Compositions and methods for non-genotoxic cell conditioning

Abstract

Compositions and methods for non-genotoxic monoclonal antibody (mAb) conditioning, wherein the methods involve altering differentiation cluster 117 (CD117; 117 ') in hematopoietic stem cells (HSCs) or progenitor cells thereof. C-KIT) polynucleotide sequences to encode a CD117 polypeptide with reduced binding to the antibody. In various embodiments, the method further comprises introducing a therapeutic alteration into the gene of the HSC or progenitor cell thereof for the treatment of hemoglobinopathy.

Description

[0001] Cross - Reference to Related Applications

[0002] This application claims priority to U.S. Provisional Application No. 63 / 500,854, filed May 8, 2023; U.S. Provisional Application No. 63 / 478,744, filed Jan. 6, 2023; U.S. Provisional Application No. 63 / 386,719, filed Dec. 9, 2022; and U.S. Provisional Application No. 63 / 355,927, filed Jun. 27, 2022, the entire contents of which are hereby incorporated by reference in their entirety.

[0003] Sequence Listing

[0004] 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 was created on Jun. 26, 2023, named 180802 - 046405PCT_SL.xml, and is 1,559,644 bytes in size. Background Art

[0005] Busulfan is a DNA - alkylating agent that induces bone marrow immunosuppression and is widely used for conditioning prior to allogeneic hematopoietic stem cell transplantation and autologous cell therapy administration. Notably, a prerequisite for ex vivo treatment of sickle cell disease (SCD), the most common monogenic inherited hemoglobinopathy, is to condition the patient prior to infusion of autologous cell therapy. Although busulfan is the current standard of care for patients requiring allogeneic or autologous transplantation and cell therapy engraftment, the use of this potent cytotoxic drug has associated risks, including genotoxicity, primary or secondary malignancies, and organ toxicities including infertility. These risks pose barriers to patients who would otherwise seek treatment. Thus, there is a need for improved methods for conditioning prior to allogeneic hematopoietic stem cell transplantation. Summary of the Invention

[0006] As described below, the present disclosure provides compositions and methods for non - genotoxic monoclonal antibody (mAb) conditioning, wherein the method involves altering the cluster of differentiation 117 (CD117; c - KIT) polynucleotide sequence in hematopoietic stem cells (HSCs) or their progenitor cells to encode a CD117 polypeptide with reduced binding to an antibody. In various embodiments, the method further includes introducing a therapeutic alteration into the gene of HSCs or their progenitor cells for the treatment of hemoglobinopathies (e.g., sickle cell disease).

[0007] In one aspect, the present disclosure provides a method of altering a nucleobase of a CD117 polynucleotide. The method involves contacting the CD117 polynucleotide with a base editor polypeptide comprising a nucleic acid programmable DNA binding protein (napDNAbp) and an adenosine deaminase domain, and a guide polynucleotide that targets the base editor to i) effect a change in a nucleobase in the codon encoding serine at amino acid position 261, wherein the change in the nucleobase encoding serine at amino acid position 261 results in the codon encoding glycine, ii) effect a change in a nucleobase in the codon encoding serine at amino acid position 251, and / or iii) effect a change in a nucleobase in the codon encoding asparagine at amino acid position 260 and effect a change in a nucleobase in the codon encoding serine at amino acid position 261 or the corresponding position in another CD117 polypeptide, thereby altering the nucleobase of the CD117 polynucleotide.

[0008] In another aspect, the present disclosure provides a method of altering a nucleobase of a CD117 polynucleotide, the method involving contacting the CD117 polynucleotide with a base editor polypeptide comprising a nucleic acid programmable DNA binding protein (napDNAbp) domain and an adenosine deaminase domain. The adenosine deaminase domain comprises a combination of alterations to TadA*7.10 selected from: a) I76Y, V82T, Y123H, Y147R, F149Y, and Q154R; and b) I76Y, V82T, Y123H, Y147D, F149Y, Q154R, T166I, and D167N. The adenosine deaminase domain has at least 85% sequence identity to TadA*7.10. The method further involves contacting the CD117 polynucleotide with a guide polynucleotide that targets the base editor to effect a change in a nucleobase in the polynucleotide encoding the CD117 polypeptide, thereby altering the nucleobase of the CD117 polynucleotide.

[0009] In another aspect, the present disclosure provides a method for hematopoietic stem cell transplantation in a subject. The method involves (a) contacting isolated hematopoietic stem cells or their progenitor cells with a guide polynucleotide and a base editor comprising a nucleic acid programmable DNA-binding protein (napDNAbp) and an adenosine deaminase domain or a polynucleotide encoding the base editor, wherein the guide polynucleotide targets a nucleic acid molecule encoding a CD117 polypeptide. (a) Results in the generation of edited cells. The method further involves (b) administering the edited cells to the subject. The method further involves (c) administering an antibody or an antigen-binding fragment thereof to the subject, wherein the antibody is selected from one or more of the following: ABTx025, ABTx030, ABTx052, ABTx061, ABTx062, ABTx070, ABTx071, ABTx196, ABTx198, ABTx202, ABTx203, ABTx205, ABTx206, ABTx248, ABTx250, ABTx251, ABTx253, ABTx254, ABTx255, ABTx256, ABTx265, ABTx268, ABTx270, ABTx271, ABTx272, ABTx273, ABTx274, ABTx307, ABTx308, ABTx309, and ABTx313.

[0010] In another aspect, the present disclosure provides a method for hematopoietic stem cell transplantation in a subject. The method involves (a) contacting isolated hematopoietic stem cells or their progenitor cells with a guide polynucleotide and a base editor comprising a nucleic acid programmable DNA-binding protein (napDNAbp) and an adenosine deaminase domain or a polynucleotide encoding the base editor. The guide polynucleotide targets a nucleic acid molecule encoding a CD117 polypeptide such that i) a change in a nucleobase is introduced in the codon encoding serine at amino acid position 261, wherein the change in the nucleobase encoding serine at amino acid position 261 results in the codon expressing glycine, ii) a change in a nucleobase is introduced in the codon encoding serine at amino acid position 251, and / or iii) a change in a nucleobase is introduced in the codon encoding asparagine at amino acid position 260 and a change in a nucleobase is introduced in the codon encoding serine at amino acid position 261 or the corresponding position in another CD117 polypeptide. (a) Results in the generation of edited cells. The method further involves (b) administering the edited cells to the subject. The method further involves (c) administering an antibody or an antigen-binding fragment thereof, an antibody-drug conjugate, or a chimeric antigen receptor T (CAR-T) cell, each of which selectively binds to the wild-type CD117 polypeptide.

[0011] In another aspect, the present disclosure provides a method for hematopoietic stem cell transplantation in a subject. The method involves (a) contacting isolated hematopoietic stem cells or their progenitor cells with a guide polynucleotide and a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) and an adenosine deaminase domain or a polynucleotide encoding the base editor. The adenosine deaminase domain comprises a combination of alterations to TadA*7.10 selected from: i) I76Y, V82T, Y123H, Y147R, F149Y, and Q154R; and ii) I76Y, V82T, Y123H, Y147D, F149Y, Q154R, T166I, and D167N. The adenosine deaminase domain has at least 85% sequence identity to TadA*7.10. The guide polynucleotide targets a nucleic acid molecule encoding a CD117 polypeptide. (a) Results in the generation of edited cells. The method further involves (b) administering the edited cells to a subject. The method further involves (c) administering to the subject an antibody or an antigen-binding fragment thereof, an antibody-drug conjugate, or a chimeric antigen receptor T (CAR-T) cell, each of which selectively binds to the wild-type CD117 polypeptide.

[0012] In another aspect, the present disclosure provides a method for treating a hemoglobinopathy in a subject. The method involves (a) contacting isolated hematopoietic stem cells or their progenitor cells with two or more guide polynucleotides and a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) and an adenosine deaminase domain or a polynucleotide encoding the base editor. One guide polynucleotide targets a nucleic acid molecule encoding a CD117 polypeptide, and another guide polynucleotide targets the base editor to effect deamination of nucleobases of the hemoglobin subunit gamma 1 and / or 2 (HBG1 / 2) promoter. (a) Results in the generation of edited cells. The method further involves (b) administering the edited cells to a subject. The method further involves (c) administering to the subject an antibody or an antigen-binding fragment thereof, wherein the antibody is selected from one or more of the following: ABTx025, ABTx030, ABTx052, ABTx061, ABTx062, ABTx070, ABTx071, ABTx196, ABTx198, ABTx202, ABTx203, ABTx205, ABTx206, ABTx248, ABTx250, ABTx251, ABTx253, ABTx254, ABTx255, ABTx256, ABTx265, ABTx268, ABTx270, ABTx271, ABTx272, ABTx273, ABTx274, ABTx307, ABTx308, ABTx309, and ABTx313.

[0013] In another aspect, the present disclosure provides a method for treating a hemoglobinopathy in a subject. The method involves (a) contacting isolated hematopoietic stem cells or their progenitor cells with two or more guide polynucleotides and a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) and an adenosine deaminase domain or a polynucleotide encoding the base editor. One guide polynucleotide targets a nucleic acid molecule encoding a CD117 polypeptide such that i) a change in a nucleobase is introduced in the codon encoding serine at amino acid position 261, wherein the change in the nucleobase encoding serine at amino acid position 261 results in the codon expressing glycine, ii) a change in a nucleobase is introduced in the codon encoding serine at amino acid position 251, and / or iii) a change in a nucleobase is introduced in the codon encoding asparagine at amino acid position 260 and a change in a nucleobase is introduced in the codon encoding serine at amino acid position 261 or at the corresponding position in another CD117 polypeptide. Another guide polynucleotide targets the base editor to effect a change in the β-globin polynucleotide (HBB) that results in the expression of a β-globin polypeptide (Hb G-Makassar) having alanine at position 6. (a) also results in the generation of edited cells. The method further involves (b) administering the edited cells to the subject. The method further involves (c) administering to the subject an antibody or an antigen-binding fragment thereof, an antibody-drug conjugate, or a chimeric antigen receptor T (CAR-T) cell, each of which selectively binds to the wild-type CD117 polypeptide.

[0014] In another aspect, the present disclosure provides a method for treating hemoglobinopathy in a subject. The method involves (a) contacting isolated hematopoietic stem cells or their progenitor cells with two or more guide polynucleotides and a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) and an adenosine deaminase domain or a polynucleotide encoding the base editor. The adenosine deaminase domain comprises a combination of alterations to TadA*7.10 selected from: i) I76Y, V82T, Y123H, Y147R, F149Y, and Q154R; and ii) I76Y, V82T, Y123H, Y147D, F149Y, Q154R, T166I, and D167N. The adenosine deaminase domain has at least 85% sequence identity to TadA*7.10. One guide polynucleotide targets a nucleic acid molecule encoding a CD117 polypeptide, and another guide polynucleotide targets the base editor to effect an alteration to the β-globin polynucleotide (HBB) that results in the expression of a β-globin polypeptide (Hb G-Makassar) having alanine at position 6. (a) Results in the generation of edited cells. The method further involves (b) administering the edited cells to the subject. The method further involves (c) administering to the subject an antibody or an antigen-binding fragment thereof, an antibody-drug conjugate, or a chimeric antigen receptor T (CAR-T) cell, each of which selectively binds to the wild-type CD117 polypeptide.

[0015] In another aspect, the present disclosure provides a cell produced by the method of any of the above aspects or its embodiments.

[0016] In another aspect, the present disclosure provides a pharmaceutical composition comprising an effective amount of a cell of any of the above aspects or its embodiments.

[0017] In another aspect, the present disclosure provides a base editor system comprising a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) and an adenosine deaminase domain or a polynucleotide encoding the base editor, and a guide polynucleotide that targets the base editor to i) effect an alteration to a nucleobase in the codon encoding serine at amino acid position 261, wherein the alteration to the nucleobase in the codon encoding serine at amino acid position 261 results in the codon expressing glycine, ii) effect an alteration to a nucleobase in the codon encoding serine at amino acid position 251, and / or iii) effect an alteration to a nucleobase in the codon encoding asparagine at amino acid position 260 and an alteration to a nucleobase in the codon encoding serine at amino acid position 261 or the corresponding position in another CD117 polypeptide, thereby altering the nucleobases of the CD117 polynucleotide.

[0018] In another aspect, the present disclosure provides a base editor system comprising a guide polynucleotide and a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) domain and an adenosine deaminase domain. The adenosine deaminase domain comprises a combination of alterations to TadA*7.10. The combination is selected from: a) I76Y, V82T, Y123H, Y147R, F149Y, and Q154R; and b) I76Y, V82T, Y123H, Y147D, F149Y, Q154R, T166I, and D167N. The guide polynucleotide targets the base editor to effect alteration of the nucleobases of a CD117 polynucleotide. The adenosine deaminase domain has at least 85% sequence identity to TadA*7.10.

[0019] In another aspect, the present disclosure provides a base editor system comprising a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) and an adenosine deaminase domain, and a guide polynucleotide comprising a polynucleotide sequence selected from one or more of the following: AUAAUAGCUGGCAUCACGGU (SEQ ID NO: 693; gRNA931); CCACUAGCUUUCCAAACGGU (SEQ ID NO: 694; gRNA889); GCUGAACUGAUAGUCAACGU (SEQ ID NO: 695; gRNA908); UUUGACAAAGCCCGGAUCAG (SEQ ID NO: 696; gRNA918); UGAAAGUGAGGCCAGGUACU (SEQ ID NO: 697; gRNA923); AAACAGUCAGGUGAGUGAAU (SEQ ID NO: 698; gRNA928); AACUACAGGAGAAAUAUAAU (SEQ ID NO: 699; gRNA929); and GAUUAAAAGGCACCGAAGGA (SEQ ID NO: 700; gRNA944).

[0020] In another aspect, the present disclosure provides a polynucleotide encoding the base editor system of any of the above aspects or embodiments thereof.

[0021] In another aspect, the present disclosure provides a guide polynucleotide comprising a spacer sequence selected from one or more of the following: AUAAUAGCUGGCAUCACGGU (SEQ ID NO: 693; gRNA931); CCACUAGCUUUCCAAACGGU (SEQ ID NO: 694; gRNA889); GCUGAACUGAUAGUCAACGU (SEQ ID NO: 695; gRNA908); UUUGACAAAGCCCGGAUCAG (SEQ ID NO: 696; gRNA918); UGAAAGUGAGGCCAGGUACU (SEQ ID NO: 697; gRNA923); AAACAGUCAGGUGAGUGAAU (SEQ ID NO: 698; gRNA928); AACUACAGGAGAAAUAUAAU (SEQ ID NO: 699; gRNA929); and GAUUAAAAGGCACCGAAGGA (SEQ ID NO: 700; gRNA944).

[0022] In another aspect, the present disclosure provides a kit comprising a cell, a base editor system, a polynucleotide, or a pharmaceutical composition of any of the above aspects or embodiments thereof.

[0023] In another aspect, the present disclosure provides an anti-CD117 antibody or an antigen-binding portion thereof, which contains one or more complementarity-determining regions (CDRs), and the CDRs contain heavy-chain variable region (VH) CDRs and / or light-chain variable region (VL) CDRs selected from the following: A) VL CDR1: QSVSSSY (SEQ ID NO: 394); VL CDR2: GAS; VL CDR3: QQYGTSLT (SEQ ID NO: 395); VH CDR1: GFTFDDYA (SEQ ID NO: 391); VH CDR2: ISWNSGTI (SEQ ID NO: 392); VH CDR3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393) (ABTx025); B) VL CDR1: QSISSY (SEQ ID NO: 409); VL CDR2: AAS; VL CDR3: QQSYSTPLT (SEQ ID NO: 410); VH CDR1: GFTFSSYS (SEQ ID NO: 406); VH CDR2: IGTISSYI (SEQ ID NO: 407); VH CDR3: ARDYYGGLFDY (SEQ ID NO: 408) (ABTx030); C) VL CDR1: QSVSSSY (SEQ ID NO: 439); VL CDR2: GAS; VL CDR3: QQYGSSPLT (SEQ ID NO: 440); VH CDR1: GFTFDDYA (SEQ ID NO: 436); VH CDR2: ISWNSGSI (SEQ ID NO: 437); VH CDR3: AKDTPLGYCSTTSCYGAFDI (SEQ ID NO: 438) (ABTx061); D) VL CDR1: QSISSY (SEQ ID NO: 454); VL CDR2: AAS; VL CDR3: QQSYSTPFT (SEQ ID NO: 455); VH CDR1: GFTFDDYA (SEQ ID NO: 451); VH CDR2: ISWNSGTI (SEQ ID NO: 452); VH CDR3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 453) (ABTx062); E) VL CDR1: QGISSY (SEQ ID NO: 469); VL CDR2: AAS; VL CDR3: QQSYSTPIT (SEQ ID NO: 470); VH CDR1: GFTFDDYG (SEQ ID NO: 466); VH CDR2: INWNGGST (SEQ ID NO: 467);VH CDR3: ARESWDGSGIYYMDV (SEQ ID NO: 468) (ABTx070); F) VL CDR1: QGISSY (SEQ ID NO: 484); VL CDR2: AAS; VL CDR3: QQLNSYPYT (SEQ ID NO: 485); VH CDR1: GFTFDDYG (SEQ ID NO: 481); VH CDR2: INWNGGST (SEQ ID NO: 482); VH CDR3: ARESWNYEGYYYMDV (SEQ ID NO: 483) (ABTx071); G) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQFNSYPLT (SEQ ID NO: 425); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012); H) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQFNSYPLT (SEQ ID NO: 425); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948); I) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQFYSYPLT (SEQ ID NO: 954); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948); J) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQFSSYPLT (SEQ ID NO: 1020); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948); K) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS;VL CDR3: QQTNSHPLT (SEQ ID NO: 1023); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012); L) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQVRSYPLT (SEQ ID NO: 1025); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948); M) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQTYSYPLT (SEQ ID NO: 1029); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO: 1027); N) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQTRSYPLT (SEQ ID NO: 1036); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012); O) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQVNSYPLT (SEQ ID NO: 952); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948); P) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQVRSYPLT (SEQ ID NO: 1025); VH CDR1: GYRFTSYW (SEQ ID NO: 421);VH CDR2: IYPGDSDTR (SEQ ID NO:958); VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO:1027); Q) VL CDR1: QGISSA (SEQ ID NO:424); VL CDR2: DAS; VL CDR3: QQTNSYPLT (SEQID NO:1044); VH CDR1: GYRFTSYW (SEQ ID NO:421); VH CDR2: IYPGDSDTR (SEQ ID NO:958); VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO:1032); R) VL CDR1: QGISSA (SEQ ID NO:424); VLCDR2: DAS; VL CDR3: QQVRSYPLT (SEQ ID NO:1025); VH CDR1: GYRFTSYW (SEQ ID NO:421); VH CDR2: IYPGDSDTK (SEQ IDNO:972); VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012); S) VL CDR1: QGISSA (SEQ ID NO:424); VL CDR2: DAS; VL CDR3: QQFRSYPLT (SEQ ID NO:953); VH CDR1: GYRFTSYW (SEQ IDNO:421); VH CDR2: IYPGDSDTR (SEQ ID NO:958); VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948); T) VL CDR1: QGISSA (SEQ ID NO:424); VL CDR2: DAS; VL CDR3: QQTNSYPLT (SEQID NO:1044); VH CDR1: GYRFTSYW (SEQ ID NO:421); VH CDR2: IYPGDSDTK (SEQ ID NO:972); VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948); U) VL CDR1: QSVSSSY (SEQ ID NO:394); VLCDR2: GAS; VL CDR3: QQSETCLT (SEQ ID NO:1074); VH CDR1: GFTFDDYA (SEQ ID NO:391)VH CDR2: ISWNSGTIG (SEQ ID NO:1070); VH CDR3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO:393);V) VL CDR1: QSVSSSY (SEQ ID NO: 394); VL CDR2: GAS; VL CDR3: QQDSLGLT (SEQ ID NO: 1074); VH CDR1: GFTFDDYA (SEQ ID NO: 391); VH CDR2: ISWNSGTIG (SEQ ID NO: 1070); VH CDR3: AKDSPPGYCASASCYGAFDI (SEQ ID NO: 1090); W) VL CDR1: QSVSSSY (SEQ ID NO: 394); VL CDR2: GSS; VL CDR3: QQYNFWPYT (SEQ ID NO: 1084); VH CDR1: GFTFDDYA (SEQ ID NO: 391); VH CDR2: ISWNSGTIG (SEQ ID NO: 1070); VH CDR3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393); X) VL CDR1: QGISSY (SEQ ID NO: 469); VL CDR2: AAS; VL CDR3: QQSYSTPYT (SEQ ID NO: 1097); VH CDR1: GFTFDDYA (SEQ ID NO: 391); VH CDR2: ISWNSGTIG (SEQ ID NO: 1070); VH CDR3: AKDWPSGFCSSAYCYGAFDI (SEQ ID NO: 1094); Y) VL CDR1: QGISSY (SEQ ID NO: 469); VL CDR2: AAS; VL CDR3: QQSYSTPYT (SEQ ID NO: 1097); VH CDR1: GFTFDDYA (SEQ ID NO: 1071); VH CDR2: ISWNSGTIG (SEQ ID NO: 1070); VH CDR3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393); Z) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQFNSYPLT (SEQ ID NO: 425); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012); AA) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS;VL CDR3: QQFSSYPLT (SEQ ID NO: 1020); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO: 1032); AB) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQTNSYPLT (SEQ ID NO: 1044); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO: 1032); and AC) VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; VL CDR3: QQFSSYPLT (SEQ ID NO: 425); VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).;

[0024] In another aspect, the present disclosure provides an isolated nucleic acid molecule encoding an antibody of any one of the above aspects or embodiments thereof.

[0025] In another aspect, the present disclosure provides an anti-CD117 antibody or an antigen-binding portion thereof, which contains complementarity-determining regions (CDRs), and the CDRs contain the following heavy-chain variable region (VH) CDR and light-chain variable region (VL) CDR amino acid sequences: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2 is IYPGDSDTR (SEQ ID NO: 958) or IYPGDSDTK (SEQ ID NO: 972); VH CDR3: ARHGRGYXYXGAFDI (SEQ ID NO: 944); VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and one or more of the following selected VL CDR3s: QQXSYPLT (SEQ ID NO: 945), QQXSHPLT (SEQ ID NO: 946), and QQXSSPLT (SEQ ID NO: 947). X represents any amino acid. The anti-CD117 antibody contains at least one amino acid alteration relative to the amino acid sequence of ABTx052.

[0026] In another aspect, the present disclosure provides an anti-CD117 antibody or an antigen-binding portion thereof, which comprises complementarity determining regions (CDRs), and the CDRs comprise or consist of the following heavy chain variable region (VH) CDRs and light chain variable region (VL) CDRs amino acid sequences:

[0027] VH CDR1: GX1X2FX3X4YX5, wherein X1 is F or Y, X2 is R or T, X3 is D, S or T, X4 is D or S, and X5 is A, G, S or W;

[0028] VH CDR2 is IX6X7X8X9X 10 X 11 X 12 X 13 , wherein X6 is G, N, S or Y, X7 is P, T or W, X8 is G, I or N, X9 is D, G or S, X 10 is G or S, X 11 is D, S, T or Y, X 12 is I or T, and X 13 is G, K, R or Y;

[0029] VH CDR3 is one or more selected from the following: ARHGRGYDX 14 YDGAFDI (SEQ ID NO:1105), ARDYYGGLFDY (SEQ ID NO:1106), ARESWX 15 X 16 X 17 GX 18 YYMDV (SEQ ID NO:1107), and AKDX 19 PX 20 GX 21 CX 22 X 23 X 24 X 25 CYGAFDI (SEQ ID NO:1108), wherein X 14 is A or G, X 15 is D or N, X 16 is G or Y, X 17 is E or S, X 18 is I or Y, X 19 is S, T or W, X 20 is L, P or S, X 21 is F or Y, X 22 is A or S, X 23 is S or T, X 24 is A or T, and X 25is S or Y;

[0030] VL CDR1 is QSX 26 SSX 27 (SEQ ID NO:1109) or QSVSSSY (SEQ ID NO:1110), wherein X 26 is G or S, and X 27 is A or Y;

[0031] VL CDR2: X 28 X 29 S, wherein X 28 is A, D or G, and X 29 is A or S; and

[0032] VL CDR3 is QQX 30 X 31 X 32 X 33 PX 34 T (SEQ ID NO:1111) or QQX 35 X 36 X 37 X 38 LT (SEQ ID NO:1112), wherein X 30 is F, L, S, T or Y, X 31 is G, N, S or Y, X 32 is S or F, X 33 is S, T, W or Y, X 34 is F, I, L or Y, X 35 is D, S or Y, X 36 is E, G or S, X 37 is L or T, and X 38 is C, G or S. Relative to the amino acid sequence of ABTx052, the anti-CD117 antibody contains at least one amino acid alteration.

[0033] In another aspect, the present disclosure provides a method for hematopoietic stem cell transplantation in a subject. The method involves (a) administering to the subject hematopoietic stem cells or their progenitor cells. The hematopoietic stem cells or their progenitor cells express a CD117 variant containing an S261G amino acid alteration or a CD117 variant containing Y259C and N260D amino acid alterations. The method further involves (b) administering to the subject an antibody or an antigen-binding fragment thereof that selectively binds to the wild-type CD117 polypeptide.

[0034] In another aspect, the present disclosure provides a method for treating a hemoglobinopathy in a subject. The method involves (a) administering to the subject hematopoietic stem cells or their progenitor cells. The hematopoietic stem cells or their progenitor cells: i) express a CD117 variant containing an S261G amino acid alteration or a CD117 variant containing Y259C and N260D amino acid alterations, and ii) contain a nucleobase alteration to the HBG1 / 2 promoter that results in increased γ-globin expression and / or expression of an HBB polypeptide containing alanine at position 6. The method further involves (b) administering to the subject an antibody or an antigen-binding fragment thereof that selectively binds to the wild-type CD117 polypeptide.

[0035] In another aspect, the present disclosure provides a hematopoietic stem cell or its progenitor cell that expresses, relative to the following amino acid sequence, i) an S261G alteration, ii) an alteration at amino acid positions 260 and 261, and / or ii) an alteration at amino acid position 251, wherein the CD117 polypeptide has at least 85% sequence identity to the following amino acid sequence:

[0036] wild-type CD117

[0037] MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDRSLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTCTIKDVSSSVYSTWKRENSQTKLQEKYNSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV(SEQ ID NO:499).

[0038] In another aspect, the present disclosure provides a hematopoietic stem cell or progenitor cell thereof that expresses a CD117 polypeptide comprising a sequence of 10, 20, 30, or 40 contiguous amino acids. The contiguous amino acid sequence contains amino acid position 260, amino acid position 261, and / or amino acid position 251 relative to the following wild-type CD117 amino acid sequence. Further, relative to the following wild-type CD117 amino acid sequence, in the contiguous amino acid sequence i) the amino acid corresponding to amino acid position 261 is replaced with glycine, ii) the amino acids corresponding to amino acid positions 260 and 261 are altered, and / or

[0039] iii) the amino acid corresponding to amino acid position 251 is altered. The contiguous amino acid sequence has at least 85% sequence identity with a fragment of the following wild-type CD117 amino acid sequence, the fragment having the same length as the contiguous amino acid sequence.

