Compositions and methods for non-genotoxic cell pretreatment

Abstract

Compositions and methods for non-genotoxic monoclonal antibody (mAb) conditioning, comprising modifying a 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 antibody binding. In various embodiments, the methods further comprise introducing a therapeutic modification into the gene of the HSCs or their progenitors for the treatment of hemoglobinopathies.

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Application Nos. 63 / 500,854, filed May 8, 2023, 63 / 478,744, filed January 6, 2023, 63 / 386,719, filed December 9, 2022, and 63 / 355,927, filed June 27, 2022, the entire contents of which are incorporated herein by reference in their entirety.

[0002] Sequence Listing

[0001] This application contains a Sequence Listing that has been submitted electronically in XML format, and is incorporated herein by reference in its entirety. The XML file for the Sequence Listing, created on June 26, 2023, is named 180802-046405PCT_SL.xml and is 1,559,644 bytes in size. [Background technology]

[0003] 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. In particular, preconditioning patients prior to the infusion of autologous cell therapy is a prerequisite for ex vivo treatment of sickle cell disease (SCD), the most common monogenic hemoglobinopathy. While busulfan is the current standard of care for patients requiring allogeneic or autologous transplants and cell therapy transplants, the use of this potent cytotoxic agent carries associated risks, including genotoxicity, primary or secondary malignancies, and organ toxicity, including infertility. These risks pose a barrier to patients seeking treatment via other methods. Therefore, improved methods for conditioning prior to allogeneic hematopoietic stem cell transplantation are needed. Summary of the Invention

[0004] As described below, the present disclosure features compositions and methods for non-genotoxic monoclonal antibody (mAb) conditioning, which involve modifying a 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 antibody binding. In various embodiments, the methods further involve introducing a therapeutic modification into the gene of the HSCs or their progenitors for the treatment of hemoglobinopathies (e.g., sickle cell disease).

[0005] In one aspect, the disclosure features a method of modifying a nucleobase of a CD117 polynucleotide, the method comprising contacting the CD117 polynucleotide with a base-editing 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) modify the nucleobase of a codon encoding serine at amino acid position 261, whereby modification of the nucleobase encoding serine at amino acid position 261 results in a codon that expresses glycine, ii) modify the nucleobase of a codon encoding serine at amino acid position 251, and / or iii) modify the nucleobase of a codon encoding asparagine at amino acid position 260 and modify the nucleobase of a codon encoding serine at amino acid position 261, or modify the corresponding positions in another CD117 polypeptide, thereby modifying the nucleobase of the CD117 polynucleotide.

[0006] In another aspect, the disclosure features a method of modifying a nucleobase of a CD117 polynucleotide, the method including contacting the CD117 polynucleotide with a base editor polypeptide including a nucleic acid programmable DNA binding protein (napDNAbp) domain and an adenosine deaminase domain. The adenosine deaminase domain contains a combination of modifications 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 also involves contacting a CD117 polynucleotide with a guide polynucleotide that targets a base editor to modify a nucleobase in a polynucleotide encoding a CD117 polypeptide, thereby modifying the nucleobase of the CD117 polynucleotide. In another aspect, the disclosure features a method for hematopoietic stem cell transplantation in a subject. The method includes: (a) contacting isolated hematopoietic stem cells or progenitor cells thereof 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, where the guide polynucleotide targets a nucleic acid molecule encoding a CD117 polypeptide. (a) generates edited cells. The method also includes (b) administering the edited cells to the subject. The method also includes (c) administering to the subject an antibody or antigen-binding fragment thereof, wherein the antibody is chosen from one or more of 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.

[0007] In another aspect, the disclosure features a method for hematopoietic stem cell transplantation in a subject. The method includes: (a) contacting isolated hematopoietic stem cells or progenitor cells thereof 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, thereby: i) introducing a nucleobase modification in the codon encoding serine at amino acid position 261, whereby the nucleobase modification in the serine at amino acid position 261 results in a codon expressing glycine; ii) introducing a nucleobase modification in the codon encoding serine at amino acid position 251; and / or iii) introducing a nucleobase modification in the codon encoding asparagine at amino acid position 260 and introducing a nucleobase modification in the codon encoding serine at amino acid position 261, or modifying the corresponding position in another CD117 polypeptide. (a) generates edited cells. The method also includes (b) administering the edited cells to the subject. The method also includes (c) administering to the subject an antibody or antigen-binding fragment thereof, an antibody-drug conjugate, or a chimeric antigen receptor T (CAR-T) cell, each of which selectively binds to a wild-type CD117 polypeptide.

[0008] In another aspect, the present disclosure features a method for hematopoietic stem cell transplantation in a subject. The method includes (a) contacting isolated hematopoietic stem cells or progenitor cells thereof 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 contains a combination of modifications 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) produces edited cells. The method also includes (b) administering the edited cells to the subject. The method also includes (c) administering to the subject an antibody or antigen-binding fragment thereof, an antibody-drug conjugate, or a chimeric antigen receptor T (CAR-T) cell, each of which selectively binds to a wild-type CD117 polypeptide.

[0009] In another aspect, the disclosure features a method for treating a hemoglobinopathy in a subject. The method includes (a) contacting isolated hematopoietic stem cells or progenitor cells thereof 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 deaminate a nucleobase in the hemoglobin subunit gamma 1 and / or 2 (HBG1 / 2) promoter. (a) generates edited cells. The method also includes (b) administering the edited cells to the subject. The method also includes (c) administering to the subject an antibody or antigen-binding fragment thereof, wherein the antibody is chosen from one or more of 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 disclosure features a method for treating a hemoglobinopathy in a subject. The method includes: (a) contacting isolated hematopoietic stem cells or progenitor cells thereof 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, thereby: i) introducing a nucleobase modification in the codon encoding serine at amino acid position 261, where the nucleobase modification in the serine at amino acid position 261 results in a codon expressing glycine; ii) introducing a nucleobase modification in the codon encoding serine at amino acid position 251; and / or iii) introducing a nucleobase modification in the codon encoding asparagine at amino acid position 260 and introducing a nucleobase modification in the codon encoding serine at amino acid position 261, or modifying the corresponding position in another CD117 polypeptide. Another guide polynucleotide targets the base editor to modify the beta globin polynucleotide (HBB), thereby expressing a beta globin polypeptide having an alanine at position 6 (Hb G-Makassar). (a) also generates an edited cell. The method also includes (b) administering the edited cell to the subject. The method further includes (c) administering to the subject an antibody or antigen-binding fragment thereof, an antibody-drug conjugate, or a chimeric antigen receptor T (CAR-T) cell, each of which selectively binds to a wild-type CD117 polypeptide.

[0011] In another aspect, the disclosure features a method for treating a hemoglobinopathy in a subject. The method includes: (a) contacting isolated hematopoietic stem cells or progenitor cells thereof with two or more guide polynucleotides, and a nucleic acid programmable DNA-binding protein (napDNAbp) and a base editor comprising an adenosine deaminase domain, or a polynucleotide encoding the base editor. The adenosine deaminase domain contains a combination of modifications 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 the other guide polynucleotide targets a base editor to modify a beta globin polynucleotide (HBB) to express a beta globin polypeptide having an alanine at position 6 (Hb G-Makassar). (a) generates edited cells. The method also includes (b) administering the edited cells to a subject. The method also includes (c) administering to a subject an antibody or antigen-binding fragment thereof, an antibody-drug conjugate, or a chimeric antigen receptor T (CAR-T) cell, each of which selectively binds to a wild-type CD117 polypeptide.

[0012] In another aspect, the disclosure features a cell produced by the method of any of the above aspects, or embodiments thereof.

[0013] In another aspect, the disclosure features a pharmaceutical composition including an effective amount of a cell of any of the above aspects, or embodiments thereof.

[0014] In another aspect, the disclosure features a base editor system 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) modify the nucleobase of the codon encoding serine at amino acid position 261, where modification of the nucleobase encoding serine at amino acid position 261 results in a codon that expresses glycine; ii) modify the nucleobase of the codon encoding serine at amino acid position 251; and / or iii) modify the nucleobase of the codon encoding asparagine at amino acid position 260 and modify the nucleobase of the codon encoding serine at amino acid position 261, or modify the corresponding position in another CD117 polypeptide, thereby modifying a nucleobase in a CD117 polynucleotide.

[0015] In another aspect, the disclosure features a base editor system including a guide polynucleotide and a base editor containing a nucleic acid programmable DNA binding protein (napDNAbp) domain and an adenosine deaminase domain. The adenosine deaminase domain comprises a combination of modifications to TadA*7.10. The combinations are 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 modify a nucleobase of a CD117 polynucleotide. The adenosine deaminase domain has at least 85% sequence identity to TadA*7.10.

[0016] In another aspect, the disclosure features a base editor system including a nucleic acid programmable DNA binding protein (napDNAbp) and a base editor comprising an adenosine deaminase domain, and a guide polynucleotide comprising a polynucleotide sequence selected from one or more of: 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).

[0017] In another aspect, the disclosure features a polynucleotide encoding the base editor system of any of the above aspects, or embodiments thereof. In another aspect, the disclosure features a guide polynucleotide that includes a spacer sequence selected from one or more of 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).

[0018] In another aspect, the disclosure features a kit including a cell, base editor system, polynucleotide, or pharmaceutical composition of any of the above aspects or embodiments thereof.

[0019] In another aspect, the disclosure features an anti-CD117 antibody, or antigen-binding portion thereof, comprising one or more complementarity determining regions (CDRs) including 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 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 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 (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); R) 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: 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 ID NO: 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 (SEQ ID 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); VL CDR2: GAS; VL CDR3: QQSETCLT (SEQ ID NO: 1074); VH CDR1: GFTFDDYA (SEQ ID NO: 391) VH V) CDR1: QSVSSSY (SEQ ID NO: 394); V) CDR2: GSS; V) CDR3: QQDSLGLT (SEQ ID NO: 1074); V) CDR1: GFTFDDYA (SEQ ID NO: 391); V) CDR2: ISWNSGTIG (SEQ ID NO: 1070); V) CDR3: AKDSPPGYCASASCYGAFDI (SEQ ID NO: 1090); V) 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). ;

[0020] In another aspect, the disclosure features an isolated nucleic acid molecule encoding the antibody of any one of the above aspects, or embodiments thereof.

[0021] In another aspect, the disclosure features an anti-CD117 antibody, or antigen-binding portion thereof, comprising complementarity-determining regions (CDRs) comprising 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 a VL CDR3 selected from one or more of QQXSYPLT (SEQ ID NO: 945), QQXSHPLT (SEQ ID NO: 946), and QQXSSPLT (SEQ ID NO: 947), where X represents any amino acid. The anti-CD117 antibody comprises at least one amino acid modification compared to the amino acid sequence of ABTx052.

[0022] In another aspect, the disclosure features an anti-CD117 antibody, or antigen-binding portion thereof, that includes complementarity-determining regions (CDRs) that include or only include the following heavy chain variable region (VH) and light chain variable region (VL) CDR amino acid sequences: 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; 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, and X 10 is G or S, and X 11 is D, S, T, or Y, and X 12 is I or T, and X 13 is G, K, R, or Y; VH CDR3 is ARHGRGYDX 14YDGAFDI (SEQ ID NO: 1105), ARDYYGLFDY (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 is G, and X 15 is D or N, and X 16 is G or Y, and X 17 is E or S, and X 18 is I or Y, and X 19 is S, T, or W, and X 20 is L, P, or S, and X 21 is F or Y and X 22 is A or S, and X 23 is S or T, and X 24 is A or T, and X 25 is S or Y, 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, VL CDR2:X 28 X 29 S (where X 28 is A, D, or G, and X 29 is A or S), 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 X30 is F, L, S, T, or Y, and X 31 is G, N, S, or Y, and X 32 is S or F, and X 33 is S, T, W, or Y, and X 34 is F, I, L, or Y, and X 35 is D, S, or Y, and X 36 is E, G, or S, and X 37 is L or T, and X 38 is C, G, or S. The anti-CD117 antibody comprises at least one amino acid modification compared to the amino acid sequence of ABTx052.

[0023] In another aspect, the present disclosure features a method for hematopoietic stem cell transplantation in a subject. The method includes (a) administering to the subject hematopoietic stem cells or progenitor cells thereof. The hematopoietic stem cells or progenitor cells thereof express a CD117 variant containing a S261G amino acid modification or a CD117 variant containing a Y259C and N260D amino acid modification. The method further includes (b) administering to the subject an antibody or antigen-binding fragment thereof that selectively binds to a wild-type CD117 polypeptide. In another aspect, the disclosure features a method for treating a hemoglobinopathy in a subject. The method includes (a) administering to the subject hematopoietic stem cells or progenitor cells thereof. The hematopoietic stem cells or progenitor cells thereof i) express either a CD117 variant containing a S261G amino acid modification or a CD117 variant containing Y259C and N260D amino acid modifications, and ii) express an HBB polypeptide containing a nucleobase modification in the HBG1 / 2 promoter that increases gamma globin expression and / or contains an alanine at position 6. The method further includes (b) administering to the subject an antibody or antigen-binding fragment thereof that selectively binds to a wild-type CD117 polypeptide.

[0024] In another aspect, the disclosure features a hematopoietic stem cell or progenitor cell expressing i) a S261G modification, ii) a modification at amino acid positions 260 and 261, and / or ii) a modification at amino acid position 251 compared to the following amino acid sequence, wherein the CD117 polypeptide has at least 85% sequence identity to the following amino acid sequence: Wild type CD117 MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDR SLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTCTIKDVSSSVYS TWKRENSQTKLQEKYNSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSE NESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGT VECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYG LIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVV PTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV (SEQ ID NO: 499).

[0025] In another aspect, the disclosure features a hematopoietic stem cell or progenitor cell expressing a CD117 polypeptide comprising a sequence of 10, 20, 30, or 40 consecutive amino acids, the sequence of consecutive amino acids containing amino acid 260, amino acid 261, and / or amino acid 251, as compared to the wild-type CD117 amino acid sequence, and further comprising: i) a substitution of the amino acid corresponding to amino acid 261 with glycine; ii) an alteration of the amino acids corresponding to amino acids 260 and 261; and / or iii) The amino acid corresponding to amino acid position 251 is modified relative to the following wild-type CD117 amino acid sequence within a sequence of consecutive amino acids that has at least 85% sequence identity to a fragment of the following wild-type CD117 amino acid sequence having the same length as the sequence of consecutive amino acids: Wild-type CD117 amino acid sequence MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDR SLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTCTIKDVSSSVYS TWKRENSQTKLQEKYNSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSE NESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGT VECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYG LIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVV PTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV (SEQ ID NO: 499).The CD117 polypeptide is capable of binding to a stem cell factor (SCF) polypeptide.

[0026] In any aspect of the disclosure, or an embodiment thereof, 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 disclosure, or an embodiment thereof, the adenosine deaminase domain comprises a series of modifications to TadA*7.10: MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO: 1). The modifications are selected from 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 to TadA*7.10.

[0027] In any aspect of the disclosure, or embodiments thereof, the deaminase is a monomer or a heterodimer. In any aspect of the disclosure, or embodiments thereof, the base editor polypeptide is an internal base editor (IBE) that comprises a deaminase domain inserted at an internal position of the napDNAbp.

[0028] In any aspect of the present disclosure, or embodiments thereof, the base editor polypeptide further comprises one or more nuclear localization sequences (NLSs). In any aspect of the present disclosure, or embodiments thereof, the base editor polypeptide further comprises a bipartite nuclear localization sequence (NLS).

[0029]

[0030] In any aspect of the disclosure, or embodiments thereof, the method includes administering to a subject an antibody or antigen-binding fragment thereof, wherein the antibody is selected from the group consisting of ABTx025, ABTx030, ABTx052, ABTx061, ABTx062, ABTx070, ABTx071, ABTx196, ABTx198, ABTx202, ABTx203, ABTx205, ABTx20 6, ABTx248, ABTx250, ABTx251, ABTx253, ABTx254, ABTx255, ABTx256, ABTx265, ABTx268, ABTx270, ABTx271, ABTx272, ABTx273, ABTx274, ABTx307, ABTx308, ABTx309, and ABTx313.

[0031] In any aspect of the present disclosure, or embodiments thereof, the subject has a hemoglobinopathy, hi certain embodiments, the hemoglobinopathy is selected from one or more of sickle cell anemia, thalassemia, Fanconi anemia, aplastic anemia, and Wiskott-Aldrich syndrome.

[0032] In any aspect or embodiment of the present disclosure, the method further comprises contacting hematopoietic stem cells or progenitor cells thereof with a guide polynucleotide that targets a nucleic acid molecule encoding a β-globin (HBB) polypeptide, thereby introducing an amino acid modification at alanine 6 of the HBB polypeptide. In any aspect or embodiment of the present disclosure, the method further comprises contacting hematopoietic stem cells or progenitor cells thereof with a guide polynucleotide that targets a base editor to result in deamination of a nucleobase in the hemoglobin subunit γ1 and / or 2 (HBG1 / 2) promoter. In any aspect or embodiment of the present disclosure, the deamination of a nucleobase interferes with repressor binding to the hemoglobin subunit γ1 and / or 2 (HBG1 / 2) promoter. In any aspect or embodiment of the present disclosure, the deamination of a nucleobase increases gamma globin (HbF) expression.

[0033] In any aspect of the disclosure, or embodiments thereof, the guide polynucleotide contacted with the CD117 polynucleotide comprises a nucleotide sequence selected from one or more of 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).

[0034] In any aspect of the disclosure, or embodiments thereof, a guide polynucleotide targeting nucleobase deamination of an HBG1 / 2 promoter or a guide polynucleotide targeting a nucleic acid molecule encoding a β-globin (HBG) polypeptide may be selected from the group consisting of ACUUCUCCACAGGAGUCAGG (SEQ ID NO: 902); GUGGGGAAGGGGCCCCCAAG (SEQ ID NO: 903); AUUGAGAUAGUGUGGGGAAG (SEQ ID NO: 904); CAUUGAGAUAGUGUGGGGAA (SEQ ID NO: 905); G CAUUGAGAUAGUGUGGGGA (SEQ ID NO: 906); GUGGGAAGGGGCCCCCAAG (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: 9 13);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 disclosure, or embodiments thereof, the guide polynucleotide contains a scaffold having the following nucleotide sequence: GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU (SEQ ID NO: 317).

[0035] In any aspect or embodiment of the present disclosure, the hematopoietic stem cells or progenitor cells thereof are autologous to the subject. In any aspect or embodiment of the present disclosure, the hematopoietic stem cells or progenitor cells thereof are allogeneic to the subject. In any aspect or embodiment of the present disclosure, the subject is a mammal. In any aspect or embodiment of the present disclosure, the mammal is a dog, a cat, a human, a non-human primate, or a rodent.

[0036] In any aspect of the present disclosure, or embodiments thereof, the guide polynucleotide is a guide RNA. In any aspect of the present disclosure, or embodiments thereof, at least one of the two or more guide polynucleotides comprises a nucleotide sequence selected from one or more of: 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).

[0033] In any aspect of the disclosure, or embodiments thereof, at least one of the two or more guide polynucleotides is selected from the group consisting of 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);GUGU GGGGAAGGGGCCCCCA (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); GGGCCCCUUCCCCACAC The nucleotide sequence includes one or more of: UAU (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 disclosure, or embodiments thereof, the guide polynucleotide is selected from one or more of 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).

[0037] In any aspect of the disclosure, or embodiments thereof, the base editor system comprises the following polynucleotide sequence: ACUUCUCCACAGGAGUCAGG (SEQ ID NO: 902) The method further comprises a guide polynucleotide comprising:

[0038] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1120; Ax025 VH), and / or the amino acid sequence: DVVMTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGTSLTFGGGTKLEIKRTV (SEQ ID NO: 1121; ABTx025 VL).

[0039] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: QVQLQESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSIGTISSYIYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARDYYGLFDYWGQGTLVTVSS (SEQ ID NO: 1118; Ax030 VH), and / or comprises a heavy chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EIVMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVDIKRTV (SEQ ID NO: 1119; ABTx030 VL).

[0040] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGSIGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCAKDTPLGYCSTTSCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1126; ABTx061 VH), and / or the amino acid sequence: EIVLAQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPLTFGGGTKLEIKRTV (SEQ ID NO: 1127; ABTx061 VL).

[0041] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCSASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTTVTVSS (SEQ ID NO: 1128; ABTx062 VH), and / or the amino acid sequence: DIQLTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTINSLQPEDFATYYCQQSYSTPFTFGPGTKVEIKRTV (SEQ ID NO: 1129; ABTx062 VL).

[0042] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGVVRPGGSLRLSCAASGFTFDDYGMSWVRQAPGKGLEWVSDINWNGGSTGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCARESWDGSGIYYMDVWGKGTTVTVSS (SEQ ID NO: 1130; ABTx070 VH), and / or the amino acid sequence: DIVMTQSPSFLSASVGDRVTITCRASQGISSYLNWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPITFGQGTRLEIKRTV (SEQ ID NO: 1131; ABTx070 VL).

[0043] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGVVRPGGSLRLSCAASGFTFDDYGMSWVRQAPGKGLEWVSGINWNGGSTGYADSVKGRFTISRDNAKNSLHLQMNSLRAEDTALYYCARESWNYEGYYYMDVWGKGTTVTVSS (SEQ ID NO: 1132; ABTx071 VH), and / or the amino acid sequence: AIQMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQLNSYPYTFGQGTKLEIKRTV (SEQ ID NO: 1133; ABTx071 VL).

[0044] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: QVQLVQSGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYCARHGRGYDGYDGAFDIWGQGTMVTVSS (SEQ ID NO: 1122; ABTx313 VH), and / or comprises a heavy chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQFSSYPLTFGGGTKVEIKRTV (SEQ ID NO: 1123; ABTx313 VL).

[0045] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: QVQLVQSGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYCARHGRGYDGYDGAFDIWGQGTMVTVSS (SEQ ID NO: 1122; ABTx307 VH), and / or comprises a heavy chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQFNSYPLTFGGGTKVEIKRTV (SEQ ID NO: 960; ABTx307 VL).

[0046] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: QVQLVQSGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTKYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYCARHGRGYDAYDGAFDIWGQGTMVTVSS (SEQ ID NO: 1124; ABTx308 VH), and / or comprises a heavy chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQFSSYPLTFGGGTKVEIKRTV (SEQ ID NO: 1123; ABTx308 VL).

