U.S. patent application number 16/443219 was filed with the patent office on 2019-12-12 for effective generation of tumor-targeted t cells derived from pluripotent stem cells.
This patent application is currently assigned to MEMORIAL SLOAN-KETTERING CANCER CENTER. The applicant listed for this patent is MEMORIAL SLOAN-KETTERING CANCER CENTER. Invention is credited to Christopher C. Kloss, Michel Sadelain, Maria Themeli.
Application Number | 20190375850 16/443219 |
Document ID | / |
Family ID | 50686211 |
Filed Date | 2019-12-12 |
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United States Patent
Application |
20190375850 |
Kind Code |
A1 |
Themeli; Maria ; et
al. |
December 12, 2019 |
EFFECTIVE GENERATION OF TUMOR-TARGETED T CELLS DERIVED FROM
PLURIPOTENT STEM CELLS
Abstract
The present invention relates to the field of adoptive
immunotherapy. The invention provides methods for generating
phenotypically defined, functional, and/or expandable T cells from
pluripotent stem cells engineered through safe genetic
modifications. The engineered cells may provide one or more of: 1)
targeting a specific predetermined antigen expressed on the cell
surface of a target cell in an HLA independent manner, 2) enhanced
survival and functional potential 3) "off-the-shelf" T cells for
administration to multiple recipients, eventually across
immunogenic barriers, and/or 4) cytotoxic potential and anti-tumor
activity.
Inventors: |
Themeli; Maria; (New York,
NY) ; Sadelain; Michel; (New York, NY) ;
Kloss; Christopher C.; (Philladelphia, PA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
MEMORIAL SLOAN-KETTERING CANCER CENTER |
New York |
NY |
US |
|
|
Assignee: |
MEMORIAL SLOAN-KETTERING CANCER
CENTER
New York
NY
|
Family ID: |
50686211 |
Appl. No.: |
16/443219 |
Filed: |
June 17, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14873836 |
Oct 2, 2015 |
10370452 |
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16443219 |
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PCT/US2014/032883 |
Apr 3, 2014 |
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14873836 |
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61808092 |
Apr 3, 2013 |
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61808992 |
Apr 5, 2013 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61K 39/001168 20180801;
C12N 5/0646 20130101; A61K 39/001102 20180801; A61K 39/001188
20180801; A61K 39/001117 20180801; A61K 39/001104 20180801; A61K
39/00118 20180801; A61K 39/001182 20180801; A61K 39/001184
20180801; C07K 14/47 20130101; A61K 39/001157 20180801; A61K
39/00117 20180801; A61K 2039/5156 20130101; C07K 14/70521 20130101;
C07K 2319/03 20130101; A61K 39/001193 20180801; A61K 39/001113
20180801; C07K 16/30 20130101; C12N 2740/13043 20130101; A61K
39/001129 20180801; A61K 39/001186 20180801; C12N 5/0638 20130101;
A61K 39/001166 20180801; A61K 39/001112 20180801; A61K 39/001171
20180801; C07K 16/2803 20130101; C12N 2740/16043 20130101; A61K
35/17 20130101; A61K 39/0011 20130101; A61K 39/001119 20180801;
C07K 2319/70 20130101; C12N 2506/45 20130101; A61K 39/001153
20180801; C07K 2319/74 20130101; A61K 39/001106 20180801; C07K
2319/33 20130101; A61K 39/001109 20180801; A61K 39/001128 20180801;
C07K 2317/622 20130101; C07K 2317/56 20130101; A61K 39/001126
20180801; A61K 39/001195 20180801; C12N 2510/00 20130101; A61K
39/001114 20180801; A61K 2035/124 20130101; C07K 14/7051 20130101;
A61K 39/001124 20180801; A61K 2039/5158 20130101; C07K 2317/24
20130101 |
International
Class: |
C07K 16/30 20060101
C07K016/30; C07K 14/705 20060101 C07K014/705; C07K 14/725 20060101
C07K014/725; C07K 14/47 20060101 C07K014/47; A61K 35/17 20060101
A61K035/17; C07K 16/28 20060101 C07K016/28; C12N 5/0783 20060101
C12N005/0783; A61K 39/00 20060101 A61K039/00 |
Claims
1.-49. (canceled)
50. A pluripotent stem cell that comprises a rearranged T-cell
receptor (TCR) locus and expresses a chimeric antigen receptor
(CAR), wherein the pluripotent stem cell is derived from a T
cell.
51. The pluripotent stem cell of claim 50, wherein (i) the
pluripotent stem cell is transduced with the CAR; (ii) pluripotent
stem cell does not express TCR on the cell surface; and/or (iii)
said CAR binds to a tumor antigen.
52. The pluripotent stem cell of claim 51, wherein said tumor
antigen is selected from the group consisting of carbonic anhydrase
IX (CA1X), carcinoembryonic antigen (CEA), CD5, CD7, CD10, CD19,
CD20, CD22, CD30, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74,
CD123, CD133, CD138, an antigen of a cytomegalovirus (CMV) infected
cell (e.g., a cell surface antigen), epithelial glycoprotein2 (EGP
2), epithelial glycoprotein-40 (EGP-40), epithelial cell adhesion
molecule (EpCAM), receptor tyrosine-protein kinases erb-B2,3,4,
folate-binding protein (FBP), fetal acetylcholine receptor (AChR),
folate receptor-a, Ganglioside G2 (GD2), Ganglioside G3 (GD3),
human Epidermal Growth Factor Receptor 2 (HER-2), human telomerase
reverse transcriptase (hTERT), Interleukin-13 receptor subunit
alpha-2 (IL-13R.alpha.2), .kappa.-light chain, kinase insert domain
receptor (KDR), Lewis A (CA19.9), Lewis Y (LeY), L1 cell adhesion
molecule (L1CAM), melanoma antigen family A, 1 (MAGE-AI), Mucin 16
(Muc-16), Mucin 1 (Muc-1), Mesothelin (MSLN), NKG2D ligands,
cancer-testis antigen NY-ESO-1, oncofetal antigen (h5T4), prostate
stem cell antigen (PSCA), prostate-specific membrane antigen
(PSMA), tumor-associated glycoprotein 72 (TAG-72), vascular
endothelial growth factor R2 (VEGF-R2), and Wilms tumor protein
(WT-1).
53. A method of producing a cell of claim 50, comprising, a)
providing, i) a pluripotent stem cell bearing a rearranged TCR
locus (T-PSC), and ii) a CAR expression vector encoding an antigen
binding domain and at least a portion of CD3.xi. polypeptide, and
b) transducing said T-PSC with said CAR expression vector under
conditions thereby obtaining a CAR-expressing and a rearranged
T-cell receptor (TCR)-bearing iPSC (CAR-T-PSC).
54. The method of claim 53, wherein said CAR expression vector
comprises a heterologous gene encoding at least one costimulatory
signaling region or a costimulatory ligand.
55. The method of claim 54, wherein (i) the at least one
costimulatory signaling region comprises a CD28 polypeptide, a
4-1BB polypeptide, an OX40 polypeptide, or an ICOS polypeptide, a
PD-1 polypeptide, a CTLA-4 polypeptide, a LAG-3 polypeptide, a 2B4
polypeptide, or a BTLA polypeptide; and/or (ii) the costimulatory
ligand is selected from the group consisting of CD80, CD86, CD70,
OX40L, 4-1BBL, CD48, TNFRSF14, and PD-L1.
56. The method of claim 53, wherein the pluripotent stem cell
bearing a rearranged TCR locus is (i) an embryonic stem cell; (ii)
an induced pluripotent stem cell; or (iii) an induced pluripotent
stem cell obtained from reprogramming a T cell.
57. The method of claim 53, further comprising: c) culturing said
CAR-T-PSC under conditions such that a CAR-expressing T-PSC-derived
T cell (CAR-T-PSC-derived T cell) is produced.
58. The method of claim 57, wherein said c) culturing said
CAR-T-PSC under conditions to obtain a CAR-T-PSCs-derived T cell
comprises: (a) providing, i) said CAR-T-PSC, ii) a first cell
culture medium for mesoderm induction, iii) a second cell culture
medium for hematopoietic specification and expansion, iv) a third
cell culture medium for T-lymphoid differentiation, and v) a feeder
cell line that induces T lymphoid commitment in hematopoietic
cells, (b) incubating said CAR-T-PSC with said first cell culture
medium for up to about 4 days under conditions such that a mesoderm
cell is produced, (c) incubating said mesoderm cell with said
second cell culture medium for up to about 6 days under conditions
such that a hematopoietic cell is produced and expanded, and (d)
incubating said expanded hematopoietic cell and said feeder cell
line with said third cell culture medium for at least about 5 days
for inducing T lymphoid commitment in said expanded hematopoietic
cell to produce a CAR-expressing T-PSC-derived T cell.
59. The method of claim 57, wherein (i) said T cell has at least
one of the following characteristics: (a) targeting specifically to
one specific antigen and antigen specificity of said T cells is
HLA-independent; (b) expresses the CAR of the CAR-T-PSC; (ii) said
CAR-T-PSC is at least one of the followings: (a) an embryonic stem
cell; (b) an induced pluripotent stem cell (iPSC); or (c) an
induced pluripotent stem cell obtained from reprogramming a T cell
(T-PSC); (d) being obtained from transducing a T-PSC with a CAR
expression vector; and/or (iii) said CAR expression vector
comprises a heterologous polynucleotide encoding a CAR comprising
an antigen binding domain, and at least one costimulatory signaling
region or a costimulatory ligand.
60. The method of claim 58, wherein (i) said first cell culture
medium comprises bone morphogenetic protein 4 (BMP-4) and basic
fibroblast growth factor (bFGF); and/or (ii) said second cell
culture medium comprises Vascular endothelial growth factor (VEGF),
bFGF, stem cell factor (SCF), FMS Like Tyrosine Kinase 3 Ligand
(Flt3L), and at least one Th1 cytokine; and/or (iii) said third
cell culture medium comprises SCF, at least one Th1 cytokine, and
Flt3L.
61. The method of claim 60, wherein said at least one Th1 cytokine
is selected from the group consisting of Interleukin-3 (IL-3),
IL-15, IL-7, IL-12 and IL-21.
62. The method of claim 59, wherein (i) said at least one
costimulatory signalling region comprises a CD28 polypeptide, a
4-1BB polypeptide, an OX40 polypeptide, an ICOS polypeptide, a PD-1
polypeptide, a CTLA-4 polypeptide, a LAG-3 polypeptide, a 2B4
polypeptide, or a BTLA polypeptide; (ii) said costimulatory ligand
is selected from the group consisting of CD80, CD86, CD70, OX40L
4-1BBL, CD48, TNFRSF14, and PD-L1; and/or (iii) said antigen
binding domain of the CAR specifically binds to a tumor antigen or
a pathogen antigen; (iv) said CAR specifically binds to a tumor
antigen selected from the group consisting of carbonic anhydrase IX
(CA1X), carcinoembryonic antigen (CEA), CD5, CD7, CD10, CD19, CD20,
CD22, CD30, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD123,
CD133, CD138, an antigen of a cytomegalovirus (CMV) infected cell
(e.g., a cell surface antigen), epithelial glycoprotein2 (EGP 2),
epithelial glycoprotein-40 (EGP-40), epithelial cell adhesion
molecule (EpCAM), receptor tyrosine-protein kinases erb B2,3,4,
folate-binding protein (FBP), fetal acetylcholine receptor (AChR),
folate receptor-a, Ganglioside G2 (GD2), Ganglioside G3 (GD3),
human Epidermal Growth Factor Receptor 2 (HER-2), human telomerase
reverse transcriptase (hTERT), Interleukin-13 receptor subunit
alpha-2 (IL-13R.alpha.2), .kappa.-light chain, kinase insert domain
receptor (KDR), Lewis A (CA19.9), Lewis Y (LeY), L1 cell adhesion
molecule (L1CAM), melanoma antigen family A, 1 (MAGE-AI), Mucin 16
(Muc-16), Mucin 1 (Muc-1), Mesothelin (MSLN), NKG2D ligands,
cancer-testis antigen NY-ESO-1, oncofetal antigen (h5T4), prostate
stem cell antigen (PSCA), prostate-specific membrane antigen
(PSMA), tumor associated glycoprotein 72 (TAG-72), vascular
endothelial growth factor R2 (VEGF R2), and Wilms tumor protein
(WT-1); (v) said CAR expression vector comprises (a) a nucleic acid
sequence that is integrated into said CAR-T-PSC's genome at a
genomic safe harbor site; and/or (b) a nucleic acid sequence
encoding a fluorescent protein for expressing in said
CAR-T-PSC.
63. The method of claim 57, further comprising: d) exposing said
CAR-T-PSC-derived T cell to an antigen-presenting cell under
conditions for stimulating an activity of said CAR-T-PSC-derived T
cell; e) inducing fluorescence in said CAR-T-PSC; and/or (f)
tracking said CAR-T-PSCs.
64. The method of claim 63, wherein said activity is selected from
the group consisting of secretion of cytokine secretion, cell
division, cytotoxicity and cytostatic inhibition of cell
growth.
65. The method of claim 64, wherein (i) said cytokine is a Th1
cytokine selected from the group consisting of IFN-.gamma., IL-2
and TNF-.alpha.; (ii) said cytotoxicity is determined by killing a
target cell expressing an antigen that binds to said CAR and
measuring target cell death; and/or (iii) cytostatic inhibition of
cell growth comprises (a) inhibition of growth of a tumor cell;
and/or (b) reduction in tumor size.
66. The method of claim 53, wherein the pluripotent stem cell is
obtained by a process comprising, a) providing, i) a cell selected
from the group consisting of an isolated peripheral blood
lymphocyte (PBL) and an isolated peripheral blood T-cell, and a
combination thereof, and ii) at least one reprogramming factor
selected from the group consisting of octamer-binding transcription
factor 4 (OCT4), Kruppel-like factor 4 (KLF4), myelocytomatosis
viral oncogene homolog (c-MYC), and transcription factor SOX-2, and
b) transducing said cell with said at least one reprogramming
factor under conditions for producing a pluripotent stem cell.
67. A pluripotent stem cell that expresses a chimeric antigen
receptor (CAR-T-PSC), wherein the cell is obtained using the method
of claim 53.
68. A CAR-expressing T-PSC-derived T cell (CAR-T-PSC-derived T
cell), wherein the cell is obtained using the method of claim
58.
69. A method of manufacturing therapeutic cells comprising a
CAR-expressing T-PSC-derived T cell (CAR-T-PSC-derived T cell)
according to claim 58.
70. A process of using therapeutic cells of claim 69 for adoptive
cell therapy, comprising administering to a subject in need of the
therapy one or multiple doses of said cells at a therapeutically
sufficient amount.
71. The process of claim 70, wherein (i) the therapeutic cells are
comprised in a pharmaceutically acceptable carrier; and/or (ii) the
subject has a neoplasia, a pathogen infection, an immune disorder,
or an allogeneic transplant.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a Divisional of U.S. patent application
Ser. No. 14/873,836, filed Oct. 2, 2015, which is a Continuation of
International Patent Application No. PCT/US2014/032883, filed Apr.
3, 2014, which claims priority to U.S. Provisional Application Nos.
61/808,092, filed Apr. 3, 2013, and 61/808,992, filed Apr. 5, 2013,
to each of which priority is claimed and the contents of each of
which are incorporated herein in their entireties.
SEQUENCE LISTING
[0002] The specification further incorporates by reference the
Sequence Listing submitted via EFS on Jun. 17, 2019. Pursuant to 37
C.F.R. .sctn. 1.52(e)(5), the Sequence Listing text file,
identified as 0727340325DIV_SL.txt is 50,390 bytes and was created
on Jun. 17, 2019. The Sequence Listing does not extend beyond the
scope of the specification and thus does not contain new
matter.
FIELD OF THE INVENTION
[0003] The present invention relates to the field of adoptive
immunotherapy. The invention provides methods for generating
phenotypically defined, functional, and/or expandable T cells from
pluripotent stem cells (embryonic stem cells or induced pluripotent
stem cells) engineered through safe genetic modifications. The
engineered cells may provide one or more of: 1) targeting a
specific predetermined antigen expressed on the cell surface of a
target cell in an HLA-independent manner, 2) enhanced survival and
functional potential 3) "off-the-shelf" T cells for administration
to multiple recipients, eventually across immunogenic barriers,
and/or 4) cytotoxic potential and anti-tumor activity.
BACKGROUND OF THE INVENTION
[0004] T lymphocytes are essential components of the immune system
whose malfunction or absence are central to multiple pathologies,
including inborn and acquired immune deficiencies, autoimmunity and
cancer. A clinically relevant supply of functional antigen-specific
T cells is thus useful for the treatment of a number of disorders,
especially in the adoptive cancer immunotherapy setting.
[0005] Essential characteristics of adoptively transferred T
lymphocytes (as in adoptive immunotherapy) required for the
successful eradication of established tumors include their
specificity for the tumor, their stimulatory capability, the number
of tumor antigen-specific T cells, and their in vivo persistence.
Current adoptive T cell therapies are limited by the lack of
patient and tumor-specific T cells, including their rarity in the
body, their failure to overcome a number of tumor immunoescape
mechanisms, and their short life span, especially when using
terminally differentiated or "exhausted" effector T cells, i.e. non
proliferating T cells even when exposed to specific antigen.
[0006] Leukapheresis of patients or allogeneic donors are current
sources of T lymphocytes used for adoptive cell therapy. However it
is difficult to isolate and expand the typically low numbers of T
cells reactive to a desired antigen, i.e. generate antigen-specific
functional T cell clones. Furthermore, in some cases peripheral
blood lymphocytes are not available, for example from
immunodeficient patients.
[0007] Therefore, there is a need for therapeutically sufficient
and functional antigen-specific T cells for effective use in
immunotherapy.
SUMMARY OF THE INVENTION
[0008] The present invention relates to the field of adoptive
immunotherapy. The invention provides methods for generating
phenotypically defined, functional, and/or expandable T cells from
pluripotent stem cells (embryonic stem cells (ESCs) or induced
pluripotent stem cells (iPSCs) engineered through safe genetic
modifications. The engineered cells may provide one or more of: 1)
targeting a specific predetermined antigen expressed on the cell
surface of a target cell in an HLA-independent manner, 2) enhanced
survival and functional potential, and/or 3) cytotoxic potential
and anti-tumor activity. In non-limiting embodiments, the
engineered cells may be used as "off-the-shelf" T cells for
administration to multiple recipients, eventually across
immunogenic barriers.
[0009] As shown herein, engineering an iPSC or ESC to express a
chimeric antigen receptor (CAR), which binds to a predetermined
antigen for stimulating proliferation and function, dramatically
augments T cell yield and provides (e.g., after differentiation
into an effector cell by cell culture systems described in the
present inventions) T cells with enhanced therapeutic properties.
Such engineered and expanded T cells, which may or not express CD4
or CD8, and may share phenotypic features of either .alpha. or
.gamma..delta. T cells, are capable of antigen specific stimulation
by target cells in an HLA-independent manner to provide T cell
functional activity including cytokine production, cytotoxicity and
cytostatic inhibition of tumor growth, e.g. as activity that
reduces the amount of tumor load, along with continued
proliferation over numerous generations of cell division. Enhanced
T cell function can be delivered to the engineered cells through a
range of costimulatory signals (e.g. CD28) provided by the CAR.
Safe genetic modification of the T-iPSC is possible by targeting a
safe genomic harbor site in the human genome. Specifically,
compositions and methods for generating CAR-modified T-iPSC-derived
T cells (or "iPSC-derived, CAR-expressing T cells) are provided for
use in adoptive immunotherapy such as adoptive cancer
immunotherapy. In some embodiments, CAR-modified T-iPSC-derived T
cells are engineered for use in allogeneic setting by genetic
manipulation of HLA cell surface expression.
[0010] The present invention provides a T cell that is generated
from a pluripotent stem cell that expresses a chimeric antigen
receptor (CAR). In certain embodiments, said T cell targets
specifically to one antigen and antigen specificity of said T cell
is HLA-independent. In one embodiment, said T cells express the
CAR. In one embodiment, said CAR is encoded by a nucleic acid
sequence that is a heterologous sequence. In one embodiment, said
heterologous sequence is integrated into said T cell's' genome at a
genomic safe harbor site. In some embodiments, the antigen is a
tumor antigen or a pathogen antigen. In certain embodiments, the
tumor antigen is selected from the group consisting of carbonic
anhydrase IX (CA1X), carcinoembryonic antigen (CEA), CD5, CD7,
CD10, CD19, CD20, CD22, CD30, CD33, CD34, CD38, CD41, CD44, CD49f,
CD56, CD74, CD123, CD133, CD138, an antigen of a cytomegalovirus
(CMV) infected cell (e.g., a cell surface antigen), epithelial
glycoprotein2 (EGP 2), epithelial glycoprotein-40 (EGP-40),
epithelial cell adhesion molecule (EpCAM), receptor
tyrosine-protein kinases erb-B2,3,4, folate-binding protein (FBP),
fetal acetylcholine receptor (AChR), folate receptor-a, Ganglioside
G2 (GD2), Ganglioside G3 (GD3), human Epidermal Growth Factor
Receptor 2 (HER-2), human telomerase reverse transcriptase (hTERT),
Interleukin-13 receptor subunit alpha-2 (IL-13R.alpha.2),
.kappa.-light chain, kinase insert domain receptor (KDR), Lewis A
(CA19.9), Lewis Y (LeY), L1 cell adhesion molecule (L1CAM),
melanoma antigen family A, 1 (MAGE-AI), Mucin 16 (Muc-16), Mucin 1
(Muc-1), Mesothelin (MSLN), NKG2D ligands, cancer-testis antigen
NY-ESO-1, oncofetal antigen (h5T4), prostate stem cell antigen
(PSCA), prostate-specific membrane antigen (PSMA), tumor-associated
glycoprotein 72 (TAG-72), vascular endothelial growth factor R2
(VEGF-R2), and Wilms tumor protein (WT-1). In one non-limiting
embodiment, said T cells comprises a silenced gene selected from
the group consisting of a HLA gene transcription factor and a
beta-2 microglobulin for an HLA gene. In some embodiments, said CAR
comprises an extracellular domain, a transmembrane domain and an
intracellular domain. In some embodiments, said extracellular
domain comprises an antigen-binding portion. In certain
embodiments, said antigen-binding portion comprises single-chain
variable fragments (scFv). In some embodiments, said transmembrane
domain comprises a CD3.xi. polypeptide, a CD4 polypeptide, a CD8
polypeptide, a CD28 polypeptide, a 4-1BB polypeptide, an OX40
polypeptide, an ICOS polypeptide, a CTLA-4 polypeptide, a PD-1
polypeptide, a LAG-3 polypeptide, a 2B4 polypeptide, and a BTLA
polypeptide. In some embodiments, the said intracellular domain
comprises a CD3.xi. polypeptide. In certain embodiments, said
intracellular domain further comprises at least one costimulatory
signaling region. Said costimulatory signaling region can comprise
a CD28 polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, an
ICOS polypeptide, a PD-1 polypeptide, a LAG-3 polypeptide, a 2B4
polypeptide, a BTLA polypeptide, or a CTLA-4 polypeptide. In one
embodiment, said CAR is 1928z. In certain embodiments, said T cells
can be selected from the group consisting of T helper cells,
cytotoxic T cells, memory T cells, regulatory T cells, Natural
killer T cells, Mucosal associated invariant T cells,
.gamma..delta. T cells, and a combination thereof. In certain
embodiments, the pluripotent stem cell is an embryonic stem cell or
an induced pluripotent stem cell. In one embodiment, the
pluripotent stem cell is an induced pluripotent stem cell.
[0011] The present invention also provides a cell population
comprising the above-described T cell.
[0012] The present invention provides methods of using
above-described T cell for the treatment of neoplasia, infectious
disease, and other pathologies.
[0013] The present invention provides a method of reducing tumor
burden in a subject. In one non-limiting embodiment, said method
comprises administering a T cell generated from a pluripotent stem
cell that expresses a chimeric antigen receptor (CAR) to a subject
having tumor, thereby inducing tumor cell death in said subject. In
certain embodiments, said T cell expresses the CAR. In some
embodiments, antigen specificity of said T cell is HLA-independent.
In certain embodiments, said T cell is cytotoxic to said tumor and
does not induce graft vs. host disease in said subject. In one
embodiment, said tumor cell expresses an tumor antigen and said T
cell targets specifically to said tumor antigen. In one embodiment,
said tumor antigen is selected from the group consisting of
carbonic anhydrase IX (CA1X), carcinoembryonic antigen (CEA), CD5,
CD7, CD10, CD19, CD20, CD22, CD30, CD33, CD34, CD38, CD41, CD44,
CD49f, CD56, CD74, CD123, CD133, CD138, an antigen of a
cytomegalovirus (CMV) infected cell (e.g., a cell surface antigen),
epithelial glycoprotein2 (EGP 2), epithelial glycoprotein-40
(EGP-40), epithelial cell adhesion molecule (EpCAM), receptor
tyrosine-protein kinases erb-B2,3,4, folate-binding protein (FBP),
fetal acetylcholine receptor (AChR), folate receptor-a, Ganglioside
G2 (GD2), Ganglioside G3 (GD3), human Epidermal Growth Factor
Receptor 2 (HER-2), human telomerase reverse transcriptase (hTERT),
Interleukin-13 receptor subunit alpha-2 (IL-13R.alpha.2),
.kappa.-light chain, kinase insert domain receptor (KDR), Lewis A
(CA19.9), Lewis Y (LeY), L1 cell adhesion molecule (L1CAM),
melanoma antigen family A, 1 (MAGE-AI), Mucin 16 (Muc-16), Mucin 1
(Muc-1), Mesothelin (MSLN), NKG2D ligands, cancer-testis antigen
NY-ESO-1, oncofetal antigen (h5T4), prostate stem cell antigen
(PSCA), prostate-specific membrane antigen (PSMA), tumor-associated
glycoprotein 72 (TAG-72), vascular endothelial growth factor R2
(VEGF-R2), and Wilms tumor protein (WT-1). In certain embodiments,
the pluripotent stem cell is an embryonic stem cell or an induced
pluripotent stem cell. In one embodiment, the pluripotent stem cell
is an induced pluripotent stem cell. In one embodiment, said method
reduces the number of tumor cells. In one embodiment, said method
reduces tumor size. In one embodiment, said method eradicates the
tumor in the subject. In certain embodiments, said T cell is
selected from the group consisting of T helper cells, cytotoxic T
cells, memory T cells, regulatory T cells, Natural killer T cells,
Mucosal associated invariant T cells, .gamma..delta. T cells, and a
combination thereof In one embodiment, said T cell has a silenced
gene selected from the group consisting of a HLA gene transcription
factor, class II transactivator (CIITA), a RAG gene, and a beta-2
microglobulin for an HLA gene. In certain embodiments, the subject
is a human. In some embodiments, wherein said T cell expresses
Foxp3. In certain embodiments, said pluripotent stem cell is
derived from a T cell. In one embodiment, said pluripotent stem
cell expresses one ligand for immunoregulatory T cell receptor,
wherein said ligand is selected from the group consisting of PD-L1,
CD48 and TNFRSF14. In another embodiment, said pluripotent stem
cell expresses HLA-G. In certain embodiments, said pluripotent stem
cell is derived from a viral-specific T cell. The viral-specific T
cell can be a EBV-specific T-cell or a CMV-specific T-cell. In
certain embodiments, said pluripotent stem cell is derived from a T
cell that does not express a rearranged T-cell receptor (TCR).
[0014] The present invention provides a method of increasing
survival of a subject having neoplasia. In one non-limiting
embodiment, said method comprises administering a T cell generated
from a pluripotent stem cell that expresses a chimeric antigen
receptor to said subject diagnosed with neoplasia, thereby treating
or preventing a neoplasia in said subject. In certain embodiments,
the pluripotent stem cell is an embryonic stem cell or an induced
pluripotent stem cell. In one embodiment, the pluripotent stem cell
is an induced pluripotent stem cell. In certain embodiments, said T
cell is cytotoxic to said neoplasia. In certain embodiments, said T
cell expresses the CAR. In certain embodiments, said neoplasia cell
expresses a tumor antigen and said T cell targets specifically to
said tumor antigen. In certain embodiments, antigen-specificity of
said T cell is HLA-independent. In certain embodiments, said
neoplasia is selected from the group consisting of blood cancer, B
cell leukemia, multiple myeloma, lymphoblastic leukemia (ALL),
chronic lymphocytic leukemia, non-Hodgkin's lymphoma, ovarian
cancer, prostate cancer, pancreatic cancer, lung cancer, breast
cancer, and sarcoma, acute myeloid leukemia (AML). In certain
embodiments, said T cell is selected from the group consisting of T
helper cells, cytotoxic T cells, memory T cells, regulatory T
cells, Natural killer T cells, Mucosal associated invariant T
cells, .gamma..delta. T cells, and a combination thereof. In one
embodiment, said T cell has a silenced gene selected from the group
consisting of a HLA gene transcription factor, class II
transactivator (CIITA), a RAG gene, and a beta-2 microglobulin for
an HLA gene. In certain embodiments, said subject is a human. In
some embodiments, wherein said T cell expresses Foxp3. In certain
embodiments, said pluripotent stem cell is derived from a T cell.
In one embodiment, said pluripotent stem cell expresses one ligand
for immunoregulatory T cell receptor, wherein said ligand is
selected from the group consisting of PD-L1, CD48 and TNFRSF14. In
another embodiment, said pluripotent stem cell expresses HLA-G. In
certain embodiments, said pluripotent stem cell is derived from a
viral-specific T cell. The viral-specific T cell can be a
EBV-specific T-cell or a CMV-specific T-cell. In certain
embodiments, said pluripotent stem cell is derived from a T cell
that does not express a rearranged T-cell receptor (TCR).
[0015] The present invention provides a method of producing a
pluirpotent stem cell bearing a rearranged T-cell receptor (TCR)
locus and expressing a chimeric antigen receptor (CAR). In one
non-limiting embodiment, said method comprises a) providing, i) a
pluirpotent stem cell bearing a rearranged TCR locus (T-PSCs), and
ii) a CAR expression vector encoding an antigen binding domain and
a CD3t polypeptide, and b) transducing said cell with said CAR
expression vector under conditions such that a CAR-expressing T-PSC
(CAR-T-PSC) is produced. In certain embodiments, said CAR
expression vector comprises a heterologous gene encoding at least
one costimulatory signaling region or a costimulatory ligand. Said
at least one costimulatory ligand can be selected from the group
consisting of CD80, CD86, CD70, OX40L, 4-1BBL, CD48, TNFRSF14, and
PD-L1. Said costimulatory signaling region can comprise a CD28
polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, an ICOS
polypeptide, or a PD-1 polypeptide, a LAG-3 polypeptide, a 2B4
polypeptide, a BTLA polypeptide, or a CTLA-4 polypeptide. In
certain embodiments, the pluripotent stem cell is an embryonic stem
cell or an induced pluripotent stem cell. In one embodiment, the
pluripotent stem cell is an induced pluripotent stem cell.
[0016] The present invention provides a method of producing a T
cell. In one non-limiting embodiment, said method comprises a)
providing, i) a pluirpotent stem cell bearing a rearranged T-cell
receptor (TCR) locus (T-PSCs), and ii) a chimeric antigen receptor
(CAR) expression vector encoding an antigen binding domain and a
CD3t polypeptide, b) transducing said T-PSC with said CAR
expression vector under conditions such that a CAR-expressing T-PSC
(CAR-T-PSC) is produced; and c) culturing said CAR-T-PSC under
conditions such that a CAR-T-PSC-derived T cell is produced. In
certain embodiments, said c) culturing said CAR-T-PSC under
conditions such that a CAR-T-PSC-derived T cell is produced
comprises: (a) providing, i) said CAR-T-PSC, ii) a first cell
culture medium for mesoderm induction, iii) a second cell culture
medium for hematopoietic specification and expansion, iii) a third
cell culture medium for T-lymphoid differentiation, and iv) a
feeder cell line that induces T lymphoid commitment in
hematopoietic cells, and (b) incubating said CAR-T-PSC with said
first cell culture medium for up to about 4 days under conditions
such that a mesoderm cell is produced, (c) incubating said mesoderm
cell with said second cell culture medium for up to about 6 days
under conditions such that a hematopoietic cell is produced and
expanded, (d) incubating said expanded hematopoietic cell and said
feeder cell line with said third cell culture medium for at least
about 5 days for inducing T lymphoid commitment in said expanded
hematopoietic cell to produce a CAR-T-PSC-derived T cell. In
certain embodiments, the pluripotent stem cell is an embryonic stem
cell or an induced pluripotent stem cell. In one embodiment, the
pluripotent stem cell is an induced pluripotent stem cell. In
certain embodiments, said T cell expresses the CAR. In some
embodiments, said T cell targets specifically to one antigen and
antigen specificity of said T cell is HLA-independent. In one
embodiment, the first cell culture medium comprises bone
morphogenetic protein 4 (BMP-4) and basic fibroblast growth factor
(bFGF). In one embodiment, the second cell culture medium comprises
Vascular endothelial growth factor (VEGF), bFGF, stem cell factor
(SCF), FMS Like Tyrosine Kinase 3 Ligand (F1t3L), and at least one
Th1 cytokine, which can be selected from the group consisting of
Interleukin-3 (IL-3), IL-15, IL-7, IL-12 and IL-21. In one
embodiment, the third cell culture medium comprises SCF, Flt3L, and
at least one Th1 cytokine, which can be selected from the group
consisting of IL-15, IL-7, IL-12 and IL-21. In certain embodiments,
said method further comprises d) exposing said CAR-T-PSC-derived T
cell to an antigen-presenting cell under conditions for stimulating
an activity of said CAR-T-PSC-derived T cell. In one embodiment,
said activity is selected from the group consisting of cytokine
secretion, cell division, cytotoxicity, cytostatic inhibition, and
inhibition of cell growth. In one embodiment, said cytokine is a
Th1 cytokine selected from the group consisting of IFN-.gamma.,
IL-2 and TNF-.alpha.. In one embodiment, said cytotoxicity is
determined by killing a target cell expressing an antigen that
binds to said CAR and measuring target cell death. In one
embodiment, said inhibition of cell growth comprises inhibition of
growth of a tumor cell. In one embodiment, said inhibition of cell
growth comprises reduction in tumor size. Said CAR can comprise an
antigen binding domain. In one embodiment, said antigen binding
domain of said is specific for an antigen. Said antigen can be a
tumor antigen or a pathogen antigen. In certain embodiments, said
antigen is selected from the group consisting of carbonic anhydrase
IX (CA1X), carcinoembryonic antigen (CEA), CD5, CD7, CD10, CD19,
CD20, CD22, CD30, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74,
CD123, CD133, CD138, an antigen of a cytomegalovirus (CMV) infected
cell (e.g., a cell surface antigen), epithelial glycoprotein2 (EGP
2), epithelial glycoprotein-40 (EGP-40), epithelial cell adhesion
molecule (EpCAM), receptor tyrosine-protein kinases erb-B2,3,4,
folate-binding protein (FBP), fetal acetylcholine receptor (AChR),
folate receptor-a, Ganglioside G2 (GD2), Ganglioside G3 (GD3),
human Epidermal Growth Factor Receptor 2 (HER-2), human telomerase
reverse transcriptase (hTERT), Interleukin-13 receptor subunit
alpha-2 (IL-13R.alpha.2), .kappa.-light chain, kinase insert domain
receptor (KDR), Lewis A (CA19.9), Lewis Y (LeY), L1 cell adhesion
molecule (L1CAM), melanoma antigen family A, 1 (MAGE-AI), Mucin 16
(Muc-16), Mucin 1 (Muc-1), Mesothelin (MSLN), NKG2D ligands,
cancer-testis antigen NY-ESO-1, oncofetal antigen (h5T4), prostate
stem cell antigen (PSCA), prostate-specific membrane antigen
(PSMA), tumor-associated glycoprotein 72 (TAG-72), vascular
endothelial growth factor R2 (VEGF-R2), and Wilms tumor protein
(WT-1). In one embodiment, said CAR expression vector comprises a
nucleic acid sequence that is integrated into said CAR-T-PSC's
genome at a genomic safe harbor site. In one embodiment, said CAR
expression vector further encodes a fluorescent protein for
expressing in said CAR-T-PSC. In one embodiment, said fluorescent
protein is mCherry. In one embodiment, said method further
comprises e) inducing florescence in said CAR-T-PSC for tracking
said CAR-T-PSC. In one embodiment, said method further comprises f)
tracking said CAR-T-PSC in vitro. In one embodiment, said method
further comprises g) tracking said CAR-T-PSC in vivo.
[0017] The present invention provides a method of producing a
pluripotent stem cell. In one non-limiting embodiment, said method
comprises a) providing, i) a cell selected from the group
consisting of an isolated peripheral blood lymphocyte (PBL) and an
isolated peripheral blood T-cell, and a combination thereof, and
ii) at least one retroviral vector encoding at least one
reprogramming factor selected from the group consisting of
octamer-binding transcription factor 4 (OCT4), Kruppel-like factor
4 (KLF4), myelocytomatosis viral oncogene homolog (c-MYC), and
transcription factor SOX-2, and b) transducing said cell with said
at least one retroviral vector under conditions for producing
apluripotent stem cell. In certain embodiments, said pluripotent
stem cell is an embryonic stem cell or an induced pluripotent stem
cell. In one embodiment, said pluripotent stem cell is an induced
pluripotent stem cell. In one embodiment, said retroviral vector
encodes in 5' to 3' direction OCT4 and KLF4. In another embodiment,
said retroviral vector encodes in 5' to 3' directionc-MYC and
SOX-2. In some embodiments, said retroviral vector is excisable. In
some embodiments, said retroviral vector comprises a loxP site
located in the 3' long terminal repeat (LTR) for use by Cre
recombinase for excising said at least one reprogramming factor. In
certain embodiments, said retroviral vector further encodes a
fluorescent marker e. In one embodiment, said fluorescent marker is
green fluorescent protein. In another embodiment, the fluorescent
marker is Citrine. A pluripotent stem cell and a cell population
comprising thereof produced by the above-described method are also
provided in the present invention.
[0018] The present invention provides an excisable retroviral
vector encoding in 5' to 3' direction, at least one reprogramming
factor selected from the group consisting of octamer-binding
transcription factor 4 (OCT4), Kruppel-like factor 4 (KLF4),
myelocytomatosis viral oncogene homolog (c-MYC), and transcription
factor SOX-2. In certain embodiments, the retroviral vector encodes
two reprogramming factors. In some embodiments, the retroviral
vector encodes in 5' to 3' direction OCT4 and KLF4. In some
embodiments, the retroviral vector encoding in 5' to 3' direction
cMYC and SOX2. In certain embodiments, said retroviral vector
further encodes a fluorescent marker. In one embodiment, the
fluorescent marker is Citrine. In one embodiment, the fluorescent
marker is GFP. In certain embodiments, the retroviral vector
comprises a loxP site in the 3' long terminal repeat (LTR) for use
by Cre recombinase for excising said at least one reprogramming
factor. In some embodiments, said retroviral vector further
comprises a promoter in operable combination with anucleic acid
sequence encoding said at least one reprogramming factor.
[0019] The present invention provides a pluripotent stem cell that
expresses a chimeric antigen receptor (CAR). In certain
embodiments, the pluripotent stem cell is an embryonic stem cell or
an induced pluripotent stem cell. In one embodiment, the
pluripotent stem cell is an induced pluripotent stem cell. The
present invention also provides a cell population comprising the
above-described pluripotent stem cell.