[0040] Wild-type CD117 amino acid sequence

[0041] MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDRSLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTCTIKDVSSSVYSTWKRENSQTKLQEKYNSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV(SEQ ID NO:499).The CD117 polypeptide is capable of binding to the stem cell factor (SCF) polypeptide.

[0042] In any aspect of the present disclosure or its embodiments, the adenosine deaminase is TadA*8.1, TadA*8.2, TadA*8.3, TadA*8.4, TadA*8.5, TadA*8.6, TadA*8.7, TadA*8.8, TadA*8.9, TadA*8.10, TadA*8.11, TadA*8.12, TadA*8.13, TadA*8.14, TadA*8.15, TadA*8.16, TadA*8.17, TadA*8.18, TadA*8.19, TadA*8.20, TadA*8.21, TadA*8.22, TadA*8.23, or TadA*8.24. In any aspect of the present disclosure or its embodiments, the adenosine deaminase domain contains a set of alterations to TadA*7.10: MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO:1). The alterations are selected from the following: a) I76Y, V82T, Y123H, Y147R, F149Y, and Q154R (ABE9v1); b) I76Y, V82T, Y123H, Y147D, F149Y, Q154R, T166I, and D167N (ABE9v1); and c) I76Y, V82S, Y123H, Y147D, F149Y, Q154R, T166I, and D167N (ABE8.20+). The adenosine deaminase domain has at least 85% sequence identity with TadA*7.10.

[0043] In any aspect of the present disclosure or its embodiments, the deaminase is a monomer or a heterodimer. In any aspect of the present disclosure or its embodiments, the base editor polypeptide is an internal base editor (IBE) that contains a deaminase domain inserted at an internal position of napDNAbp.

[0044] In any aspect of the present disclosure or its embodiments, the base editor polypeptide further contains one or more nuclear localization sequences (NLSs). In any aspect of the present disclosure or its embodiments, the base editor polypeptide further contains a bipartite nuclear localization sequence (NLS).

[0045]

[0046] In any aspect of the present disclosure or an embodiment thereof, the method involves administering an antibody or an antigen-binding fragment thereof to a subject, wherein the antibody is selected from one or more of the following: ABTx025, ABTx030, ABTx052, ABTx061, ABTx062, ABTx070, ABTx071, ABTx196, ABTx198, ABTx202, ABTx203, ABTx205, ABTx206, ABTx248, ABTx250, ABTx251, ABTx253, ABTx254, ABTx255, ABTx256, ABTx265, ABTx268, ABTx270, ABTx271, ABTx272, ABTx273, ABTx274, ABTx307, ABTx308, ABTx309, and ABTx313.

[0047] In any aspect of the present disclosure or an embodiment thereof, the subject has a hemoglobinopathy. In an embodiment, the hemoglobinopathy is selected from one or more of the following: sickle cell anemia, thalassemia, Fanconi anemia, aplastic anemia, and Wiskott-Aldrich syndrome.

[0048] In any aspect of the present disclosure or an embodiment thereof, the method further involves contacting hematopoietic stem cells or their progenitor cells with a guide polynucleotide that targets a nucleic acid molecule encoding a β-globin (HBB) polypeptide, thereby introducing an amino acid change to alanine at position 6 of the HBB polypeptide. In any aspect of the present disclosure or an embodiment thereof, the method further involves contacting hematopoietic stem cells or their progenitor cells with a guide polynucleotide that targets a base editor to effect deamination of a nucleobase of the hemoglobin subunit γ1 and / or 2 (HBG1 / 2) promoter. In any aspect of the present disclosure or an embodiment thereof, deamination of the nucleobase disrupts the binding of a repressor to the hemoglobin subunit γ1 and / or 2 (HBG1 / 2) promoter. In any aspect of the present disclosure or an embodiment thereof, deamination of the nucleobase results in increased expression of γ-globin (HbF).

[0049] In any aspect of the present disclosure or an embodiment thereof, the guide polynucleotide that contacts the CD117 polynucleotide comprises a nucleotide sequence selected from one or more of the following: AUAAUAGCUGGCAUCACGGU (SEQ ID NO:693; gRNA931; CC200); CCACUAGCUUUCCAAACGGU (SEQ ID NO:694; gRNA889); GCUGAACUGAUAGUCAACGU (SEQ ID NO:695; gRNA908); UUUGACAAAGCCCGGAUCAG (SEQ ID NO:696; gRNA918); UGAAAGUGAGGCCAGGUACU (SEQ ID NO:697; gRNA923); AAACAGUCAGGUGAGUGAAU (SEQ ID NO:698; gRNA928); AACUACAGGAGAAAUAUAAU (SEQ ID NO:699; gRNA929); and GAUUAAAAGGCACCGAAGGA (SEQ ID NO:700; gRNA944).

[0050] In any aspect of the present disclosure or an embodiment thereof, a guide polynucleotide that targets deamination of a nucleobase of the HBG1 / 2 promoter or a guide polynucleotide that targets a nucleic acid molecule encoding a β-globin (HBB) polypeptide comprises a nucleotide sequence selected from one or more of the following: ACUUCUCCACAGGAGUCAGG (SEQ ID NO:902); GUGGGGAAGGGGCCCCCAAG (SEQ ID NO:903); AUUGAGAUAGUGUGGGGAAG (SEQ ID NO:904); CAUUGAGAUAGUGUGGGGAA (SEQ ID NO:905); GCAUUGAGAUAGUGUGGGGA (SEQ ID NO:906); GUGGGGAAGGGGCCCCCAAG (SEQ ID NO:907); GCUAUUGGUCAAGGCAAGGC (SEQ ID NO:908); CAAGGCUAUUGGUCAAGGCA (SEQ ID NO:909); CUUGUCAAGGCUAUUGGUCA (SEQ ID NO:910); CUUGACCAAUAGCCUUGACA (SEQ ID NO:911); GUUUGCCUUGUCAAGGCUAU (SEQ ID NO:912); UGGUCAAGUUUGCCUUGUCA (SEQ ID NO:913); UGGGGGAAGGGGCCCCCAAGA (SEQ ID NO:914); GUGUGGGGAAGGGGCCCCCA (SEQ ID NO:915); UCAGACAGAUAUUUGCAUUG (SEQ ID NO:916); UUUCAGACAGAUAUUUGCAU (SEQ ID NO:917); CUUGCCUUGACCAAUAGCCU (SEQ ID NO:918); UAGCCUUGACAAGGCAAACU (SEQ ID NO:919); CAAACUUGACCAAUAGUCUU (SEQ ID NO:920); UGUGGGGAAGGGGCCCCCAA (SEQ ID NO:921); GGGCCCCUUCCCCACACUAU (SEQ ID NO:922); CAGACAGAUAUUUGCAUUGA (SEQ ID NO:923); UUUCAGACAGAUAUUUGCAU (SEQ ID NO:924); GCCUUGACAAGGCAAACUUG (SEQ ID NO:925); UUGACAAGGCAAACUUGACC (SEQ ID NO:926);UGACCAAUAGUCUUAGAGUA (SEQ ID NO:927); and AGACAGAUAUUUGCAUUGAGAUA (SEQ ID NO:928). In any aspect of the present disclosure or an embodiment thereof, the guide polynucleotide contains a scaffold having the following nucleotide sequence: GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU (SEQ ID NO:317).;

[0051] In any aspect of the present disclosure or an embodiment thereof, the hematopoietic stem cells or their progenitor cells are autologous to the subject. In any aspect of the present disclosure or an embodiment thereof, the hematopoietic stem cells or their progenitor cells are allogeneic to the subject. In any aspect of the present disclosure or an embodiment thereof, the subject is a mammal. In any aspect of the present disclosure or an embodiment thereof, the mammal is a canine, feline, human, non-human primate, or rodent.

[0052] In any aspect of the present disclosure or an embodiment thereof, the guide polynucleotide is a guide RNA. In any aspect of the present disclosure or an embodiment thereof, at least one of two or more guide polynucleotides comprises a nucleotide sequence selected from one or more of the following: AUAAUAGCUGGCAUCACGGU (SEQ ID NO:693; gRNA931; CC200); CCACUAGCUUUCCAAACGGU (SEQ ID NO:694; gRNA889); GCUGAACUGAUAGUCAACGU (SEQ ID NO:695; gRNA908); UUUGACAAAGCCCGGAUCAG (SEQ ID NO:696; gRNA918); UGAAAGUGAGGCCAGGUACU (SEQ ID NO:697; gRNA923); AAACAGUCAGGUGAGUGAAU (SEQ ID NO:698; gRNA928); AACUACAGGAGAAAUAUAAU (SEQ ID NO:699; gRNA929); and GAUUAAAAGGCACCGAAGGA (SEQ ID NO:700; gRNA944). In any aspect of the present disclosure or an embodiment thereof, at least one of two or more guide polynucleotides comprises a nucleotide sequence selected from one or more of the following: ACUUCUCCACAGGAGUCAGG (SEQ ID NO:902); GUGGGGAAGGGGCCCCCAAG (SEQ ID NO:903); AUUGAGAUAGUGUGGGGAAG (SEQ ID NO:904); CAUUGAGAUAGUGUGGGGAA (SEQ ID NO:905); GCAUUGAGAUAGUGUGGGGA (SEQ ID NO:906); GUGGGGAAGGGGCCCCCAAG (SEQ ID NO:907); GCUAUUGGUCAAGGCAAGGC (SEQ ID NO:908); CAAGGCUAUUGGUCAAGGCA (SEQ ID NO:909); CUUGUCAAGGCUAUUGGUCA (SEQ ID NO:910); CUUGACCAAUAGCCUUGACA (SEQ ID NO:911); GUUUGCCUUGUCAAGGCUAU (SEQ ID NO:912); UGGUCAAGUUUGCCUUGUCA (SEQ ID NO:913); UGGGGAAGGGGCCCCCAAGA (SEQ ID NO:914);GUGUGGGGAAGGGGCCCCCA (SEQ ID NO:915); UCAGACAGAUAUUUGCAUUG (SEQ ID NO:916); UUUCAGACAGAUAUUUGCAU (SEQ ID NO:917); CUUGCCUUGACCAAUAGCCU (SEQ ID NO:918); UAGCCUUGACAAGGCAAACU (SEQ ID NO:919); CAAACUUGACCAAUAGUCUU (SEQ ID NO:920); UGUGGGGAAGGGGCCCCCAA (SEQ ID NO:921); GGGCCCCUUCCCCACACUAU (SEQ ID NO:922); CAGACAGAUAUUUGCAUUGA (SEQ ID NO:923); UUUCAGACAGAUAUUUGCAU (SEQ ID NO:924); GCCUUGACAAGGCAAACUUG (SEQ ID NO:925); UUGACAAGGCAAACUUGACC (SEQ ID NO:926); UGACCAAUAGUCUUAGAGUA (SEQ ID NO:927); and AGACAGAUAUUUGCAUUGAGAUA (SEQ ID NO:928). In any aspect of the present disclosure or its embodiments, the guide polynucleotide is selected from one or more of the following: AUAAUAGCUGGCAUCACGGU (SEQ ID NO:693; gRNA931; CC200); CCACUAGCUUUCCAAACGGU (SEQ ID NO:694; gRNA889); GCUGAACUGAUAGUCAACGU (SEQ ID NO:695; gRNA908); UUUGACAAAGCCCGGAUCAG (SEQ ID NO:696; gRNA918); UGAAAGUGAGGCCAGGUACU (SEQ ID NO:697; gRNA923); AAACAGUCAGGUGAGUGAAU (SEQ ID NO:698; gRNA928); AACUACAGGAGAAAUAUAAU (SEQ ID NO:699; gRNA929); and GAUUAAAAGGCACCGAAGGA (SEQ ID NO:700; gRNA944).;

[0053] In any aspect of the present disclosure or an embodiment thereof, the base editor system further comprises a guide polynucleotide comprising the following polynucleotide sequence: ACUUCUCCACAGGAGUCAGG (SEQ ID NO: 902).

[0054] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1120; ABTx025 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence:

[0055] DVVMTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGTSLTFGGGTKLEIKRTV (SEQ ID NO: 1121; ABTx025 VL).

[0056] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: QVQLQESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSIGTISSYIYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARDYYGGLFDYWGQGTLVTVSS (SEQ ID NO: 1118; ABTx030 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EIVMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVDIKRTV (SEQ ID NO: 1119; ABTx030 VL).

[0057] In any aspect of the present disclosure or its embodiments, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGSIGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCAKDTPLGYCSTTSCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1126; ABTx061 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence:

[0058] EIVLAQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPLTFGGGTKLEIKRTV (SEQ ID NO: 1127; ABTx061 VL).

[0059] In any aspect of the present disclosure or its embodiments, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCSASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTTVTVSS (SEQ ID NO: 1128; ABTx062 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence:

[0060] DIQLTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTINSLQPEDFATYYCQQSYSTPFTFGPGTKVEIKRTV (SEQ ID NO: 1129; ABTx062 VL).

[0061] In any aspect of the present disclosure or its embodiments, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGVVRPGGSLRLSCAASGFTFDDYGMSWVRQAPGKGLEWVSDINWNGGSTGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCARESWDGSGIYYMDVWGKGTTVTVSS (SEQ ID NO: 1130; ABTx070 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence:

[0062] DIVMTQSPSFLSASVGDRVTITCRASQGISSYLNWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPITFGQGTRLEIKRTV (SEQ ID NO: 1131; ABTx070 VL).

[0063] In any aspect of the present disclosure or its embodiments, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGVVRPGGSLRLSCAASGFTFDDYGMSWVRQAPGKGLEWVSGINWNGGSTGYADSVKGRFTISRDNAKNSLHLQMNSLRAEDTALYYCARESWNYEGYYYMDVWGKGTTVTVSS (SEQ ID NO: 1132; ABTx071 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence:

[0064] AIQMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQLNSYPYTFGQGTKLEIKRTV (SEQ ID NO: 1133; ABTx071 VL).

[0065] In any aspect of the present disclosure or its embodiments, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: QVQLVQSGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYCARHGRGYDGYDGAFDIWGQGTMVTVSS (SEQ ID NO: 1122; ABTx313 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQFSSYPLTFGGGTKVEIKRTV (SEQ ID NO: 1123; ABTx313 VL).

[0066] In any aspect of the present disclosure or its embodiments, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: QVQLVQSGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYCARHGRGYDGYDGAFDIWGQGTMVTVSS (SEQ ID NO: 1122; ABTx307 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQFNSYPLTFGGGTKVEIKRTV (SEQ ID NO: 960; ABTx307 VL).

[0067] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: QVQLVQSGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTKYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYCARHGRGYDAYDGAFDIWGQGTMVTVSS (ID NO: 1124; ABTx308 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQFSSYPLTFGGGTKVEIKRTV (SEQ ID NO: 1123; ABTx308 VL).

[0068] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: QVQLVQSGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYCARHGRGYDAYDGAFDIWGQGTMVTVSS (SEQ ID NO: 1124; ABTx309 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQTNSYPLTFGGGTKVEIKRTV (SEQ ID NO: 1125; ABTx309 VL).

[0069] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1120; ABTx196 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: DVVMTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSETCLTFGGGTKLEIK (SEQ ID NO: 1068; ABTx196 VL).

[0070] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTSSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1085; ABTx202 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EIVMTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGSSTRATGIPARFSGSGSGTEFALTISSLQSEDFAVYYCQQYNFWPYTFGQGTKVEIK (SEQ ID NO: 1086; ABTx202 VL).

[0071] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCASASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1089; ABTx198 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: DVVMTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQDSLGLTFGGGTKLEIK (SEQ ID NO: 1103; ABTx198 VL).

[0072] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDWPSGFCSSAYCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1092; ABTx203, VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: DIVMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCQQSYSTPYTFGQGTKLEIK (SEQ ID NO: 1093; ABTx203, VL).

[0073] In any aspect of the present disclosure or its embodiments, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1120; ABTx205 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: DIVMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCQQSYSTPYTFGQGTKLEIK (SEQ ID NO: 1093; ABTx205 VL)

[0074] In any aspect of the present disclosure or its embodiments, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIRGQGTMVTVSS (SEQ ID NO: 1101; ABTx206 VH), and / or comprises a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the following amino acid sequence: DIVMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCQQSYSTPYTFGQGTKLEIK (SEQ ID NO: 1093).

[0075] In any aspect of the present disclosure or an embodiment thereof, at 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, and / or 12 weeks after administration of an antibody or an antigen-binding fragment thereof, the chimeric percentage of the subject for the edited cells or cells derived from or originating from the edited cells is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%. In an embodiment, the chimeric percentage of a large number of bone marrow, CD34+ cells, CD235a+ cells, CD19+ cells, and / or CD45+ cells is measured.

[0076] In any aspect of the present disclosure or an embodiment thereof, the method involves contacting a hematopoietic stem cell or a progenitor cell thereof with a guide polynucleotide containing a spacer sequence corresponding to gRNA931 (CC200) and another guide polynucleotide containing a spacer sequence corresponding to sgRNA_027. In any aspect of the present disclosure or an embodiment thereof, the base editor contains a TadA*8.20 adenosine deaminase domain. In any aspect of the present disclosure or an embodiment thereof, the base editor contains a Cas9-NRCH napDNAbp domain. In any aspect of the present disclosure or an embodiment thereof, the base editor is ABE8.20-NRCH. In any aspect of the present disclosure or an embodiment thereof, the antibody is ABTx052, contains VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2, and VL CDR3 of ABTx052, and / or contains a VH domain having at least 95% sequence identity with the VH domain of ABTx052 and a VL domain having at least 95% sequence identity with the VL domain of ABTx052. In any aspect of the present disclosure or an embodiment thereof, the composition contains a guide polynucleotide containing a spacer sequence corresponding to gRNA931 (CC200), a guide polynucleotide containing a spacer sequence corresponding to sgRNA_027, and / or an mRNA encoding the base editor ABE8.20-NRCH.

[0077] In any aspect of the present disclosure or an embodiment thereof, the method involves (A) performing base editing on a hematopoietic stem cell or a progenitor cell thereof by contacting the hematopoietic stem cell or a progenitor cell thereof with (i) a guide polynucleotide containing a spacer sequence corresponding to gRNA931 (CC200) and another guide polynucleotide containing a spacer sequence corresponding to sgRNA_027 or a polynucleotide encoding the spacer sequence, and (ii) an ABE-NRCH base editor or a polynucleotide encoding the ABE-NRCH base editor; (B) administering the base-edited hematopoietic stem cell or a progenitor cell thereof to a subject; and (C) administering the ABTx052 antibody to the subject before, after, or simultaneously with the administration of the base-edited hematopoietic stem cell.

[0078] In any aspect of the present disclosure or its embodiments, an antibody, antibody-drug conjugate, or chimeric antigen receptor contains complementarity-determining regions (CDRs) that contain the following heavy-chain variable region (VH) CDR and light-chain variable region (VL) CDR amino acid sequences: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2 is IYPGDSDTR (SEQ ID NO: 958) or IYPGDSDTK (SEQ ID NO: 972); VH CDR3: ARHGRGYXYXGAFDI (SEQ ID NO: 944); VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3 is selected from one or more of the following: QQXSYPLT (SEQ ID NO: 945), QQXSHPLT (SEQ ID NO: 946), and QQXSSPLT (SEQ ID NO: 947). X indicates any amino acid. The anti-CD117 antibody contains at least one amino acid alteration relative to the amino acid sequence of ABTx052.

[0079] In any aspect of the present disclosure or its embodiments, VH CDR3 is selected from one or more of the following: ARHGRGYDGYEGAFDI (SEQ ID NO: 948), ARHGRGYNAYEGAFDI (SEQ ID NO: 949), ARHGRGYNGYDGAFDI (SEQ ID NO: 950), ARHGRGYDGYDGAFDI (SEQ ID NO: 1012), ARHGRGYDAYEGAFDI (SEQ ID NO: 1027), and ARHGRGYDAYDGAFDI (SEQ ID NO: 1032), and / or VL CDR3 is selected from one or more of the following: QQTNSYPLT (SEQ ID NO: 951), QQVNSYPLT (SEQ ID NO: 952), QQFRSYPLT (SEQ ID NO: 953), QQFYSYPLT (SEQ ID NO: 954), QQFNSHPLT (SEQ ID NO: 955), QQFNS-SPLT (SEQ ID NO: 956), QQFSSYPLT (SEQ ID NO: 1020), QQTNSHPLT (SEQ ID NO: 1023), QQVRSYPLT (SEQ ID NO: 1025), QQTYSYPLT (SEQ ID NO: 1029), QQF-NSTPLT (SEQ ID NO: 1033), and QQTRSYPLT (SEQ ID NO: 1036).

[0080] In any aspect of the present disclosure or an embodiment thereof, the antibody selectively binds to wild-type CD117. In any aspect of the present disclosure or an embodiment thereof, the dissociation rate constant of the antibody binding to wild-type CD117 is less than about 4.0E-04 or 4.5.0E-03.

[0081] In any aspect of the present disclosure or an embodiment thereof, the binding of the antibody to a CD117 variant containing amino acid alterations Y259C, N260D, and / or S261G is reduced, wherein the reduced binding is relative to anti-CD117 antibodies ABTx052 or ABTx135. In any aspect of the present disclosure or an embodiment thereof, the binding of the antibody to a CD117 variant containing amino acid alterations Y259C and N260D and to a CD117 variant containing amino acid alteration S261G is reduced, wherein the reduced binding is relative to anti-CD117 antibodies ABTx052 or ABTx135.

[0082] In any aspect of the present disclosure or an embodiment thereof, the antibody comprises variable heavy chain (VH) and variable light chain (VL) framework regions (FRs) having the following amino acid sequences: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973); VH FR4: WGQGTMVTVSS (SEQ ID NO:429); VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431); VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0083] In any aspect of the present disclosure or an embodiment thereof, the antibody is a human IgG1 antibody.

[0084] In any aspect of the present disclosure or an embodiment thereof, the antibody or its antigen-binding fragment, antibody-drug conjugate, or chimeric antigen receptor T (CAR-T) cell is administered before, after, or simultaneously with the edited cell.

[0085] In any aspect or embodiment provided herein, the method is not a method for modifying the human germline genetic identity.

[0086] In any aspect or embodiment provided herein, the EC50 of the antibody for the target cell is less than about 0.1 nM. In any aspect or embodiment provided herein, the multispecificity of the antibody is similar to or lower than the multispecificity of ABTx052. In any aspect or embodiment provided herein, the antibody effectively reduces the viability of hematopoietic stem cells (HSCs) expressing wild-type CD117 polypeptide. In any aspect or embodiment provided herein, the IC50 value of the antibody for reducing HSC viability is less than 5E-006 moles.

[0087] In any aspect of the present disclosure or its embodiments: A) VH CDR1 is selected from one or more of the following: GYRFTSYW (SEQ ID NO: 421), GFTFSSYS (SEQ ID NO: 406), GFTFDDYG (SEQ ID NO: 466), and GFTFDDYA (SEQ ID NO: 435); B) VH CDR2 is selected from one or more of the following: IYPGDSDTK (SEQ ID NO: 972), IYPGDSDTR (SEQ ID NO: 958), IGTISSYIY (SEQ ID NO: 1113), INWNGGSTG (SEQ ID NO: 1114), ISWNSGSIG (SEQ ID NO: 1115), and ISWNSGTIG (SEQ ID NO: 1070); C) VH CDR3 is selected from one or more of the following: ARHGRGYDAYDGAFDI (SEQ ID NO: 1032), ARHGRGYDGYDGAFDI (SEQ ID NO: 1012), ARDYYGGLFDY (SEQ ID NO: 408), ARESWDGSGIYYMDV (SEQ ID NO: 468), ARESWNYEGYYYMDV (SEQ ID NO: 483), AKDTPLGYCSTTSCYGAFDI (SEQ ID NO: 438), AKDWPSGFCSSAYCYGAFDI (SEQ ID NO: 1094), AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 453), and AKDSPPGYCASASCYGAFDI (SEQ ID NO: 1090); D) VL CDR1 is selected from one or more of the following: QGISSA (SEQ ID NO: 424), QSISSY (SEQ ID NO: 409), QGISSY (SEQ ID NO: 469), and QSVSSSY (SEQ ID NO: 439); E) VL CDR2 is selected from one or more of the following: DAS, AAS, GSS, and GAS;and / or F) The VL CDR3 is selected from one or more of the following: QQTNSYPLT (SEQ ID NO: 1044), QQFSSYPLT (SEQ ID NO: 1022), QQFNSYPLT (SEQ ID NO: 425), QQSYSTPLT (SEQ ID NO: 410), QQSYSTPFT (SEQ ID NO: 455), QQLNSYPYT (SEQ ID NO: 485), QQSYSTPIT (SEQ ID NO: 470), QQSYSTPYT (SEQ ID NO: 1097), QQYNFWPYT (SEQ ID NO: 1084), QQYGSSPLT (SEQ ID NO: 440), QQYGTSLT (SEQ ID NO: 395), QQSETCLT (SEQ ID NO: 1074), and QQDSLGLT (SEQ ID NO: 1091).;

[0088] In any aspect of the present disclosure or its embodiments, an antibody comprises variable heavy chain (VH) and variable light chain (VL) framework regions (FRs), wherein A) VH FR1 is selected from one or more of the following: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426), QVQLQESGGGLVKPGGSLRLSCAAS (SEQ ID NO: 411), EVQLVESGGGVVRPGGSLRLSCAAS (SEQ ID NO: 471), EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396), and EVQLVESGGGLVQPGRSLRLSCSAS (SEQ ID NO: 456); B) VH FR2 is selected from one or more of the following: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427), MNWVRQAPGKGLEWVSS (SEQ ID NO: 412), MSWVRQAPGKGLEWVSD (SEQ ID NO: 472), MSWVRQAPGKGLEWVSG (SEQ ID NO: 487), and MHWVRQAPGKGLEWVSG (SEQ ID NO: 397); C) VH FR3 is selected from one or more of the following: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), YADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYC (SEQ ID NO: 413), YADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO: 1116), YADSVKGRFTISRDNAKNSLHLQMNSLRAEDTALYYC (SEQ ID NO: 1117), YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1077), and YADSVKGRFTSSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1065); D) VH FR4 is selected from one or more of the following: WGQGTMVTVSS (SEQ ID NO: 389), WGQGTLVTVSS (SEQ ID NO: 414), WGKGTTVTVSS (SEQ ID NO: 474), WGQGTTVTVSS (SEQ ID NO: 459), and RGQGTMVTVSS (SEQ ID NO: 1102);E) VL FR1 is selected from one or more of the following: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 430), EIVMTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 415), DIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 460), AIQMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO: 490), DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO: 475), EIVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO: 1087), EIVLAQSPGTLSLSPGERATLSCRAS (SEQ ID NO: 445), and DVVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO: 400); F) VL FR2 is selected from one or more of the following: LAWYQQKPGKAPKLLIY (SEQ ID NO: 431), LNWYQQKPGKAPKLLIY (SEQ ID NO: 416), and LAWYQQKPGQAPRLLIY (SEQ ID NO: 446); G) VL FR3 is selected from one or more of the following: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 432), SLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 417), SLQSGVPSRFSGSGSGTDFTLTINSLQPEDFATYYC (SEQ ID NO: 462), TLQNGVPSRFSGSGSGTEFTLTISSLQPEDFATYYC (SEQ ID NO: 492), TLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 477), TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC (SEQ ID NO: 1099), TRATGIPARFSGSGSGTEFALTISSLQSEDFAVYYC (SEQ ID NO: 1080), and SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO: 402);and / or H) VL FR4 is selected from one or more of the following: FGGGTKVEIKRTV (SEQ ID NO: 433), FGGGTKVDIKRTV (SEQ ID NO: 418), FGPGTKVEIKRTV (SEQ ID NO: 463), FGQGTKLEIKRTV (SEQ ID NO: 493), FGQGTRLEIKRTV (SEQ ID NO: 478), FGQGTKLEIK (SEQ ID NO: 1100), FGQGTKVEIK (SEQ ID NO: 1088), FGGGTKLEIKRTV (SEQ ID NO: 403), and FGGGTKLEIK (SEQ ID NO: 1082).;

[0089] In any aspect of the present disclosure or its embodiments, the hemoglobinopathy is selected from one or more of the following: sickle cell anemia, thalassemia, Fanconi anemia, aplastic anemia, and Wiskott - Aldrich syndrome.