[0047] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: QVQLVQSGAAVKKPGESLKISCKGSGYRFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYCARHGRGYDAYDGAFDIWGQGTMVTVSS (SEQ ID NO: 1124; ABTx309 VH), and / or comprises a heavy chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQTNSYPLTFGGGTKVEIKRTV (SEQ ID NO: 1125; ABTx309 VL).

[0048] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1120; ABTx196 VH), and / or a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: DVVMTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSETCLTFGGGTKLEIK (SEQ ID NO: 1068; ABTx196 VL).

[0049] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTSSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1085; ABTx202 VH), and / or a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EIVMTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGSSTRATGIPARFSGSGSGTEFALTISSLQSEDFAVYYCQQYNFWPYTFGQGTKVEIK (SEQ ID NO: 1086; ABTx202 VL).

[0050] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCASASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1089; ABTx198 VH), and / or a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: DVVMTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQDSLGLTFGGGTKLEIK (SEQ ID NO: 1103; ABTx198 VL).

[0051] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDWPSGFCSSAYCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1092; ABTx203, VH), and / or a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: DIVMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCQQSYSTPYTFGQGTKLEIK (SEQ ID NO: 1093; ABTx203, VL).

[0052] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIWGQGTMVTVSS (SEQ ID NO: 1120; ABTx205 VH), and / or a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: DIVMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCQQSYSTPYTFGQGTKLEIK (SEQ ID NO: 1093; ABTx205 VL).

[0053] In any aspect of the disclosure, or embodiments thereof, the antibody comprises a heavy chain variable domain (VH) sequence having at least 85% amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGTIGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYCAKDSPPGYCSSASCYGAFDIRGQGTMVTVSS (SEQ ID NO: 1101; ABTx206 VH), and / or a light chain variable domain (VL) sequence having at least 85% amino acid sequence identity to the amino acid sequence: DIVMTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCQQSYSTPYTFGQGTKLEIK (SEQ ID NO: 1093).

[0054] In any aspect of the disclosure, or embodiments thereof, the subject has at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% chimerism with the edited cells, or cells derived or lineage-derived from the edited cells, 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 the antibody or antigen-binding fragment thereof. In certain embodiments, chimerism is measured with bulk bone marrow, CD34+ cells, CD235a+ cells, CD19+ cells, and / or CD45+ cells.

[0055] In any aspect of the present disclosure, or embodiments thereof, the method comprises contacting a hematopoietic stem cell or 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 embodiments thereof, the base editor contains a TadA*8.20 adenosine deaminase domain. In any aspect of the present disclosure, or embodiments thereof, the base editor contains a napDNAbp domain of Cas9-NRCH. In any aspect of the present disclosure, or embodiments thereof, the base editor is ABE8.20-NRCH. In any aspect of the disclosure, or embodiments thereof, the antibody is ABTx052 and contains a VH CDR1, a VH CDR2, a VH CDR3, a VL CDR1, a VL CDR2, and a VL CDR3 with at least 95% sequence identity to the VH domain of ABTx052, and / or contains a VL domain with at least 95% sequence identity to the VL domain of ABTx052. In any aspect of the disclosure, or embodiments 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.

[0056] In any aspect of the present disclosure, or embodiments thereof, a method includes: (A) base-editing hematopoietic stem cells or progenitor cells thereof by contacting them with (i) a guide polynucleotide comprising a spacer sequence corresponding to gRNA931 (CC200) and another guide polynucleotide containing a spacer sequence corresponding to sgRNA_027 or a polynucleotide encoding same, and (ii) an ABE-NRCH base editor or a polynucleotide encoding same; (B) administering the base-edited hematopoietic stem cells or progenitor cells thereof to a subject; and (C) administering an ABTx052 antibody to a subject before, after, or simultaneously with administration of the base-edited hematopoietic stem cells.

[0057] In any aspect of the present disclosure, or embodiments thereof, the antibody, antibody-drug conjugate, or chimeric antigen receptor comprises complementarity-determining regions (CDRs) comprising 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 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 comprises at least one amino acid modification compared to the amino acid sequence of ABTx052.

[0058] In any aspect of the disclosure, or embodiments thereof, the VH CDR3 is selected from one or more of 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 the VL CDR3 is selected from one or more of 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), QQFNSSPLT (SEQ ID NO:956), QQFSSYPLT (SEQ ID NO:1020), QQTNSHPLT (SEQ ID NO: 1023), QQVRSYPLT (SEQ ID NO: 1025), QQTYSYPLT (SEQ ID NO: 1029), QQFNSTPLT (SEQ ID NO: 1033), and QQTRSYPLT (SEQ ID NO: 1036).

[0059] In any aspect of the disclosure, or embodiments thereof, the antibody selectively binds to wild-type CD117. In any aspect of the disclosure, or embodiments thereof, the antibody has a dissociation constant for binding to wild-type CD117 of less than about 4.0E-04 or 4.5.0E-03.

[0060] In any aspect, or embodiment, of the disclosure, the antibody has reduced binding to CD117 variants comprising the Y259C, N260D, and / or S261G amino acid modifications, wherein the reduced binding is compared to the anti-CD117 antibody ABTx052 or ABTx135. In any aspect, or embodiment, of the disclosure, the antibody has reduced binding to CD117 variants containing the amino acid modifications Y259C and N260D and CD117 variants containing the amino acid modification S261G, wherein the reduced binding is compared to the anti-CD117 antibody ABTx052 or ABTx135.

[0061] In any aspect of the disclosure, or an embodiment thereof, the antibody comprises variable heavy (VH) and variable light (VL) framework regions (FR) comprising 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).

[0062] In any aspect of the disclosure, or embodiments thereof, the antibody is a human IgG1 antibody.

[0063] In any aspect of the disclosure, or embodiments thereof, the antibody or antigen-binding fragment thereof, antibody-drug conjugate, or chimeric antigen receptor T (CAR-T) cells are administered before, after, or simultaneously with administration of the edited cells.

[0064] In any aspect or embodiment thereof provided herein, the method is not a process for altering the genetic identity of a human germline.

[0065] In any aspect or embodiment provided herein, the antibody has an EC50 of less than about 0.1 nM against target cells. In any aspect or embodiment provided herein, the antibody has a multispecificity similar to or less than that of ABTx052. In any aspect or embodiment provided herein, the antibody is effective in reducing the viability of hematopoietic stem cells (HSCs) expressing wild-type CD117 polypeptide. In any aspect or embodiment provided herein, the antibody has an IC50 value of less than 5E-006 molar for reducing HSC viability.

[0066] In any aspect of the disclosure or embodiments thereof, A) VH CDR1 is selected from one or more of 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 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); and C) VH CDR3 is selected from one or more of 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) the VL CDR1 is selected from one or more of QGISSA (SEQ ID NO:424), QSISSY (SEQ ID NO:409), QGISSY (SEQ ID NO:469), and QSVSSSY (SEQ ID NO:439); E) the VL CDR2 is selected from one or more of DAS, AAS, GSS, and GAS; and / or F) the VL CDR3 is selected from one or more of 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);

[0067] In any aspect of the disclosure, or embodiments thereof, the antibody comprises variable heavy (VH) and variable light (VL) framework regions (FR), wherein A) VH FR1 is selected from one or more of 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); and B) VH FR2 is selected from one or more of 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 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 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 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 LAWYQQKPGKAPKLLIY (SEQ ID NO:431), LNWYQQKPGKAPKLLIY (SEQ ID NO:416), and LAWYQQKPGQAPRLLIY (SEQ ID NO:446); FR3 is selected from one or more of 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 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).

[0068] In any aspect of the disclosure, or embodiments thereof, the hemoglobinopathy is selected from one or more of sickle cell anemia, thalassemia, Fanconi anemia, aplastic anemia, and Wiskott-Aldrich syndrome.

[0069] In any aspect of the disclosure, or embodiment thereof, step (b) occurs before, after, or simultaneously with step (a).

[0070] In any aspect or embodiment of the present disclosure, the CD117 polypeptide contains a S261G modification.

[0071] In any aspect of the disclosure, or embodiments thereof, the sequence of contiguous amino acids has at least 90%, 95%, 99%, 99.5%, or 99.9% sequence identity to the fragment. In any aspect of the disclosure, or embodiments thereof, the CD117 polypeptide has at least 90%, 95%, 99%, 99.5%, or 99.9% sequence identity to the amino acid sequence.

[0072] definition Unless otherwise defined, all technical and scientific terms used herein have the meanings commonly understood by those skilled in the art to which this disclosure belongs. The following references provide one of the techniques containing common definitions of many of the terms used in this disclosure: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, unless otherwise specified, the following terms have the meanings defined below.

[0073] "ABTx025" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx025, or an antibody comprising VH and / or VL CDR1-3 or antigen-binding fragments thereof of ABTx025, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to a wild-type CD117 polypeptide but has no detectable or reduced binding to a modified CD117 polypeptide. In certain 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 ABTx025. Exemplary heavy and light chain sequences for antibody ABTx025 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0074] ABTx025 Heavy Chain (HC): TIFF2025530892000002.tif60165

[0075] ABTx025 Light Chain (LC): TIFF2025530892000003.tif27165

[0076] The three CDRs of the ABTx025 antibody VH region are as follows: VH CDR1:GFTFDDYA (SEQ ID NO: 391); VH CDR2: ISWNSGTI (SEQ ID NO: 392); and VH CDR3:AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393).

[0077] The three CDRs of the ABTx025 antibody VL region are as follows: VL CDR1: QSVSSSY (SEQ ID NO: 394); VL CDR2:GAS; and VL CDR3: QQYGTSLT (SEQ ID NO: 395).

[0078] The four framework (FR) regions of the ABTx025 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx025 antibody VH region are as follows: VH FR1:EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396); VH FR2:MHWVRQAPGKGLEWVSG (SEQ ID NO: 397); VH FR3:IGYADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 398); and VH FR4:WGQGTMVTVSS (SEQ ID NO: 399).

[0079] The four FRs of the ABTx025 antibody VL region are as follows: VL FR1:DVVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO: 400); VL FR2:LAWYQQKPGQAPRLLIY (SEQ ID NO: 401); VL FR3:SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO: 402); and VL FR4:FGGGTKLEIKRTV (SEQ ID NO:403).

[0080] "ABTx025 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx025 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0081] "ABTx030" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx030, or an antibody comprising the VH and / or VL CDRs 1-3 or antigen-binding fragments of ABTx030, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to a wild-type CD117 polypeptide but has no detectable or reduced binding to a modified CD117 polypeptide. In certain embodiments, the antibody or antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity to the antibody sequence of antibody ABTx030. Exemplary heavy and light chain sequences for antibody ABTx030 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0082] ABTx030 Heavy Chain (HC): TIFF2025530892000004.tif57165

[0083] ABTx030 light chain (LC): TIFF2025530892000005.tif27165

[0084] The three CDRs of the ABTx030 antibody VH region are as follows: VH CDR1: GFTFSSYS (SEQ ID NO: 406); VH CDR2: IGTISSYI (SEQ ID NO: 407) or IGTISSYIY (SEQ ID NO: 1113); and VH CDR3: ARDYYGLFDY (SEQ ID NO: 408).

[0085] The three CDRs of the ABTx030 antibody VL region are as follows: VL CDR1: QSISSY (SEQ ID NO: 409); VL CDR2:AAS; and VL CDR3: QQSYSTPLT (SEQ ID NO: 410).

[0086] The four framework (FR) regions of the ABTx030 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx030 antibody VH region are as follows: VH FR1: QVQLQESGGGLVKPGGSLRLSCAAS (SEQ ID NO: 411); VH FR2: MNWVRQAPGKGLEWVSS (SEQ ID NO: 412); VH FR3: YYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYC (SEQ ID NO: 413); and VH FR4: WGQGTLVTVSS (SEQ ID NO: 414).

[0087] The four FRs of the ABTx030 antibody VL region are as follows: VL FR1: EIVMTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 415); VL FR2: LNWYQQKPGKAPKLLIY (SEQ ID NO: 416); VL FR3: SLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 417); and VL FR4: FGGGTKVDIKRTV (SEQ ID NO: 418).

[0088] "ABTx030 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx030 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0089] "ABTx052" or "mAb-7" refers to an antibody having at least about 85% amino acid sequence identity to the antibody sequence of antibody ABTx052, or an antibody comprising the VH and / or VL CDRs 1-3 of ABTx052, or an antigen-binding fragment thereof, wherein each of the antibody, CDRs, and antigen-binding fragment specifically binds to a wild-type CD117 polypeptide but has no detectable or only reduced binding to a modified CD117 polypeptide. In certain 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 ABTx052. Exemplary heavy and light chain sequences for antibody ABTx052 are shown below, with variable region embodiments in plain text, constant domain embodiments in bold, and complementarity determining region (CDR) embodiments, i.e., CDR1, CDR2, and CDR2, underlined.

[0090] ABTx052 heavy chain (HC): TIFF2025530892000006.tif57165

[0091] ABTx052 Light Chain (LC): TIFF2025530892000007.tif27165

[0092] The three CDRs of the ABTx052 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDT (SEQ ID NO: 422) or IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYNGYEGAFDI (SEQ ID NO: 423).

[0093] The three CDRs of the ABTx052 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQFNSYPLT (SEQ ID NO: 425).

[0094] The four framework (FR) regions of the ABTx052 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx052 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0095] The four FRs of the ABTx052 antibody VL region are as follows: 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).

[0096] "ABTx052 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx052 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0097] "ABTx061" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx061, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx061, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx061. Exemplary heavy and light chain sequences for antibody ABTx061 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0098] ABTx061 Heavy Chain (HC): TIFF2025530892000008.tif57165

[0099] ABTx061 Light Chain (LC): TIFF2025530892000009.tif27165

[0100] The three CDRs of the ABTx061 antibody VH region are as follows: VH CDR1: GFTFDDYA (SEQ ID NO: 436); VH CDR2: ISWNSGSI (SEQ ID NO: 437) or ISWNSGSIG (SEQ ID NO: 1115); and VH CDR3: AKDTPLGYCSTTSCYGAFDI (SEQ ID NO: 438).

[0101] The three CDRs of the ABTx061 antibody VL region are as follows: VL CDR1: QSVSSSY (SEQ ID NO: 439); VL CDR2: GAS; and VL CDR3: QQYGSSPLT (SEQ ID NO: 440).

[0102] The four framework (FR) regions of the ABTx061 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx061 antibody VH region are as follows: VH FR1: EVQLVESGGGLVQPGRSLRLSCAA (SEQ ID NO: 441); VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 442); VH FR3: GYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO: 443) or YADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO: 1116); and VH FR4: WGQGTMVTVSS (SEQ ID NO: 444).

[0103] The four FRs of the ABTx061 antibody VL region are as follows: VL FR1: EIVLAQSPGTLSLSPGERATLSCRAS (SEQ ID NO: 445); VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO: 446); VL FR3: SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO: 447); and VL FR4: FGGGTKLEIKRTV (SEQ ID NO: 448).

[0104] "ABTx061 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx061 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0105] "ABTx062" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx062, or an antibody comprising VH and / or VL CDR1-3 or antigen-binding fragments thereof of ABTx062, wherein each of the antibody, CDR, and antigen-binding fragment specifically binds to a wild-type CD117 polypeptide but has no detectable or reduced binding to a modified CD117 polypeptide. In certain 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 ABTx062. Exemplary heavy and light chain sequences for antibody ABTx062 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0106] ABTx062 Heavy Chain (HC): TIFF2025530892000010.tif58165

[0107] ABTx062 Light Chain (LC): TIFF2025530892000011.tif27165

[0108] The three CDRs of the ABTx062 antibody VH region are as follows: VH CDR1: GFTFDDYA (SEQ ID NO: 451); VH CDR2: ISWNSGTI (SEQ ID NO: 452); and VH CDR3: AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 453).

[0109] The three CDRs of the ABTx062 antibody VL region are as follows: VL CDR1: QSISSY (SEQ ID NO: 454); VL CDR2: AAS; and VL CDR3: QQSYSTPFT (SEQ ID NO: 455).

[0110] The four framework (FR) regions of the ABTx062 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx062 antibody VH region are as follows: VH FR1: EVQLVESGGGLVQPGRSLRLSCSAS (SEQ ID NO: 456); VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 457); VH FR3: GYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO: 458) or YADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO: 1116); and VH FR4: WGQGTTVTVSS (SEQ ID NO: 459).

[0111] The four FRs of the ABTx062 antibody VL region are as follows: VL FR1: DIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 460); VL FR2: LNWYQQKPGKAPKLLIY (SEQ ID NO: 461); VL FR3: SLQSGVPSRFSGSGSGTDFTLTINSLQPEDFATYYC (SEQ ID NO: 462); and VL FR4: FGPGTKVEIKRTV (SEQ ID NO: 463).

[0112] "ABTx062 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx062 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0113] "ABTx070" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx070, or an antibody comprising the VH and / or VL CDRs 1-3 or antigen-binding fragments of ABTx070, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to a wild-type CD117 polypeptide but has no detectable or reduced binding to a modified CD117 polypeptide. In certain embodiments, the antibody or antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity to the antibody sequence of antibody ABTx070. Exemplary heavy and light chain sequences for antibody ABTx070 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0114] ABTx070 Heavy Chain (HC): TIFF2025530892000012.tif57165

[0115] ABTx070 Light Chain (LC): TIFF2025530892000013.tif27165

[0116] The three CDRs of the ABTx070 antibody VH region are as follows: VH CDR1: GFTFDDYG (SEQ ID NO: 466); VH CDR2: INWNGGST (SEQ ID NO: 467) or INWNGGSTG (SEQ ID NO: 1114); and VH CDR3: ARESWDGSGIYYMDV (SEQ ID NO: 468).

[0117] The three CDRs of the ABTx070 antibody VL region are as follows: VL CDR1: QGISSY (SEQ ID NO: 469); VL CDR2: AAS; and VL CDR3: QQSYSTPIT (SEQ ID NO: 470).

[0118] The four framework (FR) regions of the ABTx070 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx070 antibody VH region are as follows: VH FR1: EVQLVESGGGVVRPGGSLRLSCAAS (SEQ ID NO: 471); VH FR2: MSWVRQAPGKGLEWVSD (SEQ ID NO: 472); VH FR3: GYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO: 473) or YADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYC (SEQ ID NO: 1116); and VH FR4: WGKGTTVTVSS (SEQ ID NO: 474).

[0119] The four FRs of the ABTx070 antibody VL region are as follows: VL FR1: DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO: 475); VL FR2: LNWYQQKPGKAPKLLIY (SEQ ID NO: 476); VL FR3: TLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 477); and VL FR4: FGQGTRLEIKRTV (SEQ ID NO: 478).

[0120] "ABTx070 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx070 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0121] "ABTx071" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx071, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or 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 for antibody ABTx071 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0122] ABTx071 Heavy Chain (HC): TIFF2025530892000014.tif57165

[0123] ABTx071 Light Chain (LC): TIFF2025530892000015.tif26165

[0124] The three CDRs of the ABTx071 antibody VH region are as follows: VH CDR1: GFTFDDYG (SEQ ID NO: 481); VH CDR2: INWNGGST (SEQ ID NO: 482) or INWNGGSTG (SEQ ID NO: 1114); and VH CDR3: ARESWNYEGYYYMDV (SEQ ID NO: 483).

[0125] The three CDRs of the ABTx071 antibody VL region are as follows: VL CDR1: QGISSY (SEQ ID NO: 484); VL CDR2: AAS; and VL CDR3: QQLNSYPYT (SEQ ID NO: 485).

[0126] The four framework (FR) regions of the ABTx071 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx071 antibody VH region are as follows: VH FR1: EVQLVESGGGVVRPGGSLRLSCAAS (SEQ ID NO: 486); VH FR2: MSWVRQAPGKGLEWVSG (SEQ ID NO: 487); VH FR3: GYADSVKGRFTISRDNAKNSLHLQMNSLRAEDTALYYC (SEQ ID NO: 488) or YADSVKGRFTISRDNAKNSLHLQMNSLRAEDTALYYC (SEQ ID NO: 1117); and VH FR4: WGKGTTVTVSS (SEQ ID NO: 489).

[0127] The four FRs of the ABTx071 antibody VL region are as follows: VL FR1: AIQMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO: 490); VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 491); VL FR3: TLQNGVPSRFSGSGSGTEFTLTISSLQPEDFATYYC (SEQ ID NO: 492); and VL FR4: FGQGTKLEIKRTV (SEQ ID NO: 493).

[0128] "ABTx071 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx071 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0129] "ABTx248" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx248, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx248, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx248. Exemplary heavy and light chain sequences for antibody ABTx248 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0130] ABTx248 heavy chain (HC): TIFF2025530892000016.tif57165

[0131] ABTx248 light chain (LC): TIFF2025530892000017.tif27165

[0132] The three CDRs of the ABTx248 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).

[0133] The three CDRs of the ABTx248 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQFNSYPLT (SEQ ID NO: 425).

[0134] The four framework (FR) regions of the ABTx248 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx248 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0135] The four FRs of the ABTx248 antibody VL region are as follows: 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).

[0136] "ABTx248 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx248 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0137] "ABTx249" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx249, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or 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 for antibody ABTx249 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0138] ABTx249 heavy chain (HC): TIFF2025530892000018.tif57165

[0139] ABTx249 light chain (LC): TIFF2025530892000019.tif27165

[0140] The three CDRs of the ABTx249 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0141] The three CDRs of the ABTx249 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQLNGYPLT (SEQ ID NO: 1015).

[0142] The four framework (FR) regions of the ABTx249 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx249 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0143] The four FRs of the ABTx249 antibody VL region are as follows: 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).

[0144] "ABTx249 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx249 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0145] "ABTx250" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx250, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx250, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx250. Exemplary heavy and light chain sequences for antibody ABTx250 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0146] ABTx250 heavy chain (HC): TIFF2025530892000020.tif56165

[0147] ABTx250 light chain (LC): TIFF2025530892000021.tif27165

[0148] The three CDRs of the ABTx250 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0149] The three CDRs of the ABTx250 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQFNSYPLT (SEQ ID NO: 425).

[0150] The four framework (FR) regions of the ABTx250 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx250 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0151] The four FRs of the ABTx250 antibody VL region are as follows: 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).

