U.S. patent application number 14/928134 was filed with the patent office on 2016-04-21 for genetic modification of rats.
This patent application is currently assigned to REGENERON PHARMACEUTICALS, INC.. The applicant listed for this patent is REGENERON PHARMACEUTICALS, INC.. Invention is credited to Wojtek Auerbach, David Frendewey, David Heslin, Ka-Man Venus Lai, Jeffrey D. Lee, David M. Valenzuela.
Application Number | 20160108360 14/928134 |
Document ID | / |
Family ID | 51351689 |
Filed Date | 2016-04-21 |
United States Patent
Application |
20160108360 |
Kind Code |
A1 |
Lee; Jeffrey D. ; et
al. |
April 21, 2016 |
GENETIC MODIFICATION OF RATS
Abstract
Compositions and methods are provided for making rat pluripotent
and totipotent cells, including rat embryonic stem (ES) cells.
Compositions and methods for improving efficiency or frequency of
germline transmission of genetic modifications in rats are
provided. Such methods and compositions comprise an in vitro
culture comprising a feeder cell layer and a population of rat ES
cells or a rat ES cell line, wherein the in vitro culture
conditions maintain pluripotency of the ES cell and comprises a
media having mouse leukemia inhibitory factor (LIF) or an active
variant or fragment thereof. Various methods of establishing such
rat ES cell lines are further provided. Methods of selecting
genetically modified rat ES cells are also provided, along with
various methods to generate a transgenic rat from the genetically
modified rat ES cells provided herein. Various kits and articles of
manufacture are further provided.
Inventors: |
Lee; Jeffrey D.; (New York,
NY) ; Auerbach; Wojtek; (Ridgewood, NJ) ;
Heslin; David; (Closter, NJ) ; Frendewey; David;
(New York, NY) ; Lai; Ka-Man Venus; (Tarrytown,
NY) ; Valenzuela; David M.; (Yorktown Heights,
NY) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
REGENERON PHARMACEUTICALS, INC. |
Tarrytown |
NY |
US |
|
|
Assignee: |
REGENERON PHARMACEUTICALS,
INC.
Tarrytown
NY
|
Family ID: |
51351689 |
Appl. No.: |
14/928134 |
Filed: |
October 30, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
14185703 |
Feb 20, 2014 |
|
|
|
14928134 |
|
|
|
|
61767093 |
Feb 20, 2013 |
|
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Current U.S.
Class: |
435/353 |
Current CPC
Class: |
C12N 2501/999 20130101;
A01K 67/0275 20130101; C12N 15/8509 20130101; A01K 67/02 20130101;
A01K 2217/15 20130101; C12N 2501/727 20130101; C12N 2510/00
20130101; A01K 67/0271 20130101; C12N 2501/235 20130101; A01K
2207/12 20130101; A61D 19/04 20130101; C12N 5/0606 20130101; A01K
2227/105 20130101; C12N 15/8775 20130101 |
International
Class: |
C12N 5/0735 20060101
C12N005/0735 |
Claims
1. An isolated rat embryonic stem (ES) cell obtainable by culturing
isolated rat ES cells on a feeder cell layer with a medium
comprising N2 supplement, B27 supplement, a MEK inhibitor, a GSK3
inhibitor, and about 50 U/mL to about 150 U/mL leukemia inhibitory
factor (LIF), wherein the feeder cell layer is not modified to
express LIF, and wherein the isolated rat ES cell: (i) is capable
of being modified to comprise a targeted genetic modification and
transmitting the targeted genetic modification through the
germline; (ii) has a normal karyotype; and (iii) lacks expression
of c-Myc.
2. The isolated rat ES cell of claim 1, wherein the isolated rat ES
cell has been modified to comprise the targeted genetic
modification and is capable of transmitting the targeted genetic
modification through the germline.
3. The isolated rat ES cell of claim 1, wherein the isolated rat ES
cell is derived from an ACI rat or a Dark Agouti (DA) rat.
4. The isolated rat ES cell of claim 1, wherein the isolated rat ES
cell is a male (XY) rat ES cell.
5. The isolated rat ES cell of claim 1, wherein the isolated rat ES
cell is a female (XX) rat ES cell.
6. The isolated rat ES cell of claim 2, wherein the germline
transmission efficiency of the targeted genetic modification is at
least 3%.
7. The isolated rat ES cell of claim 6, wherein germline
transmission efficiency of the targeted genetic modification is at
least 60%.
8. The isolated rat ES cell of claim 2, wherein the isolated rat ES
cell exhibits a homologous recombination targeting efficiency of at
least 2%.
9. The isolated rat ES cell of claim 2, wherein the isolated rat ES
cell is capable of transmitting the targeted genetic modification
into progeny following one or more rounds of electroporation.
10. The isolated rat ES cell of claim 2, wherein the isolated rat
ES cell comprises two or more targeted genetic modifications and
can transmit the two or more targeted genetic modifications through
the germline.
11. The isolated rat ES cell of claim 2, wherein the targeted
genetic modification comprises an insertion, a deletion, a
knockout, a knockin, a point mutation, or a combination
thereof.
12. The isolated rat ES cell of claim 11, wherein the targeted
genetic modification comprises at least one insertion of a
heterologous polynucleotide into the genome of the isolated rat ES
cell.
13. The isolated rat ES cell of claim 1, wherein the isolated rat
ES cell, when cultured in vitro, loosely adheres to the feeder cell
layer.
14. The isolated rat ES cell of claim 1, wherein the isolated rat
ES cell forms sphere-like colonies when plated on the feeder cell
layer in vitro.
15. The isolated rat ES cell of claim 1, wherein the isolated rat
ES cell does not require paracrine LIF signaling for maintenance of
pluripotency.
16. The isolated rat ES cell of claim 1, wherein the isolated rat
ES cell can be passaged up to at least 11 times in the medium
without decreasing targeting efficiency in the isolated rat ES cell
or germline transmission efficiency of the targeted genetic
modification.
17. The isolated rat ES cell of claim 1, wherein the isolated rat
ES cell expresses at least one pluripotency marker selected from
Dnmt3L, Eras, En-beta, Fbxo15, Fgf4, Gdf3, Klf4, Lef1, LIF
receptor, Lin28, Nanog, Oct4, Sox15, Sox2, and Utf1.
18. The isolated rat ES cell of claim 1, wherein the isolated rat
ES cell does not express one or more pluripotency markers selected
from Ecat1 and Rexo1.
19. The isolated rat ES cell of claim 1, wherein the isolated rat
ES cell exhibits one or more of the following characteristics: (a)
the isolated rat ES cell does not express one or more mesodermal
markers selected from Brachyury and Bmpr2; (b) the isolated rat ES
cell does not express one or more endodermal markers selected from
Gata6, Sox17, and Sox7; (c) the isolated rat ES cell does not
express one or more neural markers selected from Nestin and Pax6;
and (d) the isolated rat ES cell expresses one or more pluripotency
markers selected from Oct4, Sox2, and alkaline phosphatase.
20. The isolated rat ES cell of claim 1, wherein the isolated rat
ES cell is characterized by the expression of one or more rat
ES-cell-specific genes selected from Adherens Junctions Associate
Protein 1 (Ajap1), Claudin 5 (Cldn5), Cdc42 guanine nucleotide
exchange factor 9 (Arhgef9), Calcium/calmodulin-dependent protein
kinase IV (Camk4), ephrin-A1 (Efna1), EPH receptor A4 (Epha4), gap
junction protein beta 5 (Gjb5), Insulin-like growth factor binding
protein-like 1 (Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin
28 receptor, alpha (Il28ra), left-right determination factor 1
(Lefty1), Leukemia inhibitory factor receptor alpha (Lifr),
Lysophosphatidic acid receptor 2 (Lpar2), Neuronal pentraxin
receptor (Ntm), Protein tyrosine phosphatase non-receptor type 18
(Ptpn18), Caudal type homeobox 2 (Cdx2), Fibronectin type III and
ankyrin repeat domains 1 (Fank1), Forkhead box E1 (thyroid
transcription factor 2) (Foxe1), Hairy/enhancer-of-split related
with YRPW motif 2 (Hey2), Forkhead box E1 (thyroid transcription
factor 2) (Foxe1), Hairy/enhancer-of-split related with YRPW motif
2 (Hey2), Lymphoid enhancer-binding factor 1 (Lef1), Sal-like 3
(Drosophila) (Sall3), SATB homeobox 1 (Satb1), and miR-632.
21. The isolated rat ES cell of claim 1, wherein the concentration
of LIF in the medium is between about 75 U/mL to about 125
U/mL.
22. The isolated rat ES cell of claim 21, wherein the concentration
of LIF in the medium is between about 90 U/mL to about 110
U/mL.
23. The isolated rat ES cell of claim 22, wherein the concentration
of LIF in the medium is about 100 U/mL.
24. The isolated rat ES cell of claim 1, wherein the MEK inhibitor
is PD0325901 and/or the GSK3 inhibitor is CHIR99021.
25. The isolated rat ES cell of claim 1, wherein the medium
comprises a combination of inhibitors consisting of the MEK
inhibitor and the GSK3 inhibitor.
26. The isolated rat ES cell of claim 1, wherein the concentration
of LIF in the medium is about 100 U/mL, the MEK inhibitor is
PD0325901 at a concentration of about 1 .mu.M, and the GSK3
inhibitor is CHIR99021 at a concentration of about 3 .mu.M.
27. The isolated rat ES cell of claim 26, wherein the medium
comprises a combination of inhibitors consisting of PD0325901 and
the CHIR99021.
28. The isolated rat ES cell of claim 1, wherein the feeder cell
layer comprises mitotically inactivated mouse embryonic
fibroblasts, and the medium is a 2i medium comprising DMEM/F12
basal medium, Neurobasal medium, N2 supplement, B27 supplement,
LIF, the MEK inhibitor, and the GSK inhibitor.
29. The isolated rat ES cell of claim 28, wherein the concentration
of the LIF is 100 U/ml, the MEK inhibitor is PD0325901 at a
concentration of 1 .mu.M, and the GSK inhibitor is CHIR99021 at a
concentration of 3 .mu.M.
30. The isolated rat ES cell of claim 29, wherein the medium
comprises a combination of inhibitors consisting of PD0325901 and
CHIR99021.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 14/185,703, filed Feb. 20, 2014, which claims
priority to U.S. Provisional Application No. 61/767,093, filed Feb.
20, 2013, each of which is herein incorporated by reference in its
entirety for all purposes.
FIELD
[0002] Non-human pluripotent, totipotent, and embryonic stem (ES)
cells, in particular rat pluripotent, totipotent, and/or rat ES
cells, and methods of making them. Methods for making rat
pluripotent, totipotent, and ES cells are provided. Methods for
targeting rat pluripotent, totipotent, and/or ES cells are
provided. Methods for achieving germline transmission of a genetic
modification in a rat cell are provided. Media for deriving,
growing, and maintaining rat pluripotent, totipotent, and ES cells
are provided.
REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA
EFS-WEB
[0003] The official copy of the sequence listing is submitted
concurrently with the specification as a text file via EFS-Web, in
compliance with the American Standard Code for Information
Interchange (ASCII), with a file name of 469736SEQLIST.txt, a
creation date of Oct. 30, 2015, and a size of 2.09 kb. The sequence
listing filed via EFS-Web is part of the specification and is
hereby incorporated in its entirety by reference herein.
BACKGROUND
[0004] The rat has been a valuable model for many applications,
including, but not limited to, applications in drug discovery. The
usefulness of the rat has been mitigated somewhat by difficulty in
obtaining genetically modified rats, in particular, in developing
methods for genetically modifying rats, and generating useful rat
cells that can be used in genetic modification protocols, including
but not limited to protocols that result in germline transmission
of a genetic modification in a rat genome.
[0005] There is a need in the art for rat cells (e.g., embryonic
stem cells) that can be genetically modified such that the genetic
modification can be transmitted through the germline. There is a
need in the art for improved frequency of germline transmission of
genetic modifications in rats.
[0006] There is a need in the art for donor rat pluripotent,
totipotent, and/or ES cells from various strains of rat that are
capable of generating F0, or wholly donor cell-derived, F0 rats.
There is a need in the art for donor rat pluripotent, totipotent,
and/or ES cells that are capable of generating rats that comprise a
germline genetic modification.
SUMMARY
[0007] Compositions and methods are provided for making rat
pluripotent and/or totipotent cells, including rat embryonic stem
(ES) cells. Compositions and methods for improving efficiency or
frequency of germline transmission of genetic modifications in rats
are provided. In various aspects, the methods and compositions
comprise an in vitro culture comprising a feeder cell layer and a
population of rat ES cells or a rat ES cell line, wherein the in
vitro culture conditions allow maintenance of pluripotency of the
rat ES cell. Various methods of establishing rat ES cell lines are
further provided. Method of selecting genetically modified rat ES
cells are also provided, along with various methods to generate a
transgenic rat from the genetically modified rat ES cells are
provided herein. Various kits and articles of manufacture are
further provided.
[0008] Non-limiting embodiments are as follows:
[0009] 1. An isolated rat ES cell of a strain selected from ACI or
DA, wherein the isolated rat ES cell is and capable of transmitting
its genome through the germline.
[0010] 2. The isolated rat ES cell of embodiment 1, wherein the
cell is derived from an ACI rat.
[0011] 3. The isolated rat ES cell of embodiment 1 or 2, wherein
the cell is derived from a Dark Agouti (DA) rat.2.
[0012] 4. The isolated rat ES cell of embodiment 1, 2, or 3,
wherein the cell is euploid and capable of transmitting a targeted
genetic modification through the germline.
[0013] 5. The isolated rat ES cell of embodiment 4, wherein the rat
ES cell comprises a germline transmission efficiency of the
targeted genetic modification of at least 3%.
[0014] 6. The isolated rat ES cell of embodiment 4, wherein the rat
ES cell has a germline transmission efficiency of the targeted
genetic modification of at least 60%.
[0015] 7. The isolated rat ES cell of any one of embodiments 1-6,
wherein the rat ES cell exhibits a targeting efficiency of
homologous recombination of at least 2%.
[0016] 8. The isolated rat ES cell of any one of embodiments 1-8,
wherein the rat ES cell is capable of transmitting a targeted
genetic modification into progeny following a successive round of
electroporation.
[0017] 9. The isolated rat ES cells of any one of embodiments 1-8,
wherein the rat ES cell comprises one or more, two or more, or
three or more targeted genetic modification.
[0018] 10. The isolated rat ES cell of any one of embodiments 4-9,
wherein the targeted genetic modification comprises an insertion, a
deletion, a knockout, a knockin, a point mutation, or a combination
thereof.
[0019] 11. The isolated rat ES cell of embodiment 9, wherein the
targeted genetic modification comprises at least one insertion of a
heterologous polynucleotide into a genome of the cell.
[0020] 12. The isolated rat ES cell of embodiment 11, wherein the
heterologous polynucleotide comprises a selection marker.
[0021] 13. The isolated rat ES cell of embodiment 12, wherein (a)
the selection marker comprises a non-attenuated selection marker
gene operably linked to a promoter; or (b) the rat ES cell
comprises at least 2 copies of the polynucleotide encoding the
selection marker.
[0022] 14. The isolated rat ES cell of embodiment 12, wherein the
selection marker has an increased activity compared to a wild type
selection marker.
[0023] 15. The isolated rat ES cell of any one of embodiments 1-14,
wherein the rat ES cell forms a sphere-like colony when plated on a
feeder cell layer in culture comprising a LIF polypeptide, a GSK3
inhibitor, and a MEK inhibitor.
[0024] 16. The isolated rat ES cell of any one of embodiments 1-15,
wherein the rat ES cell, when cultured in vitro, loosely adhere to
the feeder cell layer.