[0090] In any aspect of the present disclosure or its embodiments, step (b) is carried out before, after, or simultaneously with step (a).

[0091] In any aspect of the present disclosure or its embodiments, the CD117 polypeptide contains the S261G alteration.

[0092] In any aspect of the present disclosure or its embodiments, the continuous amino acid sequence has at least 90%, 95%, 99%, 99.5%, or 99.9% sequence identity with the fragment. In any aspect of the present disclosure or its embodiments, the CD117 polypeptide has at least 90%, 95%, 99%, 99.5%, or 99.9% sequence identity with the amino acid sequence.

[0093] Definitions

[0094] Unless otherwise defined, all technical and scientific terms used herein have the meaning commonly understood by one of ordinary skill in the art to which this disclosure belongs. The following references provide one of ordinary skill in the art 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). Unless otherwise noted, as used herein, the following terms have the meanings ascribed to them below.

[0095] "ABTx025" means an antibody having at least about 85% amino acid sequence identity to the antibody sequence of antibody ABTx025 or comprising VH and / or VL CDR 1-3 of ABTx025 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to a wild-type CD117 polypeptide, but binding to an altered CD117 polypeptide is not detected or is reduced only to an altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity to the antibody sequence of antibody ABTx025. Exemplary heavy and light chain sequences of antibody ABTx025 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2 are underlined:

[0096] ABTx025 heavy chain (HC):

[0097]

[0098] ABTx025 light chain (LC):

[0099]

[0100] The three CDRs of the ABTx025 antibody VH region are as follows:

[0101] VH CDR1: GFTFDDYA (SEQ ID NO:391);

[0102] VH CDR2: ISWNSGTI (SEQ ID NO:392); and

[0103] VH CDR3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO:393).

[0104] The three CDRs of the VL region of the ABTx025 antibody are as follows:

[0105] VL CDR1: QSVSSSY (SEQ ID NO:394);

[0106] VL CDR2: GAS; and

[0107] VL CDR3: QQYGTSLT (SEQ ID NO:395).

[0108] The four framework (FR) regions of the ABTx025 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx025 antibody are as follows:

[0109] VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO:396);

[0110] VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO:397);

[0111] VH FR3: IGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO:398); and

[0112] VH FR4: WGQGTMVTVSS (SEQ ID NO:399).

[0113] The four FRs of the VL region of the ABTx025 antibody are as follows:

[0114] VL FR1: DVVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO:400);

[0115] VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO:401);

[0116] VL FR3: SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO:402); and

[0117] VL FR4: FGGGTKLEIKRTV (SEQ ID NO:403).

[0118] "ABTx025 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of an ABTx025 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0119] "ABTx030" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx030 or comprising the VH and / or VL CDR 1-3 of ABTx030 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx030. Exemplary heavy and light chain sequences of antibody ABTx030 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR2, are underlined:

[0120] ABTx030 heavy chain (HC):

[0121]

[0122]

[0123] ABTx030 light chain (LC):

[0124]

[0125] The three CDRs of the ABTx030 antibody VH region are as follows:

[0126] VH CDR1: GFTFSSYS (SEQ ID NO:406);

[0127] VH CDR2: IGTISSYI (SEQ ID NO:407) or IGTISSYIY (SEQ ID NO:1113); and

[0128] VH CDR3: ARDYYGGLFDY (SEQ ID NO:408).

[0129] The three CDRs of the ABTx030 antibody VL region are as follows:

[0130] VL CDR1: QSISSY (SEQ ID NO:409);

[0131] VL CDR2: AAS; and

[0132] VL CDR3: QQSYSTPLT (SEQ ID NO:410).

[0133] The four framework (FR) regions of the ABTx030 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx030 antibody are as follows:

[0134] VH FR1: QVQLQESGGGLVKPGGSLRLSCAAS (SEQ ID NO:411);

[0135] VH FR2: MNWVRQAPGKGLEWVSS (SEQ ID NO:412);

[0136] VH FR3: YYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYC (SEQ ID NO:413); and

[0137] VH FR4: WGQGTLVTVSS (SEQ ID NO:414).

[0138] The four FRs of the VL region of the ABTx030 antibody are as follows:

[0139] VL FR1: EIVMTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:415); VL FR2: LNWYQQKPGKAPKLLIY (SEQ ID NO:416);

[0140] VL FR3: SLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:417); and

[0141] VL FR4: FGGGTKVDIKRTV (SEQ ID NO:418).

[0142] "ABTx030 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx030 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0143] "ABTx052" or "mAb-7" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx052 or comprising the VH and / or VL CDR 1-3 of ABTx052 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or reduced only with respect to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx052. Exemplary heavy and light chain sequences of antibody ABTx052 are provided below, wherein embodiments of the variable region are represented in plain text, embodiments of the constant domain are represented in bold, and embodiments of the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0144] ABTx052 heavy chain (HC):

[0145]

[0146] ABTx052 light chain (LC):

[0147]

[0148]

[0149] The three CDRs of the ABTx052 antibody VH region are as follows:

[0150] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0151] VH CDR2: IYPGDSDT (SEQ ID NO:422) or IYPGDSDTR (SEQ ID NO:958); and

[0152] VH CDR3: ARHGRGYNGYEGAFDI (SEQ ID NO:423).

[0153] The three CDRs of the ABTx052 antibody VL region are as follows:

[0154] VL CDR1: QGISSA (SEQ ID NO:424);

[0155] VL CDR2: DAS; and

[0156] VL CDR3: QQFNSYPLT (SEQ ID NO:425).

[0157] The four framework (FR) regions of the ABTx052 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx052 antibody are as follows:

[0158] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0159] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0160] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0161] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0162] The four FRs of the VL region of the ABTx052 antibody are as follows:

[0163] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0164] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0165] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0166] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0167] "ABTx052 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx052 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0168] "ABTx061" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx061 or that contains the VH and / or VL CDR 1-3 of ABTx061 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx061. Exemplary heavy and light chain sequences of antibody ABTx061 are provided below, where the variable regions are shown in plain text, the constant domains are shown in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0169] ABTx061 heavy chain (HC):

[0170]

[0171]

[0172] ABTx061 light chain (LC):

[0173]

[0174] The three CDRs of the ABTx061 antibody VH region are as follows:

[0175] VH CDR1: GFTFDDYA (SEQ ID NO:436);

[0176] VH CDR2: ISWNSGSI (SEQ ID NO:437) or ISWNSGSIG (SEQ ID NO:1115); and

[0177] VH CDR3: AKDTPLGYCSTTSCYGAFDI (SEQ ID NO:438).

[0178] The three CDRs of the ABTx061 antibody VL region are as follows:

[0179] VL CDR1: QSVSSSY (SEQ ID NO:439);

[0180] VL CDR2: GAS; and

[0181] VL CDR3: QQYGSSPLT (SEQ ID NO:440).

[0182] The four framework (FR) regions of the ABTx061 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx061 antibody are as follows:

[0183] VH FR1: EVQLVESGGGLVQPGRSLRLSCAA (SEQ ID NO:441); VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO:442);

[0184] VH FR3: GYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO:443) or YADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO:1116); and

[0185] VH FR4: WGQGTMVTVSS (SEQ ID NO:444).

[0186] The four FRs of the VL region of the ABTx061 antibody are as follows:

[0187] VL FR1: EIVLAQSPGTLSLSPGERATLSCRAS (SEQ ID NO:445); VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO:446);

[0188] VL FR3: SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO:447); and

[0189] VL FR4: FGGGTKLEIKRTV (SEQ ID NO:448).

[0190] "ABTx061 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx061 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0191] "ABTx062" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx062 or comprising the VH and / or VL CDR 1-3 of ABTx062 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx062. Exemplary heavy and light chain sequences of antibody ABTx062 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0192] ABTx062 heavy chain (HC):

[0193]

[0194] ABTx062 light chain (LC):

[0195]

[0196] The three CDRs of the ABTx062 antibody VH region are as follows:

[0197] VH CDR1: GFTFDDYA (SEQ ID NO:451);

[0198] VH CDR2: ISWNSGTI (SEQ ID NO:452); and

[0199] VH CDR3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO:453).

[0200] The three CDRs of the ABTx062 antibody VL region are as follows:

[0201] VL CDR1: QSISSY (SEQ ID NO:454);

[0202] VL CDR2: AAS; and

[0203] VL CDR3: QQSYSTPFT (SEQ ID NO:455).

[0204] The four framework (FR) regions of the ABTx062 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx062 antibody are as follows:

[0205] VH FR1: EVQLVESGGGLVQPGRSLRLSCSAS (SEQ ID NO:456); VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO:457);

[0206] VH FR3: GYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO:458) or YADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO:1116); and

[0207] VH FR4: WGQGTTVTVSS (SEQ ID NO:459).

[0208] The four FRs of the VL region of the ABTx062 antibody are as follows:

[0209] VL FR1: DIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:460); VL FR2: LNWYQQKPGKAPKLLIY (SEQ ID NO:461);

[0210] VL FR3: SLQSGVPSRFSGSGSGTDFTLTINSLQPEDFATYYC (SEQ ID NO:462); and

[0211] VL FR4: FGPGTKVEIKRTV (SEQ ID NO:463).

[0212] "ABTx062 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx062 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0213] "ABTx070" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx070 or that contains the VH and / or VL CDR 1-3 of ABTx070 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or is reduced only with respect to the altered CD117 polypeptide. In embodiments, the antibody or antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx070. Exemplary heavy and light chain sequences of antibody ABTx070 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0214] ABTx070 heavy chain (HC):

[0215]

[0216] ABTx070 light chain (LC):

[0217]

[0218]

[0219] The three CDRs of the ABTx070 antibody VH region are as follows:

[0220] VH CDR1: GFTFDDYG (SEQ ID NO:466);

[0221] VH CDR2: INWNGGST (SEQ ID NO:467) or INWNGGSTG (SEQ ID NO:1114); and

[0222] VH CDR3: ARESWDGSGIYYMDV (SEQ ID NO:468).

[0223] The three CDRs of the ABTx070 antibody VL region are as follows:

[0224] VL CDR1: QGISSY (SEQ ID NO:469);

[0225] VL CDR2: AAS; and

[0226] VL CDR3: QQSYSTPIT (SEQ ID NO:470).

[0227] The four framework (FR) regions of the ABTx070 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx070 antibody are as follows:

[0228] VH FR1: EVQLVESGGGVVRPGGSLRLSCAAS (SEQ ID NO:471);

[0229] VH FR2: MSWVRQAPGKGLEWVSD (SEQ ID NO:472);

[0230] VH FR3: GYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO:473) or YADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO:1116); and

[0231] VH FR4: WGKGTTVTVSS (SEQ ID NO:474).

[0232] The four FRs of the VL region of the ABTx070 antibody are as follows:

[0233] VL FR1: DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO:475);

[0234] VL FR2: LNWYQQKPGKAPKLLIY (SEQ ID NO:476);

[0235] VL FR3: TLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:477); and

[0236] VL FR4: FGQGTRLEIKRTV (SEQ ID NO:478).

[0237] "ABTx070 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx070 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0238] "ABTx071" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx071 or contains the VH and / or VL CDR 1-3 of ABTx071 or its antigen-binding fragment, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx071. Exemplary heavy and light chain sequences of antibody ABTx071 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0239] ABTx071 heavy chain (HC):

[0240]

[0241]

[0242] ABTx071 light chain (LC):

[0243]

[0244] The three CDRs of the ABTx071 antibody VH region are as follows:

[0245] VH CDR1: GFTFDDYG (SEQ ID NO:481);

[0246] VH CDR2: INWNGGST (SEQ ID NO:482) or INWNGGSTG (SEQ ID NO:1114); and

[0247] VH CDR3: ARESWNYEGYYYMDV (SEQ ID NO:483).

[0248] The three CDRs of the ABTx071 antibody VL region are as follows:

[0249] VL CDR1: QGISSY (SEQ ID NO:484);

[0250] VL CDR2: AAS; and

[0251] VL CDR3: QQLNSYPYT (SEQ ID NO:485).

[0252] The four framework (FR) regions of the ABTx071 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx071 antibody are as follows:

[0253] VH FR1: EVQLVESGGGVVRPGGSLRLSCAAS (SEQ ID NO:486);

[0254] VH FR2: MSWVRQAPGKGLEWVSG (SEQ ID NO:487);

[0255] VH FR3: GYADSVKGRFTISRDNAKNSLHLQMNSLRAEDTALYYC (SEQ ID NO:488) or YADSVKGRFTISRDNAKNSLHLQMNSLRAEDTALYYC (SEQ ID NO:1117); and

[0256] VH FR4: WGKGTTVTVSS (SEQ ID NO:489).

[0257] The four FRs of the VL region of the ABTx071 antibody are as follows:

[0258] VL FR1: AIQMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO:490);

[0259] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:491);

[0260] VL FR3: TLQNGVPSRFSGSGSGTEFTLTISSLQPEDFATYYC (SEQ ID NO:492); and

[0261] VL FR4: FGQGTKLEIKRTV (SEQ ID NO:493).

[0262] "ABTx071 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx071 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0263] "ABTx248" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx248 or contains the VH and / or VL CDR 1-3 of ABTx248 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx248. Exemplary heavy and light chain sequences of antibody ABTx248 are provided below, wherein the variable regions are represented in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0264] ABTx248 heavy chain (HC):

[0265]

[0266] ABTx248 light chain (LC):

[0267]

[0268] The three CDRs of the ABTx248 antibody VH region are as follows:

[0269] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0270] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0271] VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012).

[0272] The three CDRs of the ABTx248 antibody VL region are as follows:

[0273] VL CDR1: QGISSA (SEQ ID NO:424);

[0274] VL CDR2: DAS; and

[0275] VL CDR3: QQFNSYPLT (SEQ ID NO:425).

[0276] The four framework (FR) regions of the ABTx248 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx248 antibody are as follows:

[0277] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0278] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0279] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0280] The four FRs of the VL region of the ABTx248 antibody are as follows:

[0281] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0282] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0283] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0284] "ABTx248 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx248 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0285] "ABTx249" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx249 or contains the VH and / or VL CDR 1-3 of ABTx249 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx249. Exemplary heavy and light chain sequences of antibody ABTx249 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0286] ABTx249 heavy chain (HC):

[0287]

[0288] ABTx249 light chain (LC):

[0289]

[0290] The three CDRs of the ABTx249 antibody VH region are as follows:

[0291] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0292] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0293] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0294] The three CDRs of the ABTx249 antibody VL region are as follows:

[0295] VL CDR1: QGISSA (SEQ ID NO:424);

[0296] VL CDR2: DAS; and

[0297] VL CDR3: QQLNGYPLT (SEQ ID NO:1015).

[0298] The four framework (FR) regions of the ABTx249 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx249 antibody are as follows:

[0299] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0300] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0301] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0302] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0303] The four FRs of the VL region of the ABTx249 antibody are as follows:

[0304] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0305] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0306] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0307] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0308] "ABTx249 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx249 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0309] "ABTx250" means an antibody having at least about 85% amino acid sequence identity to the antibody sequence of antibody ABTx250 or comprising the VH and / or VL CDR 1-3 of ABTx250 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 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 the antibody sequence of antibody ABTx250. Exemplary heavy and light chain sequences of antibody ABTx250 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0310] ABTx250 heavy chain (HC):

[0311]

[0312]

[0313] ABTx250 light chain (LC):

[0314]

[0315] The three CDRs of the ABTx250 antibody VH region are as follows:

[0316] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0317] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0318] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0319] The three CDRs of the ABTx250 antibody VL region are as follows:

[0320] VL CDR1: QGISSA (SEQ ID NO:424);

[0321] VL CDR2: DAS; and

[0322] VL CDR3: QQFNSYPLT (SEQ ID NO:425).

[0323] The four framework (FR) regions of the ABTx250 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx250 antibody are as follows:

[0324] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0325] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0326] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0327] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0328] The four FRs of the VL region of the ABTx250 antibody are as follows:

[0329] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0330] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0331] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0332] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0333] "ABTx250 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx250 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0334] "ABTx251" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx251 or that contains the VH and / or VL CDR 1-3 of ABTx251 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide but shows no detectable binding to the altered CD117 polypeptide or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx251. Exemplary heavy and light chain sequences of antibody ABTx251 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0335] ABTx251 heavy chain (HC):

[0336]

[0337] ABTx251 light chain (LC):

[0338]

[0339] The three CDRs of the ABTx251 antibody VH region are as follows:

[0340] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0341] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0342] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0343] The three CDRs of the ABTx251 antibody VL region are as follows:

[0344] VL CDR1: QGISSA (SEQ ID NO:424);

[0345] VL CDR2: DAS; and

[0346] VL CDR3: QQFYSYPLT (SEQ ID NO:954).

[0347] The four framework (FR) regions of the ABTx251 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx251 antibody are as follows:

[0348] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0349] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0350] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0351] The four FRs of the VL region of the ABTx251 antibody are as follows:

[0352] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0353] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0354] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0355] "ABTx251 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx251 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0356] "ABTx252" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx252 or that contains the VH and / or VL CDR 1-3 of ABTx252 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or is reduced only with respect to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx252. Exemplary heavy and light chain sequences of antibody ABTx252 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0357] ABTx252 heavy chain (HC):

[0358]

[0359] ABTx252 light chain (LC):

[0360]

[0361] The three CDRs of the ABTx252 antibody VH region are as follows:

[0362] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0363] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0364] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0365] The three CDRs of the ABTx252 antibody VL region are as follows:

[0366] VL CDR1: QGISSA (SEQ ID NO:424);

[0367] VL CDR2: DAS; and

[0368] VL CDR3: QQFNSHPLT (SEQ ID NO:955).

[0369] The four framework (FR) regions of the ABTx252 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx252 antibody are as follows:

[0370] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0371] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0372] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0373] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0374] The four FRs of the VL region of the ABTx252 antibody are as follows:

[0375] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0376] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0377] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0378] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0379] "ABTx252 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx252 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0380] "ABTx253" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx253 or contains the VH and / or VL CDR 1-3 of ABTx253 or its antigen-binding fragment, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx253. Exemplary heavy and light chain sequences of antibody ABTx253 are provided below, where the variable regions are shown in plain text, the constant domains are shown in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0381] ABTx253 heavy chain (HC):

[0382]

[0383]

[0384] ABTx253 light chain (LC):

[0385]

[0386] The three CDRs of the ABTx253 antibody VH region are as follows:

[0387] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0388] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0389] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0390] The three CDRs of the ABTx253 antibody VL region are as follows:

[0391] VL CDR1: QGISSA (SEQ ID NO:424);

[0392] VL CDR2: DAS; and

[0393] VL CDR3: QQFSSYPLT (SEQ ID NO:1020).

[0394] The four framework (FR) regions of the ABTx253 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx253 antibody are as follows:

[0395] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0396] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0397] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0398] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0399] The four FRs of the VL region of the ABTx253 antibody are as follows:

[0400] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0401] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0402] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0403] "ABTx253 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx253 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0404] "ABTx254" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx254 or that contains the VH and / or VL CDR 1-3 of ABTx254 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or is reduced only to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx254. Exemplary heavy and light chain sequences of antibody ABTx254 are provided below, where the variable regions are shown in plain text, the constant domains are shown in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0405] ABTx254 heavy chain (HC):

[0406]

[0407] ABTx254 light chain (LC):

[0408]

[0409] The three CDRs of the ABTx254 antibody VH region are as follows:

[0410] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0411] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0412] VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012).

[0413] The three CDRs of the ABTx254 antibody VL region are as follows:

[0414] VL CDR1: QGISSA (SEQ ID NO:424);

[0415] VL CDR2: DAS; and

[0416] VL CDR3: QQTNSHPLT (SEQ ID NO:1023).

[0417] The four framework (FR) regions of the ABTx254 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx254 antibody are as follows:

[0418] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0419] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0420] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0421] The four FRs of the VL region of the ABTx254 antibody are as follows:

[0422] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0423] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0424] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0425] "ABTx254 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx254 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0426] "ABTx255" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx255 or that contains the VH and / or VL CDR 1-3 of ABTx255 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or is reduced only with respect to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx255. Exemplary heavy and light chain sequences of antibody ABTx255 are provided below, where the variable regions are represented in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0427] ABTx255 heavy chain (HC):

[0428]

[0429] ABTx255 light chain (LC):

[0430]

[0431] The three CDRs of the ABTx255 antibody VH region are as follows:

[0432] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0433] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0434] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0435] The three CDRs of the ABTx255 antibody VL region are as follows:

[0436] VL CDR1: QGISSA (SEQ ID NO:424);

[0437] VL CDR2: DAS; and

[0438] VL CDR3: QQVRSYPLT (SEQ ID NO:1025).

[0439] The four framework (FR) regions of the ABTx255 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx255 antibody are as follows:

[0440] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0441] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0442] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0443] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0444] The four FRs of the VL region of the ABTx255 antibody are as follows:

[0445] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0446] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0447] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0448] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0449] "ABTx255 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx255 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0450] "ABTx256" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx256 or that contains the VH and / or VL CDR 1-3 of ABTx256 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detected or is reduced only to the altered CD117 polypeptide. In embodiments, the antibody or antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx256. Exemplary heavy and light chain sequences of antibody ABTx256 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0451] ABTx256 heavy chain (HC):

[0452]

[0453]

[0454] ABTx256 light chain (LC):

[0455]

[0456] The three CDRs of the ABTx256 antibody VH region are as follows:

[0457] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0458] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0459] VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO:1027).

[0460] The three CDRs of the ABTx256 antibody VL region are as follows:

[0461] VL CDR1: QGISSA (SEQ ID NO:424);

[0462] VL CDR2: DAS; and

[0463] VL CDR3: QQTYSYPLT (SEQ ID NO:1029).

[0464] The four framework (FR) regions of the ABTx256 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx256 antibody are as follows:

[0465] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0466] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0467] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0468] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0469] The four FRs of the VL region of the ABTx256 antibody are as follows:

[0470] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0471] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0472] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0473] "ABTx256 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx256 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0474] "ABTx257" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx257 or that contains the VH and / or VL CDR 1-3 of ABTx257 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide but no binding to the altered CD117 polypeptide is detected or only the binding to the altered CD117 polypeptide is reduced. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx257. Exemplary heavy and light chain sequences of antibody ABTx257 are provided below, wherein the variable regions are represented in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0475] ABTx257 heavy chain (HC):

[0476]

[0477] ABTx257 light chain (LC):

[0478]

[0479] The three CDRs of the ABTx257 antibody VH region are as follows:

[0480] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0481] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0482] VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO:1032).

[0483] The three CDRs of the ABTx257 antibody VL region are as follows:

[0484] VL CDR1: QGISSA (SEQ ID NO:424);

[0485] VL CDR2: DAS; and

[0486] VL CDR3: QQTNSYPLT (SEQ ID NO:1044).

[0487] The four framework (FR) regions of the ABTx257 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx257 antibody are as follows:

[0488] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0489] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0490] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0491] The four FRs of the VL region of the ABTx257 antibody are as follows:

[0492] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0493] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0494] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0495] "ABTx257 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx257 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0496] "ABTx258" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx258 or comprising the VH and / or VL CDR 1-3 of ABTx258 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99% or 100% amino acid sequence identity with the antibody sequence of antibody ABTx258. Exemplary heavy and light chain sequences of antibody ABTx258 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2 are underlined:

[0497] ABTx258 heavy chain (HC):

[0498]

[0499] ABTx258 light chain (LC):

[0500]

[0501] The three CDRs of the ABTx258 antibody VH region are as follows:

[0502] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0503] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0504] VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO:1027).

[0505] The three CDRs of the ABTx058 antibody VL region are as follows:

[0506] VL CDR1: QGISSA (SEQ ID NO:424);

[0507] VL CDR2: DAS; and

[0508] VL CDR3: QQVRSYPLT (SEQ ID NO:1025).

[0509] The four framework (FR) regions of the ABTx258 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx258 antibody are as follows:

[0510] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0511] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0512] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0513] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0514] The four FRs of the VL region of the ABTx258 antibody are as follows:

[0515] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0516] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0517] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0518] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0519] "ABTx258 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx258 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0520] "ABTx259" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx259 or comprising the VH and / or VL CDR 1-3 of ABTx259 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx259. Exemplary heavy and light chain sequences of antibody ABTx259 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0521] ABTx259 heavy chain (HC):

[0522]

[0523]

[0524] ABTx259 light chain (LC):

[0525]

[0526] The three CDRs of the ABTx259 antibody VH region are as follows:

[0527] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0528] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0529] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0530] The three CDRs of the ABTx259 antibody VL region are as follows:

[0531] VL CDR1: QGISSA (SEQ ID NO:424);

[0532] VL CDR2: DAS; and

[0533] VL CDR3: QQTRSYPLT (SEQ ID NO:1036).

[0534] The four framework (FR) regions of the ABTx259 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx259 antibody are as follows:

[0535] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0536] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0537] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0538] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0539] The four FRs of the VL region of the ABTx259 antibody are as follows:

[0540] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0541] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0542] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0543] "ABTx259 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx259 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0544] "ABTx260" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx260 or that contains the VH and / or VL CDR 1-3 of ABTx260 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide but shows no detectable binding to or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx260. Exemplary heavy and light chain sequences of antibody ABTx260 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0545] ABTx260 heavy chain (HC):

[0546]

[0547] ABTx260 light chain (LC):

[0548]

[0549] The three CDRs of the ABTx260 antibody VH region are as follows:

[0550] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0551] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0552] VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012).

