500 Da in size), organic or inorganic molecules, drugs, etc. that are to be tested for activity (e.g., ability to switch a pre-malignant or cancerous cell is in a cell state having lineage plasticity and drug resistance to a non-drug resistant proliferative cell state) in a subject assay.

[0139] The term "animal" is used herein to include all vertebrate animals, except humans. The term also includes animals at all stages of development, including embryonic, fetal, neonate, and adult stages. Animals may include any member of the subphylum Chordata, including, without limitation, non-human primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs; birds, including domestic, wild and game birds such as chickens, turkeys and other gallinaceous birds, ducks, geese, and the like.

[0140] By "transgenic animal" is meant a non-human animal, usually a mammal, having a non- endogenous (i.e., heterologous or foreign) nucleic acid sequence present as an extrachromosomal element in a portion of its cells or stably integrated into its germ line DNA (i.e., in the genomic sequence of most or all of its cells). A heterologous nucleic acid is introduced into the germ line of such transgenic animals by genetic manipulation of, for example, embryos or embryonic stem cells of the host animal according to methods well known in the art. A "transgene"is meant to refer to such a heterologous nucleic acid, e.g., heterologous nucleic acid in the form of an expression construct (e.g., for the production of a "knock-in" transgenic animal) or a heterologous nucleic acid that upon insertion within or adjacent a target gene results in a decrease in target gene expression (e.g., for production of a "knock-out" transgenic animal). Accordingly, when a DNA molecule is artificially introduced into the cells of an animal, a "transgenic animal" is produced. The DNA molecule is called a "transgene" and may contain one or many genes. By inserting a transgene into a fertilized oocyte or cells from an early embryo, the resulting transgenic animal may be able to transmit the foreign DNA stably in its germline.

[0141] The terms "tumor," "cancer" and "neoplasia" are used interchangeably and refer to a cell or population of cells whose growth, proliferation or survival is greater than growth, proliferation or survival of a normal counterpart cell, e.g., a cell proliferative, hyperproliferative or differentiative disorder. Typically, the growth is uncontrolled. The term "malignancy" refers to invasion of nearby tissue. The term "metastasis" or a secondary, recurring or recurrent tumor, cancer or neoplasia refers to spread or dissemination of a tumor, cancer or neoplasia to other sites, locations or regions within the subject, in which the sites, locations or regions are distinct from the primary tumor or cancer. Neoplasia, tumors and cancers include benign, malignant, metastatic and non- metastatic types, and include any stage (I, II, III, IV or V) or grade (G1 , G2, G3, etc.) of neoplasia, tumor, or cancer, or a neoplasia, tumor, cancer or metastasis that is progressing, worsening, stabilized or in remission. In particular, the terms "tumor," "cancer" and "neoplasia" include carcinomas, such as squamous cell carcinoma, adenocarcinoma, adenosquamous carcinoma, anaplastic carcinoma, large cell carcinoma, and small cell carcinoma, and include cancers such as, but are not limited to, pancreatic cancer, lung cancer (non-small cell lung cancer, small cell lung cancer), gastric cancer, ovarian cancer, endometrial cancer, colorectal cancer, oral cancer, skin cancer, cholangiocarcinoma, head and neck cancer, breast cancer, ovarian cancer, melanoma, peripheral neuroma, glioblastoma, adrenocortical carcinoma, AIDS-related lymphoma, anal cancer, bladder cancer, meningioma, glioma, astrocytoma, cervical cancer, chronic myeloproliferative disorders, colon cancer, endometrial cancer, ependymoma, esophageal cancer, Ewing's sarcoma, extracranial germ cell tumors, extrahepatic bile duct cancer, gallbladder cancer, gastrointestinal carcinoid tumors, gestational trophoblastic tumors, hairy cell leukemia, Hodgkin lymphoma, non-Hodgkin lymphoma, hypopharyngeal cancer, islet cell carcinoma, Kaposi sarcoma, laryngeal cancer, leukemia, lip cancer, oral cavity cancer, liver cancer, malignant mesothelioma, medulloblastoma, Merkel cell carcinoma, metastatic squamous neck cell carcinoma, multiple myeloma and other plasma cell neoplasms, mycosis fungoides and the Sezary syndrome, myelodysplastic syndromes, nasopharyngeal cancer, neuroblastoma, oropharyngeal cancer, bone cancers, including osteosarcoma and malignant fibrous histiocytoma of bone, paranasal sinus cancer, parathyroid cancer, penile cancer,pheochromocytoma, pituitary tumors, prostate cancer, rectal cancer, renal cell cancer, retinoblastoma, rhabdomyosarcoma, salivary gland cancer, small intestine cancer, soft tissue sarcoma, supratentorial primitive neuroectodermal tumors, pineoblastoma, testicular cancer, thymoma, thymic carcinoma, thyroid cancer, transitional cell cancer of the renal pelvis and ureter, urethral cancer, uterine sarcoma, vaginal cancer, vulvar cancer, and Wilm's tumor and other childhood kidney tumors.

[0142] As used herein, the term “metastatic cancer” or a secondary, recurring, or recurrent tumor or cancer are used interchangeably and refers to cancer that spreads from where it started to a distant part of the body. For many types of cancer, it is also called stage IV (4) cancer. When observed under a microscope and tested in other ways, metastatic cancer cells can have features like that of the primary cancer and not like the cells in the place where the metastatic cancer is found. Metastatic cancer is referred to by the same name as the primary cancer. For example, breast cancer that spreads to the lung is called metastatic breast cancer, not lung cancer.

[0143] As used herein, the term “metastasis” refers to the spread of cancer cells from the place where they first formed to another part of the body. In metastasis, cancer cells break away from the original (primary) tumor, travel through the blood or lymph system, and form a new tumor in other organs or tissues of the body.

[0144] The term “refractory”, used herein, refers to a disease or condition that does not respond to treatment. With regard to cancer, “refractory cancer”, as used herein, refers to cancer that does not respond to treatment. A refractory cancer may be resistant at the beginning of treatment or it may become resistant during treatment. Refractory cancer may also be called resistant cancer.

[0145] “Providing an analysis” is used herein to refer to the delivery of an oral or written analysis (i.e., a document, a report, etc.). A written analysis can be a printed or electronic document. A suitable analysis (e.g., an oral or written report) provides any or all of the following information: identifying information of the subject (name, age, etc.), a description of what type of biological sample(s) was used and / or how it was used, the technique used to assay the sample, the results of the assay (e.g., the level of the biomarker as measured, and / or the fold-change of a biomarker level over time, or in a post-treatment assay compared to a pre-treatment assay), an assessment as to whether a candidate agent can switch a cancerous or pre-malignant cell from a cell state having lineage plasticity and drug resistance to a non-drug resistant proliferative cell state that can be treated with anti-mitotic therapeutic agents, an assessment as to whether an individual is determined to have a drug resistant cancer or pre-malignant lesion, a recommendation for treatment, and / or to continue or alter therapy, a recommended strategy for additional therapy, etc. The report can be in any format including, but not limited to printed information on a suitable medium or substrate (e.g., paper); or electronic format. If in electronic format, the report can be in any computer readable medium, e.g., diskette, compact disk (CD), flash drive, and the like, onwhich the information has been recorded. In addition, the report may be present as a website address which may be used via the internet to access the information at a remote site.

[0146] A “CRISPR system" refers collectively to transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated ("Cas") genes. In some embodiments, one or more elements of a CRISPR system is derived from a type I, type II, or type III CRISPR system. In some embodiments, one or more elements of a CRISPR system is derived from a particular organism comprising an endogenous CRISPR system, such as Streptococcus pyogenes. In general, a CRISPR system is characterized by elements that promote the formation of a CRISPR complex at the site of a target sequence.

[0147] The term "Cas9" as used herein encompasses type II clustered regularly interspaced short palindromic repeats (CRISPR) system Cas9 endonucleases from any species, and also includes biologically active fragments, variants, analogs, and derivatives thereof that retain Cas9 endonuclease activity (i.e., catalyze site-directed cleavage of DNA to generate double-strand breaks).

[0148] A Cas9 endonuclease binds to and cleaves DNA at a site comprising a sequence complementary to its bound guide RNA (gRNA). For purposes of Cas9 targeting, a gRNA may comprise a sequence "complementary" to a target sequence (e.g., in an exon or an intron of a gene), capable of sufficient base-pairing to form a duplex (i.e., the gRNA hybridizes with the target sequence). Additionally, the gRNA may comprise a sequence complementary to a PAM sequence, wherein the gRNA also hybridizes with the PAM sequence in a target DNA.

[0149] The Cas 9 protein naturally contains DNA endonuclease activity that depends on association of the protein with two naturally occurring or synthetic RNA molecules called crRNA and tracrRNA (also called guide RNAs). In some cases, the two molecules are covalently linked to form a single molecule (also called a single guide RNA (“sgRNA”)). Thus, the Cas9 associates with a DNA-targeting RNA (which term encompasses both the two-molecule guide RNA configuration and the single-molecule guide RNA configuration), which activates the Cas9 or Cas9-like protein and guides the protein to a target nucleic acid sequence. If the Cas9 protein retains its natural enzymatic function, it will cleave target DNA to create a double-strand break, which can lead to genome alteration (i.e., editing: deletion, insertion (when a donor polynucleotide is present), replacement, etc.), thereby altering gene expression.

[0150] The term "CRISPR agent” as used herein encompasses any agent (or nucleic acid encoding such an agent), comprising naturally occurring and / or synthetic sequences, that can be used in a Cas9-based system (e.g., a Cas9 or Cas9-like protein; any component of a DNA- targeting RNA, e.g., a crRNA-like RNA, a tracrRNA-like RNA, a single guide RNA, etc.; a donor polynucleotide; and the like).

[0151] A Cas9 polynucleotide, nucleic acid, oligonucleotide, protein, polypeptide, or peptide refers to a molecule derived from any source. The molecule need not be physically derived from an organism, but may be synthetically or recombinantly produced. Cas9 sequences from a number of bacterial species are well known in the art and listed in the National Center for Biotechnology Information (NCBI) database. See, for example, NCBI entries for Cas9 from: Streptococcus pyogenes (WP_002989955, WP_038434062, WP_01 1528583); Campylobacter jejuni (WP_022552435, YP_002344900), Campylobacter coli (WP_060786116); Campylobacter fetus (WP_059434633); Corynebacterium ulcerans (NC_015683, NC_017317);Corynebacterium diphtheria (NC_016782, NC_016786); Enterococcus faecalis(WP_033919308); Spiroplasma syrphidicola (NC_021284); Prevotella intermedia (NC_017861 ); Spiroplasma taiwanense (NC_021846); Streptococcus iniae (NC_021314); Belliella baltica (NC_018010); Psychroflexus torquisl (NC_018721 ); Streptococcus thermophilus (YP_820832), Streptococcus mutans (WP_061046374, WP_024786433); Listeria innocua (NP_472073); Listeria monocytogenes (WP_061665472); Legionella pneumophila (WP_062726656); Staphylococcus aureus (WP_001573634); Francisella tularensis (WP_032729892, WP_014548420), Enterococcus faecalis (WP_033919308); Lactobacillus rhamnosus (WP_048482595, WP_032965177); and Neisseria meningitidis (WP_061704949,YP_002342100); all of which sequences (as entered by the date of filing of this application) are herein incorporated by reference. Any of these sequences or a variant thereof comprising a sequence having at least about 70-100% sequence identity thereto, including any percent identity within this range, such as 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, can be used for genome editing, as described herein, wherein the variant retains biological activity, such as Cas9 site-directed endonuclease activity. See also Fonfara et al. (2014) Nucleic Acids Res. 42(4):2577- 90; Kapitonov et al. (2015) J. Bacteriol. 198(5)797-807, Shmakov et al. (2015) Mol. Cell. 60(3):385-397, and Chylinski et al. (2014) Nucleic Acids Res. 42(10):6091 -6105); for sequence comparisons and a discussion of genetic diversity and phylogenetic analysis of Cas9.

[0152] By "selectively binds" with reference to a guide RNA is meant that the guide RNA binds preferentially to a target sequence of interest or binds with greater affinity to the target sequence than to other genomic sequences. For example, a gRNA will bind to a substantially complementary sequence and not to unrelated sequences. A gRNA that selectively binds to a particular target DNA sequence will selectively direct binding of Cas9 to a substantially complementary sequence at the target site and not to unrelated sequences.

[0153] The term "donor polynucleotide" refers to a polynucleotide that provides a sequence of an intended edit to be integrated into the genome at a target locus by homology directed repair (HDR).

[0154] A "target site" or "target sequence" is the nucleic acid sequence recognized (i.e., sufficiently complementary for hybridization) by a guide RNA (gRNA) or a homology arm of a donor polynucleotide. The target site may be in an exon or an intron or a specific allele.

[0155] By "homology arm" is meant a portion of a donor polynucleotide that is responsible for targeting the donor polynucleotide to the genomic sequence to be edited in a cell. The donor polynucleotide typically comprises a 5' homology arm that hybridizes to a 5' genomic target sequence and a 3' homology arm that hybridizes to a 3' genomic target sequence flanking a nucleotide sequence comprising the intended edit to the genomic DNA. The homology arms are referred to herein as 5' and 3' (i.e., upstream and downstream) homology arms, which relates to the relative position of the homology arms to the nucleotide sequence comprising the intended edit within the donor polynucleotide. The 5' and 3' homology arms hybridize to regions within the target locus in the genomic DNA to be modified, which are referred to herein as the "5' target sequence" and "3' target sequence," respectively. The nucleotide sequence comprising the intended edit is integrated into the genomic DNA by HDR or recombineering at the genomic target locus recognized (i.e., sufficiently complementary for hybridization) by the 5' and 3' homology arms.

[0156] As used herein, the terms "complementary" or "complementarity" refers to polynucleotides that are able to form base pairs with one another. Base pairs are typically formed by hydrogen bonds between nucleotide units in an anti-parallel orientation between polynucleotide strands. Complementary polynucleotide strands can base pair in a Watson-Crick manner (e.g., A to T, A to U, C to G), or in any other manner that allows for the formation of duplexes. As persons skilled in the art are aware, when using RNA as opposed to DNA, uracil (U) rather than thymine (T) is the base that is considered to be complementary to adenosine. However, when a uracil is denoted in the context of the present invention, the ability to substitute a thymine is implied, unless otherwise stated. "Complementarity" may exist between two RNA strands, two DNA strands, or between a RNA strand and a DNA strand. It is generally understood that two or more polynucleotides may be "complementary" and able to form a duplex despite having less than perfect or less than 100% complementarity. Two sequences are "perfectly complementary" or "100% complementary" if at least a contiguous portion of each polynucleotide sequence, comprising a region of complementarity, perfectly base pairs with the other polynucleotide without any mismatches or interruptions within such region. Two or more sequences are considered "perfectly complementary" or "100% complementary" even if either or both polynucleotides contain additional non-complementary sequences as long as the contiguous region of complementarity within each polynucleotide is able to perfectly hybridize with the other. "Less than perfect" complementarity refers to situations where less than all of the contiguous nucleotides within such region of complementarity are able to base pair with each other.Determining the percentage of complementarity between two polynucleotide sequences is a matter of ordinary skill in the art. For purposes of Cas9 targeting, a gRNA may comprise a sequence "complementary" to a target sequence (e.g., in an intron), capable of sufficient basepairing to form a duplex (i.e., the gRNA hybridizes with the target sequence). Additionally, the gRNA may comprise a sequence complementary to a PAM sequence, wherein the gRNA also hybridizes with the PAM sequence in a target DNA.

[0157] A “zinc-finger nuclease” or “ZFN” is an artificial DNA endonuclease generated by fusing a zinc finger DNA binding domain to a DNA cleavage domain. ZFNs can be engineered to target desired DNA sequences and this enables zinc-finger nucleases to cleave unique target sequences. When introduced into a cell, ZFNs can be used to edit target DNA in the cell (e.g, the cell's genome) by inducing double strand breaks. For more information on the use of ZFNs, see, for example: Asuri et al., Mol Ther. 2012 February; 20(2):329-38; Bibikova et al. Science. 2003 May 2; 300(5620)764; Wood et al. Science. 2011 Jul. 15; 333(6040) :307; Ochiai et al. Genes Cells. 2010 August; 15(8):875-85; Takasu et. al., Insect Biochem Mol Biol. 2010 October; 40(10)759-65; Ekker et al, Zebrafish 2008 Summer; 5(2):121 -3; Young et al, Proc Natl Acad Sci USA. 2011 Apr. 26; 108(17)7052-7; Goldberg et al, Cell. 2010 Mar. 5; 140(5):678-91 ; Geurts et al, Science. 2009 Jul. 24; 325(5939) :433; Flisikowska et al, PLoS One. 2011 ; 6(6):e21045. doi: 10.1371 / journal. pone.0021045. Epub 2011 Jun. 13; Hauschild et al, Proc Natl Acad Sci USA. 2011 Jul. 19; 108(29):12013-7; and Yu et al, Cell Res. 2011 November; 21 (11):1638-40; all of which are herein incorporated by reference for their teachings related to ZFNs. The term “ZFN agent” encompasses a zinc finger nuclease and / or a polynucleotide comprising a nucleotide sequence encoding a zinc finger nuclease.

[0158] A “transcription activator- 1 ike effector nuclease” or “TALEN” is an artificial DNA endonuclease generated by fusing a TAL (Transcription activator-like) effector DNA binding domain to a DNA cleavage domain. TALENS can be engineered to bind practically any desired DNA sequence and when introduced into a cell, TALENs can be used to edit target DNA in the cell (e.g., the cell's genome) by inducing double strand breaks. For more information on the use of TALENs, see, for example: Hockemeyer et al. Nat Biotechnol. 2011 Jul. 7; 29(8)731 -4; Wood et al. Science. 2011 Jul. 15; 333(6040) :307; Tesson et al. Nat Biotechnol. 2011 Aug. 5; 29(8):695- 6; and Huang et. al., Nat Biotechnol. 2011 Aug. 5; 29(8):699-700; all of which are herein incorporated by reference for their teachings related to TALENs. The term “TALEN agent” encompasses a TALEN and / or a polynucleotide comprising a nucleotide sequence encoding a TALEN.

[0159] "Administering" a nucleic acid, such as a vector encoding ZIP7 and / or Rpn11 , a CRISPR system or vector encoding a CRISPR system, a guide RNA, a donor polynucleotide (e.g., for HDR), a vector encoding a ZFN, or a vector encoding a TALEN to a cell comprises transducing,transfecting, electroporating, translocating, fusing, phagocytosing, shooting or ballistic methods, etc., i.e., any means by which a nucleic acid can be transported across a cell membrane.Biomarkers and Methods of Detecting Cell Type Switching

[0160] Methods of detecting whether a pre-malignant cell or cancerous cell is in a cell state having lineage plasticity and drug resistance or a proliferative cell state that can be treated with an anti-mitotic therapeutic agent are provided. Biomarkers that can be used to distinguish these cell states include, without limitation, RNA transcripts of genes of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Proml metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene. Cells in the cell state associated with increased lineage plasticity and drug resistance have increased levels of expression of genes of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene, and decreased levels of expression of genes of the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene compared to cells in the non-drug resistant, proliferative cell state. Conversely, cells in the non-drug resistant, proliferative cell state have increased proliferation, increased levels of expression of genes of the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene, and decreased levels of expression of genes of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Proml metagene, and Prom2 metagene compared to cells in the cell state having increased lineage plasticity and drug resistance.

[0161] Accordingly, methods are provided for determining whether a cancerous or pre-malignant cell or cell population will be responsive to treatment with an anti-mitotic agent. The subject methods include a step of assaying a biological sample comprising the cancerous or pre- malignant cell or cells of interest to determine the levels of expression of one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene, and the levels of expression of one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene, wherein decreased levels of expression of the one or more genes selected from Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene and increased levels of expression of the one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the cancerous or pre-malignant cell or cell population compared to reference value ranges for the levels of expression of the genes of the Sox2metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Promt metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrig 1 metagene, Lgr6 metagene, and Sox9 metagene indicate that the cancerous or pre-malignant cell or cell population is in the non-drug resistant, proliferative cell state, and wherein increased levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krtt 9 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene and decreased levels of expression of the one or more genes selected from Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the cancerous or pre-malignant cell or cell population compared to reference value ranges for the levels of expression of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Proml metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the cancerous or pre-malignant cell or cell population is in the cell state having lineage plasticity and drug resistance to the anti-mitotic agent.

[0162] In some cases, combinations of biomarkers are used in the subject methods. In some such cases, the levels of all measured biomarkers must change (as described above) in order for the cell state to be determined. In some embodiments, only some biomarkers are used in the methods described herein. For example, a single biomarker, 2 biomarkers, 3 biomarkers, 4 biomarkers, 5 biomarkers, 6 biomarkers, 7 biomarkers, 8 biomarkers, 9 biomarkers, or 10 or more biomarkers selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Promt metagene, and Prom2 metagene may be used in combination with a single biomarker, 2 biomarkers, 3 biomarkers, 4 biomarkers, 5 biomarkers, 6 biomarkers, 7 biomarkers, 8 biomarkers, 9 biomarkers, or 10 or more biomarkers selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene. In some embodiments, levels of expression of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44 e, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 are measured. Quantitative values may be combined in a linear or non-linear fashion to calculate one or more scores for classification of cell type and risk scores for drug resistance.

[0163] A biological sample comprising cancerous or pre-malignant cells such as a tumor sample or pre-malignant lesion sample can be obtained from a subject to determine if the cancerous or pre-malignant lesion is drug resistant or treatable with an anti-mitotic therapeutic agent. The sample is typically a biopsy or surgical specimen comprising the cancerous or pre-malignant cells. A "control" sample, as used herein, refers to a tissue sample that is not diseased. A control sample may be obtained from a normal or healthy subject (e.g., an individual known to not have pre-malignant lesions or cancer) or from non-diseased tissue (outside of a tumor or pre-malignantlesion) from the patient undergoing diagnostic testing. A tissue sample (e.g., normal tissue sample, tumor sample, or pre-malignant lesion sample) can be obtained from a subject by conventional techniques. For example, tumor samples and pre-malignant lesion samples can be obtained by surgical resection or by biopsy using fine needle aspiration (FNA), a core needle biopsy, or an excisional biopsy according to methods well known in the art.

[0164] When analyzing the levels of the biomarkers in a biological sample from a subject, the reference value ranges used for comparison can represent the levels of the biomarkers in one or more biological samples from one or more subjects without disease (i.e., normal or healthy control, non-diseased, non-cancerous tissue). Alternatively, the reference values can represent the levels of the biomarkers in one or more tumor samples or pre-malignant lesion samples from one or more subjects. More specifically, the reference value ranges for the biomarkers can represent the levels of the biomarkers in one or more tumor samples or pre-malignant lesion samples from one or more subjects with cancer or a pre-malignant lesion that is drug resistant (“a drug resistant biomarker expression profile”) to determine if the patient has a drug-resistant cancer or pre-malignant lesion, or the reference value ranges for the biomarkers can represent the levels of the biomarkers in one or more tumor samples or pre-malignant lesion samples from one or more subjects with cancer or a pre-malignant lesion that contains cells in a non-drug resistant, proliferative cell state that can be treated with anti-mitotic therapeutic agents (“a nondrug resistant biomarker expression profile”).

[0165] The method may further comprise determining an appropriate treatment regimen for a patient. For example, the subject methods can be used for identifying patients who will be responsive to treatment of a cancer with an anti-mitotic therapeutic agent or who have a drugresistant cancer that would benefit from treatment first with an agent that induces differentiation followed by treatment with an anti-mitotic agent. For example, if the levels of expression of one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene, and levels of expression of one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the cancer is in the non-drug resistant, proliferative cell state, the cancer is predicted to be treatable with an anti-mitotic agent. If the levels of expression of one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene, and levels of expression of one or more genes selected from metagene the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the cancer is in the cell state having lineage plasticity and drug resistance, the cancer can be treated first with anagent that induces differentiation to switch the cancer out of the high plasticity, drug-resistant state to a non-drug resistant state, followed by treatment with the anti-mitotic agent.

[0166] Exemplary anti-mitotic agents include, without limitation, alkylating agents such as cisplatin, carboplatin, cyclophosphamide, mechlorethamine, ifosfamide, chlorambucil, carmustine, lomustine, bendamustine, dacarbazine, temozolomide, thiotepa, and altretamine; taxanes such as paclitaxel, docetaxel, and cabazitaxel; vinca alkaloids such as vinblastine, vincristine, vinorelbine, and vinflunine, and combretastatins such as combretastatin A-4.

[0167] Exemplary agents that induce differentiation include, without limitation, inhibitors of protein phosphatase 2A (PP2A) such as LB100, and KRAS inhibitors such as sotorasib and adagrasib.

[0168] In certain embodiments, a patient is monitored using the biomarkers to detect cell type switching of non-drug resistant cancerous or pre-malignant cells to a drug-resistant state in response to treatment with an anti-mitotic therapeutic agent. The method comprises: (a) treating a cancerous or pre-malignant lesion with an effective amount of the anti-mitotic therapeutic agent; (b) obtaining a biological sample comprising cancerous or pre-malignant cells from the cancerous or premalignant lesion of the subject; (c) measuring levels of expression of one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene, and one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the biological sample; and (d) detecting cell state switching, wherein increased levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene and decreased levels of expression of the one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the biological sample compared to reference value ranges for the levels of expression of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Proml metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the cancerous or pre-malignant cells have switched to a drug-resistant state in response to treatment with the therapeutic agent.

[0169] Medical imaging may be used to confirm responsiveness to treatment with an anti-mitotic therapeutic agent. Medical imaging can be used, for example, to assess tumor growth, number of tumors, and metastasis. In certain embodiments, medical imaging is performed, for example, by magnetic resonance imaging (MRI), positron emission tomography (PET), single photon emission computed tomography (SPECT), computed tomography (CT), ultrasound imaging (Ul),optical imaging (01), photoacoustic imaging (PI), fluoroscopy, fluorescence imaging, or radiography.

[0170] By "responsive" is meant that the individual undergoing treatment with an anti-mitotic therapeutic agent exhibits an improvement in one or more symptoms of the cancer for which the individual is undergoing therapy. Thus, a positive therapeutic response would refer to one or more of the following improvements in the disease: (1 ) reduction in tumor size; (2) reduction in the number of cancer cells; (3) inhibition (i.e., slowing to some extent, preferably halting) of tumor growth; (4) inhibition (i.e., slowing to some extent, preferably halting) of cancer cell infiltration into peripheral organs; (5) inhibition (i.e., slowing to some extent, preferably halting) of tumor metastasis; and (6) some extent of relief from one or more symptoms associated with the cancer. Such therapeutic responses may be further characterized as to degree of improvement. Thus, for example, an improvement may be characterized as a complete response. By "complete response" is documentation of the disappearance of all symptoms and signs of all measurable or evaluable disease confirmed by physical examination, laboratory, ultrasound, nuclear, radiographic studies (i.e., CT (computer tomography), and / or MRI (magnetic resonance imaging)), and other non-invasive procedures repeated for all initial abnormalities or sites positive at the time of entry into the study. Alternatively, an improvement in the disease may be categorized as being a partial response. By "partial response" is intended a reduction of greater than 50% in the sum of the products of the perpendicular diameters of all measurable lesions when compared with pretreatment measurements.

