Non-genotoxic conditioning methods and compositions

Abstract

Compositions and methods for non-genotoxic monoclonal antibody (mAb) conditioning, where the methods involve altering a cluster of differentiation 38 (CD38) polynucleotide sequence in a hematopoietic stem cell (HSC) or progenitor thereof to encode a CD38 polypeptide with reduced binding to the antibody.

Description

[0001] ATTORNEY DOCKET NO. 180802-047501 / PCT

[0002] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0003] NON-GENOTOXIC CONDITIONING METHODS AND COMPOSITIONS

[0004] CROSS REFERENCE TO RELATED APPLICATIONS

[0005] The present application claims priority to U. S. Provisional Application No. 63 / 748,145 filed January 22, 2025, the entire contents of which are hereby incorporated by reference in its entirety.

[0006] SEQUENCE LISTING

[0007] This application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. The Sequence Listing XML file, created on January 21, 2026, is named 180802-047501PCT_SL.xml and is 1,083,076 bytes in size.

[0008] BACKGROUND

[0009] Busulfan is a DNA alkylating reagent that induces bone marrow immunosuppression and is widely used for conditioning prior to allogenic hematopoietic stem cell transplantation and administration of autologous cell therapies. While busulfan is the current standard of care for patients in need of allogenic or autologous transplants and engraftment of cell therapies, the use of this potent cytotoxic agent has associated risks including genotoxicity, primary or secondary malignancy, and organ toxicities including infertility. These risks present barriers to patients who would otherwise seek treatment. Accordingly, there is a need for improved methods for conditioning prior to allogeneic hematopoietic stem cell transplantation.

[0010] SUMMARY

[0011] As described below, the present disclosure features compositions and methods for non-genotoxic monoclonal antibody (mAb) conditioning, where the methods involve altering a cluster of differentiation 38 (CD38) polynucleotide sequence in a hematopoietic stem cell (HSC) or progenitor thereof to encode a CD38 polypeptide with reduced binding to the antibody.

[0012] In one aspect, the disclosure provides a method of altering a nucleobase of a cluster of differentiation 38 (CD38) polynucleotide. The method involves contacting the CD38 polynucleotide with a base editor system containing a base editor, or one or more polynucleotides encoding the base editor, and a guide RNA, or a polynucleotide encoding the guide RNA. The base editor contains a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain. The guide RNA directs the base editor to effectATTORNEY DOCKET NO. 180802-047501 / PCT

[0013] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0014] an alteration of the nucleobase of the CD38 polynucleotide to yield a CD38 polynucleotide variant encoding a CD38 polypeptide variant with reduced binding relative to a wild-type CD38 polypeptide to a polypeptide capable of binding to the wild-type CD38 polypeptide.

[0015] In another aspect, the present disclosure features a method for hematopoietic stem cell transplantation in a subject, the method comprising administering to the subject the engineered HSC of any aspect of the disclosure, or embodiments thereof, and a polypeptide selected from an Antibody A and an Antibody B polypeptide, a fragment of the Antibody A or Antibody B polypeptide, a variant of Antibody A or Antibody B, an immunoconjugate containing Antibody A, Antibody B, or a functional fragment thereof. The polypeptide is administered prior to, concurrent with, or subsequent to administration of the hematopoietic stem cell to the subject. In some embodiments, the method involves administering to the subject an scFv containing a fragment of Antibody A or Antibody B. In some embodiments, the method involves administering to the subject an antibody-drug conjugate containing Antibody A or Antibody B, or a functional fragment thereof.

[0016] In one aspect, the disclosure features a method of altering a nucleobase of a cluster of differentiation 38 (CD38) polynucleotide. The method involves contacting the CD38 polynucleotide with a base editor system containing a base editor, or one or more polynucleotides encoding the base editor, and a guide RNA, or a polynucleotide encoding the guide RNA. The base editor contains a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain. The guide RNA directs the base editor to effect an alteration of the nucleobase of the CD38 polynucleotide to yield a CD38 polynucleotide variant encoding a CD38 polypeptide variant with reduced binding relative to a wild-type CD38 polypeptide to a polypeptide capable of binding to the wild-type CD38 polypeptide. The CD38 polypeptide variant contains an amino acid substitution at a position selected from one or more of positions 76, 77, 78, 103, 104, 106, 107, 110, 111, 112, 114, 115, 116, 117, 120, 121, 139, 141, 142, 149, 150, 196, 201, 202, 203, 205, 231, 233, 234, 236, 237, 239, 241, 273, 274, 276, 284, 288, 292, and 296.

[0017] In another aspect, the disclosure features a cell prepared according to the method of any aspect of the disclosure, or embodiments thereof.

[0018] In another aspect, the disclosure features a method for cell transplantation in a subject. The method involves (a) contacting a cell with a base editor system containing a base editor, or one or more polynucleotides encoding the base editor, and a guide RNA, or a polynucleotide encoding the guide RNA. The base editor contains nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain. The guide RNA directs the base editor toATTORNEY DOCKET NO. 180802-047501 / PCT

[0019] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0020] effect an alteration of a nucleobase of a CD38 polynucleotide in the cell to yield a CD38 polynucleotide encoding a CD38 polypeptide variant containing an amino acid substitution at a position selected from one or more of positions 76, 77, 78, 103, 104, 106, 107, 110, 111, 112, 114, 115, 116, 117, 120, 121, 139, 141, 142, 149, 150, 196, 201, 202, 203, 205, 231, 233, 234, 236, 237, 239, 241, 273, 274, 276, 284, 288, 292, and 296, thereby producing an edited cell. The method further involves (c) administering the edited cell to the subject. The method also involves (d) administering to the subject an antibody, antibody drug conjugate, or chimeric antigen receptor expressing T cell (CAR-T) that selectively binds a wild-type version of CD38. The administering of step (d) is prior to, concurrent with, or subsequent to step (c).

[0021] In another aspect, the disclosure features a base editor system containing a base editor, or one or more polynucleotides encoding the base editor, and a guide RNA, or a polynucleotide encoding the guide RNA. The base editor contains a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain. The guide RNA directs the base editor to effect an alteration of the nucleobase of a CD38 polynucleotide to yield a CD38 polynucleotide variant, where the CD38 polypeptide variant contains an amino acid substitution at a position selected from one or more of positions 76, 77, 78, 103, 104, 106, 107, 110, 111, 112, 114, 115, 116, 117, 120, 121, 139, 141, 142, 149, 150, 196, 201, 202, 203, 205, 231, 233, 234, 236, 237, 239, 241, 273, 274, 276, 284, 288, 292, and 296.

[0022] In another aspect, the disclosure features a polynucleotide or set of polynucleotides encoding the base editor system of any aspect of the disclosure, or embodiments thereof.

[0023] In another aspect, the disclosure features a cell produced by introducing into a cell, or a progenitor thereof, the base editor system or the polynucleotide of any aspect of the disclosure, or embodiments thereof.

[0024] In another aspect, the disclosure features a guide RNA containing a spacer containing a nucleotide sequence selected from the spacer sequences listed in Table 1.

[0025] In another aspect, the disclosure features a pharmaceutical composition containing an effective amount of the polynucleotide or set of polynucleotides, the cell, or the guide polynucleotide of any aspect of the disclosure, or embodiments thereof, and a pharmaceutically acceptable excipient.

[0026] In another aspect, the disclosure features a method of treating a subject with an autoimmune disease, hemoglobinopathy, hematologic cancer, or myeloproliferative disease. The method involves administering to the subject the pharmaceutical composition of any aspect of the disclosure, or embodiments thereof.

[0027] In another aspect, the disclosure features a kit containing the polynucleotide or set ofATTORNEY DOCKET NO. 180802-047501 / PCT

[0028] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0029] polynucleotides, the cell, the guide polynucleotide, or the pharmaceutical composition of any aspect of the disclosure, or embodiments thereof, and a container.

[0030] In another aspect, the disclosure features a base editor system containing mRNA encoding a base editor, and a guide RNA. The base editor contains an SpCas9 nickase domain having protospacer-adjacent motif specificity for a PAM containing the nucleotide sequence NGG or NRCH, where “N” is A, C, T, or G, “R” is A or G, and “H” is A, C, or T, and a TadA*8 adenosine deaminase domain or a TadA*8.20 adenosine deaminase domain containing an F149Y amino acid substitution. The guide RNA contains a spacer containing a nucleotide sequence selected from the spacer sequences listed in Table 1.

[0031] In another aspect, the disclosure features a method for preparing a engineered hematopoietic stem cell (HSC). The method involves contacting an HSC with the base editor system of any aspect of the disclosure, or embodiments thereof, to effect an alteration in a CD38 polynucleotide in the cell, thereby producing an engineered HSC expressing a CD38 polypeptide variant containing an amino acid substitution(s) selected from one or more of: i) Q107R; ii) Q115R and T116A; iii) D141G and M142V; iv) E233G and K234G; v) L149P and L150P; vi) E76G, M77V, and R78G; vii) V203A; viii) T116A; ix) K234E; x) K234G; and xi) K234R.

[0032] In another aspect, the disclosure features a engineered HSC produced by the method of any aspect of the disclosure, or embodiments thereof.

[0033] In another aspect, the disclosure features a method for hematopoietic stem cell transplantation in a subject. The method involves administering to the subject the engineered HSC of any aspect of the disclosure, or embodiments thereof, and an antibody selected from Antibody A and Antibody B. The antibody is administered prior to, concurrent with, or subsequent to administration of the hematopoietic stem cell to the subject.

[0034] In any aspect of the disclosure, or embodiments thereof, the method involves altering two or more nucleobases of the CD38 polynucleotide.

[0035] In any aspect of the disclosure, or embodiments thereof, the CD38 polypeptide variant contains an amino acid substitution at a position selected from one or more of 76, 77, 78, 116, 141, and 142. In any aspect of the disclosure, or embodiments thereof, the amino acid substitution is selected from one or more of E76G, M77V, R78G, R78G, E103G, E104G, Y106C, Q107R, Q107R, M110V, K111G, K111R, L112S, T114A, T114A, Q115R, Q115R, T116A, T116A, V117A, N120D, N120G, N120G, N120G, N120S, K121E, K121G, Q139R, D141G, D141G, D141G, M142V, M142V, L149P, L149P, L150P, L150P, F196P, C201R, D202G, V203A, H205R, Q231R, Q231R, E233G, E233G, K234G, Q236R, Q236R, T237A, T237A, E239G, E239G, W241R, F273P, S274P, K276E, F284P, V288A, E292G, and C296R. InATTORNEY DOCKET NO. 180802-047501 / PCT

[0036] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0037] any aspect of the disclosure, or embodiments thereof, the CD38 polypeptide variant contains an amino acid substitution(s) selected from one or more of: i) Q107R; ii) Q115R and T116A; iii) D141G and M142V; iv) E233G and K234G; v) L149P and L150P; vi) E76G, M77V, and R78G; vii) V203A; viii) T116A; ix) K234E; x) K234G; and xi) K234R.

[0038] In any aspect of the disclosure, or embodiments thereof, the deaminase domain is an adenosine deaminase domain. In any aspect of the disclosure, or embodiments thereof, the adenosine deaminase domain is a TadA*8.8 polypeptide or a TadA*8.20 polypeptide. In any aspect of the disclosure, or embodiments thereof, the TadA*8.20 polypeptide contains an F149Y amino acid substitution.

[0039] In any aspect of the disclosure, or embodiments thereof, the napDNAbp domain is a nickase. In any aspect of the disclosure, or embodiments thereof, napDNAbp domain is a Cas9 domain. In any aspect of the disclosure, or embodiments thereof, the Cas9 domain is a Streptococcus pyogenes Cas9 (SpCas9), or a variant thereof. In any aspect of the disclosure, or embodiments thereof, the SpCas9 variant has protospacer-adjacent motif (PAM) specificity for a PAM containing the nucleotide sequence NRCH, where “N” is A, C, T, or G, “R” is A or G, and “FT is A, C, or T. In any aspect of the disclosure, or embodiments thereof, the SpCas9 contains the amino acid alterations I322V, S409I, E427G, R654L, R753G, R1114G, D1135N, E1219V, D1332N, R1335Q, T1337N, S1338T, and H1349R referenced to SEQ ID NO: 197.

[0040] In any aspect of the disclosure, or embodiments thereof, the guide RNA contains a spacer, where the spacer contains a nucleotide sequence selected from the spacer sequences listed in Table 1. In any aspect of the disclosure, or embodiments thereof, the spacer contains a nucleotide sequence selected from one or more of: ACCACAUCACAGGCAGCUUC (SEQ ID NO: 796; gRNA9234), UAUCAGCCACUAAUGAAGUU (SEQ ID NO: 728; gRNA9239), UCAGACCGUACCUUGCAACA (SEQ ID NO: 730; gRNA9240), GCGGGACAUGUUCACCCUGG (SEQ ID NO: 740; gRNA9245), AGAGAAGGUUCAGACACUAG (SEQ ID NO: 744; gRNA9247), AGCCUAGCAGCGUGUCCUCC (SEQ ID No: 756; gRNA9253), GCCUAGCAGCGUGUCCUCCA (SEQ ID NO: 758; gRNA9254), and CUGAGAUGAGGUGGGUUGGC (SEQ ID NO: 760; gRNA9255). In any aspect of the disclosure, or embodiments thereof, the guide RNA contains a gRNA sequence listed in Table 1.

[0041] In any aspect of the disclosure, or embodiments thereof, the polypeptide capable of binding to the wild-type CD38 polypeptide is an antibody. In any aspect of the disclosure, or embodiments thereof, the antibody is Antibody A or Antibody B.

[0042] In any aspect of the disclosure, or embodiments thereof, the CD38 polynucleotide is in a cell. In any aspect of the disclosure, or embodiments thereof, the cell is a hematopoietic stemATTORNEY DOCKET NO. 180802-047501 / PCT

[0043] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0044] cell. In any aspect of the disclosure, or embodiments thereof, the hematopoietic stem cell is from a subject having a disease or disorder amenable to treatment using hematopoietic stem cell transplant therapy.

[0045] In any aspect of the disclosure, or embodiments thereof, the cell is from the subject. In any aspect of the disclosure, or embodiments thereof, the subject has a disease selected from an autoimmune disease, hemoglobinopathy, hematologic cancer, or myeloproliferative disease and the edited cell is administered to the subject to treat the disease. In any aspect of the disclosure, or embodiments thereof, the subject has a disease selected from one or more of acute myeloid leukemia, acute lymphoid leukemia, amyloid light-chain (AL) amyloidosis, B-cell acute lymphoblastic leukemia (B-ALL), aplastic anemia, chronic myeloid leukemia, chronic lymphoid leukemia, diffuse large B-cell lymphoma, Fanconi anemia, lupus, multiple myeloma, a myelodysplastic syndrome, non-Hodgkin's lymphoma, rheumatoid arthritis, sickle cell anemia, T-cell acute lymphoblastic leukemia (T-ALL), thalassemia, and Wiskott-Aldrich syndrome and the edited cell is administered to the subject to treat the disease.

[0046] In any aspect of the disclosure, or embodiments thereof, the cell is a hematopoietic stem cell, common myeloid progenitor, proerythroblast, or erythroblast.

[0047] In any aspect of the disclosure, or embodiments thereof, the base editor contains two adenosine deaminase domains. In any aspect of the disclosure, or embodiments thereof, one of the two adenosine deaminase domains is a wild-type TadA.

[0048] In any aspect of the disclosure, or embodiments thereof, the base editor contains an amino acid sequence with at least 95% identity to a sequence selected from:

[0049] MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALR QGGLVMQNYRL IDATL YVTFE PCVMCAGAM IHSR I GRVVFGVRNAKTGAAGS LMDVLHHPGMNH RVEITEGILADECAALLCRFFRMPRRVFNAQKKAQSSTDSGGSSGGSSGSETPGTSESATPESS GGSSGGSDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGET AEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNI VDE VAYHEKYPT I YHLRKKLVDSTDKADLRL I YLALAHM I KFRGHFL I EGDLNPDNSDVDKLF I QLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTP NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITK APLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKP ILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEK ILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEK VLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFK KIECFDSVEISGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEE RLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHATTORNEY DOCKET NO. 180802-047501 / PCT

[0050] ELECTRONIC DEPOSIT DATE: January 21, 2026 DDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIE MARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQ ELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAK L I TQRKFDNLTKAERGGLS ELDKAGF I KRQLVETRQ I TKHVAQ I LDSRMNTKYDENDKL I RE VK VITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDV RKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFAT VRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVV AKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFELENGR KRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEI IEQIS EFSKRVILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTS TKEVLDATLIHQSITGLYETRIDLSQLGGD (SEQ ID NO: 807); and MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALR QGGLVMQNYRL YDATL YSTFE PCVMCAGAM IHSR I GRVVFGVRNAKTGAAGS LMDVLHHPGMNH RVEITEGILADECAALLCRFYRMPRRVFNAQKKAQSSTDSGGSSGGSSGSETPGTSESATPESS GGSSGGSDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGET AEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNI VDE VAYHEKYPT I YHLRKKLVDSTDKADLRL I YLALAHM I KFRGHFL I EGDLNPDNSDVDKLF I QLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTP NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITK APLSASMVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKP ILEKMDGTEELLVKLNREDLLRKQRTFDNGI IPHQIHLGELHAILRRQGDFYPFLKDNREKIEK ILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEK VLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFK KIECFDSVEISGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEE RLKTYAHLFDDKVMKQLKRLRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIH DDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGGHKPENIVIE MARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQ ELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAK L I TQRKFDNLTKAERGGLS ELDKAGF I KRQLVETRQ I TKHVAQ I LDSRMNTKYDENDKL I RE VK VITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDV RKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFAT VRKVLSMPQVNIVKKTEVQTGGFSKESILPKGNSDKLIARKKDWDPKKYGGFNSPTVAYSVLVV AKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFELENGR KRMLASAGVLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEI IEQIS EFSKRVILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTINRKQYNTATTORNEY DOCKET NO. 180802-047501 / PCT

[0051] ELECTRONIC DEPOSIT DATE: January 21, 2026 TKEVLDATLIRQSITGLYETRIDLSQLGGDEGADKRTADGSEFESPKKKRKV (SEQ ID NO: 808).

[0052] In any aspect of the disclosure, or embodiments thereof, the CD38 polypeptide variant contains an amino acid substitution selected from the group consisting of E76G, M77V, R78G, T116A, D141G, and M142V.

[0053] In any aspect provided herein, or embodiments thereof, the method is not a process for modifying the germline genetic identity of human beings.

[0054] Definitions

[0055] Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this disclosure belongs. The following references provide one of skill with a general definition of many of the terms used in this disclosure: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them below, unless specified otherwise.

[0056] By “Antibody A polypeptide” is meant an antibody having at least about 85% amino acid sequence identity to an antibody sequence of Antibody A or comprising VH and / or VL CDRs 1-3 of Antibody A or antigen binding fragments thereof, wherein each of the antibody, CDRs, and antigen binding fragments specifically bind to a wild type CD38 polypeptide but fail to detectably bind or have only reduced binding to an altered CD38 polypeptide. In embodiments, the antibody or antigen binding fragment thereof has at least 90%, 93%, 95%, 98%, 99% or 100% amino acid sequence identity to an antibody sequence of Antibody A. Exemplary heavy chain and light chain sequences for Antibody A are provided below, where the variable regions are in plain text, the constant domains are in bold, and complementarity determining regions (CDRs), i.e., CDR1, CDR2, and CDR2, are underlined:

[0057] Antibody A heavy chain (HC):

[0058] EVQLLESGGGLVQPGGSLRLSCAVSGFTFNSFAMSWVRQAPGKGLEWVSAISGSGGGTYYADSV KGRFT I SRDNS KNTL YLQMNS LRAEDTAVYFCAKDKI LWFGE PVFD YWGQGTLVTVS SASTKGP SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSWT VPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTL MISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRWSVLTVLHQDWLN GKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVATTORNEY DOCKET NO. 180802-047501 / PCT

[0059] ELECTRONIC DEPOSIT DATE: January 21, 2026 EWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL SPGK (SEQ ID NO: 687)

[0060] Antibody A light chain (LC):

[0061] E I VLTQS PATLS LS PGERATLS CRASQSVSSYLAWYQQKPGQAPRLL I YDASNRATG I PARFSG SGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSG TASWCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVY ACEVTHQGLSSPVTKSFNRGEC (SEQ ID NO: 688).

[0062] The three CDRs of the Antibody A VH region are as follows:

[0063] VH CDR1: S FAMS (SEQ ID NO: 689);

[0064] VH CDR2: AISGSGGGTYYADSVKG (SEQ ID NO: 690); and

[0065] VH CDR3: DKILWFGEPVFDY (SEQ ID NO: 691).

[0066] The three CDRs of the Antibody A VL region are as follows:

[0067] VL CDR1: RASQSVSSYLA (SEQ ID NO: 692);

[0068] VL CDR2: DASNRAT (SEQ ID NO: 693); and

[0069] VL CDR3: QQRSNWPPT (SEQ ID NO: 694).

[0070] The four framework (FR) regions, i.e., FR1, FR2, FR3, and FR4, of Antibody A are located on either side of each of the CDRs in VH and VL region sequences shown supra. In particular, the four FRs of the Antibody A VH region are as follows:

[0071] VHFR1: EVQLLESGGGLVQPGGSLRLSCAVSGFTFN (SEQ ID NO: 695);

[0072] VH FR2: WVRQAPGKGLEWVS (SEQ ID NO: 696);

[0073] VHFR3: RFTISRDNSKNTLYLQMNSLRAEDTAVYFCAK (SEQ ID NO: 697); and VH FR4: WGQGTLVTVSS (SEQ ID NO: 698).

[0074] The four FRs of the Antibody A VL region are as follows:

[0075] VL FR1: EIVLTQSPATLSLSPGERATLSC (SEQ ID NO: 699);

[0076] VL FR2: WYQQKPGQAPRLLIY (SEQ ID NO: 700);

[0077] VL FR3: GIPARFSGSGSGTDFTLTISSLEPEDFAVYYC (SEQ ID NO: 701); and VL FR4: FGQGTKVEIKRTV (SEQ ID NO: 702).

[0078] By “Antibody A polynucleotide” is meant a nucleic acid molecule (e.g., DNA) encoding at least a fragment of Antibody A. In an embodiment, the encoded fragment has antigen binding activity.

[0079] By “Antibody B polypeptide” is meant an antibody having at least about 85% amino acid sequence identity to an antibody sequence of Antibody B or comprising VH and / or VL CDRs 1-3 of Antibody B or antigen binding fragments thereof, wherein each of the antibody, CDRs, and antigen binding fragments specifically bind to a wild type CD38 polypeptide but fail toATTORNEY DOCKET NO. 180802-047501 / PCT

[0080] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0081] detectably bind or have only reduced binding to an altered CD38 polypeptide. In embodiments, the antibody or antigen binding fragment thereof has at least 90%, 93%, 95%, 98%, 99% or 100% amino acid sequence identity to an antibody sequence of Antibody B. Exemplary heavy chain and light chain sequences for Antibody B are provided below, where the variable regions are in plain text, the constant domains are in bold, and complementarity determining regions (CDRs), i.e., CDR1, CDR2, and CDR2, are underlined:

[0082] Antibody B heavy chain (HC):

[0083] Q VQLVQSGAE VAKPGTS VKLS CKASGYTFTD YWMQWVKQRPGQGLEW I GT I YPGDGDTGYAQKF QGKATLTADKS S KTVYMHLS S LAS EDS AVYYCARGD YYGSNS LD YWGQGTS VTVS SASTKGP SV FPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSWTVP SSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMI SRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRWSVLTVLHQDWLNGK EYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEW ESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSP GK (SEQ ID NO: 703)

[0084] Antibody B light chain (LC):

[0085] DIVMTQSHLSMSTSLGDPVSITCKASQDVSTVVAWYQQKPGQSPRRLIYSASYRYIGVPDRFTG SGAGTDFTFTISSVQAEDLAVYYCQQHYSPPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSG TASWCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVY ACEVTHQGLSSPVTKSFNRGEC (SEQ ID NO: 704).

[0086] The three CDRs of the Antibody B VH region are as follows:

[0087] VH CDR1: DYWMQ (SEQ ID NO: 705);

[0088] VH CDR2: TIYPGDGDTGYAQKFQG (SEQ ID NO: 706); and

[0089] VH CDR3: GDYYGSNSLDY (SEQ ID NO: 707).

[0090] The three CDRs of the Antibody B VL region are as follows:

[0091] VL CDR1: KASQDVSTVVA (SEQ ID NO: 708);

[0092] VL CDR2: SASYRYI (SEQ ID NO: 709); and

[0093] VL CDR3: QQHYSPPYT (SEQ ID NO: 710).

[0094] The four framework (FR) regions, i.e., FR1, FR2, FR3, and FR4, of Antibody B are located on either side of each of the CDRs in VH and VL region sequences shown supra. In particular, the four FRs of the Antibody B VH region are as follows:

[0095] VH FR1: QVQLVQSGAEVAKPGTSVKLSCKASGYTFT (SEQ ID NO: 711);

[0096] VH FR2: WVKQRPGQGLEWIG (SEQ ID NO: 712);

[0097] VHFR3: KATLTADKSS KTVYMHLS S LAS EDS AVYYCAR (SEQ ID NO: 713); andATTORNEY DOCKET NO. 180802-047501 / PCT

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[0099] VH FR4: WGQGTSVTVSS (SEQ ID NO: 714).

[0100] The four FRs of the Antibody B VL region are as follows:

[0101] VL FR1: DIVMTQSHLSMSTSLGDPVSITC (SEQ ID NO: 715);

[0102] VL FR2: WYQQKPGQSPRRLIY (SEQ ID NO: 716);

[0103] VL FR3: GVPDRFTGSGAGTDFTFTISSVQAEDLAVYYC (SEQ ID NO: 717); and VL FR4: FGGGTKLEIKRTV (SEQ ID NO: 718).

[0104] By “Antibody B polynucleotide” is meant a nucleic acid molecule (e.g., DNA) encoding at least a fragment of Antibody B. In an embodiment, the encoded fragment has antigen binding activity.

[0105] By “adenine” or “ 9H-Purin-6-amine” is meant a purine nucleobase with the molecular

[0106]

[0107] formula C5H5N5, having the structure, and corresponding to CAS No. 73-24-5.

[0108] By “adenosine” or “ 4-Amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2(1H)-one” is meant an adenine molecule attached to a

[0109] NH2

[0110]

[0111] ribose sugar via a glycosidic bond, having the structure OH OH, and corresponding to CAS No. 65-46-3. Its molecular formula is C10H13N5O4.

[0112] By “adenosine deaminase” or “adenine deaminase” is meant a polypeptide or fragment thereof capable of catalyzing the hydrolytic deamination of adenine or adenosine. In some embodiments, the deaminase or deaminase domain is an adenosine deaminase catalyzing the hydrolytic deamination of adenosine to inosine or deoxy adenosine to deoxyinosine. In some embodiments, the adenosine deaminase catalyzes the hydrolytic deamination of adenine or adenosine in deoxyribonucleic acid (DNA). The adenosine deaminases (e.g., engineered adenosine deaminases, evolved adenosine deaminases) provided herein may be from any organism (e.g., eukaryotic, prokaryotic), including but not limited to algae, bacteria, fungi,ATTORNEY DOCKET NO. 180802-047501 / PCT

[0113] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0114] plants, invertebrates (e.g., insects), and vertebrates (e.g., amphibians, mammals). In some embodiments, the adenosine deaminase is an adenosine deaminase variant with one or more alterations and is capable of deaminating both adenine and cytosine in a target polynucleotide e.g., DNA, RNA) and may be referred to as a “dual deaminase”. Non-limiting examples of dual deaminases include those described in PCT / US22 / 22050. In some embodiments, the target polynucleotide is single or double stranded. In some embodiments, the adenosine deaminase variant is capable of deaminating both adenine and cytosine in DNA. In some embodiments, the adenosine deaminase variant is capable of deaminating both adenine and cytosine in singlestranded DNA. In some embodiments, the adenosine deaminase variant is capable of deaminating both adenine and cytosine in RNA. In embodiments, the adenosine deaminase variant is selected from those described in PCT / US2020 / 018192, PCT / US2020 / 049975, PCT / US2017 / 045381, PCT / US2021 / 016827, PCT / US2022 / 073781, PCT / US24 / 34189, or PCT / US2020 / 028568, the full contents of which are each incorporated herein by reference in their entireties for all purposes. Further non-limiting examples of adenosine deaminases include those disclosed or referenced in Rufflow, et al., “Design of highly functional genome editors by modeling of the universe of CRISPR-Cas Sequences,” bioRxiv, posted April 22, 2024, doi: 10.1101 / 2024.04.22.590591, the disclosure of which is incorporated herein by reference in its entirety for all purposes, which were designed using artificial intelligence. Further exemplary adenosine deaminase amino acid sequenes include: TadA-8e (SEQ ID NO: 470), Tadl (SEQ ID NO: 471), Tad2 (SEQ ID NO: 472), Tad3 (SEQ ID NO: 473), Tad4 (SEQ ID NO: 474), Tad6 (SEQ ID NO: 475), Tad6-SR (SEQ ID NO: 476), TadA9 (SEQ ID NO: 477), TadA20 (SEQ ID NO: 478), Staphylococcus aureus Tad A (SEQ ID NO: 479), Bacillus subtilis Tad A (SEQ ID NO: 480), Salmonella typhimurium TadA (SEQ ID NO: 481), Shewanella putrefaciens (SEQ ID NO: 482), Haemophilus influenzae F3031 TadA (SEQ ID NO: 483), Caulobacter crescentus TadA (SEQ ID NO: 484), Geobacter sulfurreducens TadA (SEQ ID NO: 485), Streptococcus pyogenes TadA (SEQ ID NO: 486), Aquifex aeolicus TadA (SEQ ID NO: 487), and E. coll TadA deaminase (ecTadA) (SEQ ID NO: 488).

[0115] By “adenosine deaminase activity” is meant catalyzing the deamination of adenine or adenosine to guanine in a polynucleotide.

[0116] By “Adenosine Base Editor (ABE)” is meant a base editor comprising an adenosine deaminase.

[0117] By “Adenosine Base Editor (ABE) polynucleotide” is meant a polynucleotide encoding an ABE.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0118] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0119] By “Adenosine Base Editor 8 (ABE8) polypeptide” or “ABE8” is meant a base editor as defined herein comprising an adenosine deaminase or adenosine deaminase variant comprising one or more of the alterations listed in Table 5B, one of the combinations of alterations listed in Table 5B, or an alteration at one or more of the amino acid positions listed in Table 5B, where such alterations are relative to the following reference sequence:

[0120] MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALR QGGLVMQNYRL IDATL YVTFE PCVMCAGAM IHSR I GRVVFGVRNAKTGAAGS LMDVLHYPGMNH RVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO: 1), or a corresponding position in another adenosine deaminase. In embodiments, ABE8 comprises alterations at amino acids 82 and / or 166 of SEQ ID NO: 1. In some embodiments, ABE8 comprises further alterations, as described herein, relative to the reference sequence.

[0121] By “Adenosine Base Editor 8 (ABE8) polynucleotide” is meant a polynucleotide encoding an ABE8 polypeptide.

[0122] By “TadA*8.8 polypeptide” is meant an adenosine deaminase comprising an amino acid sequence with at least 85% identity to the following amino acid sequence MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALR QGGLVMQNYRL IDATL YVTFE PCVMCAGAM IHSR I GRVVFGVRNAKTGAAGS LMDVLHYPGMNH RVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO: 1) and comprising the following amino acid alterations referenced to SEQ ID NO: 1: Y123H, Y147R, and Q154R, or a functional fragment thereof. In some embodiments, the TadA*8.8 polypeptide lacks an N-terminal methionine. In some embodiments, the TadA*8.8 polypeptide comprises alterations, as described herein. By “ABE8.8” is meant a base editor as defined herein comprising a TadA*8.8 polypeptide.

[0123] By “TadA*8.8 polynucleotide” is meant a polynucleotide encoding a TadA*8.8 polypeptide.

[0124] By “TadA*8.20 polypeptide” is meant an adenosine deaminase comprising an amino acid sequence with at least 85% identity to the following amino acid sequence MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALR QGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVLHYPGMNH RVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO: 1) and comprising the following amino acid alterations referenced to SEQ ID NO: 1: I76Y, V82S, Y123H, Y147R, and Q154R, or a functional fragment thereof. In some embodiments, the TadA*8.20 polypeptide lacks an N-terminal methionine. In some embodiments, a TadA*8.20 polypeptide further comprises a F149Y alteration relative to SEQ ID NO: 1. In some embodiments, the TadA*8.20ATTORNEY DOCKET NO. 180802-047501 / PCT

[0125] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0126] polypeptide comprises alterations, as described herein. By “ABE8.20” is meant a base editor as defined herein comprising a TadA*8.20 polypeptide. By “ABE8.20 (F149Y)” is meant a base editor as defined herein comprising a TadA*8.20 polypeptide with a F149Y amino acid alteration.

[0127] By “TadA*8.20 polynucleotide” is meant a polynucleotide encoding a TadA*8.20 polypeptide.

[0128] “Administering” is referred to herein as providing one or more compositions described herein to a patient or a subject. By way of example and without limitation, composition administration (e.g., injection) can be performed by intravenous (i.v.) injection, sub-cutaneous (s.c.) injection, intradermal (i.d.) injection, intraperitoneal (i.p.) injection, or intramuscular (i.m.) injection. One or more such routes can be employed. Parenteral administration can be, for example, by bolus injection or by gradual perfusion over time. In some embodiments, parenteral administration includes infusing or injecting intravascularly, intravenously, intramuscularly, intraarterially, intrathecally, intratumorally, intradermally, intraperitoneally, transtracheally, subcutaneously, subcuticularly, intraarticularly, subcapsularly, subarachnoidly and intrasternally. Alternatively, or concurrently, administration can be by the oral route.

[0129] By “agent” is meant any small molecule chemical compound, antibody, nucleic acid molecule, polypeptide, or functional fragments thereof. Non-limiting examples of agents include base editor systems, cells modified according to methods of the disclosure, guide polynucleotides, base editors, polynucleotides encoding one or more components of a base editor system, and antibodies.