[0553] The three CDRs of the ABTx260 antibody VL region are as follows:

[0554] VL CDR1: QGISSA (SEQ ID NO:424);

[0555] VL CDR2: DAS; and

[0556] VL CDR3: QQVNSHPLT (SEQ ID NO:1038).

[0557] The four framework (FR) regions of the ABTx260 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx260 antibody are as follows:

[0558] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0559] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0560] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0561] The four FRs of the VL region of the ABTx260 antibody are as follows:

[0562] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0563] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0564] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0565] "ABTx260 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx260 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0566] "ABTx261" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx261 or comprising the VH and / or VL CDR 1-3 of ABTx261 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or reduced only to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx261. Exemplary heavy and light chain sequences of antibody ABTx261 are provided below, wherein the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0567] ABTx261 heavy chain (HC):

[0568]

[0569] ABTx261 light chain (LC):

[0570]

[0571] The three CDRs of the ABTx261 antibody VH region are as follows:

[0572] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0573] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0574] VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO:1027).

[0575] The three CDRs of the ABTx261 antibody VL region are as follows:

[0576] VL CDR1: QGISSA (SEQ ID NO:424);

[0577] VL CDR2: DAS; and

[0578] VL CDR3: QQTRSYPLT (SEQ ID NO:1036).

[0579] The four framework (FR) regions of the ABTx261 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx261 antibody are as follows:

[0580] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0581] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0582] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0583] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0584] The four FRs of the VL region of the ABTx261 antibody are as follows:

[0585] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0586] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0587] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0588] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0589] "ABTx261 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx261 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0590] "ABTx262" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx262 or comprising the VH and / or VL CDR 1-3 of ABTx262 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx262. Exemplary heavy and light chain sequences of antibody ABTx262 are provided below, wherein the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0591] ABTx262 heavy chain (HC):

[0592]

[0593]

[0594] ABTx262 light chain (LC):

[0595]

[0596] The three CDRs of the ABTx262 antibody VH region are as follows:

[0597] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0598] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0599] VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO:1027).

[0600] The three CDRs of the ABTx262 antibody VL region are as follows:

[0601] VL CDR1: QGISSA (SEQ ID NO:424);

[0602] VL CDR2: DAS; and

[0603] VL CDR3: QQFRSSPLT (SEQ ID NO:1040).

[0604] The four framework (FR) regions of the ABTx262 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx262 antibody are as follows:

[0605] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0606] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0607] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0608] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0609] The four FRs of the VL region of the ABTx262 antibody are as follows:

[0610] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0611] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0612] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0613] "ABTx262 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx262 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0614] "ABTx263" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx263 or comprising the VH and / or VL CDR 1-3 of ABTx263 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx263. Exemplary heavy and light chain sequences of antibody ABTx263 are provided below, wherein the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0615] ABTx263 heavy chain (HC):

[0616]

[0617] ABTx263 light chain (LC):

[0618]

[0619] The three CDRs of the ABTx263 antibody VH region are as follows:

[0620] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0621] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0622] VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012).

[0623] The three CDRs of the ABTx263 antibody VL region are as follows:

[0624] VL CDR1: QGISSA (SEQ ID NO:424);

[0625] VL CDR2: DAS; and

[0626] VL CDR3: QQVYSYPLT (SEQ ID NO:1042).

[0627] The four framework (FR) regions of the ABTx263 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx263 antibody are as follows:

[0628] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0629] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0630] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0631] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0632] The four FRs of the VL region of the ABTx263 antibody are as follows:

[0633] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0634] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0635] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0636] "ABTx263 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx263 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0637] "ABTx264" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx264 or that contains the VH and / or VL CDR 1-3 of ABTx264 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to a wild-type CD117 polypeptide but no binding to an altered CD117 polypeptide is detected or only reduced binding to an altered CD117 polypeptide is detected. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx264. Exemplary heavy and light chain sequences of antibody ABTx264 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0638] ABTx264 heavy chain (HC):

[0639]

[0640] ABTx264 light chain (LC):

[0641]

[0642] The three CDRs of the ABTx264 antibody VH region are as follows:

[0643] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0644] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0645] VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO:1027).

[0646] The three CDRs of the ABTx264 antibody VL region are as follows:

[0647] VL CDR1: QGISSA (SEQ ID NO:424);

[0648] VL CDR2: DAS; and

[0649] VL CDR3: QQTYSYPLT (SEQ ID NO:1029).

[0650] The four framework (FR) regions of the ABTx264 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx264 antibody are as follows:

[0651] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0652] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0653] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0654] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0655] The four FRs of the VL region of the ABTx264 antibody are as follows:

[0656] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0657] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0658] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0659] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0660] "ABTx264 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx264 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0661] "ABTx265" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx265 or that contains the VH and / or VL CDR 1-3 of ABTx265 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is reduced only in binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx265. Exemplary heavy and light chain sequences of antibody ABTx265 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0662] ABTx265 heavy chain (HC):

[0663]

[0664]

[0665] ABTx265 light chain (LC):

[0666]

[0667] The three CDRs of the ABTx265 antibody VH region are as follows:

[0668] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0669] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0670] VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012).

[0671] The three CDRs of the ABTx265 antibody VL region are as follows:

[0672] VL CDR1: QGISSA (SEQ ID NO:424);

[0673] VL CDR2: DAS; and

[0674] VL CDR3: QQTRSYPLT (SEQ ID NO:1036).

[0675] The four framework (FR) regions of the ABTx265 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx265 antibody are as follows:

[0676] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0677] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0678] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0679] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0680] The four FRs of the VL region of the ABTx265 antibody are as follows:

[0681] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0682] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0683] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0684] "ABTx265 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx265 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0685] "ABTx266" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx266 or comprising the VH and / or VL CDR 1-3 of ABTx266 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99% or 100% amino acid sequence identity with the antibody sequence of antibody ABTx266. Exemplary heavy and light chain sequences of antibody ABTx266 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2 are underlined:

[0686] ABTx266 heavy chain (HC):

[0687]

[0688] ABTx266 light chain (LC):

[0689]

[0690] The three CDRs of the ABTx266 antibody VH region are as follows:

[0691] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0692] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0693] VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO:1027).

[0694] The three CDRs of the ABTx266 antibody VL region are as follows:

[0695] VL CDR1: QGISSA (SEQ ID NO:424);

[0696] VL CDR2: DAS; and

[0697] VL CDR3: QQVRSHPLT (SEQ ID NO:1047).

[0698] The four framework (FR) regions of the ABTx266 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx266 antibody are as follows:

[0699] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0700] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0701] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0702] The four FRs of the VL region of the ABTx266 antibody are as follows:

[0703] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0704] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0705] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0706] "ABTx266 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx266 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0707] "ABTx267" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx267 or comprising the VH and / or VL CDR 1-3 of ABTx267 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx267. Exemplary heavy and light chain sequences of antibody ABTx267 are provided below, where the variable regions are represented in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0708] ABTx267 heavy chain (HC):

[0709]

[0710] ABTx267 light chain (LC):

[0711]

[0712] The three CDRs of the ABTx267 antibody VH region are as follows:

[0713] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0714] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0715] VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO:1032).

[0716] The three CDRs of the ABTx267 antibody VL region are as follows:

[0717] VL CDR1: QGISSA (SEQ ID NO:424);

[0718] VL CDR2: DAS; and

[0719] VL CDR3: QQTNSSPLT (SEQ ID NO:1050).

[0720] The four framework (FR) regions of the ABTx267 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx267 antibody are as follows:

[0721] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0722] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0723] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0724] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0725] The four FRs of the VL region of the ABTx267 antibody are as follows:

[0726] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0727] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0728] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0729] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0730] "ABTx267 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx267 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0731] "ABTx268" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx268 or comprising the VH and / or VL CDR 1-3 of ABTx268 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99% or 100% amino acid sequence identity with the antibody sequence of antibody ABTx268. Exemplary heavy and light chain sequences of antibody ABTx268 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2 are underlined:

[0732] ABTx268 heavy chain (HC):

[0733]

[0734]

[0735] ABTx268 light chain (LC):

[0736]

[0737] The three CDRs of the ABTx268 antibody VH region are as follows:

[0738] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0739] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0740] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0741] The three CDRs of the ABTx268 antibody VL region are as follows:

[0742] VL CDR1: QGISSA (SEQ ID NO:424);

[0743] VL CDR2: DAS; and

[0744] VL CDR3: QQVNSYPLT (SEQ ID NO:952).

[0745] The four framework (FR) regions of the ABTx268 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx268 antibody are as follows:

[0746] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0747] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0748] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0749] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0750] The four FRs of the VL region of the ABTx268 antibody are as follows:

[0751] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0752] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0753] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0754] "ABTx268 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx268 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0755] "ABTx269" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx269 or contains the VH and / or VL CDR 1-3 of ABTx269 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx269. Exemplary heavy and light chain sequences of antibody ABTx269 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0756] ABTx269 heavy chain (HC):

[0757]

[0758] ABTx269 light chain (LC):

[0759]

[0760] The three CDRs of the ABTx269 antibody VH region are as follows:

[0761] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0762] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0763] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0764] The three CDRs of the ABTx269 antibody VL region are as follows:

[0765] VL CDR1: QGISSA (SEQ ID NO:424);

[0766] VL CDR2: DAS; and

[0767] VL CDR3: QQVYSYPLT (SEQ ID NO:1042).

[0768] The four framework (FR) regions of the ABTx269 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx269 antibody are as follows:

[0769] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0770] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0771] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0772] The four FRs of the VL region of the ABTx269 antibody are as follows:

[0773] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0774] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0775] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0776] "ABTx269 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx269 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0777] "ABTx270" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx270 or contains the VH and / or VL CDR 1-3 of ABTx270 or its antigen-binding fragment, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx270. Exemplary heavy and light chain sequences of antibody ABTx270 are provided below, where the variable regions are represented in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2 are underlined:

[0778] ABTx270 heavy chain (HC):

[0779]

[0780] ABTx270 light chain (LC):

[0781]

[0782] The three CDRs of the ABTx270 antibody VH region are as follows:

[0783] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0784] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0785] VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO:1027).

[0786] The three CDRs of the ABTx270 antibody VL region are as follows:

[0787] VL CDR1: QGISSA (SEQ ID NO:424);

[0788] VL CDR2: DAS; and

[0789] VL CDR3: QQVRSYPLT (SEQ ID NO:1025).

[0790] The four framework (FR) regions of the ABTx270 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx270 antibody are as follows:

[0791] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0792] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0793] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0794] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0795] The four FRs of the VL region of the ABTx270 antibody are as follows:

[0796] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0797] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0798] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0799] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0800] "ABTx270 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx270 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0801] "ABTx271" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx271 or comprising the VH and / or VL CDR 1-3 of ABTx271 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx271. Exemplary heavy and light chain sequences of antibody ABTx271 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0802] ABTx271 heavy chain (HC):

[0803]

[0804]

[0805] ABTx271 light chain (LC):

[0806]

[0807] The three CDRs of the ABTx271 antibody VH region are as follows:

[0808] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0809] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0810] VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO:1032).

[0811] The three CDRs of the ABTx271 antibody VL region are as follows:

[0812] VL CDR1: QGISSA (SEQ ID NO:424);

[0813] VL CDR2: DAS; and

[0814] VL CDR3: QQTNSYPLT (SEQ ID NO:1044).

[0815] The four framework (FR) regions of the ABTx271 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx271 antibody are as follows:

[0816] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0817] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0818] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0819] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0820] The four FRs of the VL region of the ABTx271 antibody are as follows:

[0821] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0822] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0823] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0824] "ABTx271 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx271 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0825] "ABTx272" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx272 or comprising the VH and / or VL CDR 1-3 of ABTx272 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx272. Exemplary heavy and light chain sequences of antibody ABTx272 are provided below, wherein the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0826] ABTx272 heavy chain (HC):

[0827]

[0828] ABTx272 light chain (LC):

[0829]

[0830] The three CDRs of the ABTx272 antibody VH region are as follows:

[0831] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0832] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0833] VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012).

[0834] The three CDRs of the ABTx272 antibody VL region are as follows:

[0835] VL CDR1: QGISSA (SEQ ID NO:424);

[0836] VL CDR2: DAS; and

[0837] VL CDR3: QQVRSYPLT (SEQ ID NO:1025).

[0838] The four framework (FR) regions of the ABTx272 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx272 antibody are as follows:

[0839] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0840] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0841] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0842] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0843] The four FRs of the VL region of the ABTx272 antibody are as follows:

[0844] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0845] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0846] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0847] "ABTx272 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx272 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0848] "ABTx273" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx273 or contains the VH and / or VL CDR 1-3 of ABTx273 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx273. Exemplary heavy and light chain sequences of antibody ABTx273 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0849] ABTx273 heavy chain (HC):

[0850]

[0851] ABTx273 light chain (LC):

[0852]

[0853] The three CDRs of the ABTx273 antibody VH region are as follows:

[0854] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0855] VH CDR2: IYPGDSDTR (SEQ ID NO:958); and

[0856] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0857] The three CDRs of the ABTx0273 antibody VL region are as follows:

[0858] VL CDR1: QGISSA (SEQ ID NO:424);

[0859] VL CDR2: DAS; and

[0860] VL CDR3: QQFRSYPLT (SEQ ID NO:953).

[0861] The four framework (FR) regions of the ABTx273 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx273 antibody are as follows:

[0862] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0863] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0864] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0865] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0866] The four FRs of the VL region of the ABTx273 antibody are as follows:

[0867] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430);

[0868] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0869] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0870] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0871] "ABTx273 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx273 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0872] "ABTx274" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx274 or comprising the VH and / or VL CDR 1-3 of ABTx274 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or reduced only with respect to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx274. Exemplary heavy and light chain sequences of antibody ABTx274 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0873] ABTx274 heavy chain (HC):

[0874]

[0875]

[0876] ABTx274 light chain (LC):

[0877]

[0878] The three CDRs of the ABTx274 antibody VH region are as follows:

[0879] VH CDR1: GYRFTSYW (SEQ ID NO:421);

[0880] VH CDR2: IYPGDSDTK (SEQ ID NO:972); and

[0881] VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO:948).

[0882] The three CDRs of the ABTx274 antibody VL region are as follows:

[0883] VL CDR1: QGISSA (SEQ ID NO:424);

[0884] VL CDR2: DAS; and

[0885] VL CDR3: QQTNSYPLT (SEQ ID NO:1044).

[0886] The four framework (FR) regions of the ABTx274 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx274 antibody are as follows:

[0887] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426);

[0888] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427); and

[0889] VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:973);

[0890] VH FR4: WGQGTMVTVSS (SEQ ID NO:429).

[0891] The four FRs of the VL region of the ABTx274 antibody are as follows:

[0892] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431);

[0893] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432); and

[0894] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433).

[0895] "ABTx274 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx274 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0896] "ABTx313" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx313 or comprising the VH and / or VL CDR 1-3 of ABTx313 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or an antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx313. Exemplary heavy and light chain sequences of antibody ABTx313 are provided below, wherein the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0897] ABTx313 heavy chain (HC):

[0898]

[0899] ABTx313 light chain (LC):

[0900]

[0901] The three CDRs of the ABTx313 VH region are as follows:

[0902] VH CDR-1: GYRFTSYW (SEQ ID NO:421)

[0903] VH CDR-2: IYPGDSDTR (SEQ ID NO:1053)

[0904] VH CDR-3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012)

[0905] The three CDRs of the ABTx313 VL region are as follows:

[0906] VL CDR-1: QGISSA (SEQ ID NO:424)

[0907] VL CDR-2: DAS

[0908] VL CDR-3: QQFSSYPLT (SEQ ID NO:1020)

[0909] The four framework (FR) regions of the ABTx313 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx313 antibody are as follows:

[0910] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426)

[0911] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427)

[0912] VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:1059)

[0913] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[0914] The four FRs of the VL region of the ABTx313 antibody are as follows:

[0915] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430)

[0916] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431)

[0917] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432)

[0918] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433)

[0919] "ABTx313 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx313 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0920] "ABTx307" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx307 or comprising the VH and / or VL CDR 1-3 of ABTx307 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or is reduced only in binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx307. Exemplary heavy and light chain sequences of antibody ABTx307 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0921] ABTx307 heavy chain (HC):

[0922]

[0923] ABTx307 light chain (LC) (VL):

[0924]

[0925] The three CDRs of the ABTx307 VH region are as follows:

[0926] VH CDR-1: GYRFTSYW (SEQ ID NO:421)

[0927] VH CDR-2: IYPGDSDTR (SEQ ID NO:1053)

[0928] VH CDR-3: ARHGRGYDGYDGAFDI (SEQ ID NO:1012)

[0929] The three CDRs of the ABTx307 VL region are as follows:

[0930] VL CDR-1: QGISSA (SEQ ID NO:424)

[0931] VL CDR-2: DAS

[0932] VL CDR-3: QQFNSYPLT (SEQ ID NO:425)

[0933] The four framework (FR) regions of the ABTx307 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx307 antibody are as follows:

[0934] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426)

[0935] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427)

[0936] VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:1059)

[0937] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[0938] The four FRs of the VL region of the ABTx307 antibody are as follows:

[0939] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430)

[0940] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431)

[0941] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432)

[0942] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433)

[0943] "ABTx307 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx307 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0944] "ABTx308" means an antibody having at least about 85% amino acid sequence identity to the antibody sequence of antibody ABTx308 or comprising the VH and / or VL CDR 1-3 of ABTx308 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 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 the antibody sequence of antibody ABTx308. Exemplary heavy and light chain sequences of antibody ABTx308 are provided below, where the variable regions are in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR3, are underlined:

[0945] ABTx308 heavy chain (HC):

[0946]

[0947]

[0948] ABTx308 light chain (LC):

[0949]

[0950] The three CDRs of the ABTx308 VH region are as follows:

[0951] VH CDR-1: GYRFTSYW (SEQ ID NO:421)

[0952] VH CDR-2: IYPGDSDTK (SEQ ID NO:1063)

[0953] VH CDR-3: ARHGRGYDAYDGAFDI (SEQ ID NO:1032)

[0954] The three CDRs of the ABTx308 VL region are as follows:

[0955] VL CDR-1: QGISSA (SEQ ID NO:424)

[0956] VL CDR-2: DAS

[0957] VL CDR-3: QQFSSYPLT (SEQ ID NO:1020)

[0958] The four framework (FR) regions of the ABTx308 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx308 antibody are as follows:

[0959] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:426)

[0960] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:427)

[0961] VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:1059)

[0962] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[0963] The four FRs of the VL region of the ABTx308 antibody are as follows:

[0964] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:1060)

[0965] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:1061)

[0966] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:1062)

[0967] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433)

[0968] "ABTx308 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx308 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0969] "ABTx309" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx309 or comprising the VH and / or VL CDR 1-3 of ABTx309 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx309. Exemplary heavy and light chain sequences of antibody ABTx309 are provided below, wherein the variable regions are represented in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[0970] ABTx309 heavy chain (HC):

[0971]

[0972] ABTx309 light chain (LC):

[0973]

[0974] The three CDRs of the ABTx309 VH region are as follows:

[0975] VH CDR-1: GYRFTSYW (SEQ ID NO:421)

[0976] VH CDR-2: IYPGDSDTR (SEQ ID NO:1053)

[0977] VH CDR-3: ARHGRGYDAYDGAFDI (SEQ ID NO:1064)

[0978] The three CDRs of the ABTx309 VL region are as follows:

[0979] VL CDR-1: QGISSA (SEQ ID NO:424)

[0980] VL CDR-2: DAS

[0981] VL CDR-3: QQTNSYPLT (SEQ ID NO:1044)

[0982] The four framework (FR) regions of the ABTx309 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx309 antibody are as follows:

[0983] VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO:1057)

[0984] VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO:1058)

[0985] VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO:1059)

[0986] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[0987] The four FRs of the VL region of the ABTx309 antibody are as follows:

[0988] VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO:430)

[0989] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431)

[0990] VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO:432)

[0991] VL FR4: FGGGTKVEIKRTV (SEQ ID NO:433)

[0992] "ABTx309 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABTx309 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0993] "ABTx196" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx196 or comprising the VH and / or VL CDR 1-3 of ABTx196 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or antigen-binding fragment thereof has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx196. Exemplary heavy-chain variable region and light-chain variable region sequences of antibody ABTx196 are provided below, wherein the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2 are underlined:

[0994] ABTx196 heavy-chain variable region (VH):

[0995] EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCSSASCYGAFDI WGQGTMVTVSS(SEQ ID NO:1120)

[0996] ABTx196 light-chain variable region (VL):

[0997] DVVMTQSPGTLSLSPGERATLSCRAS QSVSSSY LAWYQQKPGQAPRLLIY GAS SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC QQSETCLT FGGGTKLEIK(SEQ ID NO:1068)

[0998] The three CDRs of the ABTx196 VH region are as follows:

[0999] VH CDR-1: GFTFDDYA(SEQ ID NO:391)

[1000] VH CDR-2: ISWNSGTIG(SEQ ID NO:1070)

[1001] VH CDR-3: AKDSPPGYCSSASCYGAFDI(SEQ ID NO:393)

[1002] The three CDRs of the ABTx196 VL region are as follows:

[1003] VL CDR-1: QSVSSSY (SEQ ID NO:394)

[1004] VL CDR-2: GAS

[1005] VL CDR-3: QQSETCLT (SEQ ID NO:1074)

[1006] The four framework (FR) regions of the ABTx196 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABT x196 antibody are as follows:

[1007] VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO:396)

[1008] VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO:397)

[1009] VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO:1077)

[1010] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[1011] The four FRs of the VL region of the ABT x196 antibody are as follows:

[1012] VL FR1: DVVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO:400)

[1013] VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO:446)

[1014] VL FR3: SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO:402)

[1015] VL FR4: FGGGTKLEIK (SEQ ID NO:1082)

[1016] "ABT x196 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of the ABT x196 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[1017] "ABTx202" means an antibody that has at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx202 or contains the VH and / or VL CDR 1-3 of ABTx202 or its antigen-binding fragment, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is undetectable or only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx202. Exemplary heavy-chain variable region and light-chain variable region sequences of antibody ABTx202 are provided below, wherein the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[1018] ABTx202 heavy-chain variable region (VH):

[1019] EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTSSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCSSASCYGAFDI WGQGTMVTVSS(SEQ ID NO:1085)

[1020] ABTx202 light-chain variable region (VL):

[1021] EIVMTQSPGTLSLSPGERATLSCRAS QSVSSSY LAWYQQKPGQAPRLLIY GSS TRATGIPARFSGSGSGTEFALTISSLQSEDFAVYYC QQYNFWPYT FGQGTKVEIK(SEQ ID NO:1086)

[1022] The three CDRs of the ABTx202 VH region are as follows:

[1023] VH CDR-1: GFTFDDYA(SEQ ID NO:391)

[1024] VH CDR-2: ISWNSGTIG(SEQ ID NO:1070)

[1025] VH CDR-3: AKDSPPGYCSSASCYGAFDI(SEQ ID NO:393)

[1026] The three complementarity-determining regions (CDRs) of the variable light (VL) domain of ABTx202 are as follows:

[1027] VL CDR-1: QSVSSSY (SEQ ID NO:394)

[1028] VL CDR-2: GSS

[1029] VL CDR-3: QQYNFWPYT (SEQ ID NO:1084)

[1030] The four framework (FR) regions of the ABTx202 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL domain sequences shown above. Specifically, the four FRs of the VH domain of the ABTx202 antibody are as follows:

[1031] VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO:396)

[1032] VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO:397)

[1033] VH FR3: YADSVKGRFTSSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO:1065)

[1034] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[1035] The four FRs of the VL domain of the ABTx202 antibody are as follows:

[1036] VL FR1: EIVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO:1087)

[1037] VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO:446)

[1038] VL FR3: TRATGIPARFSGSGSGTEFALTISSLQSEDFAVYYC (SEQ ID NO:1080)

[1039] VL FR4: FGQGTKVEIK (SEQ ID NO:1088)

[1040] "ABTx202 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of an ABTx202 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[1041] "ABTx198" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx198 or comprising the VH and / or VL CDR 1-3 of ABTx198 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is reduced only with the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx198. Exemplary heavy-chain variable region and light-chain variable region sequences of antibody ABTx198 are provided below, wherein the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[1042] ABTx198 heavy-chain variable region (VH):

[1043] EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCASASCYGAFDI WGQGTMVTVSS (SEQ ID NO:1089)

[1044] ABTx198 light-chain variable region (VL):

[1045] DVVMTQSPGTLSLSPGERATLSCRAS QSVSSSY LAWYQQKPGQAPRLLIY GAS SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC QQDSLGLT FGGGTKLEIK (SEQ ID NO:1103)

[1046] The three CDRs of the ABTx198 VH region are as follows:

[1047] VH CDR-1: GFTFDDYA (SEQ ID NO:391)

[1048] VH CDR-2: ISWNSGTIG (SEQ ID NO:1070)

[1049] VH CDR-3: AKDSPPGYCASASCYGAFDI (SEQ ID NO:1090)

[1050] The three CDRs of the variable light (VL) region of ABTx198 are as follows:

[1051] VL CDR-1: QSVSSSY (SEQ ID NO:394)

[1052] VL CDR-2: GAS

[1053] VL CDR-3: QQDSLGLT (SEQ ID NO:1091)

[1054] The four framework (FR) regions of the ABTx198 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx198 antibody are as follows:

[1055] VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO:396)

[1056] VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO:397)

[1057] VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO:1077)

[1058] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[1059] The four FRs of the VL region of the ABTx198 antibody are as follows:

[1060] VL FR1: DVVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO:400)

[1061] VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO:446)

[1062] VL FR3: SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO:402)

[1063] VL FR4: FGGGTKLEIK (SEQ ID NO:1082)

[1064] "ABTx198 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of an ABTx198 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[1065] "ABTx203" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx203 or comprising the VH and / or VL CDR 1-3 of ABTx203 or an antigen-binding fragment thereof, wherein each of the antibody, the CDRs, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is reduced only with the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx203. Exemplary heavy-chain variable region and light-chain variable region sequences of antibody ABTx203 are provided below, wherein the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[1066] ABTx203 heavy-chain variable region (VH):

[1067] EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDWPSGFCSSAYCYGAFDI WGQGTMVTVSS (SEQ ID NO:1092)

[1068] ABTx203 light-chain variable region (VL):

[1069] DIVMTQSPSFLSASVGDRVTITCRAS QGISSY LAWYQQKPGKAPKLLIY AAS TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC QQSYSTPYT FGQGTKLEIK (SEQ ID NO:1093)

[1070] The three CDRs of the ABTx203 VH region are as follows:

[1071] VH CDR-1: GFTFDDYA (SEQ ID NO:391)

[1072] VH CDR-2: ISWNSGTIG (SEQ ID NO:1070)

[1073] VH CDR-3: AKDWPSGFCSSAYCYGAFDI (SEQ ID NO:1094)

[1074] The three CDRs of the VL region of ABTx203 are as follows:

[1075] VL CDR-1: QGISSY (SEQ ID NO:469)

[1076] VL CDR-2: AAS

[1077] VL CDR-3: QQSYSTPYT (SEQ ID NO:1097)

[1078] The four framework (FR) regions of the ABTx203 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx203 antibody are as follows:

[1079] VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO:396)

[1080] VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO:397)

[1081] VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO:1077)

[1082] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[1083] The four FRs of the VL region of the ABTx203 antibody are as follows:

[1084] VL FR1: DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO:475)

[1085] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431)

[1086] VL FR3: TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC (SEQ ID NO:1099)

[1087] VL FR4: FGQGTKLEIK (SEQ ID NO:1100)

[1088] "ABTx203 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of an ABTx203 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[1089] "ABTx205" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx205 or comprising the VH and / or VL CDR 1-3 of ABTx205 or an antigen-binding fragment thereof, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced binding to the altered CD117 polypeptide. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx205. Exemplary heavy chain variable region and light chain variable region sequences of antibody ABTx205 are provided below, wherein the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2 are underlined:

[1090] ABTx205 heavy chain variable region (VH):

[1091] EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCSSASCYGAFDI WGQGTMVTVSS(SEQ ID NO:1120)

[1092] ABTx205 light chain variable region (VL):

[1093] DIVMTQSPSFLSASVGDRVTITCRAS QGISSY LAWYQQKPGKAPKLLIY AAS TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC QQSYSTPYT FGQGTKLEIK(SEQ ID NO:1093)

[1094] The three CDRs of the ABTx205 VH region are as follows:

[1095] VH CDR-1: GFTFDDYA(SEQ ID NO:391)

[1096] VH CDR-2: ISWNSGTIG (SEQ ID NO:1070)

[1097] VH CDR-3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO:393)

[1098] The three CDRs of the VL region of ABTx205 are as follows:

[1099] VL CDR-1: QGISSY (SEQ ID NO:1095)

[1100] VL CDR-2: AAS

[1101] VL CDR-3: QQSYSTPYT (SEQ ID NO:1097)

[1102] The four framework (FR) regions of the ABTx205 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx205 antibody are as follows:

[1103] VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO:396)

[1104] VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO:397)

[1105] VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO:1077)

[1106] VH FR4: WGQGTMVTVSS (SEQ ID NO:429)

[1107] The four FRs of the VL region of the ABTx205 antibody are as follows:

[1108] VL FR1: DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO:475)

[1109] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO:431)

[1110] VL FR3: TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC (SEQ ID NO:1099)

[1111] VL FR4: FGQGTKLEIK (SEQ ID NO:1100)

[1112] "ABTx205 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of an ABTx205 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[1113] "ABTx206" means an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx206 or comprising the VH and / or VL CDR 1-3 of ABTx206 or an antigen-binding fragment thereof, wherein each of the antibody, the CDR, and the antigen-binding fragment specifically binds to the wild-type CD117 polypeptide, but binding to the altered CD117 polypeptide is not detectable or is only reduced. In embodiments, the antibody or its antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx206. Exemplary heavy-chain variable region and light-chain variable region sequences of antibody ABTx206 are provided below, wherein the variable regions are represented in plain text, the constant domains are in bold, and the complementarity-determining regions (CDRs), namely CDR1, CDR2, and CDR2, are underlined:

[1114] ABTx206 heavy-chain variable region (VH):

[1115] EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCSSASCYGAFDI RGQGTMVTVSS (SEQ ID NO:1101)

[1116] ABTx206 light-chain variable region (VL):

[1117] DIVMTQSPSFLSASVGDRVTITCRAS QGISSY LAWYQQKPGKAPKLLIY AAS TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC QQSYSTPYT FGQGTKLEIK (SEQ ID NO:1093)

[1118] The three CDRs of the ABTx206 VH region are as follows:

[1119] VH CDR-1: GFTFDDYA (SEQ ID NO: 391)

[1120] VH CDR-2: ISWNSGTIG (SEQ ID NO: 1070)

[1121] VH CDR-3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393)

[1122] The three CDRs of the VL region of ABTx206 are as follows:

[1123] VL CDR-1: QGISSY (SEQ ID NO: 1095)

[1124] VL CDR-2: AAS

[1125] VL CDR-3: QQSYSTPYT (SEQ ID NO: 1097)

[1126] The four framework (FR) regions of the ABTx206 antibody, namely FR1, FR2, FR3, and FR4, are located on either side of each CDR in the VH and VL region sequences shown above. Specifically, the four FRs of the VH region of the ABTx206 antibody are as follows:

[1127] VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396)

[1128] VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 397)

[1129] VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1077)

[1130] VH FR4: RGQGTMVTVSS (SEQ ID NO: 1102)

[1131] The four FRs of the VL region of the ABTx206 antibody are as follows:

[1132] VL FR1: DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO: 475)

[1133] VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 431)

[1134] VL FR3: TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC (SEQ ID NO:1099)

[1135] VL FR4: FGQGTKLEIK (SEQ ID NO:1100)

[1136] "ABTx206 polynucleotide" means a nucleic acid molecule (e.g., DNA) encoding at least one fragment of an ABTx206 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[1137] "Adenine" or "9H-purin-6-amine" means the purine nucleobase with the molecular formula C5H5N5, which has the structure and corresponds to CAS number 73-24-5.

[1138] "Adenosine" or "4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2(1H)-one" means an adenine molecule attached to ribose via a glycosidic bond, which has the structure and corresponds to CAS number 65-46-3. Its molecular formula is C 10 H 13 N5O4.

[1139] "Adenosine deaminase" or "adenine deaminase" means 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 that catalyzes the hydrolytic deamination of adenosine to inosine or the hydrolytic deamination of deoxyadenosine to deoxyinosine. In some embodiments, the adenosine deaminase catalyzes the hydrolytic deamination of adenine or adenosine in deoxyribonucleic acid (DNA). The adenosine deaminases provided herein (e.g., engineered adenosine deaminases, evolved adenosine deaminases) can be from any organism (e.g., eukaryote, prokaryote), including but not limited to algae, bacteria, fungi, plants, invertebrates (e.g., insects), and vertebrates (e.g., amphibians, mammals). In some embodiments, the adenosine deaminase is an adenosine deaminase variant having one or more alterations and capable of deaminating adenine and cytosine in a target polynucleotide (e.g., DNA, RNA), and can be referred to as a "double deaminase". Non-limiting examples of double deaminases include those described in PCT / US22 / 22050. In some embodiments, the target polynucleotide is single-stranded or double-stranded. In some embodiments, the adenosine deaminase variant is capable of deaminating adenine and cytosine in DNA. In some embodiments, the adenosine deaminase variant is capable of deaminating adenine and cytosine in single-stranded DNA. In some embodiments, the adenosine deaminase variant is capable of deaminating 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, and PCT / US2020 / 028568, the entire contents of which are incorporated herein by reference in their entirety for all purposes.

[1140] "Adenosine deaminase activity" means catalyzing the deamination of adenine or adenosine in a polynucleotide to guanine. In some embodiments, the adenosine deaminase variant provided herein retains adenosine deaminase activity (e.g., at least about 30%, 40%, 50%, 60%, 70%, 80%, 90% or more of the activity of a reference adenosine deaminase (e.g., TadA*8.20 or TadA*8.19)).

[1141] "Adenosine base editor (ABE)" means a base editor that includes an adenosine deaminase.

[1142] "Adenosine base editor (ABE)" means a base editor that includes an adenosine deaminase.

[1143] "Adenosine base editor (ABE) polynucleotide" means a polynucleotide encoding an ABE. "Adenosine base editor 8 (ABE8) polypeptide" or "ABE8" means a base editor comprising an adenosine deaminase or an adenosine deaminase variant as defined herein, said adenosine deaminase variant comprising one or more of the alterations listed in Table 5B, one of the combinations of the alterations listed in Table 5B, or an alteration at one or more of the amino acid positions listed in Table 5B, such alterations being relative to the following reference sequence: MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO:1), or the corresponding positions in another adenosine deaminase. In embodiments, ABE8 comprises an alteration at amino acid 82 and / or 166 of SEQ ID NO:1. In some embodiments, as described herein, ABE8 comprises further alterations relative to the reference sequence.

[1144] "Adenosine base editor 8 (ABE8) polynucleotide" means a polynucleotide encoding an ABE8 polypeptide.

[1145] "Adenosine base editor 8 (ABE8) polynucleotide" means a polynucleotide encoding an ABE8 polypeptide.

[1146] "Administer" as used herein means to provide to a patient or subject one or more of the compositions described herein. By way of example and not limitation, administration of a composition, such as an injection, can be carried out by intravenous (i.v.) injection, subcutaneous (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 infusion over time. In some embodiments, parenteral administration includes intravascular, intravenous, intramuscular, intraarterial, intrathecal, intratumoral, intradermal, intraperitoneal, intratracheal, subcutaneous, subepidermal, intraarticular, subcapsular, subarachnoid, and intrasternal infusion or injection. Alternatively or concurrently, administration can be by the oral route.

[1147] "Agent" means any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide or fragment thereof.

[1148] As used herein, "allogeneic" refers to cells of the same species that are genetically different from the cells being compared.

[1149] As used herein, "autologous" refers to cells from the same subject.

[1150] "Alteration" means a change in the level, structure, or activity of an analyte, gene, or polypeptide as detected by methods known in the art (such as those described herein). As used herein, alteration includes a change in the level of expression (e.g., an increase or decrease). In embodiments, the level of expression is increased or decreased by 10%, 25%, 40%, 50% or more. In some embodiments, the alteration includes an insertion, deletion, or substitution of a nucleobase or amino acid (e.g., by genetic engineering).

[1151] "Ameliorate" means to reduce, inhibit, alleviate, mitigate, prevent, or stabilize the development or progression of a disease.

[1152] "Analogue" means a molecule that is not identical but has similar functional or structural characteristics. For example, a polypeptide analogue retains the biological activity of the corresponding naturally occurring polypeptide while having certain biochemical modifications that enhance the function of the analogue relative to the naturally occurring polypeptide. Such biochemical modifications can increase the protease resistance, membrane permeability, or half-life of the analogue without altering, for example, ligand binding. Analogues can include non-natural amino acids.

[1153] As used herein, the term "antibody" refers to an immunoglobulin molecule that specifically binds to a particular antigen or immunoreacts with a particular antigen, and includes polyclonal, monoclonal, genetically engineered, and other modified forms of antibodies, including but not limited to chimeric antibodies, humanized antibodies, heteroconjugate antibodies (e.g., bispecific, trispecific, and tetra-specific antibodies, diabodies, triabodies, and tetra-bodies), and antigen-binding fragments of antibodies, including, for example, Fab’, F(ab’)2, Fab, Fv, rlgG, and scFv fragments. Unless otherwise specified, the term "monoclonal antibody" (mAb) means including the intact molecule as well as antibody fragments capable of specifically binding to the target protein (including, for example, Fab and F(ab’)2 fragments). As used herein, Fab and F(ab’)2 fragments refer to antibody fragments that lack the Fc fragment of the intact antibody.

[1154] Antibodies (immunoglobulins) contain two heavy chains and two light chains linked together by disulfide bonds, where each light chain is linked to the corresponding heavy chain in a "Y" - shaped configuration by a disulfide bond. Each heavy chain has a variable domain (VH) at one end, followed by multiple constant domains (CH). Each light chain has a variable domain (VL) at one end and a constant domain (CL) at the other end. The light - chain variable domain (VL) aligns with the heavy - chain variable domain (VH), and the light - chain constant domain (CL) aligns with the first constant domain (CH1) of the heavy chain. The variable regions of each pair of light and heavy chains form the antigen - binding site. The isotype of the heavy chain (γ, α, δ, ε, or μ) determines the class of the immunoglobulin (IgG, IgA, IgD, IgE, or IgM, respectively). The light chain is one of two isotypes (kappa (κ) or lambda (λ)) found in all antibody classes. The term "antibody / antibodies" includes intact antibodies, such as polyclonal or monoclonal antibodies (mAbs), and proteolytic portions or fragments thereof that are capable of specifically binding to a target protein, such as Fab or F(ab')2 fragments. Antibodies can include chimeric antibodies; recombinant and engineered antibodies and their antigen - binding fragments. Exemplary functional antibody fragments containing the whole or substantially the whole variable regions of the light and heavy chains are defined as follows: (i) Fv, which is defined as a genetically engineered fragment consisting of the light - chain variable region and the heavy - chain variable region, represented as two chains; (ii) single - chain Fv ("scFv"), which is a genetically engineered single - chain molecule containing the light - chain variable region and the heavy - chain variable region linked by a suitable polypeptide linker; (iii) Fab, which is a fragment of an antibody molecule containing the monovalent antigen - binding portion of the antibody molecule, obtained by treating the intact antibody with the enzyme papain to produce the Fd fragment of the intact light and heavy chains, where the Fd fragment consists of the variable domain and the CH1 domain of the heavy chain; (iv) Fab', which is a fragment of an antibody molecule containing the monovalent antigen - binding portion of the antibody molecule, obtained by treating the intact antibody with the enzyme pepsin, followed by reduction (two Fab' fragments are generated per antibody molecule); and (v) F(ab')2, which is a fragment of an antibody molecule containing the monovalent antigen - binding portion of the antibody molecule, obtained by treating the intact antibody with the enzyme pepsin (i.e., a dimer of Fab' fragments linked together by two disulfide bonds).

[1155] As used herein, the term "antigen-binding fragment" refers to one or more portions or fragments of an antibody that retain the ability to specifically bind to a target antigen. In one embodiment, the target antigen is a CD117 variant polypeptide or peptide. The antigen-binding function of an antibody can be achieved by fragments of a full-length antibody. Antibody fragments can be Fab, F(ab')2, scFv, SMIP, diabody, triabody, affibody, nanobody, aptamer, or domain antibody. Examples of binding fragments encompassed by the term "antigen-binding fragment" of an antibody include, but are not limited to: (i) Fab fragment, which is a monovalent fragment consisting of V L 、V H 、C L and C H1 domains; (ii) F(ab')2 fragment, which is a divalent fragment containing two Fab fragments linked by a disulfide bond at the hinge region; (iii) Fd fragment, which consists of V H and C H1 domains; (iv) Fv fragment, which consists of the V L and V H domains of a single arm of an antibody, (v) dAb, which contains V H and V L domains; (vi) dAb fragment (Ward et al., Nature 341:544-546, 1989), which consists of V H domain; (vii) dAb, which consists of V H or V L domain; (viii) isolated complementarity-determining region (CDR); and (ix) a combination of two or more isolated CDRs, which may optionally be linked by a synthetic linker. In addition, although the two domains V L and V H of an Fv fragment are encoded by separate genes, they can be joined by a linker using recombinant methods so that they can be made into a single-chain protein, in which the V L region and V HThe regions pair to form monovalent molecules (referred to 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 utility of such fragments can be screened in the same manner as for intact antibodies. 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 of anti-CD117 antibodies (e.g., g., Fab', F(ab')2, Fab, scFab, Fv, rlgG, and scFv fragments) linked by synthetic linkers are encompassed herein.

[1156] "Base editor (BE)" or "nucleobase editor polypeptide (NBE)" means an agent that binds to a polynucleotide and has nucleobase modification activity. In various embodiments, a base editor comprises a nucleobase modification polypeptide (e.g., a deaminase) and a polynucleotide programmable nucleotide-binding domain (e.g., Cas9 or Cpf1) that binds to a guide polynucleotide (e.g., guide RNA (gRNA)). Representative nucleic acid and protein sequences of base editors include those having about or at least about 85% sequence identity to any of the base editor sequences provided in the Sequence Listing, such as those corresponding to SEQ ID NOs: 2-11.

[1157] "Base editing activity" means the activity that functions 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 a target C·G to T·A. In another embodiment, the base editing activity is adenosine or adenine deaminase activity, e.g., converting A·T to G·C.

[1158] The term "base editor system" refers to an intermolecular complex for editing nucleobases of a target nucleotide sequence. In various embodiments, a base editor (BE) system comprises (1) a polynucleotide programmable nucleotide binding domain, a deaminase domain for deaminating a nucleobase in a target nucleotide sequence (e.g., a cytidine deaminase or an adenosine deaminase); and (2) one or more guide polynucleotides (e.g., guide RNAs) that bind to the polynucleotide programmable nucleotide binding domain. In various embodiments, a 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, a 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 that bind to 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, a base editor system (e.g., a base editor system comprising a cytidine deaminase) comprises a uracil glycosylase inhibitor or other agent or peptide that inhibits the inosine base excision repair system (e.g., a uracil stabilizing protein such as that provided in WO2022015969, the disclosure of which is incorporated herein by reference in its entirety for all purposes).

[1159] "Base editing activity" means 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 adenosine or adenine deaminase activity, e.g., converting A·T to G·C.

[1160] The term "base editor system" refers to an intermolecular complex for editing nucleobases of a target nucleotide sequence. In various embodiments, a base editor (BE) system comprises (1) a polynucleotide programmable nucleotide-binding domain, a deaminase domain (e.g., adenosine deaminase) for deaminating a nucleobase in a target nucleotide sequence; and (2) one or more guide polynucleotides (e.g., guide RNAs) that bind to the polynucleotide programmable nucleotide-binding domain. In various embodiments, a base editor (BE) system comprises a nucleobase editor domain (e.g., adenosine deaminase) and a domain having nucleic acid sequence-specific binding activity. In some embodiments, a 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 that bind to 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 an adenine or adenosine base editor (ABE). In some embodiments, a base editor system (e.g., a base editor system comprising adenosine deaminase) comprises a uracil glycosylase inhibitor or other agent or peptide that inhibits the inosine base excision repair system.

[1161] The "β-globin (HBB) polypeptide" means a polypeptide having at least about 85% amino acid sequence identity with the NCBI accession number NP_000509 provided below, or a fragment thereof capable of forming a dimer with an HBA1 polypeptide. In certain embodiments, the β-globin contains one or more alterations relative to the following reference sequence. In one particular embodiment, the β-globin associated with sickle cell disease contains the E6V (also known as E7V) mutation.

[1162] MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH (SEQ ID NO:494).

[1163] "HBB polynucleotide" means a nucleic acid molecule or fragment thereof encoding an HBB polypeptide and introns, exons, 3′ untranslated region, 5′ untranslated region, and regulatory sequences associated with its expression. In embodiments, the HBB polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for HBB expression. Exemplary HBB polynucleotide sequences from Homo sapiens are provided below (NCBI Reference Sequence accession numbers NM_000518 and NG_059281).

[1164] ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGCAA(SEQ ID NO:495).

[1165] >NG_059281.1:5001-6608 Homo sapiens hemoglobin subunit beta (HBB), RefSeqGene on chromosome 11 (LRG_1232); the A changed to T in sickle cell disease is indicated in bold; the T in bold and underlined indicates an SNP that is C in some sickle cell patients.

[1166] The underlined ATG is the start codon.

[1167]

[1168]

[1169]

[1170] "Binding polypeptide" means a polypeptide or an antigen-binding portion or fragment thereof that is specific for the CD117 polypeptide and specifically binds thereto. In one embodiment, the binding polypeptide is an anti-CD117 antibody or immunoglobulin or an antigen-binding portion or fragment thereof.

[1171] "Hemoglobin gamma A (HBG1) polypeptide" means a polypeptide having at least about 85% amino acid sequence identity to Genbank accession number CAA23771.1 provided below, or a fragment thereof capable of forming a protein complex with the alpha hemoglobin subunit.

[1172] MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPKVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFGKEFTPEVQASWQKMVTAVASALSSRYH (SEQ ID NO:496).

[1173] "HBG1 polynucleotide" means a nucleic acid molecule or a fragment thereof encoding the HBG1 polypeptide and introns, exons, 3' untranslated region, 5' untranslated region, and regulatory sequences associated with its expression. In an embodiment, the HBG1 polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for HBG1 expression. Exemplary HBB polynucleotide sequences from Homo sapiens are provided on ENSEMBL, accession number GRCh38:11:5248044:5259425:1, and the sequence is provided below Reverse complementary sequence (SEQ ID NO:497). In the following sequence, the exons encoding HBG1 are shown in bold, and the exemplary HBG1 promoter region corresponds to the 5' region of the first exon encoding HBG1 (e.g., the first 100, 200, 300, or 400 nucleotides of the 5' of the first exon) or a portion thereof.

[1174]

[1175]

[1176]

[1177]

[1178]

[1179]

[1180]

[1181]

[1182]

[1183]

[1184] "Hemoglobin gamma G (HBG2) polypeptide" means a polypeptide having at least about 85% amino acid sequence identity to Genbank accession number CAA23773.1 provided below, or a fragment thereof capable of forming a protein complex with an alpha hemoglobin subunit.

[1185] MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPKVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFGKEFTPEVQASWQKMVTGVASALSSRYH (SEQ ID NO:498).

[1186] "HBG2 polynucleotide" means a nucleic acid molecule or fragment thereof encoding an HBG2 polypeptide and introns, exons, 3' untranslated regions, 5' untranslated regions, and regulatory sequences associated with its expression. In an embodiment, the HBG2 polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for HBG2 expression. An exemplary HBB polynucleotide sequence from Homo sapiens is provided on ENSEMBL, accession number GRCh38:11:5248044:5259425:1, and the reverse complementary sequence of said sequence is provided above (SEQ ID NO:497). In the above sequence (SEQ ID NO:497), the exon encoding HBG2 is shown in Bold and underlined text, and the exemplary HBG2 promoter region corresponds to the 5' region of the first exon encoding HBG2 (e.g., the first 100, 200, 300, or 400 nucleotides of the 5' of the first exon) or a portion thereof.

[1187] The term "Cas9" or "Cas9 domain" refers to an RNA-guided nuclease that includes a Cas9 protein or a fragment thereof (e.g., a protein that includes an active, inactive, or partially active DNA cleavage domain of Cas9 and / or a gRNA binding domain of Cas9). The Cas9 nuclease is sometimes also referred to as the casnl nuclease or a CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease.

[1188] The term "chimerism percentage" or "chimerism" means the proportion of a given type of cell of interest in a subject, where the cells are administered to the subject or are altered in the subject or originate from or are derived from cells administered to the subject or cells edited in the subject. In some cases, the chimerism percentage is calculated as the percentage of hCD45+ cells in the subject, where the cells are administered to the subject or are derived from or originate from cells administered to the subject. In embodiments, the cell type of interest is bulk marrow, CD34+ cells, CD235a+ cells, CD19+ cells, or CD45+ cells. In embodiments, the chimeric status of the subject is measured 1 day, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 6 months, 1 year, or longer after administration of the cells to the subject. In embodiments, the chimeric status of the subject is measured 1 day, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, 10 weeks, 11 weeks, 12 weeks, 6 months, 1 year, or longer after administration of an anti-CD117 antibody to the subject. In embodiments, the chimerism percentage measured at the time point is about or at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%. In some cases, the chimerism percentage is greater than the chimerism percentage measured for a subject administered cells expressing a wild-type CD117 polypeptide and not base edited according to the methods provided herein to express an altered CD117 polypeptide with reduced binding to the anti-CD117 antibody. As used herein, the term "complementary determining region" (CDR) refers to the hypervariable regions found in the light and heavy chain variable regions (VL and VH domains, respectively). CDRs are the non-contiguous antigen-binding sites found within the heavy and light chain polypeptide variable regions. These specific 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, 5th ed., U.S. Department of Health and Human Services, NIH Publication No. 91-3242, 1991; as well as Chothia et al., (J. Mol. Biol. 196:901-917, 1987), and MacCallum et al., (J. Mol. Biol. 262:732-745, 1996), where the definitions include an overlap or subset of amino acid residues when compared to each other. In certain embodiments, the term "CDR" is the CDR as defined by Kabat based on sequence comparison. The more highly conserved portions of the variable regions are called framework regions (FR). As is understood in the art, the amino acid positions defining the antibody hypervariable regions can vary depending on context and the various definitions known in the art.Some positions within the variable domains can be considered hybrid hypervariable positions because these positions can be considered within the hypervariable region under one set of criteria and outside the hypervariable region under another set of criteria. One or more of these positions can also be found in the extended hypervariable regions. The variable regions of native heavy and light chains each contain four framework regions (FR1, FR2, FR3, FR4), which predominantly adopt a β-sheet conformation and are connected by three CDRs (CDR1, CDR2, CDR3), which form loops connecting the β-sheet structures and in some cases form part of the β-sheet structure. The CDRs in each chain are tightly associated with each other through 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 the antibody (see Kabat et al., Sequences of Proteins of Immunological Interest (National Institute of Health, Bethesda, Md. 1987; incorporated herein by reference). Unless otherwise specified, as used herein, the numbering of immunoglobulin amino acid residues is according to the Kabat et al. immunoglobulin amino acid residue numbering system. In various embodiments, any method available to those of skill in the art, such as those 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 entire contents of which are incorporated herein by reference in their entirety for all purposes, are used to identify the complementarity-determining regions, such methods including (by way of non-limiting example) those of Kabat, Chothia, Lefranc, Honegger, Martin, MacCallum, and Zhao. CDRs can be identified using sequence- or structure-based methods. A variety of software programs are available to those of skill in the art to identify the CDRs of an antibody amino acid sequence.In various embodiments, a CDR as provided herein can be modified to include 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 additional amino acids and / or exclude 1, 2, 3, 4, 5, 6, 7, 8, or 9 amino acids at the N-terminus and / or C-terminus (e.g., in one embodiment, the VH CDR1 of ABTx025 was modified to RASQSVSS (SEQ ID NO:939) instead of QSVSSSY (SEQ ID NO:438) by extending QSVSSSY (SEQ ID NO:439) by 3 amino acids at the N-terminus and excluding two amino acids at the C-terminus). The present disclosure contemplates that the position or length of a CDR identified for a particular antibody can vary depending on the method by which they are determined).

[1189] The term “conservative amino acid substitution” or “conservative mutation” refers to the replacement of one amino acid by another amino acid having common properties. One 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)). Based on such analysis, groups of amino acids can be defined where amino acids within a group preferentially exchange with each other and are thus most similar to each other in terms of their effect on the overall protein structure (Schulz, G.E. and Schirmer, R.H., supra). Non-limiting examples of conservative mutations include amino acid substitutions of amino acids such that, for example, lysine is substituted for arginine and vice versa so that a positive charge can be maintained; glutamic acid is substituted for aspartic acid and vice versa so that a negative charge can be maintained; serine is substituted for threonine so that a free –OH can be maintained; and glutamine is substituted for asparagine so that a free –NH2 can be maintained).