[0025] 17. The isolated rat ES cell of any one of embodiments 1-16,
wherein the cell does not require paracrine LIF signaling for
maintenance of pluripotency.
[0026] 18. The isolated rat ES cell of any one of embodiments 1-17,
wherein the cell is a male (XY) rat ES cell.
[0027] 19. The isolated rat ES cell of any one of embodiments 1-19,
wherein the cell is a female (XX) rat ES cell.
[0028] 20. The isolated rat ES cell of any one of embodiments 1-19,
wherein the rat ES cell can be passaged up to at least 11 times in
a medium comprising a GSK3 inhibitor and a MEK inhibitor without
decreasing its targeting efficiency or germline transmission
efficiency of a targeted genetic modification.
[0029] 21. The isolated rat ES cell of any one of embodiments 1-20,
wherein the rat ES cells express at least one pluripotency marker
selected from Dnmt3L, Eras, Err-beta, Fbxo15, Fgf4, Gdf3, Klf4,
Lef1, LIF receptor, Lin28, Nanog, Oct4, Sox15, Sox2, Utf1, or a
combination thereof.
[0030] 22. The isolated rat ES cell of any one of embodiments 1-21,
wherein the rat ES cells do not express one or more pluripotency
markers selected from c-Myc, Ecat1, Rexo1, or a combination
thereof.
[0031] 23. The isolated rat ES cell of any one of embodiments 1-22,
wherein the rat ES cells do not express one or more mesodermal
markers selected from Brachyury, Bmpr2, or a combination
thereof.
[0032] 24. The isolated rat ES cell of any one of embodiments 1-23,
wherein the rat ES cells do not express one or more endodermal
markers selected from Gata6, Sox17, Sox7, or combination
thereof;
[0033] 25. The isolated rat ES cell of any one of embodiments 1-24,
wherein the rat ES cells do not express one or more neural markers
selected from Nestin, Pax6, or combination thereof.
[0034] 26. The isolated rat ES cell of any one of embodiments 1-25,
wherein the cell expresses a pluripotency marker comprising Oct-4,
Sox2, alkaline phosphatase, or a combination thereof.
[0035] 27. The isolated rat ES cell of any one of embodiments 1-26,
wherein the rat ES cell is characterized by the expression of one
or more of a rat ESC-specific gene selected from one or more of
Adherens Junctions Associate Protein 1 (Ajap1), Claudin 5 (Cldn5),
Cdc42 guanine nucleotide exchange factor 9 (Arhgef9),
Calcium/calmodulin-dependent protein kinase IV (Camk4), ephrin-A1
(Efna1), EPH receptor A4 (Epha4), gap junction protein beta 5
(Gjb5), Insulin-like growth factor binding protein-like 1
(Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin 28 receptor,
alpha (Il28ra), left-right determination factor 1 (Lefty1),
Leukemia inhibitory factor receptor alpha (Lifr), Lysophosphatidic
acid receptor 2 (Lpar2), Neuronal pentraxin receptor (Ntm), Protein
tyrosine phosphatase non-receptor type 18 (Ptpn18), Caudal type
homeobox 2 (Cdx2), Fibronectin type III and ankyrin repeat domains
1 (Fank1), Forkhead box E1 (thyroid transcription factor 2)
(Foxe1), Hairy/enhancer-of-split related with YRPW motif 2 (Hey2),
Forkhead box E1 (thyroid transcription factor 2) (Foxe1),
Hairy/enhancer-of-split related with YRPW motif 2 (Hey2), Lymphoid
enhancer-binding factor 1 (Lef1), Sal-like 3 (Drosophila) (Sall3),
SATB homeobox 1 (Satb1), miR-632, or a combination thereof.
[0036] 28. An isolated population of rat ES cells, wherein at least
70% of the rat ES cells are euploid and form sphere-like colonies
when plated on a feeder cell layer in vitro.
[0037] 29. The isolated population of rat ES cells of embodiment
28, wherein the rat ES cells are derived from an ACI rat.
[0038] 30. The isolated population of rat ES cells of embodiment
28, wherein the rat ES cells are derived from a Dark Agouti (DA)
rat.
[0039] 31. The isolated population of rat ES cells of any one of
embodiments 28-30, wherein the rat ES cells are capable of
transmitting their genome through the germline.
[0040] 32. The isolated population of rat ES cells of any one of
embodiments 28-31, wherein the rat ES cells have a germline
transmission efficiency of the targeted genetic modification of at
least 3%.
[0041] 33. The isolated population of rat ES cells of any one of
embodiments 28-31, wherein the rat ES cells have a germline
transmission efficiency of the targeted genetic modification of at
least 60%.
[0042] 34. The isolated population of rat ES cells of any one of
embodiments 28-31, wherein the rat ES cells exhibit a targeting
efficiency of homologous recombination of at least 2%.
[0043] 35. The isolated population of rat ES cells of any one of
embodiments 28-34, wherein the rat ES cells are capable of
transmitting a targeted genetic modification into progeny following
a successive round of electroporation.
[0044] 36. The isolated population of any one embodiments 28-35,
wherein the rat ES cells comprise one or more, two or more, or
three or more targeted genetic modification and can transmit the
targeted genetic modification through the germline.
[0045] 37. The isolated population of rat ES cells of embodiment
36, wherein the targeted genetic modification is at the rat Rosa26
locus.
[0046] 38. The isolated population of rat ES cells of embodiment
36, wherein the targeted genetic modification comprises an
insertion, a deletion, a knockout, a knockin, a point mutation, or
a combination thereof.
[0047] 39. The isolated population of rat ES cells of embodiment
36, wherein the targeted genetic modification comprises at least
one insertion of a heterologous polynucleotide into a genome of the
cell.
[0048] 40. The isolated population of rat ES cells of embodiment
39, wherein the heterologous polynucleotide comprises a selection
marker.
[0049] 41. The isolated population of rat ES cells of embodiment
40, wherein
[0050] (a) the selection marker comprises a non-attenuated
selection marker gene operably linked to a promoter; or
[0051] (b) the rat ES cell comprises at least 2 copies of the
polynucleotide encoding the selection marker.
[0052] 42. The isolated population of rat ES cells of embodiment
40, wherein the selection marker has an increased activity compared
to a wild type selection marker
[0053] 43. The isolated population of rat ES cells of any one of
embodiments 28-42, wherein the cells form a sphere-like colony when
plated on a feeder cell layer in culture comprising a LIF
polypeptide, a GSK3 inhibitor, and a MEK inhibitor.
[0054] 44. The isolated population rat ES cells of any one of
embodiments 28-43, wherein the cells, when cultured in vitro,
loosely adhere to the feeder cell layer.
[0055] 45. The isolated population of rat ES cells of any one of
embodiments 28-44, wherein the cells do not require paracrine LIF
signaling for maintenance of pluripotency.
[0056] 46. The isolated population of rat ES cells of any one of
embodiments 28-44, wherein the rat ES cells are a male (XY) rat ES
cells.
[0057] 47. The isolated population of rat ES cells of any one of
embodiments 28-44, wherein the rat ES cells are female (XX) rat ES
cells.
[0058] 48. The isolated population of rat ES cells of any one of
embodiments 28-47, wherein the rat ES cells can be passaged up to
at least 11 times in a medium comprising a GSK3 inhibitor and a MEK
inhibitor without decreasing its targeting efficiency or germline
transmission efficiency of a targeted genetic modification.
[0059] 49. The isolated population of rat ES cells of any one of
embodiments 28-48, wherein the rat ES cells express at least one
pluripotency marker selected from Dnmt3L, Eras, Err-beta, Fbxo15,
Fgf4, Gdf3, Klf4, Lef1, LIF receptor, Lin28, Nanog, Oct4, Sox15,
Sox2, Utf1, or a combination thereof.
[0060] 50. The isolated population of rat ES cells of any one of
embodiments 28-49, wherein the rat ES cells do not express one or
more pluripotency markers selected from c-Myc, Ecat1, Rexo1, or a
combination thereof.
[0061] 51. The isolated population of rat ES cells of any one of
embodiments 28-50, wherein the rat ES cells do not express one or
more mesodermal markers selected from Brachyury, Bmpr2, or a
combination thereof.
[0062] 52. The isolated population of rat ES cells of any one of
embodiments 28-51, wherein the rat ES cells do not express one or
more endodermal markers selected from Gata6, Sox17, Sox7, or
combination thereof;
[0063] 53. The isolated population of rat ES cells of any one of
embodiments 28-52, wherein the rat ES cells do not express one or
more neural markers selected from Nestin, Pax6, or combination
thereof.
[0064] 54. The isolated population of rat ES cells of any one of
embodiment 28-53, wherein the rat ES cells expresses a pluripotency
marker comprising Oct-4, Sox2, alkaline phosphatase, or a
combination thereof.
[0065] 55. The isolated population of rat ES cells of any one of
embodiments 28-54, wherein the rat ES cells are characterized by
the expression of one or more of a rat ESC-specific gene selected
from one or more of Adherens Junctions Associate Protein 1 (Ajap1),
Claudin 5 (Cldn5), Cdc42 guanine nucleotide exchange factor 9
(Arhgef9), Calcium/calmodulin-dependent protein kinase IV (Camk4),
ephrin-A1 (Efna1), EPH receptor A4 (Epha4), gap junction protein
beta 5 (Gjb5), Insulin-like growth factor binding protein-like 1
(Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin 28 receptor,
alpha (Il28ra), left-right determination factor 1 (Lefty1),
Leukemia inhibitory factor receptor alpha (Lifr), Lysophosphatidic
acid receptor 2 (Lpar2), Neuronal pentraxin receptor (Ntm), Protein
tyrosine phosphatase non-receptor type 18 (Ptpn18), Caudal type
homeobox 2 (Cdx2), Fibronectin type III and ankyrin repeat domains
1 (Fank1), Forkhead box E1 (thyroid transcription factor 2)
(Foxe1), Hairy/enhancer-of-split related with YRPW motif 2 (Hey2),
Forkhead box E1 (thyroid transcription factor 2) (Foxe1),
Hairy/enhancer-of-split related with YRPW motif 2 (Hey2), Lymphoid
enhancer-binding factor 1 (Lef1), Sal-like 3 (Drosophila) (Sall3),
SATB homeobox 1 (Satb1), miR-632, or a combination thereof.
[0066] 56. The isolated population of rat ES cells of any one of
embodiments 28-55, wherein the population comprises at least
10.sup.4 cells.
[0067] 57. The isolated population of rat ES cells of any one of
embodiments 28-56, wherein the rat ES cells have one or more
characteristic comprising:
[0068] a. at least 90% of the rat ES cells are euploid;
[0069] b. at least 70% of the rat ES cells express at least one
pluripotency marker; wherein the at least one pluripotency marker
comprises Oct-4, Sox2, alkaline phosphatase, or a combination
thereof;
[0070] c. a cell from the rat ES cell population, when combined
with a rat host embryo transmits the genome of the rat ES cell line
into an offspring;
[0071] d. the rat ES cells when cultured in vitro loosely adhere to
a feeder cell layer;
[0072] e. the rat ES cells form sphere-like colonies when plated on
a feeder cell layer in vitro; (f) the rat ES cells maintain
pluripotency when cultured in vitro in a media comprising an GSK3
inhibitor, a MEK inhibitor, LIF and a feeder cell layer that is not
genetically modified to express LIF;
[0073] f. the rat ES cell exhibits a targeting efficiency of
homologous recombination of at least 2%;
[0074] g. the rat ES cells maintain pluripotency in vitro without
requiring paracrine LIF signaling;
[0075] h. at least 70% of the rat ES cells are euploid and form
sphere-like colonies when plated on a feeder cell layer in
vitro;
[0076] i. the rat ES cells express at least one pluripotency marker
selected from Dnmt3L, Eras, Err-beta, Fbxo15, Fgf4, Gdf3, Klf4,
Lef1, LIF receptor, Lin28, Nanog, Oct4, Sox15, Sox2, Utf1, or a
combination thereof;
[0077] j. the rat ES cells do not express one or more
differentiation markers selected from c-Myc, Ecat1, Rexo1;
[0078] k. the rat ES cells do not express one or more mesodermal
markers selected from Brachyury, Bmpr2, or a combination
thereof;
[0079] l. the rat ES cells do not express one or more endodermal
markers selected from Gata6, Sox17, Sox7, or combination thereof;
and/or
[0080] m. the rat ES cells do not express one or more neural
markers selected from Nestin, Pax6, or combination thereof.
[0081] 58. The isolated population of rat ES cells of any one of
embodiments 28-57, wherein (a) the rat ES cells is derived from a
rat blastocyst; (b) the rat ES cell is derived from a rat morula
stage embryo; and/or, (c) the rat ES cell line is derived from a
superovulated rat.
[0082] 59. An in vitro culture comprising a feeder cell layer, the
population of rat embryonic stem (ES) cells, and a medium
comprising a Leukemia Inhibitory Factor (LIF), GSK3 inhibitor, and
a MEK inhibitor, wherein at least 70% of the rat ES cells are
euploid and the rat ES cell forms a sphere-like colony.
[0083] 60. The in vitro culture of embodiment 59 or 60, wherein the
rat ES cell, loosely adhere to the feeder cell layer.
[0084] 61. The in vitro culture of embodiment 59, 60, or 61,
wherein the rat ES cells are capable of transmitting their genome
through the germline.
[0085] 62. The in vitro culture of embodiment 59, 60 or 61, wherein
the rat ES cells are derived from an ACI rat.
[0086] 63. The in vitro culture of embodiment 59, 60 or 61, wherein
the rat ES cells are derived from a Dark Agouti (DA) rat.2.
[0087] 64. The in vitro culture of any one of embodiments 59-63,
wherein the rat ES cells are capable of transmitting a targeted
genetic modification through the germline.
[0088] 65. The in vitro culture of embodiment 64, wherein the rat
ES cells comprise a germline transmission efficiency of the
targeted genetic modification of at least 3%.
[0089] 66. The in vitro culture of embodiment 64, wherein the rat
ES cells have a germline transmission efficiency of the targeted
genetic modification of at least 60%.
[0090] 67. The in vitro culture of any one of embodiments 59-66,
wherein the rat ES cells exhibit a targeting efficiency of
homologous recombination of at least 2%.
[0091] 68. The in vitro culture of any one of embodiments 59-67,
wherein the rat ES cell is capable of transmitting a targeted
genetic modification into progeny following a successive round of
electroporation.
[0092] 69. The in vitro culture of any one of embodiments 59-68,
wherein the rat ES cell comprises one or more, two or more, or
three or more targeted genetic modification.
[0093] 70. The in vitro culture of embodiment 69, wherein the
targeted genetic modification comprises an insertion, a deletion, a
knockout, a knockin, a point mutation, or a combination
thereof.
[0094] 71. The in vitro culture of embodiment 69, wherein the
targeted genetic modification comprises at least one insertion of a
heterologous polynucleotide into a genome of the cell.
[0095] 72. The in vitro culture of embodiment 71, wherein the
heterologous polynucleotide comprises a selection marker.
[0096] 73. The in vitro culture of embodiment 72, wherein (a) the
selection marker comprises a non-attenuated selection marker gene
operably linked to a promoter; or (b) the rat ES cell comprises at
least 2 copies of the polynucleotide encoding the selection
marker.
[0097] 74. The in vitro culture of embodiment 72, wherein the
selection marker has an increased activity compared to a wild type
selection marker.
[0098] 75. The in vitro culture of any one of embodiments 59-74,
wherein the cell does not require paracrine LIF signaling for
maintenance of pluripotency.
[0099] 76. The in vitro culture of embodiment of any one of
embodiments 59-75, wherein the cell is a male (XY) rat ES cell.
