METHODS AND COMPOSITIONS FOR MODIFICATION OF A HLA LOCUS

• US 20120060230A1
• Filed: 07/21/2011
• Published: 03/08/2012
• Est. Priority Date: 07/21/2010
• Status: Active Grant

• Current Assignee: Sangamo Therapeutics, Inc., Board of Regents of the University of Texas System (University of Texas System)
• Original Assignee: Board of Regents of the University of Texas System (University of Texas System)
• Inventors: Collingwood, Trevor, Gregory, Philip D., Holmes, Michael C., Miller, Jeffrey C., Rebar, Edward J., Reik, Andreas, Urnov, Fyodor, Cooper, Laurence J.N.
• Granted Patent: US 8,945,868 B2
• Time in Patent Office: Days
• US Class Current: 800/9
• CPC Class Codes: A61K 35/17 Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes when activated by a specific antigen A61K39/00
• CPC Class Codes: A61K 39/4611 T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
• CPC Class Codes: A61K 39/4631 Chimeric Antigen Receptors [CAR]
• CPC Class Codes: A61K 39/464412 CD19 or B4
• CPC Class Codes: A61P 17/00 Drugs for dermatological disorders
• CPC Class Codes: A61P 17/06 Antipsoriatics
• CPC Class Codes: A61P 19/00 Drugs for skeletal disorders
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 19/04 for non-specific disorders of the connective tissue
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 3/00 Drugs for disorders of the metabolism of the blood or the extracellular fluid A61P7/00
• CPC Class Codes: A61P 31/14 for RNA viruses
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 5/14 of the thyroid hormones, e.g. T3, T4
• CPC Class Codes: A61P 5/38 of the suprarenal hormones
• CPC Class Codes: A61P 7/02 Antithrombotic agents; Anticoagulants; Platelet aggregation inhibitors
• CPC Class Codes: C07K 14/70539 MHC-molecules, e.g. HLA-molecules
• CPC Class Codes: C07K 2319/81 containing a Zn-finger domain for DNA binding
• CPC Class Codes: C12N 15/907 : in mammalian cells
• CPC Class Codes: C12N 2800/80 : Vectors containing sites for inducing double-stranded breaks, e.g. meganuclease restriction sites

Abstract

Disclosed herein are methods and compositions for modulating the expression of a HLA locus or for selectively deleting or manipulating a HLA locus or HLA regulator.

Claims

1. An isolated polypeptide comprising a non-naturally occurring zinc finger protein that binds to a target site as shown in Table 2 in an endogenous gene.

2. A fusion protein comprising the isolated polypeptide of claim 1 and a functional domain.

3. The fusion protein of claim 2 wherein the functional domain comprises an activation domain or a repression domain.

4. The fusion protein of claim 3, wherein the functional domain modulates expression of one or more HLA A, HLA B, HLA C, TAP1, TAP2, Tapasin, CTIIA, RFX5, TRAC, or TRAB genes.

6. A polynucleotide comprising a sequence encoding a polypeptide according to claim 1.

7. A gene delivery vector comprising a polynucleotide according to claim 6.

8. An isolated cell comprising a polypeptide according to claim 1.

9. The isolated cell of claim 8, wherein the cell is selected from the group consisting of a stem cell, a progenitor cell, a T-cell or an NK cell.

10. The isolated cell of claim 9, wherein the cell is a partially or fully differentiated progeny cell of the stem cell.

11. A cell fragment of an isolated cell according to claim 8.

12. The cell fragment of claim 11, wherein the fragment is a platelet.

5. The fusion protein 2, wherein the functional domain comprises a cleavage domain or cleavage half-domain.

13. A method of inactivating one or more HLA or HLA regulator genes in a cell, the method comprising;

cleaving the HLA or HLA regulator genes gene with a fusion protein according to claim 5 such that the one or more HLA or HLA regulator genes are inactivated.

14. The method of claim 13, wherein the cleavage results in a deletion or insertion within the one or more HLA or HLA regulator genes.

15. A method of treating an HLA related disorder in a subject, the method comprising

a) cleaving an endogenous HLA or HLA regulatory gene in an isolated cell according to the method of claim 13 such that the HLA or HLA regulatory gene is inactivated;

and

(b) introducing the cell into the subject, thereby treating or preventing the HLA related disorder.

16. The method of claim 15, wherein the isolated cell introduced into the subject further comprises an additional genomic modification selected from the group consisting of integration of an exogenous sequence into the genome of the cell, inactivation of one or more additional genes, and combinations thereof.

17. The method of claim 16, wherein the additional genomic modification comprises integration of an exogenous sequence and further wherein the exogenous sequence is integrated into the cleaved HLA or HLA regulatory gene.

18. The method of claim 16, wherein the additional genomic modification comprises integration of an exogenous sequence and further wherein the exogenous sequence encodes a polypeptide a chimeric antigen receptor (CAR) specific for a cancer marker.

19. The method of claim 16, wherein the additional genomic modification comprises inactivation of one or more endogenous TCR genes.

20. The method of claim 13, wherein the fusion protein is introduced into the cell as polynucleotide.

21. The method of claim 20, wherein the polynucleotide is mRNA or DNA.

22. The method of claim 15, wherein the cell is a T-cell or a stem cell.

23. The method of claim 20, wherein the stem cell is selected from the group consisting of an induced pluripotent stem cell (iPSC), a human embryonic stem cell (hES), a mesenchymal stem cell (MSC) or a neuronal stem cell.

24. A model system for HLA disorders, the model system comprising a cell line or animal in which one or more HLA or HLA regulator genes are inactivated according to the method of claim 13.

25. A method for treating a patient in need of a cell transplant, the method comprising:

inactivating one or more HLA or HLA regulator genes in isolated cells according to the method of claim 13; and

transplanting the cells or fragments of the cells into the patient in need thereof.

26. The method to claim 25 wherein the cells or cell fragments are selected from the group consisting of T-cells, stem cells and platelets.