[1190] As used herein, the terms "condition" and "conditioning" refer to the process by which a patient is prepared to receive a graft containing hematopoietic stem cells. Such procedures facilitate the engraftment of the hematopoietic stem cell graft (e.g., as inferred by the sustained increase in the number of hematopoietic stem cells surviving in blood samples isolated from the patient following the conditioning procedure and subsequent hematopoietic stem cell transplantation). According to the methods described herein, a patient can be conditioned for hematopoietic stem cell transplantation therapy by administering to the patient an antibody or antigen-binding fragment thereof that is capable of binding to an antigen expressed by hematopoietic stem cells, such as CD117. Such antibodies are expected to act via complement-mediated cytotoxicity and antibody-dependent cell-mediated cytotoxicity. As described herein, the transplanted cells have been edited such that the antibody no longer binds to the CD117 antigen. Administration of an antibody capable of binding to the CD117 antigen, an antigen-binding fragment thereof, a drug-antibody conjugate, or a T cell expressing a chimeric antigen receptor (CAR-T) to a patient in need of hematopoietic stem cell transplantation therapy can facilitate hematopoietic stem cell graft engraftment, e.g., by selectively depleting endogenous hematopoietic stem cells, thereby creating a niche to be filled by exogenous hematopoietic stem cell transplantation.

[1191] "Complex" means a combination of two or more molecules whose interaction depends on intermolecular forces. Non-limiting examples of intermolecular forces include covalent and non-covalent interactions. Non-limiting examples of non-covalent interactions include hydrogen bonds, ionic bonds, halogen bonds, hydrophobic bonds, van der Waals interactions (e.g., dipole-dipole interactions, dipole-induced dipole interactions, and London dispersion forces), and π-effects. In one embodiment, the complex comprises a polypeptide, a polynucleotide, or a combination of one or more polypeptides and one or more polynucleotides. In one embodiment, the complex comprises one or more polypeptides (e.g., a base editor comprising a nucleic acid programmable DNA-binding protein such as Cas9 and a deaminase) and a polynucleotide (e.g., a guide RNA) that associate to form a base editor. In one embodiment, the complex is held together by hydrogen bonds. It should be understood that one or more components of the base editor (e.g., the deaminase or the nucleic acid programmable DNA-binding protein) can associate covalently or non-covalently. As an example, a base editor can include a deaminase covalently linked (e.g., via a peptide bond) to a nucleic acid programmable DNA-binding protein. Alternatively, a base editor can include a deaminase and a nucleic acid programmable DNA-binding protein that associate non-covalently (e.g., where one or more components of the base editor are provided in trans and associate directly or via another molecule such as a protein or nucleic acid). In one embodiment, one or more components of the complex are bound together by hydrogen bonds.

[1192] "Cytosine" or "4-aminopyrimidin-2(1H)-one" means the purine nucleobase having the formula C4H5N3O and having the structure and corresponds to CAS number 71-30-7.

[1193] "Cytidine" means a cytosine molecule attached to ribose via a glycosidic bond and has the structure and corresponds to CAS number 65-46-3. Its molecular formula is C9H 13 N3O5.

[1194] "Cytidine base editor (CBE)" means a base editor that includes a cytidine deaminase.

[1195] "Cytidine base editor (CBE) polynucleotide" means a polynucleotide that includes a CBE.

[1196] "Cytidine deaminase" or "cytosine deaminase" means a polypeptide or a fragment thereof that is capable of deaminating cytidine or cytosine. In an embodiment, 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 this application. Petromyzon marinus cytosine deaminase 1 (PmCDA1) (SEQ ID NO: 13-14), activation-induced cytidine deaminase (AICDA) (SEQ ID NO: 15-21), and APOBEC (SEQ ID NO: 12-61) are exemplary cytidine deaminases. Other exemplary cytidine deaminase (CDA) sequences are provided in the sequence listing as SEQ ID NO: 62-66 and SEQ ID NO: 67-189. Non-limiting examples of cytidine deaminases include those described in PCT / US20 / 16288, PCT / US2018 / 021878, 180802-021804 / PCT, PCT / US2018 / 048969, and PCT / US2016 / 058344.

[1197] "Cytosine deaminase activity" means 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 one embodiment, the cytosine deaminase converts cytosine to uracil (i.e., C to U) or 5-methylcytosine to thymine (i.e., 5mC to T). In some embodiments, the cytosine deaminase as provided herein has increased cytosine deaminase activity relative to a reference cytosine deaminase (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).

[1198] As used herein, the term "deaminase" or "deaminase domain" refers to a protein or a fragment thereof that catalyzes a deamination reaction.

[1199] "Detecting" refers to identifying the presence, absence, or amount of an analyte to be detected. In one embodiment, detecting a sequence alteration in a polynucleotide or polypeptide. In another embodiment, detecting the presence of an indel.

[1200] "Detectable label" means a composition that renders a molecule of interest detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means when attached to the molecule. For example, useful labels include radioisotopes, magnetic beads, metal beads, colloidal particles, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in enzyme-linked immunosorbent assay (ELISA)), biotin, digoxin, or haptens.

[1201] "Disease" means any disorder or condition that impairs or interferes with the normal function of a cell, tissue, or organ. Exemplary diseases include diseases amenable to treatment with hematopoietic stem cell transplantation, such as β-thalassemia, sickle cell disease (SCD), or adenosine deaminase deficiency.

[1202] "Dual editing activity" or "dual deaminase activity" means having adenosine deaminase and cytidine deaminase activities. In one embodiment, a base editor having dual editing activity has both A→G and C→T activities, where the two activities are approximately equal or within about 10% or 20% of each other. In another embodiment, the A→G activity of the dual editor is not more than about 10% or 20% higher than the C→T activity. In another embodiment, the A→G activity of the dual editor is not more than about 10% or 20% lower than the C→T activity. In some embodiments, the adenosine deaminase variant predominantly has cytidine deaminase activity and little or no adenosine deaminase activity. In some embodiments, the adenosine deaminase variant has cytidine deaminase activity and no significant or no detectable adenosine deaminase activity.

[1203] "Effective amount" means the amount of an agent or active compound (e.g., a base editor or an antibody as described herein) that improves the symptoms of a disease relative to an untreated patient or an individual not suffering from the disease (i.e., a healthy individual), or is an amount of an agent or active compound sufficient to elicit a desired biological response. The effective amount of an active compound for practicing an embodiment of the present disclosure for therapeutic treatment of a disease varies depending on the mode of administration, the age, weight, and general health of the subject. Ultimately, the attending physician or veterinarian will determine the appropriate amount and dosage regimen. This amount is referred to as an "effective" amount. In one embodiment, the effective amount is an amount of a base editor of the present disclosure sufficient to introduce a change in a gene of interest in a cell (e.g., an in vitro or in vivo cell). In one embodiment, the effective amount is the amount of a base editor required to achieve a therapeutic effect. Such a therapeutic effect does not require sufficient change in the pathogenic gene in all cells of a subject, tissue, or organ, but only requires change in the pathogenic gene in about 1%, 5%, 10%, 25%, 50%, 75% or more of the cells present in the subject, tissue, or organ. In one embodiment, the effective amount is sufficient to improve one or more symptoms of a disease.

[1204] "Fragment" means a portion of a polypeptide or nucleic acid molecule. The portion contains at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the full length of the reference nucleic acid molecule or polypeptide. Fragments can 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.

[1205] As used herein, the term "framework region" or "FR region" encompasses the amino acid residues adjacent to the CDRs. FR region residues may be present, for example, in human antibodies, rodent-derived antibodies (e.g., murine antibodies), humanized antibodies, primatized antibodies, chimeric antibodies, antibody fragments (e.g., Fab fragments), single-chain antibody fragments (e.g., scFv fragments), antibody domains, and bispecific antibodies.

[1206] "Guide polynucleotide" means a polynucleotide or polynucleotide complex that is specific for a target sequence and can form a complex with a polynucleotide programmable nucleotide binding domain protein (e.g., Cas9 or Cpf1). In one embodiment, the guide polynucleotide is a guide RNA (gRNA). The gRNA can exist as a complex of two or more RNAs, or as a single RNA molecule.

[1207] As used herein, the term "hematopoietic stem cell" ("HSC") refers to an immature blood cell that has the ability to self-renew and differentiate into mature blood cells, which include multiple lineages, including but not limited to granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), thrombocytes (e.g., megakaryocytes, 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 thought to include a subset of cells with stem cell properties as defined above, while in mice, HSCs are CD34-. In addition, HSC also refers to long-term repopulating HSCs (LT-HSCs) and short-term repopulating HSCs (ST-HSCs). LT-HSCs and ST-HSCs are distinguished based on functional potential and based 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, CD11B, CD19, 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 Ter119, CD11b, Gr1, CD3, CD4, CD8, B220, IL7ra), while ST-HSCs are CD34+, SCA-1+, C-kit+, CD135-, Slamf1 / CD150+, and lin- (negative for mature lineage markers, including Ter119, CD11b, Gr1, CD3, CD4, CD8, B220, IL7ra). In addition, under steady-state conditions, ST-HSCs have lower quiescence but higher proliferative capacity than LT-HSCs. However, LT-HSCs have a stronger self-renewal potential (i.e., they can survive throughout adulthood and can be serially transplanted through successive recipients), while ST-HSCs have a limited self-renewal potential (i.e., they can only survive for a limited period of time and do not have the potential for serial transplantation). Any of these HSCs can be used in the methods described herein. ST-HSCs are particularly useful because they are highly proliferative and can thus produce differentiated progeny more quickly.

[1208] As used herein, the term "hematopoietic stem cell functional potential" refers to the functional characteristics of hematopoietic stem cells, which include: 1) pluripotency (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, red blood cells), thrombocytes (e.g., megakaryocytes, 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 produce daughter cells with the same potential as the mother cell, and this ability can further occur repeatedly throughout the life of an individual without exhaustion), and 3) the ability to reintroduce hematopoietic stem cells or their progeny into a transplant recipient, whereupon they home to the hematopoietic stem cell niche (e.g., the bone marrow niche) and re-establish productive and sustained hematopoiesis.”

[1209] "Increase" means a positive change 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.

[1210] The term "inhibitor of base repair", "base repair inhibitor", "IBR", or grammatical equivalents thereof refers to a protein capable of inhibiting the activity of a nucleic acid repair enzyme, such as a base excision repair enzyme.

[1211] "Intein" is a segment of a protein that is capable of excising itself during a process called protein splicing and joining the remaining segments (exteins) with a peptide bond.

[1212] The terms "isolated", "purified", or "biologically pure" refer to a substance that is, to varying degrees, free from the components that are normally associated with it in its natural state. An "isolate" represents the degree of separation from the original source or the surrounding environment. "Purification" represents a higher degree of separation than isolation. A "purified" or "biologically pure" protein is sufficiently free of other substances so that any contaminants do not substantially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide of the present disclosure is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or is substantially free of chemical precursors or other chemicals when chemically synthesized. Purity and homogeneity are generally determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. The term "purified" can mean that a nucleic acid or protein gives rise to substantially a single band in an electrophoretic gel. For proteins that can be modified (e.g., phosphorylated or glycosylated), different modifications may result in different isolated proteins, which can be purified separately.

[1213] "Isolated polynucleotide" means a nucleic acid molecule that does not contain the genes that flank the gene in the naturally occurring genome of the organism from which the nucleic acid molecule of the present disclosure is derived. Thus, the term includes, for example, recombinant DNA incorporated into a vector; incorporated into an autonomously replicating plasmid or virus; or incorporated into the genomic DNA of a prokaryote or eukaryote; or existing as a separate molecule independent of other sequences (e.g., a cDNA or genomic or cDNA fragment produced by PCR or restriction endonuclease digestion). In addition, the term includes RNA molecules transcribed from a DNA molecule, and recombinant DNA that is part of a hybrid gene encoding an additional polypeptide sequence.

[1214] "Isolated polypeptide" means that the polypeptide of the present disclosure has been separated from the components that naturally accompany it. Generally, a polypeptide is isolated when it is at least 60% by weight free of the proteins and naturally occurring organic molecules with which it is naturally associated. In some embodiments, the preparation is at least 75%, 90%, or 99% by weight of the polypeptide of the present disclosure. The isolated polypeptides of the present disclosure can be obtained, for example, by extraction from natural sources, by expression of recombinant nucleic acids encoding such polypeptides; or by chemical synthesis of the protein. Purity can be measured by any suitable method, such as column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.

[1215] "Cluster of Differentiation 117 (CD117; C-kit; SCFR) polypeptide" means a polypeptide or a fragment thereof that binds to an anti-CD117 antibody and has at least about 85% amino acid sequence identity to the amino acid sequence provided by Genbank accession number NP_000213 provided below. CD117 (KIT) is a type III receptor tyrosine kinase that is involved in cell signal transduction in a variety of cell types. Under normal circumstances, KIT is activated (phosphorylated) by binding to its ligand, stem cell factor (SCF). This leads to a phosphorylation cascade that ultimately activates various transcription factors in different cell types. This activation regulates apoptosis, cell differentiation, proliferation, chemotaxis, and cell adhesion. In some embodiments, the CD117 polypeptide or a fragment thereof has SCF signaling activity.

[1216] >NP_000213.1 mast cell / stem cell growth factor receptor Kit isoform 1 precursor [Homo sapiens]

[1217] MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDRSLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTCTIKDVSSSVYSTWKRENSQTKLQEKYNSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV(SEQ ID NO:499)

[1218] >CD117 variant having S261G alteration and N260D alteration (shown in bold and underlined)

[1219]

[1220]

[1221] >CD117 variant having S261G alteration (shown in bold and underlined)

[1222]

[1223]

[1224] >CD117 variant having Y259C and N260D alterations (shown in bold and underlined)

[1225]

[1226]

[1227] >CD117 variant having N260D alteration (shown in bold and underlined)

[1228]

[1229]

[1230] >CD117 variant having S251G alteration (shown in bold and underlined)

[1231]

[1232] "Cluster of Differentiation 117 (CD117; C-kit; SCFR) polynucleotide" means a nucleic acid molecule or fragment thereof encoding a CD117 polypeptide and introns, exons, 3' untranslated region, 5' untranslated region, and regulatory sequences associated with its expression. In embodiments, the CD117 polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for CD117 expression. Exemplary CD117 polynucleotide sequences from Homo sapiens are provided below (NCBI Reference Sequence accession number NM_000222.2), and an exemplary CD117 gene sequence is provided in ENSEMBL accession number ENSG00000157404.

[1233]

[1234] As used herein, the term "linker" refers to a molecule that connects two moieties. In one embodiment, the term "linker" refers to a covalent linker (e.g., a covalent bond) or a non-covalent linker.

[1235] "Makassar" or "Hb G-Makassar" refers to a human β-globin variant, i.e., a human hemoglobin (Hb) of the G-Makassar variant or mutation (HB Makassar variant), which is an asymptomatic, naturally occurring variant (E6A) hemoglobin. Hb G-Makassar was first identified in Indonesia. (Mohamad, A.S. et al., 2018, Hematol. Rep., 10(3):7210 (doi:10.4081 / hr.2018.7210)). When subjected to electrophoresis, Hb G-Makassar migrates more slowly. The Makassar β-globin variant has an anatomical anomaly at the β-6 or A3 position, where the glutamyl residue is usually replaced by an alanyl residue. Substitution of the single amino acid β-6 glutamyl group in the gene encoding the β-globin subunit with valine will result in sickle cell disease. Conventional procedures, such as isoelectric focusing, hemoglobin electrophoretic separation by cation-exchange high-performance liquid chromatography (HPLC), and cellulose acetate electrophoresis, are unable to separate Hb G-Makassar and HbS globin forms because they have been found to have the same properties when analyzed by these methods. Therefore, Hb G-Makassar and HbS cannot be correctly discriminated and are confused with each other by those skilled in the art, thus leading to misdiagnosis of sickle cell disease (SCD). In one embodiment, the valine at amino acid position 6 that causes sickle cell disease is replaced with alanine, thereby generating an Hb variant (Hb Makassar) that does not generate a sickle cell phenotype. In some embodiments, substitutions (i.e., HbMakassar variants) can be generated using an A·T to G·C base editor (ABE).

[1236] Accordingly, the present disclosure includes compositions and methods for base editing the thymidine (T) base in the codon of the sixth amino acid (sickle Hb S; E6V) of the β-globin sickle cell variant to cytidine (C), thereby replacing the valine (V6A) at that amino acid position with alanine. Replacing the valine at position 6 of HbS with alanine generates a β-globin variant that does not have a sickle cell phenotype (e.g., does not have the potential to polymerize like the pathogenic variant HbS). Thus, the compositions and methods of the present disclosure are useful for treating sickle cell disease (SCD).

[1237] "Marker" means any protein or polynucleotide having an altered expression, level, structure, or activity that is associated with a disease or disorder. In some cases, the disease or disorder is sickle cell disease. Non-limiting examples of markers include the Makassar variant of β-globin, β-globin, fetal hemoglobin, CD117, and the CD117 variants provided herein.

[1238] As used herein, the term "mutation" refers to the substitution of a residue within a sequence (e.g., a nucleic acid or amino acid sequence) with another residue, or the deletion or insertion of one or more residues within the sequence. Mutations are typically described herein by identifying the original residue, then the position of the residue within the sequence, and then the identity of the newly substituted residue. The various methods for making amino acid substitutions (mutations) provided herein are well known in the art and are provided, for example, by Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)).

[1239] As used herein, the terms "nucleic acid" and "nucleic acid molecule" refer to compounds that contain nucleobases and acidic moieties, such as nucleosides, nucleotides, or polymers of nucleotides. Generally, polymeric nucleic acids (e.g., nucleic acid molecules that contain three or more nucleotides) are linear molecules in which adjacent nucleotides are linked to each other via phosphodiester bonds. In some embodiments, "nucleic acid" refers to a single nucleic acid residue (e.g., nucleotide and / or nucleoside). In some embodiments, "nucleic acid" refers to an oligonucleotide chain that contains three or more single nucleotide residues. As used herein, the terms "oligonucleotide" and "polynucleotide" are used interchangeably and refer to polymers of nucleotides (e.g., a string of at least three nucleotides). In some embodiments, "nucleic acid" encompasses RNA as well as single-stranded and / or double-stranded DNA. Nucleic acids can be naturally occurring, e.g., in the case of genomic, transcript, mRNA, tRNA, rRNA, siRNA, snRNA, plasmid, cosmid, chromosome, chromatid, or other naturally occurring nucleic acid molecules. On the other hand, nucleic acid molecules can be non-naturally occurring molecules, such as recombinant DNA or RNA, artificial chromosomes, engineered genomes or fragments thereof, or synthetic DNA, RNA, DNA / RNA hybrids, or those that include non-naturally occurring nucleotides or nucleosides. In addition, the terms "nucleic acid", "DNA", "RNA", and / or similar terms include nucleic acid analogs, such as analogs that have components other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems, and optionally are purified, chemically synthesized, etc. Where appropriate, e.g., in the case of chemically synthesized molecules, nucleic acids contain nucleoside analogs, such as analogs that have chemically modified bases or sugars and backbone modifications. Unless otherwise indicated, nucleic acid sequences are presented in the 5′ to 3′ direction. In some embodiments, the nucleic acid is or contains natural nucleosides (e.g., adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolopyrimidine, 3-methyladenosine, 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′-N-phosphoramidite linkages).

[1240] The term "nuclear localization sequence", "nuclear localization signal", or "NLS" refers to an amino acid sequence that facilitates the import of a protein into the nucleus. Nuclear localization sequences are known in the art and are described, for example, in International PCT application PCT / EP2000 / 011690, filed Nov. 23, 2000, and published as WO / 2001 / 038547 on May 31, 2001, the contents of which are incorporated herein by reference as they disclose exemplary nuclear localization sequences. In other embodiments, the NLS is an optimized NLS, such as described by Koblan et al., Nature Biotech. 2018 doi:10.1038 / nbt.4172. In some embodiments, the NLS comprises the amino acid sequence 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), RKSGKIAAIVVKRPRKPKKKRKV (SEQ ID NO:329), or MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO:196).

[1241] The terms "nucleobase", "nitrogenous base", or "base", which are used interchangeably herein, refer to nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides. The ability of nucleobases to form base pairs and stack on top of each other directly results in long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases, namely adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U), are referred to as 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 modified (non-basic) bases. Non-limiting examples of modified nucleobases can include hypoxanthine, xanthine, 7-methylguanine, 5,6-dihydrouracil, 5-methylcytosine (m5C), and 5-hydroxymethylcytosine. Hypoxanthine and xanthine can be produced in the presence of mutagens, and they are both produced by deamination (replacing the amine group with a carbonyl group). Hypoxanthine can be modified from adenine. Xanthine can be modified from guanine. Uracil can be produced by the deamination of cytosine. A "nucleoside" consists of a nucleobase and a five-carbon sugar (ribose or deoxyribose). Examples of nucleosides include adenosine, guanosine, uridine, cytidine, 5-methyluridine (m5U), deoxyadenosine, deoxyguanosine, thymidine, deoxyuridine, and deoxycytidine. Examples of nucleosides with modified nucleobases include inosine (I), xanthosine (X), 7-methylguanosine (m7G), dihydrouridine (D), 5-methylcytidine (m5C), and pseudouridine (Ψ). A "nucleotide" consists of a nucleobase, a five-carbon sugar (ribose or deoxyribose), and at least one phosphate group. Non-limiting examples of chemical modifications that modified nucleobases and / or modified nucleobases can include are as follows: pseudouridine, 5-methyl-cytosine, 2′-O-methyl-3′-phosphonoacetate, 2′-O-methylthioPACE (MSP), 2′-O-methyl-PACE (MP), 2′-fluoro RNA (2′-F-RNA), restricted ethyl (S-cEt), 2′-O-methyl (‘M’), 2′-O-methyl-3′-thiophosphate (‘MS’), 2′-O-methyl-3′-thiophosphonoacetate (‘MSP’), 5-methoxyuridine, thiophosphate, and N1-methylpseudouridine.

[1242] The term "nucleic acid programmable DNA binding protein" or "napDNAbp" can be used interchangeably with "polynucleotide programmable nucleotide binding domain" and refers to a protein that associates with a nucleic acid (e.g., DNA or RNA), such as a guide nucleic acid or guide polynucleotide (e.g., gRNA) that directs 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. The Cas9 protein can associate with a guide RNA that directs the Cas9 protein to a specific DNA sequence that is complementary to the guide RNA. In some embodiments, the napDNAbp is a Cas9 domain, such as nuclease-active Cas9, Cas9 nickase (nCas9), or nuclease-inactive Cas9 (dCas9). Non-limiting examples of nucleic acid programmable DNA binding proteins include Cas9 (e.g., dCas9 and nCas9), Cas12a / Cpfl, Cas12b / C2cl, Cas12c / C2c3, Cas12d / CasY, Cas12e / CasX, Cas12g, Cas12h, Cas12i, and Cas12j / CasΦ (Cas12j / Casphi).Non-limiting examples of Cas enzymes include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas5d, Cas5t, Cas5h, Cas5a, Cas6, Cas7, Cas8, Cas8a, Cas8b, Cas8c, Cas9 (also known as Csn1 or Csx12), Cas10, Cas10d, Cas12a / Cpfl, Cas12b / C2cl, Cas12c / C2c3, Cas12d / CasY, Cas12e / CasX, Cas12g, Cas12h, Cas12i, Cas12j / CasΦ, Cpf1, Csy1, Csy2, Csy3, Csy4, Cse1, Cse2, Cse3, Cse4, Cse5e, Csc1, Csc2, Csa5, Csn1, Csn2, Csm1, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx1S, Csx11, Csf1, Csf2, CsO, Csf4, Csd1, Csd2, Cst1, Cst2, Csh1, Csh2, Csa1, Csa2, Csa3, Csa4, Csa5, type II Cas effector proteins, type V Cas effector proteins, type VI Cas effector proteins, CARF, DinG, homologs thereof, or modified or engineered forms thereof. Other nucleic acid programmable DNA-binding proteins are also within the scope of the present disclosure, although they may not be specifically listed in the present disclosure. See, for example, Makarova et al., "Classification and Nomenclature of CRISPR-Cas Systems: Wherefrom Here?" CRISPR J. October 2018; 1:325-336. doi:10.1089 / crispr.2018.0033; Yan et al., "Functionally diverse type V CRISPR-Cas systems" Science. January 4, 2019; 363(6422):88-91. doi:10.1126 / science.aav7271, the entire contents of each of which 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 NO: 197-230 and 378.

[1243] As used herein, the term "nucleobase editing domain" or "nucleobase editing protein" refers to a protein or enzyme that can catalyze nucleobase modifications in RNA or DNA, such as deamination of cytosine (or cytidine) to uracil (or uridine) or thymine (or thymidine) and adenine (or adenosine) to inosine, as well as non-templated nucleotide addition and insertion. In some embodiments, the nucleobase editing domain is a deaminase domain (e.g., an adenine deaminase or adenosine deaminase).

[1244] As used herein, "obtaining an agent" includes synthesizing, purchasing, or otherwise acquiring the agent.

[1245] "Stem cell factor (SCF) polypeptide" means a polypeptide or fragment thereof having at least about 85% amino acid sequence identity to the amino acid sequence provided by NCBI Reference Sequence Accession No. NP_000890, which functions in hematopoiesis. In some embodiments, the SCF polypeptide or fragment thereof binds to CD117.

[1246] >NP_000890.1 kit ligand isoform b precursor [Homo sapiens]

[1247] MKKTQTWILTCIYLQLLLFNPLVKTEGICRNRVTNNVKDVTKLVANLPKDYMITLKYVPGMDVLPSHCWISEMVVQLSDSLTDLLDKFSNISEGLSNYSIIDKLVNIVDDLVECVKENSSKDLKKSFKSPEPRLFTPEEFFRIFNRSIDAFKDFVVASETSDCVVSSTLSPEKDSRVSVTKPFMLPPVAASSLRNDSSSSNRKAKNPPGDSSLHWAAMALPALFSLIIGFAFGALYWKKRQPSLTRAVENIQINEEDNEISMLQEKEREFQEV (SEQ ID NO:501).

[1248] "Stem cell factor (SCF) polynucleotide" means a nucleic acid molecule or fragment thereof that encodes an SCF polypeptide, as well as introns, exons, 3' untranslated regions, 5' untranslated regions, and regulatory sequences associated with its expression. In an embodiment, the SCF polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for SCF expression. An exemplary SCF polynucleotide sequence from Homo sapiens is provided below (NCBI Reference Sequence Accession No. NM_003994.5).

[1249] >NM_003994.5 Homo sapiens KIT ligand (KITLG), transcript variant a, mRNA

[1250]

[1251] "Subject" or "patient" means a mammal. Non-limiting examples of mammals include primates (e.g., human or cynomolgus monkey) or non-human mammals. In an embodiment, the mammal is a bovine, equine, canine, ovine, rabbit, rodent, non-human primate or feline. In one embodiment, a "patient" is a mammalian subject having a higher than average likelihood of developing a disease or disorder. Exemplary patients can be human, non-human primates (e.g., cynomolgus monkey), cats, dogs, pigs, cows, cats, horses, camels, llamas, goats, sheep, rodents (e.g., mice, rabbits, rats or guinea pigs) and other mammals that can benefit from the therapies disclosed herein. Exemplary human patients can be male and / or female.

