Methods and compositions for modification of a HLA locus

• US 8,945,868 B2
• Filed: 07/21/2011
• Issued: 02/03/2015
• 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: Sangamo Biosciences, Inc., 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.
• Primary Examiner(s): LEAVITT, MARIA GOMEZ
• Application Number:
  US13/188,417
• Publication Number:
  US 20120060230A1
• Time in Patent Office: 1,293 Days
• Field of Search: 435/69.1, 435/252.3, 435/440, 435/455, 435/350
• US Class Current: 435/69.1
• 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. A protein comprising an engineered zinc finger DNA-binding domain, wherein the engineered zinc finger DNA-binding domain comprises four, five or six zinc finger DNA recognition regions designated and ordered F1 to F4, F1 to F5 or F1 to F6 from N-terminus to C-terminus and further wherein the engineered zinc finger DNA-binding domain comprises the zinc finger DNA recognition regions selected from the group consisting of:

(i) F1;

QSSHLTR (SEQ ID NO;

1);

F2;

RSDHLTT (SEQ ID NO;

2);

F3;

RSDTLSQ (SEQ ID NO;

3);

F4;

RSADLSR (SEQ ID NO;

4);

F5;

QSSDLSR (SEQ ID NO;

5); and

F6;

RSDALTQ (SEQ ID NO;

6), wherein the protein binds to the target site set forth in SEQ ID NO;

97 in an endogenous human leukocyte antigen (HLA) A2 gene;

(ii) F1;

QKTHLAK (SEQ ID NO;

7);

F2;

RSDTLSN (SEQ ID NO;

8);

F3;

RKDVRIT (SEQ ID NO;

9);

F4;

RSDHLST (SEQ ID NO;

10); and

F5;

DSSARKK (SEQ ID NO;

11), wherein the protein binds to the target site set forth in SEQ ID NO;

98 in an endogenous HLA A2 gene;

(iii) F1;

QNAHRKT (SEQ ID NO;

12);

F2;

RSDSLLR (SEQ ID NO;

13);

F3;

RNDDRKK (SEQ ID NO;

14);

F4;

RSDHLST (SEQ ID NO;

10); and

F5;

DSSARKK (SEQ ID NO;

11), wherein the protein binds to the target site set forth in SEQ ID NO;

99 in an endogenous HLA A2 gene;

(iv) F1;

DRSHLSR (SEQ ID NO;

15);

F2;

RSDDLTR (SEQ ID NO;

16);

F3;

DRSDLSR (SEQ ID NO;

17); and

F4;

QSGHLSR (SEQ ID NO;

18), wherein the protein binds to the target site set forth in SEQ ID NO;

100 in an endogenous HLA A3 gene;

(v) F1;

DRSALSR (SEQ ID NO;

19);

F2;

QSSDLRR (SEQ ID NO;

20);

F3;

DRSALSR (SEQ ID NO;

19);

F4;

DRSHLAR (SEQ ID NO;

21);

F5;

RSDDLSK (SEQ ID NO;

22); and

F6;

DRSHLAR (SEQ ID NO;

21), wherein the protein binds to the target site set forth in SEQ ID NO;

101 in an endogenous HLA A3 gene;

(vi) F1;

SSELLNE (SEQ ID NO;

23);

F2;

TSSHLSR (SEQ ID NO;

24);

F3;

QSGDRNK (SEQ ID NO;

25);

F4;

RSANLAR (SEQ ID NO;

26); and

F5;

RSDNLRE (SEQ ID NO;

27), wherein the protein binds to the target site set forth in SEQ ID NO;

102 in an endogenous HLA B gene;

(vii) F1;

QSGDLTR (SEQ ID NO;

28);

F2;

RSDDLTR (SEQ ID NO;

16);

F3;

DQSTLRN (SEQ ID NO;

29);

F4;

DRSNLSR (SEQ ID NO;

30); and

F5;

DAFTRTR (SEQ ID NO;

31), wherein the protein binds to the target site set forth in SEQ ID NO;

103 in an endogenous HLA B gene;

(viii) F1;

RSDNLSE (SEQ ID NO;

32);

F2;

ASKTRKN (SEQ ID NO;

33);

F3;

TSGNLTR (SEQ ID NO;

34); and

F4;

RSDALAR (SEQ ID NO;

