U.S. patent application number 14/155963 was filed with the patent office on 2014-07-10 for expansion of definitive endoderm cells.
This patent application is currently assigned to ViaCyte, Inc.. The applicant listed for this patent is ViaCyte, Inc.. Invention is credited to Emmanuel E. Baetge, Melissa Carpenter, Olivia Kelly.
Application Number | 20140193905 14/155963 |
Document ID | / |
Family ID | 46323450 |
Filed Date | 2014-07-10 |
United States Patent
Application |
20140193905 |
Kind Code |
A1 |
Kelly; Olivia ; et
al. |
July 10, 2014 |
EXPANSION OF DEFINITIVE ENDODERM CELLS
Abstract
Disclosed herein are cell cultures comprising expanded
definitive endoderm cells as well as methods for expanding
definitive endoderm cells in culture.
Inventors: |
Kelly; Olivia; (San Diego,
CA) ; Baetge; Emmanuel E.; (Encinitas, CA) ;
Carpenter; Melissa; (San Diego, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
ViaCyte, Inc. |
San Diego |
CA |
US |
|
|
Assignee: |
ViaCyte, Inc.
San Diego
CA
|
Family ID: |
46323450 |
Appl. No.: |
14/155963 |
Filed: |
January 15, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12582600 |
Oct 20, 2009 |
8658151 |
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14155963 |
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11317387 |
Dec 22, 2005 |
7625753 |
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12582600 |
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11021618 |
Dec 23, 2004 |
7510876 |
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11317387 |
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60587942 |
Jul 14, 2004 |
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60586566 |
Jul 9, 2004 |
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60532004 |
Dec 23, 2003 |
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Current U.S.
Class: |
435/366 |
Current CPC
Class: |
C12N 5/0606 20130101;
C12N 2500/90 20130101; C12N 2502/13 20130101; C12N 2501/385
20130101; C12N 2501/115 20130101; C12N 5/0603 20130101; C12N
2501/155 20130101; C12N 2501/415 20130101; C12N 2501/16 20130101;
C12N 2506/02 20130101 |
Class at
Publication: |
435/366 |
International
Class: |
C12N 5/073 20060101
C12N005/073 |
Claims
1.-11. (canceled)
12. An in vitro population of passaged human definitive endoderm
cells.
13. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells expresses SOX17, GSC,
MIXL1 or CXCR4.
14. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells expresses SOX17 and
CXCR4.
15. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells does not express Oct4,
Brachyury, ZIC1 or SOX1.
16. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells is a population of cells
that has been passaged at least twice.
17. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells is in contact with a
surface coated with human fibronectin.
18. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells is in a medium comprising
less than 2% (v/v) serum.
19. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells is in a medium comprising
at least one growth factor from the TGF.beta. superfamily or a
member of the epidermal growth factor family.
20. The cell population of claim 19, wherein the at least one
growth factor from the TGF.beta. superfamily comprises activin
A.
21. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells has been passaged using a
protease or by disrupting contacts between cells.
22. The cell population of claim 21, wherein the protease is
trypsin.
23. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells is derived from human
embryonic stem cells (hESCs).
24. The cell population of claim 12, wherein the population of
passaged human definitive endoderm cells is substantially free of
pluripotent cells.
25. The cell population of claim 24, wherein at least 1 passaged
human definitive endoderm cell is present for every 5 pluripotent
cells.
26. A method of making passaged human definitive endoderm cells in
vitro comprising passaging definitive endoderm cells thereby
forming passaged human definitive endoderm cells.
27. The method of claim 26, wherein the passaged human definitive
endoderm cells express SOX17, GSC, MIXL1 or CXCR4.
28. The method of claim 26, wherein the passaged human definitive
endoderm cells do not express Oct4, Brachyury, ZIC1 or SOX1.
29. The method of claim 26, wherein the definitive endoderm cells
are passaged at least twice.
30. The method of claim 26, wherein the definitive endoderm cells
are derived from human embryonic stem cells (hESCs).
31. The method of claim 26, wherein 1 passaged human definitive
endoderm cell is present for every 5 pluripotent cell.
32. A method of expanding human definitive endoderm cells in vitro
comprising passaging definitive endoderm cells thereby expanding
human definitive endoderm cells.
Description
RELATED APPLICATIONS
[0001] This application is a division of and claims priority to
U.S. patent application Ser. No. 11/317,387, entitled EXPANSION OF
DEFINITIVE ENDODERM CELLS, filed Dec. 22, 2005, which is a
continuation-in-part of and claims priority to U.S. patent
application Ser. No. 11/021,618, entitled DEFINITIVE ENDODERM,
filed Dec. 23, 2004, now U.S. Pat. No. 7,510,876, issued Mar. 31,
2009, which claims priority under 35 U.S.C. .sctn.119(e) as a
nonprovisional application to U.S. Provisional Patent Application
No. 60/587,942, entitled CHEMOKINE CELL SURFACE RECEPTOR FOR THE
ISOLATION OF DEFINITIVE ENDODERM, filed Jul. 14, 2004, U.S.
Provisional Patent Application No. 60/586,566, entitled CHEMOKINE
CELL SURFACE RECEPTOR FOR THE ISOLATION OF DEFINITIVE ENDODERM,
filed Jul. 9, 2004 and U.S. Provisional Patent Application No.
60/532,004, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2003; U.S.
patent application Ser. No. 11/317,387 is also a nonprovisional
application of and claims priority to U.S. Provisional Patent
Application No. 60/693,317, entitled EXPANSION OF ISOLATED
DEFINITIVE ENDODERM CELLS, filed Jun. 23, 2005 and a nonprovisional
application of and claims priority to U.S. Provisional Patent
Application No. 60/736,598, entitled MARKERS OF DEFINITIVE
ENDODERM, filed Nov. 14, 2005.
FIELD OF THE INVENTION
[0002] The present invention relates to the fields of medicine and
cell biology. In particular, the present invention relates to
compositions of definitive endoderm cells which have been expanded
either prior to or subsequent to enrichment, isolation and/or
purification as well as methods of producing and using such
cells.
BACKGROUND
[0003] Human pluripotent stem cells, such as embryonic stem (ES)
cells and embryonic germ (EG) cells, were first isolated in culture
without fibroblast feeders in 1994 (Bongso et al., 1994) and with
fibroblast feeders (Hogan, 1997). Later, Thomson, Reubinoff and
Shamblott established continuous cultures of human ES and EG cells
using mitotically inactivated mouse feeder layers (Reubinoff et
al., 2000; Shamblott et al., 1998; Thomson et al., 1998).
[0004] Human ES and EG cells (hESCs) offer unique opportunities for
investigating early stages of human development as well as for
therapeutic intervention in several disease states, such as
diabetes mellitus and Parkinson's disease. For example, the use of
insulin-producing .beta.-cells derived from hESCs would offer a
vast improvement over current cell therapy procedures that utilize
cells from donor pancreases for the treatment of diabetes. However,
presently it is not known how to generate an insulin-producing
.beta.-cell from hESCs. As such, current cell therapy treatments
for diabetes mellitus, which utilize islet cells from donor
pancreases, are limited by the scarcity of high quality islet cells
needed for transplant. Cell therapy for a single Type I diabetic
patient requires a transplant of approximately 8.times.10.sup.8
pancreatic islet cells. (Shapiro et al., 2000; Shapiro et al.,
2001a; Shapiro et al., 2001b). As such, at least two healthy donor
organs are required to obtain sufficient islet cells for a
successful transplant. Human embryonic stem cells offer a source of
starting material from which to develop substantial quantities of
high quality differentiated cells for human cell therapies.
[0005] Two properties that make hESCs uniquely suited to cell
therapy applications are pluripotence and the ability to maintain
these cells in culture for prolonged periods. Pluripotency is
defined by the ability of hESCs to differentiate to derivatives of
all 3 primary germ layers (endoderm, mesoderm, ectoderm) which, in
turn, form all somatic cell types of the mature organism in
addition to extraembryonic tissues (e.g. placenta) and germ cells.
Although pluripotency imparts extraordinary utility upon hESCs,
this property also poses unique challenges for the study and
manipulation of these cells and their derivatives. Owing to the
large variety of cell types that may arise in differentiating hESC
cultures, the vast majority of cell types are produced at very low
efficiencies in mixed cell populations. In order to use hESCs as a
starting material to generate cells that are useful in cell therapy
applications, it would be advantageous to overcome the foregoing
problems.
SUMMARY OF THE INVENTION
[0006] Embodiments of the present invention relate to cell cultures
comprising expanded definitive endoderm cells. Further embodiments
described herein relate to methods for expanding enriched, isolated
and/or purified definitive endoderm cells in culture.
[0007] Some of the methods described herein relate to the
maintenance, growth, passage and/or expansion of definitive
endoderm cells in cell culture. In such embodiments, cell cultures
comprising definitive endoderm cells are obtained. The cells are
then isolated so that at least some of the definitive endoderm
cells are separated from at least some of the other cells in the
cell culture, thereby producing a cell population that is enriched
in definitive endoderm cells. In some embodiments, the enriched
cell populations of definitive endoderm cells are cultured under
conditions that permit the expansion of the definitive endoderm
cells.
[0008] In other embodiments of the methods described herein, the
definitive endoderm cells are multipotent cells that can
differentiate into cells of the gut tube or organs derived
therefrom. In preferred embodiments, the definitive endoderm cells
are human definitive endoderm cells that are obtained by
differentiating human embryonic stem cells (hESCs). In such
embodiments, definitive endoderm cells can be derived from hESCs by
contacting such cells with at least one growth factor from the
TGF.beta. superfamily, such as activin A. In other embodiments,
human and/or other definitive endoderm cells can be obtained from a
pre-existing culture of definitive endoderm cells. In such
embodiments, either a portion of or the entire culture may be used
in the definitive endoderm expansion methods described herein.
[0009] In addition to obtaining cell cultures comprising definitive
endoderm cells, some embodiments of the expansion methods described
herein also comprise the step of producing enriched definitive
endoderm cell populations. In some embodiments, such enriched
definitive endoderm cell populations are produced by separating at
least some of the definitive endoderm cells from at least some of
the other cells in the cell cultures. As such, the at least some of
the definitive endoderm cells are isolated from at least some of
the other cells which remain in the cell culture. In some
embodiments, the isolating step comprises providing the cells in
the cell culture with a reagent which binds to a marker expressed
in said definitive endoderm cells but which is not substantially
expressed in said other cells present in the cell culture. The
reagent-bound definitive endoderm cells are then separated from the
non-reagent-bound cells, thereby producing an enriched definitive
endoderm cell population. In some embodiments, the marker is CXCR4
and the reagent is an antibody with an affinity for CXCR4. In some
embodiments, the definitive endoderm cells are separated by
fluorescence activated cell sorting (FACS).
[0010] In still other embodiments, at least some of the definitive
endoderm cells are separated from at least some of the other cells
in the culture by specifically fluorescently labeling the
definitive endoderm cells in culture and then separating the
labeled cells from the unlabeled cells by FACS. In some
embodiments, the fluorescence is produced by green fluorescent
protein (GFP) or enhanced green fluorescent protein (EGFP). In some
embodiments, the GFP and/or EGFP is expressed under the control of
the SOX17 or the CXCR4 promoter.
[0011] In some embodiments, the enriched definitive endoderm cell
populations that are produced as described above are substantially
free of cells other than definitive endoderm cells. In other
embodiments, the enriched definitive endoderm cell populations
comprise from at least about 96% to at least about 100% definitive
endoderm cells.
[0012] Additional embodiments of the methods described herein also
include a culturing step that comprises plating the population
enriched in definitive endoderm cells or a portion of the
population. In some embodiments, the cells are plated on a surface
coated with human fibronectin and/or poly-ornithine. In other
embodiments, the culturing step comprises incubating the enriched
definitive endoderm cell population or portion thereof in a medium
comprising about 2% (v/v) serum. In some embodiments, the medium
also comprises at least one growth factor. In certain embodiments,
the at least one growth factor is a growth factor comprises a
member of the TGF.beta. superfamily, such as activin A.
Alternatively, the growth factor can be IGF1, bFGF, EGF or another
growth factor. In such embodiments, the growth factor can be
present in the medium at a concentration ranging from about 1 ng/ml
to about 5000 ng/ml. In some embodiments, a combination of growth
factors is present in the culture medium.
[0013] Additional embodiments described herein relate to methods of
expanding definitive endoderm cells in culture by obtaining a cell
culture comprising definitive endoderm cells and then passaging the
definitive endoderm cells so as to produce a plurality of cell
cultures comprising definitive endoderm cells. In some embodiments,
the definitive endoderm cells obtained in cell culture are attached
to a substrate, such as the surface of a cell culture flask or the
surface of a microtiter plate. In some embodiments, the definitive
endoderm cells are passaged using enzymatic methods. In other
embodiments, the definitive endoderm cells are mechanically
passaged. In yet other embodiments, the definitive endoderm cells
are passage using a cell dispersal buffer.
[0014] Still other embodiments described herein relate to expanded
definitive endoderm cell cultures and/or populations produced by
the methods described herein. In such embodiments, the definitive
endoderm cells are multipotent cells that can differentiate into
cells of the gut tube or organs derived therefrom.
[0015] In certain jurisdictions, there may not be any generally
accepted definition of the term "comprising." As used herein, the
term "comprising" is intended to represent "open" language which
permits the inclusion of any additional elements. With this in
mind, additional embodiments of the present inventions are
described with reference to the numbered paragraphs below:
[0016] 1. A method of expanding definitive endoderm cells in
culture, said method comprising the steps of: (a) obtaining a cell
culture comprising definitive endoderm cells, (b) isolating at
least some of the definitive endoderm cells from at least some of
the other cells in the cell culture, thereby producing a cell
population enriched in definitive endoderm cells; and (c) culturing
said cell population enriched in definitive endoderm cells under
conditions that permit the expansion of said definitive endoderm
cells.
[0017] 2. The method of paragraph 1, wherein said definitive
endoderm cells being multipotent cells that can differentiate into
cells of the gut tube or organs derived therefrom.
[0018] 3. The method of paragraph 1, wherein said definitive
endoderm cells are human definitive endoderm cells.
[0019] 4. The method of paragraph 3, wherein said definitive
endoderm cells are derived from human embryonic stem cells
(hESCs).
[0020] 5. The method of paragraph 4, wherein the obtaining step
comprises contacting hESCs with at least one growth factor from the
TGF.beta. superfamily so as to permit differentiation of at least
some of said hESCs to definitive endoderm cells.
[0021] 6. The method of paragraph 5, wherein said at least one
growth factor from the TGF.beta. superfamily comprises activin
A.
[0022] 7. The method of paragraph 1, wherein the step of obtaining
said cell culture comprising definitive endoderm further comprises
obtaining a portion of an existing definitive endoderm culture.
[0023] 8. The method of paragraph 1, wherein said cell population
enriched in definitive endoderm cells is substantially free of
cells other than definitive endoderm cells.
[0024] 9. The method of paragraph 1, wherein said cell population
enriched in definitive endoderm cells comprises at least about 96%
definitive endoderm cells.
[0025] 10. The method of paragraph 1, wherein said cell population
enriched in definitive endoderm cells comprises at least about 97%
definitive endoderm cells.
[0026] 11. The method of paragraph 1, wherein said cell population
enriched in definitive endoderm cells comprises at least about 98%
definitive endoderm cells.
[0027] 12. The method of paragraph 1, wherein said cell population
enriched in definitive endoderm cells comprises at least about 99%
definitive endoderm cells.
[0028] 13. The method of paragraph 1, wherein said cell population
enriched in definitive endoderm cells comprises about 100%
definitive endoderm cells.
[0029] 14. The method of paragraph 1, wherein said isolating step
comprises providing said cell culture with a reagent which binds to
a marker expressed in said definitive endoderm cells but which is
not substantially expressed in said other cells present in the cell
culture, and separating said definitive endoderm cells bound to
said reagent from said other cells present in the cell culture,
thereby producing a cell population enriched in definitive endoderm
cells.
[0030] 15. The method of paragraph 14, wherein said marker is
CXCR4.
[0031] 16. The method of paragraph 14, wherein said reagent is an
antibody.
[0032] 17. The method of paragraph 16, wherein said antibody has
affinity for CXCR4.
[0033] 18. The method of paragraph 14, wherein said definitive
endoderm cells bound to said reagent are separated from said other
cells present in the cell culture by fluorescence activated cell
sorting (FACS).
[0034] 19. The method of paragraph 1, wherein said isolating step
comprises separating fluorescently-labeled definitive endoderm
cells from unlabeled cells.
[0035] 20. The method of paragraph 19, wherein said
fluorescently-labeled definitive endoderm cells are labeled as a
result of the expression of enhanced green fluorescent protein
(EGFP).
[0036] 21. The method of paragraph 20, wherein the expression of
EGFP is under control of the SOX17 promoter.
[0037] 22. The method of paragraph 20, wherein the expression of
EGFP is under control of the CXCR4 promoter.
[0038] 23. The method of paragraph 19, wherein said
fluorescently-labeled definitive endoderm cells are separated from
unlabeled cells by FACS.
[0039] 24. The method of paragraph 1, wherein said culturing step
comprises plating said population enriched in definitive endoderm
cells or a portion thereof.
[0040] 25. The method of paragraph 24, wherein said population
enriched in definitive endoderm cells or a portion thereof is
plated on a surface coated with human fibronectin.
[0041] 26. The method of paragraph 25, wherein said surface is
coated with poly-ornithine.
[0042] 27. The method of paragraph 1, wherein said culturing step
comprises incubating said population enriched in definitive
endoderm cells or a portion thereof in a medium comprising about 2%
(v/v) serum.
[0043] 28. The method of paragraph 1, wherein said culturing step
comprises incubating said population enriched in definitive
endoderm cells or a portion thereof in a medium comprising greater
than about 2% (v/v) serum.
[0044] 29. The method of paragraph 1, wherein said culturing step
comprises incubating said population enriched in definitive
endoderm cells or a portion thereof in a medium comprising less
than about 2% (v/v) serum.
[0045] 30. The method of paragraph 1, wherein said culturing step
comprises incubating said population enriched in definitive
endoderm cells or a portion thereof in a medium comprising at least
one growth factor.
[0046] 31. The method of paragraph 30, wherein said at least one
growth factor is a growth factor from the TGF.beta. superfamily of
growth factors.
[0047] 32. The method of paragraph 31, wherein said at least one
growth factor from the TGF.beta. superfamily of growth factors
comprises activin A.
[0048] 33. The method of paragraph 32, wherein said activin A is
present in said medium at a concentration of about 100 ng/ml.
[0049] 34. The method of paragraph 30, wherein said at least one
growth factor comprises IGF1.
[0050] 35. The method of paragraph 34, wherein said IGF1 is present
in said medium at a concentration of about 100 ng/ml.
[0051] 36. The method of paragraph 30, wherein said at least one
growth factor comprises a combination of activin A and IGF1.
[0052] 37. The method of paragraph 30, wherein said at least one
growth factor comprises bFGF.
[0053] 38. The method of paragraph 37, wherein said bFGF is present
in said medium at a concentration of about 12 ng/ml.
[0054] 39. The method of paragraph 30, wherein said at least one
growth factor comprises EGF.
[0055] 40. The method of paragraph 39, wherein said EGF is present
in said medium at a concentration of about 10 ng/ml.
