Methods and compositions for modification of a HLA locus

• US 10,072,062 B2
• Filed: 01/05/2015
• Issued: 09/11/2018
• Est. Priority Date: 07/21/2010
• Status: Active Grant

• Current Assignee: Sangamo Therapeutics, Inc.
• Original Assignee: Sangamo Therapeutics, Inc., Board of Regents of the University of Texas System (University of Texas System)
• Inventors: Collingwood, Trevor, Cooper, Laurence J. N., Gregory, Philip D., Holmes, Michael C., Miller, Jeffrey C., Rebar, Edward J., Reik, Andreas, Urnov, Fyodor
• Primary Examiner(s): LEAVITT, MARIA GOMEZ
• Application Number:
  US14/589,632
• Publication Number:
  US 20150252094A1
• Time in Patent Office: 1,345 Days
• Field of Search: None
• 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. A genetically modified mammalian cell comprising an endogenous human leukocyte antigen (HLA) class I gene comprising a sequence selected from the group consisting of any one of the nucleotides of SEQ ID NOs:

97 to 111 and an endogenous HLA class II gene comprising a sequence selected from the group consisting of any one of the nucleotides of SEQ ID NOs;

112 to 115, the genetically modified cell comprising;

(i) a first genomic modification comprising an integrated exogenous nucleotide sequence encoding a chimeric antigen receptor (CAR) or T-cell receptor gene, and

(ii) a second genomic modification comprising an inactivated HLA gene following zinc finger nuclease-mediated cleavage of the active HLA class I gene and/or HLA class II gene with a pair of zinc finger nucleases, each zinc finger nuclease comprising a cleavage domain and the recognition helix regions of the zinc finger proteins designated 18889, which binds to a target site within SEQ ID NO;

97;

11881, which binds to a target site within SEQ ID NO;

98;

24859, which binds to a target site within SEQ ID NO;

99;

25191, which binds to a target site within SEQ ID NO;

100;

25190, which binds to a target site within SEQ ID NO;

101;

25316, which binds to a target site within SEQ ID NO;

102;

25317, which binds to a target site within SEQ ID NO;

103;

15267, which binds to a target site within SEQ ID NO;

104;

15265, which binds to a target site within SEQ ID NO;

105;

17454, which binds to a target site within SEQ ID NO;

106;

17456, which binds to a target site within SEQ ID NO;

107;

15296, which binds to a target site within SEQ ID NO;

108;

15298, which binds to a target site within SEQ ID NO;

109;

25588, which binds to a target site within SEQ ID NO;

110;

25589, which binds to a target site within SEQ ID NO;

111;

15872, which binds to a target site within SEQ ID NO;

112;

15873, which binds to a target site within SEQ ID NO;

113;

15909, which binds to a target site within SEQ ID NO;

114;

or 15910, which binds to a target site within SEQ ID NO;

115,

wherein the pair of zinc finger nucleases includes 18889 and 18881;

18889 and 24859;

25191 and 25190;

25316 and 25317;

15267 and 15265;

17454 and 17456;

15296 and 15298;

25588 and 25589;

15872 and 15873;

or 15909 and 15910;

and wherein the HLA gene is inactivated by the second genomic modification.

2. The genetically modified cell of claim 1, wherein the HLA class I gene is selected from the group consisting of an HLA A2 gene, an HLA A3 gene, an HLA B gene and an HLC gene.

3. The genetically modified cell of claim 1, wherein the integrated exogenous nucleotide sequence encodes a CAR.

4. The genetically modified cell of claim 1, wherein the integrated exogenous nucleotide sequence comprises a TCR gene.

5. The genetically modified cell of claim 1, wherein a donor sequence is inserted into the inactivated HLA gene following targeted cleavage with the pair of zinc finger nucleases proteins.

6. The genetically modified cell of claim 1, wherein the CAR targets CD19 (CD19CAR).

7. The genetically modified cell of claim 1, wherein the cell is a T-cell or a stem cell.

8. The genetically modified cell of claim 7, wherein the stem cell is a hematopoietic stem cell.

9. The genetically modified cell of claim 1, further comprising a third genomic modification comprising inactivation of a second gene using one or more zinc finger nucleases.

10. The genetically modified cell of claim 9, wherein the inactivated second gene is selected from the group consisting of a DBP2 gene;

a DRA gene;

transporter associated antigen processing (TAP) gene;

tapasin gene;

class 2 transactivator (CTIIA) gene;

regulatory factor X protein 5 (RFX5) gene;

T-cell receptor alpha (TRAC) or a T-cell receptor beta (TRBC) gene.

11. A pharmaceutical composition comprising the genetically modified mammalian cell of claim 1.