[0100] 77. The in vitro culture of embodiment of any one of
embodiments 59-75, wherein the cell is a female (XX) rat ES
cell.
[0101] 78. The in vitro culture of embodiment of any one of
embodiments 59-77, wherein the rat ES cell can be passaged up to at
least 11 times in a medium comprising a GSK3 inhibitor and a MEK
inhibitor without decreasing its targeting efficiency or germline
transmission efficiency of a targeted genetic modification.
[0102] 79. The in vitro culture of any one of embodiments 59-78,
wherein the rat ES cells express at least one pluripotency marker
selected from Dnmt3L, Eras, Err-beta, Fbxo15, Fgf4, Gdf3, Klf4,
Lef1, LIF receptor, Lin28, Nanog, Oct4, Sox15, Sox2, Utf1, or a
combination thereof.
[0103] 80. The in vitro culture of any one of embodiments 59-79,
wherein the rat ES cells do not express one or more pluripotency
markers selected from c-Myc, Ecat1, Rexo1, or a combination
thereof.
[0104] 81. The in vitro culture of any one of embodiments 59-80,
wherein the rat ES cells do not express one or more mesodermal
markers selected from Brachyury, Bmpr2, or a combination
thereof.
[0105] 82. The in vitro culture of any one of embodiments 59-81,
wherein the rat ES cells do not express one or more endodermal
markers selected from Gata6, Sox17, Sox7, or combination
thereof;
[0106] 83. The in vitro culture of any one of embodiments 59-82,
wherein the rat ES cells do not express one or more neural markers
selected from Nestin, Pax6, or combination thereof.
[0107] 84. The in vitro culture of any one of embodiments 59-83,
wherein the cell expresses a pluripotency marker comprising Oct-4,
Sox2, alkaline phosphatase, or a combination thereof.
[0108] 85. The in vitro culture of any one of embodiments 59-84,
wherein the rat ES cells are characterized by the expression of one
or more of a rat ESC-specific gene selected from one or more of
Adherens Junctions Associate Protein 1 (Ajap1), Claudin 5 (Cldn5),
Cdc42 guanine nucleotide exchange factor 9 (Arhgef9),
Calcium/calmodulin-dependent protein kinase IV (Camk4), ephrin-A1
(Efna1), EPH receptor A4 (Epha4), gap junction protein beta 5
(Gjb5), Insulin-like growth factor binding protein-like 1
(Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin 28 receptor,
alpha (Il28ra), left-right determination factor 1 (Lefty1),
Leukemia inhibitory factor receptor alpha (Lifr), Lysophosphatidic
acid receptor 2 (Lpar2), Neuronal pentraxin receptor (Ntm), Protein
tyrosine phosphatase non-receptor type 18 (Ptpn18), Caudal type
homeobox 2 (Cdx2), Fibronectin type III and ankyrin repeat domains
1 (Fank1), Forkhead box E1 (thyroid transcription factor 2)
(Foxe1), Hairy/enhancer-of-split related with YRPW motif 2 (Hey2),
Forkhead box E1 (thyroid transcription factor 2) (Foxe1),
Hairy/enhancer-of-split related with YRPW motif 2 (Hey2), Lymphoid
enhancer-binding factor 1 (Lef1), Sal-like 3 (Drosophila) (Sall3),
SATB homeobox 1 (Satb1), miR-632, or a combination thereof.
[0109] 86. The in vitro culture of any one of embodiments 59-84,
wherein the concentration of LIF is 50 U/ml to 150 U/ml.
[0110] 87. The in vitro culture of any one of embodiments 59-85,
wherein the concentration of LIF is 100 U/ml.
[0111] 88. The in vitro culture of any one of embodiments 59-87,
wherein the LIF is from mouse or comprises at least 92% sequence
identity to SEQ ID NO: 1.
[0112] 89. The in vitro culture of any one of embodiments 59-88,
wherein the rat ES cell is capable of maintaining a pluripotency
without requiring a paracrine LIF signaling.
[0113] 90. The in vitro culture of any one of embodiments 59-89,
wherein the feeder cell layer is not genetically modified to
express LIF.
[0114] 91. The in vitro culture of any one of embodiments 59-90,
wherein the feeder cell layer comprises a monolayer of mitotically
inactivated mouse embryonic fibroblasts (MEFs)
[0115] 92. The in vitro culture of any one of embodiments 59-91,
wherein the MEK inhibitor comprises PD0325901.
[0116] 93. The in vitro culture of any one of embodiment 59-92,
wherein the GSK-3 inhibitor comprises CHIR99021.
[0117] 94. The in vitro culture of any one of embodiments 59-93,
wherein the population of rat ES cells is derived from a rat
blastocyst-stage embryo or a rat morula-stage embryo.
[0118] 95. The in vitro culture of embodiment 94, wherein the
blastocyst-stage or the morula-stage rat embryo further comprises
an outgrowth of an amorphous undifferentiated mass of rat ES
cells.
[0119] 96. The in vitro culture of embodiment 94, wherein the
population of rat ES cells comprises an isolated outgrowth of an
amorphous undifferentiated mass of rat ES cells.
[0120] 97. A method for generating a rat embryonic stem (ES) cell
line comprising: (a) culturing in vitro a first feeder cell layer
and a morula or a blastocyst-stage rat embryo, wherein the zona
pellucida of the morula or blastocyst-stage rat embryo has been
removed, and wherein the culture conditions maintain pluripotency
of a rat ES cell and comprise a medium having mouse leukemia
inhibitory factor (LIF) or a sequence having at least 91% sequence
identity to SEQ ID NO:1 and having LIF activity, and a GSK3
inhibitor, and a MEK inhibitor; and, (b) transferring an outgrowth
of an amorphous undifferentiated mass of rat ES cells to an in
vitro culture well comprising a second feeder cell layer and
culturing the outgrowth under conditions comprising the medium
having the mouse LIF or an active variant of the mouse LIF, and
thereby maintaining pluripotency of the rat ES cells; and,
establishing a rat ES cell line therefrom.
[0121] 98. The method of embodiment 97, wherein the rat ES cell
line is passaged at least 5 times.
[0122] 99. The method of embodiment 97 or 98, wherein the rat ES
cell line is passaged at least 10 times.
[0123] 100. The method of embodiment 97, 98, or 99, wherein the
medium comprises about 50 U/ml to about 150 U/ml of mouse LIF.
[0124] 101. The method of any one of embodiments 97-100, wherein
the medium comprises about 100 U/ml of mouse LIF.
[0125] 102. The method of any one of embodiments 97-101, wherein
the feeder cell layer is not genetically modified to express
LIF.
[0126] 103. The method of any one of embodiments 97-102, wherein
the feeder cell layer comprises a monolayer of mitotically
inactivated mouse embryonic fibroblasts (MEFs).
[0127] 104. The method of any one of embodiments 97-103, wherein
the MEK inhibitor comprises PD0325901.
[0128] 105. The method of any one of embodiments 97-104, wherein
the GSK-3 inhibitor comprises CHIR99021.
[0129] 106. The method of any one of embodiment 97-105, wherein (a)
the rat ES cell line is derived from an ACI rat or derived from a
Dark Agouti (DA) rat; (b) the rat ES cell line is derived from a
morula-stage or a blastocyst-stage rat embryo; and/or, (c) the rat
ES cell line is derived from a morula-stage or a blastocyst-stage
embryo from a superovulated rat.
[0130] 107. The method of any one of embodiments 97-106, wherein
the medium further comprises at least one of an FGF receptor
inhibitor, a ROCK inhibitor, or an ALK inhibitor.
[0131] 108. The method of embodiment 107, wherein the FGF receptor
inhibitor comprises PD184352, the ROCK inhibitor comprises Y-27632,
or the ALK inhibitor comprises A-83-01.
[0132] 109. The method any one of embodiments 97-108, wherein at
least one rat ES cell has a germline transmission efficiency of the
targeted genetic modification is at least 3%.
[0133] 110. The method of embodiment any one of embodiments 97-109,
wherein the germline transmission efficiency of the targeted
genetic modification is at least 60%.
[0134] 111. A method of selecting a rat embryonic stem (ES) cells
having stably incorporated into its genome a heterologous
polynucleotide comprising: (a) providing an in vitro population of
rat ES cells; (b) introducing into at least one rat ES cell a
heterologous polynucleotide comprising a selection marker operably
linked to a promoter active the rat ES cell; and, (c) culturing in
vitro the rat ES cell population in an alternating first and second
culture media, wherein the first culture medium comprises an
effective amount of a selection agent for a first time period and
the second culture medium does not comprise the selection agent,
wherein the in vitro culture conditions are sufficient to maintain
pluripotency; thereby selecting the rat ES cell having stably
integrated into its genome the heterologous polynucleotide.
[0135] 112. The method of embodiment 111, wherein the first and
second culture media are alternated every 24 hours.
[0136] 113. The method of embodiment 111 or 112, wherein the
selection marker imparts resistance to an antibiotic.
[0137] 114. The method of any one of embodiments 111-113, wherein
the antibiotic comprises G418.
[0138] 115. The method of any one of embodiment 111-114, wherein
the selection marker comprises neomycin phosphotransferase
(neo.sup.r), hygromycin B phosphotransferase (hyg.sup.r),
puromycin-N-acetyltransferase (puro.sup.r), blasticidin S deaminase
(bsr.sup.r), xanthine/guanine phosphoribosyl transferase (gpt), and
herpes simplex virus thymidine kinase (HSV-k), or a combination
thereof.
[0139] 116. The method of any one of embodiments 111-115, wherein
(a) the selection marker has an increased activity compared to the
wild type selection marker; and/or (b) multiple copies of the
selection marker are stably incorporated into the genome of the rat
ES cell.
[0140] 117. The method of embodiment 116, wherein the selection
marker is a non-attenuated selection marker.
[0141] 118. A method for genetically modifying an isolated rat
embryonic stem (ES) cell comprising introducing into the genome of
an isolated rat ES cell of any one of embodiment 1-58 a
heterologous polynucleotide to form a genetically modified rat ES
cell.
[0142] 119. A method of making a genetically modified rat
comprising:
[0143] (a) introducing into the genome of the isolated rat
embryonic stem (ES) cell of any one of embodiments 1-58, a
heterologous polynucleotide to form a rat ES cell having a genetic
modification;
[0144] (b) introducing at least one of the rat ES cells comprising
the targeted genetic modification into a rat host embryo to produce
an F0 embryo;
[0145] (c) implanting the F0 embryo into a surrogate mother;
[0146] (d) gestating the F0 embryo in the surrogate mother to term;
and, (e) identifying an F0 rat having the targeted genetic
modification.
[0147] 120. The method of embodiment 119, further comprising
breeding a male F0 rat with a wild type female rat to produce an F1
progeny that is heterozygous for the targeted genetic
modification.
[0148] 121. The method of embodiment 120, further comprising
breeding a male F0 rat with a wild type female rat to produce an F1
progeny that is heterozygous for the targeted genetic
modification.
[0149] 122. The method of embodiment 119, further comprising
breeding a male rat of the F1 progeny with a female rat of the F1
progeny to obtain an F2 progeny that is homozygous for the genetic
modification.
[0150] 123. The method of any one of embodiments 119-122, wherein
at least 3% of the F0 rats having the genetic modification transmit
the genetic modification to the F1 progeny.
[0151] 124. The method of any one of embodiments 119-123, wherein
at least 10% of the F0 rats having the genetic modification
transmit the genetic modification to the F1 progeny.
[0152] 125. The method of any one of embodiments 119-124, wherein
at least 60% of the F0 rats having the genetic modification
transmit the genetic modification to the F1 progeny.
[0153] 126. The method of any one of embodiments 119-125, wherein
the genetically modified rat ES cell is from the same rat strain as
the rat host embryo.
[0154] 127. The method of any one of embodiments 119-127, wherein
the genetically modified rat ES cell is from a different rat strain
as the rat host embryo.
[0155] 128. The isolated population of rat ES cells of any of the
preceding claims, the in vitro culture of any of the preceding
claims, or the method of any of the preceding claims, wherein the
rat ES cells in the population comprise: [0156] (a) at least 90% of
the rat ES cells are euploid; [0157] (b) at least 70% of the rat ES
cells express at least one pluripotency marker; wherein the at
least one pluripotency marker comprises Oct-4, Sox2, alkaline
phosphatase, or a combination thereof; [0158] (c) a cell from the
rat ES cell population, when combined with a rat host embryo
transmits the genome of the rat ES cell line into an offspring;
[0159] (d) the rat ES cells when cultured in vitro loosely adhere
to a feeder cell layer; [0160] (e) the rat ES cells form
sphere-like colonies when plated on a feeder cell layer in vitro;
[0161] (f) the rat ES cells maintain pluripotency when cultured in
vitro in a media comprising an GSK3 inhibitor, a MEK inhibitor, LIF
and a feeder cell layer that is not genetically modified to express
LIF; [0162] (g) the rat ES cell exhibits a targeting efficiency of
homologous recombination of at least 2%; [0163] (h) the rat ES
cells maintain pluripotency in vitro without requiring paracrine
LIF signaling; [0164] (i) at least 70% of the rat ES cells are
euploid and form sphere-like colonies when plated on a feeder cell
layer in vitro; [0165] (j) the rat ES cells express at least one
pluripotency marker selected from Dnmt3L, Eras, Err-beta, Fbxo15,
Fgf4, Gdf3, Klf4, Lef1, LIF receptor, Lin28, Nanog, Oct4, Sox15,
Sox2, Utf1, or a combination thereof; [0166] (k) the rat ES cells
do not express one or more differentiation markers selected from
c-Myc, Ecat1, Rexo1. [0167] (l) the rat ES cells do not express one
or more mesodermal markers selected from Brachyury, Bmpr2, or a
combination thereof; [0168] (m) the rat ES cells do not express one
or more endodermal markers selected from Gata6, Sox17, Sox7, or
combination thereof; and/or [0169] (n) the rat ES cells do not
express one or more neural markers selected from Nestin, Pax6, or
combination thereof.
BRIEF DESCRIPTION OF THE FIGURES
[0170] The patent or application file contains at least one drawing
executed in color. Copies of this patent or patent application
publication with color drawing(s) will be provided by the Office
upon request and payment of the necessary fee.
[0171] FIG. 1 depicts rESCs, which grow as compact spherical
colonies that routinely detach and float in the dish.
[0172] FIG. 2A through D depicts various pluripotency markers
expressed by rESCs: FIG. 2A depicts Oct-4 (green); FIG. 2B depicts
Sox-2 (red); FIG. 2C depicts DAPI (blue); FIG. 2D depicts an
overlay of pluripotency markers expressed by rESCs.
[0173] FIG. 3 depicts that the rESCs express light levels of
alkaline phosphatase (a pluripotency marker) (left), and the
karyotype for line DA.2B is 42X,Y (right). Karyotyping was done
because rESCs often become tetraploid; lines were thus pre-screened
by counting metaphase chromosome spreads, and lines with mostly
normal counts were then formally karyotyped.
[0174] FIG. 4 depicts a closer view of a rESC of FIG. 1.
[0175] FIG. 5 depicts production of chimeras by blastocyst
injection and transmission of the rESC genome through the germline;
chimeras produced by blastocyst injection using parental ACI.G1
rESC; high percentage chimeras usually have albino snouts.
[0176] FIG. 6 depicts F1 agouti pups with albino littermates, sired
by ACI/SD chimera labeled with an asterisk (*) in FIG. 5.