[0020] In a related aspect, the present invention provides a
pharmaceutical composition containing an effective amount of a cell
population of T cells of any aspect of the present invention
delineated herein in a pharmaceutically acceptable excipient. In
another related aspect, the invention provides a pharmaceutical
composition for the treatment of a neoplasia containing an
effective amount of tumor antigen-specific T cells of any aspect of
the invention delineated herein in a pharmaceutically acceptable
excipient.
[0021] In an additional aspect, the invention provides a kit for
treatment of a neoplasia, pathogen infection, an autoimmune
disorder, or an allogeneic transplant, the kit comprising a cell
population comprising T cells that are generated from induced
pluripotent stem cells (iPSCs), wherein said T cells target
specifically to one antigen, and antigen recognition by said T
cells is HLA-independent. In certain embodiments, the kit further
comprises written instructions for using the cell for the treatment
of a subject having a neoplasia, a pathogen infection, an
autoimmune disorder, or an allogeneic transplant.
DEFINITIONS
[0022] To facilitate understanding of the present invention, a
number of terms are defined below.
[0023] As used herein, "a" or "an" means "at least one" or "one or
more."
[0024] As used herein, the term "about" or "approximately" means
within an acceptable error range for the 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. For example, "about" can
mean within 3 or more than 3 standard deviations, per the practice
in the art. Alternatively, "about" can mean a range of up to 20%,
preferably up to 10%, more preferably up to 5%, and more preferably
still up to 1% of a given value. Alternatively, particularly with
respect to biological systems or processes, the term can mean
within an order of magnitude, preferably within 5-fold, and more
preferably within 2-fold, of a value.
[0025] As used herein, the term "cell population" refers to a group
of at least two cells expressing similar or different phenotypes.
In non-limiting examples, a cell population can include at least
about 10, at least about 100, at least about 200, at least about
300, at least about 400, at least about 500, at least about 600, at
least about 700, at least about 800, at least about 900, at least
about 1000 cells expressing similar or different phenotypes.
[0026] As used herein, the term "clone" in reference to a cell
clone refers to a cell that is genetically identical to another
cell, for example T cell clones are daughter cells genetically
identical to the parental cell.
[0027] As used herein, the term "peripheral blood lymphocyte(s)" or
"PBL(s)" refers to white blood cell(s) comprising T cells and B
cells of a range of differentiation and functional stages, plasma
cells, monocytes, macrophages, natural killer cells, basocytes,
eosinophyils, etc.
[0028] As used herein, the term "isolated" in reference to a
population refers to the removal of a smaller desired cell
population from a larger starting population. As one example,
isolated peripheral blood lymphocytes may refer to a specific white
blood cell layer located in a gradient of Ficol. As another
example, "isolated peripheral blood T-cells" may refer to a
population of CD3.sup.+ cells isolated from a larger white blood
cell population, as one example, CD3.sup.+ cells may be isolated
using anti CD3.sup.+ antibodies, such as by flow cytometry sorting
or magnetic bead separation, etc. As one example, a CD3.sup.+ T
cell population may be isolated from peripheral blood mononuclear
cells (PBMCs) or other cell population by magnetic separation using
CD3 antibody directly or indirectly attached to magnetic
particles.
[0029] As used herein, the term "pluripotent" refers to a cell line
capable of differentiating into multiple differentiated cell
types.
[0030] As used herein, the term "pluripotent stem cell (PSC)" or
"pluripotent stem cells (PSCs)" refers to stem cell(s) that have
the potential to differentiate into any of the three germ layers:
endoderm (interior stomach lining, gastrointestinal tract, the
lungs), mesoderm (muscle, bone, blood, urogenital), or ectoderm
(epidermal tissues and nervous system). In non-limiting examples, a
PSC can be an embryonic stem cell or an induced pluripotent stem
cell.
[0031] As used herein, the term "multipotent" refers to a cell line
capable of differentiating into at least two differentiated cell
types.
[0032] As used herein, the term "embryonic stem cell (ESC)" or
"embryonic stem cells (ESCs)" refers to a pluripotent stem cell
derived from the inner cell mass of a blastocyst.
[0033] As used herein, the term "adult stem cell" or "adult stem
cells" refers to stem cell(s) derived from an organism after
birth.
[0034] As used herein, the term "T lymphocyte" or "T cell" refers
to a cell expressing CD3 (CD3.sup.+) and a T Cell Receptor
(TCR.sup.+).
[0035] As used herein, the term "TCR" or "T cell receptor" refers
to a dimeric heterologous cell surface signaling protein forming an
alpha-beta or gamma-delta receptor typically involved in
recognizing an antigen presented by an MEW molecule (i.e. antigen
recognition in the context of an MEW molecule).
[0036] As used herein, the term "CD3 complex" refers to a cell
surface molecule assembly comprising numerous proteins for
transmembrane signaling of TCR activation.
[0037] As used herein, the terms "region" or "portion" when used in
reference to a nucleic acid molecule refers to a set of linked
nucleotides that is less than the entire length of the molecule,
such as a CD3 signaling region described herein.
[0038] As used herein, the term "cell culture system" refers to
compositions and methods of culturing cells to produce a more
specific homogenous cell type. A cell culture system can comprise
certain cell culture factors in cell growth medium, and methods of
incubation for a time period for culturing cells in specific
culture factors for producing specific cells. In one non-limiting
example, a cell culture system can provide compositions and methods
for producing cells of a non-default cell type, such as producing
more differentiated T cells with a specific antigen recognition. In
another non-limiting example, a cell culture system can be used for
dedifferentiating T cells for producing induced pluripotent T
cells.
[0039] As used herein, the term "precursor T cell" in reference to
a cell produced by compositions and methods of the present
inventions refers to a cell expressing CD34 (CD34.sup.+) and CD7
(CD7.sup.+).
[0040] As used herein, the term "induced pluripotent stem cell(s)"
or "iPSC(s)" refers to pluripotent stem cell(s) artificially
derived in vitro from a somatic cell through forced expression
(transformed or induced) of specific reprogramming transcription
factors (such as, OCT-4, KLF-4, SOX-2, c-Myc). iPSCs are similar to
embryonic stem cells in morphology, stem cell gene expression
pattern, chromatin methylation pattern and pluripotency (teratoma
formation, embryoid body formation, etc.).
[0041] As used herein, the term "T-PSC" or "T-PSCs" refers to
pluirpotent stem cell(s) bearing a rearranged TCR locus, such that
a T cell is reprogrammed or dedifferentiated to a pluirpotent stem
cell (PSC). A T-PSC cell may derive from any isolated endogenously
developed mature T cell.
[0042] As used herein, the term "T-iPSC" or "T-iPSCs" refers to
induced pluirpotent stem cell(s) bearing a rearranged TCR locus,
such that a T cell is reprogrammed or dedifferentiated to an iPSC.
A T-iPSC cell may derive from any isolated endogenously developed
mature T cell.
[0043] As used herein, the term "CAR-T-PSC" or "CAR-T-PSCs" refers
to pluirpotent stem cell(s) bearing a pre-rearranged TCR locus and
expressing a chimeric antigen receptor (CAR) (CAR.sup.+). The
CAR-T-PSC does not express a TCR on the cell surface. There
typically is expression of the TCR after re-differentiation using a
cell culture method for producing committed T cells and effector T
cells. CAR-T-PSC can be produced by transducing T-PSC with a CAR
vector.
[0044] As used herein, the term "CAR-T-iPSC" or "CAR-T-iPSCs"
refers to induced pluirpotent stem cell(s) bearing a pre-rearranged
TCR locus and expressing a chimeric antigen receptor (CAR)
(CAR.sup.+). The CAR-T-iPSC does not express a TCR on the cell
surface. There typically is expression of the TCR after
re-differentiation using a cell culture method for producing
committed T cells and effector T cells. CAR-T-iPSCs can be produced
by transducing T-iPSC with a CAR vector.
[0045] As used herein, the term "CAR-T-PSC-derived T cell(s)"
refers to T cell(s) produced or derived from CAR-T-PSC(s) as
described above. For example, CAR-T-PSC-derived T cell can be
derived from CAR-T-PSC after induction of differentiation using a
cell culture system of the present invention. CAR-T-PSC-derived T
cell can recognize an antigen, for which the CAR is specific or
which can be recognized by the CAR.
[0046] As used herein, the term "CAR-T-iPSC-derived T cell(s)"
refers to T cell(s) produced or derived from CAR-T-iPSC(s) as
described above. For example, CAR-T-iPSC-derived T cells can be
derived from CAR-T-iPSCs after induction of differentiation using a
cell culture system of the present invention. CAR-T-iPSC-derived T
cells can recognize an antigen, for which the CAR is specific or
which can be recognized by the CAR.
[0047] As used herein, the term "CAR-T-PSC-derived T cell(s)"
refers to T cell(s) produced or derived from CAR-T-PSC(s) as
described above. For example, CAR-T-PSC-derived T cell can be
derived from CAR-T-PSC after induction of differentiation using a
cell culture system of the present invention. CAR-T-PSC-derived T
cell can recognize an antigen, for which the CAR is specific or
which can be recognized by the CAR.
[0048] As used herein, the term "CAR-T-PSC effector T cell(s)"
refers to effector T cell(s) produced from CAR-T-PSC(s) as
described above, e.g., CAR-T-PSC-derived T cells. CAR-T-PSC
effector T cells can possess at least one of the following
activities: cytokine secretion (including, but not limited to,
IL-2, IFN-.gamma., TNF-.alpha.), proliferation when exposing an
antigen that can be recognized by the CAR, cytoxicity, and
cytostatic inhibition.
[0049] As used herein, the term "CAR-T-iPSC effector T cell(s)"
refers to effector T cell(s) produced from CAR-T-iPSC(s), e.g.,
CAR-T-iPSC-derived T cells. CAR-T-iPSC effector T cells can possess
at least one of the following activities: cytokine secretion
(including, but not limited to, IL-2, IFN-.gamma., TNF-.gamma.),
proliferation when exposing an antigen that can be recognized by
the CAR, cytoxicity, and cytostatic inhibition.
[0050] As used herein, the term "cytotoxic" or "cytostatic" or
"cytostatic inhibition" refers to one or more of an inhibition of
tumor growth and a reduction in tumor load, i.e. the amount of
tumor cells in a subject, such as measured by diagnostic means.
[0051] As used herein, the term "contacting" or "exposing" in
reference to an antigen and its binding region on a CAR refers to
the interaction between the antigen binding region expressed by a
CAR and its antigen that stimulates a response in a CAR.sup.+
cell.
[0052] As used herein, the term "single-chain variable fragment" or
"scFv" is a fusion protein of the variable regions of the heavy
(V.sub.H) and light chains (V.sub.L) of an immunoglobulin (e.g.,
mouse or human) covalently linked to form a VH:: VL heterodimer.
The heavy (V.sub.H) and light chains (V.sub.L) are either joined
directly or joined by a peptide-encoding linker (e.g., 10, 15, 20,
25 amino acids), which connects the N-terminus of the V.sub.H with
the C-terminus of the V.sub.L, or the C-terminus of the V.sub.H
with the N-terminus of the V.sub.L. The linker is usually rich in
glycine for flexibility, as well as serine or threonine for
solubility. Despite removal of the constant regions and the
introduction of a linker, scFv proteins retain the specificity of
the original immunoglobulin. Single chain Fv polypeptide antibodies
can be expressed from a nucleic acid including V.sub.H- and
V.sub.L-encoding sequences as described by Huston, et al. (Proc.
Nat. Acad. Sci. USA, 85:5879-5883, 1988). See, also, U.S. Pat. Nos.
5,091,513, 5,132,405 and 4,956,778; and U.S. Patent Publication
Nos. 20050196754 and 20050196754. Antagonistic scFvs having
inhibitory activity have been described (see, e.g., Zhao et al.,
Hyrbidoma (Larchmt) 2008 27(6):455-51; Peter et al., J Cachexia
Sarcopenia Muscle 2012 Aug. 12; Shieh et al., J Imunol. 2009
183(4):2277-85; Giomarelli et al., Thromb Haemost 2007
97(6):955-63; Fife eta., J Clin Invst 2006 116(8):2252-61; Brocks
et al., Immunotechnology 1997 3(3):173-84; Moosmayer et al., Ther
Immunol 1995 2(10:31-40). Agonistic scFvs having stimulatory
activity have been described (see, e.g., Peter et al., J Bioi Chern
2003 25278(38):36740-7; Xie et al., Nat Biotech 1997 15(8):768-71;
Ledbetter et al., Crit Rev Immuno11997 17(5-6):427-55; Ho et al.,
BioChim Biophys Acta 2003 1638(3):257-66).
[0053] As used herein, "F(ab)" refers to a fragment of an antibody
structure that binds to an antigen but is monovalent and does not
have a Fc portion, for example, an antibody digested by the enzyme
papain yields two F(ab) fragments and an Fc fragment (e.g., a heavy
(H) chain constant region; Fc region that does not bind to an
antigen).
[0054] As used herein, "F(ab').sub.2" refers to an antibody
fragment generated by pepsin digestion of whole IgG antibodies,
wherein this fragment has two antigen binding (ab') (bivalent)
regions, wherein each (ab') region comprises two separate amino
acid chains, a part of a H chain and a light (L) chain linked by an
S--S bond for binding an antigen and where the remaining H chain
portions are linked together. A "F(ab').sub.2" fragment can be
split into two individual Fab' fragments.
[0055] As used herein, the term "Cluster of Differentiation" or
"CD" refers to a cell surface marker, e.g., a leukocyte. CD can be
used to distinguish cell lineages, developmental stages, and
functional subsets. The CAR of the present invention can target to
a CD, including, but not limited to, CD10, CD19, etc.
[0056] As used herein, the term "selectable marker" refers to the
use of a gene that encodes a protein which delivers a
distinguishable activity to the cell such as the ability to grow in
medium containing an antibiotic that would otherwise kill a cell
(e.g. a neomycin phosphoryltransferase (Neo) gene in transformed or
transduced cells) or the ability to emit fluorescent light. For one
example, a selectable marker may confer resistance to an antibiotic
or drug upon the cell, such as when a selectable marker, such as a
neomycin phosphoryltransferase (Neo) gene, is expressed. Another
type of marker is a fluorescent marker, such as enhanced GFP
(eGFP), mCherry, etc., which can be detected by flow cytometry or
fluorescence microscopy. Fluorescent markers include green
fluorescent protein, blue fluorescent protein, cyan fluorescent
protein, and yellow fluorescent protein. Blue fluorescent proteins
include EBFP, EBFP2, Azurite, and mKalamal. Cyan fluorescent
proteins include ECFP, Cerulean, and CyPet. Yellow fluorescent
proteins include YFP, Citrine, Venus, and YPet.
[0057] As used herein, the term "differentiation" as used with
respect to cells in a differentiating cell system refers to a
process by which cells differentiate from one cell type (e.g., a
multipotent, totipotent or pluripotent differentiable cell) to
another cell type such as a target differentiated cell (e.g., a T
cell). As such, differentiation may be by default or a nondefault
cell type. In vitro, a default cell type is the majority cell type
in a cell population when not exposed to a certain differentiation
factor or group of factors in contrast to a non-default cell type
or different cell type in the majority of cells when exposed to
certain differentiation factor(s).
[0058] As used herein, "inducing hematopoietic differentiation" in
reference to a cell culture system refers to compositions and
methods of the present inventions as described herein, for
producing CD34.sup.+ hematopoietic precursor cells from T-iPSCs,
see Example I for an exemplary description.
[0059] As used herein, "reprogramming" in reference to a cell
culture system refers to compositions and methods for producing
T-PSC cells from peripheral blood mature T lymphocytes of the
present inventions as described herein, wherein said reprogrammed
cells initially express reprogramming transcription factors
(consisting of Oct-4, KLF-4, Sox-2 and c-Myc),see Example I for an
exemplary description.
[0060] As used herein, "re-differentiate" or "T lymphoid
differentiation" or "T lymphoid commitment" in reference to a cell
culture system refers to compositions and methods described herein,
for producing cells with T lymphoid specific markers that were
expressed but then silenced during reprogramming (CD7, CD5, CD3,
TCR) from T-PSC-derived CD34.sup.+ cells. In particular, T cells of
the present inventions were produced by compositions and methods of
a re-differentiation or cell culture system as describe in Example
I.
[0061] As used herein, the term "cell culture" refers to any in
vitro culture of cells. Included within this term are continuous
cell lines (e.g., with an immortal phenotype), primary cell
cultures, finite cell lines (e.g., non-transformed cells), and any
other cell population maintained in vitro, including stem cells,
embryonic cord blood cells, transduced cells, etc.
[0062] As used herein, " Embryoid body" or "EB" refers to
three-dimensional aggregates of pluripotent stem cells that form
during certain cell culture systems.
[0063] As used herein, the term "vector" refers to any genetic
element, such as a plasmid, phage, transposon, cosmid, chromosome,
virus, virion, etc., which is capable of replication when
associated with the proper control elements and which can transfer
gene sequences into cells. Thus, the term includes cloning and
expression vehicles, as well as viral vectors and plasmid
vectors.
[0064] The term "expression vector" as used herein refers to a
recombinant nucleic acid sequence, i.e. recombinant DNA molecule,
containing a desired coding sequence and appropriate nucleic acid
sequences necessary for the expression of the operably linked
coding sequence in a particular host organism. Nucleic acid
sequences necessary for expression in prokaryotes usually include a
promoter, an operator (optional), and a ribosome binding site,
often along with other sequences. Eukaryotic cells are known to
utilize promoters, enhancers, and termination and polyadenylation
signals.
[0065] As used herein, the term "Lentivirus" refers to a virus that
can transduce both actively proliferating and non-dividing
cells.
[0066] As used herein, the term "SFG vectors" refer to
gammaretroviral vectors which also find use in the present
inventions, such vectors include but are not limited to vectors
derived from the Moloney murine leukemia virus, including vectors
and vector construction described, for examples, by Riviere, PNAS,
1995, Gallardo, Blood, 1997, herein incorporated by reference in
their entirety.
[0067] As used herein, the term "excisable" in reference to a
vector refers to a vector that can be removed from a genome after
integration (transduction), wherein said vector has a loxP site in
a 3'LTR for use by Cre recombinase for excising the vector
sequences.
[0068] As used herein, the term "lentiviral " or "lentivirus" in
reference to a vector refers to viral vectors derived from the
Lentiviridae family that are capable of integrating into dividing
and non-dividing cells, including but not limited to pLM vectors,
(For examples, see, e.g., Papapetrou & Sadelain, Nature
Protocols, 6(9):1274-1289 (2011); U.S. Pat. Nos. 5,994,136 and
6,013,516, all of which are incorporated herein by reference). A
variety of lentiviral vectors and packaging cell lines are known in
the art and find use in the present invention (See, e.g., U.S. Pat.
Nos. 5,994,136 and 6,013,516, both of which are herein incorporated
in their entirety by reference) however it is not meant to limit
the type of vector so long as it is capable of stably integrating a
CAR into the genome of a cell.
[0069] The term "transduction" as used herein refers to the process
where heterologous nucleic acid sequences are introduced into
another cell using a viral vector.
[0070] The term "transfection" as used herein refers to the process
of introducing nucleic acids into cells by non-viral methods.
Transfection may be accomplished by a variety of means known to the
art including calcium phosphate-DNA co-precipitation,
DEAE-dextran-mediated transfection, polybrene-mediated
transfection, electroporation, microinjection, liposome fusion,
lipofection, protoplast fusion, and biolistics.
[0071] The term "stable transduction" or "stably transduced" refers
to a cell that has stably integrated the foreign DNA into the
genome after infection with a viral vector.
[0072] The term "silenced" in reference to a gene or protein refers
to the downregulation or absence of gene expression and/or protein
expression. The term "silenced" in reference to a cell having a
silenced gene refers to a cell that has at least one downregulated
or absent gene as compared to an equivalent cell that does not have
the silenced gene.
[0073] As used herein, "adoptive cell transfer therapy" or "ACT"
refers to administration of ex vivo-activated and -expanded
autologous tumor-reactive T lymphocytes.
[0074] As used herein, "autologous" refers to genetically identical
cells derived from the same donor.
[0075] As used herein, "allogeneic" refers to cells derived from a
genetically non-identical donor. Allogeneic cells typically cause
graft-host disease when used for cell or organ transplantation.
[0076] As used herein, "MHC" or "major histocompatibility complex"
refers to cell surface molecules encoded by a large number of genes
in mammals. WIC molecules include Class I and Class II. Class I
molecules are alternatively refered to in humans as "HLA" or "human
leukocyte antigen." In part due to the complexity of HLA molecule
expression HLA may also be referred to as an HLA system. Humans
express HLA-A, HLA-B and HLA-C molecules that are typically
involved with presenting processed antigen to CD8 cells, i.e. HLA
resticted. Class II molecules, such as DR, DQ, DP, etc., are
typically involved with presenting externally derived peptides to
CD4+ cells, i.e. MHC Class II resticted. MHC restricted in general
encompasses both Class I and Class II as in transplantation (bone
marrow) matching.
[0077] As used herein, "HLA-restricted" or "MHC-restricted" refers
to antigen recognition requiring both MHC molecule and it's
peptide. Unlike antigen recognition that is "not HLA-restricted" or
"HLA-independent" or "not WIC-restricted."
[0078] As used herein, the term "in vitro" refers to an artificial
environment and to processes or reactions that occur within an
artificial environment. In vitro environments can consist of, but
are not limited to, test tubes and cell culture. Alternatively, the
term "in vivo" refers to the natural environment (e.g., an animal
or a cell) and to processes or reaction that occur within a natural
environment.
[0079] As used herein, the term "subject" refers to any animal
(e.g., a mammal), including, but not limited to, humans, non-human
primates, rodents, and the like (e.g., which is to be the recipient
of a particular treatment, or from whom cells are harvested).
[0080] As used herein, the term "effective amount" refers to an
amount sufficient to have a therapeutic effect. In one embodiment,
an "effective amount" is an amount sufficient to arrest,
ameliorate, or inhibit the continued proliferation, growth, or
metastasis (e.g., invasion, or migration) of a neoplasia. An
effective amount can be administered in one or more
administrations, applications or dosages and is not intended to be
limited to a particular formulation or administration route.
[0081] As used herein, the term "therapeutically effective amount"
refers to an amount sufficient to reduce by a least about 15
percent, preferably by at least 50 percent, more preferably by at
least 90 percent, and most preferably prevents a clinically
significant harmful effect or activity or response of disease
causing cells in a host patient, such as a reduction in tumor load
or cancer, or at least slowing or stopping the development of
additional tumor growth or spread of cancer. Alternatively, a
therapeutically effective amount is sufficient to cause an
improvement in a clinically significant condition in a host
patient, i.e. such as when a CAR+ cell of the present inventions is
administered to a patient having cancer and cancer cells are
killed.
[0082] As used herein, the term "treatment" or "treating" refers to
clinical intervention in an attempt to alter the disease course of
the individual or cell being treated, and can be performed either
for prophylaxis or during the course of clinical pathology.
Therapeutic effects of treatment include, without limitation,
preventing occurrence or recurrence of disease, alleviation of
symptoms, diminishment of any direct or indirect pathological
consequences of the disease, preventing metastases, decreasing the
rate of disease progression, amelioration or palliation of the
disease state, and remission or improved prognosis. By preventing
progression of a disease or disorder, a treatment can prevent
deterioration due to a disorder in an affected or diagnosed subject
or a subject suspected of having the disorder, but also a treatment
may prevent the onset of the disorder or a symptom of the disorder
in a subject at risk for the disorder or suspected of having the
disorder.
[0083] As used herein, the term "subject diagnosed with a cancer"
refers to a subject who has been tested and found to have cancerous
cells. The cancer may be diagnosed using any suitable method,
including but not limited to, biopsy, x-ray, blood test, and the
diagnostic methods of the present invention. A "preliminary
diagnosis" is one based only on visual (e.g., CT scan or the
presence of a lump) and antigen tests. The subject may be in need
of anticancer adoptive immunotherapy comprising the T cells of the
present invention.
[0084] As used herein, the term "administered" or "administering"
refers to any method of providing a composition (i.e., for example,
a biological cell) to a patient such that the composition has its
intended effect on the patient. For example, one method of
administering is by an indirect mechanism using a medical device
such as, but not limited to a catheter, applicator gun, syringe
etc. A second exemplary method of administering is by a direct
mechanism such as, local tissue administration (i.e., for example,
extravascular placement), oral ingestion, transdermal patch,
topical, inhalation, suppository, etc, however it is not meant to
limit the type of administering a cell produced by methods of the
present inventions to a patient.
[0085] As used herein, the term "cancer cells" or "cancerous cells"
refers to individual cells of a cancer. Such cells may include, for
example, tumorigenic cells (e.g., capable of generating a tumor),
leukemogenic cells (e.g., capable of generating leukemia), cancer
stem cells (e.g., capable of forming new tumors or transferring
disease upon transplantation into an immunocompromised host), as
well as cells that are not tumorigenic, leukemogenic or that are
capable of forming new tumors or transferring disease upon
transplantation (e.g., mesenchymal and endothelial cells) including
but not limited to prostate cancer, breast cancer, etc.
[0086] As used herein, the term "nucleic acid molecule" refers to
any nucleic acid containing molecule, including but not limited to,
DNA or RNA. The term encompasses sequences that include any of the
known base analogs of DNA and RNA
[0087] As used herein, the terms "nucleic acid molecule encoding,"
"DNA sequence encoding," and "DNA encoding" refer to the order or
sequence of deoxyribonucleotides along a strand of deoxyribonucleic
acid. The order of these deoxyribonucleotides determines the order
of amino acids along the polypeptide (protein) chain. The DNA
sequence thus codes for the amino acid sequence.
[0088] As used herein, the term "heterologous gene" refers to a
gene that is not in its natural environment. For example, a
heterologous gene includes a gene from one species introduced into
another species. A heterologous gene also includes a gene native to
an organism that has been altered in some way (e.g., mutated, added
in multiple copies, linked to non-native regulatory sequences,
etc). As another example, a heterologous gene includes a gene
expressed in a previous or future cell lineage or differentiation
state of a cell. Heterologous genes are distinguished from
endogenous genes in that the heterologous gene sequences are
typically joined to DNA sequences that are not found naturally
associated with the gene sequences in the chromosome or are
associated with portions of the chromosome not found in nature
(e.g., genes expressed in loci where the gene is not normally
expressed).
[0089] As used herein, the term "transgene" refers to a
heterologous gene that is integrated into the genome of an organism
(e.g., a non-human animal) and that is transmitted to progeny of
the organism during sexual reproduction.
[0090] As used herein, "amino acid sequence" and terms such as
"polypeptide" or "protein" are not meant to limit the amino acid
sequence to the complete, native amino acid sequence associated
with the recited protein molecule.
[0091] As used herein, the term "substantially identical" refers to
a polypeptide or nucleic acid molecule exhibiting at least 50%
identity to a reference amino acid sequence (for example, any one
of the amino acid sequences described herein) or nucleic acid
sequence (for example, any one of the nucleic acid sequences
described herein). Preferably, such a sequence is at least 60%,
more preferably 80% or 85%, and more preferably 90%, 95% or even
99% identical at the amino acid level or nucleic acid to the
sequence used for comparison.
[0092] Sequence identity is typically measured using sequence
analysis software (for example, Sequence Analysis Software Package
of the Genetics Computer Group, University of Wisconsin
Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705,
BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs). Such software
matches identical or similar sequences by assigning degrees of
homology to various substitutions, deletions, and/or other
modifications. Conservative substitutions typically include
substitutions within the following groups: glycine, alanine;
valine, isoleucine, leucine; aspartic acid, glutamic acid,
asparagine, glutamine; serine, threonine; lysine, arginine; and
phenylalanine, tyrosine. In an exemplary approach to determining
the degree of identity, a BLAST program may be used, with a
probability score between e-3 and e-100 indicating a closely
related sequence.
[0093] As used herein, the term "ligand" refers to a molecule that
binds to a receptor. In particular, the ligand binds a receptor on
another cell, allowing for cell-to-cell recognition and/or
interaction.
[0094] As used herein, the term "neoplasia" is meant a disease
characterized by the pathological proliferation of a cell or tissue
and its subsequent migration to or invasion of other tissues or
organs. Neoplasia growth is typically uncontrolled and progressive,
and occurs under conditions that would not elicit, or would cause
cessation of, multiplication of normal cells. Neoplasias can affect
a variety of cell types, tissues, or organs, including but not
limited to an organ selected from the group consisting of bladder,
bone, brain, breast, cartilage, glia, esophagus, fallopian tube,
gallbladder, heart, intestines, kidney, liver, lung, lymph node,
nervous tissue, ovaries, pancreas, prostate, skeletal muscle, skin,
spinal cord, spleen, stomach, testes, thymus, thyroid, trachea,
urogenital tract, ureter, urethra, uterus, and vagina, or a tissue
or cell type thereof. Neoplasias include cancers, such as sarcomas,
carcinomas, or plasmacytomas (malignant tumor of the plasma
cells).
[0095] As used herein, the term "pathogen" is meant a virus,
bacteria, fungi, parasite or protozoa capable of causing
disease.
[0096] Exemplary viruses include, but are not limited to,
Retroviridae (e.g. human immunodeficiency viruses, such as HIV-1
(also referred to as HDTV-III, LAVE or HTLV-III/LAV, or HIV-III;
and other isolates, such as HIV-LP; Picornaviridae (e.g. polio
viruses, hepatitis A virus; enteroviruses, human Coxsackie viruses,
rhinoviruses, echoviruses); Calciviridae (e.g. strains that cause
gastroenteritis); Togaviridae (e.g. equine encephalitis viruses,
rubella viruses); Flaviridae (e.g. dengue viruses, encephalitis
viruses, yellow fever viruses); Coronoviridae (e.g. coronaviruses);
Rhabdoviridae (e.g. vesicular stomatitis viruses, rabies viruses);
Filoviridae (e.g. ebola viruses); Paramyxoviridae (e.g.
parainfluenza viruses, mumps virus, measles virus, respiratory
syncytial virus); Orthomyxoviridae (e.g. influenza viruses);
Bungaviridae (e.g. Hantaan viruses, bunga viruses, phleboviruses
and Naira viruses); Arena viridae (hemorrhagic fever viruses);
Reoviridae (e.g. reoviruses, orbiviurses and rotaviruses);
Birnaviridae; Hepadnaviridae (Hepatitis B virus); Parvovirida
(parvoviruses); Papovaviridae (papilloma viruses, polyoma viruses);
Adenoviridae (most adenoviruses); Herpesviridae (herpes simplex
virus (HSV) 1 and 2, varicella zoster virus, cytomegalovirus (CMV),
herpes virus; Poxviridae (variola viruses, vaccinia viruses, pox
viruses); and Iridoviridae (e.g. African swine fever virus); and
unclassified viruses (e.g. the agent of delta hepatitis (thought to
be a defective satellite of hepatitis B virus), the agents of
non-A, non-B hepatitis (class 1=internally transmitted; class 2
parenterally transmitted (i.e. Hepatitis C); Norwalk and related
viruses, and astroviruses).
[0097] Exemplary bacteria include, but are not limited to,
Pasteurella, Staphylococci, Streptococcus, Escherichia coli,
Pseudomonas species, and Salmonella species. Specific examples of
infectious bacteria include but are not limited to, Helicobacter
pyloris, Borelia burgdorferi, Legionella pneumophilia, Mycobacteria
sps (e.g. M. tuberculosis, M. avium, M. intracellulare, M. kansaii,
M. gordonae), Staphylococcus aureus, Neisseria gonorrhoeae,
Neisseria meningitidis, Listeria monocytogenes, Streptococcus
pyogenes (Group A Streptococcus), Streptococcus agalactiae (Group B
Streptococcus), Streptococcus (viridans group), Streptococcus
faecalis, Streptococcus bovis, Streptococcus (anaerobic sps.),
Streptococcus pneumoniae, pathogenic Campylobacter sp.,
Enterococcus sp., Haemophilus influenzae, Bacillus antracis,
corynebacterium diphtherias, corynebacterium sp., Erysipelothrix
rhusiopathiae, Clostridium perfringens, Clostridium tetani,
Enterobacter aerogenes, Klebsiella pneumoniae, Pasturella
multocida, Bacteroides sp., Fusobacterium nucleatum,
Streptobacillus moniliformis, Treponema pallidium, Treponema
pertenue, Leptospira, Rickettsia, and Actinomyces israelli.
[0098] As used herein, the term "receptor" refers to a polypeptide,
or portion thereof, present on a cell membrane that selectively
binds one or more ligand.
[0099] As used herein, the term "reduce" is meant to alter
negatively by at least 5%. An alteration may be by 5%, 10%, 25%,
30%, 50%, 75%, or even by 100%.
[0100] As used herein, the term "recognize" refers to selectively
binds a target. A T cell that recognizes a virus typically
expresses a receptor that binds an antigen expressed by the
virus.
[0101] As used herein, the term "tumor antigen" refers to an
antigen (e.g., a polypeptide) that is uniquely or differentially
expressed on a tumor cell compared to a normal or non-IS neoplastic
cell. With reference to the invention, a tumor antigen includes any
polypeptide expressed by a tumor that is capable of activating or
inducing an immune response via an antigen recognizing receptor
(e.g., CD19, MUCI) or capable of suppressing an immune response via
receptor-ligand binding (e.g., CD47, PD-L1/L2, B7.1/2).
[0102] As used herein, the term "virus antigen" refers to a
polypeptide expressed by a virus that is capable of inducing an
immune response.
[0103] As used herein, "treatment" refers to clinical intervention
in an attempt to alter the disease course of the individual or cell
being treated, and can be performed either for prophylaxis or
during the course of clinical pathology. Therapeutic effects of
treatment include, without limitation, preventing occurrence or
recurrence of disease, alleviation of symptoms, diminishment of any
direct or indirect pathological consequences of the disease,
preventing metastases, decreasing the rate of disease progression,
amelioration or palliation of the disease state, and remission or
improved prognosis. By preventing progression of a disease or
disorder, a treatment can prevent deterioration due to a disorder
in an affected or diagnosed subject or a subject suspected of
having the disorder, but also a treatment may prevent the onset of
the disorder or a symptom of the disorder in a subject at risk for
the disorder or suspected of having the disorder.
[0104] Other aspects of the present invention are described in the
following disclosure and are within the ambit of the present
invention.
BRIEF DESCRIPTION OF THE DRAWINGS
[0105] The following Detailed Description, given by way of example,
but not intended to limit the present invention to specific
embodiments described, may be understood in conjunction with the
accompanying drawings.
[0106] FIGS. 1A-1F show differentiation of 1928z CAR-engineered
T-iPSCs into CD19-specific functional T lymphocytes. FIG. 1A shows
the study concept. Peripheral blood lymphocytes are reprogrammed to
pluripotency by transduction with retroviruses encoding c-MYC,
SOX2, KLF4 and OCT-4 (7). The resulting T-iPSCs are genetically
engineered to express a CAR and are then differentiated into T
cells that express both the CAR and an endogenous TCR. FIG. 1B
shows in vitro T-lymphoid differentiation protocol. T-iPSCs were
stably transduced with a bicistronic lentiviral vector encoding the
19-28z CAR and the fluorescent marker mCherry. mCherry+ CAR+
T-iPSCs are differentiated in three steps: (i) mesoderm formation
(days 1-4), (ii) hematopoietic specification and expansion (days
5-10) and (iii) T-lymphoid commitment (days 10-30). Fluorescence
microscopy images (below) show mCherry expression was maintained
throughout the differentiation process. Scale bars, 100 .mu.M. FIG.
1C shows flow cytometric analysis of 1928z-T-iPSC-derived cells at
day 30 of differentiation. Representative plots are of at least
five independent differentiations. FIG. 1D shows 1928z-T-iPSC-T
cells were seeded into cultures of 3T3 cells or 3T3 cells
expressing CD19 (3T3-CD19). Co-cultures shown 24 h after T-cell
seeding; formation of T-cell clusters and elimination of the
3T3-CD19 monolayer are visible. Scale bars, 100 mM. FIG. 1E shows
flow cytometric analysis of CD25 and CD69 expression on the surface
of 1928z-T-iPSC-T cells 48 h after exposure to 3T3 or 3T3-CD19
cells. FIG. 1F shows luminex multiplex cytokine analysis of culture
supernatant 24 h after seeding of 1928z-T-iPSC-T cells on 3T3 or
3T3-CD19 cells. Data are presented as mean of two independent
experiments.+-.s.d.
[0107] FIGS. 2A-2G show phenotypic profiling of 1928z-T-iPSC-T
cells before and after CD19-induced expansion. FIG. 2A shows
unsupervised hierarchical clustering of 35 total transcriptomes,
generated by an mRNA gene expression microarray, from 1928z-TiPCS-T
cells at days 30-35 of differentiation (1928z-T-iPSC-T) and other
human lymphoid cell subsets isolated for this study
[CD3.sup.+TCR.gamma..delta..sup.+ cells (.gamma..delta.-T),
CD3.sup.+CD56.sup.- cells, CD8.sup.+ cells and CD4.sup.+ cells] or
downloaded from the NCBI repository GEO database (naive B cells,
TCRV.gamma.9 .gamma..delta. T-cells before activation
(.gamma..delta.-T GEO) and after activation with BrHPP/IL-2
(bromohydrin pyrophosphate/interleukin-2) for 6 h (.gamma..delta.-T
6 h activ) or 7 days (.gamma..delta.-T 7 d activ) and resting NK
cells). FIG. 2B shows heatmap comparing the expression of indicated
mRNA transcripts expressed in lymphoid and/or NK cells. Transcripts
are classified according to known function and expression patterns.
FIG. 2C shows intracellular expression of the transcription factor
PLZF (red histogram), compared to isotype control (black
histogram), and surface expression of CD161 and CD3 in
1928z-T-iPSC-T cells, as assessed by flow cytometry. FIG. 2D shows
expansion of 1928z-T-iPSC-T cells after weekly stimulations with
3T3-CD19 cells in the presence of IL-7 (10 ng/ml) and IL-15 (10
ng/ml) for 4 weeks. Absolute cell numbers are shown. Arrows
indicate restimulations with freshly irradiated 3T3-CD19 AAPCs.
FIG. 2E shows flow cytometric analysis of cell surface molecules
and cytotoxic receptors in gated CD3+ 1928z-T-iPSC-T cells before
and 7 d after expansion on 3T3-CD19 AAPCs. FIGS. 2F and 2G show
qRT-PCR analysis of the expression of the indicated mRNA
transcripts in 1928z-T-iPSC-T cells before and 7 d after expansion
on 3T3-CD19 AAPCs. Data were normalized to the values of endogenous
GAPDH and pre-expansion expression levels were used as reference.
Graphs represent average of intra-assay technical triplicates.
Error bars, mean.+-.s.d.
[0108] FIGS. 3A-3E show 1928z-T-iPSC-T cells lyse CD19-positive
tumor cells in vitro and in vivo. FIG. 3A shows in vitro 51Cr
release assay of 7 d-expanded 1928z-T-iPSC-T cells (effectors) and
the murine lymphoma cell line EL-4 expressing ovalbumin (EL4-OVA)
or human CD19 (EL4-CD19) (targets). E/T, effector/target ratio.