[0056] 41. The method of paragraph 30, wherein said at least one
growth factor comprises a combination of activin A, bFGF and
EGF.
[0057] 42. An expanded definitive endoderm cell population produced
by the method of paragraph 1.
[0058] 43. A method of expanding definitive endoderm cells in
culture, said method comprising the steps of: (a) obtaining a cell
culture comprising definitive endoderm cells, and (b) passaging
said definitive endoderm cells, thereby producing a plurality of
cell cultures comprising definitive endoderm cells.
[0059] 44. The method of paragraph 43, wherein the step of
passaging said definitive endoderm cells comprises providing at
least one enzyme to said cell culture.
[0060] 45. The method of paragraph 44, wherein said at least one
enzyme comprises at least one protease.
[0061] 46. The method of paragraph 45, wherein said at least one
protease comprises trypsin.
[0062] 47. The method of paragraph 43, wherein the step of
passaging said definitive endoderm cells comprises mechanically
disrupting contacts between said definitive endoderm cells.
[0063] 48. The method of paragraph 43, wherein the step of
passaging said definitive endoderm cells comprises incubating said
definitive endoderm cells in a cell dispersal buffer.
[0064] 49. The method of paragraph 43, wherein said definitive
endoderm cells are attached to a substrate.
[0065] 50. The method of paragraph 49, wherein the step of
passaging said definitive endoderm cells comprises detaching said
definitive endoderm cells from said substrate.
[0066] 51. The method of paragraph 50, wherein said substrate is a
surface of a tissue culture flask.
[0067] 52. The method of paragraph 50, wherein said substrate is a
surface of a microtiter plate.
[0068] 53. An expanded definitive endoderm cell population produced
by the method of paragraph 43.
[0069] It will be appreciated that the methods and compositions
described above relate to cells cultured in vitro. However, the
above-described in vitro differentiated cell compositions may be
used for in vivo applications.
[0070] Additional embodiments of the present invention may also be
found in U.S. Provisional Patent Application No. 60/532,004,
entitled DEFINITIVE ENDODERM, filed Dec. 23, 2003; U.S. Provisional
Patent Application No. 60/566,293, entitled PDX1 EXPRESSING
ENDODERM, filed Apr. 27, 2004; U.S. Provisional Patent Application
No. 60/586,566, entitled CHEMOKINE CELL SURFACE RECEPTOR FOR THE
ISOLATION OF DEFINITIVE ENDODERM, filed Jul. 9, 2004; U.S.
Provisional Patent Application No. 60/587,942, entitled CHEMOKINE
CELL SURFACE RECEPTOR FOR THE ISOLATION OF DEFINITIVE ENDODERM,
filed Jul. 14, 2004; U.S. patent application Ser. No. 11/021,618,
entitled DEFINITIVE ENDODERM, filed Dec. 23, 2004; U.S. patent
application Ser. No. 11/115,868, entitled PDX1 EXPRESSING ENDODERM,
filed Apr. 26, 2005; U.S. patent application Ser. No. 11/165,305,
entitled METHODS FOR IDENTIFYING FACTORS FOR DIFFERENTIATING
DEFINITIVE ENDODERM, filed Jun. 23, 2005; U.S. Provisional Patent
Application No. 60/693,364, entitled PREPRIMITIVE STREAK AND
MESENDODERM CELLS, filed Jun. 23, 2005; U.S. Provisional Patent
Application No. 60/693,317, entitled EXPANSION OF ISOLATED
DEFINITIVE ENDODERM CELLS, filed Jun. 23, 2005; and U.S.
Provisional Patent Application No. 60/736,598, entitled MARKERS OF
DEFINITIVE ENDODERM, filed Nov. 14, 2005, the disclosures of which
are incorporated herein by reference in their entireties.
BRIEF DESCRIPTION OF THE DRAWINGS
[0071] FIG. 1 is a schematic of a proposed differentiation pathway
for the production of beta-cells from hESCs. The first step in the
pathway commits the ES cell to the definitive endoderm lineage and
represents one of the earliest known steps in the further
differentiation of ES cells to pancreatic endoderm, endocrine
endoderm, or islet/beta-cell. Some factors useful for mediating
this transition are members of the TGF.beta. family which include,
but are not limited to, activins and nodals. Exemplary markers for
defining the definitive endoderm target cell are SOX17, GATA4,
HNF3b, MIX1 and CXCR4.
[0072] FIG. 2 is a diagram of the human SOX17 cDNA which displays
the positions of conserved motifs and highlights the region used
for the immunization procedure by GENOVAC.
[0073] FIG. 3 is a relational dendrogram illustrating that SOX17 is
most closely related to SOX7 and somewhat less to SOX18. The SOX17
proteins are more closely related among species homologs than to
other members of the SOX group F subfamily within the same
species.
[0074] FIG. 4 is a Western blot probed with the rat anti-SOX17
antibody. This blot demonstrates the specificity of this antibody
for human SOX17 protein over-expressed in fibroblasts (lane 1) and
a lack of immunoreactivity with EGFP (lane 2) or the most closely
related SOX family member, SOX7 (lane 3).
[0075] FIGS. 5A-B are micrographs showing a cluster of SOX17.sup.+
cells that display a significant number of AFP.sup.+ co-labeled
cells (A). This is in striking contrast to other SOX17.sup.+
clusters (B) where little or no AFP.sup.+ cells are observed.
[0076] FIGS. 6A-C are micrographs showing parietal endoderm and
SOX17. Panel A shows immunocytochemistry for human Thrombomodulin
(TM) protein located on the cell surface of parietal endoderm cells
in randomly differentiated cultures of hES cells. Panel B is the
identical field shown in A double-labeled for TM and SOX17. Panel C
is the phase contrast image of the same field with DAPI labeled
nuclei. Note the complete correlation of DAPI labeled nuclei and
SOX17 labeling.
[0077] FIGS. 7A-B are bar charts showing SOX17 gene expression by
quantitative PCR (Q-PCR) and anti-SOX17 positive cells by
SOX17-specific antibody. Panel A shows that activin A increases
SOX17 gene expression while retinoic acid (RA) strongly suppresses
SOX17 expression relative to the undifferentiated control media
(SR20). Panel B shows the identical pattern as well as a similar
magnitude of these changes is reflected in SOX17.sup.+ cell number,
indicating that Q-PCR measurement of SOX17 gene expression is very
reflective of changes at the single cell level.
[0078] FIG. 8A is a bar chart which shows that a culture of
differentiating hESCs in the presence of activin A maintains a low
level of AFP gene expression while cells allowed to randomly
differentiate in 10% fetal bovine serum (FBS) exhibit a strong
upregulation of AFP. The difference in expression levels is
approximately 7-fold.
[0079] FIGS. 8B-C are images of two micrographs showing that the
suppression of AFP expression by activin A is also evident at the
single cell level as indicated by the very rare and small clusters
of AFP.sup.+ cells observed in activin A treatment conditions
(bottom) relative to 10% FBS alone (top).
[0080] FIGS. 9A-B are comparative images showing the quantitation
of the AFP.sup.+ cell number using flow cytometry. This figure
demonstrates that the magnitude of change in AFP gene expression
(FIG. 8A) in the presence (right panel) and absence (left panel) of
activin A exactly corresponds to the number of AFP.sup.+ cells,
further supporting the utility of Q-PCR analyses to indicate
changes occurring at the individual cell level.
[0081] FIGS. 10A-F are micrographs which show that exposure of
hESCs to nodal, activin A and activin B (NAA) yields a striking
increase in the number of SOX17.sup.+ cells over the period of 5
days (A-C). By comparing to the relative abundance of SOX17.sup.+
cells to the total number of cells present in each field, as
indicated by DAPI stained nuclei (D-F), it can be seen that
approximately 30-50% of all cells are immunoreactive for SOX17
after five days treatment with NAA.
[0082] FIG. 11 is a bar chart which demonstrates that activin A (0,
10, 30 or 100 ng/ml) dose-dependently increases SOX 17 gene
expression in differentiating hESCs. Increased expression is
already robust after 3 days of treatment on adherent cultures and
continues through subsequent 1, 3 and 5 days of suspension culture
as well.
[0083] FIGS. 12A-C are bar charts which demonstrate the effect of
activin A on the expression of MIXL1 (panel A), GATA4 (panel B) and
HNF3b (panel C). Activin A dose-dependent increases are also
observed for three other markers of definitive endoderm; MIXL1,
GATA4 and HNF3b. The magnitudes of increased expression in response
to activin dose are strikingly similar to those observed for SOX17,
strongly indicating that activin A is specifying a population of
cells that co-express all four genes (SOX17.sup.+, MIXL1.sup.+,
GATA4.sup.+ and HNF3b.sup.+).
[0084] FIGS. 13A-C are bar charts which demonstrate the effect of
activin A on the expression of AFP (panel A), SOX7 (panel B) and
SPARC (panel C). There is an activin A dose-dependent decrease in
expression of the visceral endoderm marker AFP. Markers of
primitive endoderm (SOX7) and parietal endoderm (SPARC) remain
either unchanged or exhibit suppression at some time points
indicating that activin A does not act to specify these
extra-embryonic endoderm cell types. This further supports the fact
that the increased expression of SOX17, MIXL1, GATA4, and HNF3b are
due to an increase in the number of definitive endoderm cells in
response to activin A.
[0085] FIGS. 14A-B are bar charts showing the effect of activin A
on ZIC1 (panel A) and Brachyury expression (panel B) Consistent
expression of the neural marker ZIC1 demonstrates that there is not
a dose-dependent effect of activin A on neural differentiation.
There is a notable suppression of mesoderm differentiation mediated
by 100 ng/ml of activin A treatment as indicated by the decreased
expression of brachyury. This is likely the result of the increased
specification of definitive endoderm from the mesendoderm
precursors. Lower levels of activin A treatment (10 and 30 ng/ml)
maintain the expression of brachyury at later time points of
differentiation relative to untreated control cultures.
[0086] FIGS. 15A-B are micrographs showing decreased parietal
endoderm differentiation in response to treatment with activins.
Regions of TM.sup.hi parietal endoderm are found through the
culture (A) when differentiated in serum alone, while
differentiation to TM.sup.+ cells is scarce when activins are
included (B) and overall intensity of TM immunoreactivity is
lower.
[0087] FIGS. 16A-D are micrographs which show marker expression in
response to treatment with activin A and activin B. hESCs were
treated for four consecutive days with activin A and activin B and
triple labeled with SOX17, AFP and TM antibodies. Panel A--SOX17;
Panel B--AFP; Panel C--TM; and Panel D--Phase/DAPI. Notice the
numerous SOX17 positive cells (A) associated with the complete
absence of AFP (B) and TM (C) immunoreactivity.
[0088] FIG. 17 is a micrograph showing the appearance of definitive
endoderm and visceral endoderm in vitro from hESCs. The regions of
visceral endoderm are identified by AFP.sup.hi/SOX17.sup.lo/- while
definitive endoderm displays the complete opposite profile,
SOX17.sup.hi/AFP.sup.lo/-. This field was selectively chosen due to
the proximity of these two regions to each other. However, there
are numerous times when SOX17.sup.hi/AFP.sup.lo/- regions are
observed in absolute isolation from any regions of AFP.sup.hi
cells, suggesting the separate origination of the definitive
endoderm cells from visceral endoderm cells.
[0089] FIG. 18 is a diagram depicting the TGF.beta. family of
ligands and receptors. Factors activating AR Smads and BR Smads are
useful in the production of definitive endoderm from human
embryonic stem cells (see, J Cell Physiol. 187:265-76).
[0090] FIG. 19 is a bar chart showing the induction of SOX17
expression over time as a result of treatment with individual and
combinations of TGF.beta. factors.
[0091] FIG. 20 is a bar chart showing the increase in SOX17.sup.+
cell number with time as a result of treatment with combinations of
TGF.beta. factors.
[0092] FIG. 21 is a bar chart showing induction of SOX17 expression
over time as a result of treatment with combinations of TGF.beta.
factors.
[0093] FIG. 22 is a bar chart showing that activin A induces a
dose-dependent increase in SOX17.sup.+ cell number.
[0094] FIG. 23 is a bar chart showing that addition of Wnt3a to
activin A and activin B treated cultures increases SOX17 expression
above the levels induced by activin A and activin B alone.
[0095] FIGS. 24A-C are bar charts showing differentiation to
definitive endoderm is enhanced in low FBS conditions. Treatment of
hESCs with activins A and B in media containing 2% FBS (2AA) yields
a 2-3 times greater level of SOX17 expression as compared to the
same treatment in 10% FBS media (10AA) (panel A). Induction of the
definitive endoderm marker MIXL1 (panel B) is also affected in the
same way and the suppression of AFP (visceral endoderm) (panel C)
is greater in 2% FBS than in 10% FBS conditions.
[0096] FIGS. 25A-D are micrographs which show SOX17.sup.+ cells are
dividing in culture. SOX17 immunoreactive cells are present at the
differentiating edge of an hESC colony (C, D) and are labeled with
proliferating cell nuclear antigen (PCNA) (panel B) yet are not
co-labeled with OCT4 (panel C). In addition, clear mitotic figures
can be seen by DAPI labeling of nuclei in both SOX17.sup.+ cells
(arrows) as well as OCT4.sup.+, undifferentiated hESCs (arrowheads)
(D).
[0097] FIG. 26 is a bar chart showing the relative expression level
of CXCR4 in differentiating hESCs under various media
conditions.
[0098] FIGS. 27A-D are bar charts that show how a panel of
definitive endoderm markers share a very similar pattern of
expression to CXCR4 across the same differentiation treatments
displayed in FIG. 26.
[0099] FIGS. 28A-E are bar charts showing how markers for mesoderm
(BRACHYURY, MOX1), ectoderm (SOX1, ZIC1) and visceral endoderm
(SOX7) exhibit an inverse relationship to CXCR4 expression across
the same treatments displayed in FIG. 26.
[0100] FIGS. 29A-F are micrographs that show the relative
difference in SOX17 immunoreactive cells across three of the media
conditions displayed in FIGS. 26-28.
[0101] FIGS. 30A-C are flow cytometry dot plots that demonstrate
the increase in CXCR4.sup.+ cell number with increasing
concentration of activin A added to the differentiation media.
[0102] FIGS. 31A-D are bar charts that show the CXCR4.sup.+ cells
isolated from the high dose activin A treatment (A100-CX+) are even
further enriched for definitive endoderm markers than the parent
population (A100).
[0103] FIG. 32 is a bar chart showing gene expression from
CXCR4.sup.+ and CXCR4.sup.- cells isolated using
fluorescence-activated cell sorting (FACS) as well as gene
expression in the parent populations. This demonstrates that the
CXCR4.sup.+ cells contain essentially all the CXCR4 gene expression
present in each parent population and the CXCR4.sup.- populations
contain very little or no CXCR4 gene expression.
[0104] FIGS. 33A-D are bar charts that demonstrate the depletion of
mesoderm (BRACHYURY, MOX1), ectoderm (ZIC1) and visceral endoderm
(SOX7) gene expression in the CXCR4+ cells isolated from the high
dose activin A treatment which is already suppressed in expression
of these non-definitive endoderm markers.
[0105] FIGS. 34A-M are bar charts showing the expression patterns
of marker genes that can be used to identify definitive endoderm
cells. The expression analysis of definitive endoderm markers,
FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1 is shown in panels G-L,
respectively. The expression analysis of previously described
lineage marking genes, SOX17, SOX7, SOX17/SOX7, TM, ZIC1, and MOX1
is shown in panels A-F, respectively. Panel M shows the expression
analysis of CXCR4. With respect to each of panels A-M, the column
labeled hESC indicates gene expression from purified human
embryonic stem cells; 2NF indicates cells treated with 2% FBS, no
activin addition; 0.1A100 indicates cells treated with 0.1% FBS,
100 ng/ml activin A; 1A100 indicates cells treated with 1% FBS, 100
ng/ml activin A; and 2A100 indicates cells treated with 2% FBS, 100
ng/ml activin A.
[0106] FIGS. 35A-D are bar charts showing the expression patterns
of definitive endoderm marker genes in cell cultures maintained for
36 days under various growth conditions. The expression analysis of
definitive endoderm markers SOX17, GSC, MIXL1 and CXCR4 is shown in
panels A-D, respectively. EB and EV are used to designate to
separate cell populations each from the hCyT25 hESC line. The
abbreviation NF indicates cells grown in the absence of activin A,
whereas A100 indicates cells grown in the presence of 100 ng/ml
this factor. EGF indicates 50 ng/ml epidermal growth factor.
[0107] FIG. 36 is a diagram showing the cell differentiation,
isolation and expansion procedure for definitive endoderm cells.
The abbreviations are as follows: hESC refers to human embryonic
stem cells; d5 hESC-DE refers to unpurified definitive endoderm
cells; d6 FACS-DE refers to CXCR4 antibody/FACS purified definitive
endoderm cells; and p1 d10 FACS-DE refers to purified definitive
endoderm cells that have been passaged once and grown for 10
additional days subsequent to passage. RNA samples are taken and
analyzed for marker expression at each of the indicated days.
[0108] FIGS. 37A-F are bar charts showing the expression patterns
of various embryonic cell lineage marker genes in cell cultures
that have been differentiated to definitive endoderm then
subsequently purified using the CXCR4 antibody in conjunction with
fluorescence activated cell sorting (FACS). The abbreviations are
as follows: p96 hESC refers to mRNA from the 96.sup.th passage of
CyT25 human embryonic stem cells; d5 DE refers to mRNA from
unpurified definitive endoderm cells on the fifth day of
differentiation from p96 hESCs; NF d6-FACS refers to mRNA taken 11
days post differentiation from CXCR4 antibody/FACS purified
definitive endoderm cells incubated in the absence of activin A; A
refers to mRNA taken 11 days post differentiation from CXCR4
antibody/FACS purified definitive endoderm cells incubated in the
presence of 100 ng/ml activin A; AI refers to mRNA taken 11 days
post differentiation from CXCR4 antibody/FACS purified definitive
endoderm cells incubated in the presence of 100 ng/ml activin A and
100 ng/ml IGF1; AFE refers to mRNA taken 11 days post
differentiation from CXCR4 antibody/FACS purified definitive
endoderm cells incubated in the presence of 100 ng/ml activin A, 12
ng/ml bFGF and 10 ng/ml EGF; NF p1-d10-FACS refers to mRNA taken 10
days post passage of CXCR4 antibody/FACS purified definitive
endoderm cells incubated in the absence of activin A; A refers to
mRNA taken 10 days post passage from CXCR4 antibody/FACS purified
definitive endoderm cells incubated in the presence of 100 ng/ml
activin A; AI refers to mRNA taken 10 days post passage from CXCR4
antibody/FACS purified definitive endoderm cells incubated in the
presence of 100 ng/ml activin A and 100 ng/ml IGF1; and AFE refers
to mRNA taken 10 days post passage from CXCR4 antibody/FACS
purified definitive endoderm cells incubated in the presence of 100
ng/ml activin A, 12 ng/ml bFGF and 10 ng/ml EGF. Panel A--SOX17;
B--GSC; C--OCT4; D--Brachyury; E--ZIC1; F--SOX1.