[0152] "ABTx250 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx250 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0153] "ABTx251" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx251, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein the antibody, CDRs, and antigen-binding fragment, respectively, specifically bind to wild-type CD117 polypeptide but have no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx251. Exemplary heavy and light chain sequences for antibody ABTx251 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0154] ABTx251 heavy chain (HC): TIFF2025530892000022.tif57165

[0155] ABTx251 light chain (LC): TIFF2025530892000023.tif26165

[0156] The three CDRs of the ABTx251 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0157] The three CDRs of the ABTx251 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQFYSYPLT (SEQ ID NO: 954).

[0158] The four framework (FR) regions of the ABTx251 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx251 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0159] The four FRs of the ABTx251 antibody VL region are as follows: 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).

[0160] "ABTx251 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx251 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0161] "ABTx252" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx252, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx252, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or antigen-binding fragment 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 for antibody ABTx252 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0162] ABTx252 heavy chain (HC): TIFF2025530892000024.tif57165

[0163] ABTx252 light chain (LC): TIFF2025530892000025.tif27165

[0164] The three CDRs of the ABTx252 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0165] The three CDRs of the ABTx252 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQFNSHPLT (SEQ ID NO: 955).

[0166] The four framework (FR) regions of the ABTx252 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx252 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0167] The four FRs of the ABTx252 antibody VL region are as follows: 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).

[0168] "ABTx252 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx252 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0169] "ABTx253" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx253, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or 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 for antibody ABTx253 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0170] ABTx253 heavy chain (HC): TIFF2025530892000026.tif57165

[0171] ABTx253 light chain (LC): TIFF2025530892000027.tif27165

[0172] The three CDRs of the ABTx253 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0173] The three CDRs of the ABTx253 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQFSSYPLT (SEQ ID NO: 1020).

[0174] The four framework (FR) regions of the ABTx253 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx253 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0175] The four FRs of the ABTx253 antibody VL region are as follows: 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).

[0176] "ABTx253 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx253 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0177] "ABTx254" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx254, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx254, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or antigen-binding fragment 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 for antibody ABTx254 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0178] ABTx254 heavy chain (HC): TIFF2025530892000028.tif59165

[0179] ABTx254 light chain (LC): TIFF2025530892000029.tif27165

[0180] The three CDRs of the ABTx254 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).

[0181] The three CDRs of the ABTx254 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTNSHPLT (SEQ ID NO: 1023).

[0182] The four framework (FR) regions of the ABTx254 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx254 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0183] The four FRs of the ABTx254 antibody VL region are as follows: 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).

[0184] "ABTx254 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx254 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0185] "ABTx255" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx255, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx255, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx255. Exemplary heavy and light chain sequences for antibody ABTx255 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0186] ABTx255 heavy chain (HC): TIFF2025530892000030.tif57165

[0187] ABTx255 light chain (LC): TIFF2025530892000031.tif27165

[0188] The three CDRs of the ABTx255 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0189] The three CDRs of the ABTx255 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVRSYPLT (SEQ ID NO: 1025).

[0190] The four framework (FR) regions of the ABTx255 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx255 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0191] The four FRs of the ABTx255 antibody VL region are as follows: 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).

[0192] "ABTx255 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx255 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0193] "ABTx256" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx256, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx256, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 for antibody ABTx256 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0194] ABTx256 Heavy Chain (HC): TIFF2025530892000032.tif57165

[0195] ABTx256 light chain (LC): TIFF2025530892000033.tif27165

[0196] The three CDRs of the ABTx256 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO: 1027).

[0197] The three CDRs of the ABTx256 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTYSYPLT (SEQ ID NO: 1029).

[0198] The four framework (FR) regions of the ABTx256 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx256 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0199] The four FRs of the ABTx256 antibody VL region are as follows: 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).

[0200] "ABTx256 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx256 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0201] "ABTx257" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx257, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx257, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx257. Exemplary heavy and light chain sequences for antibody ABTx257 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0202] ABTx257 Heavy Chain (HC): TIFF2025530892000034.tif57165

[0203] ABTx257 light chain (LC): TIFF2025530892000035.tif27165

[0204] The three CDRs of the ABTx257 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO: 1032).

[0205] The three CDRs of the ABTx257 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTNSYPLT (SEQ ID NO: 1044).

[0206] The four framework (FR) regions of the ABTx257 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx257 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0207] The four FRs of the ABTx257 antibody VL region are as follows: 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).

[0208] "ABTx257 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx257 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0209] "ABTx258" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx258, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx258, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx258. Exemplary heavy and light chain sequences for antibody ABTx258 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0210] ABTx258 Heavy Chain (HC): TIFF2025530892000036.tif57165

[0211] ABTx258 light chain (LC): TIFF2025530892000037.tif28165

[0212] The three CDRs of the ABTx258 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO: 1027).

[0213] The three CDRs of the ABTx058 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVRSYPLT (SEQ ID NO: 1025).

[0214] The four framework (FR) regions of the ABTx258 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx258 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0215] The four FRs of the ABTx258 antibody VL region are as follows: 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).

[0216] "ABTx258 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx258 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0217] "ABTx259" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx259, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or antigen-binding fragment 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 for antibody ABTx259 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0218] ABTx259 Heavy Chain (HC): TIFF2025530892000038.tif57165

[0219] ABTx259 light chain (LC): TIFF2025530892000039.tif27165

[0220] The three CDRs of the ABTx259 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0221] The three CDRs of the ABTx259 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTRSYPLT (SEQ ID NO: 1036).

[0222] The four framework (FR) regions of the ABTx259 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx259 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0223] The four FRs of the ABTx259 antibody VL region are as follows: 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).

[0224] "ABTx259 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx259 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0225] "ABTx260" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx260, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx260, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx260. Exemplary heavy and light chain sequences for antibody ABTx260 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0226] ABTx260 heavy chain (HC): TIFF2025530892000040.tif57165

[0227] ABTx260 light chain (LC): TIFF2025530892000041.tif28165

[0228] The three CDRs of the ABTx260 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).

[0229] The three CDRs of the ABTx260 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVNSHPLT (SEQ ID NO: 1038).

[0230] The four framework (FR) regions of the ABTx260 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx260 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0231] The four FRs of the ABTx260 antibody VL region are as follows: 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).

[0232] "ABTx260 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx260 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0233] "ABTx261" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx261, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or 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 for antibody ABTx261 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0234] ABTx261 heavy chain (HC): TIFF2025530892000042.tif57165

[0235] ABTx261 light chain (LC): TIFF2025530892000043.tif28165

[0236] The three CDRs of the ABTx261 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO: 1027).

[0237] The three CDRs of the ABTx261 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTRSYPLT (SEQ ID NO: 1036).

[0238] The four framework (FR) regions of the ABTx261 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx261 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0239] The four FRs of the ABTx261 antibody VL region are as follows: 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).

[0240] "ABTx261 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx261 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0241] "ABTx262" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx262, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx262, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or antigen-binding fragment 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 for antibody ABTx262 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0242] ABTx262 heavy chain (HC): TIFF2025530892000044.tif57165

[0243] ABTx262 light chain (LC): TIFF2025530892000045.tif26165

[0244] The three CDRs of the ABTx262 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO: 1027).

[0245] The three CDRs of the ABTx262 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQFRSSPLT (SEQ ID NO: 1040).

[0246] The four framework (FR) regions of the ABTx262 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx262 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0247] The four FRs of the ABTx262 antibody VL region are as follows: 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).

[0248] "ABTx262 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx262 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0249] "ABTx263" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx263, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx263, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx263. Exemplary heavy and light chain sequences for antibody ABTx263 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0250] ABTx263 heavy chain (HC): TIFF2025530892000046.tif57165

[0251] ABTx263 light chain (LC): TIFF2025530892000047.tif26165

[0252] The three CDRs of the ABTx263 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).

[0253] The three CDRs of the ABTx263 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVYSYPLT (SEQ ID NO: 1042).

[0254] The four framework (FR) regions of the ABTx263 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx263 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0255] The four FRs of the ABTx263 antibody VL region are as follows: 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).

[0256] "ABTx263 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx263 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0257] "ABTx264" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx264, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx264, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to a wild-type CD117 polypeptide but has no detectable or reduced binding to a modified CD117 polypeptide. In certain 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 ABTx264. Exemplary heavy and light chain sequences for antibody ABTx264 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0258] ABTx264 heavy chain (HC): TIFF2025530892000048.tif57165

[0259] ABTx264 light chain (LC): TIFF2025530892000049.tif27165

[0260] The three CDRs of the ABTx264 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO: 1027).

[0261] The three CDRs of the ABTx264 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTYSYPLT (SEQ ID NO: 1029).

[0262] The four framework (FR) regions of the ABTx264 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx264 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0263] The four FRs of the ABTx264 antibody VL region are as follows: 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).

[0264] "ABTx264 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx264 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0265] "ABTx265" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx265, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx265, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx265. Exemplary heavy and light chain sequences for antibody ABTx265 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0266] ABTx265 heavy chain (HC): TIFF2025530892000050.tif60165

[0267] ABTx265 light chain (LC): TIFF2025530892000051.tif27165

[0268] The three CDRs of the ABTx265 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).

[0269] The three CDRs of the ABTx265 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTRSYPLT (SEQ ID NO: 1036).

[0270] The four framework (FR) regions of the ABTx265 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx265 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0271] The four FRs of the ABTx265 antibody VL region are as follows: 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).

[0272] "ABTx265 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx265 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0273] "ABTx266" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx266, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or antigen-binding fragment 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 for antibody ABTx266 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0274] ABTx266 Heavy Chain (HC): TIFF2025530892000052.tif57165

[0275] ABTx266 light chain (LC): TIFF2025530892000053.tif27165

[0276] The three CDRs of the ABTx266 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO: 1027).

[0277] The three CDRs of the ABTx266 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVRSHPLT (SEQ ID NO: 1047).

[0278] The four framework (FR) regions of the ABTx266 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx266 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0279] The four FRs of the ABTx266 antibody VL region are as follows: 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).

[0280] "ABTx266 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx266 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0281] "ABTx267" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx267, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx267, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx267. Exemplary heavy and light chain sequences for antibody ABTx267 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0282] ABTx267 Heavy Chain (HC): TIFF2025530892000054.tif56165

[0283] ABTx267 light chain (LC): TIFF2025530892000055.tif27165

[0284] The three CDRs of the ABTx267 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO: 1032).

[0285] The three CDRs of the ABTx267 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTNSSPLT (SEQ ID NO: 1050).

[0286] The four framework (FR) regions of the ABTx267 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx267 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0287] The four FRs of the ABTx267 antibody VL region are as follows: 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).

[0288] "ABTx267 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx267 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0289] "ABTx268" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx268, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or 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 for antibody ABTx268 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0290] ABTx268 heavy chain (HC): TIFF2025530892000056.tif57165

[0291] ABTx268 light chain (LC): TIFF2025530892000057.tif27165

[0292] The three CDRs of the ABTx268 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0293] The three CDRs of the ABTx268 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVNSYPLT (SEQ ID NO: 952).

[0294] The four framework (FR) regions of the ABTx268 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx268 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0295] The four FRs of the ABTx268 antibody VL region are as follows: 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).

[0296] "ABTx268 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx268 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0297] "ABTx269" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx269, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or antigen-binding fragment 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 for antibody ABTx269 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0298] ABTx269 Heavy Chain (HC): TIFF2025530892000058.tif58165

[0299] ABTx269 light chain (LC): TIFF2025530892000059.tif28165

[0300] The three CDRs of the ABTx269 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0301] The three CDRs of the ABTx269 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVYSYPLT (SEQ ID NO: 1042).

[0302] The four framework (FR) regions of the ABTx269 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx269 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0303] The four FRs of the ABTx269 antibody VL region are as follows: 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).

[0304] "ABTx269 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx269 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0305] "ABTx270" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx270, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx270, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx270. Exemplary heavy and light chain sequences for antibody ABTx270 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0306] ABTx270 heavy chain (HC): TIFF2025530892000060.tif56165

[0307] ABTx270 light chain (LC): TIFF2025530892000061.tif27165

[0308] The three CDRs of the ABTx270 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDAYEGAFDI (SEQ ID NO: 1027).

[0309] The three CDRs of the ABTx270 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVRSYPLT (SEQ ID NO: 1025).

[0310] The four framework (FR) regions of the ABTx270 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx270 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0311] The four FRs of the ABTx270 antibody VL region are as follows: 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).

[0312] "ABTx270 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx270 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0313] "ABTx271" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx271, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity to the antibody sequence of antibody ABTx271. Exemplary heavy and light chain sequences for antibody ABTx271 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0314] ABTx271 heavy chain (HC): TIFF2025530892000062.tif59165

[0315] ABTx271 light chain (LC): TIFF2025530892000063.tif26165

[0316] The three CDRs of the ABTx271 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDAYDGAFDI (SEQ ID NO: 1032).

[0317] The three CDRs of the ABTx271 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTNSYPLT (SEQ ID NO: 1044).

[0318] The four framework (FR) regions of the ABTx271 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx271 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0319] The four FRs of the ABTx271 antibody VL region are as follows: 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).

[0320] "ABTx271 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx271 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0321] "ABTx272" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx272, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx272, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or 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 for antibody ABTx272 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0322] ABTx272 heavy chain (HC): TIFF2025530892000064.tif57165

[0323] ABTx272 light chain (LC): TIFF2025530892000065.tif27165

[0324] The three CDRs of the ABTx272 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).

[0325] The three CDRs of the ABTx272 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQVRSYPLT (SEQ ID NO: 1025).

[0326] The four framework (FR) regions of the ABTx272 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx272 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0327] The four FRs of the ABTx272 antibody VL region are as follows: 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).

[0328] "ABTx272 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx272 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0329] "ABTx273" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx273, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or 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 for antibody ABTx273 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0330] ABTx273 heavy chain (HC): TIFF2025530892000066.tif57165

[0331] ABTx273 light chain (LC): TIFF2025530892000067.tif27165

[0332] The three CDRs of the ABTx273 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTR (SEQ ID NO: 958); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0333] The three CDRs of the ABTx0273 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQFRSYPLT (SEQ ID NO: 953).

[0334] The four framework (FR) regions of the ABTx273 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx273 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0335] The four FRs of the ABTx273 antibody VL region are as follows: 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).

[0336] "ABTx273 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx273 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0337] "ABTx274" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx274, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or antigen-binding fragment 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 for antibody ABTx274 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0338] ABTx274 heavy chain (HC): TIFF2025530892000068.tif57165

[0339] ABTx274 light chain (LC): TIFF2025530892000069.tif27165

[0340] The three CDRs of the ABTx274 antibody VH region are as follows: VH CDR1: GYRFTSYW (SEQ ID NO: 421); VH CDR2: IYPGDSDTK (SEQ ID NO: 972); and VH CDR3: ARHGRGYDGYEGAFDI (SEQ ID NO: 948).

[0341] The three CDRs of the ABTx274 antibody VL region are as follows: VL CDR1: QGISSA (SEQ ID NO: 424); VL CDR2: DAS; and VL CDR3: QQTNSYPLT (SEQ ID NO: 1044).

[0342] The four framework (FR) regions of the ABTx274 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx274 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426); VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427); and VH FR3: RYSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 428) or YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 973), VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0343] The four FRs of the ABTx274 antibody VL region are as follows: 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).

[0344] "ABTx274 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx274 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0345] "ABTx313" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx313, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx313, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx313. Exemplary heavy and light chain sequences for antibody ABTx313 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0346] ABTx313 heavy chain (HC): TIFF2025530892000070.tif57165

[0347] ABTx313 light chain (LC): TIFF2025530892000071.tif27165

[0348] The three CDRs of the ABTx313 VH region are as follows: VH CDR-1: GYRFTSYW (SEQ ID NO: 421); VH CDR-2: IYPGDSDTR (SEQ ID NO: 1053) VH CDR-3:ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).

[0349] The three CDRs of the ABTx313 VL region are as follows: VL CDR-1: QGISSA (SEQ ID NO: 424) VL CDR-2:DAS VL CDR-3: QQFSSYPLT (SEQ ID NO: 1020).

[0350] The four framework (FR) regions of the ABTx313 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx313 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426) VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427) VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 1059) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429) The four FRs of the ABTx313 antibody VL region are as follows: VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 430) VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 431) VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 432) VL FR4: FGGGTKVEIKRTV (SEQ ID NO: 433).

[0351] "ABTx313 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx313 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0352] "ABTx307" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx307, or an antibody comprising the VH and / or VL CDRs 1-3 or antigen-binding fragments of ABTx307, where each of the antibody, CDRs, and antigen-binding fragments specifically binds to a wild-type CD117 polypeptide but has no detectable or reduced binding to a modified CD117 polypeptide. In certain embodiments, the antibody or antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity to the antibody sequence of antibody ABTx307. Exemplary heavy and light chain sequences for antibody ABTx307 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0353] ABTx307 Heavy Chain (HC): TIFF2025530892000072.tif57165

[0354] ABTx307 Light Chain (LC) (VL): TIFF2025530892000073.tif29165

[0355] The three CDRs of the ABTx307 VH region are as follows: VH CDR-1: GYRFTSYW (SEQ ID NO: 421) VH CDR-2: IYPGDSDTR (SEQ ID NO: 1053) VH CDR-3:ARHGRGYDGYDGAFDI (SEQ ID NO: 1012).

[0356] The three CDRs of the ABTx307 VL region are as follows: VL CDR-1: QGISSA (SEQ ID NO: 424) VL CDR-2:DAS VL CDR-3: QQFNSYPLT (SEQ ID NO: 425).

[0357] The four framework (FR) regions of the ABTx307 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx307 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426) VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427) VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 1059) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429) The four FRs of the ABTx307 antibody VL region are as follows: VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 430) VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 431) VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 432) VL FR4: FGGGTKVEIKRTV (SEQ ID NO: 433).

[0358] "ABTx307 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx307 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0359] "ABTx308" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx308, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx308, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx308. Exemplary heavy and light chain sequences for antibody ABTx308 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0360] ABTx308 heavy chain (HC): TIFF2025530892000074.tif59165

[0361] ABTx308 light chain TIFF2025530892000075.tif27165

[0362] The three CDRs of the ABTx308 VH region are as follows: VH CDR-1: GYRFTSYW (SEQ ID NO: 421) VH CDR-2: IYPGDSDTK (SEQ ID NO: 1063) VH CDR-3:ARHGRGYDAYDGAFDI (SEQ ID NO: 1032).

[0363] The three CDRs of the ABTx308 VL region are as follows: VL CDR-1: QGISSA (SEQ ID NO: 424) VL CDR-2:DAS VL CDR-3: QQFSSYPLT (SEQ ID NO: 1020).

[0364] The four framework (FR) regions of the ABTx308 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx308 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 426) VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 427) VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 1059) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429)

[0365] The four FRs of the ABTx308 antibody VL region are as follows: VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 1060) VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 1061) VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 1062) VL FR4: FGGGTKVEIKRTV (SEQ ID NO: 433).

[0366] "ABTx308 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx308 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0367] "ABTx309" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx309, or an antibody comprising the VH and / or VL CDRs 1-3 or antigen-binding fragments of ABTx309, where each of the antibody, CDRs, and antigen-binding fragments specifically binds to a wild-type CD117 polypeptide but has no detectable or reduced binding to a modified CD117 polypeptide. In certain embodiments, the antibody or 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 for antibody ABTx309 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0368] ABTx309 Heavy Chain (HC): TIFF2025530892000076.tif58165

[0369] ABTx309 light chain (LC): TIFF2025530892000077.tif29165

[0370] The three CDRs of the ABTx309 VH region are as follows: VH CDR-1: GYRFTSYW (SEQ ID NO: 421) VH CDR-2: IYPGDSDTR (SEQ ID NO: 1053) VH CDR-3:ARHGRGYDAYDGAFDI (SEQ ID NO: 1064).

[0371] The three CDRs of the ABTx309 VL region are as follows: VL CDR-1: QGISSA (SEQ ID NO: 424) VL CDR-2:DAS VL CDR-3: QQTNSYPLT (SEQ ID NO: 1044).

[0372] The four framework (FR) regions of the ABTx309 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx309 antibody VH region are as follows: VH FR1: QVQLVQSGAAVKKPGESLKISCKGS (SEQ ID NO: 1057) VH FR2: IGWVRQMPGKGLEWMGI (SEQ ID NO: 1058) VH FR3: YSPSFQGQVTISAGKSISTAYLQWSSLKASDTAMYYC (SEQ ID NO: 1059) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0373] The four FRs of the ABTx309 antibody VL region are as follows: VL FR1: AIQLTQSPSSLSASVGDRVTITCRAS (SEQ ID NO: 430) VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 431) VL FR3: SLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 432) VL FR4: FGGGTKVEIKRTV (SEQ ID NO: 433).