[0177] FIG. 7A depicts targeting of the rat Rosa 26 locus, which
lies between the Setd5 and Thumpd3 genes as in mouse, with the same
spacing. FIG. 7A shows the structure of the mouse Rosa 26 locus.
mRosa26 transcripts consist of 2 or 3 exons. FIG. 7B depicts the
structure of the rRosa26 locus; the rat locus contains a second
exon 1 (Ex1b) in addition to the homologous exon to mouse exon1
(Ex1a); no third exon has been identified in rat. FIG. 7C depicts a
targeted rRosa26 allele; homology arms of 5 kb each were cloned by
PCR using genomic DNA from DA rESC; the targeted allele contains a
SA-lacZ-hUB-neo cassette replacing a 117 bp deletion in the rRosa26
intron.
[0178] FIG. 8A depicts a control brain of a 14-week-old wild type
rat, which was treated with X-gal. The control brain showed a low
level of background staining for LacZ (dorsal view).
[0179] FIG. 8B depicts LacZ expression in the brain of an rRosa26
heterozygous rat (14-week old). The lacZ reporter was expressed
ubiquitously throughout the brain of the rRosa26 heterozygote.
[0180] FIG. 8C depicts a control heart and thymus (inset) of a
14-week-old wild type rat, which were treated with X-gal. The
control heart and thymus showed a low level of background staining
for LacZ.
[0181] FIG. 8D depicts LacZ expression in the heart and thymus
(inset) of a 14-week-old rRosa26 heterozygous rat. The lacZ
reporter was expressed ubiquitously throughout the heart and thymus
of the rROSA26 heterozygote.
[0182] FIG. 8E depicts a control lung of a 14-week-old wild type
rat, which were treated with X-gal. The control lung showed a low
level of background staining for LacZ.
[0183] FIG. 8F depicts LacZ expression in the lung of a 14-week-old
rRosa26 heterozygote rat. The lacZ reporter was expressed
ubiquitously throughout the lung of the rRosa26 heterozygote.
[0184] FIGS. 8G and H depict LacZ expression in e12.5 embryos. In
contrast to the wild-type control embryo (FIG. 8H), which shows a
low level of background LacZ staining, the rRosa26 heterozygous
embryo exhibited ubiquitous expression of the LacZ reporter
throughout the embryo.
[0185] FIGS. 8I and J depict LacZ expression in e14.5 embryos. In
contrast to the wild-type control embryo (FIG. 8J), which shows a
low level of background LacZ staining, the rRosa26 heterozygous rat
embryo exhibited ubiquitous expression of the LacZ reporter
throughout the embryo.
[0186] FIG. 9A-B provides a photograph showing the analysis of the
chromosome number of the ACI.G1 rat ES cell line.
[0187] FIG. 10A-B provides a photograph showing the analysis of the
chromosome number of the DA.2B rat ES cell line.
[0188] FIG. 11A-B provides a photograph showing the analysis of the
chromosome number of the DA.C2 rat ES cell line.
DETAILED DESCRIPTION
[0189] The present methods and compositions now will be described
more fully hereinafter with reference to the accompanying drawings,
in which some, but not all embodiments of the methods and
compositions are shown. Indeed, these methods and compositions may
be embodied in many different forms and should not be construed as
limited to the embodiments set forth herein; rather, these
embodiments are provided so that this disclosure will satisfy
applicable legal requirements. Like numbers refer to like elements
throughout.
[0190] Many modifications and other embodiments of the methods and
compositions set forth herein will come to mind to one skilled in
the art to which this methods and compositions pertains having the
benefit of the teachings presented in the foregoing descriptions
and the associated drawings. Therefore, it is to be understood that
the methods and compositions are not to be limited to the specific
embodiments disclosed and that modifications and other embodiments
are included within the scope of the appended claims. Although
specific terms are employed herein, they are used in a generic and
descriptive sense only and not for purposes of limitation.
[0191] I. Overview
[0192] The rat has long been the preferred rodent model organism
for several fields of biomedical research such as cardiovascular
disease, metabolism, toxicology, neurobiology and behavior.
Hundreds of strains of rat have been developed; some are excellent
models for complex human diseases such as hypertension, diabetes
and cancer. However, progress in understanding the genetics of
these models has been severely hampered by the difficulty of
modifying the rat genome in a controlled manner. Through the use of
site-specific endonucleases it is possible to produce mutations in
a gene of interest, but this method remains imprecise and
expensive. Targeting and germline transmission of rat ES cells
remains a difficult task to achieve.
[0193] Isolation of rat ES cells (rESC) from two inbred strains of
rat is described herein. rESC from the DA and ACI strains were
derived. These cells express pluripotency markers and exhibit a
normal 42X,Y karyotype. High percentage chimeras have been
produced, by microinjection into SD host embryos at the blastocyst
stage, and transmission of the rESC genome has been demonstrated
through the germline for both strains. Using plasmid targeting
vectors, we have produced targeted mutations in the rat equivalent
of the ROSA26 locus, and we have achieved germline transmission of
the targeted allele in both strains. These heterozygous animals
express lacZ in all tissues at all stages examined.
[0194] In various aspects, ES cells were derived from the ACI
strain in order to obtain a favorable number of male progeny from
ACI donor ES cells. In one embodiment, the amount of male progeny
is about 50%.
[0195] In various aspects, ES cells were derived from the DA strain
in order to obtain primarily female progeny.
[0196] II. Rat Embryonic Stem (ES) Cells
[0197] Various compositions and methods are provided herein which
comprise embryonic stem (ES) cells from rat. Stem cells are a cell
population possessing the capability to self-renew indefinitely and
are pluripotent. An "embryonic stem cell" or an "ES cell" comprises
a stem cell obtained from an embryo or a fetus. The various rat ES
cells provided herein can have one or more of any of the following
properties: [0198] (a) have germ-line competency, meaning when the
rat ES cell is implanted into a rat host embryo, the genome of the
rat ES cell line is transmitted into an offspring; [0199] (b) have
germ-line competency following at least one targeted genetic
modification, meaning when the rat ES cell having the targeted
genetic modification is implanted into a rat host embryo, the
targeted genetic modification within the genome of the rat ES cell
line is transmitted into an offspring; [0200] (c) have pluripotency
in vitro; [0201] (d) have totipotency in vitro; [0202] (e) when
cultured in vitro loosely adhere to a feeder cell layer; [0203] (f)
when cultured in vitro form sphere-like colonies when plated on a
feeder cell layer in vitro; [0204] (g) maintain pluripotency when
cultured in vitro under conditions comprising a feeder cell layer
that is not genetically modified to express leukemia inhibitory
factor (LIF), wherein the culture media comprises a sufficient
concentration of LIF; [0205] (h) maintain pluripotency when
cultured in vitro under conditions comprising a feeder cell layer,
wherein the culture media comprises mouse LIF or an active variant
or fragment thereof; [0206] (i) comprise a molecular signature that
is characterized by [0207] i) the expression of one or more of rat
ES cell-specific genes comprising Adherens Junctions Associate
Protein 1 (Ajap1), Claudin 5 (Cldn5), Cdc42 guanine nucleotide
exchange factor 9 (Arhgef9), Calcium/calmodulin-dependent protein
kinase IV (Camk4), ephrin-A1 (Efna1), EPH receptor A4 (Epha4), gap
junction protein beta 5 (Gjb5), Insulin-like growth factor binding
protein-like 1 (Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin
28 receptor, alpha (1128ra), left-right determination factor 1
(Lefty1), Leukemia inhibitory factor receptor alpha (Lifr),
Lysophosphatidic acid receptor 2 (Lpar2), Neuronal pentraxin
receptor (Ntm), Protein tyrosine phosphatase non-receptor type 18
(Ptpn18), Caudal type homeobox 2 (Cdx2), Fibronectin type III and
ankyrin repeat domains 1 (Fank1), Forkhead box E1 (thyroid
transcription factor 2) (Foxe1), Hairy/enhancer-of-split related
with YRPW motif 2 (Hey2), Forkhead box E1 (thyroid transcription
factor 2) (Foxe1), Hairy/enhancer-of-split related with YRPW motif
2 (Hey2), Lymphoid enhancer-binding factor 1 (Lef1), Sal-like 3
(Drosophila) (Sall3), SATB homeobox 1 (Satb1), miR-632, or a
combination thereof; [0208] ii) the expression of at least 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25 or more of the rat ES cell-specific genes comprising
Adherens Junctions Associate Protein 1 (Ajap1), Claudin 5 (Cldn5),
Cdc42 guanine nucleotide exchange factor 9 (Arhgef9),
Calcium/calmodulin-dependent protein kinase IV (Camk4), ephrin-A1
(Efna1), EPH receptor A4 (Epha4), gap junction protein beta 5
(Gjb5), Insulin-like growth factor binding protein-like 1
(Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin 28 receptor,
alpha (1128ra), left-right determination factor 1 (Lefty1),
Leukemia inhibitory factor receptor alpha (Lifr), Lysophosphatidic
acid receptor 2 (Lpar2), Neuronal pentraxin receptor (Ntm), Protein
tyrosine phosphatase non-receptor type 18 (Ptpn18), Caudal type
homeobox 2 (Cdx2), Fibronectin type III and ankyrin repeat domains
1 (Fank1), Forkhead box E1 (thyroid transcription factor 2)
(Foxe1), Hairy/enhancer-of-split related with YRPW motif 2 (Hey2),
Forkhead box E1 (thyroid transcription factor 2) (Foxe1),
Hairy/enhancer-of-split related with YRPW motif 2 (Hey2), Lymphoid
enhancer-binding factor 1 (Lef1), Sal-like 3 (Drosophila) (Sall3),
SATB homeobox 1 (Satb1), miR-632, or a combination thereof; [0209]
iii) at least a 20-fold increase in the expression of one or more
of the rat ES cell-specific genes as set forth in Table 14 when
compared to a F1H4 mouse ES cell; [0210] iv) at least a 20-fold
increase in the expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more
of the rat ES cell-specific genes as set forth in Table 14 when
compared to a F1H4 mouse ES cell; [0211] v) the expression of one
or more of rat ES cell-specific genes as set forth in Table 13;
[0212] vi) the expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35,
40, 45, 50 or more of the rat ES cell-specific genes as set forth
in Table 13; [0213] vii) at least a 20-fold increase in the
expression of one or more of the rat ES cell-specific genes as set
forth in Table 13 when compared to a F1H4 mouse ES cell; [0214]
viii) at least a 20-fold increase in the expression of at least 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more of the rat ES
cell-specific genes as set forth in Table 13 when compared to a
F1H4 mouse ES cell; [0215] ix) at least a 20-fold decrease in the
expression of one or more of the rat ES cell-specific genes as set
forth in Table 12 when compared to a F1H4 mouse ES cell; and/or
[0216] x) at least a 20-fold decrease in the expression of at least
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more of the rat ES
cell-specific genes as set forth in Table 12 when compared to a
F1H4 mouse ES cell; [0217] xi) any combination of expression of the
rat ES cell-specific genes of parts (i)-(x); [0218] xii) a relative
expression level of pluripotency markers as shown in Table 15 for
at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 or
18 of the listed pluripotency markers. See, pluripotency ranking
column of Table 15 for relative expression levels; [0219] xiii) a
relative expression level of the mesodermal markers as shown in
Table 15 for at least 2, 3, or 4 of the listed mesodermal markers.
See, mesodermal ranking column in Table 15 for relative expression
levels; [0220] xiv) a relative expression level of endodermal
markers as shown in Table 15 for at least 2, 3, 4, 5, or 6 of the
listed endodermal markers. See, endodermal ranking column in Table
15 for relative expression levels; [0221] xv) a relative expression
level of neural markers as shown in Table 15 for at least 2 and 3
of the listed neural markers. See, neural ranking column in table
15 for relative expression levels; [0222] xvi) a relative
expression level of trophectoderm markers as shown in Table 15 for
the listed trophectoderm markers. See, trophectoderm ranking column
in table 15 for relative expression levels; [0223] xvii) any
relative expression level of one or more (2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, 29 or 30) of the pluripotency markers, mesodermal markers,
endodermal markers, neural markers and/or trophectoderm markers set
forth in Table 15; [0224] xviii) the relative expression level of
each of the markers set forth in table 15; [0225] xix) any
combination of the signatures set forth in xii-xiix; and/or [0226]
xx) any combination of the signature set forth in i-xiix; [0227]
(j) have the ability to produce a F0 rat; [0228] (k) are capable of
being subcultured and maintaining the undifferentiated state;
[0229] (l) have the same number of chromosomes as a normal rat
cell; [0230] (m) maintain pluripotency in vitro without requiring
paracrine LIF signaling; and/or [0231] (n) have self renewal,
meaning they divide indefinitely while maintaining
pluripotency.
[0232] One or more of the characteristics outlined in (a)-(n) can
be present in an isolated rat ES cell, a rat ES cell population or
a rat ES cell line provided herein, wherein the rat ES cells have
not undergone a targeted genetic modification. In other
embodiments, one or more of the characteristics outlined in (a)-(n)
can be present in an isolated rat ES cell, a rat ES cell population
or a rat ES cell line provided herein that has one or more targeted
genetic modifications. A targeted genetic modification comprises an
alteration in the genome of the rat ES cell and includes, for
example, an insertion, a deletion, a knockout, a knockin, a
mutation, or a combination thereof. In other instances, the
targeted genetic modification comprises at least one insertion of a
heterologous polynucleotide into the genome of the rat ES cell. A
further description of such targeted genetic modifications are
discussed elsewhere herein.
[0233] In specific embodiments, the various rat ES cells and cell
lines provided herein are germ-line competent, meaning when the rat
ES cell is implanted into a rat host embryo, the genome of the rat
ES cell is transmitted into an offspring. Such transmission into
the offspring (i.e., the F1 population) can occur when the rat ES
cell has not undergone a targeted genetic modification. In
addition, a rat ES cell having a targeted genetic modification are
also germ-line competent, meaning when the rat ES cell having the
targeted genetic modification is implanted into a rat host embryo,
the targeted genetic modification of the rat ES cell is transmitted
to the offspring (i.e., the F1 population.) Thus, in various
aspects, the rat ES cells and methods described herein are employed
to obtain a high frequency, or high efficiency, of germline
transmission of a rat cell genome from both rat ES cells that have
not undergone a targeted genetic modification and also from rat ES
cells that have undergone a targeted genetic modification. In
various embodiments, the frequency of germline transmission is
greater than 1:600, greater than 1:500, greater than 1:400, greater
than 1:300, greater than 1:200, and greater than 1:100. In various
embodiments, the frequency of germline transmission is greater than
1%, greater than 2%, greater than 3%, greater than 4%, greater than
5%, greater than 6%, greater than 7%, greater than 8%, greater than
9%, greater than 10%, up to about 16%, greater than 25%, greater
than 50%, greater than 60%, greater than 65%, greater than 70%,
greater than 75% or greater. In various embodiments, the frequency
of germline transmission ranges from 9% to 16%. In various aspects,
percent of donor rESC-derived progeny in the F1 generation is 1% or
more, 2% or more, 3% or more, 10% or more, 20% or more, 30% or
more, 40% or more, 50% or more, 60% or more, from 3% to about 10%
or more; from 3% or more to about 63%, from about 10% to about 30%,
from about 10% to about 50%, from about 30% to about 70%, from
about 30% to about 60%, from about 20% to about 40%, from about 20%
to 65%, or from about 40% to 70%. Thus, a rat ES cell provided
herein that has not undergone a targeted genetic modification or,
alternatively, a rat ES cell that has a targeted genetic
modification have the ability to transmit their genome into the F1
population.
[0234] A rat ES cell that has not undergone a targeted genetic
modification or a rat ES cell that has a targeted genetic
modification can be pluripotent and/or totipotent. "Pluripotent" or
"pluripotency" refers to a stem cell that has the potential to
differentiate into any of the three germ layers: endoderm,
mesoderm, or ectoderm. Cell potency is a general term which
describes a cell's ability to differentiate into other cell types.