DETAILED DESCRIPTION
[0109] A crucial stage in early human development termed
gastrulation occurs 2-3 weeks after fertilization. Gastrulation is
extremely significant because it is at this time that the three
primary germ layers are first specified and organized (Lu et al.,
2001; Schoenwolf and Smith, 2000). The ectoderm is responsible for
the eventual formation of the outer coverings of the body and the
entire nervous system whereas the heart, blood, bone; skeletal
muscle and other connective tissues are derived from the mesoderm.
Definitive endoderm is defined as the germ layer that is
responsible for formation of the entire gut tube which includes the
esophagus, stomach and small and large intestines, and the organs
which derive from the gut tube such as the lungs, liver, thymus,
parathyroid and thyroid glands, gall bladder and pancreas
(Grapin-Botton and Melton, 2000; Kimelman and Griffin, 2000;
Tremblay et al., 2000; Wells and Melton, 1999; Wells and Melton,
2000). A very important distinction should be made between the
definitive endoderm and the completely separate lineage of cells
termed primitive endoderm. The primitive endoderm is primarily
responsible for formation of extra-embryonic tissues, mainly the
parietal and visceral endoderm portions of the placental yolk sac
and the extracellular matrix material of Reichert's membrane.
[0110] During gastrulation, the process of definitive endoderm
formation begins with a cellular migration event in which
mesendoderm cells (cells competent to form mesoderm or endoderm)
migrate through a structure called the primitive streak. Definitive
endoderm is derived from cells, which migrate through the anterior
portion of the streak and through the node (a specialized structure
at the anterior-most region of the streak). As migration occurs,
definitive endoderm populates first the most anterior gut tube and
culminates with the formation of the posterior end of the gut
tube.
[0111] Definitive endoderm and endoderm cells derived therefrom
represent important multipotent starting points for the derivation
of cells which make up terminally differentiated tissues and/or
organs derived from the definitive endoderm lineage. Such cells,
tissues and/or organs are extremely useful in cell therapies.
Because large numbers of cells are usually necessary for successful
cell therapy applications, it is beneficial to begin
differentiation procedures with large numbers of cells of a single
cell type. As embryonic stem cells in culture differentiate to
definitive endoderm, not every embryonic stem cell is converted to
the definitive endoderm cell type. To overcome this problem,
definitive endoderm cells growing in mixed cell cultures can be
enriched, isolated and/or purified using the methodology described
herein. After such enrichment, isolation and/or purification, the
resulting definitive endoderm cells may not be easy to grow in
culture. Methods described herein improve the ability of enriched,
isolated and/or purified definitive endoderm cells to grow and
expand in cell culture. Because definitive endoderm cells can now
be expanded in culture subsequent to enrichment, isolation and/or
purification, cells, tissues and/or organs derived from definitive
endoderm cells can be produced in greater numbers.
[0112] Some embodiments of the present invention relate to methods
of expanding definitive endoderm cells in cell culture. In some
embodiments, definitive endoderm cells are enriched by separating
these cells from other cells in a mixed cell culture. The enriched
definitive endoderm cells are then cultured under conditions which
permit their expansion.
DEFINITIONS
[0113] Certain terms and phrases as used throughout this
application have the meanings provided as follows:
[0114] As used herein, "embryonic" refers to a range of
developmental stages of an organism beginning with a single zygote
and ending with a multicellular structure that no longer comprises
pluripotent or totipotent cells other than developed gametic cells.
In addition to embryos derived by gamete fusion, the term
"embryonic" refers to embryos derived by somatic cell nuclear
transfer.
[0115] As used herein, "multipotent" or "multipotent cell" refers
to a cell type that can give rise to a limited number of other
particular cell types.
[0116] As used herein, "expression" refers to the production of a
material or substance as well as the level or amount of production
of a material or substance. Thus, determining the expression of a
specific marker refers to detecting either the relative or absolute
amount of the marker that is expressed or simply detecting the
presence or absence of the marker.
[0117] As used herein, "marker" refers to any molecule that can be
observed or detected. For example, a marker can include, but is not
limited to, a nucleic acid, such as a transcript of a specific
gene, a polypeptide product of a gene, a non-gene product
polypeptide, a glycoprotein, a carbohydrate, a glycolipd, a lipid,
a lipoprotein or a small molecule (for example, molecules having a
molecular weight of less than 10,000 amu)
[0118] When used in connection with cell cultures and/or cell
populations, the term "portion" means any non-zero amount of the
cell culture or cell population, which ranges from a single cell to
the entirety of the cell culture or cells population.
[0119] With respect to cells in cell cultures or in cell
populations, the phrase "substantially free of" means that the
specified cell type of which the cell culture or cell population is
free, is present in an amount of less than about 5% of the total
number of cells present in the cell culture or cell population.
[0120] With respect to cell culture medium, as used herein, "low
serum RPMI" refers to a low serum containing medium, wherein the
serum concentration is gradually increased over a defined time
period. For example, in one embodiment, low serum RPMI comprises a
concentration of about 0.2% fetal bovine serum (FBS) on the first
day of cell growth, about 0.5% FBS on the second day of cell growth
and about 2% FBS on the third through fifth day of cell growth. In
another embodiment, low serum RPMI comprises a concentration of
about 0% on day one, about 0.2% on day two and about 2% on the
third and subsequent days.
[0121] As used herein, the terms "bFGF" and "FGF2" are used
interchangeably.
Definitive Endoderm Cells and Processes Related Thereto
[0122] Embodiments described herein relate to novel, defined
processes for the production of definitive endoderm cells in
culture by differentiating pluripotent cells, such as stem cells
into multipotent definitive endoderm cells. As described above,
definitive endoderm cells do not differentiate into tissues
produced from ectoderm or mesoderm, but rather, differentiate into
the gut tube as well as organs that are derived from the gut tube.
In certain preferred embodiments, the definitive endoderm cells are
derived from hESCs. Such processes can provide the basis for
efficient production of human endodermal derived tissues such as
pancreas, liver, lung, stomach, intestine, thyroid and thymus. For
example, production of definitive endoderm may be the first step in
differentiation of a stem cell to a functional insulin-producing
.beta.-cell. To obtain useful quantities of insulin-producing
.beta.-cells, high efficiency of differentiation is desirable for
each of the differentiation steps that occur prior to reaching the
pancreatic islet/.beta.-cell fate. Since differentiation of stem
cells to definitive endoderm cells represents perhaps the earliest
step towards the production of functional pancreatic
islet/.beta.-cells (as shown in FIG. 1), high efficiency of
differentiation at this step is particularly desirable.
[0123] In view of the desirability of efficient differentiation of
pluripotent cells to definitive endoderm cells, some aspects of the
differentiation processes described herein relate to in vitro
methodology that results in approximately 50-80% conversion of
pluripotent cells to definitive endoderm cells. Typically, such
methods encompass the application of culture and growth factor
conditions in a defined and temporally specified fashion. Further
enrichment of the cell population for definitive endoderm cells can
be achieved by isolation and/or purification of the definitive
endoderm cells from other cells in the population by using a
reagent that specifically binds to definitive endoderm cells. As
such, some embodiments described herein relate to definitive
endoderm cells as well as methods for producing and isolating
and/or purifying such cells.
[0124] In order to determine the amount of definitive endoderm
cells in a cell culture or cell population, a method of
distinguishing this cell type from the other cells in the culture
or in the population is desirable. Accordingly, certain embodiments
described herein relate to cell markers whose presence, absence
and/or relative expression levels are specific for definitive
endoderm and methods for detecting and determining the expression
of such markers.
[0125] In some embodiments described herein, the presence, absence
and/or level of expression of a marker is determined by
quantitative PCR (Q-PCR). For example, the amount of transcript
produced by certain genetic markers, such as SOX17, CXCR4, OCT4,
AFP, TM, SPARC, SOX7, MIXL1, GATA4, HNF3b, GSC, FGF17, VWF, CALCR,
FOXQ1, CMKOR1, CRIP1 and other markers described herein is
determined by quantitative Q-PCR. In other embodiments,
immunohistochemistry is used to detect the proteins expressed by
the above-mentioned genes. In still other embodiments, Q-PCR and
immunohistochemical techniques are both used to identify and
determine the amount or relative proportions of such markers.
[0126] By using methods, such as those described above, to
determine the expression of one or more appropriate markers, it is
possible to identify definitive endoderm cells, as well as
determine the proportion of definitive endoderm cells in a cell
culture or cell population. For example, in some embodiments of the
present invention, the definitive endoderm cells or cell
populations that are produced express the SOX17 and/or the CXCR4
gene at a level of about 2 orders of magnitude greater than
non-definitive endoderm cell types or cell populations. In other
embodiments, the definitive endoderm cells or cell populations that
are produced express the SOX17 and/or the CXCR4 gene at a level of
more than 2 orders of magnitude greater than non-definitive
endoderm cell types or cell populations. In still other
embodiments, the definitive endoderm cells or cell populations that
are produced express one or more of the markers selected from the
group consisting of SOX17, CXCR4, GSC, FGF17, VWF, CALCR, FOXQ1,
CMKOR1 and CRIP1 at a level of about 2 or more than 2 orders of
magnitude greater than non-definitive endoderm cell types or cell
populations. In some embodiments described herein, definitive
endoderm cells do not substantially express PDX1.
[0127] Embodiments described herein also relate to definitive
endoderm compositions. For example, some embodiments relate to cell
cultures comprising definitive endoderm, whereas others relate to
cell populations enriched in definitive endoderm cells. Some
preferred embodiments relate to cell cultures which comprise
definitive endoderm cells, wherein at least about 50-80% of the
cells in culture are definitive endoderm cells. An especially
preferred embodiment relates to cells cultures comprising human
cells, wherein at least about 50-80% of the human cells in culture
are definitive endoderm cells. Because the efficiency of the
differentiation procedure can be adjusted by modifying certain
parameters, which include but are not limited to, cell growth
conditions, growth factor concentrations and the timing of culture
steps, the differentiation procedures described herein can result
in about 5%, about 10%, about 15%, about 20%, about 25%, about 30%,
about 35%, about 40%, about 45%, about 50%, about 55%, about 60%,
about 65%, about 70%, about 75%, about 80%, about 85%, about 90%,
about 95%, or greater than about 95% conversion of pluripotent
cells to definitive endoderm. In other preferred embodiments,
conversion of a pluripotent cell population, such as a stem cell
population, to substantially pure definitive endoderm cell
population is contemplated.
[0128] The compositions and methods described herein have several
useful features. For example, the cell cultures and cell
populations comprising definitive endoderm as well as the methods
for producing such cell cultures and cell populations are useful
for modeling the early stages of human development. Furthermore,
the compositions and methods described herein can also serve for
therapeutic intervention in disease states, such as diabetes
mellitus. For example, since definitive endoderm serves as the
source for only a limited number of tissues, it can be used in the
development of pure tissue or cell types.
Production of Definitive Endoderm from Pluripotent Cells
[0129] Processes for differentiating pluripotent cells to produce
cell cultures and enriched cell populations comprising definitive
endoderm is described below and in U.S. patent Ser. No. 11/021,618,
entitled DEFINITIVE ENDODERM, filed Dec. 23, 2004, the disclosure
of which is incorporated herein by reference in its entirety. In
some of these processes, the pluripotent cells used as starting
material are stem cells. In certain processes, definitive endoderm
cell cultures and enriched cell populations comprising definitive
endoderm cells are produced from embryonic stem cells. A preferred
method for deriving definitive endoderm cells utilizes human
embryonic stem cells as the starting material for definitive
endoderm production. Such pluripotent cells can be cells that
originate from the morula, embryonic inner cell mass or those
obtained from embryonic gonadal ridges. Human embryonic stem cells
can be maintained in culture in a pluripotent state without
substantial differentiation using methods that are known in the
art. Such methods are described, for example, in U.S. Pat. Nos.
5,453,357, 5,670,372, 5,690,926 5,843,780, 6,200,806 and 6,251,671
the disclosures of which are incorporated herein by reference in
their entireties.
[0130] In some processes for producing definitive endoderm cells,
hESCs are maintained on a feeder layer. In such processes, any
feeder layer which allows hESCs to be maintained in a pluripotent
state can be used. One commonly used feeder layer for the
cultivation of human embryonic stem cells is a layer of mouse
fibroblasts. More recently, human fibroblast feeder layers have
been developed for use in the cultivation of hESCs (see US Patent
Application No. 2002/0072117, the disclosure of which is
incorporated herein by reference in its entirety). Alternative
processes for producing definitive endoderm permit the maintenance
of pluripotent hESC without the use of a feeder layer. Methods of
maintaining pluripotent hESCs under feeder-free conditions have
been described in US Patent Application No. 2003/0175956, the
disclosure of which is incorporated herein by reference in its
entirety.
[0131] The human embryonic stem cells used herein can be maintained
in culture either with or without serum. In some embryonic stem
cell maintenance procedures, serum replacement is used. In others,
serum free culture techniques, such as those described in US Patent
Application No. 2003/0190748, the disclosure of which is
incorporated herein by reference in its entirety, are used.
[0132] Stem cells are maintained in culture in a pluripotent state
by routine passage until it is desired that they be differentiated
into definitive endoderm. In some processes, differentiation to
definitive endoderm is achieved by providing to the stem cell
culture a growth factor of the TGF.beta. superfamily in an amount
sufficient to promote differentiation to definitive endoderm.
Growth factors of the TGF.beta. superfamily which are useful for
the production of definitive endoderm are selected from the
Nodal/Activin or BMP subgroups. In some preferred differentiation
processes, the growth factor is selected from the group consisting
of Nodal, activin A, activin B and BMP4. Additionally, the growth
factor Wnt3a and other Wnt family members are useful for the
production of definitive endoderm cells. In certain differentiation
processes, combinations of any of the above-mentioned growth
factors can be used.
[0133] With respect to some of the processes for the
differentiation of pluripotent stem cells to definitive endoderm
cells, the above-mentioned growth factors are provided to the cells
so that the growth factors are present in the cultures at
concentrations sufficient to promote differentiation of at least a
portion of the stem cells to definitive endoderm cells. In some
processes, the above-mentioned growth factors are present in the
cell culture at a concentration of at least about 5 ng/ml, at least
about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml,
at least about 75 ng/ml, at least about 100 ng/ml, at least about
200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at
least about 500 ng/ml, at least about 1000 ng/ml, at least about
2000 ng/ml, at least about 3000 ng/ml, at least about 4000 ng/ml,
at least about 5000 ng/ml or more than about 5000 ng/ml.
[0134] In certain processes for the differentiation of pluripotent
stem cells to definitive endoderm cells, the above-mentioned growth
factors are removed from the cell culture subsequent to their
addition. For example, the growth factors can be removed within
about one day, about two days, about three days, about four days,
about five days, about six days, about seven days, about eight
days, about nine days or about ten days after their addition. In a
preferred processes, the growth factors are removed about four days
after their addition.
[0135] Cultures of definitive endoderm cells can be grown in medium
containing reduced serum or no serum. Under certain culture
conditions, serum concentrations can range from about 0.05% v/v to
about 20% v/v. For example, in some differentiation processes, the
serum concentration of the medium can be less than about 0.05%
(v/v), less than about 0.1% (v/v), less than about 0.2% (v/v), less
than about 0.3% (v/v), less than about 0.4% (v/v), less than about
0.5% (v/v), less than about 0.6% (v/v), less than about 0.7% (v/v),
less than about 0.8% (v/v), less than about 0.9% (v/v), less than
about 1% (v/v), less than about 2% (v/v), less than about 3% (v/v),
less than about 4% (v/v), less than about 5% (v/v), less than about
6% (v/v), less than about 7% (v/v), less than about 8% (v/v), less
than about 9% (v/v), less than about 10% (v/v), less than about 15%
(v/v) or less than about 20% (v/v). In some processes, definitive
endoderm cells are grown without serum or with serum replacement.
In still other processes, definitive endoderm cells are grown in
the presence of B27. In such processes, the concentration of B27
supplement can range from about 0.1% v/v to about 20% v/v.
Monitoring the Differentiation of Pluripotent Cells to Definitive
Endoderm
[0136] The progression of the hESC culture to definitive endoderm
can be monitored by determining the expression of markers
characteristic of definitive endoderm. In some processes, the
expression of certain markers is determined by detecting the
presence or absence of the marker. Alternatively, the expression of
certain markers can be determined by measuring the level at which
the marker is present in the cells of the cell culture or cell
population. In such processes, the measurement of marker expression
can be qualitative or quantitative. One method of quantitating the
expression of markers that are produced by marker genes is through
the use of quantitative PCR (Q-PCR). Methods of performing Q-PCR
are well known in the art. Other methods which are known in the art
can also be used to quantitate marker gene expression. For example,
the expression of a marker gene product can be detected by using
antibodies specific for the marker gene product of interest. In
certain processes, the expression of marker genes characteristic of
definitive endoderm as well as the lack of significant expression
of marker genes characteristic of hESCs and other cell types is
determined.
[0137] As described further in the Examples below, a reliable
marker of definitive endoderm is the SOX17 gene. As such, the
definitive endoderm cells produced by the processes described
herein express the SOX17 marker gene, thereby producing the SOX17
gene product. Other markers of definitive endoderm are MIXL1,
GATA4, HNF3b, GSC, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1.
Since definitive endoderm cells express the SOX17 marker gene at a
level higher than that of the SOX7 marker gene, which is
characteristic of primitive and visceral endoderm (see Table 1), in
some processes, the expression of both SOX17 and SOX7 is monitored.
In other processes, expression of the both the SOX17 marker gene
and the OCT4 marker gene, which is characteristic of hESCs, is
monitored. Additionally, because definitive endoderm cells express
the SOX17 marker gene at a level higher than that of the AFP, SPARC
or Thrombomodulin (TM) marker genes, the expression of these genes
can also be monitored.
[0138] Another marker of definitive endoderm is the CXCR4 gene. The
CXCR4 gene encodes a cell surface chemokine receptor whose ligand
is the chemoattractant SDF-1. The principal roles of the CXCR4
receptor-bearing cells in the adult are believed to be the
migration of hematopoetic cells to the bone marrow, lymphocyte
trafficking and the differentiation of various B cell and
macrophage blood cell lineages [Kim, C., and Broxmeyer, H. J.
Leukocyte Biol. 65, 6-15 (1999)]. The CXCR4 receptor also functions
as a coreceptor for the entry of HIV-1 into T-cells [Feng, Y., et
al. Science, 272, 872-877 (1996)]. In an extensive series of
studies carried out by [McGrath, K. E. et al. Dev. Biology 213,
442-456 (1999)], the expression of the chemokine receptor CXCR4 and
its unique ligand, SDF-1 [Kim, C., and Broxmyer, H., J. Leukocyte
Biol. 65, 6-15 (1999)], were delineated during early development
and adult life in the mouse. The CXCR4/SDF1 interaction in
development became apparent when it was demonstrated that if either
gene was disrupted in transgenic mice [Nagasawa et al. Nature, 382,
635-638 (1996)], Ma, Q., et al Immunity, 10, 463-471 (1999)] it
resulted in late embryonic lethality. McGrath et al. demonstrated
that CXCR4 is the most abundant chemokine receptor messenger RNA
detected during early gastrulating embryos (E7.5) using a
combination of RNase protection and in situ hybridization
methodologies. In the gastrulating embryo, CXCR4/SDF-1 signaling
appears to be mainly involved in inducing migration of
primitive-streak germlayer cells and is expressed on definitive
endoderm, mesoderm and extraembryonic mesoderm present at this
time. In E7.2-7.8 mouse embryos, CXCR4 and alpha-fetoprotein are
mutually exclusive indicating a lack of expression in visceral
endoderm [McGrath, K. E. et al. Dev. Biology 213, 442-456
(1999)].