[1252] "Patient in need" or "subject in need" as used herein refers to a patient diagnosed with a disease or disorder, at risk of developing a disease or disorder, or having, pre-determined to have, or suspected of having a disease or disorder.

[1253] The terms "pathogenic mutation", "pathogenic variant", "disease causing mutation", "disease causing variant", "deleterious mutation" or "predisposing mutation" refer to a genetic alteration or mutation that is associated with a disease or disorder or increases an individual's susceptibility or predisposition to a particular disease or disorder. In some embodiments, a pathogenic mutation comprises the substitution of at least one wild-type amino acid in a protein encoded by a gene with at least one pathogenic amino acid. In some embodiments, the pathogenic mutation is in a termination region (e.g., a stop codon). In some embodiments, the pathogenic mutation is in a non-coding region (e.g., an intron, a promoter, etc.).

[1254] The terms "protein", "peptide", "polypeptide" and their grammatical equivalents are used interchangeably herein and refer to a polymer of amino acid residues joined together by peptide (amide) bonds. A protein, peptide or polypeptide can be naturally occurring, recombinant or synthetic, or any combination thereof.

[1255] As used herein, the term "fusion protein" refers to a hybrid polypeptide comprising protein domains from at least two different proteins.

[1256] As used herein, the term "human antibody" refers to an antibody in which substantially every part of the protein (e.g., CDRs, frameworks, C L region, C H domain (e.g., C H1 region, C H2 region, C H3 domain), hinge, (V L region, V H region)) is substantially non-immunogenic in humans and has only minor sequence changes or variations. Human antibodies can be produced in human cells (e.g., by recombinant expression), or by non-human animals or prokaryotic or eukaryotic cells (e.g., yeast) capable of expressing functional rearranged human immunoglobulin (e.g., heavy and / or light chain) genes. In addition, when a human antibody is a single-chain antibody, it may include a linker peptide not found in native human antibodies. For example, an Fv may contain a linker peptide, such as two to about eight glycine or other amino acid residues, that joins the heavy chain variable region and the light chain variable region. Such linker peptides are considered to be of human origin. Human antibodies can be prepared by a variety of methods known in the art, including phage display methods using antibody libraries derived from human immunoglobulin sequences. See U.S. Patent 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, which are incorporated herein by reference. Human antibodies can also be produced using transgenic mice that cannot express functional endogenous immunoglobulins but can express human immunoglobulin genes. See, e.g., PCT Publications WO 98 / 24893; WO 92 / 01047; WO 96 / 34096; WO 96 / 33735; U.S. Patent Nos. 5,413,923; 5,625,126; 5,633,425; 5,569,825; 5,661,016; 5,545,806; 5,814,318; 5,885,793; 5,916,771; and 5,939,598, which are incorporated herein by reference.

[1257] As used herein, the term "humanized" antibody refers to a form of a non-human (e.g., murine) antibody that is a chimeric immunoglobulin, immunoglobulin chain, or fragment thereof (such as an Fv, Fab, Fab', F(ab')2, or other target-binding subdomain of an antibody) that contains a minimal sequence derived from a non-human immunoglobulin. Generally, a humanized antibody will contain substantially all of at least one and usually two variable regions, wherein all or substantially all of the CDR regions correspond to those of the non-human immunoglobulin. All or substantially all of the FR regions may also be those of human immunoglobulin sequences. A humanized antibody optionally may also contain at least a portion of an immunoglobulin constant region (Fc), usually at least a portion of the immunoglobulin constant region (Fc) of a human immunoglobulin consensus sequence. Methods for humanizing antibodies are known in the art. See, e.g., Riechmann et al., Nature 332:323-7, 1988; U.S. Patent Nos. 5,530,101; 5,585,089; 5,693,761; 5,693,762; and U.S. Patent No. 6,180,370 to Queen et al.; EP239400; PCT Publication WO 91 / 09967; U.S. Patent No. 5,225,539; EP592106; and EP519596; which are incorporated herein by reference.

[1258] As used herein in the context of a protein or nucleic acid, the term "recombinant" refers to a protein or nucleic acid that does not exist in nature but is the product of human engineering. For example, in some embodiments, a recombinant protein or nucleic acid molecule contains an amino acid or nucleotide sequence that contains at least one, at least two, at least three, at least four, at least five, at least six, or at least seven mutations compared to any naturally occurring sequence.

[1259] "Reduce" means a negative change of at least 10%, 25%, 50%, 75%, or 100%.

[1260] "Reference" means a standard or control condition. In one embodiment, the reference is a wild-type or healthy cell. In other embodiments and without limitation, the reference is an untreated cell that has not been treated under the test conditions, or has been treated with a placebo or saline, medium, buffer, and / or a control vector that does not contain a polynucleotide of interest. In some cases, the "reference" is an untreated subject, such as a subject who has not been administered hematopoietic stem cells edited according to the methods of the present disclosure. In some cases, the subject is a healthy subject (e.g., a subject who does not have sickle cell disease). In some embodiments, the reference is an unedited or wild-type cell, polypeptide, or polynucleotide.

[1261] "Reference sequence" is a defined sequence used as a basis for sequence comparison. The reference sequence can be a subset or the entirety of a specified sequence; for example, a segment of a full-length cDNA or gene sequence or a full-length cDNA or gene sequence. For polypeptides, the length of the reference polypeptide sequence will typically 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 typically 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 near or between them. In some embodiments, the reference sequence is the wild-type sequence of a protein of interest. In other embodiments, the reference sequence is a polynucleotide sequence encoding a wild-type protein.

[1262] The terms "RNA-programmable nuclease" and "RNA-guided nuclease" refer to a nuclease that forms a complex (e.g., binds or associates) with one or more RNAs that are not the target to be cleaved. In some embodiments, when forming a complex with an RNA, the RNA-programmable nuclease can be referred to as a nuclease:RNA complex. Generally, the bound RNA is referred to as guide RNA (gRNA). In some embodiments, the RNA-programmable nuclease is a (CRISPR-associated system) Cas9 endonuclease, such as Cas9 (Csn1) from Streptococcus pyogenes (e.g., SEQ ID NO: 197), Cas9 from Neisseria meningitidis (NmeCas9; SEQ ID NO: 208), Nme2Cas9 (SEQ ID NO: 209), or derivatives thereof (e.g., sequences having at least about 85% sequence identity to Cas9 such as Nme2Cas9 or spCas9).

[1263] As used herein, the term "scFv" refers to a single-chain Fv antibody in which the variable regions of the heavy and light chains of the antibody have been joined to form a single chain. The scFv fragment contains a single polypeptide chain that comprises the variable region of the antibody light chain (VL) (e.g., CDR-L1, CDR-L2, and / or CDR-L3) and the variable region of the antibody heavy chain (VH) (e.g., CDR-H1, CDR-H2, and / or CDR-H3) separated by a linker. The linker that joins the VL and VH regions of the scFv fragment can be a peptide linker composed of protein amino acids. Alternative linkers can be used to increase the resistance of the scFv fragment to proteolytic degradation (e.g., linkers containing D-amino acids) in order to enhance the solubility of the scFv fragment (e.g., hydrophilic linkers such as linkers containing polyethylene glycol or polypeptides containing repeating glycine and serine residues), to increase the biophysical stability of the molecule (e.g., linkers containing cysteine residues that form intra- or intermolecular disulfide bonds), or to reduce the immunogenicity of the scFv fragment (e.g., linkers containing glycosylation sites). One of ordinary skill in the art will also understand that the variable regions of the scFv molecules described herein can be modified such that their amino acid sequences are different from those of the antibody molecules from which they are derived. For example, nucleotide or amino acid substitutions can be made that result in conservative substitutions or changes at amino acid residues (e.g., in CDRs and / or framework residues) in order to retain or enhance the ability of the scFv to bind to the antigen recognized by the corresponding antibody.

[1264] Amino acids can generally be grouped as follows according to the following common side-chain characteristics:

[1265] (1) Hydrophobic: norleucine, Met, Ala, Val, Leu, Ile;

[1266] (2) Neutral hydrophilic: Cys, Ser, Thr, Asn, Gln;

[1267] (3) Acidic: Asp, Glu;

[1268] (4) Basic: His, Lys, Arg;

[1269] (5) Residues affecting chain orientation: Gly, Pro;

[1270] (6) Aromatic: Trp, Tyr, Phe.

[1271] In some embodiments, conservative substitutions can involve exchanging a member of one of these categories for another member of the same category. In some embodiments, non-conservative amino acid substitutions can involve exchanging a member of one of these categories for a member of another category.

[1272] "Selectively binds" means specifically binds to the wild-type form of a cell surface protein, but exhibits reduced binding to a cell surface protein comprising a mutation or fails to detectably bind to a cell surface protein comprising a mutation. In an embodiment, an antibody of the present disclosure selectively binds to a wild-type CD117 polypeptide, but relative to the wild-type CD117 polypeptide, the antibody exhibits reduced binding to a CD117 polypeptide comprising one or more amino acid alterations (such as those provided herein). In an embodiment, the antibody of the present disclosure binds to the wild-type CD117 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 stronger than to the altered CD117 polypeptide of the present disclosure (e.g., as quantified using KD(M), where a lower KD(M) indicates stronger binding).

[1273] "Specifically binds" means a nucleic acid molecule, polypeptide, polypeptide / nucleotide complex, compound, or molecule recognizes and binds to a polypeptide and / or nucleic acid molecule of the present disclosure, but does not substantially recognize and bind to other molecules in a sample (e.g., a biological sample).

[1274] "Substantially identical" means a polypeptide or nucleic acid molecule exhibits at least 50% identity to a reference amino acid sequence. In one embodiment, the reference sequence is a wild-type amino acid or nucleic acid sequence. In another embodiment, the reference sequence is any of the amino acid or nucleic acid sequences described herein. In one embodiment, such a sequence has at least about 60%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or even 99.99% identity at the amino acid level or nucleic acid level to the sequence being compared.

[1275] Nucleic acid molecules that can be used in the methods of the present disclosure include any nucleic acid molecule encoding a polypeptide of the present disclosure or a functional fragment thereof. Such nucleic acid molecules need not have 100% identity with an endogenous nucleic acid sequence, but will generally exhibit substantial identity. A polynucleotide having "substantial identity" with an endogenous sequence is generally capable of hybridizing to at least one strand of a double-stranded nucleic acid molecule. Nucleic acid molecules that can be used in the methods of the present disclosure include any nucleic acid molecule encoding a polypeptide of the present disclosure or a functional fragment thereof. Such nucleic acid molecules need not have 100% identity with an endogenous nucleic acid sequence, but will generally exhibit substantial identity. A polynucleotide having "substantial identity" with an endogenous sequence is generally capable of hybridizing to at least one strand of a double-stranded nucleic acid molecule. "Hybridization" means the pairing between complementary polynucleotide sequences (e.g., the genes described herein) or portions thereof to form a double-stranded molecule under various stringent conditions. (See, e.g., Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A.R. (1987) Methods Enzymol. 152:507).

[1276] "Cleavage" means to divide into two or more segments.

[1277] A "split polypeptide" or "split protein" refers to a protein provided as an N-terminal fragment and a C-terminal fragment translated from a nucleotide sequence into two separate polypeptides. In some embodiments, the polypeptides corresponding to the N-terminal and C-terminal portions of the split protein can be spliced to form a "reconstituted" protein. In an embodiment, the split polypeptide is a nucleic acid programmable DNA binding protein (e.g., Cas9) or a base editor.

[1278] The term "target site" refers to the sequence within a nucleic acid molecule that is modified. In an embodiment, the modification is deamination of a base. The deaminase can be an adenine deaminase. A fusion protein or base editing complex comprising a deaminase can comprise a dCas9-adenosine deaminase fusion protein, a Cas12b-adenosine deaminase fusion, or a base editor disclosed herein.

[1279] As used herein, the term "treat / treating / treatment, etc." refers to reducing or ameliorating a disorder and / or its associated symptoms or obtaining a desired pharmacological and / or physiological effect. It will be understood that treating a disorder or condition does not require complete elimination of the disorder, condition or its associated symptoms, although this is not excluded. In some embodiments, the effect is therapeutic, i.e., (but not limited to) the effect partially or completely reduces, attenuates, eliminates, alleviates, mitigates, decreases the intensity of the disease and / or the adverse symptoms attributable to the disease or cures the disease and / or the adverse symptoms attributable to the disease. In some embodiments, the effect is prophylactic, i.e., the effect protects or prevents the occurrence or recurrence of a disease or disorder. To this end, the methods disclosed herein include administering a therapeutically effective amount of a composition as described herein.

[1280] "Uracil glycosylase inhibitor" or "UGI" means an agent that inhibits the uracil excision repair system. Base editors containing cytidine deaminase convert cytosine to uracil, which is then converted to thymine by DNA replication or repair. In various embodiments, uracil DNA glycosylase (UGI) prevents base excision repair that would convert U back to C. In some cases, contacting a cell and / or polynucleotide with UGI and a base editor prevents base excision repair that would convert U back to C. Exemplary UGIs include the following amino acid sequences:

[1281] >splP14739IUNGI_BPPB2 Uracil-DNA glycosylase inhibitor

[1282] MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML (SEQ ID NO:231).

[1283] In some embodiments, the agent that inhibits the uracil excision repair system is uracil stabilizing protein (USP). See, e.g., WO 2022015969 A1, which is incorporated herein by reference.

[1284] The ranges provided herein are to be understood as shorthand expressions for all values within the range. For example, a range of 1 to 50 is to be understood as including any number, combination of numbers, or sub-range from the group consisting of: 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.

[1285] The terms “transfecting” or “transfection” are used interchangeably and, in some aspects and embodiments herein, mean introducing heterologous nucleic acid (DNA / RNA) into a eukaryotic cell, particularly a yeast cell.

[1286] In some aspects and embodiments herein, an antibody fragment is understood to mean a functional portion of an antibody, such as Fc, Fab, Fab', Fv, F(ab')2, scFv. In some aspects and embodiments herein, a corresponding bioactive fragment is understood to mean those portions of an antibody that are capable of binding to an antigen, such as Fab, Fab', Fv, F(ab')2, and scFv.

[1287] As used herein, the term "vector" means a means of introducing a nucleic acid sequence into a cell, thereby producing a transformed cell. Vectors include plasmids, transposons, bacteriophages, viruses, liposomes, lipid nanoparticles, and episomes. An "expression vector" is a nucleic acid sequence that contains a nucleotide sequence to be expressed in a recipient cell. An expression vector contains a polynucleotide sequence and additional nucleic acid sequences to facilitate and / or enable the expression of the introduced sequence, such as initiation, termination, enhancer, promoter, and secretion sequences, in the mammalian cell genome. Examples of vectors include nucleic acid vectors, such as DNA vectors, such as plasmids, RNA vectors, viruses, or other suitable replicons (e.g., viral vectors). A variety of vectors have been developed for delivering polynucleotides encoding foreign proteins into prokaryotic or eukaryotic cells. Examples of such expression vectors are disclosed, for example, in WO1994 / 11026; which is incorporated herein by reference. Certain vectors useful for expressing antibodies, antibody fragments, base editors, guide polynucleotides, and / or base editor systems of some aspects and embodiments herein include plasmids containing regulatory sequences that direct gene transcription, such as promoter and enhancer regions. Other useful vectors for expressing antibodies and antibody fragments contain polynucleotide sequences that enhance the translation rate of these genes or improve the stability or nuclear export of the mRNA produced by gene transcription. These sequence elements include, for example, 5' and 3' untranslated regions, internal ribosome entry sites (IRES), and polyadenylation signal sites to direct the efficient transcription of genes carried on an expression vector. Expression vectors of some aspects and embodiments herein may also contain a polynucleotide encoding a marker for selecting cells containing such a vector. Examples of suitable markers include genes encoding antibiotic resistance, such as ampicillin, chloramphenicol, kanamycin, or nourseothricin.

[1288] As used herein, the term "VH" refers to the variable region of the immunoglobulin heavy chain of an antibody, including the heavy chain of an Fv, scFv, or Fab. Reference to "VL" refers to the variable region of the immunoglobulin light chain, including the light chain of an Fv, scFv, dsFv, or Fab. Antibodies (Ab) and immunoglobulins (Ig) are glycoproteins with the same structural characteristics. While antibodies exhibit binding specificity for a particular target, immunoglobulins include antibodies lacking target specificity and other antibody-like molecules. Native antibodies and immunoglobulins are typically about 150,000 Dalton heterotetrameric glycoproteins composed of two identical light (L) chains and two identical heavy (H) chains. Each heavy chain of a native antibody has a variable domain (VH) at the amino terminus, followed by a plurality of constant domains. Each light chain of a native antibody has a variable domain (VL) at the amino terminus and a constant domain at the carboxyl terminus.

[1289] In any definition of a variable herein, a reference to a list of chemical groups includes the definition of the variable as any single group or combination of the listed groups. A reference to an embodiment of a variable or aspect herein includes the embodiment as any single embodiment or in combination with any other embodiment or portion thereof.

[1290] All terms are intended to be understood as would be understood by one of ordinary skill in the art. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains.

[1291] 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, unless otherwise indicated, the use of “or” means “and / or.” Additionally, the use of the term “including” and other forms such as “include,” “includes,” and “included” is not limiting.

[1292] As used in this specification and the claims, 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. The phrasing indicates the presence of the specified elements, features, components, and / or method steps, but does not preclude the presence of other elements, features, components, and / or method steps. In some embodiments, any embodiment designated as “comprising” a particular component or element is also contemplated to be “consisting of” or “consisting essentially of” the particular component or element. 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. Additionally, the compositions of the present disclosure can be used to implement the methods of the present disclosure.

[1293] The terms "about" or "approximately" mean that a particular value as determined by a person of ordinary skill in the art is within an acceptable error range, which will depend in part on how the value is measured or determined, i.e., the limitations of the measuring system.

[1294] References in the specification to "some embodiments", "embodiments", "one embodiment" or "other embodiments" mean that a particular feature, structure, or characteristic described in connection with the embodiments is included in at least some embodiments, but not necessarily in all embodiments. BRIEF DESCRIPTION OF THE DRAWINGS

[1295] Figure 1A and Figure 1B Schematic diagrams are provided showing the engineered stem cell antibody pairing escape method (ESCAPE). Figure 1A Schematic diagrams are provided showing opsonization with mAb. The bone marrow microenvironment may be depleted with mAbs that interfere with essential proteins expressed on the surface of stem cells. After myeloablation, hematopoietic stem cells (HSCs) containing mutations in the mAb target protein are available for engraftment, and the mutations render the cells resistant to mAb ablation. In some cases, the method involves more than one administration of the antibody (i.e., readministration). Figure 1B Schematic diagrams are provided showing the selective enrichment of engineered hematopoietic stem cells (eHSCs) containing mutations in essential cell surface proteins (e.g., CD117). HSCs can be engineered by base editing to contain nonsynonymous mutations that do not inhibit normal cell function and are resistant to mAb ablation. Due to sensitivity to mAb binding and interference, unedited cells or endogenous cells remaining in the microenvironment can be selectively eliminated.

[1296] Figures 2A - 2D Schematic diagrams are provided showing Engineered stem cells cell Antibody ligand Escape pair for non-genotoxic cell conditioning Figure 2ASchematic diagrams are provided showing how base editing can be used to generate cells with increased fetal hemoglobin production (HbF) and an altered CD117 (c-KIT) polypeptide, the binding of which to an antibody (e.g., a non-genotoxic stem cell factor-(SCF-) blocking antibody) is reduced. In embodiments, the cell conditioning strategy eliminates the need for busulfan conditioning by replacing the chemotherapeutic agent with a non-genotoxic SCF blocking antibody. The strategy involves modifying the CD117 (c-KIT) antigen by creating a single nucleotide or polynucleotide polymorphism (SNP or nucleotide alteration) via base editing. In embodiments, the SNP in c-KIT (e.g., a non-synonymous mutation) prevents or reduces the binding of an antibody (Ab) (e.g., ABTx052). In embodiments, editing of a sickle cell disease (SCD) target (e.g., an edit associated with upregulation of fetal hemoglobin (HbF) expression, such as an edit to the promoter region) is multiplexed with the modification of the CD117 antigen. In some cases, both edits are performed using a combination of the same adenosine base editor (ABE) with two or more guide RNAs (gRNAs) (e.g., sgRNA_015 and a CD117-targeting gRNA). In various cases, the edited cells are derived from the patient to whom the cells are to be administered. Figure 2B and Figure 2C Schematic diagrams are provided showing how the combination of an SCF blocking antibody specific for the wild-type c-KIT antigen will ablate cells displaying wild-type c-KIT. Thus, ESCAPE enables the selective enrichment of c-KIT-edited cells. Figure 2C Schematic diagrams are provided showing that unedited cells are depleted when an SCF blocking antibody is present. In embodiments, cells containing the modified c-KIT polypeptide are not depleted by the SCF blocking antibody but instead repopulate and engraft. In embodiments, the multiplex-edited cells (i.e., cells having an edit for the treatment of sickle cell disease and an edit to the CD117 antigen) are administered simultaneously with, after, or before the administration of the SCF blocking antibody, wherein the administration of the antibody is associated with the enrichment of the edited cells in the subject. Figure 2D Schematic diagrams are provided showing how alteration of the CD117 epitope encoded by HSCs using base editing allows the HSCs to selectively escape binding to an antibody that binds the CD117 epitope.

[1297] Figure 3Schematic diagrams are provided that summarize the completed screening to identify ABE8.8-compatible guides for introducing alterations to the CD117 antigen (left), antibodies that show reduced binding to the altered antigen (right), and the ESCAPE method suitable for non-genotoxic cell conditioning. Guides identified in the screening include CC128, CC79, and CC89. Antibodies identified in the screening include ABTx052, ABTx062, ABTx025, ABTx030, ABTx070, and ABTx071. As Figure 3 shown on the left, 102 guide RNAs capable of installing missense mutations were computationally identified. Among them, 27 gRNAs were selected based on the highest editing efficiency in HEK293 cells. 8 gRNAs were selected based on high editing efficiency in CD34+ cells. The CD117 mutations generated by these gRNAs were characterized, and 5 gRNAs were selected based on retaining normal ligand binding and phosphorylation ability in vitro. In addition, as Figure 3 shown on the right, 188 mAb clones were identified, 72 of which had unique variable heavy chains (VH). 66 clones were screened from these clones for binding to wild-type and variant CD117 proteins. 6 such antibodies were selected based on binding to wild-type CD117 and lack of binding to variant CD117. One of the primary antibodies blocked the binding of CD117 to its native ligand SCF and did not bind to one of the primary edits.

[1298] Figure 4 Crystallographic images of CD117 are provided, showing the positions of the amino acid residue alterations of the present disclosure. The alterations include T144A (sgRNA CC89); Y249C and N260D (sgRNA CC128); and M351T (sgRNA CC79). The edits Y259C and N260D are located near the stem cell factor (SCF) binding site. In Figure 4 the following altered positions are highlighted from top to bottom in the structural image: sites highlighted from top to bottom: (CC89) T144A; (CC128) Y259C N260D; (CC79) M351T; and (CC78) Y418C. The protospacer corresponding to guide RNA CC128 is provided in the figure and corresponds to SEQ ID NO:830.

[1299] Figures 5A - 5F Charts and histograms are provided showing that ABTx052 lacks binding to CD117 edited with guide CC128 and ABE8.8 (CC128-edited CD117) and blocks the binding of stem cell factor (SCF) to wild-type CD117. Figure 5ACharts are provided showing biolayer interferometry (BLI) measurements demonstrating that ABTx052 (mAB-7) does not bind to CC128-edited CD117 as a purified protein. ABTx052 does bind with high affinity (20 pM) to wtCD117 expressed on M07e cells. ABTx052 dissociates rapidly from CC128-edited CD117. Monoclonal antibody mAb-7 binds with high affinity (KD < 1E-12) to wtCD117 but has minimal binding to CC128-edited CD117. Figure 5B and Figure 5F Charts are provided showing that ABTx052 (mAB-7) blocks the binding of SCF to CD117. Figure 5C Histograms are provided showing that ABTx052 does not bind to CC128-edited CD117 as expressed in M07e cells. Figure 5D Charts are provided showing that ABTx052 has an EC50 of approximately 20 pM. Figure 5A and Figure 5B The vertical lines in indicate the substrate addition times (e.g., ABTx052 or SCF addition). Figure 5ECharts showing flow cytometry data are provided, demonstrating high binding (EC50 0.02 nM) of unedited CD34+ cells to mAb-7 modified to contain the LALADA Fc alteration (i.e., ABTx135), while CD34+ cells edited with CD117 sgRNA show minimal binding to the antibody. ABTx135 shows minimal binding to CD34+ cells expressing the CD117 variant prepared using the guide CC128. 100,000 unedited or CD117-edited human CD34+ hematopoietic stem and progenitor cells were incubated with different concentrations of ABTx135 (which corresponds to ABTx052 containing the LALADA alteration in the Fc domain) for 20 minutes at 4°C in a total staining volume of 100 μL in PBS + 2.5% FBS. After 20 minutes, the cells were pelleted by centrifugation at 500 x g for 5 minutes at 4°C. The supernatant was removed, and the cells were washed 2 times with PBS + 2.5% FBS. After 2 washes, 100 μL of a secondary detection antibody at a concentration of 25 μg / mL was added to the cell pellet. The cells were incubated with the secondary antibody for 20 minutes at 4°C. Then the cells were washed 2 times with PBS + 2.5% FBS at 4°C. Finally, the cells were resuspended in 100 μL of PBS + 2.5% FBS and analyzed using flow cytometry. A chart of the geometric mean fluorescence intensity of the stain (y-axis) versus the log of the ABTx135 concentration (x-axis) was plotted. Cell staining with the secondary antibody alone (dashed line) was used as a negative control. Flow cytometry shows binding of mAb-7 to unedited CD34+ cells and lack of binding to CD117-edited CD34+ cells. Secondary antibody details: Goat anti-human IgG Fc cross-adsorbed secondary antibody, DyLight 650, ThermoFisher, catalog number SA5-10137.

[1300] Figure 6A and Figure 6B SDS-PAGE gel images and size exclusion chromatograms are provided, respectively, showing the purity of the ABTx052 antibody.

[1301] Figure 7A and Figure 7BCharts are provided showing an in vitro assessment of mAb binding at increasing doses between unedited human hematopoietic stem cells (HSCs) and HSCs base-edited to contain a mutation in CD117 to block mAb binding. Human CD34+ cells edited with ABE8.8 and a CD117-targeting guide RNA escaped recognition by the antibodies ABTx062 and ABTx052, which bind to unedited human HSCs expressing wild-type CD117. The mAbs ABTx062 and ABTx052 showed loss of binding to CD34+ hematopoietic stem and progenitor cells (HSPCs; HSCs) edited with the gRNA CC128. The edited cells expressed CD117*Y259C / N260D. The desired nucleotide edit using the CC128 guide was 5G+7G.