See, for example, Hans et al. (2007). "The Potential of Stem Cells:
An Inventory". Human biotechnology as Social Challenge. Ashgate
Publishing, Ltd. p. 28, herein incorporate by reference. The term
"totipotency" or "totipotent" is the ability of a single cell to
divide and produce all of the differentiated cells in an organism.
See, for example, Western P (2009). Int. J. Dev. Biol. 53 (2-3):
393-409, herein incorporated by reference. In specific embodiments,
the various ES cells disclosed herein can be either pluripotent
and/or totipotent.
[0235] Various methods can be used to determine if a rat ES cell is
pluripotent. For example, the ES cell can be assayed for the
expression of various pluripotent markers including, but not
limited to, Oct-4, Sox2, alkaline phosphatase, or a combination
thereof. See, for example, Okamoto, K. et al., Cell, 60: 461-472
(1990), Scholer, H. R. et al., EMBO J. 9: 2185-2195 (1990)) and
Nanog (Mitsui, K. et al., Cell, 113: 631-642 (2003), Chambers, I.
et al., Cell, 113: 643-655 (2003) for various methods of assaying
for the presence or the level of such markers. See, also FIGS. 2
and 3 provided herein. Other pluripotency markers include, for
example, the presence of at least 1, 2, 3, 4, or 5 pluripotency
marker comprising Nanog, Klf4, Dppa2, Fgf4, Rex1, Eras, Err-beta
and/or Sall3. Other pluripotency markers include, for example, the
absence of at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 pluripotency
marker comprising T/Brachyury, Flk1, Nodal, Bmp4, Bmp2, Gata6,
Sox17, Hhex1, Sox7, and/or Pax6.
[0236] In specific embodiments, the expression and/or the level of
expression of these markers can be determined using RT-PCR. Various
kits are available to determine the level and/or presence of
alkaline phosphatase, including, for example, an ALP tissue
staining kit (Sigma) and Vector Red Alkaline Phosphatase Substrate
Kit I (Funakoshi) and the like. Additional assays include in situ
hybridization, immunohistochemistry, immunofluorescence. In
specific embodiments, the rat ES cell is characterized by
expression of at least one pluripotency marker, including for
example expression of Oct-4, Sox2, alkaline phosphatase, or a
combination thereof, and preferably all three of these markers.
[0237] The various rat ES cell provided herein (i.e. rat ES cells
that have not undergone a targeted genetic modification and/or rat
ES cells that have a targeted genetic modification) are capable of
maintaining pluripotency and/or totipotency while being maintained
in in vitro culturing conditions. Thus, the various rat ES cells
provide herein can, in some embodiments, be subcultured while still
maintaining the undifferentiated state. Various methods of
culturing the rat ES cells are discussed in further detail
elsewhere herein.
[0238] The rat embryonic stem cells provided herein have been
isolated from the rat embryo employing various isolation,
purification, and culture expansion techniques which are discussed
in detail elsewhere herein. The term "cell" as used herein refers
to individual cells, cell lines, or cultures derived from such
cells. An "isolated" rat ES cell or rat embryo has been removed
from its natural environment. The term "isolated" can mean free
from 70%, 80%, 90%, 95%, 96%, 97%, 98% or 99% of the constituents
with which a component is found in its natural state. As used
herein, a rat ES "cell line" comprises a population of isolated rat
cells that were developed from a single rat ES cell and therefore
the population of cells within a given cell line have a uniform
genetic makeup other than for mutations or karyotypic changes
occurring during propagation or during targeted genetic
modifications. For example, as indicated elsewhere, the disclosed
rat ES cells are characterized by a high level of euploidy.
Nevertheless, in some cell lines the level of euploidy is less than
100% due to karyotypic changes in propagation of the line from a
single cell. Moreover, a given population of rat ES cells can
comprise at least 10 exp 3, 10 exp4, 10.times.10.sup.4,
10.times.10.sup.5, 10.times.10.sup.6, 10.times.10.sup.7,
10.times.10.sup.8, 10.times.10.sup.9, or 10.times.10.sup.10 cells
or greater. Some cell populations have sufficient cells to permit
selection of a desired modified cell but not an excessively greater
number so as to reduce the possibility of mutations or karyotypic
changes developing in the cell line. For example, some cell
populations have 10exp3 to 10exp6 cells.
[0239] As discussed elsewhere herein, various methods are provided
for the targeted genetic modification of a rat ES cell line. When
such methods are carried out, at least one cell within a rat ES
cell line contains the targeted genetic modification. Through
various culturing and/or selection techniques rat ES cell lines
having one or more desired targeted genetic modifications are
produced.
[0240] In specific embodiments, a rat ES cell, a population of rat
ES cell or a rat ES cell line (that have not undergone a targeted
genetic modification and/or have a targeted genetic modification)
are euploid, and thus have a chromosome number that is an exact
multiple of the haploid number. In further embodiment, a rat ES
cell, a population of rat ES cells or a rat ES cell line (that have
not undergone a targeted genetic modification and/or have a
targeted genetic modification) are diploid, and thus have two
haploid sets of homologous chromosomes. When referring to a rat ES
cell population or a population of cells from a given population of
rat ES cells or a rat ES cell line (that have not undergone a
targeted genetic modification and/or have a targeted genetic
modification), at least about 50%, 60%, 65%, 70%, 75%, 80%, 85%,
86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99% or 100% of the cells with the given population or euploid
and/or diploid. In other instances, when referring to a rat ES cell
population or a population of cells from a given rat ES cell line
(that have not undergone a targeted genetic modification and/or
have a targeted genetic modification), at least about 50% to 95%,
about 60% to 90%, about 60% to 95%, about 60% to 85%, about 60% to
80%, about 70% to 80%, about 70% to 85%, about 70% to about 90%,
about 70% to about 95%, about 70% to about 100%, about 80% to about
100%, about 80% to about 95%, about 80% to about 90%, about 90% to
about 100%, about 90% to about 99%, about 90% to about 98%, about
90% to about 97%, about 90% to about 95% of the cells within the
given population are euploid and/or diploid.
[0241] In still further embodiments, a rat ES cell, a population of
rat ES cells or a rat ES cell line (that have not undergone a
targeted genetic modification and/or have a targeted genetic
modification) have 42 chromosomes. When referring to a rat ES cell
population or a population of cells from a given rat ES cell line
(that have not undergone a targeted genetic modification and/or
have a targeted genetic modification) at least about 50%, 60%, 65%,
70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99% or 100% of the cells with the given
population have 42 chromosomes. In other instances, when referring
to a rat ES cell population or a population of cells from a given
rat ES cell line (that have not undergone a targeted genetic
modification and/or have a targeted genetic modification) at least
about 50% to 95%, about 60% to 90%, about 60% to 95%, about 60% to
85%, about 60% to 80%, about 70% to 80%, about 70% to 85%, about
70% to about 90%, about 70% to about 95%, about 70% to about 100%,
about 80% to about 100%, about 80% to about 95%, about 80% to about
90%, about 90% to about 100%, about 90% to about 99%, about 90% to
about 98%, about 90% to about 97%, about 90% to about 95% of the
cells within the given population have 42 chromosomes.
[0242] In further embodiments, a rat ES cell, a population of rat
ES cells or a rat ES cell line (that have not undergone a targeted
genetic modification and/or have a targeted genetic modification)
provided herein form sphere-like colonies when plated on a feeder
cell layer in vitro. The "sphere-like" morphology refers to the
shape of rat ES cell colonies in culture, rather than the shape of
individual ES cells. The rat ES cell colonies are spherical-like.
Colonies which are loosely attached to the feeder cells appear
circular (have a circular-like morphology). Free-floating colonies
are spherical-like. The rat ES cell colonies are spherical-like and
very compact, meaning: the boundaries between cells are very hard
to see. The edge of the colony appears bright and sharp. Individual
nuclei are difficult to distinguish because the cells are very
small (so that the nucleus takes up most of the volume of the
cell). Mouse ES Cells form elongated colonies and attach strongly
to feeder cells. mESC morphology can vary with strain; e.g. B6
colonies are rounder and more domed than F1H4 colonies but are
still more elongated than rESC. Human ES cell colonies are flatter
and more spread out than mESC colonies. The instant rat ES colonies
are not flat and do not resemble human ES cell colonies.
[0243] In still further embodiments, a rat ES cell, a population of
rat ES cells or a rat ES cell line (that have not undergone a
targeted genetic modification and/or have a targeted genetic
modification) have a circular morphology. A morphology scale for a
circle is provided below, where a score of a 10 represents a
perfect circle and a score of a 1 represents an ellipse.
[0244] Morphology scale of a circle: [0245] 10=A circle with a
structure having a longitudinal axis and a vertical axis that run
through the center of the structure and are of equal length. [0246]
9=A structure having a longitudinal axis and vertical axis that run
through the center of the structure, wherein one of the axis is
between 0.9999 to 0.9357 the length of the other axis. [0247] 8=A
structure having a longitudinal axis and vertical axis that run
through the center of the structure, wherein one of the axis is
between 0.9357 to 0.875 the length of the other axis. [0248] 7=A
structure having a longitudinal axis and vertical axis that run
through the center of the structure, wherein one of the axis is
between 0.875 to about 0.8125 the length of the other axis. [0249]
6=A structure having a longitudinal axis and vertical axis that run
through the center of the structure, wherein one of the axis is
between 0.8125 to 0.750 the length of the other axis. [0250] 5=A
structure having a longitudinal axis and vertical axis that run
through the center of the structure, wherein one of the axis is
between 0.750 to 0.6875 the length of the other axis. [0251] 4=A
structure having a longitudinal axis and vertical axis that run
through the center of the structure, wherein one of the axis is
between 0.6875 to 0.625 the length of the other axis. [0252] 3=A
structure having a longitudinal axis and vertical axis that run
through the center of the structure, wherein one of the axis is
between 0.625 to 0.5625 the length of the other axis. [0253] 2=A
structure having a longitudinal axis and vertical axis that run
through the center of the circle, wherein one of the axis is
between 0.5625 to 0.523 the length of the other axis. [0254] 1=An
ellipse is defined as having a longitudinal axis and vertical axis
that run through the center of the structure, wherein one of the
axis is between 0.523 to 0.500 the length of the other axis.
[0255] In one non-limiting embodiment, the rat ES cell population
or a population of cells from a given rat ES cell line (that have
not undergone a targeted genetic modification and/or have a
targeted genetic modification) have at least about 50%, 60%, 65%,
70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99% or 100% of the cells with the given
population have a circular morphology score of a 10, 9 or 8. In
other embodiments, the rat ES cell population or a population of
cells from a given rat ES cell line (that have not undergone a
targeted genetic modification and/or have a targeted genetic
modification) have at least about 50% to 95%, about 60% to 90%,
about 60% to 95%, about 60% to 85%, about 60% to 80%, about 70% to
80%, about 70% to 85%, about 70% to about 90%, about 70% to about
95%, about 70% to about 100%, about 80% to about 100%, about 80% to
about 95%, about 80% to about 90%, about 90% to about 100%, about
90% to about 99%, about 90% to about 98%, about 90% to about 97%,
about 90% to about 95% of the cells within the given population
have a circular morphology score of a 10, 9, or 8.
[0256] In another non-limiting embodiment, the rat ES cell
population or a population of cells from a given rat ES cell line
(that have not undergone a targeted genetic modification and/or
have a targeted genetic modification) have at least about 50%, 60%,
65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99% or 100% of the cells with the given
population have a circular morphology score of a 7, 6, 5, 4 or 3.
In other non-limiting embodiments, the rat ES cell population or a
population of cells from a given rat ES cell line (that have not
undergone a targeted genetic modification and/or have a targeted
genetic modification) have at least about 50% to 95%, about 60% to
90%, about 60% to 95%, about 60% to 85%, about 60% to 80%, about
70% to 80%, about 70% to 85%, about 70% to about 90%, about 70% to
about 95%, about 70% to about 100%, about 80% to about 100%, about
80% to about 95%, about 80% to about 90%, about 90% to about 100%,
about 90% to about 99%, about 90% to about 98%, about 90% to about
97%, about 90% to about 95% of the cells within the given
population have a circular morphology score of a 7, 6, 5, 4, or
3.
[0257] In still further embodiments, sphere-like colonies form when
the rat ES cells (that have not undergone a targeted genetic
modification and/or have a targeted genetic modification) are
plated on a feeder cell layer in vitro. A morphology scale for a
sphere is provided below, where a score of a 10 represents a
perfect sphere and a score of a 1 represents a three dimensional
elliptical structure.
[0258] Morphology scale of a sphere-like structure: [0259] 10=A
sphere is a structure having an X-axis and a Y-axis and a Z-axis
each of which runs through the center of the structure and are of
equal length. [0260] 9=A structure having an X axis and a Y-axis
and a Z-axis that run through the center of the structure, wherein
one of the axis is between 0.9999 to 0.9357 the length of at least
one of the other axes. [0261] 8=A structure having an X axis and a
Y-axis and a Z-axis that run through the center of the structure,
wherein one of the axis is between 0.9357 to 0.875 the length of at
least one or both of the other axes. [0262] 7=A structure having an
X axis and a Y-axis and a Z-axis that run through the center of the
structure, wherein one of the axis is between 0.875 to 0.8125 the
length of at least one or both of the other axes. [0263] 6=A
structure having an X axis and a Y-axis and a Z-axis that run
through the center of the structure, wherein one of the axis is
between 0.8125 to 0.750 the length of at least one or both of the
other axes. [0264] 5=A structure having an X axis and a Y-axis and
a Z-axis that run through the center of the structure, wherein one
of the axis is 0.750 to 0.6875 the length of at least one or both
of the other axes. [0265] 4=A structure having an X axis and a
Y-axis and a Z-axis that run through the center of the structure,
wherein one of the axis is 0.6875 to 0.625 the length of at least
one or both of the other axes. [0266] 3=A structure having an X
axis and a Y-axis and a Z-axis that run through the center of the
structure, wherein one of the axis is between 0.625 to 0.5625 the
length of at least one or both of the other axes. [0267] 2=A
structure having an X axis and a Y-axis and a Z-axis that run
through the center of the structure, wherein one of the axis is
between 0.5625 to 0.523 the length of at least one or both of the
other axes. [0268] 1=A structure having an X axis and a Y-axis and
a Z-axis that run through the center of the structure, wherein one
of the axis is between 0.523 to 0.500 the length of at least one or
both of the other axes.
[0269] In one non-limiting embodiment, the rat ES cell population
or a population of cells from a given rat ES cell line (that have
not undergone a targeted genetic modification and/or have a
targeted genetic modification) have at least about 50%, 60%, 65%,
70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99% or 100% of the colonies that form when the
cells are plated on a feeder cell layer in vitro have a sphere-like
morphology of a 10, 9 or 8. In other embodiments, the rat ES cell
population or a population of cells from a given rat ES cell line
(that have not undergone a targeted genetic modification and/or
have a targeted genetic modification) have at least about 50% to
95%, about 60% to 90%, about 60% to 95%, about 60% to 85%, about
60% to 80%, about 70% to 80%, about 70% to 85%, about 70% to about
90%, about 70% to about 95%, about 70% to about 100%, about 80% to
about 100%, about 80% to about 95%, about 80% to about 90%, about
90% to about 100%, about 90% to about 99%, about 90% to about 98%,
about 90% to about 97%, about 90% to about 95% of the colonies that
form when the cells are plated on a feeder cell layer in vitro have
a sphere-like morphology of a 10, 9 or 8.