[0171] The level of a biomarker in a pre-treatment biological sample comprising cancerous or pre-malignant cells such as from a tumor sample or pre-malignant lesion sample can be referred to as a “pre-treatment value” because the first biological sample is isolated from the individual prior to the administration of the therapy (i.e., “pre-treatment”). The level of a biomarker in the pre-treatment biological sample can also be referred to as a “baseline value” because this value is the value to which “post-treatment” values are compared. In some cases, the baseline value (i.e., “pre-treatment value”) is determined by determining the level of a biomarker in multiple (i.e., more than one, e.g., two or more, three or more, for or more, five or more, etc.) pre-treatment biological samples. In some cases, the multiple pre-treatment biological samples are isolated from an individual at different time points in order to assess natural fluctuations in biomarker levels prior to treatment. As such, in some cases, one or more (e.g., two or more, three or more, for or more, five or more, etc.) pre-treatment biological samples are isolated from the individual. In some embodiments, all of the pre-treatment biological samples will be the same type of biological sample (e.g., a tissue sample, tumor sample, pre-malignant lesion sample). In some cases, two or more pre-treatment biological samples are pooled prior to determining the level of the biomarker in the biological samples. In some cases, the level of the biomarker is determinedseparately for two or more pre-treatment biological samples and a “pre-treatment value” is calculated by averaging the separate measurements.

[0172] A post-treatment biological sample is isolated from an individual after the administration of a therapy. Thus, the level of a biomarker in a post-treatment sample can be referred to as a “post-treatment value”. In some embodiments, the level of a biomarker is measured in additional post-treatment biological samples (e.g., a second, third, fourth, fifth, etc. post-treatment biological sample). Because additional post-treatment biological samples are isolated from the individual after the administration of a treatment, the levels of a biomarker in the additional biological samples can also be referred to as “post-treatment values.”

[0173] The determination that an individual has a drug resistant cancer or a non-drug resistant cancer is an active clinical application of the correlation between the levels of expression of the genes of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene and cell state. For example, “determining” requires the active step of reviewing the data, which is produced during the active assaying step(s), and determining whether an individual does or does not have a drug resistant cancer, Additionally, in some cases, a decision is made to proceed with a current treatment (e.g., anti-mitotic therapy), or instead to alter the treatment. In some cases, the subject methods include the step of continuing therapy or altering therapy.

[0174] The term “continue treatment” (i.e., continue therapy) is used herein to mean that the current course of treatment (e.g., continued administration of a therapy) is to continue. If the current course of treatment is not effective in treating the cancer, the treatment may be altered. “Altering therapy” is used herein to mean “discontinuing therapy” or “changing the therapy” (e.g., changing the type of treatment, changing the particular dose and / or frequency of administration of medication, e.g., increasing or decreasing the dose and / or frequency). In some cases, therapy can be altered until the individual is deemed to be responsive. In some embodiments, altering therapy means changing which type of treatment is administered, discontinuing a particular treatment altogether, etc.

[0175] As a non-limiting illustrative example, a patient may be initially treated for cancer with an anti-mitotic chemotherapeutic agent. Then to “continue treatment” would be to continue with this type of treatment. If the levels of expression of one or more genes of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in a tumor sample indicate that the current course of treatment is leading to development of drug resistance to the anti-mitotic chemotherapeutic agent, the treatment may be altered, e.g., switching treatment to an agent thatinduces differentiation, or a different type of treatment, such as radiosurgery or stereotactic radiation therapy.

[0176] In other words, the level of one or more biomarkers may be monitored in order to determine when to continue therapy and / or when to alter therapy. As such, a post-treatment biological sample (e.g., tumor sample) can be isolated after any of the administrations of the antimitotic chemotherapeutic agent and the biological sample can be assayed to determine the levels of expression of the genes of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene. Accordingly, the subject methods can be used to determine whether an individual being treated with an anti-mitotic chemotherapeutic agent is developing drug resistance due to tumor cells switching to a cell state having lineage plasticity and drug resistance.

[0177] The therapy can be administered to an individual any time after a pre-treatment biological sample is isolated from the individual, but it is preferable for the therapy to be administered simultaneous with or as soon as possible (e.g., about 7 days or less, about 3 days or less, e.g., 2 days or less, 36 hours or less, 1 day or less, 20 hours or less, 18 hours or less, 12 hours or less, 9 hours or less, 6 hours or less, 3 hours or less, 2.5 hours or less, 2 hours or less, 1 .5 hours or less, 1 hour or less, 45 minutes or less, 30 minutes or less, 20 minutes or less, 15 minutes or less, 10 minutes or less, 5 minutes or less, 2 minutes or less, or 1 minute or less) after a pretreatment biological sample is isolated (or, when multiple pre-treatment biological samples are isolated, after the final pre-treatment biological sample is isolated).

[0178] In some embodiments, the subject methods include providing an analysis (e.g., an oral or written report) having any or all of the following information: identifying information of the subject (name, age, etc.), a description of what type of biological sample(s) was used and / or how it was used, the technique used to assay the sample, the results of the assay (e.g., the levels of the biomarkers as measured, and / or the fold-change of a biomarker level over time, or in a posttreatment assay compared to a pre-treatment assay), an assessment as to whether a candidate agent can switch a cancerous or pre-malignant cell from a cell state having lineage plasticity and drug resistance to a non-drug resistant proliferative cell state that can be treated with anti-mitotic therapeutic agents, an assessment as to whether an individual is determined to have a drug resistant cancer or pre-malignant lesion, a recommendation for treatment, and / or to continue or alter therapy, a recommended strategy for additional therapy, etc. As described above, an analysis can be an oral or written report (e.g., written or electronic document). The analysis can be provided to the subject, to the subject’s physician, to a testing facility, etc. The analysis can also be accessible as a website address via the internet. In some such cases, the analysis canbe accessible by multiple different entities (e.g., the subject, the subject’s physician, a testing facility, etc.).Detecting and Measuring Biomarkers

[0179] It is understood that the biomarkers in a sample can be measured by any suitable method known in the art. Measurement of levels of transcription of an RNA transcript biomarker can be direct or indirect. In some embodiments, the amount or level in the sample of nascent RNA or RNA transcripts encoded by a gene of interest is determined. A number of exemplary methods for measuring RNA (e.g., nascent RNA or mRNA) levels in a sample are known by one of ordinary skill in the art, and any convenient method can be used.

[0180] For example, RNA-seg can be used to measure levels of RNA transcripts in a sample. In an exemplary embodiment, RNA-seq involves lysis of cells, RNA capture, reverse transcription (conversion of RNA into cDNA), cDNA amplification, and sequencing of cDNA amplicons. For a further description of RNA-seq techniques, see, e.g., Hrdlickova et al. (2017) Wiley Interdiscip Rev RNA 8(1 ):10.1002 / wrna.1364, Wang et al. (2009) Nat. Rev. Genet. 10(1 ):57-63; Withanage et al. (2022) Methods Mol. Biol. 2418:405-424; Owens et al. (2019) Cold Spring Harb Protoc. 2019(6); herein incorporated by reference in their entireties.

[0181] Single-cell RNA sequencing (scRNA-seq) additionally involves the step of isolating single cells, followed by lysis of cells, RNA capture, reverse transcription (conversion of RNA into cDNA), cDNA amplification, and sequencing of cDNA amplicons. For a description of scRNA-seq techniques, see, e.g., Jovic et al. (2022) Clin. Transl. Med. 12(3):e694, Papalexi et al. (2018) Nat. Rev. Immunol. 18(1 ):35-45 Li et al. (2021) Int. J. Oral Sci. 13(1 ):36, Yamada et al. (2020) Int. J. Mol. Sci. 21 (21 ):8345, Eberwine et al. (2014). Nature Methods. 11 (1 ):25-27, Saliba et al. (2014) Nucleic Acids Research 42(14):8845-8860, Shintaku et al. (2014) Analytical Chemistry 86 (4):1953-1957, Nawy et al. (2014). "Single-cell sequencing". Nature Methods. 1 1 (1 ):18; herein incorporated by reference in their entireties).

[0182] GRO-seq can be used to measure levels of nascent RNA transcripts. In an exemplary embodiment, GRO-seq involves lysis of cells to release nuclei, isolation of nuclei, incorporation of Br-UTP into nascent RNA molecules by RNA polymerases, affinity purification of RNA molecules using antibodies against bromodeoxyuridine, reverse transcription (conversion of RNA into cDNA), cDNA amplification, and sequencing of cDNA amplicons. For a further description of GRO-seq techniques, see, e.g., Gardini et al. (2017) Methods Mol. Biol. 1468:1 1 1 -120, Tzerpos et al. (2021 ) Methods Mol. Biol. 2351 :25-39.Jordan-Pla et al. (2019) Methods 159-160:177-182, Cardiello et al. (2020) Transcription 1 1 (1 ):3-18; herein incorporated by reference in their entireties.

[0183] Cellular indexing of transcriptomes and epitopes sequencing (CITE-seq) can be used to measure levels of both RNA transcripts and proteins of single cells. CITE-seq utilizes antibody- oligonucleotide conjugates, known as antibody-derived tags (ADTs), in combination with scRNA- seq. Each ADT comprises an antibody specific for a cell surface protein of interest and an oligonucleotide for barcoding the antibody, which can be amplified by PCR and sequenced to identify the antibody. The oligonucleotide is typically linked to the antibody non-covalently by conjugating the antibody with streptavidin and the oligonucleotide with biotin. A plurality of ADTs are used for immunostaining cells, which in combination with scRNA-seq allows multiplex protein and transcriptome co-profiling. For a further description of CITE-seq, see, e.g., Mercatelli et al. (2021 ) Methods and Protocols 4 (2):28, Stoeckius et al. (2017) Nature Methods. 14 (9) :865-868, Scheyltjens et al. (2022) Nat. Protoc. 17(10):2354-2388, Xu et al. (2021 ) Methods 189:65-73, Liu et al. (2023) Nat. Biotechnol. 41 (10) :1405-1409; herein incorporated by reference in their entireties.

[0184] RNA expression and protein sequencing (REAP-seq) is very similar to CITE-seq except for using antibody-oligonucleotide conjugates in which the antibody is covalently linked to an aminated DNA barcode. For a further description of REAP-seq, see, e.g., Peterson, et al. (2017) Nature Biotechnology 35 (10): 936-939; herein incorporated by reference in its entirety.

[0185] Any high-throughput technique for sequencing can be used to sequence RNA transcripts isolated from cells. DNA sequencing techniques include dideoxy sequencing reactions (Sanger method) using labeled terminators or primers and gel separation in slab or capillary, sequencing by synthesis using reversibly terminated labeled nucleotides, pyrosequencing, 454 sequencing, sequencing by synthesis using allele specific hybridization to a library of labeled clones followed by ligation, real time monitoring of the incorporation of labeled nucleotides during a polymerization step, polony sequencing, SOLID sequencing, and the like.

[0186] Certain high-throughput methods of sequencing comprise a step in which individual molecules are spatially isolated on a solid surface where they are sequenced in parallel. Such solid surfaces may include nonporous surfaces (such as in Solexa sequencing, e.g. Bentley et al, Nature, 456: 53-59 (2008) or Complete Genomics sequencing, e.g. Drmanac et al, Science, 327: 78-81 (2010)), arrays of wells, which may include bead- or particle-bound templates (such as with 454, e.g. Margulies et al, Nature, 437: 376-380 (2005) or Ion Torrent sequencing, e.g., U.S. patent publication 2010 / 0137143 or 2010 / 0304982), micromachined membranes (such as with SMRT sequencing, e.g. Eid et al, Science, 323: 133-138 (2009)), or bead arrays (as with SOLiD sequencing or polony sequencing, e.g. Kim et al, Science, 316: 1481 -1414 (2007)). Such methods may comprise amplifying the isolated molecules either before or after they are spatially isolated on a solid surface. Prior amplification may comprise emulsion-based amplification, such as emulsion PCR or rolling circle amplification.

[0187] Of particular interest is sequencing on the Illumina MiSeq, NextSeq, and HiSeq platforms, which use reversible-terminator sequencing by synthesis technology (see, e.g., Shen et al. (2012) BMC Bioinformatics 13:160; Junemann et al. (2013) Nat. Biotechnol. 31 (4):294-296; Glenn (201 1 ) Mol. Ecol. Resour. 11 (5) :759-769; Thudi et al. (2012) Brief Funct. Genomics 1 1 (1):3-11 ; herein incorporated by reference); the Oxford Nanopore Technologies Inc. MinlON, GridlON, and PromethlON nanopore sequencing platforms, which can be used to determine the sequences of DNA or RNA by monitoring changes in electrical current as nucleic acids are passed through a protein nanopore (see, e.g., Lu et al. (2016) Genomics Proteomics Bioinformatics 14(5):265-279, Petersen et al. (2019) J. Clin. Microbiol. 58(1 ) :e01315-19, Kono et al. (2019) Dev Growth Differ. 61 (5):316-326, Deamer et al. (2016) Nat. Biotechnol. 34(5):518-24, Madoui et al. (2015) BMC Genomics 16:327, Szalay et al. (2015) Nat. Biotechnol 33, 1087-1091 ; herein incorporated by reference); the PacBIO Single Molecule, Real-Time (SMRT) sequencing platforms, including the Sequel, HiFi, and RS II sequencing platforms (see, e.g., Ardui et al. (2018) Nucleic Acids Res. 46(5):2159-2168, An et al. (2018) Genes (Basel) 9(1 ):43), Nakano et al. (2017) Hum Cell. 30(3):149-161 ; herein incorporated by reference), the Omniome sequencing by binding (SBB®) short-read sequencing platform using high fidelity plasmonic nanohole arrays (see, e.g., Cetin et al. (2018) ACS Sens. 3(3):561 -568; herein incorporated by reference), the Gynapsys compact DNA sequencer, which uses metal oxide semiconductor (CMOS) sequencing chips for electronic data detection and sequencing by synthesis (SBS) chemistry, the Singular Genomics G4 benchtop sequencing platform, which uses SBS chemistry, and the Element Biosciences AVITI™ benchtop sequencer, which uses a modified form of SBS chemistry that reduces reagent usage.

[0188] Other methods of detecting levels of RNA transcripts include hybridization-based methods such as Northern blotting, array hybridization (e.g., microarray); in situ hybridization; and in situ hybridization followed by FACS, and the like (see, e.g., Parker & Barnes (1999) Methods in Molecular Biology 106:247-283); RNAse protection assays (Hod (1992) Biotechniques 13:852-854); PCR-based methods such as reverse transcription PCR (RT-PCR), quantitative RT-PCR (qRT-PCR), real-time RT-PCR, and the like (see, e.g., Weis et al. (1992) Trends in Genetics 8:263-264); and the like. See also, Robert E. Farrell Jr, RNA Methodologies: A Laboratory Guide for Isolation and Characterization (6thEdition, Academic Press, November 22, 2022; herein incorporated by reference in its entirety.

[0189] For measuring mRNA levels, the starting material is typically total RNA or poly A+ RNA isolated from a biological sample (e.g., cancerous cells from a tumor biopsy or surgical specimen, or from a homogenized tissue, e.g. a homogenized biopsy sample, an aspirate, a homogenized paraffin- or OCT-embedded sample, etc.). General methods for mRNA extraction are well known in the art and are disclosed in standard textbooks of molecular biology, including Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997). RNA isolation can also beperformed using a purification kit, buffer set and protease from commercial manufacturers, according to the manufacturer’s instructions. For example, RNA from cell suspensions can be isolated using Qiagen RNeasy mini-columns, and RNA from cell suspensions or homogenized tissue samples can be isolated using the TRIzol reagent-based kits (Invitrogen), MasterPure™ Complete DNA and RNA Purification Kit (Epicentre, Madison, Wl), Paraffin Block RNA Isolation Kit (Ambion, Inc.) or RNA Stat-60 kit (Tel-Test).

[0190] A variety of different manners of measuring mRNA levels are known in the art, e.g., as employed in the field of differential gene expression analysis. One representative and convenient type of protocol for measuring mRNA levels is array-based gene expression profiling. Such protocols are hybridization assays in which a nucleic acid that displays “probe” nucleic acids for each of the genes to be assayed / profiled in the profile to be generated is employed. In these assays, a sample of target nucleic acids is first prepared from the initial nucleic acid sample being assayed, where preparation may include labeling of the target nucleic acids with a label, e.g., a member of signal producing system. Following target nucleic acid sample preparation, the sample is contacted with the array under hybridization conditions, whereby complexes are formed between target nucleic acids that are complementary to probe sequences attached to the array surface. The presence of hybridized complexes is then detected, either qualitatively or quantitatively.

[0191] Specific hybridization technology which may be practiced to generate the expression profiles employed in the subject methods includes the technology described in U.S. Patent Nos.: 5,143,854; 5,288,644; 5,324,633; 5,432,049; 5,470,710; 5,492,806; 5,503,980; 5,510,270; 5,525,464; 5,547,839; 5,580,732; 5,661 ,028; 5,800,992; the disclosures of which are herein incorporated by reference; as well as WO 95 / 21265; WO 96 / 31622; WO 97 / 10365; WO 97 / 27317; EP 373 203; and EP 785 280. In these methods, an array of “probe” nucleic acids that includes a probe for each of the phenotype determinative genes whose expression is being assayed is contacted with target nucleic acids as described above. Contact is carried out under hybridization conditions, e.g., stringent hybridization conditions, and unbound nucleic acid is then removed. The term “stringent assay conditions” as used herein refers to conditions that are compatible to produce binding pairs of nucleic acids, e.g., surface bound and solution phase nucleic acids, of sufficient complementarity to provide for the desired level of specificity in the assay while being less compatible to the formation of binding pairs between binding members of insufficient complementarity to provide for the desired specificity. Stringent assay conditions are the summation or combination (totality) of both hybridization and wash conditions.

[0192] The resultant pattern of hybridized nucleic acid provides information regarding expression for each of the genes that have been probed, where the expression information is in terms of whether or not the gene is expressed and, typically, at what level, where the expression data,i.e., expression profile (e.g., in the form of a transcriptosome), may be both qualitative and quantitative.

[0193] Alternatively, non-array based methods for quantitating the level of one or more nucleic acids in a sample may be employed. These include those based on amplification protocols, e.g., Polymerase Chain Reaction (PCR)-based assays, including quantitative PCR, reversetranscription PCR (RT-PCR), real-time PCR, and the like, e.g. TaqMan® RT-PCR, MassARRAY® System, BeadArray® technology, and Luminex technology; and those that rely upon hybridization of probes to filters, e.g. Northern blotting and in situ hybridization.Data Analysis

[0194] In some embodiments, one or more pattern recognition methods are used in analyzing the data for biomarker levels. The quantitative values may be combined in linear or non-linear fashion to classify the cell state of a cell (e.g., cell state having lineage plasticity and drug resistance or non-drug resistant proliferative cell state). In some embodiments, measurements for a biomarker or combinations of biomarkers are formulated into linear or non-linear models or algorithms (e.g., a 'biomarker signature') and converted into a likelihood score. This likelihood score indicates the probability that a sample is from a cell in a cell state having lineage plasticity and drug resistance, a non-drug resistant proliferative cell state, or a non-cancerous, non- premalignant, normal cell state. The models and / or algorithms can be provided in machine readable format, and may be used to correlate biomarker levels or a biomarker profile with a cell state, predict resistance to treatment of a cancer with an anti-mitotic therapeutic agent, and / or to designate a treatment modality for a patient or class of patients (e.g., treatment of a cancer with a therapeutic agent that induces cell differentiation before treatment of the cancer with an antimitotic therapeutic agent if diagnostic testing of cells from a cancer biopsy indicates a cell state having lineage plasticity and drug resistance).

[0195] In some embodiments, a machine learning algorithm is used to classify the cell state of a cell (e.g., cell state having lineage plasticity and drug resistance or non-drug resistant proliferative cell state). The machine learning algorithm may comprise a supervised learning algorithm. Examples of supervised learning algorithms may include Average One-Dependence Estimators (AODE), Artificial neural network (e.g., Backpropagation), Bayesian statistics (e.g., Naive Bayes classifier, Bayesian network, Bayesian knowledge base), Case-based reasoning, Decision trees, Inductive logic programming, Gaussian process regression, Group method of data handling (GMDH), Learning Automata, Learning Vector Quantization, Minimum message length (decision trees, decision graphs, etc.), Lazy learning, Instance-based learning Nearest Neighbor Algorithm, Analogical modeling, Probably approximately correct learning (PAC) learning, Ripple down rules, a knowledge acquisition methodology, Symbolic machine learningalgorithms, Subsymbolic machine learning algorithms, Support vector machines, Random Forests, Ensembles of classifiers, Bootstrap aggregating (bagging), and Boosting. Supervised learning may comprise ordinal classification such as regression analysis and Information fuzzy networks (IFN). Alternatively, supervised learning methods may comprise statistical classification, such as AODE, Linear classifiers (e.g., Fisher's linear discriminant, Logistic regression, Naive Bayes classifier, Perceptron, and Support vector machine), quadratic classifiers, k-nearest neighbor, Boosting, Decision trees (e.g., C4.5, Random forests), Bayesian networks, and Hidden Markov models.

[0196] The machine learning algorithm may also comprise an unsupervised learning algorithm. Examples of unsupervised learning algorithms may include artificial neural network, Data clustering, Expectation-maximization algorithm, Self-organizing map, Radial basis function network, Vector Quantization, Generative topographic map, Information bottleneck method, and IBSEAD. Unsupervised learning may also comprise association rule learning algorithms such as Apriori algorithm, Eclat algorithm and FP-growth algorithm. Hierarchical clustering, such as Single-linkage clustering and Conceptual clustering, may also be used. Alternatively, unsupervised learning may comprise partitional clustering such as K-means algorithm and Fuzzy clustering.

[0197] In some instances, the machine learning algorithm comprises a reinforcement learning algorithm. Examples of reinforcement learning algorithms include, but are not limited to, temporal difference learning, Q-learning and Learning Automata. Alternatively, the machine learning algorithm may comprise Data Pre-processing.

[0198] In some embodiments, the machine learning algorithm uses artificial neural networks. In some embodiments, the machine learning algorithm uses a deep learning algorithm, which may include the use of convolutional neural networks, deep neural networks, recurrent neural networks, efficient neural networks, deep residual neural networks, long short-term memory networks, deep belief networks, multilayer perceptrons, or deep reinforcement learning, and the like. See, e.g., Pedrycz et al. Deep Learning: Algorithms and Applications (Studies in Computational Intelligence Book 865, Springer, 2019), Goodfellow et al. Deep Learning (Adaptive Computation and Machine Learning series, The MIT Press, 2016), and Various Deep Learning Algorithms in Computational Intelligence (edited by Oscar Humberto Montiel Ross, Mdpi AG, 2023); herein incorporated by reference in their entireties.Reporter Gene Assay for Detecting Cell Type Switching

[0199] A reporter gene assay is provided for identifying the cell state of a cell to determine if the cell in in a cell state having lineage plasticity and drug resistance or a non-drug resistant proliferative cell state. A first lineage tracing reporter gene is operably linked to a promoter of afirst gene whose expression is positively correlated with a stem cell plasticity state, wherein expression of the first lineage tracing reporter gene coincides with the expression of the first gene; and a second lineage tracing reporter gene is operably linked to a promoter of a second gene whose expression is positively correlated with a proliferative state, wherein expression of the second lineage tracing reporter gene coincides with the expression of the second gene.

[0200] In certain embodiments, the first gene is selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Prom1 metagene, and a Prom2 metagene; and the second gene is selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene.

[0201] In certain embodiments, the Sox2 metagene comprises genes selected from Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, Mtrnrl O, Esd, Sox13, Nfe2l2, Pls1 , Tom1 l2, Bink, Suox, Sid 6a1 1 , Xrcc5, Chst15, Krt12, Eval c, Nppc, Esd, Ddx59, Nop2, Krt13, Plekhh3, Osbpl6, Aldh5a1 , Cirhl a, Wnk4, Arntl2, Fam110c, Tmem180, Dili , Galnt12, Pitxl , Caleb, Ankrd9, Isl1 , Btc, Gss, Ociad2, Klra33, Aldh3a1 , Minkl , Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl , Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrl a, Pthlh, Usp6nl, Ufspl , Irgq, Nkiras2, Grtpl , Nqo1 , Krt20, Snord42b, Avpil , Ifrdl , Srd5a2, Cpn1 , Bail , Sprr3, Rap1gap2, Rassf7, Fetub, Ramp3, Arl4d, Tle1 , Krt76, Ptprzl , Pradd , Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl , G6pdx, Tsg101 , Nmrkl , Ralgapb, A430105119Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik.

[0202] In certain embodiments, the Foxal metagene comprises genes selected from Foxal , Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1 , Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1 , Tjp3, Plekhg6, Bspry, Ocln, Ceacaml , Marveld3, Cldn3, Mal2, Tmem30b, Sowahb, Spns2, Slc9a3r1 , Kctdl , Cwh43, Cystml , Rab17, S100a2, Ppbp, Padil , Caleb, Gstol , S100a16, Spint2, Slc52a3, Slc16a1 1 , Crispl , Mall, Aldh1 a3, Entpd3, Tmprss1 1 g, Anxal , Pgapl , Prss22, Kif21 a, Omp, Liph, Epb4.1 l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, Arhgefl Ol, Tmprss1 1 d, Mxd1 , Elf5, Acss2, Leprell , Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppfibp2, Mboatl , Zdhhc13, Dgka, Ehf, Mst1 , St14, Ap1 s3, Maltl , Spintl , Sprr3, Pllp, AA986860, Prss27, Tmprssl 1 a, Serpinb11 , Hs3st1 , Stardl O, Arhgap40, lldrl , Ppi, Fbp2, Cnksrt , Map7, and 1700001 C19Rik, E330009J07Rik.

[0203] In certain embodiments, the Krt15 metagene comprises genes selected from Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrd , Zfp750, Lipm, Ocln, Paqr5, GrhH , Erbb3, PsapH , Aldh3b2, Ppi, RapgefH , Aldh3b2, Efna3, Mud 5, Liph, 2610528A1 1 Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1 pr5, Klhl29, 4833423E24Rik, Nccrpl , Slc27a4, Barx2, Aim11, Wnt4, L1 cam, Leprell , Rnf43, Ckmtl , Lipk, Mapk13, Il22ra1 , Padil , Ripk4, Prom2, Adtrp,Caszl , 1700055N04Rik, Scnnl a, Ptprf, Arhgef I, Tmprss11 e, Slc25a48, Mall, Mst1 , Crnn, Celsrl , Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinbl 1 , VsnH , Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprss13, Sowahb, Celsr2, Ly6g6e, SytH , Tprg, AA986860, and Sptbn2.

[0204] In certain embodiments, the Krt19 metagene comprises genes selected from Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal , Mall, Slc37a1 , Cblc, Marveld3, Marveld2, Gstol , Ceacaml , Gm9573, Ocln, Slc9a3r1 , Mal2, Tmprss1 1 g, Spns2, Anxal , 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, Arhgefl 01, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, Upk3bl, Gsta4, Ppbp, Tmprss11d, Spintl , Tmem30b, S100a2, Pgapl , Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1 , Kif21 a, Krt13, Padil , Tmprss11 bnl, Foxql , S100a16, L1cam, Seel, Ehf, Sarndl O, Epb4.1 l5, Rab27b, Plekha7, Llgl2, Erbb2, Stap2, Rab25, Hebp2, Cnksrl , 1117re, Pllp, Cystml , Tnk1 , Mboatl , Tmprss11 e, Tacstd2, Plekha6, Arg1 , Ltf, Evpl, S100a14, Plekhhl , Slc25a48, Ap1s3, Zdhhc13, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl , Ppfibp2, Nipal2, Rab27a, Rbm47, and Stardl O.