[0130] By “alteration” is meant a change in the level, structure, or activity of an analyte, gene or polypeptide as detected by standard art known methods such as those described herein. As used herein, an alteration includes a change (e.g., increase or reduction) in expression levels. In embodiments, the increase or reduction in expression levels is by 10%, 25%, 40%, 50% or greater. In some embodiments, an alteration includes an insertion, deletion, or substitution of a nucleobase or amino acid (by, e.g., genetic engineering).

[0131] By “ameliorate” is meant reduce, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.

[0132] By “analog” is meant a molecule that is not identical but has analogous functional or structural features. For example, a polypeptide analog retains the biological activity of a corresponding naturally-occurring polypeptide, while having certain biochemical modifications that enhance the analog’s function relative to a naturally occurring polypeptide. Such biochemical modifications could increase the analog’s protease resistance, membraneATTORNEY DOCKET NO. 180802-047501 / PCT

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[0134] permeability, or half-life, without altering, for example, ligand binding. An analog may include an unnatural amino acid.

[0135] As used herein, the term “antibody” refers to an immunoglobulin molecule that specifically binds to, or is immunologically reactive with, a particular antigen, and includes polyclonal, monoclonal, genetically engineered, and otherwise modified forms of antibodies, including but not limited to chimeric antibodies, humanized antibodies, heteroconjugate antibodies (e.g., bi- tri- and quad-specific antibodies, diabodies, triabodies, and tetrabodies), and antigen binding fragments of antibodies, including, for example, Fab’, F(ab’)2, Fab, Fv, rlgG, and scFv fragments. Further non-limiting examples of antibodies include VHH domains. Unless otherwise indicated, the term “monoclonal antibody” (mAb) is meant to include both intact molecules, as well as antibody fragments (including, for example, Fab and F(ab’)2 fragments) that are capable of specifically binding to a target protein. As used herein, the Fab and F(ab’)2 fragments refer to antibody fragments that lack the Fc fragment of an intact antibody.

[0136] Antibodies (immunoglobulins) comprise two heavy chains linked together by disulfide bonds, and two light chains, with each light chain being linked to a respective heavy chain by disulfide bonds in a " Y" shaped configuration. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains (CH). Each light chain has a variable domain (VL) at one end and a constant domain (CL) at its other end. The variable domain of the light chain (VL) is aligned with the variable domain of the heavy chain (VL), and the light chain constant domain (CL) is aligned with the first constant domain of the heavy chain (CHI). The variable domains of each pair of light and heavy chains form the antigen binding site. The isotype of the heavy chain (gamma, alpha, delta, epsilon or mu) determines the immunoglobulin class (IgG, IgA, IgD, IgE or IgM, respectively). The light chain is either of two isotypes (kappa (K) or lambda (1)) found in all antibody classes. The terms "antibody" or "antibodies" include intact antibodies, such as polyclonal antibodies or monoclonal antibodies (mAbs), as well as proteolytic portions or fragments thereof, such as the Fab or F(ab')2 fragments, that are capable of specifically binding to a target protein. Antibodies may include chimeric antibodies, recombinant and engineered antibodies, and antigen binding fragments thereof. Exemplary functional antibody fragments comprising whole or essentially whole variable regions of both the light and heavy chains are defined as follows: (i) Fv, defined as a genetically engineered fragment consisting of the variable region of the light chain and the variable region of the heavy chain expressed as two chains; (ii) single-chain Fv (“scFv”), a genetically engineered singlechain molecule including the variable region of the light chain and the variable region of the heavy chain, linked by a suitable polypeptide linker; (iii) Fab, a fragment of an antibodyATTORNEY DOCKET NO. 180802-047501 / PCT

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[0138] molecule containing a monovalent antigen-binding portion of an antibody molecule, obtained by treating an intact antibody with the enzyme papain to yield the intact light chain and the Fd fragment of the heavy chain, which consists of the variable and CHI domains thereof; (iv) Fab', a fragment of an antibody molecule containing a monovalent antigen-binding portion of an antibody molecule, obtained by treating an intact antibody with the enzyme pepsin, followed by reduction (two Fab' fragments are generated per antibody molecule); and (v) F(ab')2, a fragment of an antibody molecule containing a monovalent antigen-binding portion of an antibody molecule, obtained by treating an intact antibody with the enzyme pepsin (i.e., a dimer of Fab' fragments held together by two disulfide bonds).

[0139] The term “antigen-binding fragment,” as used herein, refers to one or more portions or fragments of an antibody that retain the ability to specifically bind to a target antigen. In an embodiment, the target antigen is a wild-type CD38 polypeptide or peptide. The antigen-binding function of an antibody can be performed by fragments of a full-length antibody. The antibody fragments can be a Fab, F(ab')2, scFv, SMIP, diabody, a triabody, an affibody, a nanobody, an aptamer, or a domain antibody. Examples of binding fragments encompassed by the term "antigen-binding fragment" of an antibody include, but are not limited to: (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL, and Cm domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and Cm domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb including VH and VL domains; (vi) a dAb fragment (Ward et al., Nature 341:544-546, 1989), which consists of a VH domain; (vii) a dAb which consists of a VH or a VL domain; (viii) an isolated complementarity determining region (CDR); and (ix) a combination of two or more isolated CDRs which may optionally be joined by a synthetic linker. Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single-chain Fv (scFv); see, e.g., Bird et al., Science 242:423-426, 1988, and Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883, 1988). Such antibody fragments can be obtained using conventional techniques known to those of skill in the art, and the fragments can be screened for utility in the same manner as intact antibodies.

[0140] Antigen-binding fragments can be produced by recombinant DNA techniques, enzymatic or chemical cleavage of intact immunoglobulins, or, in some cases, by chemical peptide synthesis procedures known in the art. In some embodiments, antigen-binding fragments (e.g., Fab',ATTORNEY DOCKET NO. 180802-047501 / PCT

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[0142] F(ab')2, Fab, scFab, Fv, rlgG, and scFv fragments) of an anti-CD38 antibody, which are joined by a synthetic linker, are encompassed herein.

[0143] By “base editor (BE),” or “nucleobase editor polypeptide (NBE)” is meant an agent that binds a polynucleotide and has nucleobase modifying activity. In various embodiments, the base editor comprises a nucleobase modifying polypeptide (e.g., a deaminase) and a polynucleotide programmable nucleotide binding domain (e.g., Cas9 or Cpfl). Representative nucleic acid and protein sequences of base editors include those sequences having about or at least about 85% sequence identity to any base editor sequence provided in the sequence listing, such as those corresponding to SEQ ID NOs: 2-11.

[0144] By “BE4 cytidine deaminase (BE4) polypeptide,” is meant a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) domain, a cytidine deaminase domain, and two uracil glycosylase inhibitor domains (UGIs). In embodiments, the napDNAbp domain is a Cas9n (D10A) polypeptide. Non-limiting examples of cytidine deaminase domains include rAPOBEC, ppAPOBEC, RrA3F, AmAPOBECl, and SsAPOBEC3B.

[0145] By “BE4 cytidine deaminase (BE4) polynucleotide,” is meant a polynucleotide encoding a BE4 polypeptide.

[0146] By “base editing activity” is meant acting to chemically alter a base within a polynucleotide. In one embodiment, a first base is converted to a second base. In one embodiment, the base editing activity is cytidine deaminase activity, e.g., converting target OG to T»A. In another embodiment, the base editing activity is adenosine or adenine deaminase activity, e.g., converting A•T to G•C.

[0147] By “base editing efficiency” is meant the total percent of one or more target bases in a sample that have been modified using a base editor. In some cases, the base editing efficiency is calculated as the total percent of target polynucleotides in a sample containing a modified target base. In some instances, the base editing efficiency is calculated as the total percent of target polynucleotides in a sample containing a modification to one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9 or 10) of 2, 3, 4, 5, 6, 7, 8, 9, or 10 target bases. Methods for measuring base editing efficiency for a base editor are known in the art (see, e.g., Gaudelli, etal. Nature 551:464-471 (2017), the disclosure of which is incorporated herein in its entirety for all purposes). In some cases, a base editing efficiency is a median base editing efficiency calculated across 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or more target sites.

[0148] By “base editing window” for a base editor is meant bases within a target polynucleotide sequence that can be modified using the base editor. In some embodiments, the position of the nucleobases in the target polynucleotide sequence are numbered relative to a protospacerATTORNEY DOCKET NO. 180802-047501 / PCT

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[0150] adjacent motif (PAM) for which a nucleic acid programmable DNA binding protein (napDNAbp) domain of the base editor has specificity, where base 1 corresponds to the base immediately adjacent to the PAM. In some embodiments, the position of the nucleobases in the target polynucleotide sequence are numbered relative to the 5' or 3' end of a spacer of a guide polynucleotide used to guide a nucleic acid programmable DNA binding protein (napDNAbp) domain of the base editor to a target site, where base 1 corresponds to the 5' or 3' terminal base of the spacer. The term “base editor system” refers to an intermolecular complex for editing a nucleobase of a target nucleotide sequence. In various embodiments, the base editor (BE) system comprises (1) a polynucleotide programmable nucleotide binding domain, a deaminase domain e.g., cytidine deaminase or adenosine deaminase) for deaminating nucleobases in the target nucleotide sequence; and (2) one or more guide polynucleotides (e.g., guide RNA) in conjunction with the polynucleotide programmable nucleotide binding domain. In various embodiments, the base editor (BE) system comprises a nucleobase editor domain selected from an adenosine deaminase or a cytidine deaminase, and a domain having nucleic acid sequence specific binding activity. In some embodiments, the base editor system comprises (1) a base editor (BE) comprising a polynucleotide programmable DNA binding domain and a deaminase domain for deaminating one or more nucleobases in a target nucleotide sequence; and (2) one or more guide RNAs in conjunction with the polynucleotide programmable DNA binding domain. In some embodiments, the polynucleotide programmable nucleotide binding domain is a polynucleotide programmable DNA binding domain. In some embodiments, the base editor is a cytidine base editor (CBE). In some embodiments, the base editor is an adenine or adenosine base editor (ABE). In some embodiments, the base editor is an adenine or adenosine base editor (ABE) or a cytidine or cytosine base editor (CBE). In some embodiments, the base editor system (e.g., a base editor system comprising a cytidine deaminase) comprises a uracil glycosylase inhibitor or other agent or peptide (e.g., a uracil stabilizing protein such as provided in W02022015969, the disclosure of which is incorporated herein by reference in its entirety for all purposes) that inhibits the inosine base excision repair system.

[0151] A “CD38-binding polypeptide” refers to a polypeptide, or an antigen binding portion or fragment thereof, that has specificity for and specifically binds to a wild-type CD38 polypeptide. In an embodiment, a binding polypeptide is an anti-CD38 antibody or immunoglobulin, or an antigen binding portion or fragment thereof.

[0152] The term “Cas9” or “Cas9 domain” refers to an RNA guided nuclease comprising a Cas9 protein, or a fragment thereof (e.g., a protein comprising an active, inactive, or partially active DNA cleavage domain of Cas9, and / or the gRNA binding domain of Cas9). A Cas9 nuclease isATTORNEY DOCKET NO. 180802-047501 / PCT

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[0154] also referred to sometimes as a casnl nuclease or a CRISPR (clustered regularly interspaced short palindromic repeat) associated nuclease.

[0155] As used herein, the term “complementarity determining region (CDR)” refers to noncontiguous antigen-binding sites within an antibody. In various embodiments, amino acids in a CDR are identified using sequence or structure based methods. These particular regions have been described by Kabat et al., J. Biol. Chem. 252:6609-6616, 1977 and Kabat, et al., Sequences of Proteins of Immunological Interest, Fifth Edition, U. S. Department of Health and Human Services, NIH Publication No. 91-3242, 1991; by Chothia et al., (J. Mol. Biol. 196:901-917, 1987), and by MacCallum et al., (J. Mol. Biol. 262:732-745, 1996) where the definitions include overlapping or subsets of amino acid residues when compared against each other. As used herein, numbering of immunoglobulin amino acid residues is done according to the immunoglobulin amino acid residue numbering system of Kabat, unless otherwise indicated. In certain embodiments, the term “CDR” is a CDR as defined by Kabat based on sequence comparisons. Highly conserved portions of antibody variable regions are called the framework regions (FRs). As is appreciated in the art, the amino acid positions that delineate a hypervariable region of an antibody (i.e., CDRs) can vary, depending on the context and the various definitions known in the art. Some positions within a variable domain may be viewed as hybrid hypervariable positions in that these positions can be deemed to be within a hypervariable region under one set of criteria while being deemed to be outside a hypervariable region under a different set of criteria. One or more of these positions can also be found in extended hypervariable regions. The variable regions of native heavy and light chains each comprise four framework regions (FR1, FR2, FR3, FR4) that primarily adopt a beta-sheet configuration, connected by three CDRs (CDR1, CDR2, CDR3), which form loops that connect, and in some cases form part of, the beta-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions in the order FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4. and the CDRs in each antibody chain contribute to the formation of the target binding site of antibodies (see Kabat et al, Sequences of Proteins of Immunological Interest (National Institute of Health, Bethesda, Md. 1987; incorporated herein by reference). In various embodiments, complementarity determining regions are identified using any of the methodologies available to one of skill in the art such as those methods described in “Antibody Structure-Function Relationships.” Therapeutic Antibody Engineering, edited by William R. Strohl and Lilia M. Strohl, Woodhead Publishing Series in Biomedicine, 2012, 37-56, 459-595, the entirety of which is incorporated herein in its entirety for all purposes, where such methods include, as nonlimiting examples, those of Kabat, Chothia, Lefranc, Honegger, Martin, MacCallum, and Zhao.ATTORNEY DOCKET NO. 180802-047501 / PCT

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[0157] CDRs can be identified using sequence or structure based methods. Various software programs are available to one of skill in the art to identify CDRs for an antibody amino acid sequence. In various embodiments, a CDR as provided herein may be modified to include 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 additional amino acids and / or to exclude 1, 2, 3, 4, 5, 6, 7, 8, or 9 amino acids at the N-terminal and / or C-terminal end. The present disclosure contemplates that the CDRs identified for a particular antibody can vary in location or length depending upon the method by which they are determined.

[0158] By “chimeric antigen receptor” or “CAR” is meant a synthetic or engineered receptor comprising an extracellular antigen binding domain operationally joined to one or more intracellular signaling domains where the CAR confers specificity for an antigen bound by the extracellular antigen binding domain onto an immune effector cell. In some cases, the intracellular signaling domain is a T cell signaling domain. In embodiments, the immune effector cell is a T cell, an NK cell, or a macrophage. In embodiments, the CAR is a SUPRA CAR, an anti-tag CAR, a TCR-CAR, or a TCR-like CAR (see, e.g., Guedan, etal. “Engineering and Design of Chimeric Antigen Receptors,” Methods and Clinical Development, 12: 145-156 (2019); Poorebrahim, et al., “TCR-like CARs and TCR-CARs targeting neoepitopes: an emerging potential,” Cancer Gene Therapy, 28:581-589 (2021); and Minutolo, et al. “The Emergence of Universal Immune Receptor T Cell Therapy for Cancer,” Front Oncol., 9:176 (2019), the disclosures of which are incorporated herein by reference in their entireties for all purposes).

[0159] By “chimeric antigen receptor (CAR) T cell” or “CAR-T cell” is meant a T cell expressing a CAR that has antigen specificity determined by the antibody-derived targeting domain of the CAR. As used herein, “CAR-T cells” include T cells, regulatory T cells (TREG), macrophages, or NK cells. As used herein, the term “CAR-T cells” includes cells engineered to express a CAR or a T cell receptor (TCR, sometimes referred to as TCR-CARs or TCR-like CARs). Methods of making CARs (e.g., for treatment of cancer) are publicly available (see, e.g., Park et al., Trends Biotechnol., 29:550-557, 2011; Grupp et al., N Engl JMed., 368:1509-1518, 2013; Han etal, J. Hematol Oncol. 6:47, 2013; Haso etal, (2013) Blood, 121, 1165-1174; Mohseni, et al., (2020) Front. Immunol., 11, art. 1608, doi: 10.3389 / fimmu.2020.01608;

[0160] Eggenhuizen, et al. Int. J. Mol. Sci. (2020), 21:7015, doi: 10.3390 / ijms21197015; Poorebrahim, et al., Cancer Gene Ther 28, 581-589 (2021), doi.org / 10.1038 / s41417-021-00307-7, PCT Pubs. W02012 / 079000, WO2013 / 059593; and U. S. Pub. 2012 / 0213783, the disclosure of each of which is incorporated herein by reference herein in its entirety).ATTORNEY DOCKET NO. 180802-047501 / PCT

[0161] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0162] By “cluster of differentiation 38 (CD38) polypeptide” is meant a polypeptide having at least about 85% amino acid sequence identity to an amino acid sequence provided at GenBank Accession No. AAA68482.1, which is provided below, or a functional fragment thereof. In various embodiments, a functional CD38 polypeptide is capable of binding a cluster of differentiation 31 (CD31) polypeptide and / or capable of catalyzing the synthesis of ADP ribose and cyclic ADP-ribose from NAD+. In various embodiments, a CD38 polypeptide contains one or more amino acid alterations selected from M76G, M77V, R78G, Q107R, Q115R, T116A, D141G, M142V, E233G, K234G, K234E, K234R, L149P, L150P, and V203A, referenced to the below amino acid sequence or one or more amino acid alterations at an amino acid position selected from 76, 77, 78, 107, 115, 116, 141, 142, 233, 234, 149, 150, and 203 referenced to the below amino acid sequence. In some embodiments, the CD38 polypeptide contains one or more alterations in an extracellular domain compared to the below sequence. In various embodiments, the extracellular domain contains one or more amino acids selected from R78, H79, El 04, QI 07, MHO, Kill, L112, G113, T114, QI 15, T116, V117, Pl 18, C119, L150, R194, R195, F196, E197, A199, C201, Q231, E233, S274, F284, V288, P291, E292, and C296. In some embodiments, the CD8 polypeptide contains an alteration at an amino acid position selected from R78, H79, E104, Q107, Ml 10, KI 11, LI 12, G113, T114, QI 15, T116, VI 17, Pl 18, Cl 19, L150, R194, R195, F196, E197, A199, C201, Q231, E233, S274, F284, V288, P291, E292, and C296.

[0163] > AAA68482.1 lymphocyte differentiation antigen CD38 [Homo sapiens] MANCEFSPVSGDKPCCRLSRRAQLCLGVSILVLILVVVLAVVVPRWRQTWSGPGTTKRFPETVL ARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCNITEEDYQPLMKLGTQTVPCNKILLWSRI KDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFNTSKINYQSCPDWRKDCSNNPVSVFWKTV SRRFAEAACDVVHVMLNGSRSKIFDKNSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQD PTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI (SEQ IDNO: 719)

[0164] By “cluster of differentiation 38 (CD38) polynucleotide” is meant a nucleic acid molecule that encodes a CD38 polypeptide as well as the introns, exons, 3' untranslated regions, 5' untranslated regions, and regulatory sequences associated with its expression, or fragments thereof. In embodiments, a CD38 polynucleotide is the genomic sequence, cDNA, mRNA, or gene associated with and / or required for CD38 expression. An exemplary CD38 polynucleotide sequence from Homo sapiens is provided below (GenBank Accession No. M34461.1), and an exemplary CD38 gene sequence is provided at ENSEMBL Accession No. ENSG00000004468 (SEQ ID NO:720).

[0165] > M34461.1:70-972 Human lymphocyte differentiation antigen CD38 mRNA, complete cdsATTORNEY DOCKET NO. 180802-047501 / PCT

[0166] ELECTRONIC DEPOSIT DATE: January 21, 2026 ATGGCCAACTGCGAGTTCAGCCCGGTGTCCGGGGACAAACCCTGCTGCCGGCTCTCTAGGAGAG CCCAACTCTGTCTTGGCGTCAGTATCCTGGTCCTGATCCTCGTCGTGGTGCTCGCGGTGGTCGT CCCGAGGTGGCGCCAGACGTGGAGCGGTCCGGGCACCACCAAGCGCTTTCCCGAGACCGTCCTG GCGCGATGCGTCAAGTACACTGAAATTCATCCTGAGATGAGACATGTAGACTGCCAAAGTGTAT GGGATGCTTTCAAGGGTGCATTTATTTCAAAACATCCTTGCAACATTACTGAAGAAGACTATCA GCCACTAATGAAGTTGGGAACTCAGACCGTACCTTGCAACAAGATTCTTCTTTGGAGCAGAATA AAAGATCTGGCCCATCAGTTCACACAGGTCCAGCGGGACATGTTCACCCTGGAGGACACGCTGC TAGGCTACCTTGCTGATGACCTCACATGGTGTGGTGAATTCAACACTTCCAAAATAAACTATCA ATCTTGCCCAGACTGGAGAAAGGACTGCAGCAACAACCCTGTTTCAGTATTCTGGAAAACGGTT TCCCGCAGGTTTGCAGAAGCTGCCTGTGATGTGGTCCATGTGATGCTCAATGGATCCCGCAGTA AAATCTTTGACAAAAACAGCACTTTTGGGAGTGTGGAAGTCCATAATTTGCAACCAGAGAAGGT TCAGACACTAGAGGCCTGGGTGATACATGGTGGAAGAGAAGATTCCAGAGACTTATGCCAGGAT CCCACCATAAAAGAGCTGGAATCGATTATAAGCAAAAGGAATATTCAATTTTCCTGCAAGAATA TCTACAGACCTGACAAGTTTCTTCAGTGTGTGAAAAATCCTGAGGATTCATCTTGCACATCTGA GATCTGA (SEQ ID NO: 721)

[0167] The term “conservative amino acid substitution” or “conservative mutation” refers to the replacement of one amino acid by another amino acid with a common property. A functional way to define common properties between individual amino acids is to analyze the normalized frequencies of amino acid changes between corresponding proteins of homologous organisms (Schulz, G. E. and Schirmer, R. H., Principles of Protein Structure, Springer-Verlag, New York (1979)). According to such analyses, groups of amino acids can be defined where amino acids within a group exchange preferentially with each other, and therefore resemble each other most in their impact on the overall protein structure (Schulz, G. E. and Schirmer, R. H., supra). Nonlimiting examples of conservative mutations include amino acid substitutions of amino acids, for example, lysine for arginine and vice versa such that a positive charge can be maintained; glutamic acid for aspartic acid and vice versa such that a negative charge can be maintained; serine for threonine such that a free -OH can be maintained; and glutamine for asparagine such that a free -NH2 can be maintained.

[0168] Amino acids generally can be grouped into classes according to the following common side- chain properties:

[0169] (1) hydrophobic: Norleucine, Met, Ala, Vai, Leu, He;

[0170] (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gin;

[0171] (3) acidic: Asp, Glu;

[0172] (4) basic: His, Lys, Arg;

[0173] (5) residues that influence chain orientation: Gly, Pro;ATTORNEY DOCKET NO. 180802-047501 / PCT

[0174] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0175] (6) aromatic: Trp, Tyr, Phe.

[0176] In some embodiments, conservative substitutions can involve the exchange of a member of one of these classes for another member of the same class. In some embodiments, nonconservative amino acid substitutions can involve exchanging a member of one of these classes with a member of another class.

[0177] The term “coding sequence” or “protein coding sequence” as used interchangeably herein refers to a segment of a polynucleotide that codes for a protein. Coding sequences can also be referred to as open reading frames. The region or sequence is bounded nearer the 5' end by a start codon and nearer the 3' end with a stop codon. Stop codons useful with the base editors described herein include the following: TAG, TAA, and TGA.

[0178] As used herein, the terms “condition” and “conditioning” refer to processes by which a patient is prepared for receipt of a transplant containing hematopoietic stem cells. Such procedures promote the engraftment of a hematopoietic stem cell transplant (for instance, as inferred from a sustained increase in the quantity of viable hematopoietic stem cells within a blood sample isolated from a patient following a conditioning procedure and subsequent hematopoietic stem cell transplantation). According to the methods described herein, a patient may be conditioned for hematopoietic stem cell transplant therapy by administration to the patient of an antibody or antigen-binding fragment thereof capable of binding a CD38 antigen expressed by hematopoietic stem cells. Such antibodies may act via complement-mediated cytotoxicity and antibody-dependent cell-mediated cytotoxicity. As described herein, the transplanted cells have been edited so that the antibody has reduced or undetectable binding to a CD38 variant expressed on the cells compared to a wild-type CD38 variant. Administration of an antibody, antigen-binding fragment thereof, drug-antibody conjugate, or chimeric antigen receptor expressing T-cell (CAR-T) capable of binding a wild-type CD38 antigen to a patient in need of hematopoietic stem cell transplant therapy can promote the engraftment of a hematopoietic stem cell graft, for example, by selectively depleting endogenous hematopoietic stem cells, thereby creating a vacancy filled by an exogenous hematopoietic stem cell transplant.

[0179] By “complex” is meant a combination of two or more molecules whose interaction relies on inter-molecular forces. Non-limiting examples of inter-molecular forces include covalent and non-covalent interactions. Non-limiting examples of non-covalent interactions include hydrogen bonding, ionic bonding, halogen bonding, hydrophobic bonding, van der Waals interactions (e.g., dipole-dipole interactions, dipole-induced dipole interactions, and London dispersion forces), and 7t-effects. In an embodiment, a complex comprises polypeptides, polynucleotides, or a combination of one or more polypeptides and one or more polynucleotides. In oneATTORNEY DOCKET NO. 180802-047501 / PCT

[0180] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0181] embodiment, a complex comprises one or more polypeptides that associate to form a base editor (e.g., base editor comprising a nucleic acid programmable DNA binding protein, such as Cas9, and a deaminase) and a polynucleotide (e.g., a guide RNA). In an embodiment, the complex is held together by hydrogen bonds. It should be appreciated that one or more components of a base editor (e.g., a deaminase, or a nucleic acid programmable DNA binding protein) may associate covalently or non-covalently. As one example, a base editor may include a deaminase covalently linked to a nucleic acid programmable DNA binding protein (e.g., by a peptide bond).

[0182] Alternatively, a base editor may include a deaminase and a nucleic acid programmable DNA binding protein that associate noncovalently (e.g., where one or more components of the base editor are supplied in trans and associate directly or via another molecule such as a protein or nucleic acid). In an embodiment, one or more components of the complex are held together by hydrogen bonds.

[0183] By “cytosine” or “4-Aminopyrimidin-2(1H)-one” is meant a purine nucleobase with the o

[0184] N^NH

[0185] molecular formula C₄H₅N₃O, having the structure

[0186]

[0187] 2anc[ corresponding to CAS No. 71-30-7.

[0188] By “cytidine” is meant a cytosine molecule attached to a ribose sugar via a glycosidic NH2

[0189] HO.

[0190] - oN 0

[0191]

[0192] OH OH

[0193] bond, having the structure, and corresponding to CAS No. 65-46-3. Its molecular formula is C₉H₁₃N₃O₅.

[0194] By “Cytidine Base Editor (CBE)” is meant a base editor comprising a cytidine deaminase. Non-limiting examples of cytidine deaminase base editor amino acid sequences include amino acid sequences for BE4max (SEQ ID NO: 553), YE1-BE4 (SEQ ID NO: 554), YE2-BE4 (SEQ ID NO: 555), YEE-BE4 (SEQ ID NO: 556), EE-BE4 (SEQ ID NO: 557), R33A-BE4 (SEQ ID NO: 558), R33A+K34A-BE4 (SEQ ID NO: 559), APOBEC3A (A3A)-BE4 (SEQ ID NO: 560), APOBEC3B (A3B)-BE4 (SEQ ID NO: 561), APOBEC3G (A3G)-BE4 (SEQ ID NO: 562), AID-BE4 (SEQ ID NO: 563), CDA-BE4 (SEQ ID NO: 564), FERNY-BE4ATTORNEY DOCKET NO. 180802-047501 / PCT

[0195] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0196] (SEQ ID NO: 565), evolved APOBEC3A (eA3A)-BE4 (SEQ ID NO: 566), AALN-BE4 (SEQ ID NO: 567), BE4max modified with SpCas9-NG (SEQ ID NO: 568), YEl-SpCas9-NG (YE1-NG) (SEQ ID NO: 569), YE2-SpCas9-NG (SEQ ID NO: 570), YEE-SpCas9-NG (SEQ ID NO: 571), EE-SpCas9-NG (SEQ ID NO: 572), R33A+K34A-SpCas9-NG (SEQ ID NO: 573), YE1-CP1028 (YE1-BE4-CP1028, or YE1-CP) (SEQ ID NO: 574), YE2-CP1028 (YE2-BE4-CP1028) (SEQ ID NO: 575), YEE-CP1028 (YEE-BE4-CP1028) (SEQ ID NO: 576), EE-CP1028 (EE-BE4-CP1028) (SEQ ID NO: 577), R33A+K34A-CP1028 (R33A+K34A-BE4-CP1028) (SEQ ID NO: 578), BE4max (with nickase) (SEQ ID NO: 597), BE4 (SEQ ID NO: 598), BE4 with His tag (SEQ ID NO: 599), BE4max (SEQ ID NO: 600), AncBE4max 689 (SEQ ID NO: 601), and AncBE4max 687 (SEQ ID NO: 602).

[0197] By “Cytidine Base Editor (CBE) polynucleotide” is meant a polynucleotide encoding a CBE. Non-limiting examples of polynucleotide sequences encoding cytidine deaminase base editors include those encoding BE4max (SEQ ID NO: 616), AncBE4max689 (SEQ ID NO: 617), and AncBE4max687 (SEQ ID NO: 618).

[0198] By “cytidine deaminase” or “cytosine deaminase” is meant a polypeptide or fragment thereof capable of deaminating cytidine or cytosine. In embodiments, the cytidine or cytosine is present in a polynucleotide. In one embodiment, the cytidine deaminase converts cytosine to uracil or 5-methylcytosine to thymine. The terms “cytidine deaminase” and “cytosine deaminase” are used interchangeably throughout the application. Petromyzon marinus cytosine deaminase 1 (PmCDAl) (SEQ ID NO: 12-13), Activation-induced cytidine deaminase (AICDA) (SEQ ID NOs: 14-20), and APOBEC (SEQ ID NOs: 21-61) are exemplary cytidine deaminases. Further exemplary cytidine deaminase (CD A) sequences are provided in the Sequence Listing as SEQ ID NOs: 62-66 and SEQ ID NOs: 67-189. Non-limiting examples of cytidine deaminases include those described in PCT / US20 / 16288, PCT / US2018 / 021878, 180802-021804 / PCT, PCT / US2018 / 048969, PCT / US2016 / 058344, PCT / US2020 / 062428, and PCT / US2019 / 033848, the disclosures of which are incorporated herein by reference in their entireties for all purposes. Non-limiting examples of cytidine deaminase amino acid sequences include amino acid sequences for Rat APOBEC1 (SEQ ID NO: 579), Human APOBEC1 (SEQ ID NO: 580), Human APOBEC3 (SEQ ID NO: 581), Human APOBEC3B (SEQ ID NO: 582), Human APOBEC3G (SEQ ID NO: 583), evoAPOBEC3A(eA3A) (SEQ ID NO: 584), evoCDA (SEQ ID NO: 585), evoAPOBECl (SEQ ID NO: 586), YE1 (SEQ ID NO: 587), YE2 (SEQ ID NO: 588), YEE (SEQ ID NO: 589), EE (SEQ ID NO: 590), R33A (SEQ ID NO: 591), R33A+K34A (SEQ ID NO: 592), AALN (SEQ ID NO: 593), FERNY (SEQ ID NO: 594), evoFERNY (SEQ ID NO: 595), APOBEC (SEQ ID NO: 619), Anc686 APOBEC (SEQ ID NO: 620), Human APOBEC-ATTORNEY DOCKET NO. 180802-047501 / PCT

[0199] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0200] 3G D316R D317R (SEQ ID NO: 621), Human APOBEC-3G chain A (SEQ ID NO: 622), Human APOBEC3-G chain A D120R D121R (SEQ ID NO: 623), Mouse APOBEC3 (SEQ ID NO: 624), Rat APOBEC3 (SEQ ID NO: 625), Rhesus macaque APOBEC-3G (SEQ ID NO: 626), Chimpanzee APOBEC-3G (SEQ ID NO: 627), Green Monkey APOBEC-3G (SEQ ID NO: 628), Human APOBEC-3G (SEQ ID NO: 629), Human APOBEC-3F (SEQ ID NO: 630), Human APOBEC-3B (SEQ ID NO: 631), Rat APOBEC-3B (SEQ ID NO: 632), Bovine APOBEC-3B (SEQ ID NO: 633), Chimpanzee APOBEC-3B (SEQ ID NO: 634), Gorilla APOBEC-3C (SEQ ID NO: 635), Human APOBEC-3A (SEQ ID NO: 636), Rhesus macaque APOBEC-3A (SEQ ID NO: 637), Bovine APOBEC-3A (SEQ ID NO: 638), Human APOBEC-3H (SEQ ID NO: 639), Human APOBEC-3D (SEQ ID NO: 640), Rat ABOPEC1 (SEQ ID NO: 641), Anc689 APOBEC (SEQ ID NO: 642), Anc687 APOBEC (SEQ ID NO: 643), Anc686 APOBEC (SEQ ID NO: 644), Anc655 APOBEC (SEQ ID NO: 645), and Anc733 APOBEC (SEQ ID NO: 646).

[0201] By “cytidine deaminase polynucleotide” is meant a polynucleotide encoding a cytidine deaminase. Non-limiting examples of polynucleotide sequences encoding cytidine deaminase domains include those encoding Rat APOBEC 1 (SEQ ID NO: 604), Anc689 APOBEC (SEQ ID NO: 605), Anc687 APOBEC (SEQ ID NO: 606), Anc686 APOBEC (SEQ ID NO: 607), Anc655 APOBEC (SEQ ID NO: 608), Anc733 APOBEC (SEQ ID NO: 609), Rat APOBEC 1 (SEQ ID NO: 610), Anc689 APOBEC (SEQ ID NO: 611), Anc687 APOBEC (SEQ ID NO: 612), Anc686 APOBEC (SEQ ID NO: 613), Anc655 APOBEC (SEQ ID NO: 614), and Anc733 APOBEC (SEQ ID NO: 615).

