Crispr/cas-related methods and compositions for improving transplantation
AssigneeEditas Medicine, Inc.
InventorsJennifer Leah Gori, Tongyao Wang, Hariharan Jayaram, Penrose ODonnell
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Abstract
Disclosed herein are compositions and methods for increasing the immunocompatibility of donor cells (e.g., HSCs or T-cells) for transplantation to a recipient subject, as well as database schemes for use in the methods. The methods and compositions described herein result in the allele-specific modification of one or more immunogenicity genes (e.g., an HLA gene) of a cell, resulting in cells that are suitable for transplantation into a recipient subject.
Claims46
1-102. (canceled)
A method of reducing the cell surface expression of a protein encoded by a first allele of an endogenous immunogenicity gene in a cell, the method comprising:
- contacting the cell with a first allele-specific gRNA molecule and a Cas9 molecule, wherein the allele-specific gRNA molecule and the Cas9 molecule associate with the first allele of the endogenous immunogenicity gene,
- thereby reducing the cell surface expression of the protein encoded by the first allele of the endogenous immunogenicity gene.
An ex vivo method of making a composition comprising a population of cells having an allele-specific gene modification, comprising:
- contacting a population of cells with an allele-specific gRNA molecule and a Cas9 molecule, wherein the allele-specific gRNA molecule and the Cas9 molecule associate with a first allele of a gene encoding an identifiable gene product;
- and
- enriching for cells that express the identifiable gene product but do not express the first allele.
A blood cell comprising a modification in a first allele of an endogenous immunogenicity gene, wherein the blood cell has been contacted with a first allele-specific modified gRNA molecule and a Cas9 molecule.
A blood cell comprising a first allele-specific gRNA molecule and a Cas9 molecule, wherein the allele-specific gRNA molecule and the Cas9 molecule associate with a first allele of an endogenous immunogenicity gene and reduce the cell surface expression of a protein encoded by the first allele of the endogenous immunogenicity gene.
A non-transitory computer readable storage medium storing instructions for execution by a processing device for implementing a database schema, the database schema comprising:
- an allele table storing data related to major HLA alleles;
- a gRNA table storing data related to gRNAs;
- an allele-gRNA-relation table storing relationships between records of the allele table and records of the gRNA table, the allele table having a one-to-many relationship with the allele-gRNA-relation table, and the gRNA table having a one-to-many relationship with the allele-gRNA-relation table;
- a haplotype table storing data related to haplotypes, the allele table having a one-to-many relationship with the haplotype table;
- a haplotype-frequency table storing data related to frequency of a haplotype occurring within a plurality of ancestries, the haplotype table having a one-to-one relationship with the haplotype-frequency table;
- an ancestry table storing data related to ancestry;
- an ancestry-haplotype-relation table storing relationships between records of the haplotype-frequency table and records of the ancestry table, the haplotype-frequency table having a one-to-many relationship with the ancestry-haplotype-relation table, the ancestry table having a one-to-many relationship with the an ancestry-haplotype-relation table;
- an allele frequency table storing data related to frequency of an allele occurring within a plurality of ancestries, the allele table having a one-to-one relationship with the allele frequency table;
- and
- an allele-ancestry-relation table storing relationships between records of the allele frequency table and records of the ancestry table, the allele frequency table having a one-to-many relationship with the allele-ancestry-relation table and the ancestry table having a one-to-many relationship with the allele-ancestry-relation table.
A system for identifying gRNAs for editing one or more alleles, the system comprising:
- a processor;
- and
- a memory storing instructions that when executed causes the processor to:
- receive a listing of a first plurality of alleles of a targeted transplant recipient;
- receive a listing of a second plurality of alleles of a targeted transplant donor;
- process the listings of the first and second pluralities of alleles to identify one or more mismatched alleles between the first plurality of alleles and the second plurality of alleles;
- query a database to determine whether one or more gRNAs are suitable for editing the one or more mismatched alleles of the second plurality of alleles;
- in response to determining that one or more gRNAs from the database are suitable to edit the one or more mismatched alleles, generate a list of gRNAs that identifies the one or more gRNAs found to be suitable;
- rank the list of gRNAs;
- and
- display the ranked list of gRNAs.
A method performed in a computational system for identifying gRNAs for editing one or more alleles comprising:
- receiving, via an interface of the computational system, a listing of a first plurality of alleles of a targeted transplant recipient;
- receiving, via the interface of the computational system, a listing of a second plurality of alleles of a targeted transplant donor;
- processing the listings of the first and second pluralities of alleles to identify one or more mismatched alleles between the first plurality of alleles and the second plurality of alleles;
- querying a database to determine whether one or more gRNAs are suitable for editing the one or more mismatched alleles of the second plurality of alleles;
- in response to determining that one or more gRNAs from the database are suitable to edit the one or more mismatched alleles, generating a list of gRNAs that identifies the one or more gRNAs found to be suitable;
- ranking the list of gRNAs;
- and
- displaying the ranked list of gRNAs.
Dependencies are inferred from the claim text.