[0270] In another non-limiting embodiment, the rat ES cell
population or a population of cells from a given rat ES cell line
(that have not undergone a targeted genetic modification and/or
have a targeted genetic modification) have at least about 50%, 60%,
65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99% or 100% of the colonies that form when
the cells are plated on a feeder cell layer in vitro have a
sphere-like morphology of a 7, 6, 5, 4, or 3. In other embodiments,
the rat ES cell population or a population of cells from a given
rat ES cell line (that have not undergone a targeted genetic
modification and/or have a targeted genetic modification) have at
least about 50% to 95%, about 60% to 90%, about 60% to 95%, about
60% to 85%, about 60% to 80%, about 70% to 80%, about 70% to 85%,
about 70% to about 90%, about 70% to about 95%, about 70% to about
100%, about 80% to about 100%, about 80% to about 95%, about 80% to
about 90%, about 90% to about 100%, about 90% to about 99%, about
90% to about 98%, about 90% to about 97%, about 90% to about 95% of
the colonies that form when the cells are plated on a feeder cell
layer in vitro have a sphere-like morphology of a 7, 6, 5, 4, or
3.
[0271] A given rat ES cell, a population of rat ES cells or a rat
ES cell line provided herein can be a male (XY) rat ES cell, a male
(XY) population of rat ES cells, or a male (XY) rat ES cell line.
In other embodiments, a population of rat ES cells or a rat ES cell
line provided herein can be a female (XX) rat ES cell, a female
(XX) population of rat ES cells, or a female (XX) rat ES cell line.
Any such rat ES cell, population of rat ES cells or rat ES cell
line can comprise the euploidy and/or diploidy as described
above.
[0272] The various rat ES cell provided herein can be from any rat
strain, including but not limited to, an ACI rat strain, a Dark
Agouti (DA) rat strain, a Wistar rat strain, a LEA rat strain, a
Sprague Dawley (SD) rat strain, or a Fischer rat strain such as
Fisher F344 or Fisher F6. The various rat ES cells can also be
obtained from a strain derived from a mix of two or more strains
recited above. In one embodiment, the rat ES cell is derived from a
strain selected from a DA strain and an ACI strain. In a specific
embodiment, the rat ES cell is derived from an ACI strain. The ACI
rat strain is are characterized as having black agouti, with white
belly and feet and an RT1.sup.av1 haplotype. Such strains are
available from a variety of sources including Harlan Laboratories.
In other embodiments, the various rat ES cells are from a Dark
Agouti (DA) rat strain which is characterized as having an agouti
coat and an RT1.sup.av1 haplotype. Such rats are available from a
variety of source including Charles River and Harlan Laboratories.
In a further embodiment, the various rat ES cells provided herein
are from an inbred rat strain.
[0273] In specific embodiments the rat ES cell line is from an ACI
rat and comprises the ACI.G1 rat ES cell as described herein. In
another embodiment, the rat ES cell line is from a DA rat and
comprises the DA.2B rat ES cell line or the DA.2C rat ES cell line
as described herein. A given rat ES cell provided herein can be
obtained from a rat embryo at any stage of rat embryo development.
Representative stages of rat embryo development are outline below
in Table 1. The rat embryos employed to derive the rat ES cells can
be a morula-stage embryo, a blastocyst-stage embryo, or a rat
embryo at a developmental stage between a morula-stage embryo and a
blastocyst-stage embryo. Thus, in specific embodiments, the rat
embryo employed is at or between the Witschi stages of 5 and 7. In
other embodiments, the rat embryo employed is at the Witschi stage
5, 6, or 7.
[0274] In one embodiment, the rat ES cell is obtained from a rat
blastocyst. In other embodiments, the rat ES cell is obtained from
a blastocyst from a superovulated rat. In other embodiments, the
rat ES cells are obtained from an 8-cell stage embryo which is then
cultured in vitro until it develops into a morula-stage, blastocyst
stage, an embryo between the Witschi stages 5 and 7, or into an
embryo at the Witschi stage 5, 6, or 7. At which time the embryos
are then plated. Morula-stage embryos comprise a compact ball of
cells with no internal cavity. Blastocyst-stage embryos have a
visible internal cavity (the blastocoel) and contain an inner cell
mass (ICM). The ICM cells form ES cells.
TABLE-US-00001 TABLE 1 Stages of Rat Embryo Development Standard
Stages Age (Witschi) (days) Identification of Stages Cleavage and
Blastula 1 1 1 cell (in oviduct) 2 2 2 cells (in oviduct) 3 3 4
cells (in oviduct) 4 3.25 8-12 cells (in oviduct) 5 3.5 Morula (in
uterus) 6 4 Early blastocyst (in uterus) 7 5 Free blastocyst (in
uterus) Gastrula 8 6 Implanting blastocyst, with trophoblastic cone
and inner cell mass; outgrowth of endoderm (hypoblast) 9 6.75
Diplotrophoblast; inner cell mass (pendant), covered with endoderm
10 7.25 Near complete implantation; pendant begins differentiation
into embryonic and extra-embryonic parts 11 7.75 Completion of
implantation; primary amniotic cyst; ectoplacental cone
[0275] Further provided are various rat ES cells (that have not
undergone a targeted genetic modification and/or have a targeted
genetic modification) which are characterized by
The rat ES cell is characterized by:
[0276] i) the expression of one or more of rat ES cell-specific
genes comprising Adherens Junctions Associate Protein 1 (Ajap1),
Claudin 5 (Cldn5), Cdc42 guanine nucleotide exchange factor 9
(Arhgef9), Calcium/calmodulin-dependent protein kinase IV (Camk4),
ephrin-A1 (Efna1), EPH receptor A4 (Epha4), gap junction protein
beta 5 (Gjb5), Insulin-like growth factor binding protein-like 1
(Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin 28 receptor,
alpha (1128ra), left-right determination factor 1 (Lefty1),
Leukemia inhibitory factor receptor alpha (Lifr), Lysophosphatidic
acid receptor 2 (Lpar2), Neuronal pentraxin receptor (Ntm), Protein
tyrosine phosphatase non-receptor type 18 (Ptpn18), Caudal type
homeobox 2 (Cdx2), Fibronectin type III and ankyrin repeat domains
1 (Fank1), Forkhead box E1 (thyroid transcription factor 2)
(Foxe1), Hairy/enhancer-of-split related with YRPW motif 2 (Hey2),
Forkhead box E1 (thyroid transcription factor 2) (Foxe1),
Hairy/enhancer-of-split related with YRPW motif 2 (Hey2), Lymphoid
enhancer-binding factor 1 (Lef1), Sal-like 3 (Drosophila) (Sall3),
SATB homeobox 1 (Satb1), miR-632, or a combination thereof;
[0277] ii) the expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more
of the rat ES cell-specific genes comprising Adherens Junctions
Associate Protein 1 (Ajap1), Claudin 5 (Cldn5), Cdc42 guanine
nucleotide exchange factor 9 (Arhgef9),
Calcium/calmodulin-dependent protein kinase IV (Camk4), ephrin-A1
(Efna1), EPH receptor A4 (Epha4), gap junction protein beta 5
(Gjb5), Insulin-like growth factor binding protein-like 1
(Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin 28 receptor,
alpha (Il28ra), left-right determination factor 1 (Lefty1),
Leukemia inhibitory factor receptor alpha (Lifr), Lysophosphatidic
acid receptor 2 (Lpar2), Neuronal pentraxin receptor (Ntm), Protein
tyrosine phosphatase non-receptor type 18 (Ptpn18), Caudal type
homeobox 2 (Cdx2), Fibronectin type III and ankyrin repeat domains
1 (Fank1), Forkhead box E1 (thyroid transcription factor 2)
(Foxe1), Hairy/enhancer-of-split related with YRPW motif 2 (Hey2),
Forkhead box E1 (thyroid transcription factor 2) (Foxe1),
Hairy/enhancer-of-split related with YRPW motif 2 (Hey2), Lymphoid
enhancer-binding factor 1 (Lef1), Sal-like 3 (Drosophila) (Sall3),
SATB homeobox 1 (Satb1), miR-632, or a combination thereof;
[0278] iii) at least a 20-fold increase in the expression of one or
more of the rat ES cell-specific genes as set forth in Table 14
when compared to a F1H4 mouse ES cell;
[0279] iv) at least a 20-fold increase in the expression of at
least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25 or more of the rat ES cell-specific
genes as set forth in Table 14 when compared to a F1H4 mouse ES
cell;
[0280] v) the expression of one or more of rat ES cell-specific
genes as set forth in Table 13;
[0281] vi) the expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35,
40, 45, 50 or more of the rat ES cell-specific genes as set forth
in Table 13;
[0282] vii) at least a 20-fold increase in the expression of one or
more of the rat ES cell-specific genes as set forth in Table 13
when compared to a F1H4 mouse ES cell;
[0283] viii) at least a 20-fold increase in the expression of at
least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more of the rat
ES cell-specific genes as set forth in Table 13 when compared to a
F1H4 mouse ES cell;
[0284] ix) at least a 20-fold decrease in the expression of one or
more of the rat ES cell-specific genes as set forth in Table 12
when compared to a F1H4 mouse ES cell; and/or
[0285] x) at least a 20-fold decrease in the expression of at least
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more of the rat ES
cell-specific genes as set forth in Table 12 when compared to a
F1H4 mouse ES cell;
[0286] xi) any combination of expression of the rat ES
cell-specific genes of parts (i)-(x);
[0287] xii) a relative expression level of pluripotency markers as
shown in Table 15 for at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17 or 18 of the listed pluripotency markers. See,
pluripotency ranking column of Table 15 for relative expression
levels;
[0288] xiii) a relative expression level of the mesodermal markers
as shown in Table 15 for at least 2, 3, or 4 of the listed
mesodermal markers. See, mesodermal ranking column in Table 15 for
relative expression levels;
[0289] xiv) a relative expression level of endodermal markers as
shown in Table 15 for at least 2, 3, 4, 5, or 6 of the listed
endodermal markers. See, endodermal ranking column in Table 15 for
relative expression levels;
[0290] xv) a relative expression level of neural markers as shown
in Table 15 for at least 2 and 3 of the listed neural markers. See,
neural ranking column in table 15 for relative expression
levels;
[0291] xvi) a relative expression level of trophectoderm markers as
shown in Table 15 for the listed trophectoderm markers. See,
trophectoderm ranking column in table 15 for relative expression
levels;
[0292] xvii) any relative expression level of one or more (2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29 or 30) of the pluripotency markers,
mesodermal markers, endodermal markers, neural markers and/or
trophectoderm markers set forth in Table 15;
[0293] xviii) the relative expression level of each of the markers
set forth in table 15;
[0294] xix) any combination of the signatures set forth in
xii-xiix; and/or
[0295] xx) any combination of the signature set forth in
i-xiix.
[0296] In one embodiment, when transplanted into a pre-morula stage
rat embryo, the rat ES cell (that have not undergone a targeted
genetic modification and/or have a targeted genetic modification)
can contribute to at least 90% of the cells in an F0 generation,
contribute to at least 95% of the cells in an F0 generation,
contribute to at least 96% of the cells in an F0 generation,
contribute to at least 97% of the cells in an F0 generation,
contribute to at least 98% of the cells in an F0 generation, or
contribute to at least 99% of the cells in an F0 generation.
[0297] III. Derivation and Propagation of Rat Embryonic Stem (ES)
Cells
[0298] Various methods are provided for obtaining the rat ES cells
disclosed herein. In specific embodiments, such methods comprise
(a) providing an in vitro culture comprising a feeder cell layer
and a population of isolated rat embryonic stem (ES) cells; (b)
culturing in vitro under conditions which are sufficient to
maintain pluipotency and/or totipotency of the isolated rat ES
cell. Such methods thereby allow for the propagation of a rat ES
cell population and/or a rat ES cell line.
[0299] In one embodiment, a method for culturing a rat embryonic
stem cell line is provided. Such methods comprises culturing in
vitro a feeder cell layer and a rat ES cell line, wherein the
culture conditions maintain pluripotency of the rat ES cells and
comprise a media having mouse leukemia inhibitory factor (LIF) or
an active variant or fragment thereof. The various methods further
comprise passaging and culturing in vitro the cells of the rat ES
cell line, wherein each subsequent in vitro culturing comprises
culturing the rat ES cells on the feeder cell layer under
conditions that maintain pluripotency of the rat ES cells and
comprises a media having mouse LIF or an active variant or fragment
thereof.
[0300] i. Culture Conditions
[0301] The culture media employed in the various methods and
compositions will maintain the rat ES cells. The terms
"maintaining" and "maintenance" refer to the stable preservation of
at least one or more of the characteristics or phenotypes of the
rat ES cells outline herein. Such phenotypes can include
maintaining pluripotency and/or totipotency, cell morphology, gene
expression profiles and the other functional characteristics of the
rat stem cells described herein. The term "maintain" can also
encompass the propagation of stem cells, or an increase in the
number of stem cells being cultured. The term further contemplates
culture conditions that permit the stem cells to remain
pluripotent, while the stem cells may or may not continue to divide
and increase in number.
[0302] The term "feeder cell" or "feeder cell layer" refers to a
culture of cells that grow in vitro and secrete at least one factor
into the culture medium that is used to support the growth of
another cell of interest in the culture. The feeder cells employed
herein aid in maintaining the pluripotency of the rat ES cells, and
in specific embodiments, one or more of the other characteristics
or phenotypes described herein. Various feeder cells can be used
including, for example, mouse embryonic fibroblasts, including
mouse embryonic fibroblasts obtained between the 12.sup.th and
16.sup.th day of pregnancy. In specific embodiments, feeder cell
layer comprises a monolayer of mitotically inactivated mouse
embryonic fibroblasts (MEFs).
[0303] The in vitro cultures of the rat ES cells further comprise
an effective amount of Leukemia Inhibitory Factor (LIF) or an
active variant or fragment thereof. Leukemia inhibitory factor
(LIF) belongs to the IL-6 receptor family. LIF binds to a
heterodimeric membrane receptor made up of a LIF-specific subunit,
gp190 or LIFR, and the subunit gp130, which is shared with the
other members of the IL-6 family. LIF inhibits the differentiation
of embryonic stem cells in mice and contribute to stem cell
self-renewal. Human and mouse LIF share 79% sequence homology and
exhibit cross-species activity. Rat LIF (rtLIF) is a 22.1 kDa
protein containing 202 amino acid residues that exhibits 91% amino
acid sequence identity with murine LIF (Takahama et al. 1998).
There are six possible asparagine-linked glycosylation
(N-glycosylation) sites which are conserved among the LIF
polypeptide from the various species and an additional site of
Asn150 which is specific for rat LIF. The tertiary structure of the
mouse LIF and its function is described in further detail in Aikawa
et al. (1998) Biosci. Biotechnol. Biochem. 62 1318-1325 and Senturk
et al. (2005) Immunology of Pregnancy, editor Gil Mor., U.S. Pat.
No. 5,750,654 and D P Gearing (1987) EMBO Journal 1987-12-20, each
of which is herein incorporated by reference in their entirety. A
partial mouse LIF sequence is reported on the SwissProt website
under the accession number P09056.
[0304] Mouse LIF activity is assessed by its ability to induce
differentiation of M1 myeloid leukemia cells. The specific activity
is 1.times.10.sup.6 units/ml (Cat. No. 03-0011 from Stemgent) and
1.times.10.sup.7 units/ml (Cat. No. 03-0011-100 from Stemgent),
where 50 units is defined as the amount of mouse LIF required to
induce differentiation in 50% of the M1 colonies in 1 ml of medium.
See, also, Williams, R. L. et al. (1988) Nature 336: 684-687.;
Metcalf, D. et al. (1988) Leukemia 2: 216-221; Niwa, H. et al.