[0205] In certain embodiments, the Pitxl metagene comprises genes selected from Pitxl , Cldn8, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1 , Klf5, Cep170b,Llgl2, 1700001 C19Rik, Tmprss1 1d, Dsc2, Fam160a1 , Erbb2, Gsta4, Shb, Duoxal , Rab27b, Barx2, Fhdcl , Tmprss11 bnl, Krt13, Plekhg6, Fam57a, Gstol , Ppp1 r13l, Dsg3, Epn3, Als2cl, Grhl3, Myo5b, Arhgef5, Tmem63b, Phldb3, Tmprss11 a, Gstal , Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinbl 1 , Foxql , Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhc13, Tgm1 , Gclm, Rhov, Gsta2, Samd12, Spns2, Proser2, Ehf, Sostdcl , Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl , Arhgap27, Lpar5, Duoxl , Sult2b1 , Jup, 2200002D01 Rik, Map3k9, Ppap2c, Anxal , Arhgap27, Foxql , Mir200a, Cnksrl , Tmprss11 g, Dennd2c, Lztsl , S100a16, Arhgap32, Sox15, Spintl , Clic3, Crb3, and Rtkn.

[0206] In certain embodiments, the Klf5 metagene comprises genes selected from Klf5, Dsg3, Tmprssl 1 bnl, Grhl3, Dsp, Jup, Pkp1 , Ripk4, Esrpl , Tgm1 , Ehf, Aqp3, Cdh1 , Spintl , Tjp2, Foxql , 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll , Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1 , Rab25, Duoxal , Plekhg6, Slc9a3r1 , Pkp3, Tnk1 , Krtcap3, Fam160a1 , Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1 r13l, Sult2b1 , Celsrl , Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1 g, Col17a1 , Grb7, Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2, Llgl2, Anxa8, Krt5, Tmprssl 1 e, Ppi, Dennd2c, Tacstd2, Sprrl a, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl , Tmem63b, Grhl2, Cldn4, Krt14, TtlH O, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1 , and Itgb4.

[0207] In certain embodiments, the Psca metagene comprises genes selected from Psca, Mal, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1 d, Cblc, Ceacaml , Gstol , Tmprssl 1 g, Anxal , Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1 bnl, Krt13,Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, Upk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinbl 1 , Rab25, Dsg3, Prss22, Tmprss11a, Calml3, Epn3, Slc6a20a, Tmprss11e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl , Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rabi 1fip1 , Ocln, Crispl , Prss8, Pglyrp4, Kif21 a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1, Gstal, Gstal, Pvrl4, ArhgefWI, Elf5, Mapk13, Ikzf2, Tjp3, Osginl , Gsta2, Cldn7, Epb4.115, Duoxa2, Zfp750, Zdhhc13, GmW639, Klk11 , Arhgap40, Arg1, Ltf, Rnf223, and St14.

[0208] In certain embodiments, the Cd44 metagene comprises genes selected from Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Fam83h, Col17a1, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpzl2, Arhgef5, Spint2, 1810019J16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltHb, Grb7, Esrp2, Lsr, Itga3, Plekha7, Dsg3, Clca5, Ap1m2, Plch2, Arhgef5, Celsrl, Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5, Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgef16, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1, Lypd3, Trim29, Tmprss11g, Cnksrl, Tmprss11bnl, Mir200b, Ptprf, Gm9908, Dlg1, Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, Il17re, Fat1, Nrg1, Mdfi, and Nipal2.

[0209] In certain embodiments, the Promt metagene comprises genes selected from Promt, Ceacaml, Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca, Tmprss11d, Cwh43, Slc37a1, Marveld2, ArhgefWI, Gclm, Ocln, Mctp2, Lrrc26, Fxyd3, lldrl, Cblc, Spintl, Cldn4, Slc52a3, Tmprss11g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, Upk3bl, Slc9a3r1, Mall, Sostdcl, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2l1, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO, Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprss11bnl, Gpx2, Gstol, Spns2, Serpinbl 1, Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N1 ORik, Sh3yl1 , Slc5a9, SarndlO, Elf3, St14, Ikzf2, Kif21 a, and Erbb3.

[0210] In certain embodiments, the Prom2 metagene comprises genes selected from Prom2, Clic3, Tmem54, Evpl, Zfp750, GrhH, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8l1, Gltp, Llgl2, Ovoll, Tmprss13, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14, Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinbl 1, H22ra1, Erbb2, Dsc2, Rnf39, Tmprss11e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, Arhgef I, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl, Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1, Ttc39a, Spintl, Ppfia3, S100a7a, Dsp, Chitl, Pinlyp, Grb7,Tmem79, Barx2, Klk10, Perp, Efna3, CcbH, Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml , Slc6a20a, SytH , Rnf223, Ide, Calml3, Caszl , and Celsr2.

[0211] In certain embodiments, the Bmi1 metagene comprises genes selected from Bmi1, Klhdc2, Bbx, Tusc3, Glg1 , Bloc1s6, Wdr34, 5730455P16Rik, Hs2st1 , Terf2, Fut8, Zmym4, Pcm1 , Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajdO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301 B20Rik, Mib1, Tiam2, Cers2, Stk3, Hspa13, Txndc12, Dock7, Psmd5, Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1 , Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy1911 , Ilf3, Bbs4, Slc30a4, InppH , Inf2, Zmynd11, Atp8b2, Gludl , Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, Kifap3, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7.

[0212] In certain embodiments, the Sox4 metagene comprises genes selected from Sox4, Abl1 , Rab34, Fgfrll, Ptovl, Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl, Tcf3, Tcf12, Clip2, Bbx, Nf1, Spats2, Farpl , Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl , Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl, MicalH, Ubxn7, Mvb12b, Trio, Stonl, Dok1, Fam65a, Fmnl3, Hsf2, Sestdl, Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1, Cep120, Rnf139, Dpy19l1, Dbn1, Ctps2, Magedl, Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbl , AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl , Staul , Mecp2, Phf20, Pex11 b, Ehmt2, Cep170, Fgf r1 , Txndc5, Zmym4, Samdl 4, Kansl2, Teadl , Zkscanl 7, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdm1 a, Loxl3, Acvrl , Wwtrl , AsxH , and Phf2.

[0213] In certain embodiments, the Lrigl metagene comprises genes selected from Lrigl, Rgmb, Zcchc24, Teadl, Lambi, Cep170, Evalb, Sept9, Farpl, Satb2, Maplb, Ccdc88a, Axl, Loxl3, Pdgfra, list, Lgalsl, Kifap3, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamd, Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1, Stx2, Lbh, Wipfl, Igfbp4, Myo9a, Cul7, Abl1, Phf20, Xxyltl, Myo9a, Dok1, Dst, Gkapl, Tspan11, Phldbl, Sydel, Teadl, Rab34, Stxbpl, AI597468, St6gal1, Ilk, Zeb1, Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl, Ank, Displ, Fhl3, Fermt2, Cdr2, Dock5, Crabpl, S1pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl, Sdccag8, Gliprl, and Nnt.

[0214] In certain embodiments, the Lgr6 metagene comprises genes selected from Lgr6, Tnnt2, Cnnm4, Prss12, Sox9, Itga2, Shf, I Bhlhe41, Fzd7, Krt18, Arid5a, Tgfbl, Tes, Raplgap, Add2, Sdd, Jam2, Gpr Ertd82e, Plekhg3, Lamc2, Socs2, Rampl, Etv6, Lamb3, Egr3, Dusp6, Foxpl, a, Pip4k2c, Rnf181 , Anol, A130010J15Rik, 1118r1, Chst2, Jag1, 1600029D21 Runxl, Rhbddl, Smad7, Itga6, Socs2,Slco2a1 , Aplp2, Cd9, Rail 4, Smurfl , Nedd9, C1 galt1 , Pmepal , Padi3, Gpr25, Fermtl , Nav2, Arhgef3, Capnsl , Foxp4, Ubald2, Gm7367, Gm7367, Ctnnal , Cd80, Hivep2, Dyrk3, Rab6a, Runx2, Iqgapl , Ggct, Lrch4, Skil, Frrsl , Slc20a2, Ncmap, Reep3, Nadsynl , Bhlhe40, Gprc5a, Slc39a4, Hes6, Acsl3, Erc1 , Lama5, Ephb4, Rmnd5b, Plekhal , Bcr, Zbtb18, Shq1 , Scyl2, Padi4, Scin, Dhcr7, and Atpl Od.

[0215] In certain embodiments, the Sox9 metagene comprises genes selected from Sox9, Lgr6, Shf, Cnnm4, Runxl , Ctnnal , Capnsl , Rail 4, Itpr3, Runx2, Iqgapl , Bhlhe41 , Rnf181 , Ccndl , Prss12, Tes, Aig1 , Foxc2, Rapl gap, Krt18, Rab6a, Etv6, Dusp6, IgsfS, Tubgcp2, Alcam, Sos2, Dusp4, Bzw2, Nck2, Add2, Foxpl , Ubald2, Tnnt2, Kcnn4, Fzd7, Reep3, Nav2, Cpe, Casp3, Cnot7, Cttn, Anol , Bcarl , Cyth2, Myof, Egr3, Nadsynl , Nt5e, Dnaja4, Plekhal , Capg, Phc2, I tga2, B4galnt1 , Smurfl , Gtf2i rd 1 , Pwwp2b, Phldal , Enppl , Nfat5, Cd151 , Hivep2, Ppmel , Tgif 1 , Gm7367, Gm7367, Zbtb18, Sdc4, D630045J12Rik, Smad7, Slc20a2, Igfl r, Rsf1 , Tnfrsf12a, Slc27a1 , Chst2, 2810408A1 1 Rik, Igfbp3, Kdelrl , Ern1 , Atxn2l,Dyrk3, Tgfbl , Bhlhe40, Phrfl , Tnfrsf22, Ddhdl , Traf4, A130010J15Rik, Papd7, Mast4, Skil, Pyroxdl , Fubp3, Nr1 h2, Ctnnbl , Foxci , Tbc1 d1 , and 181001101 ORik.

[0216] In certain embodiments, a cell is provided, the cell comprising: a first lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf 5 , Psca, Cd44, Prom1 , and Prom2, wherein expression of the first lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2; and a second lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9, wherein expression of the second lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9.

[0217] The reporter gene encodes a gene product that provides a readily detectable signal such as fluorescence, bioluminescence, or enzymatic activity to track expression of a biomarker gene. Exemplary reporter genes include genes encoding fluorescent proteins such as, but not limited to, green fluorescent protein (GFP), enhanced green fluorescent protein (EGFP), yellow fluorescent protein (YFP), yellow-green fluorescent protein, blue fluorescent protein (BFP), cyan fluorescent protein (CFP), violet fluorescent protein, red fluorescent protein (RFP), mCherry, mStrawberry, mOrange, mPlum, Venus, dsRed, and tdTomato; genes encoding bioluminescent proteins such as, but not limited to, luciferases from Photinus pyralis, Renilla reniformis, Metridia longa, Vibrio fischeri, Vibrio haweyi, Vibrio harveyi, and dinoflagellates, engineered luciferases such as NanoLuc, QLuc, Antares, and teLuc; and genes encoding enzymes such as, but not limited to, p-galactosidase (lacZ), alkaline phosphatase (AP), and chloramphenicol acetyltransferase (CAT). See also, Jiang et al. (2008) Biotechnol Genet Eng Rev 25:41 -75, Xuet al. (2020) Apoptosis 25(7-8) :459-473, Kang et al. (2008) J Nucl Med 49 Suppl 2:164S-79S, Zhang et al. (2002) Nat Rev Mol Cell Biol 3(12):906-18. Preferably, a reporter gene is selected that is not expressed endogenously in the cell.

[0218] In certain embodiments, the first lineage tracing reporter gene encodes a first fluorescent protein, and the second lineage tracing reporter gene encodes a second fluorescent protein, wherein the first fluorescent protein and the second fluorescent protein have different fluorescent emission wavelengths to allow expression of a gene selected from a Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Promt metagene, and Prom2 metagene, and a gene selected from a Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene to be distinguished. In an exemplary embodiment, the first fluorescent protein is a green fluorescent protein, and the second fluorescent protein is a red fluorescent protein. In another exemplary embodiment, the first fluorescent protein is a blue fluorescent protein, and the second fluorescent protein is a yellow fluorescent protein. As well be clear to one of skill in the art, other combinations of fluorescent proteins may be used as long as the fluorescent emissions from different fluorescent reporters are distinguishable. Florescent emissions of reporter fluorescent proteins may be detected using any suitable technique such as, but not limited to, fluorescence microscopy, fluorometry, or flow cytometry. In some embodiments, a microplate fluorescence scanner is used for multiplex reporter gene assays.

[0219] In some embodiments, one or more reporter genes are used to track expression of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more genes of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Promt metagene, and Prom2 metagene, and one or more reporter genes are used to track expression of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more genes of the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene, wherein each reporter gene encodes a different reporter protein (e.g., fluorescent protein with different emission wavelength) to allow the expression of the genes to be distinguished from one another. In some embodiments, a first reporter gene is used to track expression of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or all 10 of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 genes, and a second reporter gene is used to track expression of 1 , 2, or all 3 of the Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 genes, wherein expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 genes can be distinguished from expression of the Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 genes. In some embodiments, a first reporter gene encoding a first fluorescent protein is used to track expression of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2, and a second reporter gene encoding a second fluorescent protein is used to track expression of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 to provide a two color assay for distinguishing cell states.

[0220] In some embodiments, the reporter gene is fused to a regulatory region of a target biomarker gene such that the reporter gene and the target biomarker gene are under the control of the same promoter. In some embodiments, a gene fusion is created, wherein the reporter gene and the target biomarker gene are transcribed into a single messenger RNA molecule, wherein the mRNA is translated into a fusion protein comprising the protein encoded by the target biomarker gene covalently linked to a reporter protein encoded by the reporter gene. In some cases, a polynucleotide encoding a flexible linker region is included in constructs such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the target biomarker gene to minimize interference of the reporter protein with the expressed protein of the target biomarker gene whose expression is being monitored.

[0221] Reporter genes can be inserted into the genome of a cell at a target location (e g., regulatory region or coding region of a target biomarker gene whose expression is to be monitored) using any suitable gene editing method. Various gene editing approaches can be used for this purpose, including, without limitation, the use of genome editing systems comprising clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR-associated (Cas) nucleases, meganucleases, zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs). See, e.g., CRISPR Gene Editing: Methods and Protocols (edited by Luo, Humana, 2019), Genome Editing and Engineering: From TALENs, ZFNs and CRISPRs to Molecular Surgery (edited by Appasani and Church, Cambridge University Press, 2018); herein incorporated by reference in their entireties. These gene editing techniques involve creating a double-strand break (DSB) in the DNA at a target site of the intended gene edit. In some embodiments, the DSB is repaired by homology-directed repair (HDR) using a donor DNA template comprising the reporter gene that is inserted into the genome at the target locus using homologous recombination to replace a portion of the genomic sequence with a modified sequence.

[0222] In some embodiments, the donor polynucleotide comprises the reporter gene flanked by a pair of homology arms, which are responsible for targeting the donor polynucleotide to a genomic locus (e.g., in target biomarker gene whose expression is to be monitored) where the reporter gene is integrated into the genome. The donor polynucleotide typically comprises a 5' homology arm that hybridizes to a 5' genomic target sequence and a 3' homology arm that hybridizes to a 3' genomic target sequence. The homology arms are referred to herein as 5' and 3' (i.e., upstream and downstream) homology arms, which relates to the relative position of the homology arms to the reporter gene within the donor polynucleotide. The 5' and 3' homology arms hybridize to regions within the target locus in the genomic DNA to be modified, which are referred to herein as the "5' target sequence" and "3' target sequence," respectively.

[0223] The homology arm must be sufficiently complementary for hybridization to the target sequence to mediate homologous recombination between the donor polynucleotide and genomic DNA at the target locus. For example, a homology arm may comprise a nucleotide sequence having at least about 80-100% sequence identity to the corresponding genomic target sequence, including any percent identity within this range, such as at least 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity thereto, wherein the reporter gene is integrated into the genomic DNA by HDR at the genomic target locus recognized (i.e. , sufficiently complementary for hybridization) by the 5' and 3' homology arms.

[0224] In certain embodiments, the corresponding homologous nucleotide sequences in the genomic target sequence (i.e., the "5' target sequence" and "3' target sequence") flank a specific site for cleavage and / or a specific site for introducing the reporter gene. The distance between the specific cleavage site and the homologous nucleotide sequences (e.g., each homology arm) can be several hundred nucleotides. In some embodiments, the distance between a homology arm and the cleavage site is 200 nucleotides or less (e.g., 0, 10, 20, 30, 50, 75, 100, 125, 150, 175, and 200 nucleotides). In most cases, a smaller distance may give rise to a higher gene targeting rate. In a preferred embodiment, the donor polynucleotide is substantially identical to the target genomic sequence, across its entire length except for the sequence changes to be introduced to a portion of the genome that encompasses both the specific cleavage site and the portions of the genomic target sequence to be altered.

[0225] A homology arm can be of any length, e.g., 10 nucleotides or more, 50 nucleotides or more, 100 nucleotides or more, 250 nucleotides or more, 300 nucleotides or more, 350 nucleotides or more, 400 nucleotides or more, 450 nucleotides or more, 500 nucleotides or more, 1000 nucleotides (1 kb) or more, 5000 nucleotides (5 kb) or more, 10000 nucleotides (10 kb) or more, etc. In some instances, the 5' and 3' homology arms are substantially equal in length to one another, e.g. one may be 30% shorter or less than the other homology arm, 20% shorter or less than the other homology arm, 10% shorter or less than the other homology arm, 5% shorter or less than the other homology arm, 2% shorter or less than the other homology arm, or only a few nucleotides less than the other homology arm. In other instances, the 5' and 3' homology arms are substantially different in length from one another, e.g., one may be 40% shorter or more, 50% shorter or more, sometimes 60% shorter or more, 70% shorter or more, 80% shorter or more, 90% shorter or more, or 95% shorter or more than the other homology arm.

[0226] An RNA-guided nuclease can be targeted to a particular genomic sequence (i.e., genomic target sequence to be modified) by altering its guide RNA sequence. A target-specific guide RNA comprises a nucleotide sequence that is complementary to a genomic target sequence, and thereby mediates binding of the nuclease-gRNA complex by hybridization at the target site. Forexample, the gRNA can be designed with a sequence complementary to a sequence of the genomic target locus to target the nuclease-gRNA complex to a target site.

[0227] In certain embodiments, the RNA-guided nuclease used for genome modification is a clustered regularly interspersed short palindromic repeats (CRISPR) system Cas nuclease. Any RNA-guided Cas nuclease capable of catalyzing site-directed cleavage of DNA to allow integration of donor polynucleotides by the HDR mechanism can be used in genome editing, including CRISPR system type I, type II, or type III Cas nucleases. Examples of Cas proteins include Cas1 , Cas1 B, Cas2, Cas3, Cas4, Cas5, Cas5e (CasD), Cas6, Cas6e, Cas6f, Cas7, Cas8a1 , Cas8a2, Cas8b, Cas8c, Cas9 (Csn1 or Csx12), Cas10, Cas10d, CasF, CasG, CasH, Csy1 , Csy2, Csy3, Cse1 (CasA), Cse2 (CasB), Cse3 (CasE), Cse4 (CasC), Csc1 , Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1 , Cmr3, Cmr4, Cmr5, Cmr6, Csb1 , Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1 , Csx15, Csf1 , Csf2, Csf3, Csf4, and Cu1966, and homologs or modified versions thereof.

[0228] In certain embodiments, a type II CRISPR system Cas9 endonuclease is used. Cas9 nucleases from any species, or biologically active fragments, variants, analogs, or derivatives thereof that retain Cas9 endonuclease activity (i.e., catalyze site-directed cleavage of DNA to generate double-strand breaks) may be used to perform genome modification as described herein. The Cas9 need not be physically derived from an organism, but may be synthetically or recombinantly produced. Cas9 sequences from a number of bacterial species are well known in the art and listed in the National Center for Biotechnology Information (NCBI) database. See, for example, NCBI entries for Cas9 from: Streptococcus pyogenes (WP_002989955, WP_038434062, WP_011528583); Campylobacter jejuni (WP_022552435, YP_002344900), Campylobacter coli (WP_060786116); Campylobacter fetus (WP_059434633); Corynebacterium ulcerans (NC_015683, NC_017317); Corynebacterium diphtheria (NC_016782, NC_016786); Enterococcus faecalis (WP_033919308); Spiroplasma syrphidicola (NC_021284); Prevotella intermedia (NC_017861 ); Spiroplasma taiwanense (NC_021846); Streptococcus iniae (NC_021314); Belliella baltica (NC_018010); Psychroflexus torquisl (NC_018721 ); Streptococcus thermophilus (YP_820832), Streptococcus mutans (WP_061046374, WP_024786433); Listeria innocua (NP_472073); Listeria monocytogenes (WP_061665472); Legionella pneumophila (WP 062726656); Staphylococcus aureus (WP_001573634); Francisella tularensis (WP 032729892, WP_014548420), Enterococcus faecalis(WP_033919308); Lactobacillus rhamnosus (WP_048482595, WP_032965177); and Neisseria meningitidis (WP_061704949, YP_002342100); all of which sequences (as entered by the date of filing of this application) are herein incorporated by reference. Any of these sequences or a variant thereof comprising a sequence having at least about 70-100% sequence identity thereto, including any percent identity within this range, such as 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80,81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, can be used for genome editing, as described herein. See also Fonfara et al. (2014) Nucleic Acids Res. 42(4):2577-90; Kapitonov et al. (2015) J. Bacteriol. 198(5):797-807, Shmakov et al. (2015) Mol. Cell. 60(3):385-397, and Chylinski et al. (2014) Nucleic Acids Res. 42(10) :6091 - 6105); for sequence comparisons and a discussion of genetic diversity and phylogenetic analysis of Cas9.

[0229] The CRISPR-Cas system naturally occurs in bacteria and archaea where it plays a role in RNA-mediated adaptive immunity against foreign DNA. The bacterial type II CRISPR system uses the endonuclease, Cas9, which forms a complex with a guide RNA (gRNA) that specifically hybridizes to a complementary genomic target sequence, where the Cas9 endonuclease catalyzes cleavage to produce a double-stranded break. Targeting of Cas9 typically further relies on the presence of a 5' protospacer-adjacent motif (PAM) in the DNA at or near the gRNA-binding site.

[0230] The genomic target site will typically comprise a nucleotide sequence that is complementary to the gRNA, and may further comprise a protospacer adjacent motif (PAM). In certain embodiments, the target site comprises 20-30 base pairs in addition to a 3 base pair PAM. Typically, the first nucleotide of a PAM can be any nucleotide, while the two other nucleotides will depend on the specific Cas9 protein that is chosen. Exemplary PAM sequences are known to those of skill in the art and include, without limitation, NNG, NGN, NAG, and NGG, wherein N represents any nucleotide. In certain embodiments, the intron sequence of the TCR gene targeted by a gRNA comprises a mutation that creates a PAM within the intron, wherein the PAM promotes binding of the Cas9-gRNA complex to the intron.

[0231] In certain embodiments, the gRNA is 5-50 nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22 nucleotides, or 19-21 nucleotides in length, or any length between the stated ranges, including, for example, 10, 1 1 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, or 35 nucleotides in length. The guide RNA may be a single guide RNA comprising crRNA and tracrRNA sequences in a single RNA molecule, or the guide RNA may comprise two RNA molecules with crRNA and tracrRNA sequences residing in separate RNA molecules.

[0232] In another embodiment, the CRISPR nuclease from Prevotella and Francisella 1 (Cpf1 ) also referred to as CRISPR associated protein 12a (Cas12a) may be used. Cas12a is another class II CRISPR / Cas system RNA-guided nuclease with similarities to Cas9 and may be used analogously. Unlike Cas9, Cas12a does not require a tracrRNA and only depends on a crRNA in its guide RNA, which provides the advantage that shorter guide RNAs can be used with Cas12a for targeting than Cas9. Cas12a is capable of cleaving either DNA or RNA. The PAM sites recognized by Cas12a have the sequences 5'-YTN-3' (where "Y" is a pyrimidine and "N" is anynucleobase) or 5'-TTN-3', in contrast to the G-rich PAM site recognized by Cas9. Cas12a cleavage of DNA produces double-stranded breaks with sticky-ends having a 4 or 5 nucleotide overhang. For a discussion of Cas12a, see, e.g., Ledford et al. (2015) Nature. 526 (7571 ) :17-17, Zetsche et al. (2015) Cell. 163 (3):759-771 , Murovec et al. (2017) Plant Biotechnol. J. 15(8):917- 926, Zhang et al. (2017) Front. Plant Sci. 8:177, Fernandes et al. (2016) Postepy Biochem. 62(3):315-326; herein incorporated by reference.

[0233] C2c1 is another class II CRISPR / Cas system RNA-guided nuclease that may be used. C2c1 , similarly to Cas9, depends on both a crRNA and tracrRNA for guidance to target sites. For a description of C2c1 , see, e.g., Shmakov et al. (2015) Mol Cell. 60(3):385-397, Zhang et al. (2017) Front Plant Sci. 8:177; herein incorporated by reference.

[0234] In yet another embodiment, an engineered RNA-guided Fokl nuclease may be used. RNA-guided Fokl nucleases comprise fusions of inactive Cas9 (dCas9) and the Fokl endonuclease (Fokl-dCas9), wherein the dCas9 portion confers guide RNA-dependent targeting on Fokl. For a description of engineered RNA-guided Fokl nucleases, see, e.g., Havlicek et al. (2017) Mol. Then 25(2):342-355, Pan et al. (2016) Sci Rep. 6:35794, Tsai et al. (2014) Nat Biotechnol. 32(6):569-576; herein incorporated by reference.

[0235] The RNA-guided nuclease can be provided in the form of a protein, such as the nuclease complexed with a gRNA, or provided by a nucleic acid encoding the RNA-guided nuclease, such as an RNA (e.g., messenger RNA) or DNA (expression vector such as a plasmid or viral vector). Codon usage may be optimized to improve production of an RNA-guided nuclease in a particular cell, organoid, or organism. For example, a nucleic acid encoding an RNA-guided nuclease can be modified to substitute codons having a higher frequency of usage in a human cell or a nonhuman mammalian cell, such as a non-human primate cell, a rodent cell, a mouse cell, a rat cell, or any other host cell of interest, as compared to the naturally occurring polynucleotide sequence. When a nucleic acid encoding the gRNA and / or RNA-guided nuclease is introduced into cells, the gRNA and / or RNA-guided nuclease can be transiently, conditionally, or constitutively expressed in the cell. Recombinant nucleic acids encoding the gRNA, RNA-guided nuclease, and / or donor polynucleotide can be introduced into a cell using any suitable transfection technique such as, but not limited to electroporation, nucleofection, or lipofection. Alternatively, a ribonucleoprotein complex of the gRNA and the RNA-guided nuclease may be introduced into a cell by microinjection into the cytoplasm or nucleus.

[0236] In some embodiments, the CRISPR system is introduced into cells with a viral vector that encodes the RNA-guided nuclease and guide RNA (gRNA). Viral delivery of CRISPR components has been demonstrated using lentiviral, retroviral, adenovirus, and adeno- associated virus (AAV) vectors. For a description of methods of introducing a CRISPR system into cells with various viral vectors, see, e.g., Shalem et al. (2014) Science 343:84-87, Williamset al. (2016) Sci Rep. 6:2561 1 , Ran et al. (2015) Nature 520:186-191 , Swiech et al. (2015) Nat Biotechnol. 33:102-106; herein incorporated by reference.