[0202] By “cytosine deaminase activity” is meant catalyzing the deamination of cytosine or cytidine. In one embodiment, a polypeptide having cytosine deaminase activity converts an amino group to a carbonyl group. In an embodiment, a cytosine deaminase converts cytosine to uracil ( / .<., C to U) or 5-methylcytosine to thymine ( / .<., 5mC to T). In some embodiments, a cytosine deaminase as provided herein has increased cytosine deaminase activity (e.g., at least 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold or more) relative to a reference cytosine deaminase.

[0203] The term “deaminase” or “deaminase domain,” as used herein, refers to a protein or fragment thereof that catalyzes a deamination reaction.

[0204] The term, “detect” refers to identifying the presence, absence or amount of the analyte to be detected. In one embodiment, a sequence alteration in a polynucleotide or polypeptide is detected. In another embodiment, the presence of indels is detected.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0205] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0206] By “detectable label” is meant a composition that when linked to a molecule of interest renders the latter detectable, via spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include radioactive isotopes, magnetic beads, metallic beads, colloidal particles, fluorescent dyes, electron-dense reagents, enzymes (for example, as commonly used in an enzyme linked immunosorbent assay (ELISA)), biotin, digoxigenin, or haptens.

[0207] By “disease” is meant any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. Exemplary diseases include autoimmune diseases or neoplasias, such as multiple myeloma or other B cell-related hematologic malignancies, autoimmune diseases (e.g., amyloid light chains (AL) amyloidosis), CD38-related diseases, and hemoglobinopathies. In some embodiments, the disease is a disease amenable to treatment using a hematopoietic stem cell transplant (HSCT) therapy. In some cases, the disease is selected from acute myeloid leukemia, acute lymphoid leukemia, amyloid light-chain (AL) amyloidosis, B-cell acute lymphoblastic leukemia (B-ALL), aplastic anemia, chronic myeloid leukemia, chronic lymphoid leukemia, diffuse large B-cell lymphoma, Fanconi anemia, lupus, multiple myeloma, a myelodysplastic syndrome, non-Hodgkin's lymphoma, rheumatoid arthritis, sickle cell anemia, T-cell acute lymphoblastic leukemia (T-ALL), thalassemia, and Wiskott-Aldrich syndrome. In some embodiments, the disease is a hemoglobinopathy, hematologic cancer, or myeloproliferative disease. In some embodiments, the neoplasia is a hematologic cancer, such as acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphoid leukemia, multiple myeloma, diffuse large B-cell lymphoma, or non-Hodgkin's lymphoma. In some cases, the hemoglobinopathy is selected from sickle cell anemia, thalassemia, Fanconi anemia, aplastic anemia, and Wiskott-Aldrich syndrome. In some cases, the disease is a B cell-related hematologic malignancy.

[0208] By “dual editing activity” or “dual deaminase activity” is meant having adenosine deaminase and cytidine deaminase activity. In one embodiment, a base editor having dual editing activity has both A~> G and C- T activity, wherein the two activities are approximately equal or are within about 10% or 20% of each other. In another embodiment, a dual editor has A→G activity that no more than about 10% or 20% greater than C→T activity. In another embodiment, a dual editor has A-> G activity that is no more than about 10% or 20% less than C- T activity. In some embodiments, the adenosine deaminase variant has predominantly cytosine deaminase activity, and little, if any, adenosine deaminase activity. In some embodiments, the adenosine deaminase variant has cytosine deaminase activity, and no significant or no detectable adenosine deaminase activity. Non-limiting examples of proteins having dual deaminase activity includeATTORNEY DOCKET NO. 180802-047501 / PCT

[0209] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0210] those described in International Patent Application Publications No. WO 2024 / 040083 and WO 2022 / 204574, the disclosures of which are hereby incorporated by reference in their entireties for all purposes.

[0211] By “effective amount” is meant the amount of an agent (e.g., a base editor, cell) as described herein, that is required to ameliorate the symptoms of a disease relative to an untreated patient or an individual without disease, z.e., a healthy individual, or is the amount of the agent sufficient to elicit a desired biological response. The effective amount of active compound(s) used to practice embodiments of the present disclosure for therapeutic treatment of a disease varies depending upon the manner of administration, the age, body weight, and general health of the subject. Ultimately, the attending physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an “effective” amount. In one embodiment, an effective amount is the amount of a base editor of the disclosure sufficient to introduce an alteration in a gene of interest in a cell (e.g., a cell in vitro or in vivo). In one embodiment, an effective amount is the amount of a base editor required to achieve a therapeutic effect. Such therapeutic effect need not be sufficient to alter a pathogenic gene in all cells of a subject, tissue or organ, but only to alter the pathogenic gene in about 1%, 5%, 10%, 25%, 50%, 75% or more of the cells present in a subject, tissue or organ. In one embodiment, an effective amount is sufficient to ameliorate one or more symptoms of a disease.

[0212] By “fragment” is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotides or amino acids. In some embodiments, the fragment is a functional fragment.

[0213] As used herein, the term “framework region” or “FR region” includes amino acid residues that are adjacent to the CDRs. FR region residues may be present in, for example, human antibodies, rodent-derived antibodies (e.g., murine antibodies), humanized antibodies, primatized antibodies, chimeric antibodies, antibody fragments (e.g., Fab fragments), singlechain antibody fragments (e.g., scFv fragments), antibody domains, and bispecific antibodies, among others.

[0214] By “guide polynucleotide” is meant a polynucleotide or polynucleotide complex which is specific for a target sequence and can form a complex with a polynucleotide programmable nucleotide binding domain protein (e.g., Cas9 or Cpfl). In an embodiment, the guide polynucleotide is a guide RNA (gRNA). gRNAs can exist as a complex of two or more RNAs, or as a single RNA molecule.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0215] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0216] As used herein, the term “hematopoietic stem cells” (“HSCs”) refers to immature blood cells having the capacity to self-renew and to differentiate into mature blood cells containing diverse lineages including but not limited to granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), thrombocytes (e.g., megakary oblasts, platelet producing megakaryocytes, platelets), monocytes (e.g., monocytes, macrophages), dendritic cells, microglia, osteoclasts, and lymphocytes (e.g., NK cells, B-cells and T-cells). Such cells may include CD34+ cells. CD34+ cells are immature cells that express the CD34 cell surface marker. In humans, CD34+ cells are believed to include a subpopulation of cells with the stem cell properties defined above, whereas in mice, HSCs are CD34-. In addition, HSCs also refer to long term repopulating HSCs (LT-HSC) and short term repopulating HSCs (ST-HSC). LT-HSCs and ST-HSCs are differentiated, based on functional potential and on cell surface marker expression. For example, human HSCs are CD34+, CD38-, CD45RA-, CD90+, CD49F+, and lin-(negative for mature lineage markers including CD2, CD3, CD4, CD7, CD8, CD10, CD1 1 B, CD 19, CD20, CD56, CD235A). In mice, bone marrow LT-HSCs are CD34-, SCA-1 +, C-kit+, CD135-, SLAMF1 / CD150+, CD48-, and lin- (negative for mature lineage markers including Teri 19, CDllb, Grl, CD3, CD4, CD8, B220, IL7ra), whereas ST-HSCs are CD34+, SCA-1+, C-kit+, CD135-, SLAMF1 / CD150+, and lin-(negative for mature lineage markers including Teri 19, CD1 1 b, Grl, CD3, CD4, CD8, B220, IL7ra). In addition, ST-HSCs are less quiescent and more proliferative than LT-HSCs under homeostatic conditions. However, LT-HSC have greater self-renewal potential ( / .<., they survive throughout adulthood, and can be serially transplanted through successive recipients), whereas ST-HSCs have limited self-renewal ( / .<., they survive for only a limited period of time, and do not possess serial transplantation potential). Any of these HSCs can be used in the methods described herein. ST-HSCs are particularly useful because they are highly proliferative and thus, can more quickly give rise to differentiated progeny.

[0217] As used herein, the term “hematopoietic stem cell functional potential” refers to the functional properties of hematopoietic stem cells which include 1 ) multi-potency (which refers to the ability to differentiate into multiple different blood lineages including, but not limited to, granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), thrombocytes (e.g., megakary oblasts, platelet producing megakaryocytes, platelets), monocytes (e.g., monocytes, macrophages), dendritic cells, microglia, osteoclasts, and lymphocytes (e.g., NK cells, B-cells and T-cells), 2) self-renewal (which refers to the ability of hematopoietic stem cells to give rise to daughter cells that have equivalent potential as the mother cell, and further that this ability can repeatedly occurATTORNEY DOCKET NO. 180802-047501 / PCT

[0218] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0219] throughout the lifetime of an individual without exhaustion), and 3) the ability of hematopoietic stem cells or progeny thereof to be reintroduced into a transplant recipient whereupon they home to the hematopoietic stem cell niche and re-establish productive and sustained hematopoiesis.” As used herein, the term “human antibody” refers to an antibody in which substantially every part of the protein (e.g., CDR, framework, CL, CH domains (e.g., Cm, Cm, Cm), hinge, (VL, VH)) is substantially non-immunogenic in humans, with only minor sequence changes or variations. A human antibody can be produced in a human cell (e.g., by recombinant expression), or by a non-human animal or a prokaryotic or eukaryotic cell (e.g., yeast) that is capable of expressing functionally rearranged human immunoglobulin (e.g., heavy chain and / or light chain) genes. Further, when a human antibody is a single-chain antibody, it can include a linker peptide that is not found in native human antibodies. For example, an Fv can comprise a linker peptide, such as two to about eight glycine or other amino acid residues, which connects the variable region of the heavy chain and the variable region of the light chain. Such linker peptides are considered to be of human origin. Human antibodies can be made by a variety of methods known in the art including phage display methods using antibody libraries derived from human immunoglobulin sequences. See U. S. Pat. Nos. 4,444,887 and 4,716,111; and PCT publications WO 1998 / 46645; WO 1998 / 50433; WO 1998 / 24893; WO 1998 / 16654; WO 1996 / 34096; WO 1996 / 33735; and WO 1991 / 10741; incorporated herein by reference. Human antibodies can also be produced using transgenic mice that are incapable of expressing functional endogenous immunoglobulins, but which can express human immunoglobulin genes. See, e.g., PCT publications WO 98 / 24893; WO 92 / 01047; WO 96 / 34096; WO 96 / 33735; U. S. Pat. Nos.

[0220] 5,413,923; 5,625,126; 5,633,425; 5,569,825; 5,661,016; 5,545,806; 5,814,318; 5,885,793;

[0221] 5,916,771; and 5,939,598; incorporated by reference herein.

[0222] As used herein, the term “humanized” antibodies refers to forms of non-human (e.g., murine) antibodies that are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or other target-binding subdomains of antibodies) which contain minimal sequences derived from non-human immunoglobulin. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable regions, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin. All or substantially all of the FR regions may also be those of a human immunoglobulin sequence. The humanized antibody can also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin consensus sequence. Methods of antibody humanization are known in the art. See, e.g., Riechmann et al., Nature 332:323-7, 1988; U. S. Pat. Nos. 5,530,101; 5,585,089; 5,693,761; 5,693,762; and U. S.ATTORNEY DOCKET NO. 180802-047501 / PCT

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[0224] Pat. No. 6,180,370 to Queen et al; EP239400; PCT publication WO 91 / 09967; U. S. Pat. No. 5,225,539; EP592106; and EP519596; incorporated herein by reference.

[0225] “Hybridization” means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases. For example, adenine and thymine are complementary nucleobases that pair through the formation of hydrogen bonds.

[0226] By “increases” is meant a positive alteration of at least 10%, 25%, 50%, 75%, or 100%, or about 1.5 fold, about 2 fold, about 3-fold, about 4-fold, about 5-fold, about 6-fold, about 7-fold, about 8-fold, about 9-fold, about 10-fold, about 15-fold, about 20-fold, about 25-fold, about 30-fold, about 35-fold, about 40-fold, about 45-fold, about 50-fold, or about 100-fold.

[0227] The terms “inhibitor of base repair”, “base repair inhibitor”, “IBR” or their grammatical equivalents refer to a protein that is capable in inhibiting the activity of a nucleic acid repair enzyme, for example a base excision repair enzyme.

[0228] An “intein” is a fragment of a protein that is able to excise itself and join the remaining fragments (the exteins) with a peptide bond in a process known as protein splicing.

[0229] The terms “isolated,” “purified,” or “biologically pure” refer to material that is free to varying degrees from components which normally accompany it as found in its native state. “Isolate” denotes a degree of separation from original source or surroundings. “Purify” denotes a degree of separation that is higher than isolation. A “purified” or “biologically pure” protein is sufficiently free of other materials such that any impurities do not materially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide of this disclosure is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Purity and homogeneity are typically determined using analytical chemistry techniques, for example, polyacrylamide gel electrophoresis or high performance liquid chromatography. The term “purified” can denote that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. For a protein that can be subjected to modifications, for example, phosphorylation or glycosylation, different modifications may give rise to different isolated proteins, which can be separately purified.

[0230] By “isolated polynucleotide” is meant a nucleic acid molecule that is free of the genes which, in the naturally-occurring genome of the organism from which the nucleic acid molecule of the disclosure is derived, flank the gene. The term therefore includes, for example, a recombinant DNA that is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or that exists as a separateATTORNEY DOCKET NO. 180802-047501 / PCT

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[0232] molecule (for example, a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. In addition, the term includes an RNA molecule that is transcribed from a DNA molecule, as well as a recombinant DNA that is part of a hybrid gene encoding additional polypeptide sequence.

[0233] By an “isolated polypeptide” is meant a polypeptide of the disclosure that has been separated from components that naturally accompany it. Typically, the polypeptide is isolated when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. In embodiments, the preparation is at least 75%, at least 90%, or at least 99%, by weight, a polypeptide of the disclosure. An isolated polypeptide of the disclosure may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding such a polypeptide; or by chemically synthesizing the protein. Purity can be measured by any appropriate method, for example, column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.

[0234] The term “linker”, as used herein, refers to a molecule that links two moieties. In one embodiment, the term “linker” refers to a covalent linker (e.g., covalent bond) or a non-covalent linker.

[0235] By “marker” is meant any protein or polynucleotide having an alteration in expression, level, structure, or activity that is associated with a disease or disorder. In some cases, the marker is CD38 or a CD38 variant containing one or more amino acid alterations described herein.

[0236] The term “mutation,” as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues within a sequence. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art, and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4thed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y. (2012)).

[0237] The terms “nucleic acid” and “nucleic acid molecule,” as used herein, refer to a compound comprising a nucleobase and an acidic moiety, e.g., a nucleoside, a nucleotide, or a polymer of nucleotides. Typically, polymeric nucleic acids, e.g., nucleic acid molecules comprising three or more nucleotides are linear molecules, in which adjacent nucleotides are linked to each other via a phosphodiester linkage. In some embodiments, “nucleic acid” refers to individual nucleic acid residues (e.g., nucleotides and / or nucleosides). In some embodiments, “nucleic acid” refers to an oligonucleotide chain comprising three or more individual nucleotideATTORNEY DOCKET NO. 180802-047501 / PCT

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[0239] residues. As used herein, the terms “oligonucleotide” and “polynucleotide” can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least three nucleotides). In some embodiments, “nucleic acid” encompasses RNA as well as single and / or doublestranded DNA. Nucleic acids may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid, chromosome, chromatid, or other naturally occurring nucleic acid molecule. On the other hand, a nucleic acid molecule may be a non-naturally occurring molecule, e.g., a recombinant DNA or RNA, an artificial chromosome, an engineered genome, or fragment thereof, or a synthetic DNA, RNA, DNA / RNA hybrid, or including non-naturally occurring nucleotides or nucleosides.

[0240] Furthermore, the terms “nucleic acid,” “DNA,” “RNA,” and / or similar terms include nucleic acid analogs, e.g., analogs having other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc. Where appropriate, e.g, in the case of chemically synthesized molecules, nucleic acids comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications. A nucleic acid sequence is presented in the 5' to 3' direction unless otherwise indicated. In some embodiments, a nucleic acid is or comprises natural nucleosides (e.g. adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, O(6)-methylguanine, and 2 -thiocytidine); chemically modified bases; biologically modified bases (e.g., methylated bases); intercalated bases; modified sugars (e.g., 2'-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose); and / or modified phosphate groups (e.g., phosphorothioates and 5'-A-phosphoramidite linkages).

[0241] The term “nuclear localization sequence,” “nuclear localization signal,” or “NLS” refers to an amino acid sequence that promotes import of a protein into the cell nucleus. Nuclear localization sequences are known in the art and described, for example, in Plank et al., International PCT application, PCT / EP2000 / 011690, filed November 23, 2000, published as W 0 / 2001 / 038547 on May 31, 2001, the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences. In other embodiments, the NLS is an optimized NLS described, for example, by Koblan et al., Nature Biotech. 2018 doi:10.1038 / nbt.4172. In some embodiments, an NLS comprises the amino acid sequenceATTORNEY DOCKET NO. 180802-047501 / PCT

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[0243] KRTADGSEFESPKKKRKV (SEQ ID NO: 190), KRPAATKKAGQAKKKK (SEQ ID NO: 191), KKTELQTTNAENKTKKL (SEQ ID NO: 192), KRGINDRNFWRGENGRKTR (SEQ ID NO: 193), RKSGKIAAIVVKRPRK (SEQ ID NO: 194), PKKKRKV (SEQ ID NO: 195), MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO: 196), PKKKRKVEGADKRTADGSEFESPKKKRKV (SEQ ID NO: 328), or RKSGKIAAIVVKRPRKPKKKRKV (SEQ ID NO: 329).

[0244] The term “nucleobase,” “nitrogenous base,” or “base,” used interchangeably herein, refers to a nitrogen-containing biological compound that forms a nucleoside, which in turn is a component of a nucleotide. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases - adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) - are called primary or canonical. Adenine and guanine are derived from purine, and cytosine, uracil, and thymine are derived from pyrimidine. DNA and RNA can also contain other (non-primary) bases that are modified. Non-limiting exemplary modified nucleobases can include hypoxanthine, xanthine, 7-methylguanine, 5,6-dihydrouracil, 5-methylcytosine (m5C), and 5-hydromethylcytosine. Hypoxanthine and xanthine can be created through mutagen presence, both of them through deamination (replacement of the amine group with a carbonyl group). Hypoxanthine can be modified from adenine. Xanthine can be modified from guanine. Uracil can result from deamination of cytosine. A “nucleoside” consists of a nucleobase and a five carbon sugar (either ribose or deoxyribose). Examples of a nucleoside include adenosine, guanosine, uridine, cytidine, 5-methyluridine (m5U), deoxyadenosine, deoxyguanosine, thymidine, deoxyuridine, and deoxycytidine. Examples of a nucleoside with a modified nucleobase includes inosine (I), xanthosine (X), 7-methylguanosine (m7G), dihydrouridine (D), 5-methylcytidine (m5C), and pseudouridine (T). A “nucleotide” consists of a nucleobase, a five carbon sugar (either ribose or deoxyribose), and at least one phosphate group. Non-limiting examples of modified nucleobases and / or chemical modifications that a modified nucleobase may include are the following: pseudo-uridine, 5-Methyl-cytosine, 2'-O-methyl-3'-phosphonoacetate, 2'-O-methyl thioPACE (MSP), 2'-O-methyl-PACE (MP), 2'-fluoro RNA (2'-F-RNA), constrained ethyl (S-cEt), 2'-O-methyl (‘M’), 2'-O-methyl-3'-phosphorothioate (‘MS’), 2'-O-methyl-3'-thiophosphonoacetate (‘MSP’), 5-methoxyuridine, phosphorothioate, and N1 -Methylpseudouridine.

[0245] The term “nucleic acid programmable DNA binding protein” or “napDNAbp” may be used interchangeably with “polynucleotide programmable nucleotide binding domain” to refer to a protein that associates with a nucleic acid (e.g., DNA or RNA), such as a guide nucleic acid orATTORNEY DOCKET NO. 180802-047501 / PCT

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[0247] guide polynucleotide (e.g., gRNA), that guides the napDNAbp to a specific nucleic acid sequence. In some embodiments, the polynucleotide programmable nucleotide binding domain is a polynucleotide programmable DNA binding domain. In some embodiments, the polynucleotide programmable nucleotide binding domain is a polynucleotide programmable RNA binding domain. In some embodiments, the polynucleotide programmable nucleotide binding domain is a Cas9 protein. A Cas9 protein can associate with a guide RNA that guides the Cas9 protein to a specific DNA sequence that is complementary to the guide RNA. In some embodiments, the napDNAbp is a Cas9 domain, for example a nuclease active Cas9, a Cas9 nickase (nCas9), or a nuclease inactive Cas9 (dCas9). Non-limiting examples of nucleic acid programmable DNA binding proteins include, Cas9 (e.g., dCas9 and nCas9), Casl2a / Cpfl, Casl2b / C2cl, Casl2c / C2c3, Casl2d / CasY, Casl2e / CasX, Casl2g, Casl2h, Casl2i, and Casl2j / Cas (Casl2j / Casphi). Non-limiting examples of Cas enzymes include Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas5d, Cas5t, Cas5h, Cas5a, Cas6, Cas7, Cas8, Cas8a, Cas8b, Cas8c, Cas9 (also known as Csnl or Csxl2), CaslO, CaslOd, Casl2a / Cpfl, Casl2b / C2cl, Casl2c / C2c3, Casl2d / CasY, Casl2e / CasX, Casl2g, Casl2h, Casl2i, Casl2j / Cas, Cpfl, Csyl, Csy2, Csy3, Csy4, Csel, Cse2, Cse3, Cse4, Cse5e, Cscl, Csc2, Csa5, Csnl, Csn2, Csml, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, CsxlS, Csxll, Csfl, Csf2, CsO, Csf4, Csdl, Csd2, Cstl, Cst2, Cshl, Csh2, Csal, Csa2, Csa3, Csa4, Csa5, Type II Cas effector proteins, Turbo Cas9 (i.e., an SpCas9 with the amino acid alterations Q844R, V842L, F846Y, L847M, and I852F), Type V Cas effector proteins, Type VI Cas effector proteins, CARF, DinG, homologues thereof, or modified or engineered versions thereof. Other nucleic acid programmable DNA binding proteins are also within the scope of this disclosure, although they may not be specifically listed in this disclosure. See, e.g., Makarova et al. “Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?” CRISPRJ. 2018 Oct; 1:325-336. doi: 10.1089 / crispr.2018.0033; Yan et al., “Functionally diverse type V CRISPR-Cas systems” Science. 2019 Jan 4;363(6422):88-91. doi: 10.1126 / science.aav7271, the entire contents of each are hereby incorporated by reference. Exemplary nucleic acid programmable DNA binding proteins and nucleic acid sequences encoding nucleic acid programmable DNA binding proteins are provided in the Sequence Listing as SEQ ID NOs: 197-231, 232-245, 254-257, 260, and 378. In some embodiments, the napDNAbp is a (CRISPR-associated system) Cas9 endonuclease, for example, Cas9 (Csnl) from Streptococcus pyogenes (e.g., SEQ ID NO: 197), Cas9 from Neisseria meningitidis (NmeCas9; SEQ ID NO: 208), Nme2Cas9 (SEQ ID NO: 209), Streptococcus constellatus (ScoCas9), or derivatives thereof (e.g., a sequence with at least about 85% sequenceATTORNEY DOCKET NO. 180802-047501 / PCT

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[0249] identity to a Cas9, such as Nme2Cas9 or spCas9). Further non-limiting examples of nucleic acid programmable DNA binding proteins include those disclosed or referenced in Rufflow, et al., “Design of highly functional genome editors by modeling of the universe of CRISPR-Cas Sequences,” bioRxiv, posted April 22, 2024, doi: 10.1101 / 2024.04.22.590591, the disclosure of which is incorporated herein by reference in its entirety for all purposes, which were designed using artificial intelligence. In some embodiments, the napDNAbp is OpenCRISPR-1, or a variant thereof (e.g., a variant comprising a D10A amino acid alteration and / or lacking an N-terminal methionine). Further non-limiting examples of nucleic acid programmable DNA binding proteins include those disclosed in International Patent Application No.

[0250] PCT / US2019 / 047996.

[0251] The terms “nucleobase editing domain” or “nucleobase editing protein,” as used herein, refers to a protein or enzyme that can catalyze a nucleobase modification in RNA or DNA, such as cytosine (or cytidine) to uracil (or uridine) or thymine (or thymidine), and adenine (or adenosine) to hypoxanthine (or inosine) deaminations, as well as non-templated nucleotide additions and insertions. In some embodiments, the nucleobase editing domain is a deaminase domain (e.g., an adenine deaminase or an adenosine deaminase; or a cytidine deaminase or a cytosine deaminase).

[0252] As used herein, “obtaining” as in “obtaining an agent” includes synthesizing, purchasing, or otherwise acquiring the agent.

[0253] By “OpenCRISPR-1 polypeptide” is meant a protein with an amino acid sequence having at least about 85% amino acid sequence identity to SEQ ID NO: 463, or a fragment thereof that associates with a nucleic acid, such as a guide nucleic acid or guide polynucleotide, that guides the napDNAbp to a specific nucleic acid sequence. Further details relating to the OpenCRISPR-1 polypeptide are disclosed in Rufflow, et al., “Design of highly functional genome editors by modeling of the universe of CRISPR-Cas Sequences,” bioRxiv, posted April 22, 2024, doi: 10.1101 / 2024.04.22.590591, the disclosure of which is incorporated herein by reference in its entirety for all purposes.

[0254] By “OpenCRISPR-1 polynucleotide” is meant a nucleic acid molecule encoding an OpenCRISPR-1 polypeptide, as well as the introns, exons, 3' untranslated regions, 5' untranslated regions, and regulatory sequences associated with its expression, or fragments thereof. In embodiments, an OpenCRISPR-1 polynucleotide is the genomic sequence, cDNA, mRNA, or gene associated with and / or required for OpenCRISPR-1 expression. An exemplary OpenCRISPR-1 nucleotide sequence is provided at SEQ ID NO: 464.ATTORNEY DOCKET NO. 180802-047501 / PCT

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[0256] In various embodiments, a guide RNA suitable for use in combination with an OpenCRISPR-1 polypeptide contains a scaffold having at least 85% sequence identity to a nucleotide sequence selected from the following, or fragments thereof capable of binding to an OpenCRISPR-1 polypeptide:

[0257] GUUUUAGAGCUGUGUUGAAAAACACAGCAAGUUAAAAUAAGGCUUUGUCCGUAUCCAACUUGAA AAAGUGAGCACCGAUUCGGUGC (SEQ ID NO: 465);

[0258] GUUUUAGAGCUGGAAACAGCAAGUUAAAAUAAGGCUUUGUCCGUAUCCAACUUGAAAAAGUGAG CACCGAUUCGGUGC (SEQ ID NO: 466); and GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGC (SEQ ID NO: 467).

[0259] By “subject” or “patient” is meant a mammal, including, but not limited to, a human or non-human mammal. In embodiments, the mammal is a bovine, equine, canine, ovine, rabbit, rodent, nonhuman primate, or feline. In an embodiment, “patient” refers to a mammalian subject with a higher than average likelihood of developing a disease or a disorder. Exemplary patients can be humans, non-human primates, cats, dogs, pigs, cattle, cats, horses, camels, llamas, goats, sheep, rodents (e.g., mice, rabbits, rats, or guinea pigs) and other mammalians that can benefit from the therapies disclosed herein. Exemplary human patients can be male and / or female.

[0260] “Patient in need thereof’ or “subject in need thereof’ is referred to herein as a patient diagnosed with, at risk or having, predetermined to have, or suspected of having a disease or disorder.

[0261] The terms “pathogenic mutation”, “pathogenic variant”, “disease causing mutation”, “disease causing variant”, “deleterious mutation”, or “predisposing mutation” refers to a genetic alteration or mutation that is associated with a disease or disorder or that increases an individual’s susceptibility or predisposition to a certain disease or disorder. In some embodiments, the pathogenic mutation comprises at least one wild-type amino acid substituted by at least one pathogenic amino acid in a protein encoded by a gene.

[0262] The terms “protein”, “peptide”, “polypeptide”, and their grammatical equivalents are used interchangeably herein, and refer to a polymer of amino acid residues linked together by peptide (amide) bonds. A protein, peptide, or polypeptide can be naturally occurring, recombinant, or synthetic, or any combination thereof.

[0263] The term “fusion protein” as used herein refers to a hybrid polypeptide which comprises protein domains from at least two different proteins.

[0264] The term “recombinant” as used herein in the context of proteins or nucleic acids refers to proteins or nucleic acids that do not occur in nature but are the product of human engineering.ATTORNEY DOCKET NO. 180802-047501 / PCT

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[0266] For example, in some embodiments, a recombinant protein or nucleic acid molecule comprises an amino acid or nucleotide sequence that comprises at least one, at least two, at least three, at least four, at least five, at least six, or at least seven mutations as compared to any naturally occurring sequence.

[0267] By “reduces” is meant a negative alteration of at least 10%, 25%, 50%, 75%, or 100%. By “reference” is meant a standard or control condition. In one embodiment, the reference is a wild type or healthy cell. In other embodiments and without limitation, a reference is an untreated cell that is not subjected to a test condition, or is subjected to placebo or normal saline, medium, buffer, and / or a control vector that does not harbor a polynucleotide of interest. In some cases, a “reference” is an untreated subject, such as a subject not administered a hematopoietic stem cell edited according to the methods of the present disclosure. In some cases, the subject is a healthy subject. In some embodiments, the reference is an unedited or wild type cell, polypeptide, or polynucleotide.

[0268] A “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset of or the entirety of a specified sequence; for example, a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence. For polypeptides, the length of the reference polypeptide sequence will generally be at least about 16 amino acids, at least about 20 amino acids, at least about 25 amino acids, about 35 amino acids, about 50 amino acids, or about 100 amino acids. For nucleic acids, the length of the reference nucleic acid sequence will generally be at least about 50 nucleotides, at least about 60 nucleotides, at least about 75 nucleotides, about 100 nucleotides or about 300 nucleotides or any integer thereabout or therebetween. In some embodiments, a reference sequence is a wild-type sequence of a protein of interest. In other embodiments, a reference sequence is a polynucleotide sequence encoding a wild-type protein.

[0269] The terms “RNA-programmable nuclease,” and “RNA-guided nuclease” refer to a nuclease that forms a complex with (e.g., binds or associates with) one or more RNA(s) that is not a target for cleavage. In some embodiments, an RNA-programmable nuclease, when in a complex with an RNA, may be referred to as a nuclease-RNA complex. Typically, the bound RNA(s) is referred to as a guide RNA (gRNA).

[0270] As used herein, the term “scFv” refers to a single chain Fv antibody in which the variable domains of the heavy chain and the light chain from an antibody have been joined to form one chain. scFv fragments contain a single polypeptide chain that includes the variable region of an antibody light chain (VL) (e.g, CDR-L1, CDR- L2, and / or CDR-L3) and the variable region of an antibody heavy chain (VH) (e.g, CDR-H1, CDR-H2, and / or CDR-H3) separated by a linker.ATTORNEY DOCKET NO. 180802-047501 / PCT

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[0272] The linker that joins the VL and VH regions of a scFv fragment can be a peptide linker composed of proteinogenic amino acids. Alternative linkers can be used to so as to increase the resistance of the scFv fragment to proteolytic degradation (for example, linkers containing D-amino acids), in order to enhance the solubility of the scFv fragment (for example, hydrophilic linkers such as polyethylene glycol-containing linkers or polypeptides containing repeating glycine and serine residues), to improve the biophysical stability of the molecule (for example, a linker containing cysteine residues that form intramolecular or intermolecular disulfide bonds), or to attenuate the immunogenicity of the scFv fragment (for example, linkers containing glycosylation sites). It will also be understood by one of ordinary skill in the art that the variable regions of the scFv molecules described herein can be modified such that they vary in amino acid sequence from the antibody molecule from which they were derived. For example, nucleotide or amino acid substitutions leading to conservative substitutions or changes at amino acid residues can be made (e.g., in CDR and / or framework residues) so as to preserve or enhance the ability of the scFv to bind to the antigen recognized by the corresponding antibody.

[0273] By “selectively binds” is meant specifically binds a wild type version of the cell surface protein but exhibits reduced binding or fails to detectably bind to the cell surface protein comprising a mutation. In embodiments, an antibody of the present disclosure selectively binds to a wild type CD38 polypeptide but exhibits reduced binding to a CD38 polypeptide comprising one or more amino acid alterations, such as those provided herein, relative to the wild type CD38 polypeptide. In embodiments, an antibody of the present disclosure binds a wild type CD38 polypeptide 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1-fold, 5-fold, 1.75-fold, 2-fold, 3-fold, 4-fold, 5 -fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold more strongly (e.g., as quantified using KD(M), where a lower KD(M) indicates stronger binding) than to an altered CD38 polypeptide of the present disclosure.

[0274] By “specifically binds” is meant a nucleic acid molecule, polypeptide, polypeptide / polynucleotide complex, compound, or molecule that recognizes and binds a polypeptide and / or nucleic acid molecule of the disclosure, but which does not substantially recognize and bind other molecules in a sample, for example, a biological sample.

[0275] By “substantially identical” is meant a polypeptide or nucleic acid molecule exhibiting at least 50% identity to a reference amino acid sequence. In one embodiment, a reference sequence is a wild-type amino acid or nucleic acid sequence. In another embodiment, a reference sequence is any one of the amino acid or nucleic acid sequences described herein. In one embodiment, such a sequence is at least about 60%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, orATTORNEY DOCKET NO. 180802-047501 / PCT

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[0277] even 99.99%, identical at the amino acid level or nucleic acid level to the sequence used for comparison.

[0278] Sequence identity is typically measured using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, or PILEUP / PRETTYBOX programs). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and / or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.