[0139] Since definitive endoderm cells produced by differentiating
pluripotent cells express the CXCR4 marker gene, expression of
CXCR4 can be monitored in order to track the production of
definitive endoderm cells. Additionally, definitive endoderm cells
produced by the methods described herein express other markers of
definitive endoderm including, but not limited to, SOX17, MIXL1,
GATA4, HNF3b, GSC, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1.
Since definitive endoderm cells express the CXCR4 marker gene at a
level higher than that of the SOX7 marker gene, the expression of
both CXCR4 and SOX7 can be monitored. In other processes,
expression of both the CXCR4 marker gene and the OCT4 marker gene,
is monitored. Additionally, because definitive endoderm cells
express the CXCR4 marker gene at a level higher than that of the
AFP, SPARC or Thrombomodulin (TM) marker genes, the expression of
these genes can also be monitored.
[0140] It will be appreciated that expression of CXCR4 in
endodermal cells does not preclude the expression of SOX17. As
such, definitive endoderm cells produced by the processes described
herein will substantially express SOX17 and CXCR4 but will not
substantially express AFP, TM, SPARC or PDX1.
[0141] It will be appreciated that SOX17 and/or CXCR4 marker
expression is induced over a range of different levels in
definitive endoderm cells depending on the differentiation
conditions. As such, in some embodiments described herein, the
expression of the SOX17 marker and/or the CXCR4 marker in
definitive endoderm cells or cell populations is at least about
2-fold higher to at least about 10,000-fold higher than the
expression of the SOX17 marker and/or the CXCR4 marker in
non-definitive endoderm cells or cell populations, for example
pluripotent stem cells. In other embodiments, the expression of the
SOX 17 marker and/or the CXCR4 marker in definitive endoderm cells
or cell populations is at least about 4-fold higher, at least about
6-fold higher, at least about 8-fold higher, at least about 10-fold
higher, at least about 15-fold higher, at least about 20-fold
higher, at least about 40-fold higher, at least about 80-fold
higher, at least about 100-fold higher, at least about 150-fold
higher, at least about 200-fold higher, at least about 500-fold
higher, at least about 750-fold higher, at least about 1000-fold
higher, at least about 2500-fold higher, at least about 5000-fold
higher, at least about 7500-fold higher or at least about
10,000-fold higher than the expression of the SOX17 marker and/or
the CXCR4 marker in non-definitive endoderm cells or cell
populations, for example pluripotent stem cells. In some
embodiments, the expression of the SOX17 marker and/or CXCR4 marker
in definitive endoderm cells or cell populations is infinitely
higher than the expression of the SOX17 marker and/or the CXCR4
marker in non-definitive endoderm cells or cell populations, for
example pluripotent stem cells.
[0142] It will also be appreciated that in some embodiments
described herein, the expression of markers selected from the group
consisting of GATA4, MIXL1, HNF3b, GSC, FGF17, VWF, CALCR, FOXQ1,
CMKOR1 and CRIP1 in definitive endoderm cells or cell populations
is increased as compared to the expression of GATA4, MIXL1, HNF3b,
GSC, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1 in non-definitive
endoderm cells or cell populations.
[0143] Additionally, it will be appreciated that there is a range
of differences between the expression level of the SOX17 marker and
the expression levels of the OCT4, SPARC, AFP, TM and/or SOX7
markers in definitive endoderm cells. Similarly, there exists a
range of differences between the expression level of the CXCR4
marker and the expression levels of the OCT4, SPARC, AFP, TM and/or
SOX7 markers in definitive endoderm cells. As such, in some
embodiments described herein, the expression of the SOX17 marker or
the CXCR4 marker is at least about 2-fold higher to at least about
10,000-fold higher than the expression of OCT4, SPARC, AFP, TM
and/or SOX7 markers. In other embodiments, the expression of the
SOX17 marker or the CXCR4 marker is at least about 4-fold higher,
at least about 6-fold higher, at least about 8-fold higher, at
least about 10-fold higher, at least about 15-fold higher, at least
about 20-fold higher, at least about 40-fold higher, at least about
80-fold higher, at least about 100-fold higher, at least about
150-fold higher, at least about 200-fold higher, at least about
500-fold higher, at least about 750-fold higher, at least about
1000-fold higher, at least about 2500-fold higher, at least about
5000-fold higher, at least about 7500-fold higher or at least about
10,000-fold higher than the expression of OCT4, SPARC, AFP, TM
and/or SOX7 markers. In some embodiments, OCT4, SPARC, AFP, TM
and/or SOX7 markers are not significantly expressed in definitive
endoderm cells.
[0144] It will also be appreciated that in some embodiments
described herein, the expression of markers selected from the group
consisting of GATA4, MIXL1, HNF3b, GSC, FGF17, VWF, CALCR, FOXQ1,
CMKOR1 and CRIP1 in definitive endoderm cells is increased as
compared to the expression of OCT4, SPARC, AFP, TM and/or SOX7 in
definitive endoderm cells.
Enrichment, Isolation and/or Purification of Definitive
Endoderm
[0145] Definitive endoderm cells produced by any of the
above-described processes can be enriched, isolated and/or purified
by using an affinity tag that is specific for such cells. Examples
of affinity tags specific for definitive endoderm cells are
antibodies, ligands or other binding agents that are specific to a
marker molecule, such as a polypeptide, that is present on the cell
surface of definitive endoderm cells but which is not substantially
present on other cell types that would be found in a cell culture
produced by the methods described herein. In some processes, an
antibody which binds to CXCR4 is used as an affinity tag for the
enrichment, isolation or purification of definitive endoderm cells.
In other processes, the chemokine SDF-1 or other molecules based on
SDF-1 can also be used as affinity tags. Such molecules include,
but not limited to, SDF-1 fragments, SDF-1 fusions or SDF-1
mimetics.
[0146] Methods for making antibodies and using them for cell
isolation are known in the art and such methods can be implemented
for use with the antibodies and definitive endoderm cells described
herein. In one process, an antibody which binds to CXCR4 is
attached to a magnetic bead and then allowed to bind to definitive
endoderm cells in a cell culture which has been enzymatically
treated to reduce intercellular and substrate adhesion. The
cell/antibody/bead complexes are then exposed to a movable magnetic
field which is used to separate bead-bound definitive endoderm
cells from unbound cells. Once the definitive endoderm cells are
physically separated from other cells in culture, the antibody
binding is disrupted and the cells are replated in appropriate
tissue culture medium.
[0147] Additional methods for obtaining enriched, isolated or
purified definitive endoderm cell cultures or populations can also
be used. For example, in some embodiments, the CXCR4 antibody is
incubated with a definitive endoderm-containing cell culture that
has been treated to reduce intercellular and substrate adhesion.
The cells are then washed, centrifuged and resuspended. The cell
suspension is then incubated with a secondary antibody, such as an
FITC-conjugated antibody that is capable of binding to the primary
antibody. The cells are then washed, centrifuged and resuspended in
buffer. The cell suspension is then analyzed and sorted using a
fluorescence activated cell sorter (FACS). CXCR4-positive cells are
collected separately from CXCR4-negative cells, thereby resulting
in the isolation of such cell types. If desired, the isolated cell
compositions can be further purified by using an alternate
affinity-based method or by additional rounds of sorting using the
same or different markers that are specific for definitive
endoderm.
[0148] In still other processes, definitive endoderm cells are
enriched, isolated and/or purified using a ligand or other molecule
that binds to CXCR4. In some processes, the molecule is SDF-1 or a
fragment, fusion or mimetic thereof.
[0149] In some embodiments of the processes described herein,
definitive endoderm cells are fluorescently labeled then isolated
from non-labeled cells by using a fluorescence activated cell
sorter (FACS). In such embodiments, a nucleic acid encoding green
fluorescent protein (GFP) or another nucleic acid encoding an
expressible fluorescent marker gene is used to label PDX1-positive
cells. For example, in some embodiments, at least one copy of a
nucleic acid encoding GFP or a biologically active fragment thereof
is introduced into a pluripotent cell, preferably a human embryonic
stem cell, downstream of the SOX17 or CXCR4 promoter such that the
expression of the GFP gene product or biologically active fragment
thereof is under control of the SOX17 or CXCR4 promoter. In some
embodiments, the entire coding region of the nucleic acid, which
encodes SOX17 or CXCR4, is replaced by a nucleic acid encoding GFP
or a biologically active fragment thereof. In other embodiments,
the nucleic acid encoding GFP or a biologically active fragment
thereof is fused in frame with at least a portion of the nucleic
acid encoding SOX17 or CXCR4, thereby generating a fusion protein.
In such embodiments, the fusion protein retains a fluorescent
activity similar to GFP.
[0150] Fluorescently marked cells, such as the above-described
pluripotent cells, are differentiated to definitive endoderm as
described previously above. Because definitive endoderm cells
express the fluorescent marker gene, whereas other cell types do
not, definitive endoderm cells can be separated from the other cell
types. In some embodiments, cell suspensions comprising a mixture
of fluorescently-labeled definitive endoderm cells and unlabeled
non-definitive endoderm cells are sorted using a FACS. Definitive
endoderm cells are collected separately from non-fluorescing cells,
thereby resulting in the isolation of definitive endoderm. If
desired, the isolated cell compositions can be further purified by
additional rounds of sorting using the same or different markers
that are specific for definitive endoderm.
[0151] In preferred processes, definitive endoderm cells are
enriched, isolated and/or purified from other non-definitive
endoderm cells after the stem cell cultures are induced to
differentiate towards the definitive endoderm lineage. It will be
appreciated that the above-described enrichment, isolation and
purification procedures can be used with such cultures at any stage
of differentiation.
[0152] In addition to the procedures just described, definitive
endoderm cells may also be isolated by other techniques for cell
isolation. Additionally, definitive endoderm cells may also be
enriched or isolated by methods of serial subculture in growth
conditions which promote the selective survival or selective
expansion of the definitive endoderm cells.
[0153] Using the methods described herein, enriched, isolated
and/or purified populations of definitive endoderm cells and or
tissues can be produced in vitro from pluripotent cell cultures or
cell populations, such as stem cell cultures or populations, which
have undergone at least some differentiation. In some methods, the
cells undergo random differentiation. In a preferred method,
however, the cells are directed to differentiate primarily into
definitive endoderm. Some preferred enrichment, isolation and/or
purification methods relate to the in vitro production of
definitive endoderm from human embryonic stem cells.
[0154] Using the methods described herein, cell populations or cell
cultures can be enriched in definitive endoderm content by at least
about 2- to about 1000-fold as compared to untreated cell
populations or cell cultures. In some embodiments, definitive
endoderm cells can be enriched by at least about 5- to about
500-fold as compared to untreated cell populations or cell
cultures. In other embodiments, definitive endoderm cells can be
enriched from at least about 10- to about 200-fold as compared to
untreated cell populations or cell cultures. In still other
embodiments, definitive endoderm cells can be enriched from at
least about 20- to about 100-fold as compared to untreated cell
populations or cell cultures. In yet other embodiments, definitive
endoderm cells can be enriched from at least about 40- to about
80-fold as compared to untreated cell populations or cell cultures.
In certain embodiments, definitive endoderm cells can be enriched
from at least about 2- to about 20-fold as compared to untreated
cell populations or cell cultures.
Compositions Comprising Definitive Endoderm
[0155] Cell compositions produced by the above-described methods
include cell cultures comprising definitive endoderm and cell
populations enriched in definitive endoderm. For example, cell
cultures which comprise definitive endoderm cells, wherein at least
about 50-80% of the cells in culture are definitive endoderm cells,
can be produced. Because the efficiency of the differentiation
process can be adjusted by modifying certain parameters, which
include but are not limited to, cell growth conditions, growth
factor concentrations and the timing of culture steps, the
differentiation procedures described herein can result in about 5%,
about 10%, about 15%, about 20%, about 25%, about 30%, about 35%,
about 40%, about 45%, about 50%, about 55%, about 60%, about 65%,
about 70%, about 75%, about 80%, about 85%, about 90%, about 95%,
or greater than about 95% conversion of pluripotent cells to
definitive endoderm. In processes in which isolation of definitive
endoderm cells is employed, for example, by using an affinity
reagent that binds to the CXCR4 receptor, a substantially pure
definitive endoderm cell population can be recovered.
[0156] Some embodiments described herein relate to compositions,
such as cell populations and cell cultures, that comprise both
pluripotent cells, such as stem cells, and definitive endoderm
cells. For example, using the methods described herein,
compositions comprising mixtures of hESCs and definitive endoderm
cells can be produced. In some embodiments, compositions comprising
at least about 5 definitive endoderm cells for about every 95
pluripotent cells are produced. In other embodiments, compositions
comprising at least about 95 definitive endoderm cells for about
every 5 pluripotent cells are produced. Additionally, compositions
comprising other ratios of definitive endoderm cells to pluripotent
cells are contemplated. For example, compositions comprising at
least about 1 definitive endoderm cell for about every 1,000,000
pluripotent cells, at least about 1 definitive endoderm cell for
about every 100,000 pluripotent cells, at least about 1 definitive
endoderm cell for about every 10,000 pluripotent cells, at least
about 1 definitive endoderm cell for about every 1000 pluripotent
cells, at least about 1 definitive endoderm cell for about every
500 pluripotent cells, at least about 1 definitive endoderm cell
for about every 100 pluripotent cells, at least about 1 definitive
endoderm cell for about every 10 pluripotent cells, at least about
1 definitive endoderm cell for about every 5 pluripotent cells, at
least about 1 definitive endoderm cell for about every 2
pluripotent cells, at least about 2 definitive endoderm cells for
about every 1 pluripotent cell, at least about 5 definitive
endoderm cells for about every 1 pluripotent cell, at least about
10 definitive endoderm cells for about every 1 pluripotent cell, at
least about 20 definitive endoderm cells for about every 1
pluripotent cell, at least about 50 definitive endoderm cells for
about every 1 pluripotent cell, at least about 100 definitive
endoderm cells for about every 1 pluripotent cell, at least about
1000 definitive endoderm cells for about every 1 pluripotent cell,
at least about 10,000 definitive endoderm cells for about every 1
pluripotent cell, at least about 100,000 definitive endoderm cells
for about every 1 pluripotent cell and at least about 1,000,000
definitive endoderm cells for about every 1 pluripotent cell are
contemplated. In some embodiments, the pluripotent cells are human
pluripotent stem cells. In certain embodiments the stem cells are
derived from a morula, the inner cell mass of an embryo or the
gonadal ridges of an embryo. In certain other embodiments, the
pluripotent cells are derived from the gondal or germ tissues of a
multicellular structure that has developed past the embryonic
stage.
[0157] Some embodiments described herein relate to cell cultures or
cell populations comprising from at least about 5% definitive
endoderm cells to at least about 95% definitive endoderm cells. In
some embodiments the cell cultures or cell populations comprise
mammalian cells. In preferred embodiments, the cell cultures or
cell populations comprise human cells. For example, certain
specific embodiments relate to cell cultures comprising human
cells, wherein from at least about 5% to at least about 95% of the
human cells are definitive endoderm cells. Other embodiments relate
to cell cultures comprising human cells, wherein at least about 5%,
at least about 10%, at least about 15%, at least about 20%, at
least about 25%, at least about 30%, at least about 35%, at least
about 40%, at least about 45%, at least about 50%, at least about
55%, at least about 60%, at least about 65%, at least about 70%, at
least about 75%, at least about 80%, at least about 85%, at least
about 90% or greater than 90% of the human cells are definitive
endoderm cells. In embodiments where the cell cultures or cell
populations comprise human feeder cells, the above percentages are
calculated without respect to the human feeder cells in the cell
cultures or cell populations.
[0158] Further embodiments described herein relate to compositions,
such as cell cultures or cell populations, comprising human cells,
such as human definitive endoderm cells, wherein the expression of
either the SOX17 or the CXCR4 marker is greater than the expression
of the OCT4, SPARC, alpha-fetoprotein (AFP), Thrombomodulin (TM)
and/or SOX7 marker in at least about 5% of the human cells. In
other embodiments, the expression of either the SOX17 or the CXCR4
marker is greater than the expression of the OCT4, SPARC, AFP, TM
and/or SOX7 marker in at least about 10% of the human cells, in at
least about 15% of the human cells, in at least about 20% of the
human cells, in at least about 25% of the human cells, in at least
about 30% of the human cells, in at least about 35% of the human
cells, in at least about 40% of the human cells, in at least about
45% of the human cells, in at least about 50% of the human cells,
in at least about 55% of the human cells, in at least about 60% of
the human cells, in at least about 65% of the human cells, in at
least about 70% of the human cells, in at least about 75% of the
human cells, in at least about 80% of the human cells, in at least
about 85% of the human cells, in at least about 90% of the human
cells, in at least about 95% of the human cells or in greater than
95% of the human cells. In embodiments where the cell cultures or
cell populations comprise human feeder cells, the above percentages
are calculated without respect to the human feeder cells in the
cell cultures or cell populations.
[0159] It will be appreciated that some embodiments described
herein relate to compositions, such as cell cultures or cell
populations, comprising human cells, such as human definitive
endoderm cells, wherein the expression of one or more markers
selected from the group consisting of GATA4, MIXL1, HNF3b, GSC,
FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1 is greater than the
expression of the OCT4, SPARC, AFP, TM and/or SOX7 markers in from
at least about 5% to greater than at least about 95% of the human
cells. In embodiments where the cell cultures or cell populations
comprise human feeder cells, the above percentages are calculated
without respect to the human feeder cells in the cell cultures or
cell populations.
[0160] Still other embodiments described herein relate to
compositions, such as cell cultures or cell populations, comprising
human cells, such as human definitive endoderm cells, wherein the
expression both the SOX17 and the CXCR4 marker is greater than the
expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at
least about 5% of the human cells. In other embodiments, the
expression of both the SOX17 and the CXCR4 marker is greater than
the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker in at
least about 10% of the human cells, in at least about 15% of the
human cells, in at least about 20% of the human cells, in at least
about 25% of the human cells, in at least about 30% of the human
cells, in at least about 35% of the human cells, in at least about
40% of the human cells, in at least about 45% of the human cells,
in at least about 50% of the human cells, in at least about 55% of
the human cells, in at least about 60% of the human cells, in at
least about 65% of the human cells, in at least about 70% of the
human cells, in at least about 75% of the human cells, in at least
about 80% of the human cells, in at least about 85% of the human
cells, in at least about 90% of the human cells, in at least about
95% of the human cells or in greater than 95% of the human cells.
In embodiments where the cell cultures or cell populations comprise
human feeder cells, the above percentages are calculated without
respect to the human feeder cells in the cell cultures or cell
populations.
[0161] It will be appreciated that some embodiments described
herein relate to compositions, such as cell cultures or cell
populations, comprising human cells, such as human definitive
endoderm cells, wherein the expression of the GATA4, MIXL1, HNF3b,
GSC, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1 markers is greater
than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 markers
in from at least about 5% to greater than at least about 95% of the
human cells. In embodiments where the cell cultures or cell
populations comprise human feeder cells, the above percentages are
calculated without respect to the human feeder cells in the cell
cultures or cell populations.