Representative of two independent experiments. FIG. 3B shows flow
cytometric analysis of 1928z-T-iPSC-T cells and syngeneic
1928z-transduced .gamma..delta. (1928z-.gamma..delta.) and
.alpha..beta. (1928z-.alpha..beta.) T cells before their injection
into tumor-bearing mice. Bottom: black histogram, un-transduced
cells; red histogram, transduced cells. Representative plots of two
independent experiments. FIG. 3C shows NOD-SCID
IL2R.gamma.c.sup.null mice were inoculated intraperitoneally with
CD19.sup.+ Raji human Burkitt lymphoma cell line expressing a green
fluorescent protein-firefly luciferase fusion protein (GFP/Luc).
Four days later, T cells (4.times.10.sup.5) described in B were
injected intraperitoneally. No treatment indicates mice that were
injected with tumor cells but not T cells. Tumor burden was
measured biweekly by bioluminescent imaging. Images of
representative time points are shown. Images of three mice from
each group were intentionally selected to show mice relapsing after
treatment. Disappearance of a mouse from the sequence of images
indicates death of that mouse. FIG. 3D shows kaplan-Meier curve
representing the percent survival of the experimental groups
described in B (1928z-T-iPSC-T: n=4, 1928z-.gamma..delta.: n=5,
1928z-.alpha..beta.: n=7, no treatment: n=6). Color-coded arrows
depict death events not related to tumor growth in the
corresponding groups. Statistical analysis between the treated
experimental and the untreated control group, depicted here, was
done using the log-rank test and P<0.05 was considered
significant. FIG. 3E shows exemplary CAR-T-iPSC-T cells that
delayed tumor growth in a murine xenograft model of CD19.sup.+ Raji
Burkit's Lymphoma compared to an untreated control. Peripheral
Blood TCR.alpha..beta. and TCR.gamma..delta. cells transduced with
the 1928z CAR served as positive controls. NOD scid gamma (NSG)
mice were inoculated intraperitoneally with 10.sup.5 Raji cells
which are expressing GFP and firefly-luciferase, so that tumor
burden could be monitored by in vivo bioluminescence imaging (IVIS
100 Imaging System). Four days later 10.sup.5 T cells of the
respective groups were also injected intraperitoneally together
with IL-2 (50.000 U/mouse) and IL-15 (0.25 .mu.g/mouse). IL-2
administration was continued daily and IL-15 every 2 days.
[0109] FIGS. 4A-4G show generation of T-iPSCs. FIG. 4A shows
schematic representation of the two tricistronic retroviral vectors
used for reprogramming peripheral blood T lymphocytes (PBL). Each
of the vectors encodes 2 of the Yamanaka's reprogramming factors
and a fluorescent marker (vexGFP or mCitrine) linked with 2A
peptides. LTR: long terminal repeat, wpre: woodchuck hepatitis
virus posttranscriptional regulatory element. FIG. 4B shows
reprogramming vector copy number in different T-iPSC lines assessed
by qPCR. FIG. 4C shows silencing of reprogramming vectors in
T-iPSCs assessed by qRT-PCR. Expression of the vector-encoded
transcripts vexGFP-P2A-Oct4-E2A-KLF4 and mCitrine-P2A-cMyc-T2A-SOX2
in PBL before transduction (PBL d0), 3 days post-transduction (PBL
d3) and in 3 different T-iPSC clones. FIG. 4D shows expression of
pluripotent cell markers Tra-1-81, Tra-1-60, SSEA-3 and SSEA-4 in
clone T-iPSC-1.10 assessed by flow cytometry. The pluripotency
marker-negative/HLA-ABC-negative population corresponds to MEFs.
FIG. 4E shows expression of endogenous pluripotency-associated
genes in clone TiPSC-1.10 (listed below the X axis) assessed by
qRT-PCR. Data were normalized to the values of endogenous GAPDH and
are shown as relative expression against the expression levels of
PBL d0. hES: human embryonic stem cell line H1. FIG. 4F shows
karyotypic analysis of clone TiPSC-1.10. FIG. 4G shows
representative hematoxylin and eosin staining of histological
sections of a teratoma derived from clone T-iPSC-1.10 comprising
tissues of all three germ layers. Black arrows show ectoderm:
neuronal rosettes, mesoderm: cartilage and mesoderm: gland-like
epithelium.
[0110] FIGS. 5A and 5B show T cell receptor (TCR) .beta. and
.gamma. chain rearrangements. FIG. 5A shows TCR.beta. and
TCR.gamma. rearrangement analysis of the parental line T-iPSC-1.10
and 1928z-T-iPSC-T lymphocytes using multiplexed PCR primers
targeted to conserved regions within the V-J region of the TCR
.beta. and .gamma. loci and PCR fragment analysis. FIG. 5A shows
TCR.beta. rearrangement analysis of lines T-iPSC-1.3 and
T-iPSC-1.4. X-axis: fragment size (bp), Y-axis: fluorescence
intensity (RFU). Red brackets depict the valid PCR fragment size
range on the electropherogram.
[0111] FIGS. 6A-6C show generation of 1928z CAR expressing T-iPSCs.
FIG. 6A shows Schematic representation of the lentiviral vector
encoding the 1928z CAR and the mCherry fluorescent marker linked
with a P2A peptide. LTR: long terminal repeat, Ubi-c: Ubiquitin-C
promoter, wpre: woodchuck hepatitis virus posttranscriptional
regulatory element. FIG. 6B shows T-iPSC-1.10 line transduced with
the mCherry-P2A-1928z lentiviral vector (1928z-T-iPSC) as seen
under a fluorescent microscope. Top image: bright field, bottom
image: epi-fluorescence. Scale bar, 100 .mu.M. FIG. 6C shows
expression mCherry and the CAR in 1928z-T-iPSCs assessed by flow
cytometry. Surface expression of the CAR was determined after
staining with a goat-anti-mouse IgG F(ab')2 antibody that binds to
the murine derived extracellular domain of the CAR.
[0112] FIGS. 7A and 7B show generation of hematopoietic progenitors
with lymphoid potential. FIG. 7A shows expression of Notch1 and
GATA-3 in isolated CD34.sup.+ cells from day 10 and day 12 of
differentiation of clone T-iPSC-1.10, assessed by qRT-PCR using
Taqman Gene Expression Assays (Applied Biosystems). Data were
normalized to the values of endogenous GAPDH and are shown as
relative expression against the expression levels of clone
T-iPSC-1.10. FIG. 7B shows flow cytometric analysis of Notch1 and
CD127 (IL-7R.alpha.) expression in the CD34.sup.+CD43.sup.-
hematopoietic progenitors and CD34-CD43- cells at day 10 of
differentiation of clone T-iPSC-1.10. Representative plots of at
least 5 independent differentiations.
[0113] FIGS. 8A-8C show expression of surface markers and receptors
on 1928z-T-cells. FIG. 8A shows expression of TCR.gamma..delta. and
CD3 by flow cytometry. FIG. 8B shows expression of NK cell-specific
surface markers and receptors was assessed by flow cytometry on
1928z-T-iPSC-T cells before (pre-expansion) and 7 days after
(post-expansion) stimulation with irradiated 3T3-CD19 cells. FIG.
8C shows expression of CD27 and CD28 on 1928z-T-iPSC-T cells before
and 7 days after stimulation with irradiated 3T3-CD19 cells.
[0114] FIGS. 9A and 9B show comparison of mRNA gene expression
between 1928z-T-CC-T cells and control peripheral blood lymphoid
subsets. FIG. 9A shows plots demonstrating the gene expression
similarity, computed as Pearson's correlation coefficients, between
1928z-T-iPSCT cells and other lymphoid subsets as depicted. Dataset
1: samples collected for this study, Dataset 2: samples downloaded
from the NCBI repository GEO (Gene Expression Omnibus) database.
FIG. 9B shows expression of major transcription factors, cytolytic
molecules and surface molecules, that are characteristic of the T,
NK and .gamma..delta.-T lineages in NK cells, CD4, CD8 and
.gamma..delta. T cells and 1928z-T-iPSC-T cells before and after 1
week of expansion on 3T3-CD19, as assessed by qRT-PCR. Data were
normalized to the values of endogenous GAPDH and are shown as
relative expression compared to the expression in .gamma..delta. T
cells. Graphs represent average of intra-assay technical
triplicates (error bars=SD).
[0115] FIG. 10 shows 1928z-T-iPSC-T cells significantly delay
CD19-positive tumor progression in vivo. NSG mice were inoculated
intraperitoneally with the CD19.sup.+ Raji human Burkitt lymphoma
cell line expressing a green fluorescent protein-firefly luciferase
fusion protein (GFP/Luc). Four days later they were injected i.p.
with syngeneic 1928z-T-iPSC-T, 1928z-.gamma..delta. or
1928z-.alpha..beta. T cells. No treatment indicates tumor-bearing
mice not injected with T cells. Total tumor burden at day 22 after
tumor injection was measured by Bioluminescence imaging (BLI) and
total flux (photons/sec) is represented. Median.+-.range is
plotted. Variances differed between the 1928z-T-iPSC-T and the no
treatment group (F test, p=0.0016) but did not differ between the
1928z-T-iPSC-T and 1928z-.gamma..delta. group (F test, p=0.408).
Statistical significance was determined using two-tailed
Mann-Whitney test to compare ranks between the 1928z-T-iPSC-T, no
treatment and 1928z-.gamma..delta. groups. Each dot represents one
recipient mouse. p<0.05 was considered significant.
[0116] FIG. 11 shows early expression of TCR in T lymphoid
differentiation of different T-iPSC clones. Flow cytometric
analysis of cells derived from independent clones T-iPSC-1.3 and
T-iPSC-1.4 at day 25 of differentiation (day 15 on OP9-DL1
coculture).
[0117] FIG. 12 shows immunophenotype of T lymphocytes derived from
non-CAR-engineered T-iPSCs. Flow cytometric analysis of T
lymphocytes derived from clone T-iPSC-1.10 at day 30 of
differentiation (day 20 on OP9-DL1 co-culture). Figure shows
representative plots of at least 5 independent differentiations.
Black histogram: isotype control.
DETAILED DESCRIPTION OF THE INVENTION
[0118] The present invention relates to the field of adoptive
immunotherapy. The present invention provides phenotypically
defined, functional, and/or expandable T cells that possess at
least one of the following immunotherapeutic features: 1) targeting
a specific predetermined antigen expressed on the cell surface of a
target cell in an HLA independent manner, 2) enhanced survival and
functional potential and 3) available "off-the-shelf" T cells for
administration to multiple recipients, eventually across
immunogenic barriers, and 4) cytotoxic potential and anti-tumor
activity.
[0119] In summary, although there are numerous examples of
publications describing the generation of antigen-specific T cells
or NK cells from human ESCs and iPSCs, none of these examples of
publications describe the production and use of an iPSC or ESC
expressing a CAR (including an antigen recognition region (domain),
a CD3z chain, and optionally at least one costimulatory signal
provided either within in the CAR protein or as a costimulatory
ligand protein co-expressed with a CAR protein, i.e. to provides at
least two proteins with extracellular binding sites, the CAR
protein and the costimulatory ligand protein) as an in vitro
determined antigen-specificity that is further differentiated then
expanded by using CAR stimulation for use as described herein. The
present invention relates to engineering antigen-specificity
through the use of vectors comprising CARs transduced into T-iPSCs
or NK cells produced by compositions and methods the present
invention.
[0120] The present invention also provides methods for generating
phenotypically defined, functional, and/or expandable T cells from
human T-iPSCs engineered through safe genetic modifications, e.g.,
iPSCs that are modified to express a chimeric antigen receptor
(CAR) (CAR-T-iPSCs). The CAR-T-iPSCs can be further differentiated
and expanded in cell numbers using a CAR binding antigen for
stimulation (instead of through TCR activation or non-specific
activation) of the CAR.sup.+ cell for producing CAR-T-iPSC-derived
T cells (CAR-T-iPSC-T cells) having effector activity (function) in
numbers contemplated for therapeutically effective adoptive cell
therapy, e.g., CAR-T-iPSC-derived effector T cells.
[0121] The present invention provides antigen-specific T
lymphocytes for immunotherapy including but not limited to
antigen-specific T lymphocytes capable of removing established
tumor cells in vivo. In accordance with the present invention, the
antigen-specific T lymphocytes can reduce the growth of cancerous
cells. In some embodiments, the antigen-specific T lymphocytes can
kill virus infected cells, including but not limited to HIV
infected cells in vivo.
[0122] Currently, use of T cells that express an endogenous
antigen-specific TCR (or other antigen presenting molecule) in
adoptive immunotherapy relies upon MHC-dependent self-recognition
and antigen (i.e. in the context of antigen) for stimulation. This
MHC matching requirement along with antigen-specific binding
results in limitations of effector function when a tumor (cancer)
cell escapes immunoregulation when expression of its MHC molecules
containing antigen is reduced or absent, i.e. one example of a
tumor escape mechanism. Therefore, use of CAR.sup.+ cells of the
present inventions can overcome such tumor escape because CAR based
antigen recognition does not depend upon MHC recognition, merely
the capability of an extracellular expressed antigen to bind to the
CAR.
[0123] Further, use of T cells and other effector cells that
express endogenous MHC molecules in adoptive immunotherapy limits
such cells for immunotherapy to autologous use, i.e. subject to the
limitations of MHC haplotypes matching as does tissue
transplantation. In certain embodiments, the CAR.sup.+ cells of the
present invention have reduced or undetectable cell surface
expression of MHC molecules. In certain embodiments, the CAR.sup.+
cells of the present invention have reduced or undetectable cell
surface expression of HLA molecules. In some embodiments, the
CAR.sup.+ cells of the present invention have reduced or
undetectable cell surface expression of HLA class I molecules.
[0124] The antigen-specific T lymphocytes of the present invention
express CAR, and target specifically to one antigen through the
interaction between CAR and the antigen. The CAR of the present
invention can provide antigen-specific stimulation to the T
lymphocytes expressing the CAR, which results in cell proliferation
and/or an effector function. The CAR-expressing T cells of the
present invention can overcome the limitations of T cells having an
endogenous antigen-specific TCR, which have limited proliferative
and functional capability in vivo even if an antigen-specific T
cell present in vivo and then happens to be present in isolated
PBMCs. The CAR-expressing T cells of the present invention have
long term survival rates (increased proliferative capability) both
in vitro and in vivo for providing therapeutically relevant numbers
of antigen-specific cells for both short term and long term
adoptive cell therapies. This is unlike the shorter term (fewer
cycles of proliferation) when mature (endogenously isolated) source
effector cells are used for in vitro expansion methods. Cells
having shorter term survival rates result in antigen "exhaustion"
when they have reduced or non-existent proliferation in vitro. The
present invention provides methods for producing therapeutically
relevant (effective) numbers of antigen-specific T cells from small
amounts of isolated blood cells isolated from one sample of blood
cells drawn from a subject. In some embodiments, the amount of the
blood sample drawn from a patient is at least about 0.5 mls, at
least about 1 ml, at least about 5 mls, or up to about 10 mls of
blood, in contrast to collecting multiple tubes of blood from the
subject. In some embodiments, the methods for producing
antigen-specific CAR.sup.+ T cells of the present invention
comprise producing up to about 10.sup.8, up to about 10.sup.9, up
to about 10.sup.10, up to about 10.sup.11, up to about 10.sup.12,
or greater than 10.sup.12 antigen-specific CAR.sup.+ T cells from
one subject. The present invention provides dedifferentiation
(reprogramming) of peripheral blood T cells to T-PSCs (ESCs or
iPSCs) for use with engineered vector constructs comprising a
chimeric antigen-specific regions CAR to produce CAR-expressing
T-PSCs. Furthermore, the present invention provides methods of
producing CAR-expressing T cells from CAR-expressing or
CAR-modified PSCs (e.g., ESCs or iPSCs). In some embodiments, the
methods comprises providing a differentiation cell culture system
for producing CAR-PSC-T-derived T effector cells from CAR-T-PSCs.
The produced CAR-PSC-T-derived T effector cells can be used
immunotherapy treatments.
[0125] In certain embodiments, the present invention includes
providing genetic modifications to T cells. The genetically
modified (engineered) T cells can be used in clinical therapy, as
they are considered "safe" for in vivo use. The genetic
modification includes inserting of one or more heterologous genes
in one or more genomic safe harbour sites.As used herein, a "a
genomic safe harbor site" refers to a location in the human genome
where foreign genetic material can be added where transgene
expression is sustained (i.e., not silenced) and does not perturb
expression of endogenous genes. See Sadelain, Nat Rev Cancer,
2012.
[0126] Furthermore, the present invention provides methods of
producing PSCs (e.g., ESCs, iPSCs, T-iPSCs) that can be used to
produce naive T cells, e.g., phenotypically defined, functional,
and/or expandable T cells that possess at least one of the
following immunotherapeutic features: 1) targeting one specific
predetermined antigen expressed on the cell surface of a target
cell in an HLA independent manner, 2) enhanced survival and
functional potential and 3) available "off-the-shelf" T cells for
administration to multiple recipients, eventually across
immunogenic barriers, and 4) cytotoxic potential and anti-tumor
activity.
I. Differentiation Of T Lymphocytes Having Antigen-Specificity From
Endogenous TCR Gene Rearrangements.
[0127] T cells gain antigen-specificity through functional
rearrangements of antigen recognition regions in their T cell
receptors (TCRs). The T cell receptor or TCR is a molecule found on
the surface of T lymphocytes (or T cells) that is responsible for
recognizing antigens bound to major histocompatibility complex
(WIC) molecules. The TCR can be composed of two different protein
chains (e.g., a heterodimer). In most (e.g., 95%) T cells, this
consists of an alpha (.alpha.) and beta (.beta.) chain, whereas in
some (e.g., 5%) of T cells, this consists of gamma (.gamma.) and
delta (.gamma./.delta.) chains. Such T cells having
antigen-specificity in cell surface TCR molecules differentiate in
vivo into different phenotypic subsets, including, but not limited
to, classical CD3.sup.+ alpha-beta TCR CD4.sup.+, CD3.sup.-
alpha-beta TCR CD8.sup.+, gamma-delta T cells, Natural Killer T
cells, etc. In addition, T cell populations have numerous types for
activation states, including, but not limited to, naive, central
memory, effector memory, terminal effector, etc. each with distinct
functional properties and proliferative capacities in response to
antigen-specific interactions, i.e. stimulation. T cells have
antigen-specific interactions (reactions) that can be triggered
when a specific antigen recognition region on the TCR (including
the variable region of each chain which governs
antigen-specificity) interacts with a major histocompatibility
complex (MHC) molecule capable of triggering the TCR's activation
with or without TCR recognition with regions on MHC molecules. The
interaction between TCR and a MHC molecule must be just right for
certain types of functional activation. The type of activation
triggered by the TCR is controlled by many factors, including, but
not limited to, strength of antigen to antigen binding/recognition
region, e.g., TCR binding to an antigenic peptide within the
context of an MHC molecule, the location or binding strength of the
antigenic peptide within the MHC molecule, the degree, if any, of
HLA or MHC matching to the TCR in the context of the antigenic
peptide, costimulatory molecule binding (e.g., CD28), the phenotype
of the T cell when it is activated, and cytokines present in the
environment. Some of these activation factors can be controlled at
least in part, by a target cell, e.g., a tumor or cancerous cell,
which often limits cytotoxic activities of T cells (e.g., harming
or killing the target cell). In one non-limiting example, T cell
activation by a target cell can alternatively result in suppressor
T cell activity, where the T cell becomes activated but this
activation may not result in harming or killing the target cell. In
fact, under certain conditions of stimulation, TCR binding and
signaling may result in triggering suicide of the activated T cell
(e.g., cell death). Therefore, there is a delicate balance of T
cell antigen recognition, TCR signaling, and costimulatory molecule
action, along with co-factor contributions for producing functional
antigen-specific effector T cells. In addition, similar
considerations related to producing antigen-specific effector
memory T cells for long term control of tumor cells or viruses.
[0128] When the TCR engages with an antigenic peptide and a MHC
molecule, the T lymphocyte can be activated through a series of
biochemical events mediated by associated enzymes, co-receptors,
specialized adaptor molecules, and activated or released
transcription factors. Furthermore, activation of a T cell can
induce cell proliferation, e.g., cell mitosis to produce daughter
cells (e.g., clones). Depending upon the differentiation stage of a
T cell and types of activation factors present, activation can
result in any of the phenotypic subsets as mentioned above.
[0129] Similar to transplantation, adoptive immunotherapy (e.g.,
adoptive T cell therapy) is often restricted by HLA/MHC matching.
Thus, there is often a requirement for HLA/MHC matched T cells in
adoptive immunotherapy. Both autologous and non-autologous (e.g.,
allogeneic, syngenic, or xenogenic) T cells can be used in the
adoptive T cell therapy (e.g., methods for treating cancers) of the
present invention. In certain embodiments, at least one Human
leukocyte antigen (HLA) gene is silenced, knocked out or absent in
the CAR-expressing T cells of the present invention.
[0130] Known methods for generating autologous functional
antigen-specific T cells include activating antigen (including a
tumor antigen and a pathogen antigen) specific cytotoxic T
lymphocytes (CTLs) isolated from a subject ex vivo in order to
increase cell numbers and provide functionally active killer T
cells to boost that immune function of the subject. These activated
antigen-specific CTLs can be phenotypically characterized as
CD3+CD4-CD8+(CD8 single positive: CD8SP) cells (Sensi and Anichini,
2006). Although the activated CTLs can kill or harm tumor cells in
vitro, they often are not sufficiently substantial enough to stop
tumor cell growth or stop tumor development in the subject. A major
limiting factor in this type of approach is the short life span of
activated CTLs, which are frequently inactivated quite rapidly by
antigen-induced cell death (Mescher et al., 2007; Willimsky and
Blankenstein, 2005). For example, isolated CD8.sup.+ T cells at
least of the naive subset reactive to a specific antigen are of
limited use in adoptive immunotherapy since they have limited in
vitro expansion and in vivo persistence. Furthermore, use of these
activated CTLs ex vivo in cell therapy is limited mostly due to the
difficulty in finding a CD8.sup.+ T cell that can target
specifically to one specific antigen. Antigen-specific T cells can
be obtained by isolation from a subject and non-specific
stimulation with CD3 and CD28 or other stimulatory factors. These
activated T cells may divide in the present of the antigen for
producing endogenously generated antigen-specific T cells. However,
these antigen-specific T cells do not always continue to expand in
sufficient numbers when further stimulated, e.g., they do not
always divide in cell culture to produce more antigen-specific T
cells for use in adoptive immunotherapy. For example, the
antigen-specific T cells can be exposed to factors preventing
expansion in vitro and/or in vivo due to prolonged effect of tumor
cell factors present when the T cells are exposed to at least one
tumor antigens. Alternatively, these T cell may be terminally
differentiated such that they cannot undergo further proliferation.
Furthermore, the endogenous numbers of antigen-specific T cells may
be limited. Other limitations include, but are not limited to, the
target antigen (e.g., a tumor antigen)'s capability to continue to
evade or escape from the cytotoxicity of the injected functional T
cells from in vitro expansion and activation even when present in
higher numbers in the subject.
[0131] Isolation of peripheral blood T lymphocytes (PBL) through
leukapheresis can provide a source of T lymphocytes (cells) for use
in producing antigen-specific T cells that are suitable for
adoptive T cell therapy. However, in many cases, e.g., in the case
of immune-deficient subjects, autologous T-cell isolation and
expansion is problmatic or impossible. Also, in cases of rare
HLA/MHC subtypes, it is difficult to obtain HLA/MHC-matched
autologous donors.
[0132] The antigen-specific T cells generated from CAR-expressing
T-iPSCs can circumvent the tolerance (escape) mechanisms utilized
by tumor antigens. Differentiated CAR.sup.+ T cells of the present
invention can target specifically to one specific antigen,
including, but not limited to, a tumor antigen and a pathogen
antigen. Furthermore, the antigen-specificity of the T cells of the
present invention is, not HLA-restricted or is HLA-independent.
CARs used in producing the T cells of the present invention do not
requires MHC/HLA antigen recognition e.g., CAR does not require the
antigen to be presented by a specific MHC/HLA molecule in order to
activate or stimulate T cells because antigen-specific stimulation
or activation is through the CAR. CAR.sup.+ T cells undergo
differentiation and commitment to a T cell lineage, and no antigen
stimulation is required or necessary before at least about 20 days
or at least about 30 days after T lymphoid differentiation.
Therefore, CAR+ T cells can be used in adoptive immunotherapy,
including treating cancers and treating viral infections, etc.
II. CAR-Expressing PSCs and Methods of Producing Thereof
[0133] The present invention provides compositions and methods for
producing (providing) precursor T cells, e.g., dedifferentiated
(reprogrammed) T cells for producing T-PSCs (e.g, ESCs or iPSCs)
that can be modified by a CAR, and compositions and methods for
providing a differentiation system including differentiation,
expansion, and T cell commitment from dedifferentiated T-PSCs (e.g,
ESCs or iPSCs) and CAR-T-PSCs. Compositions include, but are not
limited to, cell culture systems and expression vectors. The cell
culture systems of the present invention include, but are not
limited to, cell culture system for reprogramming a cell's
differentiation state (e.g., directing a committed somatic cell to
express markers of pluripotent cells). cell culture system for
mesoderm induction (e.g., initiating embryoid body formation for
mesoderm induction), cell culture systems for hematopoietic
specification and expansion, and cell culture systems for
T-lymphoid differentiation (inducing committed to a T cell lineage,
including inducing effector function in a redifferentiated T cell).
The compositions of the present invention include an expression
vector (e.g., a CAR vector) for transducing T-PSCs with a CAR.
[0134] Human embryonic stem cells (ESCs) and human induced
pluripotent stem cells (iPSCs) can be produced by various methods
known in the art. PSCs (ESCs or iPSCs) can be used to produce or
generate T-PSCs that can be modified by a CAR by, e.g., transducing
T-PSCs with a CAR.
[0135] PSCs include ESCs and iPSCs. iPSCs can be generated directly
from adult cells (e.g., somatic cells). PSCs can be used broadly in
regenerative medicine. Since PSCs can propagate indefinitely, as
well as give rise to every other cell type in the body (such as
neurons, heart, pancreatic, and liver cells), they represent a
single source of cells that could be used to replace those lost to
damage or disease. iPSCs can be derived or generated by introducing
a specific set of pluripotency-associated genes, or "reprogramming
factors", into a given cell type. Reprogramming factors include,
but are not limited to, OCT4 (also known as "POU5FL"), SOX2, cMYC,
and KLF4, which are also known as Yamanaka factors. See Takahashi,
K; Yamanaka, S (2006). "Induction of pluripotent stem cells from
mouse embryonic and adult fibroblast cultures by defined factors".
Cell 126 (4): 663-76. Each of the reprogramming factors can be
functionally replaced by related transcription factors, miRNAs,
small molecules, or even non-related genes such as lineage
specifiers. Upon introduction of reprogramming factors, cells begin
to form colonies that resemble PSCs, which can be isolated based on
their morphology, conditions that select for their growth, or
through expression of surface markers or reporter genes. In certain
embodiments, the PSCs used in the methods of the present invention
are subject-specific.
[0136] There are known technologies for producing PSCs from various
types of somatic cells by reprogramming using the Yamanaka factors
(OCT4, SOX2, KLF4, and cMYC). For example, reprogramming of mature
lymphocytes into iPSCs was accomplished for murine B cells (Hanna
et al., 2008; Wada et al., 2011), for murine T cells and mature NK
T cells (Watarai et al., 2010a), and for human T cells (Loh et al.,
2010; Seki et al., 2010). iPSCs can be produced from human T cells
by using whole peripheral mononuclear cells (PBMCs) or CD3.sup.+
cells as a source cell population (Loh et al., 2010; Seki et al.,
2010, Staerk et al. 2010, Brown et al, 2010)). The starting T cell
population of the known technology often includes about one million
cells. In contrast, T-PSCs of the present invention (prior to cell
number expansion) can be obtained from about 0.5 million PBMCs or
less, which can be from less than about 1 ml of whole blood drawn
from a subject.
[0137] The CAR-expressing T-PSCs of the present invention can be
generated by transducing peripheral blood lymphocytes collected
from a subject with at least one retroviral vector. In some
embodiments, the retroviral vector is excisable. The retroviral
vector can encode at least one reprogramming factors as described
above, e.g., ones selected from the group consisting of OCT4, SOX2,
KLF4, and cMYC. The retroviral vector can encode a florescent
marker. Said fluorescent marker can be selected from the group
consisting of green fluorescent protein, blue fluorescent protein,
cyan fluorescent protein, yellow fluorescent protein, and a
combination thereof. Blue fluorescent protein can be selected from
the group consisting of EBFP, EBFP2, Azurite, and mKalamal. Said
cyan fluorescent protein can be selected from the group consisting
of ECFP, Cerulean, and CyPet. Said yellow fluorescent protein can
be selected from the group consisting of YFP, Citrine, Venus, and
YPet. In one embodiment, said fluorescent marker is green
fluorescent protein. In another embodiment, the fluorescent marker
is Citrine.
[0138] Use of CAR-expressing T-PSCs to produce T cells can avoid
HLA restriction. In accordance with the present invention, the
CAR-expressing T-PSCs can be engineered for specific clinical uses.
In some embodiments, CAR-expressing T-PSCs can be engineered to
down regulate or knock out HLA expression and down regulate or
knock out Rag gene expression, in order to generate CAR-expressing
T cells that can be used in multiple hosts without rejection or
symptoms of graft vs. host disease or to be used as
immunosuppressive drugs (e.g., for allogenic cell immunotherapy).
In some embodiments, the CAR-expressing T-PSCs can be engineered to
not express the transactivator CIITA, which is necessary for
transcription of HLA class II genes (e.g., CIITA can be knocked
down). In some embodiments, the CAR-expressing T-PSCs can be
engineered to not express beta-2 microglobulin, which is necessary
for a HLA class I molecules' surface expression (e.g., beta-2
microglobulin can be knocked down). The engineered CAR-expressing
T-PSCs can be used to generate T cells suitable for many subjects
regardless of their HLA haplotypes, and can be used to target tumor
cells that have downregulated HLA expression. In addition, the
CAR-expressing PSCs can be engineered to express cell surface
molecules for effecting the type of activation, for example by
transducing cells to express suppressive or tolerogenic ligands
using known methods.
III. T Cells Derived From CAR-Expressing PSCs
[0139] Use of the T cells derived from ESCs and/or iPSCs by known
technologies is limited. The functional characterization of T cells
derived from ESCs and iPSCs is complicated by not knowing their
antigen-specificity (i.e. TCR antigen-specificity) and/or HLA
restriction. For example, T cells generated in vitro from ESCs or
iPSCs have an unpredictable TCR repertoire because TCR gene
rearrangements are random and the cells are positively selected by
unclear mechanisms during their in vitro differentiation
(Timmermans, 2009). For example, there is difficulty in finding a
CD5.sup.+T cell that target specifically to an antigen (e.g., a
tumor antigen or a pathogen antigen) on the cell surface. One or
more of the limitations can be circumvented by using iPSCs bearing
a rearranged endogenous TCR of known antigen specificity (Vizcardo,
2013; and Nishimura, 2013). However, this approach requires
laborious cloning of antigen-specific T cells and is limited to
antigens for which patient-specific T cells can be detected.
[0140] Additionally, the procedure for isolating a T cell clone
typically takes about 4-6 months. Furthermore, although numerous
attempts have been made to expand antigen-specific T cells ex vivo
in order to boost levels of antigen-responsive T cells that are
sufficient to induce a response to a virus or cancerous cell,
expanded antigen-specific T cells have been found not effective
mainly due to rapid loss of function and low cell numbers (June, C.
H. J. Clin. Invest. 117, 1466-1476 (2007)). For example, Brown
reported treating patients with advanced melanoma with CD8.sup.+ T
cell adoptive immunotherapy, eradication of tumors correlated with
increased presence of stem cell-like CD8.sup.+ T cells (Brown, M.
E. et al. PLoS ONE 5, el1373; published online Jun. 29, 2010).
Further limitations of using T cells derived from ESCs or iPSCs
include 1) not being able to find endogenous T cell clones for
every desired antigen, 2) even when a T cell clone for a specific
antigen is obtained, it takes months to expand and establish the
cell line for use in characterization and/or therapy, 3) antigen
recognition is still subject to HLA-restriction or is still
HLA-dependent. Thus, these T cells derived from ESCs or iPSCs only
recognize antigen in autologous or MHC/HLA-matched systems and
these T cells derived from ESCs or iPSCs do not overcome tumor
escape of MHC/HLA-downregulation. Furthermore, as TCRs recognize
antigens presented by specific HLA molecules, the clinical use of T
cells that recognize antigen through an endogenous TCR is
constrained by the need to match their specificity to the HLA of
the recipient.
[0141] Additionally, while numerous attempts have been made to
produce iPSCs-derived T cells having endogenous antigen-specificity
for use in adoptive immunotherapy, these cells cannot be
differentiated into committed effector T cells (Brown, et al. PLoS
ONE 5, el1373 2010; Loh, Cell Stem Cell 7, 15-19 (2010); Seki, Cell
Stem Cell 7, 11-14 (2010); and Staerk, et al. Cell Stem Cell 7,
20-24 (2010)). Use of mature antigen-specific CD8.sup.+ T cells
isolated from patients then reprogrammed into iPSCs are reported in
Nishimura (2013) and Vizcardo (2013). As reported in Nishimura
(2013) and Vizcardo (2013, these antigen-specific iPSCs-derived T
cells were redifferentiated into "rejuvenated" proliferative T
cells. Nishimura (2013) used mature HIV p27 (nef)-specific
CD8.sup.+ T cells obtained from a patient infected with HIV-1 to
produce iPSCs. Vizcardo (2013) used a melanoma patient-derived T
cell line expressing the melanoma epitope melan-A (MLANA; MART1) to
produce iPSCs. These iPSCs were then differentiated into mature
CD8.sup.+ T cells by cytokine exposure along with co-culturing with
mouse feeder cells. Because these cells were exposed to murine
feeder cells prior to use in mice, these cells may not be
acceptable for use in human clinical therapy. Antigen-specificity
encoded in the genomic DNA of the parent mature T cells was shown
to be conserved in the reprogrammed iPSCs and then by the
differentiated mature CD8.sup.+ cells.
[0142] Further, use of known systems relies upon finding and
culturing antigen-specific T cell clones from a subject for each
desired antigen. This takes painstaking culturing efforts over long
time periods. This process may include multiple blood draws from a
subject, especially when the antigen-specificity is in a rare T
cell population. Success of this type of method depends upon the
presence of antigen-specific T cells, and the number of these
antigen-specific T cells circulating in the blood of the subject.
The present invention provides T cells that are derived from T-PSCs
(ESCs or iPSCs) modified by a chimeric antigen receptor (CAR),
e.g., CAR-expressing T-PSCs. These T cells target specifically to
one antigen, and antigen-specificity of these T cells is
HLA-independent. One advantage of the methods of the present
invention for producing CAR-expressing T cells by using
CAR-expressing T-PSCs is that no antigen-specific T cell clones are
necessary in the starting cell population because
antigen-specificity is achieved through interaction of the antigen
and the antigen-binding domain of the CAR. In some embodiments,
CAR-expressing T cells are produced from one blood draw not
multiple blood draw from a subject. Therefore, a few peripheral
blood T cells are necessary or required in the starting cell
population. In accordance with the present invention, starting cell
population can have cell numbers ranging from about
2.times.10.sup.5 to about 5.times.10.sup.5 peripheral blood T cells
from about 0.5 ml to about 1 ml of peripheral blood from a
subject.
[0143] In addition, one advantage of the methods of the present
invention for producing CAR-expressing T cells by using
CAR-expressing T-PSCs (ESCs or iPSCs) is the expansion of
antigen-specific effector T cells. Unlike known methods for
producing T cells from ESCs or iPSCs, where there is no expansion
of antigen-specific effector T cells (e.g., using
non-antigen-specific T-PSCs, or co-culturing T-PSCs with allo-PBMCs
to stimulate cell division to expand T cell populations),
CAR-induced antigen-specific signals can stimulate cell division
that results in significant expansion of effector T cells.
[0144] The methods of the present invention include engeering or
modifying T-PSCs with a CAR, which includesan antigen binding or
recognition region that binds to one specific antigen. Thus,
another advantage of the methods of the present invention is that
the tareget of the T cells does not depend upon the subject's
endogenous T cell repertoire or frequency of antigen-specific T
cells.
[0145] An obstacle of TCRa chain further rearrangement due to Rag
gene expression during differentiation, was reported. This type of
event typically leads to altered specificity of an antigen
recognition region of the TCR. Altered antigen recognition during
cell proliferation can be overcome in the methods of the present
invention including the use of CAR-expressing T-PSCs through, for
example, the constant (stable) expression of the CAR.
[0146] In some embodiments, t using a subject's blood cells (e.g.,
peripheral blood lymphocytes) as a source for reprogramming
antigen-specific T cell (e.g., effector T cells) complies with the
same rules of HLA compatibility that exist for BMT. Antigen
recognition/specificity of CAR-expressing T cells is not dependent
on HLA presentation. When using cells from a single clone with the
same TCR then the antigen typically must be presented by a certain
matching HLA-type in order to be recognized by the T cell, i.e.
stimulation. In this situation, tumor cells that frequently down
regulate their HLA expression then escape T cell recognition.
However, since CAR-based stimulation does not rely upon HLA
presentation, the methods of the present invention can overcome HLA
down-regulation by tumor cells.
[0147] Additionally, phenotypic and functional characterization of
the T cells produced by the known technolgoies are limited. This
limitation can be overcome by using CAR-expressing T-PSCs of the
present invention, as the CAR-expressing T-PSCs can be expanded in
substantial amounts used for in vitro and in vivo functional
characterization, phenotyping and for future use in the clinic.
[0148] There are known technologies for generating T lymphocytes
from human ESCs and/or iPSCs: Gali , et al., Stem Cells, 2009;
Timmermans, et al., Journal of Immunology, 2009; Kennedy, et al.,
Cell Reports, 2012, Nishimura et al. Cell Stem Cell 2013, Vizcardo
et al, Cell Stem Cell 2013 and Wakao et al. Cell Stem Cell 2013.
However, as the antigen-specificity of these T cells is not known,
their therapeutic utility is not known or limited. Further, none of
the known technologies use a CAR-expressing ESCs or iPSCs. Since
the yield of mature T cells in the known technologies is often
extremely low, the potential for further functional investigation
is limited and the possibility for in vivo therapeutic application
in animal models or for use in generating cells for human
immunotherapy is extremely low.
[0149] Gali , et al., Stem Cells. 27(1):100-107 (2009) describe
using human embryonic stem cells (hESC) as a source through
embryoid body (EB) formation for producing T-cell progenitor cells.
Galic et al. reported T-cell differentiation from human ESCs
through EB-derived T-cell progenitors gave rise to phenotypically
and functionally normal cells of the T lineage when transferred
into human thymic tissue implanted in immunocompromised mice.
Furthermore, Galic et al. showed that following lentiviral-mediated
introduction of a vector expressing enhanced green fluorescent
protein into hESC, stable transgene expression was maintained
throughout differentiation. However, unlike the cell culture
systems of the present invention, Gali , et al., added BMP-4 into
the cell culture media at Day 4 instead of at the start of
differentiation. Further, T cell differentiation in Galic et al.
used a murine carrier which renders the produced T cells
incompatible for clinical application.
[0150] Timmermans, et al. (2009). Generation of T cells from human
embryonic stem cell-derived hematopoietic zones. Journal of
Immunology, 182, 6879-6888 reported hESC-derived T cells that
proliferated in response to PHA stimulation, suggesting that hESCs
can give rise to functional T cells. However, Timmermans, et al.
used an OP9 feeder culture to induce hematopoietic differentiation
instead of the defined cytokine cocktail used in the present
invention.