[0237] Alternatively, a gRNA and a messenger RNA encoding the RNA-guided nuclease can be introduced into cells, wherein the RNA-guided nuclease is produced by translation of the mRNA in the cytoplasm. The gRNA and RNA-guided nuclease then form a complex in the cytoplasm and enter the nucleus. RNA transfection of cells can be performed using electroporation, cationic- lipid-mediated transfection, or using liposomes or lipid nanoparticles (LNPs) encapsulating the gRNA and mRNA. See, e.g., Billingsley et al. (2022) Nano Lett 22(1 ):533-542, Tchou et al. (2017) Cancer Immunol Res. 5(12) :1152-1161 , Ye et al. (2022) ACS Biomater Sci Eng. 8(2)722-733, Guevara et al. (2020) Front. Chem. 8:589959; herein incorporated by reference.

[0238] Donor polynucleotides and gRNAs are readily synthesized by standard techniques, e.g., solid phase synthesis via phosphoramidite chemistry, as disclosed in U.S. Patent Nos. 4,458,066 and 4,415,732, incorporated herein by reference; Beaucage et al., Tetrahedron (1992) 48:2223- 2311 ; and Applied Biosystems User Bulletin No. 13 (1 April 1987). Other chemical synthesis methods include, for example, the phosphotriester method described by Narang et al., Meth. Enzymol. (1979) 68:90 and the phosphodiester method disclosed by Brown et al., Meth. Enzymol. (1979) 68:109. In view of the short lengths of gRNAs (typically about 20 nucleotides in length) and donor polynucleotides (typically about 100-150 nucleotides), gRNA-donor polynucleotide cassettes can be produced by standard oligonucleotide synthesis techniques and subsequently ligated into vectors.

[0239] Zinc-finger nucleases (ZFNs) are artificial DNA endonucleases generated by fusing a zinc finger DNA binding domain to a DNA cleavage domain. ZFNs can be engineered to target desired DNA sequences, which enables zinc-finger nucleases to cleave unique target sequences. When introduced into a cell, ZFNs can be used to edit target DNA in the cell (e.g., the cell's genome) by inducing double strand breaks. For more information on the use of ZFNs, see, for example: Asuri et al., Mol Ther. 2012 February; 20(2):329-38; Bibikova et al. Science. 2003 May 2; 300(5620)764; Wood et al. Science. 201 1 Jul. 15; 333(6040) :307; Ochiai et al. Genes Cells.2010 August; 15(8):875-85; Takasu et. al., Insect Biochem Mol Biol. 2010 October; 40(10)759- 65; Ekker et al, Zebrafish 2008 Summer; 5(2) : 121 -3; Young et al, Proc Natl Acad Sci USA. 201 1 Apr. 26; 108(17)7052-7; Goldberg et al, Cell. 2010 Mar. 5; 140(5):678-91 ; Geurts et al, Science. 2009 Jul. 24; 325(5939) :433; Flisikowska et al, PLoS One. 2011 ; 6(6):e21045. doi: 10.1371 / journal. pone.0021045. Epub 201 1 Jun. 13; Hauschild et al, Proc Natl Acad Sci USA.2011 Jul. 19; 108(29):12013-7; and Yu et al, Cell Res. 201 1 November; 21 (11 ):1638-40; all of which are herein incorporated by reference for their teachings related to ZFNs. The term “ZFN agent” encompasses a zinc finger nuclease and / or a polynucleotide comprising a nucleotide sequence encoding a zinc finger nuclease.

[0240] Transcription activator-like effector nucleases (TALENs) are artificial DNA endonucleases generated by fusing a TAL (Transcription activator-like) effector DNA binding domain to a DNA cleavage domain. TALENS can be quickly engineered to bind practically any desired DNA sequence and when introduced into a cell, TALENs can be used to edit target DNA in the cell (e.g., the cell's genome) by inducing double strand breaks. For more information on the use of TALENs, see, for example: Hockemeyer et al. Nat Biotechnol. 2011 Jul. 7; 29(8):731 -4; Wood et al. Science. 201 1 Jul. 15; 333(6040) :307; Tesson et al. Nat Biotechnol. 2011 Aug. 5; 29(8):695- 6; and Huang et. al., Nat Biotechnol. 201 1 Aug. 5; 29(8):699-700; all of which are herein incorporated by reference for their teachings related to TALENs. The term “TALEN agent” encompasses a TALEN and / or a polynucleotide comprising a nucleotide sequence encoding a TALEN.

[0241] The cell that is genetically modified to include reporter genes for use in reporter gene assays, as described herein, may be derived from a pre-malignant lesion such as, but not limited to a papilloma, actinic keratosis, adenoma, polyp, hyperplasia, or dysplasia lesion. In certain embodiments, the cell is a pre-malignant epithelial cell. In certain embodiments, the pre- malignant cell is a mammalian pre-malignant cell, such as, but not limited to, a rodent, non-human primate, or human pre-malignant cell. In some embodiments, the cell is a cancerous cell. In some embodiments, the cell is derived from a cancerous cell that was previously treated with a chemotherapeutic agent.

[0242] Reporter gene assays can be used for high throughput screening to identify agents that switch the pre-malignant cell from one cell state to another, as described further below.Screening Candidate Agents

[0243] Screening methods are provided for identifying an agent that switches a pre-malignant cell or a cancerous cell from a cell state having lineage plasticity and drug resistance to a proliferative cell state or vice versa. As discussed above, cell type switching in response to treatment of a pre-malignant cell or a cancerous cell with a candidate agent can be detected by measuring expression levels of genes selected from a Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene either directly or indirectly using a reporter gene assay. Assays may further include suitable controls (e.g., a pre-malignant cell or a cancerous cell in the absence of the candidate agent). Generally, a plurality of assays are run in parallel with different agent concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection.

[0244] A variety of different test agents may be screened. Candidate agents encompass numerous chemical classes, e.g., small organic compounds having a molecular weight of more than 50 daltons and less than about 10,000 daltons, less than about 5,000 daltons, or less than about 2,500 daltons. Test agents can comprise functional groups necessary for structural interaction with proteins, e.g., hydrogen bonding, and can include at least an amine, carbonyl, hydroxyl or carboxyl group, or at least two of the functional chemical groups. The test agents can comprise cyclical carbon or heterocyclic structures and / or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Test agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.

[0245] Test agents are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs. Moreover, screening may be directed to known pharmacologically active compounds and chemical analogs thereof, or to new agents with unknown properties such as those created through rational drug design.

[0246] In some embodiments, test agents are synthetic compounds. A number of techniques are available for the random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides. See for example WO 94 / 24314, hereby expressly incorporated by reference, which discusses methods for generating new compounds, including random chemistry methods as well as enzymatic methods.

[0247] In another embodiment, the test agents are provided as libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts that are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means. Known pharmacological agents may be subjected to directed or random chemical modifications, including enzymatic modifications, to produce structural analogs.

[0248] In some embodiments, the test agents are organic moieties. In this embodiment, test agents are synthesized from a series of substrates that can be chemically modified. “Chemically modified” herein includes traditional chemical reactions as well as enzymatic reactions. Thesesubstrates generally include, but are not limited to, alkyl groups (including alkanes, alkenes, alkynes and heteroalkyl), aryl groups (including arenes and heteroaryl), alcohols, ethers, amines, aldehydes, ketones, acids, esters, amides, cyclic compounds, heterocyclic compounds (including purines, pyrimidines, benzodiazepins, beta-lactams, tetracylines, cephalosporins, and carbohydrates), steroids (including estrogens, androgens, cortisone, ecodysone, etc.), alkaloids (including ergots, vinca, curare, pyrollizdine, and mitomycines), organometallic compounds, hetero-atom bearing compounds, amino acids, and nucleosides. Chemical (including enzymatic) reactions may be done on the moieties to form new substrates or candidate agents which can then be tested using the present invention.

[0249] In some embodiments test agents are assessed for any cytotoxic activity they may exhibit toward a living eukaryotic cell, using well-known assays, such as trypan blue dye exclusion, an MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2 H-tetrazolium bromide) assay, and the like. Agents that do not exhibit significant cytotoxic activity are considered candidate agents.

[0250] In certain embodiments, the candidate agent inhibits mitosis or induces cell differentiation. In some embodiments, the candidate agent inhibits KRAS4A or protein phosphatase 2A (PP2A). In some embodiments, the candidate agent selectively inhibits a PP2A subunit. In some embodiments, the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.Kits

[0251] Also provided are kits for use in the methods, disclosed herein, for assaying a pre- malignant or cancerous cell to determine whether the cell is in a cell state having lineage plasticity and drug resistance or a non-drug resistant proliferative cell state. In some embodiments, the kit includes agents for performing RT-PCR, RNA-Seq, or GRO-SEQ (e.g., 5-bromouridine 5'- triphosphate (Br-UTP), a nuclear lysis buffer containing sarkosyl, RNase inhibitors, antibodies against bromouridine (BrdU), magnetic beads, DNA polymerase, reverse transcriptase, primers, dNTPs, and appropriate buffers for washes and purification, and the like) to determine the levels of mRNA transcripts of a gene of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene.

[0252] In certain embodiments, the kit comprises a cell comprising a first lineage tracing reporter gene operably linked to a promoter of a first gene whose expression is positively correlated with a stem cell plasticity state, wherein expression of the first lineage tracing reporter gene coincides with the expression of the first gene; and a second lineage tracing reporter gene operably linked to a promoter of a second gene whose expression is positively correlated with a proliferativestate, wherein expression of the second lineage tracing reporter gene coincides with the expression of the second gene. In some embodiments, the first gene is selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Prom1 metagene, and a Prom2 metagene; and the second gene is selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene.

[0253] In some embodiments, the kit comprises a cell comprising: a first lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf 5 , Psca, Cd44, Prom1 , and Prom2, wherein expression of the first lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Sox2, Foxal , Krt 15, Krt19, Pitxl , Klf 5, Psca, Cd44, Proml , and Prom2; and a second lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9, wherein expression of the second lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9. In some embodiments, the first lineage tracing reporter gene encodes a first fluorescent protein, and wherein the second lineage tracing reporter gene encodes a second fluorescent protein. In some embodiments, the first fluorescent protein and the second fluorescent protein have different fluorescent emission wavelengths. In some embodiments, the cell is a cancerous cell or a pre-malignant cell. In some embodiments, the cell is a mammalian cell. In some embodiments, the mammalian cell is a rodent, non-human primate, or human cell. In some embodiments, the cell is derived from a cancerous cell that was previously treated with a chemotherapeutic agent. In some embodiments, the cell is derived from a pre-neoplasia lesion, optionally wherein the pre-neoplasia lesion is a papilloma. In some embodiments, the cell is a pre-malignant epithelial cell.

[0254] In addition to the above components, the subject kits may further include (in certain embodiments) instructions for practicing the subject methods. These instructions may be present in the subject kits in a variety of forms, one or more of which may be present in the kit. One form in which these instructions may be present is as printed information on a suitable medium or substrate, e.g., a piece or pieces of paper on which the information is printed, in the packaging of the kit, in a package insert, and the like. Yet another form of these instructions is a computer- readable medium, e.g., diskette, compact disk (CD), DVD, flash drive, and the like, on which the information has been recorded. Yet another form of these instructions that may be present is a website address which may be used via the internet to access the information at a removed site.Examples of Non-Limiting Aspects of the Disclosure