[0279] Nucleic acid molecules useful in the methods of the disclosure include any nucleic acid molecule that encodes a polypeptide of the disclosure or a functional fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence but will typically exhibit substantial identity. Polynucleotides having “substantial identity” to an endogenous sequence are typically capable of hybridizing with at least one strand of a doublestranded nucleic acid molecule. Nucleic acid molecules useful in the methods of the disclosure include any nucleic acid molecule that encodes a polypeptide of the disclosure or a functional fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence but will typically exhibit substantial identity. Polynucleotides having “substantial identity” to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. By “hybridize” is meant pair to form a double-stranded molecule between complementary polynucleotide sequences (e.g., a gene described herein), or portions thereof, under various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A. R. (1987) Methods Enzymol. 152:507).

[0280] By “split” is meant divided into two or more fragments.

[0281] A “split polypeptide” or “split protein” refers to a protein that is provided as an N-terminal fragment and a C-terminal fragment translated as two separate polypeptides from a nucleotide sequence(s). The polypeptides corresponding to the N-terminal portion and the C-terminal portion of the split protein may be spliced in some embodiments to form a “reconstituted” protein. In embodiments, the split polypeptide is a nucleic acid programmable DNA binding protein (e.g. a Cas9) or a base editor.

[0282] By “ Streptococcus pyogenes Cas9 (spCas9) polypeptide” is meant a nucleic acid programmable DNA binding domain (napDNAbp) comprising an amino acid sequence with atATTORNEY DOCKET NO. 180802-047501 / PCT

[0283] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0284] least 85% identity to the following amino acid sequence:

[0285] MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRL KRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAY HEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTY NQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNF DLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMD GTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRI PYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHS LLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFD SVEISGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTF KEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQ TTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINR LSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRK FDNLTKAERGGLS ELDKAGF I KRQLVETRQ I TKHVAQ I LDSRMNTKYDENDKL I RE VKVI TLKS KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAK SEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLS MPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKG KSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFELENGRKRMLAS AGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEI IEQISEFSKRV ILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLD ATLIHQSITGLYETRIDLSQLGGD (SEQ ID NO: 197), or a functional fragment thereof. In some embodiments, the spCas9 polypeptide lacks an N-terminal methionine. In some embodiments, spCas9 polypeptide comprises alterations, as described herein. In some embodiments, spCas9 contains a D10A amino acid alteration. In some embodiments the SpCas9 polypeptide has PAM specificity for a PAM containing the nucleotide sequence NGG, where “N” is A, C, T, or G. In some embodiments, the SpCas9 polypeptide further comprises the amino acid alterations I322V, S409I, E427G, R654L, R753G, R1114G, D1135N, E1219V, D1332N, R1335Q, T1337N, S1338T, and H1349R referenced to SEQ ID NO: 197 and has protospacer-adjacent motif (PAM) specificity for a PAM containing the nucleotide sequence NRCH, where “N” is A, C, T, or G, “R” is A or G, and “FT is A, C, or T.

[0286] By “ Streptococcus pyogenes Cas9 (spCas9) polynucleotide” is meant a polynucleotide encoding an spCas9 polypeptide.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0287] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0288] The term “target site” refers to a nucleotide sequence or nucleobase of interest within a nucleic acid molecule that is modified. In embodiments, the modification is deamination of a base.

[0289] The term “transfecting” or “transfection” is used synonymously and according to some aspects and embodiments herein means the introduction of heterologous nucleic acid (DNA / RNA) into a eukaryotic cell, in particular yeast cells.

[0290] As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and / or symptoms associated therewith or obtaining a desired pharmacologic and / or physiologic effect. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated. In some embodiments, the effect is therapeutic, / .<., without limitation, the effect partially or completely reduces, diminishes, abrogates, abates, alleviates, reduces the intensity of, or cures a disease and / or adverse symptom attributable to the disease. In some embodiments, the effect is preventative, / .<., the effect protects or prevents an occurrence or reoccurrence of a disease or condition. To this end, the presently disclosed methods comprise administering a therapeutically effective amount of a composition as described herein.

[0291] By “uracil glycosylase inhibitor” or “UGI” is meant an agent that inhibits the uracil-excision repair system. Base editors comprising a cytidine deaminase convert cytosine to uracil, which is then converted to thymine through DNA replication or repair. In various embodiments, a uracil DNA glycosylase (UGI) prevent base excision repair which changes the U back to a C. In some instances, contacting a cell and / or polynucleotide with a UGI and a base editor prevents base excision repair which changes the U back to a C. An exemplary UGI comprises an amino acid sequence as follows:

[0292] >splP14739IUNGI_BPPB2 Uracil-DNA glycosylase inhibitor MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPE YKPWALVIQDSNGENKIKML (SEQ ID NO: 231).

[0293] In some embodiments, the agent inhibiting the uracil-excision repair system is a uracil stabilizing protein (USP). See, e.g., WO 2022015969 Al, incorporated herein by reference.

[0294] As used herein, the term “vector” refers to a means of introducing a nucleic acid molecule into a cell, resulting in a transformed cell. Vectors include plasmids, transposons, phages, viruses, liposomes, lipid nanoparticles, and episomes.

[0295] Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination ofATTORNEY DOCKET NO. 180802-047501 / PCT

[0296] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0297] numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.

[0298] As used herein, the term “VH” refers to the variable region of an immunoglobulin heavy chain of an antibody, including the heavy chain of an Fv, scFv, or Fab. References to “VL” refer to the variable region of an immunoglobulin light chain, including the light chain of an Fv, scFv, dsFv or Fab. Antibodies (Abs) and immunoglobulins (Igs) are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific target, immunoglobulins include both antibodies and other antibody-like molecules which lack target specificity. Native antibodies and immunoglobulins are usually heterotetrameric glycoproteins of about 150,000 Daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each heavy chain of a native antibody has at the amino terminus a variable domain (VH) followed by a number of constant domains. Each light chain of a native antibody has a variable domain at the amino terminus (VL) and a constant domain at the carboxy terminus.

[0299] The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.

[0300] All terms are intended to be understood as they would be understood by a person skilled in the art. 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 the disclosure pertains

[0301] In this application, the use of the singular includes the plural unless specifically stated otherwise. It must be noted that, as used in the specification, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. In this application, the use of “or” means “and / or” unless stated otherwise. Furthermore, use of the term “including” as well as other forms, such as “include”, “includes,” and “included,” is not limiting.

[0302] As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended. This wording indicates that specified elements, features, components, and / or method steps are present, but does not exclude the presence of other elements, features, components, and / or method steps. Any embodiments specified as “comprising” a particularATTORNEY DOCKET NO. 180802-047501 / PCT

[0303] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0304] component(s) or element(s) are also contemplated as “consisting of’ or “consisting essentially of’ the particular component(s) or element(s) in some embodiments. It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method or composition of the present disclosure, and vice versa. Furthermore, compositions of the present disclosure can be used to achieve methods of the present disclosure.

[0305] The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, z.e., the limitations of the measurement system.

[0306] Reference in the specification to “some embodiments,” “an embodiment,” “one embodiment” or “other embodiments” means that a particular feature, structure, or characteristic described in connection with the embodiments is included in at least some embodiments, but not necessarily all embodiments, of the present disclosures.

[0307] BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 provides a bar graph showing percent maximum A-to-G editing (i.e., percent of total cells having an A-to-G base change at a target site) measured in CD34+ cells transfected with the indicated base editor systems to alter a CD38 polynucleotide sequence in the cells. The base editor systems contained one of the guide RNAs indicated along the x-axis and an mRNA molecule encoding the adenosine base editor ABE8.8 having specificity for the protospacer-adjacent motif (PAM) NGG or encoding the base editor ABE8.20 (F149Y) having specificity for the PAM NRCH, where “N” represents A, C, G, or T and “R” represents A or G. Sequences for the guide RNAs and base editors are provided in Tables 1 and 2. In FIG. 1, the term “MaxCyte” indicates the MaxCyte® device used to transfect the cells with the base editor systems using electroporation. Base editing rates were measured at 5-days following electroporation (EP) using next-generation sequencing (NGS). Amino acid alterations introduced to the CD38 polynucleotide sequence using each guide are indicated in FIG. 1 by the arrows, namely base editor systems containing gRNA9239 introduced a base edit resulting in a Q107R amino acid alteration in CD38, the base editor systems containing gRNA9240 introduced a base edit(s) resulting in one or more of Q115R and T116A amino acid alterations in CD38, the base editor systems containing gRNA9245 introduced a base edit(s) resulting in one or more of D141G and Ml 42V amino acid alterations in CD38, the base editor systems containing gRNA9247 introduced a base edit(s) resulting in one or more of E233G and K234G amino acid alterations in CD38, the base editor systems containing gRNA9253 or gRNA9254 introduced a base edit(s) resulting in one or more of L149P and L150P amino acid alterations in CD38, the base editorATTORNEY DOCKET NO. 180802-047501 / PCT

[0308] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0309] system containing gRNA9255 introduced a base edit(s) resulting in one or more of E76G, M77V, and R78G amino acid alterations in CD38, and the base editor system containing gRNA9232 introduced a base edit(s) resulting in a V203A amino acid alteration in CD38. Amino acid alterations introduced to the CD38 polypeptide using each guide are also listed in Table 1.

[0310] FIG. 2 provides a schematic diagram summarizing the experiment undertaken to gather the data presented in FIG. 1. In FIG. 2, “X VIVO 10” refers to the medium in which the CD34+ cells were cultured, “EP” indicates “electroporation,” and “Mobilized PB CD34+” indicates CD34+ hematopoietic stem cells (HSCs) collected from mobilized peripheral blood (PB) of a donor.

[0311] FIGs. 3A to 3C provide plots and a bar graph demonstrating that CD34+ cells surfaceexpressing CD38 variants (namely, CD38 variants containing one of the following amino acid alterations: Q107R; T116A; D141G and / or M142V; K234E, K234G, or K234R; L149P and / or L150P; E76G, M77V, and / or R78G; or V203A) prepared using base editor systems listed in FIG. 1 showed reduced levels of binding to Antibody A and / or Antibody B, which were monoclonal antibodies capable of binding to a wild-type CD38 protein. FIG. 3A provides a plot showing secondary antibody mean fluorescence intensity (MFI) for CD34+ cells expressing the indicated CD38 variant polypeptides and contacted with different concentrations of Antibody A.

[0312] FIG. 3B provides a plot showing secondary antibody mean fluorescence intensity (MFI) for CD34+ cells expressing the indicated CD38 variant polypeptides and contacted with different concentrations of Antibody B. FIG. 3C provides a bar graph showing on-target editing rates for the base editor systems used to prepare the CD34+ cells of FIGs. 3A and 3B, where the cells were transfected with base editor systems containing one of the guide RNAs indicated along the x-axis and an mRNA molecule encoding the adenosine base editor ABE8.8 having specificity for the protospacer-adjacent motif (PAM) NGG or encoding the base editor ABE8.20 (F149Y) having specificity for the PAM NRCH, where “N” represents A, C, G, or T and “R” represents A or G. In FIG. 3C, the CD38 alterations introduced using each guide are indicated in parenthesis. On-target editing was assessed at day 5 post-electroporation using next-generation sequencing.

[0313] FIGs. 4A to 4C provide plots and a bar graph demonstrating that RPMI8224 and RPMI8226 multiple myeloma (MM) cells surface-expressing CD38 variants (namely, CD38 variants containing one of the following amino acid alterations: T116A; D141G and / or M142V; E76G, M77V, and / or R78G) prepared using base editor systems listed in FIG. 1 showed reduced levels of binding to Antibody A and / or Antibody B, which were monoclonal antibodies capable of binding to a wild-type CD38 protein. FIG. 4A provides a plot showing secondary antibody mean fluorescence intensity (MFI) for RPMI8224 cells expressing the indicated CD38 variantATTORNEY DOCKET NO. 180802-047501 / PCT

[0314] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0315] polypeptides and contacted with different concentrations of Antibody A. FIG. 4B provides a plot showing secondary antibody mean fluorescence intensity (MFI) for RPMI8226 cells expressing the indicated CD38 variant polypeptides and contacted with different concentrations of Antibody B. FIG. 4C provides a bar graph showing on-target editing rates for the base editor systems used to prepare the RPMI8226 MM cells of FIG. 4B, where the cells were transfected with base editor systems containing one of the guide RNAs indicated along the x-axis and an mRNA molecule encoding the adenosine base editor ABE8.8 having specificity for the protospacer-adjacent motif (PAM) NGG or encoding the base editor ABE8.20 (F149Y) having specificity for the PAM NRCH, where “N” represents A, C, G, or T and “R” represents A or G. In FIG. 4C, the CD38 alterations introduced using each guide are indicated in parenthesis. On-target editing was assessed at day 4 post-electroporation using next-generation sequencing.

[0316] DETAILED DESCRIPTION

[0317] The disclosure features compositions and methods for non-genotoxic monoclonal antibody (mAb) conditioning, where the methods involve altering a cluster of differentiation 38 (CD38) polynucleotide sequence in a hematopoietic stem cell (HSC) or progenitor thereof to encode a CD38 polypeptide with reduced binding to the antibody. In various embodiments, the methods further include introducing a therapeutic alteration to a gene of the HSC or progenitor thereof for treatment of a disease or disorder.

[0318] The embodiments of the disclosure are based, at least in part, upon the development of a non-genotoxic, busulfan-free, conditioning approach. The embodiments of the disclosure were developed with the goal, among others, of reducing challenges associated with the standard of care conditioning regimen. The non-genotoxic conditioning efforts aimed to leverage base editing technologies to engineer hemopoietic stem cells (eHSCs) that can be coupled with an anti-CD38 monoclonal antibody (mAb) reagent capable of conditioning a patient prior to, during, or subsequent to transplantation. Through base editing, an engineered stem cell antibody paired evasion, or “ESCAPE”, approach was developed that enables the engineered HSCs to be resistant to an anti-CD38 mAb still present in the system and / or allows the ability to administer a second dose of the anti-CD38 mAb after administration of the HSCs. The ESCAPE (Engineered Stem Cell Antibody Paired Evasion) strategy provides a non-genotoxic alternative to conventional conditioning regimens by creating base-edited hematopoietic stem cells (HSCs) that are resistant to antibody -mediated targeting, enabling selective elimination of unedited cells. In embodiments, the engineered hematopoietic stem cells (eHSCs) can selectively escape ablation.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0319] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0320] The methods described herein provide for the selective targeting of endogenous HSCs, while sparing edited HSCs. Accordingly, antibody or antibody-drug conjugate (ADC) treatment used for conditioning prior to hematopoietic stem cell transplantation (HSCT) can continue to be administered following HSCT to expand gene edited cells in vivo or treat malignant disease with repeated dosing. This minimizes the risk of killing edited cells. Edited cells would allow for the administration of antibody or ADC without Fc modifications to reduce their half-life. This has the potential to enable the use of antibodies with longer half-lives and simplify the development of ADCs. Clinical trial design is also simplified - HSCs could be infused prior to or concurrently with conditioning with little or no risk of being depleted. The methods provide a benefit for all patients regardless of immune status.

[0321] In one embodiment, CD38 is altered (e.g., using base editing) in a cell for transplantation to prevent binding of anti-CD38 antibody. In various embodiments, the alterations to the CD38 polypeptide are in the extracellular domain of CD38. In some embodiments, the alterations to CD38 do not interfere with normal functioning of CD38. Using base editing, a nucleobase change may be generated to create an amino acid substitution in CD38. Administering a polypeptide capable of binding to CD38 results in depleting unedited HSCs and progenitor cells in the patient (conditioning). Autologous gene edited HSCs are transplanted into the patient. Gene-edited cells compete with residual host HSCs to repopulate bone marrow (BM). The polypeptides capable of binding to CD38 bind to wild-type CD38 but cannot bind to HSCs expressing an edited CD38 polypeptide. Thus, native, wild-type HSCs are targeted by the CD38-binding polypeptide, but gene edited HSCs are not. In embodiments, both the edited and unedited cells express active CD38 polypeptides. In contrast, gene-edited HSCs are refractory to the CD38-binding polypeptide because amino acid substitution(s) introduced in the altered CD38 polypeptide prevents the binding of CD38-binding polypeptide but, in various embodiments, does not interfere with normal CD38 activity.

[0322] In embodiments, the methods of the disclosure enable a reduction or elimination of use of alkylating agents for conditioning. In some instances, the reduction is a reduction of about, or at least about, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%. In some instances, the methods of the disclosure are associated with a reduction in or avoidance of side effects associated with an alkylating agent (e.g., busulfan). In some cases, the side effect is selected from one or more of intestinal mucosal damage, alopecia, pancytopenia, anemia, amenorrhea, impaired spermatogenesis, increased risk of malignancy, and infertility.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0323] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0324] CLUSTER OF DIFFERENTIATION 38

[0325] CD38 is a type II transmembrane glycoprotein expressed on the surface of various immune cells, including plasma cells, B cells, T cells, and NK cells, as well as on some non-hematopoietic cells. Its expression is particularly high on plasma cells, which has made it a valuable target in treating multiple myeloma and other B cell-related hematologic malignancies. In clinical applications, anti-CD38 antibodies have been developed to target CD38 on malignant plasma cells, aiding in the elimination of these cells in multiple myeloma therapy. CD38 may also be useful as a target in autoimmune diseases such as AL amyloidosis.

[0326] One approach to eliminate hematopoietic stem cells from a niche is to contact the cells with an anti-CD38 polypeptide (e.g., an antibody or chimeric antigen receptor) or antibody-drug conjugate that interferes with proper functioning of the CD38 polypeptide and / or mediates killing of cells expressing a wild-type CD38 polypeptide. Accordingly, CD38 is a target for hematopoietic stem cell transplantation (HSCT) antibody-based conditioning. Non-limiting examples of antibodies suitable for use in the methods of the disclosure include Antibody A and Antibody B, an Antibody A or Antibody B polypeptide, or an Antibody A or Antibody B fragment or variant thereof.

[0327] METHODS OF TREATMENT

[0328] The methods and compositions disclosed herein may be used to condition a subject's tissues (e.g., bone marrow) for engraftment or transplant and following such conditioning, a stem cell population is administered to the subject. The transplanted cells (e.g., HSCs) can be autologous cells or allogeneic cells. In some aspects, or embodiments thereof, the HSCs have been altered according to the methods of the disclosure to express a CD38 polypeptide variant having reduced binding to a polypeptide (e.g., an antibody) capable of binding to a wild-type CD38 polypeptide. In certain aspects, the stem cell population comprises an exogenous stem cell population. In some embodiments, the stem cell population comprises the subject's endogenous stem cells (e.g., endogenous stem cells that have been genetically modified to correct a disease or genetic defect). Such methods and compositions may be useful for treating such diseases without causing the toxicities that are observed in response to traditional conditioning therapies, such as irradiation.

[0329] Hematopoietic stem cell transplant therapy can be administered to a subject in need of treatment so as to populate or re-populate one or more blood cell types. Hematopoietic stem cells generally exhibit multi-potency, and can thus differentiate into multiple different blood lineages including, but not limited to, granulocytes (e.g., promyelocytes, neutrophils, eosinophils,ATTORNEY DOCKET NO. 180802-047501 / PCT

[0330] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0331] basophils), erythrocytes (e.g., reticulocytes, erythrocytes), thrombocytes (e.g., megakary oblasts, platelet producing megakaryocytes, platelets), monocytes (e.g., monocytes, macrophages), dendritic cells, microglia, osteoclasts, and lymphocytes (e.g., NK cells, B-cells and T-cells). Hematopoietic stem cells are additionally capable of self-renewal and can thus give rise to daughter cells that have equivalent potential as the mother cell, and also feature the capacity to be reintroduced into a transplant recipient whereupon they home to the hematopoietic stem cell niche and re-establish productive and sustained hematopoiesis.

[0332] Hematopoietic stem cells can thus be administered to a patient defective or deficient in one or more cell types of the hematopoietic lineage in order to reconstitute the defective or deficient population of cells in vivo, thereby treating the pathology associated with the defect or depletion in the endogenous blood cell population. The compositions and methods described herein can thus be used to treat a non-malignant hemoglobinopathy (e.g., a hemoglobinopathy selected from the group consisting of sickle cell anemia, thalassemia, Fanconi anemia, aplastic anemia, and Wiskott-Aldrich syndrome) or a hematologic malignancy (e.g., a B bell-related hematologic malignancy, such as multiple myeloma). The compositions and methods described herein can be used to treat a malignancy or proliferative disorder, such as a hematologic cancer and / or myeloproliferative disease. The compositions and methods described herein may be used to treat an autoimmune disease, such as AL amyloidosis. In the case of cancer or autoimmune disease treatment, the compositions and methods described herein may be administered to a patient so as to deplete a population of endogenous hematopoietic stem cells prior to hematopoietic stem cell transplantation therapy, in which case the transplanted cells can home to a niche created by the endogenous cell depletion step and establish productive hematopoiesis and / or a healthy immune system. This, in turn, can re-constitute a population of cells depleted during cancer cell eradication, such as during systemic chemotherapy. Exemplary hematological cancers that can be treated using the compositions and methods described herein include, without limitation, acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphoid leukemia, multiple myeloma, diffuse large B-cell lymphoma, B cell-related hematologic malignancies (e.g., multiple myeloma), and non-Hodgkin's lymphoma, as well as other cancerous conditions, including neuroblastoma.

[0333] Antibodies, antigen-binding fragments thereof, and ligands described herein can be administered to a patient (e.g., a human patient suffering from cancer, an autoimmune disease, or in need of hematopoietic stem cell transplant therapy) in a variety of dosage forms. For instance, antibodies, antigen-binding fragments thereof, and ligands described herein can be administered to a patient suffering from cancer, an autoimmune disease, or in need of hematopoietic stem cellATTORNEY DOCKET NO. 180802-047501 / PCT

[0334] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0335] transplant therapy in the form of an aqueous solution, such as an aqueous solution containing one or more pharmaceutically acceptable excipients. Pharmaceutically acceptable excipients for use with the compositions and methods described herein include viscosity-modifying agents. The aqueous solution may be sterilized using techniques known in the art. Non-limiting examples of antibodies suitable for use in the methods of the disclosure include Antibody A and Antibody B.

[0336] In various embodiments, an antibody of the disclosure is administered to a subject before, after, or concurrently with administration of transplanted cells (e.g., HSCs) to the subject (e.g., HSCs altered according to the methods provided herein to express a CD38 polypeptide variant with reduced or undetectable binding to a polypeptide (e.g., an anti-CD38 antibody) relative to the binding of the polypeptide to a wild-type CD38 polypeptide). In embodiments, the methods of the disclosure involve administering cells (e.g., HSCs of the disclosure) to a subject previously that was previously administered an anti-CD38 antibody of the disclosure. In some cases, the blood of the subject contains a therapeutically effective amount of the anti-CD38 antibody at the time at which the cells are administered to the subject. The antibody of the disclosure may persist at a therapeutically effective level in a subject (e.g., in the blood of the subject) for about or at least about 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 1 wk, 2 wks, 3 wks, 4 wks, 5 wks, 10 wks, 15 wks, or 20 wks after administration of the antibody to the subject. An antibody or antigen binding fragment thereof, immunoconjugate (e.g., one selected from those described below, such as an antibody drug conjugate), or a chimeric antigen receptor T (CAR-T) cell may be administered to a subject before, after, or concurrently with an edited cell of the disclosure.

[0337] IgGl antibodies targeting CD38 can cause mast cell degranulation, which can result from Fey receptor interactions. Accordingly, in some embodiments an antibody can be modified to include one or more amino acid residue alterations in an Fc domain to reduce or eliminate binding to FcyR, binding to FcRn, and / or mast cell activation. In embodiments, an antibody is modified to include amino acid alterations that prevent or reduce hypersensitivity reactions (HSRs). In some embodiments, an antibody (e.g., Antibody A or Antibody B) is modified to include an amino acid alteration at one or more of the following sites: L234, L235, G236, D265, N297, and P329. In some cases, the antibody includes an amino acid alteration and / or combination of amino acid alterations selected from: N297Q (aglycosylated); L234A and L235A (LALA); L234A, L235A, and P329G (LALAPG); L234A, L235A, and D265A (LALADA); L234S, L235T, and G236R (STR or LSLTGR); M252Y, S254T, and T256E (YTE); and LS M428L and N434S (LS) (see, e.g., Rosenberg, et al., PloS One, 14:e0212649, the disclosure of which is incorporated herein by reference in its entirety for all purposes); where the amino acidATTORNEY DOCKET NO. 180802-047501 / PCT

[0338] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0339] positions are referenced to the following amino acid sequence:

[0340] SGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTI SAGKSISTAYLQWSSLKASDTAMYYCARHGRGYNGYEGAFDIWGQGTMVTVSSASTKGPSVFPL APSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSS LGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRT PEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK CKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESN GQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPG

[0341] (SEQ IDNO: 722).

[0342] The antibodies, antigen-binding fragments, and ligands described herein may be administered by a variety of routes, such as orally, transdermally, subcutaneously, intranasally, intravenously, intramuscularly, intraocularly, or parenterally. The most suitable route for administration in any given case will depend on the particular antibody, antigen-binding fragment, or ligand administered, the patient, pharmaceutical formulation methods, administration methods (e.g., administration time and administration route), the patient's age, body weight, sex, severity of the diseases being treated, the patient's diet, and the patient's excretion rate.

[0343] One of ordinary skill in the art would recognize that multiple administrations of the pharmaceutical compositions contemplated in particular embodiments may be required to affect the desired therapy. For example, a composition may be administered to the subject 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more times over a span of 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 1 year, 2 years, 5, years, 10 years, or more.

[0344] Administration of the pharmaceutical compositions contemplated herein may be carried out using conventional techniques including, but not limited to, infusion, transfusion, or parenterally. In some embodiments, parenteral administration includes infusing or injecting intravascularly, intravenously, intramuscularly, intraarterially, intrathecally, intratumorally, intradermally, intraperitoneally, transtracheally, subcutaneously, subcuticularly, intraarticularly, subcapsularly, subarachnoidly and intrastemally.

[0345] Immunoconjugates

[0346] In some embodiments, the methods of the disclosure involve administering an immunoconjugate to a subject, where an immunoconjugate contains an antibody conjugated to one or more heterologous molecule(s), such as, but not limited to, a cytotoxic or an imaging agent. The fusion of the cytotoxic agent with an antibody may have therapeutic value. CytotoxicATTORNEY DOCKET NO. 180802-047501 / PCT

[0347] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0348] agents include, but are not limited to, radioactive isotopes (e.g., At211, 1131, 1125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212and radioactive isotopes of Lu); chemotherapeutic agents (e.g., maytansinoids, taxanes, methotrexate, adriamicin, vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin, melphalan, mitomycin C, chlorambucil, daunorubicin or other intercalating agents); growth inhibitory agents; enzymes and fragments thereof such as nucleolytic enzymes; antibiotics; toxins such as small molecule toxins or enzymatically active toxins. In some embodiments, the antibody is conjugated to one or more cytotoxic agents, such as chemotherapeutic agents or drugs, growth inhibitory agents, toxins (e.g., protein toxins, enzymatically active toxins of bacterial, fungal, plant, or animal origin, or fragments thereof), or radioactive isotopes.

[0349] Among the antibody immunoconjugates contemplated herein are antibody-drug conjugates (ADCs), in which an antibody is conjugated to one or more drugs, including but not limited to a maytansinoid (see U. S. Patent Nos. 5,208,020, 5,416,064 and European Patent EP 0 425235 B 1); an auristatin such as monomethylauristatin drug moieties DE and DF (MMAE and MMAF) (see U. S. Patent Nos. 5,635,483 and 5,780,588, and 7,498,298); a dolastatin; a calicheamicin or derivative thereof (see U. S. Patent Nos. 5,712,374, 5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001, and 5,877,296; Hinman et al., Cancer Res. 53: 3336-3342 (1993); and Lode et al, Cancer Res. 58: 2925-2928 (1998)); an anthracycline such as daunomycin or doxorubicin (see Kratz et al., Current Med. Chem. 13: 477- 523 (2006); Jeffrey et al., Bioorganic & Med. Chem. Letters 16: 358-362 (2006); Torgov et al., Bioconj. Chem. 16: 717-721 (2005); Nagy et al, Proc. Natl. Acad. Sci. USA 97: 829-834 (2000); Dubowchik et al, Bioorg. & Med. Chem. Letters 12: 1529-1532 (2002); King et al, J. Med. Chem. 45: 4336-4343 (2002); and U. S. Patent No. 6,630,579); methotrexate; vindesine; ataxane such as docetaxel, paclitaxel, larotaxel, tesetaxel, and ortataxel; a trichothecene; and CC1065.

[0350] Also among the antibody immunoconjugates contemplated herein are those in which the antibody is conjugated to an enzymatically active toxin or fragment thereof, including but not limited to diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes.

[0351] In some embodiments, an antibody is conjugated to a protein degrader, such as those described in Frere, G., et al. Methods in Cell Biology, 167: 1-26 (2022) and Sasso, J., et al.

[0352] Biochemistry, 62:601-623 (2023), or in International Patent Applications No. WO 2021 / 053555,ATTORNEY DOCKET NO. 180802-047501 / PCT

[0353] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0354] WO 2021 / 249517, WO 2020 / 006264, WO 2008 / 115516, WO 2021 / 126805, WO 2021 / 178920, WO 2021 / 127080, WO 2014 / 094138, WO 2015 / 200795, WO 2017 / 117118, and WO 2020 / 079103 the disclosures of which is incorporated herein by reference in their entireties for all purposes. In some embodiments, the degrader is CC-122, CC-220, CC-99282, CFT7455, DKY709, CR8, GlueOl, HQ005, FPFT-2216, TMX-4116, Eragidomide, BTX-1188, MG-277, ZHX-1-161, Indisulam, E7820, dCeMMl, CQS, NRX-252114, NRX-252262, BI-3802, CCT369260, Cyclosporin A, Lupkynis, Sanglifehrin A, Auxin, Jasmonate, lenalidomide (Revlimid), lenalidomide, pomalidomide (Pomalyst), or thalidomide. Non-limiting examples of types of protein degraders suitable for use in compositions, conjugates, and / or methods of the disclosure include heterobifunctional degraders and molecular glue degraders.

[0355] Also among the antibody immunoconjugates contemplated herein are those in which the antibody is conjugated to a radioactive atom to form a radioconjugate. Exemplary radioactive isotopes include At211, 1131, 1125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212and radioactive isotopes of Lu.

[0356] Conjugates of an antibody and cytotoxic agent may be made using any of a number of known protein coupling agents, e.g., linkers, (see Vitetta et al., Science 238: 1098 (1987)). The linker may be a "cleavable linker" facilitating release of a cytotoxic drug in the cell, such as acid-labile linkers, peptidase- sensitive linkers, photolabile linkers, dimethyl linkers, and disulfide-containing linkers (Chari et al., Cancer Res. 52: 127-131 (1992); U. S. Patent No. 5,208,020).

[0357] EDITING OF TARGET GENES

[0358] To produce the gene edits described herein, cells are collected from a subject and contacted with one or more guide RNAs and a nucleobase editor polypeptide comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a cytidine deaminase or adenosine deaminase or comprising one or more deaminases with cytidine deaminase and / or adenosine deaminase activity (e.g., a “dual deaminase” which has cytidine and adenosine deaminase activity). In some embodiments, cells to be edited are contacted with at least one nucleic acid, wherein the at least one nucleic acid encodes one or more guide RNAs and a nucleobase editor polypeptide comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a cytidine deaminase. In some embodiments, the gRNA comprises nucleotide analogs. In some instances, the gRNA is added directly to a cell. These nucleotide analogs can inhibit degradation of the gRNA from cellular processes. In various embodiments, editing a cell involves contacting the cell with an mRNA molecule encoding a base editor together with one orATTORNEY DOCKET NO. 180802-047501 / PCT

[0359] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0360] more guide RNAs capable of directing the base editor to alter a target nucleotide(s) at a target site(s) in the cell.

[0361] Variants of the spacer sequences listed in Table 1 comprising 1, 2, 3, 4, or 5 nucleobase alterations are contemplated. For example, variation of a target polynucleotide sequence within a population (e.g., single nucleotide polymorphisms) may require said alterations to a spacer sequence to allow the spacer to better bind a variant of a target sequence in a subject.

[0362] In various instances, it is advantageous for a spacer sequence to include a 5' and / or a 3' “G” nucleotide. In some cases, for example, any spacer sequence or guide polynucleotide provided herein comprises or further comprises a 5' “G”, where, in some embodiments, the 5' “G” is or is not complementary to a target sequence. In some embodiments, the 5' “G” is added to a spacer sequence that does not already contain a 5' “G” For example, it can be advantageous for a guide RNA to include a 5' terminal “G” when the guide RNA is expressed under the control of a U6 promoter or the like because the U6 promoter prefers a “G” at the transcription start site (see Cong, L. el al. “Multiplex genome engineering using CRISPR / Cas systems. Science 339:819-823 (2013) doi: 10.1126 / science.l231143). In some cases, a 5' terminal “G” is added to a guide polynucleotide that is to be expressed under the control of a promoter but is optionally not added to the guide polynucleotide if or when the guide polynucleotide is not expressed under the control of a promoter.