[0374] "ABTx309 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx309 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0375] "ABTx196" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx196, or an antibody comprising the VH and / or VL CDRs 1-3 or antigen-binding fragments of ABTx196, where each of the antibody, CDRs, and antigen-binding fragments specifically binds to a wild-type CD117 polypeptide but has no detectable or reduced binding to a modified CD117 polypeptide. In certain embodiments, the antibody or antigen-binding fragment has at least 90%, 93%, 95%, 98%, 99%, or 100% amino acid sequence identity with the antibody sequence of antibody ABTx196. Exemplary heavy chain and light chain variable region sequences for antibody ABTx196 are shown below, with the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0376] ABTx196 heavy chain variable region (VH): EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCSSASCYGAFDI WGQGTMVTVSS (SEQ ID NO: 1120)

[0377] ABTx196 light chain variable region (VL): DVVMTQSPGTLSLSPGERATLSCRAS QSVSSSY LAWYQQKPGQAPRLLIY GAS SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC QQSETCLT FGGGTKLEIK (SEQ ID NO: 1068)

[0378] The three CDRs of the ABTx196 VH region are as follows: VH CDR-1: GFTFDDYA (SEQ ID NO: 391) VH CDR-2: ISWNSGTIG (SEQ ID NO: 1070) VH CDR-3:AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393)

[0379] The three CDRs of the ABTx196 VL region are as follows: VL CDR-1: QSVSSSY (SEQ ID NO: 394) VL CDR-2:GAS VL CDR-3: QQSETCLT (SEQ ID NO: 1074)

[0380] The four framework (FR) regions of the ABTx196 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx196 antibody VH region are as follows: VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396) VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 397) VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1077) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0381] The four FRs of the ABTx196 antibody VL region are as follows: VL FR1: DVVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO: 400) VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO: 446) VL FR3: SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO: 402) VL FR4: FGGGTKLEIK (SEQ ID NO: 1082)

[0382] "ABTx196 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx196 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0383] "ABTx202" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx202, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx202, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx202. Exemplary heavy chain and light chain variable region sequences for antibody ABTx202 are shown below, with the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0384] ABTx202 heavy chain variable region (VH): EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTSSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCSSASCYGAFDI WGQGTMVTVSS (SEQ ID NO: 1085)

[0385] ABTx202 light chain variable region (VL): EIVMTQSPGTLSLSPGERATLSCRAS QSVSSSY LAWYQQKPGQAPRLLIY GSS TRATGIPARFSGSGSGTEFALTISSLQSEDFAVYYC QQYNFWPYT FGQGTKVEIK (SEQ ID NO: 1086)

[0386] The three CDRs of the ABTx202 VH region are as follows: VH CDR-1: GFTFDDYA (SEQ ID NO: 391) VH CDR-2: ISWNSGTIG (SEQ ID NO: 1070) VH CDR-3:AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393)

[0387] The three CDRs of the ABTx202 light chain variable region (VL) region are as follows: VL CDR-1: QSVSSSY (SEQ ID NO: 394) VL CDR-2:GSS VL CDR-3: QQYNFWPYT (SEQ ID NO: 1084)

[0388] The four framework (FR) regions of the ABTx202 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx202 antibody VH region are as follows: VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396) VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 397) VH FR3: YADSVKGRFTSSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1065) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0389] The four FRs of the ABTx202 antibody VL region are as follows: VL FR1: EIVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO: 1087) VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO: 446) VL FR3: TRATGIPARFSGSGSGTEFALTISSLQSEDFAVYYC (SEQ ID NO: 1080) VL FR4: FGQGTKVEIK (SEQ ID NO: 1088)

[0390] "ABTx202 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx202 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0391] "ABTx198" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx198, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx198, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx198. Exemplary heavy chain and light chain variable region sequences for antibody ABTx198 are shown below, with the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0392] ABTx198 heavy chain variable region (VH): EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCASASCYGAFDI WGQGTMVTVSS (SEQ ID NO: 1089)

[0393] ABTx198 light chain variable region (VL): DVVMTQSPGTLSLSPGERATLSCRAS QSVSSSY LAWYQQKPGQAPRLLIY GAS SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC QQDSLGLT FGGGTKLEIK (SEQ ID NO: 1103)

[0394] The three CDRs of the ABTx198 VH region are as follows: VH CDR-1: GFTFDDYA (SEQ ID NO: 391) VH CDR-2: ISWNSGTIG (SEQ ID NO: 1070) VH CDR-3:AKDSPPGYCASASCYGAFDI (SEQ ID NO: 1090)

[0395] The three CDRs of the ABTx198 light chain variable region (VL) region are as follows: VL CDR-1: QSVSSSY (SEQ ID NO: 394) VL CDR-2:GAS VL CDR-3: QQDSLGLT (SEQ ID NO: 1091)

[0396] The four framework (FR) regions of the ABTx198 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx198 antibody VH region are as follows: VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396) VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 397) VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1077) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0397] The four FRs of the ABTx198 antibody VL region are as follows: VL FR1: DVVMTQSPGTLSLSPGERATLSCRAS (SEQ ID NO: 400) VL FR2: LAWYQQKPGQAPRLLIY (SEQ ID NO: 446) VL FR3: SRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYC (SEQ ID NO: 402) VL FR4: FGGGTKLEIK (SEQ ID NO: 1082)

[0398] "ABTx198 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx198 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0399] "ABTx203" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx203, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx203, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx203. Exemplary heavy chain and light chain variable region sequences for antibody ABTx203 are shown below, with the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0400] ABTx203 heavy chain variable region (VH): EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDWPSGFCSSAYCYGAFDI WGQGTMVTVSS (SEQ ID NO: 1092)

[0401] ABTx203 light chain variable region (VL): DIVMTQSPSFLSASVGDRVTITCRAS QGISSY LAWYQQKPGKAPKLLIY AAS TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC QQSYSTPYTFGQGTKLEIK (SEQ ID NO: 1093)

[0402] The three CDRs of the ABTx203 VH region are as follows: VH CDR-1: GFTFDDYA (SEQ ID NO: 391) VH CDR-2: ISWNSGTIG (SEQ ID NO: 1070) VH CDR-3:AKDWPSGFCSSAYCYGAFDI (SEQ ID NO: 1094)

[0403] The three CDRs of the ABTx203 VL region are as follows: VL CDR-1: QGISSY (SEQ ID NO: 469) VL CDR-2:AAS VL CDR-3: QQSYSTPYT (SEQ ID NO: 1097)

[0404] The four framework (FR) regions of the ABTx203 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx203 antibody VH region are as follows: VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396) VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 397) VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1077) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0405] The four FRs of the ABTx203 antibody VL region are as follows: VL FR1: DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO: 475) VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 431) VL FR3: TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC (SEQ ID NO: 1099) VL FR4: FGQGTKLEIK (SEQ ID NO: 1100)

[0406] "ABTx203 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx203 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0407] "ABTx205" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx205, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx205, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain embodiments, the antibody or 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 and light chain variable region sequences for antibody ABTx205 are shown below, with the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0408] ABTx205 heavy chain variable region (VH): EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCSSASCYGAFDI WGQGTMVTVSS (SEQ ID NO: 1120)

[0409] ABTx205 light chain variable region (VL): DIVMTQSPSFLSASVGDRVTITCRAS QGISSY LAWYQQKPGKAPKLLIY AAS TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC QQSYSTPYT FGQGTKLEIK (SEQ ID NO: 1093)

[0410] The three CDRs of the ABTx205 VH region are as follows: VH CDR-1: GFTFDDYA (SEQ ID NO: 391) VH CDR-2: ISWNSGTIG (SEQ ID NO: 1070) VH CDR-3:AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393)

[0411] The three CDRs of the ABTx205 VL region are as follows: VL CDR-1: QGISSY (SEQ ID NO: 1095) VL CDR-2:AAS VL CDR-3: QQSYSTPYT (SEQ ID NO: 1097)

[0412] The four framework (FR) regions of the ABTx205 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx205 antibody VH region are as follows: VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396) VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 397) VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1077) VH FR4: WGQGTMVTVSS (SEQ ID NO: 429).

[0413] The four FRs of the ABTx205 antibody VL region are as follows: VL FR1: DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO: 475) VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 431) VL FR3: TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC (SEQ ID NO: 1099) VL FR4: FGQGTKLEIK (SEQ ID NO: 1100)

[0414] "ABTx205 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx205 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0415] "ABTx206" refers to an antibody having at least about 85% amino acid sequence identity with the antibody sequence of antibody ABTx206, or an antibody comprising VH and / or VL CDRs 1-3 or antigen-binding fragments thereof of ABTx206, wherein each of the antibody, CDRs, and antigen-binding fragments specifically binds to wild-type CD117 polypeptide but has no detectable or reduced binding to modified CD117 polypeptides. In certain 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 ABTx206. Exemplary heavy and light chain variable region sequences for antibody ABTx206 are shown below, with the variable regions in plain text, the constant domains in bold, and the complementarity-determining regions (CDRs), i.e., CDR1, CDR2, and CDR3, underlined.

[0416] ABTx206 heavy chain variable region (VH): EVQLVESGGGLVQPGRSLRLSCAAS GFTFDDYA MHWVRQAPGKGLEWVSG ISWNSGTIG YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC AKDSPPGYCSSASCYGAFDI RGQGTMVTVSS (SEQ ID NO: 1101)

[0417] ABTx206 light chain variable region (VL): DIVMTQSPSFLSASVGDRVTITCRAS QGISSY LAWYQQKPGKAPKLLIY AAS TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC QQSYSTPYT FGQGTKLEIK (SEQ ID NO: 1093)

[0418] The three CDRs of the ABTx206 VH region are as follows: VH CDR-1: GFTFDDYA (SEQ ID NO: 391) VH CDR-2: ISWNSGTIG (SEQ ID NO: 1070) VH CDR-3:AKDSPPGYCSSASCYGAFDI (SEQ ID NO: 393)

[0419] The three CDRs of the ABTx206 VL region are as follows: VL CDR-1: QGISSY (SEQ ID NO: 1095) VL CDR-2:AAS VL CDR-3: QQSYSTPYT (SEQ ID NO: 1097)

[0420] The four framework (FR) regions of the ABTx206 antibody, i.e., FR1, FR2, FR3, and FR4, are located on either side of the CDRs of each of the VH and VL region sequences described above. In particular, the four FRs of the ABTx206 antibody VH region are as follows: VH FR1: EVQLVESGGGLVQPGRSLRLSCAAS (SEQ ID NO: 396) VH FR2: MHWVRQAPGKGLEWVSG (SEQ ID NO: 397) VH FR3: YADSVKGRFTNSRDNAKNSLYLEMNSLRAEDTALYYC (SEQ ID NO: 1077) VH FR4: RGQGTMVTVSS (SEQ ID NO: 1102)

[0421] The four FRs of the ABTx206 antibody VL region are as follows: VL FR1: DIVMTQSPSFLSASVGDRVTITCRAS (SEQ ID NO: 475) VL FR2: LAWYQQKPGKAPKLLIY (SEQ ID NO: 431) VL FR3: TLQNGVPSRFSGSGSGTDFTLTITSLQPEDFATYYC (SEQ ID NO: 1099) VL FR4: FGQGTKLEIK (SEQ ID NO: 1100)

[0422] "ABTx206 polynucleotide" refers to a nucleic acid molecule (e.g., DNA) that encodes at least a fragment of the ABTx206 antibody. In one embodiment, the encoded fragment has antigen-binding activity.

[0423] "Adenine" or "9H-purin-6-amine" has the molecular formula C5H5N5 and the structure [ka] and refers to the purine nucleobase having the formula:

[0424] "Adenosine" or "4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2(1H)-one" is a compound attached to a ribose sugar via a glycosidic bond and has the structure [ka] It refers to the adenine molecule having the formula C and corresponding to the CAS number 65-46-3. 10 H 13 It is N5O4.

[0425] "Adenosine deaminase" or "adenine deaminase" refers to a polypeptide or fragment thereof that can catalyze 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 deoxyadenosine to deoxyinosine. In some embodiments, the adenosine deaminase catalyzes the hydrolytic deamination of adenine or adenosine in deoxyribonucleic acid (DNA). The adenosine deaminases (e.g., engineered adenosine deaminases, evolved adenosine deaminases) provided herein can be derived from any organism (e.g., eukaryotes, prokaryotes), 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 modifications and capable of deaminating both adenine and cytosine in a target polynucleotide (e.g., DNA, RNA), and may be referred to as a "dual deaminase." Non-limiting examples of dual deaminases include those described in PCT / US22 / 22050. In some embodiments, the target polynucleotide is single-stranded or double-stranded. In some embodiments, the adenosine deaminase variant is capable of deaminating both adenine and cytosine in DNA. In some embodiments, the adenosine deaminase variant is capable of deaminating both adenine and cytosine in single-stranded DNA. In some embodiments, the adenosine deaminase variant is capable of deaminating both adenine and cytosine in RNA. In some 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.

[0426] "Adenosine deaminase activity" means catalyzing the deamination of adenine or adenosine to guanine in a polynucleotide. In some embodiments, the adenosine deaminase variants provided herein maintain 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)).

[0427] "Adenosine base editor (ABE)" means a base editor that includes an adenosine deaminase.

[0428] "Adenosine base editor (ABE)" means a base editor that includes an adenosine deaminase.

[0429] "Adenosine base editor (ABE) polynucleotide" refers to a polynucleotide encoding an ABE. "Adenosine base editor 8 (ABE8) polypeptide" or "ABE8" refers to a base editor as defined herein, comprising an adenosine deaminase or adenosine deaminase variant that includes one or more modifications listed in Table 5B, one of the combinations of modifications listed in Table 5B, or a modification at one or more amino acid positions listed in Table 5B, or a corresponding position in another adenosine deaminase (such modifications are with respect to the following reference sequence: MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVLHYPGMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO: 1)). In certain embodiments, ABE8 comprises modifications at amino acids 82 and / or 166 of SEQ ID NO: 1. In some embodiments, ABE8 comprises additional modifications relative to the reference sequence, as described herein.

[0430] By "adenosine base editor 8 (ABE8) polynucleotide" is meant a polynucleotide that encodes an ABE8 polypeptide.

[0431] By "adenosine base editor 8 (ABE8) polynucleotide" is meant a polynucleotide that encodes an ABE8 polypeptide.

[0432] "Administering" refers herein to providing one or more compositions described herein to a patient or subject. By way of example, and not limitation, administration, e.g., injection, of a composition can be performed by intravenous (iv), subcutaneous (sc), intradermal (id), intraperitoneal (ip), or intramuscular (im) injection. One or more such routes can be used. Parenteral administration can be performed, for example, by bolus injection or gradual perfusion over time. In some embodiments, parenteral administration includes intravascular, intravenous, intramuscular, intraarterial, intrathecal, intratumoral, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, and intrasternal infusion or injection. Alternatively, or concurrently, administration can be performed by the oral route.

[0433] By "agent" is meant any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide, or fragment thereof.

[0434] As used herein, "allogeneic" refers to cells of the same species that are genetically distinct from the cells to which they are being compared.

[0435] As used herein, "autologous" refers to cells derived from the same subject.

[0436] "Alteration" refers to a change in the level, structure, or activity of an analyte, gene, or polypeptide, as detected by standard methods known in the art, such as those described herein. As used herein, modification includes a change (e.g., an increase or decrease) in expression levels. In certain embodiments, the increase or decrease in expression levels is 10%, 25%, 40%, 50%, or more. In some embodiments, modification includes an insertion, deletion, or substitution (e.g., by genetic modification) of a nucleic acid base or amino acid.

[0437] "Ameliorate" means to reduce, suppress, attenuate, decrease, arrest, or stabilize the onset or progression of a disease.

[0438] "Analog" refers to a molecule that has similar, but not identical, functional or structural characteristics. For example, a polypeptide analog retains the biological activity of the corresponding naturally occurring polypeptide while possessing certain biochemical modifications that enhance the analog's function relative to the naturally occurring polypeptide. Such biochemical modifications may increase the analog's protease resistance, membrane permeability, or half-life, for example, without altering ligand binding. Analogs may also contain unnatural amino acids.

[0439] As used herein, the term "antibody" refers to an immunoglobulin molecule that specifically binds to or immunologically reacts with a particular antigen, including polyclonal, monoclonal, genetically engineered, and other modified forms of antibodies, including, but not limited to, chimeric antibodies, humanized antibodies, heteroconjugate antibodies (e.g., diabodies, triabodies, and tetrabodies), and antigen-binding fragments of antibodies, including, for example, Fab', F(ab')2, Fab, Fv, rIgG, and scFv fragments. Unless otherwise specified, the term "monoclonal antibody" (mAb) is intended to include not only intact molecules but also antibody fragments (e.g., Fab fragments and F(ab')2 fragments) that are capable of specifically binding to a target protein. As used herein, Fab and F(ab')2 fragments refer to antibody fragments that lack the Fc fragment of an intact antibody.

[0440] An antibody (immunoglobulin) comprises two heavy chains linked together by disulfide bonds and two light chains, with each light chain linked to a respective heavy chain by a disulfide bond in a "Y" configuration. Each heavy chain has a variable domain (VH) at one end followed by several constant domains (CH). Each light chain has a variable domain (VL) at one end and a constant domain (CL) at the other end. The variable domain (VL) of the light chain is aligned with the variable domain (VL) of the heavy chain, and the light chain constant domain (CL) is aligned 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 heavy chain isotype (γ, α, δ, ε, or μ) determines the immunoglobulin class (IgG, IgA, IgD, IgE, or IgM, respectively). Light chains are of one of two isotypes, kappa (κ) or lambda (λ), present in all antibody classes. The term "antibody" includes intact antibodies, such as polyclonal or monoclonal antibodies (mAbs), as well as proteolytic portions or fragments thereof, such as Fab or F(ab')2 fragments, that are capable of specific binding to a target protein. Antibodies can include chimeric, recombinant, and modified antibodies, and antigen-binding fragments thereof.Exemplary functional antibody fragments comprising all or essentially all of the variable regions of both the light and heavy chains are defined as follows: (i) Fv, defined as a genetically engineered fragment consisting of the variable region of the light chain and the variable region of the heavy chain, expressed as two chains; (ii) single-chain Fv (“scFv”), a genetically engineered single-chain molecule comprising the variable region of the light chain and the variable region of the heavy chain linked by a suitable polypeptide linker; and (iii) a fragment of an antibody molecule comprising a monovalent antigen-binding portion of an antibody molecule, obtained by treating an intact antibody with the enzyme papain to produce an Fv consisting of its variable domain and CH1 domain. (iv) Fab', the fragment of an antibody molecule that contains a monovalent antigen-binding portion of an antibody molecule, which can be obtained by treating an intact antibody with the enzyme pepsin, followed by reduction (to produce two Fab' fragments per antibody molecule); and (v) F(ab')2, the fragment of an antibody molecule that contains a monovalent antigen-binding portion of an antibody molecule, which can be obtained by treating an intact antibody with the enzyme pepsin (i.e., a dimer of Fab' fragments held together by two disulfide bonds).

[0441] 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 may be performed by a fragment of a full-length antibody. An antibody fragment may be a 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) V L , V H , C L , and C H1 (ii) a Fab fragment, which is a monovalent fragment consisting of two Fab fragments linked by a disulfide bridge at the hinge region; and (iii) a V H and C H1(iv) a V fragment of a single arm of an antibody; L and V H Fv fragment consisting of domains, (v) V H and V L (vi) dAb containing domain V H (vii) a dAb fragment consisting of the V domain (Ward et al., Nature 341:544-546, 1989); H or V L (viii) an isolated complementarity-determining region (CDR), and (ix) a combination of two or more isolated CDRs, optionally joined by a synthetic linker. Additionally, the two domains of an Fv fragment, V L and V H Although the V and V proteins are encoded by separate genes, they can be joined by a linker that allows them to be made as a single protein chain using recombinant methods. L and V H The domains pair to form a monovalent molecule (known as a single-chain Fv (scFv); see, e.g., Bird et al., Science 242:423-426, 1988, and Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883, 1988). Such antibody fragments can be obtained using conventional techniques known to those of skill in the art, and the fragments can be screened for utility in the same manner as intact antibodies. Antigen-binding fragments can be produced by recombinant DNA techniques, enzymatic or chemical cleavage of intact immunoglobulins, or, in some cases, chemical peptide synthesis procedures known in the art. In some embodiments, antigen-binding fragments of anti-CD117 antibodies (e.g., Fab', F(ab')2, Fab, scFab, Fv, rIgG, and scFv fragments) linked by synthetic linkers are encompassed herein.

[0442] "Base editor (BE)" or "nucleobase editor polypeptide (NBE)" refers to an agent that binds to a polynucleotide and has nucleobase-modifying activity. In various embodiments, a base editor comprises a polynucleotide-programmable nucleotide-binding domain (e.g., Cas9 or Cpf1) in combination with a nucleobase-modifying polypeptide (e.g., a deaminase) and a guide polynucleotide (e.g., a guide RNA (gRNA)). Exemplary nucleic acid and protein sequences of base editors include those having about 85%, or at least about 85%, sequence identity to any base editor sequence set forth in the Sequence Listing, such as sequences corresponding to SEQ ID NOS: 2-11.

[0443] "Base editing activity" refers to acting to chemically modify 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 targeted 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.

[0444] 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., cytidine deaminase or adenosine deaminase) for deaminating nucleobases in a target nucleotide sequence; and (2) one or more guide polynucleotides (e.g., guide RNAs) in combination with the polynucleotide-programmable nucleotide-binding domain. In various embodiments, the base editor (BE) system comprises a nucleobase editor domain selected from adenosine deaminase or cytidine deaminase, and a domain with nucleic acid sequence-specific binding activity. In some embodiments, the base editor system comprises: (1) a base editor (BE) comprising a polynucleotide-programmable DNA-binding domain and a deaminase domain for deaminating one or more nucleobases in a target nucleotide sequence; and (2) one or more guide RNAs in combination with the polynucleotide-programmable DNA-binding domain. In some embodiments, the polynucleotide-programmable nucleotide-binding domain is a polynucleotide-programmable DNA-binding domain. In some embodiments, the base editor is a cytidine base editor (CBE). In some embodiments, the base editor is an adenine or adenosine base editor (ABE). In some embodiments, the base editor is an adenine or adenosine base editor (ABE) or a cytidine or cytosine base editor (CBE). In some embodiments, the base editor system (e.g., a base editor system comprising 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 provided in WO2022015969, the disclosure of which is incorporated herein by reference in its entirety for all purposes).

[0445] "Base editing activity" refers to acting to chemically modify 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.

[0446] 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 includes (1) a polynucleotide-programmable nucleotide-binding domain, a deaminase domain (e.g., adenosine deaminase) for deaminating nucleobases in a target nucleotide sequence, and (2) one or more guide polynucleotides (e.g., guide RNAs) in combination with the polynucleotide-programmable nucleotide-binding domain. In various embodiments, a base editor (BE) system includes a nucleobase editor domain (e.g., adenosine deaminase) and a domain with nucleic acid sequence-specific binding activity. In some embodiments, a base editor system includes (1) a base editor (BE) including a polynucleotide-programmable DNA-binding domain and a deaminase domain for deaminating one or more nucleobases in a target nucleotide sequence, and (2) one or more guide RNAs in combination with the polynucleotide-programmable DNA-binding domain. In some embodiments, the polynucleotide-programmable nucleotide-binding domain is a polynucleotide-programmable DNA-binding domain. In some embodiments, the base editor is an adenine or adenosine base editor (ABE). In some embodiments, the base editor system (e.g., a base editor system comprising an adenosine deaminase) comprises a uracil glycosylase inhibitor or other agent or peptide that inhibits the inosine base excision repair system.

[0447] By "β-globin (HBB) polypeptide" is meant a polypeptide having at least about 85% amino acid sequence identity to NCBI Accession No. NP_000509, shown below, or a fragment thereof capable of dimerizing with an HBA1 polypeptide. In certain embodiments, the β-globin protein comprises one or more modifications relative to the following reference sequence: In one particular embodiment, the β-globin protein associated with sickle cell disease comprises an E6V (also referred to as E7V) mutation. MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH (SEQ ID NO: 494).