[0162] Additional embodiments described herein relate to
compositions, such as cell cultures or cell populations, comprising
mammalian endodermal cells, such as human endoderm cells, wherein
the expression of either the SOX17 or the CXCR4 marker is greater
than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker
in at least about 5% of the endodermal cells. In other embodiments,
the expression of either the SOX17 or the CXCR4 marker is greater
than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker
in at least about 10% of the endodermal cells, in at least about
15% of the endodermal cells, in at least about 20% of the
endodermal cells, in at least about 25% of the endodermal cells, in
at least about 30% of the endodermal cells, in at least about 35%
of the endodermal cells, in at least about 40% of the endodermal
cells, in at least about 45% of the endodermal cells, in at least
about 50% of the endodermal cells, in at least about 55% of the
endodermal cells, in at least about 60% of the endodermal cells, in
at least about 65% of the endodermal cells, in at least about 70%
of the endodermal cells, in at least about 75% of the endodermal
cells, in at least about 80% of the endodermal cells, in at least
about 85% of the endodermal cells, in at least about 90% of the
endodermal cells, in at least about 95% of the endodermal cells or
in greater than 95% of the endodermal cells.
[0163] It will be appreciated that some embodiments described
herein relate to compositions, such as cell cultures or cell
populations comprising mammalian endodermal cells, wherein the
expression of one or more markers selected from the group
consisting of GATA4, MIXL1, HNF3b, GSC, FGF17, VWF, CALCR, FOXQ1,
CMKOR1 and CRIP1 is greater than the expression of the OCT4, SPARC,
AFP, TM and/or SOX7 markers in from at least about 5% to greater
than at least about 95% of the endodermal cells.
[0164] Still other embodiments described herein relate to
compositions, such as cell cultures or cell populations, comprising
mammalian endodermal cells, such as human endodermal cells, wherein
the expression of both the SOX17 and the CXCR4 marker is greater
than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker
in at least about 5% of the endodermal cells. In other embodiments,
the expression of both the SOX17 and the CXCR4 marker is greater
than the expression of the OCT4, SPARC, AFP, TM and/or SOX7 marker
in at least about 10% of the endodermal cells, in at least about
15% of the endodermal cells, in at least about 20% of the
endodermal cells, in at least about 25% of the endodermal cells, in
at least about 30% of the endodermal cells, in at least about 35%
of the endodermal cells, in at least about 40% of the endodermal
cells, in at least about 45% of the endodermal cells, in at least
about 50% of the endodermal cells, in at least about 55% of the
endodermal cells, in at least about 60% of the endodermal cells, in
at least about 65% of the endodermal cells, in at least about 70%
of the endodermal cells, in at least about 75% of the endodermal
cells, in at least about 80% of the endodermal cells, in at least
about 85% of the endodermal cells, in at least about 90% of the
endodermal cells, in at least about 95% of the endodermal cells or
in greater than 95% of the endodermal cells.
[0165] It will be appreciated that some embodiments described
herein relate to compositions, such as cell cultures or cell
populations comprising mammalian endodermal cells, wherein the
expression of the GATA4, MIXL1, HNF3b, GSC, FGF17, VWF, CALCR,
FOXQ1, CMKOR1 and CRIP1 markers is greater than the expression of
the OCT4, SPARC, AFP, TM and/or SOX7 markers in from at least about
5% to greater than at least about 95% of the endodermal cells.
[0166] Using the methods described herein, compositions comprising
definitive endoderm cells substantially free of other cell types
can be produced. In some embodiments described herein, the
definitive endoderm cell populations or cell cultures produced by
the methods described herein are substantially free of cells that
significantly express the OCT4, SOX7, AFP, SPARC, TM, ZIC1 or BRACH
marker genes.
[0167] In one embodiment, a description of a definitive endoderm
cell based on the expression of marker genes is, SOX17 high, MIXL1
high, AFP low, SPARC low, Thrombomodulin low, SOX7 low, CXCR4
high.
Expansion of Definitive Endoderm Cells
[0168] According to some of the in vitro methods described herein,
definitive endoderm cells are maintained, grown, passaged and/or
expanded while in cell culture. In some embodiments the definitive
endoderm cells are maintained, grown, passaged and/or expanded
without any significant differentiation. In other words, in such
embodiments, the definitive endoderm cells maintain the definitive
endoderm phenotype while being maintained, grown, passaged and/or
expanded in cell culture.
[0169] In some embodiments, definitive endoderm cells used in the
expansion methods described herein, are multipotent cells that can
differentiate into cells of the gut tube or organs derived
therefrom. Such cells include, but are not limited to, cells of the
pancreas, liver, lungs, stomach, intestine, thyroid, thymus,
pharynx, gallbladder and urinary bladder as well as precursors of
such cells. Additionally, these cells can further develop into
higher order structures such as tissues and/or organs. In some
embodiments, the definitive endoderm cells are human definitive
endoderm cells.
[0170] Some embodiments of the methods described herein comprise a
step of obtaining a cell culture comprising definitive endoderm
cells. The cell culture can be a pure culture of definitive
endoderm cells or a mixed cell culture that comprises definitive
endoderm cells as well as cells of other types. For example, the
cell culture can be a culture comprising both definitive endoderm
cells and human embryonic stem cells (hESCs). In some embodiments,
the definitive endoderm cell culture is obtained by differentiating
in vitro cell cultures of hESCs. In certain embodiments, the hESCs
are derived from a morula, the inner cell mass of an embryo or the
gonadal ridges of an embryo. In certain other embodiments, the
pluripotent cells are derived from the gonadal or germ tissues of a
multicellular structure that has developed past the embryonic
stage.
[0171] Methods of differentiating hESCs so as to produce cell
cultures comprising human definitive endoderm cells have been
described throughout this application and in U.S. patent
application Ser. No. 11/021,618, entitled DEFINITIVE ENDODERM,
filed Dec. 23, 2004, the disclosure of which is incorporated herein
by reference in its entirety. However, it will be appreciated that
any known methods for producing human definitive endoderm cells
from hESCs or from other human cell types can be used. In some
embodiments described herein, the cultures of definitive endoderm
cells produced by differentiating hESCs can be mixed definitive
endoderm cultures, which comprise definitive endoderm cells and one
or more types of other cells, enriched definitive endoderm cell
cultures and/or purified definitive endoderm cell cultures. Some
methods for obtaining definitive endoderm cells from hESCs comprise
contacting or otherwise providing the hESCs with at least one
growth factor from the TGF.beta. superfamily. Such growth factors
can include, but are not limited to, Nodal, activin A and activin
B. In some embodiments, the growth factor is provided to the hESCs
at a concentration ranging from 5 ng/ml to 5000 ng/ml. In certain
embodiments the growth factor is provided to the hESCs in culture
at a concentration of at least about 5 ng/ml, at least about 10
ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least
about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml,
at least about 300 ng/ml, at least about 400 ng/ml, at least about
500 ng/ml, at least about 1000 ng/ml, at least about 2000 ng/ml, at
least about 3000 ng/ml, at least about 4000 ng/ml, at least about
5000 ng/ml or more than about 5000 ng/ml.
[0172] In other embodiments of the methods described herein,
definitive endoderm cells can be obtained from a pre-existing
culture of definitive endoderm cells. In such embodiments, either a
portion of or the entire culture may be used in the definitive
endoderm expansion methods described herein.
[0173] In addition to obtaining cell cultures comprising definitive
endoderm cells, some embodiments of the expansion methods described
herein also comprise the step of isolating at least some of the
definitive endoderm cells from the cell culture. In such
embodiments, at least some of the definitive endoderm cells are
separated from at least some of the other cells in the cell
culture, thereby producing a cell population enriched in definitive
endoderm cells. In some embodiments, at least some of the
definitive endoderm cell are removed from the cell culture while at
least some of the other cells remain in the cell culture. Other
cells that are present in the cell culture can include, but are not
limited to, hESCs, primitive endoderm, trophectoderm, mesoderm and
ectoderm.
[0174] In other embodiments described herein, the isolating step
comprises providing the cells in the cell culture with a reagent
which binds to a marker expressed in said definitive endoderm cells
but which is not substantially expressed in said other cells
present in the cell culture. As described previously herein, in
some embodiments, the marker can be any cell surface marker that is
specific to definitive endoderm cells. One such marker that is
described throughout this application (see especially the Examples
below) is the CXCR4 marker. As described previously herein, the
reagent-bound definitive endoderm cells can be separated from the
non-reagent-bound cells by numerous methods. For example, an
antibody against the CXCR4 receptor that is selectively present on
the surface of definitive endoderm cells, can be provided to
definitive endoderm cells in a cell culture. Antibody-bound
definitive endoderm cells can then be separated from other cells in
the culture by, for example, fluorescent activated cell sorting
(FACS), binding the antibody to a solid support or isolating
appropriately tagged antibody in a magnetic field. In some
embodiments, the antibody is released from the definitive endoderm
cells after the separation process.
[0175] As an alternative means of separation, at least some of the
definitive endoderm cells are separated from at least some of the
other cells in the culture by specifically fluorescently labeling
the definitive endoderm cells in culture and then separating the
labeled cells from the unlabeled cells by FACS. As described
previously above and in the Examples, in such embodiments, hESCs
are transfected with a vector comprising a fluorescent reporter
gene under the control of the promoter of a marker gene that is
highly expressed in definitive endoderm cells but not significantly
expressed in other cell types. In some embodiments, the fluorescent
reporter gene is the gene encoding green fluorescent protein (GFP)
or enhanced green fluorescent protein (EGFP). In some embodiments,
the GFP and/or EGFP is expressed under the control of the SOX17 or
the CXCR4 promoter. Transfected hESCs are then grown in culture in
the presence of a differentiation factor that specifically induces
the production of definitive endoderm. In preferred embodiments,
the differentiation factor is activin A. In other preferred
embodiments, activin A is added to the cell culture at a
concentration of 100 ng/ml.
[0176] In some embodiments described herein, the enriched
definitive endoderm cell populations that are produced as a result
of the isolating step are substantially free of cells other than
definitive endoderm cells. In other embodiments, the enriched
definitive endoderm cell populations comprise from at least about
96% to at least about 100% definitive endoderm cells. In still
other embodiments, the enriched definitive endoderm cell
populations comprise from at least about 96%, at least about 97%,
at least about 98%, at least about 99% and at least about 100%
definitive endoderm cells.
[0177] According to further embodiments of the expansion methods
described herein a cell culture step is contemplated. For example,
some embodiments include a culturing step that comprises plating
the population enriched in definitive endoderm cells or a portion
of the population. In some embodiments, the cells are plated on a
surface coated with human fibronectin. In other embodiments the
plates are coated with poly-ornithine. In still other embodiments,
the plates are coated with poly-ornithine and human fibronectin. In
preferred embodiments, the plates are IVF plates coated with both
poly-ornithine and human fibronectin. It will be appreciated that
although human fibronectin is a preferred coating for the plates
described herein, fibronectin from other sources is sufficient for
coating plates.
[0178] In other embodiments, the culturing step comprises
incubating the enriched definitive endoderm cell population or
portion thereof in an expansion medium comprising about 2% (v/v)
serum. In some embodiments, the serum concentration can range from
about 0% (v/v) to about 20% (v/v). For example, in some methods
described herein, the serum concentration of the medium can be
about 0.05% (v/v), about 0.1% (v/v), about 0.2% (v/v), about 0.3%
(v/v), about 0.4% (v/v), about 0.5% (v/v), about 0.6% (v/v), about
0.7% (v/v), about 0.8% (v/v), about 0.9% (v/v), about 1% (v/v),
about 2% (v/v), about 3% (v/v), about 4% (v/v), about 5% (v/v),
about 6% (v/v), about 7% (v/v), about 8% (v/v), about 9% (v/v),
about 10% (v/v), about 15% (v/v) or about 20% (v/v). In some
embodiments, serum replacement is included in the medium.
[0179] In still other embodiments of the expansion methods
described herein, the expansion medium also comprises at least one
growth factor. In certain embodiments, the at least one growth
factor is a growth factor comprises a member of the TGF.beta.
superfamily. In such embodiments, the at least one growth factor of
the TGF.beta. superfamily includes, but is not limited to Nodal,
activin A, activin B and combinations of these growth factors.
Alternatively, in some embodiments, the at least one growth factor
can be IGF1 or a combination of IGF and a growth factor of the
TGF.beta. superfamily. In other embodiments, the at least one
growth factor can be bFGF, EGF or another growth factor. In yet
other embodiments, the at least one growth factor can be a
combination of bFGF, EGF and a growth factor of the TGF.beta.
superfamily. In each of the above embodiments, one or more of the
growth factors can be present at a concentration ranging from about
1 ng/ml to about 5000 ng/ml. In such embodiments, the concentration
of growth factor in the medium is at least about 5 ng/ml, at least
about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml,
at least about 75 ng/ml, at least about 100 ng/ml, at least about
200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at
least about 500 ng/ml, at least about 1000 ng/ml, at least about
2000 ng/ml, at least about 3000 ng/ml, at least about 4000 ng/ml,
at least about 5000 ng/ml or more than about 5000 ng/ml. In certain
embodiments, a combination of growth factors is present in the
culture medium. In such embodiments, each growth factor is present
in the medium at a concentration of at a concentration of at least
about 5 ng/ml, at least about 10 ng/ml, at least about 25 ng/ml, at
least about 50 ng/ml, at least about 75 ng/ml, at least about 100
ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least
about 400 ng/ml, at least about 500 ng/ml, at least about 1000
ng/ml, at least about 2000 ng/ml, at least about 3000 ng/ml, at
least about 4000 ng/ml, at least about 5000 ng/ml or more than
about 5000 ng/ml.
[0180] In addition to the above-described expansion methods, in
some embodiments definitive endoderm cells are expanded by first
obtaining a cell culture comprising definitive endoderm cells and
then passaging the definitive endoderm cells so as to produce a
plurality of cell cultures comprising definitive endoderm cells.
These methods of expanding definitive endoderm cells by passaging
the cells can be performed using any definitive endoderm culture
regardless of how such culture is obtained. For example, these
methods can be performed as part of the culturing step that follows
the cell isolation step in the above-described expansion methods,
or alternatively, this methods can be performed using definitive
endoderm cells that have been freshly differentiated from
hESCs.
[0181] In accordance with certain aspects of the expansion methods
described herein, the step of passaging definitive endoderm cells
comprises providing at least one enzyme to a cell culture
comprising definitive endoderm cells. For example, the at least one
enzyme can be one or more enzymes selected from the group
consisting of papain, pronase, type I collagenase, type II
collagenase, type III collagenase, type IV collagenase, trypsin,
hyaluronidase, elastase, DNase I, and dispase. In some embodiments,
the at least one enzyme comprises at least one protease. In
preferred embodiments, the at least one protease comprises trypsin.
For example, in certain embodiments, definitive endoderm cells
growing in a culture vessel are passaged with trypsin by first
removing the culture medium from the cells. Next, a sterile trypsin
solution is provided to the definitive endoderm cells for several
minutes at room temperature. The trypsin solution is then gently
removed so as not to disturb the cells. After the trypsin solution
has been removed, the definitive endoderm cells are provided with a
culture medium, such as RPMI with 2% (v/v) serum, and the cell
culture vessel is then agitated so as to disrupt cell adhesions and
generate a cell suspension. In some embodiments, the cell culture
medium comprises trypsin inhibitor to inactivate residual
trypsin.
[0182] It will be appreciated that trypsin can be provided in a
variety of sterile solutions, for example, trypsin can be provided
to the definitive endoderm cells in a balanced salt solution, such
as Hanks balanced salt solution. Alternatively, trypsin can be
provided to the definitive endoderm in a medium with or without
serum, for example in low serum RPMI.
[0183] In accordance with other aspects of the expansion methods
described herein, the step of passaging definitive endoderm cells
comprises mechanically disrupting contacts between said definitive
endoderm cells. Such mechanical disruption techniques should be
sufficient to substantially disrupt cell contacts and the
substrate, however, these techniques should not be so harsh as to
affect cell viability. Mechanical cell disruption techniques, such
as trituration, are known to those of ordinary skill in the
art.
[0184] In accordance with yet other aspects of the expansion
methods described herein, the step of passaging definitive endoderm
cells comprises incubating said definitive endoderm cells in a cell
dispersal buffer. The cell dispersal buffer can be any dispersal
buffer known in the art, for example, commercially available
chemical dissociation buffers.
[0185] In some embodiments of the expansion methods described
herein, the definitive endoderm cells are grown in a cell culture
vessel. Cell culture vessels can include, but are not limited to,
tissue culture flasks and cell culture plate, such as microtiter
plates. In some embodiments, the definitive endoderm cells in
culture are attached to a substrate. In certain embodiments, the
step of passaging said definitive endoderm cells comprises
detaching said definitive endoderm cells from the substrate. In
preferred embodiments, the substrate is a surface of a tissue
culture flask. In other preferred embodiments, the substrate is a
surface of a microtiter plate.
EXAMPLES
[0186] Many of the examples below describe the use of pluripotent
human cells. Methods of producing pluripotent human cells are well
known in the art and have been described numerous scientific
publications, including U.S. Pat. Nos. 5,453,357, 5,670,372,
5,690,926, 6,090,622, 6,200,806 and 6,251,671 as well as U.S.
Patent Application Publication No. 2004/0229350, the disclosures of
which are incorporated herein by reference in their entireties.
Example 1
Human ES cells
[0187] For our studies of endoderm development we employed human
embryonic stem cells, which are pluripotent and can divide
seemingly indefinitely in culture while maintaining a normal
karyotype. ES cells were derived from the 5-day-old embryo inner
cell mass using either immunological or mechanical methods for
isolation. In particular, the human embryonic stem cell line
hESCyt-25 was derived from a supernumerary frozen embryo from an in
vitro fertilization cycle following informed consent by the
patient. Upon thawing the hatched blastocyst was plated on mouse
embryonic fibroblasts (MEF), in ES medium (DMEM, 20% FBS, non
essential amino acids, beta-mercaptoethanol, and FGF2). The embryo
adhered to the culture dish and after approximately two weeks,
regions of undifferentiated hESCs were transferred to new dishes
with MEFs. Transfer was accomplished with mechanical cutting and a
brief digestion with dispase, followed by mechanical removal of the
cell clusters, washing and re-plating. Since derivation, hESCyt-25
has been serially passaged over 100 times. We employed the
hESCyt-25 human embryonic stem cell line as our starting material
for the production of definitive endoderm.
[0188] It will be appreciated by those of skill in the art that
stem cells or other pluripotent cells can also be used as starting
material for the differentiation procedures described herein. For
example, cells obtained from embryonic gonadal ridges, which can be
isolated by methods known in the art, can be used as pluripotent
cellular starting material.