[0363] Exemplary guide RNAs are provided in the following Table 1 and exemplary base editor sequences are provided in the following Table 2.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0364] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0365] Table 1 Guide RNAs

[0366] sgRNA Target gRNA Sequence2SEQ Spacer Sequence SEQ Amino ID NO ID NO Acid

[0367] Change

[0368] (s)1

[0369] gRNA R78G mAsmUsmGsAGGUGGGUUGGCGACUA 723 AUGAGGUGGGU 724 9237 GUUUUAGAGCUAGAAAUAGCAAGUUA UGGCGACUA

[0370] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0371] smUsmUsU

[0372] gRNA Y106C, mCsmUsmAsUCAGCCACUAAUGAAGU 725 CUAUCAGCCAC 726 9238 Q107R GUUUUAGAGCUAGAAAUAGCAAGUUA UAAUGAAGU

[0373] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0374] smUsmUsU

[0375] gRNA Q107R mUsmAsmUsCAGCCACUAAUGAAGUU 727 UAUCAGCCACU 728 9239 GUUUUAGAGCUAGAAAUAGCAAGUUA AAUGAAGUU

[0376] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0377] smUsmUsU

[0378] gRNA Q115R, mUsmCsmAsGACCGUACCUUGCAACA 729 UCAGACCGUAC 730 9240 T116A GUUUUAGAGCUAGAAAUAGCAAGUUA CUUGCAACA

[0379] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0380] smUsmUsU

[0381] gRNA N120D mUsmAsmCsCUUGCAACAAGGUAAUU 731 UACCUUGCAAC 732 9241 GUUUUAGAGCUAGAAAUAGCAAGUUA AAGGUAAUU

[0382] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0383] smUsmUsU

[0384] gRNA N120G mAsmCsmCsUUGCAACAAGGUAAUUG 733 ACCUUGCAACA 734 9242 GUUUUAGAGCUAGAAAUAGCAAGUUA AGGUAAUUG

[0385] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0386] smUsmUsU

[0387] gRNA N120G mCsmCsmUsUGCAACAAGGUAAUUGG 735 CCUUGCAACAA 736 9243 GUUUUAGAGCUAGAAAUAGCAAGUUA GGUAAUUGG

[0388]

[0389] AAAU AAGG CU AGUC CGUU AU C AACUU

[0390] 1The target amino acid changes are each referenced to the following CD38 polypeptide sequence:

[0391] MANCEFSPVSGDKPCCRLSRRAQLCLGVSILVLILVVVLAVVVPRWRQTWSGPGTTKRFPETVL ARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCNITEEDYQPLMKLGTQTVPCNKILLWSRI KDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFNTSKINYQSCPDWRKDCSNNPVSVFWKTV SRRFAEAACDVVHVMLNGSRSKIFDKNSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQD PTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI (SEQ ID NO: 719).

[0392] 2“mN” indicates a 2'-0Me modification of the nucleotide “N”, and “Ns” indicates that the nucleotide “N” is linked to the following (i.e., 3') nucleotide by a phosphorothioate (PS).ATTORNEY DOCKET NO. 180802-047501 / PCT

[0393] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0394] sgRNA Target gRNA Sequence2SEQ Spacer Sequence SEQ Amino ID NO ID NO Acid

[0395] Change

[0396] (s)1

[0397] GAAAAAGUGGCACCGAGUCGGUGCmU

[0398] smUsmUsU

[0399] gRNA Q139R, mCsmCsmAsGCGGGACAUGUUCACCC 737 CCAGCGGGACA 738 9244 D141G GUUUUAGAGCUAGAAAUAGCAAGUUA UGUUCACCC

[0400] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0401] smUsmUsU

[0402] gRNA D141G, mGsmCsmGsGGACAUGUUCACCCUGG 739 GCGGGACAUGU 740 9245 M142V GUUUUAGAGCUAGAAAUAGCAAGUUA UCACCCUGG

[0403] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0404] smUsmUsU

[0405] gRNA H205R mGsmUsmGsGUCCAUGUGAUGCUCAA 741 GUGGUCCAUGU 742 9246 GUUUUAGAGCUAGAAAUAGCAAGUUA GAUGCUCAA

[0406] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0407] smUsmUsU

[0408] gRNA E233G, mAsmGsmAsGAAGGUUCAGACACUAG 743 AGAGAAGGUUC 744 9247 K234G GUUUUAGAGCUAGAAAUAGCAAGUUA AGACACUAG

[0409] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0410] smUsmUsU

[0411] gRNA Q236R, mAsmGsmGsUUCAGACACUAGAGGCC 745 AGGUUCAGACA 746 9248 T237A GUUUUAGAGCUAGAAAUAGCAAGUUA CUAGAGGCC

[0412] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0413] smUsmUsU

[0414] gRNA Q236R, mGsmGsmUsUCAGACACUAGAGGCCU 747 GGUUCAGACAC 748 9249 T237A GUUUUAGAGCUAGAAAUAGCAAGUUA UAGAGGCCU

[0415] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0416] smUsmUsU

[0417] gRNA E239G mCsmUsmAsGAGGCCUGGGUGAUACA 749 CUAGAGGCCUG 750 9250 GUUUUAGAGCUAGAAAUAGCAAGUUA GGUGAUACA

[0418] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0419] smUsmUsU

[0420] gRNA K276E mUsmUsmUsCCUGCAAGAAUAUCUAC 751 UUUCCUGCAAG 752 9251 GUUUUAGAGCUAGAAAUAGCAAGUUA AAUAUCUAC

[0421] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0422] smUsmUsU

[0423] gRNA C296R mGsmAsmUsGUGCAAGAUGAAUCCUC 753 GAUGUGCAAGA 754 9252 GUUUUAGAGCUAGAAAUAGCAAGUUA UGAAUCCUC

[0424] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0425] smUsmUsU

[0426] gRNA L149P, mAsmGsmCsCUAGCAGCGUGUCCUCC 755 AGCCUAGCAGC 756 9253 L150P GUUUUAGAGCUAGAAAUAGCAAGUUA GUGUCCUCC

[0427]

[0428] AAAU AAGG CU AGUC CGUU AU C AACUUATTORNEY DOCKET NO. 180802-047501 / PCT

[0429] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0430] sgRNA Target gRNA Sequence2SEQ Spacer Sequence SEQ Amino ID NO ID NO Acid

[0431] Change

[0432] (s)1

[0433] GAAAAAGUGGCACCGAGUCGGUGCmU

[0434] smUsmUsU

[0435] gRNA L149P, mGsmCsmCsUAGCAGCGUGUCCUCCA 757 GCCUAGCAGCG 758 9254 L150P GUUUUAGAGCUAGAAAUAGCAAGUUA UGUCCUCCA

[0436] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0437] smUsmUsU

[0438] gRNA E76G, mCsmUsmGsAGAUGAGGUGGGUUGGC 759 CUGAGAUGAGG 760 9255 M77V, GUUUUAGAGCUAGAAAUAGCAAGUUA UGGGUUGGC

[0439] R78G AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0440] smUsmUsU

[0441] gRNA E103G, mUsmAsmCsUGAAGAAGACUAUCAGC 761 UACUGAAGAAG 762 9256 E104G GUUUUAGAGCUAGAAAUAGCAAGUUA ACUAUCAGC

[0442] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0443] smUsmUsU

[0444] gRNA M110V mCsmUsmAsAUGAAGUUGGGAACUCA 763 CUAAUGAAGUU 764 9257 GUUUUAGAGCUAGAAAUAGCAAGUUA GGGAACUCA K111G AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0445] smUsmUsU

[0446] gRNA K111R mGsmAsmAsGUUGGGAACUCAGACCG 765 GAAGUUGGGAA 766 9258 GUUUUAGAGCUAGAAAUAGCAAGUUA CUCAGACCG

[0447] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0448] smUsmUsU

[0449] gRNA T114A mUsmGsmGsGAACUCAGACCGUACCU 767 UGGGAACUCAG 768 9229 GUUUUAGAGCUAGAAAUAGCAAGUUA ACCGUACCU

[0450] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0451] smUsmUsU

[0452] gRNA T114A, mGsmAsmAsCUCAGACCGUACCUUGC 769 GAACUCAGACC 770 9259 Q115R, GUUUUAGAGCUAGAAAUAGCAAGUUA GUACCUUGC T116A AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0453] smUsmUsU

[0454] gRNA N120G, mCsmUsmUsGCAACAAGGUAAUUGGG 771 CUUGCAACAAG 772 9230 K121E GUUUUAGAGCUAGAAAUAGCAAGUUA GUAAUUGGG

[0455] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0456] smUsmUsU

[0457] gRNA N120S, mCsmAsmAsCAAGGUAAUUGGGGGCA 773 CAACAAGGUAA 774 9231 K121G GUUUUAGAGCUAGAAAUAGCAAGUUA UUGGGGGCA

[0458] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0459] smUsmUsU

[0460] gRNA D141G, mGsmGsmGsACAUGUUCACCCUGGAG 775 GGGACAUGUUC 776 9260 M142V GUUUUAGAGCUAGAAAUAGCAAGUUA ACCCUGGAG

[0461]

[0462] AAAU AAGG CU AGUC CGUU AU C AACUUATTORNEY DOCKET NO. 180802-047501 / PCT

[0463] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0464] sgRNA Target gRNA Sequence2SEQ Spacer Sequence SEQ Amino ID NO ID NO Acid

[0465] Change

[0466] (s)1

[0467] GAAAAAGUGGCACCGAGUCGGUGCmU

[0468] smUsmUsU

[0469] gRNA D202G mCsmUsmGsUGAUGUGGUCCAUGUGA 777 CUGUGAUGUGG 778 9232 GUUUUAGAGCUAGAAAUAGCAAGUUA UCCAUGUGA

[0470] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0471] smUsmUsU

[0472] gRNA Q231R mUsmUsmGsCAACCAGAGAAGGUUCA 779 UUGCAACCAGA 780 9261 GUUUUAGAGCUAGAAAUAGCAAGUUA GAAGGUUCA

[0473] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0474] smUsmUsU

[0475] gRNA Q231R, mGsmCsmAsACCAGAGAAGGUUCAGA 781 GCAACCAGAGA 782 9262 E233G GUUUUAGAGCUAGAAAUAGCAAGUUA AGGUUCAGA

[0476] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0477] smUsmUsU

[0478] gRNA E239G mGsmAsmCsACUAGAGGCCUGGGUGA 783 GACACUAGAGG 784 9263 GUUUUAGAGCUAGAAAUAGCAAGUUA CCUGGGUGA

[0479] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0480] smUsmUsU

[0481] gRNA E292G mAsmAsmUsCCUGAGGAUUCAUCUUG 785 AAUCCUGAGGA 786 9264 GUUUUAGAGCUAGAAAUAGCAAGUUA UUCAUCUUG

[0482] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0483] smUsmUsU

[0484] gRNA V288A mGsmAsmUsUUUUCACACACUGAAGA 787 GAUUUUUCACA 788 9265 GUUUUAGAGCUAGAAAUAGCAAGUUA CACUGAAGA

[0485] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0486] smUsmUsU

[0487] gRNA F284P mAsmAsmGsAAACUUGUCAGGUCUAU 789 AAGAAACUUGU 790 9266 GUUUUAGAGCUAGAAAUAGCAAGUUA CAGGUCUAU

[0488] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0489] smUsmUsU

[0490] gRNA F273P, mGsmGsmAsAAAUUGAAUAUUCCUUU 791 GGAAAAUUGAA 792 9233 S274P GUUUUAGAGCUAGAAAUAGCAAGUUA UAUUCCUUU

[0491] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0492] smUsmUsU

[0493] gRNA W241R mAsmCsmCsCAGGCCUCUAGUGUCUG 793 ACCCAGGCCUC 794 9267 GUUUUAGAGCUAGAAAUAGCAAGUUA UAGUGUCUG

[0494] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0495] smUsmUsU

[0496] gRNA V203A mAsmCsmCsACAUCACAGGCAGCUUC 795 ACCACAUCACA 796 9234 GUUUUAGAGCUAGAAAUAGCAAGUUA GGCAGCUUC

[0497]

[0498] AAAU AAGG CU AGUC CGUU AU C AACUUATTORNEY DOCKET NO. 180802-047501 / PCT

[0499] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0500] sgRNA Target gRNA Sequence2SEQ Spacer Sequence SEQ Amino ID NO ID NO Acid

[0501] Change

[0502] (s)1

[0503] GAAAAAGUGGCACCGAGUCGGUGCmU

[0504] smUsmUsU

[0505] gRNA C201R mCsmAsmUsCACACGGCAGCUUCUGCA 797 CAUCACAGGCA 798 9268 GUUUUAGAGCUAGAAAUAGCAAGUUA GCUUCUGCA

[0506] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0507] smUsmUsU

[0508] gRNA F196P mUsmGsmCsAAAUUAAAAAAAAAAAA 799 UGCAAACUUAA 800 9235 GUUUUAGAGCUAGAAAUAGCAAGUUA AAAAAAAAA

[0509] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0510] smUsmUsU

[0511] gRNA V117A mAsmAsmGsGUACGGUCUGAGUUCCC 801 AAGGUACGGUC 802 9269 GUUUUAGAGCUAGAAAUAGCAAGUUA UGAGUUCCC

[0512] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0513] smUsmUsU

[0514] gRNA L112S mGsmAsmGsUUCCCAACUUCAUUAGU 803 GAGUUCCCAAC 804 9236 GUUUUAGAGCUAGAAAUAGCAAGUUA UUCAUUAGU

[0515] AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0516] smUsmUsU

[0517] sgRNA Positive mCsmAsmGsGAUCCGCACAGACUCCA 805 CAGGAUCCGCA 806 _088 control GUUUUAGAGCUAGAAAUAGCAAGUUA CAGACUCCA

[0518] for AAAU AAGG CU AGUC CGUU AU C AACUU GAAAAAGUGGCACCGAGUCGGUGCmU

[0519] editing

[0520]

[0521] smUsmUsU

[0522] Table 2: Exemplary base editor sequences

[0523] mRNA Deaminase SpCas9 Domain Amino Acid Sequence3

[0524] Encoding the Domain Protospacer- Base Editor Adjacent Motif

[0525] (PAM)

[0526] Specificity

[0527] mRNA3944 TadA*8.8 NGG msevefsheywmrhaltlakrarderevpvgavlvl (encoding nnrvigegwnraiglhdptahaeimalrqgglvmqn NGG yrlidatlyvtfepcvmcagamihsrigrvvfgvrn ABE8.8) aktgaagslmdvlhhpgmnhrveitegiladecaal lerf f rmprrvfnaqkkaqsstdSGGSSGGSSGSET PGTSESATPES SGGS SGGSDKKYS I GLAI GTNS VGW AV I TDE YKVP S KK FK VL GNTDRH S I KKNL I GAL L FD SGETAEATRLKRTARRRYTRRKNRI CYLQE I FSNEM AKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEV AYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMI

[0528]

[0529] KFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEE3Adenosine deaminase domains are shown as lowercase plain text, nuclear localization sequences (NLS) are shown as UPPERCASE UNDERLINED TEXT, SpCas9 domains are shown as BOLD UPPERCASE TEXT, and linkers are shown as UPPERCASE PLAIN TEXT.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0530] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0531] NPINASGVDAEAILSARLSESRRLENLIAQLPGEEE NGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDT YDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDIL RVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQ LPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKP ILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQI HLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPY YVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGA SAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYN E LTKVKYVTEGMRKP AF LS GEQKKA I VDL LFKTNRK VTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTY HDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDRE MIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKL INGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSL TFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGIL QTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQ KNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEK LYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNY WRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIK RQL VETRQ I TKHVAQ I LDS RMNTKYDENDKL I REVK VITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLN A WGT AL IKKYPKLESE F V YGD YKV YD VRKM I AKS E QE I GRATAE YF F YSN IMNF FETE I TLANGE I RERP L IETNGETGEIVWDEGRDFATVREVLSMPQVNIVEET EVQTGGFSEES I LPERNSDEL I AREEDWDPEEYGGF DSPTVAYSVLVVAEVEEGESEELESVEELLGITIME RSSFEENPIDFLEAEGYEEVEEDLI IELPEYSLFEL ENGRERMLAS AGE LQEGNE LALP SE YVNF L YLASH Y EELEGSPEDNEQEQLFVEQHEHYLDEIIEQISEFSE RVILADANLDEVLSAYNEHRDEPIREQAENI IHLFT LTNLGAPAAFEYFDTTIDRERYTSTEEVLDATLIHQ SITGLYETRIDLSQLGGD (SEQ ID NO: 807) H1RNA3311 TadA*8.20 NRCH msevefsheywmrhaltlakrarderevpvgavlvl (encoding (F149Y) nnr vi ge gwnr a i g 1 hdp t ahae i ma 1 r qgg 1 vmqn NRCH yrlydatlystf epcvmcagamihsrigrvvfgvrn ABE8.20 aktgaagslmdvlhhpgmnhrveitegiladecaal (F149Y)) lcrffrmprrvfnaqkkaqsstdSGGSSGGSSGSET PGTSESATPES SGGS SGGSDEEYS I GLAI GTNS VGW AV I TDE YEVP S EE FE VL GNTDRH S I EENL I GAL L FD SGETAEATRLERTARRRYTRRENRI CYLQE I FSNEM AEVDDSFFHRLEESFLVEEDEEHERHPIFGNIVDEV AYHEEYPTIYHLREELVDSTDEADLRLIYLALAHMI EFRGHFLIEGDLNPDNSDVDELFIQLVQTYNQLFEE NPINASGVDAEAILSARLSESRRLENLIAQLPGEEE NGLFGNLIALSLGLTPNFESNFDLAEDAELQLSEDT YDDDLDNLLAQIGDQYADLFLAAENLSDAILLSDIL RVNTEITEAPLSASMVERYDEHHQDLTLLEALVRQQ LPEEYEEIFFDQSENGYAGYIDGGASQEEFYEFIEP ILEEMDGTEELLVELNREDLLREQRTFDNGI IPHQI HLGELHAILRRQGDFYPFLEDNREEIEEILTFRIPY YVGPLARGNSRFAWMTRESEETITPWNFEEVVDEGA SAQSFIERMTNFDENLPNEEVLPEHSLLYEYFTVYN E LTEVEYVTEGMREP AF LS GEQEEA I VDL LFETNRE VTVEQLEEDYFEEIECFDSVEISGVEDRFNASLGTY

[0532]

[0533] HDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREATTORNEY DOCKET NO. 180802-047501 / PCT

[0534] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0535] MIEERLETYAHLFDDEVMEQLERLRYTGWGRLSREL INGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSL TFEEDIQEAQVSGQGDSLHEHIANLAGSPAIEEGIL QTVEVVDELVEVMGGHEPENIVIEMARENQTTQEGQ KNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEK LYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNY WRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIK RQL VETRQ I TKHVAQ I LDS RMNTKYDENDKL I REVK VITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLN A WGT AL IKKYPKLESE F V YGD YKV YD VRKM I AKS E QE I GRATAE YF F YSN IMNF FETE I TLANGE I RERP L IETNGETGEIVWDEGRDFATVREVLSMPQVNIVEET EVQTGGFSEES I LPEGNSDEL I AREEDWDPEEYGGF NSPTVAYSVLVVAEVEEGESEELESVEELLGITIME RSSFEENPIDFLEAEGYEEVEEDLI IELPEYSLFEL ENGRERMLASAGVLQEGNELALPSEYVNFLYLASHY EELEGSPEDNEQEQLFVEQHEHYLDEIIEQISEFSE RVILADANLDEVLSAYNEHRDEPIREQAENI IHLFT LTNLGAP AAFE YFDTT I NREQ YNTTEE VLDATL I RQ S I T G L YE T R I D L S Q L GGD EGADKRTADGSEFESPKK KRKV (SEQ ID NO: 808)

[0536]

[0537] NUCLEOBASE EDITORS

[0538] Useful in the methods and compositions described herein are nucleobase editors that edit, modify or alter a target nucleotide sequence of a polynucleotide. Nucleobase editors described herein typically include a polynucleotide programmable nucleotide binding domain and a nucleobase editing domain (e.g, adenosine deaminase, cytidine deaminase, or a dual deaminase). A polynucleotide programmable nucleotide binding domain, when in conjunction with a bound guide polynucleotide (e.g, gRNA), can specifically bind to a target polynucleotide sequence and thereby localize the base editor to the target nucleic acid sequence desired to be edited.

[0539] Polynucleotide Programmable Nucleotide Binding Domain

[0540] Disclosed herein are base editors comprising a polynucleotide programmable nucleotide binding domain comprising all or a portion (e.g., a functional portion) of a CRISPR protein (i.e., a base editor comprising as a domain all or a portion (e.g., a functional portion) of a CRISPR protein (e.g., a Cas protein), also referred to as a “CRISPR protein-derived domain” of the base editor). A CRISPR protein-derived domain incorporated into a base editor can be modified compared to a wild-type or natural version of the CRISPR protein. A CRISPR protein-derived domain can comprise one or more mutations, insertions, deletions, rearrangements and / or recombinations relative to a wild-type or natural version of the CRISPR protein.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0541] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0542] A CRISPR enzyme can direct cleavage of one or both strands at a target sequence, such as within a target sequence and / or within a complement of a target sequence. For example, a CRISPR enzyme can direct cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence.

[0543] A Cas protein (e.g., Cas9, Cas12) or a Cas domain (e.g, Cas9, Cas12) can refer to a polypeptide or domain with at least or at least about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity and / or sequence homology to a wild-type exemplary Cas polypeptide or Cas domain. Cas (e.g., Cas9, Cas12) can refer to the wild-type or a modified form of the Cas protein that can comprise an amino acid change such as a deletion, insertion, substitution, variant, mutation, fusion, chimera, or any combination thereof.

[0544] Typically, Cas9 proteins, such as Cas9 from S. pyogenes (spCas9), require a “protospacer adjacent motif (PAM)” or PAM-like motif, which is a 2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system. The presence of an NGG PAM sequence is required to bind a particular nucleic acid region, where the “N” in “NGG” is adenosine (A), thymidine (T), or cytosine (C), and the G is guanosine. In some embodiments, any of the fusion proteins or complexes provided herein may contain a Cas9 domain that is capable of binding a nucleotide sequence that does not contain a canonical (e.g., NGG) PAM sequence. Cas9 domains that bind to non-canonical PAM sequences have been described in the art and would be apparent to the skilled artisan. For example, Cas9 domains that bind non-canonical PAM sequences have been described in Kleinstiver, B. P., et al., “Engineered CRISPR-Cas9 nucleases with altered PAM specificities” Nature 523, 481-485 (2015); and Kleinstiver, B. P., et al., “Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition” Nature Biotechnology 33, 1293-1298 (2015); the entire contents of each are hereby incorporated by reference.

[0545] In some embodiments, the polynucleotide programmable nucleotide binding domain comprises a nickase domain. For example, where a polynucleotide programmable nucleotide binding domain comprises a nickase domain derived from Cas9, the Cas9-derived nickase domain can include a D10A mutation and / or a histidine at position 840.

[0546] In some embodiments, a Cas9 nuclease has an inactive (e.g, an inactivated) DNA cleavage domain, that is, the Cas9 is a nickase, referred to as an “nCas9” protein (for “nickase” Cas9; SEQ ID NO: 201). In some embodiments the Cas9 nickase comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at leastATTORNEY DOCKET NO. 180802-047501 / PCT

[0547] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0548] 99.5% identical to any one of the Cas9 polypeptides provided herein. Additional suitable Cas9 nickases will be apparent to those of skill in the art based on this disclosure and knowledge in the field and are within the scope of this disclosure.

[0549] Also provided herein are base editors comprising a polynucleotide programmable nucleotide binding domain which is catalytically dead (i.e., incapable of cleaving a target polynucleotide sequence). dCas9 domains are known in the art and described, for example, in Qi et al., “Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.” Cell. 2013; 152(5): 1173-83, the entire contents of which are incorporated herein by reference.

[0550] The term “protospacer adjacent motif (PAM)” or PAM-like motif refers to a 2-6 base pair DNA sequence immediately following the DNA sequence targeted by a nucleic acid programmable DNA binding protein. In some embodiments, the PAM can be a 5' PAM (i.e., located upstream of the 5' end of the protospacer). In other embodiments, the PAM can be a 3' PAM (i.e., located downstream of the 5' end of the protospacer). The PAM sequence can be any PAM sequence known in the art. Suitable PAM sequences include, but are not limited to, NGG, NGA, NGC, NGN, NRN, NGT, NGTT, NGCG, NGAG, NGAN, NGNG, NGCN, NGCG, NGTN, NNGRRT, NNNRRT, NNGRR(N), TTTV, TYCV, TYCV, TATV, NNNNGATT, NNAGAAW, or NAAAAC. R is A or G; Y is a pyrimidine; N is any nucleotide base (A, C, G, or T); W is A or T.

[0551] A base editor provided herein may comprise a CRISPR protein-derived domain that is capable of binding a nucleotide sequence that contains a canonical or non-canonical protospacer adjacent motif (PAM) sequence.

[0552] Cas9 domains that bind non-canonical PAM sequences have been described in Kleinstiver, B. P., et al., “Engineered CRISPR-Cas9 nucleases with altered PAM specificities” Nature 523, 481-485 (2015); and Kleinstiver, B. P., et al., “Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition” Nature Biotechnology 33, 1293-1298 (2015); R. T. Walton et al. “Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants” Science 10.1126 / science.aba8853 (2020); Hu et al. “Evolved Cas9 variants with broad PAM compatibility and high DNA specificity,” Nature, 2018 Apr. 5, 556(7699), 57-63; Miller et al., “Continuous evolution of SpCas9 variants compatible with non-G PAMs” Nat. Biotechnol., 2020 Apr;38(4):471-481; the entire contents of each are hereby incorporated by reference.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0553] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0554] Fusion Proteins or Complexes Comprising a NapDNAbp and a Cytidine Deaminase and / or Adenosine Deaminase

[0555] Some aspects of the disclosure provide fusion proteins or complexes comprising a Cas9 domain or other nucleic acid programmable DNA binding protein (e.g., Cas12) and one or more cytidine deaminase, adenosine deaminase, or cytidine adenosine deaminase domains. It should be appreciated that the Cas9 domain may be any of the Cas9 domains or Cas9 proteins (e.g., dCas9 or nCas9) provided herein.

[0556] Exemplary, yet nonlimiting, fusion proteins are described in International PCT Application Nos. PCT / US2017 / 045381, PCT / US2019 / 044935, and PCT / US2020 / 016288, each of which is incorporated herein by reference for its entirety.

[0557] Fusion Proteins or Complexes with Internal Insertions

[0558] Provided herein are fusion proteins or complexes comprising a heterologous polypeptide fused to a nucleic acid programmable nucleic acid binding protein, for example, a napDNAbp. The heterologous polypeptide can be fused to the napDNAbp at a C-terminal end of the napDNAbp, an N-terminal end of the napDNAbp, or inserted at an internal location of the napDNAbp. In some embodiments, the heterologous polypeptide is a deaminase (e.g., cytidine or adenosine deaminase) or a functional fragment thereof. For example, a fusion protein may comprise a deaminase flanked by an N- terminal fragment and a C-terminal fragment of a Cas9 or Cas12 (e.g., Cas12b / C2c1), polypeptide.

[0559] The fusion protein or complexes can comprise more than one deaminase. The fusion protein or complex can comprise, for example, 1, 2, 3, 4, 5 or more deaminases. The deaminases in a fusion protein or complex can be adenosine deaminases, cytidine deaminases, or a combination thereof.

[0560] In some embodiments, the napDNAbp in the fusion protein or complex contains a Cas9 polypeptide or a fragment thereof.

[0561] Exemplary, yet nonlimiting, fusion proteins are described in International PCT Application Nos. PCT / US2020 / 016285 and U. S. Provisional Application Nos. 62 / 852,228 and 62 / 852,224, the contents of which are incorporated by reference herein in their entireties.

[0562] A to G Editing

[0563] In some embodiments, a base editor described herein comprises an adenosine deaminase domain. Such an adenosine deaminase domain of a base editor can facilitate the editing of anATTORNEY DOCKET NO. 180802-047501 / PCT

[0564] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0565] adenine (A) nucleobase to a guanine (G) nucleobase by deaminating the A to form inosine (I), which exhibits base pairing properties of G.

[0566] The adenosine deaminase can be derived from any suitable organism (e.g., E. coli). In some embodiments, the adenosine deaminase is from Escherichia coli, Staphylococcus aureus, Salmonella typhi, Shewanella putrefaciens, Haemophilus influenzae, Caulobacter crescentus, or Bacillus subtilis. In some embodiments, the adenine deaminase is a naturally-occurring adenosine deaminase that includes one or more mutations corresponding to any of the mutations provided herein (e.g, mutations in ecTadA). The corresponding residue in any homologous protein can be identified by e.g., sequence alignment and determination of homologous residues. The mutations in any naturally-occurring adenosine deaminase (e.g, having homology to ecTadA) that correspond to any of the mutations described herein (e.g., any of the mutations identified in ecTadA) can be generated accordingly.

[0567] In some embodiments, the adenosine deaminase comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of the amino acid sequences set forth in any of the adenosine deaminases provided herein. In some embodiments, the adenosine deaminase comprises an amino acid sequence that has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more mutations compared to a reference sequence, or any of the adenosine deaminases provided herein.

[0568] It should be appreciated that any of the mutations provided herein (e.g., based on a TadA reference sequence, such as TadA*7.10 (SEQ ID NO: 1)) can be introduced into other adenosine deaminases, such as A. coli TadA (ecTadA), S. aureus TadA (saTadA), or other adenosine deaminases (e.g., bacterial adenosine deaminases). In some embodiments, the TadA reference sequence is TadA*7.10 (SEQ ID NO: 1). It would be apparent to the skilled artisan that additional deaminases may similarly be aligned to identify homologous amino acid residues that can be mutated as provided herein. Thus, any of the mutations identified in a TadA reference sequence can be made in other adenosine deaminases (e.g., ecTada) that have homologous amino acid residues. It should also be appreciated that any of the mutations provided herein can be made individually or in any combination in a TadA reference sequence or another adenosine deaminase.

[0569] In some embodiments, the adenosine deaminase comprises an alteration or set of alterations selected from those listed in Table 3A or 3B below:ATTORNEY DOCKET NO. 180802-047501 / PCT

[0570] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0571] Table 3A. TadA*8 Adenosine Deaminase Variants. Residue positions in the E. coli TadA variant (TadA*) are indicated. Alterations are referenced to TadA*7.10 (first row).

[0572] 2 3 4 5 7 8 8 10 10 12 14 14 15 15 15 15 15

[0573] 166 3 6 8 1 6 2 4 6 8 3 6 7 2 4 5 6 7 TadA* 7.10 R L A L I V F V N Y C Y P Q V F N T TadA* 8.1 T

[0574] TadA* 8.2 R

[0575] TadA* 8.3 S

[0576] TadA* 8.4 H

[0577] TadA* 8.5 S

[0578] TadA* 8.6 R TadA* 8.7 R

[0579] TadA* 8.8 H R R

[0580] TadA* 8.9 Y R R

[0581] TadA* 8.10 R R R TadA* 8.11 T R

[0582] TadA* 8.12 T S

[0583] TadA* 8.13 Y H R R

[0584] TadA* 8.14 Y s

[0585] TadA* 8.15 s R

[0586] TadA* 8.16 s H R

[0587] TadA* 8.17 s R

[0588] TadA* 8.18 s H R

[0589] TadA* 8.19 s H R R

[0590] TadA* 8.20 Y s H R R

[0591] TadA* 8.21 R S

[0592] TadA* 8.22 s S

[0593] TadA* 8.23 s H

[0594] TadA* 8.24

[0595] Table 3B. TadA*9 Adenosine Deaminase Variants. Alterations are referenced to TadA*7.10. Additional details of TadA*9 adenosine deaminases are described in International PCT Application No. PCT / US2020 / 049975, which is incorporated herein by reference in its entirety for all purposes.

[0596] TadA*9 Description Alterations

[0597] TadA*9.1 E25F, V82S, Y123H, T133K, Y147R, Q154R

[0598] TadA*9.2 E25F, V82S, Y123H, Y147R, Q154R

[0599] TadA*9.3 V82S, Y123H, P124W, Y147R, Q154R

[0600] TadA*9.4 L51W, V82S, Y123H, C146R, Y147R, Q154R

[0601] TadA*9.5 P54C, V82S, Y123H, Y147R, Q154R

[0602] TadA*9.6 Y73S, V82S, Y123H, Y147R, Q154R

[0603] TadA*9.7 N38G, V82T, Y123H, Y147R, Q154R

[0604] TadA*9.8 R23H, V82S, Y123H, Y147R, Q154R

[0605]

[0606] TadA*9.9 R21N, V82S, Y123H, Y147R, Q154RATTORNEY DOCKET NO. 180802-047501 / PCT

[0607] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0608] TadA*9 Description Alterations

[0609] TadA*9.10 V82S, Y123H, Y147R, Q154R, A158K TadA*9.11 N72K, V82S, Y123H, D139L, Y147R, Q154R, TadA*9.12 E25F, V82S, Y123H, D139M, Y147R, Q154R TadA*9.13 M70V, V82S, M94V, Y123H, Y147R, Q154R TadA*9.14 Q71M, V82S, Y123H, Y147R, Q154R TadA*9.15 E25F, V82S, Y123H, T133K, Y147R, Q154R TadA*9.16 E25F, V82S, Y123H, Y147R, Q154R TadA*9.17 V82S, Y123H, P124W, Y147R, Q154R TadA*9.18 L51W, V82S, Y123H, C146R, Y147R, Q154R TadA*9.19 P54C, V82S, Y123H, Y147R, Q154R TadA*9.2 Y73S, V82S, Y123H, Y147R, Q154R TadA*9.21 N38G, V82T, Y123H, Y147R, Q154R TadA*9.22 R23H, V82S, Y123H, Y147R, Q154R TadA*9.23 R21N, V82S, Y123H, Y147R, Q154R TadA*9.24 V82S, Y123H, Y147R, Q154R, A158K TadA*9.25 N72K, V82S, Y123H, D139L, Y147R, Q154R, TadA*9.26 E25F, V82S, Y123H, D139M, Y147R, Q154R TadA*9.27 M70V, V82S, M94V, Y123H, Y147R, Q154R TadA*9.28 Q71M, V82S, Y123H, Y147R, Q154R TadA*9.29 E25F, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.30 I76Y, V82T, Y123H, Y147R, Q154R TadA*9.31 N38G, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.32 N38G, I76Y, V82T, Y123H, Y147R, Q154R TadA*9.33 R23H, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.34 P54C, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.35 R21N, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.36 I76Y, V82S, Y123H, D138M, Y147R, Q154R TadA*9.37 Y72S, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.38 E25F, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.39 I76Y, V82T, Y123H, Y147R, Q154R TadA*9.40 N38G, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.41 N38G, I76Y, V82T, Y123H, Y147R, Q154R TadA*9.42 R23H, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.43 P54C, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.44 R21N, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.45 I76Y, V82S, Y123H, D138M, Y147R, Q154R TadA*9.46 Y72S, I76Y, V82S, Y123H, Y147R, Q154R TadA*9.47 N72K, V82S, Y123H, Y147R, Q154R TadA*9.48 Q71M, V82S, Y123H, Y147R, Q154R TadA*9.49 M70V, V82S, M94V, Y123H, Y147R, Q154R TadA*9.50 V82S, Y123H, T133K, Y147R, Q154R TadA*9.51 V82S, Y123H, T133K, Y147R, Q154R, A158K TadA*9.52 M70V, Q71M, N72K, V82S, Y123H, Y147R, Q154R TadA*9.53 N72K, V82S, Y123H, Y147R, Q154R TadA*9.54 Q71M, V82S, Y123H, Y147R, Q154R TadA*9.55 M70V, V82S, M94V, Y123H, Y147R, Q154R TadA*9.56 V82S, Y123H, T133K, Y147R, Q154R

[0610]

[0611] TadA*9.57 V82S, Y123H, T133K, Y147R, Q154R, A158KATTORNEY DOCKET NO. 180802-047501 / PCT

[0612] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0613] TadA*9 Description Alterations

[0614]

[0615] TadA*9.58 M70V, Q71M, N72K, V82S, Y123H, Y147R, Q154R

[0616] In some embodiments, the adenosine deaminase comprises a TadA*8.20 adenosine deaminase variant further comprising an F149Y amino acid alteration. In some embodiments, the adenosine deaminase comprises a TadA*8.20 adenosine deaminase variant further comprising the amino acid alterations R147D, F149Y, T166I, and D167N (TadA*8.10+). In some embodiments, the adenosine deaminase comprises a TadA*8.20 adenosine deaminase variant further comprising the amino acid alterations S82T and F149Y (TadA*9vl). In some embodiments, the adenosine deaminase comprises a TadA*8.20 adenosine deaminase variant further comprising the amino acid alterations Y147D, F149Y, T166I, D167N and S82T (TadA*9v2).