(2009) Nature 460: 118-122; Xu, J. et al. (2010) Cell Biol Int. 34:
791-797; Fukunaga, N. et al. (2010) Cell Reprogram. 12: 369-376;
and, Metcalf D. (2003) Stem Cells 21: 5-14, each of which is herein
incorporated by reference in their entirety. An "effective amount
of LIF" comprises a concentration of LIF that allows the rat ES
cells of an in vitro culture to remain in an undifferentiated
pluripotent state. Various markers that can be used to assay for
the cells remaining in a pluripotent state are discussed elsewhere
herein.
[0305] The LIF polypeptide employed in the various methods and
compositions provided herein can be from any organism, including
from a mammal, a rodent, a human, a rat or a mouse. In one
embodiment, the LIF polypeptide is from a mouse. In still further
embodiments, the mouse LIF polypeptide comprises the amino acid
sequence set forth in SwissProt Accession number: P09056, which is
herein incorporated by reference in its entirety and is also set
forth in SEQ ID NO: 1.
[0306] In other embodiments, an active variant or fragment of the
mouse LIF polypeptide as set forth in SEQ ID NO: 1 or in SwissProt
Accession number: P09056 can be used. Such active variants and
fragments (including active variants having at least 75%, 80%, 85%
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence
identity to SEQ ID NO: 1) are discussed in further detail elsewhere
herein.
[0307] LIF polypeptide or the active variant or fragment thereof
can be provided to the in vitro culture in a variety of ways. In
one embodiment, the effective amount of the LIF polypeptide or the
active variant or fragment thereof is added to the culture media.
In other embodiments, the feeder cells have been genetically
modified to overexpress the LIF polypeptide or the active variant
or fragment thereof. Such feeder cells include feeder cells
prepared from gamma-irradiated or mitomycin-C treated DIA-M mouse
fibroblasts that express matrix-associated LIF. Method of
generating and using such genetically modified feeder cells can be
found, for example, in See, Buehr et al. (2003) Biol Reprod
68:222-229, Rathjen et al. (1990) Cell 62 1105-1115, and Buehr et
al. (2008) Cell 135:1287-1298, each of which is herein incorporated
by reference. The heterologous LIF expressed in the feeder cells
can be from the same organism as the feeder cells or from an
organism that is different from that of the feeder cell. In
addition, the heterologous LIF expressed in the feeder cells can be
from the same or from a different organism than the ES cells the
feeder layer is supporting.
[0308] In still other embodiments, the feeder cells employed in the
various methods disclosed herein are not genetically modified to
express a heterologous LIF polypeptide or an active variant or
fragment thereof. Thus, in particular embodiments, the monolayer of
mitotically inactivated mouse embryonic fibroblast employed in the
methods has not been genetically modified to express a heterologous
LIF polypeptide.
[0309] In other embodiments, the LIF polypeptide or the active
variant or fragment thereof is added to the culture media. When LIF
is added to the culture media, the LIF can be from any organism,
including from a mammal, a rodent, a human, a rat or a mouse. In
one embodiment, the LIF present in the culture media is from a
mouse. In still further embodiments, the mouse LIF polypeptide
comprises the amino acid sequence set forth in SEQ ID NO:1. In
other embodiments, an active variant or fragment of the mouse LIF
polypeptide as set forth in SEQ ID NO:1 can be used. Such active
variants and fragments (including active variants having at least
75%, 80%, 85% 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%
sequence identity to SEQ ID NO: 1) are discussed in further detail
elsewhere herein.
[0310] In specific embodiments, the rat ES cells and rat ES cell
lines provided herein maintain pluripotency in vitro without
requiring paracrine LIF signaling.
[0311] In specific embodiments, LIF or an active variant or
fragment thereof is present in the culture media at any
concentration that maintains the rat ES cells. LIF polypeptide or
active variant or fragment thereof is present in the culture media
at about 25 U/ml to about 50 U/ml, at about 50 U/ml to about 100
U/ml, at about 100 U/ml to about 125 U/ml, at about 125 U/ml to
about 150 U/ml, at about 150 U/ml to about 175 U/ml, at about 175
U/ml to about 200 U/ml, at about 200 U/ml to about 225 U/ml, at
about 225 U/ml to about 250 U/ml, at about 250 U/ml to about 300
U/ml, to about 300 U/ml to about 325 U/ml, at about 325 U/ml to
about 350 U/ml, at about 350 U/ml to about 400 U/ml, at about 400
U/ml to about 425 U/ml, at about 425 U/ml to about 450 U/ml, at
about 450 U/ml to about 475 U/ml, at about 475 U/ml to about 500
U/ml, at about 75 U/ml to about 500 U/ml or greater. In other
embodiments, LIF polypeptide or active variant or fragment thereof
is present in the culture media at about 25 U/ml to about 50 U/ml,
at about 25 U/ml to about 100 U/ml, at about 75 U/ml to about 125
U/ml, at about 50 U/ml to about 150 U/ml, at about 90 U/ml to about
125 U/ml, at about 90 U/ml to about 110 U/ml, at about 80 U/ml to
about 150 U/ml, at about 80 U/ml to about 125 U/ml. In a specific
embodiment, LIF polypeptide or active variant or fragment thereof
is present in the culture media at about 100 U/ml.
[0312] When mouse LIF is employed, the mouse LIF polypeptide or
active variant or fragment thereof is present in the culture media
at any concentration that maintains the rat ES cells. Mouse LIF
polypeptide or active variant or fragment thereof is present at
about 25 U/ml to about 50 U/ml, at about 50 U/ml to about 100 U/ml,
at about 100 U/ml to about 125 U/ml, at about 125 U/ml to about 150
U/ml, at about 150 U/ml to about 175 U/ml, at about 175 U/ml to
about 200 U/ml, at about 200 U/ml to about 225 U/ml, at about 225
U/ml to about 250 U/ml, at about 250 U/ml to about 300 U/ml, to
about 300 U/ml to about 325 U/ml, at about 325 U/ml to about 350
U/ml, at about 350 U/ml to about 400 U/ml, at about 400 U/ml to
about 425 U/ml, at about 425 U/ml to about 450 U/ml, at about 450
U/ml to about 475 U/ml, at about 475 U/ml to about 500 U/ml, at
about 75 U/ml to about 500 U/ml or greater. In other embodiments,
mouse LIF polypeptide or active variant or fragment thereof is
present at about 25 U/ml to about 50 U/ml, at about 25 U/ml to
about 100 U/ml, at about 75 U/ml to about 125 U/ml, at about 50
U/ml to about 150 U/ml, at about 90 U/ml to about 125 U/ml, at
about 90 U/ml to about 110 U/ml, at about 80 U/ml to about 150
U/ml, at about 80 U/ml to about 125 U/ml. In a specific embodiment,
mouse LIF polypeptide or active variant or fragment thereof is
present in the culture media at about 100 U/ml.
[0313] The culture media employed maintains rat ES cells. As such,
in specific embodiments, the culture media employed in the various
method and compositions will maintain the pluripotency of all or
most of (i.e., over 50%) of the rat ES cells in a cell line for a
period of a at least 5, 10 or 15 passages. In one embodiment, the
culture media comprises one or more compounds that assist in
maintaining pluripotency. In one embodiment, the culture media
comprises a MEK pathway inhibitor and a glycogen synthase kinase-3
(GSK-3) inhibitor. The media can further comprise additional
components that aid in maintaining the ES cells, including for
example, FGF receptor inhibitors, ROCK inhibitors, and/or ALK (TGFb
receptor) inhibitors. A non-limiting example of an FGF receptor
inhibitors includes PD184352. A non-limiting example of a ROCK
inhibitor includes Y-27632, and non-limiting example of an ALK
(TGFb receptor) inhibitor includes A-83-01. In specific
embodiments, 2i media (table 2) is used with 10 uM ROCKi when
thawing cryopreserved rESC or when re-plating rESC after
dissociation with trypsin.
[0314] In other embodiments, the media comprises a combination of
inhibitors consisting of a MEK pathway inhibitor and a glycogen
synthase kinase-3 (GSK-3) inhibitor.
[0315] In one non-limiting embodiment, the culture media comprises
a GSK-3 inhibitor comprising CHIR99021 and/or comprises a MEK
inhibitor comprising PD0325901. In other embodiments, the media
comprises a combination of inhibitors consisting of CHIR99021 and
PD0325901. Either of these compounds can be obtained, for example,
from Stemgent. In specific embodiments, CHIR99021 is present in the
culture media at a concentration of about 0.5.mu. to about 3 .mu.M,
about 0.5.mu. to about 3.5 .mu.M, about 0.5 .mu.M to about 4 .mu.M,
about 0.5 .mu.M to about 1 .mu.M, about 1 .mu.M to about 1.5 .mu.M,
about 1.5 .mu.M to about 2 .mu.M, about 2 .mu.M to about 2.5 .mu.M,
about 2.5 to about 3 .mu.M, 3 .mu.M to about 3.5 .mu.M. In further
embodiments, CHIR99021 is present in the culture media at a
concentration of about 3 .mu.M. In other embodiments, PD0325901 is
present in the culture media at a concentration of about 0.4 .mu.M
to about 1 uM, about 0.4 .mu.M to about 1.5 uM, about 0.4 .mu.M to
about 2 .mu.M, about 0.4 .mu.M to about 0.8 .mu.M, 0.8 .mu.M to
about 1.2 .mu.M, about 1.2 to about 1.5 .mu.M. In further
embodiments, PD0325901 is present in the culture media at a
concentration of about 1 .mu.M. In specific embodiments, CHIR99021
is present in the culture media at a concentration of about 3 .mu.M
and PD0325901 is present at a concentration of about 1 .mu.M.
[0316] In one non-limiting embodiment, the culture media employed
in the various methods and compositions disclosed herein is set
forth in Table 2. Within the context of this application, the media
described in Table 2 is referred to as 2i media.
TABLE-US-00002 TABLE 2 Non-limiting rat ES culture media. Reagent
Concentration DMEM/F12 basal media 1x (50%) Neurobasal media 1x
(50%) Penicillin/streptomycin 1% L-Glutamine 4 mM 2-Mercaptoethanol
0.1 mM N2 supplement 1x B27 supplement 1x LIF 100 U/ml PD0325901
(MEK inhibitor). 1 .mu.M CHIR99021 (GSK inhibitor). 3 .mu.M
[0317] Additional media that can be employed include those
disclosed in Li et al. (2008) Cell 135:1299-1310, Yamamoto et al.
(2012) Transgenic Rats 21:743-755, Ueda et al. (2008) PLoS ONE
3(6):e2800, Meek et al. (2010) PLoS ONE 4 (12): e14225; Tong et al.
(2010) Nature 467:211-213; US Patent Publication 2012/0142092,
Buehr et al. (2008) Cell 135:1287-1298, Li et al. (135) Cell
1299-1310, each of which is herein incorporated by reference in
their entirety. When employing such media, the concentration and
the source of LIF can be modified as outlined herein. In specific
embodiments, the various culture media are used in combination with
mouse LIF or an active variant or fragment thereof, and in even
further embodiments, the various culture media comprise a mouse LIF
or an active variant or fragment thereof at a concentration of
about 50 U/ml to about 100 U/ml, about 50 U/ml to about 150 U/ml,
or about 100 U/ml.
[0318] The temperature of the cultures of rat ES cells, both for
the production of the ES cell line and for the culturing and
maintaining of the ES line it typically carried out at about
35.degree. C. to about 37.5.degree. C. In specific embodiment, the
temperature is 37.0.degree. C. The culture is typically carried out
at 7.5% CO.sub.2.
[0319] ii. Establishing a Rat ES Cell Line
[0320] Methods for generating a rat embryonic stem (ES) cell line
are provided. Such methods comprises (a) culturing in vitro a first
feeder cell layer and a morula-stage embryo, a blastocyst-stage
embryo, or a rat embryo at a developmental stage between a
morula-stage embryo and a blastocyst-stage embryo, wherein the zona
pellucida of the rat embryo has been removed and wherein the
culture conditions maintain pluripotency of the rat ES cell and
comprises a media having mouse leukemia inhibitory factor (LIF) or
an active variant or fragment thereof; and, (b) transferring an
outgrowth of an amorphous undifferentiated mass of rat ES cells to
an in vitro culture well comprising a second feeder cell layer and
culturing the outgrowth under conditions that maintain pluripotency
of the rat ES cells and comprises a media having mouse LIF or an
active variant or fragment thereof, and thereby establishing a rat
ES cell line. The various methods further comprise passaging and
culturing in vitro the cells of the rat ES cell line, wherein each
subsequent in vitro culturing comprises culturing the rat ES cells
on the feeder cell layer under conditions that maintain
pluripotency of the rat ES cells and comprises a media having mouse
LIF or an active variant or fragment thereof. Rat ES cell lines
made by such methods are also provided.
[0321] Non-limiting examples of methods to establish a rat ES cell
line having the various characteristics discussed herein are set
forth in Example 3. Briefly, a rat embryo (i.e., a morula-stage
embryo, a blastocyst-stage embryo, or a rat embryo at a
developmental stage between a morula-stage embryo and a
blastocyst-stage embryo) is flushed from the uteruses of a female
rat. In specific embodiments, a blastocyst or an 8 cell embryo is
obtained. The zona pellucida is removed and the rat embryos are
cultured on feeder cells (as discussed elsewhere herein) which, in
specific embodiments, comprise a monolayer of mitotically
inactivated mouse embryonic fibroblasts (MEFs). The cells of the
morula-stage embryo, the blastocyst-stage embryo, or the rat embryo
at a developmental stage between a morula-stage embryo and a
blastocyst-stage embryo are cultured in vitro under conditions that
maintain the ES rat cells and thereby are sufficient to maintain
pluripotency and/or totipotency of the ES cells. Various media can
be employed at this stage, including any of the various media
discussed above which have LIF, including mouse LIF or an active
variant or fragment thereof, in the media.
[0322] The cultures are monitored for the presence of an outgrowth
(an amorphous undifferentiated mass of cells). Once the outgrowth
reaches an appropriate size, a given outgrowth is transferred to
new feeder plate and cultured. Transfer is accompanied by enzymatic
dissociation using trypsin in order to produce multiple colonies.
This transfer is commonly referred to as "passage 1". The speed at
which each line expands varies. The media is changed as needed in
order to maintain the pluripotency or totipotency of the rat ES
cells. The culture is monitored for the presence of colonies having
embryonic stem cell morphology. Such morphology includes one or
more of the following characteristics: (a) round, circular mounds
that rise above the monolayer of feeder cells; (b) cells that are
packed tightly together such that cell boarders are difficult to
see; (c) smaller cell size; (d) small amount of cytoplasm and
enlarged nucleus, (e) form sphere-like colonies when plated on
feeder cells in vitro. Once such colonies appear, the culturing can
continue until reaching approximately 50% confluency. The colonies
are then transferred to a new feeder plate. Transfer is accompanied
by enzymatic dissociation using trypsin in order to expand the
number of colonies. This is referred to as "passage 2". The cells
are continued to be cultured with feeder cells until they reach
approximately 50% confluent, at which point the cells can undergo
further passages to maintain the cell lines or the lines can be
frozen. See, also Tong et al. (2010) Nature 467 (9):211-215; Li et
al. (2008) Cell 135:1299-1310, and Buehr et al. (2008) Cell
135:1287-1298, each of which is herein incorporated by reference.
Thus, in specific embodiments, the various rat ES cells, cell lines
and cell populations disclosed herein are capable of being
subcultured and maintaining the undifferentiated state.