35), wherein the protein binds to the target site set forth in SEQ ID NO;

104 in an endogenous HLA B gene;

(ix) F1;

DRSALSR (SEQ ID NO;

19);

F2;

QSGNLAR (SEQ ID NO;

36);

F3;

DRSALSR (SEQ ID NO;

19);

F4;

QSGHLSR (SEQ ID NO;

18), wherein the protein binds to the target site set forth in SEQ ID NO;

105 in an endogenous HLA B gene;

(x) F1;

RSDNLSE (SEQ ID NO;

32);

F2;

ASKTRKN (SEQ ID NO;

33);

F3;

QSGHLSR (SEQ ID NO;

18);

F4;

TSGHLSR (SEQ ID NO;

37); and

F5;

QSGHLSR (SEQ ID NO;

18), wherein the protein binds to the target site set forth in SEQ ID NO;

106 in an endogenous HLA B gene;

(xi) F1;

RSADLTR (SEQ ID NO;

38);

F2;

QSGDLTR (SEQ ID NO;

28);

F3;

QSGNLAR (SEQ ID NO;

36); and

F4;

QSGDLTR (SEQ ID NO;

28), wherein the protein binds to the target site set forth in SEQ ID NO;

107 in an endogenous HLA B gene;

(xii) F1;

QSGHLSR (SEQ ID NO;

18);

F2;

RSDHLST (SEQ ID NO;

10);

F3;

QSADRTK (SEQ ID NO;

39);

F4;

TSGSLSR (SEQ ID NO;

40); and

F5;

QSADRTK (SEQ ID NO;

39), wherein the protein binds to the target site set forth in SEQ ID NO;

108 in an endogenous HLA C gene;

(xiii) F1;

QSGDLTR (SEQ ID NO;

28);

F2;

RSDHLST (SEQ ID NO;

10);

F3;

QSADRTK (SEQ ID NO;

39);

F4;

RSDNLSA (SEQ ID NO;

41); and

F5;

RSDNRTT (SEQ ID NO;

42), wherein the protein binds to the target site set forth in SEQ ID NO;

109 in an endogenous HLA C gene;

(xiv) F1;

QRSNLVR (SEQ ID NO;

43);

F2;

DRSALAR (SEQ ID NO;

44);

F3;

QSSDLRR (SEQ ID NO;

20);

F4;

RSDDLTR (SEQ ID NO;

16); and

F5;

RSDDLTR (SEQ ID NO;

16), wherein the protein binds to the target site set forth in SEQ ID NO;

110 in an endogenous HLA C gene;

(xv) F1;

RSDDLTR (SEQ ID NO;

16);

F2;

DRSDLSR (SEQ ID NO;

17);

F3;

QSGHLSR (SEQ ID NO;

18);

F4;

RSDHLSA (SEQ ID NO;

45); and

F5;

ESRYLMV (SEQ ID NO;

46), wherein the protein binds to the target site set forth in SEQ ID NO;

111 in an endogenous HLA C gene;

(xvi) F1;

RSDHLST (SEQ ID NO;

10);

F2;

DNANRTK (SEQ ID NO;

47);

F3;

QSGDLTR (SEQ ID NO;

28);

F4;

RSDALST (SEQ ID NO;

48); and

F5;

ASSNRKT (SEQ ID NO;

49), wherein the protein binds to the target site set forth in SEQ ID NO;

112 in an endogenous DBP2 gene;

(xvii) F1;

TSGNLTR (SEQ ID NO;

34);

F2;

DRSDLSR (SEQ ID NO;

17);

F3;

RSDNLSE (SEQ ID NO;

32);

F4;

RSANLTR (SEQ ID NO;

50); and

F5;

QSGHLSR (SEQ ID NO;

18), wherein the protein binds to the target site set forth in SEQ ID NO;

113 in an endogenous DBP2 gene;

(xviii) F1;

RSDNLSE (SEQ ID NO;

32);

F2;

TSGSLTR (SEQ ID NO;

51);

F3;

TSGHLSR (SEQ ID NO;

37);

F4;

RSDNLSQ (SEQ ID NO;

52); and

F5;

ASNDRKK (SEQ ID NO;

53), wherein the protein binds to the target site set forth in SEQ ID NO;

114 in an endogenous DRA gene;