[0617] Additional representative adenosine deaminase mutations are described in U. S. Patent Application Publication No. 2022 / 0307003 Al U. S. Patent No. 11,155,803, and International Patent Application Publications No. WO 2023 / 288304 A2, PCT / CN2022 / 143408, WO 2018 / 027078 Al, WO 2021 / 158921 Al, WO 2024 / 259364 A2, and WO 2023 / 034959 A2, and in M. Richter, etal. 2020, Nature Biotechnology, doi.org / 10.1038 / s41587-020-0453-z the disclosures of which are incorporated herein by reference in their entirety for all purposes.

[0618] In various embodiments, an adenosine deaminase of the disclosure lacks an N-terminal methionine.

[0619] In some embodiments, the disclosure provides TadA variants comprising a V82T, Y147T, and / or a Q154S mutation. In some embodiments, the disclosure provides TadA variants comprising a V82T, Y147T, and / or a Q154S mutation. In some embodiments, the disclosure provides TadA*8.8 further comprising a V82T mutation. In some embodiments, the disclosure provides TadA*8.8 further comprising a V82T, a Y147T, and a Q154S mutation. In some embodiments, the disclosure provides TadA*8.17 further comprising a V82T mutation. In some embodiments, the disclosure provides TadA*8.17 further comprising a V82T, a Y147T, and a Q154S mutation. In some embodiments, the disclosure provides TadA*8.20 further comprising a V82T mutation. In some embodiments, the disclosure provides TadA*8.20 further comprising a V82T, a Y147T, and a Q154S mutation.

[0620] In embodiments, a variant of TadA*7.10 comprises one or more alterations selected from any of those alterations provided herein.

[0621] In particular embodiments, an adenosine deaminase heterodimer comprises a TadA*8 domain and an adenosine deaminase domain selected from Staphylococcus aureus (S. aureus) TadA, Bacillus subtilis (B. subtilis) TadA, Salmonella typhimurium (S. typhimurium) TadA,ATTORNEY DOCKET NO. 180802-047501 / PCT

[0622] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0623] Shewanella putrefaciens (S. putrefaciens TadA, Haemophilus influenzae F3031 (H. influenzae) TadA, Caulobacter crescentus (C. crescentus) TadA, Geobacter sulfurreducens (G. sulfurreducens) TadA, or TadA*7.10.

[0624] In particular embodiments, the fusion proteins or complexes comprise a single (e.g., provided as a monomer) TadA* (e.g., TadA*8 or TadA*9). In some embodiments, the fusion proteins or complexes of the disclosure comprise as a heterodimer comprising two adenosine deaminase domains (e.g., a wild-type TadA and a TadA variant provided herein).

[0625] Details of A to G nucleobase editing proteins are described in International PCT Application No. PCT / US2017 / 045381 (WO2018 / 027078) and Gaudelli, N. M., etaL, “Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage” Nature, 551, 464-471 (2017), the entire contents of which are hereby incorporated by reference.

[0626] Cto T Editing

[0627] In some embodiments, a base editor disclosed herein comprises a fusion protein or complex comprising cytidine deaminase capable of deaminating a target cytidine (C) base of a polynucleotide to produce uridine (U), which has the base pairing properties of thymine. In some embodiments, for example where the polynucleotide is double-stranded (e.g., DNA), the uridine base can then be substituted with a thymidine base e.g., by cellular repair machinery) to give rise to a C: G to a T: A transition. In other embodiments, deamination of a C to U in a nucleic acid by a base editor cannot be accompanied by substitution of the U to a T.

[0628] The base editor can comprise additional domains which facilitate conversion of the U resulting from deamination to, in some embodiments, a T or a G. For example, a base editor comprising a cytidine deaminase domain can further comprise a uracil glycosylase inhibitor (UGI) domain to mediate substitution of a U by a T, completing a C-to-T base editing event.

[0629] A base editor comprising a cytidine deaminase as a domain can deaminate a target C in any polynucleotide, including DNA, RNA and DNA-RNA hybrids.

[0630] In some embodiments, an APOB EC deaminase incorporated into a base editor can comprise one or more mutations selected from the group consisting of R33A, K34A, E63A, H102P, D104N, H121R, H122R, H122L, D124N; R126A, R126E, R118A, W90A, W90Y, and R132E of rAPOBECl; D316R, D317R, R320A, R320E, R313A, W285A, W285Y, and R326E of hAPOBEC3G; and any alternative mutation at the corresponding position, or one or more corresponding mutations in another APOBEC deaminase. In some embodiments, an APOBEC deaminase incorporated into a base editor can comprise one or more combinations of mutations selected from K34A, H122L, and D124N (AALN); H102P and D104N (evoFERNY derivedATTORNEY DOCKET NO. 180802-047501 / PCT

[0631] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0632] from FERNY); W90Y and R126E (YE1); W90Y and R132E (YE2); R126E and R132E (EE); W90Y, R126E, and R132E (YEE), or rAPOBECl; and any alternative mutation at the corresponding positions, or one or more corresponding mutations in another APOBEC deaminase.

[0633] In some embodiments, the fusion proteins or complexes of the disclosure comprise one or more cytidine deaminase domains.

[0634] In some embodiments, the cytidine deaminase comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of the cytidine deaminase amino acid sequences set forth herein. It should be appreciated that cytidine deaminases provided herein may include one or more mutations (e.g., any of the mutations provided herein). Some embodiments provide a polynucleotide molecule encoding the cytidine deaminase nucleobase editor polypeptide of any previous aspect or as delineated herein. In some embodiments, the polynucleotide is codon optimized.

[0635] Details of C to T nucleobase editing proteins are described in International PCT Application No. PCT / US2016 / 058344 (WO2017 / 070632) and Komor, A. C., et al., “Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage” Nature 533, 420-424 (2016), the entire contents of which are hereby incorporated by reference. Further non-limiting examples of C to T nucleobase editing proteins are described in PCT Applications No. PCT / US2020 / 062428 and PCT / US2019 / 033848, the entire contents of which are hereby incorporated by reference.

[0636] Cytidine Adenosine Base Editors (CABEs)

[0637] In some embodiments, a base editor described herein comprises an adenosine deaminase variant that has increased cytidine deaminase activity. Such base editors may be referred to as “cytidine adenosine base editors (CABEs)” or “cytosine base editors derived from TadA* (CBE-Ts),” and their corresponding deaminase domains may be referred to as “TadA* acting on DNA cytosine (TADC)” domains or TadA-derived cytidine deaminases (TadA-CD). Base editors containing adenosine deaminase variants having both cytidine deaminase and adenosine deaminase activity (i.e., TadA-Dual deaminases) may be referred to as TadA-based dual editors (TadDE). In some instances, an adenosine deaminase variant has both adenine and cytosine deaminase activity (i.e., is a dual deaminase). In some embodiments, the adenosine deaminase variants deaminate adenine and cytosine in DNA. In some embodiments, theATTORNEY DOCKET NO. 180802-047501 / PCT

[0638] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0639] adenosine deaminase variants deaminate adenine and cytosine in single-stranded DNA. In some embodiments, the adenosine deaminase variants deaminate adenine and cytosine in RNA. In some embodiments, the adenosine deaminase variant predominantly deaminates cytosine in DNA and / or RNA (e.g., greater than 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 99% of all deaminations catalyzed by the adenosine deaminase variant, or the number of cytosine deaminations catalyzed by the variant is about or at least about 2-fold, 3 -fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 25-fold, 50-fold, 75-fold, 100-fold, 500-fold, or 1,000-fold greater than the number adenine deaminations catalyzed by the variant). In some embodiments, the adenosine deaminase variant has approximately equal cytosine and adenosine deaminase activity (e.g., the two activities are within about 10% or 20% of each other). In some embodiments, the adenosine deaminase variant has predominantly cytosine deaminase activity, and little, if any, adenosine deaminase activity. In some embodiments, the adenosine deaminase variant has cytosine deaminase activity, and no significant or no detectable adenosine deaminase activity. In some embodiments, the target polynucleotide is present in a cell in vitro or in vivo. In some embodiments, the cell is a bacteria, yeast, fungi, insect, plant, or mammalian cell.

[0640] Examples of adenosine deaminase variants having increased cytidine deaminase activity include those described in International Patent Application Publications No. WO 2024 / 040083 and WO 2022 / 204574, the disclosures of which are hereby incorporated by reference in their entireties for all purposes.

[0641] In some embodiments, an adenosine deaminase variant of the disclosure is a TadA adenosine deaminase comprising one or more alterations that increase cytosine deaminase activity (e.g., at least about 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold or more increase) while maintaining adenosine deaminase activity (e.g., at least about 30%, 40%, 50% or more of the activity of a reference adenosine deaminase (e.g., TadA*8.20 or TadA*8.19)). In some instances, the adenosine deaminase variant comprises one or more alterations that increase cytosine deaminase activity (e.g., at least about 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold or more increase) relative to the activity of a reference adenosine deaminase and comprise undetectable adenosine deaminase activity or adenosine deaminase activity that is less than 30%, 20%, 10%, or 5% of that of a reference adenosine deaminase. In some embodiments, the reference adenosine deaminase is TadA*8.20 or TadA*8.19.

[0642] Guide Polynucleotides

[0643] A polynucleotide programmable nucleotide binding domain, when in conjunction with a bound guide polynucleotide (e.g., gRNA), can specifically bind to a target polynucleotideATTORNEY DOCKET NO. 180802-047501 / PCT

[0644] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0645] sequence (i.e., via complementary base pairing between bases of the bound guide nucleic acid and bases of the target polynucleotide sequence) and thereby localize the base editor to the target nucleic acid sequence desired to be edited.

[0646] A guide polynucleotide may include natural or non-natural (or unnatural) nucleotides (e.g., peptide nucleic acid or nucleotide analogs). In some cases, the targeting region of a guide nucleic acid sequence (e.g., a spacer) can be at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length.

[0647] A guide RNA (gRNA) is a short synthetic RNA composed of a scaffold sequence necessary for Cas-binding and a user-defined spacer that defines the genomic target to be modified. Exemplary gRNA scaffold sequences are provided in the sequence listing as SEQ ID NOs: 317-327 and 425. In embodiments, the spacer is about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, or more nucleotides in length.

[0648] Modified Polynucleotides

[0649] To enhance expression, stability, and / or genomic / base editing efficiency, and / or reduce possible toxicity, the base editor-coding sequence (e.g., mRNA) and / or the guide polynucleotide (e.g., gRNA) can be modified to include one or more modified nucleotides and / or chemical modifications, e.g. using pseudo-uridine, 5-Methyl-cytosine, 2'-O-methyl-3'-phosphonoacetate, 2'-O-methyl thioPACE (MSP), 2'-O-methyl-PACE (MP), 2'-fluoro RNA (2'-F-RNA), =constrained ethyl (S-cEt), 2'-O-methyl (‘M’), 2'-O-methyl-3'-phosphorothioate (‘MS’), 2'-O-methyl-3'-thiophosphonoacetate (‘MSP’), 5-methoxyuridine, phosphorothioate, and N1-Methylpseudouridine. Chemically protected gRNAs can enhance stability and editing efficiency in vivo and ex vivo. Methods for using chemically modified mRNAs and guide RNAs are known in the art and described, for example, by Jiang et al., Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope. Nat Commun 11, 1979 (2020). doi.org / 10.1038 / s41467-020-15892-8, Callum et al., N1-Methylpseudouridine substitution enhances the performance of synthetic mRNA switches in cells, Nucleic Acids Research, Volume 48, Issue 6, 06 April 2020, Page e35, by Andries et al., Journal of Controlled Release, Volume 217, 10 November 2015, Pages 337-344, and in PCT / US2024 / 0226601, the disclosures of each of which is incorporated herein by reference in its entirety for all purposes.

[0650] In some embodiments, the guide polynucleotide comprises one or more modified nucleotides at the 5' end and / or the 3' end of the guide. In some embodiments, the guide polynucleotide comprises two, three, four or more modified nucleosides at the 5' end and / or the 3' end of the guide.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0651] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0652] In embodiments, the gRNA comprises 2'-O-methyl and / or phosphorothioate modifications.

[0653] Fusion Proteins or Complexes Comprising a Nuclear Localization Sequence (NLS)

[0654] In some embodiments, the fusion proteins or complexes provided herein further comprise one or more (e.g., 2, 3, 4, 5) nuclear targeting sequences, for example a nuclear localization sequence (NLS). In one embodiment, a bipartite NLS is used. In some embodiments, the NLS is fused to the N-terminus or the C-terminus of the fusion protein or a component of a complex. NLS sequences are described in Plank et al., PCT / EP2000 / 011690, the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences.

[0655] In some embodiments, the NLS is present in a linker or the NLS is flanked by linkers, for example described herein. A bipartite NLS comprises two basic amino acid clusters, which are separated by a relatively short spacer sequence (hence bipartite - 2 parts, while monopartite NLSs are not). The NLS of nucleoplasmin, KR [PAATKKAGQA] KKKK (SEQ ID NO: 191), is the prototype of the ubiquitous bipartite signal: two clusters of basic amino acids, separated by a spacer of about 10 amino acids. The sequence of an exemplary bipartite NLS follows:

[0656] PKKKRKVEGADKRTADGSEFESPKKKRKV (SEQ ID NO: 328).

[0657] In some embodiments, any of the fusion proteins or complexes provided herein comprise an NLS comprising the amino acid sequence EGADKRTADGSEFESPKKKRKV (SEQ ID NO 893). In some embodiments, any of the adenosine base editors provided herein comprise an NLS comprising the amino acid sequence EGADKRTADGSEFESPKKKRKV (SEQ ID NO: 893). In some embodiments, the NLS is at a C-terminal portion of the adenosine base editor. In some embodiments, the NLS is at the C-terminus of the adenosine base editor.

[0658] Additional Domains

[0659] A base editor described herein can include any domain which helps to facilitate the nucleobase editing, modification or altering of a nucleobase of a polynucleotide.

[0660] This disclosure contemplates a base editor fusion protein or complex comprising a UGI domain and / or a uracil stabilizing protein (USP) domain.

[0661] BASE EDITOR SYSTEM

[0662] Provided herein are systems, compositions, and methods for editing a nucleobase using a base editor system.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0663] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0664] Use of the base editor system provided herein comprises the steps of: (a) contacting a target nucleotide sequence of a polynucleotide (e.g., double- or single stranded DNA or RNA) of a subject with a base editor system comprising a deaminase domain and a guide polynucleotide (e.g., gRNA), wherein the target nucleotide sequence comprises a targeted nucleobase pair; (b) inducing strand separation of said target region; (c) converting a first nucleobase of said target nucleobase pair in a single strand of the target region to a second nucleobase; and (d) cutting no more than one strand of said target region, where a third nucleobase complementary to the first nucleobase base is replaced by a fourth nucleobase complementary to the second nucleobase. It should be appreciated that in some embodiments, step (b) is omitted. In some embodiments, the base editor system provided herein is capable of multiplex editing of a plurality of nucleobase pairs in one or more genes.

[0665] The components of a base editor system (e.g., a deaminase domain, a guide RNA, and / or a polynucleotide programmable nucleotide binding domain) may be associated with each other covalently or non-covalently (see, e.g., International Patent Application Publications no.

[0666] WO2022148955A1, WO2022150367A1, and WO2022150372A1, the disclosures of each of which is incorporated in its entirety for all purposes). In some embodiments, a polynucleotide programmable nucleotide binding domain can target a deaminase domain to a target nucleotide sequence by non-covalently interacting with or associating with the deaminase domain. For example, in some embodiments, the nucleobase editing component (e.g., the deaminase component) comprises an additional heterologous portion or domain that is capable of interacting with, associating with, or capable of forming a complex with a corresponding heterologous portion, antigen, or domain that is part of a polynucleotide programmable nucleotide binding domain and / or a guide polynucleotide (e.g., a guide RNA) complexed therewith. In some embodiments, the polynucleotide programmable nucleotide binding domain, and / or a guide polynucleotide (e.g., a guide RNA) complexed therewith, comprises an additional heterologous portion or domain that is capable of interacting with, associating with, or capable of forming a complex with a corresponding heterologous portion, antigen, or domain that is part of a nucleobase editing domain (e.g., the deaminase component). In some embodiments, the additional heterologous portion may be capable of binding to, interacting with, associating with, or forming a complex with a polypeptide or polynucleotide.

[0667] Linkers

[0668] In certain embodiments, linkers may be used to link any of the peptides or peptide domains of the disclosure. The linker may be as simple as a covalent bond, or it may be a polymeric linker many atoms in length. In certain embodiments, the linker is a polypeptide orATTORNEY DOCKET NO. 180802-047501 / PCT

[0669] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0670] based on amino acids. In other embodiments, the linker is not peptide-like. In certain embodiments, the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbonheteroatom bond, etc.).

[0671] In some embodiments, any of the fusion proteins provided herein, comprise a cytidine or adenosine deaminase and a Cas9 domain that are fused to each other via a linker. Various linker lengths and flexibilities between the cytidine or adenosine deaminase and the Cas9 domain can be employed (e.g., ranging from very flexible linkers of the form (GGGS )n(SEQ ID NO: 246), (GGGGS)n (SEQ ID NO: 247), and (G)n to more rigid linkers of the form (EAAAK)n(SEQ ID NO: 248), (SGGS)n (SEQ ID NO: 355), SGSETPGTSESATPES (SEQ ID NO: 249) (see, e.g., Guilinger JP, et al. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat. Biotechnol. 2014; 32(6): 577-82; the entire contents are incorporated herein by reference) and (XP)n) in order to achieve the optimal length for activity for the cytidine or adenosine deaminase nucleobase editor. In some embodiments, n is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15. In some embodiments, the linker comprises a (GGS)n motif, wherein n is 1, 3, or 7. In some embodiments, cytidine deaminase or adenosine deaminase and the Cas9 domain of any of the fusion proteins provided herein are fused via a linker comprising the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 249), which can also be referred to as the XTEN linker.

[0672] In some embodiments, the domains of the base editor are fused via a linker that comprises the amino acid sequence of:

[0673] SGGSSGSETPGTSESATPESSGGS (SEQ ID NO: 356), SGGSSGGSSGSETPGTSESATPESSGGSSGGS (SEQ ID NO: 357), GGSGGSPGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEG SAPGTSTEPSEGSAPGTSESATPESGPGSEPATSGGSGGS (SEQ ID NO: 358), EGGSEEEEESGS (SEQ ID NO: 468), or KGPKPKKEESEK (SEQ ID NO: 469).

[0674] In some embodiments, domains of the base editor are fused via a linker comprising the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 249), which may also be referred to as the XTEN linker. In some embodiments, a linker comprises the amino acid sequence SGGS (SEQ ID NO: 355). In some embodiments, the linker is 24 amino acids in length. In some embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPES (SEQ ID NO: 359). In some embodiments, the linker is 40 amino acids in length. In some embodiments, the linker comprises the amino acid sequence:

[0675] SGGSSGGSSGSETPGTSESATPESSGGSSGGSSGGSSGGS (SEQ ID NO: 360). In some embodiments, the linker is 64 amino acids in length. In some embodiments, the linker comprisesATTORNEY DOCKET NO. 180802-047501 / PCT

[0676] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0677] the amino acid sequence:

[0678] SGGSSGGSSGSETPGTSESATPESSGGSSGGSSGGSSGGSSGSETPGTSESATPESSGGSSGGS

[0679] (SEQ ID NO: 361). In some embodiments, the linker is 92 amino acids in length. In some embodiments, the linker comprises the amino acid sequence:

[0680] PGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTS TEPSEGSAPGTSESATPESGPGSEPATS (SEQ ID NO: 362).

[0681] In some embodiments, a linker comprises a plurality of proline residues and is 5-21, 5-14, 5-9, 5-7 amino acids in length, e.g., PAPAP (SEQ ID NO: 363), PAPAPA (SEQ ID NO: 364), PAPAPAP (SEQ ID NO: 365), PAPAPAPA (SEQ ID NO: 366), P(AP)4(SEQ ID NO: 367), P(AP)7(SEQ ID NO: 368), P(AP)10(SEQ ID NO: 369) (see, e.g., Tan J, Zhang F, Karcher D, Bock R. Engineering of high-precision base editors for site-specific single nucleotide replacement. Nat Commun. 2019 Jan 25;10(l):439; the entire contents are incorporated herein by reference). Such proline-rich linkers are also termed “rigid” linkers.

[0682] In various embodiments, a linker of the disclosure comprises 8, 9, 10, 11, 12, 13, 14, or 15 amino acids. In some cases, the linker comprises a sequence selected from one or more of EGSSSKEEEEPG (SEQ ID NO: 647), NSISSSNGQK (SEQ ID NO: 648), GEEGEGSGGGEK (SEQ ID NO: 649), EGEGGKESGSSE (SEQ ID NO: 650), GGGGSSKSPGSE (SEQ ID NO: 651), PIGSDQDD (SEQ ID NO: 652), TEKGQVPHGS (SEQ ID NO: 653), ESGEGGGGSEKK (SEQ ID NO: 654), EEGKPKEGEGSG (SEQ ID NO: 655), ASREPKDSS (SEQ ID NO: 656), KQGSEHDE (SEQ ID NO: 657), SESKSEKGSSEK (SEQ ID NO: 658), QYDSGERSDQ (SEQ ID NO: 659), PGANEEIPGQ (SEQ ID NO: 660), NSPTDEK (SEQ ID NO: 661), EGANEEIPGQ (SEQ ID NO: 662), EGEKEKKKSGES (SEQ ID NO: 663), PGRHEEVPGQ (SEQ ID NO: 664), SKHQTEQDDS (SEQ ID NO: 665), ESEDDSSGRK (SEQ ID NO: 666), KESEKKESESKS (SEQ ID NO: 667), KGEGKSSIKD (SEQ ID NO: 668), DRSQKQDQQD (SEQ ID NO: 669), GPSSTSSS (SEQ ID NO: 670), GSSGEKEEGEPS (SEQ ID NO: 671), GEPKSKKSGSGS (SEQ ID NO: 672), SSGEGGKSESGP (SEQ ID NO: 673), SPQPTSSD (SEQ ID NO: 674), EGGSEEEEESGS (SEQ ID NO: 675), KGPKPKKEESEK (SEQ ID NO: 676), SKSQQFVTYE (SEQ ID NO: 677), TGNSKYQTGK (SEQ ID NO: 678), PQPIPHTNPT (SEQ ID NO: 679), ANAHSDISTG (SEQ ID NO: 680), KSQQTEDQSK (SEQ ID NO: 681), QSQDQKQKEH (SEQ ID NO: 682), NQQRPSSD (SEQ ID NO: 683), TTKDTSPKPQ (SEQ ID NO: 684), EGKDNQQTGE (SEQ ID NO: 685), or EPQPDSSE (SEQ ID NO: 686).ATTORNEY DOCKET NO. 180802-047501 / PCT

[0683] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0684] Base Editor Efficiency

[0685] The base editors of the disclosure advantageously modify a specific nucleotide base encoding a protein without generating a significant proportion of indels (i.e., insertions or deletions) and / or other non-target modifications.

[0686] In some embodiments, a target modification, e.g., a base edit, results in about or at least about a 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% reduction, or reduction to an undetectable level, of the gene targeted expression.

[0687] In some embodiments, any of the base editing system comprising one of the base editor variants described herein has reduced bystander editing or mutations by at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% compared to a reference base editor system.10.

[0688] In some embodiments, any of the base editor variants described herein has higher base editing efficiency compared to a reference base editor. In some embodiments, any of the base editor variants described herein have at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, 100%, 105%, 110%, 115%, 120%, 125%, 130%, 135%, 140%, 145%, 150%, 155%, 160%, 165%, 170%, 175%, 180%, 185%, 190%, 195%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 450%, or 500% higher base editing efficiency compared the reference base editor (e.g., ABE7.10).

[0689] In some embodiments, the method described herein, for example, the base editing methods has minimum to no off-target effects. In some embodiments, the method described herein, for example, the base editing methods, has minimal to no chromosomal translocations.

[0690] In some embodiments, the base editing method described herein results in about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% of a cell population that have been successfully edited.

[0691] In some embodiments, the percent of viable cells in a cell population following base editing is about 90%, or about 91%, 92%, 93%, 94% 95%, 96%, 97%, 98%, 99%, or 100% of the viable cells in the population prior to base editing.

[0692] The number of intended mutations and indels can be determined using any suitable method, for example, as described in International PCT Application Nos. PCT / US2017 / 045381 (WO2018 / 027078) and PCT / US2016 / 058344 (WO2017 / 070632); Komor, A. C., et al., “Programmable editing of a target base in genomic DNA without double-stranded DNAATTORNEY DOCKET NO. 180802-047501 / PCT

[0693] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0694] cleavage” Nature 533, 420-424 (2016); Gaudelli, N. M., et al., “Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage” Nature 551, 464-471 (2017); and Komor, A. C., et al., “Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C: G-to-T: A base editors with higher efficiency and product purity” Science Advances 3:eaao4774 (2017); the entire contents of which are hereby incorporated by reference.

[0695] CD38-BINDING POL YPEPTIDES

[0696] Generation and Screening of Antibodies that Bind to a wild type CD38 Polypeptide or Peptide Antibodies, including recombinantly produced antibodies, that specifically bind to wild type CD38 but show reduced binding to a CD38 variant polypeptide or peptide thereof (e.g., a variant produced by the methods provided herein) are provided and described herein. In embodiments, the antibodies are Antibody A, Antibody B, or antigen binding portions thereof, as described herein.

[0697] Methods for generating antibodies against a protein or peptide of interest are known and practiced in the art. When animals are immunized with antigens they respond by generating a polyclonal antibody response comprised of many individual monoclonal antibody specificities. It is the sum of these individual specificities that make polyclonal antibodies useful in so many different assays. Individual monoclonal antibodies were originally isolated by immortalizing individual B cells using hybridoma technology (Kohler and Milstein, Nature 256, 495, 2011), in which B cells from an immunized animal are fused with a myeloma cell. With the advent of molecular biology, in vitro methods to generate antibodies against proteins of interest, such as wild type CD38, have been developed.

[0698] The terms "antigen of interest" or "target protein" are used herein interchangeably and refer generally to the agent recognized and specifically bound by an antibody. In an embodiment, such an antigen of interest or target protein is the wild type CD38 polypeptide, or an antigenic and / or immunogenic portion thereof.

[0699] An antibody is a polypeptide chain-containing molecular structure with a specific shape that specifically binds an epitope, where one or more non-covalent binding interactions stabilize the complex between the molecular structure and the epitope. In one embodiment, an antibody molecule is an immunoglobulin (e.g., IgG, IgM, IgA, IgE, IgD). Antibodies from a variety of sources, e.g., human, camel, rodent, rabbit, cow, sheep, pig, dog, or fowl are considered “antibodies.” Numerous antibody coding sequences have been described; and others may be raised by methods well-known in the art.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0700] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0701] For example, antibodies or antigen binding fragments may be produced by genetic engineering. Antibody coding sequences of interest include those encoded by native sequences, as well as nucleic acids that, by virtue of the degeneracy of the genetic code, are not identical in sequence to a wild type nucleic acid sequence. Variant polypeptides can include amino acid (aa) substitutions, additions or deletions. The amino acid substitutions can be conservative amino acid substitutions or substitutions to eliminate non-essential amino acids, such as to alter a glycosylation site, or to minimize misfolding by substitution or deletion of one or more cysteine residues that are not necessary for function. Variants can be designed so as to retain or have enhanced biological activity of a particular region of the protein (e.g., a functional domain, catalytic amino acid residues). Variants also include fragments of the polypeptides disclosed herein, particularly biologically active fragments and / or fragments corresponding to functional domains. Techniques for in vitro mutagenesis of cloned genes are known. Also included in some aspects and embodiments herein are polypeptides that have been modified using ordinary molecular biological techniques so as to improve their resistance to proteolytic degradation or to optimize solubility properties or to render them more suitable as a therapeutic agent.

[0702] Chimeric antibodies may be made by recombinant means by combining the variable light and heavy chain regions obtained from antibody producing cells of one species with the constant light and heavy chain regions from another. Typically, chimeric antibodies utilize rodent or rabbit variable regions and human constant regions, in order to produce an antibody with predominantly human domains. The production of such chimeric antibodies is well known in the art and may be achieved by standard means (as described, e.g., in U. S. Pat. No. 5,624,659, incorporated fully herein by reference).

[0703] Humanized antibodies are engineered to contain even more human-like immunoglobulin domains and incorporate only the complementarity-determining regions of the animal-derived antibody. This is accomplished by carefully examining the sequence of the hyper-variable loops of the variable regions of the monoclonal antibody and fitting them to the structure of the human antibody chains. Although apparently complex, the process is straightforward in practice. See, e.g., U. S. Patent No. 6,187,287, incorporated fully herein by reference.

[0704] In addition to entire immunoglobulins (or their recombinant counterparts), immunoglobulin fragments comprising the epitope binding site (e.g., Fab', F(ab')2, or other fragments) may be synthesized. " Fragment," or minimal immunoglobulins may be designed utilizing recombinant immunoglobulin techniques. For instance, " Fv" immunoglobulins for use in some aspects and embodiments herein may be produced by synthesizing a variable light chainATTORNEY DOCKET NO. 180802-047501 / PCT

[0705] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0706] region and a variable heavy chain region. Combinations of antibodies are also of interest, e.g., diabodies, which comprise two distinct Fv specificities.

[0707] Immunoglobulins may be modified post-translationally, e.g., to add chemical linkers, detectable moieties, such as fluorescent dyes, enzymes, substrates, chemiluminescent moieties and the like, or specific binding moieties, such as streptavidin, avidin, or biotin, and the like may be utilized in the methods and compositions of some aspects and embodiments herein.

[0708] Screening of libraries for CD38-binding polypeptides or peptides

[0709] Methods for high throughput screening of polypeptide (e.g., antibody or antigen-binding antibody fragment) libraries for molecules capable of binding to the wild type CD38 polypeptide or peptide (and / or epitopes within the CD38 polypeptide or peptide) include, without limitation, display techniques including phage display, bacterial display, yeast display, mammalian display, ribosome display, mRNA display, and cDNA display. The use of phage display to isolate ligands that bind biologically relevant molecules has been reviewed, e.g., in Felici et al.

[0710] (Biotechnol. Annual Rev. 1:149-183, 1995), Katz (Annual Rev. Biophys. Biomol. Struct. 26:27-45, 1997), and Hoogenboom et al. (Immunotechnology 4:1-20, 1998). Several randomized combinatorial peptide libraries have been constructed to select for polypeptides that bind different targets, e.g., cell surface receptors or DNA (reviewed by Kay (Perspect. Drug Discovery Des. 2, 251-268, 1995), Kay et al., (Mol. Divers. 1:139-140, 1996)). Proteins and multimeric proteins have been successfully phage-displayed as functional molecules (see, e.g., EP 0349578A, EP 4527839A, EP 0589877A; Chiswell and McCafferty (Trends Biotechnol. 10, 80-84 1992)). In addition, functional antibody fragments (e.g., Fab, single-chain Fv [scFv]) have been expressed as reported by McCafferty et al. (Nature 348: 552-554, 1990), Barbas et al.

[0711] (Proc. Natl. Acad Sci. USA 88:7978-7982, 1991), and Clackson et al. (Nature 352:624-628, 1991). These references are hereby incorporated by reference in their entirety.

[0712] In addition to generating CD38 binding polypeptides (e.g., CD38 binding polypeptides, antibodies, and antigen-binding fragments thereof) of some aspects and embodiments herein, in vitro display techniques, which are known and practiced in the art, also provide methods for improving the affinity of an anti-CD38 variant-binding polypeptide, antibody, or antigen-binding fragments thereof. For instance, rather than screening libraries of antibodies and fragments thereof containing completely randomized hypervariable regions, narrower libraries of antibodies and antigen-binding fragments thereof that feature targeted mutations at specific sites within hypervariable regions can be screened. This can be accomplished, for example, by assembling libraries of polynucleotides encoding antibodies or antigen-binding fragments thereofATTORNEY DOCKET NO. 180802-047501 / PCT

[0713] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0714] that encode random mutations only at particular sites within hypervariable regions. These polynucleotides can then be expressed in, e.g., filamentous phage, bacterial cells, yeast cells, mammalian cells, or in vitro using, e.g., ribosome display, mRNA display, or cDNA display techniques in order to screen for antibodies or antigen-binding fragments thereof that specifically bind to the wild type CD38 polypeptide or peptide (and epitopes thereof) with improved binding affinity. Yeast display, for instance, is well-suited for affinity maturation, and has been used previously to improve the affinity of a single-chain antibody to a KD of 48 fM (Boder et al. (Proc Natl Acad Sci USA 97:10701, 2000)).