[1302] Figures 8A to 8G Charts and bar graphs are provided showing that the CC128-engineered CD117 epitope is protected from ligand blockade by ABTx052 in vitro. Figure 8A and Figure 8B Charts are provided showing that cells edited with the CC128 guide showed improved viability in the presence of ABTx052 relative to unedited cells at 2 days and 5 days post-transfection. In the presence (and absence) of stem cell factor (SCF), the cell viability of primary CD34+-derived edited cells cultured with the CC128 guide alone was retained as the concentration of the ABTx052 Ab increased. Unedited cells exposed to ABTx052 showed a viability similar to that of complete SCF withdrawal (dashed line). Figure 8C Shows that over time, cells containing the target 5G+7G dinucleotide edit combination introduced using the CC128 guide were enriched in a 1:1 mixture of edited and unedited cells in the presence of ABTx052. Next-generation sequencing (NGS) of the 1:1 mixture showed enrichment by demonstrating an increased editing frequency. Figure 8D and 8E Charts are provided showing that contacting cells expressing wild-type CD117 polypeptide ("unedited cells") with ABTx052 mimicked complete SCF withdrawal and resulted in a ~85% loss of viability in vitro, while edited cells showed increased viability relative to unedited cells. Unedited, CD117-edited, and a 1:1 mixture of unedited and CD117-edited CD34+ cells were cultured for 7 days in the presence of different concentrations of mAb-7. mAb-7 treatment depleted unedited cells to the level of complete SCF starvation (dashed line), while CD117-edited cells retained viability. The cell viability level of the mixed population remained at an intermediate value. Figure 8FBar graphs are provided showing the enrichment of base-edited cells containing the engineered CC128 CD117 epitope in co-cultures of edited and unedited cells in contact with mAb-7 at concentrations ranging from 100 ng / mL to 10,000 ng / mL. After 7 days of co-culture in the presence and absence of mAb-7, genomic DNA was isolated from the co-culture and next-generation sequencing (NGS) was performed. NGS showed enrichment of CD117 editing in the treated cells compared to untreated controls. Figure 8G Graphs are provided showing that mAb-7 selectively depletes unedited hematopoietic stem cells while cells expressing engineered CD117 (engineered by base editing using guide CC128) retain viability in vitro. In Figure 8G the dotted horizontal line represents cell viability corresponding to complete SCF starvation, and the control corresponds to cells not treated with mAb-7.

[1303] Figure 9 Schematic diagrams are provided showing in vivo study designs to determine whether CD117-edited cells have similar functions to wild-type CD117 cells. Unedited or CD117-edited CD34+ cells were transplanted into NBSGW mice. Mice were sacrificed 16 weeks after transplantation and bone marrow was harvested for flow cytometry and NGS analysis. The bone marrow hematopoietic compartment was sorted.

[1304] Figure 10A and Figure 10B Bar graphs and flow cytometry plots are provided showing that engraftment of CD117 variants prepared using guides CC79, CC84, CC89, CC90, CC119, and CC128 was not altered by base editing, as measured by flow cytometry 8 weeks after engraftment. Figure 10B Representative flow cytometry plots are provided demonstrating engraftment of edited human CD45+ cells (hCD45+) in mice to which the cells were administered. In Figure 10B the plots, unedited mouse CD45+ cells are denoted by the term "mCD45+".

[1305] Figure 11A and 11B Stacked bar graphs are provided showing that CD117 editing was retained in a large fraction of the bone marrow at the 8-week time point after engraftment. Figure 11A Shows the percentage of editing 48 hours after electroporation (EP) in cells edited using ABE8.8 and guides CC79, CC84, CC89, CC90, CC119, and CC128. Editing was 5G, 6G, 7G, 8G, 5G+7G, 6G+7G, and 6G+8G. Figure 11B Shows editing in bulk bone marrow (BM) measured 8 weeks after engraftment. In Figure 11AIn it, from top to bottom and from left to right of each stacked bar chart, the edits represented in each bar are as follows, where each bar is separated by a semicolon: 6G + 8G, 8G; 6G + 8G, 6G; 5G; 6G + 7G, 7G, 6G; 5G; 5G + 7G, 7G, 5G; and 7G. In Figure 11B In it, from top to bottom and from left to right of each stacked bar chart, the edits represented in each bar are as follows, where each bar is separated by a semicolon: 6G + 8G, 8G, 6G; 6G + 8G, 6G; 5G; 6G + 7G, 7G, 6G; 5G; 5G + 7G, 5G; and 7G.

[1306] Figure 12 Schematic diagrams are provided showing that multiplex editing advantageously preserves the level of therapeutic editing in hematopoietic stem cells (HSCs) and the content of the desired multiplex editing (i.e., "multiplex-edited HSCs"). In one embodiment, cells are multiplex-edited using a combination of ABE8.8 and guide RNAs to introduce an edit to the CD117 polynucleotide and the sgRNA_015 guide (HPFH editing). The therapeutic edit is introduced into the cells using the guide sgRNA_015 and targets the HBG1 / 2 promoter, and the conditioning edit is introduced into the cells using sgRNA CC128 and targets the CD117 polynucleotide. In Figure 12 In it, SCF is represented by filled gray circles, and +BEAM-101 gRNA indicates sgRNA_015.

[1307] Figure 13A and Figure 13B Stacked bar charts are provided showing that multiplex editing with sgRNA HBG1 / 2a-114 (sgRNA_015) and gRNA CC128 produces efficient A:T to G:C base editing. Figure 13A Stacked bar charts are provided showing the editing rate at the CD117 locus targeted by the CC128 guide. Figure 13B Stacked bar charts are provided showing the editing rate at the HBG1 / 2a-114 locus targeted by sgRNA_015.

[1308] Figure 14 Schematic diagrams are provided showing a strategy for generating single-cell clones to reduce the risk of single CC128 editing.

[1309] Figure 15A and Figure 15B Bar charts are provided showing the editing rate of M07e clones and the staining of M07e clones with the antibody ABTx052. Figure 15AA stacked bar graph is provided, showing allelic editing in the indicated clones. The edits depicted for each bar are as follows, from top to bottom and left to right, where each bar is separated by a semicolon: 7G, 5G+7G, 5G; 7G, 5G+7G, 5G; 7G, 5G+7G, 5G; 7G, 5G+7G, 5G; 5G; 5G; 7G, 5G+7G+10G, 5G+7G, 5G; 7G, 5G+7G, 5G; and 7G, 5G+7G (where the positions of the nucleotide edits are indicated by the subscripts in the following sequence: 5’-AAATA5TA7ATA 10 GCTGGCATCA-3’ (SEQ ID NO:830)). Figure 15B A bar graph is provided, showing that some M07e clones show reduced ABTx052 staining. The genotypes of the clones indicated on the x-axis of Table 12 are provided Figure 15A and Figure 15B in Table 12.

[1310] Figures 16A - 16D Protein blot images and graphs are provided, showing that cells with Y259C (5G) and Y259C+N260D (5G+7G) CD117 monoallelic editing can bind ligand (stem cell factor (SCF)) and induce phosphorylation in the presence of ABTx052, and thus, the edited CD117 polypeptide is functional. Figure 16A Protein blot images are provided, demonstrating phosphorylation of CD117 in the indicated clones (see Table 12 for a description of the clone allelic editing compositions). Cells were incubated with 1 μg / mL of the ABTx052 antibody for 5 min, then 100 ng / mL of SCF was added for 10 min. Phospho-CD117 was probed with anti-phospho CD117 abY719. Figure 16B Graphs are provided, showing how cells edited with guide CC128 show increased viability relative to unedited (UN) cells under the same conditions in the presence of the indicated concentrations of ABTx052 on the x-axis and 100 ng / mL SCF. The monoclonal antibody ABTx052 (mAb ABTx052) reduces cell proliferation of unedited cells by blocking the binding of c-KIT to SCF. A significant difference in cell survival was observed between unedited and CC128 variant primary hematopoietic stem cells (HSCs) when cultured with ABTx052. CC128-edited cells showed higher survival relative to unedited cells. Figure 16CProtein blot images are provided showing phosphorylation of CD117 in cells edited with the indicated guide (CC128 or CC295) in combination with ABE8.8. The protein blot also shows that ABTx052 does not block the binding of SCF to CD117 polypeptides altered with the CC128 guide. The cells are M07e cells. The cells were stimulated with 100 ng / mL SCF for 10 minutes. c-KIT was probed with mAB332. Phospho-c-KIT was probed with mAb Y719. CD117 edited with guide CC128 was phosphorylated upon SCF stimulation. ABTx052 blocked phosphorylation of unedited c-KIT polypeptides. Figure 16D Protein blot images are provided showing the results of an experiment in which unedited, CD117-sgRNA base-edited, or CD117 knockout (KO) M07e cell lines were treated with 100 ng / mL SCF in the presence or absence of mAb-7. Phosphorylated CD117 was probed with anti-phospho CD117 mAb Y719. Cells expressing wild-type CD117 were phosphorylated after SCF stimulation, as were cells containing monoallelic and biallelic editing of CD117. mAb-7 inhibited phosphorylation of WT CD117. Biallelically edited cells were phosphorylated at normal levels even in the presence of mAb-7. mAb-7 decreased but did not completely inhibit CD117 phosphorylation in cells containing monoallelic CD117 editing. CD117-KO cells were used as a negative control.

[1311] Figure 17 Schematic diagrams are provided depicting that a screen has been completed to identify new guides for use with the ABE-NRCH non-G PAM editor to alter polynucleotides encoding CD117 polypeptides. The selection criteria for guide screening in HEK293 T cells were as follows: 1) achieve the desired editing at a frequency > 25% with good next-generation sequencing quality, 2) generate final protein variants with low heterogeneity, 3) protein sequence conservation among cynomolgus monkey genomes (required at the positively targeted amino acid and preferred if 100% conserved).

[1312] Figure 18A and Figure 18B Flow cytometry histograms are provided. Figure 18A Overlapping flow cytometry histograms are provided showing that overall CD117 expression in cells remained constant after editing with guides gRNA931 (CC200) and CC128. Expression was measured using monoclonal antibody (mAb) 104D2. Figure 18B Flow cytometry histograms are provided showing that CD34+ cells edited with gRNA931 lack binding to ABTx052.

[1313] Figure 19 Charts are provided showing that the CD117 S261G engineered epitope is protected from ligand blockade by ABTx052 in vitro. Cells edited with gRNA931 (CC200) showed increased viability when contacted with ABTx052 at the concentrations indicated on the x-axis, relative to unedited cells.

[1314] Figures 20A - 20H Bar charts are provided showing the percentage of human CD34+ ( Figure 20A ), CD15+ ( Figure 20B ), CD19+ ( Figure 20C ), Lin-CD34+ ( Figure 20D ), CD3+ ( Figure 20E ), hCD33+SSC-Alow ( Figure 20F ), GlyA ( Figure 20G ), and CD33+SSC-Ahi ( Figure 20H ) cells in mice 8 weeks after implantation of cells edited with the indicated guides (CC79, CC84, CC90, CC119, and CC128).

[1315] Figure 21A and Figure 21B Stacked bar charts and bar charts are provided demonstrating efficient bi-allelic editing in CD34+ cells and that the cells have normal colony-forming unit (CFU) capacity. Figure 21A Stacked bar charts are provided showing that cells edited with the indicated guides (CC79, CC128, CC84, CC90, CC89, and CC119) have normal colony-forming unit capacity, which is consistent with retained CD117 function, and disruption of CD117 function (e.g., by editing with guide 291 or 295) adversely affects the colony-forming ability of the edited cells. Disruption of CD117 function affects the colony-forming ability of the erythroid population. CFU assays indicate that editing c-KIT has a minimal impact on myeloid colony formation. Figure 21B Bar charts are provided showing the percentage of A>G editing achieved using the indicated guides (CC79, CC128, CC84, CC90, CC89, and CC119) after 24 hours (3 bars per group, first from the left), 48 hours (3 bars per group, second from the left), and 120 hours (3 bars per group, third from the left). Greater than 85% bi-allelic editing was achieved.

[1316] Figures 22A - 22D Bar charts are provided demonstrating that c-KIT knockout significantly affects erythroid in vitro differentiation. Figure 22AShows the total number of burst-forming unit-erythroid (BFU-E) measured after editing cells with the indicated guides (HFPH (sgRNA_015), CC119, CC126, CC290, CC291, CC292, CC293, CC294, and CC295). Figure 22B Shows the number of granulocyte-macrophage progenitor (GMP) colony-forming units (CFU-GM) measured after editing cells with the indicated guides (HFPH (sgRNA_015), CC119, CC126, CC290, CC291, CC292, CC293, CC294, and CC295). Figure 22C and Figure 22D Show the levels of in vitro differentiation and myeloid lineage 7 days after transfection with the indicated editors. In Figure 22C and Figure 22D , the bars from left to right correspond to the following: unedited, HPFH (sgRNA_015), CC119, CC126, CC290, CC291, CC292, CC293, CC294, and CC295. Knockout editing resulted in severe defects in in vitro erythroid differentiation and less severe defects in myeloid differentiation.

[1317] Figure 23A and Figure 23B Provide stacked bar charts and bar charts showing the results associated with editing CD34+ HSPCs to install c-KIT mutations. Figure 23A Provide a stacked bar chart showing the editing efficiency with selected c-KIT guides (CC79, CC84, CC89, CC90, CC119, and CC128). Efficient editing was achieved in CD34+ HSPCs and resulted in the expression of mutant c-KIT polypeptides in the edited cells. Figure 23B Provide a bar chart showing that knockout of c-KIT (using guides CC291 and CC295) disrupts in vitro erythroid differentiation, but editing with guides HPFH (sgRNA_015), CC78, CC79, CC94, CC89, CC90, CC119, CC128, or CC84 + CC90 does not disrupt erythroid differentiation. Selected c-KIT mutations do not disrupt HSPC function and differentiation.

[1318] Figure 24Western blots are provided showing that guide RNAs 291 and 295, when used in combination with ABE8.8, can be used to successfully knock out the expression of CD117. Unedited and edited CD34 cells were stimulated with stem cell factor (SCF) for 10 minutes, and Western blots of cell lysates were performed using anti-CD117 antibody (MAB332) and anti-phospho CD117 antibody (Y719). Editing of CD34+ HSCs with KO sgRNAs 291 and 295 and ABE8.8 mRNA did not show CD117 phosphorylation.

[1319] Figure 25 Cell fluorescence images are provided showing that CD117 altered using guide RNA CC128 is internalized when bound to stem cell factor (SCF), which is consistent with an altered CD117 polypeptide maintaining its function. SCF is conjugated to the pH-sensitive dye pHrodo-green. pHrodo-green fluoresces only when it enters the cell. Measurement of pHrodo-green fluorescence indicates that ligand-bound SCF is internalized.

[1320] Figure 26 Stacked bar graphs are provided showing the percentages of target, bystander, and non-synonymous bystander A>G edits corresponding to the indicated base editors. In Figure 26 , each bar indicates "other non-synonymous bystander", "1G bystander", and "favorable" edits from top to bottom. In Figure 26 , "XVIVO" refers to a serum-free stem cell culture medium for cell growth, "IVD" refers to "in vitro differentiated erythroid culture (IVD)", and "d5" and "d7" refer to five days and seven days, respectively.

[1321] Figure 27 Stacked bar graphs are provided showing the editing efficiency (A to G%) of base editors ABE8.20-NRCH(1570), ABE9v1-NRCH(2517), and ABE9v2(2518) when used in combination with guide gRNA931 (CC200). In each stacked bar graph of Figure 27 , the following edits are shown in order from top to bottom: "3G_4G_6G", "4G_6G", "3G_6G", and "6G".

[1322] Figure 28 Histograms are provided showing that cells expressing CD117 polypeptides altered using a combination of ABE8.20-NRCH(1570), ABE9v1-NRCH(2517), or ABE9v2(2518) and guide gRNA931 (CC200) show reduced binding to antibody ABTx052. Cells were evaluated 2 days after electroporation (EP). In Figure 28Among them, "1" indicates cells edited with ABE8.20-NRCH, "2" indicates cells edited with ABE9v1-NRCH, and "3" indicates cells edited with ABE9v2.

[1323] Figures 29A - 29C Bar graphs, flow cytometry histograms, and charts are provided, showing efficient multiplex editing of CD117 and HBG1 / 2 in CD34+ hematopoietic stem cells (HSPCs). Figure 29A Bar graphs are provided, showing successful multiplex base editing of CD34+ cells using sgRNAs against the polynucleotides encoding CD117 and HBG1 / 2. For the two sgRNAs used, the multiplex base editing efficiency is equivalent to that of single editing. Multiplex editing of the HBG1 / 2 and CD117 polynucleotides results in efficient editing of both, with an efficiency exceeding 85%. Monoclonal analysis shows that all cells were edited for HBG1 / 2 under multiplex editing conditions. The results of CD117 multiplex editing are: >97% biallelic, 1.5% monoallelic, and 1.5% unedited. Figure 29B Charts are provided, showing that the combination of multiplex base editing of the CD117 polynucleotide and editing of the HBG1 / 2 polynucleotide does not hinder γ-globin induction in the edited cells. Approximately 60% γ-globin induction was detected in IVED cells differentiated from multiplex-edited CD34+ cells. Figure 29C Flow cytometry histograms are provided, showing that multiplex-edited cells evade recognition by mAb-7.

[1324] Figure 30 Bar graphs are provided, showing that mAb-7 blocking SCF significantly inhibits erythroid colony formation. Contacting cells with mAb-7 (i.e., ABTx052) results in enrichment of cells with CD117 base editing. A 1:1 mixture of unedited cells and cells base edited using the combination of the guide CC128 and a base editor was seeded in semi-solid medium in the presence of different concentrations of mAb-7. On day 14, individual erythroid colonies (BFU-E) were picked and sequenced (n = 24 colonies were sequenced in each case). In the absence of mAB-7, an even distribution of edited and unedited colonies was observed. As the mAB-7 concentration increased, the proportion of edited colonies produced also increased. When the mAB-7 concentration was 100 ng / mL or higher, 100% of the colonies contained 5G or 5G_7G editing. Very few BFU-E colonies were observed when incubated with SR1. A few colonies selected at higher antibody concentrations contained CD117 editing in only one allele, indicating that monoallelic editing may be sufficient to evade antibody blockade by mAb.

[1325] Figure 31A andFigure 31B Bar graphs and stacked histograms are provided showing successful multiplex editing of CD117 polynucleotides and β-globin genes in CD34+ hematopoietic stem cells. Figure 31A Bar graphs are provided showing high multiplex editing at sites targeted by guide sgRNA_017 (Makassar sgRNA) and gRNA931 (CD117 sgRNA; CC200). Using a combination of a base editor and two guide polynucleotides (sgRNAs), efficient CD117 and Makassar editing was achieved in mobilized peripheral blood-derived (mPB) CD34+ cells (n = 3). Figure 31B Flow cytometry histograms are provided showing that both edited and unedited cells bind to a pan CD117 antibody (Pan CD117 Ab), but edited cells show reduced binding to the antibody mAb-7 (i.e., ABTx052).

[1326] Figures 32A - 32C Structural images and diagrams are provided. Figure 32A and Figure 32B The image corresponds to the approximate Cryo-EM structural image of the CD117 / c-KIT and ABTx052-Fab complex in solution state. In Figure 32A each domain is numbered and each number is placed next to the corresponding domain in the figure, where "1" represents the ABTx052 Fab - heavy chain domain, "2" represents the ABTx052 Fab - light chain, "3" represents the D3 domain of CD117, "4" represents the D2 domain of CD117, and "5" represents the D1 domain of CD117. Figure 32B Structural images are provided with the shaded portion indicating the structural resolution estimated by window FSC in RELION 3. Figure 32C A Fourier shell correlation versus resolution

[1327] Figures 33A - 33D Bar graphs and diagrams are provided demonstrating that alteration of the Fc domain of mAb-7 generates an efficient mAb that does not cause mast cell degranulation in vitro. Figure 33ABar graphs are provided showing that the Fc-engineered forms of anti-CD117 ABTx052 do not produce mast cell degranulation in vitro. Mast cells generated by in vitro differentiation of CD34+ cells were contacted with IgE or interferon γ to increase the expression of Fc-γ receptors and then treated with native and Fc-engineered mAb-7. The absorbance at 405 nM measured β-hexosaminidase release and thus indicated mast cell degranulation. The known positive control antibodies 104D2 and NEG085 cause mast cell degranulation when incubated with mast cells and were thus used as positive controls for degranulation. In Figure 33A , mAb-7-FcEng-1, mAB-7-FcEng-2, and mAb-7-FcEng-3 refer to ABTx052 with Fc modifications LALAPG, LSLTRG, and LALADA, respectively. Figure 33B Charts are provided demonstrating that mAb-7 selectively depletes unedited CD34+ cells in vitro while cells edited for CD117 retain viability upon contact with the antibody. Figure 33C and Figure 33D Charts are provided showing that the Fc-engineered mAb-7 (ABTx135; mAb-7 with an LALADA Fc domain alteration) causes similar levels of cell depletion in human and cynomolgus macaque CD34+ cells. In Figure 33C and Figure 33D , CD34+ cells from human and cynomolgus macaque sources were cultured for 7 days in the presence of 100 ng / mL SCF and different concentrations of ABTx135. As a control, some cells were cultured without any SCF. Cell viability was assessed using the CellTiter-Glo reagent on day 7 according to the manufacturer's instructions. ABTx135 caused similar levels of cell depletion in human and cynomolgus macaque CD34+ cells. CellTiter-Glo measurements on day 7 showed that mAb-7 treatment depleted unedited cells to levels comparable to complete SCF starvation while CD117-edited cells retained viability.

[1328] Figure 34A and Figure 34B Schematic diagrams are provided showing how an adenine base editor (ABE) can be used to chemically modify a target base in a polynucleotide sequence. Figure 34A Schematic diagrams are provided showing that in an embodiment, the ABE is a fusion protein comprising an evolved TadA* deaminase linked to a CRISPR-Cas enzyme. The base editor binds to a target sequence complementary to the guide RNA and exposes a single-stranded DNA fragment. The deaminase converts the target adenine to inosine (which is read as guanine by DNA polymerase), and the Cas enzyme nicks the opposite strand. The nicked strand is repaired, completing the A:T to G:C base pair conversion. Figure 34BSchematic diagrams are provided showing how naturally occurring base changes can lead to hereditary persistence of fetal hemoglobin (HPFH), thereby protecting patients from SCD / B-Thal. Base editors can recapitulate these changes, resulting in high and consistent fetal hemoglobin levels. Higher fetal hemoglobin may be associated with further reduction of the symptoms of hemoglobinopathies (e.g., sickle cell disease).

[1329] Figure 35A and Figure 35B Bar graphs are provided showing that editing the CD117 polynucleotide in CD34+ cells does not alter long-term engraftment and multi-lineage reconstitution in a rodent model. Figure 35A Bar graphs are provided showing that CD117 base-edited cells result in stable long-term (16-week) engraftment in NBSGW mice. Unedited (light gray bars) and CD117 base-edited (dark gray bars) CD34+ cells resulted in similar levels of multi-lineage reconstitution. Figure 35B Bar graphs are provided showing next-generation sequencing (NGS) results demonstrating high levels of CD117 editing in different hematopoietic compartments.

[1330] Figures 36A to 36D Schematic diagrams and bar graphs are provided demonstrating that mAb-7 selectively depletes unedited cells from the bone marrow (BM) of mice transplanted with hCD34+ cells. Figure 36A Schematic diagrams of in vivo studies evaluating anti-CD117-mAb-mediated depletion of bone marrow cells are provided. Irradiated NSG mice were humanized first with unedited cells or a 1:1 mixture of unedited and multiply edited CD34+ cells. Four weeks after transplantation, the mice were left untreated or treated with an isotype control antibody or mAb-7 according to the mouse groups listed on the right. Mouse bone marrow was harvested at the indicated time points and analyzed using flow cytometry. Next-generation sequencing (NGS) was performed on bulk bone marrow and sorted CD34+ cells. Figure 36B Bar graphs are provided showing a significant reduction in human chimerism observed at 8 weeks (upper panel) and 12 weeks (lower panel) after dosing. Figure 36C Bar graphs are provided showing that the CD34+ cell population was also eliminated at the 8-week (upper panel) and 12-week (lower panel) time points. Figure 36D Bar graphs are provided showing editing at the HBG1 / 2 and CD117 target sites in bulk bone marrow (left) and sorted CD34+ cells (right), and demonstrating significant enrichment of editing in the mAb-7-treated group compared to the isotype control group, indicating in vivo selection of multiply edited cells. In Figure 36D each, the four bars from left to right in each group represent the following mouse groups: D, E, D, E. In Figures 36A - 36DIn this study, the letters "A" through "E" were used to refer to the following groups of mice: A) unedited cells without antibody treatment; B) unedited cells treated with a control isotype antibody; C) unedited cells treated with mAb-7; D) a 1:1 ratio of edited and unedited cells treated with a control isotype antibody; E) a 1:1 ratio of edited and unedited cells treated with mAb-7.

[1331] Figure 37 Schematic diagrams were provided showing the in vivo experimental design to evaluate ABTx052-mediated enrichment of multiply base-edited cells in NSG mice. The multiply base-edited cells contained an altered CD117 polynucleotide and an altered HBG1 / 2 polynucleotide.

[1332] Figure 38 Bar graphs were provided showing engraftment data measured over time for human CD45+ cell chimerism in mice. Depletion of unedited cells was observed after administration of mAb (ABTx052) to the mice. The mice were treated as Figure 37 described. Figure 38 The study conditions cited in

[1333] Figure 39 Bar graphs were provided showing the results of HSC bone marrow analysis demonstrating selective depletion of unedited CD34+ hematopoietic stem cells (HSCs) in mice implanted with cells and exposed to ABTx052 after implantation. The mice were treated as Figure 37 described. Figure 38 The study conditions cited in

[1334] Figure 40A and Figure 40B Stacked bar graphs were provided showing the allelic frequencies of HBG1 / 2 editing and CD117 editing measured in the bone marrow ( Figure 37 ) and in CD34+ cells ( Figure 40A ) eight weeks after administration of ABTx052 in mice treated as Figure 40B described. The groups cited in Figure 38

[1335] Figure 41A Figure 41B and Figure 41A Charts were provided showing ABTx052 cell binding as measured on M07e cells expressing wild-type (WT) or base-edited (ESCAPE-2 variant) CD117 ( Figure 41A ), and on mobilized peripheral blood (mPB) human CD34 + expressing wild-type (WT) or base-edited (ESCAPE-2 variant) CD117 as m...

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