Example 2
hESCyt-25 Characterization
[0189] The human embryonic stem cell line, hESCyt-25 has maintained
a normal morphology, karyotype, growth and self-renewal properties
over 18 months in culture. This cell line displays strong
immunoreactivity for the OCT4, SSEA-4 and TRA-1-60 antigens, all of
which, are characteristic of undifferentiated hESCs and displays
alkaline phosphatase activity as well as a morphology identical to
other established hESC lines. Furthermore, the human stem cell
line, hESCyt-25, also readily forms embryoid bodies (EBs) when
cultured in suspension. As a demonstration of its pluripotent
nature, hESCyT-25 differentiates into various cell types that
represent the three principal germ layers. Ectoderm production was
demonstrated by Q-PCR for ZIC1 as well as immunocytochemistry (ICC)
for nestin and more mature neuronal markers. Immunocytochemical
staining for .beta.-III tubulin was observed in clusters of
elongated cells, characteristic of early neurons. Previously, we
treated EBs in suspension with retinoic acid, to induce
differentiation of pluripotent stem cells to visceral endoderm
(VE), an extra-embryonic lineage. Treated cells expressed high
levels of .alpha.-fetoprotein (AFP) and SOX7, two markers of VE, by
54 hours of treatment. Cells differentiated in monolayer expressed
AFP in sporadic patches as demonstrated by immunocytochemical
staining. As will be described below, the hESCyT-25 cell line was
also capable of forming definitive endoderm, as validated by
real-time quantitative polymerase chain reaction (Q-PCR) and
immunocytochemistry for SOX17, in the absence of AFP expression. To
demonstrate differentiation to mesoderm, differentiating EBs were
analyzed for Brachyury gene expression at several time points.
Brachyury expression increased progressively over the course of the
experiment. In view of the foregoing, the hESCyT-25 line is
pluripotent as shown by the ability to form cells representing the
three germ layers.
Example 3
Production of SOX17 Antibody
[0190] A primary obstacle to the identification of definitive
endoderm in hESC cultures is the lack of appropriate tools. We
therefore undertook the production of an antibody raised against
human SOX17 protein.
[0191] The marker SOX17 is expressed throughout the definitive
endoderm as it forms during gastrulation and its expression is
maintained in the gut tube (although levels of expression vary
along the A-P axis) until around the onset of organogenesis. SOX17
is also expressed in a subset of extra-embryonic endoderm cells. No
expression of this protein has been observed in mesoderm or
ectoderm. It has now been discovered that SOX17 is an appropriate
marker for the definitive endoderm lineage when used in conjunction
with markers to exclude extra-embryonic lineages.
[0192] As described in detail herein, the SOX17 antibody was
utilized to specifically examine effects of various treatments and
differentiation procedures aimed at the production of SOX17
positive definitive endoderm cells. Other antibodies reactive to
AFP, SPARC and Thrombomodulin were also employed to rule out the
production of visceral and parietal endoderm (extra-embryonic
endoderm).
[0193] In order to produce an antibody against SOX17, a portion of
the human SOX17 cDNA (SEQ ID NO: 1) corresponding to amino acids
172-414 (SEQ ID NO: 2) in the carboxyterminal end of the SOX17
protein (FIG. 2) was used for genetic immunization in rats at the
antibody production company, GENOVAC (Freiberg, Germany), according
to procedures developed there. Procedures for genetic immunization
can be found in U.S. Pat. Nos. 5,830,876, 5,817,637, 6,165,993 and
6,261,281 as well as International Patent Application Publication
Nos. WO00/29442 and WO99/13915, the disclosures of which are
incorporated herein by reference in their entireties.
[0194] Other suitable methods for genetic immunization are also
described in the non-patent literature. For example, Barry et al.
describe the production of monoclonal antibodies by genetic
immunization in Biotechniques 16: 616-620, 1994, the disclosure of
which is incorporated herein by reference in its entirety. Specific
examples of genetic immunization methods to produce antibodies
against specific proteins can be found, for example, in Costaglia
et al., (1998) Genetic immunization against the human thyrotropin
receptor causes thyroiditis and allows production of monoclonal
antibodies recognizing the native receptor, J. Immunol. 160:
1458-1465; Kilpatrick et al (1998) Gene gun delivered DNA-based
immunizations mediate rapid production of murine monoclonal
antibodies to the Flt-3 receptor, Hybridoma 17: 569-576; Schmolke
et al., (1998) Identification of hepatitis G virus particles in
human serum by E2-specific monoclonal antibodies generated by DNA
immunization, J. Virol. 72: 4541-4545; Krasemann et al., (1999)
Generation of monoclonal antibodies against proteins with an
unconventional nucleic acid-based immunization strategy, J.
Biotechnol. 73: 119-129; and Ulivieri et al., (1996) Generation of
a monoclonal antibody to a defined portion of the Heliobacter
pylori vacuolating cytotoxin by DNA immunization, J. Biotechnol.
51: 191-194, the disclosures of which are incorporated herein by
reference in their entireties.
[0195] SOX7 and SOX18 are the closest Sox family relatives to SOX17
as depicted in the relational dendrogram shown in FIG. 3. We
employed the human SOX7 polypeptide as a negative control to
demonstrate that the SOX17 antibody produced by genetic
immunization is specific for SOX17 and does not react with its
closest family member. In particular, SOX7 and other proteins were
expressed in human fibroblasts, and then, analyzed for cross
reactivity with the SOX17 antibody by Western blot and ICC. For
example, the following methods were utilized for the production of
the SOX17, SOX7 and EGFP expression vectors, their transfection
into human fibroblasts and analysis by Western blot. Expression
vectors employed for the production of SOX17, SOX7, and EGFP were
pCMV6 (OriGene Technologies, Inc., Rockville, Md.), pCMV-SPORT6
(Invitrogen, Carlsbad, Calif.) and pEGFP-N1 (Clonetech, Palo Alto,
Calif.), respectively. For protein production, telomerase
immortalized MDX human fibroblasts were transiently transfected
with supercoiled DNA in the presence of Lipofectamine 2000
(Invitrogen, Carlsbad, Calif.). Total cellular lysates were
collected 36 hours post-transfection in 50 mM TRIS-HCl (pH 8), 150
mM NaCl, 0.1% SDS, 0.5% deoxycholate, containing a cocktail of
protease inhibitors (Roche Diagnostics Corporation, Indianapolis,
Ind.). Western blot analysis of 100 .mu.g of cellular proteins,
separated by SDS-PAGE on NuPAGE (4-12% gradient polyacrylamide,
Invitrogen, Carlsbad, Calif.), and transferred by electro-blotting
onto PDVF membranes (Hercules, Calif.), were probed with a 1/1000
dilution of the rat SOX17 anti-serum in 10 mM TRIS-HCl (pH 8), 150
mM NaCl, 10% BSA, 0.05% Tween-20 (Sigma, St. Louis, Mo.), followed
by Alkaline Phosphatase conjugated anti-rat IgG (Jackson
ImmunoResearch Laboratories, West Grove, Pa.), and revealed through
Vector Black Alkaline Phosphatase staining (Vector Laboratories,
Burlingame, Calif.). The proteins size standard used was wide range
color markers (Sigma, St. Louis, Mo.).
[0196] In FIG. 4, protein extracts made from human fibroblast cells
that were transiently transfected with SOX17, SOX7 or EGFP cDNA's
were probed on Western blots with the SOX17 antibody. Only the
protein extract from hSOX17 transfected cells produced a band of
.about.51 Kda which closely matched the predicted 46 Kda molecular
weight of the human SOX17 protein. There was no reactivity of the
SOX17 antibody to extracts made from either human SOX7 or EGFP
transfected cells. Furthermore, the SOX17 antibody clearly labeled
the nuclei of human fibroblast cells transfected with the hSOX17
expression construct but did not label cells transfected with EGFP
alone. As such, the SOX17 antibody exhibits specificity by ICC.
Example 4
Validation of SOX17 Antibody as a Marker of Definitive Endoderm
[0197] Partially differentiated hESCs were co-labeled with SOX17
and AFP antibodies to demonstrate that the SOX17 antibody is
specific for human SOX17 protein and furthermore marks definitive
endoderm. It has been demonstrated that SOX17, SOX7 (which is a
closely related member of the SOX gene family subgroup F (FIG. 3))
and AFP are each expressed in visceral endoderm. However, AFP and
SOX7 are not expressed in definitive endoderm cells at levels
detectable by ICC, and thus, they can be employed as negative
markers for bonifide definitive endoderm cells. It was shown that
SOX17 antibody labels populations of cells that exist as discrete
groupings of cells or are intermingled with AFP positive cells. In
particular, FIG. 5A shows that small numbers of SOX17 cells were
co-labeled with AFP; however, regions were also found where there
were little or no AFP.sup.+ cells in the field of SOX17.sup.+ cells
(FIG. 5B). Similarly, since parietal endoderm has been reported to
express SOX17, antibody co-labeling with SOX17 together with the
parietal markers SPARC and/or Thrombomodulin (TM) can be used to
identify the SOX17.sup.+ cells that are parietal endoderm. As shown
in FIGS. 6A-C, Thrombomodulin and SOX17 co-labeled parietal
endoderm cells were produced by random differentiation of hES
cells.
[0198] In view of the above cell labeling experiments, the identity
of a definitive endoderm cell can be established by the marker
profile SOX17.sup.hi/AFP.sup.lo/[TM.sup.lo or SPARC.sup.lo]. In
other words, the expression of the SOX17 marker is greater than the
expression of the AFP marker, which is characteristic of visceral
endoderm, and the TM or SPARC markers, which are characteristic of
parietal endoderm. Accordingly, those cells positive for SOX17 but
negative for AFP and negative for TM or SPARC are definitive
endoderm.
[0199] As a further evidence of the specificity of the
SOX17.sup.hi/AFP.sup.lo/TM.sup.lo/SPARC.sup.lo marker profile as
predictive of definitive endoderm, SOX17 and AFP gene expression
was quantitatively compared to the relative number of antibody
labeled cells. As shown in FIG. 7A, hESCs treated with retinoic
acid (visceral endoderm inducer), or activin A (definitive endoderm
inducer), resulted in a 10-fold difference in the level of SOX17
mRNA expression. This result mirrored the 10-fold difference in
SOX17 antibody-labeled cell number (FIG. 7B). Furthermore, as shown
in FIG. 8A, activin A treatment of hESCs suppressed AFP gene
expression by 6.8-fold in comparison to no treatment. This was
visually reflected by a dramatic decrease in the number of AFP
labeled cells in these cultures as shown in FIGS. 8B-C. To quantify
this further, it was demonstrated that this approximately 7-fold
decrease in AFP gene expression was the result of a similar 7-fold
decrease in AFP antibody-labeled cell number as measured by flow
cytometry (FIGS. 9A-B). This result is extremely significant in
that it indicates that quantitative changes in gene expression as
seen by Q-PCR mirror changes in cell type specification as observed
by antibody staining.
[0200] Incubation of hESCs in the presence of Nodal family members
(Nodal, activin A and activin B--NAA) resulted in a significant
increase in SOX17 antibody-labeled cells over time. By 5 days of
continuous activin treatment greater than 50% of the cells were
labeled with SOX17 (FIGS. 10A-F). There were few or no cells
labeled with AFP after 5 days of activin treatment.
[0201] In summary, the antibody produced against the
carboxy-terminal 242 amino acids of the human SOX17 protein
identified human SOX17 protein on Western blots but did not
recognize SOX7, it's closest Sox family relative. The SOX17
antibody recognized a subset of cells in differentiating hESC
cultures that were primarily SOX17.sup.+/AFP.sup.lo/- (greater than
95% of labeled cells) as well as a small percentage (<5%) of
cells that co-label for SOX17 and AFP (visceral endoderm).
Treatment of hESC cultures with activins resulted in a marked
elevation of SOX17 gene expression as well as SOX17 labeled cells
and dramatically suppressed the expression of AFP mRNA and the
number of cells labeled with AFP antibody.
Example 5
Q-PCR Gene Expression Assay
[0202] In the following experiments, real-time quantitative RT-PCR
(Q-PCR) was the primary assay used for screening the effects of
various treatments on hESC differentiation. In particular,
real-time measurements of gene expression were analyzed for
multiple marker genes at multiple time points by Q-PCR. Marker
genes characteristic of the desired as well as undesired cell types
were evaluated to gain a better understanding of the overall
dynamics of the cellular populations. The strength of Q-PCR
analysis includes its extreme sensitivity and relative ease of
developing the necessary markers, as the genome sequence is readily
available. Furthermore, the extremely high sensitivity of Q-PCR
permits detection of gene expression from a relatively small number
of cells within a much larger population. In addition, the ability
to detect very low levels of gene expression provides indications
for "differentiation bias" within the population. The bias towards
a particular differentiation pathway, prior to the overt
differentiation of those cellular phenotypes, is unrecognizable
using immunocytochemical techniques. For this reason, Q-PCR
provides a method of analysis that is at least complementary and
potentially much superior to immunocytochemical techniques for
screening the success of differentiation treatments. Additionally,
Q-PCR provides a mechanism by which to evaluate the success of a
differentiation protocol in a quantitative format at semi-high
throughput scales of analysis.
[0203] The approach taken here was to perform relative quantitation
using SYBR Green chemistry on a Rotor Gene 3000 instrument (Corbett
Research) and a two-step RT-PCR format. Such an approach allowed
for the banking of cDNA samples for analysis of additional marker
genes in the future, thus avoiding variability in the reverse
transcription efficiency between samples.
[0204] Primers were designed to lie over exon-exon boundaries or
span introns of at least 800 bp when possible, as this has been
empirically determined to eliminate amplification from
contaminating genomic DNA. When marker genes were employed that do
not contain introns or they possess pseudogenes, DNase I treatment
of RNA samples was performed.
[0205] We routinely used Q-PCR to measure the gene expression of
multiple markers of target and non-target cell types in order to
provide a broad profile description of gene expression in cell
samples. The markers relevant for the early phases of hESC
differentiation (specifically ectoderm, mesoderm, definitive
endoderm and extra-embryonic endoderm) and for which validated
primer sets are available are provided below in Table 1. The human
specificity of these primer sets has also been demonstrated. This
is an important fact since the hESCs were often grown on mouse
feeder layers. Most typically, triplicate samples were taken for
each condition and independently analyzed in duplicate to assess
the biological variability associated with each quantitative
determination.
[0206] To generate PCR template, total RNA was isolated using
RNeasy (Qiagen) and quantitated using RiboGreen (Molecular Probes).
Reverse transcription from 350-500 ng of total RNA was carried out
using the iScript reverse transcriptase kit (BioRad), which
contains a mix of oligo-dT and random primers. Each 20 .mu.L
reaction was subsequently diluted up to 100 .mu.L total volume and
3 .mu.L was used in each 10 .mu.L Q-PCR reaction containing 400 nM
forward and reverse primers and 5 .mu.L 2.times.SYBR Green master
mix (Qiagen). Two step cycling parameters were used employing a 5
second denature at 85-94.degree. C. (specifically selected
according to the melting temp of the amplicon for each primer set)
followed by a 45 second anneal/extend at 60.degree. C. Fluorescence
data was collected during the last 15 seconds of each extension
phase. A three point, 10-fold dilution series was used to generate
the standard curve for each run and cycle thresholds (Ct's) were
converted to quantitative values based on this standard curve. The
quantitated values for each sample were normalized to housekeeping
gene performance and then average and standard deviations were
calculated for triplicate samples. At the conclusion of PCR
cycling, a melt curve analysis was performed to ascertain the
specificity of the reaction. A single specific product was
indicated by a single peak at the T.sub.m appropriate for that PCR
amplicon. In addition, reactions performed without reverse
transcriptase served as the negative control and do not
amplify.
[0207] A first step in establishing the Q-PCR methodology was
validation of appropriate housekeeping genes (HGs) in the
experimental system. Since the HG was used to normalize across
samples for the RNA input, RNA integrity and RT efficiency, it was
of value that the HG exhibited a constant level of expression over
time in all sample types in order for the normalization to be
meaningful. We measured the expression levels of Cyclophilin G,
hypoxanthine phosphoribosyltransferase 1 (HPRT),
beta-2-microglobulin, hydroxymethylbiane synthase (HMBS),
TATA-binding protein (TBP), and glucoronidase beta (GUS) in
differentiating hESCs. Our results indicated that
beta-2-microglobulin expression levels increased over the course of
differentiation and therefore we excluded the use of this gene for
normalization. The other genes exhibited consistent expression
levels over time as well as across treatments. We routinely used
both Cyclophilin G and GUS to calculate a normalization factor for
all samples. The use of multiple HGs simultaneously reduces the
variability inherent to the normalization process and increases the
reliability of the relative gene expression values.
[0208] After obtaining genes for use in normalization, Q-PCR was
then utilized to determine the relative gene expression levels of
many marker genes across samples receiving different experimental
treatments. The marker genes employed have been chosen because they
exhibit enrichment in specific populations representative of the
early germ layers and in particular have focused on sets of genes
that are differentially expressed in definitive endoderm and
extra-embryonic endoderm. These genes as well as their relative
enrichment profiles are highlighted in Table 1.
TABLE-US-00001 TABLE 1 Germ Layer Gene Expression Domains Endoderm
SOX17 definitive, visceral and parietal endoderm MIXL1 endoderm and
mesoderm GATA4 definitive and primitive endoderm HNF3b definitive
endoderm and primitive endoderm, mesoderm, neural plate GSC
endoderm and mesoderm Extra- SOX7 visceral endoderm embryonic AFP
visceral endoderm, liver SPARC parietal endoderm TM parietal
endoderm/ trophectoderm Ectoderm ZIC1 neural tube, neural Mesoderm
progenitors BRACH nascent mesoderm
[0209] Since many genes are expressed in more than one germ layer
it is useful to quantitatively compare expression levels of many
genes within the same experiment. SOX17 is expressed in definitive
endoderm and to a smaller extent in visceral and parietal endoderm.
SOX7 and AFP are expressed in visceral endoderm at this early
developmental time point. SPARC and TM are expressed in parietal
endoderm and Brachyury is expressed in early mesoderm.
[0210] Definitive endoderm cells were predicted to express high
levels of SOX17 mRNA and low levels of AFP and SOX7 (visceral
endoderm), SPARC (parietal endoderm) and Brachyury (mesoderm). In
addition, ZIC1 was used here to further rule out induction of early
ectoderm. Finally, GATA4 and HNF3b were expressed in both
definitive and extra-embryonic endoderm, and thus, correlate with
SOX17 expression in definitive endoderm (Table 1). A representative
experiment is shown in FIGS. 11-14 which demonstrates how the
marker genes described in Table 1 correlate with each other among
the various samples, thus highlighting specific patterns of
differentiation to definitive endoderm and extra-embryonic endoderm
as well as to mesodermal and neural cell types.
[0211] In view of the above data it is clear that increasing doses
of activin resulted in increasing SOX17 gene expression. Further
this SOX17 expression predominantly represented definitive endoderm
as opposed to extra-embryonic endoderm. This conclusion stems from
the observation that SOX17 gene expression was inversely correlated
with AFP, SOX7, and SPARC gene expression.
Example 6
Directed Differentiation of Human ES Cells to Definitive
Endoderm
[0212] Human ES cell cultures randomly differentiate if cultured
under conditions that do not actively maintain their
undifferentiated state. This heterogeneous differentiation results
in production of extra-embryonic endoderm cells comprised of both
parietal and visceral endoderm (AFP, SPARC and SOX7 expression) as
well as early ectodermal and mesodermal derivatives as marked by
ZIC1 and Nestin (ectoderm) and Brachyury (mesoderm) expression.
Definitive endoderm cell appearance has not been examined or
specified for lack of specific antibody markers in ES cell
cultures. As such, and by default, early definitive endoderm
production in ES cell cultures has not been well studied. Since
satisfactory antibody reagents for definitive endoderm cells have
been unavailable, most of the characterization has focused on
ectoderm and extra-embryonic endoderm. Overall, there are
significantly greater numbers of extra-embryonic and neurectodermal
cell types in comparison to SOX17.sup.hi definitive endoderm cells
in randomly differentiated ES cell cultures.