[0715] Additional in vitro techniques that can be used for the generation and affinity maturation of CD38-binding polypeptides, antibodies, and antigen-binding fragments thereof (e.g., singlechain polypeptides, antibodies, and antigen-binding fragments thereof) of some aspects and embodiments herein include the screening of combinatorial libraries of antibodies or antigenbinding fragments thereof for functional molecules capable of specifically binding to peptides derived from the CD38 polypeptide. Combinatorial antibody libraries can be obtained, e.g., by expression of polynucleotides encoding randomized hypervariable regions of an antibody or antigen-binding fragment thereof in a eukaryotic or prokaryotic cell. This can be achieved, e.g., using gene expression techniques described herein or known in the art. Heterogeneous mixtures of antibodies can be purified, e.g., by Protein A or Protein G selection, sizing column chromatography), centrifugation, differential solubility, and / or by any other standard technique for the purification of proteins. Libraries of combinatorial libraries thus obtained can be screened, e.g., by incubating a heterogeneous mixture of these antibodies with a peptide derived from the CD38 polypeptide that has been immobilized to a surface for a period of time sufficient to allow antibody-antigen binding. Non-binding antibodies or fragments thereof can be removed by washing the surface with an appropriate buffer (e.g., a solution buffered at physiological pH (approximately 7.4) and containing physiological salt concentrations and ionic strength, and optionally containing a detergent, such as TWEEN-20®). Antibodies that remain bound can subsequently be detected, e.g., using an ELISA-based detection protocol (see, e.g., U. S. Patent No. 4,661,445; incorporated herein by reference).

[0716] Additional techniques for screening combinatorial libraries of polypeptides (e.g., antibodies, and antigen-binding fragments thereof) for those that specifically bind to CD38 polypeptide-derived peptides include the screening of one-bead-one-compound libraries of antibody fragments. Antibody fragments can be chemically synthesized on a solid bead (e.g., using established split-and-pool solid phase peptide synthesis protocols) composed of a hydrophilic, water-swellable material such that each bead displays a single antibody fragment.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0717] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0718] Heterogeneous bead mixtures can then be incubated with a CD38 polypeptide-derived peptide that is optionally labeled with a detectable moiety (e.g., a fluorescent dye) or that is conjugated to an epitope tag (e.g., biotin, avidin, FLAG tag, HA tag) that can later be detected by treatment with a complementary tag (e.g., avidin, biotin, anti-FLAG antibody, anti-HA antibody, respectively). Beads containing antibody portions or fragments that specifically bind to CD38 polypeptide-derived peptide can be identified by analyzing the fluorescent properties of the beads following incubation with a fluorescently-labeled antigen or complementary tag (e.g., by confocal fluorescent microscopy or by fluorescence-activated bead sorting; see, e.g., Muller et al. (J. Biol. Chem., 16500-16505, 1996); incorporated herein by reference). Beads containing antibody fragments that specifically bind to CD38 polypeptide-derived peptides can thus be separated from those that do not contain high-affinity antibody fragments. The sequence of an antibody fragment that specifically binds to a CD38 polypeptide-derived peptide can be determined by techniques known in the art, including, e.g., Edman degradation, tandem mass spectrometry, matrix-assisted laser-desorption time-of-flight mass spectrometry (MALDI-TOF MS), nuclear magnetic resonance (NMR), and 2D gel electrophoresis, among others (see, e.g., WO 2004 / 062553; incorporated herein by reference).

[0719] Methods of Identifying Antibodies and Ligands

[0720] Methods for high throughput screening of antibody, antibody fragment, and ligand libraries for molecules capable of binding the CD38 polypeptide or peptide can be used to identify antibodies suitable for the uses as described herein. Such methods include in vitro display techniques known in the art, such as phage display, bacterial display, yeast display, mammalian cell display, ribosome display, mRNA display, and cDNA display, among others. The use of phage display to isolate ligands that bind biologically relevant molecules has been reviewed, for example, in Felici et al., Biotechnol. Annual Rev. 1:149-183, 1995; Katz, Annual Rev. Biophys. Biomol. Struct. 26:27-45, 1997; and Hoogenboom et al., Immunotechnology 4:1-20, 1998, the disclosures of each of which are incorporated herein by reference as they pertain to in vitro display techniques. Randomized combinatorial peptide libraries have been constructed to select for polypeptides that bind cell surface antigens as described in Kay, Perspect. Drug Discovery Des. 2:251-268, 1995 and Kay et al., Mol. Divers. 1:139-140, 1996, the disclosures of each of which are incorporated herein by reference as they pertain to the discovery of antigenbinding molecules. Proteins, such as multimeric proteins, have been successfully phage-displayed as functional molecules (see, for example, EP 0349578; EP 4527839; and EP 0589877, as well as Chiswell and McCafferty, Trends Biotechnol. 10:80-84 1992, the disclosures of eachATTORNEY DOCKET NO. 180802-047501 / PCT

[0721] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0722] of which are incorporated herein by reference as they pertain to the use of in vitro display techniques for the discovery of antigen-binding molecules). In addition, functional antibody fragments, such as Fab and scFv fragments, have been expressed in in vitro display formats (see, for example, McCafferty et al., Nature 348:552-554, 1990; Barbas et al., Proc. Natl. Acad. Sci. USA 88:7978-7982, 1991; and Clackson et al., Nature 352:624-628, 1991, the disclosures of each of which are incorporated herein by reference as they pertain to in vitro display platforms for the discovery of antigen-binding molecules). These techniques, among others, can be used to identify and improve the affinity of antibodies that bind to the CD38 polypeptide or peptide.

[0723] Host Cells for Expression of Antibodies

[0724] Mammalian cells can be co-transfected with polynucleotides encoding the antibodies of some aspects and embodiments herein, which are expressed as recombinant polypeptides, and assembled into anti-CD38 antibodies by the host cell. In one embodiment, a mammalian cell is co-transfected with polynucleotides encoding the heavy and light chains of an anti-CD38 polypeptide antibody, which are expressed in the cell and assembled as the anti-CD38 antibody.

[0725] It is possible to express antibodies or antigen-binding fragments thereof in either prokaryotic or eukaryotic host cells. In certain embodiments, expression of polypeptides or antigen-binding fragments thereof is performed in eukaryotic cells, e.g., mammalian host cells, for optimal secretion of a properly folded and immunologically active antibody. Exemplary, nonlimiting mammalian host cells for expressing the recombinant antibodies or antigen-binding fragments thereof of some aspects and embodiments herein include Chinese Hamster Ovary (CHO cells) (including DHFR CHO cells, described in Urlaub and Chasin (1980, Proc. Natl. Acad. Sci. USA 77:4216-4220), used with a DHFR selectable marker, e.g., as described in Kaufman and Sharp (1982, Mol. Biol. 159:601-621), NSO myeloma cells, COS cells, HEK293T cells, SP2 / 0, NIH3T3, and BaF3 cells. Additional, nonlimiting cell types that may be useful for the expression of antibodies and fragments thereof include bacterial cells, such as BL-21(DE3) E. coli cells, which can be transformed with vectors containing foreign DNA according to established protocols. Additional eukaryotic cells that may be useful for expression of antibodies include yeast cells, such as auxotrophic strains of S. cerevisiae, which can be transformed and selectively grown in incomplete medium according to established procedures known in the art. When recombinant expression vectors encoding antibody genes are introduced into mammalian host cells, the antibodies are produced by culturing the host cells for a period of time sufficient to allow for expression of the antibody protein in the host cells or secretion of the antibody into the culture medium in which the host cells are grown.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0726] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0727] Polypeptides (e.g., antibodies or antigen-binding fragments thereof) can be recovered from the culture medium using standard protein purification methods. Host cells can also be used to produce portions of intact antibodies, such as Fab fragments or scFv molecules. Also included in some aspects and embodiments herein are methods in which the above procedure is varied according to established protocols known in the art. For example, it may be desirable to transfect a host cell with DNA encoding either the light chain or the heavy chain (but not both) of an anti-CD38 antibody of some aspects and embodiments herein in order to produce an antigen-binding fragment of the antibody.

[0728] Once a CD38-binding polypeptide (e.g., an anti-CD38 polypeptide antibody or an antigen-binding fragment thereof) of some aspects and embodiments herein has been produced by recombinant expression, it can be purified by any method known in the art, such as a method useful for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, affinity for antigen (e.g., a CD38 polypeptide or peptide) after Protein A or Protein G selection, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. Further, a CD38 polypeptide (e.g., an anti-CD38 antibody of some aspects and embodiments described herein ) or an antigen-binding portion or fragment thereof, can be fused to heterologous polypeptide sequences as known in the art, for example, to facilitate purification, e.g., a histidine tag, a detectable / detectably labeled marker, and the like.

[0729] Once isolated, an anti-CD38 antibody, or antigen-binding portion or fragment thereof can, if desired, be further purified, e.g., by high performance liquid chromatography (see, e.g., Fisher, Laboratory Techniques in Biochemistry and Molecular Biology (Work and Burdon, eds., Elsevier, 1980); incorporated herein by reference), or by gel filtration chromatography, such as on a Superdex. TM. 75 column (Pharmacia Biotech AB, Uppsala, Sweden).

[0730] Mapping Epitopes of the CD38 Polypeptide

[0731] Anti-CD38 antibodies, and antigen-binding fragments thereof, can be produced by screening libraries of polypeptides (e.g., antibodies and antigen-binding fragments thereof) for functional molecules that are capable of binding to a wild type CD38 polypeptide or peptide that selectively bind to the wild type CD38 polypeptide or peptide compared with CD38 polypeptide variant polypeptides or peptides containing alterations, such as those provided herein. Epitopes can be modeled by screening antibodies or antigen-binding fragments thereof against a series of linear or cyclic peptides containing residues that correspond to a desired epitope within a CD38 polypeptide or peptide.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0732] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0733] As an example, peptides containing individual fragments isolated from the CD38 polypeptide or peptide can be synthesized by peptide synthesis techniques known in the art. These peptides can be immobilized on a solid surface and screened for molecules that bind to anti-CD38 antibodies and antigen-binding fragments thereof, such as representative antibodies Antibody A or Antibody B, or antigen binding portions thereof, as described herein, e.g., using an ELISA-based screening platform using established procedures. Using this assay, peptides that specifically bind to the anti-CD38 antibodies with high affinity therefore contain residues within epitopes of the CD38 polypeptide antigen that preferentially bind these antibodies.

[0734] Peptides identified in this manner can be used to screen libraries of antibodies and antigenbinding fragments thereof in order to identify anti-CD38 antibodies useful in generating anti-CD38 antibodies of some aspects and embodiments herein.

[0735] DELIVERY SYSTEMS

[0736] Nucleic Acid-Based Delivery of Base Editor Systems

[0737] Nucleic acid molecules encoding a base editor system or a component thereof (e.g., mRNA encoding a base editor) according to the present disclosure can be administered to subjects or delivered into cells in vitro or in vivo by art-known methods or as described herein. For example, a base editor system comprising a deaminase (e.g., cytidine or adenine deaminase) can be delivered by vectors (e.g., viral or non-viral vectors), or by naked DNA, DNA complexes, lipid nanoparticles, or a combination of the aforementioned compositions. A base editor system may be delivered to a cell using any methods available in the art including, but not limited to, physical methods (e.g., electroporation, particle gun, calcium phosphate transfection), viral methods, non-viral methods (e.g., liposomes, cationic methods, lipid nanoparticles, polymeric nanoparticles), or biological non-viral methods (e.g., attenuated bacterial, engineered bacteriophages, mammalian virus-like particles, biological liposomes, erythrocyte ghosts, exosomes).

[0738] Nanoparticles, which can be organic or inorganic, are useful for delivering a base editor system or component thereof. Nanoparticles are well known in the art and any suitable nanoparticle can be used to deliver a base editor system or component thereof, or a nucleic acid molecule encoding such components. In one example, organic (e.g., lipid and / or polymer) nanoparticles are suitable for use as delivery vehicles in certain embodiments of this disclosure. Non-limiting examples of lipid nanoparticles suitable for use in the methods of the present disclosure include those described in International Patent Application Publications No.

[0739] WO 2025 / 038864, WO 2025 / 038855, WO 2024 / 019936, WO 2023 / 121975, WO 2023 / 121964,ATTORNEY DOCKET NO. 180802-047501 / PCT

[0740] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0741] WO 2023 / 121971, WO 2023 / 121970, WO 2022 / 140239, WO 2022 / 140252, WO 2022 / 140238, WO 2022 / 159421, WO 2022 / 159472, WO 2022 / 159475, WO 2022 / 159463, WO 2021 / 113365, WO 2024 / 019936, and WO 2021 / 141969, the disclosures of each of which is incorporated herein by reference in its entirety for all purposes.

[0742] Viral Vectors

[0743] A base editor described herein can be delivered with a viral vector. In some embodiments, a base editor disclosed herein can be encoded on a nucleic acid that is contained in a viral vector. In some embodiments, one or more components of the base editor system can be encoded on one or more viral vectors.

[0744] Viral vectors can include lentivirus (e.g., HIV and FIV-based vectors), Adenovirus (e.g, AD 100), Retrovirus (e.g., Maloney murine leukemia virus, MML-V), herpesvirus vectors (e.g., HSV-2), rabies virus (see, e.g., U. S. Patent Application Publication No. US 2022 / 0290164 Al, the disclosure of which is incorporated herein by reference in its entirety for all purposes), and Adeno-associated viruses (AAVs), or other plasmid or viral vector types, in particular, using formulations and doses from, for example, U. S. Patent No. 8,454,972 (formulations, doses for adenovirus), U. S. Patent No. 8,404,658 (formulations, doses for AAV) and U. S. Patent No.

[0745] 5,846,946 (formulations, doses for DNA plasmids) and from clinical trials and publications regarding the clinical trials involving lentivirus, AAV and adenovirus. For example, for AAV, the route of administration, formulation and dose can be as in U. S. Patent No. 8,454,972 and as in clinical trials involving AAV. For Adenovirus, the route of administration, formulation and dose can be as in U. S. Patent No. 8,404,658 and as in clinical trials involving adenovirus. For plasmid delivery, the route of administration, formulation and dose can be as in U. S. Patent No.

[0746] 5,846,946 and as in clinical studies involving plasmids. Doses can be based on or extrapolated to an average 70 kg individual (e.g., a male adult human), and can be adjusted for patients, subjects, mammals of different weight and species. Frequency of administration is within the ambit of the medical or veterinary practitioner (e.g, physician, veterinarian), depending on usual factors including the age, sex, general health, other conditions of the patient or subject and the particular condition or symptoms being addressed. The viral vectors can be injected into the tissue of interest. For cell-type specific base editing, the expression of the base editor and optional guide nucleic acid can be driven by a cell-type specific promoter.

[0747] Viral vectors can be selected based on the application. For example, for in vivo gene delivery, AAV can be advantageous over other viral vectors. In some embodiments, AAV allows low toxicity, which can be due to the purification method not requiring ultra-centrifugation ofATTORNEY DOCKET NO. 180802-047501 / PCT

[0748] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0749] cell particles that can activate the immune response. In some embodiments, AAV allows low probability of causing insertional mutagenesis because it doesn’t integrate into the host genome. Adenoviruses are commonly used as vaccines because of the strong immunogenic response they induce. Packaging capacity of the viral vectors can limit the size of the base editor that can be packaged into the vector.

[0750] AAV has a packaging capacity of about 4.5 Kb or 4.75 Kb including two 145 base inverted terminal repeats (ITRs). This means disclosed base editor as well as a promoter and transcription terminator can fit into a single viral vector. Constructs larger than 4.5 or 4.75 Kb can lead to significantly reduced virus production. For example, SpCas9 is quite large, the gene itself is over 4.1 Kb, which makes it difficult for packing into AAV. Therefore, embodiments of the present disclosure include utilizing a disclosed base editor which is shorter in length than conventional base editors. In some examples, the base editors are less than 4 kb. Disclosed base editors can be less than 4.5 kb, 4.4 kb, 4.3 kb, 4.2 kb, 4.1 kb, 4 kb, 3.9 kb, 3.8 kb, 3.7 kb, 3.6 kb, 3.5 kb, 3.4 kb, 3.3 kb, 3.2 kb, 3.1 kb, 3 kb, 2.9 kb, 2.8 kb, 2.7 kb, 2.6 kb, 2.5 kb, 2 kb, or 1.5 kb. In some embodiments, the disclosed base editors are 4.5 kb or less in length.

[0751] An AAV can be AAV1, AAV2, AAV5, AAV6, AAV9, PHP. EB, PHP. B, AAV.CAP-B10, AAV.CAP-B22, AAV-rhlO, a PAL family AAV, or any combination thereof. In embodiments, the AAV is capable of crossing the blood-brain barrier (see, e.g., those AAV vectors disclosed in Liu, et al. “Crossing the blood-brain barrier with AAV vectors,” Metabolic Brain Disease, 36:45-52 (2021), the disclosure of which is incorporated herein by reference in its entirety for all purposes). One can select the type of AAV with regard to the cells to be targeted; e.g., one can select AAV serotypes 1, 2, 5 or a hybrid capsid AAV1, AAV2, AAV5 or any combination thereof for targeting brain or neuronal cells; and one can select AAV4 for targeting cardiac tissue. AAV8 is useful for delivery to the liver. A tabulation of certain AAV serotypes as to these cells can be found in Grimm, D. et al, J. Virol. 82: 5887-5911 (2008)).

[0752] In some embodiments, the AAV vector contains a PAL family AAV capsid (see, Stanton, A., et al. Med 4:31-50 (2023) (doi: doi.org / 10.1016 / j.medj.2022.11.002), the disclosure of which is incorporated herein by reference in its entirety for all purposes).

[0753] In some embodiments, lentiviral vectors are used to transduce a cell of interest with a polynucleotide encoding a base editor or base editor system as provided herein. Lentiviruses are complex retroviruses that have the ability to infect and express their genes in both mitotic and post-mitotic cells. The most commonly known lentivirus is the human immunodeficiency virus (HIV), which uses the envelope glycoproteins of other viruses to target a broad range of cell types.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0754] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0755] Any RNA of the systems, for example a guide RNA or a base editor-encoding mRNA, can be delivered in the form of RNA. Base editor-encoding mRNA can be generated using any methods available to the skilled practitioner, such as in vitro transcription, PCR, or chemical synthesis.

[0756] Non-Viral Platforms for Gene Transfer

[0757] Non-viral platforms for introducing a heterologous polynucleotide into a cell of interest are known in the art.

[0758] For example, the disclosure provides a method of inserting a heterologous polynucleotide into the genome of a cell using a Cas9 or Casl2 (e.g., Casl2b) ribonucleoprotein complex (RNP)-DNA template complex where an RNP including a Cas9 or Cas12 nuclease domain and a guide RNA, wherein the guide RNA specifically hybridizes to a target region of the genome of the cell, and wherein the Cas nuclease domain cleaves the target region to create an insertion site in the genome of the cell. A DNA template is then used to introduce a heterologous polynucleotide.

[0759] In some embodiments, a heterologous polynucleotide may be inserted into the genome of a cell using a transposable element such as a transposon, as described, for example, in Tipanee, et al. Human Gene Therapy, Nov. 2017, 1087-1104, DOI: 10.1089 / hum.2017.128. Non-limiting examples of transposons include the Sleeping Beauty (SB) transposon, the piggyBac (PB) transposon, and Tol2 transposable elements.

[0760] PHARMACEUTICAL COMPOSITIONS

[0761] In some aspects, the present disclosure provides a pharmaceutical composition comprising any of the cells, polynucleotides, vectors, base editors, base editor systems, guide polynucleotides, fusion proteins, complexes, or the fusion protein-guide polynucleotide complexes described herein.

[0762] The pharmaceutical compositions of the present disclosure can be prepared in accordance with known techniques. See, e.g, Remington, The Science and Practice of Pharmacy (21st ed.

[0763] 2005). In general, the cell, or population thereof is admixed with a suitable carrier prior to administration or storage, and in some embodiments, the pharmaceutical composition further comprises a pharmaceutically acceptable carrier. Suitable pharmaceutically acceptable carriers generally comprise inert substances that aid in administering the pharmaceutical composition to a subject, aid in processing the pharmaceutical compositions into deliverable preparations, or aid in storing the pharmaceutical composition prior to administration. Pharmaceutically acceptableATTORNEY DOCKET NO. 180802-047501 / PCT

[0764] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0765] carriers can include agents that can stabilize, optimize or otherwise alter the form, consistency, viscosity, pH, pharmacokinetics, solubility of the formulation. Such agents include buffering agents, wetting agents, emulsifying agents, diluents, encapsulating agents, and skin penetration enhancers. For example, carriers can include, but are not limited to, saline, buffered saline, dextrose, arginine, sucrose, water, glycerol, ethanol, sorbitol, dextran, sodium carboxymethyl cellulose, and combinations thereof.

[0766] In some embodiments, the pharmaceutical composition is formulated for delivery to a subject. Suitable routes of administrating the pharmaceutical composition described herein include, without limitation: topical, subcutaneous, transdermal, intradermal, intralesional, intraarticular, intraperitoneal, intravesical, transmucosal, gingival, intradental, intracochlear, transtympanic, intraorgan, epidural, intrathecal, intramuscular, intravenous, intravascular, intraosseus, periocular, intratumoral, intracerebral, and intracerebroventricular administration.

[0767] In some embodiments, the pharmaceutical composition described herein is administered locally to a diseased site. In some embodiments, the pharmaceutical composition described herein is administered to a subject by injection, by means of a catheter, by means of a suppository, or by means of an implant, the implant being of a porous, non-porous, or gelatinous material, including a membrane, such as a sialastic membrane, or a fiber.

[0768] In some embodiments, any of the fusion proteins, gRNAs, and / or complexes described herein are provided as part of a pharmaceutical composition. In some embodiments, the pharmaceutical composition comprises any of the fusion proteins or complexes provided herein. In some embodiments pharmaceutical composition comprises a gRNA, a nucleic acid programmable DNA binding protein, a cationic lipid, and a pharmaceutically acceptable excipient. In embodiments, pharmaceutical compositions comprise a lipid nanoparticle and a pharmaceutically acceptable excipient. In embodiments, the lipid nanoparticle contains a gRNA, a base editor, a complex, a base editor system, or a component thereof of the present disclosure, and / or one or more polynucleotides encoding the same. Pharmaceutical compositions can optionally comprise one or more additional therapeutically active substances.

[0769] The compositions, as described above, can be administered in effective amounts. The effective amount will depend upon the mode of administration, the particular condition being treated, and the desired outcome. It may also depend upon the stage of the condition, the age and physical condition of the subject, the nature of concurrent therapy, if any, and like factors well-known to the medical practitioner. For therapeutic applications, it is that amount sufficient to achieve a medically desirable result.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0770] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0771] In some embodiments, compositions in accordance with the present disclosure can be used for treatment of any of a variety of diseases, disorders, and / or conditions.

[0772] KITS

[0773] The disclosure provides kits for the treatment of a disease (e.g., a melanoma or hemoglobinopathy) in a subject. In some embodiments, the kit further includes a base editor system or a polynucleotide encoding a base editor system, wherein the base editor polypeptide system a nucleic acid programmable DNA binding protein (napDNAbp), a deaminase, and a guide RNA. In some embodiments, the napDNAbp is Cas9 or Casl2. In some embodiments, the polynucleotide encoding the base editor is a mRNA sequence. In some embodiments, the deaminase is a cytidine deaminase or an adenosine deaminase. In some embodiments, the kit comprises an edited cell and instructions regarding the use of such cell. In some instances, the kit comprises an anti-CD38 antibody (e.g., Antibody A or Antibody B).

[0774] The kits may further comprise written instructions for using a base editor, base editor system and / or edited cell as described herein. In other embodiments, the instructions include at least one of the following: precautions; warnings; clinical studies; and / or references. The instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container. In a further embodiment, a kit comprises instructions in the form of a label or separate insert (package insert) for suitable operational parameters. In yet another embodiment, the kit comprises one or more containers with appropriate positive and negative controls or control samples, to be used as standard(s) for detection, calibration, or normalization. The kit can further comprise a second container comprising a pharmaceutically-acceptable buffer, such as (sterile) phosphate-buffered saline, Ringer’s solution, or dextrose solution. It can further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.

[0775] The practice of embodiments of the present disclosure employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are well within the purview of the skilled artisan. Such techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, second edition (Sambrook, 1989); “Oligonucleotide Synthesis” (Gait, 1984); “Animal Cell Culture” (Freshney, 1987); “Methods in Enzymology” “Handbook of Experimental Immunology” (Weir, 1996); “Gene Transfer Vectors for Mammalian Cells”ATTORNEY DOCKET NO. 180802-047501 / PCT

[0776] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0777] (Miller and Calos, 1987); “Current Protocols in Molecular Biology” (Ausubel, 1987); “PCR: The Polymerase Chain Reaction”, (Mullis, 1994); “Current Protocols in Immunology” (Coligan, 1991). These techniques are applicable to the production of the polynucleotides and polypeptides of the disclosure, and, as such, may be considered in making and practicing embodiments of the disclosure. Particularly useful techniques for particular embodiments will be discussed in the sections that follow.

[0778] 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 assay, screening, and therapeutic methods of the disclosure, and are not intended to limit the scope of what the inventors regard as their invention.

[0779] EXAMPLES

[0780] Example 1: Development of an Engineered Stem Cell Antibody-Paired Evasion (ESCAPE) Approach for Engraftment of Hematopoietic Stem Cells (HSCs)

[0781] Experiments were undertaken to leverage base editing technologies to produce engineered hemopoietic stem cells (eHSCs) that could be coupled with a monoclonal antibody (mAb) strategy capable of clearing the niche of a patient’s bone marrow to levels sufficient for eHSC engraftment and preserving eHSC viability in the presence of the conditioning mAb. Using base editing technology, methods were developed to enhance the flexibility and potency of a non-genotoxic conditioning approach (e.g., use of monoclonal antibodies) through intentional, non-synonymous mutations within an epitope of an essential protein expressed on the surface of HSCs (e.g., CD38). This essential, cell-surface protein was designed to selectively escape mAb-induced ablation. Because the CD38 epitope-engineered HSCs were designed for transplant and to be resistant to a conditioning reagent, high concentrations of mAb can be used to clear the niche for engraftment, long half-lives of administered mAb conditioning reagent can be tolerated, and additional doses of mAb can be administered if required.

[0782] An experiment was undertaken to screen guide RNAs predicted in silico to be suitable for use with ABE8.8 having specificity for the protospacer adjacent motif (PAM) NGG or ABE8.20 (F149Y) having specificity for the PAM NRCH, for introducing an alteration selected from those listed in Table 1 to a CD38 polynucleotide in hematopoietic stem cells (HSCs) (FIG. 2). Each of ABE8.8 and ABE8.20 (F149Y) contained an SpCas9 nickase containing a D10A amino acid alterations referenced to SEQ ID NO: 197. Mobilized peripheral blood (PB) CD34+ cells were seeded at Day -2 (FIG. 2) and grown in X VIVO 10 culture medium. At day O, the cells were transfected with base editor systems containing mRNA encoding ABE8.8 (mRNA3944) orATTORNEY DOCKET NO. 180802-047501 / PCT

[0783] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0784] ABE8.20 (F149Y) (mRNA3311) and a guide RNA (gRNA9239, gRNA9240, gRNA9245, gRNA9247, gRNA9253, gRNA9254, gRNA9255, or gRNA9234) (see Tables 1 and 2 for guide and base editor sequences) using electroporation. Max A-to-G editing was measured at day 5 post electroporation using next-generation sequencing (FIGs. 1 and 3C). The amino acid alterations introduced to the CD38 polynucleotide sequence using each guide are indicated in FIG. 1, where base editor systems containing gRNA9239 introduced a base edit resulting in a Q107R amino acid alteration in CD38, the base editor systems containing gRNA9240 introduced a base edit(s) resulting in one or more of Q115R and T116A amino acid alterations in CD38, the base editor systems containing gRNA9245 introduced a base edit(s) resulting in one or more of D141G and M142V amino acid alterations in CD38, the base editor systems containing gRNA9247 introduced a base edit(s) resulting in one or more of E233G and K234G amino acid alterations in CD38, the base editor systems containing gRNA9253 or gRNA9254 introduced a base edit(s) resulting in one or more of L149P and L150P amino acid alterations in CD38, the base editor system containing gRNA9255 introduced a base edit(s) resulting in one or more of E76G, M77V, and R78G amino acid alterations in CD38, and the base editor system containing gRNA9232 introduced a base edit(s) resulting in a V203A amino acid alteration in CD38.

[0785] Several of the base editor systems were associated with maximum A-to-G editing rates of greater than 50% (FIGs. 1 and 3C).

[0786] HSCs expressing the CD38 polypeptides altered through base editing showed reduced levels of binding to the anti-CD38 antibodies Antibody A and Antibody B (FIGs. 3A and 3B).

[0787] For example, cells expressing a CD38 polypeptide containing one of the following alterations or combinations of alterations showed reduced binding to Antibody A and / or Antibody B: D141G and / or M142V; E76G, M77V, and / or R78G; or T116A. The base edited HSCs were capable of evading therapeutic antibody binding.

[0788] Experiments were next undertaken to demonstrate that myeloma cells (RPMI8224 or RPMI8226) base edited as described above to express CD38 polypeptide variants showed reduced levels of binding to the anti-CD38 antibodies Antibody A and Antibody B. The myeloma cells were transfected with base editor systems containing mRNA encoding ABE8.8 (mRNA3944) or ABE8.20 (F149Y) (mRNA3311) and a guide RNA (gRNA9240, gRNA9245, or gRNA9255) (see Tables 1 and 2 for guide and base editor sequences) using electroporation. Max A-to-G editing was measured at day 4 post electroporation using next-generation sequencing, and the base editor systems were all associated with maximum A-to-G editing rates of greater than 50% (FIG. 4C). RPMI8226 or RPMI8224 multiple myeloma cells expressing a CD38 polypeptide containing one of the following alterations or combinations of alterationsATTORNEY DOCKET NO. 180802-047501 / PCT

[0789] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0790] showed reduced binding to Antibody A and / or Antibody B: D141G and / or M142V; E76G, M77V, and / or R78G; or T116A. The base edited HSCs were capable of evading therapeutic antibody binding (FIGs. 4A and 4B).

[0791] The following methods were employed in the above examples.

[0792] CD34+ cell culture

[0793] Plerixafor and G-CSF mobilized peripheral blood CD34+ cells were thawed and put into X-VIVO 10 culture medium containing 1% GlutaMAX and 100 ng / ml each of human stem cell factor (SCF), Flt3 -ligand (Flt3-L), and thrombopoietin (TPO), and were cultured for 48 hours prior to electroporation.

[0794] R PM 1-8226 myeloma cell culture

[0795] RPMI-8226 myeloma cells were thawed and put into RPMI-1640 culture medium containing 10% of fetal bovine serum. Cell density was maintained between 5 * 105and 2 * 106viable cells / ml, and medium was renewed every 2 to 3 days.

[0796] Electroporation of CD34+ cells and RPMI-8226 myeloma cell line

[0797] At 48 hours post-thaw, the cells were centrifuged to remove the culture medium and washed in MaxCyte® buffer with 0.1% human serum albumin. The cells were then resuspended in cold MaxCyte® buffer at 50 * 106cells per ml and split into multiple 20 pl aliquots. The ABE mRNA (i.e., mRNA encoding the adenosine base editor) (0.05 pM) and CD38 sgRNA (5 pM) were then aliquoted according to the experimental conditions and were raised to a total of 5 pl in MaxCyte® buffer. Then, 20 pl of cells were added into the 5 pl RNA mixture and these were loaded into each chamber of an OC25x3 MaxCyte® cuvette for electroporation using program ‘HSC-3’ for CD34+ cells and program ‘B Cell 2’ for RPMI-8226 myeloma cell line. After receiving the charge, 25 pl was collected from each chamber and was placed in the center of the wells in a 12-well untreated culture plate. The cells were recovered for 20 min in an incubator (37 °C, 5% CO2). After the 20 min recovery, X-VIVO 10 culture medium was added to CD34+ cells and RPMI-1640 culture medium was added to the RPMI-8226 myeloma cell line to produce a concentration of 1 x 106cells / ml. The cells were then further recovered in an incubator (37 °C, 5% CO2) for 48 hours.ATTORNEY DOCKET NO. 180802-047501 / PCT

[0798] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0799] Genomic DNA extraction for CD34+ cells and RPMI-8226 myeloma cell line

[0800] Genomic DNA was extracted from CD34+ cells and RPMI-8226 myeloma cells at 96 or 120 hours after electroporation. A total of 1 x 105cells were collected and centrifuged to form a pellet. The pellet was resuspended in 50 pL of Quick Extract buffer, and the mixture was transferred to a 96-well PCR plate. The lysates were subjected to heat treatment at 65 °C for 15 minutes, followed by 98 °C for 10 minutes. The resulting lysates were stored at -20 °C for further use.

[0801] Next generation sequencing of genomic DNA samples

[0802] Genomic DNA samples were prepared for high-throughput sequencing following protocols described in Gaudelli, et al., “Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage,” Nature, 551:464-471 (2017). Briefly, 4 pL of genomic DNA (gDNA) was added to a 25 pL PCR reaction containing Phusion U Green Multiplex PCR Master Mix and 0.5 pM of each forward and reverse primer. After amplification, the resulting PCR products were barcoded using unique, combinatorial Illumina barcoding primer pairs. Each barcoding reaction consisted of 0.5 pM of Illumina forward and reverse primers, 2 pL of PCR-amplified product containing the target genomic region, and Q5 Hot Start High-Fidelity 2X Master Mix in a total volume of 25 pL. All PCR steps followed the conditions outlined in Gaudelli, et al. The primers used for amplifying site-specific genomic DNA from mammalian cells transfected with base editor systems containing particular guide RNAs are listed in Table 9.

[0803] DNA concentrations were measured using a NanoDrop 1000 Spectrophotometer, and sequencing was performed on an Illumina MiSeq instrument in accordance with the manufacturer’s protocols.

[0804] Table 9. Target site amplification primers.