[0151] Nishimura (2013), Vizcardo (2013) and Wakao (2013) reported
the generation of T cells from T-iPSCs bearing specific TCRs.
However the functional characterization of those T cells is
limited. Nishimura (2013) and Vizcardo (2013) merely showed in
vitro functionality as IFN-.gamma. production and cytotoxic
activity against peptide pulsed EBV-transformed B cell lines. The T
cells generated in Wakao (2013)showed in vivo function, however
they targeted mycobacterium infection in a non-antigen-specific
manner. In contrast, the CAR-expressing T cells of the present
invention possess not only cytokine secretion activity (e.g.,
secretion of type 1 cytokines, including IL-2, TNF-.alpha., and
IFN-.gamma.), but also in vitro and in vivo cytotoxic activity
against tumor cells in mouse and in humans.
[0152] However, major issues remain to be resolved before the T
cells generated from ESCs and iPSCs of the known technologies can
be applied to human regenerative medicine. In addition, T cells
generated from ESCs display a polyclonal TCR pattern as random TCR
rearrangements take place during differentiation. Therefore,
without knowing the TCR specificity, testing the antigen-specific
mediated cytotoxic capacity of the generated T cells becomes a
random chance occurrence if the matching antigen happens to be
present in the assay. It becomes futile when a desired
antigen-specific cell is not present. Antigen recognition is an
important component of functional evaluation of T cells. In
addition, no effective positive selection can take place in such an
in vitro differentiation system due to the lack of HLA presentation
of matching peptide antigens. In accordance with the present
invention, the T cells derived from CAR-expressing T-PSCs can be
any type of T cells, including, but not limited to, T helper cells,
cytotoxic T cells, memory T cells (including central memory T
cells, stem-cell-like memory T cells (or stem-like memory T cells),
and two types of effector memory T cells: e.g., T.sub.EM cells and
T.sub.EMRA cells), Regulatory T cells (also known as suppressor T
cells), Natural killer T cells, Mucosal associated invariant T
cells, and .gamma..delta. T cells. In some embodiments, the
CAR-T-PSCs express Foxp3 to achieve and maintain a T regulatory
phenotype. Foxp3-expressing regulatory T cells hold the promise to
replace and/or supplement indiscriminatory immunosuppression by the
CAR-T-PSCs.
IV. Natural Killer (NK) Cells Derived From CAR-Expressing PSCs.
[0153] Embryonic stem cell (ESC)-derived natural killer (NK) cells
and iPSCs-derived natural killer (NK) cells are another source of
anti-tumor lymphocytes for use as immunotherapeutic CAR.sup.+
cells. In some embodiments, ESC-derived or iPSC-derived NK cells
are used as a source for inducing with a CAR.
[0154] NK cells can be derived from ESCs and/or iPSCs, as described
in Woll, et al., Journal of Immunology 175:5095-103(2005); Ni, et
al., Journal of Virology 85:43-50 (2011); and Knorr, et al.,
Translational Research 156:147-154 (2010). hESC-derived and
iPSC-derived NK cells can have the ability to kill diverse tumor
cells both in vitro and in vivo (See Woll (2005); Ni (2011); Woll,
et al., Blood 113:6094-6101 (2009)). ESC-derived NK cells can
mediate complete tumor clearance in mice engrafted with human
leukemia cells (See Woll (2009).
[0155] 1. Production of NK Cells From ESCs and iPSCs Lines.
[0156] ESCs (e.g., H9 line) can be maintained on low-density
(90,000 cells/well of a 6 well plate) mouse embryonic fibroblasts
(MEF). Generation of hematopoietic progenitor cells from ESCs can
be accomplished by using any suitable methods known in the art,
e.g., the method described in Ng, et al., (2008). A protocol
describing the use of a recombinant protein-based, animal
product-free medium (APEL) for human embryonic stem cell
differentiation as spin embryoid bodies. Nature Protocols
3:768-776. As described in Ng (2008), spin EBs amenable to
aggregation generate can be generated for ESCs and iPSCs lines by
passage in TrypLE Select (Invitrogen) on low density mouse
embryonic fibroblasts (MEFs, 90,000 cells/well). TrypLE adapted
ESCs around 60-70% confluency can be dissociated and filtered
through a 70 micron sterile filter. Cells can be counted and placed
at a concentration of 3000 cells per well (100 .mu.l volume) of a
round-bottom 96-well plate in BPEL medium containing stem cell
factor (SCF, 40 ng/ml), vascular endothelial growth factor (VEGF,
20 ng/ml), and bone morphogenic protein 4 (BMP4, 20 ng/ml. The
outer wells of the plate can be filled with sterile water to
prevent any evaporation of the media. Plates can be spin aggregated
at 1,500 RPMs for 5 minutes at room temperature and placed
undisturbed in a 37.degree. C. incubator with 5% CO2.
[0157] 2. NK Cell Differentiation From SpAin EBs.
[0158] As described in Woll, et al., (2009). Human embryonic stem
cells differentiate into a homogeneous population of natural killer
cells with potent in vivo antitumor activity. Blood 113:6094-6101,
at day 11 differentiation, 6 wells of a 96 well plate can be
directly transferred to one well of a 24-well plate in NK cell
initiating cytokines (IL-3, IL-7, IL-15, stem cell factor (SCF),
fms-like tyrosine kinase receptor-3 ligand (FLT3L). NK cell
cultures can be refreshed with 0.5 mL of cytokine containing media
every 4-5 days. Mature NK cells can be measured at 28-35 days of
culture. Following 4 weeks of NK cell culture, cells can be further
expanded using artificial antigen presenting cells (aAPCs) (See
Denman, et al., (2012). Membrane-bound IL-21 promotes sustained ex
vivo proliferation of human natural killer cells. PLoS ONE
7:e30264).
V. Cell Culture Systems
[0159] There are known cell culture systems for T-cell
differentiation. See e.g., Salvagiotto, et al., describes a
Defined, Feeder-Free, Serum-Free System to Generate In Vitro
Hematopoietic Progenitors and Differentiated Blood Cells from hESCs
and hiPSCs. PLoS One 2011. and Brown et al. Derivation of induced
pluripotent stem cells from human peripheral blood T lymphocytes.
PLoS One 5: e11373 (2010).
[0160] The cell culture systems for generating CAR-expressing T
cells used in the present invention can be serum-free, feeder-free,
and/or include feeder cells that are compatible for co-culturing
cells for human clinical therapy. In certain embodiments, the cell
culture system for generating hematopoietic precursors from human
cells is serum-free and feeder-free. This serum-free and
feeder-free system relies upon the formation of embryoid bodies
(EBs) in cultures of starting cell populations. Starting cell
populations include human pluripotent stem cells, e.g., human ESCs
and human iPSCs. The cell culture system of the present invention
can overcome limitations of known cell culture systems, including
but not limited to, donor cell shortages, viral contamination of
cells, such as when a patient has in vivo infected cells.
[0161] In certain embodiments, the cell culture system of the
present invention uses erythroid body (EB) formation in defined
serum-free and/or feed-free conditions for generating hematopoietic
precursors from T-PSCs (e.g., CAR-expressing T-PSCs). Such cell
culture system can result in at least about 70% or at least about
80% of CD3.sup.+TCR.sup.+ cells in about 30 days of
differentiation. For example, in some embodiments, as early as
about day 25 of differentiation, CD3.sup.+TCR.sup.+ can be
detected. At about day 30 of differentiation, about 80%
CD3.sup.+TCR.sup.+ cells all express a CAR. Therefore,
CAR-expressing T-PSCs can be generated in about 20 days to about 30
days, which is much shorter than the time period (several months or
more) required to establish a T cell clone reactive to a specific
antigen, if one is found, by known technologies. T-PSCs can be
expanded for about 10 days, about 20 days, or for up to about one
month. The expanded T-PSCs can be cultured for about 10 days, about
20 days, or up to about one month. Subsequently, for about 10 days,
about 20 days, about 30 days, or up to about 35 days, these T-PSCs
(e.g., CAR-expressing T-PSCs) can be differentiated into functional
T cells (e.g., CAR-expressing T-iPSC-derived effector T cells).
Thus, functional CAR-expressing T cells (e.g., CAR-expressing
PSCs-derived effector T cells) can be produced within about 4
months, or about 5 months, or up to 6 months after removal of a
blood sample from a subject.
[0162] T cell differentiation can inlcude four stages: 1) Mesoderm
induction (at about days 1-4), 2) Hematopoietic Specification (at
about days 4-8) and 3) Hematopoietic commitment and expansion (at
about days 8-10), and 4) T-lymphoid differntiation. The cell
culture system of the present invention use CAR-expressing
undifferentiated PSCs (iPSCs or ESCs) as starting cell population
for mesoderm differentiation. These CAR-expressing iPSCs are
further differentiated into mesoderm cells. The mesoderm cells are
further differentiated into Hematopoietic cells which are expanded
in cell numbers followed by inducing these CAR-expressing
T-PSCs-derived cells into committed CAR-expressing T-PSC-derived T
cells for producing effector T cells capable of long term survival
in culture. The cell culture systems of the present invention
include, but are not limited to, a first cell culture media for
mesoderm induction, a second cell culture media for hematopoietic
specificaiton and expansion, and a third cell culture media for
T-lymphoid diferentiation. The first cell culture media can include
BMP-4 (e.g., human BMP-4) and bFGF (e.g., human bFGF).
Undifferentiated T-iPSCs or undiffentiated ESCs can be used as the
starting cell population. Undifferentiated T-iPSCs or ESCs can be
transferred to low-attachment plates to allow for the formation of
embryoid bodies (EBs). The formation of EBs during the first stage
can be facilitated by an overnight incubation in the presence of
hBMP-4. EBs can then be cultured with BMP-4 and bFGF until day 4 to
allow for mesoderm induction. The successful induction of mesoderm
can be tested by, e.g., measuring the percentage of
KDR.sup.+PDGFR.sup.- cells.
[0163] The second cell culture media can include VEGF (e.g.,
hVEGF), and a cocktail of hematopoietic cytokines. The cocktail of
hematopoietic cytokines can include SCF (e.g., hSCF), Flt3L (e.g.,
hFlt3L), at least one cytokine, and bFGF for hematopoietic
specification. The cytokine can be a Th1 cytokine, which includes,
but is not limited to IL-3, IL-15, IL-7, IL-12 and IL-21. EBs can
be cultured in the second cell culture media for hematopoietic
specification until about day 10. The EBs can be
immunophenotypically analyzed by FACS for expression of CD34, CD31,
CD43, CD45, CD41a, ckit, Notch1, IL7R.alpha.. In some embodiments,
CD34.sup.+ cells from about day 10 EBs express the highest levels
of key transcription factors for lymphoid differentiation, e.g.,
CD127 (IL7R.alpha.) and Notch1. The cell culture system of the
present invention can produce a surprisingly high yield of
hematopoietic progenitors from in vitro directed differentiation of
iPSCs or ESCs.
[0164] The third cell culture media can include a feeder cell and
SCF, Flt3L and at least one cytokine. The cytokine can be a Th1
cytokine, which includes, but is not limited to, IL-3, IL-15, IL-7,
IL-12 and IL-21. In some embodiments, the cytokine can add genetic
modification(s) to the CAR-T-PSCs in order to enhance the survival
and functional potential of the CAR-T-PSC-T cells. In some
embodiments, at about day 10, the EBs are dissociated and the
hematopoietic precursors are transferred onto a feeder cell to
induce T-lymphoid differentiation in an established co-culture
system in the presence of the SCF, Flt3L and Th1 cytokine(s) (e.g.,
IL-7). In some embodiments, the feeder cell is compatible for
co-culturing cells for human clinical therapy and expresses a
recombinant protein, including, but not limited to, a Delta-like
protein (DL)-1, or a delta-like (DL) protein-4 (DL-4). In one
embodiment, the feeder cell is a DL-1-expressing OP9 (IP9-DL1)
feeder cell.
VI. Chimeric Antigen Receptor (CAR).
[0165] Chimeric antigen receptors (CARs) are engineered receptors,
which graft an arbitrary specificity onto an immune effector cell.
CARs can be used to graft the specificity of a monoclonal antibody
onto a T cell; with transfer of their coding sequence facilitated
by retroviral vectors.
[0166] Any CARs that are suitable for engineering effector cells
(e.g., T cells or NK cells) for use in adoptive immunotherapy
therapy can be used in the present invention. CARs that can be used
in the present invention to engineer or modify PSCs (iPSCs or ESCs)
include those described in Sadelain, et al., "The Basic Principles
of Chimeric Antigen Receptor Design." Cancer Discovery, OF1-11,
(2013), Chicaybam, et al., (2011), Brentjens et al. Nature Medicine
9:279-286 (2003),and U.S. Pat. No. 7,446,190, which are herein
incorporated by reference in their entireties, Non-limiting
examples of suitable CDRs include, but are not limited to,
CD19-targeted CARs (see U.S. Pat. No. 7,446,190; United States
Patent Application Publication No. 2013/0071414,), HER2-targeted
CARs (see Ahmed, et al., Clin Cancer Res., 2010), MUC16-targeted
CARs (see Chekmasova, et al., 2011), prostate-specific membrane
antigen (PSMA)-targeted CARs (for example, Zhong, et al., Molecular
Therapy, 18(2):413-420 (2010), all of which are herein incorporated
by reference in their entireties.
[0167] CARs can include an extracellular domain, a transmembrane
domain and an intracellular domain. The extracellular domain can
include an antigen binding/recognition region/domain. The antigen
binding domain of the CAR can bind to a specific antigen, e.g., a
tumor antigen, a pathogen antigen (e.g.,viral antigen), a CD
antigen. The extracellular domain can also include a signal peptide
that directs the nascent protein into the endoplasmic reticulum.
Signal peptide can be essential if the CAR is to be glycosylated
and anchored in the cell membrane. The transmembrane domain is a
hydrophobic alpha helix that spans the membrane. Different
transmembrane domains result in different receptor stability. After
antigen recognition, receptors cluster and a signal is transmitted
to the cell. The most commonly used intracellular component is
CD3.xi. which contains 3 ITAMs. This transmits an activation signal
to the T cell after antigen is bound. CARs can also include a
spacer region that links the antigen binding domain to the
transmembrane domain. The spacer region should be flexible enough
to allow the antigen binding domain to orient in different
directions to facilitate antigen recognition. The spacer can be the
hinge region from IgG1, or the CH.sub.2CH.sub.3 region of
immunoglobulin and portions of CD3.
[0168] When used to reprogram T-cell specificity, CARs permit
MHC-independent and/or HLA-independent recognition of native rather
than processed antigen (Eshhar, et al., Specific activation and
targeting of cytotoxic lymphocytes through chimeric single chains
consisting of antibody-binding domains and the gamma or zeta
subunits of the immunoglobulin and T-cell receptors. Proc. Natl.
Acad. Sci. USA 90, 720-724 (1993); Altenschmidt, et al., Specific
cytotoxic T lymphocytes in gene therapy. J. Mol. Med. 75, 259-266
(1997); Paillard, F. Immunotherapy with T cells bearing chimeric
antitumor receptors. Hum. Gene Ther. 10, 151-153 (1999)).
[0169] After antigen recognition, the intracellular domain of the
CARs delivers or transmits an activation stimulus or signal to the
T cells (Eshhar, (1993); Altenschmidt (1999)). In certain
embodiments, one or more costimulatory receptors are included in
the intracellular domain other than CD3.xi. chain to provide
optimal lymphocyte activation. In some examples, lack of a
costimulatory signaling can result in poor T-cell proliferative
response or in the induction of anergy or apoptosis (Hardin, et
al., CD28-mediated signaling co-stimulates murine T cells and
prevents induction of anergy in T cell clones. Nature 356, 607-609
(1992); Lenschow, et al., CD28/B7 system of T cell co-stimulation.
Annu. Rev. Immunol. 14, 233-258 (1996);. Ward, S. G. CD28: a
signaling perspective. Biochem. J. 318, 361-377 (1996); Greenfield,
et al., CD28/B7 co-stimulation: a review. Crit. Rev. Immunol. 18,
389-418 (1998)). Therefore, it may be valuable to engineer human T
cells so that they receive a costimulatory signal in an
antigen-dependent manner. An important development in this regard
has been the successful design of ScFv-CD28 fusion receptors that
transduce a functional antigen-dependent costimulatory signal in
human primary T cells, permitting sustained T-cell proliferation
when both the endogenous TCR and the chimeric CD28 receptor are
engaged (Krause, et al. Antigen-dependent CD28 signaling
selectively enhances survival and proliferation in genetically
modified activated human primary T lymphocytes. J. Exp. Med. 188,
619-626 (1998). U.S. Patent Publication No. 2002/0018783, which are
herein incorporated by reference in their entireties.
[0170] There are three generations of CARs. "First generation" CARs
are typically composed of an antibody derived antigen recognition
domain (e.g., a single-chain variable fragments (scFv)) fused to a
transmembrane domain, fused to cytoplasmic signaling domain of the
T cell receptor chain. "First generation" CARs typically have the
intracellular domain from the CD3 .xi.-chain, which is the primary
transmitter of signals from endogenous TCRs. "First generation"
CARs can provide de novo antigen recognition and cause activation
of both CD4.sup.+ and CD8.sup.+ T cells through their CD3.xi. chain
signaling domain in a single fusion molecule, independent of
HLA-mediated antigen presentation. In one non-limiting example, T
lymphocytes can be genetically engineered to express artificial
TCRs that direct cytotoxicity toward tumor cells (See Eshhar, et
al., Specific activation and targeting of cytotoxic lymphocytes
through chimeric single chains consisting of antibody-binding
domains and the gamma or zeta subunits of the immunoglobulin and
T-cell receptors. Proc. Natl. Acad. Sci. USA 90, 720-724 (1993);
Altenschmidt, et al., Specific cytotoxic T lymphocytes in gene
therapy. J. Mol. Med. 75, 259-266 (1997)).
[0171] "Second generation" CARs add intracellular signaling domains
from various costimulatory protein receptors (e.g., CD28, 41BB,
ICOS, OX40) to the cytoplasmic tail of the CAR to provide
additional signals to the T cell. Maher, Nat Biotechnol, 2002;
Brentjens, et al., Clin Cancer Res. (2007) and Stephan, et al., Nat
Med., 13(12):1440-9 (2007). "Second generation" CARs can.
Preclinical studies have indicated that the "Second generation"
CARs improve the antitumor activity of T cells. For example, robust
efficacy of "Second Generation" CAR modified T cells was
demonstrated in clinical trials targeting the CD19 molecule in
patients with chronic lymphoblastic leukemia (CLL) and acute
lymphoblastic leukemia (ALL).
[0172] Antigen-specific CAR receptor stimulation does not induce
"exhaustion" as demonstrated with TCR-based antigen stimulation or
non-specific anti-CD3 antibody based stimulation or allo-PBMC
stimulation. Thus, CAR antigen recognition is not limited to
endogenous TCR-based antigen recognition but depends upon the
antigen-specificity chosen for engineering into antigen specific
CAR.sup.+ cells.
[0173] In accordance with the present invention, the CAR can
include an extracellular domain, a transmembrane domain, and an
intracellular domain. The extracellular domain of the CAR can
include an antigen-binding region that binds to an antigen, which
can be, e.g., a tumor antigen or a pathogen antigen. Examples of
suitable tumor antigens include, but are not limited to, carbonic
anhydrase IX (CA1X), carcinoembryonic antigen (CEA), CD5, CD7,
CD10, CD19, CD20, CD22, CD30, CD33, CD34, CD38, CD41, CD44, CD49f,
CD56, CD74, CD123, CD133, CD138, an antigen of a cytomegalovirus
(CMV) infected cell (e.g., a cell surface antigen), epithelial
glycoprotein2 (EGP 2), epithelial glycoprotein-40 (EGP-40),
epithelial cell adhesion molecule (EpCAM), receptor
tyrosine-protein kinases erb-B2,3,4, folate-binding protein (FBP),
fetal acetylcholine receptor (AChR), folate receptor-a, Ganglioside
G2 (GD2), Ganglioside G3 (GD3), human Epidermal Growth Factor
Receptor 2 (HER-2), human telomerase reverse transcriptase (hTERT),
Interleukin-13 receptor subunit alpha-2 (IL-13R.alpha.2),
.kappa.-light chain, kinase insert domain receptor (KDR), Lewis A
(CA19.9), Lewis Y (LeY), L1 cell adhesion molecule (L1CAM),
melanoma antigen family A, 1 (MAGE-AI), Mucin 16 (Muc-16), Mucin 1
(Muc-1), Mesothelin (MSLN), NKG2D ligands, cancer-testis antigen
NY-ESO-1, oncofetal antigen (h5T4), prostate stem cell antigen
(PSCA), prostate-specific membrane antigen (PSMA), tumor-associated
glycoprotein 72 (TAG-72), vascular endothelial growth factor R2
(VEGF-R2), and Wilms tumor protein (WT-1). In certain embodiments,
the antigen-binding region of CAR includes a single-chain variable
fragment (scFv). The scFv can be derived from a heavy chain
variable region and a light chain variable region of an antibody
that binds to the desired antigen. Alternatively, ScFvs can be
derived from Fab's (e.g., from Fab libraries). In some embodiments,
the CAR is selected to have high affinity or avidity for the
antigen.
[0174] The transmembrane domain of the CAR can include a CD3.xi.
polypeptide, a CD4 polypeptide, a CD8 polypeptide, a CD28
polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, an ICOS
polypeptide, a CTLA-4 polypeptide, a PD-1 polypeptide, a LAG-3
polypeptide, a 2B4 polypeptide, and a BTLA polypeptide.
[0175] The CD3.xi. polypeptide can have an amino acid sequence that
is at least about 85%, about 90%, about 95%, about 96%, about 97%,
about 98%, about 99% or about 100% homologous to SEQ ID NO. 1, or
the sequence having a NCBI Reference No: NP_932170, or fragments
thereof, which has activating or stimulatory activity.
[0176] SEQ ID NO:1 is provided below:
TABLE-US-00001 1 mkwkalftaa ilqaqlpite aqsfglldpk lcylldgilf
iygviltalf lrvkfsrsad 61 apayqqgqnq lynelnlgrr eeydvldkrr
grdpemggkp qrrknpqegl ynelqkdkma 121 eayseigmkg errrgkghdg
lyqgistatk dtydalhmqa lppr
[0177] In accordance with the present invention, a "CD3.xi. nucleic
acid molecule" refers to a polynucleotide encoding a CD3.xi.
polypeptide.
[0178] The CD8 polypeptide can have an amino acid sequence that is
at least about 85%, about 90%, about 95%, about 96%, about 97%,
about 98%, about 99% or about 100% homologous to SEQ ID NO: 2 as
provided below:
TABLE-US-00002 MALPVTALLLPLALLLHAARPSQFRVSPLDRTWNLGETVELKCQVLLSNP
TSGCSWLFQPRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLGDTFVL
TLSDFRRENEGYYFCSALSNSIMYFSHFVPVFLPAKPTTTPAPRPPTPAP
TIASQPLSLRPEACRPAAGGAVHTRGLDFACDIYIWAPLAGTCGVLLLSL
VITLYCNHRNRRRVCKCPRPVVKSGDKPSLSARYV
[0179] In some embodiments, the transmembrane domain of the CAR
includes a CD8 polypeptide having an acid sequence of amino acids
137 to 209 of SEQ ID NO: 2.
[0180] In accordance with the present invention, a "CD8 nucleic
acid molecule" refers to a polynucleotide encoding a CD8
polypeptide.
[0181] The intracellular domain of the CAR can include a CD3
polypeptide that can activate or stimulate a cell (e.g., a cell of
the lymphoid lineage, e.g., a T cell). In certain embodiments, the
intracellular domain of the CAR can further include at least one
costimulatory signaling region comprising at least one
costimulatory molecule. As used herein, "Costimulatory molecules"
refer to cell surface molecules other than antigen receptors or
their ligands that are required for an efficient response of
lymphocytes to antigen. The costimulatory signaling region can
include a CD28 polypeptide, a 4-1BB polypeptide, an OX40
polypeptide, an ICOS polypeptide, a DAP-10 polypeptide, a PD-1
polypeptide, a LAG-3 polypeptide, a 2B4 polypeptide, a BTLA
polypeptide, or a CTLA-4 polypeptide. For example, CARs containing
the intracellular domain of 4-1BB, ICOS or DAP-10 are disclosed in
U.S. Pat. No. 7,446,190 (e.g., the nucleotide sequence encoding
4-1BB is set forth in SEQ ID No: 15, the nucleotide sequence
encoding ICOS is set forth in SEQ ID No: 16, and the nucleotide
sequence encoding DAP-10 is set forth in SEQ ID No: 17 in U.S. Pat.
No. 7,446,190), which is herein incorporated by reference in its
entirety. In some embodiments, the intracellular domain of the CAR
includes two costimulatory signaling regions comprising CD28 and
4-1BB (Sadelain, et al., Cancer Discovery, OF1-11, (2013)), and
CD28-OX40. The costimulatory molecule can bind to a costimulatory
ligand, which is a protein expressed on cell surface that upon
binding to its receptor produces a costimulatory response, i.e. an
intracellular response that effects the stimulation provided when
an antigen binds to its CAR molecule of the present invention.
Costimulatory ligands, include, but is not limited to CD80, CD86,
CD70, OX40L, 4-1BBL, CD48, TNFRSF14, and PD-L1. As one example, a
4-1BB ligand (i.e., 4-1BBL) may bind to 4-1BB (also known as
"CD137") for providing an intracellular signal that in combination
with a CAR signal induces an effector cell function of the
CAR.sup.+ T cell.
[0182] A CD28 polypeptide can have an amino acid sequence that is
at least about 85%, about 90%, about 95%, about 96%, about 97%,
about 98%, about 99% or 100% homologous to the sequence having a
NCBI Reference No: or P10747 or NP_006130 (SEQ ID No. 3), or
NP_001230006 (SEQ ID NO:4), or fragments thereof, which has
stimulatory activity.
[0183] SEQ ID NO:3 is provided below:
TABLE-US-00003 1 MLRLLLALNL FPSIQVTGNK ILVKQSPMLV AYDNAVNLSC
KYSYNLFSRE FRASLHKGLD 61 SAVEVCVVYG NYSQQLQVYS KTGFNCDGKL
GNESVTFYLQ NLYVNQTDIY FCKIEVMYPP 121 PYLDNEKSNG TIIHVKGKHL
CPSPLFPGPS KPFWVLVVVG GVLACYSLLV TVAFIIFWVR 181 SKRSRLLHSD
YMNMTPRRPG PTRKHYQPYA PPRDFAAYRS
[0184] SEQ ID NO:4 is provided below:
TABLE-US-00004 1 MLRLLLALNL FPSIQVTGNK ILVKQSPMLV AYDNAVNLSW
KHLCPSPLFP GPSKPFWVLV 61 VVGGVLACYS LLVTVAFIIF WVRSKRSRLL
HSDYMNMTPR RPGPTRKHYQ PYAPPRDFAA 121 YRS
[0185] In accordance with the present invention, a "CD28 nucleic
acid molecule" refers to a polynucleotide encoding a CD28
polypeptide.
[0186] An OX40 polypeptide can have an amino acid sequence that is
at least about 85%, about 90%, about 95%, about 96%, about 97%,
about 98%, about 99% or 100% homologous to the sequence having a
NCBI Reference No: P43489 or NP_003318 (SEQ ID No:5), or fragments
thereof, which has stimulatory activity.
[0187] SEQ ID NO:5 is provided below:
TABLE-US-00005 1 MCVGARRLGR GPCAALLLLG LGLSTVTGLH CVGDTYPSND
RCCHECRPGN GMVSRCSRSQ 61 NTVCRPCGPG FYNDVVSSKP CKPCTWCNLR
SGSERKQLCT ATQDTVCRCR AGTQPLDSYK 121 PGVDCAPCPP GHFSPGDNQA
CKPWTNCTLA GKHTLQPASN SSDAICEDRD PPATQPQETQ 181 GPPARPITVQ
PTEAWPRTSQ GPSTRPVEVP GGRAVAAILG LGLVLGLLGP LAILLALYLL 241
RRDQRLPPDA HKPPGGGSFR TPIQEEQADA HSTLAKI
[0188] In accordance with the present invention, an "OX40 nucleic
acid molecule" refers to a polynucleotide encoding an OX40
polypeptide.
[0189] A 4-1BB polypeptide can have an amino acid sequence that is
at least about 85%, about 90%, about 95%, about 96%, about 97%,
about 98%, about 99% or 100% homologous to the sequence having a
NCBI Reference No: P41273 or NP_001552 or fragments thereof (SEQ ID
NO:6), which acts as s tumor necrosis factor (TNF) ligand and has
stimulatory activity.
[0190] SEQ ID NO:6 is provided below:
TABLE-US-00006 1 MGNSCYNIVA TLLLVLNFER TRSLQDPCSN CPAGTFCDNN
RNQICSPCPP NSFSSAGGQR 61 TCDICRQCKG VFRTRKECSS TSNAECDCTP
GFHCLGAGCS MCEQDCKQGQ ELTKKGCKDC 121 CFGTFNDQKR GICRPWTNCS
LDGKSVLVNG TKERDVVCGP SPADLSPGAS SVTPPAPARE 181 PGHSPQIISF
FLALTSTALL FLLFFLTLRF SVVKRGRKKL LYIFKQPFMR PVQTTQEEDG 241
CSCRFPEEEE GGCEL
[0191] In accordance with the present invention, a "4-1BB nucleic
acid molecule" refers to a polynucleotide encoding a 4-1BB
polypeptide.
[0192] An ICOS polypeptide can have an amino acid sequence that is
at least about 85%, about 90%, about 95%, about 96%, about 97%,
about 98%, about 99% or 100% homologous to the sequence having a
NCBI Reference No: NP_036224 (SEQ ID NO:7) or fragments thereof,
which has stimulatory activity.
[0193] SEQ ID NO:7 is provided below:
TABLE-US-00007 1 MKSGLWYFFL FCLRIKVLTG EINGSANYEM FIFHNGGVQI
LCKYPDIVQQ FKMQLLKGGQ 61 ILCDLIKTKG SGNTVSIKSL KFCHSQLSNN
SVSFFLYNLD HSHANYYFCN LSIFDPPPFK 121 VTLTGGYLHI YESQLCCQLK
FWLPIGCAAF VVVCILGCIL ICWLTKKKYS SSVHDPNGEY 181 MFMRAVNTAK
KSRLTDVTL
[0194] In accordance with the present invention, a "ICOS nucleic
acid molecule" refers to a polynucleotide encoding a ICOS
polypeptide.
[0195] CTLA-4 is an inhibitory receptor expressed by activated T
cells, which when engaged by its corresponding ligands (CD80 and
CD86; B7-1 and B7-2, respectively), mediates activated T cell
inhibition or anergy. In both preclinical and clinical studies,
CTLA-4 blockade by systemic antibody infusion, enhanced the
endogenous anti-tumor response albeit, in the clinical setting,
with significant unforeseen toxicities.
[0196] CTLA-4 contains an extracellular V domain, a transmembrane
domain, and a cytoplasmic tail. Alternate splice variants, encoding
different isoforms, have been characterized. The membrane-bound
isoform functions as a homodimer interconnected by a disulfide
bond, while the soluble isoform functions as a monomer. The
intracellular domain is similar to that of CD28, in that it has no
intrinsic catalytic activity and contains one YVKM motif able to
bind PI3K, PP2A and SHP-2 and one proline-rich motif able to bind
SH3 containing proteins. One role of CTLA-4 in inhibiting T cell
responses seem to be directly via SHP-2 and PP2A dephosphorylation
of TCR-proximal signaling proteins such as CD3 and LAT. CTLA-4 can
also affect signaling indirectly via competing with CD28 for
CD80/86 binding. CTLA-4 has also been shown to bind and/or interact
with PI3K, CD80, AP2M1, and PPP2R5A.
[0197] A CTLA-4 polypeptide can have an amino acid sequence as set
forth in SEQ ID NO:8.
TABLE-US-00008 1 MACLGFQRHK AQLNLATRTW PCTLLFFLLF IPVFCKAMHV
AQPAVVLASS RGIASFVCEY 61 ASPGKATEVRVTVLRQADSQ VTEVCAATYM MGNELTFLDD
SICTGTSSGN QVNLTIQGLR 121 AMDTGLYICK VELMYPPPYY LGIGNGTQTY
VIDPEPCPDS DFLLWILAAV SSGLFFYSFL 181 LTAVSLSKML KKRSPLTTGV
YVKMPPTEPE CEKQFQPYFI PIN
[0198] In accordance with the present invention, a CTLA-4
polypeptide can have an amino acid sequence that is at least 85%,
90%, 95%, 96%, 97%, 98%, 99% or 100% homologous to SEQ ID NO:8
(homology herein may be determined using standard software such as
BLAST or FASTA). In non-limiting embodiments, a CTLA-4 polypeptide
can have an amino acid sequence that is a consecutive portion of
SEQ ID NO:8 which is at least 20, or at least 30, or at least 40,
or at least 50, and up to 222 amino acids in length. Alternatively
or additionally, in non-limiting various embodiments, the CTLA-4
polypeptide has an amino acid sequence of amino acids 1 to 223, 1
to 50, 50 to 100, 100 to 140, 141 to 161, 162 to 182, 183 to 223,
141 to 223, 162 to 223, or 183 to 223 of SEQ ID NO:8. In one
embodiment, the CTLA-4 polypeptide has an amino acid sequence of
amino acids 183 to 223 of SEQ ID NO:8. In certain embodiments, the
intracellular signaling domain of the CAR includes a CTLA-4
polypeptide having an amino acid sequence of amino acids 183 to 223
of SEQ ID NO:8. In certain embodiments, the transmembrane domain of
the CAR includes a CTLA-4 polypeptide having an amino acid sequence
of amino acids 162 to 182 of SEQ ID NO:8.
[0199] In accordance with the present invention, a "CTLA-4 nucleic
acid molecule" refers to a polynucleotide encoding a CTLA-4
polypeptide.
[0200] PD-1 is a negative immune regulator of activated T cells
upon engagement with its corresponding ligands PD-L1 and PD-L2
expressed on endogenous macrophages and dendritic cells. PD-1 is a
type I membrane protein of 268 amino acids. PD-1 has two ligands,
PD-L1 and PD-L2, which are members of the B7 family. The protein's
structure includes an extracellular IgV domain followed by a
transmembrane region and an intracellular tail. The intracellular
tail contains two phosphorylation sites located in an
immunoreceptor tyrosine-based inhibitory motif and an
immunoreceptor tyrosine-based switch motif, that PD-1 negatively
regulates TCR signals. SHP-I and SHP-2 phosphatases bind to the
cytoplasmic tail of PD-1 upon ligand binding. Upregulation of PD-L1
is one mechanism tumor cells may evade the host immune system. In
pre-clinical and clinical trials, PD-1 blockade by antagonistic
antibodies induced anti-tumor responses mediated through the host
endogenous immune system.
[0201] A PD-1 polypeptide can have an amino acid sequence as set
forth in SEQ ID NO:9.
TABLE-US-00009 1 mqipqapwpv vwavlqlgwr pgwfldspdr pwnpptfspa
llvvtegdna tftcsfsnts 61 esfvlnwyrm spsnqtdkla afpedrsqpg
qdcrfrvtql pngrdfhmsv vrarrndsgt 121 ylcgaislap kaqikeslra
elrvterrae vptahpspsp rpagqfqtlv vgvvggllgs 181 lvllvwvlav
icsraargti garrtgqplk edpsavpvfs vdygeldfqw rektpeppvp 241
cvpeqteyat ivfpsgmgts sparrgsadg prsaqplrpe dghcswpl
[0202] In accordance with the present invention, a PD-1 polypeptide
can have an amino acid sequence that is at least 85%, 90%, 95%,
96%, 97%, 98%, 99% or 100% homologous to SEQ ID NO:9. In
non-limiting embodiments, a PD-1 polypeptide can have an amino acid
sequence that is a consecutive portion of SEQ ID NO:9 which is at
least 20, or at least 30, or at least 40, or at least 50, and up to
287 amino acids in length. Alternatively or additionally, in
non-limiting various embodiments, a PD-1 polypeptide has an amino
acid sequence of amino acids 1 to 288, 1 to 50, 50 to 100, 100 to
144, 145 to 170, 171 to 191, 192 to 288, 145 to 288, 171 to 288, or
192 to 288 of SEQ ID NO:9. In one embodiment, the PD-1 polypeptide
has an amino acid sequence of amino acids 192 to 288 of SEQ ID
NO:9. In certain embodiments, the intracellular signaling domain of
the CAR includes a PD-1 polypeptide having an amino acid sequence
of amino acids 192 to 288 of SEQ ID NO:9. In certain embodiments,
the transmembrane domain of the CAR includes a PD-1 polypeptide
having an amino acid sequence of amino acids 171 to 191 of SEQ ID
NO:9.
[0203] In accordance with the present invention, a "PD-1 nucleic
acid molecule" refers to a polynucleotide encoding a PD-1
polypeptide.
[0204] Lymphocyte-activation protein 3 (LAG-3) is a negative immune
regulator of immune cells. LAG-3 belongs to the immunoglobulin (1g)
superfamily and contains 4 extracellular Ig-like domains. The LAG3
gene contains 8 exons. The sequence data, exon/intron organization,
and chromosomal localization all indicate a close relationship of
LAG3 to CD4. LAG3 has also been designated CD223 (cluster of
differentiation 223).
[0205] A LAG-3 polypeptide can have an amino acid sequence as set
forth in SEQ ID NO:10.
TABLE-US-00010 1 mweagflgll flqplwvapv kplqpgaevp vvwaqegapa
qlpcsptipl qdlsllrrag 61 vtwqhqpdsg ppaaapghpl apgphpaaps
swgprprryt vlsvgpgglr sgrlplqpry 121 qldergrqrg dfslwlrpar
radageyraa vhlrdralse rlrlrlgqas mtasppgslr 181 asdwvilncs
fsrpdrpasv hwfrnrgqgr vpvresphhh laesflflpq vspmdsgpwg 241
ciltyrdgfn vsimynltvl glepptpltv yagagsrvgl pcrlpagvgt rsfltakwtp
301 pgggpdllvt gdngdftlrl edvsqaqagt ytchihlqeq qlhatvtlai
itvtpksfgs 361 pgslgkllce vtpvsgqerf vwssldtpsq rsfsgpwlea
qeaqllsqpw qcqlyqgerl 421 lgaavyftel sspgaqrsgr apgalpaghl
llflilgvls llllvtgafg fhlwrrqwrp 481 rrfsaleqgi hppqaqskie
eleqepepep epepepepep epeql
[0206] In accordance with the present invention, a LAG-3
polypeptide can have an amino acid sequence that is at least 85%,
90%, 95%, 96%, 97%, 98%, 99% or 100% homologous to SEQ ID NO:10. In
non-limiting embodiments, a LAG-3 polypeptide can have an amino
acid sequence that is a consecutive portion of SEQ ID NO:10 which
is at least 20, or at least 30, or at least 40, or at least 50, and
up to 524 amino acids in length. Alternatively or additionally, in
non-limiting various embodiments, a LAG-3 polypeptide has an amino
acid sequence of amino acids 1 to 525, 1 to 50, 50 to 100, 100 to
150, 150 to 200, 200 to 250, 250 to 300, 300 to 350, 350 to 400,
400 to 420, 421 to 450, 451 to 471, 472 to 525, 421 to 525, 451 to
525, or 472 to 525 of SEQ ID NO:10. In one embodiment, the LAG-3
polypeptide has an amino acid sequence of amino acids 472 to 525 of
SEQ ID NO:10. In certain embodiments, the intracellular signaling
domain of the CAR includes a LAG-3 polypeptide having an amino acid
sequence of amino acids 472 to 525 of SEQ ID NO:10. In certain
embodiments, the transmembrane domain of the CAR includes a LAG-3
polypeptide having an amino acid sequence of amino acids 451 to 471
of SEQ ID NO:10.