(xix) F1;

RSDNLSR (SEQ ID NO;

54);

F2;

DNNARIN (SEQ ID NO;

55);

F3;

RSDSLSV (SEQ ID NO;

56);

F4;

QNQHRIN (SEQ ID NO;

57); and

F5;

RSDHLSR (SEQ ID NO;

58), wherein the protein binds to the target site set forth in SEQ ID NO;

115 in an endogenous DRA gene;

(xx) F1;

DSSDRKK (SEQ ID NO;

59);

F2;

DRSHLTR (SEQ ID NO;

60);

F3;

RSDALAR (SEQ ID NO;

35);

F4;

QSSDLSR (SEQ ID NO;

5); and

F5;

RSDNLTT (SEQ ID NO;

61), wherein the protein binds to the target site set forth in SEQ ID NO;

116 in an endogenous transporter associated with antigen processing 1 (TAP1) gene;

(xxi) F1;

RSANLAR (SEQ ID NO;

26);

F2;

QSGHLSR (SEQ ID NO;

18);

F3;

TSGNLTR (SEQ ID NO;

34);

F4;

QSGALVI (SEQ ID NO;

62);

F5;

RSDHLSE (SEQ ID NO;

63); and

F6;

RKHDRTK (SEQ ID NO;

64), wherein the protein binds to the target site set forth in SEQ ID NO;

117 in an endogenous TAP1 gene;

(xxii) F1;

QSSDLSR (SEQ ID NO;

5);

F2;

QSGDLTR (SEQ ID NO;

28);

F3;

QSSHLTR (SEQ ID NO;

1);

F4;

RSDDRKT (SEQ ID NO;

65);

F5;

TSGNLTR (SEQ ID NO;

34); and

F6;

RSDDLTR (SEQ ID NO;

16), wherein the protein binds to the target site set forth in SEQ ID NO;

118 in an endogenous transporter associated with antigen processing 2(TAP2) gene;

(xxiii) F1;

RSDNLST (SEQ ID NO;

66);

F2;

RSDALAR (SEQ ID NO;

35);

F3;

RSDVLSA (SEQ ID NO;

67);

F4;

DRSNRIK (SEQ ID NO;

68);

F5;

RREDLIT (SEQ ID NO;

69); and

F6;

TSSNLSR (SEQ ID NO;

70), wherein the protein binds to the target site set forth in SEQ ID NO;

119 in an endogenous TAP2 gene;

(xxiv) F1;

RSDNLSE (SEQ ID NO;

32);

F2;

KRCNLRC (SEQ ID NO;

71);

F3;

DRSDLSR (SEQ ID NO;

17);

F4;

QTTHRNR (SEQ ID NO;

72);

F5;

DRSDLSR (SEQ ID NO;

17), and

F6;

QSSTRAR (SEQ ID NO;

73), wherein the protein binds to the target site set forth in SEQ ID NO;

120 in an endogenous tapasin gene;

(xxv) F1;

QSSDLR (SEQ ID NO;

5);

F2;

RSDNLTR (SEQ ID NO;

74);

F3;

QSSHLTR (SEQ ID NO;

1);

F4;

QSSDLTR (SEQ ID NO;

75);

F5;

RSDNLAR (SEQ ID NO;

76); and

F6;

QKVNLMS (SEQ ID NO;

77), wherein the protein binds to the target site set forth in SEQ ID NO;

121 in an endogenous tapasin gene;

(xxvi) F1;

TSGNLTR (SEQ ID NO;

34);

F2;

LSQDLNR (SEQ ID NO;

78);

F3;

RSDSLSA (SEQ ID NO;

79);

F4;

DRSHLAR (SEQ ID NO;

21);

F5;

RSDHLST (SEQ ID NO;

10); and

F6;

QSGHLSR (SEQ ID NO;

18), wherein the protein binds to the target site set forth in SEQ ID NO;

122 in an endogenous tapasin gene;

(xxvii) F1;

RSDDLTR (SEQ ID NO;

16);

F2;

SSSNLTK (SEQ ID NO;

80);

F3;

TSGSLSR (SEQ ID NO;

40);

F4;

QSGDLTR (SEQ ID NO;

28);

F5;

RSDHLSE (SEQ ID NO;

63); and

F6;

RNRDRIT (SEQ ID NO;