[0805] sgRNA Forward Primer SEQ Reverse Primer SEQ ID NO ID NO

[0806] gRNA9237 ACACTCTTTCCCTACACGACG 809 TGGAGTTCAGACGTGTGCTCTT 810 CTCTTCCGATCTGGCGCGATG CCGATCTCCGAGCCCGGGACTC CGTCAAGTACACTGA CCTACTCA

[0807] gRNA9238 ACACTCTTTCCCTACACGACG 811 TGGAGTTCAGACGTGTGCTCTT 812 CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0808] gRNA9239 ACACTCTTTCCCTACACGACG 813 TGGAGTTCAGACGTGTGCTCTT 814 CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0809] gRNA9240 ACACTCTTTCCCTACACGACG 815 TGGAGTTCAGACGTGTGCTCTT 816 CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT

[0810]

[0811] CATGTTAGACGAGATAATA CCCCAGTTTTAAATTORNEY DOCKET NO. 180802-047501 / PCT

[0812] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0813] sgRNA Forward Primer SEQ Reverse Primer SEQ ID NO ID NO

[0814] gRNA9241 ACACTCTTTCCCTACACGACG 817 TGGAGTTCAGACGTGTGCTCTT 818

[0815] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0816] gRNA9242 ACACTCTTTCCCTACACGACG 819 TGGAGTTCAGACGTGTGCTCTT 820

[0817] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0818] gRNA9243 ACACTCTTTCCCTACACGACG 821 TGGAGTTCAGACGTGTGCTCTT 822

[0819] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0820] gRNA9244 ACACTCTTTCCCTACACGACG 823 TGGAGTTCAGACGTGTGCTCTT 824

[0821] CTCTTCCGATCTCTTCCTTAG CCGATCTGGCCTCCAGCAGAAG ATTCTTCTTTGGAGCAGA TCACTCTGTTCA

[0822] gRNA9245 ACACTCTTTCCCTACACGACG 825 TGGAGTTCAGACGTGTGCTCTT 826

[0823] CTCTTCCGATCTCTTCCTTAG CCGATCTGGCCTCCAGCAGAAG ATTCTTCTTTGGAGCAGA TCACTCTGTTCA

[0824] gRNA9246 ACACTCTTTCCCTACACGACG 827 TGGAGTTCAGACGTGTGCTCTT 828

[0825] CTCTTCCGATCTCCTTCCTTA CCGATCTAGGATACTTGCAAAC ACC AG CTATTG CTAAGTAT AGGATGCAAAATA

[0826] gRNA9247 ACACTCTTTCCCTACACGACG 829 TGGAGTTCAGACGTGTGCTCTT 830

[0827] CTCTTCCGATCTCTATTTTAG CCGATCTTTTCATTTCCTGAGT CACTTTTGGGAGTGTGGAA CAATTTGTTCCCA

[0828] gRNA9248 ACACTCTTTCCCTACACGACG 831 TGGAGTTCAGACGTGTGCTCTT 832

[0829] CTCTTCCGATCTCTATTTTAG CCGATCTTTTCATTTCCTGAGT CACTTTTGGGAGTGTGGAA CAATTTGTTCCCA

[0830] gRNA9249 ACACTCTTTCCCTACACGACG 833 TGGAGTTCAGACGTGTGCTCTT 834

[0831] CTCTTCCGATCTCTATTTTAG CCGATCTTTTCATTTCCTGAGT CACTTTTGGGAGTGTGGAA CAATTTGTTCCCA

[0832] gRNA9250 ACACTCTTTCCCTACACGACG 835 TGGAGTTCAGACGTGTGCTCTT 836

[0833] CTCTTCCGATCTCTATTTTAG CCGATCTTTTCATTTCCTGAGT CACTTTTGGGAGTGTGGAA CAATTTGTTCCCA

[0834] gRNA9251 ACACTCTTTCCCTACACGACG 837 TGGAGTTCAGACGTGTGCTCTT 838

[0835] CTCTTCCGATCTACTTATGCC CCGATCTGTGATCATCATCAAG AGGATCCCACCATAAAAGA GCCCAAGAAAGA

[0836] gRNA9252 ACACTCTTTCCCTACACGACG 839 TGGAGTTCAGACGTGTGCTCTT 840

[0837] CTCTTCCGATCTCATTAGCGA CCGATCTAGCAGGTATGCTGAG ATTGGACGACAGATGTA TCATGTATGATGA

[0838] gRNA9253 ACACTCTTTCCCTACACGACG 841 TGGAGTTCAGACGTGTGCTCTT 842

[0839] CTCTTCCGATCTCTTCCTTAG CCGATCTGGCCTCCAGCAGAAG ATTCTTCTTTGGAGCAGA TCACTCTGTTCA

[0840] gRNA9254 ACACTCTTTCCCTACACGACG 843 TGGAGTTCAGACGTGTGCTCTT 844

[0841] CTCTTCCGATCTCTTCCTTAG CCGATCTGGCCTCCAGCAGAAG ATTCTTCTTTGGAGCAGA TCACTCTGTTCA

[0842] gRNA9255 ACACTCTTTCCCTACACGACG 845 TGGAGTTCAGACGTGTGCTCTT 846

[0843] CTCTTCCGATCTGGCGCGATG CCGATCTCCGAGCCCGGGACTC CGTCAAGTACACTGA CCTACTCA

[0844] gRNA9256 ACACTCTTTCCCTACACGACG 847 TGGAGTTCAGACGTGTGCTCTT 848

[0845] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0846] gRNA9257 ACACTCTTTCCCTACACGACG 849 TGGAGTTCAGACGTGTGCTCTT 850

[0847] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0848] gRNA9258 ACACTCTTTCCCTACACGACG 851 TGGAGTTCAGACGTGTGCTCTT 852

[0849] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT

[0850]

[0851] CATGTTAGACGAGATAATA CCCCAGTTTTAAATTORNEY DOCKET NO. 180802-047501 / PCT

[0852] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0853] sgRNA Forward Primer SEQ Reverse Primer SEQ ID NO ID NO

[0854] gRNA9229 ACACTCTTTCCCTACACGACG 853 TGGAGTTCAGACGTGTGCTCTT 854

[0855] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0856] gRNA9259 ACACTCTTTCCCTACACGACG 855 TGGAGTTCAGACGTGTGCTCTT 856

[0857] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0858] gRNA9230 ACACTCTTTCCCTACACGACG 857 TGGAGTTCAGACGTGTGCTCTT 858

[0859] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0860] gRNA9231 ACACTCTTTCCCTACACGACG 859 TGGAGTTCAGACGTGTGCTCTT 860

[0861] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0862] gRNA9260 ACACTCTTTCCCTACACGACG 861 TGGAGTTCAGACGTGTGCTCTT 862

[0863] CTCTTCCGATCTCTTCCTTAG CCGATCTGGCCTCCAGCAGAAG ATTCTTCTTTGGAGCAGA TCACTCTGTTCA

[0864] gRNA9232 ACACTCTTTCCCTACACGACG 863 TGGAGTTCAGACGTGTGCTCTT 864

[0865] CTCTTCCGATCTCCTTCCTTA CCGATCTAGGATACTTGCAAAC ACC AG CTATTG CTAAGTAT AGGATGCAAAATA

[0866] gRNA9261 ACACTCTTTCCCTACACGACG 865 TGGAGTTCAGACGTGTGCTCTT 866

[0867] CTCTTCCGATCTCTATTTTAG CCGATCTTTTCATTTCCTGAGT CACTTTTGGGAGTGTGGAA CAATTTGTTCCCA

[0868] gRNA9262 ACACTCTTTCCCTACACGACG 867 TGGAGTTCAGACGTGTGCTCTT 868

[0869] CTCTTCCGATCTCTATTTTAG CCGATCTTTTCATTTCCTGAGT CACTTTTGGGAGTGTGGAA CAATTTGTTCCCA

[0870] gRNA9263 ACACTCTTTCCCTACACGACG 869 TGGAGTTCAGACGTGTGCTCTT 870

[0871] CTCTTCCGATCTCTATTTTAG CCGATCTTTTCATTTCCTGAGT CACTTTTGGGAGTGTGGAA CAATTTGTTCCCA

[0872] gRNA9264 ACACTCTTTCCCTACACGACG 871 TGGAGTTCAGACGTGTGCTCTT 872

[0873] CTCTTCCGATCTCATTAGCGA CCGATCTAGCAGGTATGCTGAG ATTGGACGACAGATGTA TCATGTATGATGA

[0874] gRNA9265 ACACTCTTTCCCTACACGACG 873 TGGAGTTCAGACGTGTGCTCTT 874

[0875] CTCTTCCGATCTCATTAGCGA CCGATCTAGCAGGTATGCTGAG ATTGGACGACAGATGTA TCATGTATGATGA

[0876] gRNA9266 ACACTCTTTCCCTACACGACG 875 TGGAGTTCAGACGTGTGCTCTT 876

[0877] CTCTTCCGATCTCATTAGCGA CCGATCTAGCAGGTATGCTGAG ATTGGACGACAGATGTA TCATGTATGATGA

[0878] gRNA9233 ACACTCTTTCCCTACACGACG 877 TGGAGTTCAGACGTGTGCTCTT 878

[0879] CTCTTCCGATCTACTTATGCC CCGATCTGTGATCATCATCAAG AGGATCCCACCATAAAAGA GCCCAAGAAAGA

[0880] gRNA9267 ACACTCTTTCCCTACACGACG 879 TGGAGTTCAGACGTGTGCTCTT 880

[0881] CTCTTCCGATCTCTATTTTAG CCGATCTTTTCATTTCCTGAGT CACTTTTGGGAGTGTGGAA CAATTTGTTCCCA

[0882] gRNA9234 ACACTCTTTCCCTACACGACG 881 TGGAGTTCAGACGTGTGCTCTT 882

[0883] CTCTTCCGATCTCCTTCCTTA CCGATCTAGGATACTTGCAAAC ACC AG CTATTG CTAAGTAT AGGATGCAAAATA

[0884] gRNA9268 ACACTCTTTCCCTACACGACG 883 TGGAGTTCAGACGTGTGCTCTT 884

[0885] CTCTTCCGATCTCCTTCCTTA CCGATCTAGGATACTTGCAAAC ACC AG CTATTG CTAAGTAT AGGATGCAAAATA

[0886] gRNA9235 ACACTCTTTCCCTACACGACG 885 TGGAGTTCAGACGTGTGCTCTT 886

[0887] CTCTTCCGATCTCCTTCCTTA CCGATCTAGGATACTTGCAAAC ACC AG CTATTG CTAAGTAT AGGATGCAAAATA

[0888] gRNA9269 ACACTCTTTCCCTACACGACG 887 TGGAGTTCAGACGTGTGCTCTT 888

[0889] CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT

[0890]

[0891] CATGTTAGACGAGATAATA CCCCAGTTTTAAATTORNEY DOCKET NO. 180802-047501 / PCT

[0892] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0893] sgRNA Forward Primer SEQ Reverse Primer SEQ ID NO ID NO

[0894] gRNA9236 ACACTCTTTCCCTACACGACG 889 TGGAGTTCAGACGTGTGCTCTT 890 CTCTTCCGATCTGGTAGACTG C CG ATCTAC CATTGG CTTTTAT CATGTTAGACGAGATAATA CCCCAGTTTTAA

[0895] sgRNA_088 GTACATCGCCAGCACGAGTTC 891 GGCCGGCATCCATTAGCATCTG 892

[0896]

[0897] TCTGA TCTCA

[0898] Antibody affinity screen

[0899] At 48 hours prior to electroporation, CD34+ cells or RPMI-8226 myeloma cells were thawed, counted, and resuspended at a density of 5 * 105cells / mL for culture in the corresponding culture medium. On Day 0, cells were subjected to electroporation to introduce CD38 edits. At 96- or 120-hours post-electroporation, the cells were harvested for analysis. The cells were collected, counted, and assessed for viability. Remaining cells were pelleted and resuspended in Dulbecco's phosphate-buffered saline (DPBS) at a concentration of 1 x 106cells / mL. Fifty microliters of the cell suspension (5 x 104cells) were seeded into each well of a 96-well plate. For cell staining, the cells were centrifuged and resuspended in 100 pL of Zombie dye (1:800 dilution in DPBS). The cells were incubated for 20 minutes at room temperature in the dark. Following incubation, 100 pL of cell staining buffer (CSB) was added to each well, and the cells were centrifuged and washed before antibody binding. Antibody dilutions were prepared in 96-well plates by serial dilutions using CSB as the diluent. Diluted nanobody solution were added to each well. The cells were mixed thoroughly and incubated at 4°C for 1 hour. Post-incubation, 100 pL of CSB was added to each well, and the cells were centrifuged, resuspended in 100 pL of secondary antibody (fluorochrome conjugated anti-human IgGFc) buffer (1:200 dilution in CSB), and incubated at 4°C for 30 minutes. After the final wash, the cells were resuspended in 100 pL of CSB and analyzed using a flow cytometer to evaluate antibody binding and cell viability.

[0900] Flow cytometry

[0901] To assess cell surface receptor expression, 1 × 106cells were taken from culture 4- or 5-days post-electroporation and stained with an anti -human CD38 antibody (e.g., Antibody A or Antibody B) along with Zombie Aqua viability dye. Data were acquired using an Attune NxT Flow Cytometer (Thermo Fisher Scientific) and were analyzed using FlowJo Single Cell Analysis Software vlO.7.1 (FlowJo).ATTORNEY DOCKET NO. 180802-047501 / PCT

[0902] ELECTRONIC DEPOSIT DATE: January 21, 2026

[0903] OTHER EMBODIMENTS

[0904] From the foregoing description, it will be apparent that variations and modifications may be made to the aspects or embodiments described herein to adopt it to various usages and conditions. Such embodiments are also within the scope of the following claims.

[0905] The recitation of a listing of elements in any definition of a variable herein includes definitions of that variable as any single element or combination (or subcombination) of listed elements. The recitation of an embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.

[0906] All patents and publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent and publication was specifically and individually indicated to be incorporated by reference.

Claims

ATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026CLAIMSWhat is claimed:

1. A method of altering a nucleobase of a cluster of differentiation 38 (CD38) polynucleotide, the method comprising:contacting the CD38 polynucleotide with a base editor system comprising a base editor, or one or more polynucleotides encoding the base editor, wherein the base editor comprises a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain, and a guide RNA, or a polynucleotide encoding the guide RNA, wherein the guide RNA directs said base editor to effect an alteration of the nucleobase of the CD38 polynucleotide to yield a CD38 polynucleotide variant encoding a CD38 polypeptide variant with reduced binding relative to a wild-type CD38 polypeptide to a polypeptide capable of binding to the wild-type CD38 polypeptide, wherein the CD38 polypeptide variant comprises an amino acid substitution at a position selected from the group consisting of positions 76, 77, 78, 103, 104, 106, 107, 110, 111, 112, 114, 115, 116, 117, 120, 121, 139, 141, 142, 149, 150, 196, 201, 202, 203, 205, 231, 233, 234, 236, 237, 239, 241, 273, 274, 276, 284, 288, 292, and 296.

2. The method of claim 1, wherein the method comprises altering two or more nucleobases of the CD38 polynucleotide.

3. The method of claim 1, wherein the CD38 polypeptide variant comprises an amino acid substitution at a position selected from the group consisting of 76, 77, 78, 116, 141, and 142.

4. The method of claim 1, wherein the amino acid substitution is selected from the group consisting ofE76G, M77V, R78G, R78G, E103G, E104G, Y106C, Q107R, Q107R, M110V, K111G, K111R, L112S, T114A, T114A, Q115R, Q115R, T116A, T116A, V117A, N120D, N120G, N120G, N120G, N120S, K121E, K121G, Q139R, D141G, D141G, D141G, M142V, M142V, L149P, L149P, L150P, L150P, F196P, C201R, D202G, V203A, H205R, Q231R, Q231R, E233G, E233G, K234G, Q236R, Q236R, T237A, T237A, E239G, E239G, W241R, F273P, S274P, K276E, F284P, V288A, E292G, and C296R.

5. The method of claim 4, wherein the CD38 polypeptide variant comprises an amino acid substitution(s) selected from the group consisting of:i) Q107R;ATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026ii) Q115R and T116A;iii) D141G and M142V;iv) E233G and K234G;v) L149P and L150P;vi) E76G, M77V, and R78G;vii) V203A;viii) T116A;ix) K234E;x) K234G; andxi) K234R.

6. The method of claim 1, wherein the deaminase domain is an adenosine deaminase domain.

7. The method of claim 6, wherein the adenosine deaminase domain is a TadA*8.8 polypeptide or a TadA*8.20 polypeptide.

8. The method of claim 7, wherein the TadA*8.20 polypeptide comprises an F149Y amino acid substitution.

9. The method of claim 1, wherein the napDNAbp domain is a nickase.

10. The method of claim 1, wherein the napDNAbp domain is a Cas9 domain.

11. The method of claim 10, wherein the Cas9 domain is a Streptococcus pyogenes Cas9 (SpCas9), or a variant thereof.

12. The method of claim 11, wherein the SpCas9 variant has protospacer-adjacent motif (PAM) specificity for a PAM containing the nucleotide sequence NRCH, where “N” is A, C, T, or G, “R” is A or G, and “H” is A, C, or T.

13. The method of claim 12, wherein the SpCas9 comprises the amino acid alterations I322V, S409I, E427G, R654L, R753G, R1114G, D1135N, E1219V, D1332N, R1335Q, T1337N, S1338T, and H1349R referenced to SEQ ID NO: 197.ATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 202614. The method of claim 1, wherein the guide RNA comprises a spacer, wherein the spacer comprises a nucleotide sequence selected from the spacer sequences listed in Table 1.

15. The method of claim 14, wherein the spacer comprises a nucleotide sequence selected from the group consisting of: ACCACAUCACAGGCAGCUUC (SEQ ID NO: 796; gRNA9234), UAUCAGCCACUAAUGAAGUU (SEQ ID NO: 728; gRNA9239), UCAGACCGUACCUUGCAACA (SEQ ID NO: 730; gRNA9240), GCGGGACAUGUUCACCCUGG (SEQ ID NO: 740; gRNA9245), AGAGAAGGUUCAGACACUAG (SEQ ID NO: 744; gRNA9247), AGCCUAGCAGCGUGUCCUCC (SEQ ID No: 756; gRNA9253), GCCUAGCAGCGUGUCCUCCA (SEQ ID NO: 758; gRNA9254), and CUGAGAUGAGGUGGGUUGGC (SEQ ID NO: 760; gRNA9255).

16. The method of claim 1 or claim 15, wherein the guide RNA comprises a gRNA sequence listed in Table 1.

17. The method of claim 1, wherein the polypeptide capable of binding to the wild-type CD38 polypeptide is an antibody.

18. The method of claim 17, wherein the antibody is Antibody A or Antibody B.

19. The method of claim 1, wherein the CD38 polynucleotide is in a cell.

20. The method of claim 19, wherein the cell is a hematopoietic stem cell.

21. The method of claim 20, wherein the hematopoietic stem cell is from a subject having a disease or disorder amenable to treatment using hematopoietic stem cell transplant therapy.

22. A cell prepared according to the method of any one of claims 19-21.

23. A method for cell transplantation in a subject, the method comprising:(a) contacting a cell with a base editor system comprising a base editor, or one or more polynucleotides encoding the base editor, wherein the base editor comprises a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain, and a guide RNA, or a polynucleotide encoding the guide RNA, wherein the guide RNA directs said baseATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026editor to effect an alteration of a nucleobase of a CD38 polynucleotide in the cell to yield a CD38 polynucleotide encoding a CD38 polypeptide variant comprising an amino acid substitution at a position selected from the group consisting of positions 76, 77, 78, 103, 104, 106, 107, 110, 111, 112, 114, 115, 116, 117, 120, 121, 139, 141, 142, 149, 150, 196, 201, 202, 203, 205, 231, 233, 234, 236, 237, 239, 241, 273, 274, 276, 284, 288, 292, and 296, thereby producing an edited cell;(c) administering the edited cell to the subject; and(d) administering to the subject an antibody, antibody drug conjugate, or chimeric antigen receptor expressing T cell (CAR-T) that selectively binds a wild-type version of CD38, wherein the administering of step (d) is prior to, concurrent with, or subsequent to step (c).

24. The method of claim 23, wherein the cell is from the subject.

25. The method of claim 23, wherein the method comprises altering two or more nucleobases of the CD38 polynucleotide.

26. The method of claim 23, wherein the CD38 polypeptide variant comprises an amino acid substitution at a position selected from the group consisting of 76, 77, 78, 116, 141, and 142.

27. The method of claim 23, wherein the amino acid substitution is selected from the group consisting ofE76G, M77V, R78G, R78G, E103G, E104G, Y106C, Q107R, Q107R, M110V, K111G, K111R, L112S, T114A, T114A, Q115R, Q115R, T116A, T116A, V117A, N120D, N120G, N120G, N120G, N120S, K121E, K121G, Q139R, D141G, D141G, D141G, M142V, M142V, L149P, L149P, L150P, L150P, F196P, C201R, D202G, V203A, H205R, Q231R, Q231R, E233G, E233G, K234G, Q236R, Q236R, T237A, T237A, E239G, E239G, W241R, F273P, S274P, K276E, F284P, V288A, E292G, and C296R.

28. The method of claim 27, wherein the CD38 polypeptide variant comprises an amino acid substitution(s) selected from the group consisting of:i) Q107R;ii) Q115R and T116A;iii) D141G and M142V;iv) E233G and K234G;v) L149P and L150P;ATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026vi) E76G, M77V, and R78G;vii) V203A;viii) T116A;ix) K234E;x) K234G; andxi) K234R.

29. The method of claim 23, wherein the deaminase domain is an adenosine deaminase domain.

30. The method of claim 29, wherein the adenosine deaminase domain is a TadA*8.8 polypeptide or a TadA*8.20 polypeptide.

31. The method of claim 30, wherein the TadA*8.20 polypeptide comprises an F149Y amino acid substitution.

32. The method of claim 23, wherein the napDNAbp domain is a SpCas9 variant with protospacer-adjacent motif (PAM) specificity for a PAM containing the nucleotide sequence NRCH, where “N” is A, C, T, or G, “R” is A or G, and “H” is A, C, or T.

33. The method of claim 23, wherein the guide RNA comprises a spacer, wherein the spacer comprises a nucleotide sequence selected from the spacer sequences listed in Table 1.

34. The method of claim 33, wherein the spacer comprises a nucleotide sequence selected from the group consisting of: ACCACAUCACAGGCAGCUUC (SEQ ID NO: 796; gRNA9234), UAUCAGCCACUAAUGAAGUU (SEQ ID NO: 728; gRNA9239), UCAGACCGUACCUUGCAACA (SEQ ID NO: 730; gRNA9240), GCGGGACAUGUUCACCCUGG (SEQ ID NO: 740; gRNA9245), AGAGAAGGUUCAGACACUAG (SEQ ID NO: 744; gRNA9247), AGCCUAGCAGCGUGUCCUCC (SEQ ID No: 756; gRNA9253), GCCUAGCAGCGUGUCCUCCA (SEQ ID NO: 758; gRNA9254), and CUGAGAUGAGGUGGGUUGGC (SEQ ID NO: 760; gRNA9255).ATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 202635. The method of claim 23 or claim 34, wherein the guide RNA comprises a gRNA sequence listed in Table 1.

36. The method of claim 23, wherein the antibody is Antibody A or Antibody B.

37. The method of claim 23, wherein the subject has a disease selected from an autoimmune disease, hemoglobinopathy, hematologic cancer, or myeloproliferative disease and the edited cell is administered to the subject to treat the disease.

38. The method of claim 23, wherein the subject has a disease selected from the group consisting of acute myeloid leukemia, acute lymphoid leukemia, amyloid light-chain (AL) amyloidosis, B-cell acute lymphoblastic leukemia (B-ALL), aplastic anemia, chronic myeloid leukemia, chronic lymphoid leukemia, diffuse large B-cell lymphoma, Fanconi anemia, lupus, multiple myeloma, a myelodysplastic syndrome, non-Hodgkin's lymphoma, rheumatoid arthritis, sickle cell anemia, T-cell acute lymphoblastic leukemia (T-ALL), thalassemia, and Wiskott-Aldrich syndrome and the edited cell is administered to the subject to treat the disease.

39. The method of claim 23, wherein the cell is a hematopoietic stem cell, common myeloid progenitor, proerythroblast, or erythroblast.

40. The method of any one of claims 1-38, wherein the base editor comprises two adenosine deaminase domains.

41. The method of claim 40, wherein one of the two adenosine deaminase domains is a wildtype Tad A.

42. A base editor system comprising a base editor, or one or more polynucleotides encoding the base editor, wherein the base editor comprises a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain, and a guide RNA, or a polynucleotide encoding the guide RNA, wherein the guide RNA directs said base editor to effect an alteration of the nucleobase of a CD38 polynucleotide to yield a CD38 polynucleotide variant, wherein the CD38 polypeptide variant comprises an amino acid substitution at a position selected from the group consisting of positions 76, 77, 78, 103, 104, 106, 107, 110, 111, 112, 114, 115, 116, 117, 120, 121, 139, 141, 142, 149, 150, 196, 201, 202, 203, 205, 231, 233, 234, 236, 237, 239, 241,ATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026273, 274, 276, 284, 288, 292, and 296.

43. The base editor system of claim 42, wherein the deaminase domain is an adenosine deaminase domain.

44. The base editor system of claim 43, wherein the adenosine deaminase domain is a TadA*8.8 polypeptide or a TadA*8.20 polypeptide.

45. The base editor system of claim 44, wherein the TadA*8.20 polypeptide comprises an F149Y amino acid substitution.

46. The base editor system of claim 42, wherein the napDNAbp domain is an SpCas9 variant having protospacer-adjacent motif (PAM) specificity for a PAM containing the nucleotide sequence NRCH, where “N” is A, C, T, or G, “R” is A or G, and “H” is A, C, or T.

47. The base editor system of claim 42, wherein the guide RNA comprises a spacer, wherein the spacer comprises a nucleotide sequence selected from the spacer sequences listed in Table 1.

48. The base editor system of claim 47, wherein the spacer comprises a nucleotide sequence selected from the group consisting of: ACCACAUCACAGGCAGCUUC (SEQ ID NO: 796; gRNA9234), UAUCAGCCACUAAUGAAGUU (SEQ ID NO: 728; gRNA9239), UCAGACCGUACCUUGCAACA (SEQ ID NO: 730; gRNA9240), GCGGGACAUGUUCACCCUGG (SEQ ID NO: 740; gRNA9245), AGAGAAGGUUCAGACACUAG (SEQ ID NO: 744; gRNA9247), AGCCUAGCAGCGUGUCCUCC (SEQ ID No: 756; gRNA9253), GCCUAGCAGCGUGUCCUCCA (SEQ ID NO: 758; gRNA9254), and CUGAGAUGAGGUGGGUUGGC (SEQ ID NO: 760; gRNA9255).

49. The base editor system of claim 42 or claim 48 wherein the guide RNA comprises a gRNA sequence listed in Table 1.

50. A polynucleotide or set of polynucleotides encoding the base editor system of any one of claims 42-49.

51. A cell produced by introducing into a cell, or a progenitor thereof, the base editor systemATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026of any one of claims 42-49 or the polynucleotide of claim 50.

52. A guide RNA comprising a spacer comprising a nucleotide sequence selected from the spacer sequences listed in Table 1.

53. The guide RNA of claim 52, wherein the guide RNA comprises a spacer, wherein the spacer comprises a nucleotide sequence selected from the spacer sequences listed in Table 1.

54. The guide RNA of claim 53, wherein the spacer comprises a nucleotide sequence selected from the group consisting of: ACCACAUCACAGGCAGCUUC (SEQ ID NO: 796; gRNA9234), UAUCAGCCACUAAUGAAGUU (SEQ ID NO: 728; gRNA9239), UCAGACCGUACCUUGCAACA (SEQ ID NO: 730; gRNA9240), GCGGGACAUGUUCACCCUGG (SEQ ID NO: 740; gRNA9245), AGAGAAGGUUCAGACACUAG (SEQ ID NO: 744; gRNA9247), AGCCUAGCAGCGUGUCCUCC (SEQ ID No: 756; gRNA9253), GCCUAGCAGCGUGUCCUCCA (SEQ ID NO: 758; gRNA9254), and CUGAGAUGAGGUGGGUUGGC (SEQ ID NO: 760; gRNA9255).

55. The guide RNA of claim 52, wherein the guide RNA comprises a gRNA sequence listed in Table 1.

56. A pharmaceutical composition comprising an effective amount of the polynucleotide or set of polynucleotides of claim 50, the cell of claim 22 or claim 51, or the guide polynucleotide of any one of claims 52-55, and a pharmaceutically acceptable excipient.

57. A method of treating a subject with an autoimmune disease, hemoglobinopathy, hematologic cancer, or myeloproliferative disease, the method comprising administering to the subject the pharmaceutical composition of claim 56.

58. A kit comprising the polynucleotide or set of polynucleotides of claim 50, the cell of claim 22 or claim 51, the guide polynucleotide of any one of claims 52-55, or the pharmaceutical composition of claim 56, and a container.

59. A base editor system comprising mRNA encoding a base editor, wherein the base editor comprises an SpCas9 nickase domain having protospacer-adjacent motif specificity for a PAMATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026containing the nucleotide sequence NGG or NRCH, wherein “N” is A, C, T, or G, “R” is A or G, and “H” is A, C, or T, and a TadA*8 adenosine deaminase domain or a TadA*8.20 adenosine deaminase domain comprising an F149Y amino acid substitution, and a guide RNA comprising a spacer comprising a nucleotide sequence selected from the spacer sequences listed in Table 1.

60. The base editor system of claim 59, wherein the base editor comprises an amino acid sequence with at least 95% identity to a sequence selected from:MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALR QGGLVMQNYRL IDATL YVTFE PCVMCAGAM IHSR I GRVVFGVRNAKTGAAGS LMDVLHHPGMNH RVEITEGILADECAALLCRFFRMPRRVFNAQKKAQSSTDSGGSSGGSSGSETPGTSESATPESS GGSSGGSDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGET AEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNI VDE VAYHEKYPT I YHLRKKLVDSTDKADLRL I YLALAHM I KFRGHFL I EGDLNPDNSDVDKLF I QLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTP NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITK APLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKP ILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEK ILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEK VLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFK KIECFDSVEISGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEE RLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIH DDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIE MARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQ ELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAK L I TQRKFDNLTKAERGGLS ELDKAGF I KRQLVETRQ I TKHVAQ I LDSRMNTKYDENDKL I RE VK VITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDV RKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFAT VRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVV AKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFELENGR KRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEI IEQIS EFSKRVILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDRKRYTS TKEVLDATLIHQSITGLYETRIDLSQLGGD (SEQ ID NO: 807); and MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALR QGGLVMQNYRL YDATLYSTFE PCVMCAGAM IHSR I GRVVFGVRNAKTGAAGS LMDVLHHPGMNH RVEITEGILADECAALLCRFYRMPRRVFNAQKKAQSSTDSGGSSGGSSGSETPGTSESATPESSATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026 GGSSGGSDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGET AEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNI VDE VAYHEKYPT I YHLRKKLVDSTDKADLRL I YLALAHM I KFRGHFL I EGDLNPDNSDVDKLF I QLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTP NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITK APLSASMVKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKP ILEKMDGTEELLVKLNREDLLRKQRTFDNGI IPHQIHLGELHAILRRQGDFYPFLKDNREKIEK ILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEK VLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFK KIECFDSVEISGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEE RLKTYAHLFDDKVMKQLKRLRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIH DDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGGHKPENIVIE MARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQ ELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAK L I TQRKFDNLTKAERGGLS ELDKAGF I KRQLVETRQ I TKHVAQ I LDSRMNTKYDENDKL I RE VK VITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDV RKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFAT VRKVLSMPQVNIVKKTEVQTGGFSKESILPKGNSDKLIARKKDWDPKKYGGFNSPTVAYSVLVV AKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFELENGR KRMLASAGVLQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEI IEQIS EFSKRVILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTINRKQYNT TKEVLDATLIRQSITGLYETRIDLSQLGGDEGADKRTADGSEFESPKKKRKV (SEQ ID NO: 808).

61. The base editor system of claim 59, wherein the spacer comprises a nucleotide sequence selected from the group consisting of: ACCACAUCACAGGCAGCUUC (SEQ ID NO: 796; gRNA9234), UAUCAGCCACUAAUGAAGUU (SEQ ID NO: 728; gRNA9239), UCAGACCGUACCUUGCAACA (SEQ ID NO: 730; gRNA9240), GCGGGACAUGUUCACCCUGG (SEQ ID NO: 740; gRNA9245), AGAGAAGGUUCAGACACUAG (SEQ ID NO: 744; gRNA9247), AGCCUAGCAGCGUGUCCUCC (SEQ ID No: 756; gRNA9253), GCCUAGCAGCGUGUCCUCCA (SEQ ID NO: 758; gRNA9254), and CUGAGAUGAGGUGGGUUGGC (SEQ ID NO: 760; gRNA9255).

62. The base editor system of claim 59 or claim 61, wherein the guide RNA comprises aATTORNEY DOCKET NO. 180802-047501 / PCTELECTRONIC DEPOSIT DATE: January 21, 2026gRNA sequence listed in Table 1.

63. A method for preparing a engineered hematopoietic stem cell (HSC), the method comprising contacting an HSC with the base editor system of any one of claims 59-62 to effect an alteration in a CD38 polynucleotide in the cell, thereby producing an engineered HSC expressing a CD38 polypeptide variant comprises an amino acid substitution(s) selected from the group consisting of:i) Q107R;ii) Q115R and T116A;iii) D141G and M142V;iv) E233G and K234G;v) L149P and L150P;vi) E76G, M77V, and R78G;vii) V203A;viii) T116A;ix) K234E;x) K234G; andxi) K234R.

64. An engineered HSC produced by the method of claim 63.

65. A method for hematopoietic stem cell transplantation in a subject, the method comprising administering to the subject the engineered HSC of claim 64 and an antibody selected from Antibody A and Antibody B, wherein the antibody is administered prior to, concurrent with, or subsequent to administration of the hematopoietic stem cell to the subject.

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