[0207] In accordance with the present invention, a "LAG-3 nucleic
acid molecule" refers to a polynucleotide encoding a LAG-3
polypeptide.
[0208] Natural Killer Cell Receptor 2B4 (2B4) mediates non-MHC
restricted cell killing on NK cells and subsets of T cells. To
date, the function of 2B4 is still under investigation, with the
2B4-S isoform believed to be an activating receptor, and the 2B4-L
isoform believed to be a negative immune regulator of immune cells.
2B4 becomes engaged upon binding its high-affinity ligand, CD48.
2B4 contains a tyrosine-based switch motif, a molecular switch that
allows the protein to associate with various phosphatases. 2B4 has
also been designated CD244 (cluster of differentiation 244).
[0209] A 2B4 polypeptide can have an amino acid sequence as set
forth in SEQ ID NO:11.
TABLE-US-00011 1 mlgqvvtlil llllkvyqgk gcqgsadhvv sisgvplqlq
pnsiqtkvds iawkkllpsq 61 ngfhhilkwe ngslpsntsn drfsfivknl
sllikaaqqq dsglyclevt sisgkvqtat 121 fqvfvfesll pdkvekprlq
gqgkildrgr cqvalsclvs rdgnvsyawy rgskliqtag 181 nltyldeevd
ingthtytcn vsnpvswesh tlnltqdcqn ahqefrfwpf lviivilsal 241
flgtlacfcv wrrkrkekqs etspkeflti yedvkdlktr rnheqeqtfp gggstiysmi
301 qsqssaptsq epaytlysli qpsrksgsrk rnhspsfnst iyevigksqp
kaqnparlsr 361 kelenfdvys
[0210] In accordance with the present invention, a 2B4 polypeptide
can have an amino acid sequence that is at least 85%, 90%, 95%,
96%, 97%, 98%, 99% or 100% homologous to SEQ ID NO:11. In
non-limiting embodiments, a 2B4 polypeptide can have an amino acid
sequence that is a consecutive portion of SEQ ID NO:11 which is at
least 20, or at least 30, or at least 40, or at least 50, and up to
369 amino acids in length. Alternatively or additionally, in
non-limiting various embodiments, a 2B4 polypeptide has an amino
acid sequence of amino acids 1 to 370, 1 to 50, 50 to 100, 100 to
150, 150 to 215, 216 to 229, 230 to 250, 251 to 370, 216 to 370,
230 to 370, or 251 to 370 of SEQ ID NO:11. In one embodiment, the
2B4 polypeptide has an amino acid sequence of amino acids 251 to
370 of SEQ ID NO:11. In certain embodiments, the intracellular
signaling domain of the CAR includes a 2B4 polypeptide having an
amino acid sequence of amino acids 251 to 370 of SEQ ID NO:11. In
certain embodiments, the transmembrane domain of the CAR includes a
2B4 polypeptide having an amino acid sequence of amino acids 230 to
250 of SEQ ID NO:11.
[0211] In accordance with the present invention, a "2B4 nucleic
acid molecule" refers to a polynucleotide encoding a 2B4
polypeptide.
[0212] B- and T-lymphocyte attenuator (BTLA) expression is induced
during activation of T cells, and BTLA remains expressed on Th1
cells but not Th2 cells. Like PD1 and CTLA4, BTLA interacts with a
B7 homolog, B7H4. However, unlike PD-1 and CTLA-4, BTLA displays
T-Cell inhibition via interaction with tumor necrosis family
receptors (TNF-R), not just the B7 family of cell surface
receptors. BTLA is a ligand for tumour necrosis factor (receptor)
superfamily, member 14 (TNFRSF14), also known as herpes virus entry
mediator (HVEM). BTLA-HVEM complexes negatively regulate T-cell
immune responses. BTLA activation has been shown to inhibit the
function of human CD8.sup.+ cancer-specific T cells. BTLA has also
been designated as CD272 (cluster of differentiation 272).
[0213] A BTLA polypeptide can have an amino acid sequence as set
forth in SEQ ID NO:12.
TABLE-US-00012 1 MKTLPAMLGT GKLFWVFFLI PYLDIWNIHG KESCDVQLYI
KRQSEHSILA GDPFELECPV 61 KYCANRPHVT WCKLNGTTCV KLEDRQTSWK
EEKNISFFIL HFEPVLPNDN GSYRCSANFQ 121 SNLIESHSTT LYVTDVKSAS
ERPSKDEMAS RPWLLYRLLP LGGLPLLITT CFCLFCCLRR 181 HQCKQNELSD
TAGREINLVD AHLKSEQTEA STRQNSQVLL SETGIYDNDP DLCFRMQEGS 241
EVYSNPCLEE NKPGIVYASL NHSVIGPNSR LARNVKEAPT EYASICVRS
[0214] In accordance with the present invention, a BTLA polypeptide
can have an amino acid sequence that is at least 85%, 90%, 95%,
96%, 97%, 98%, 99% or 100% homologous to SEQ ID NO:12. In
non-limiting embodiments, a BTLA polypeptide can have an amino acid
sequence that is a consecutive portion of SEQ ID NO:12 which is at
least 20, or at least 30, or at least 40, or at least 50, and up to
288 amino acids in length. Alternatively or additionally, in
non-limiting various embodiments, a BTLA polypeptide has an amino
acid sequence of amino acids 1 to 289, 1 to 50, 50 to 100, 100 to
134, 135 to 157, 158 to 178, 179 to 289, 135 to 289, 158 to 289, or
179 to 289 of SEQ ID NO:12. In one embodiment, the BTLA polypeptide
has an amino acid sequence of amino acids 179 to 289 of SEQ ID
NO:12. In certain embodiments, the intracellular signaling domain
of the CAR includes a BTLA polypeptide having an amino acid
sequence of amino acids 179 to 289 of SEQ ID NO:12. In certain
embodiments, the transmembrane domain of the CAR includes a BTLA
polypeptide having an amino acid sequence of amino acids 158 to 178
of SEQ ID NO:12.
[0215] In accordance with the present invention, a "BTLA nucleic
acid molecule" refers to a polynucleotide encoding a BTLA
polypeptide.
[0216] An OX40L polypeptide can have an amino acid sequence that is
at least about 85%, about 90%, about 95%, about 96%, about 97%,
about 98%, about 99% or 100% homologous to the sequence having a
NCBI Reference No: BAB18304 or NP_003317 (SEQ ID NO: 13), or
fragments thereof that is a tumor necrosis factor (TNF) ligand.
[0217] SEQ ID NO:13 is provided below:
TABLE-US-00013 1 mervqpleen vgnaarprfe rnklllvasv iqglglllcf
tyiclhfsal qvshrypriq 61 sikvqfteyk kekgfiltsq kedeimkvqn
nsviincdgf ylislkgyfs qevnislhyq 121 kdeeplfqlk kvrsvnslmv
asltykdkvy lnvttdntsl ddfhvnggel ilihqnpgef 181 cvl
[0218] In accordance with the present invention, an "OX40L nucleic
acid molecule" refers to a polynucleotide encoding an OX40L
polypeptide.
[0219] A 4-1BB polypeptide can have an amino acid sequence that is
at least about 85%, about 90%, about 95%, about 96%, about 97%,
about 98%, about 99% or 100% homologous to the sequence having a
NCBI Reference No: P41273 or NP_001552.2 (SEQ ID NO:14) or a
fragment thereof that that acts as a tumor necrosis factor (TNF)
ligand.
[0220] SEQ ID NO:14 is provided below:
TABLE-US-00014 1 mgnscyniva tlllvlnfer trslqdpcsn cpagtfcdnn
rnqicspcpp nsfssaggqr 61 tcdicrqckg vfrtrkecss tsnaecdctp
gfhclgagcs mceqdckqgq eltkkgckdc 121 cfgtfndqkr gicrpwtncs
ldgksvlvng tkerdvvcgp spadlspgas svtppapare 181 pghspqiisf
flaltstall fllffltlrf svvkrgrkkl lyifkqpfmr pvqttqeedg 241
cscrfpeeee ggcel
[0221] In accordance with the present invention, a "4-1BB nucleic
acid molecule" refers to a polynucleotide encoding a 4-1BB
polypeptide.
[0222] In one embodiment, the CAR is 1928z, which comprises an
antigen binding region that binds to a B-cell lineage antigen CD19,
and a costimulatory signaling domain that comprises a CD28
polypeptide. "1928z" refers to a protein having at least about 85%,
about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or
about 100% homologous to SEQ ID NO:15, which includes a CDS leader
sequence at amino acids 1-18, and is able to bind to CD19.
[0223] SEQ ID NO:15 is provided below:
TABLE-US-00015 MALPVTALLLPLALLLHAEVKLQQSGAELVRPGSSVKISCKASGYAFSSY
WMNWVKQRPGQGLEWIGQIYPGDGDTNYNGKFKGQATLTADKSSSTAYMQ
LSGLTSEDSAVYFCARKTISSVVDFYFDYWGQGTTVTVSSGGGGSGGGGS
GGGGSDIELTQSPKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPK
PLIYSATYRNSGVPDRFTGSGSGTDFTLTITNVQSKDLADYFCQQYNRYP
YTSGGGTKLEIKRAAAIEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFP
GPSKPFWVLVVVGGVLACYSLLVTVAFIIFWVRSKRSRLLHSDYMNMTPR
RPGPTRKHYQPYAPPRDFAAYRSRVKFSRSAEPPAYQQGQNQLYNELNLG
RREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNELQKDKMAEAYSEIGMK
GERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRX
[0224] An exemplary nucleic acid sequence encoding a 1928z
polypeptide, including a CDS leader sequence, is provided in SEQ ID
NO:16, which is provided below.
TABLE-US-00016 ccatggctctcccagtgactgccctactgcttcccctagcgcttctcctg
catgcagaggtgaagctgcagcagtctggggctgagctggtgaggcctgg
gtcctcagtgaagatttcctgcaaggcttctggctatgcattcagtagct
actggatgaactgggtgaagcagaggcctggacagggtcttgagtggatt
ggacagatttatcctggagatggtgatactaactacaatggaaagttcaa
gggtcaagccacactgactgcagacaaatcctccagcacagcctacatgc
agctcagcggcctaacatctgaggactctgcggtctatttctgtgcaaga
aagaccattagttcggtagtagatttctactttgactactggggccaagg
gaccacggtcaccgtctcctcaggtggaggtggatcaggtggaggtggat
ctggtggaggtggatctgacattgagctcacccagtctccaaaattcatg
tccacatcagtaggagacagggtcagcgtcacctgcaaggccagtcagaa
tgtgggtactaatgtagcctggtatcaacagaaaccaggacaatctccta
aaccactgatttactcggcaacctaccggaacagtggagtccctgatcgc
ttcacaggcagtggatctgggacagatttcactctcaccatcactaacgt
gcagtctaaagacttggcagactatttctgtcaacaatataacaggtatc
cgtacacgtccggaggggggaccaagctggagatcaaacgggcggccgca
attgaagttatgtatcctcctccttacctagacaatgagaagagcaatgg
aaccattatccatgtgaaagggaaacacctttgtccaagtcccctatttc
ccggaccttctaagcccttttgggtgctggtggtggttggtggagtcctg
gcttgctatagcttgctagtaacagtggcctttattattttctgggtgag
gagtaagaggagcaggctcctgcacagtgactacatgaacatgactcccc
gccgccccgggcccacccgcaagcattaccagccctatgccccaccacgc
gacttcgcagcctatcgctccagagtgaagttcagcaggagcgcagagcc
ccccgcgtaccagcagggccagaaccagctctataacgagctcaatctag
gacgaagagaggagtacgatgttttggacaagagacgtggccgggaccct
gagatggggggaaagccgagaaggaagaaccctcaggaaggcctgtacaa
tgaactgcagaaagataagatggcggaggcctacagtgagattgggatga
aaggcgagcgccggaggggcaaggggcacgatggcctttaccagggtctc
agtacagccaccaaggacacctacgacgcccttcacatgcaggccctgcc ccctcgcg
[0225] In some embodiments, the CAR of the present invention can
further comprise an inducible promoter, for expressing nucleic acid
sequences in human cells. Promoters for use in expressing CAR genes
can be a constitutive promoters, such as ubiquitin C (UbiC)
promoter.
[0226] In some embodiments, the extracellular domain of the CAR of
the present invention can further include a signal peptide that
directs the nascent protein into the endoplasmic reticulum. The CAR
of the present invention can also include a spacer region that
links the antigen binding domain to the transmembrane domain. The
spacer region should be flexible enough to allow the antigen
binding domain to orient in different directions to facilitate
antigen recognition. The spacer can be the hinge region from IgG1,
or the CH.sub.2CH.sub.3 region of immunoglobulin and portions of
CD3
[0227] PSCs (iPSCs or ESCs) can be transduced with the CAR to
generate CAR-expressing PSCs. The generation of CAR-expressing PSCs
can be evaluated in stimulation assays with artificial antigen
presenting cells (AAPCs) expressing the antigen to which the CAR
antigen binding region can bind and recognize. The T cells derived
from CAR-expressing T-PSCs have a TCR-like strong survival and
proliferative signal through the CD3 .sub.t chain and further
through co-stimulation provided by CD28.
[0228] Using a CAR for antigen recognition can avoid the potential
for future TCR gene rearrangement. Further, by reprogramming a T
cell into a T-PSC which has a greater proliferation and
differentiation potential than a T cell, these T-PSCs (e.g.,
CAR-expressing T-PSCs can be used for genetic manipulations. T-PSCs
can be transduced by a molecule, including, but not limited to, a
CAR, a specific TCR, a costimulatory ligand, a suicide gene
(e.g.,hsvtk, inducible caspase), an inducible cytokine and an
imaging gene. In one embodiment, the T-PSC are transduced with a
CAR. These molecules can be inserted within a genomic safe harbor
such as the one identified in Papapetrou, Nat Biotech (2011).
Targeting of a specific safe genomic harbor can be achieved by
homologous recombination using a nuclease (e.g. Transcription
activator-like effector nucleases (TALENs)). Additionally, MHC/HLA
expression may be manipulated as described herein, and by knocking
out or silencing Rag genes in order to provide the CAR.sup.+ T cell
with a universal application potential, i.e. allogeneic use.
Therefore, cell effector function of CAR.sup.+ T cells is amendable
for manipulation and enhancement in a clinically safe manner.
Moreover, the engineering process (vector construction) provides an
opportunity to engineer the vector to integrate into a selected
chromosomal integration site for the CAR by targeting specific
"genomic safe harbor" sites (see, Papapetrou et al Nat Biotech
2011). In some embodiments, the vectors comprise targeting
sequences for integration into a genomic safe harbor site.
[0229] In one non-limiting embodiment, T-PSCs are produced from
peripheral blood T-cells, which are stably transduced with a vector
encoding a CAR, and a fluorescent marker. Suitable vectors include,
but are not limited to a lentiviral vector, a retroviral vector.
Other approaches that can target DNAs to a selected "genomic safe
harbor", e.g., Thal5.10 (Papapetrou, 2011 or 2012) and AAVS1, can
also be used to produce T-PSCs from T cells. In some embodiments,
the fluorescent marker is mCherry. An exemplary mCherry encoding
sequence is provided in SEQ ID NO:17:
TABLE-US-00017 Atggtgagcaagggcgaggaggataacatggccatcatcaaggagttcat
gcgcttcaaggtgcacatggagggctccgtgaacggccacgagttcgaga
tcgagggcgagggcgagggccgcccctacgagggcacccagaccgccaag
ctgaaggtgaccaagggtggccccctgcccttcgcctgggacatcctgtc
ccctcagttcatgtacggctccaaggcctacgtgaagcaccccgccgaca
tccccgactacttgaagctgtccttccccgagggcttcaagtgggagcgc
gtgatgaacttcgaggacggcggcgtggtgaccgtgacccaggactcctc
cctgcaggacggcgagttcatctacaaggtgaagctgcgcggcaccaact
tcccctccgacggccccgtaatgcagaagaagaccatgggctgggaggcc
tcctccgagcggatgtaccccgaggacggcgccctgaagggcgagatcaa
gcagaggctgaagctgaaggacggcggccactacgacgctgaggtcaaga
ccacctacaaggccaagaagcccgtgcagctgcccggcgcctacaacgtc
aacatcaagttggacatcacctcccacaacgaggactacaccatcgtgga
acagtacgaacgcgccgagggccgccactccaccggcggcatggacgagc tgtacaag.
The fluorescent marker can be used to sort CAR-expressing T-PSCs by
sorting for high expression of the fluorescent marker,
identification, tracking, in vitro and in vivo. The CAR-expressing
T-PSCs can be re-differentiated to hematopoietic precursors, which
can be further differentiated to T lymphoid lineage. The T cells
derived or produced from CAR-expressing T-PSCs of the present
invention express the CAR on their surface and can respond to,
target to, or recognize the specific antigen to which the antigen
binding region of the CAR target. For example, the T cells produced
or derived from 1928ZCAR-expressing T-PSCs can target to or
recognize CD19, e.g., the CD19 expressed on cell surface of NIH-3T3
cells (AAPCs) (Latouche et al. Nat Biotech 2000). After antigen
recognition, the intracellular domain of the CAR (e.g., CD3.xi.
alone or CD3.xi. combined with one or more costimulatory signaling
peptides (e.g., CD28, 4-1BB, ICOS, and/or OX40) transmits an
activation signal to the T cells. The CAR-expressing T cells of the
present invention can secrete cytokines, e.g., Th1 cytokines
including, but not limited to IFN-.gamma., IL-2 and TNF-.alpha.. In
addition, the CAR-expressing T cells of the present invention can
be expanded 10- to 50-fold after one stimulation (e.g., day 30
differentiation) and up to about 1,000-fold after three rounds of
stimulations. Additional activities possessed by the CAR-expressing
T cells of the present invention include cytotoxicity and
cytostatic inhibition of cell growth. Cytostatic inhibition of cell
growth can result in killing the cells that express the antigen
recognized by the CAR. Due to the cytostatic inhibition of cell
growth activity, the CAR-expressing T cells of the present
invention can be used for treating tumors or cancers. In addition,
antigen recognition of CARs does not require HLA class I
presentation, and thus, the CAR-expressing T cells derived from
CAR-expressing T-PSCs can recognize tumors across MEW barriers. For
at least the above, the CAR-expressing T cells of the present
invention can be in adoptive immunotherapy (adoptive T cell
therapy).
[0230] Through the use of cell culture systems described herein for
differentiation and dedifferentiation of source cells, including,
but not limited to, PSCs, iPSCs, ESCs, cord blood, peripheral blood
cells, peripheral blood T cells, etc., the yield obstacle of in
vitro T-cell differentiation of PSCs for a specific antigen
reactivity was overcome. Thus, the CAR-expressing T cells of the
present invention can be used for in vivo functional assessment in
mouse models and for clinical use.
VII. Vectors
[0231] Genetic modification of cells (e.g., T cells, NK cells and
iPSCs and ESCs) can be accomplished by transducing a substantially
homogeneous cell composition with a recombinant DNA or RNA
construct. Preferably, a retroviral vector (either gamma retroviral
or lentiviral) is employed for the introduction of the DNA or RNA
construct into the host cell genome. For example, a polynucleotide
encoding a receptor that binds an antigen (e.g., a tumor antigen,
or a variant, or a fragment thereof), can be cloned into a
retroviral vector and expression can be driven from its endogenous
promoter, from the retroviral long terminal repeat, or from an
alternative internal promoter. Non-viral vectors or RNA may be used
as well. Random chromosomal integration, or targeted integration
(e.g., using a nuclease, transcription activator-like effector
nucleases (TALENs), Zinc-finger nucleases (ZFNs), and/or clustered
regularly interspaced short palindromic repeats (CRISPRs), or
transgene expression (e.g., using a natural or chemically modified
RNA) can be used.
[0232] For initial genetic modification of the cells to provide
tumor or viral antigen-specific cells, a retroviral vector is
generally employed for transduction, however any other suitable
viral vector or non-viral delivery system can be used. For
subsequent genetic modification of the cells to provide cells
comprising an antigen presenting complex comprising at least two
co-stimulatory ligands, retroviral gene transfer (transduction)
likewise proves effective. Combinations of retroviral vector and an
appropriate packaging line are also suitable, where the capsid
proteins will be functional for infecting human cells. Various
amphotropic virus-producing cell lines are known, including, but
not limited to, PA12 (Miller, et al. (1985) Mol. Cell. Biol.
5:431-437); PA317 (Miller, et al. (1986) Mol. Cell. Biol.
6:2895-2902); and CRIP (Danos, et al. (1988) Proc. Natl. Acad. Sci.
USA 85:6460-6464). Non-amphotropic particles are suitable too,
e.g., particles pseudotyped with VSVG, RD114 or GALV envelope and
any other known in the art.
[0233] Possible methods of transduction also include direct
co-culture of the cells with producer cells, e.g., by the method of
Bregni, et al. (1992) Blood 80:1418-1422, or culturing with viral
supernatant alone or concentrated vector stocks with or without
appropriate growth factors and polycations, e.g., by the method of
Xu, et al. (1994) Exp. Hemat. 22:223-230; and Hughes, et al. (1992)
J. Clin. Invest. 89:1817.
[0234] Transducing viral vectors can be used to express a
co-stimulatory ligand in an immunoresponsive cell. Preferably, the
chosen vector exhibits high efficiency of infection and stable
integration and expression (see, e.g., Cayouette et al., Human Gene
Therapy 8:423-430, 1997; Kido et al., Current Eye Research
15:833-844, 1996; Bloomer et al., Journal of Virology 71:6641-6649,
1997; Naldini et al., Science 272:263 267, 1996; and Miyoshi et
al., Proc. Natl. Acad. Sci. U.S.A. 94:10319, 1997). Other viral
vectors that can be used include, for example, adenoviral,
lentiviral, and adeno-associated viral vectors, vaccinia virus, a
bovine papilloma virus, or a herpes virus, such as Epstein-Barr
Virus (also see, for example, the vectors of Miller, Human Gene
Therapy 15-14, 1990; Friedman, Science 244:1275-1281, 1989; Eglitis
et al., BioTechniques 6:608-614, 1988; Tolstoshev et al., Current
Opinion in Biotechnology 1:55-61, 1990; Sharp, The Lancet
337:1277-1278, 1991; Cornetta et al., Nucleic Acid Research and
Molecular Biology 36:311-322, 1987; Anderson, Science 226:401-409,
1984; Moen, Blood Cells 17:407-416, 1991; Miller et al.,
Biotechnology 7:980-990, 1989; Le Gal La Salle et al., Science
259:988-990, 1993; and Johnson, Chest 107:77S-83S, 1995).
Retroviral vectors are particularly well developed and have been
used in clinical settings (Rosenberg et al., N. Engl. J. Med
323:370, 1990; Anderson et al., U.S. Pat. No. 5,399,346).
[0235] Non-viral approaches can also be employed for the expression
of a protein in cell. For example, a nucleic acid molecule can be
introduced into a cell by administering the nucleic acid in the
presence of lipofection (Feigner et al., Proc. Natl. Acad. Sci.
U.S.A. 84:7413, 1987; Ono et al., Neuroscience Letters 17:259,
1990; Brigham et al., Am. J. Med. Sci. 298:278, 1989; Staubinger et
al., Methods in Enzymology 101:512, 1983),
asialoorosomucoid-polylysine conjugation (Wu et al., Journal of
Biological Chemistry 263:14621, 1988; Wu et al., Journal of
Biological Chemistry 264:16985, 1989), or by micro-injection under
surgical conditions (Wolff et al., Science 247:1465, 1990). Other
non-viral means for gene transfer include transfection in vitro
using calcium phosphate, DEAE dextran, electroporation, and
protoplast fusion. Liposomes can also be potentially beneficial for
delivery of DNA into a cell. Transplantation of normal genes into
the affected tissues of a subject can also be accomplished by
transferring a normal nucleic acid into a cultivatable cell type ex
vivo (e.g., an autologous or heterologous primary cell or progeny
thereof), after which the cell (or its descendants) are injected
into a targeted tissue or are injected systemically. Recombinant
receptors can also be derived or obtained using transposases or
targeted nucleases (e.g. Zinc finger nucleases, meganucleases, or
TALE nucleases). Transient expression may be obtained by RNA
electroporation.
[0236] cDNA expression for use in polynucleotide therapy methods
can be directed from any suitable promoter (e.g., the human
cytomegalovirus (CMV), simian virus 40 (SV40), or metallothionein
promoters), and regulated by any appropriate mammalian regulatory
element or intron (e.g. the elongation factor 1 .alpha.
enhancer/promoter/intron structure). For example, if desired,
enhancers known to preferentially direct gene expression in
specific cell types can be used to direct the expression of a
nucleic acid. The enhancers used can include, without limitation,
those that are characterized as tissue- or cell-specific enhancers.
Alternatively, if a genomic clone is used as a therapeutic
construct, regulation can be mediated by the cognate regulatory
sequences or, if desired, by regulatory sequences derived from a
heterologous source, including any of the promoters or regulatory
elements described above.
[0237] The resulting cells can be grown under conditions similar to
those for unmodified cells, whereby the modified cells can be
expanded and used for a variety of purposes.
VIII. Administration
[0238] Cell populations comprising T cells derived from
CAR-expressing T-PSCs and compositions comprising thereof of the
present invention can be provided systemically or directly to a
subject for the treatment of a neoplasia, pathogen infection, or
infectious disease. In one embodiment, T cells of the present
invention are directly injected into an organ of interest (e.g., an
organ affected by a neoplasia). Alternatively, T cells and
compositions comprising thereof of the present invention are
provided indirectly to the organ of interest, for example, by
administration into the circulatory system (e.g., the tumor
vasculature). Expansion and differentiation agents can be provided
prior to, during or after administration of cells and compositions
to increase production of T cells in vitro or in vivo.
[0239] T cells and compositions comprising thereof of the present
invention can be administered in any physiologically acceptable
vehicle, normally intravascularly, although they may also be
introduced into bone or other convenient site where the cells may
find an appropriate site for regeneration and differentiation
(e.g., thymus). Usually, at least 1.times.10.sup.5 cells will be
administered, eventually reaching 1.times.10.sup.10 or more. A cell
population comprising T cells can comprise a purified population of
cells. Those skilled in the art can readily determine the
percentage of T cells in a population using various well-known
methods, such as fluorescence activated cell sorting (FACS).
Preferable ranges of purity in populations comprising genetically
modified immunoresponsive cells are about 50 to about 55%, about 55
to about 60%, and about 65 to about 70%. More preferably the purity
is about 70 to about 75%, about 75 to about 80%, about 80 to about
85%; and still more preferably the purity is about 85 to about 90%,
about 90 to about 95%, and about 95 to about 100%. Dosages can be
readily adjusted by those skilled in the art (e.g., a decrease in
purity may require an increase in dosage). The cells can be
introduced by injection, catheter, or the like. If desired, factors
can also be included, including, but not limited to, interleukins,
e.g. IL-2, IL-3, IL 6, IL-11, IL-7, IL-12, IL-15, IL-21, as well as
the other interleukins, the colony stimulating factors, such as G-,
M- and GM-CSF, interferons, e.g. gamma.-interferon and
erythropoietin.
[0240] Compositions of the invention include pharmaceutical
compositions comprising T cells derived from CAR-expressing T-PSCs
and a pharmaceutically acceptable carrier. Administration can be
autologous or non-autologous. For example, T cells and compositions
comprising thereof can be obtained from one subject, and
administered to the same subject or a different, compatible
subject. Peripheral blood derived T cells of the present invention
or their progeny (e.g., in vivo, ex vivo or in vitro derived) can
be administered via localized injection, including catheter
administration, systemic injection, localized injection,
intravenous injection, or parenteral administration. When
administering a therapeutic composition of the present invention
(e.g., a pharmaceutical composition comprising T cells derived from
CAR-expressing T-PSCs), it will generally be formulated in a unit
dosage injectable form (solution, suspension, emulsion).
IX. Formulations
[0241] Cell populations comprising T cells derived from
CAR-expressing T-PSCs and compositions comprising thereof of the
present invention can be conveniently provided as sterile liquid
preparations, e.g., isotonic aqueous solutions, suspensions,
emulsions, dispersions, or viscous compositions, which may be
buffered to a selected pH. Liquid preparations are normally easier
to prepare than gels, other viscous compositions, and solid
compositions. Additionally, liquid compositions are somewhat more
convenient to administer, especially by injection. Viscous
compositions, on the other hand, can be formulated within the
appropriate viscosity range to provide longer contact periods with
specific tissues. Liquid or viscous compositions can comprise
carriers, which can be a solvent or dispersing medium containing,
for example, water, saline, phosphate buffered saline, polyol (for
example, glycerol, propylene glycol, liquid polyethylene glycol,
and the like) and suitable mixtures thereof.
[0242] Sterile injectable solutions can be prepared by
incorporating the compositions comprising T cells derived from
CAR-expressing T-PSCs of the present invention in the required
amount of the appropriate solvent with various amounts of the other
ingredients, as desired. Such compositions may be in admixture with
a suitable carrier, diluent, or excipient such as sterile water,
physiological saline, glucose, dextrose, or the like. The
compositions can also be lyophilized. The compositions can contain
auxiliary substances such as wetting, dispersing, or emulsifying
agents (e.g., methylcellulose), pH buffering agents, gelling or
viscosity enhancing additives, preservatives, flavoring agents,
colors, and the like, depending upon the route of administration
and the preparation desired. Standard texts, such as "REMINGTON'S
PHARMACEUTICAL SCIENCE", 17th edition, 1985, incorporated herein by
reference, may be consulted to prepare suitable preparations,
without undue experimentation.
[0243] Various additives which enhance the stability and sterility
of the compositions, including antimicrobial preservatives,
antioxidants, chelating agents, and buffers, can be added.
Prevention of the action of microorganisms can be ensured by
various antibacterial and antifungal agents, for example, parabens,
chlorobutanol, phenol, sorbic acid, and the like. Prolonged
absorption of the injectable pharmaceutical form can be brought
about by the use of agents delaying absorption, for example,
aluminum monostearate and gelatin. According to the present
invention, however, any vehicle, diluent, or additive used would
have to be compatible with the T cells derived from CAR-expressing
T-iPSCs of the present invention.
[0244] The compositions can be isotonic, i.e., they can have the
same osmotic pressure as blood and lacrimal fluid. The desired
isotonicity of the compositions of this invention may be
accomplished using sodium chloride, or other pharmaceutically
acceptable agents such as dextrose, boric acid, sodium tartrate,
propylene glycol or other inorganic or organic solutes. Sodium
chloride is preferred particularly for buffers containing sodium
ions.
[0245] Viscosity of the compositions, if desired, can be maintained
at the selected level using a pharmaceutically acceptable
thickening agent. Methylcellulose is preferred because it is
readily and economically available and is easy to work with. Other
suitable thickening agents include, for example, xanthan gum,
carboxymethyl cellulose, hydroxypropyl cellulose, carbomer, and the
like. The preferred concentration of the thickener will depend upon
the agent selected. The important point is to use an amount that
will achieve the selected viscosity. Obviously, the choice of
suitable carriers and other additives will depend on the exact
route of administration and the nature of the particular dosage
form, e.g., liquid dosage form (e.g., whether the composition is to
be formulated into a solution, a suspension, gel or another liquid
form, such as a time release form or liquid-filled form).
[0246] Those skilled in the art will recognize that the components
of the compositions should be selected to be chemically inert and
will not affect the viability or efficacy of the T cells as
describe in the present invention. This will present no problem to
those skilled in chemical and pharmaceutical principles, or
problems can be readily avoided by reference to standard texts or
by simple experiments (not involving undue experimentation), from
this disclosure and the documents cited herein.
[0247] One consideration concerning the therapeutic use of T cells
of the present invention is the quantity of cells necessary to
achieve an optimal effect. The quantity of cells to be administered
will vary for the subject being treated. In a one embodiment,
between 10.sup.4 to 10.sup.10 between 10.sup.5 to 10.sup.9 or
between 10.sup.6 and 10.sup.8 T cells of the present invention are
administered to a human subject. More effective cells may be
administered in even smaller numbers. In some embodiments, at least
about 1.times.10.sup.8, 2.times.10.sup.8, 3.times.10.sup.8,
4.times.10.sup.8, and 5.times.10.sup.8 T cells of the present
invention are administered to a human subject. The precise
determination of what would be considered an effective dose may be
based on factors individual to each subject, including their size,
age, sex, weight, and condition of the particular subject. Dosages
can be readily ascertained by those skilled in the art from this
disclosure and the knowledge in the art.
[0248] The skilled artisan can readily determine the amount of
cells and optional additives, vehicles, and/or carrier in
compositions and to be administered in methods of the invention.
Typically, any additives (in addition to the active cell(s) and/or
agent(s)) are present in an amount of 0.001 to 50% (weight)
solution in phosphate buffered saline, and the active ingredient is
present in the order of micrograms to milligrams, such as about
0.0001 to about 5 wt %, preferably about 0.0001 to about 1 wt %,
still more preferably about 0.0001 to about 0.05 wt% or about 0.001
to about 20 wt %, preferably about 0.01 to about 10 wt %, and still
more preferably about 0.05 to about 5 wt %. Of course, for any
composition to be administered to an animal or human, and for any
particular method of administration, it is preferred to determine
therefore: toxicity, such as by determining the lethal dose (LD)
and LD50 in a suitable animal model e.g., rodent such as mouse;
and, the dosage of the composition(s), concentration of components
therein and timing of administering the composition(s), which
elicit a suitable response. Such determinations do not require
undue experimentation from the knowledge of the skilled artisan,
this disclosure and the documents cited herein. And, the time for
sequential administrations can be ascertained without undue
experimentation.
X. Methods of Treatment
[0249] The present invention provides methods for treating
neoplasia in a subject. The present invention also provides methods
for treating a pathogen infection or other infectious disease in a
subject, such as an immunocompromised human subject. The methods
comprise administering T cells derived from CAR-expressing T-PSCs
of the present invention in an amount effective to achieve the
desired effect, be it palliation of an existing condition or
prevention of recurrence. For treatment, the amount administered is
an amount effective in producing the desired effect. An effective
amount can be provided in one or a series of administrations. An
effective amount can be provided in a bolus or by continuous
perfusion.
[0250] An "effective amount" (or, "therapeutically effective
amount") is an amount sufficient to effect a beneficial or desired
clinical result upon treatment. An effective amount can be
administered to a subject in one or more doses. In terms of
treatment, an effective amount is an amount that is sufficient to
palliate, ameliorate, stabilize, reverse or slow the progression of
the disease, or otherwise reduce the pathological consequences of
the disease. The effective amount is generally determined by the
physician on a case-by-case basis and is within the skill of one in
the art. Several factors are typically taken into account when
determining an appropriate dosage to achieve an effective amount.
These factors include age, sex and weight of the subject, the
condition being treated, the severity of the condition and the form
and effective concentration of the antigen-binding fragment
administered.
[0251] For adoptive immunotherapy using antigen-specific T cells,
cell doses in the range of 10.sup.6-10.sup.10 (e.g., 10.sup.9) are
typically infused. Upon administration of the T cells into the
subject and subsequent differentiation, T cells are induced that
are specifically directed against one specific antigen. "Induction"
of T cells can include inactivation of antigen-specific T cells
such as by deletion or anergy. Inactivation is particularly useful
to establish or reestablish tolerance such as in autoimmune
disorders. The T cells of the present invention can be administered
by any methods known in the art, including, but not limited to,
intravenous administration, subcutaneous administration, intranodal
administration, intratumoral administration, intrathecal
administration, intrapleural administration, intraperitoneal
administration, and direct administration to the thymus.
[0252] The invention provides methods for increasing an immune
response in a subject in need thereof. In one embodiment, the
invention provides methods for treating or preventing a neoplasia
in a subject. The invention provides therapies that are
particularly useful for the treatment of subjects having blood
cancers (e.g. leukemias, lymphomas, and myelomas) or ovarian
cancer, that are not amenable to conventional therapeutic
interventions. Suitable human subjects for therapy typically
comprise two treatment groups that can be distinguished by clinical
criteria. Subjects with "advanced disease" or "high tumor burden"
are those who bear a clinically measurable tumor. A clinically
measurable tumor is one that can be detected on the basis of tumor
mass (e.g., by palpation, CAT scan, sonogram, mammogram or X-ray;
positive biochemical or histopathologic markers on their own are
insufficient to identify this population). A pharmaceutical
composition embodied in this invention is administered to these
subjects to elicit an anti-tumor response, with the objective of
palliating their condition. Ideally, reduction in tumor mass occurs
as a result, but any clinical improvement constitutes a benefit.
Clinical improvement includes decreased risk or rate of progression
or reduction in pathological consequences of the tumor.
[0253] A second group of suitable subjects is known in the art as
the "adjuvant group." These are individuals who have had a history
of neoplasia, but have been responsive to another mode of therapy.
The prior therapy can have included, but is not restricted to,
surgical resection, radiotherapy, and traditional chemotherapy. As
a result, these individuals have no clinically measurable tumor.
However, they are suspected of being at risk for progression of the
disease, either near the original tumor site, or by metastases.
This group can be further subdivided into high-risk and low-risk
individuals. The subdivision is made on the basis of features
observed before or after the initial treatment. These features are
known in the clinical arts, and are suitably defined for each
different neoplasia. Features typical of high-risk subgroups are
those in which the tumor has invaded neighboring tissues, or who
show involvement of lymph nodes.
[0254] Another group have a genetic predisposition to neoplasia but
have not yet evidenced clinical signs of neoplasia. For instance,
women testing positive for a genetic mutation associated with
breast cancer, but still of childbearing age, can wish to receive
one or more of the antigen-binding fragments described herein in
treatment prophylactically to prevent the occurrence of neoplasia
until it is suitable to perform preventive surgery.
[0255] Human neoplasia subjects having any of the following
neoplasias: glioblastoma, melanoma, neuroblastom a, adenocarcinoma,
glioma, soft tissue sarcoma, and various carcinomas (including
prostate and small cell lung cancer) are especially appropriate
subjects. Suitable carcinomas further include any known in the
field of oncology, including, but not limited to, astrocytoma,
fibrosarcoma, myxosarcoma, liposarcoma, oligodendroglioma,
ependymoma, medulloblastoma, primitive neural ectodermal tumor
(PNET), chondrosarcoma, osteogenic sarcoma, pancreatic ductal
adenocarcinoma, small and large cell lung adenocarcinomas,
chordoma, angiosarcoma, endotheliosarcoma, squamous cell carcinoma,
bronchoalveolar carcinoma, epithelial adenocarcinoma, and liver
metastases thereof, lymphangiosarcoma, lymphangioendothelio
sarcoma, hepatoma, cholangiocarcinoma, synovioma, mesothelioma,
Ewing's tumor, rhabdomyosarcoma, colon carcinoma, basal cell
carcinoma, sweat gland carcinoma, papillary carcinoma, sebaceous
gland carcinoma, papillary adenocarcinoma, cystadenocarcinoma,
medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma,
bile duct carcinoma, choriocarcinoma, seminoma, embryonal
carcinoma, Wilms' tumor, testicular tumor, medulloblastoma,
craniopharyngioma, ependymoma, pinealoma, hemangioblastoma,
acoustic neuroma, oligodendroglioma, meningioma, neuroblastoma,
retinoblastoma, leukemia, multiple myeloma, Waldenstrom's
macroglobulinemia, and heavy chain disease, breast tumors such as
ductal and lobular adenocarcinoma, squamous and adenocarcinomas of
the uterine cervix, uterine and ovarian epithelial carcinomas,
prostatic adenocarcinomas, transitional squamous cell carcinoma of
the bladder, B and T cell lymphomas (nodular and diffuse)
plasmacytoma, acute and chronic leukemias, malignant melanoma, soft
tissue sarcomas and leiomyosarcomas.