[0448] "HBB polynucleotide" refers to a nucleic acid molecule encoding an HBB polypeptide, as well as introns, exons, 3' untranslated regions, 5' untranslated regions, and regulatory sequences associated with its expression, or fragments thereof. In certain embodiments, an HBB polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for the expression of HBB. Exemplary HBB polynucleotide sequences from Homo sapiens are shown below (NCBI Reference Sequence Accession Nos. NM_000518 and NG_059281): ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTA CCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACA CTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATG CCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGCAA (SEQ ID NO: 495).

[0449] >NG_059281.1:5001-6608 Homo sapiens hemoglobin subunit beta (HBB), RefSeqGene (LRG_1232) (chromosome 11); the A to T change in sickle cell disease is shown in bold, and the bold underlined T indicates a SNP, which is a C in some sickle cell disease patients. The underlined ATG is the start codon. TIFF2025530892000080.tif197165

[0450] "Binding polypeptide" refers to a polypeptide that has specificity for and specifically binds to a CD117 polypeptide, or an antigen-binding portion or fragment thereof. In one embodiment, the binding polypeptide is an anti-CD117 antibody or immunoglobulin, or an antigen-binding portion or fragment thereof.

[0451] By "hemoglobin γA (HBG1) polypeptide" is meant a polypeptide having at least about 85% amino acid sequence identity to Genbank Accession No. CAA23771.1 shown below, or a fragment thereof capable of forming a protein complex with an alpha hemoglobin subunit. MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPKVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFGKEFTPEVQASWQKMVTAVASALSSRYH (SEQ ID NO: 496).

[0452] "HBG1 polynucleotide" refers to a nucleic acid molecule encoding an HBG1 polypeptide, as well as introns, exons, 3' untranslated regions, 5' untranslated regions, and regulatory sequences associated with its expression, or fragments thereof. In certain embodiments, an HBG1 polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for the expression of HBG1. An exemplary HBG1 polynucleotide sequence from Homo sapiens is set forth in ENSEMBL Accession No. GRCh38:11:5248044:5259425:1, and its reverse complement (SEQ ID NO:497) is set forth below. In the sequence below, the exons encoding HBG1 are shown in bold, and an 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 5' of the first exon), or a portion thereof.

[0453] TIFF2025530892000081.tif224165TIFF2025530892000082.tif225165TIFF20255308920 00083.tif217164TIFF2025530892000084.tif224164TIFF2025530892000085.tif219165

[0454] By "hemoglobin γG (HBG2) polypeptide" is meant a polypeptide having at least about 85% amino acid sequence identity to Genbank Accession No. CAA23773.1 shown below, or a fragment thereof capable of forming a protein complex with an α-hemoglobin subunit. MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPKVKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFGKEFTPEVQASWQKMVTGVASALSSRYH (SEQ ID NO: 498).

[0455] "HBG2 polynucleotide" refers to a nucleic acid molecule encoding an HBG2 polypeptide, as well as introns, exons, 3' untranslated regions, 5' untranslated regions, and regulatory sequences associated with its expression, or fragments thereof. In certain embodiments, an HBG2 polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for the expression of HBG2. An exemplary HBG2 polynucleotide sequence from Homo sapiens is set forth in ENSEMBL Accession No. GRCh38:11:5248044:5259425:1, and its reverse complement sequence (SEQ ID NO:497) is set forth above. In the sequence (SEQ ID NO:497), the exons encoding HBG2 are indicated in underlined bold text, and an 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 5' of the first exon), or a portion thereof.

[0456] 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). Cas9 nucleases are also sometimes referred to as casnl nucleases or CRISPR (clustered regularly interspaced short palindromic repeats)-associated nucleases.

[0457] "Percent chimeric" or "chimerism" refers to the percentage of cells of a given type(s) of interest in a subject that are administered to or modified in the subject, or that are lineage-derived or derived from cells administered to or edited in the subject. In some cases, "percent chimeric" is calculated as the percentage of hCD45+ cells in the subject that are administered to or that are lineage-derived or derived from cells administered to the subject. In some embodiments, the cell type of interest is bulk bone marrow, CD34+ cells, CD235a+ cells, CD19+ cells, or CD45+ cells. In some embodiments, chimerism is measured in a subject 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 cells to the subject. In some embodiments, chimerism is measured in a subject 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 some embodiments, the chimeric rate measured at that time point is about, or at least about, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%. In some cases, the chimeric rate is higher than the value measured in a subject that expresses a wild-type CD117 polypeptide and that has not been base-edited according to the methods provided herein to express a modified CD117 polypeptide that has reduced binding to an anti-CD117 antibody. As used herein, the term "complementarity-determining region" (CDR) refers to the hypervariable regions found in both the light and heavy chain variable regions (VL and VH domains, respectively). CDRs are noncontiguous antigen-binding sites found within the variable regions of both heavy and light chain polypeptides.These specific regions are described by Kabat et al., J.Biol.Chem. 252:6609-6616, 1977 and Kabat, et al., Sequences of Proteins of Immunological Interest, Fifth Edition, USDapartment of Health and Human Services, NIH Publication No. 91-3242, 1991, by Chothia et al., (J.Mol.Biol. 196:901-917, 1987), and by MacCallum et al., (J.Mol.Biol. 262:732-745, 1996), and these definitions include overlapping or subsets of amino acid residues when compared with each other. In certain embodiments, the term "CDR" refers to the CDR defined by Kabat based on sequence comparison. The more highly conserved portions of the variable regions are called framework regions (FR). As recognized in the art, the amino acid positions that designate hypervariable regions of an antibody can vary depending on the context and the various definitions known in the art. Some positions within variable domains can be considered hybrid hypervariable positions, because they can be considered within a hypervariable region under one set of criteria, but outside of a hypervariable region under a different set of criteria. One or more of these positions can also be found in extended hypervariable regions. Naturally occurring heavy and light chain variable regions each contain four framework regions (FR1, FR2, FR3, FR4) that adopt a primarily β-sheet configuration, connected by three CDRs (CDR1, CDR2, CDR3) that form loops that connect, and in some cases form part of, the β-sheet structure.The CDRs of each chain are held in close proximity by FR regions in the order FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4, and the CDRs of each antibody chain contribute to forming the target binding site of the antibody (see Kabat et al., Sequences of Proteins of Immunological Interest (National Institutes of Health, Bethesda, Md. 1987; incorporated herein by reference). As used herein, immunoglobulin amino acid residue numbering is done according to the immunoglobulin amino acid residue numbering system of Kabat et al., unless otherwise indicated. In various embodiments, the complementarity determining regions are numbered as 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). CDRs can be identified using any of the methods available to those skilled in the art, such as those described in (the entirety of which is incorporated herein by reference for all purposes), including, by way of non-limiting example, the methods of Kabat, Chothia, Lefranc, Honegger, Martin, MacCallum, and Zhao. Sequence- or structure-based methods can be used to identify CDRs. Various software programs are available to those skilled in the art to identify CDRs in antibody amino acid sequences.In various embodiments, the CDRs provided herein may be modified to include 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 additional amino acids at the N-terminus and / or C-terminus, and / or to exclude 1, 2, 3, 4, 5, 6, 7, 8, or 9 amino acids (e.g., in one embodiment, the VH CDR1 of ABTx025 is modified to be RASQSVSS (SEQ ID NO:939), rather than QSVSSSY (SEQ ID NO:438), by extending QSVSSSY (SEQ ID NO:439) by 3 amino acids at the N-terminus and omitting 2 amino acids at the C-terminus). The present disclosure contemplates that the CDRs identified for a particular antibody may vary in location or length, depending on how they are determined.

[0458] The term "conservative amino acid substitution" or "conservative mutation" refers to the substitution of one amino acid for another amino acid that shares common properties. A functional method for defining common properties between individual amino acids is to analyze the normalized frequency of amino acid changes between corresponding proteins of homologous organisms (Schulz, GE and Schirmer, RH, Principles of Protein Structure, Springer-Verlag, New York (1979)). According to such analysis, groups of amino acids can be defined when amino acids within the group are preferentially exchanged with each other, and therefore have the most similar effects on the overall protein structure (Schulz, GE and Schirmer, RH, supra). Non-limiting examples of conservative mutations include amino acid substitutions such as arginine to lysine, and vice versa, to maintain a positive charge; aspartic acid to glutamic acid, and vice versa, to maintain a negative charge; threonine to serine, to maintain a free -OH; and asparagine to glutamine, to maintain a free -NH.

[0459] As used herein, the terms "conditioning" and "conditioning" refer to the process of preparing a patient to receive a graft containing hematopoietic stem cells. Such procedures promote hematopoietic stem cell transplant engraftment (e.g., as inferred from a sustained increase in the amount of viable hematopoietic stem cells in a blood sample isolated from the patient after the conditioning procedure and subsequent hematopoietic stem cell transplant). According to the methods described herein, a patient may be conditional treated for hematopoietic stem cell transplantation therapy by administering to the patient an antibody or antigen-binding fragment thereof capable of binding to an antigen expressed by hematopoietic stem cells, such as CD117. Such antibodies are expected to act via complement-dependent cytotoxicity and antibody-dependent cellular cytotoxicity. As described herein, the transplanted cells have been edited so 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 chimeric antigen receptor-expressing T cells (CAR-T) to a patient in need of hematopoietic stem cell transplantation therapy can promote hematopoietic stem cell graft engraftment, for example, by selectively depleting endogenous hematopoietic stem cells, thereby creating a void that can be filled by exogenous hematopoietic stem cell transplantation.

[0460] A "complex" refers to a combination of two or more molecules whose interaction relies 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 the π effect. In one embodiment, a complex comprises a polypeptide, a polynucleotide, or a combination of one or more polypeptides and one or more polynucleotides. In one embodiment, a complex comprises one or more polypeptides that associate to form a base editor (e.g., a nucleic acid-programmable DNA-binding protein such as Cas9, and a base editor comprising a deaminase) and a polynucleotide (e.g., a guide RNA). In one embodiment, the complex is held together by hydrogen bonds. It should be understood that one or more components of a base editor (e.g., a deaminase, or a nucleic acid-programmable DNA-binding protein) can be covalently or non-covalently associated. As an example, a base editor can include a deaminase covalently linked (e.g., by 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 are non-covalently associated (e.g., when one or more components of the base editor are provided in trans and associated directly or via another molecule, such as a protein or nucleic acid). In one embodiment, one or more components of the complex are held together by hydrogen bonds.

[0461] "Cytosine" or "4-aminopyrimidin-2(1H)-one" has the molecular formula C4H5N3O and the structure [ka] and refers to the purine nucleobase having the formula:

[0462] "Cytidine" is attached to the ribose sugar via a glycosidic bond and has the structure [ka] and corresponds to CAS number 65-46-3. Its molecular formula is CH 13 It is N3O5.

[0463] "Cytidine base editor (CBE)" means a base editor that includes a cytidine deaminase.

[0464] By "cytidine base editor (CBE) polynucleotide" is meant a polynucleotide that comprises a CBE.

[0465] "Cytidine deaminase" or "cytosine deaminase" refers to a polypeptide or fragment thereof capable of deaminating cytidine or cytosine. In certain embodiments, the cytidine or cytosine is present in a polynucleotide. In one embodiment, the cytidine deaminase converts cytosine to uracil or 5-methylcytosine to thymine. The terms "cytidine deaminase" and "cytosine deaminase" are used interchangeably throughout this application. Petromyzon marinus cytosine deaminase 1 (PmCDA1) (SEQ ID NOS: 13-14), activation-induced cytidine deaminase (AICDA) (SEQ ID NOS: 15-21), and APOBEC (SEQ ID NOS: 12-61) are exemplary cytidine deaminases. Further exemplary cytidine deaminase (CDA) sequences are set forth in the Sequence Listing as SEQ ID NOS: 62-66 and 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.

[0466] "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, a 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 provided herein has increased cytosine deaminase activity (e.g., at least 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, or more) relative to a reference cytosine deaminase.

[0467] As used herein, the term "deaminase" or "deaminase domain" refers to a protein or fragment thereof that catalyzes a deamination reaction.

[0468] "Detection" refers to identifying the presence, absence, or amount of the analyte being detected. In one embodiment, a change in the sequence of a polynucleotide or polypeptide is detected. In another embodiment, the presence of an indel is detected.

[0469] "Detectable label" refers to a composition that, when linked to a molecule of interest, renders the molecule of interest detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include radioisotopes, magnetic beads, metal beads, colloidal particles, fluorescent dyes, electron-dense reagents, enzymes (e.g., enzymes commonly used in enzyme-linked immunosorbent assays (ELISAs)), biotin, digoxigenin, or haptens.

[0470] "Disease" means any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. Exemplary diseases include those amenable to treatment with hematopoietic stem cell transplantation, such as β-thalassemia, sickle cell disease (SCD), or adenosine deaminase deficiency.

[0471] "Dual editing activity" or "dual deaminase activity" means having adenosine deaminase and cytidine deaminase activity. In one embodiment, a base editor with dual editing activity has both A→G and C→T activity, and these two activities are about equal or within about 10% or 20% of each other. In another embodiment, the dual editor has A→G activity that is no more than about 10% or 20% greater than its C→T activity. In another embodiment, the dual editor has A→G activity that is no more than about 10% or 20% less than its C→T activity. In some embodiments, the adenosine deaminase variant has primarily cytosine deaminase activity and little, if any, adenosine deaminase activity. In some embodiments, the adenosine deaminase variant has cytosine deaminase activity and no significant or detectable adenosine deaminase activity.

[0472] An "effective amount" refers to the amount of a drug or active compound, e.g., a base editor or antibody described herein, required to ameliorate disease symptoms compared to an untreated patient or an individual not afflicted with the disease, i.e., a healthy individual, or the amount of a drug or active compound sufficient to elicit a desired biological response. The effective amount of an active compound(s) used to practice embodiments of the present disclosure for the therapeutic treatment of a disease will vary 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 dosing regimen. Such an amount is referred to as an "effective" amount. In one embodiment, an effective amount is the amount of a base editor of the present disclosure that is sufficient to introduce a modification in a gene of interest in a cell (e.g., a cell in vitro or in vivo). In one embodiment, an effective amount is the amount of a base editor required to achieve a therapeutic effect. Such a therapeutic effect need not be sufficient to modify pathogenic genes in all cells of a subject, tissue, or organ, but need only be sufficient to modify pathogenic genes 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 ameliorate one or more symptoms of the disease.

[0473] By "fragment" is meant a portion of a polypeptide or nucleic acid molecule, which portion contains at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide. 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, a fragment is a functional fragment.

[0474] As used herein, the term "framework region" or "FR region" includes amino acid residues adjacent to the CDRs. FR region residues may be present in, for example, human antibodies, rodent-derived antibodies (e.g., murine antibodies), humanized antibodies, primatized antibodies, chimeric antibodies, antibody fragments (e.g., Fab fragments), single-chain antibody fragments (e.g., scFv fragments), antibody domains, and bispecific antibodies.

[0475] "Guide polynucleotide" refers to a polynucleotide or polynucleotide complex that is specific to 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.

[0476] As used herein, the term "hematopoietic stem cells" ("HSCs") refers to immature blood cells that have the capacity for self-renewal and the ability to differentiate into mature blood cells comprising a variety of lineages, including, but not limited to, granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), platelets (e.g., megakaryoblasts, 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 considered to comprise a subpopulation of cells with the stem cell properties defined above, while in mice, HSCs are CD34-. Furthermore, HSCs also refer to long-term bone marrow-reconstituting HSCs (LT-HSCs) and short-term bone marrow-reconstituting HSCs (ST-HSCs). LT-HSCs and ST-HSCs differentiate based on functional potential and cell surface marker expression. For example, human HSCs are CD34+, CD38-, CD45RA-, CD90+, CD49F+, and lin- (negative for mature lineage markers including CD2, CD3, CD4, CD7, CD8, CD10, CD1 1B, CD19, CD20, CD56, and CD235A). In mice, bone marrow LT-HSCs are CD34-, SCA-1+, C-kit+, CD135-, Slamfl / CD150+, CD48-, and lin- (negative for mature lineage markers, including Ter119, CD11b, Gr1, CD3, CD4, CD8, B220, and IL7ra), whereas ST-HSCs are CD34+, SCA-1+, C-kit+, CD135-, Slamfl / CD150+, and lin- (negative for mature lineage markers, including Ter119, CD11b, Gr1, CD3, CD4, CD8, B220, and IL7ra). Furthermore, ST-HSCs are less quiescent and more proliferative than LT-HSCs under homeostatic conditions. However, LT-HSCs have a high self-renewal capacity (i.e., they survive throughout adulthood and can be serially transplanted through successive recipients), whereas ST-HSCs have limited self-renewal capacity (i.e., they survive only for a limited period of time and do not have serial transplantation capacity).Any of these HSCs can be used in the methods described herein. ST-HSCs are particularly useful because they are highly proliferative and therefore can give rise to differentiated progeny more quickly.

[0477] As used herein, the term "functional potential of hematopoietic stem cells" refers to the functional properties of hematopoietic stem cells, including: 1) multipotency (which refers to the ability to differentiate into multiple different blood lineages, including, but not limited to, granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), platelets (e.g., megakaryoblasts, platelet-producing megakaryocytes, platelets), monocytes (e.g., monocytes, macrophages), dendritic cells, microglia, osteoclasts, and lymphocytes (e.g., NK cells, B cells, and T cells)); 2) self-renewal (which refers to the ability of hematopoietic stem cells to give rise to daughter cells with potential equivalent to that of the parent cell, and further, this ability may occur repeatedly throughout an individual's lifetime without becoming exhausted); and 3) the ability of hematopoietic stem cells or their progeny to be reintroduced into a transplant recipient, home to the hematopoietic stem cell niche (e.g., bone marrow niche), and reconstitute productive and sustained hematopoiesis.

[0478] By "increase" is meant 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.

[0479] The terms "inhibitor of base repair," "base repair inhibitor," "IBR," or grammatical equivalents thereof, refer to proteins capable of inhibiting the activity of nucleic acid repair enzymes, e.g., base excision repair enzymes.

[0480] An "intein" is a fragment of a protein that can excise itself and join the remaining fragment (an extein) with a peptide bond in a process known as protein splicing.

[0481] The terms "isolated," "purified," or "biologically pure" refer to material that is free, to varying degrees, from components that normally accompany it as found in its native state. "Isolated" refers to a degree of separation from the original source or surroundings. "Purified" refers to a degree of separation greater than isolation. A "purified" or "biologically pure" protein is sufficiently free from other substances so that any impurities do not substantially affect the biological properties of the protein or cause other adverse events. That is, a nucleic acid or peptide of the present disclosure, if produced by recombinant DNA technology, is purified to be substantially free of cellular material, viral material, or culture medium, or, if chemically synthesized, is purified to be substantially free of chemical precursors or other chemicals. Purity and homogeneity are typically measured using analytical chemistry techniques, such as polyacrylamide gel electrophoresis or high-performance liquid chromatography. The term "purified" can indicate that the nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. For example, in the case of proteins that can be subject to modifications such as phosphorylation or glycosylation, different modifications can give rise to different isolated proteins that can be separately purified.

[0482] An "isolated polynucleotide" refers to a nucleic acid molecule that is free of the genes that flank it in the naturally occurring genome of the organism from which it is derived. Thus, the term includes, for example, recombinant DNA that is integrated into a vector, an autonomously replicating plasmid, or virus, or into the genomic DNA of a prokaryote or eukaryote, or that exists as a separate molecule independent of other sequences (e.g., cDNA, or genomic or cDNA fragments produced by PCR or restriction endonuclease digestion). Additionally, the term includes RNA molecules transcribed from DNA molecules, and recombinant DNA that is part of a hybrid gene encoding additional polypeptide sequences.

[0483] "Isolated polypeptide" refers to a polypeptide of the present disclosure that has been separated from components that naturally accompany it. Typically, a polypeptide is isolated when it is at least 60%, by weight, free from the proteins and naturally occurring organic molecules with which it is naturally associated. In some embodiments, preparations are at least 75%, 90%, or 99%, by weight, of a polypeptide of the present disclosure. Isolated polypeptides of the present disclosure may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding such a polypeptide, or by chemically synthesizing the protein. Purity can be measured by any appropriate method, for example, column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.

[0484] A "cluster of differentiation 117 (CD117; C-kit; SCFR) polypeptide" refers to a polypeptide having at least about 85% amino acid sequence identity to the amino acid sequence set forth in GenBank Accession No. NP_000213, shown below, or a fragment thereof that binds to an anti-CD117 antibody. CD117 (KIT) is a type III receptor tyrosine kinase that functions in cell signaling in several cell types. Normally, KIT is activated (phosphorylated) by binding of its ligand, stem cell factor (SCF). This results in a phosphorylation cascade that ultimately activates various transcription factors in different cell types. Such activation regulates apoptosis, cell differentiation, proliferation, chemotaxis, and cell adhesion. In some embodiments, the CD117 polypeptide or a fragment thereof has SCF signaling activity.