[0255] Aspects, including embodiments, of the present subject matter described above may be beneficial alone or in combination, with one or more other aspects or embodiments. Without limiting the foregoing description, certain non-limiting aspects of the disclosure numbered 1 -69 are provided below. As will be apparent to those of skill in the art upon reading this disclosure, each of the individually numbered aspects may be used or combined with any of the preceding or following individually numbered aspects. This is intended to provide support for all such combinations of aspects and is not limited to combinations of aspects explicitly provided below:1. A cell comprising: a first lineage tracing reporter gene operably linked to a promoter of a first gene whose expression is positively correlated with a stem cell plasticity state, wherein expression of the first lineage tracing reporter gene coincides with the expression of the first gene; and a second lineage tracing reporter gene operably linked to a promoter of a second gene whose expression is positively correlated with a proliferative state, wherein expression of the second lineage tracing reporter gene coincides with the expression of the second gene.2. The cell of aspect 1 , wherein the first gene is selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Promt metagene, and a Prom2 metagene; and the second gene is selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene.3. The cell of aspect 2, wherein the Sox2 metagene comprises genes selected from Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, MtmrI O, Esd, Sox13, Nfe2l2, Pls1 , Tom1 l2, Bink, Suox, Slc16a11 , Xrcc5, Chstl 5, Krtt 2, Eval c, Nppc, Esd, Ddx59, Nop2, Krtt 3, Plekhh3, Osbpl6, Aldh5a1 , Ci rh 1 a, Wnk4, Arntl2, Fam110c, Tmem180, Dili , Galnt12, Pitxl , Caleb, Ankrd9, Isl1 , Btc, Gss, Ociad2, Klra33, Aldh3a1 , Minkl , Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl , Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrl a, Pthlh, Usp6nl, Ufspl , Irgq, Nkiras2, Grtpl , Nqo1 , Krt20, Snord42b, Avpil , Ifrdl , Srd5a2, Cpn1 , Bail , Sprr3, Rap1gap2, Rassf7, Fetub, Ramp3, Arl4d, Tle1 , Krt76, Ptprzl , Pradd , Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl , G6pdx, Tsg101 , Nmrkl , Ralgapb, A430105119Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik; wherein the Foxal metagene comprises genes selected from Foxal , Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1 , Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1 , Tjp3, Plekhg6, Bspry, Ocln, Ceacaml , Marveld3, Cldn3, Mal2, Tmem30b, Sowahb,Spns2, Slc9a3r1 , Kctdl , Cwh43, Cystml , Rab17, S100a2, Ppbp, Padil , Caleb, Gstol , S100a16, Spint2, Slc52a3, Slc16a11 , Crispl , Mall, Aldh1a3, Entpd3, Tmprss11g, Anxal , Pgapl , Prss22, Kif21a, Omp, Liph, Epb4.1 l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, ArhgeflOl, Tmprss11d, Mxd1 , Elf5, Acss2, Leprell , Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppfibp2, Mboatl , Zdhhc13, Dgka, Ehf, Mst1 , St14, Ap1s3, Maltl , Spintl , Sprr3, Pllp, AA986860, Prss27, Tmprssl 1a, Serpinbl 1 , Hs3st1 , StardlO, Arhgap40, lldrl , Ppi, Fbp2, Cnksrl , Map7, and 1700001 C19Rik, E330009J07Rik; wherein the Krt15 metagene comprises genes selected from Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrcl , Zfp750, Lipm, Ocln, Paqr5, GrhH , Erbb3, PsapH , Aldh3b2, Ppi, Rapgefh , Aldh3b2, Efna3, Muc15, Liph, 2610528A11 Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1pr5, Klhl29, 4833423E24Rik, Nccrpl , Slc27a4, Barx2, Aind l, Wnt4, L1cam, Leprell , Rnf43, Ckmtl , Lipk, Mapk13, H22ra1 , Zfp185, Cds1 , Arhgap40, Krt80, Dsc3, Prss8, Fgfr3, Hsd17b2, Padil , Ripk4, Prom2, Adtrp, Caszl , 1700055N04Rik, Scnnla, Ptprf, Arhgefl Ol, Tmprssl 1 e, Slc25a48, Mall, Mst1 , Crnn, Celsrl , Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinbl 1 , Vsnll , Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprssl 3, Sowahb, Celsr2, Ly6g6e, SytH , Tprg, AA986860, and Sptbn2; wherein the Krt19 metagene comprises genes selected from Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal , Mall, Slc37a1 , Cblc, Marveld3, Marveld2, Gstol , Ceacaml , Gm9573, Ocln, Slc9a3r1 , Mal2, Tmprssl 1g, Spns2, Anxal , 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, ArhgeflOl, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, Upk3bl, Gsta4, Ppbp, Tmprssl 1d, Spintl , Tmem30b, S100a2, Pgapl , Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1 , Kif21 a, Krt13, Padil , Tmprssl 1 bnl, Foxql , S100a16, L1cam, Seel, Ehf, Sarndl O, Epb4.115, Rab27b, Plekha7, Llgl2, Erbb2, Stap2, Rab25, Hebp2, Cnksrl , 1117re, Pllp, Cystml , Tnk1 , Mboatl , Tmprss11 e, Tacstd2, Plekha6, Arg1 , Ltf, Evpl, S100a14, Plekhhl , Slc25a48, Ap1s3, Zdhhc13, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl , Ppfibp2, Nipal2, Rab27a, Rbm47, and StardlO; wherein the Pitxl metagene comprises genes selected from Pitxl , Cldn8, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1 , Klf5, Cep170b,Llgl2, 1700001C19Rik, Tmprss11d, Dsc2, Fam160a1 , Erbb2, Gsta4, Shb, Duoxal , Rab27b, Barx2, Fhdd , Tmprssl 1 bnl, Krt13, Plekhg6, Fam57a, Gstol , Ppp1 r13l, Dsg3, Epn3, Als2cl, Grhl3, Myo5b, Arhgef5, Tmem63b, Phldb3, Tmprssl 1 a, Gstal , Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinbl 1 , Foxql , Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhc13, Tgm1 , Gclm, Rhov, Gsta2, Samd12, Spns2, Proser2, Ehf, Sostd , Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl , Arhgap27, Lpar5, Duoxl , Sult2b1 , Jup,2200002D01 Rik, Map3k9, Ppap2c, Anxal, Arhgap27, Foxql, Mir200a, Cnksrl, Tmprss11g, Dennd2c, Lztsl, S100a16, Arhgap32, Sox15, Spintl , Clic3, Crb3, and Rtkn; wherein the Klf5 metagene comprises genes selected from Klf5, Dsg3, Tmprss11bnl, Grhl3, Dsp, Jup, Pkp1, Ripk4, Esrpl, Tgm1, Ehf, Aqp3, Cdh1, Spintl, Tjp2, Foxql, 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll, Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1, Rab25, Duoxal, Plekhg6, Slc9a3r1, Pkp3, Tnk1, Krtcap3, Fam160a1, Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1r13l, Sult2b1 , Celsrl , Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1g, Col17a1, Grb7, Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2, Llgl2, Anxa8, Krt5, Tmprssl 1e, Ppi, Dennd2c, Tacstd2, Sprrla, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl , Tmem63b, Grhl2, Cldn4, Krt14, TtlHO, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1 , and Itgb4; wherein the Psca metagene comprises genes selected from Psca, Mai, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1d, Cblc, Ceacaml, Gstol, Tmprssl 1g, Anxal, Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1bnl, Krt13, Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, L)pk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinb11, Rab25, Dsg3, Prss22, Tmprss11a, Calml3, Epn3, Slc6a20a, Tmprssl 1e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl, Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rabi 1fip1 , Ocln, Crispl, Prss8, Pglyrp4, Kif21a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1, Gstal, Gstal, Pvrl4, Arhgef I, Elf5, Mapk13, Ikzf2, Tjp3, Osginl, Gsta2, Cldn7, Epb4.1l5, Duoxa2, Zfp750, Zdhhc13, Gm10639, Klk11 , Arhgap40, Arg1 , Ltf, Rnf223, and St14; wherein the Cd44 metagene comprises genes selected from Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Fam83h, Col17a1, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpzl2, Arhgef5, Spint2, 1810019J16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltHb, Grb7, Esrp2, Lsr, Itga3, Plekha7, Dsg3, Clca5, Ap1m2, Plch2, Arhgef5, Celsrl, Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5, Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgef16, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1, Lypd3, Trim29, Tmprssl 1g, Cnksrl, Tmprssl 1bnl, Mir200b, Ptprf, Gm9908, Dlg1, Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, 1117re, Fat1, Nrg1, Mdfi, and Nipal2; wherein the Prom1 metagene comprises genes selected from Prom1, Ceacaml, Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca, Tmprssl 1d, Cwh43, Slc37a1, Marveld2, Arhgef I, Gclm, Ocln, Mctp2, Lrrc26, Fxyd3, lldrl, Cblc, Spintl, Cldn4, Slc52a3, Tmprssl 1g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, Upk3bl, Slc9a3r1, Mall, Sostdcl, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2l1, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO,Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprss11bnl, Gpx2, Gstol, Spns2, Serpinbl 1 , Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N10Rik, Sh3yl1, Slc5a9, SamdIO, Elf3, St14, Ikzf2, Kif21 a, and Erbb3; wherein the Prom2 metagene comprises genes selected from Prom2, Clic3, Tmem54, Evpl, Zfp750, GrhH, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8l1, Gltp, Llgl2, Ovol1, Tmprss13, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14, Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinbl 1, H22ra1, Erbb2, Dsc2, Rnf39, Tmprss11e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, ArhgeflOl, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl , Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1, Ttc39a, Spintl, Ppfia3, S100a7a, Dsp, Chitl, Pinlyp, Grb7, Tmem79, Barx2, Klk10, Perp, Efna3, CcbH, Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml, Slc6a20a, SytH, Rnf223, Ide, Calml3, Caszl, and Celsr2; wherein the Bmi1 metagene comprises genes selected from Bmi1, Klhdc2, Bbx, Tusc3, Glg1, Bloc1s6, Wdr34, 5730455P16Rik, Hs2st1, Terf2, Fut8, Zmym4, Pcm1, Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajcIO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301 B20Rik, Mib1, Tiam2, Cers2, Stk3, Hspa13, Txndc12, Dock7, Psmd5, Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1, Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy19l1, Ilf3, Bbs4, Slc30a4, Inpph, Inf2, Zmynd11, Atp8b2, Gludl, Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, Kifap3, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7; wherein the Sox4 metagene comprises genes selected from Sox4, Abl1 , Rab34, Fgf rl1 , Ptovl, Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl, Tcf3, Tcf12, Clip2, Bbx, Nf1, Spats2, Farpl, Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl, Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl, MicalU, Ubxn7, Mvb12b, Trio, Stonl, Dok1, Fam65a, Fmnl3, Hsf2, Sestdl, Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1, Cep120, Rnf139, Dpy19l1, Dbn1, Ctps2, Magedl, Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbl, AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl, Staid, Mecp2, Phf20, Pex11b, Ehmt2, Cep170, Fgfrl, Txndc5, Zmym4, Samd14, Kansl2, Teadl, Zkscan17, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdrr a, Loxl3, Acvrl, Wwtrl, Asxll, and Phf2; and wherein the Lrigl metagene comprises genes selected from Lrigl, Rgmb, Zcchc24, Teadl, Lambl, Cep170, Evalb, Sept9, Farpl, Satb2, Maplb, Ccdc88a, Axl, Loxl3, Pdgfra, list,Lgalsl , KifapS, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamcl , Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1 , Stx2, Lbh, Wipfl , Igfbp4, Myo9a, Cul7, Abl1 , Phf20, Xxyltl , Myo9a, Dok1 , Dst, Gkapl , Tspanl 1 , Phldbl , Sydel , Teadl , Rab34, Stxbpl , AI597468, St6gal1 , Ilk, Zeb1 , Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl , Ank, Displ , Fhl3, Fermt2, Cdr2, Dock5, Crabpl , S1 pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl , Sdccag8, Gliprl , and Nnt.4. The cell of aspect 1 , wherein the cell comprises: a first lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2, wherein expression of the first lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2; and a second lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9, wherein expression of the second lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9.5. The cell of any one of aspects 1 -4, wherein the first lineage tracing reporter gene encodes a first fluorescent protein, and wherein the second lineage tracing reporter gene encodes a second fluorescent protein.6. The cell of aspect 5, wherein the first fluorescent protein and the second fluorescent protein have different fluorescent emission wavelengths.7. The cell of any one of aspects 1 -6, wherein the cell is a cancerous cell or a pre- malignant cell.8. The cell of any one of aspects 1 -7, wherein the cell is a mammalian cell.9. The cell of aspect 8, wherein the mammalian cell is a rodent, non-human primate, or human cell.10. The cell of any one of aspects 1 -9, wherein the cell is derived from a cancerous cell that was previously treated with a chemotherapeutic agent.11 . The cell of any one of aspects 1 -9, wherein the cell is derived from a pre-neoplasia lesion, optionally wherein the pre-neoplasia lesion is a papilloma.12. The cell of any one of aspects 1 -11 , wherein the cell is a pre-malignant epithelial cell.13. The cell of any one of aspects 1 -12, wherein the first lineage tracing reporter gene is fused to a regulatory region of the first gene whose expression is positively correlated with a stem cell plasticity state such that the first lineage tracing reporter gene is under the control of the promoter of the first gene.14. The cell of any one of aspects 1-13, wherein the second lineage tracing reporter gene is fused to a regulatory region of the second gene whose expression is positively correlated with a proliferative state such that the second lineage tracing reporter gene is under the control of the promoter of the second gene.15. The cell of any one of aspects 1 -12, wherein the first lineage tracing reporter gene is fused in frame to a coding region of the first gene whose expression is positively correlated with a stem cell plasticity state such that the first lineage tracing reporter gene and the first gene are transcribed into a single messenger RNA (mRNA), wherein the mRNA is translated into a fusion protein comprising a protein encoded by the first gene covalently linked to a reporter protein encoded by the first lineage tracing reporter gene.16. The cell of aspect 15, further comprising an insertion of a polynucleotide encoding a flexible linker region between the first lineage tracing reporter gene and the first gene such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the first gene.17. The cell of any one of aspects 1-12, wherein the second lineage tracing reporter gene is fused in frame to a coding region of the second gene whose expression is positively correlated with a proliferative state such that the second lineage tracing reporter gene and the second gene are transcribed into a single messenger RNA (mRNA), wherein the mRNA is translated into a fusion protein comprising a protein encoded by the second gene covalently linked to a reporter protein encoded by the second lineage tracing reporter gene.18. The cell of aspect 17, further comprising an insertion of a polynucleotide encoding a flexible linker region between the second lineage tracing reporter gene and the second gene such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the second gene.19. A method of detecting whether the cell of any one of aspects 1 -18 is in a cell state having lineage plasticity and drug resistance or a proliferative cell state, the method comprising:(a) contacting the cell of any one of aspects 1 -18 with a candidate agent; and(b) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the first lineage tracing reporter gene compared to the second lineage tracing reporter gene indicates that the cell is in the cell state having lineage plasticity and drug resistance, and wherein increased expression of the second lineage tracing reporter gene compared to the first lineage tracing reporter gene indicates that the cell is in the proliferative cell state.20. The method of aspect 19, further comprising screening for an agent that switches the cell identified as being in the cell state having lineage plasticity and drug resistance to the proliferative cell state, the method comprising:(a) contacting the cell with a candidate agent; and(b) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the second lineage tracing reporter gene compared to the first lineage tracing reporter gene indicates that the cell has switched to the proliferative cell state.21 . The method of aspect 20, wherein the candidate agent induces cell differentiation.22. The method of aspect 20, wherein the candidate agent is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A.23. The method of aspect 20, wherein the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.24. The method of aspect 19, further comprising screening for an agent that switches the cell identified as being in the proliferative cell state to the cell state having lineage plasticity and drug resistance, the method comprising:(a) contacting the cell with a candidate agent; and(b) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the first lineage tracing reporter gene compared to the second lineage tracing reporter gene indicates that the cell has switched to the cell state having lineage plasticity and drug resistance.25. The method of aspect 24, wherein the candidate agent is an anti-mitotic agent.26. The method of aspect 25, wherein the anti-mitotic agent is an alkylating agent, a taxane, or a vinca alkaloid.27. The method of aspect 24, wherein the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.28. The method of any one of aspects 19-27, wherein the first lineage tracing reporter gene encodes a first fluorescent protein, and wherein the second lineage tracing reporter gene encodes a second fluorescent protein.29. The method of aspect 28, wherein the first fluorescent protein and the second fluorescent protein have different fluorescent emission wavelengths.30. A method of screening for an agent that switches cells between cell states, the method comprising:(a) providing a first population of cells and a second population of cells, wherein the first population of cells has increased lineage plasticity, increased levels of expression of a gene selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Promt metagene, and a Prom2 metagene, and decreased levels of expression of a gene selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene compared to the second population of cells, and wherein the second population of cells has increased proliferation, increased levels of expression of a gene selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene, and decreased levels of expression of a gene selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Prom1 metagene, and a Prom2 metagene compared to the first population of cells;(b) contacting the first population of cells and the second population of cells with a candidate agent;(c) measuring levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxf metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene, and one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the first population of cells and the second population of cells; and(d) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene and increased levels of expression of the one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the first population of cells in presence of the candidate agent compared to reference value ranges for the levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Proml metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein increased levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene and decreased levels of expression of the one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the second population of cells in the presence of the candidate agent compared to the reference value ranges for the levels of expression of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the candidate agent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.31 . The method of aspect 30, wherein the Sox2 metagene comprises genes selected from Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, MtmrI O, Esd, Sox13, Nfe2l2, Pls1 , Tom1 l2, Bink, Suox, Slc16a1 1 , Xrcc5, Chstl 5, Krt12, Eval c, Nppc, Esd, Ddx59, Nop2, Krt13, Plekhh3, Osbpl6, Aldh5a1 , Ci rh 1 a, Wnk4, Arntl2, Fam110c, Tmem180, Dili , Galnt12, Pitxl , Caleb, Ankrd9, Isl1 , Btc, Gss, Ociad2, Klra33, Aldh3a1 , Minkl , Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl , Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrl a, Pthlh, Usp6nl, Ufspl , Irgq, Nkiras2, Grtpl , Nqo1 , Krt20, Snord42b, Avpil , Ifrdl , Srd5a2, Cpn1 , Bail , Sprr3, Rap1gap2, Rassf7, Fetub, Ramp3, Arl4d,Tle1 , Krt76, Ptprzl , Pradcl , Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl , G6pdx, Tsg101 , Nmrkl , Ralgapb, A430105119Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik; wherein the Foxal metagene comprises genes selected from Foxal , Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1 , Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1 , Tjp3, Plekhg6, Bspry, Ocln, Ceacaml , Marveld3, Cldn3, Mal2, Tmem30b, Sowahb, Spns2, Slc9a3r1 , Kctdl , Cwh43, Cystml , Rab17, S100a2, Ppbp, Padil , Caleb, Gstol , S100a16, Spint2, Slc52a3, Sid 6a11 , Crispl , Mall, Aldh1a3, Entpd3, Tmprss11g, Anxal , Pgapl , Prss22, Kif21a, Omp, Liph, Epb4.1 l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, Arhgefl Ol, Tmprss11d, Mxd1 , Elf5, Acss2, LepreH , Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppfibp2, Mboatl , Zdhhc13, Dgka, Ehf, Mst1 , St14, Ap1s3, Maltl , Spintl , Sprr3, Pllp, AA986860, Prss27, Tmprssl 1a, Serpinbl 1 , Hs3st1 , StardlO, Arhgap40, lldrl , Ppi, Fbp2, Cnksrl , Map7, and 1700001 C19Rik, E330009J07Rik; wherein the Krt15 metagene comprises genes selected from Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrd , Zfp750, Lipm, Ocln, Paqr5, GrhH , Erbb3, PsapH , Aldh3b2, Ppi, RapgefH , Aldh3b2, Efna3, Muc15, Liph, 2610528A11 Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1pr5, Klhl29, 4833423E24Rik, Nccrpl , Slc27a4, Barx2, Aind l, Wnt4, L1cam, LepreH , Rnf43, Ckmtl , Lipk, Mapk13, H22ra1 , Zfp185, Cds1 , Arhgap40, Krt80, Dsc3, Prss8, Fgfr3, Hsd17b2, Padil , Ripk4, Prom2, Adtrp, Caszl , 1700055N04Rik, Scnnla, Ptprf, Arhgefl Ol, Tmprssl 1 e, Slc25a48, Mall, Mst1 , Crnn, Celsrl , Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinbl 1 , Vsnll , Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprssl 3, Sowahb, Celsr2, Ly6g6e, SytH , Tprg, AA986860, and Sptbn2; wherein the Krt19 metagene comprises genes selected from Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal , Mall, Slc37a1 , Cblc, Marveld3, Marveld2, Gstol , Ceacaml , Gm9573, Ocln, Slc9a3r1 , Mal2, Tmprssl 1g, Spns2, Anxal , 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, ArhgeflOl, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, Upk3bl, Gsta4, Ppbp, Tmprssl 1d, Spintl , Tmem30b, S100a2, Pgapl , Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1 , Kif21 a, Krt13, Padil , Tmprssl 1 bnl, Foxql , S100a16, L1cam, Seel, Ehf, Sarndl O, Epb4.115, Rab27b, Plekha7, Llgl2, Erbb2, Stap2, Rab25, Hebp2, Cnksrl , 1117re, Pllp, Cystml , Tnk1 , Mboatl , Tmprss11 e, Tacstd2, Plekha6, Arg1 , Ltf, Evpl, S100a14, Plekhhl , Slc25a48, Ap1s3, Zdhhc13, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl , Ppfibp2, Nipal2, Rab27a, Rbm47, and StardlO; wherein the Pitxl metagene comprises genes selected from Pitxl , CldnS, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1 , Klf5, Cep170b,Llgl2, 1700001 C19Rik, Tmprss11d, Dsc2, Fam160a1 , Erbb2, Gsta4, Shb, Duoxal , Rab27b, Barx2, Fhdd , Tmprssl 1 bnl, Krt13, Plekhg6, Fam57a, Gstol ,Gstal, Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinbl 1, Foxql, Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhc13, Tgm1, Gclm, Rhov, Gsta2, Samd12, Spns2, Proser2, Ehf, Sostdcl , Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl, Arhgap27, Lpar5, Duox1, Sult2b1 , Jup, 2200002D01 Rik, Map3k9, Ppap2c, Anxal, Arhgap27, Foxql, Mir200a, Cnksrl, Tmprss11g, Dennd2c, Lztsl, S100a16, Arhgap32, Sox15, Spintl , Clic3, Crb3, and Rtkn; wherein the Klf5 metagene comprises genes selected from Klf5, Dsg3, Tmprss11bnl, Grhl3, Dsp, Jup, Pkp1, Ripk4, Esrpl, Tgm1, Ehf, Aqp3, Cdh1, Spintl, Tjp2, Foxql, 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll, Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1, Rab25, Duoxal, Plekhg6, Slc9a3r1, Pkp3, Tnk1, Krtcap3, Fam160a1, Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1r13l, Sult2b1 , Celsrl , Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1g, Col17a1 , Grb7, Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2, Llgl2, Anxa8, Krt5, Tmprssl 1e, Ppi, Dennd2c, Tacstd2, Sprrla, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl , Tmem63b, Grhl2, Cldn4, Krt14, TtlHO, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1 , and Itgb4; wherein the Psca metagene comprises genes selected from Psca, Mai, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1d, Cblc, Ceacaml, Gstol, Tmprssl 1g, Anxal, Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1bnl, Krt13, Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, Upk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinbl 1, Rab25, Dsg3, Prss22, Tmprss11a, Calml3, Epn3, Slc6a20a, Tmprssl 1e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl, Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rab11fip1, Ocln, Crispl, Prss8, Pglyrp4, Kif21a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1, Gstal, Gstal, Pvrl4, Arhgef I, Elf5, Mapk13, Ikzf2, Tjp3, Osginl, Gsta2, Cldn7, Epb4.1l5, Duoxa2, Zfp750, Zdhhc13, Gm10639, Klk11 , Arhgap40, Arg1 , Ltf, Rnf223, and St14; wherein the Cd44 metagene comprises genes selected from Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Fam83h, Col17a1, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpzl2, Arhgef5, Spint2, 1810019J16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltUb, Grb7, Esrp2, Lsr, Itga3, Plekha7, Dsg3, Clca5, Ap1m2, Plch2, Arhgef5, Celsrl, Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5, Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgef16, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1, Lypd3, Trim29, Tmprssl 1g, Cnksrl, Tmprssl 1bnl, Mir200b, Ptprf, Gm9908, Dlg1, Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, 1117re, Fat1, Nrg1, Mdfi, and Nipal2; wherein the Prom1 metagene comprises genes selected from Prom1, Ceacaml, Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca,Tmprss11d, Cwh43, Slc37a1, Marveld2, ArhgeflOl, Gclm, Ocln, Mctp2, Lrrc26, Fxyd3, lldrl, Cblc, Spintl , Cldn4, Slc52a3, Tmprss11g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, Upk3bl, Slc9a3r1, Mall, Sostdd, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2l1, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO, Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprss11bnl, Gpx2, Gstol, Spns2, Serpinb11, Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N10Rik, Sh3yl1, Slc5a9, SamdIO, Elf3, St14, Ikzf2, Kif21 a, and Erbb3; wherein the Prom2 metagene comprises genes selected from Prom2, Clic3, Tmem54, Evpl, Zfp750, Grhll, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8l1, Gltp, Llgl2, Ovol1, Tmprss13, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14, Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinb11, H22ra1, Erbb2, Dsc2, Rnf39, Tmprss11e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, ArhgeflOl, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl , Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1 , Ttc39a, Spintl, Ppfia3, S100a7a, Dsp, Chitl, Pinlyp, Grb7, Tmem79, Barx2, Klk10, Perp, Efna3, CcbH, Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml, Slc6a20a, SytH, Rnf223, Ide, Calml3, Caszl, and Celsr2; wherein the Bmi1 metagene comprises genes selected from Bmi1, Klhdc2, Bbx, Tusc3, Glg1, Bloc1s6, Wdr34, 5730455P16Rik, Hs2st1, Terf2, Fut8, Zmym4, Pcm1, Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajcIO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301 B20Rik, Mib1, Tiam2, Cers2, Stk3, Hspa13, Txndc12, Dock7, Psmd5, Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1, Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy19l1, Ilf3, Bbs4, Slc30a4, Inppd, Inf2, Zmynd11, Atp8b2, Gludl , Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, KifapS, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7; wherein the Sox4 metagene comprises genes selected from Sox4, Abl1 , Rab34, Fgfrll , Ptovl, Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl, Tcf3, Tcf12, Clip2, Bbx, Nf1, Spats2, Farpl, Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl, Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl, MicalH, L)bxn7, Mvb12b, Trio, Stonl, Dok1, Fam65a, Fmnl3, Hsf2, Sestdl, Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1, Cep120, Rnf139, Dpy19l1, Dbn1, Ctps2, Magedl, Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbl, AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl, Staid, Mecp2, Phf20, Pex11b, Ehmt2, Cep170, Fgfrl, Txndc5, Zmym4, Samd14, Kansl2, Teadl,Zkscan17, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdml a, Loxl3, Acvrl , Wwtrl , AsxH , and Phf2; and wherein the Lrigl metagene comprises genes selected from Lrigl , Rgmb, Zcchc24, Teadl , Lambl , Cep170, Eval b, Sept9, Farpl , Satb2, Mapl b, Ccdc88a, Axl, Loxl3, Pdgfra, list, Lgalsl , KifapS, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamcl , Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1 , Stx2, Lbh, Wipf 1 , Igfbp4, Myo9a, Cul7, Abl1 , Phf20, Xxyltl , Myo9a, Dok1 , Dst, Gkapl , Tspanl 1 , Phldbl , Sydel , Teadl , Rab34, Stxbpl , AI597468, St6gal1 , Ilk, Zeb1 , Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl , Ank, Displ , Fhl3, Fermt2, Cdr2, Dock5, Crabpl , S1 pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl , Sdccag8, Gliprl , and Nnt.32. The method of aspect 30, wherein the method comprises:(a) providing a first population of cells and a second population of cells, wherein the first population of cells has increased lineage plasticity, increased levels of expression of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Proml , and Prom2, and decreased levels of expression of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 compared to the second population of cells, and wherein the second population of cells has increased proliferation, increased levels of expression of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9, and decreased levels of expression of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 compared to the first population of cells;(b) contacting the first population of cells and the second population of cells with a candidate agent;(c) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf 5, Psca, Cd44, Prom1 , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the first population of cells and the second population of cells; and(d) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the first population of cells in presence of the candidate agent compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Prom1 , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6,and Sox9 in the second population of cells in the presence of the candidate agent compared to the reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.33. The method of aspect 32, further comprising measuring proliferation of the first population of cells and the second population of cells, wherein an increased level of proliferation in combination with decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2, and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the first population of cells in the presence of the candidate agent compared to reference value ranges for the level of proliferation and the levels of expression of the Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Prom1 , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein a decreased level of proliferation in combination with increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Proml , and Prom2, and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the second population of cells in the presence of the candidate agent compared to reference value ranges for the level of proliferation and the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.34. The method of any one of aspects 30-33, wherein said measuring levels of expression comprises performing reverse transcription polymerase chain reaction, RNA sequencing, global run-on sequencing, microarray analysis, or any combination thereof.35. The method of aspect 34, wherein the RNA sequencing is single cell RNA sequencing.36. The method of any one of aspects 30-35, wherein the candidate agent inhibits mitosis or induces cell differentiation.37. The method of any one of aspects 30-36, wherein the candidate agent inhibits KRAS4A or protein phosphatase 2A (PP2A).38. The method of aspect 37, wherein the candidate agent selectively inhibits a PP2A subunit.39. The method of any one of aspects 30-38, wherein the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.40. The method of any one of aspects 30-39, wherein the first population of cells and the second population of cells are cancerous cells or pre-malignant cells.41 . The method of any one of aspects 30-40, wherein the first population of cells and the second population of cells are mammalian cells.42. The method of aspect 41 , wherein the mammalian cells are rodent, non-human primate, or human cells.43. The method of any one of aspects 30-42, wherein the first population of cells or the second population of cells is derived from a cancerous cell that was previously treated with a chemotherapeutic agent.44. The method of any one of aspects 30-43, wherein the first population of cells or the second population of cells is derived from a pre-neoplasia lesion, optionally wherein the preneoplasia lesion is a papilloma.45. The method of any one of aspects 30-44, wherein the first population of cells and the second population of cells are pre-malignant epithelial cells.46. A method of detecting cell type switching of a cancerous cell in response to treatment with a therapeutic agent;(a) treating the cancerous cell with an effective amount of the therapeutic agent;(b) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf 5, Psca, Cd44, Prom1 , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9 in progeny of the cancerous cell; and(c) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigf , Lgr6, and Sox9 in the progeny of the cancerous cell after said treating the cancerous cell compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigt , Lgr6, and Sox9 indicate that the progeny of the cancerous cell are in a proliferative cell state susceptible to treatment with an antimitotic agent, and wherein increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the progeny of the cancerous cell after said treating the cancerous cell compared to the reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the progeny of the cancerous cell are in a cell state having lineage plasticity and drug resistance.47. The method of aspect 46, further comprising treating the cancerous cell and the progeny thereof with an anti-mitotic agent if the progeny of the cancerous cell are in the proliferative cell state susceptible to treatment with the anti-mitotic agent, or treating the cancerous cell with an inducer of differentiation if the progeny of the cancerous cell are in the cell state having lineage plasticity and drug resistance.48. The method of aspect 47, further comprising treating the cancerous cell and the progeny thereof with the anti-mitotic agent after said treating the cancerous cell with the inducer of differentiation if the progeny of the cancerous cell are in the cell state having lineage plasticity and drug resistance.49. The method of aspect 47 or 48, wherein the inducer of differentiation is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A.50. The method of aspect 49, wherein the inhibitor of PP2A is LB100.51 . The method of any one of aspects 47-50, wherein the anti-mitotic agent is cisplatin, cyclophosphamide, chlorambucil, vinblastine, vincristine, vinorelbine, vinflunine, paclitaxel, docetaxel, or a combretastatin.52. The method of any one of aspects 46-51 , wherein the cancerous cell is a carcinoma cell.53. The method of aspect 52, wherein the carcinoma cell is a squamous cell carcinoma cell.54. The method of aspect 53, wherein the squamous cell carcinoma cell is a cutaneous squamous cell carcinoma cell.55. The method of any one of aspects 46-54, wherein the cancerous cell is in vivo or in vitro.56. The method of any one of aspects 46-55, wherein the cancerous cell comprises a reporter gene for lineage tracing of the progeny of the cancerous cell.57. The method of aspect 56, wherein the reporter gene encodes a fluorescent protein.58. The method of any one of aspects 46-57, wherein said measuring levels of expression comprises performing reverse transcription polymerase chain reaction, RNA sequencing, global run-on sequencing, microarray analysis, or any combination thereof.59. The method of aspect 58, wherein the RNA sequencing is single cell RNA sequencing.60. A method of treating a cancerous or pre-malignant lesion in a patient, the method comprising:(a) administering a therapeutically effective amount of an anti-mitotic therapeutic agent to the patient;(b) obtaining a biological sample comprising cancerous or pre-malignant cells from the cancerous or premalignant lesion of the patient;(c) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf 5, Psca, Cd44, Prom1 , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the biological sample, wherein increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and decreased levels of expression of the one or more genes selectedfrom Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the biological sample compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxt , Klf5, Psca, Cd44, Proml , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the cancerous or pre-malignant cells are in a drug resistant state, and wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the biological sample compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the cancerous or pre-malignant cells are in non-drug resistant state; and(d) continuing treatment of the patient with the anti-mitotic therapeutic agent if the patient is in the non-drug resistant state; or discontinuing treatment of the patient with the anti-mitotic therapeutic agent if the patient is in the drug resistant state, and administering a therapeutically effective amount of an agent that induces differentiation to the patient to switch the cell state of the cancerous or pre-malignant cells from the drug resistant state to the non-drug resistant state before subsequently administering another therapeutically effective amount of the anti-mitotic agent to the patient.61 . The method of aspect 60, wherein the inducer of differentiation is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A.62. The method of aspect 61 , wherein the inhibitor of PP2A is LB100.63. The method of any one of aspects 60-62, wherein the anti-mitotic agent is cisplatin, cyclophosphamide, chlorambucil, vinblastine, vincristine, vinorelbine, vinflunine, paclitaxel, docetaxel, or a combretastatin.64. A composition comprising an RNA transcript of a gene selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Prom1 metagene, a Prom2 metagene, a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene for use in a method of diagnosing development of drug resistance of a cancer in response to treatment with a therapeutic agent.65. The composition of aspect 64,wherein the Sox2 metagene comprises genes selected from Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, MtmrIO, Esd, Sox13, Nfe2l2, Pls1, Tom1l2, Bink, Suox, Sid 6a11 , Xrcc5, Chstl 5, Krt12, Eval c, Nppc, Esd, Ddx59, Nop2, Krt13, Plekhh3, Osbpl6, Aldh5a1 , Ci rh 1 a, Wnk4, Arntl2, Fam110c, Tmem180, Dili, Galnt12, Pitxl, Caleb, Ankrd9, Isl1 , Btc, Gss, Ociad2, Klra33, Aldh3a1, Minkl, Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl, Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrla, Pthlh, Usp6nl, Ufspl, Irgq, Nkiras2, Grtpl, Nqo1, Krt20, Snord42b, Avpil, Ifrdl, Srd5a2, Cpn1, Bail, Sprr3, Rap1gap2, Rassf7, Fetub, Ramp3, Arl4d, Tle1, Krt76, Ptprzl, Pradd, Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl, G6pdx, Tsg101, Nmrkl, Ralgapb, A430105119Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik; wherein the Foxal metagene comprises genes selected from Foxal , Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1, Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1, Tjp3, Plekhg6, Bspry, Ocln, Ceacaml, Marveld3, Cldn3, Mal2, Tmem30b, Sowahb, Spns2, Slc9a3r1, Kctdl, Cwh43, Cystml, Rab17, S100a2, Ppbp, Padil, Caleb, Gstol, S100a16, Spint2, Slc52a3, Sid 6a11 , Crispl, Mall, Aldh1a3, Entpd3, Tmprss11g, Anxal, Pgapl, Prss22, Kif21a, Omp, Liph, Epb4.1l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, ArhgeflOl, Tmprss11d, Mxd1, Elf5, Acss2, Leprell, Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppfibp2, Mboatl, Zdhhc13, Dgka, Ehf, Mst1, St14, Ap1s3, Maltl, Spintl, Sprr3, Pllp, AA986860, Prss27, Tmprssl 1a, Serpinbl 1 , Hs3st1 , StardlO, Arhgap40, lldrl , Ppi, Fbp2, Cnksrl , Map7, and 1700001 C19Rik, E330009J07Rik; wherein the Krt15 metagene comprises genes selected from Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrd , Zfp750, Lipm, Ocln, Paqr5, GrhH , Erbb3, PsapH , Aldh3b2, Ppi, Rapgefh , Aldh3b2, Efna3, Muc15, Liph, 2610528A11Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1pr5, Klhl29, 4833423E24Rik, Nccrpl, Slc27a4, Barx2, Aindl, Wnt4, L1cam, Leprell, Rnf43, Ckmtl, Lipk, Mapk13, H22ra1, Zfp185, Cds1, Arhgap40, Krt80, Dsc3, Prss8, Fgfr3, Hsd17b2, Padil, Ripk4, Prom2, Adtrp, Caszl, 1700055N04Rik, Scnnla, Ptprf, ArhgeflOl, Tmprssl 1 e, Slc25a48, Mall, Mst1, Crnn, Celsrl, Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinbl 1, Vsnll, Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprssl 3, Sowahb, Celsr2, Ly6g6e, SytH, Tprg, AA986860, and Sptbn2; wherein the Krt19 metagene comprises genes selected from Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal, Mall, Slc37a1, Cblc, Marveld3, Marveld2, Gstol, Ceacaml, Gm9573, Ocln, Slc9a3r1, Mal2, Tmprssl 1g, Spns2, Anxal, 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, ArhgeflOl, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, Upk3bl, Gsta4, Ppbp, Tmprssl 1d, Spintl, Tmem30b, S100a2, Pgapl, Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1, Kif21 a, Krt13, Padil, Tmprssl 1 bnl, Foxql, S100a16, L1cam, Seel, Ehf, SarndlO,Rab25, Hebp2, Cnksrl, 1117re, Flip, Cystml, Tnk1, Mboatl, Tmprss11e, Tacstd2, Plekha6, Arg1, Ltf, Evpl, S100a14, Plekhhl , Slc25a48, Ap1s3, Zdhhc13, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl, Ppfibp2, Nipal2, Rab27a, Rbm47, and StardlO; wherein the Pitxl metagene comprises genes selected from Pitxl , Cldn8, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1, Klf5, Cep170b,Llgl2, 1700001C19Rik, Tmprss11d, Dsc2, Fam160a1, Erbb2, Gsta4, Shb, Duoxal, Rab27b, Barx2, Fhdd, Tmprss11bnl, Krt13, Plekhg6, Fam57a, Gstol, Ppp1r13l, Dsg3, Epn3, Als2cl, Grhl3, Myo5b, Arhgef5, Tmem63b, Phldb3, Tmprss11a, Gstal, Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinbl 1, Foxql, Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhc13, Tgm1, Gclm, Rhov, Gsta2, Samd12, Spns2, Proser2, Ehf, Sostdcl , Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl, Arhgap27, Lpar5, Duoxl, Sult2b1, Jup, 2200002D01Rik, Map3k9, Ppap2c, Anxal, Arhgap27, Foxql, Mir200a, Cnksrl, Tmprss11g, Dennd2c, Lztsl, S100a16, Arhgap32, Sox15, Spintl, Clic3, Crb3, and Rtkn; wherein the Klf5 metagene comprises genes selected from Klf5, Dsg3, Tmprss11bnl, Grhl3, Dsp, Jup, Pkp1, Ripk4, Esrpl, Tgm1, Ehf, Aqp3, Cdh1, Spintl, Tjp2, Foxql, 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll, Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1, Rab25, Duoxal, Plekhg6, Slc9a3r1, Pkp3, Tnk1, Krtcap3, Fam160a1, Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1r13l, Sult2b1 , Celsrl , Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1g, Col17a1 , Grb7, Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2, Llgl2, Anxa8, Krt5, Tmprssl 1e, Ppi, Dennd2c, Tacstd2, Sprrla, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl , Tmem63b, Grhl2, Cldn4, Krt14, TtlHO, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1 , and Itgb4; wherein the Psca metagene comprises genes selected from Psca, Mai, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1d, Cblc, Ceacaml, Gstol, Tmprssl 1g, Anxal, Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1bnl, Krt13, Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, Upk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinbl 1, Rab25, Dsg3, Prss22, Tmprss11a, Calml3, Epn3, Slc6a20a, Tmprssl 1e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl, Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rab11fip1, Ocln, Crispl, Prss8, Pglyrp4, Kif21a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1, Gstal, Gstal, Pvrl4, ArhgefWI, Elf5, Mapk13, Ikzf2, Tjp3, Osginl, Gsta2, Cldn7, Epb4.1l5, Duoxa2, Zfp750, Zdhhc13, Gm10639, Klk11 , Arhgap40, Arg1 , Ltf, Rnf223, and St14; wherein the Cd44 metagene comprises genes selected from Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpz 1810019J16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltHb, Gr , Plekha7, Dsg3, Clca5, Ap1m2,Plch2, Arhgef5, Celsrl, Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5, Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgef16, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1 , Lypd3, Trim29, Tmprss11g, Cnksrl, Tmprss11bnl, Mir200b, Ptprf, Gm9908, Dlg1, Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, 1117re, Fat1, Nrg1, Mdfi, and Nipal2; wherein the Promt metagene comprises genes selected from Promt , Ceacaml , Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca, Tmprss11d, Cwh43, Slc37a1, Marveld2, ArhgeflOl, Gclm, Ocln, Mctp2, Lrrc26, Fxyd3, lldrl, Cblc, Spintl, Cldn4, Slc52a3, Tmprss11g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, L)pk3bl, Slc9a3r1, Mall, Sostdd, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2l1, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO, Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprss11bnl, Gpx2, Gstol, Spns2, Serpinb11, Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N10Rik, Sh3yl1, Slc5a9, SamdIO, Elf3, St14, Ikzf2, Kif21 a, and Erbb3; wherein the Prom2 metagene comprises genes selected from Prom2, Clic3, Tmem54, Evpl, Zfp750, Grhll, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8l1, Gltp, Llgl2, Ovol1, Tmprss13, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14, Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinb11, H22ra1, Erbb2, Dsc2, Rnf39, Tmprss11e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, ArhgeflOl, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl , Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1 , Ttc39a, Spintl, Ppfia3, S100a7a, Dsp, Chitl, Pinlyp, Grb7, Tmem79, Barx2, Klk10, Perp, Efna3, CcbH, Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml, Slc6a20a, SytH, Rnf223, Ide, Calml3, Caszl, and Celsr2; wherein the Bmi1 metagene comprises genes selected from Bmi1, Klhdc2, Bbx, Tusc3, Glg1, Bloc1s6, Wdr34, 5730455P16Rik, Hs2st1, Terf2, Fut8, Zmym4, Pcm1, Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajcIO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301 B20Rik, Mib1, Tiam2, Cers2, Stk3, Hspa13, Txndc12, Dock7, Psmd5, Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1, Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy19l1, Ilf3, Bbs4, Slc30a4, InppH, Inf2, Zmynd11, Atp8b2, Gludl , Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, Kifap3, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7;wherein the Sox4 metagene comprises genes selected from Sox4, Abl1 , Rab34, FgfrH , Ptovl , Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl , Tcf3, Tcf12, Clip2, Bbx, Nf1 , Spats2, Farpl , Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl , Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl , MicalU , Ubxn7, Mvb12b, Trio, Stonl , Dok1 , Fam65a, Fmnl3, Hsf2, Sestdl , Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1 , Cep120, Rnf139, Dpy19l1 , Dbn1 , Ctps2, Magedl , Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbf , AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl , Staid , Mecp2, Phf20, Pex1 1 b, Ehmt2, Cep170, Fgfrl , Txndc5, Zmym4, Samd14, Kansl2, Teadl , Zkscan17, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdml a, Loxl3, Acvrl , Wwtrl , Asxll , and Phf2; and wherein the Lrigl metagene comprises genes selected from Lrigl , Rgmb, Zcchc24, Teadl , Lambl , Cep170, Eval b, Sept9, Farpl , Satb2, Mapl b, Ccdc88a, Axl, Loxl3, Pdgfra, Ust, Lgalsl , Kifap3, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamcl , Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1 , Stx2, Lbh, Wipfl , Igfbp4, Myo9a, Cul7, Abl1 , Phf20, Xxyltl , Myo9a, Dok1 , Dst, Gkapl , Tspanl 1 , Phldbl , Sydel , Teadl , Rab34, Stxbpl , AI597468, St6gal1 , Ilk, Zeb1 , Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl , Ank, Displ , Fhl3, Fermt2, Cdr2, Dock5, Crabpl , S1 pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl , Sdccag8, Gliprl , and Nnt.66. A composition comprising an RNA transcript of a gene selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 for use in a method of diagnosing development of drug resistance of a cancer in response to treatment with a therapeutic agent.67. The composition of any one of aspects 64-66, wherein the cancer is a carcinoma.68. The composition of aspect 67, wherein the carcinoma is squamous cell carcinoma.69. The composition of aspect 68, wherein the squamous cell carcinoma is cutaneous squamous cell carcinoma cell.