[0256] The subjects can have an advanced form of disease, in which
case the treatment objective can include mitigation or reversal of
disease progression, and/or amelioration of side effects. The
subjects can have a history of the condition, for which they have
already been treated, in which case the therapeutic objective will
typically include a decrease or delay in the risk of recurrence. In
some embodiments, the subjects are immune-deficient patients, such
as HIV-infected or highly immunosuppressed patients with
malignancies, where autologous T-cell isolation and expansion is
problematic or impossible. In some embodiments, the subjects have
failed isolation of autologous tumor-infiltrating T lymphocytes. In
some embodiments, the patients have acute leukemia and have
relapsed after allogeneic hematopoietic cell transplantation, for
whom the use of allogeneic donor lymphocyte infusions (DLI) is
problematic. Thus, the methods can provide an additional option for
patients who do not respond to DLI or for whom DLI use is not
indicated due to high risk for graft-versus-host disease.
[0257] Accordingly, the invention provides a method of treating or
preventing a neoplasia in a subject, the method comprising
administering to the subject an effective amount of the T cells
derived from CAR-expressing T-iPSCs of the present invention.
Examples of neoplasia that can be treated or prevented by
administration of the T cells of the present invention include, but
are not limited to, blood cancers (e.g. leukemias, lymphomas, and
myelomas), ovarian cancer, sarcoma, and acute myeloid leukemia
(AML), prostate cancer, breast cancer, bladder cancer, brain
cancer, colon cancer, intestinal cancer, liver cancer, lung cancer,
pancreatic cancer, prostate cancer, skin cancer, stomach cancer,
glioblastoma, and throat cancer. In another embodiment, the tumor
antigen is one or more of carbonic anhydrase IX (CA1X),
carcinoembryonic antigen (CEA), CD5, CD7, CD10, CD19, CD20, CD22,
CD30, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD123,
CD133, CD138, an antigen of a cytomegalovirus (CMV) infected cell
(e.g., a cell surface antigen), epithelial glycoprotein2 (EGP 2),
epithelial glycoprotein-40 (EGP-40), epithelial cell adhesion
molecule (EpCAM), receptor tyrosine-protein kinases erb-B2,3,4,
folate-binding protein (FBP), fetal acetylcholine receptor (AChR),
folate receptor-a, Ganglioside G2 (GD2), Ganglioside G3 (GD3),
human Epidermal Growth Factor Receptor 2 (HER-2), human telomerase
reverse transcriptase (hTERT), Interleukin-13 receptor subunit
alpha-2 (IL-13R.alpha.2), .kappa.-light chain, kinase insert domain
receptor (KDR), Lewis A (CA19.9), Lewis Y (LeY), L1 cell adhesion
molecule (L1CAM), melanoma antigen family A, 1 (MAGE-AI), Mucin 16
(Muc-16), Mucin 1 (Muc-1), Mesothelin (MSLN), NKG2D ligands,
cancer-testis antigen NY-ESO-1, on cofetal antigen (h5T4), prostate
stem cell antigen (PSCA), prostate-specific membrane antigen
(PSMA), tumor-associated glycoprotein 72 (TAG-72), vascular
endothelial growth factor R2 (VEGF-R2), or Wilms tumor protein
(WT-1).
[0258] In other embodiments, the invention provides methods for
treating subjects with a pathogen infection (e.g., viral infection,
bacterial infection, fungal infection, parasite infection, or
protozoal infection). The invention is particularly useful for
enhancing an immune response in an immunocompromised subject.
Exemplary viral infections susceptible to treatment using a method
of the invention include, but are not limited to, Cytomegalovirus
(CMV), Epstein Barr Virus (EBV), Human Immunodeficiency Virus
(HIV), and influenza virus infections. Accordingly, the invention
provides a method of treating or preventing a pathogen infection in
a subject, the method comprising administering an effective amount
of the CAR-expressing T cells of the present invention.
[0259] Several steps can be taken to avert or minimize the risks of
immunological complications in the context of an "off-the-shelf"
allogeneic CAR-T-PSC-T therapy. Generation of "off-the-shelf" T
cells for administration to multiple recipients can be achieved by
prevention of allo-rejection of adoptively transferred CAR-T-PSC T
cells. For example, The alloreactivity of T-PSC-derived T cells,
which express an endogenous TCR (FIG. 1A), can be minimized or
preempted by generating PSCs from common HLA haplotypes to ensure
their histocompatibility with matched unrelated recipients) or
homozygous HLA haplotypes (Turner at al Cell Stem Cell 2013 and
Stacey et al Cell Stem Cell 2013), and/or by repressing HLA
expression on the CAR-T-PSC-derived T cells, e.g., knocking out the
HLA transcription factor and/or b2-microglobulin, e.g., by using
zinc-finger nucleases, meganucleases, TALENs or CRISPR. Rejection
of CAR-T-PSC-derived T cells from the recipient's T lymphocytes can
be prevented by genetic modification of the T-PSCs to express
ligands for immunoregulatory T cell receptors, including, but not
limited to, PD-L1, CD48, TNFRSF14. Furthermore, rejection of
CAR-T-PSC-derived T cells from the recipient's NK cells can be
prevented by genetic modification of the T-PSCs to express the
non-classical class I, e.g., HLA-G. Additionally or alternatively,
generation of "off-the-shelf" T cells for administration to
multiple recipients can be achieved by prevention of graft
versus-host disease (GvHD). For example, prevention of GvHD can be
achieved by selection of a desirable endogenous TCR, e.g, by
generating T-PSCs from virus-specific T cells, which due to their
recognition of a pathogen-derived antigen, are less likely to cause
GvHD. The already rearranged TCR is already directed against viral
antigens, with which large population has been infected (e.g., EBV,
CMV), and thus, there is little or no risk for GvHD reaction after
administration of the product. There are already well-characterized
banks of EBV- and CMV-specific T cells, which can be used for the
generation of such PSCs. In addition, prevention of GvHD can be
achieved by eliminating the expression of the endogenous TCR by
disruption of the TRAC gene, e.g., by using zinc-finger nucleases,
meganucleases, TALENs or CRISPR. Furthermore, prevention of GvHD
can be achieved by preventing the surface expression of TCR, e.g.,
by knocking out (e.g., by zinc-finger nucleases, meganucleases,
TALENs or CRISPR) or knocking down (e.g., with shRNAs) of the CD3
gene expression. The risk of insertional oncogenesis secondary to
gene transfer can be decreased by integrating the CAR cDNA and
other genes, such as suicide genes and noninvasive imaging
reporters at genomic safe harbor sites. Suitable suicide genes
include, but are not limited to, Herpes simplex virus thymidine
kinase (hsv-tk) and inducible Caspase 9 Suicide gene (iCasp-9).
XI. Kits
[0260] The invention provides kits for the treatment or prevention
of a neoplasia, pathogen infection, immune disorder or allogeneic
transplant. In one embodiment, the kit includes a therapeutic or
prophylactic composition containing an effective amount of T cells
derived from CAR-expressing T-PSCs in unit dosage form. In some
embodiments, the kit comprises a sterile container which contains a
therapeutic or prophylactic vaccine; such containers can be boxes,
ampules, bottles, vials, tubes, bags, pouches, blister-packs, or
other suitable container forms known in the art. Such containers
can be made of plastic, glass, laminated paper, metal foil, or
other materials suitable for holding medicaments.
[0261] If desired, the T cells is provided together with
instructions for administering the T cells to a subject having or
at risk of developing a neoplasia, pathogen infection, immune
disorder or allogeneic transplant. The instructions generally
include information about the use of the composition for the
treatment or prevention of neoplasia, pathogen infection, immune
disorder or allogeneic transplant. In other embodiments, the
instructions include at least one of the following: description of
the therapeutic agent; dosage schedule and administration for
treatment or prevention of a neoplasia, pathogen infection, immune
disorder or allogeneic transplant or symptoms thereof; precautions;
warnings; indications; counter-indications; over-dosage
information; adverse reactions; animal pharmacology; clinical
studies; and/or references. The instructions may be printed
directly on the container (when present), or as a label applied to
the container, or as a separate sheet, pamphlet, card, or folder
supplied in or with the container.
EXAMPLES
[0262] The following examples serve to illustrate certain
embodiments and aspects of the present invention and are not to be
construed as limiting the scope thereof In the experimental
disclosures which follow, the following abbreviations apply: N
(normal); M (molar); mM (millimolar); .mu.M (micromolar); mol
(moles); mmol (millimoles); .mu.mol (micromoles); nmol (nanomoles);
pmol (picomoles); g (grams); mg (milligrams); .mu.g (micrograms);
ng (nanograms); pg (picograms); L and (liters); ml (milliliters);
.mu.l (microliters); cm (centimeters); mm (millimeters); .mu.m
(micrometers); nm (nanometers); U (units); min (minute); s and sec
(second); deg (degree); pen (penicillin), strep (streptomycin) and
.degree. C. (degrees Centigrade/Celsius).
Example 1
Generation of Tumor-Targeted Human T Lymphocytes From Induced
Pluripotent Stem Cells For Cancer Therapy
1. Summary
[0263] This Example provides exemplary cell culture methods for use
in producing exemplary cells of the present invention. These cell
culture systems result in differentiation when using ES or iPS
cells as starting populations. When peripheral blood T cells are
used as a starting population this cell culture system additionally
dedifferentiates T cells to iPS like cells that are then
differentiated into T like cells for use with CARs of the present
inventions.
[0264] Progress in adoptive T-cell therapy for cancer and
infectious diseases (1, 2) is hampered by the lack of readily
available, antigen-specific, human T lymphocytes. Pluripotent stem
cells could provide an unlimited source of T lymphocytes, but the
therapeutic potential of human pluripotent stem cell-derived
lymphoid cells generated to date remains uncertain (3-6). As shown
in this Example, induced pluripotent stem cell (iPSC) was combined
with chimeric antigen receptor (CAR) technologies to generate human
T cells targeted to CD19, an antigen expressed by malignant B
cells, in tissue culture (7, 8). These iPSC-derived, CAR-expressing
T cells display a phenotype resembling that of innate
.gamma..delta. T cells. Similar to CAR-transduced, peripheral blood
.gamma..delta. T cells, the iPSC-derived T cells potently inhibit
tumor growth in a xenograft model. This approach of generating
therapeutic human T cells `in the dish` may be useful for cancer
immunotherapy and other medical applications.
2. Introduction
[0265] Current approaches to adoptive T-cell therapy require the
labor-intensive generation of T-cell lines from carefully selected
donors or the genetic engineering of autologous T cells from each
individual patient, hindering the facile and broad use of T cells
with pre-determined antigen specificity. Having rapid access to
unlimited antigen-specific T lymphocytes with optimized therapeutic
features would greatly advance the scope and delivery of T-cell
therapies. Previous studies support the feasibility of generating T
lymphocytes from human embryonic stem cells (ESCs) and iPSCs in
vitro, although the yield of lymphoid cells has been low and their
nature only partially defined (3, 4). More specifically, the
functional characterization of T cells derived from ESCs and iPSCs
is complicated by not knowing their antigen specificity and HLA
restriction. For example, T cells generated in vitro from ESCs or
iPSCs have an unpredictable T-cell receptor (TCR) repertoire
because TCR gene rearrangements are random and the cells are
positively selected by unclear mechanisms during their in vitro
differentiation (3). This limitation can be circumvented by using
iPSCs bearing a rearranged endogenous TCR of known antigen
specificity (5, 6). Unfortunately, this approach requires laborious
cloning of antigen-specific T cells and is limited to antigens for
which patient-specific T cells can be detected. Furthermore, as
TCRs recognize antigens presented by specific HLA molecules, the
clinical use of T cells that recognize antigen through an
endogenous TCR is constrained by the need to match their
specificity to the HLA of the recipient patient.
[0266] Genetic engineering of T lymphocytes to express CARs has
recently emerged as a promising approach to rapidly generate
tumor-targeted T cells endowed with enhanced anti-tumor properties
(8). For example, CARs redirect T-cell specificity in
HLA-independent fashion, thereby eliminating the need to consider
HLA restriction and overcoming some tumor escape mechanisms (8). It
was previously demonstrated that human T cells expressing a CAR
targeted to the CD19 antigen, which is expressed on the vast
majority of leukemias and lymphomas, can eradicate B-cell
malignancies in mice (9). Importantly, second-generation CARs,
combining both activation and co-stimulatory signaling domains,
enhanced T-cell expansion and in vivo persistence (8, 10). It has
been demonstrated in clinical trials that second-generation CD19
CAR-modified T cells efficiently induce complete remissions in
patients with acute or chronic lymphoblastic leukemias (11-14).
[0267] It was hypothesized that genetic engineering of iPSCs with
second-generation CARs would be an efficient strategy to
concomitantly harness the unlimited availability of iPSCs and to
generate phenotypically defined, functional and expandable T cells
that are genetically targeted to a tumor antigen of interest (FIG.
1A) (8).
3. Methods and Materials
[0268] 3.1. Generation of 1928z-T-iPSC
[0269] Peripheral blood lymphocytes (PBL) were collected from a
volunteer donor after informed consent was obtained. PBLs were
activated with phytohaemagglutinin (PHA, 2 .mu.g/ml) and transduced
with two tri-cistronic excisable Moloney murine leukemia
virus-based (SFG) retroviral vectors, each one encoding
reprogramming factors and a different fluorescent marker
(f-Citrine-P2A-cMYC-E2A-SOX2 and f-vexGFP-P2A-OCT4-T2A-KLF4) (FIG.
4A). The Citrine-P2A-cMYC-E2A-SOX2 sequence and
vexGFP-P2A-OCT4-T2A-KLF4 were constructed by overlapping PCR
fragments and introduced in the Ncol and BamHI sites of an SFG
retroviral vector (see, Riviere et al PNAS 1995 for compositions
and methods of constructing an SFG vector). A wpre element was
introduced after the transgenes and before the 3'LTR. A loxP site
was introduced in the 3'LTR, so that the vector can be excised by
transient expression of Cre recombinase through an
integrase-deficient lentiviral vector (IDLV) (43). A loxP site was
introduced in the 3'LTR, so that the vector was excised by
transient expression of Cre recombinase through an
integrase-deficient lentiviral vector (IDLV).
[0270] An exemplary nucleic acid sequence for encoding
reprogramming factors MYC and SOX-2, wherein an exemplary marker is
Citrine: SFG-fCMS (f-Citrine-P2A-cMYC-E2A-SOX2) which includes:
TABLE-US-00018 [SEQ ID NO: 18]
atggtgagcaagggcgaggagctgttcaccggggtggtgcccatcctggt
cgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagg
gcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcacc
accggcaagctgcccgtgccctggcccaccctcgtgaccaccttcggcta
cggcctgatgtgcttcgcccgctaccccgaccacatgaagcagcacgact
tcttcaagtccgccatgcccgaaggctacgtccaggagcgcaccatcttc
ttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgaggg
cgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggagg
acggcaacatcctggggcacaagctggagtacaactacaacagccacaac
gtctatatcatggccgacaagcagaagaacggcatcaaggtgaacttcaa
gatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactacc
agcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccac
tacctgagctaccagtccgccctgagcaaagaccccaacgagaagcgcga
tcacatggtcctgctggagttcgtgaccgccgccgggatcactctcggca
tggacgagctgtacaagGGATCTGGAGCAACAAACTTCTCACTACTCAAA
CAAGCAGGTGACGTGGAGGAGAATCCCGGCCCTatgcccctcaacgttag
cttcaccaacaggaactatgacctcgactacgactcggtgcagccgtatt
tctactgcgacgaggaggagaacttctaccagcagcagcagcagagcgag
ctgcagcccccggcgcccagcgaggatatctggaagaaattcgagctgct
gcccaccccgcccctgtcccctagccgccgctccgggctctgctcgccct
cctacgttgcggtcacacccttctcccttcggggagacaacgacggcggt
ggcgggagcttctccacggccgaccagctggagatggtgaccgagctgct
gggaggagacatggtgaaccagagtttcatctgcgacccggacgacgaga
ccttcatcaaaaacatcatcatccaggactgtatgtggagcggcttctcg
gccgccgccaagctcgtctcagagaagctggcctcctaccaggctgcgcg
caaagacagcggcagcccgaaccccgcccgcggccacagcgtctgctcca
cctccagcttgtacctgcaggatctgagcgccgccgcctcagagtgcatc
gacccctcggtggtcttcccctaccctctcaacgacagcagctcgcccaa
gtcctgcgcctcgcaagactccagcgccttctctccgtcctcggattctc
tgctctcctcgacggagtcctccccgcagggcagccccgagcccctggtg
ctccatgaggagacaccgcccaccaccagcagcgactctgaggaggaaca
agaagatgaggaagaaatcgatgttgtttctgtggaaaagaggcaggctc
ctggcaaaaggtcagagtctggatcaccttctgctggaggccacagcaaa
cctcctcacagcccactggtcctcaagaggtgccacgtctccacacatca
gcacaactacgcagcgcctccctccactcggaaggactatcctgctgcca
agagggtcaagttggacagtgtcagagtcctgagacagatcagcaacaac
cgaaaatgcaccagccccaggtcctcggacaccgaggagaatgtcaagag
gcgaacacacaacgtcttggagcgccagaggaggaacgagctaaaacgga
gcttttttgccctgcgtgaccagatcccggagttggaaaacaatgaaaag
gcccccaaggtagttatccttaaaaaagccacagcatacatcctgtccgt
ccaagcagaggagcaaaagctcatttctgaagaggacttgttgcggaaac
gacgagaacagttgaaacacaaacttgaacagctacggaactcttgtgcg
GGATCTGGACAATGTACTAACTACGCTTTGTTGAAACTCGCTGGCGATGT
TGAAAGTAACCCCGGTCCCatgtacaacatgatggagacggagctgaagc
cgccgggcccgcagcaaacttcggggggcggcggcggcaactccaccgcg
gcggcggccggcggcaaccagaaaaacagcccggaccgcgtcaagcggcc
catgaatgccttcatggtgtggtcccgcgggcagcggcgcaagatggccc
aggagaaccccaagatgcacaactcggagatcagcaagcgcctgggcgcc
gagtggaaacttttgtcggagacggagaagcggccgttcatcgacgaggc
taagcggctgcgagcgctgcacatgaaggagcacccggattataaatacc
ggccccggcggaaaaccaagacgctcatgaagaaggataagtacacgctg
cccggcgggctgctggcccccggcggcaatagcatggcgagcggggtcgg
ggtgggcgccggcctgggcgcgggcgtgaaccagcgcatggacagttacg
cgcacatgaacggctggagcaacggcagctacagcatgatgcaggaccag
ctgggctacccgcagcacccgggcctcaatgcgcacggcgcagcgcagat
gcagcccatgcaccgctacgacgtgagcgccctgcagtacaactccatga
ccagctcgcagacctacatgaacggctcgcccacctacagcatgtcctac
tcgcagcagggcacccctggcatggctcttggctccatgggttcggtggt
caagtccgaggccagctccagcccccctgtggttacctcttcctcccact
ccagggcgccctgccaggccggggacctccgggacatgatcagcatgtat
ctccccggcgccgaggtgccggaacccgccgcccccagcagacttcacat
gtcccagcactaccagagcggcccggtgcccggcacggccattaacggca
cactgcccctctcacacatgtga.
[0271] This annotated vector sequence shows an exemplary nucleic
acid sequence of: underlined=fluorescent marker; Capital letters=2A
peptides; bold=first reprogramming gene; italic=second
reprogramming gene.
[0272] An exemplary nucleic acid sequence for encoding
reprogramming factors OCT4 and OCT, wherein an exemplary marker is
vexGFP: SFG-GOK (f-vexGFP-P2A-OCT4-T2A-KLF4):
TABLE-US-00019 [SEQ ID NO: 19]
atggtgagcaagggcgaggagctgttcaccggggtggtgcccatcctggt
cgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagg
gcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcacc
accggcaagctgcccgtgccctggcccaccctcgtgaccaccttcagcta
cggcgtgcagtgcttcagccgctaccccgaccacatgaagcagcacgact
tcttcaagtccgccatgcccgaaggctacgtccaggagcgcaccatcagc
ttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgaggg
cgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggagg
acggcaacatcctggggcacaagctggagtacaactacaacagccacaac
gtctatatcacggccgacaagcagaagaacggcatcaaggcgaacttcaa
gatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactacc
agcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccac
tacctgttcatccagtccgccctgagcaaagaccccaacgagaagcgcga
tcacatggtcctgctggagttcgtgaccgccgccgggatcactcacggca
tggacgagctgtacaagGGATCTGGAGCAACAAACTTCTCACTACTCAAA
CAAGCAGGTGACGTGGAGGAGAATCCCGGCCCTatggcgggacacctggc
ttcggatttcgccttctcgccccctccaggtggtggaggtgatgggccag
gggggccggagccgggctgggttgatcctcggacctggctaagcttccaa
ggccctcctggagggccaggaatcgggccgggggttgggccaggctctga
ggtgtgggggattcccccatgccccccgccgtatgagttctgtgggggga
tggcgtactgtgggccccaggttggagtggggctagtgccccaaggcggc
ttggagacctctcagcctgagggTgaagcaggagtcggggtggagagcaa
ctccgatggggctccccggagccctgcaccgtcacccctggtgccgtgaa
gctggagaaggagaagctggagcaaaacccggaggagtcccaggacatca
aagctctgcagaaagaactcgagcaatttgccaagctcctgaagcagaag
aggatcaccctgggatatacacaggccgatgtggggctcaccctgggggt
tctatttgggaaggtattcagccaaacgaccatctgccgctttgaggctc
tgcagcttagcttcaagaacatgtgtaagctgcggcccttgctgcagaag
tgggtggaggaagctgacaacaatgaaaatcttcaggagatatgcaaagc
agaaaccctcgtgcaggcccgaaagagaaagcgaaccagtatcgagaacc
gagtgagaggcaacctggagaatttgttcctgcagtgcccgaaacccaca
ctgcagcagatcagccacatcgcccagcagcttgggctcgagaaggatgt
ggtccgagtgtggttctgtaaccggcgccagaagggcaagcgatcaagca
gcgactatgcacaacgagaggattttgaggctgctgggtctcctttctca
gggggaccagtgtcctttcctctggccccagggccccattttggtacccc
aggctatgggagccctcacttcactgcactgtactcctcggtccctttcc
ctgagggggaagcctttccccctgtctctgtcaccactctgggctctccc
atgcattcaaacGGATCTGGAGAGGGCAGAGGAAGTCTTCTAACATGCGG
TGACGTGGAGGAGAATCCCGGCCCCatggctgtcagcgacgcgctgctcc
catctttctccacgttcgcgtctggcccggcgggaagggagaagacactg
cgtcaagcaggtgccccgaataaccgctggcgggaggagctctcccacat
gaagcgacttcccccagtgcttcccggccgcccctatgacctggcggcgg
cgaccgtggccacagacctggagagcggcggagccggtgcggcttgcggc
ggtagcaacctggcgcccctacctcggagagagaccgaggagttcaacga
tctcctggacctggactttattctctccaattcgctgacccatcctccgg
agtcagtggccgccaccgtgtcctcgtcagcgtcagcctcctcttcgtcg
tcgccgtcgagcagcggccctgccagcgcgccctccacctgcagcttcac
ctatccgatccgggccgggaacgacccgggcgtggcgccgggcggcacgg
gcggaggcctcctctatggcagggagtccgctccccctccgacggctccc
ttcaacctggcggacatcaacgacgtgagcccctcgggcggcttcgtggc
cgagctcctgcggccagaattggacccggtgtacattccgccgcagcagc
cgcagccgccaggtggcgggctgatgggcaagttcgtgctgaaggcgtcg
ctgagcgcccctggcagcgagtacggcagcccgtcggtcatcagcgtcag
caaaggcagccctgacggcagccacccggtggtggtggcgccctacaacg
gcgggccgccgcgcacgtgccccaagatcaagcaggaggcggtctcttcg
tgcacccacttgggcgctggaccccctctcagcaatggccaccggccggc
tgcacacgacttccccctggggcggcagctccccagcaggactaccccga
ccctgggtcttgaggaagtgctgagcagcagggactgtcaccctgccctg
ccgcttcctcccggcttccatccccacccggggcccaattacccatcctt
cctgcccgatcagatgcagccgcaagtcccgccgctccattaccaagagc
tcatgccacccggttcctgcatgccagaggagcccaagccaaagagggga
agacgatcgtggccccggaaaaggaccgccacccacacttgtgattacgc
gggctgcggcaaaacctacacaaagagttcccatctcaaggcacacctgc
gaacccacacaggtgagaaaccttaccactgtgactgggacggctgtgga
tggaaattcgcccgctcagatgaactgaccaggcactaccgtaaacacac
ggggcaccgcccgttccagtgccaaaaatgcgaccgagcattttccaggt
cggaccacctcgccttacacatgaagaggcatttttaa.
This annotated vector sequence shows an exemplary nucleic acid
sequence of: underlined=fluorescent marker; Capital letters=2A
peptides; bold=first reprogramming gene; italic=second
reprogramming gene.
[0273] Transduced cells were seeded on MEF feeder cells and
cultured in T-cell medium (RPMI-1640 supplemented with 10% FBS, 2
mM 1-glutamine, 100 U/ml penicillin and 100 ng/ml streptomycin).
The medium was changed to human ESC medium (DMEM/F12 with 20% of
knockout serum replacement, 1 mM 1-glutamine, 1% nonessential amino
acids, 10 mM 2-mercaptoethanol and 8 ng/ml basic fibroblast growth
factor (bFGF)) on day 5 after transduction and was then refreshed
daily. T-iPSC colonies appeared at .about.22-25 days after
transduction. Clone T-iPSC-1.10 was stably transduced with a
lentiviral vector encoding 19-28z, a second-generation CAR, and a
fluorescent marker (mCherry) linked by a 2A peptide (FIG. 6A). The
1928z-T-iPSC line was established after sorting for high expression
of the mCherry marker. All T-iPSC lines were maintained in culture
on MEF feeder cells with human ESC medium and passaged every 3 to 4
days. T-iPSC lines were tested for mycoplasma contamination every 2
months.
3.2. Characterization and Assessment of Pluripotency of
T-iPSCs.
[0274] To determine the reprogramming vectors' copy numbers (VCN),
isolated genomic DNA was isolated from the T-iPSC lines and
multiplex quantitative PCR (qPCR) using sets of primers and probes
specific for the SFG vector and for the human albumin gene (Table
1) was performed. To determine absolute VCN, a standard curve was
generated using serial dilutions of a plasmid containing both SFG
vector and albumin gene amplicons. Reactions were carried out in
triplicate in an ABI 7500 detection system (Applied
Biosystems).
TABLE-US-00020 TABLE 1 List of Oligonucleotides used for vector
copy number qPCR SFG forward 5'-AGAACCTAGAACCTCGCTGGA-3' (SEQ ID
NO: 20) SFG reverse 5'-CTGCGATGCCGTTCTACTTTG-3' (SEQ ID NO: 21)
hALB forward 5'-TGAAACATACGTTCCCAAAGAGTTT-3' (SEQ ID NO: 22) hALB
reverse 5'-CTCTCCTTCTCAGAAAGTGTGCATAT-3' (SEQ ID NO: 23) SFG probe
5' FAM-AGGACCTTACACAGTCCTGCTGAC-3' (SEQ ID NO: 24) hALB probe 5'
VIC-TGCTGAAACATTCACCTTCCATGCAGA- TAMRA-3' (SEQ ID NO: 25)
For assessment of expression of endogenous pluripotency genes,
total mRNA from T-iPSC was isolated with Trizol (Invitrogen).
Reverse transcription was performed with Superscript III
(Invitrogen) and qRT-PCR was performed with previously described
primers using SYBR Green (38). Reactions were carried out in
duplicate in an ABI PRISM 7500 Sequence Detection System (Applied
Biosystems). Expression was calculated by relative quantification
using the DDCt method with GAPDH as endogenous control.
[0275] For flow cytometric analysis, T-iPSCs were stained with the
following fluorophore-conjugated antibodies: SSEA-3-AlexaFluor647
(MC-631) purchased from Biolegend, SSEA-4-AlexaFluor647 (MC813-70),
Tra-1-81-AlexaFluor647 (TRA-1-81), Tra-1-60-AlexaFluor647
(TRA-1-60) and HLA-ABC-PE (Cat #555553) purchased from BD
Biosciences. All flow cytometry analysis was done on a LSRII
cytometer (BD Biosciences) and analyzed using FlowJo software, Ver.
9.5.2 (TreeStar).
[0276] For teratoma formation assays, undifferentiated T-iPSCs were
suspended in human ESC medium containing 10 mM of the
Rho-associated kinase (Rock) inhibitor Y-27632 (Tocris).
Approximately 2.times.10.sup.6 cells were injected subcutaneously
into 6- to 12-week-old female NOD-SCID IL2R.gamma.c.sup.null mice
obtained from the MSKCC Mouse Genetics Core facility. Five to six
weeks later, teratomas were surgically dissected and fixed in 4%
formaldehyde. Paraffin-embedded samples were stained with
hematoxylin and eosin for histological analysis.
[0277] For karyotyping, standard G-banding analysis was done at the
MSKCC molecular cytogenetics core facility. Chromosome analysis was
done on a minimum of 12 4,6-diamidino-2-phenylindole (DAPI)-banded
metaphases.
[0278] For the assessment of silencing of the reprogramming
vectors, qRT-PCR was done using primers and probes that detect
GFP-derivative (vexGFP and mCitrine) transcripts as previously
described (38). Reactions were carried out in duplicate in an ABI
PRISM 7500 Sequence Detection System (Applied Biosystems).
Expression was calculated by relative quantification using the DDCt
method with GAPDH as endogenous control.
3.3 TCR .beta. and .gamma. Chain Rearrangement
[0279] Genomic DNA was isolated from T-iPSCs and 1928z-T-iPSC-T
cells using Qiagen DNeasy Blood and Tissue kit (Qiagen). PCR was
performed using multiplex primer kits (Invivoscribe Technologies,
San Diego, Calif.) specific for a majority of clonal TCR .beta. and
.gamma. chain rearrangements. Capillary electrophoresis and PCR
product fragment analysis was performed at MSKCC Genomic's Core
Facility using an ABI 3730 DNA analyzer. Data were analyzed using
Peak Scanner software (ABI, Foster City, Calif.).
3.4 T-Cell Differentiation from 1928z-T-iPSCs and Expansion of
1928z-T-iPSC-T Cells
[0280] For the differentiation of 1928z-T-iPSCs to hematopoietic
precursors, an optimized serum- and feeder-free in vitro
differentiation protocol was used. Briefly, undifferentiated T-iPSC
colonies were treated with dispase (Worthington) for 6 min and
transferred to low-attachment plates to allow for the formation of
embryoid bodies (EBs) in embryoid body differentiation medium
(StemPro-34, Invitrogen, with 2 mM 1-glutamine, 1% nonessential
amino acids, 10 mM 2-mercaptoethanol, 100 U/ml penicillin and 100
ng/ml streptomycin and 50 mg/ml ascorbic acid). The formation of
embryoid bodies was facilitated by an overnight incubation in the
presence of 30 ng/ml of hBMP-4. embryoid bodies were then cultured
with BMP-4 and hbFGF (5 ng/ml) until day 4 to allow for mesoderm
induction. Next, hematopoietic specification and expansion was
achieved in the presence of hVEGF (20 ng/ml) and a cocktail of
hematopoietic cytokines (hSCF 100 ng/ml, hFlt3L 20 ng/ml, hIL-3 20
ng/ml and bFGF 5 ng/ml) as indicated. Day 10 embryoid bodies
containing hematopoietic progenitor cells were dissociated by
treatment with Accutase for 20 min and single cells were then
seeded on OP9-DL1 monolayers to allow for their T-lymphoid
differentiation in OP9 medium (a-MEM with 20% FBS, 2 mM
1-glutamine, 1% nonessential amino acids, 10 mM 2-mercaptoethanol,
100 U/ml penicillin and 100 ng/ml streptomycin and 50 mg/ml
ascorbic acid) supplemented with SCF 10 ng/ml, IL-7 5 ng/ml and
Flt3L 10 ng/ml (39). For the stimulation and expansion of
1928z-T-iPSC-T cells, we used previously described CD19-expressing
3T3 cells as artificial antigen presenting cells (3T3-CD19) (9,
40). The generated 1928z-T-iPSC-T cells were seeded on a monolayer
of irradiated 3T3-CD19 in a 3:1 E/T ratio in T-cell medium with
IL-7 (10 ng/ml) and IL-15 (10 ng/ml). All recombinant factors were
purchased from R&D Systems (Minneapolis).
3.5 Flow Cytometric Analysis
[0281] The following conjugated antibodies were used for flow
cytometric phenotyping and analysis: CD34-PECy.7 (8G12), CD43-FITC
(1G10), CD7-V450 (MT701), CD8.beta.-PE (2ST8.5H7), CD69-PECy.7
(FN50), CD161-FITC (DX12), CD16-PerCPCy5.5 (3G8),
TCR.gamma..delta.-FITC (11F2), CD122-FITC (TU27), CD94-PE (HP-3D9)
purchased from BD Biosciences, CD3-PE/FITC/Pacific Blue (UCTH1),
CD5-PE (5D7), CD4-PECy.7 (S3.5), CD8.alpha.-PE/FITC (3B5), CD25-APC
(3G10), CD62L-PE (Dreg-56), CD27-APC (0323), CD28-PE (10F3),
goat-anti-mouse-AlexaFluor647 purchased from Invitrogen,
TCR.alpha..beta.-APC (IP26), CD56-PECy.7 (CMSSB) and
CD45RA-PerCPCy5.5 (HI100) purchased from eBioscience, NKp44-PE
(P44-8), NKp46-PE (9E2), NKG2DAPC (1D11), CD158a/h-PE (HP-MA4),
CD158b-PE (OX27) purchased from BioLegend, PLZF-APC (20102) and
CCR7-FITC (150503) purchased from R&D. All antibodies were used
in a 1:20 dilution. Dead cells were excluded from analysis in all
experiments by staining with DAPI. All flow cytometry analysis was
done on a LSRII cytometer (BD Biosciences) and analyzed on FlowJo
software, Ver. 9.5.2 (TreeStar).
3.6. Cytokine Release and Cytotoxicity Assays
[0282] To measure cytokine production 6.times.10.sup.4
1928z-T-iPSC-T cells were seeded on irradiated CD19.sup.- or
3T3-CD19 cells in a 3:1 ratio (E/T ratio) per well of a 96-well
plate in T-cell medium with IL-7 (10 ng/ml) and IL-15 (10 ng/ml).
Culture supernatants were collected after 24 h and the
concentration of type I and/or type II cytokines was quantified
with a Luminex assay kit (Invitrogen) according to manufacturer
instructions. Cytotoxic potential of 1928z-Ti-T cells was evaluated
in standard .sup.51Cr release assays. Target cells were labeled
with .sup.51Cr and co-cultured with 1928z-T-iPSC-T cells at
decreasing effector/target (E/T) ratios. After 4 h of culture,
supernatant was removed and radioactivity released from chromium
was measured. Specific lysis was determined by subtracting
background radioactivity of target cells not cultured with T cells
and dividing by the radioactivity measured from target cells
completely lysed by treatment with 0.2% Triton X-100. The murine
lymphoma cell line EL4, engineered to express ovalbumin (EL4-OVA)
or human CD19 (EL4-CD19), was used as target (41).
3.7 Microarray Procedure and Gene Expression Analysis
[0283] Whole PBLs were isolated from two healthy donors by Ficoll
density centrifugation after informed consent was obtained. The
following subpopulations: CD3.sup.+CD4.sup.+, CD3.sup.+CD8.sup.+,
CD3.sup.+CD56.sup.+, CD3.sup.- CD56.sup.+ (NK) and
CD3.sup.+TCR.gamma..delta..sup.+ (.gamma..delta. T cells) were
purified (98%) from PBL by cell sorting. Total mRNA was extracted
from 1928z-T-iPSC-T cells at days 30-35 of differentiation and from
the sorted PBL subpopulations using TRIzol.TM. Reagent (Invitrogen
Life Technologies, Paisley, UK). Microarray analyses were performed
at the MSKCC Genomics Core facility using 75 ng of total RNA as the
starting material, amplified and labeled following the standard
Affymetrix protocol (Affymetrix, Santa Clara, Calif., USA). The
labeled complementary RNA was then fragmented and hybridized to
Affymetrix GeneChip arrays HG-U133 plus 2.0.
[0284] For the gene expression analysis the raw data (Affymetrix
CEL files) produced using HG U133-Plus 2.0 platform were used. For
comparison purposes, additional raw data files obtained on the same
platform were downloaded from the NCBI repository GEO database:
five samples of normal naive B cells (GSE12195), five samples of
.alpha..beta. CD4.sup.+ cells (GSE15659), one sample of resting
.alpha..beta. CD8.sup.+ cells (GSE8059), one sample of resting NK
cells (GSE8059), 12 samples of TCRV.gamma.9.gamma..delta. T cells
(GSE27291), before activation and after activation with BrHPP/IL-2
(bromohydrin pyrophosphate and IL-2) for 6 h or 7 d. Robust
Multi-array Average (RMA) procedure was applied to all CEL files
and comparisons of different samples were performed upon z-scores
normalization. Gene-centric expression values were obtained using a
CDF file based on remapping of probes to the human genome. Gene
expression levels were compared both between single samples and by
grouping samples of the same type in an unbiased way. Similarity
between samples was evaluated by Pearson's correlation coefficient
computed between a selected list of probes: 1,163 probes were
selected based on their variability across samples (s.d.>0.75)
and consistency among 1928z-T-iPSC-T cells (s.d.<1).
Correlations between groups were computed after averaging probe
expression levels of single samples of the same type. Using the
computed set of correlations, hierarchical clustering of the single
samples was performed. The clustering was performed using the R
package hclust with the default settings (Euclidean distance).
Second, a comparison between the analyzed samples on a selected
panel of genes was performed.
3.8 Quantitative Real-Time PCR
[0285] Total mRNA was extracted using TRIzol.TM. Reagent
(Invitrogen Life Technologies, Paisley, UK). Reverse transcription
was done using the Superscript III First-Strand Synthesis supermix
for qRT-PCR (Invitrogen). Quantitative-PCR for specific genes were
done using the respective probe-based TaqMan Gene Expression assays
(Applied Biosystems). Reactions were carried out in duplicate in an
ABI PRISM 7500 Sequence Detection System (Applied Biosystems).
Expression was calculated by relative quantification using the DDCt
method with GAPDH as endogenous control.