[0485] >NP_000213.1 Mast cell / stem cell growth factor receptor Kit isoform 1 precursor [Homo sapiens] MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDR SLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTCTIKDVSSSVYS TWKRENSQTKLQEKYNSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSE NESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGT VECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYG LIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVV PTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV (SEQ ID NO: 499)

[0486] >CD117 variant with S261G and N260D alterations (underlined and bold) MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDRSLYGKED NDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTCTIKDVSSSVYSTWKRENSQTKLQEKY DGWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTID WYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAM TVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARN ILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV (SEQ ID NO: 1134)

[0487] CD117 variant with a >S261G alteration (shown in bold and underlined) MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDRSLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTTCTIKDVSSSVYSTWKRENSQTKLQEKYN GWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTID WYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAM TVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARN ILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV (SEQ ID NO: 1135)

[0488] CD117 variants with >Y259C and N260D alterations (shown in bold and underlined) MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDRSLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTTCTIKDVSSSVYSTWKRENSQTKLQEK CDSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTID WYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAM TVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARN ILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV (SEQ ID NO: 1136)

[0489] CD117 variant with >N260D alteration (underlined and bold) MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGEPSPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDRSLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTTCTIKDVSSSVYSTWKRENSQTKLQEKY DSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTID WYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAM TVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARN ILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV (SEQ ID NO: 1137)

[0490] CD117 variant with a >S251G alteration (underlined and bold) MRGARGAWDFLCVLLLLLRVQTGSSQPSVSPGESPPSIHPGKSDLIVRVGDEIRLLCTDPGFVKWTFEILDETNENKQNEWITEKAEATNTGKYTCTNKHGLSNSIYVFVRDPAKLFLVDRSLYGKEDNDTLVRCPLTDPEVTNYSLKGCQGKPLPKDLRFIPDPKAGIMIKSVKRAYHRLCLHCSVDQEGKSVLSEKFILKVRPAFKAVPVVSVSKASYLLREGEEFTVTTCTIKDVSSSVYSTWKREN GQTKLQEKYNSWHHGDFNYERQATLTISSARVNDSGVFMCYANNTFGSANVTTTLEVVDKGFINIFPMINTTVFVNDGENVDLIVEYEAFPKPEHQQWIYMNRTFTDKWEDYPKSENESNIRYVSELHLTRLKGTEGGTYTFLVSNSDVNAAIAFNVYVNTKPEILTYDRLVNGMLQCVAAGFPEPTIDWYFCPGTEQRCSASVLPVDVQTLNSSGPPFGKLVVQSSIDSSAFKHNGTVECKAYNDVGKTSAYFNFAFKGNNKEQIHPHTLFTPLLIGFVIVAGMMCIIVMILTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHIYSNLANCSPNRQKPVVDHSVRINSVGSTASSSQPLLVHDDV (SEQ ID NO: 1138)

[0491] By "cluster of differentiation 117 (CD117; C-kit; SCFR) polynucleotide" is meant a nucleic acid molecule encoding a CD117 polypeptide, as well as introns, exons, 3' untranslated region, 5' untranslated region, and regulatory sequences associated with its expression, or fragments thereof. In certain embodiments, a CD117 polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for the expression of CD117. An exemplary CD117 polynucleotide sequence from Homo sapiens is shown below (NCBI Reference Sequence Accession No. NM_000222.2), and an exemplary CD117 gene sequence is shown in ENSEMBL Accession No. ENSG00000157404.

[0492]

[0493] 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.

[0494] "Makassar" or "Hb G-Makassar" refers to the human beta hemoglobin variant, the G-Makassar variant or mutant form of human hemoglobin (Hb) (HB Makassar variant), which is an asymptomatic, naturally occurring variant (E6A) hemoglobin. Hb G-Makassar was first identified in Indonesia. (Mohamad, ASet et al., 2018, Hematol. Rep., 10(3):7210 (doi:10.4081 / hr.2018.7210). When subjected to electrophoresis, Hb G-Makassar migrates slowly. The Makassar β-hemoglobin variant has an anatomical abnormality at the β-6 or A3 position, where a glutamyl residue is usually replaced by an alanyl residue. A single amino acid substitution of valine in the gene encoding the β-globin subunit β-6 glutamyl results in sickle cell disease. Conventional procedures, such as isoelectric focusing, cation-exchange high-performance liquid chromatography (HPLC) hemoglobin electrophoretic separation, and cellulose acetate electrophoresis, have failed to separate the Hb G-Makassar and Hb S globin forms, because these forms have been found to have identical properties when analyzed by these methods. Consequently, Hb G-Makassar and HbS have been misidentified and confused with each other by those skilled in the art, leading to misdiagnosis of sickle cell disease (SCD). In one embodiment, the sickle cell-causing amino acid at position 6, valine, is replaced with alanine, thereby generating an Hb variant (Hb Makassar) that does not produce the sickle cell phenotype. In some embodiments, Val→Ala (G T G → G CG) substitutions (i.e., Hb Makassar variants) can be generated using an A·T to G·C base editor (ABE).

[0495] Thus, the present disclosure includes compositions and methods for base editing the codon for the sixth amino acid of the sickle cell disease variant of the β-globin protein (sickle HbS; E6V) from thymidine (T) to cytidine (C), thereby substituting valine for alanine at this amino acid position (V6A). Substituting valine for alanine at position 6 of HbS generates a β-globin protein variant that does not have the sickle cell phenotype (e.g., does not have the potential to polymerize, as does pathogenic variant HbS). Thus, the compositions and methods of the present disclosure are useful for treating sickle cell disease (SCD).

[0496] By "marker" is meant any protein or polynucleotide having an altered expression level, structure, or activity 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 beta globin, beta globin, fetal hemoglobin, CD117, and variants of CD117 provided herein.

[0497] As used herein, the term "mutation" refers to the substitution of a residue in a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or the deletion or insertion of one or more residues in a sequence. Mutations are typically described herein by identifying the original residue, followed by the position of the residue in the sequence, and then identifying the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art and can be found, for example, in Green and Sambrook, Molecular Cloning: A Laboratory Manual (4 th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (2012)).

[0498] As used herein, the terms "nucleic acid" and "nucleic acid molecule" refer to a compound comprising a nucleobase and an acidic moiety, e.g., a nucleoside, a nucleotide, or a polymer of nucleotides. Typically, polymeric nucleic acids, e.g., nucleic acid molecules comprising three or more nucleotides, are linear molecules in which adjacent nucleotides are linked to each other via phosphodiester bonds. In some embodiments, "nucleic acid" refers to an individual nucleic acid residue (e.g., a nucleotide and / or a nucleoside). In some embodiments, "nucleic acid" refers to an oligonucleotide chain comprising three or more individual nucleotide residues. As used herein, the terms "oligonucleotide" and "polynucleotide" can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least three nucleotides). In some embodiments, "nucleic acid" encompasses RNA and single- and / or double-stranded DNA. Nucleic acids can occur naturally, for example, in the context of a genome, a transcript, mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, a cosmid, a chromosome, a chromatid, or other naturally occurring nucleic acid molecule. On the other hand, nucleic acid molecules include non-naturally occurring molecules, such as recombinant DNA or RNA, artificial chromosomes, modified genomes, or fragments thereof, as well as synthetic DNA, RNA, DNA / RNA hybrids, or non-naturally occurring nucleotides or nucleosides. Furthermore, "nucleic acid," "DNA," "RNA," and / or similar terms include nucleic acid analogs, e.g., analogs having other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems, and optionally purified or chemically synthesized. Optionally, for example, in the case of chemically synthesized molecules, nucleic acids include nucleoside analogs, such as analogs with chemically modified bases or sugars, and backbone modifications. Nucleic acid sequences are presented in the 5' to 3' direction unless otherwise indicated.In some embodiments, nucleic acids are selected from natural nucleosides (e.g., adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine), nucleotide analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyladenosine, 5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C ...bromouridine, C5-bromouridine, C5-bromouridine, C5-bromouridine, C5-bromouridine, C5-brom -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., phosphorothioate and 5'-N-phosphoramidite linkages).

[0499] The term "nuclear localization sequence," "nuclear localization signal," or "NLS" refers to an amino acid sequence that promotes the import of proteins into the cell nucleus.Nuclear localization sequences are known in the art and are described, for example, in International PCT Application PCT / EP2000 / 011690, filed November 23, 2000 by Plank et al. (published May 31, 2001 as WO / 2001 / 038547), the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences.In other embodiments, the NLS is, for example, the optimized NLS 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).

[0500] The terms "nucleobase," "nitrogenous base," or "base" are used interchangeably herein to refer to nitrogen-containing biological compounds that form nucleosides, the building blocks of nucleotides. The ability of nucleobases to base pair and stack with one another directly gives rise to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). The five nucleobases (adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)) are referred to as primary or standard nucleobases. Adenine and guanine are derived from purines, while cytosine, uracil, and thymine are derived from pyrimidines. DNA and RNA can also contain other (non-primary) modified bases. Non-limiting exemplary modified nucleobases may include hypoxanthine, xanthine, 7-methylguanine, 5,6-dihydrouracil, 5-methylcytosine (m5C), and 5-hydromethylcytosine. Hypoxanthine and xanthine are produced in the presence of mutagens, and both are produced by deamination (replacement of an amine group with a carbonyl group). Hypoxanthine can be modified from adenine. Xanthine can be modified from guanine. Uracil can result from the deamination of cytosine. A "nucleoside" consists of a nucleobase and a five-carbon sugar (either 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 (either ribose or deoxyribose), and at least one phosphate group.Non-limiting examples of modified nucleobases and / or chemical modifications that a modified nucleobase may contain may include: pseudouridine, 5-methyl-cytosine, 2'-O-methyl-3'-phosphonoacetate, 2'-O-methylthioPACE (MSP), 2'-O-methyl-PACE (MP), 2'-fluoroRNA (2'-F-RNA), constrained ethyl (S-cEt), 2'-O-methyl ("M"), 2'-O-methyl-3'-phosphorothioate ("MS"), 2'-O-methyl-3'-thiophosphonoacetate ("MSP"), 5-methoxyuridine, phosphorothioate, and N1-methylpseudouridine.

[0501] The term "nucleic acid programmable DNA binding protein" or "napDNAbp" may be used interchangeably with "polynucleotide programmable nucleotide binding domain" and may refer 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 guides the napDNAbp to a specific nucleic acid sequence. In some embodiments, the polynucleotide programmable nucleotide binding domain is a polynucleotide programmable DNA binding domain. In some embodiments, the polynucleotide programmable nucleotide binding domain is a polynucleotide programmable RNA binding domain. In some embodiments, the polynucleotide programmable nucleotide binding domain is a Cas9 protein. The Cas9 protein can associate with a guide RNA that guides the Cas9 protein to a specific DNA sequence complementary to the guide RNA. In some embodiments, the napDNAbp is a Cas9 domain, e.g., a nuclease-active Cas9, a Cas9 nickase (nCas9), or a nuclease-inactive Cas9 (dCas9). Non-limiting examples of nucleic acid programmable DNA binding proteins include Cas9 (e.g., dCas9 and nCas9), 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, Csn3, Csn4, Csn5, Csn6, Csn7, Csn8, Csn9, Csn10, Csn11, Csn12, Csn13, Csn14, Csn15, Csn16, Csn17, Csn18, Csn19, Csn11, Csn11, Csn12, Csn13, Csn14, Csn15, Csn16, Csn17, Csn18, Csn19 ...9, Csn11, Csn12, Csn13, Csn14, Csn15, Csn Examples include sn1, 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 versions thereof. Other nucleic acid programmable DNA binding proteins are also within the scope of the present disclosure, but may not be specifically listed in the present disclosure.See, for example, Makarova et al. "Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?" CRISPR J.2018 Oct;1:325-336.doi:10.1089 / crispr.2018.0033; Yan et al., "Functionally diverse type V CRISPR-Cas systems" Science.2019 Jan 4;363(6422):88-91.doi:10.1126 / science.aav7271 (the entire contents of each are incorporated herein by reference).Exemplary nucleic acid programmable DNA binding proteins and nucleic acid sequences encoding the nucleic acid programmable DNA binding proteins are provided in the Sequence Listing as SEQ ID NOs: 197-230, and 378.

[0502] 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 the deamination of cytosine (or cytidine) to uracil (or uridine) or thymine (or thymidine), and the deamination of adenine (or adenosine) to hypoxanthine (or inosine), as well as non-templated nucleotide addition and insertion. In some embodiments, the nucleobase editing domain is a deaminase domain (e.g., adenine deaminase or adenosine deaminase).

[0503] As used herein, "obtaining" in "obtaining a drug" includes synthesizing, purchasing, or otherwise obtaining a drug.

[0504] "Stem cell factor (SCF) polypeptide" means a polypeptide having at least about 85% amino acid sequence identity to the amino acid sequence set forth in NCBI reference accession number NP_000890 (reproduced below), or a fragment thereof that functions in hematopoiesis. In some embodiments, the SCF polypeptide or fragment thereof binds to CD117.

[0505] >NP_000890.1 kit ligand isoform b precursor [Homo sapiens] MKKTQTWILTCIYLQLLLFNPLVKTEGICRNRVTNNVKDVTKLVANLPKDYMITLKYVPGMDVLPSHCWISEMVVQLSDSLTDLLDKFSNISEGLSNYSIIDKLVNIVDDLVECVKENSSKDLKKSFKSPEPRLFTPEEFFRIFNRSIDAFKDFVVASETSDCVVSSTLSPEKDSRVSVTKPFMLPPVAASSLRNDSSSSNRKAKNPPGDSSLHWAAMALPALFSLIIGFAFGALYWKKRQPSLTRAVENIQINEEDNEISMLQEKEREFQEV (SEQ ID NO: 501).

[0506] "Stem cell factor (SCF) polynucleotide" refers to a nucleic acid molecule encoding an SCF polypeptide, as well as the introns, exons, 3' untranslated region, 5' untranslated region, and regulatory sequences associated with its expression, or fragments thereof. In certain embodiments, an SCF polynucleotide is a genomic sequence, cDNA, mRNA, or gene associated with and / or required for the expression of SCF. An exemplary SCF polynucleotide sequence from Homo sapiens is shown below (NCBI Reference Sequence Accession No. NM_003994.5):

[0507] >NM_003994.5 Homo sapiens KIT ligand (KITLG), transcript variant a, mRNA

[0508] "Subject" or "patient" means a mammal. Non-limiting examples of mammals include primates (e.g., humans or cynomolgus monkeys) or non-human mammals. In certain embodiments, the mammal is a cow, horse, dog, sheep, rabbit, rodent, non-human primate, or cat. In one embodiment, "patient" refers to a mammalian subject who has a higher than average likelihood of developing a disease or disorder. Exemplary patients can be humans, non-human primates (e.g., cynomolgus monkeys), 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.

[0509] A "patient in need thereof" or "subject in need thereof" as used herein refers to a patient who has been diagnosed with, is at risk of or has, has been predetermined to have, or is suspected of having a disease or disorder.

[0510] The terms "pathogenic mutation," "pathogenic variant," "disease-causing mutation," "pathogenic variant," "deleterious mutation," or "predisposing mutation" refer to a genetic alteration or mutation associated with a disease or disorder that increases an individual's susceptibility or predisposition to a particular disease or disorder. In some embodiments, a pathogenic mutation comprises at least one wild-type amino acid substituted with at least one pathogenic amino acid in a protein encoded by the gene. In some embodiments, a pathogenic mutation is in a termination region (e.g., a stop codon). In some embodiments, a pathogenic mutation is in a non-coding region (e.g., an intron, promoter, etc.).

[0511] The terms "protein," "peptide," "polypeptide," and their grammatical equivalents are used interchangeably herein to refer to a polymer of amino acid residues linked together by peptide (amide) bonds. A protein, peptide, or polypeptide may be naturally occurring, recombinant, or synthetic, or any combination thereof.

[0512] As used herein, the term "fusion protein" refers to a hybrid polypeptide that contains protein domains derived from at least two different proteins.

[0513] As used herein, the term "human antibody" refers to a human antibody that contains substantially all portions of the protein (e.g., CDRs, framework, C L , C H Domain (e.g., C H1 , C H2 , C H3 ), hinge, (V L , V H)) refers to antibodies that are substantially non-immunogenic in humans and have only minor sequence changes or variations. Human antibodies can be produced in human cells (e.g., by recombinant expression) or in non-human animals or prokaryotic or eukaryotic cells (e.g., yeast) capable of expressing functionally rearranged human immunoglobulin (e.g., heavy and / or light chain) genes. Furthermore, when a human antibody is a single-chain antibody, the antibody can contain a linker peptide not found in naturally occurring human antibodies. For example, an Fv can contain a linker peptide, such as two to about eight glycine or other amino acid residues, connecting the heavy chain variable region and the light chain variable region. Such a linker peptide is considered to be of human origin. Human antibodies can be produced by various methods known in the art, including phage display, using antibody libraries derived from human immunoglobulin sequences. See U.S. Patent Nos. 4,444,887 and 4,716,111, and PCT publications WO1998 / 46645, WO1998 / 50433, WO1998 / 24893, WO1998 / 16654, WO1996 / 34096, WO1996 / 33735, and WO1991 / 10741, which are incorporated herein by reference. Human antibodies can also be produced using transgenic mice which are incapable of expressing functional endogenous immunoglobulins, but which can express human immunoglobulin genes. See, e.g., PCT Publications WO98 / 24893, WO92 / 01047, WO96 / 34096, WO96 / 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.

[0514] As used herein, the term "humanized" antibody refers to forms of non-human (e.g., murine) antibodies that are chimeric immunoglobulins, immunoglobulin chains, or fragments thereof (such as Fv, Fab, Fab', F(ab')2, or other target-binding subdomains of antibodies) that contain minimal sequence derived from non-human immunoglobulin. Generally, humanized antibodies will contain substantially all of at least one, and usually two, variable regions, with all or substantially all of the CDR regions corresponding to those of a non-human immunoglobulin. All or substantially all of the FR regions may also be those of a human immunoglobulin sequence. A humanized antibody may also contain at least a portion of an immunoglobulin constant region (Fc), typically a portion 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. Pat. Nos. 5,530,101, 5,585,089, 5,693,761, 5,693,762, and Queen et al., U.S. Pat. No. 6,180,370, EP 239400, PCT Publication WO 91 / 09967, U.S. Pat. No. 5,225,539, EP 592106, and EP 519596 (incorporated herein by reference).

[0515] The term "recombinant" as used herein in the context of a protein or nucleic acid refers to a protein or nucleic acid that does not occur in nature but is the product of human engineering. For example, in some embodiments, a recombinant protein or nucleic acid molecule comprises 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.

[0516] By "reduction" is meant a negative change of at least 10%, 25%, 50%, 75%, or 100%.

[0517] "Reference" refers to a standard or control condition. In one embodiment, the reference is a wild-type or healthy cell. In other embodiments, the reference is an untreated cell that is not subjected to the test condition, or is subjected to a placebo or saline, medium, buffer, and / or a control vector that does not carry the polynucleotide of interest. In some cases, the "reference" is an untreated subject, such as a subject that 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 that does not have sickle cell disease). In some embodiments, the reference is an unedited or wild-type cell, polypeptide, or polynucleotide.

[0518] A "reference sequence" is a defined sequence used as the basis for sequence comparison. A reference sequence may be a subset of a particular sequence or its entirety, for example, a segment of a full-length cDNA or gene sequence, or a complete cDNA or gene sequence. For polypeptides, the length of a reference polypeptide sequence is generally at least about 16 amino acids, at least about 20 amino acids, at least about 25 amino acids, at least about 35 amino acids, at least about 50 amino acids, or at least about 100 amino acids. For nucleic acids, the length of a reference nucleic acid sequence is generally at least about 50 nucleotides, at least about 60 nucleotides, at least about 75 nucleotides, at least about 100 nucleotides, or at least about 300 nucleotides, or any integer thereabout or therebetween. 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.

[0519] The terms "RNA-programmable nuclease" and "RNA-guided nuclease" refer to a nuclease that forms a complex with (e.g., binds to or associates with) one or more RNA(s) that are not targets for cleavage. In some embodiments, when an RNA-programmable nuclease is complexed with an RNA, it may be referred to as a nuclease:RNA complex. Typically, the bound RNA(s) are referred to as guide RNAs (gRNAs). In some embodiments, the RNA-programmable nuclease is a (CRISPR-associated system) Cas9 endonuclease, such as Cas9 from Streptococcus pyogenes (Csnl) (e.g., SEQ ID NO: 197), Cas9 from Neisseria meningitidis (NmeCas9; SEQ ID NO: 208), Nme2Cas9 (SEQ ID NO: 209), or a derivative thereof (e.g., a sequence having at least about 85% sequence identity to Cas9, e.g., Nme2Cas9 or spCas9).

[0520] As used herein, the term "scFv" refers to a single-chain Fv antibody in which the variable regions of the heavy and light chains from an antibody are joined to form a single chain. An scFv fragment contains a single polypeptide chain comprising 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 connecting the VL and VH regions of the scFv fragment can be a peptide linker composed of proteinogenic amino acids. Alternative linkers can be used to increase the resistance of the scFv fragment to proteolysis (e.g., linkers comprising D-amino acids), to increase the solubility of the scFv fragment (e.g., hydrophilic linkers such as linkers comprising polyethylene glycol or polypeptides comprising glycine repeats and serine residues), to improve the biophysical stability of the molecule (e.g., linkers comprising cysteine ​​residues that form intramolecular or intermolecular disulfide bonds), or to reduce the immunogenicity of the scFv fragment (e.g., linkers comprising glycosylation sites). Those skilled in the art will also appreciate that the variable regions of the scFv molecules described herein can be engineered to differ in amino acid sequence from the antibody molecule from which they are derived. For example, nucleotide or amino acid substitutions (e.g., within CDR and / or framework residues) resulting in conservative substitutions or changes in amino acid residues can be made to maintain or enhance the ability of the scFv to bind to the antigen recognized by the corresponding antibody.

[0521] Amino acids can generally be classified according to common side chain properties as follows: (1) Hydrophobic: Norleucine, Met, Ala, Val, Leu, He, (2) Neutral hydrophilicity: Cys, Ser, Thr, Asn, Gin, (3) Acidic: Asp, Glu, (4) Basic: His, Lys, Arg, (5) Residues that affect chain orientation: Gly, Pro, (6) Aromatic: Trp, Tyr, Phe.

[0522] In some embodiments, conservative substitutions may involve exchanging a member of any of these classes for another member of the same class, hi some embodiments, non-conservative amino acid substitutions may involve exchanging a member of any of these classes for another class. By "selectively binds" is meant specifically binding to a wild-type version of a cell surface protein but exhibiting reduced binding or no detectable binding to a cell surface protein containing a mutation. In certain embodiments, an antibody of the present disclosure selectively binds to a wild-type CD117 polypeptide but exhibits reduced binding to a CD117 polypeptide containing one or more amino acid modifications, such as those provided herein, compared to the wild-type CD117 polypeptide. In certain embodiments, an antibody of the present disclosure binds 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 1,000,000-fold stronger to a wild-type CD117 polypeptide compared to a modified CD117 polypeptide of the present disclosure (e.g., as quantified using KD(M) (a lower KD(M) indicates stronger binding)).

[0523] By "specifically binds" is meant that in a sample, e.g., a biological sample, a nucleic acid molecule, polypeptide, polypeptide / polynucleotide complex, compound, or molecule recognizes and binds to a polypeptide and / or nucleic acid molecule of the disclosure, but does not substantially recognize or substantially bind to other molecules.