[0256] It will be apparent to one of ordinary skill in the art that various changes and modifications can be made without departing from the spirit or scope of the invention.EXPERIMENTAL

[0257] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.

[0258] All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

[0259] The present invention has been described in terms of particular embodiments found or proposed by the present inventor to comprise preferred modes for the practice of the invention. It will be appreciated by those of skill in the art that, in light of the present disclosure, numerous modifications and changes can be made in the particular embodiments exemplified without departing from the intended scope of the invention. For example, due to codon redundancy, changes can be made in the underlying DNA sequence without affecting the protein sequence. Moreover, due to biological functional equivalency considerations, changes can be made in protein structure without affecting the biological action in kind or amount. All such modifications are intended to be included within the scope of the appended claims.Example 1Stem-Cell States Converge in Multi-Stage Cutaneous Squamous Cell Carcinoma DevelopmentIntroduction

[0260] Here, we address these questions using mouse skin, which has over several decades been the most widely studied solid tissue for analysis of stem-cell function in normal homeostasis and during oncogenic transformation ( 11- 13). In the mouse, a number of distinct stem-cell markers have been identified which contribute to homeostasis by repopulating specific compartments within the epithelium ( 14, 15). Certain healthy-skin stem-cell markers, including Lgr5( 16), Lgr6( 17), Twistl ( 18), Sox2( 19), and Pitx1(20), mark cancer stem cells (CSCs) in several tumor types (9, 21) To identify the cell plasticity states that arise during transitions from normal tissue through pre-neoplasia to malignant carcinomas, we developed a model system that encompasses both germline genetic and somatic genetic diversity to construct gene expressionnetworks in each stage, and visualized these networks in single cells representing the continuum of steps in carcinogenesis. Our data identify connections between different stem-cell populations in the skin, leading to a more unified model of cell state transitions during tumorigenesis.ResultsRewiring of stem-cell gene expression networks in tumors

[0261] Although progress has been made in unravelling gene expression networks in single cells (22), understanding global dysregulation of these networks in cancer continues to rely upon bulktissue data(23). Bulk-tissue data are useful when inferring gene networks since they encompass hundreds of independent samples and thus are likely general features of a system, occurring repeatedly across independent instantiations of carcinogenesis. On the other hand, features in single cells are usually assayed in a small number of samples because of the throughput tradeoff between the number of samples and the number of cells that single-cell ‘-omics’ can measure. Thus, single-cell datasets often represent specific contingent outcomes of a particular sample rather than general system features (24). Together, the sampling breadth of bulk-tissue data and high resolution of single-cell data are complementary. We leveraged this complementarity by generating gene networks from hundreds of bulk samples and resolving their expression in single cells. Combined with stem cell biology, we are thus able to elucidate how these conserved features operate in single cells to drive initiated cells from normal homeostasis to cancer.

[0262] We previously carried out genetic and gene expression analysis of multistage chemically- induced carcinogenesis in genetically heterogeneous mice (25-27). These chemical carcinogenesis models capture a realistic view of cancer development in human populations since 1 ) tumors are induced by environmental insult, rather than genetic modification, and carry thousands of somatic mutations including many cancer driver mutations that are also seen in human tumors (26, 28, 29); 2) they are autochthonous to the animals in which they are generated, rather than transplanted into immunodeficient host animals; and 3) the treated mice are from a genetically heterogeneous mouse population that mimics human germline diversity. From this, we generated a transcriptomic database from several hundred samples that span progression from normal skin to benign pre-neoplasia (papillomas in the skin) to malignant tumors (squamous cell carcinomas) and finally metastasis (25, 26). A similar database has been used to infer functions for specific genes based on their network structures in bulk-tissue samples (25, 27, 30, 31). Here, we profiled gene expression of 106 normal skin and 157 carcinoma samples from interspecific Mus spretus x FVB / N backcross mice, generated as previously described (32) (FIG. 1A). These networks are based on gene-gene correlations across samples, and thus capture direct and indirect interactions among genes. For the present analysis, we considered indirectinteractions to be the biologically relevant effects of a gene’s function, so we did not seek to limit network inference to specific physical interactions such as transcription factors and their targets (33) or among their protein-protein interactions (34). Furthermore, since bulk samples contain mixtures of different cell types, these networks capture the extended function of network seed genes expressed across different cell types (FIG. 9).

[0263] To gain an unbiased view of the global gene expression network, we implemented the unsupervised inference algorithm WGCNA, which clusters genes sharing similar expression from bulk-tissue samples into gene modules (35) (Data S1 ). We then tested these modules for functional enrichment using biological process gene ontologies (GO) (Data S2). One large module in carcinomas, Module 3 (Ngene=1720), was highly enriched for genes associated with wound healing. This wound healing module included several known stem-cell marker genes that have been implicated in carcinogenesis, including Sox9, Psca, Pitxl, Krt15, Krt19, and Lgr6. Lgr6 is of particular interest in this system since Lgr6+ cells are highly clonogenic in squamous carcinomas ( 17), play an important role in wound healing (36), and can drive extreme lineage plasticity by repopulating all skin cell types (37).

[0264] We next examined the correlation structure of these well-characterized stem-cell marker genes in normal tissues and tumors. This revealed three clusters of genes that were correlated with each other in tumors but not in matched normal tissues (FIGS. 1 B, 1 C). We refer to these groups of correlated stem-cell genes that are co-expressed at the bulk- tissue level as ‘Spearman groups.’ These Spearman groups recapitulated the gene modules identified by WGCNA (Data53). Importantly, Spearman group 1 , consisting of Bmi1, Sox4, and Lrigl, was strongly anticorrelated to Spearman group 3, the latter containing multiple known adult stem-cell markers.

[0265] Each stem-cell marker was then used as a “seed gene” to generate normal skin- and carcinoma-specific gene correlation networks (called “metagenes,” Supplementary Text, Data54), which can capture the downstream function of specific genes in bulk-tissue samples (25, 27, 30, 31). The Lgr6 metagene showed major network rewiring between normal skin and carcinoma. In normal skin, the Lgr6 network included of several epidermal lineage markers including Krt15 (p=0.78) and Klf5 (p=0.63), as well as Zn rf 3 (p=0.51 ) and Rnf43 (p=0.55), the two E3-ligases that act as R-spondin coreceptors to mediate Wnt signaling(38). However, during carcinogenic rewiring, these correlations were lost, replaced by Sox9 (p=0.67), as well as other important drivers of cancer phenotypes including Tgfbl (p=0.60) (table S1 ). Tgfbl is a growth factor known to play multiple roles in tumor development, acting as a growth inhibitor at early stages and switching roles to become an inducer of the epithelial-mesenchymal transition (EMT) during tumor progression (39). It is also a major mediator of immunosuppression that, when inhibited with blocking antibodies, improves immunotherapy outcomes in mouse models (40, 41). Thus,changes in the correlation network architecture of the Lgr6 metagene during tumor development revealed biologically functional rewiring associated with cancer progression and immune escape.Single-cell transcriptomes in multi-stage carcinogenesis

[0266] Since our goal was to understand how gene networks inferred from hundreds of bulk samples can be visualized in single cells, we then obtained single-cell RNA sequencing (scRNAseq) for 57,807 cells, of which 33,234 (57.5%) cells were normal skin from 4 mice, 15,280 (26.4%) were papilloma from 1 mouse, and 9,293 (16.1%) were carcinoma from 1 mouse (FIG. 1 C), and plotted metagene expression within the resulting UMAP. Additionally, we included in this analysis single epithelial cells from normal skin, benign papillomas, and carcinomas that were selected by lineage tracing in the Lgr6-eGFP-tdTomato mouse strain ( 17), in order to mark and separate Lgr6+ stem cells (eGFP+) from their direct progeny (tdTomato). Later, we replicated these data with an additional 7,883 cells from 4 carcinomas and 7 papillomas (see below). Critically for our first analysis, to make their transitional relationships analytically tractable, the proportion of Lgr6+ and progeny cells were increased relative to unsorted cells by loading equal numbers of Lgr6+, progeny, and unsorted cells for scRNAseq. We identified 21 low-resolution single cell clusters by unsupervised clustering, of which cell clusters 1 -4 dominated the assembly, predominantly populated by normal skin (clusters 1 ,2), papilloma (cluster 3), and carcinoma (cluster 4), which we consider to be tissue- specific parenchymal cells (FIGS. 10A, 10B). We classified normal skin cell types with canonical markers and re-analyzed the carcinoma parenchyma alone, which showed two distinct keratinocyte subpopulations corresponding to squamous (20.8% of carcinoma parenchyma) and spindle phases (79.2%) that had undergone an epithelial- mesenchymal transition (FIGS. 10C-10E,1 1 ) (42, 43).Scaling gene networks from bulk tissue to single cells: metagenes quantify extended gene function

[0267] To visualize how metagenes are expressed at the single-cell level, we first examined Lgr6 and its closely related family member Lgr5. Both genes are known stem-cell markers in the skin, but Lgr6 is clonogenic in squamous cell carcinomas whereas Lgr5 is not ( 17). Lgr6 as an individual gene was expressed in the isthmus region of the upper hair follicle (arrow, FIG. 2A), as well as in the interfollicular epithelium (If E). Prior lineage tracing studies have shown that Lgr6+ cells repopulate these regions during normal homeostasis and wound healing(37, 44, 45). These cells then differentiate into the overlying specialized epidermal strata. The Lgr6 normal-skin metagene (the aggregate expression of the 100 genes most highly rank-correlated with Lgr6 across multiple bulk- tissue samples of normal skin) reflects this developmental pattern, showing increasing expression across interfollicular keratinocytes that peaks in terminally keratinized cellsfrom the granular layer of the epidermis (arrow, FIG. 2B) . Since this metagene consists of a gene network derived from independent bulk-skin samples, which contain mixtures of interfollicular and follicular cells, we tested whether this metagene was expressed in hair follicle cells as well. Indeed, it was robustly expressed in normal skin (NSk) hair follicle cells (FIGS. 12A, 12B), although its expression was highest in terminal keratinocytes (FIG. 12C). Furthermore, the individual genes that constitute the Lgr6 normal-skin metagene are enriched for keratinocyte proliferation and differentiation (Data S5), implying that this network captures Lgr6’s function to establish epidermal cell layer patterning more strongly than its complex functions in other skin compartments such as the sebaceous gland or hair follicle(46). The Lgr6 carcinoma metagene, on the other hand, shows high expression in the carcinoma parenchyma (arrow, FIG. 2C), reflecting the functional switch during tumor progression from normal homeostasis to malignancy (see also table S1 ).

[0268] Lgr5 is highly expressed in the lower bulge region of the hair follicle, reflecting its known follicular stem-cell function (arrow, FIG. 2D). Unlike Lgr6, the Lgr5 carcinoma metagene shows low expression across all stages of carcinogenesis (FIG. 2E, FIG. 13). Thus, metagene expression of the Lgr6 carcinoma network increases, while that of the Lgr5 carcinoma network decreases, in parenchymal cells during tumor progression (FIG. 2F). This demonstrates that metagene expression in single cells traces the functional role of these stem-cell markers in normal tissue and reflects functional rewiring that occurs during malignant transformation.Convergent expression of multiple stem-cell metagenes in the same cell populations.

[0269] Since Spearman groups 1 and 3 of stem-cell genes were strongly anticorrelated in tumor samples (FIG. 1 C), we reasoned that they may represent two mutually exclusive stem-cell states expressed in distinct single-cell populations. To test this hypothesis, we examined whether stemcell markers and their metagenes were expressed in different cell populations in the single-cell data. The expression of individual stem genes was notably variable across single cells, with sparse and divergent expression in disparate cell populations (seed gene panels in FIG. 14). However, metagene expression dramatically altered this landscape. Spearman group 3 carcinoma metagenes co- localized to a specific “spike” cell population corresponding to cell cluster 33 in the UMAP of the papilloma (lower spike, FIG. 2G). “Spike” refers to the appearance of this cell population in the UMAP. For example, carcinoma metagenes for Pitxl, Krt15, and Psca were highly and specifically expressed in this lower spike population.

[0270] To investigate possible overlapping functions of stem networks in the lower spike, we tested for gene ontology (GO) enrichment in genes of the ten stem-cell Spearman group 3 metagenes that co-localized to the lower spike. GO analysis showed that this gene set was highly enriched in functions related to oxidative stress (Duoxa1 / 2), skin barrier formation (Sprrla,Sprr3), wound healing ( Wnt4, Klf5), cell migration (Cd44, Ceacaml), apoptosis (Anxal), and immune responses (Arg1) (table S2). Notably, normal wound healing is associated with oxidative stress and lineage infidelity, the latter indicative of stem cell plasticity and characterized by de novo co-expression of genes representing different hair follicle and epidermal lineages(27). Several genes associated with stem-cell plasticity were prominent in this set of lower spike metagenes (including Sox15, Foxal, Klf5, Cd44, Wnt4), consistent with the development of lineage infidelity in the lower spike region. Despite the individual seed genes being expressed in disparate cell populations, these stem-cell markers converged at the metagene level with high expression in the same single-cell population, and this convergence cohered around lineage plasticity and wound healing.

[0271] In contrast, carcinoma metagenes for Bmi1 (Spearman group 1 ) and Lgr6 (Spearman group 2) were almost absent from the lower-spike cell population (FIG. 14). The upper spike cells showed higher expression for Spearman group 1 metagenes, with distinct enrichment in expression of metagenes corresponding to markers of cell cycle progression, including E2f1 and Foxml, known as a master regulator of proliferation and malignant progression (FIG. 2G) (47) . The upper spike was composed of a much larger proportion of cells in the G2M phase than the lower spike or other neoplastic cells: 20.6% versus 0.52% and 13.29%, respectively (table S3, FIGS. 15 and 16). Furthermore, mitotic metagenes such as E2f1, Foxml, and Mki67 were significantly (p<0.01 ) more highly expressed in G2M cells than in G1 - or S-phase cells (FIGS. 15E-15G). Similar metagene patterns were seen for multiple markers of DNA damage / genomic instability, for example those corresponding to Atm and Atr (FIG. 17). Together, we take this to indicate that the upper spike cells highly express gene networks related to DNA replication, mitosis, and cell division.

[0272] We then hypothesized that if the stem-cell Spearman groups 1 and 3, which were negatively correlated at the bulk-tissue level, were truly mutually exclusive gene programs at the single-cell level, then their anticorrelated genes would be expressed primarily in mutually exclusive cell populations. We refer to the set of a seed gene’s most highly anticorrelated genes as the ‘negative metagene.’ Strikingly, plotting Spearman group 1 ’s negative metagenes showed high expression in the lower spike region (FIG. 18). This points to the mutually exclusive relationship between Spearman groups 1 and 3 carcinoma metagenes in these distinct singlecell populations.Alternative stem cell populations arise from / _gr6-positive papilloma cells.

[0273] Having identified two distinct single-cell populations with high expression of alternate stem programs (the upper and lower spikes), we then asked how they relate to Lgr6, which is a major driver of clonogenicity in this system. We tested this directly through lineage tracing andimmunofluorescent analysis of normal skin, papillomas, and carcinomas (FIG. 3). This showed that in normal skin Lgr6+ cells repopulated the upper hair follicle and interfollicular epidermis (FIG. 3A), but during neoplastic progression, expression was more widespread and disorganized as Lgr6 marked clone-initiating cancer stem cells( 17). In papillomas, rare Lgr6-GFP+ cells were primarily located at the basement membrane, and their tdTomato-i- progeny formed streaks that extended into the upper different...

Claims

What is claimed is:

1. A cell comprising: a first lineage tracing reporter gene operably linked to a promoter of a first gene whose expression is positively correlated with a stem cell plasticity state, wherein expression of the first lineage tracing reporter gene coincides with the expression of the first gene; and a second lineage tracing reporter gene operably linked to a promoter of a second gene whose expression is positively correlated with a proliferative state, wherein expression of the second lineage tracing reporter gene coincides with the expression of the second gene.

2. The cell of claim 1 , wherein the first gene is selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Prom1 metagene, and a Prom2 metagene; and the second gene is selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene.

3. The cell of claim 2, wherein the Sox2 metagene comprises genes selected from Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, MtmrI O, Esd, Sox13, Nfe2l2, Pls1 , Tom1 l2, Bink, Suox, Slc16a11 , Xrcc5, Chstl 5, Krt12, Eval c, Nppc, Esd, Ddx59, Nop2, Krt13, Plekhh3, Osbpl6, Aldh5a1 , Ci rh 1 a, Wnk4, Arntl2, Fam110c, Tmem180, Dili , Galnt12, Pitxl , Caleb, Ankrd9, Isl1 , Btc, Gss, Ociad2, Klra33, Aldh3a1 , Minkl , Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl , Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrl a, Pthlh, Usp6nl, Ufspl , Irgq, Nkiras2, Grtpl , Nqo1 , Krt20, Snord42b, Avpil , Ifrdl , Srd5a2, Cpn1 , Bail , Sprr3, Rap1gap2, Rassf7, Fetub, Ramp3, Arl4d, Tle1 , Krt76, Ptprzl , Pradd , Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl , G6pdx, Tsg101 , Nmrkl , Ralgapb, A430105l19Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik; wherein the Foxal metagene comprises genes selected from Foxal , Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1 , Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1 , Tjp3, Plekhg6, Bspry, Ocln, Ceacaml , Marveld3, Cldn3, Mal2, Tmem30b, Sowahb, Spns2, Slc9a3r1 , Kctdl , Cwh43, Cystml , Rab17, S100a2, Ppbp, Padil , Caleb, Gstol , S100a16, Spint2, Slc52a3, Slc16a1 1 , Crispl , Mall, Aldh1 a3, Entpd3, Tmprss11 g, Anxal , Pgapl , Prss22, Kif21a, Omp, Liph, Epb4.1 l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, Arhgef I, Tmprss11 d, Mxd1 , Elf5, Acss2, LepreH , Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppfibp2, Mboatl , Zdhhc13, Dgka, Ehf, Mst1 , St14, Ap1 s3, Maltl , Spintl , Sprr3, Pllp, AA986860, Prss27, Tmprssl 1 a, Serpinbl 1 , Hs3st1 , StardlO, Arhgap40, lldrl , Ppi, Fbp2, Cnksrl , Map7, and 1700001 C19Rik, E330009J07Rik;wherein the Krt15 metagene comprises genes selected from Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrcl , Zfp750, Lipm, Ocln, Paqr5, GrhH , Erbb3, Psapll , Aldh3b2, Ppi, RapgefH , Aldh3b2, Efna3, Muc15, Liph, 2610528A11 Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1pr5, Klhl29, 4833423E24Rik, Nccrpl , Slc27a4, Barx2, Aimll, Wnt4, L1cam, Leprell , Rnf43, Ckmtl , Lipk, Mapk13, H22ra1 , Zfp185, Cds1, Arhgap40, Krt80, Dsc3, Prss8, Fgfr3, Hsd17b2, Padil , Ripk4, Prom2, Adtrp, Caszl , 1700055N04Rik, Scnnla, Ptprf, Arhgefl Ol, Tmprss11 e, Slc25a48, Mall, Mst1 , Crnn, Celsrl , Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinbl 1 , Vsnll , Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprss13, Sowahb, Celsr2, Ly6g6e, SytH , Tprg, AA986860, and Sptbn2; wherein the Krt19 metagene comprises genes selected from Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal , Mall, Slc37a1 , Cblc, Marveld3, Marveld2, Gstol , Ceacaml , Gm9573, Ocln, Slc9a3r1 , Mal2, Tmprss11g, Spns2, Anxal , 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, ArhgeflOl, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, L)pk3bl, Gsta4, Ppbp, Tmprss11d, Spintl , Tmem30b, S100a2, Pgapl , Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1 , Kif21 a, Krt13, Padil , Tmprss11 bnl, Foxql , S100a16, L1cam, Seel, Ehf, Sarndl O, Epb4.115, Rab27b, Plekha7, Llgl2, Erbb2, Stap2, Rab25, Hebp2, Cnksrl , 1117re, Pllp, Cystml , Tnk1 , Mboatl , Tmprss11 e, Tacstd2, Plekha6, Arg1 , Ltf, Evpl, S100a14, Plekhhl , Slc25a48, Ap1s3, Zdhhc13, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl , Ppfibp2, Nipal2, Rab27a, Rbm47, and StardlO; wherein the Pitxl metagene comprises genes selected from Pitxl , Cldn8, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1 , Klf5, Cep170b,Llgl2, 1700001C19Rik, Tmprss11d, Dsc2, Fam160a1 , Erbb2, Gsta4, Shb, Duoxal , Rab27b, Barx2, Fhdd , Tmprss11 bnl, Krt13, Plekhg6, Fam57a, Gstol , Ppp1 r13l, Dsg3, Epn3, Als2cl, Grhl3, Myo5b, Arhgef5, Tmem63b, Phldb3, Tmprss11 a, Gstal , Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinbl 1 , Foxql , Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhc13, Tgm1 , Gclm, Rhov, Gsta2, Samd12, Spns2, Proser2, Ehf, Sostdcl , Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl , Arhgap27, Lpar5, Duoxl , Sult2b1 , Jup, 2200002D01 Rik, Map3k9, Ppap2c, Anxal , Arhgap27, Foxql , Mir200a, Cnksrl , Tmprss11g, Dennd2c, Lztsl , S100a16, Arhgap32, Sox15, Spintl , Clic3, Crb3, and Rtkn; wherein the Klf5 metagene comprises genes selected from Klf5, Dsg3, Tmprss11 bnl, Grhl3, Dsp, Jup, Pkp1 , Ripk4, Esrpl , Tgm1 , Ehf, Aqp3, Cdh1 , Spintl , Tjp2, Foxql , 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll , Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1 , Rab25, Duoxal , Plekhg6, Slc9a3r1 , Pkp3, Tnk1 , Krtcap3, Fam160a1 , Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1 r13l, Sult2b1 , Celsrl , Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1g, Col17a1 , Grb7,Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2, Llgl2, Anxa8, Krt5, Tmprssl 1e, Ppi, Dennd2c, Tacstd2, Sprrla, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl , Tmem63b, Grhl2, Cldn4, Krt14, TtlHO, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1 , and Itgb4; wherein the Psca metagene comprises genes selected from Psca, Mai, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1d, Cblc, Ceacaml, Gstol, Tmprssl 1g, Anxal, Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1bnl, Krt13, Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, Upk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinbl 1 , Rab25, Dsg3, Prss22, Tmprssl 1a, Calml3, Epn3, Slc6a20a, Tmprssl 1e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl, Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rab11fip1, Ocln, Crispl, Prss8, Pglyrp4, Kif21a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1, Gstal, Gstal, Pvrl4, ArhgeflOl, Elf5, Mapk13, Ikzf2, Tjp3, Osginl, Gsta2, Cldn7, Epb4.1l5, Duoxa2, Zfp750, Zdhhc13, Gm10639, Klk11 , Arhgap40, Arg1, Ltf, Rnf223, and St14; wherein the Cd44 metagene comprises genes selected from Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Fam83h, Col17a1, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpzl2, Arhgef5, Spint2, 1810019J16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltHb, Grb7, Esrp2, Lsr, Itga3, Plekha7, Dsg3, Clca5, Ap1m2, Plch2, Arhgef5, Celsrl, Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5, Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgef16, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1 , Lypd3, Trim29, Tmprssl 1g, Cnksrl, Tmprssl 1bnl, Mir200b, Ptprf, Gm9908, Dlg1, Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, 1117re, Fat1, Nrg1, Mdfi, and Nipal2; wherein the Prom1 metagene comprises genes selected from Prom1, Ceacaml, Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca, Tmprssl 1d, Cwh43, Slc37a1, Marveld2, ArhgeflOl, Gclm, Ocln, Mctp2, Lrrc26, Fxyd3, lldrl, Cblc, Spintl, Cldn4, Slc52a3, Tmprssl 1g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, Upk3bl, Slc9a3r1, Mall, Sostdd, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2l1, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO, Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprss11bnl, Gpx2, Gstol, Spns2, Serpinbl 1, Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N10Rik, Sh3yl1, Slc5a9, Samd10, Elf3, St14, Ikzf2, Kif21 a, and Erbb3; wherein the Prom2 metagene comprises genes selected from Prom2, Clic3, Tmem54, Evpl, Zfp750, Grhll, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8l1, Gltp, Llgl2, Ovol1, Tmprssl 3, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14,Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinb11, H22ra1, Erbb2, Dsc2, Rnf39, Tmprss11e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, ArhgeHOI, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl , Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1, Ttc39a, Spintl , Ppfia3, S100a7a, Dsp, Chitl , Pinlyp, Grb7, Tmem79, Barx2, Klk10, Perp, Efna3, Ccbll , Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml, Slc6a20a, SytH, Rnf223, Ide, Calml3, Caszl, and Celsr2; wherein the Bmi1 metagene comprises genes selected from Bmi1, Klhdc2, Bbx, Tusc3, Glg1, Bloc1s6, Wdr34, 5730455P16Rik, Hs2st1, Terf2, Fut8, Zmym4, Pcm1, Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajcIO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301 B20Rik, Mib1, Tiam2, Cers2, Stk3, Hspa13, Txndc12, Dock7, Psmd5, Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1, Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy19l1, Ilf3, Bbs4, Slc30a4, Inpph, Inf2, Zmynd11, Atp8b2, Gludl, Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, Kifap3, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7; wherein the Sox4 metagene comprises genes selected from Sox4, Abl1 , Rab34, Fgf rl1 , Ptovl, Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl, Tcf3, Tcf12, Clip2, Bbx, Nf1, Spats2, Farpl, Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl, Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl, MicalH, Ubxn7, Mvb12b, Trio, Stonl, Dok1, Fam65a, Fmnl3, Hsf2, Sestdl, Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1, Cep120, Rnf139, Dpy19l1, Dbn1, Ctps2, Magedl, Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbl, AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl, Staul, Mecp2, Phf20, Pex11b, Ehmt2, Cep170, Fgfrl, Txndc5, Zmym4, Samd14, Kansl2, Teadl, Zkscan17, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdmla, Loxl3, Acvrl , Wwtrl , AsxH , and Phf2; wherein the Lrigl metagene comprises genes selected from Lrigl, Rgmb, Zcchc24, Teadl, Lambl, Cep170, Evalb, Sept9, Farpl, Satb2, Maplb, Ccdc88a, Axl, Loxl3, Pdgfra, Ust, Lgalsl, Kifap3, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamcl, Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1 , Stx2, Lbh, Wipfl , Igfbp4, Myo9a, Cul7, Abl1 , Phf20, Xxyltl , Myo9a, Dok1 , Dst, Gkapl , Tspanl 1 , Phldbl , Sydel , Teadl , Rab34, Stxbpl , AI597468, St6gal1 , Ilk, Zeb1, Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl, Ank, Displ , Fhl3, Fermt2, Cdr2, Dock5, Crabpl , S1pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl, Sdccag8, Gliprl, and Nnt; wherein the Lgr6 metagene comprises genes selected from Lgr6, Tnnt2, Cnnm4, Prss12, Tgfbl, Tes, Raplgap, Add2,Sdc1 , Jam2, Gpr39, B4galnt1 , D8Ertd82e, Plekhg3, Lamc2, Socs2, Rampl , Etv6, Lamb3, Egr3, Dusp6, Foxpl, Dnaja4, Tnfrsf12a, Pip4k2c, Rnf181, Anol, A130010J15Rik, 1118r1 , Chst2, Jag1, 1600029D21 Rik, Tnfsf9, Src, Runxl , Rhbddl , Smad7, Itga6, Socs2, Slco2a1 , Aplp2, Cd9, Rail 4, Smurf 1, Nedd9, C1galt1, Pmepal, Padi3, Gpr25, Fermtl, Nav2, Arhgef3, Capnsl, Foxp4, Ubald2, Gm7367, Gm7367, Ctnnal, Cd80, Hivep2, Dyrk3, Rab6a, Runx2, Iqgapl, Ggct, Lrch4, Skil, Frrsl, Slc20a2, Ncmap, Reep3, Nadsynl, Bhlhe40, Gprc5a, Slc39a4, Hes6, Acsl3, Erc1, Lama5, Ephb4, Rmnd5b, Plekhal, Bcr, Zbtb18, Shq1, Scyl2, Padi4, Scin, Dhcr7, and AtplOd; and wherein the Sox9 metagene comprises genes selected from Sox9, Lgr6, Shf, Cnnm4, Runxl, Ctnnal, Capnsl, Rail 4, Itpr3, Runx2, Iqgapl, Bhlhe41, Rnf181, Ccndl, Prss12, Tes, Aig1, Foxc2, Raplgap, Krt18, Rab6a, Etv6, Dusp6, Igsf8, Tubgcp2, Alcam, Sos2, Dusp4, Bzw2, Nck2, Add2, Foxpl, Ubald2, Tnnt2, Kcnn4, Fzd7, Reep3, Nav2, Cpe, Casp3, Cnot7, Cttn, Anol, Bcarl, Cyth2, Myof, Egr3, Nadsynl, Nt5e, Dnaja4, Plekhal, Capg, Phc2, Itga2, B4galnt1, Smurfl, Gtf2ird1, Pwwp2b, Phldal, Enppl, Nfat5, Cd151, Hivep2, Ppmel, Tgifl, Gm7367, Gm7367, Zbtb18, Sdc4, D630045J12Rik, Smad7, Slc20a2, Igf 1 r, Rsf1, Tnfrsf12a, Slc27a1, Chst2, 2810408A11 Rik, Igfbp3, Kdelrl, Ern1, Atxn2l,Dyrk3, Tgfbl, Bhlhe40, Phrfl, Tnfrsf22, Ddhdl, Traf4, A130010J15Rik, Papd7, Mast4, Skil, Pyroxdl, Fubp3, Nr1h2, Ctnnbl, Foxci, Tbc1d1, and 1810011O10Rik.