3.9 Isolation and Retroviral Transduction of .gamma..delta. and
.alpha..beta.-T Cells
[0286] PBL were isolated from the same donor as the T-iPSC.
TCR.gamma..delta. T cells were isolated with magnetic cell sorting
(negative selection) using the TCR.gamma..delta..sup.+ T-cell
Isolation Kit (Miltenyi Biotec) according the manufacturer's
instructions. Next, TCR.gamma..delta. T cells were stimulated with
5 mM zoledronic acid (Zometa, Novartis) and 1,000 IU/ml IL-2 for 48
h. The TCR.alpha..beta. fraction of PBLs (obtained as the positive
fraction after negative selection of TCR.gamma..delta. T cells) was
activated with PHA 2 mg/ml for 48 h. Synthesis of the
1928z-CAR-encoding 1928z-IRES-LNGFR vector has been described (41).
Retroviral producers were prepared from plasmid-transfected H29
cell supernatants as previously described (41). Activated
.gamma..delta. and .alpha..beta. T cells were transduced with
retroviral supernatants on two consecutive days by spin-infection
in retronectin (Takara)-coated oncoretroviral vector-bound plates.
Cells were fed every 3 d with T-cell medium supplemented with 1,000
IU/ml or 20 IU/ml of IL-2 for .gamma..delta. and .alpha..beta. T
cells, respectively.
3.10 In Vivo Tumor Model
[0287] 6- to 12-week-old male NOD-SCID IL2R.gamma.c.sup.null mice,
obtained from the MSKCC Mouse Genetics Core facility, were
inoculated i.p. with 10.sup.5 Raji human CD19+ Burkitt lymphoma
cells expressing a green fluorescent protein-firefly luciferase
fusion protein (GFP/Luc) as previously described (9, 40). Four days
later 4.times.10.sup.5 expanded (1-week stimulation on irradiated
3T3-CD19) 1928z-T-iPSC-T cells or CAR-transduced syngeneic or
.gamma..delta. T cells were injected i.p. along with IL-2 (50,000
U/mouse) and IL-15 (0.25 mg/mouse). Only mice that had equal tumor
burden (2.times.10.sup.6.+-.0.5.times.10.sup.6 photons/sec) before
T-cell injection were used. Mice with lesser or greater tumor
burden were excluded from the study. Tumor-bearing mice retained in
the study were randomized to the different treatment groups (at
least four mice per group). No blinding method was used. T-cell
dose was based on the percentage of CAR.sup.+ cells as measured by
pre-injection flow cytometric analysis. IL-2 administration was
continued daily and IL-15 every 2 d for 2 weeks. Tumor burden was
monitored twice per week by in vivo bioluminescence imaging (IVIS
100 Imaging System). Living Image software Version 4.3.1 was used
to acquire and quantify the bioluminescence imaging data sets. All
animal experiments were conducted in accordance with protocols
approved by MSKCC Institutional Animal Care and Use Committee
(IACUC) and following National Institutes of Health guidelines for
animal welfare.
3.11 Statistical Methods
[0288] No pre-specified effect size was used to determine sample
sizes. The use of statistical tests was chosen according to the
nature of the data. The Wilcoxon rank-sum test (Mann-Whitney U
test) was used to compare the tumor burden across multiple groups.
This test was chosen because of its robustness to the underlying
distribution of the observations. Comparison of survival curves was
done using the log-rank test. Partial likelihood ratio test from a
Cox regression model was also used to compare the survival between
1928z-T-iPSCT and no treatment groups after ensuring that the data
were consistent with the proportional hazards assumption (P=0.15
using the weighted-residuals test) (42). As it was unable to fit a
Cox model for the remaining treatment groups due to the paucity of
events, the reported P-values are those provided by the log-rank
test. Statistical significance was defined as P<0.05.
Statistical analyses were done on Prism software (GraphPad) (tumor
burden comparison and log-rank) or R (microarray analysis and Cox
proportional hazards regression).
4. Results
[0289] iPSC clones (T-iPSCs) was generated by transducing
peripheral blood T lymphocytes (PBL) from a healthy volunteer with
two retroviral vectors each encoding two of the reprogramming
factors KLF4, SOX2, OCT-4 and C-MYC (FIG. 4A) (7). Multiple
randomly selected T-iPSC clones were analyzed, and their
pluripotency (FIGS. 4B to 4G) and T-cell origin (FIGS. 5A and 5B)
were confirmed. Clone T-iPSC-1.10 was stably transduced with a
bicistronic lentiviral vector encoding 19-28z (1928z-T-iPSC), a
second-generation CAR specific for CD19, and the fluorescent marker
mCherry (FIGS. 6A to 6C) (14). To direct the differentiation of
1928z-T-iPSC to the T-lymphoid lineage, a serum- and feeder-free in
vitro differentiation protocol for the generation of hematopoietic
precursors through embryoid body formation was first optimized
(FIG. 1B).
[0290] Similar to previous reports (3, 4, 15), it was found that
CD34+ cells from day 10 embryoid bodies expressed the highest
levels of key transcription factors for lymphoid differentiation
(FIG. 7A), specifically showing increased expression of Notch 1 and
CD127 (IL7R.alpha.) in the CD34.sup.+CD43.sup.- subset compared to
CD34.sup.-CD43.sup.- cells (FIG. 7B). Day 10 embryoid bodies were
dissociated and the hematopoietic precursors were transferred onto
Delta-like 1-expressing OP9(OP9-DL1) feeder cells to induce
T-lymphoid differentiation in an established co-culture system in
the presence of the cytokines stem cell factor (SCF), Flt3L and
interleukin (IL)-7 (FIG. 1B). mCherry expression was ascertained
throughout the differentiation process and no substantial silencing
of mCherry expression was detected (FIG. 1B). As early as day 25 of
differentiation, CD7.sup.+CD3.sup.+ TCR.alpha..beta.+ cells were
detected (Table 2). As shown in Table 2, the expression of each
surface marker on cells gated as indicated was measured by flow
cytometry at day 25 and 30 of differentiation and 7 days after
expansion on 3T3-CD19 cells (expanded). These cells harbored the
same TCR .beta. and .gamma. chain rearrangements as the parental
T-iPSC-1.10 line (FIG. 5C). By day 30, CD3+TCR.alpha..beta..sup.+
cells typically accounted for .about.80% of the cultures (FIG. 1c
and Supplementary Table 1), and all of them expressed the
CD19-specific CAR on their surface; day 30 cells are referred to
hereafter as 1928z-T-iPSC-T cells (FIG. 1C). A substantial fraction
expressed CD8.alpha. (10.4.+-.3.5%) and CD56 (20.7.+-.9.5%),
whereas very few cells expressed low amounts of CD4 and almost no
cells expressed detectable CD8.beta. (FIG. 1C and Table 2). Further
surface phenotyping showed most cells to be CD5.sup.low and
negative for CD122 and TCR.gamma..delta. (FIG. 1C, FIGS. 8A and 8B
and Table 2).
TABLE-US-00021 TABLE 2 Summary of Flow Cytometric Data Analysis
Surface Marker day 25 day 30 expanded CD7+ 53 .+-. 16.7 6 64.2 .+-.
10.5 5 na na CD7+ CD5 32.6 .+-. 2.9 3 39.6 .+-. 8.7 na na CD56 8
.+-. 2.8 2 na na na CD3+TCR+ 54.4 .+-. 16.4 6 78 .+-. 1.7 4 88.4
.+-. 6.1 3 CD3+ CD56 16.7 .+-. 6.3 6 20.7 .+-. 9.5 3 89.6 .+-. 7.5
2 CD8.alpha. 14.3 .+-. 3.6 5 10.4 .+-. 3.5 2 48.7 .+-. 11.5 3 CD4
3.5 .+-. 0.7 3 2.6 .+-. 0.5 3 11.1 .+-. 1.9 3 CD5 33.7 .+-. 3.1 2
41.5 .+-. 10.3 4 na na CD161 39.6 .+-. 12.3 3 na na 15.7 .+-. 6.08
2 CD122 0 2 na na 2.5 1 CD16 23.3 .+-. 6.8 2 na na 24.5 1 CD94 13.2
.+-. 2.1 2 na na 14.3 1
[0291] Taking advantage of the CD19-specific CAR, the functional
response of 1928z-T-iPSC-T cells to cell-bound CD19 was evaluated.
1928z-T-iPSC-T cells harvested on days 30-35 of differentiation
were cultured on NIH-3T3-based artificial antigen-presenting cells
(AAPCs) expressing the CD19 antigen (3T3-CD19) where indicated (9).
The 1928z-T-iPSC-T cells rapidly bound to 3T3-CD19 cells, forming
clusters and eliminating the 3T3-CD19 monolayer (FIG. 1D). No such
adhesion was observed when 1928z-T-iPSC-T cells were placed on
CD19-negative 3T3 cells (FIG. 1D). Exposure to 3T3-CD19 cells also
prompted 1928z-T-iPSC-T-cell surface expression of T-cell
activation markers CD25 and CD69 (FIG. 1E) and secretion of type 1
cytokines such as IL-2, tumor-necrosis factor (TNF)-.alpha. and
interferon (IFN)-.gamma. (FIG. 1F). These results show that
1928z-T-iPSC-T cells displayed canonical features of T-lymphocyte
function and specificity for the CD19 antigen.
[0292] To better elucidate the phenotype of 1928z-T-iPSC-T cells, a
gene expression microarray was carried out, and the mRNA expression
profile of days 30-35 1928z-T-iPSC-T cells was compared to that of
naive B cells, CD4 T cells, CD8 T cells, CD3.sup.+CD56.sup.+ T
cells and natural killer (NK) cells isolated from peripheral blood.
The profile was also compared to freshly isolated or in
vitro-activated peripheral blood .gamma..delta. T cells.
Hierarchical clustering using the set of genes with most variable
mRNA expression (s.d.>0.75) showed that 1928z-T-iPSC-T cells
were distinct from B cells and more closely related to the other
T-lymphoid subsets and NK cells (FIG. 2A). Next, 1928z-T-iPSC-T
cells were compared to particular lymphoid cell subsets by
correlating mRNA expression levels of the most variable genes in
the data set. This pairwise correlation analysis indicated that
1928z-T-iPSC-T cells were more similar to fresh or activated (for 7
d) .gamma..delta. T cells (FIG. 9A). This correlation was further
confirmed upon examining expression of key lymphoid differentiation
genes. The 1928z-T-iPSC-T cells expressed genes characteristic of
the T-lymphoid lineage (e.g., GATA3, CD3.delta., CD3.epsilon.,
LEF1, LCK and BCL11B) at levels comparable to those of peripheral
blood .gamma..delta. T cells; however, the 1928z-T-iPSC-T cells did
not express many genes characteristic of the NK cell lineage (e.g.,
CD94, CD16 and killer-cell immunoglobulin-like receptors) (FIGS.
2B, 8 and 9B). Moreover, pronounced expression of FASLG, TYROBP,
CCL20, TNFSF11 (RANKL), CXCR6 and RORC, genes that are highly
expressed in .gamma..delta. T cells versus .alpha..beta. T cells
and/or NK cells, was detected in 1928z-T-iPSC-T cells (FIGS. 2B and
9B) (16). The innate immune cell property of 1928z-T-iPSC-T cells
was further supported by their expression of the transcription
factor PLZF and the surface marker CD161 (FIG. 2C). Interestingly,
1928z-T-iPSC-T cells also showed high cytotoxic potential as
indicated by high expression of TNFSF10 (TRAIL), GNLY, GZMB, FASL,
LTA and low expression of co-inhibitory or exhaustion markers PD1,
CTLA-4 and LAG3 (FIG. 2B). The majority of the CD3.sup.+ cells had
a CD45RA.sup.+CD62L.sup.-CCR7.sup.- effector memory phenotype
(TEMRA), although a small percentage (.about.6%) had a more naive
CD45RA.sup.+CD62L.sup.+ phenotype (FIG. 2D). No expression of CD27
or CD28 receptors was detected on the surface of 1928z-T-iPSC-T
cells (FIG. 8C).
[0293] iPSC-derived T cells will be therapeutically relevant only
if they can be expanded while retaining functional properties.
Therefore, 1928z-T-iPSC-T cells were expanded using 3T3-CD19 cells
and the expanded T cells were characterized. Starting from
3.times.10.sup.6 1928z-T-iPSC, .about.1-2.times.10.sup.5
1928z-T-iPSC-T cells were obtained by day 30 of differentiation.
Those 1928z-T-iPSC-T cells were expanded 10- to 50-fold (mean=20,
s.d.=15, n=6) after one stimulation and up to 1,000-fold after
three weekly stimulations (FIG. 2E). Therefore, although the
differentiation efficiency at day 30 is around 0.05, it was
increased to 0.5-1.0 by 1 week and up to 50.0 after 3 weeks of
expansion. The expanded cells maintained their effector memory
phenotype and upregulated the expression of natural cytotoxicity
receptors such as NKp44, NKp46 and NKG2D (FIG. 2E). Interestingly,
the expanded cells upregulated expression of T-lymphoid
lineage-specific genes (ZAP70, GATA3, CD3.delta., CD3.epsilon.,
TRGC2) and downregulated expression of RORC, indicative of a switch
toward a type 1 (Tbet/IFN-.gamma. expressing) phenotype (FIGS. 2F
and 2G). CD161 surface expression was also reduced after expansion
(FIGS. 2D and 2E). In aggregate these findings suggest that
CAR-mediated proliferation polarized the 1928z-T-iPSC-T cells
toward a type 1 response. A similar phenotype switch has been shown
for RORC-expressing T17 .gamma..delta. T cells, IL-17-producing
fetal innate lymphoid cells and murine TCR-transgenic Th17 cells,
which polarize to type 1 cells after antigen or cytokine
stimulation (17-19).
[0294] The cytotoxic potential of expanded 1928z-T-iPSCT cells was
first evaluated using an in vitro .sup.51Cr release assay with EL4
murine lymphoma cells expressing CD19 or ovalbumin (nonspecific
negative control) as targets (9). Expanded 1928z-T-iPSC-T cells
displayed high antigen-specific cytotoxic activity, even at low
effector-to-target (E/T) ratios (FIG. 3A). To investigate the
anti-tumor activity of 1928z-T-iPSC-T cells in vivo, a xenogeneic
tumor model was established. Nonobese diabetic-severe combined
immunodeficient NOD-SCID IL2R.gamma.c.sup.null mice were inoculated
with the CD19.sup.+ Raji human Burkitt lymphoma cell line
expressing a fluorescent luciferase fusion protein. For comparison
to 1928z-T-iPSC-T cells, TCR-.alpha..beta. and TCR-.alpha..delta.
peripheral blood lymphocytes from the same donor as the T-iPSC line
expressing the 1928z CD19 CAR were transduced.
[0295] These three T-cell populations showed some phenotypic
similarities and some differences. When 1928z-T-iPSC-T cells were
expanded for a week, they displayed a TEMRA phenotype
(CD45RA.sup.+CD27.sup.-CD28.sup.-CCR7.sup.-), similar to the
expanded 1928z-.alpha..delta. T cells. In contrast, a sizeable
fraction (33%) of 1928z-.alpha..beta. T cells displayed a
CD45RACD27.sup.+CD28.sup.+CCR7.sup.+ phenotype indicative of
central memory cells (FIG. 3B). CAR expression was much lower on
1928z-T-iPSC-T cells (mean fluorescence intensity (MFI)=395) than
on 1928z-.gamma..delta. (MFI=1,212) or 1928z-.alpha..beta. cells
(MFI=2,010) (FIG. 3B), which may influence therapeutic activity
(20).
[0296] As shown by bioluminescent imaging, infusion of
1928z-T-iPSC-T cells delayed tumor progression to an extent similar
to that induced by peripheral blood 1928z-.alpha..delta. cells
(FIGS. 3C and 10), and resulted in a significant survival advantage
compared to tumor-bearing mice that were not treated with T cells
(log-rank P=0.042, Cox proportional hazards regression P=0.036;
FIG. 3D and 3E). Bioluminescence imaging further revealed that
1928z-T-iPSC-T and 1928z-.gamma..delta. T cells initiated tumor
regression more rapidly than 1928z-.alpha..beta. cells (FIG. 3C).
However, although initially slower at inducing tumor regression,
the 1928z-.alpha..beta. T cells did eventually induce complete
tumor regression (FIG. 3C). These findings demonstrate that
CAR+T-iPSC-T cells can lyse tumor cells in vitro, elicit strong
anti-tumor responses in vivo and provide a survival benefit in
tumor-bearing animals, to the same degree as their closest natural
counterparts.
5. Discussion
[0297] The iPSC and CAR technologies, combined as shown here,
potentially provide an unlimited source of T lymphocytes targeted
to a chosen antigen, independent of HLA restriction. Under the
present conditions, starting from T-iPSCs encoding a rearranged
endogenous .alpha..beta. TCR, it was determined that the generated
T cells have the properties of .gamma..delta. T cells, although
they express their endogenous .alpha..beta. TCR on their surface
(17, 21). A similar lineage diversion has been observed in mice
expressing TCR.alpha. and .beta. transgenes, wherein T cells
distinct from wild-type NK, NK T cells, or CD4.sup.+ or CD8.sup.+
.alpha. .beta. T cells displayed .alpha..delta. T-cell features,
including expression of CD8.alpha. and low expression of CD5, CD122
and NK1.1 (22-24). T cells differentiated in vitro from human
CD34.sup.+ hematopoietic progenitors genetically engineered to
express an antigen-specific TCR display an NK cell-like phenotype
(25). Together these observations suggest a possible effect of
premature expression of TCR.alpha..beta., which may skew
development toward innate lymphoid-like lineages. Although
T-iPSC-derived expanded T cells have been reported to have a
CD3.sup.+CD7.sup.+CD5.sup.lowTCR.alpha..beta..sup.+CD56.sup.+
phenotype associated with expression of CD8.alpha. but not
CD8.beta., they were not identified as .gamma..delta.-like T cells
(6). Interestingly, expression of the pre-rearranged endogenous
TCR.alpha..beta. was observed on day 15 of differentiation on
OP9-DL1 cells (Table 2), earlier than in some other reports
describing T-cell differentiation from human ESC- or iPSC-derived T
cells (3, 4). Importantly, the same kinetics of T-cell development
as in T-iPSC-1.10 were observed in two other independent T-iPSC
lines bearing different TCR rearrangements (FIGS. 5B and 11), but
not in cord blood-derived iPSC or in ESCs (data not shown).
Altogether, these observations suggest that early expression of a
transgenic or endogenous TCR.alpha..beta. influences the T-cell
differentiation process (22-25). In addition, some subtle features
of our 1928z-T-iPSC-T cells, such as their
CD8.alpha..sup.+CD8.beta..sup.- phenotype, expression of CD161 and
low expression of CD5, are shared between adult .gamma..delta. T
cells and innate-like T cells generated in fetal development (17,
18, 21, 26). Together with previous reports, these observations
suggest that these lymphoid cells may originate from a fetal
cell-like hematopoietic stem cell intermediate committed to
innate-like lymphopoiesis and that in vitro differentiation from
pluripotent stem cells may be intrinsically skewed toward embryonic
characteristics (4, 27, 28). Notably, the CAR, which effectively
supported T-cell expansion, did not seem to influence the
acquisition of the .gamma..delta. phenotype, as non-CAR-transduced
T-iPSC-1.10 cells also yielded TCR.alpha..beta.-expressing,
.gamma..delta.-like T cells (FIG. 12). A complete understanding of
the maturation of T-iPSC-derived T lymphocytes can further optimize
their development and differentiation, generate different T-cell
lineages and shape their functional attributes.
[0298] Tumor specificity is one of the essential characteristics of
T lymphocytes used in adoptive T-cell therapy. Using the protocol
described in this Example, any HLA-independent antigen specificity
can be imparted to any iPSC through an appropriate CAR, without
requiring the establishment of a patient-specific T-cell clone (8).
The inventors was not aware of any previously published study
reporting that genetic modification of human pluripotent stem cells
with a receptor for antigen is an effective approach to generate T
cells with therapeutic potential. 1928z-T-iPSC-T cells delayed
tumor progression in vivo to a similar extent as peripheral
blood-derived 1928z-.gamma..delta.-T cells from the same donor.
.gamma..delta. T cells have some advantageous properties, such as
low graft-versus-host reactivity and the ability to infiltrate
solid tumors (29, 30). Their anti-tumor activity has been
demonstrated in several clinical settings, mainly against
hematological malignancies (30).
[0299] CAR-modified T-iPSC-derived T cells may be especially
valuable in situations where autologous or allogeneic T cells are
not available. This is, for example, the case in immune-deficient
patients such as HIV-infected or highly immunosuppressed patients
with malignancies; in these scenarios autologous T-cell isolation
and expansion is problematic or impossible. CAR-T-iPSC-T cells may
also be useful in patients from whom the isolation of autologous
tumor-infiltrating T lymphocytes has failed, while providing the
additional benefit of targeting alternative antigens recognized by
CARs (8, 31). Other patients who could benefit from CAR-T-iPSC-T
cells include those with acute leukemia who relapse after
allogeneic hematopoietic cell transplantation and for whom the use
of allogeneic donor lymphocyte infusions (DLI) is problematic. The
efficacy of DLI in those patients is minimal, yet fraught with the
risk of graft-versus-host disease (32). CAR-T-iPSC-T cells could
thus represent an additional option for patients who do not respond
to DLI or for whom DLI use is not indicated due to high risk for
graft-versus-host disease.
[0300] Several steps can be taken to avert the risks of
immunological complications in the context of an off-the-shelf
allogeneic CAR-T-iPSC-T therapy. The alloreactivity of
T-iPSC-derived T cells, which express an endogenous TCR (FIG. 1A),
can be eliminated by either disrupting the TCR, using target
site-specific nucleases after T-cell differentiation, or by
generating T-iPSCs from virus-specific T cells, which due to their
recognition of a pathogen-derived antigen, are less likely to cause
graftversus-host disease (33, 34). Allorejection of CAR-iPSC-T
cells (which express HLA molecules) can be minimized by generating
iPSCs from common HLA haplotypes (to ensure their
histocompatibility with matched unrelated recipients) or by
repressing HLA expression through additional genetic modification
(35, 36). Finally, the risk of insertional oncogenesis secondary to
gene transfer can be decreased by integrating the CAR cDNA and
other genes, such as suicide genes and noninvasive imaging
reporters, at genomic safe harbor sites (37, 38).
[0301] In summary, the combination of iPSC and CAR technologies as
disclosed in the present invention offers a potential new source of
off-the-shelf T cells of predetermined antigen specificity.
Considering the versatility of pluripotent stem cells and CAR
engineering, this system may facilitate production of different
T-cell subpopulations with additional genetic modifications and
specificities suitable for a range of therapeutic indications.
Example 2
[0302] This example provides exemplary compositions and methods for
engineering and providing chimeric T cell receptors (CARs).
[0303] Chimeric antigen receptors (CARs) are provided that combine,
in a single chimeric species, the intracellular domain of CD3
.zeta.-chain, a signaling region from a costimulatory protein, such
as CD28, and a binding element that specifically interacts with a
selected target antigen. The engineered construct may further
comprise nucleic acid sequences encoding a fluorescent marker. Such
as mCherry, eGFP, etc.
[0304] For this example, a chimeric T cell receptor was provided
comprising nucleic acid sequences for encoding a nucleic acid
sequence encoding a protein for B-cell lineage cell surface
receptor CD19 antigen recognition, a CD28 costimulatory molecule,
and mCherry. Such sequences for CD19 and CD28 are provided in U.S.
Pat. No. 7,446,190, which is herein incorporated by reference in
its entirety including sequences, viral vectors and methods of
using viral vectors for transducing cells and testing function and
phenotypes of resulting cells.
[0305] Specifically, to construct a CD19 specific CAR, ScFv, the
heavy (VH) and light (VL) chain variable regions were cloned from
hybridoma cell line SJ25C1 derived cDNA by the polymerase chain
reaction (PCR) using degenerate primers described by Orlandi (43)
and fused these coding regions with a DNA fragment encoding for a
(Gly3 Ser) (4) spacer region. A costimulatory signaling element
from human CD28, including transmembrane and extracellular portions
(U.S. Pat. No. 7,446,190: SEQ ID NO: 6) was ligated to the 3' end
of the resulting ScFv and the cytoplasmic domain of the
human-.zeta. (U.S. Pat. No. 7,446,190: SEQ ID NO: 3) to the 3' end
of the CD28 portion to form fusion gene 19-28z (also termed
1928z).
[0306] The mCherry sequence was linked with a P2A peptide upstream
of the 1928z fusion gene and the construct was then ligated into
the AgeI/SalI restriction sites of a pLM lentiviral vector
(Papapetrou et al PNAS 2009) driven by a constitutive ubiquitin C
(UbC) promoter.
[0307] Lentiviral vector production was done by triple
co-transfection of 293T producer cells plated on poly-L-lysine
coated 100-mm tissue culture dishes. When the cells were .about.80%
confluent, the medium (DMEM with 10% FBS and 1 mM L-Glut) was
gently replaced with 7 ml of prewarmed medium and incubated for an
hour. A plasmid/CaCl2 mix was prepared by adding 10 .mu.g of the
lentiviral vector plasmid, 7.5 .mu.g of pCMV.DELTA.R8.91, 2.5 .mu.g
of pUCMDG, 50 .mu.l of 2.5 M CaCl2 and WFI to a total volume of 500
.mu.l. To transfect, 0.5 ml of plasmid/CaCl2 mix was transferred
into a 50-ml conical tube. While vortexing at low speed, 0.5 ml of
the 2.times. HBS buffer was added dropwise using a P1000 pipette.
Then 1 ml of the new mix was added to the 100-mm dish of 293T using
a P1000 pipette dropwise, scattering the drops uniformly to the
entire surface of the dish. 293T cells were incubate at 37.degree.
C., 5% CO2 for .about.16 h. After 16 h the medium was aspirated and
replaced gently with 10 ml prewarmed medium per plate. Cells were
incubate at 37.degree. C., 5% CO2 for .about.24 h. The following
day the vector-containing supernatant is collected and the dishes
discarded. The supernatant was centrifuged at 1,000 g at 4.degree.
C. for 5 min to pellet cell debris. Then the supernatant was
filtered through a 0.45-.mu.m filter, aliquoted and stored at
.about.80.degree. C.
Example 3
[0308] This example describes prophetic compositions and methods
for providing a "universal" CAR.sup.+ cell which is "edited" so
that it would not induce graft vs. host symptoms in an allogeneic
system or host.
[0309] Thus, in one embodiment, compositions and methods are
provided to knocking out HLA (class I) cell surface expression in a
cell before or after expression of a CAR. In further embodiments,
compositions and methods are provided to knocking out HLA (class
II) cell surface expression in a cell before or after expression of
a CAR.
[0310] In one embodiment, a TCR is silenced or knocked in. In one
embodiment, a costimulatory ligand is silenced or knocked out. in
one embodiment, a suicide gene is knocked-in. in one embodiment, a
sequence for an inducible cytokine is transduced into a CAR+ cells.
in one embodiment, a sequence for an imaging gene is transduced
into a CAR+ cells. In some embodiments, a heterologous gene is
placed inside of genomic safe harbor site of a cell's genome, In
some embodiments inside of a CAR.sup.+ cell's genome (Papapetrou,
et al., Nat Biotech (2011), herein incorporated by reference).
Targeting of this specific safe genomic harbor was achieved by
homologous recombination using a nuclease (e.g. TALEN). Further
manipulation of CAR-T-PSC includes silencing or knocking out Rag
genes in order to avoid re-rearrangement of TCRa chain during
redifferentiation and the risk of new TCR.alpha..beta. pairs to
appear. In this way the produced CAR-T-iPSC-derived T cells will
express a unique endogenous TCR therefore minimizing the risk of
alloreactivity. Throught these manipulations the present invention
aims to provide CAR-T-PSC-T cells with a universal application
potential for including allogeneic transplantation.
[0311] Therefore, the compositions and methods as described herein
were used to produce engineered antigen spedific cells capable of
antgen stimulation of effector functions. Further, these engineered
cells overcome a yield obstacle of other types of in vitro T-cell
differentiation of iPS cells into antigen-specific effector
cells.
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[0355] All publications and patents disclosed in the above
specification are herein incorporated by reference. Various
modifications and variations of the described method and system of
the invention will be apparent to those skilled in the art without
departing from the scope and spirit of the invention. Although the
present invention has been described in connection with some
specific preferred embodiments, it should be understood that the
invention as claimed should not be unduly limited to such specific
embodiments. Indeed, various modifications of the described modes
for carrying out the invention that are obvious to those skilled in
immunology, adoptive cell therapy, cellular biology, cancer cell
biology, biochemistry, chemistry, organic synthesis, imaging
diagnostics or related fields are intended to be within the scope
of the following claims.