[0213] As undifferentiated hESC colonies expand on a bed of
fibroblast feeders, the cells at the edges of the colony take on
alternative morphologies that are distinct from those cells
residing within the interior of the colony. Many of these outer
edge cells can be distinguished by their less uniform, larger cell
body morphology and by the expression of higher levels of OCT4. It
has been described that as ES cells begin to differentiate they
alter the levels of OCT4 expression up or down relative to
undifferentiated ES cells. Alteration of OCT4 levels above or below
the undifferentiated threshold may signify the initial stages of
differentiation away from the pluripotent state.
[0214] When undifferentiated colonies were examined by SOX17
immunocytochemistry, occasionally small 10-15-cell clusters of
SOX17-positive cells were detected at random locations on the
periphery and at the junctions between undifferentiated hESC
colonies. As noted above, these scattered pockets of outer colony
edges appeared to be some of the first cells to differentiate away
from the classical ES cell morphology as the colony expanded in
size and became more crowded. Younger, smaller fully
undifferentiated colonies (<1 mm; 4-5 days old) showed no SOX17
positive cells within or at the edges of the colonies while older,
larger colonies (1-2 mm diameter, >5 days old) had sporadic
isolated patches of SOX17 positive, AFP negative cells at the
periphery of some colonies or in regions interior to the edge that
did not display the classical hESC morphology described previously.
Given that this was the first development of an effective SOX17
antibody, definitive endoderm cells generated in such early
"undifferentiated" ES cell cultures have never been previously
demonstrated.
[0215] Based on negative correlations of SOX17 and SPARC gene
expression levels by Q-PCR, the vast majority of these SOX17
positive, AFP negative cells will be negative for parietal endoderm
markers by antibody co-labeling. This was specifically demonstrated
for TM-expressing parietal endoderm cells as shown in FIGS. 15A-B.
Exposure to Nodal factors activin A and B resulted in a dramatic
decrease in the intensity of TM expression and the number of TM
positive cells. By triple labeling using SOX17, AFP and TM
antibodies on an activin treated culture, clusters of SOX17
positive cells that were also negative for AFP and TM were observed
(FIGS. 16A-D). These are the first cellular demonstrations of SOX17
positive definitive endoderm cells in differentiating hESC cultures
(FIGS. 16A-D and 17).
[0216] With the SOX17 antibody and Q-PCR tools described above we
have explored a number of procedures capable of efficiently
programming hESCs to become SOX17.sup.hi/AFP.sup.lo/SPARC/TM.sup.lo
definitive endoderm cells. We applied a variety of differentiation
protocols aimed at increasing the number and proliferative capacity
of these cells as measured at the population level by Q-PCR for
SOX17 gene expression and at the level of individual cells by
antibody labeling of SOX17 protein.
[0217] We were the first to analyze and describe the effect of
TGF.beta. family growth factors, such as Nodal/activin/BMP, for use
in creating definitive endoderm cells from embryonic stem cells in
in vitro cell cultures. In typical experiments, activin A, activin
B, BMP or combinations of these growth factors were added to
cultures of undifferentiated human stem cell line hESCyt-25 to
begin the differentiation process.
[0218] As shown in FIG. 19, addition of activin A at 100 ng/ml
resulted in a 19-fold induction of SOX17 gene expression vs.
undifferentiated hESCs by day 4 of differentiation. Adding activin
B, a second member of the activin family, together with activin A,
resulted in a 37-fold induction over undifferentiated hESCs by day
4 of combined activin treatment. Finally, adding a third member of
the TGF.beta. family from the Nodal/Activin and BMP subgroups,
BMP4, together with activin A and activin B, increased the fold
induction to 57 times that of undifferentiated hESCs (FIG. 19).
When SOX17 induction with activins and BMP was compared to no
factor medium controls 5-, 10-, and 15-fold inductions resulted at
the 4-day time point. By five days of triple treatment with
activins A, B and BMP, SOX17 was induced more than 70 times higher
than hESCs. These data indicate that higher doses and longer
treatment times of the Nodal/activin TGF.beta. family members
results in increased expression of SOX17.
[0219] Nodal and related molecules activin A, B and BMP facilitate
the expression of SOX17 and definitive endoderm formation in vivo
or in vitro. Furthermore, addition of BMP results in an improved
SOX17 induction possibly through the further induction of Cripto,
the Nodal co-receptor.
[0220] We have demonstrated that the combination of activins A and
B together with BMP4 result in additive increases in SOX17
induction and hence definitive endoderm formation. BMP4 addition
for prolonged periods (>4 days), in combination with activin A
and B may induce SOX17 in parietal and visceral endoderm as well as
definitive endoderm. In some embodiments of the present invention,
it is therefore valuable to remove BMP4 from the treatment within 4
days of addition.
[0221] To determine the effect of TGF.beta. factor treatment at the
individual cell level, a time course of TGF.beta. factor addition
was examined using SOX17 antibody labeling. As previously shown in
FIGS. 10A-F, there was a dramatic increase in the relative number
of SOX17 labeled cells over time. The relative quantification (FIG.
20) shows more than a 20-fold increase in SOX17-labeled cells. This
result indicates that both the numbers of cells as well SOX17 gene
expression level are increasing with time of TGF.beta. factor
exposure. As shown in FIG. 21, after four days of exposure to
Nodal, activin A, activin B and BMP4, the level of SOX17 induction
reached 168-fold over undifferentiated hESCs. FIG. 22 shows that
the relative number of SOX17-positive cells was also dose
responsive. activin A doses of 100 ng/ml or more were capable of
potently inducing SOX17 gene expression and cell number.
[0222] In addition to the TGF.beta. family members, the Wnt family
of molecules may play a role in specification and/or maintenance of
definitive endoderm. The use of Wnt molecules was also beneficial
for the differentiation of hESCs to definitive endoderm as
indicated by the increased SOX17 gene expression in samples that
were treated with activins plus Wnt3a over that of activins alone
(FIG. 23).
[0223] All of the experiments described above were performed using
a tissue culture medium containing 10% serum with added factors.
Surprisingly, we discovered that the concentration of serum had an
effect on the level of SOX17 expression in the presence of added
activins as shown in FIGS. 24A-C. When serum levels were reduced
from 10% to 2%, SOX17 expression tripled in the presence of
activins A and B.
[0224] Finally, we demonstrated that activin induced SOX17.sup.+
cells divide in culture as depicted in FIGS. 25A-D. The arrows show
cells labeled with SOX17/PCNA/DAPI that are in mitosis as evidenced
by the PCNA/DAPI-labeled mitotic plate pattern and the phase
contrast mitotic profile.
Example 7
Chemokine Receptor 4 (CXCR4) Expression Correlates with Markers for
Definitive Endoderm and not Markers for Mesoderm, Ectoderm or
Visceral Endoderm
[0225] As described above, hESCs can be induced to differentiate to
the definitive endoderm germ layer by the application of cytokines
of the TGF.beta. family and more specifically of the activin/nodal
subfamily. Additionally, we have shown that the proportion of fetal
bovine serum (FBS) in the differentiation culture medium effects
the efficiency of definitive endoderm differentiation from hESCs.
This effect is such that at a given concentration of activin A in
the medium, higher levels of FBS will inhibit maximal
differentiation to definitive endoderm. In the absence of exogenous
activin A, differentiation of hESCs to the definitive endoderm
lineage is very inefficient and the FBS concentration has much
milder effects on the differentiation process of hESCs.
[0226] In these experiments, hESCs were differentiated by growing
in RPMI medium (Invitrogen, Carlsbad, Calif.; cat#61870-036)
supplemented with 0.5%, 2.0% or 10% FBS and either with or without
100 ng/ml activin A for 6 days. In addition, a gradient of FBS
ranging from 0.5% to 2.0% over the first three days of
differentiation was also used in conjunction with 100 ng/ml of
activin A. After the 6 days, replicate samples were collected from
each culture condition and analyzed for relative gene expression by
real-time quantitative PCR. The remaining cells were fixed for
immunofluorescent detection of SOX17 protein.
[0227] The expression levels of CXCR4 varied dramatically across
the 7 culture conditions used (FIG. 26). In general, CXCR4
expression was high in activin A treated cultures (A100) and low in
those which did not receive exogenous activin A (NF). In addition,
among the A100 treated cultures, CXCR4 expression was highest when
FBS concentration was lowest. There was a remarkable decrease in
CXCR4 level in the 10% FBS condition such that the relative
expression was more in line with the conditions that did not
receive activin A (NF).
[0228] As described above, expression of the SOX17, GSC, MIXL1, and
HNF3.beta. genes is consistent with the characterization of a cell
as definitive endoderm. The relative expression of these four genes
across the 7 differentiation conditions mirrors that of CXCR4
(FIGS. 27A-D). This demonstrates that CXCR4 is also a marker of
definitive endoderm.
[0229] Ectoderm and mesoderm lineages can be distinguished from
definitive endoderm by their expression of various markers. Early
mesoderm expresses the genes Brachyury and MOX1 while nascent
neuro-ectoderm expresses SOX1 and ZIC1. FIGS. 28A-D demonstrate
that the cultures which did not receive exogenous activin A were
preferentially enriched for mesoderm and ectoderm gene expression
and that among the activin A treated cultures, the 10% FBS
condition also had increased levels of mesoderm and ectoderm marker
expression. These patterns of expression were inverse to that of
CXCR4 and indicated that CXCR4 was not highly expressed in mesoderm
or ectoderm derived from hESCs at this developmental time
period.
[0230] Early during mammalian development, differentiation to
extra-embryonic lineages also occurs. Of particular relevance here
is the differentiation of visceral endoderm that shares the
expression of many genes in common with definitive endoderm,
including SOX17. To distinguish definitive endoderm from
extra-embryonic visceral endoderm one should examine a marker that
is distinct between these two. SOX7 represents a marker that is
expressed in the visceral endoderm but not in the definitive
endoderm lineage. Thus, culture conditions that exhibit robust
SOX17 gene expression in the absence of SOX7 expression are likely
to contain definitive and not visceral endoderm. It is shown in
FIG. 28E that SOX7 was highly expressed in cultures that did not
receive activin A, SOX7 also exhibited increased expression even in
the presence of activin A when FBS was included at 10%. This
pattern is the inverse of the CXCR4 expression pattern and suggests
that CXCR4 is not highly expressed in visceral endoderm.
[0231] The relative number of SOX17 immunoreactive (SOX17.sup.+)
cells present in each of the differentiation conditions mentioned
above was also determined. When hESCs were differentiated in the
presence of high dose activin A and low FBS concentration
(0.5%-2.0%) SOX17.sup.+ cells were ubiquitously distributed
throughout the culture. When high dose activin A was used but FBS
was included at 10% (v/v), the SOX17.sup.+ cells appeared at much
lower frequency and always appeared in isolated clusters rather
than evenly distributed throughout the culture (FIGS. 29A and C as
well as B and E). A further decrease in SOX17.sup.+ cells was seen
when no exogenous activin A was used. Under these conditions the
SOX17.sup.+ cells also appeared in clusters and these clusters were
smaller and much more rare than those found in the high activin A,
low FBS treatment (FIGS. 29 C and F). These results demonstrate
that the CXCR4 expression patterns not only correspond to
definitive endoderm gene expression but also to the number of
definitive endoderm cells in each condition.
Example 8
Differentiation Conditions that Enrich for Definitive Endoderm
Increase the Proportion of CXCR4 Positive Cells
[0232] The dose of activin A also effects the efficiency at which
definitive endoderm can be derived from hESCs. This example
demonstrates that increasing the dose of activin A increases the
proportion of CXCR4.sup.+ cells in the culture.
[0233] hESCs were differentiated in RPMI media supplemented with
0.5%-2% FBS (increased from 0.5% to 1.0% to 2.0% over the first 3
days of differentiation) and either 0, 10, or 100 ng/ml of activin
A. After 7 days of differentiation the cells were dissociated in
PBS without Ca.sup.2+/Mg.sup.2+ containing 2% FBS and 2 mM (EDTA)
for 5 minutes at room temperature. The cells were filtered through
35 .mu.m nylon filters, counted and pelleted. Pellets were
resuspended in a small volume of 50% human serum/50% normal donkey
serum and incubated for 2 minutes on ice to block non-specific
antibody binding sites. To this, 1 .mu.l of mouse anti-CXCR4
antibody (Abeam, cat#ab10403-100) was added per 50 .mu.l
(containing approximately 10.sup.5 cells) and labeling proceeded
for 45 minutes on ice. Cells were washed by adding 5 ml of PBS
containing 2% human serum (buffer) and pelleted. A second wash with
5 ml of buffer was completed then cells were resuspended in 50
.mu.l buffer per 10.sup.5 cells. Secondary antibody (FITC
conjugated donkey anti-mouse; Jackson ImmunoResearch,
cat#715-096-151) was added at 5 .mu.g/ml final concentration and
allowed to label for 30 minutes followed by two washes in buffer as
above. Cells were resuspended at 5.times.10.sup.6 cells/ml in
buffer and analyzed and sorted using a FACS Vantage (Beckton
Dickenson) by the staff at the flow cytometry core facility (The
Scripps Research Institute). Cells were collected directly into RLT
lysis buffer (Qiagen) for subsequent isolation of total RNA for
gene expression analysis by real-time quantitative PCR.
[0234] The number of CXCR4.sup.+ cells as determined by flow
cytometry were observed to increase dramatically as the dose of
activin A was increased in the differentiation culture media (FIGS.
30A-C). The CXCR4.sup.+ cells were those falling within the R4 gate
and this gate was set using a secondary antibody-only control for
which 0.2% of events were located in the R4 gate. The dramatically
increased numbers of CXCR4.sup.+ cells correlates with a robust
increase in definitive endoderm gene expression as activin A dose
is increased (FIGS. 31A-D).
Example 9
Isolation of CXCR4 Positive Cells Enriches for Definitive Endoderm
Gene Expression and Depletes Cells Expressing Markers of Mesoderm,
Ectoderm and Visceral Endoderm
[0235] The CXCR4 and CXCR4.sup.- cells identified in Example 8
above were collected and analyzed for relative gene expression and
the gene expression of the parent populations was determined
simultaneously.
[0236] The relative levels of CXCR4 gene expression was
dramatically increased with increasing dose of activin A (FIG. 32).
This correlated very well with the activin A dose-dependent
increase of CXCR4.sup.+ cells (FIGS. 30A-C). It is also clear that
isolation of the CXCR4.sup.+ cells from each population accounted
for nearly all of the CXCR4 gene expression in that population.
This demonstrates the efficiency of the FACS method for collecting
these cells.
[0237] Gene expression analysis revealed that the CXCR4.sup.+ cells
contain not only the majority of the CXCR4 gene expression, but
they also contained gene expression for other markers of definitive
endoderm. As shown in FIGS. 31A-D, the CXCR4.sup.+ cells were
further enriched over the parent A100 population for SOX17, GSC,
HNF3B, and MIXL1. In addition, the CXCR4.sup.- fraction contained
very little gene expression for these definitive endoderm markers.
Moreover, the CXCR4.sup.+ and CXCR4.sup.- populations displayed the
inverse pattern of gene expression for markers of mesoderm,
ectoderm and extra-embryonic endoderm. FIGS. 33A-D shows that the
CXCR4.sup.+ cells were depleted for gene expression of Brachyury,
MOX1, ZIC1, and SOX7 relative to the A100 parent population. This
A100 parent population was already low in expression of these
markers relative to the low dose or no activin A conditions. These
results show that the isolation of CXCR4.sup.+ cells from hESCs
differentiated in the presence of high activin A yields a
population that is highly enriched for and substantially pure
definitive endoderm.
Example 10
Quantitation of Definitive Endoderm Cells in a Cell Population
Using CXCR4
[0238] To confirm the quantitation of the proportion of definitive
endoderm cells present in a cell culture or cell population as
determined previously herein and as determined in U.S. Provisional
Patent Application No. 60/532,004, entitled DEFINITIVE ENDODERM,
filed Dec. 23, 2003, the disclosure of which is incorporated herein
by reference in its entirety, cells expressing CXCR4 and other
markers of definitive endoderm were analyzed by FACS.
[0239] Using the methods such as those described in the above
Examples, hESCs were differentiated to produce definitive endoderm.
In particular, to increase the yield and purity in differentiating
cell cultures, the serum concentration of the medium was controlled
as follows: 0.2% FBS on day 1, 1.0% FBS on day 2 and 2.0% FBS on
days 3-6. Differentiated cultures were sorted by FACS using three
cell surface epitopes, E-Cadherin, CXCR4, and Thrombomodulin.
Sorted cell populations were then analyzed by Q-PCR to determine
relative expression levels of markers for definitive and
extraembryonic-endoderm as well as other cell types. CXCR4 sorted
cells taken from optimally differentiated cultures resulted in the
isolation of definitive endoderm cells that were >98% pure.
[0240] Table 2 shows the results of a marker analysis for a
definitive endoderm culture that was differentiated from hESCs
using the methods described herein.
TABLE-US-00002 TABLE 2 Composition of Definitive Endoderm Cultures
Percent Percent Percent Percent of Definitive Extraembryonic hES
Marker(s) culture Endoderm endoderm cells SOX17 70-80 100
Thrombomodulin <2 0 75 AFP <1 0 25 CXCR4 70-80 100 0 ECAD 10
0 100 other (ECAD neg.) 10-20 Total 100 100 100 100
[0241] In particular, Table 2 indicates that CXCR4 and SOX17
positive cells (endoderm) comprised from 70%-80% of the cells in
the cell culture. Of these SOX17-expressing cells, less than 2%
expressed TM (parietal endoderm) and less than 1% expressed AFP
(visceral endoderm). After subtracting the proportion of
TM-positive and AFP-positive cells (combined parietal and visceral
endoderm; 3% total) from the proportion of SOX17/CXCR4 positive
cells, it can be seen that about 67% to about 77% of the cell
culture was definitive endoderm. Approximately 10% of the cells
were positive for E-Cadherin (ECAD), which is a marker for hESCs,
and about 10-20% of the cells were of other cell types.
[0242] We have discovered that the purity of definitive endoderm in
the differentiating cell cultures that are obtained prior to FACS
separation can be improved as compared to the above-described low
serum procedure by maintaining the FBS concentration at
.ltoreq.0.5% throughout the 5-6 day differentiation procedure.
However, maintaining the cell culture at .ltoreq.0.5% throughout
the 5-6 day differentiation procedure also results in a reduced
number of total definitive endoderm cells that are produced.
[0243] Definitive endoderm cells produced by methods described
herein have been maintained and expanded in culture in the presence
of activin for greater than 50 days without appreciable
differentiation. In such cases, SOX17, CXCR4, MIXL1, GATA4,
HNF3.beta. expression is maintained over the culture period.
Additionally, TM, SPARC, OCT4, AFP, SOX7, ZIC1 and BRACH were not
detected in these cultures. It is likely that such cells can be
maintained and expanded in culture for substantially longer than 50
days without appreciable differentiation.