[0524] "Substantially identical" refers to a polypeptide or nucleic acid molecule that 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 one of the amino acid or nucleic acid sequences described herein. In one embodiment, such a sequence is at least about 60%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or even 99.99% identical at the amino acid or nucleic acid level to the sequence used for comparison.

[0525] Nucleic acid molecules useful 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 be 100% identical to an endogenous nucleic acid sequence, but will typically exhibit substantial identity. A polynucleotide having "substantial identity" to an endogenous sequence is typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. Nucleic acid molecules useful 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 be 100% identical to an endogenous nucleic acid sequence, but will typically exhibit substantial identity. A polynucleotide having "substantial identity" to an endogenous sequence is typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. "Hybridizing" means that the pair forms a double-stranded molecule between complementary polynucleotide sequences (e.g., genes described herein) or portions thereof under various stringency conditions. (See, e.g., Wahl, GM and SL Berger (1987) Methods Enzymol. 152:399; Kimmel, AR (1987) Methods Enzymol. 152:507).

[0526] "Split" means divided into two or more pieces.

[0527] A "split polypeptide" or "split protein" refers to a protein that is provided as an N-terminal fragment and a C-terminal fragment that are translated from a nucleotide sequence(s) as two separate polypeptides. The polypeptides corresponding to the N-terminal and C-terminal portions of the split protein can, in some embodiments, be spliced ​​to form a "reassembled" protein. In certain embodiments, the split polypeptide is a nucleic acid-programmable DNA-binding protein (e.g., Cas9) or a base editor.

[0528] The term "target site" refers to a sequence within a nucleic acid molecule that is modified. In some embodiments, the modification is base deamination. The deaminase can be adenine deaminase. The fusion protein or base editing complex comprising the deaminase can include a dCas9-adenosine deaminase fusion protein, a Cas12b-adenosine deaminase fusion, or a base editor disclosed herein.

[0529] As used herein, terms such as "treat," "treating," and "treatment" refer to reducing or ameliorating a disorder and / or its associated symptoms, or achieving a desired pharmacological and / or physiological effect. It will be understood that treating a disorder or condition does not necessarily require, although does not exclude, that the disorder, condition, or its associated symptoms be completely eliminated. In some embodiments, the effect is therapeutic, i.e., without limitation, the effect partially or completely reduces, diminishes, suppresses, alleviates, relieves, reduces the intensity of, or cures, the disease and / or adverse symptoms resulting from the disease. In some embodiments, the effect is prophylactic, i.e., the effect protects against or prevents the occurrence or recurrence of the disease or condition. To this end, the methods disclosed herein comprise administering a therapeutically effective amount of a composition as described herein.

[0530] "Uracil glycosylase inhibitor" or "UGI" refers to an agent that inhibits the uracil excision repair system. Base editors, including cytidine deaminase, convert cytosine to uracil, which is then converted to thymine during DNA replication or repair. In various embodiments, uracil DNA glycosylase (UGI) prevents base excision repair, which results in a U back to C. In some examples, contacting a cell and / or polynucleotide with a UGI and a base editor prevents base excision repair, which results in a U back to C. Exemplary

[0531] The UGI contains the following amino acid sequence: >splP14739IUNGI_BPPB2 Uracil DNA glycosylase inhibitor MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML (SEQ ID NO: 231).

[0532] In some embodiments, the agent that inhibits the uracil excision repair system is a uracil stabilizing protein (USP). See, e.g., WO2022015969A1, which is incorporated herein by reference. Ranges provided herein are understood to be shorthand for all values ​​within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or subrange 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.

[0533] The terms "transfect" or "transfection" are used interchangeably and, according to some aspects and embodiments herein, refer to the introduction of heterologous nucleic acid (DNA / RNA) into eukaryotic cells, particularly yeast cells.

[0534] According to 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, etc. According to some aspects and embodiments herein, a corresponding biologically active fragment should be understood to mean a portion of an antibody that is capable of binding to an antigen, such as Fab, Fab', Fv, F(ab')2, and scFv.

[0535] As used herein, the term "vector" refers to a means for introducing a nucleic acid sequence into a cell, resulting in a transformed cell. Vectors include plasmids, transposons, phages, viruses, liposomes, lipid nanoparticles, and episomes. An "expression vector" is a nucleic acid sequence containing a nucleotide sequence to be expressed in a recipient cell. In addition to the polynucleotide sequence, an expression vector contains additional nucleic acid sequences, such as initiation sequences, termination sequences, enhancer sequences, promoter sequences, and secretion sequences, that promote and / or facilitate expression of the introduced sequence in the genome of a mammalian cell. Examples of vectors include nucleic acid vectors, e.g., DNA vectors such as plasmids, RNA vectors, viruses, or other suitable replicons (e.g., viral vectors). Various 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 WO 1994 / 11026 (incorporated herein by reference). Particular vectors that can be used to express the antibodies, antibody fragments, base editors, guide polynucleotides, and / or base editor systems of some aspects and embodiments herein include plasmids containing regulatory sequences, such as promoter and enhancer regions, that direct gene transcription. Other vectors useful for expressing antibodies and antibody fragments contain polynucleotide sequences that increase the translation rate of these genes or improve the stability or nuclear export of mRNA resulting from gene transcription. To enable efficient transcription of genes carried by the expression vector, these sequence elements include, for example, 5' and 3' untranslated regions, internal ribosome entry sites (IRES), and polyadenylation signal sites. Expression vectors of some aspects and embodiments herein may also contain a polynucleotide encoding a marker for selection of cells harboring such a vector. Examples of suitable markers include genes encoding resistance to antibiotics such as ampicillin, chloramphenicol, kanamycin, or nourseothricin.

[0536] As used herein, the term "VH" refers to the variable region of an immunoglobulin heavy chain of an antibody, including the heavy chain of an Fv, scFv, or Fab. Reference to "VL" refers to the variable region of an 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 to a specific target, immunoglobulins include both antibodies and other antibody-like molecules that lack target specificity. Natural antibodies and immunoglobulins are typically heterotetrameric glycoproteins of approximately 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each heavy chain of a natural antibody has a variable domain (VH) at the amino terminus, followed by several constant domains. Each light chain of a natural antibody has a variable domain (VL) at the amino terminus and a constant domain at the carboxy terminus.

[0537] The recitation of a list of chemical groups within any definition of a variable herein includes the definition of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiment or portion thereof.

[0538] 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.

[0539] In this application, the use of the singular includes the plural unless specifically stated otherwise. It should be noted that as used herein, the singular forms "a," "an," and "the" include plural references unless the context clearly dictates otherwise. In this application, the use of "or" means "and / or" unless specifically stated otherwise. Furthermore, the use of the term "including," as well as other forms such as "include," "includes," and "included," is not limiting.

[0540] As used in this specification and claims, the words "comprising" (and any of its forms, such as "comprise" and "comprises"), "having" (and any of its forms, such as "have" and "has"), "including" (and any of its forms, such as "includes" and "include"), or "containing" (and any of its forms, such as "contains" and "contain") are inclusive or open-ended. This language indicates the presence of specified elements, features, components, and / or method steps, but does not exclude the presence of other elements, features, components, and / or method steps. Any embodiment specified as "comprising" particular component(s) or elements also contemplates, in some embodiments, "consisting of" or "consisting essentially of" the specified component(s) or elements. It is contemplated that any embodiment discussed herein can be implemented with respect to any method or composition of the present disclosure, and vice versa. Furthermore, the compositions of the present disclosure can be used to achieve the methods of the present disclosure.

[0541] The term "about" or "approximately" means within an acceptable error range for a particular value as determined by one of ordinary skill in the art, which will depend, in part, on how the value is measured or determined (i.e., the limitations of the measurement system).

[0542] References herein to "some embodiments," "embodiments," "one embodiment," or "other embodiments" mean that the particular feature, structure, or characteristic described in connection with the embodiment is included in at least some embodiments of the present disclosure, but not necessarily in all embodiments. [Brief explanation of the drawings]

[0543] [Figure 1] Figure 1 shows a schematic diagram illustrating the engineered stem cell antibody-paired evasion approach (ESCAPE). Figure 2 shows a schematic diagram illustrating mAb pretreatment. The bone marrow niche can be depleted with mAbs that inhibit essential proteins expressed on the surface of stem cells. Following bone marrow ablation, hematopoietic stem cells (HSCs) containing mutations in the mAb target protein that confer resistance to mAb ablation can be provided for transplantation. In some cases, this method involves multiple administrations (i.e., re-administration) of the antibody. Figure 3 shows a schematic diagram illustrating selective enrichment of engineered hematopoietic stem cells (eHSCs) carrying mutations in essential cell surface proteins (e.g., CD117). Base editing can be used to engineer HSCs to contain nonsynonymous mutations that do not inhibit normal cell function and are resistant to mAb ablation. Unedited or endogenous cells remaining within the niche can be selectively eliminated due to their susceptibility to mAb binding and interference. [Figure 2A]A schematic diagram illustrating the engineered stem cell antibody paired evasion (ESCAPE) approach to non-genotoxic cell pretreatment is shown. The diagram shows a method for using base editing to generate cells with modified CD117 (c-KIT) polypeptides that have increased fetal hemoglobin production (HbF) and reduced binding to antibodies (e.g., non-genotoxic stem cell factor (SCF)-inhibiting antibodies). In one embodiment, a cell pretreatment strategy eliminates the need for busulfan pretreatment by replacing chemotherapeutic agents with non-genotoxic SCF-blocking antibodies. This strategy involves modifying the CD117 (c-KIT) antigen by creating single-nucleotide polymorphisms or multiple-nucleotide polymorphisms (SNPs or nucleotide alterations) through base editing. In one embodiment, a SNP (e.g., a non-synonymous mutation) in c-KIT prevents or reduces antibody (Ab) (e.g., ABTx052) binding. In some embodiments, modifications to the CD117 antigen are multiplexed with edits to a sickle cell disease (SCD) target (e.g., edits associated with upregulating fetal hemoglobin (HbF) expression, such as edits to a promoter region). In some cases, both edits are made using the same adenosine base editor (ABE) in combination with two or more guide RNAs (gRNAs) (e.g., sgRNA_015 and a CD117-targeting gRNA). In various examples, the edited cells are derived from the patient to whom they are administered. [Figure 2B] A schematic diagram illustrating the engineered stem cell antibody paired evasion (ESCAPE) approach for non-genotoxic cell pretreatment is shown. The diagram shows how cells displaying wild-type c-KIT are destroyed by combining an SCF-blocking antibody specific for the wild-type c-KIT antigen. ESCAPE therefore allows for the selective enrichment of c-KIT-edited cells. [Figure 2C]A schematic diagram illustrating the engineered stem cell antibody paired evasion (ESCAPE) approach to non-genotoxic cell pretreatment is shown. The diagram shows how cells displaying wild-type c-KIT are destroyed by combining an SCF-blocking antibody specific for the wild-type c-KIT antigen. ESCAPE thus allows for the selective enrichment of c-KIT-edited cells. The diagram shows a schematic diagram illustrating that unedited cells are depleted in the presence of an SCF-blocking antibody. In one embodiment, cells containing modified c-KIT polypeptides are not depleted by the SCF-blocking antibody and repopulate and engraft. In one embodiment, multi-edited cells (i.e., cells with edits for the treatment of sickle cell disease and edits for the CD117 antigen) are administered simultaneously with, after, or before administration of an SCF-blocking antibody, where administration of the antibodies is associated with enrichment of edited cells in the subject. [Figure 2D] Figure 1 shows a schematic illustrating the engineered stem cell antibody paired evasion (ESCAPE) approach to non-genotoxic cell pretreatment. Figure 2 shows a schematic illustrating how base editing can be used to modify the CD117 epitope encoded by HSCs, allowing the HSCs to selectively avoid binding by antibodies that bind to the CD117 epitope. [Figure 3]A schematic diagram summarizing the screen completed to identify guides compatible with ABE8.8 for use in introducing modifications to the CD117 antigen (left panel) and antibodies (right panel) that exhibited reduced binding to the modified antigen and were suitable for use in the ESCAPE approach for non-genotoxic cell pretreatment. Guides identified in the screen included C128, CC79, and CC89. Antibodies identified in the screen included ABTx052, ABTx062, ABTx025, ABTx030, ABTx070, and ABTx071. As shown in the left panel of the figure, 102 guide RNAs capable of introducing missense mutations were computationally identified. From these, 27 gRNAs were selected based on their highest editing efficiency in HEK293 cells. Eight gRNAs were selected based on their high editing efficiency in CD34+ cells. The CD117 mutations generated by these gRNAs were characterized, and five were selected based on their retention of normal ligand binding and phosphorylation ability in vitro. Also, as shown in the right panel of Figure 3, 188 mAb clones were identified, of which 72 clones had unique variable heavy chains (VH). 66 of these clones were screened for binding to wild-type and variant CD117 proteins. Six such antibodies were selected based on their binding to wild-type CD117 and lack of binding to variant CD117. One of the lead antibodies blocked CD117 from binding to its natural ligand, SCF, and did not bind to one of the lead antibodies. [Figure 4]4 shows a crystallographic image of CD117 indicating the locations of the amino acid residue modifications of the present disclosure. The modifications included T144A (sgRNA CC89), Y249C and N260D (sgRNA CCl28), and M351T (sgRNA CC79). The Y259C and N260D edits were located near the stem cell factor (SCF) binding site. In Figure 4, the following modification locations are highlighted in the structural image from top to bottom: Highlighted sites (top to bottom): (CC89) T144A, (C128) Y259C N260D, (CC79) M351T, and (CC78) Y418C. The protospacer corresponding to guide RNA C128 is shown in the figure and corresponds to SEQ ID NO: 830. [Figure 5A] Plots and histograms show that ABTx052 does not bind to CD117 edited using the guides CC128 and ABE8.8 (CC128-edited CD117) and inhibits stem cell factor (SCF) binding to wild-type CD117. The figure shows plots showing biolayer interferometry (BLI) measurements demonstrating that ABTx052 (mAB-7) did not bind to CC128-edited CD117 as purified protein. ABTx052 bound with high affinity (20 pM) to wtCD117 expressed in M07e cells. ABTx052 rapidly dissociated from CC128-edited CD117. The monoclonal antibody mAb-7 bound with high affinity (KD < 1E-12) to wtCD117, but showed minimal binding to CC128-edited CD117. Vertical lines indicate the time of substrate addition (e.g., addition of ABTx052 or SCF). [Figure 5B] Figure 1 shows plots and histograms demonstrating that ABTx052 does not bind to CD117 edited using the guides CC128 and ABE8.8 (CC128-edited CD117) and inhibits stem cell factor (SCF) binding to wild-type CD117. The figure shows plots demonstrating that ABTx052 (mAB-7) blocks SCF binding to CD117. Vertical lines indicate the time of substrate addition (e.g., addition of ABTx052 or SCF). [Figure 5C]Figure 1 shows plots and histograms demonstrating that ABTx052 does not bind to CD117 edited using the guides CC128 and ABE8.8 (CC128-edited CD117) and inhibits stem cell factor (SCF) binding to wild-type CD117. The figure shows a histogram demonstrating that ABTx052 did not bind to CC128-edited CD117 expressed in M07e cells. [Figure 5D]

[0039] Figure 1 shows plots and histograms demonstrating that ABTx052 does not bind to CD117 edited using the guides CC128 and ABE8.8 (CC128-edited CD117) and inhibits stem cell factor (SCF) binding to wild-type CD117. The figure shows plots demonstrating that ABTx052 had an EC50 of approximately 20 pM. [Figure 5E]Plots and histograms show that ABTx052 does not bind to CD117 edited using guides CC128 and ABE8.8 (CC128-edited CD117) and inhibits stem cell factor (SCF) binding to wild-type CD117. The figure also shows plots of flow cytometry data demonstrating that unedited CD34+ cells bound strongly (EC50 0.02 nM) to a mAb-7 engineered antibody (i.e., ABTx135) containing the LALADA Fc modification, whereas CD34+ cells edited with CD117 sgRNA showed minimal antibody binding. ABTx135 showed minimal binding to CD34+ cells expressing the CD117 variant prepared using guide CC128. 100,000 unedited or CD117-edited human CD34+ hematopoietic stem and progenitor cells were incubated with various concentrations of ABTx135 (corresponding to ABTx052, which contains the LALADA modification in the Fc domain) in PBS + 2.5% FBS in a total volume of 100 μL for 20 minutes at 4°C. After 20 minutes, the cells were pelleted by centrifugation at 500 × G for 5 minutes at 4°C. The supernatant was removed, and the cells were washed twice with PBS + 2.5% FBS. After the two washes, 100 μL of 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. The cells were then washed twice with PBS + 2.5% FBS at 4°C. Finally, the cells were suspended in 100 μL of PBS + 2.5% FBS and analyzed using flow cytometry. The geometric mean fluorescence intensity of staining (y-axis) was plotted against the logarithm of ABTx135 concentration (x-axis). Staining of cells with secondary antibody alone (dotted line) was used as a negative control. Flow cytometry demonstrated binding of mAb-7 to unedited CD34+ cells and a lack of binding to CD117-edited CD34+ cells. Secondary antibody details: Goat anti-human IgG Fc cross-adsorbed secondary antibody, DyLight650, ThermoFisher, catalog number SA5-10137. [Figure 5F]Figure 1 shows plots and histograms demonstrating that ABTx052 does not bind to CD117 edited using guides CC128 and ABE8.8 (CC128-edited CD117) and inhibits stem cell factor (SCF) binding to wild-type CD117. The figure shows plots demonstrating that ABTx052 (mAB-7) blocks SCF binding to CD117.

[0544] [Figure 6A] An SDS-PAGE gel image and size exclusion chromatography plot are shown, demonstrating the purity of the ABTx052 antibody. [Figure 6B] An SDS-PAGE gel image and size exclusion chromatography plot are shown, demonstrating the purity of the ABTx052 antibody. [Figure 7A] Figure 1 shows a plot depicting in vitro assessment of mAb binding at increasing doses between unedited human hematopoietic stem cells (HSCs) and HSCs base-edited to contain mutations in CD117 to block mAb binding. Human CD34+ cells edited with ABE8.8 and a CD117-targeting guide RNA avoided recognition by antibodies ABTx062 and ABTx052, which bind to unedited human HSCs expressing wild-type CD117. mAbs ABTx062 and ABTx052 showed loss of binding to CD34+ hematopoietic stem and progenitor cells (HSCs) edited using gRNA CC128. Edited cells expressed CD117*Y259C / N260D. The desired nucleotide edits performed using the CC128 guide were 5G+7G. [Figure 7B]Figure 1 shows a plot depicting in vitro assessment of mAb binding at increasing doses between unedited human hematopoietic stem cells (HSCs) and HSCs base-edited to contain mutations in CD117 to block mAb binding. Human CD34+ cells edited with ABE8.8 and a CD117-targeting guide RNA avoided recognition by antibodies ABTx062 and ABTx052, which bind to unedited human HSCs expressing wild-type CD117. mAbs ABTx062 and ABTx052 showed loss of binding to CD34+ hematopoietic stem and progenitor cells (HSCs) edited using gRNA CC128. Edited cells expressed CD117*Y259C / N260D. The desired nucleotide edits performed using the CC128 guide were 5G+7G. [Figure 8A] Figures 8A-8G show plots and bar graphs demonstrating that the CC128-modified CD117 epitope was protective from ligand blocking by ABTx052 in vitro. Figure 8A shows plots and bar graphs demonstrating that the CC128-modified CD117 epitope was protective from ligand blocking by ABTx052 in vitro. The figures show plots demonstrating that cells edited using the CC128 guide showed improved viability in the presence of ABTx052 compared to unedited cells at days 2 and 5 post-transfection. Cell viability was preserved for CD34+-derived edited primary cells bearing only the CC128 guide cultured with increasing concentrations of ABTx052 Ab in the presence (and absence) of stem cell factor (SCF). Unedited cells exposed to ABTx052 showed similar viability to those obtained with complete removal of SCF (dotted line). [Figure 8B]Figure 1 shows a plot and bar graph demonstrating that the CD117 epitope engineered with CC128 was protective from ligand blocking by ABTx052 in vitro. The figure shows plots demonstrating that cells edited using the CC128 guide showed improved viability in the presence of ABTx052 compared to unedited cells at days 2 and 5 post-transfection. Cell viability was preserved for edited primary CD34+ cells bearing only the CC128 guide cultured with increasing concentrations of ABTx052 Ab in the presence (and absence) of stem cell factor (SCF). Unedited cells exposed to ABTx052 showed similar viability to those with complete removal of SCF (dotted line). [Figure 8C] Plots and bar graphs show that the CD117 epitope modified with CC128 was protective against ligand blocking by ABTx052 in vitro. The figure shows that cells containing the targeted 5G+7G dual nucleotide edit combination introduced using CC128 guide were enriched over time in a 1:1 mixture of edited and unedited cells in the presence of ABTx052. Next-generation sequencing (NGS) of the 1:1 mixture demonstrated enrichment by showing increased editing frequency. [Figure 8D] Figure 1 shows a plot and bar graph demonstrating that the CD117 epitope engineered with CC128 was protective against ligand blocking by ABTx052 in vitro. The figure shows plots demonstrating that contacting cells expressing wild-type CD117 polypeptide ("unedited cells") with ABTx052 mimicked complete SCF deprivation, resulting in approximately 85% loss of viability in vitro, while edited cells exhibited increased viability compared 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 various concentrations of mAb-7. mAb-7 treatment depleted unedited cells to the level of complete SCF starvation (dotted line), while CD117-edited cells retained viability. Cell viability levels in the mixed population remained intermediate. [Figure 8E]Figure 1 shows a plot and bar graph demonstrating that the CD117 epitope engineered with CC128 was protective against ligand blocking by ABTx052 in vitro. The figure shows plots demonstrating that contacting cells expressing wild-type CD117 polypeptide ("unedited cells") with ABTx052 mimicked complete SCF deprivation, resulting in approximately 85% loss of viability in vitro, while edited cells exhibited increased viability compared 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 various concentrations of mAb-7. mAb-7 treatment depleted unedited cells to the level of complete SCF starvation (dotted line), while CD117-edited cells retained viability. Cell viability levels in the mixed population remained intermediate. [Figure 8F] Plots and bar graphs show that the CC128-modified CD117 epitope was protective against ligand blocking by ABTx052 in vitro. The figure also shows a bar graph demonstrating enrichment of base-edited cells containing the CC128-modified CD117 epitope in co-cultures of edited and non-edited cells exposed to mAb-7 at concentrations ranging from 100 ng / mL to 10,000 ng / mL. After 7 days of co-culture in the presence or absence of mAb-7, genomic DNA was isolated from the co-cultures and subjected to next-generation sequencing (NGS). NGS showed enrichment of CD117 editing in treated cells compared to untreated controls. [Figure 8G]

[0049] Figure 1 shows a plot and bar graph demonstrating that the CC128-modified CD117 epitope was protective against ligand blocking by ABTx052 in vitro. The figure shows plots demonstrating that mAb-7 selectively depleted unedited hematopoietic stem cells, while cells expressing modified CD117 (modified by base editing using the guide CC128) retained viability in vitro. In the figure, the horizontal dotted line represents cell viability corresponding to complete SCF starvation, and the control corresponded to cells not treated with mAb-7. [Figure 9]A schematic diagram showing the in vivo study design to confirm whether CD117-edited cells have similar functionality to wild-type CD117 cells is shown. Unedited or CD117-edited CD34+ cells were transplanted into NBSGW mice. Mouse bone marrow was harvested and subjected to flow cytometry and NGS analysis 16 weeks after transplantation. The bone marrow hematopoietic compartment was sorted. [Figure 10A] 1 shows bar graphs and flow cytometry plots demonstrating that engraftment of CD117 variants prepared using guides CC79, CC84, CC89, CC90, CC119, and CC128 was unaltered by base editing, as measured using flow cytometry after 8 weeks of engraftment. [Figure 10B]

[0039] Figure 1 shows a bar graph and flow cytometry plots demonstrating that the engraftment of CD117 variants prepared using guides CC79, CC84, CC89, CC90, CC119, and CC128 was unaltered by base editing, as measured by flow cytometry after 8 weeks of engraftment. The figure shows representative flow cytometry plots demonstrating the engraftment of edited human CD45+ cells (hCD45+) in mice administered the cells. In the figure, unedited mouse CD45+ cells are designated by the term "mCD45+."