4. The cell of claim 1 , wherein the cell comprises: a first lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Sox2, Foxal, Krt15, Krt19, Pitxl, Klf5, Psca, Cd44, Prom1, and Prom2, wherein expression of the first lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Sox2, Foxal, Krt15, Krt19, Pitxl, Klf5, Psca, Cd44, Proml, and Prom2; and a second lineage tracing reporter gene operably linked to a promoter of a gene selected from the group consisting of Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9, wherein expression of the second lineage tracing reporter gene coincides with expression of the gene selected from the group consisting of Bmi1, Sox4, Lrigl, Lgr6, and Sox9.

5. The cell of any one of claims 1-4, wherein the first lineage tracing reporter gene encodes a first fluorescent protein, and wherein the second lineage tracing reporter gene encodes a second fluorescent protein.

6. The cell of claim 5, wherein the first fluorescent protein and the second fluorescent protein have different fluorescent emission wavelengths.

7. The cell of any one of claims 1 -6, wherein the cell is a cancerous cell or a pre- malignant cell.

8. The cell of any one of claims 1-7, wherein the cell is a mammalian cell.

9. The cell of claim 8, wherein the mammalian cell is a rodent, non-human primate, or human cell.

10. The cell of any one of claims 1 -9, wherein the cell is derived from a cancerous cell that was previously treated with a chemotherapeutic agent.11 . The cell of any one of claims 1 -9, wherein the cell is derived from a pre-neoplasia lesion, optionally wherein the pre-neoplasia lesion is a papilloma.

12. The cell of any one of claims 1 -11 , wherein the cell is a pre-malignant epithelial cell.

13. The cell of any one of claims 1 -12, wherein the first lineage tracing reporter gene is fused to a regulatory region of the first gene whose expression is positively correlated with a stem cell plasticity state such that the first lineage tracing reporter gene is under the control of the promoter of the first gene.

14. The cell of any one of claims 1 -13, wherein the second lineage tracing reporter gene is fused to a regulatory region of the second gene whose expression is positively correlated with a proliferative state such that the second lineage tracing reporter gene is under the control of the promoter of the second gene.

15. The cell of any one of claims 1 -12, wherein the first lineage tracing reporter gene is fused in frame to a coding region of the first gene whose expression is positively correlated with a stem cell plasticity state such that the first lineage tracing reporter gene and the first gene are transcribed into a single messenger RNA (mRNA), wherein the mRNA is translated into a fusion protein comprising a protein encoded by the first gene covalently linked to a reporter protein encoded by the first lineage tracing reporter gene.

16. The cell of claim 15, further comprising an insertion of a polynucleotide encoding a flexible linker region between the first lineage tracing reporter gene and the first gene such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the first gene.

17. The cell of any one of claims 1 -12, wherein the second lineage tracing reporter gene is fused in frame to a coding region of the second gene whose expression is positively correlated with a proliferative state such that the second lineage tracing reporter gene and the second gene are transcribed into a single messenger RNA (mRNA), wherein the mRNA is translated into a fusion protein comprising a protein encoded by the second gene covalently linked to a reporter protein encoded by the second lineage tracing reporter gene.

18. The cell of claim 17, further comprising an insertion of a polynucleotide encoding a flexible linker region between the second lineage tracing reporter gene and the second gene such that the fusion protein comprises a flexible linker between the reporter protein and the protein encoded by the second gene.

19. A method of detecting whether the cell of any one of claims 1 -18 is in a cell state having lineage plasticity and drug resistance or a proliferative cell state, the method comprising:(a) contacting the cell of any one of claims 1 -18 with a candidate agent; and(b) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the first lineage tracing reporter gene compared to the second lineage tracing reporter gene indicates that the cell is in the cell state having lineage plasticity and drug resistance, and wherein increased expression of the second lineage tracing reporter gene compared to the first lineage tracing reporter gene indicates that the cell is in the proliferative cell state.

20. The method of claim 19, further comprising screening for an agent that switches the cell identified as being in the cell state having lineage plasticity and drug resistance to the proliferative cell state, the method comprising:(a) contacting the cell with a candidate agent; and(b) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the second lineage tracing reporter gene compared to the first lineage tracing reporter gene indicates that the cell has switched to the proliferative cell state.21 . The method of claim 20, wherein the candidate agent induces cell differentiation.

22. The method of claim 20, wherein the candidate agent is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A.

23. The method of claim 20, wherein the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.

24. The method of claim 19, further comprising screening for an agent that switches the cell identified as being in the proliferative cell state to the cell state having lineage plasticity and drug resistance, the method comprising:(a) contacting the cell with a candidate agent; and(b) detecting levels of expression of the first lineage tracing reporter gene and the second lineage tracing reporter gene, wherein increased expression of the first lineage tracing reporter gene compared to the second lineage tracing reporter gene indicates that the cell has switched to the cell state having lineage plasticity and drug resistance.

25. The method of claim 24, wherein the candidate agent is an anti-mitotic agent.

26. The method of claim 25, wherein the anti-mitotic agent is an alkylating agent, a taxane, or a vinca alkaloid.

27. The method of claim 24, wherein the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.

28. The method of any one of claims 19-27, wherein the first lineage tracing reporter gene encodes a first fluorescent protein, and wherein the second lineage tracing reporter gene encodes a second fluorescent protein.

29. The method of claim 28, wherein the first fluorescent protein and the second fluorescent protein have different fluorescent emission wavelengths.

30. A method of screening for an agent that switches cells between cell states, the method comprising:(a) providing a first population of cells and a second population of cells, wherein the first population of cells has increased lineage plasticity, increased levels of expression of a geneselected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Promt metagene, and a Prom2 metagene, and decreased levels of expression of a gene selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene compared to the second population of cells, and wherein the second population of cells has increased proliferation, increased levels of expression of a gene selected from a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene, and decreased levels of expression of a gene selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Proml metagene, and a Prom2 metagene compared to the first population of cells;(b) contacting the first population of cells and the second population of cells with a candidate agent;(c) measuring levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Promt metagene, and Prom2 metagene, and one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the first population of cells and the second population of cells; and(d) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene and increased levels of expression of the one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the first population of cells in presence of the candidate agent compared to reference value ranges for the levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein increased levels of expression of the one or more genes selected from the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene, and Prom2 metagene and decreased levels of expression of the one or more genes selected from the Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene in the second population of cells in the presence of the candidate agent compared to the reference value ranges for the levels of expression of the Sox2 metagene, Foxal metagene, Krt15 metagene, Krt19 metagene, Pitxl metagene, Klf5 metagene, Psca metagene, Cd44 metagene, Prom1 metagene,Prom2 metagene, Bmi1 metagene, Sox4 metagene, Lrigl metagene, Lgr6 metagene, and Sox9 metagene indicate that the candidate agent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.

31. The method of claim 30, wherein the Sox2 metagene comprises genes selected from Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, MtmrIO, Esd, Sox13, Nfe2l2, Pls1, Tom1l2, Bink, Suox, Sid 6a11 , Xrcc5, Chstl 5, Krt12, Eval c, Nppc, Esd, Ddx59, Nop2, Krt13, Plekhh3, Osbpl6, Aldh5a1 , Ci rh 1 a, Wnk4, Arntl2, Fam110c, Tmem180, Dili, Galnt12, Pitxl, Caleb, Ankrd9, Isl1, Btc, Gss, Ociad2, Klra33, Aldh3a1, Minkl, Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl, Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrla, Pthlh, Usp6nl, Ufspl, Irgq, Nkiras2, Grtpl, Nqo1, Krt20, Snord42b, Avpil, Ifrdl, Srd5a2, Cpn1, Bail, Sprr3, Rap1gap2, Rassf7, Fetub, Ramp3, Arl4d, Tle1, Krt76, Ptprzl, Pradcl, Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl, G6pdx, Tsg101, Nmrkl, Ralgapb, A430105l19Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik; wherein the Foxal metagene comprises genes selected from Foxal , Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1, Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1, Tjp3, Plekhg6, Bspry, Ocln, Ceacaml, Marveld3, Cldn3, Mal2, Tmem30b, Sowahb, Spns2, Slc9a3r1, Kctdl, Cwh43, Cystml, Rab17, S100a2, Ppbp, Padil, Caleb, Gstol, S100a16, Spint2, Slc52a3, Sid 6a11 , Crispl, Mall, Aldh1a3, Entpd3, Tmprss11g, Anxal, Pgapl, Prss22, Kif21a, Omp, Liph, Epb4.1l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, ArhgeflOl, Tmprss11d, Mxd1, Elf5, Acss2, Leprell, Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppfibp2, Mboatl, Zdhhc13, Dgka, Ehf, Mst1, St14, Ap1s3, Maltl, Spintl, Sprr3, Pllp, AA986860, Prss27, Tmprssl 1a, Serpinbl 1 , Hs3st1 , StardlO, Arhgap40, lldrl , Ppi, Fbp2, Cnksrl , Map7, and 1700001 C19Rik, E330009J07Rik; wherein the Krt15 metagene comprises genes selected from Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrd , Zfp750, Lipm, Ocln, Paqr5, GrhH , Erbb3, PsapH , Aldh3b2, Ppi, Rapgefh , Aldh3b2, Efna3, Muc15, Liph, 2610528A11Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1pr5, Klhl29, 4833423E24Rik, Nccrpl, Slc27a4, Barx2, Aimll, Wnt4, L1cam, Leprell, Rnf43, Ckmtl, Lipk, Mapk13, H22ra1 , Zfp185, Cds1, Arhgap40, Krt80, Dsc3, Prss8, Fgfr3, Hsd17b2, Padil, Ripk4, Prom2, Adtrp, Caszl, 1700055N04Rik, Scnnla, Ptprf, ArhgeflOl, Tmprssl 1e, Slc25a48, Mall, Mst1, Crnn, Celsrl, Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinbl 1, Vsnll, Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprssl 3, Sowahb, Celsr2, Ly6g6e, SytH, Tprg, AA986860, and Sptbn2; wherein the Krt19 metagene comprises genes selected from Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal, Mall, Slc37a1, Cblc, Marveld3, Marveld2, Gstol,Ceacaml, Gm9573, Ocln, Slc9a3r1, Mal2, Tmprss11g, Spns2, Anxal, 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, Arhgefl 01, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, Upk3bl, Gsta4, Ppbp, Tmprss11d, Spintl , Tmem30b, S100a2, Pgapl, Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1, Kif21 a, Krt13, Padil , Tmprss11bnl, Foxql, S100a16, L1cam, Seel, Ehf, SamdIO, Epb4.115, Rab27b, Plekha7, Llgl2, Erbb2, Stap2, Rab25, Hebp2, Cnksrl, 1117re, Pllp, Cystml, Tnk1, Mboatl, Tmprss11e, Tacstd2, Plekha6, Arg1, Ltf, Evpl, S100a14, Plekhhl , Slc25a48, Ap1s3, Zdhhc13, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl, Ppfibp2, Nipal2, Rab27a, Rbm47, and StardlO; wherein the Pitxl metagene comprises genes selected from Pitxl , Cldn8, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1, Klf5, Cep170b,Llgl2, 1700001C19Rik, Tmprss11d, Dsc2, Fam160a1, Erbb2, Gsta4, Shb, Duoxal, Rab27b, Barx2, Fhdd, Tmprss11bnl, Krt13, Plekhg6, Fam57a, Gstol, Ppp1r13l, Dsg3, Epn3, Als2cl, Grhl3, Myo5b, Arhgef5, Tmem63b, Phldb3, Tmprss11a, Gstal, Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinb11, Foxql, Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhc13, Tgm1, Gclm, Rhov, Gsta2, Samd12, Spns2, Proser2, Ehf, Sostdcl , Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl, Arhgap27, Lpar5, Duoxl, Sult2b1 , Jup, 2200002D01Rik, Map3k9, Ppap2c, Anxal, Arhgap27, Foxql, Mir200a, Cnksrl, Tmprss11g, Dennd2c, Lztsl, S100a16, Arhgap32, Sox15, Spintl, Clic3, Crb3, and Rtkn; wherein the Klf5 metagene comprises genes selected from Klf5, Dsg3, Tmprss11bnl, Grhl3, Dsp, Jup, Pkp1, Ripk4, Esrpl, Tgm1, Ehf, Aqp3, Cdh1, Spintl, Tjp2, Foxql, 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll, Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1, Rab25, Duoxal, Plekhg6, Slc9a3r1, Pkp3, Tnk1, Krtcap3, Fam160a1, Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1r13l, Sult2b1 , Celsrl , Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1g, Col17a1 , Grb7, Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2, Llgl2, Anxa8, Krt5, Tmprssl 1e, Ppi, Dennd2c, Tacstd2, Sprrla, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl , Tmem63b, Grhl2, Cldn4, Krt14, TtlHO, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1 , and Itgb4; wherein the Psca metagene comprises genes selected from Psca, Mai, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1d, Cblc, Ceacaml, Gstol, Tmprssl 1g, Anxal, Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1bnl, Krt13, Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, Upk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinb11, Rab25, Dsg3, Prss22, Tmprss11a, Calml3, Epn3, Slc6a20a, Tmprssl 1e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl, Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rab11fip1, Ocln, Crispl, Prss8, Pglyrp4, Kif21a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1, Gstal, Gstal, Pvrl4, Arhgefl 01, Elf5,Mapk13, Ikzf2, Tjp3, Osginl, Gsta2, Cldn7, Epb4.1l5, Duoxa2, Zfp750, Zdhhc13, Gm10639, Klk11 , Arhgap40, Arg1 , Ltf, Rnf223, and St14; wherein the Cd44 metagene comprises genes selected from Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Fam83h, Col17a1, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpzl2, Arhgef5, Spint2, 1810019J16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltUb, Grb7, Esrp2, Lsr, Itga3, Plekha7, Dsg3, Clca5, Ap1m2, Plch2, Arhgef5, Celsrl, Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5, Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgef16, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1 , Lypd3, Trim29, Tmprss11g, Cnksrl, Tmprss11bnl, Mir200b, Ptprf, Gm9908, Dlg1, Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, 1117re, Fat1, Nrg1, Mdfi, and Nipal2; wherein the Promt metagene comprises genes selected from Promt , Ceacaml , Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca, Tmprss11d, Cwh43, Slc37a1, Marveld2, ArhgeflOl, Gclm, Ocln, Mctp2, Lrrc26, Fxyd3, lldrl, Cblc, Spintl, Cldn4, Slc52a3, Tmprss11g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, Upk3bl, Slc9a3r1, Mall, Sostdcl, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2l1, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO, Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprss11bnl, Gpx2, Gstol, Spns2, Serpinb11, Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N10Rik, Sh3yl1, Slc5a9, SarndlO, Elf3, St14, Ikzf2, Kif21 a, and Erbb3; wherein the Prom2 metagene comprises genes selected from Prom2, Clic3, Tmem54, Evpl, Zfp750, Grhll, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8l1, Gltp, Llgl2, Ovol1, Tmprss13, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14, Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinb11, H22ra1, Erbb2, Dsc2, Rnf39, Tmprss11e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, ArhgeflOl, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl , Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1 , Ttc39a, Spintl, Ppfia3, S100a7a, Dsp, Chitl, Pinlyp, Grb7, Tmem79, Barx2, Klk10, Perp, Efna3, CcbH, Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml, Slc6a20a, SytH, Rnf223, Ide, Calml3, Caszl, and Celsr2; wherein the Bmi1 metagene comprises genes selected from Bmi1, Klhdc2, Bbx, Tusc3, Glg1, Bloc1s6, Wdr34, 5730455P16Rik, Hs2st1, Terf2, Fut8, Zmym4, Pcm1, Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajcIO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1, Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy19l1, Ilf3, Bbs4, Slc30a4, InppH, Inf2, Zmynd11, Atp8b2, Gludl , Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, Kifap3, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7; wherein the Sox4 metagene comprises genes selected from Sox4, Abl1 , Rab34, Fgfrll , Ptovl, Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl, Tcf3, Tcf12, Clip2, Bbx, Nf1, Spats2, Farpl, Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl, Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl, MicalH, Ubxn7, Mvb12b, Trio, Stonl, Dok1, Fam65a, Fmnl3, Hsf2, Sestdl, Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1, Cep120, Rnf139, Dpy19l1, Dbn1, Ctps2, Magedl, Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbl, AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl, Staul, Mecp2, Phf20, Pex11b, Ehmt2, Cep170, Fgfrl, Txndc5, Zmym4, Samd14, Kansl2, Teadl, Zkscan17, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdmla, Loxl3, Acvrl , Wwtrl , AsxH , and Phf2; wherein the Lrigl metagene comprises genes selected from Lrigl, Rgmb, Zcchc24, Teadl, Lambl, Cep170, Evalb, Sept9, Farpl, Satb2, Maplb, Ccdc88a, Axl, Loxl3, Pdgfra, list, Lgalsl, Kifap3, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamcl, Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1 , Stx2, Lbh, Wipfl , Igfbp4, Myo9a, Cul7, Abl1 , Phf20, Xxyltl , Myo9a, Dok1 , Dst, Gkapl , Tspanl 1 , Phldbl , Sydel , Teadl , Rab34, Stxbpl , AI597468, St6gal1 , Ilk, Zeb1, Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl, Ank, Displ , Fhl3, Fermt2, Cdr2, Dock5, Crabpl , S1pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl , Sdccag8, Gliprl, and Nnt; wherein the Lgr6 metagene comprises genes selected from Lgr6, Tnnt2, Cnnm4, Prss12, Sox9, Itga2, Shf, Igsf8, Itpr3, Nt5e, Bhlhe41, Fzd7, Krt18, Arid5a, Tgfbl, Tes, Raplgap, Add2, Sdc1 , Jam2, Gpr39, B4galnt1 , D8Ertd82e, Plekhg3, Lamc2, Socs2, Rampl , Etv6, Lamb3, Egr3, Dusp6, Foxpl, Dnaja4, Tnfrsf12a, Pip4k2c, Rnf181, Anol, A130010J15Rik, 1118r1 , Chst2, Jag1, 1600029D21 Rik, Tnfsf9, Src, Runxl , Rhbddl , Smad7, Itga6, Socs2, Slco2a1 , Aplp2, Cd9, Rail 4, Smurf 1, Nedd9, C1galt1, Pmepal, Padi3, Gpr25, Fermtl, Nav2, Arhgef3, Capnsl, Foxp4, Ubald2, Gm7367, Gm7367, Ctnnal, Cd80, Hivep2, Dyrk3, Rab6a, Runx2, Iqgapl, Ggct, Lrch4, Skil, Frrsl, Slc20a2, Ncmap, Reep3, Nadsynl, Bhlhe40, Gprc5a, Slc39a4, Hes6, Acsl3, Erc1, Lama5, Ephb4, Rmnd5b, Plekhal, Bcr, Zbtb18, Shq1, Scyl2, Padi4, Scin, Dhcr7, and AtplOd; and wherein the Sox9 metagene comprises genes selected from Sox9, Lgr6, Shf, Cnnm4, Runxl, Ctnnal, Capnsl, Rail 4, Itpr3, Runx2, Iqgapl, Bhlhe41, Rnf181 , Ccndl, Prss12, Tes, Aig1 , Foxc2, Raplgap, Krt18, Rab6a, Etv6, Dusp6, Igsf8, Tubgcp2, Alcam, Sos2, Dusp4, Bzw2,Nck2, Add2, Foxpl , Ubald2, Tnnt2, Kcnn4, Fzd7, Reep3, Nav2, Cpe, Casp3, Cnot7, Cttn, Anol , Bcarl , Cyth2, Myof, Egr3, Nadsynl , Nt5e, Dnaja4, Plekhal , Capg, Phc2, Itga2, B4galnt1 , Smurfl , Gtf2ird1 , Pwwp2b, Phldal , Enppl , Nfat5, Cd151 , Hivep2, Ppmel , Tgifl , Gm7367, Gm7367, Zbtb18, Sdc4, D630045J12Rik, Smad7, Slc20a2, Igf 1 r, Rsf1 , Tnfrsf12a, Slc27a1 , Chst2, 2810408A1 1 Rik, IgfbpS, Kdelrl , Ern1 , Atxn2l,Dyrk3, Tgfbl , Bhlhe40, Phrfl , Tnfrsf22, Ddhdl , Traf4, A130010J15Rik, Papd7, Mast4, Skil, Pyroxdl , Fubp3, Nr1 h2, Ctnnbl , Foxci , Tbc1d1 , and 181001 1 O10Rik.

32. The method of claim 30, wherein the method comprises:(a) providing a first population of cells and a second population of cells, wherein the first population of cells has increased lineage plasticity, increased levels of expression of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2, and decreased levels of expression of Bmi1 , Sox4, and Lrigl compared to the second population of cells, and wherein the second population of cells has increased proliferation, increased levels of expression of Bmi1 , Sox4, Lrigl , Lgr6, and Sox9, and decreased levels of expression of Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 compared to the first population of cells;(b) contacting the first population of cells and the second population of cells with a candidate agent;(c) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf 5, Psca, Cd44, Promt , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the first population of cells and the second population of cells; and(d) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the first population of cells in presence of the candidate agent compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the second population of cells in the presence of the candidate agent compared to the reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom! , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidateagent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.

33. The method of claim 32, further comprising measuring proliferation of the first population of cells and the second population of cells, wherein an increased level of proliferation in combination with decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2, and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9 in the first population of cells in the presence of the candidate agent compared to reference value ranges for the level of proliferation and the levels of expression of the Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the first population of cells to a more proliferative cell state having decreased lineage plasticity, and wherein a decreased level of proliferation in combination with increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2, and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the second population of cells in the presence of the candidate agent compared to reference value ranges for the level of proliferation and the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the candidate agent is effective in switching the second population of cells to a less proliferative cell state having increased lineage plasticity.

34. The method of any one of claims 30-33, wherein said measuring levels of expression comprises performing reverse transcription polymerase chain reaction, RNA sequencing, global run-on sequencing, microarray analysis, or any combination thereof.

35. The method of claim 34, wherein the RNA sequencing is single cell RNA sequencing.

36. The method of any one of claims 30-35, wherein the candidate agent inhibits mitosis or induces cell differentiation.

37. The method of any one of claims 30-36, wherein the candidate agent inhibits KRAS4A or protein phosphatase 2A (PP2A).

38. The method of claim 37, wherein the candidate agent selectively inhibits a PP2A subunit.

39. The method of any one of claims 30-38, wherein the candidate agent affects a DNA damage response, protein translation, RNA splicing, or telomere length.

40. The method of any one of claims 30-39, wherein the first population of cells and the second population of cells are cancerous cells or pre-malignant cells.41 . The method of any one of claims 30-40, wherein the first population of cells and the second population of cells are mammalian cells.

42. The method of claim 41 , wherein the mammalian cells are rodent, non-human primate, or human cells.

43. The method of any one of claims 30-42, wherein the first population of cells or the second population of cells is derived from a cancerous cell that was previously treated with a chemotherapeutic agent.

44. The method of any one of claims 30-43, wherein the first population of cells or the second population of cells is derived from a pre-neoplasia lesion, optionally wherein the preneoplasia lesion is a papilloma.

45. The method of any one of claims 30-44, wherein the first population of cells and the second population of cells are pre-malignant epithelial cells.

46. A method of detecting cell type switching of a cancerous cell in response to treatment with a therapeutic agent;(a) treating the cancerous cell with an effective amount of the therapeutic agent;(b) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt 15, Krt 19, Pitxl , Klf 5, Psca, Cd44, Prom1 , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrig 1 , Lgr6, and Sox9 in progeny of the cancerous cell; and(c) detecting cell state switching, wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the progeny of the cancerous cell after said treating the cancerous cellcompared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt 19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the progeny of the cancerous cell are in a proliferative cell state susceptible to treatment with an antimitotic agent, and wherein increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Proml , and Prom2 and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the progeny of the cancerous cell after said treating the cancerous cell compared to the reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Prom1 , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the progeny of the cancerous cell are in a cell state having lineage plasticity and drug resistance.

47. The method of claim 46, further comprising treating the cancerous cell and the progeny thereof with an anti-mitotic agent if the progeny of the cancerous cell are in the proliferative cell state susceptible to treatment with the anti-mitotic agent, or treating the cancerous cell with an inducer of differentiation if the progeny of the cancerous cell are in the cell state having lineage plasticity and drug resistance.