Example 11
Additional Marker of Definitive Endoderm Cells
[0244] In the following experiment, RNA was isolated from purified
definitive endoderm and human embryonic stem cell populations. Gene
expression was then analyzed by gene chip analysis of the RNA from
each purified population. Q-PCR was also performed to further
investigate the potential of genes expressed in definitive
endoderm, but not in embryonic stem cells, as a marker for
definitive endoderm.
[0245] Human embryonic stem cells (hESCs) were maintained in
DMEM/F12 media supplemented with 20% KnockOut Serum Replacement, 4
ng/ml recombinant human basic fibroblast growth factor (bFGF), 0.1
mM 2-mercaptoethanol, L-glutamine, non-essential amino acids and
penicillin/streptomycin. hESCs were differentiated to definitive
endoderm by culturing for 5 days in RPMI media supplemented with
100 ng/ml of recombinant human activin A, fetal bovine serum (FBS),
and penicillin/streptomycin. The concentration of FBS was varied
each day as follows: 0.1% (first day), 0.2% (second day), 2% (days
3-5).
[0246] Cells were isolated by fluorescence activated cell sorting
(FACS) in order to obtain purified populations of hESCs and
definitive endoderm for gene expression analysis.
Immuno-purification was achieved for hESCs using SSEA4 antigen
(R&D Systems, cat# FAB1435P) and for definitive endoderm using
CXCR4 (R&D Systems, cat# FAB170P). Cells were dissociated using
trypsin/EDTA (Invitrogen, cat#25300-054), washed in phosphate
buffered saline (PBS) containing 2% human serum and resuspended in
100% human serum on ice for 10 minutes to block non-specific
binding. Staining was carried out for 30 minutes on ice by adding
200 .mu.l of phycoerythrin-conjugated antibody to 5.times.10.sup.6
cells in 800 .mu.l human serum. Cells were washed twice with 8 ml
of PBS buffer and resuspended in 1 ml of the same. FACS isolation
was carried out by the core facility of The Scripps Research
Institute using a FACS Vantage (BD Biosciences). Cells were
collected directly into RLT lysis buffer and RNA was isolated by
RNeasy according to the manufacturers instructions (Qiagen).
[0247] Purified RNA was submitted in duplicate to Expression
Analysis (Durham, N.C.) for generation of the expression profile
data using the Affymetrix platform and U133 Plus 2.0 high-density
oligonucleotide arrays. Data presented is a group comparison that
identifies genes differentially expressed between the two
populations, hESCs and definitive endoderm. Genes that exhibited a
robust upward change in expression level over that found in hESCs
were selected as new candidate markers that are highly
characteristic of definitive endoderm. Select genes were assayed by
Q-PCR, as described above, to verify the gene expression changes
found on the gene chip and also to investigate the expression
pattern of these genes during a time course of hESC
differentiation.
[0248] FIGS. 34A-M show the gene expression results for certain
markers. Results are displayed for cell cultures analyzed 1, 3 and
5 days after the addition of 100 ng/ml activin A, CXCR4-expressing
definitive endoderm cells purified at the end of the five day
differentiation procedure (CXDE), and in purified hESCs. A
comparison of FIGS. 34C and G-M demonstrates that the six marker
genes, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1, exhibit an
expression pattern that is almost identical to each other and which
is also identical to the pattern of expression of CXCR4 and the
ratio of SOX17/SOX7. As described previously, SOX17 is expressed in
both the definitive endoderm as well as in the SOX7-expressing
extra-embryonic endoderm. Since SOX7 is not expressed in the
definitive endoderm, the ratio of SOX17/SOX7 provides a reliable
estimate of definitive endoderm contribution to the SOX17
expression witnessed in the population as a whole. The similarity
of panels G-L and M to panel C indicates that FGF17, VWF, CALCR,
FOXQ1, CMKOR1 and CRIP1 are likely markers of definitive endoderm
and that they are not significantly expressed in extra-embryonic
endoderm cells.
[0249] It will be appreciated that the Q-PCR results described
herein can be further confirmed by ICC.
Example 12
Generation of SOX17 Promoter-EGFP Transgenic hESC Lines and CXCR4
Promoter-EGFP Transgenic hESC Lines
[0250] As an alternative to purification of definitive endoderm
using the CXCR4-specific antibody, EGFP fusions to either the SOX17
or the CXCR4 promoters can be used. In particular, this Example
describes the construction of a vector comprising a reporter
cassette which comprises a reporter gene under the control of the
SOX17 regulatory region. Additionally, the construction of a vector
comprising a reporter cassette which comprises a reporter gene
under the control of the CXCR4 regulatory region is described. This
Example also describes the preparation of a cell, such as a human
embryonic stem cell, transfected with one or more of these vectors
as well as a cell having this one or both of these reporter
cassettes integrated into its genome.
[0251] SOX17-expressing definitive endoderm cell lines and
CXRC4-expressing definitive endoderm cell lines genetically tagged
with a reporter gene are constructed by placing a GFP reporter gene
under the control of the regulatory region (promoter) of the SOX17
gene or the CXCR4 gene, respectively. First, a plasmid construct in
which EGFP expression is driven by the human SOX17 or CXCR4 gene
promoter is generated by replacing the CMV promoter of vector
pEGFP-N1 (Clontech) with the human SOX17 or CXCR4 control region.
These control regions contain the characterized regulatory elements
of either the SOX17 or the CXCR4 gene, and they is sufficient to
confer the normal expression pattern of these genes in transgenic
mice. In the resulting vector, expression of EFGP is driven by
either the SOX17 promoter or the CXCR4 promoter. In some
experiments, this vector can be transfected into hESCs.
[0252] The SOX17 promoter/EGFP cassette or the CXCR4 promoter/EGFP
cassette is excised from the above vector, and then subcloned into
a selection vector containing the neomycin phosphotransferase gene
under control of the phosphoglycerate kinase-1 promoter. The
selection cassette is flanked by flp recombinase recognition sites
to allow removal of the cassette. This selection vector is
linearized, and then introduced into hESCs using standard
lipofection methods. Following 10-14 days of selection in G418,
undifferentiated transgenic hESC clones is isolated and
expanded.
[0253] It will be appreciated that reporter genes other than GFP or
EGFP can be used in any of the above-described constructs provided
that the reporter allows for cell separation by FACS
Example 13
Alternative Isolation of Definitive Endoderm
[0254] The following Example demonstrates that hESCs comprising a
SOX17 or CXCR4 promoter/EGFP cassette can be differentiated into
definitive endoderm cells and then subsequently isolated by
fluorescence-activated cell sorting (FACS).
[0255] SOX17 or CXCR4 promoter/EGFP transgenic hESCs are
differentiated for approximately 6, 12 and 18 hours in growth
medium containing 100 ng/ml activin A and no serum. The
differentiated cells are then harvested by trypsin digestion and
sorted on a Becton Dickinson FACS Diva directly into RNA lysis
buffer or PBS. A sample of single live cells is taken without
gating for EGFP and single live cells are gated into EGFP positive
and GFP negative populations. In a separate experiment, the EGFP
positive fraction is separated into two equally sized populations
according to fluorescence intensity (Hi and Lo).
[0256] Following sorting, cell populations are analyzed by both
Q-PCR and immunocytochemistry. For Q-PCR analysis, RNA is prepared
using Qiagen RNeasy columns and then converted to cDNA. Q-PCR is
conducted as described previously. For immunocytochemistry
analysis, cells are sorted into PBS, fixed for 10 minutes in 4%
paraformaldehyde, and adhered to glass slides using a Cytospin
centrifuge. The primary antibody SOX17 or CXCR4. An appropriate
secondary antibody conjugated to FITC (green) or Rhodamine (Red) is
used to detect binding of the primary antibody.
[0257] Sorted cells are further subjected to Q-PCR analysis.
Differentiated cells show a correlation of EGFP fluorescence with
endogenous SOX17 or CXCR4 expression gene expression. Compared to
non-fluorescing cells, the EGFP positive cells show a greater than
2-fold increase in SOX17 or CXCR4 expression levels. The separation
of high and low EGFP intensity cells indicates that EGFP expression
level correlates with SOX17 or CXCR4 expression level. In addition
to SOX17 or CXCR4 mRNA analysis, sorted cells are subjected to
immunocytochemistry analysis of SOX17 or CXCR4 polypeptide (in
embodiments where CXCR4/EGFP fusions are used, SOX17 polypeptide
expression is analyzed and in cases where SOX17/EGFP fusions are
used, CXCR4 polypeptide expression is analyzed). Substantial
expression of either the SOX17 or CXCR4 polypeptides can be seen in
the enriched in the EGFP positive fraction. In contrast, little
expression of either the SOX17 or CXCR4 polypeptides is seen in the
EGFP negative fraction.
[0258] Given these results, at least about 5% of the cells present
in the differentiated cell cultures prior to sorting are
SOX17/CXCR4-positive definitive endoderm cells. At least about 90%
of the cells in the sorted cell populations are
SOX17/CXCR4-positive definitive endoderm cells.
Example 14
Passage of Definitive Endoderm Cells in Culture
[0259] This Example demonstrates that the definitive endoderm cells
described herein can be maintained in cell culture and passaged
without further differentiation.
[0260] Definitive endoderm cells were differentiated from two
related passages, designated EB and EV, of the CyT25 hESC line in
the presence of 100 ng/ml activin A in low serum RMPI. The low
serum RPMI contained 0% (v/v) fetal bovine serum (FBS) on day 1,
0.2% (v/v) FBS on day two and 2% serum on each day thereafter.
After four days of differentiation, the cells maintained in culture
in either the presence or absence of 100 ng/ml activin A for a
total of 36 days as measured from induction of differentiation.
During the 36 day culture period, the definitive endoderm cells
were passaged twice. Furthermore, on days 29-36 the cells of the
group designated EV were additionally contacted with 50 mg/ml EGF.
On days 4, 9, 23, 29 and 36 of culture, Q-PCR was used to measure
the expression of marker genes indicative of definitive
endoderm.
[0261] FIGS. 35A-D show that, in cell cultures provided with 100
ng/ml activin A, expression of the definitive endoderm markers
SOX17, GSC, MIXL1 and CXCR4 was maintained during the 32 day
culture period subsequent to the derivation of the definitive
endoderm cells from hESCs (days 4 to 36). Little expression of
these markers was observed in the cell cultures grown in the
absence of activin A. Addition of 50 ng/ml EGF did not appear to
significantly increase the expression of any of the definitive
endoderm markers.
Example 15
Expansion of Purified Definitive Endoderm Cells
[0262] This Example demonstrates that the definitive endoderm cells
described herein can be differentiated from hESCs, purified and
then regrown and expanded in cell culture.
[0263] FIG. 36 shows the design of a definitive endoderm
purification/expansion experiment. In particular, definitive
endoderm cells were differentiated from the 96.sup.th passage of
hESC line CyT25 in the presence of 100 ng/ml activin A in low serum
RMPI. The low serum RPMI contained 0% (v/v) fetal bovine serum
(FBS) on day 1, 0.2% (v/v) FBS on day two and 2% serum on each day
thereafter. After five days of differentiation, the cells were
subjected to FACS purification using antibody against CXCR4 as
described in previous Examples. The purified cell population was
then cultured on IVF dishes coated with poly-ornithine and 10
.mu.g/ml human fibronectin in RPMI containing 2% FBS under one of
the following four growth factor conditions: no added factor (NF);
100 ng/ml activin A (A); 100 ng/ml activin A and 100 ng/ml IGF1
(AI); or 100 ng/ml activin A, 12 ng/ml bFGF and 10 ng/ml EGF (AFE).
On day 11, the expanded definitive endoderm cells were passaged
using the standard trypsinization method. Each of the cell cultures
were then grown for an additional 10 days after passage (a total of
21 days subsequent to the first contact with activin A). Samples of
mRNA were obtained at days 0, 5, 11 and 21 as indicated in FIG.
36.
[0264] FIGS. 37A-E show the expression of marker genes for various
embryonic cell types at each of the sample time points for each of
the culture conditions. As shown in FIGS. 37A-B, the definitive
endoderm markers SOX17 and GSC were highly expressed five day old
unpurified definitive endoderm cultures but were not expressed in
hESCs. This expression is in contrast to that of the hESC marker,
OCT4 (FIG. 37C). Six days after the purification of definitive
endoderm cells (day 11) the expression of SOX17 and GSC expression
remained high in each of the cell cultures treated with growth
factor(s) but not in cell cultures grown in the absence of activin
A (FIG. 37A-B). A similar pattern of expression was observed for
these markers 10 days after passage (day 21) (FIGS. 37A-B). No
expression of mRNA for markers of hESCs (OCT4), mesoderm
(brachyury), or ectoderm (ZIC1 and SOX1) was observed in any of the
cell cultures subsequent to purification. This result indicates
that purified definitive endoderm cells do not form hESCs or cells
of the other two embryonic cell lineages even in the absence of
activin A (FIGS. 37C-F).
[0265] The methods, compositions, and devices described herein are
presently representative of preferred embodiments and are exemplary
and are not intended as limitations on the scope of the invention.
Changes therein and other uses will occur to those skilled in the
art which are encompassed within the spirit of the invention and
are defined by the scope of the disclosure. Accordingly, it will be
apparent to one skilled in the art that varying substitutions and
modifications may be made to the invention disclosed herein without
departing from the scope and spirit of the invention.
[0266] As used in the claims below and throughout this disclosure,
by the phrase "consisting essentially of" is meant including any
elements listed after the phrase, and limited to other elements
that do not interfere with or contribute to the activity or action
specified in the disclosure for the listed elements. Thus, the
phrase "consisting essentially of" indicates that the listed
elements are required or mandatory, but that other elements are
optional and may or may not be present depending upon whether or
not they affect the activity or action of the listed elements.
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Sequence CWU 1
1
211245DNAHomo sapiens 1atgagcagcc cggatgcggg atacgccagt gacgaccaga
gccagaccca gagcgcgctg 60cccgcggtga tggccgggct gggcccctgc ccctgggccg
agtcgctgag ccccatcggg 120gacatgaagg tgaagggcga ggcgccggcg
aacagcggag caccggccgg ggccgcgggc 180cgagccaagg gcgagtcccg
tatccggcgg ccgatgaacg ctttcatggt gtgggctaag 240gacgagcgca
agcggctggc gcagcagaat ccagacctgc acaacgccga gttgagcaag
300atgctgggca agtcgtggaa ggcgctgacg ctggcggaga agcggccctt
cgtggaggag 360gcagagcggc tgcgcgtgca gcacatgcag gaccacccca
actacaagta ccggccgcgg 420cggcgcaagc aggtgaagcg gctgaagcgg
gtggagggcg gcttcctgca cggcctggct 480gagccgcagg cggccgcgct
gggccccgag ggcggccgcg tggccatgga cggcctgggc 540ctccagttcc
ccgagcaggg cttccccgcc ggcccgccgc tgctgcctcc gcacatgggc
600ggccactacc gcgactgcca gagtctgggc gcgcctccgc tcgacggcta
cccgttgccc 660acgcccgaca cgtccccgct ggacggcgtg gaccccgacc
cggctttctt cgccgccccg 720atgcccgggg actgcccggc ggccggcacc
tacagctacg cgcaggtctc ggactacgct 780ggccccccgg agcctcccgc
cggtcccatg cacccccgac tcggcccaga gcccgcgggt 840ccctcgattc
cgggcctcct ggcgccaccc agcgcccttc acgtgtacta cggcgcgatg
900ggctcgcccg gggcgggcgg cgggcgcggc ttccagatgc agccgcaaca
ccagcaccag 960caccagcacc agcaccaccc cccgggcccc ggacagccgt
cgccccctcc ggaggcactg 1020ccctgccggg acggcacgga ccccagtcag
cccgccgagc tcctcgggga ggtggaccgc 1080acggaatttg aacagtatct
gcacttcgtg tgcaagcctg agatgggcct cccctaccag 1140gggcatgact
ccggtgtgaa tctccccgac agccacgggg ccatttcctc ggtggtgtcc
1200gacgccagct ccgcggtata ttactgcaac tatcctgacg tgtga
12452414PRTHomo sapiens 2Met Ser Ser Pro Asp Ala Gly Tyr Ala Ser
Asp Asp Gln Ser Gln Thr 1 5 10 15 Gln Ser Ala Leu Pro Ala Val Met
Ala Gly Leu Gly Pro Cys Pro Trp 20 25 30 Ala Glu Ser Leu Ser Pro
Ile Gly Asp Met Lys Val Lys Gly Glu Ala 35 40 45 Pro Ala Asn Ser
Gly Ala Pro Ala Gly Ala Ala Gly Arg Ala Lys Gly 50 55 60 Glu Ser
Arg Ile Arg Arg Pro Met Asn Ala Phe Met Val Trp Ala Lys 65 70 75 80
Asp Glu Arg Lys Arg Leu Ala Gln Gln Asn Pro Asp Leu His Asn Ala 85
90 95 Glu Leu Ser Lys Met Leu Gly Lys Ser Trp Lys Ala Leu Thr Leu
Ala 100 105 110 Glu Lys Arg Pro Phe Val Glu Glu Ala Glu Arg Leu Arg
Val Gln His 115 120 125 Met Gln Asp His Pro Asn Tyr Lys Tyr Arg Pro
Arg Arg Arg Lys Gln 130 135 140 Val Lys Arg Leu Lys Arg Val Glu Gly
Gly Phe Leu His Gly Leu Ala 145 150 155 160 Glu Pro Gln Ala Ala Ala
Leu Gly Pro Glu Gly Gly Arg Val Ala Met 165 170 175 Asp Gly Leu Gly
Leu Gln Phe Pro Glu Gln Gly Phe Pro Ala Gly Pro 180 185 190 Pro Leu
Leu Pro Pro His Met Gly Gly His Tyr Arg Asp Cys Gln Ser 195 200 205
Leu Gly Ala Pro Pro Leu Asp Gly Tyr Pro Leu Pro Thr Pro Asp Thr 210
215 220 Ser Pro Leu Asp Gly Val Asp Pro Asp Pro Ala Phe Phe Ala Ala
Pro 225 230 235 240 Met Pro Gly Asp Cys Pro Ala Ala Gly Thr Tyr Ser
Tyr Ala Gln Val 245 250 255 Ser Asp Tyr Ala Gly Pro Pro Glu Pro Pro
Ala Gly Pro Met His Pro 260 265 270 Arg Leu Gly Pro Glu Pro Ala Gly
Pro Ser Ile Pro Gly Leu Leu Ala 275 280 285 Pro Pro Ser Ala Leu His
Val Tyr Tyr Gly Ala Met Gly Ser Pro Gly 290 295 300 Ala Gly Gly Gly
Arg Gly Phe Gln Met Gln Pro Gln His Gln His Gln 305 310 315 320 His
Gln His Gln His His Pro Pro Gly Pro Gly Gln Pro Ser Pro Pro 325 330
335 Pro Glu Ala Leu Pro Cys Arg Asp Gly Thr Asp Pro Ser Gln Pro Ala
340 345 350 Glu Leu Leu Gly Glu Val Asp Arg Thr Glu Phe Glu Gln Tyr
Leu His 355 360 365 Phe Val Cys Lys Pro Glu Met Gly Leu Pro Tyr Gln
Gly His Asp Ser 370 375 380 Gly Val Asn Leu Pro Asp Ser His Gly Ala
Ile Ser Ser Val Val Ser 385 390 395 400 Asp Ala Ser Ser Ala Val Tyr
Tyr Cys Asn Tyr Pro Asp Val 405 410
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