[0545] [Figure 11A] A stacked graph shows that CD117 editing was maintained in bulk bone marrow at 8 weeks of engraftment. The figure shows the editing rate 48 hours post-electroporation (EP) in cells edited using ABE8.8 and guides CC79, CC84, CC89, CC90, CC119, and CC128. Edits were 5G, 6G, 7G, 8G, 5G + 7G, 6G + 7G, and 6G + 8G. From top to bottom and left to right in each stacked bar, the edits represented in each bar are separated by semicolons: 6G + 8G, 8G, 6G + 8G, 6G, 5G, 6G + 7G, 7G, 6G, 5G, 5G + 7G, 7G, 5G, and 7G. [Figure 11B]Figure 1 shows a stacked graph demonstrating that CD117 editing was maintained in bulk bone marrow at 8 weeks post-engraftment. The figure shows bulk bone marrow (BM) editing measured 8 weeks post-engraftment. In the figure, from top to bottom and left to right of each stacked bar, the edits represented in each bar are separated by semicolons: 6G + 8G, 8G, 6G; 6G + 8G, 6G; 5G; 6G + 7G, 7G, 6G; 5G; 5G + 7G, 7G, 5G; and 7G. [Figure 12]

[0033] Figure 1 shows a schematic diagram demonstrating that multiplex editing advantageously maintained therapeutic editing levels in hematopoietic stem cells (HSCs) and what the desired multiplex editing (i.e., "multiple-edited HSCs") was. In one embodiment, cells are multiplex-edited using ABE8.8 in combination with a guide RNA and sgRNA_015 guide (HPFH editing) to introduce edits into the CD117 polynucleotide. Guide sgRNA_015 was used to introduce therapeutic edits into the cells, targeting the HBG1 / 2 promoter, and sgRNA CC128 was used to introduce pre-treatment edits into the cells, targeting the CD117 polynucleotide. In the diagram, SCF is represented by a solid gray circle, and +BEAM-101 gRNA indicates sgRNA_015. [Figure 13] Stacked bar graphs show that multiplex editing with sgRNA HBG1 / 2a-114 (sgRNA_015) and gRNA CC128 resulted in highly efficient A:T to G:C base editing. (A) Stacked bar graphs show the editing rate at the CD117 site targeted by the CC128 guide. (B) Stacked bar graphs show the editing rate at the HBG1 / 2a-114 site targeted by sgRNA_015. [Figure 14] A schematic diagram illustrating the strategy for generating single-cell clones to remove the risk of individual CC128 editing is shown. [Figure 15A]

[0033] Figure 1 shows a bar graph depicting editing rates for M07e clones and staining of M07e clones with antibody ABTx052. The figure shows stacked bar graphs depicting allelic editing in the indicated clones. From top to bottom, left to right, the edits depicted in each bar (each bar separated by a semicolon) are as follows: 7G, 5G + 7G, 5G; 7G, 5G + 7G, 5G; 7G, 5G + 7G, 5G; 7G, 5G + 7G, 5G; 5G; 7G, 5G + 7G + 10G, 5G + 7G, 5G; 7G, 5G + 7G, 5G; and 7G, 5G + 7G (the position of the nucleotide edit is indicated by a subscript in the following sequence: 5'-AAATA5TA7ATA10GCTGGCATCA-3' (SEQ ID NO: 830)). The genotypes of the clones depicted on the x-axis of the figure are shown in Table 12. [Figure 15B]

[0023] Figure 12 shows a bar graph depicting the editing rate for M07e clones and staining of M07e clones with antibody ABTx052. The figure shows a bar graph demonstrating that a portion of the M07e clones showed reduced ABTx052 staining. The genotypes of the clones shown on the x-axis of the figure are shown in Table 12. [Figure 16A] Western blot images and plots are shown showing that Y259C (5G) and Y259C+N260D (5G+7G) CD117 single allele-edited cells were able to bind the ligand (stem cell factor (SCF)) and induce phosphorylation in the presence of ABTx052, thus indicating that the edited CD117 polypeptide was functional. The figure shows Western blot images demonstrating CD117 phosphorylation in the indicated clones (see Table 12 for a description of the clone allele-edited composition). Cells were incubated with 1 μg / mL ABTx052 antibody for 5 minutes, followed by the addition of 100 ng / mL SCF for 10 minutes. Phosphorylated CD117 was probed with the anti-phospho-CD117 antibody Y719.

[0546] [Figure 16B]Western blot images and plots are shown showing that Y259C (5G) and Y259C+N260D (5G+7G) CD117 monoallelic edited cells were able to bind the ligand (stem cell factor (SCF)) and induce phosphorylation in the presence of ABTx052, thus indicating that the edited CD117 polypeptide was functional. The figure shows plots showing how cells edited using the guide CC128 exhibited increased viability compared to unedited (UN) cells under identical conditions in the presence of ABTx052 at the concentrations indicated on the x-axis and 100 ng / mL SCF. Monoclonal antibody ABTx052 (mAbABTx052) reduced cell proliferation of unedited cells by blocking c-KIT binding with SCF. A clear difference in cell viability was observed between unedited primary hematopoietic stem cells (HSCs) and those containing the CC128 variant when cultured with ABTx052. CC128-edited cells showed increased viability compared to unedited cells. [Figure 16C] Western blot images and plots are shown showing that Y259C (5G) and Y259C+N260D (5G+7G) CD117 monoallelic edited cells were able to bind the ligand (stem cell factor (SCF)) and induce phosphorylation in the presence of ABTx052, thus indicating that the edited CD117 polypeptide was functional. The figure shows Western blot images showing CD117 phosphorylation in cells edited using the indicated guide (CC128 or CC295) in combination with ABE8.8. The Western blot also shows that ABTx052 did not block SCF binding to CD117 polypeptides modified using the CC128 guide. Cells were M07e cells. Cells were stimulated with 100 ng / mL SCF for 10 minutes. mAb 332 was used to probe c-KIT. mAb Y719 was used to probe phosphorylated c-KIT. CD117 edited with the guide CC128 was phosphorylated upon SCF stimulation, and ABTx052 blocked phosphorylation of the unedited c-KIT polypeptide. [Figure 16D]Western blot images and plots are shown showing that Y259C (5G) and Y259C+N260D (5G+7G) CD117 monoallelic edited cells were able to bind the ligand (stem cell factor (SCF)) and induce phosphorylation in the presence of ABTx052, thus indicating that the edited CD117 polypeptide was functional. The figure shows Western blot images depicting the results of experiments in which unedited, CD117-sgRNA-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, as well as cells containing monoallelic and biallelic edits of CD117, were phosphorylated upon SCF stimulation. mAb-7 inhibited the phosphorylation of WT CD117. Biallelicly edited cells underwent normal levels of phosphorylation in the presence of mAb-7. mAb-7 reduced but did not completely inhibit CD117 phosphorylation in cells containing monoallelic CD117 editing. CD117-KO cells served as a negative control. [Figure 17] A schematic diagram showing the screening completed to identify novel guides for use with the ABE-NRCH non-G PAM editor to modify the polynucleotide encoding the CD117 polypeptide is shown. Selection criteria for guide screening in HEK293 T cells were as follows: 1) the intended edit was achieved at a frequency greater than 25% with good next-generation sequencing quality, 2) low heterogeneity of the resulting protein variants, and 3) conservation of the protein sequence between cynomolgus macaque genomes (required in the targeted amino acids, with 100% conservation preferred). [Figure 18A]Figure 1 shows flow cytometry histograms. Figure 1 shows overlay histograms of flow cytometry showing that overall CD117 expression in cells remained constant after editing with guide gRNA931 (CC200) and CC128. Expression was measured using monoclonal antibody (mAb) 104D2. [Figure 18B] Figure 1 shows flow cytometry histograms. Figure 2 shows overlay histograms of flow cytometry demonstrating that CD34+ cells edited with gRNA 931 lack binding to ABTx052. [Figure 19] Figure 1 shows a plot demonstrating that the CD117 S261G modified epitope was protective from ligand blockade by ABTx052 in vitro. Cells edited with gRNA931 (CC200) showed increased viability compared to unedited cells when contacted with ABTx052 at the concentrations indicated on the x-axis. [Figure 20A] 1 shows a bar graph depicting the percentage of human CD34+ cells in mice after 8 weeks of engraftment with cells edited using the guides indicated on the x-axis (CC79, CC84, CC90, CC119, and CC128). [Figure 20B] 1 shows a bar graph depicting the percentage of human CD15+ cells in mice after 8 weeks of engraftment of cells edited using the guides indicated on the x-axis (CC79, CC84, CC90, CC119, and CC128). [Figure 20C] 1 shows a bar graph depicting the percentage of human CD19+ cells in mice after 8 weeks of engraftment of cells edited using the guides indicated on the x-axis (CC79, CC84, CC90, CC119, and CC128). [Figure 20D] A bar graph showing the percentage of human Lin-CD34+ cells in mice after 8 weeks of engraftment of cells edited using the guides indicated on the x-axis (CC79, CC84, CC90, CC119, and CC128). [Figure 20E]1 shows a bar graph depicting the percentage of human CD3+ cells in mice after 8 weeks of engraftment with cells edited using the guides indicated on the x-axis (CC79, CC84, CC90, CC119, and CC128). [Figure 20F] 1 shows a bar graph depicting the percentage of human hCD33+SSC-Alow cells in mice after 8 weeks of engraftment of cells edited using the guides indicated on the x-axis (CC79, CC84, CC90, CC119, and CC128). [Figure 20G] 1 shows a bar graph depicting the percentage of human GlyA cells in mice after 8 weeks of engraftment of cells edited using the guides indicated on the x-axis (CC79, CC84, CC90, CC119, and CC128). [Figure 20H] 1 shows a bar graph depicting the percentage of human CD33+ SSC-Ahi cells in mice after 8 weeks of engraftment of cells edited using the guides indicated on the x-axis (CC79, CC84, CC90, CC119, and CC128).

[0547] [Figure 21A] The stacked bar graphs and bar graphs show that highly efficient biallelic editing was achieved in CD34+ cells, and that the cells had normal colony-forming unit (CFU) performance. The figure shows that cells edited using the indicated guides (CC79, CC128, CC84, CC90, CC89, and CC119) had normal CFU performance (consistent with retained CD117 function), and that disrupting CD117 function (e.g., by editing with guides 291 or 295) adversely affected the colony-forming ability of edited cells. Disruption of CD117 function affected the colony-forming ability of erythroid populations. CFU assays showed that c-KIT editing had minimal impact on myeloid colony formation. [Figure 21B]Figure 1 shows stacked bar graphs and bar graphs demonstrating that highly efficient biallelic editing was achieved in CD34+ cells, and the cells had normal colony-forming unit (CFU) performance. The figure shows bar graphs depicting the percentage of A>G editing achieved after 24 hours (first bar from the left in each triplicate), 48 hours (second bar from the left in each triplicate), and 120 hours (third bar from the left in each triplicate) using the indicated guides (CC79, CC128, CC84, CC90, CC89, and CC119). Over 85% biallelic editing was achieved. [Figure 22A] A bar graph showing that c-KIT knockout significantly affected erythroid differentiation in vitro. The figure shows the total number of burst-forming units-erythroid cells (BFU-E) measured after editing cells with the indicated guides: HFPH (sgRNA_015), CC119, CC126, CC290, CC291, CC292, CC293, CC294, and CC295. [Figure 22B] A bar graph showing that c-KIT knockout significantly affected erythroid differentiation in vitro. The figure 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]

[0049] Figure 1 shows a bar graph demonstrating that c-KIT knockout significantly affected in vitro erythroid differentiation. The figure shows in vitro differentiation and myeloid levels 7 days after transfection with the indicated editors. In the figure, the bars correspond, from left to right, to the following: unedited, HPFH (sgRNA_015), CC119, CC126, CC290, CC291, CC292, CC293, CC294, and CC295. Knockout editing results in severe impairment of erythroid in vitro differentiation and less severe impairment of myeloid differentiation. [Figure 22D]

[0049] Figure 1 shows a bar graph demonstrating that c-KIT knockout significantly affected in vitro erythroid differentiation. The figure shows in vitro differentiation and myeloid levels 7 days after transfection with the indicated editors. In the figure, the bars correspond, from left to right, to the following: unedited, HPFH (sgRNA_015), CC119, CC126, CC290, CC291, CC292, CC293, CC294, and CC295. Knockout editing results in severe impairment of erythroid in vitro differentiation and less severe impairment of myeloid differentiation. [Figure 23A] Figure 1 shows stacked bar plots and bar plots depicting results related to editing of CD34+ HSPCs to install c-KIT mutations. The figure shows stacked bar plots demonstrating editing efficiency with selected c-KIT guides (CC79, CC84, CC89, CC90, CC119, and CC128). High efficiency of editing in CD34+ HSPCs was achieved, and mutant c-KIT polypeptides were expressed in the edited cells. [Figure 23B] Stacked bar plots and bar plots show results associated with editing CD34+ HSPCs to install c-KIT mutations. The figure shows a bar graph demonstrating that knocking out c-KIT (using guides CC291 and CC295) disrupted in vitro erythroid differentiation, but editing with guides HPFH (sgRNA_015), CC78, CC79, CC94, CC89, CC90, CC119, CC128, or CC84+CC90 did not. Mutations in c-KIT that did not disrupt HSPC function and differentiation were selected. [Figure 24]Western blots show that guides 291 and 295, used in combination with ABE8.8, were useful for successfully knocking out CD117 expression. Unedited and edited CD34+ cells were stimulated with stem cell factor (SCF) for 10 minutes, and cell lysates were subjected to Western blot analysis using anti-CD117 antibody (MAB332) and anti-phospho-CD117 antibody (Y719). Editing CD34+ HSCs with KO sgRNAs 291 and 295 and ABE8.8 mRNA did not demonstrate CD117 phosphorylation. [Figure 25] Fluorescence images of cells are shown showing that CD117 engineered with the guide CC128 was internalized upon binding to stem cell factor (SCF), consistent with the engineered CD117 polypeptide retaining functionality. SCF was conjugated to the pH-sensitive dye pHrodo-green, which fluoresces only upon entering cells. When pHrodo-green fluorescence is measured, it indicates that the ligand-bound SCF has been internalized.

[0548] [Figure 26] 26 shows a stacked bar graph depicting the proportion of target, bystander, and nonsynonymous bystander A>G edits corresponding to the indicated base editor. In the figure, each bar represents, from top to bottom, "other nonsynonymous bystander," "1G bystander," and "favorable" edits. In Figure 26, "XVIVO" refers to the serum-free stem cell medium in which cells were grown, "IVD" refers to "in vitro differentiated erythroid culture (IVD)," and "d5" and "d7" refer to days 5 and 7, respectively. [Figure 27] A stacked bar graph showing the editing efficiency (A to G (%)) of the base editors ABE8.20-NRCH (1570), ABE9v1-NRCH (2517), and ABE9v2 (2518) used in combination with guide gRNA931 (CC200) is shown. Each stacked bar in the figure shows the following editing contents from top to bottom: "3G_4G_6G", "4G_6G", "3G_6G", and "6G". [Figure 28] Figure 28 shows histograms demonstrating that cells expressing CD117 polypeptides modified using ABE8.20-NRCH (1570), ABE9v1-NRCH (2517), or ABE9v2 (2518) in combination with guide gRNA931 (CC200) exhibited reduced binding to antibody ABTx052. Cells were assessed 2 days post-electroporation (EP). In Figure 28, "1" indicates cells edited using ABE8.20-NRCH, "2" indicates cells edited using ABE9v1-NRCH, and "3" indicates cells edited using ABE9v2. [Figure 29A] Bar graphs, flow cytometry histograms, and plots demonstrate that highly efficient multiplex editing of CD117 and HBG1 / 2 was achieved in CD34+ hematopoietic stem cells (HSPCs). The figure shows a bar graph demonstrating successful multiplex base editing of CD34+ cells using sgRNAs against polynucleotides encoding CD117 and HBG1 / 2. The efficiency of multiplex base editing was comparable to single editing for both sgRNAs used. Multiplex editing of HBG1 / 2 and CD117 polynucleotides resulted in efficient editing of both with an efficiency of over 85%. Single-clone analysis revealed that all cells had HBG1 / 2 editing in the multiplex editing condition. Outcomes of CD117 multiplex editing were >97% biallelic, 1.5% monoallelic, and 1.5% unedited. [Figure 29B] Bar graphs, flow cytometry histograms, and plots show that highly efficient multiplex editing of CD117 and HBG1 / 2 was achieved in CD34+ hematopoietic stem cells (HSPCs). The figure also shows plots demonstrating that multiplex base editing of CD117 polynucleotides in combination with HBG1 / 2 polynucleotide editing did not interfere with gamma-globin induction in the edited cells. Approximately 60% gamma-globin induction was detected in IVED cells differentiated from multiply-edited CD34+ cells. [Figure 29C]Figure 1 shows bar graphs, flow cytometry histograms, and plots demonstrating that highly efficient multi-editing of CD117 and HBG1 / 2 was achieved in CD34+ hematopoietic stem cells (HSPCs). The figure shows flow cytometry histograms demonstrating that multi-edited cells escape recognition by mAb-7. [Figure 30] A bar graph shows that SCF blockade with mAb-7 significantly inhibited erythroid colony formation. Exposing cells to mAb-7 (i.e., ABTx052) enriched for CD117 base-edited cells. A 1:1 mixture of unedited cells and cells base-edited using the guide CC128 in combination with a base editor was plated on semi-solid medium in the presence of various concentrations of mAb-7. Individual erythroid colonies (BFU-E) were picked and sequenced on day 14 (n = 24 colonies were sequenced for each condition). In the absence of mAb-7, an equal distribution of edited and unedited colonies was observed. As the concentration of mAb-7 increased, the proportion of edited colonies became higher. At 100 ng / mL or higher concentrations of mAb-7, 100% of colonies contained either 5G or 5G_7G edits. Upon incubation with SR1, few BFU-E colonies were observed. Some of the selected colonies contained CD117 editing in only one allele, indicating that single-allele editing may be sufficient to circumvent antibody blockade by mAbs.

[0549] [Figure 31A]Figure 1 shows bar graphs and stacked histograms demonstrating successful multiplex editing of both the CD117 polynucleotide and the β-globin gene in CD34+ hematopoietic stem cells. The figure shows bar graphs demonstrating high levels of multiplex editing at sites targeted by guide sgRNA_017 (Makassar sgRNA) and gRNA931 (CD117 sgRNA; CC200). Highly efficient CD117 and Makassar editing (n=3) was achieved in mobilized peripheral blood-derived (mPB) CD34+ cells using a single base editor in combination with two guide polynucleotides (sgRNAs). [Figure 31B] Figure 1 shows a bar graph and stacked histograms demonstrating successful multiplex editing of both the CD117 polynucleotide and the β-globin gene in CD34+ hematopoietic stem cells. The figure shows flow cytometry histograms demonstrating that both edited and unedited cells bound to a pan-CD117 antibody (Pan CD117 Ab), but edited cells showed reduced binding to the antibody mAb-7 (i.e., ABTx052). [Figure 32A] Structural images and plots are shown. The image in the figure corresponds to a cryo-EM structural image of CD117 / c-KIT complexed with ABTx052-Fab in solution at approximately 3.0 Å. In the figure, each domain is numbered and each number is located next to the corresponding domain in the figure, with "1" representing the ABTx052 Fab-heavy chain domain, "2" representing the ABTx052 Fab-light chain domain, "3" representing the D3 domain of CD117, "4" representing the D2 domain of CD117, and "5" representing the D1 domain of CD117. [Figure 32B] Structural images and plots are shown. The image in the figure corresponded to a ~3.0 Å cryo-EM structural image of CD117 / c-KIT complexed with ABTx052-Fab in solution. The figure shows the structural image shaded to indicate the structural resolution estimated by windowed FSC of RELION3. [Figure 32C]Structural images and plots are shown. The figure shows a plot of Fourier shell correlation versus resolution (1 / Angstrom), indicating that the final resolution of the structure was approximately 3 Angstroms. [Figure 33A] The figure shows a bar graph and plot demonstrating that modification of the Fc domain of mAb-7 generated a highly potent mAb that did not cause mast cell degranulation in vitro. The figure shows a bar graph demonstrating that an Fc-modified version of anti-CD117 ABTx052 did not cause mast cell degranulation in vitro. Mast cells generated through in vitro differentiation of CD34+ cells contacted with IgE or interferon-γ to increase Fcγ receptor expression were treated with nati...

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