Sequence CWU 1
1
271164PRTHomo sapiens 1Met Lys Trp Lys Ala Leu Phe Thr Ala Ala Ile
Leu Gln Ala Gln Leu1 5 10 15Pro Ile Thr Glu Ala Gln Ser Phe Gly Leu
Leu Asp Pro Lys Leu Cys 20 25 30Tyr Leu Leu Asp Gly Ile Leu Phe Ile
Tyr Gly Val Ile Leu Thr Ala 35 40 45Leu Phe Leu Arg Val Lys Phe Ser
Arg Ser Ala Asp Ala Pro Ala Tyr 50 55 60Gln Gln Gly Gln Asn Gln Leu
Tyr Asn Glu Leu Asn Leu Gly Arg Arg65 70 75 80Glu Glu Tyr Asp Val
Leu Asp Lys Arg Arg Gly Arg Asp Pro Glu Met 85 90 95Gly Gly Lys Pro
Gln Arg Arg Lys Asn Pro Gln Glu Gly Leu Tyr Asn 100 105 110Glu Leu
Gln Lys Asp Lys Met Ala Glu Ala Tyr Ser Glu Ile Gly Met 115 120
125Lys Gly Glu Arg Arg Arg Gly Lys Gly His Asp Gly Leu Tyr Gln Gly
130 135 140Leu Ser Thr Ala Thr Lys Asp Thr Tyr Asp Ala Leu His Met
Gln Ala145 150 155 160Leu Pro Pro Arg2235PRTHomo sapiens 2Met Ala
Leu Pro Val Thr Ala Leu Leu Leu Pro Leu Ala Leu Leu Leu1 5 10 15His
Ala Ala Arg Pro Ser Gln Phe Arg Val Ser Pro Leu Asp Arg Thr 20 25
30Trp Asn Leu Gly Glu Thr Val Glu Leu Lys Cys Gln Val Leu Leu Ser
35 40 45Asn Pro Thr Ser Gly Cys Ser Trp Leu Phe Gln Pro Arg Gly Ala
Ala 50 55 60Ala Ser Pro Thr Phe Leu Leu Tyr Leu Ser Gln Asn Lys Pro
Lys Ala65 70 75 80Ala Glu Gly Leu Asp Thr Gln Arg Phe Ser Gly Lys
Arg Leu Gly Asp 85 90 95Thr Phe Val Leu Thr Leu Ser Asp Phe Arg Arg
Glu Asn Glu Gly Tyr 100 105 110Tyr Phe Cys Ser Ala Leu Ser Asn Ser
Ile Met Tyr Phe Ser His Phe 115 120 125Val Pro Val Phe Leu Pro Ala
Lys Pro Thr Thr Thr Pro Ala Pro Arg 130 135 140Pro Pro Thr Pro Ala
Pro Thr Ile Ala Ser Gln Pro Leu Ser Leu Arg145 150 155 160Pro Glu
Ala Cys Arg Pro Ala Ala Gly Gly Ala Val His Thr Arg Gly 165 170
175Leu Asp Phe Ala Cys Asp Ile Tyr Ile Trp Ala Pro Leu Ala Gly Thr
180 185 190Cys Gly Val Leu Leu Leu Ser Leu Val Ile Thr Leu Tyr Cys
Asn His 195 200 205Arg Asn Arg Arg Arg Val Cys Lys Cys Pro Arg Pro
Val Val Lys Ser 210 215 220Gly Asp Lys Pro Ser Leu Ser Ala Arg Tyr
Val225 230 2353220PRTHomo sapiens 3Met Leu Arg Leu Leu Leu Ala Leu
Asn Leu Phe Pro Ser Ile Gln Val1 5 10 15Thr Gly Asn Lys Ile Leu Val
Lys Gln Ser Pro Met Leu Val Ala Tyr 20 25 30Asp Asn Ala Val Asn Leu
Ser Cys Lys Tyr Ser Tyr Asn Leu Phe Ser 35 40 45Arg Glu Phe Arg Ala
Ser Leu His Lys Gly Leu Asp Ser Ala Val Glu 50 55 60Val Cys Val Val
Tyr Gly Asn Tyr Ser Gln Gln Leu Gln Val Tyr Ser65 70 75 80Lys Thr
Gly Phe Asn Cys Asp Gly Lys Leu Gly Asn Glu Ser Val Thr 85 90 95Phe
Tyr Leu Gln Asn Leu Tyr Val Asn Gln Thr Asp Ile Tyr Phe Cys 100 105
110Lys Ile Glu Val Met Tyr Pro Pro Pro Tyr Leu Asp Asn Glu Lys Ser
115 120 125Asn Gly Thr Ile Ile His Val Lys Gly Lys His Leu Cys Pro
Ser Pro 130 135 140Leu Phe Pro Gly Pro Ser Lys Pro Phe Trp Val Leu
Val Val Val Gly145 150 155 160Gly Val Leu Ala Cys Tyr Ser Leu Leu
Val Thr Val Ala Phe Ile Ile 165 170 175Phe Trp Val Arg Ser Lys Arg
Ser Arg Leu Leu His Ser Asp Tyr Met 180 185 190Asn Met Thr Pro Arg
Arg Pro Gly Pro Thr Arg Lys His Tyr Gln Pro 195 200 205Tyr Ala Pro
Pro Arg Asp Phe Ala Ala Tyr Arg Ser 210 215 2204123PRTHomo sapiens
4Met Leu Arg Leu Leu Leu Ala Leu Asn Leu Phe Pro Ser Ile Gln Val1 5
10 15Thr Gly Asn Lys Ile Leu Val Lys Gln Ser Pro Met Leu Val Ala
Tyr 20 25 30Asp Asn Ala Val Asn Leu Ser Trp Lys His Leu Cys Pro Ser
Pro Leu 35 40 45Phe Pro Gly Pro Ser Lys Pro Phe Trp Val Leu Val Val
Val Gly Gly 50 55 60Val Leu Ala Cys Tyr Ser Leu Leu Val Thr Val Ala
Phe Ile Ile Phe65 70 75 80Trp Val Arg Ser Lys Arg Ser Arg Leu Leu
His Ser Asp Tyr Met Asn 85 90 95Met Thr Pro Arg Arg Pro Gly Pro Thr
Arg Lys His Tyr Gln Pro Tyr 100 105 110Ala Pro Pro Arg Asp Phe Ala
Ala Tyr Arg Ser 115 1205277PRTHomo sapiens 5Met Cys Val Gly Ala Arg
Arg Leu Gly Arg Gly Pro Cys Ala Ala Leu1 5 10 15Leu Leu Leu Gly Leu
Gly Leu Ser Thr Val Thr Gly Leu His Cys Val 20 25 30Gly Asp Thr Tyr
Pro Ser Asn Asp Arg Cys Cys His Glu Cys Arg Pro 35 40 45Gly Asn Gly
Met Val Ser Arg Cys Ser Arg Ser Gln Asn Thr Val Cys 50 55 60Arg Pro
Cys Gly Pro Gly Phe Tyr Asn Asp Val Val Ser Ser Lys Pro65 70 75
80Cys Lys Pro Cys Thr Trp Cys Asn Leu Arg Ser Gly Ser Glu Arg Lys
85 90 95Gln Leu Cys Thr Ala Thr Gln Asp Thr Val Cys Arg Cys Arg Ala
Gly 100 105 110Thr Gln Pro Leu Asp Ser Tyr Lys Pro Gly Val Asp Cys
Ala Pro Cys 115 120 125Pro Pro Gly His Phe Ser Pro Gly Asp Asn Gln
Ala Cys Lys Pro Trp 130 135 140Thr Asn Cys Thr Leu Ala Gly Lys His
Thr Leu Gln Pro Ala Ser Asn145 150 155 160Ser Ser Asp Ala Ile Cys
Glu Asp Arg Asp Pro Pro Ala Thr Gln Pro 165 170 175Gln Glu Thr Gln
Gly Pro Pro Ala Arg Pro Ile Thr Val Gln Pro Thr 180 185 190Glu Ala
Trp Pro Arg Thr Ser Gln Gly Pro Ser Thr Arg Pro Val Glu 195 200
205Val Pro Gly Gly Arg Ala Val Ala Ala Ile Leu Gly Leu Gly Leu Val
210 215 220Leu Gly Leu Leu Gly Pro Leu Ala Ile Leu Leu Ala Leu Tyr
Leu Leu225 230 235 240Arg Arg Asp Gln Arg Leu Pro Pro Asp Ala His
Lys Pro Pro Gly Gly 245 250 255Gly Ser Phe Arg Thr Pro Ile Gln Glu
Glu Gln Ala Asp Ala His Ser 260 265 270Thr Leu Ala Lys Ile
2756255PRTHomo sapiens 6Met Gly Asn Ser Cys Tyr Asn Ile Val Ala Thr
Leu Leu Leu Val Leu1 5 10 15Asn Phe Glu Arg Thr Arg Ser Leu Gln Asp
Pro Cys Ser Asn Cys Pro 20 25 30Ala Gly Thr Phe Cys Asp Asn Asn Arg
Asn Gln Ile Cys Ser Pro Cys 35 40 45Pro Pro Asn Ser Phe Ser Ser Ala
Gly Gly Gln Arg Thr Cys Asp Ile 50 55 60Cys Arg Gln Cys Lys Gly Val
Phe Arg Thr Arg Lys Glu Cys Ser Ser65 70 75 80Thr Ser Asn Ala Glu
Cys Asp Cys Thr Pro Gly Phe His Cys Leu Gly 85 90 95Ala Gly Cys Ser
Met Cys Glu Gln Asp Cys Lys Gln Gly Gln Glu Leu 100 105 110Thr Lys
Lys Gly Cys Lys Asp Cys Cys Phe Gly Thr Phe Asn Asp Gln 115 120
125Lys Arg Gly Ile Cys Arg Pro Trp Thr Asn Cys Ser Leu Asp Gly Lys
130 135 140Ser Val Leu Val Asn Gly Thr Lys Glu Arg Asp Val Val Cys
Gly Pro145 150 155 160Ser Pro Ala Asp Leu Ser Pro Gly Ala Ser Ser
Val Thr Pro Pro Ala 165 170 175Pro Ala Arg Glu Pro Gly His Ser Pro
Gln Ile Ile Ser Phe Phe Leu 180 185 190Ala Leu Thr Ser Thr Ala Leu
Leu Phe Leu Leu Phe Phe Leu Thr Leu 195 200 205Arg Phe Ser Val Val
Lys Arg Gly Arg Lys Lys Leu Leu Tyr Ile Phe 210 215 220Lys Gln Pro
Phe Met Arg Pro Val Gln Thr Thr Gln Glu Glu Asp Gly225 230 235
240Cys Ser Cys Arg Phe Pro Glu Glu Glu Glu Gly Gly Cys Glu Leu 245
250 2557199PRTHomo sapiens 7Met Lys Ser Gly Leu Trp Tyr Phe Phe Leu
Phe Cys Leu Arg Ile Lys1 5 10 15Val Leu Thr Gly Glu Ile Asn Gly Ser
Ala Asn Tyr Glu Met Phe Ile 20 25 30Phe His Asn Gly Gly Val Gln Ile
Leu Cys Lys Tyr Pro Asp Ile Val 35 40 45Gln Gln Phe Lys Met Gln Leu
Leu Lys Gly Gly Gln Ile Leu Cys Asp 50 55 60Leu Thr Lys Thr Lys Gly
Ser Gly Asn Thr Val Ser Ile Lys Ser Leu65 70 75 80Lys Phe Cys His
Ser Gln Leu Ser Asn Asn Ser Val Ser Phe Phe Leu 85 90 95Tyr Asn Leu
Asp His Ser His Ala Asn Tyr Tyr Phe Cys Asn Leu Ser 100 105 110Ile
Phe Asp Pro Pro Pro Phe Lys Val Thr Leu Thr Gly Gly Tyr Leu 115 120
125His Ile Tyr Glu Ser Gln Leu Cys Cys Gln Leu Lys Phe Trp Leu Pro
130 135 140Ile Gly Cys Ala Ala Phe Val Val Val Cys Ile Leu Gly Cys
Ile Leu145 150 155 160Ile Cys Trp Leu Thr Lys Lys Lys Tyr Ser Ser
Ser Val His Asp Pro 165 170 175Asn Gly Glu Tyr Met Phe Met Arg Ala
Val Asn Thr Ala Lys Lys Ser 180 185 190Arg Leu Thr Asp Val Thr Leu
1958223PRTHomo sapiens 8Met Ala Cys Leu Gly Phe Gln Arg His Lys Ala
Gln Leu Asn Leu Ala1 5 10 15Thr Arg Thr Trp Pro Cys Thr Leu Leu Phe
Phe Leu Leu Phe Ile Pro 20 25 30Val Phe Cys Lys Ala Met His Val Ala
Gln Pro Ala Val Val Leu Ala 35 40 45Ser Ser Arg Gly Ile Ala Ser Phe
Val Cys Glu Tyr Ala Ser Pro Gly 50 55 60Lys Ala Thr Glu Val Arg Val
Thr Val Leu Arg Gln Ala Asp Ser Gln65 70 75 80Val Thr Glu Val Cys
Ala Ala Thr Tyr Met Met Gly Asn Glu Leu Thr 85 90 95Phe Leu Asp Asp
Ser Ile Cys Thr Gly Thr Ser Ser Gly Asn Gln Val 100 105 110Asn Leu
Thr Ile Gln Gly Leu Arg Ala Met Asp Thr Gly Leu Tyr Ile 115 120
125Cys Lys Val Glu Leu Met Tyr Pro Pro Pro Tyr Tyr Leu Gly Ile Gly
130 135 140Asn Gly Thr Gln Ile Tyr Val Ile Asp Pro Glu Pro Cys Pro
Asp Ser145 150 155 160Asp Phe Leu Leu Trp Ile Leu Ala Ala Val Ser
Ser Gly Leu Phe Phe 165 170 175Tyr Ser Phe Leu Leu Thr Ala Val Ser
Leu Ser Lys Met Leu Lys Lys 180 185 190Arg Ser Pro Leu Thr Thr Gly
Val Tyr Val Lys Met Pro Pro Thr Glu 195 200 205Pro Glu Cys Glu Lys
Gln Phe Gln Pro Tyr Phe Ile Pro Ile Asn 210 215 2209288PRTHomo
sapiens 9Met Gln Ile Pro Gln Ala Pro Trp Pro Val Val Trp Ala Val
Leu Gln1 5 10 15Leu Gly Trp Arg Pro Gly Trp Phe Leu Asp Ser Pro Asp
Arg Pro Trp 20 25 30Asn Pro Pro Thr Phe Ser Pro Ala Leu Leu Val Val
Thr Glu Gly Asp 35 40 45Asn Ala Thr Phe Thr Cys Ser Phe Ser Asn Thr
Ser Glu Ser Phe Val 50 55 60Leu Asn Trp Tyr Arg Met Ser Pro Ser Asn
Gln Thr Asp Lys Leu Ala65 70 75 80Ala Phe Pro Glu Asp Arg Ser Gln
Pro Gly Gln Asp Cys Arg Phe Arg 85 90 95Val Thr Gln Leu Pro Asn Gly
Arg Asp Phe His Met Ser Val Val Arg 100 105 110Ala Arg Arg Asn Asp
Ser Gly Thr Tyr Leu Cys Gly Ala Ile Ser Leu 115 120 125Ala Pro Lys
Ala Gln Ile Lys Glu Ser Leu Arg Ala Glu Leu Arg Val 130 135 140Thr
Glu Arg Arg Ala Glu Val Pro Thr Ala His Pro Ser Pro Ser Pro145 150
155 160Arg Pro Ala Gly Gln Phe Gln Thr Leu Val Val Gly Val Val Gly
Gly 165 170 175Leu Leu Gly Ser Leu Val Leu Leu Val Trp Val Leu Ala
Val Ile Cys 180 185 190Ser Arg Ala Ala Arg Gly Thr Ile Gly Ala Arg
Arg Thr Gly Gln Pro 195 200 205Leu Lys Glu Asp Pro Ser Ala Val Pro
Val Phe Ser Val Asp Tyr Gly 210 215 220Glu Leu Asp Phe Gln Trp Arg
Glu Lys Thr Pro Glu Pro Pro Val Pro225 230 235 240Cys Val Pro Glu
Gln Thr Glu Tyr Ala Thr Ile Val Phe Pro Ser Gly 245 250 255Met Gly
Thr Ser Ser Pro Ala Arg Arg Gly Ser Ala Asp Gly Pro Arg 260 265
270Ser Ala Gln Pro Leu Arg Pro Glu Asp Gly His Cys Ser Trp Pro Leu
275 280 28510525PRTHomo sapiens 10Met Trp Glu Ala Gln Phe Leu Gly
Leu Leu Phe Leu Gln Pro Leu Trp1 5 10 15Val Ala Pro Val Lys Pro Leu
Gln Pro Gly Ala Glu Val Pro Val Val 20 25 30Trp Ala Gln Glu Gly Ala
Pro Ala Gln Leu Pro Cys Ser Pro Thr Ile 35 40 45Pro Leu Gln Asp Leu
Ser Leu Leu Arg Arg Ala Gly Val Thr Trp Gln 50 55 60His Gln Pro Asp
Ser Gly Pro Pro Ala Ala Ala Pro Gly His Pro Leu65 70 75 80Ala Pro
Gly Pro His Pro Ala Ala Pro Ser Ser Trp Gly Pro Arg Pro 85 90 95Arg
Arg Tyr Thr Val Leu Ser Val Gly Pro Gly Gly Leu Arg Ser Gly 100 105
110Arg Leu Pro Leu Gln Pro Arg Val Gln Leu Asp Glu Arg Gly Arg Gln
115 120 125Arg Gly Asp Phe Ser Leu Trp Leu Arg Pro Ala Arg Arg Ala
Asp Ala 130 135 140Gly Glu Tyr Arg Ala Ala Val His Leu Arg Asp Arg
Ala Leu Ser Cys145 150 155 160Arg Leu Arg Leu Arg Leu Gly Gln Ala
Ser Met Thr Ala Ser Pro Pro 165 170 175Gly Ser Leu Arg Ala Ser Asp
Trp Val Ile Leu Asn Cys Ser Phe Ser 180 185 190Arg Pro Asp Arg Pro
Ala Ser Val His Trp Phe Arg Asn Arg Gly Gln 195 200 205Gly Arg Val
Pro Val Arg Glu Ser Pro His His His Leu Ala Glu Ser 210 215 220Phe
Leu Phe Leu Pro Gln Val Ser Pro Met Asp Ser Gly Pro Trp Gly225 230
235 240Cys Ile Leu Thr Tyr Arg Asp Gly Phe Asn Val Ser Ile Met Tyr
Asn 245 250 255Leu Thr Val Leu Gly Leu Glu Pro Pro Thr Pro Leu Thr
Val Tyr Ala 260 265 270Gly Ala Gly Ser Arg Val Gly Leu Pro Cys Arg
Leu Pro Ala Gly Val 275 280 285Gly Thr Arg Ser Phe Leu Thr Ala Lys
Trp Thr Pro Pro Gly Gly Gly 290 295 300Pro Asp Leu Leu Val Thr Gly
Asp Asn Gly Asp Phe Thr Leu Arg Leu305 310 315 320Glu Asp Val Ser
Gln Ala Gln Ala Gly Thr Tyr Thr Cys His Ile His 325 330 335Leu Gln
Glu Gln Gln Leu Asn Ala Thr Val Thr Leu Ala Ile Ile Thr 340 345
350Val Thr Pro Lys Ser Phe Gly Ser Pro Gly Ser Leu Gly Lys Leu Leu
355 360 365Cys Glu Val Thr Pro Val Ser Gly Gln Glu Arg Phe Val Trp
Ser Ser 370 375 380Leu Asp Thr Pro Ser Gln Arg Ser Phe Ser Gly Pro
Trp Leu Glu Ala385 390 395 400Gln Glu Ala Gln Leu Leu Ser Gln Pro
Trp Gln Cys Gln Leu Tyr Gln 405 410 415Gly Glu Arg Leu Leu Gly Ala
Ala Val Tyr Phe Thr Glu Leu Ser Ser 420 425 430Pro Gly Ala Gln Arg
Ser Gly Arg Ala Pro Gly Ala Leu Pro Ala Gly 435 440 445His Leu Leu
Leu Phe Leu Ile Leu Gly Val Leu Ser Leu Leu Leu Leu 450 455 460Val
Thr Gly Ala Phe Gly Phe His Leu Trp Arg Arg Gln Trp Arg Pro465
470 475 480Arg Arg Phe Ser Ala Leu Glu Gln Gly Ile His Pro Pro Gln
Ala Gln 485 490 495Ser Lys Ile Glu Glu Leu Glu Gln Glu Pro Glu Pro
Glu Pro Glu Pro 500 505 510Glu Pro Glu Pro Glu Pro Glu Pro Glu Pro
Glu Gln Leu 515 520 52511370PRTHomo sapiens 11Met Leu Gly Gln Val
Val Thr Leu Ile Leu Leu Leu Leu Leu Lys Val1 5 10 15Tyr Gln Gly Lys
Gly Cys Gln Gly Ser Ala Asp His Val Val Ser Ile 20 25 30Ser Gly Val
Pro Leu Gln Leu Gln Pro Asn Ser Ile Gln Thr Lys Val 35 40 45Asp Ser
Ile Ala Trp Lys Lys Leu Leu Pro Ser Gln Asn Gly Phe His 50 55 60His
Ile Leu Lys Trp Glu Asn Gly Ser Leu Pro Ser Asn Thr Ser Asn65 70 75
80Asp Arg Phe Ser Phe Ile Val Lys Asn Leu Ser Leu Leu Ile Lys Ala
85 90 95Ala Gln Gln Gln Asp Ser Gly Leu Tyr Cys Leu Glu Val Thr Ser
Ile 100 105 110Ser Gly Lys Val Gln Thr Ala Thr Phe Gln Val Phe Val
Phe Glu Ser 115 120 125Leu Leu Pro Asp Lys Val Glu Lys Pro Arg Leu
Gln Gly Gln Gly Lys 130 135 140Ile Leu Asp Arg Gly Arg Cys Gln Val
Ala Leu Ser Cys Leu Val Ser145 150 155 160Arg Asp Gly Asn Val Ser
Tyr Ala Trp Tyr Arg Gly Ser Lys Leu Ile 165 170 175Gln Thr Ala Gly
Asn Leu Thr Tyr Leu Asp Glu Glu Val Asp Ile Asn 180 185 190Gly Thr
His Thr Tyr Thr Cys Asn Val Ser Asn Pro Val Ser Trp Glu 195 200
205Ser His Thr Leu Asn Leu Thr Gln Asp Cys Gln Asn Ala His Gln Glu
210 215 220Phe Arg Phe Trp Pro Phe Leu Val Ile Ile Val Ile Leu Ser
Ala Leu225 230 235 240Phe Leu Gly Thr Leu Ala Cys Phe Cys Val Trp
Arg Arg Lys Arg Lys 245 250 255Glu Lys Gln Ser Glu Thr Ser Pro Lys
Glu Phe Leu Thr Ile Tyr Glu 260 265 270Asp Val Lys Asp Leu Lys Thr
Arg Arg Asn His Glu Gln Glu Gln Thr 275 280 285Phe Pro Gly Gly Gly
Ser Thr Ile Tyr Ser Met Ile Gln Ser Gln Ser 290 295 300Ser Ala Pro
Thr Ser Gln Glu Pro Ala Tyr Thr Leu Tyr Ser Leu Ile305 310 315
320Gln Pro Ser Arg Lys Ser Gly Ser Arg Lys Arg Asn His Ser Pro Ser
325 330 335Phe Asn Ser Thr Ile Tyr Glu Val Ile Gly Lys Ser Gln Pro
Lys Ala 340 345 350Gln Asn Pro Ala Arg Leu Ser Arg Lys Glu Leu Glu
Asn Phe Asp Val 355 360 365Tyr Ser 37012289PRTHomo sapiens 12Met
Lys Thr Leu Pro Ala Met Leu Gly Thr Gly Lys Leu Phe Trp Val1 5 10
15Phe Phe Leu Ile Pro Tyr Leu Asp Ile Trp Asn Ile His Gly Lys Glu
20 25 30Ser Cys Asp Val Gln Leu Tyr Ile Lys Arg Gln Ser Glu His Ser
Ile 35 40 45Leu Ala Gly Asp Pro Phe Glu Leu Glu Cys Pro Val Lys Tyr
Cys Ala 50 55 60Asn Arg Pro His Val Thr Trp Cys Lys Leu Asn Gly Thr
Thr Cys Val65 70 75 80Lys Leu Glu Asp Arg Gln Thr Ser Trp Lys Glu
Glu Lys Asn Ile Ser 85 90 95Phe Phe Ile Leu His Phe Glu Pro Val Leu
Pro Asn Asp Asn Gly Ser 100 105 110Tyr Arg Cys Ser Ala Asn Phe Gln
Ser Asn Leu Ile Glu Ser His Ser 115 120 125Thr Thr Leu Tyr Val Thr
Asp Val Lys Ser Ala Ser Glu Arg Pro Ser 130 135 140Lys Asp Glu Met
Ala Ser Arg Pro Trp Leu Leu Tyr Ser Leu Leu Pro145 150 155 160Leu
Gly Gly Leu Pro Leu Leu Ile Thr Thr Cys Phe Cys Leu Phe Cys 165 170
175Cys Leu Arg Arg His Gln Gly Lys Gln Asn Glu Leu Ser Asp Thr Ala
180 185 190Gly Arg Glu Ile Asn Leu Val Asp Ala His Leu Lys Ser Glu
Gln Thr 195 200 205Glu Ala Ser Thr Arg Gln Asn Ser Gln Val Leu Leu
Ser Glu Thr Gly 210 215 220Ile Tyr Asp Asn Asp Pro Asp Leu Cys Phe
Arg Met Gln Glu Gly Ser225 230 235 240Glu Val Tyr Ser Asn Pro Cys
Leu Glu Glu Asn Lys Pro Gly Ile Val 245 250 255Tyr Ala Ser Leu Asn
His Ser Val Ile Gly Pro Asn Ser Arg Leu Ala 260 265 270Arg Asn Val
Lys Glu Ala Pro Thr Glu Tyr Ala Ser Ile Cys Val Arg 275 280
285Ser13183PRTHomo sapiens 13Met Glu Arg Val Gln Pro Leu Glu Glu
Asn Val Gly Asn Ala Ala Arg1 5 10 15Pro Arg Phe Glu Arg Asn Lys Leu
Leu Leu Val Ala Ser Val Ile Gln 20 25 30Gly Leu Gly Leu Leu Leu Cys
Phe Thr Tyr Ile Cys Leu His Phe Ser 35 40 45Ala Leu Gln Val Ser His
Arg Tyr Pro Arg Ile Gln Ser Ile Lys Val 50 55 60Gln Phe Thr Glu Tyr
Lys Lys Glu Lys Gly Phe Ile Leu Thr Ser Gln65 70 75 80Lys Glu Asp
Glu Ile Met Lys Val Gln Asn Asn Ser Val Ile Ile Asn 85 90 95Cys Asp
Gly Phe Tyr Leu Ile Ser Leu Lys Gly Tyr Phe Ser Gln Glu 100 105
110Val Asn Ile Ser Leu His Tyr Gln Lys Asp Glu Glu Pro Leu Phe Gln
115 120 125Leu Lys Lys Val Arg Ser Val Asn Ser Leu Met Val Ala Ser
Leu Thr 130 135 140Tyr Lys Asp Lys Val Tyr Leu Asn Val Thr Thr Asp
Asn Thr Ser Leu145 150 155 160Asp Asp Phe His Val Asn Gly Gly Glu
Leu Ile Leu Ile His Gln Asn 165 170 175Pro Gly Glu Phe Cys Val Leu
18014255PRTHomo sapiens 14Met Gly Asn Ser Cys Tyr Asn Ile Val Ala
Thr Leu Leu Leu Val Leu1 5 10 15Asn Phe Glu Arg Thr Arg Ser Leu Gln
Asp Pro Cys Ser Asn Cys Pro 20 25 30Ala Gly Thr Phe Cys Asp Asn Asn
Arg Asn Gln Ile Cys Ser Pro Cys 35 40 45Pro Pro Asn Ser Phe Ser Ser
Ala Gly Gly Gln Arg Thr Cys Asp Ile 50 55 60Cys Arg Gln Cys Lys Gly
Val Phe Arg Thr Arg Lys Glu Cys Ser Ser65 70 75 80Thr Ser Asn Ala
Glu Cys Asp Cys Thr Pro Gly Phe His Cys Leu Gly 85 90 95Ala Gly Cys
Ser Met Cys Glu Gln Asp Cys Lys Gln Gly Gln Glu Leu 100 105 110Thr
Lys Lys Gly Cys Lys Asp Cys Cys Phe Gly Thr Phe Asn Asp Gln 115 120
125Lys Arg Gly Ile Cys Arg Pro Trp Thr Asn Cys Ser Leu Asp Gly Lys
130 135 140Ser Val Leu Val Asn Gly Thr Lys Glu Arg Asp Val Val Cys
Gly Pro145 150 155 160Ser Pro Ala Asp Leu Ser Pro Gly Ala Ser Ser
Val Thr Pro Pro Ala 165 170 175Pro Ala Arg Glu Pro Gly His Ser Pro
Gln Ile Ile Ser Phe Phe Leu 180 185 190Ala Leu Thr Ser Thr Ala Leu
Leu Phe Leu Leu Phe Phe Leu Thr Leu 195 200 205Arg Phe Ser Val Val
Lys Arg Gly Arg Lys Lys Leu Leu Tyr Ile Phe 210 215 220Lys Gln Pro
Phe Met Arg Pro Val Gln Thr Thr Gln Glu Glu Asp Gly225 230 235
240Cys Ser Cys Arg Phe Pro Glu Glu Glu Glu Gly Gly Cys Glu Leu 245
250 25515486PRTArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polypeptide"MOD_RES(486)..(486)Any
amino acid 15Met Ala Leu Pro Val Thr Ala Leu Leu Leu Pro Leu Ala
Leu Leu Leu1 5 10 15His Ala Glu Val Lys Leu Gln Gln Ser Gly Ala Glu
Leu Val Arg Pro 20 25 30Gly Ser Ser Val Lys Ile Ser Cys Lys Ala Ser
Gly Tyr Ala Phe Ser 35 40 45Ser Tyr Trp Met Asn Trp Val Lys Gln Arg
Pro Gly Gln Gly Leu Glu 50 55 60Trp Ile Gly Gln Ile Tyr Pro Gly Asp
Gly Asp Thr Asn Tyr Asn Gly65 70 75 80Lys Phe Lys Gly Gln Ala Thr
Leu Thr Ala Asp Lys Ser Ser Ser Thr 85 90 95Ala Tyr Met Gln Leu Ser
Gly Leu Thr Ser Glu Asp Ser Ala Val Tyr 100 105 110Phe Cys Ala Arg
Lys Thr Ile Ser Ser Val Val Asp Phe Tyr Phe Asp 115 120 125Tyr Trp
Gly Gln Gly Thr Thr Val Thr Val Ser Ser Gly Gly Gly Gly 130 135
140Ser Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Asp Ile Glu Leu
Thr145 150 155 160Gln Ser Pro Lys Phe Met Ser Thr Ser Val Gly Asp
Arg Val Ser Val 165 170 175Thr Cys Lys Ala Ser Gln Asn Val Gly Thr
Asn Val Ala Trp Tyr Gln 180 185 190Gln Lys Pro Gly Gln Ser Pro Lys
Pro Leu Ile Tyr Ser Ala Thr Tyr 195 200 205Arg Asn Ser Gly Val Pro
Asp Arg Phe Thr Gly Ser Gly Ser Gly Thr 210 215 220Asp Phe Thr Leu
Thr Ile Thr Asn Val Gln Ser Lys Asp Leu Ala Asp225 230 235 240Tyr
Phe Cys Gln Gln Tyr Asn Arg Tyr Pro Tyr Thr Ser Gly Gly Gly 245 250
255Thr Lys Leu Glu Ile Lys Arg Ala Ala Ala Ile Glu Val Met Tyr Pro
260 265 270Pro Pro Tyr Leu Asp Asn Glu Lys Ser Asn Gly Thr Ile Ile
His Val 275 280 285Lys Gly Lys His Leu Cys Pro Ser Pro Leu Phe Pro
Gly Pro Ser Lys 290 295 300Pro Phe Trp Val Leu Val Val Val Gly Gly
Val Leu Ala Cys Tyr Ser305 310 315 320Leu Leu Val Thr Val Ala Phe
Ile Ile Phe Trp Val Arg Ser Lys Arg 325 330 335Ser Arg Leu Leu His
Ser Asp Tyr Met Asn Met Thr Pro Arg Arg Pro 340 345 350Gly Pro Thr
Arg Lys His Tyr Gln Pro Tyr Ala Pro Pro Arg Asp Phe 355 360 365Ala
Ala Tyr Arg Ser Arg Val Lys Phe Ser Arg Ser Ala Glu Pro Pro 370 375
380Ala Tyr Gln Gln Gly Gln Asn Gln Leu Tyr Asn Glu Leu Asn Leu
Gly385 390 395 400Arg Arg Glu Glu Tyr Asp Val Leu Asp Lys Arg Arg
Gly Arg Asp Pro 405 410 415Glu Met Gly Gly Lys Pro Arg Arg Lys Asn
Pro Gln Glu Gly Leu Tyr 420 425 430Asn Glu Leu Gln Lys Asp Lys Met
Ala Glu Ala Tyr Ser Glu Ile Gly 435 440 445Met Lys Gly Glu Arg Arg
Arg Gly Lys Gly His Asp Gly Leu Tyr Gln 450 455 460Gly Leu Ser Thr
Ala Thr Lys Asp Thr Tyr Asp Ala Leu His Met Gln465 470 475 480Ala
Leu Pro Pro Arg Xaa 485161458DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 16ccatggctct cccagtgact gccctactgc ttcccctagc
gcttctcctg catgcagagg 60tgaagctgca gcagtctggg gctgagctgg tgaggcctgg
gtcctcagtg aagatttcct 120gcaaggcttc tggctatgca ttcagtagct
actggatgaa ctgggtgaag cagaggcctg 180gacagggtct tgagtggatt
ggacagattt atcctggaga tggtgatact aactacaatg 240gaaagttcaa
gggtcaagcc acactgactg cagacaaatc ctccagcaca gcctacatgc
300agctcagcgg cctaacatct gaggactctg cggtctattt ctgtgcaaga
aagaccatta 360gttcggtagt agatttctac tttgactact ggggccaagg
gaccacggtc accgtctcct 420caggtggagg tggatcaggt ggaggtggat
ctggtggagg tggatctgac attgagctca 480cccagtctcc aaaattcatg
tccacatcag taggagacag ggtcagcgtc acctgcaagg 540ccagtcagaa
tgtgggtact aatgtagcct ggtatcaaca gaaaccagga caatctccta
600aaccactgat ttactcggca acctaccgga acagtggagt ccctgatcgc
ttcacaggca 660gtggatctgg gacagatttc actctcacca tcactaacgt
gcagtctaaa gacttggcag 720actatttctg tcaacaatat aacaggtatc
cgtacacgtc cggagggggg accaagctgg 780agatcaaacg ggcggccgca
attgaagtta tgtatcctcc tccttaccta gacaatgaga 840agagcaatgg
aaccattatc catgtgaaag ggaaacacct ttgtccaagt cccctatttc
900ccggaccttc taagcccttt tgggtgctgg tggtggttgg tggagtcctg
gcttgctata 960gcttgctagt aacagtggcc tttattattt tctgggtgag
gagtaagagg agcaggctcc 1020tgcacagtga ctacatgaac atgactcccc
gccgccccgg gcccacccgc aagcattacc 1080agccctatgc cccaccacgc
gacttcgcag cctatcgctc cagagtgaag ttcagcagga 1140gcgcagagcc
ccccgcgtac cagcagggcc agaaccagct ctataacgag ctcaatctag
1200gacgaagaga ggagtacgat gttttggaca agagacgtgg ccgggaccct
gagatggggg 1260gaaagccgag aaggaagaac cctcaggaag gcctgtacaa
tgaactgcag aaagataaga 1320tggcggaggc ctacagtgag attgggatga
aaggcgagcg ccggaggggc aaggggcacg 1380atggccttta ccagggtctc
agtacagcca ccaaggacac ctacgacgcc cttcacatgc 1440aggccctgcc ccctcgcg
145817708DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 17atggtgagca
agggcgagga ggataacatg gccatcatca aggagttcat gcgcttcaag 60gtgcacatgg
agggctccgt gaacggccac gagttcgaga tcgagggcga gggcgagggc
120cgcccctacg agggcaccca gaccgccaag ctgaaggtga ccaagggtgg
ccccctgccc 180ttcgcctggg acatcctgtc ccctcagttc atgtacggct
ccaaggccta cgtgaagcac 240cccgccgaca tccccgacta cttgaagctg
tccttccccg agggcttcaa gtgggagcgc 300gtgatgaact tcgaggacgg
cggcgtggtg accgtgaccc aggactcctc cctgcaggac 360ggcgagttca
tctacaaggt gaagctgcgc ggcaccaact tcccctccga cggccccgta
420atgcagaaga agaccatggg ctgggaggcc tcctccgagc ggatgtaccc
cgaggacggc 480gccctgaagg gcgagatcaa gcagaggctg aagctgaagg
acggcggcca ctacgacgct 540gaggtcaaga ccacctacaa ggccaagaag
cccgtgcagc tgcccggcgc ctacaacgtc 600aacatcaagt tggacatcac
ctcccacaac gaggactaca ccatcgtgga acagtacgaa 660cgcgccgagg
gccgccactc caccggcggc atggacgagc tgtacaag 708183123DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 18atggtgagca agggcgagga gctgttcacc ggggtggtgc
ccatcctggt cgagctggac 60ggcgacgtaa acggccacaa gttcagcgtg tccggcgagg
gcgagggcga tgccacctac 120ggcaagctga ccctgaagtt catctgcacc
accggcaagc tgcccgtgcc ctggcccacc 180ctcgtgacca ccttcggcta
cggcctgatg tgcttcgccc gctaccccga ccacatgaag 240cagcacgact
tcttcaagtc cgccatgccc gaaggctacg tccaggagcg caccatcttc
300ttcaaggacg acggcaacta caagacccgc gccgaggtga agttcgaggg
cgacaccctg 360gtgaaccgca tcgagctgaa gggcatcgac ttcaaggagg
acggcaacat cctggggcac 420aagctggagt acaactacaa cagccacaac
gtctatatca tggccgacaa gcagaagaac 480ggcatcaagg tgaacttcaa
gatccgccac aacatcgagg acggcagcgt gcagctcgcc 540gaccactacc
agcagaacac ccccatcggc gacggccccg tgctgctgcc cgacaaccac
600tacctgagct accagtccgc cctgagcaaa gaccccaacg agaagcgcga
tcacatggtc 660ctgctggagt tcgtgaccgc cgccgggatc actctcggca
tggacgagct gtacaaggga 720tctggagcaa caaacttctc actactcaaa
caagcaggtg acgtggagga gaatcccggc 780cctatgcccc tcaacgttag
cttcaccaac aggaactatg acctcgacta cgactcggtg 840cagccgtatt
tctactgcga cgaggaggag aacttctacc agcagcagca gcagagcgag
900ctgcagcccc cggcgcccag cgaggatatc tggaagaaat tcgagctgct
gcccaccccg 960cccctgtccc ctagccgccg ctccgggctc tgctcgccct
cctacgttgc ggtcacaccc 1020ttctcccttc ggggagacaa cgacggcggt
ggcgggagct tctccacggc cgaccagctg 1080gagatggtga ccgagctgct
gggaggagac atggtgaacc agagtttcat ctgcgacccg 1140gacgacgaga
ccttcatcaa aaacatcatc atccaggact gtatgtggag cggcttctcg
1200gccgccgcca agctcgtctc agagaagctg gcctcctacc aggctgcgcg
caaagacagc 1260ggcagcccga accccgcccg cggccacagc gtctgctcca
cctccagctt gtacctgcag 1320gatctgagcg ccgccgcctc agagtgcatc
gacccctcgg tggtcttccc ctaccctctc 1380aacgacagca gctcgcccaa
gtcctgcgcc tcgcaagact ccagcgcctt ctctccgtcc 1440tcggattctc
tgctctcctc gacggagtcc tccccgcagg gcagccccga gcccctggtg
1500ctccatgagg agacaccgcc caccaccagc agcgactctg aggaggaaca
agaagatgag 1560gaagaaatcg atgttgtttc tgtggaaaag aggcaggctc
ctggcaaaag gtcagagtct 1620ggatcacctt ctgctggagg ccacagcaaa
cctcctcaca gcccactggt cctcaagagg 1680tgccacgtct ccacacatca
gcacaactac gcagcgcctc cctccactcg gaaggactat 1740cctgctgcca
agagggtcaa gttggacagt gtcagagtcc tgagacagat cagcaacaac
1800cgaaaatgca ccagccccag gtcctcggac accgaggaga atgtcaagag
gcgaacacac 1860aacgtcttgg agcgccagag gaggaacgag ctaaaacgga
gcttttttgc cctgcgtgac 1920cagatcccgg agttggaaaa caatgaaaag
gcccccaagg tagttatcct taaaaaagcc 1980acagcataca tcctgtccgt
ccaagcagag gagcaaaagc tcatttctga agaggacttg 2040ttgcggaaac
gacgagaaca gttgaaacac aaacttgaac agctacggaa ctcttgtgcg
2100ggatctggac aatgtactaa ctacgctttg ttgaaactcg ctggcgatgt
tgaaagtaac 2160cccggtccca tgtacaacat gatggagacg gagctgaagc
cgccgggccc gcagcaaact 2220tcggggggcg gcggcggcaa ctccaccgcg
gcggcggccg gcggcaacca gaaaaacagc 2280ccggaccgcg tcaagcggcc
catgaatgcc ttcatggtgt ggtcccgcgg gcagcggcgc 2340aagatggccc
aggagaaccc caagatgcac aactcggaga tcagcaagcg cctgggcgcc
2400gagtggaaac
ttttgtcgga gacggagaag cggccgttca tcgacgaggc taagcggctg
2460cgagcgctgc acatgaagga gcacccggat tataaatacc ggccccggcg
gaaaaccaag 2520acgctcatga agaaggataa gtacacgctg cccggcgggc
tgctggcccc cggcggcaat 2580agcatggcga gcggggtcgg ggtgggcgcc
ggcctgggcg cgggcgtgaa ccagcgcatg 2640gacagttacg cgcacatgaa
cggctggagc aacggcagct acagcatgat gcaggaccag 2700ctgggctacc
cgcagcaccc gggcctcaat gcgcacggcg cagcgcagat gcagcccatg
2760caccgctacg acgtgagcgc cctgcagtac aactccatga ccagctcgca
gacctacatg 2820aacggctcgc ccacctacag catgtcctac tcgcagcagg
gcacccctgg catggctctt 2880ggctccatgg gttcggtggt caagtccgag
gccagctcca gcccccctgt ggttacctct 2940tcctcccact ccagggcgcc
ctgccaggcc ggggacctcc gggacatgat cagcatgtat 3000ctccccggcg
ccgaggtgcc ggaacccgcc gcccccagca gacttcacat gtcccagcac
3060taccagagcg gcccggtgcc cggcacggcc attaacggca cactgcccct
ctcacacatg 3120tga 3123193339DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 19atggtgagca agggcgagga gctgttcacc ggggtggtgc
ccatcctggt cgagctggac 60ggcgacgtaa acggccacaa gttcagcgtg tccggcgagg
gcgagggcga tgccacctac 120ggcaagctga ccctgaagtt catctgcacc
accggcaagc tgcccgtgcc ctggcccacc 180ctcgtgacca ccttcagcta
cggcgtgcag tgcttcagcc gctaccccga ccacatgaag 240cagcacgact
tcttcaagtc cgccatgccc gaaggctacg tccaggagcg caccatcagc
300ttcaaggacg acggcaacta caagacccgc gccgaggtga agttcgaggg
cgacaccctg 360gtgaaccgca tcgagctgaa gggcatcgac ttcaaggagg
acggcaacat cctggggcac 420aagctggagt acaactacaa cagccacaac
gtctatatca cggccgacaa gcagaagaac 480ggcatcaagg cgaacttcaa
gatccgccac aacatcgagg acggcagcgt gcagctcgcc 540gaccactacc
agcagaacac ccccatcggc gacggccccg tgctgctgcc cgacaaccac
600tacctgttca tccagtccgc cctgagcaaa gaccccaacg agaagcgcga
tcacatggtc 660ctgctggagt tcgtgaccgc cgccgggatc actcacggca
tggacgagct gtacaaggga 720tctggagcaa caaacttctc actactcaaa
caagcaggtg acgtggagga gaatcccggc 780cctatggcgg gacacctggc
ttcggatttc gccttctcgc cccctccagg tggtggaggt 840gatgggccag
gggggccgga gccgggctgg gttgatcctc ggacctggct aagcttccaa
900ggccctcctg gagggccagg aatcgggccg ggggttgggc caggctctga
ggtgtggggg 960attcccccat gccccccgcc gtatgagttc tgtgggggga
tggcgtactg tgggccccag 1020gttggagtgg ggctagtgcc ccaaggcggc
ttggagacct ctcagcctga gggtgaagca 1080ggagtcgggg tggagagcaa
ctccgatggg gcctccccgg agccctgcac cgtcacccct 1140ggtgccgtga
agctggagaa ggagaagctg gagcaaaacc cggaggagtc ccaggacatc
1200aaagctctgc agaaagaact cgagcaattt gccaagctcc tgaagcagaa
gaggatcacc 1260ctgggatata cacaggccga tgtggggctc accctggggg
ttctatttgg gaaggtattc 1320agccaaacga ccatctgccg ctttgaggct
ctgcagctta gcttcaagaa catgtgtaag 1380ctgcggccct tgctgcagaa
gtgggtggag gaagctgaca acaatgaaaa tcttcaggag 1440atatgcaaag
cagaaaccct cgtgcaggcc cgaaagagaa agcgaaccag tatcgagaac
1500cgagtgagag gcaacctgga gaatttgttc ctgcagtgcc cgaaacccac
actgcagcag 1560atcagccaca tcgcccagca gcttgggctc gagaaggatg
tggtccgagt gtggttctgt 1620aaccggcgcc agaagggcaa gcgatcaagc
agcgactatg cacaacgaga ggattttgag 1680gctgctgggt ctcctttctc
agggggacca gtgtcctttc ctctggcccc agggccccat 1740tttggtaccc
caggctatgg gagccctcac ttcactgcac tgtactcctc ggtccctttc
1800cctgaggggg aagcctttcc ccctgtctct gtcaccactc tgggctctcc
catgcattca 1860aacggatctg gagagggcag aggaagtctt ctaacatgcg
gtgacgtgga ggagaatccc 1920ggccccatgg ctgtcagcga cgcgctgctc
ccatctttct ccacgttcgc gtctggcccg 1980gcgggaaggg agaagacact
gcgtcaagca ggtgccccga ataaccgctg gcgggaggag 2040ctctcccaca
tgaagcgact tcccccagtg cttcccggcc gcccctatga cctggcggcg
2100gcgaccgtgg ccacagacct ggagagcggc ggagccggtg cggcttgcgg
cggtagcaac 2160ctggcgcccc tacctcggag agagaccgag gagttcaacg
atctcctgga cctggacttt 2220attctctcca attcgctgac ccatcctccg
gagtcagtgg ccgccaccgt gtcctcgtca 2280gcgtcagcct cctcttcgtc
gtcgccgtcg agcagcggcc ctgccagcgc gccctccacc 2340tgcagcttca
cctatccgat ccgggccggg aacgacccgg gcgtggcgcc gggcggcacg
2400ggcggaggcc tcctctatgg cagggagtcc gctccccctc cgacggctcc
cttcaacctg 2460gcggacatca acgacgtgag cccctcgggc ggcttcgtgg
ccgagctcct gcggccagaa 2520ttggacccgg tgtacattcc gccgcagcag
ccgcagccgc caggtggcgg gctgatgggc 2580aagttcgtgc tgaaggcgtc
gctgagcgcc cctggcagcg agtacggcag cccgtcggtc 2640atcagcgtca
gcaaaggcag ccctgacggc agccacccgg tggtggtggc gccctacaac
2700ggcgggccgc cgcgcacgtg ccccaagatc aagcaggagg cggtctcttc
gtgcacccac 2760ttgggcgctg gaccccctct cagcaatggc caccggccgg
ctgcacacga cttccccctg 2820gggcggcagc tccccagcag gactaccccg
accctgggtc ttgaggaagt gctgagcagc 2880agggactgtc accctgccct
gccgcttcct cccggcttcc atccccaccc ggggcccaat 2940tacccatcct
tcctgcccga tcagatgcag ccgcaagtcc cgccgctcca ttaccaagag
3000ctcatgccac ccggttcctg catgccagag gagcccaagc caaagagggg
aagacgatcg 3060tggccccgga aaaggaccgc cacccacact tgtgattacg
cgggctgcgg caaaacctac 3120acaaagagtt cccatctcaa ggcacacctg
cgaacccaca caggtgagaa accttaccac 3180tgtgactggg acggctgtgg
atggaaattc gcccgctcag atgaactgac caggcactac 3240cgtaaacaca
cggggcaccg cccgttccag tgccaaaaat gcgaccgagc attttccagg
3300tcggaccacc tcgccttaca catgaagagg catttttaa
33392021DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 20agaacctaga acctcgctgg a
212121DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 21ctgcgatgcc gttctacttt g
212225DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 22tgaaacatac gttcccaaag agttt
252326DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 23ctctccttct cagaaagtgt gcatat
262424DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic probe" 24aggaccttac acagtcctgc tgac
242527DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic probe" 25tgctgaaaca ttcaccttcc atgcaga
27264PRTHomo sapiens 26Tyr Val Lys Met12716PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 27Gly Gly Gly Ser Gly Gly Gly Ser Gly Gly Gly Ser Gly Gly
Gly Ser1 5 10 15
* * * * *