48. The method of claim 47, further comprising treating the cancerous cell and the progeny thereof with the anti-mitotic agent after said treating the cancerous cell with the inducer of differentiation if the progeny of the cancerous cell are in the cell state having lineage plasticity and drug resistance.

49. The method of claim 47 or 48, wherein the inducer of differentiation is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A.

50. The method of claim 49, wherein the inhibitor of PP2A is LB100.51 . The method of any one of claims 47-50, wherein the anti-mitotic agent is cisplatin, cyclophosphamide, chlorambucil, vinblastine, vincristine, vinorelbine, vinflunine, paclitaxel, docetaxel, or a combretastatin.

52. The method of any one of claims 46-51 , wherein the cancerous cell is a carcinoma cell.

53. The method of claim 52, wherein the carcinoma cell is a squamous cell carcinoma cell.

54. The method of claim 53, wherein the squamous cell carcinoma cell is a cutaneous squamous cell carcinoma cell.

55. The method of any one of claims 46-54, wherein the cancerous cell is in vivo or in vitro.

56. The method of any one of claims 46-55, wherein the cancerous cell comprises a reporter gene for lineage tracing of the progeny of the cancerous cell.

57. The method of claim 56, wherein the reporter gene encodes a fluorescent protein.

58. The method of any one of claims 46-57, wherein said measuring levels of expression comprises performing reverse transcription polymerase chain reaction, RNA sequencing, global run-on sequencing, microarray analysis, or any combination thereof.

59. The method of claim 58, wherein the RNA sequencing is single cell RNA sequencing.

60. A method of treating a cancerous or pre-malignant lesion in a patient, the method comprising:(a) administering a therapeutically effective amount of an anti-mitotic therapeutic agent to the patient;(b) obtaining a biological sample comprising cancerous or pre-malignant cells from the cancerous or premalignant lesion of the patient;(c) measuring levels of expression of one or more genes selected from Sox2, Foxal , Krt 15, Krt 19, Pitxl , Klf 5, Psca, Cd44, Prom1 , and Prom2, and one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the biological sample, wherein increased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and decreased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 in the biological sample compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krtt 5, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the cancerous or pre-malignant cells are in a drug resistant state, and wherein decreased levels of expression of the one or more genes selected from Sox2, Foxal , Krt15, Krtt 9, Pitxl , Klf5, Psca, Cd44, Promt , and Prom2 and increased levels of expression of the one or more genes selected from Bmi1 , Sox4, Lrigl , Lgr6,and Sox9 in the biological sample compared to reference value ranges for the levels of expression of the Sox2, Foxal , Krt15, Krt19, Pitxl , Klf5, Psca, Cd44, Promt , Prom2, Bmi1 , Sox4, Lrigl , Lgr6, and Sox9 indicate that the cancerous or pre-malignant cells are in non-drug resistant state; and(d) continuing treatment of the patient with the anti-mitotic therapeutic agent if the patient is in the non-drug resistant state; or discontinuing treatment of the patient with the anti-mitotic therapeutic agent if the patient is in the drug resistant state, and administering a therapeutically effective amount of an agent that induces differentiation to the patient to switch the cell state of the cancerous or pre-malignant cells from the drug resistant state to the non-drug resistant state before subsequently administering another therapeutically effective amount of the anti-mitotic agent to the patient.61 . The method of claim 60, wherein the inducer of differentiation is an inhibitor of protein phosphatase 2A (PP2A) or a subunit thereof or an inhibitor of KRAS4A.

62. The method of claim 61 , wherein the inhibitor of PP2A is LB100.

63. The method of any one of claims 60-62, wherein the anti-mitotic agent is cisplatin, cyclophosphamide, chlorambucil, vinblastine, vincristine, vinorelbine, vinflunine, paclitaxel, docetaxel, or a combretastatin.

64. A composition comprising an RNA transcript of a gene selected from a Sox2 metagene, a Foxal metagene, a Krt15 metagene, a Krt19 metagene, a Pitxl metagene, a Klf5 metagene, a Psca metagene, a Cd44 metagene, a Prom1 metagene, a Prom2 metagene, a Bmi1 metagene, a Sox4 metagene, a Lrigl metagene, a Lgr6 metagene, and a Sox9 metagene for use in a method of diagnosing development of drug resistance of a cancer in response to treatment with a therapeutic agent.

65. The composition of claim 64, wherein the Sox2 metagene comprises genes selected from Sox2, Aspa, Snx15, Krt4, Ngef, Pax9, Dlg3, MtmrI O, Esd, Sox13, Nfe2l2, Pls1 , Tom1 l2, Bink, Suox, Slc16a1 1 , Xrcc5, Chstl 5, Krt12, Eval c, Nppc, Esd, Ddx59, Nop2, Krt13, Plekhh3, Osbpl6, Aldh5a1 , Ci rh 1 a, Wnk4, Arntl2, Fam110c, Tmem180, Dili , Galnt12, Pitxl , Caleb, Ankrd9, Isl1 , Btc, Gss, Ociad2, Klra33, Aldh3a1 , Minkl , Capn5, Clock, Plcd3, Slc35e4, Rnf207, Chac2, Bag2, Lxn, Mix, Itpkl , Paip2b, Gipc2, Gpd2, Thsd4, Qars, Ggh, Polrl a, Pthlh, Usp6nl, Ufspl , Irgq, Nkiras2, Grtpl , Nqo1 , Krt20, Snord42b, Avpil , Ifrdl , Srd5a2, Cpn1 , Bail , Sprr3, Rap1gap2, Rassf7, Fetub, Ramp3, Arl4d,Tle1 , Krt76, Ptprzl , Pradcl , Otud4, Cyp3a13, Nme4, Eps8l2, Bpntl , G6pdx, Tsg101 , Nmrkl , Ralgapb, A430105119Rik, 2300002M23Rik, 2200002D01 Rik, and 4930452B06Rik; wherein the Foxal metagene comprises genes selected from Foxal , Krt19, Slc44a4, Elf3, Cldn7, Rhpn2, Krt7, Lrrc26, Arg1 , Duoxa2, Gm9573, Psca, Ikzf2, Cblc, Marveld2, Tmprss2, Slc37a1 , Tjp3, Plekhg6, Bspry, Ocln, Ceacaml , Marveld3, Cldn3, Mal2, Tmem30b, Sowahb, Spns2, Slc9a3r1 , Kctdl , Cwh43, Cystml , Rab17, S100a2, Ppbp, Padil , Caleb, Gstol , S100a16, Spint2, Slc52a3, Sid 6a11 , Crispl , Mall, Aldh1a3, Entpd3, Tmprss11g, Anxal , Pgapl , Prss22, Kif21a, Omp, Liph, Epb4.1 l5, Rnf144b, Upk3bl, Duox2, Gsta4, Rab27a, Krt13, Arhgefl Ol, Tmprss11d, Mxd1 , Elf5, Acss2, LepreH , Cldn4, Rab27b, Erbb3, Plekha7, Mctp2, Rbm47, Stap2, Pard6b, Ppfibp2, Mboatl , Zdhhc13, Dgka, Ehf, Mst1 , St14, Ap1s3, Maltl , Spintl , Sprr3, Pllp, AA986860, Prss27, Tmprssl 1a, Serpinbl 1 , Hs3st1 , StardlO, Arhgap40, lldrl , Ppi, Fbp2, Cnksrl , Map7, and 1700001 C19Rik, E330009J07Rik; wherein the Krt15 metagene comprises genes selected from Krt15, Dhcr24, Gpr115, Sh3rf2, Lrrd , Zfp750, Lipm, Ocln, Paqr5, GrhH , Erbb3, PsapH , Aldh3b2, Ppi, RapgefH , Aldh3b2, Efna3, Muc15, Liph, 2610528A11 Rik, S100a14, Tmem184a, Bnipl, Evpl, Cwh43, St14, Spink5, Seel, Mfsd2a, Ly6g6c, Reep6, Camsap3, S1pr5, Klhl29, 4833423E24Rik, Nccrpl , Slc27a4, Barx2, Aind l, Wnt4, L1cam, LepreH , Rnf43, Ckmtl , Lipk, Mapk13, H22ra1 , Zfp185, Cds1 , Arhgap40, Krt80, Dsc3, Prss8, Fgfr3, Hsd17b2, Padil , Ripk4, Prom2, Adtrp, Caszl , 1700055N04Rik, Scnnla, Ptprf, Arhgefl Ol, Tmprssl 1 e, Slc25a48, Mall, Mst1 , Crnn, Celsrl , Rnf39, 2310007B03Rik, Fam83b, Rab25, Tmprss4, Krt23, 1700001 C19Rik, Rnf208, Rhbg, Nipal2, Tmem30b, Calml3, Perp, Dmkn, Cblc, Serpinbl 1 , Vsnll , Esrp2, Fam83c, Dsp, Clic3, Map7, Tmprssl 3, Sowahb, Celsr2, Ly6g6e, SytH , Tprg, AA986860, and Sptbn2; wherein the Krt19 metagene comprises genes selected from Krt19, Krt7, Elf3, Lrrc26, Plekhg6, Psca, Cldn7, Cwh43, Foxal , Mall, Slc37a1 , Cblc, Marveld3, Marveld2, Gstol , Ceacaml , Gm9573, Ocln, Slc9a3r1 , Mal2, Tmprssl 1g, Spns2, Anxal , 1700001 C19Rik, Tjp3, Wfdc2, Slc44a4, Bspry, Grb7, Slc52a3, Spint2, Sowahb, ArhgeflOl, Mai, Prss22, Rhpn2, Cldn4, Tmprss2, Upk3bl, Gsta4, Ppbp, Tmprssl 1d, Spintl , Tmem30b, S100a2, Pgapl , Erbb3, Tmem184a, Ikzf2, Cldn3, Prss27, St14, Liph, Acss2, Mxd1 , Kif21 a, Krt13, Padil , Tmprssl 1 bnl, Foxql , S100a16, L1cam, Seel, Ehf, Sarndl O, Epb4.115, Rab27b, Plekha7, Llgl2, Erbb2, Stap2, Rab25, Hebp2, Cnksrl , 1117re, Pllp, Cystml , Tnk1 , Mboatl , Tmprss11 e, Tacstd2, Plekha6, Arg1 , Ltf, Evpl, S100a14, Plekhhl , Slc25a48, Ap1s3, Zdhhc13, Cldn8, Arhgap27, Duoxa2, Ppi, Nccrpl , Ppfibp2, Nipal2, Rab27a, Rbm47, and StardlO; wherein the Pitxl metagene comprises genes selected from Pitxl , CldnS, Pitpnm3, B4galnt3, Wnt4, Slc9a3r1 , Klf5, Cep170b,Llgl2, 1700001 C19Rik, Tmprss11d, Dsc2, Fam160a1 , Erbb2, Gsta4, Shb, Duoxal , Rab27b, Barx2, Fhdd , Tmprssl 1 bnl, Krt13, Plekhg6, Fam57a, Gstol ,Gstal, Arhgef5, Limk2, Epha2, Jag2, Chmp4c, Serpinbl 1, Foxql, Mai, Glt28d2, Gm10639, Tmem125, Cblc, Fam83h, Zdhhc13, Tgm1, Gclm, Rhov, Gsta2, Samd12, Spns2, Proser2, Ehf, Sostdcl , Fam84b, Plekha7, Cdc42bpg, Vps53, Sprr3, Ccdc120, Abhd6, Tmem79, Ripk4, Zfp185, Anxa8, Mall, Evpl, Prss27, Ndufa4, Cwh43, Ptprzl, Arhgap27, Lpar5, Duox1, Sult2b1 , Jup, 2200002D01 Rik, Map3k9, Ppap2c, Anxal, Arhgap27, Foxql, Mir200a, Cnksrl, Tmprss11g, Dennd2c, Lztsl, S100a16, Arhgap32, Sox15, Spintl , Clic3, Crb3, and Rtkn; wherein the Klf5 metagene comprises genes selected from Klf5, Dsg3, Tmprss11bnl, Grhl3, Dsp, Jup, Pkp1, Ripk4, Esrpl, Tgm1, Ehf, Aqp3, Cdh1, Spintl, Tjp2, Foxql, 1700001 C19Rik, Lypd3, Esrp2, Erbb2, S100a14, Fam83h, Tmem79, Dsc2, Perp, Erbb3, Als2cl, Cd44, Galnt3, Fam83b, Pvrll, Mpzl2, Ccdc120, Epn3, Gsta4, Pitpnm3, Sox15, Proser2, Lad1, Rab25, Duoxal, Plekhg6, Slc9a3r1, Pkp3, Tnk1, Krtcap3, Fam160a1, Cwh43, Cdc42bpg, Ptprf, Syt8, Ppp1r13l, Sult2b1 , Celsrl , Rab27b, Tmprssl 1 d, Clic3, Cnksrl , Tmprssl 1g, Col17a1 , Grb7, Arap2, Fat2, Cblc, Zdhhc5, Wnt4, Spint2, Llgl2, Anxa8, Krt5, Tmprssl 1e, Ppi, Dennd2c, Tacstd2, Sprrla, Nbeal2, Has3, Jag2, Mall, Limk2, Zfp750, Trp63, Cast, Trim29, Duoxl , Tmem63b, Grhl2, Cldn4, Krt14, TtlHO, Cpeb2, Myo5b, Seel, Slc25a48, Itgb6, St14, Tns4, Prss22, Mxd1 , and Itgb4; wherein the Psca metagene comprises genes selected from Psca, Mai, Mal2, Prss27, Gm9573, Gsta4, Mall, Tmprssl 1d, Cblc, Ceacaml, Gstol, Tmprssl 1g, Anxal, Elf3, Cwh43, Plekhg6, Sprr3, 1700001 C19Rik, Ppbp, Seel, Spns2, Sowahb, Tmprssl 1bnl, Krt13, Mxd1, Ppi, Slc37a1, Nccrpl, Bspry, Upk3bl, Krt7, Lrrc26, S100a16, Marveld3, Slc9a3r1, Serpinbl 1, Rab25, Dsg3, Prss22, Tmprss11a, Calml3, Epn3, Slc6a20a, Tmprssl 1e, S100a7a, Plekha7, Tacstd2, Dsc2, Spintl, Cldn8, S100a14, AA986860, Ehf, Slc52a3, Evpl, Hebp2, Clic3, Llgl2, Rab11fip1, Ocln, Crispl, Prss8, Pglyrp4, Kif21a, Ppfibp2, Spint2, Foxql, Grhl3, Hsd17b2, Liph, Zfp185, Slc5a9, Cldn4, Sprrla, Grb7, Acss2, Slc25a48, Tgm1, Gstal, Gstal, Pvrl4, Arhgef I, Elf5, Mapk13, Ikzf2, Tjp3, Osginl, Gsta2, Cldn7, Epb4.1l5, Duoxa2, Zfp750, Zdhhc13, Gm10639, Klk11 , Arhgap40, Arg1 , Ltf, Rnf223, and St14; wherein the Cd44 metagene comprises genes selected from Cd44, Galnt3, Lama3, Krtcap3, Sox15, Slc4a11, Grhl2, Snai3, Fam83h, Col17a1, Tgfa, Lad1, Fermtl, Zdhhc5, Cdcp1,Cdh1, Fat2, Cdh3, Irf6, Tns4, Mpzl2, Arhgef5, Spint2, 1810019J16Rik, Krt5, Samd12, Epcam, Pvrll, Duoxal, Cldn4, GyltUb, Grb7, Esrp2, Lsr, Itga3, Plekha7, Dsg3, Clca5, Ap1m2, Plch2, Arhgef5, Celsrl, Tjp2, S100a14, Dusp7, Beam, Cdc42bpg, Esrpl, Foxql, Klf5, Tnk1, Urah, Itgb4, Inadl, Prrg4, Tacstd2, Arhgef16, Spintl, Pkp3, Pak6, Itgb6, Tmc7, Duoxl, Cwh43, Plek2, Sult2b1, Lypd3, Trim29, Tmprssl 1g, Cnksrl, Tmprssl 1bnl, Mir200b, Ptprf, Gm9908, Dlg1, Krt17, Lamb3, Pgap2, Elmo3, Fam83a, Syt8, Fgfbpl, Fam188a, Srd5a1, Sfn, St14, Rgs12, Plxnbl, Cblc, Rab25, Stra6, Dsg2, Erbb2, Hook2, Dgka, 1117re, Fat1, Nrg1, Mdfi, and Nipal2; wherein the Prom1 metagene comprises genes selected from Prom1, Ceacaml, Cldn7, Marveld3, Gsta4, Duoxal, Plekhg6, Crispl, Bspry, Ltf, Eya2, Tmem184a, Wfdc2, Mai, Psca,Tmprss11d, Cwh43, Slc37a1, Marveld2, ArhgeflOl, Gclm, Ocln, Mctp2, Lrrc26, Fxyd3, lldrl, Cblc, Spintl , Cldn4, Slc52a3, Tmprss11g, Ehf, Nipal2, 1117re, Zbtb7c, Phyhipl, Vtcnl, Foxql, Krt7, Upk3bl, Slc9a3r1, Mall, Sostdd, Gm9573, Alox12, Mal2, Cldn8, Tacstd2, Tnk1, Tfcp2l1, Tspan12, Arvcf, Llgl2, Seel, Anxal, Myo5b, Ppbp, 1700001 C19Rik, Cnksrl, Rbm47, StardlO, Sell 13, Plekha7, Entpd3, Cib2, Sprr3, Prss27, Beam, Usp53, Tmem30b, Spint2, Ppfibp2, Sowahb, Mapk13, Grb7, Mxd1, Myh14, Atp9a, Mir200b, Tmprss11bnl, Gpx2, Gstol, Spns2, Serpinb11, Lpar5, Reep6, Dsg2, Krt13, Hnflb, Rab27a, Rnf144b, 4732456N10Rik, Sh3yl1, Slc5a9, SamdIO, Elf3, St14, Ikzf2, Kif21 a, and Erbb3; wherein the Prom2 metagene comprises genes selected from Prom2, Clic3, Tmem54, Evpl, Zfp750, Grhll, Zfp185, Bnipl, Mapk13, Epn3, Cyp4f39, 1700001 C19Rik, Tmem184a, Sh3rf2, Arhgap40, Chmp4c, Ccdc120, Ppi, Sptbn2, Slc27a4, Gpr115, Esrp2, Seel, RapgefH, Mpzl3, Eps8l1, Gltp, Llgl2, Ovol1, Tmprss13, Rab25, Esrpl, Erbb3, Dmkn, Grhl3, S100a14, Fam57a, Fut2, St14, Ripk4, Ttc22, Ccdc64b, Klk11 , Ocln, Serpinb11, H22ra1, Erbb2, Dsc2, Rnf39, Tmprss11e, Wnt4, Spink5, B4galnt3, Tgm1, Scnnla, Cpeb2, ArhgeflOl, Cers3, Pvrl4, 4833423E24Rik, Hsd17b2, Nccrpl , Prss8, Proser2, Ehf, Mall, Mfsd2a, Tmem125, Ly6d, Cwh43, Dsg3, Tmem40, Sult2b1 , Ttc39a, Spintl, Ppfia3, S100a7a, Dsp, Chitl, Pinlyp, Grb7, Tmem79, Barx2, Klk10, Perp, Efna3, CcbH, Pard6b, Fam83c, Mpzl2, Map7, 2310002J15Rik, Tiaml, Slc6a20a, SytH, Rnf223, Ide, Calml3, Caszl, and Celsr2; wherein the Bmi1 metagene comprises genes selected from Bmi1, Klhdc2, Bbx, Tusc3, Glg1, Bloc1s6, Wdr34, 5730455P16Rik, Hs2st1, Terf2, Fut8, Zmym4, Pcm1, Zbtb25, Rock2, Mta1, Kif2a, Arhgap21, Galntl, Sept9, Tmem237, Akap11, Mecp2, Slc25a4, Hp1bp3, Synj2, Cnep1r1, Msi2, Akap11, Ing1, Nfic, Plekha3, Sestdl, DnajcIO, Tmem67, Zfhx3, Septi 0, Ccdc104, Tcf3, 2610301 B20Rik, Mib1, Tiam2, Cers2, Stk3, Hspa13, Txndc12, Dock7, Psmd5, Zfp639, Rnf2, Trappc6b, Ehmt2, Fxr1, Slc35b3, Vdac3, Spredl, Nf1, Phip, E2f5, Pias2, Dok1, Zc3h14, Prkd3, Gtl3, Cep120, Rab4a, Dpy19l1, Ilf3, Bbs4, Slc30a4, Inppd, Inf2, Zmynd11, Atp8b2, Gludl , Fam64a, Vdac3, Ttc26, Arl2, Zdhhc20, Trdmtl, Arfgap3, Mbtps2, Dnall, Uxs1, Cdc27, Abhd2, Rnf139, KifapS, Nphpl, Tmem55a, Snx4, Elp3, Hnrnpll, Gm13375, 2510003E04Rik, Teadl, Ptprs, and Kat7; wherein the Sox4 metagene comprises genes selected from Sox4, Abl1 , Rab34, Fgfrll , Ptovl, Zdhhc8, Klhdc2, Mex3d, Arfgap3, Ctxnl, Tcf3, Tcf12, Clip2, Bbx, Nf1, Spats2, Farpl, Cbfa2t2, Rab4a, Zfp9, Usp22, Rest, Ncs1 , Kif3c, Nlgn2, Smarcdl, Mras, Zswim8, Lrrc58, Rbfox2, Tmem9, Josdl, MicalH, L)bxn7, Mvb12b, Trio, Stonl, Dok1, Fam65a, Fmnl3, Hsf2, Sestdl, Frmd4a, Pcbp2, Kirrel, Kansl2, Ank, Ptprs, Rab33b, Axl, Pcbp4, Sept9, Gatad2b, Pias2, Plekha3, Cbfa2t2, St6gal1, Cep120, Rnf139, Dpy19l1, Dbn1, Ctps2, Magedl, Prkd3, Cttnbp2nl, Atp8b2, Fermt2, Bbs4, Phldbl, AI597468, Ttbk2, Adcy6, Zc3h7b, Sh3pxd2b, Rab12, Aaedl, Staid,Mecp2, Phf20, Pex11b, Ehmt2, Cep170, Fgfrl, Txndc5, Zmym4, Samd14, Kansl2, Teadl, Zkscan17, Arhgef2, Zmym3, Sfxn3, Pja2, Lzts2, Kdmla, Loxl3, Acvrl , Wwtrl , AsxH , and Phf2; wherein the Lrigl metagene comprises genes selected from Lrigl, Rgmb, Zcchc24, Teadl, Lambl, Cep170, Evalb, Sept9, Farpl, Satb2, Maplb, Ccdc88a, Axl, Loxl3, Pdgfra, list, Lgalsl, Kifap3, Myo9a, Gnb4, Kank2, Txndc5, Sema3a, Dock7, Zmym4, Atp8b2, Hsf2, Kirrel, Srgap2, Nfic, Lamcl, Ikbip, Gng2, Sema7a, Ryk, Tcf12, Clip2, Calu, Sdc2, Dennd2a, Dennd5a, Kdelc2, Cntln, Arhgef40, Sfxn3, Eml1 , Stx2, Lbh, Wipf 1 , Igfbp4, Myo9a, Cul7, Abl1 , Phf20, Xxyltl , Myo9a, Dok1 , Dst, Gkapl , Tspanl 1 , Phldbl , Sydel , Teadl , Rab34, Stxbpl , AI597468, St6gal1 , Ilk, Zeb1, Mxra7, Stard3nl, Ccdc66, Gamt, Gfra4, Zdhhc17, Aida, Synpo, Trim35, Ptovl, Ank, Displ, Fhl3, Fermt2, Cdr2, Dock5, Crabpl , S1 pr2, 4930503L19Rik, Ddr2, Zdhhc8, Gpr124, Pja2, Zfp639, Adcy7, Mras, Pcdh19, Ctdpl, Sdccag8, Gliprl, and Nnt; wherein the Lgr6 metagene comprises genes selected from Lgr6, Tnnt2, Cnnm4, Prss12, Sox9, Itga2, Shf, Igsf8, Itpr3, Nt5e, Bhlhe41, Fzd7, Krt18, Arid5a, Tgfbl, Tes, Raplgap, Add2, Sdc1 , Jam2, Gpr39, B4galnt1 , D8Ertd82e, Plekhg3, Lamc2, Socs2, Rampl , Etv6, Lamb3, Egr3, Dusp6, Foxpl, Dnaja4, Tnfrsf12a, Pip4k2c, Rnf181, Anol, A130010J15Rik, 1118r1 , Chst2, Jag1, 1600029D21 Rik, Tnfsf9, Src, Runxl , Rhbddl , Smad7, Itga6, Socs2, Slco2a1 , Aplp2, Cd9, Rail 4, Smurf 1, Nedd9, C1galt1, Pmepal, Padi3, Gpr25, Fermtl, Nav2, Arhgef3, Capnsl, Foxp4, Ubald2, Gm7367, Gm7367, Ctnnal, Cd80, Hivep2, Dyrk3, Rab6a, Runx2, Iqgapl, Ggct, Lrch4, Skil, Frrsl, Slc20a2, Ncmap, Reep3, Nadsynl, Bhlhe40, Gprc5a, Slc39a4, Hes6, Acsl3, Erc1, Lama5, Ephb4, Rmnd5b, Plekhal, Bcr, Zbtb18, Shq1, Scyl2, Padi4, Scin, Dhcr7, and AtplOd; and wherein the Sox9 metagene comprises genes selected from Sox9, Lgr6, Shf, Cnnm4, Runxl, Ctnnal, Capnsl, Rail 4, Itpr3, Runx2, Iqgapl, Bhlhe41, Rnf181 , Ccndl, Prss12, Tes, Aig1, Foxc2, Raplgap, Krt18, Rab6a, Etv6, Dusp6, Igsf8, Tubgcp2, Alcam, Sos2, Dusp4, Bzw2, Nck2, Add2, Foxpl, Ubald2, Tnnt2, Kcnn4, Fzd7, Reep3, Nav2, Cpe, Casp3, Cnot7, Cttn, Anol, Bcarl, Cyth2, Myof, Egr3, Nadsynl, Nt5e, Dnaja4, Plekhal, Capg, Phc2, Itga2, B4galnt1, Smurfl, Gtf2ird1, Pwwp2b, Phldal, Enppl, Nfat5, Cd151, Hivep2, Ppmel, Tgifl, Gm7367, Gm7367, Zbtb18, Sdc4, D630045J12Rik, Smad7, Slc20a2, Igf 1 r, Rsf1, Tnfrsf12a, Slc27a1, Chst2, 2810408A11 Rik, IgfbpS, Kdelrl, Ern1, Atxn2l,Dyrk3, Tgfbl, Bhlhe40, Phrfl, Tnfrsf22, Ddhdl, Traf4, A130010J15Rik, Papd7, Mast4, Skil, Pyroxdl, Fubp3, Nr1h2, Ctnnbl, Foxci, Tbc1d1, and 1810011O10Rik.

66. A composition comprising an RNA transcript of a gene selected from Sox2, Foxal , Krt15, Krt19, Pitxl, Klf5, Psca, Cd44, Prom1, Prom2, Bmi1, Sox4, Lrigl, Lgr6, and Sox9 for use in a method of diagnosing development of drug resistance of a cancer in response to treatment with a therapeutic agent.

67. The composition of any one of claims 64-66, wherein the cancer is a carcinoma.

68. The composition of claim 67, wherein the carcinoma is squamous cell carcinoma.

69. The composition of claim 68, wherein the squamous cell carcinoma is cutaneous squamous cell carcinoma cell.

Images