81), wherein the protein binds to the target site set forth in SEQ ID NO;

123 in an endogenous tapasin gene;

(xxviii) F1;

RSDDLTR (SEQ ID NO;

16);

F2;

RSDHLSE (SEQ ID NO;

63);

F3;

NSRNRKT (SEQ ID NO;

82);

F4;

RSDNLSQ (SEQ ID NO;

52); and

F5;

ASNDRKK (SEQ ID NO;

53), wherein the protein binds to the target site set forth in SEQ ID NO;

124 in an endogenous class 2 transactivator (CTIIA) gene;

(xxvix) F1;

RSDDLSR (SEQ ID NO;

83);

F2;

RNDDRKK (SEQ ID NO;

14);

F3;

DRSDLSR (SEQ ID NO;

17);

F4;

RSDHLSE (SEQ ID NO;

63); and

F5;

ARSTRTN (SEQ ID NO;

84), wherein the protein binds to the target site set forth in SEQ ID NO;

125 in an endogenous CTIIIA gene;

(xxx) F1;

TSGNLTR (SEQ ID NO;

34);

F2;

QSGNLAR (SEQ ID NO;

36);

F3;

RSDHLTQ (SEQ ID NO;

85);

F4;

ASMALNE (SEQ ID NO;

86); and

F5;

TSSNLSR (SEQ ID NO;

70), wherein the protein binds to the target site set forth in SEQ ID NO;

126 in an endogenous regulatory factor X protein 5 (RXF5) gene;

(xxxi) F1;

RSDVLSE (SEQ ID NO;

87);

F2;

RNQHRKT (SEQ ID NO;

88);

F3;

RSDHLST (SEQ ID NO;

10);

F4;

QSSDLRR (SEQ ID NO;

20);

F5;

RSDNLST (SEQ ID NO;

66); and

F6;

RSADRKN (SEQ ID NO;

89), wherein the protein binds to the target site set forth in SEQ ID NO;

127 in an endogenous RXF5 gene;

(xxxii) F1;

QSGDLTR (SEQ ID NO;

28);

F2;

QWGTRYR (SEQ ID NO;

90);

F3;

ERGTLAR (SEQ ID NO;

91);

F4;

RSDNLRE (SEQ ID NO;

27);

F5;

QSGDLTR (SEQ ID NO;

28); and

F6;

TSGSLTR (SEQ ID NO;

51), wherein the protein binds to the target site set forth in SEQ ID NO;

128 in an endogenous T-cell receptor alpha (TRAC) gene;

(xxxiii) F1;

QSGDLTR (SEQ ID NO;

28);

F2;

WRSSLAS (SEQ ID NO;

92);

F3;

QSGDLTR (SEQ ID NO;

28);

F4;

HKWVLRQ (SEQ ID NO;

93); and

F5;

DRSNLTR (SEQ ID NO;

94), wherein the protein binds to the target site set forth in SEQ ID NO;

129 in an endogenous TRAC gene;

(xxxiv)F1;

RSDVLSA (SEQ ID NO;

67);

F2;

DRSNRIK (SEQ ID NO;

68);

F3;

RSDVLSE (SEQ ID NO;

87);

F4;

QSGNLAR (SEQ ID NO;

36); and

F5;

QSGSLTR (SEQ ID NO;

95), wherein the protein binds to the target site set forth in SEQ ID NO;

130 in an endogenous T-cell receptor beta (TRBC) gene; and

(xxxv) F1;

RSDHLST (SEQ ID NO;

10);

F2;

RSDNLTR (SEQ ID NO;

74);

F3;

DRSNLSR (SEQ ID NO;

30);

F4;

TSSNRKT (SEQ ID NO;

96);

F5;

RSANLAR (SEQ ID NO;

26); and

F6;

RNDDRKK (SEQ ID NO;

14), wherein the protein binds to the target site set forth in SEQ ID NO;

131 in an endogenous TRBC gene.

2. A fusion protein comprising the engineered zinc finger DNA-binding domain of claim 1 and a transcriptional regulatory domain or a nuclease domain.

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

4. An isolated cell comprising the fusion protein of claim 2.

6. A polynucleotide encoding the protein of claim 1.

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

8. An isolated cell comprising the protein 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 a Natural Killer (NK) cell.

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