[0323] In one non-limiting embodiment, the derivation of the rat ES
cells occurs as follows. At day 0, female rats are euthanized and
the oviducts and uterine horns are dissected out and place into a
tissue culture dish containing warm N2B27 media. Media is flushed
through the uterine horns and oviducts to eject blastocysts into
the media. The blastocysts are collected and transfer to embryo
culture dish containing KSOM+2i (1 .mu.MPD0325901, 3 .mu.M
CHIR99021). KSOM can be purchased from Millipore, catalog number is
MR-106-D. The 2i media referred to herein comprises the media set
forth in Table 2. The cells are culture overnight at 37.degree. at
7.5% CO.sub.2.
[0324] In other non-limiting embodiments, the rat ES cells are
derived from 8-cell embryos or frozen 8-cell embryos. The embryos
are cultured in M2 medium for 10 minutes at room temperature and
are then transfer to KSOM+2i and culture overnight.
[0325] A non-limiting example for derivation of the rat ES cells is
as follows: on Day 1, transferring cavitated embryos to 2i medium
(Table 2) and culture overnight. The culturing is continued
un-cavitated in KSOM+2i. On day 2, all remaining embryos are
transferred to 2i medium, whether or not they have cavitated.
Culture continues overnight in 2i medium. On day 3, embryos are
incubated with acid tyrodes to remove the zona pellucida and washed
3 times in 2i medium to remove the acid tyrodes. Each embryo is
deposited into a separate well feeder plate, in which each well
contains a monolayer of mitotically inactivated mouse embryonic
fibroblasts (MEFs). The cells are cultured overnight in 2i medium.
On day 4 and 5, the cells plated embryos are monitored for the
presence of an outgrowth, an amorphous undifferentiated mass of
cells. Outgrowths are ready for transfer when they are
approximately twice the size of the plated embryo. Each day, spent
media is removed and replaced with fresh 2i media. The outgrowths
are transferred to new feeder wells, and again spent media is
removed and the wells are washed with PBS. The PBS is removed and
trypsin is added and incubated for about 10 minutes. The trypsin
reaction is stopped by the addition of 30 .mu.l 2i media and 10%
FBS. The cells are gently dissociated and the entire content is
transferred to a well in a feeder plate. This is referred to as
Passage 1 (P1). The cells are cultured overnight in 2i medium. On
day 5-8, depending on how fast each line expands, the 2i media is
changed each day and culture is monitored for the presence of
colonies with an ESC morphology. Such ESC morphology is discussed
in detail elsewhere herein. Culturing continues until colonies
expand to about 50% confluency. The colonies are then trypsinzied
and passaged as before into feeder wells. This is referred to as
passage 2. Feeding and monitoring each line is continued until they
are approximately 50% confluent. The cells are trypsinized as
usual. The trypsin is stopped with 2i media+10% FBS. The cells are
pelleted by centrifugation, and the cells in 400 .mu.l Freezing
Medium (70% 2i, 20% FBS, 10% DMSO). The cells can then be frozen.
This is referred to passage 3.
[0326] iii. Maintaining and Passaging a Rat ES Cell Line
[0327] Further provided are methods for maintaining or culturing a
rat embryonic stem cell line. The method comprises culturing in
vitro a feeder cell layer and a rat ES cell line, wherein the
culture conditions maintain pluripotency of a rat embryonic stem
(ES) cell and comprise a media having mouse leukemia inhibitory
factor (LIF) or an active variant or fragment thereof. Such methods
employ the culture media and feeder cell layer as outlined above.
In one embodiment, the rat ES cell line can be passaged at least 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 30, 40, 50 or more times. In specific embodiments, the rat
ES cells can be passaged up to at least 11 times in a medium
comprising a GSK3 inhibitor and a MEK inhibitor without decreasing
its targeting efficiency or germline transmission efficiency of a
targeted genetic modification.
[0328] The rat ES cell lines are fed and monitored. In specific
embodiments, passage occurs when the culture is approximately 30%,
40%, 50%, or 60% confluent. In other embodiments, passage occurs
when the culture is 50% confluent. Depending on how fast each line
expands, the passages can occur every 24, 25, 26, 27, 28, 29, 30,
40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 95 or 100 hours. In other
embodiments, the time between passages ranges between 24 hours and
96 hours, between about 30 and 50 hours, between about 25 and 75
hours, between about 50 and 96 hours, between about 25 and 75
hours, between about 35 and 85 hours, or between about 40 and 70
hours. In one embodiment, the rat ES cell, cell line or cell
population as disclosed herein has a doubling time ranging from
about 24 hours to about 36 hours. In one embodiment, the rat ES
cell has a doubling time of 25 hours.
[0329] The various rat ES cell lines when derived and maintained as
outlined herein can have one or more any the following
properties:
[0330] (a) have germ-line competency, meaning when the rat ES cell
is implanted into a rat host embryo, the genome of the rat ES cell
line is transmitted into an offspring;
[0331] (b) have germ-line competency following targeted genetic
modification, meaning when the rat ES cell is implanted into a rat
host embryo, the targeted genetic modification within the genome of
the rat ES cell line, is transmitted into an offspring;
[0332] (c) have pluripotency in vitro;
[0333] (d) have totipotency in vitro;
[0334] (e) when cultured in vitro loosely adhere to a feeder cell
layer;
[0335] (f) when cultured in vitro form sphere-like colonies when
plated on a feeder cell layer in vitro;
[0336] (g) maintain pluripotency when cultured in vitro under
conditions comprising a feeder cell layer that is not genetically
modified to express leukemia inhibitory factor (LIF), wherein the
culture media comprises a sufficient concentration of LIF;
[0337] (h) maintain pluripotency when cultured in vitro under
conditions comprising a feeder cell layer, wherein the culture
media comprises mouse LIF or an active variant or fragment
thereof;
[0338] (i) comprise a molecular signature characterized by [0339]
i) the expression of one or more of rat ES cell-specific genes
comprising Adherens Junctions Associate Protein 1 (Ajap1), Claudin
5 (Cldn5), Cdc42 guanine nucleotide exchange factor 9 (Arhgef9),
Calcium/calmodulin-dependent protein kinase IV (Camk4), ephrin-A1
(Efna1), EPH receptor A4 (Epha4), gap junction protein beta 5
(Gjb5), Insulin-like growth factor binding protein-like 1
(Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin 28 receptor,
alpha (1128ra), left-right determination factor 1 (Lefty1),
Leukemia inhibitory factor receptor alpha (Lifr), Lysophosphatidic
acid receptor 2 (Lpar2), Neuronal pentraxin receptor (Ntm), Protein
tyrosine phosphatase non-receptor type 18 (Ptpn18), Caudal type
homeobox 2 (Cdx2), Fibronectin type III and ankyrin repeat domains
1 (Fank1), Forkhead box E1 (thyroid transcription factor 2)
(Foxe1), Hairy/enhancer-of-split related with YRPW motif 2 (Hey2),
Forkhead box E1 (thyroid transcription factor 2) (Foxe1),
Hairy/enhancer-of-split related with YRPW motif 2 (Hey2), Lymphoid
enhancer-binding factor 1 (Lef1), Sal-like 3 (Drosophila) (Sall3),
SATB homeobox 1 (Satb1), miR-632, or a combination thereof; [0340]
ii) the expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more of the
rat ES cell-specific genes comprising Adherens Junctions Associate
Protein 1 (Ajap1), Claudin 5 (Cldn5), Cdc42 guanine nucleotide
exchange factor 9 (Arhgef9), Calcium/calmodulin-dependent protein
kinase IV (Camk4), ephrin-A1 (Efna1), EPH receptor A4 (Epha4), gap
junction protein beta 5 (Gjb5), Insulin-like growth factor binding
protein-like 1 (Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin
28 receptor, alpha (1128ra), left-right determination factor 1
(Lefty1), Leukemia inhibitory factor receptor alpha (Lifr),
Lysophosphatidic acid receptor 2 (Lpar2), Neuronal pentraxin
receptor (Ntm), Protein tyrosine phosphatase non-receptor type 18
(Ptpn18), Caudal type homeobox 2 (Cdx2), Fibronectin type III and
ankyrin repeat domains 1 (Fank1), Forkhead box E1 (thyroid
transcription factor 2) (Foxe1), Hairy/enhancer-of-split related
with YRPW motif 2 (Hey2), Forkhead box E1 (thyroid transcription
factor 2) (Foxe1), Hairy/enhancer-of-split related with YRPW motif
2 (Hey2), Lymphoid enhancer-binding factor 1 (Lef1), Sal-like 3
(Drosophila) (Sall3), SATB homeobox 1 (Satb1), miR-632, or a
combination thereof; [0341] iii) at least a 20-fold increase in the
expression of one or more of the rat ES cell-specific genes as set
forth in Table 14 when compared to a F1H4 mouse ES cell; [0342] iv)
at least a 20-fold increase in the expression of at least 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25 or more of the rat ES cell-specific genes as set forth
in Table 14 when compared to a F1H4 mouse ES cell; [0343] v) the
expression of one or more of rat ES cell-specific genes as set
forth in Table 13; [0344] vi) the expression of at least 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 30, 35, 40, 45, 50 or more of the rat ES cell-specific
genes as set forth in Table 13; [0345] vii) at least a 20-fold
increase in the expression of one or more of the rat ES
cell-specific genes as set forth in Table 13 when compared to a
F1H4 mouse ES cell; [0346] viii) at least a 20-fold increase in the
expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or
more of the rat ES cell-specific genes as set forth in Table 13
when compared to a F1H4 mouse ES cell; [0347] ix) at least a
20-fold decrease in the expression of one or more of the rat ES
cell-specific genes as set forth in Table 12 when compared to a
F1H4 mouse ES cell; and/or [0348] x) at least a 20-fold decrease in
the expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50
or more of the rat ES cell-specific genes as set forth in Table 12
when compared to a F1H4 mouse ES cell; [0349] xi) any combination
of expression of the rat ES cell-specific genes of parts (i)-(x);
[0350] xii) a relative expression level of pluripotency markers as
shown in Table 15 for at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17 or 18 of the listed pluripotency markers. See,
pluripotency ranking column of Table 15 for relative expression
levels; [0351] xiii) a relative expression level of the mesodermal
markers as shown in Table 15 for at least 2, 3, or 4 of the listed
mesodermal markers. See, mesodermal ranking column in Table 15 for
relative expression levels; [0352] xiv) a relative expression level
of endodermal markers as shown in Table 15 for at least 2, 3, 4, 5,
or 6 of the listed endodermal markers. See, endodermal ranking
column in Table 15 for relative expression levels; [0353] xv) a
relative expression level of neural markers as shown in Table 15
for at least 2 and 3 of the listed neural markers. See, neural
ranking column in table 15 for relative expression levels; [0354]
xvi) a relative expression level of trophectoderm markers as shown
in Table 15 for the listed trophectoderm markers. See,
trophectoderm ranking column in table 15 for relative expression
levels; [0355] xvii) any relative expression level of one or more
(2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30) of the pluripotency
markers, mesodermal markers, endodermal markers, neural markers
and/or trophectoderm markers set forth in Table 15; [0356] xviii)
the relative expression level of each of the markers set forth in
table 15; [0357] xix) any combination of the signatures set forth
in xii-xiix; and/or [0358] xx) any combination of the signature set
forth in i-xiix;
[0359] (j) have the ability to produce a F0 rat;
[0360] (k) capable of being subcultured and maintaining the
undifferentiated state;
[0361] (l) have the same number of chromosomes a normal rat cell;
and/or
[0362] (m) maintain pluripotency in vitro without requiring
paracrine LIF signaling.
[0363] (n) have self renewal, meaning they divide indefinitely
while maintaining pluripotency.
[0364] Such properties of a given rat ES cell line can be present
at any one of the passage, including at passages 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 40,
50 or later.
[0365] Thus, in one non-limiting embodiment, an in vitro culture
comprising a feeder cell layer and a population of rat ES cells is
provided, wherein the in vitro culture conditions maintain
pluripotency of the rat ES cells and comprises a media having mouse
leukemia inhibitory factor (LIF) or an active variant or fragment
thereof. In specific embodiments, the rat ES cells cultured under
such conditions maintains pluripotency of at least 50% of cell
population over a period of at least 10 passages, maintains
pluripotency of at least 60% of cell population over a period of at
least 10 passages, maintains pluripotency of at least 70% of cell
population over a period of at least 10 passages, maintains
pluripotency of at least 75% of cell population over a period of at
least 10 passages, maintains pluripotency of at least 80% of cell
population over a period of at least 10 passages, maintains
pluripotency of at least 85% of cell population over a period of at
least 10 passages, maintains pluripotency of at least 90% of cell
population over a period of at least 10 passages, or maintains
pluripotency of at least 95% of cell population over a period of at
least 10 passages.
[0366] Further provided herein are in vitro cultures comprising the
various rat ES cells, cell populations and cell lines disclosure
herein, as well as, culturing kits for these various ES cells. For
example, as discussed above, in specific embodiments, the various
rat ES cells provided herein have a one or more of the following
characteristics: (1) when cultured in vitro loosely adhere to a
feeder cell layer; (2) when cultured in vitro they form sphere-like
colonies when plated on a feeder cell layer in vitro; (3) they
maintain pluipotency when cultured in vitro under conditions
comprising a feeder cell layer that is not genetically modified to
express leukemia inhibitory factor (LIF), wherein the culture media
comprises a sufficient concentration of LIF; and/or (4) they
capable of being subcultured and maintaining the undifferentiated
state. Moreover, the rat ES cell populations of any of these in
vitro cultures can comprise, for example, a population of cells in
which at least 70%, 75%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99% or 100% of the cells within the population are
euploid, are diploid and/or have 42 chromosomes.
[0367] One method of culturing a rat embryonic stem cells in vitro
comprises (a) providing an in vitro culture comprising a feeder
cell layer and a population of isolated rat embryonic stem (ES)
cells; and (b) culturing the in vitro culture under conditions
which are sufficient to maintain pluipotency or totipotency of the
isolated rat embryonic stem (ES) cell, and wherein the rat ES cells
form colonies that loosely adhere to the feeder cell layer. "Loose
adherence" or "adhere loosely" means that, if the culture dish is
undisturbed for a period of time (minimum 8 hours), some colonies
will adhere to the feeders such that they can maintain adherence if
the dish is gently moved. In smaller wells (where the media moves
less), loose adherence can happen faster. In either case, these
colonies can be dislodged by either a) swirling the media in the
dish or by gently pipetting media across the surface of the
feeders. The morphology of these loosely adherent colonies is still
spherical. In such instances the rat ES cells form sphere-like
colonies when plated on a feeder cell layer in vitro. Such
sphere-like colonies are shown for example in FIG. 1.
[0368] iv. Kits and In Vitro Cultures
[0369] The rat ES cells and rat ES cell lines provided herein can
be contained within a kit or an article of manufacture. In specific
embodiments, the kit or article of manufacture comprises any of the
rat ES cell lines or populations disclosed herein. The kit can
further comprise any culture media that maintains the rat ES cell,
including media that maintains the pluripotency of the rat ES
cells. Such media can comprise culture media having mouse LIF or an
active variant or fragment thereof, as discussed in greater detail
elsewhere herein. The media within the kit can further comprise a
MEK inhibitor and a GSK-3 inhibitor, or alternatively, the media
within the kit can further comprise a combination of inhibitors
consisting of a MEK inhibitor and a GSK-3 inhibitor. In specific
embodiments, the media in the kit comprises a MEK inhibitor
comprising PD0325901 and/or a GSK-3 inhibitor comprising CHIR99021.
Any of the various media discussed herein, can be contained within
the kit.
[0370] Further provided is a kit or article of manufacture that
comprises any of the rat ES cell lines or populations disclosed
herein, any of the various media disclosed herein, and a population
of feeder cells. In one embodiment, the feeder cells in the kit or
article of manufacture are not genetically modified to express LIF
and/or the feeder cells comprises mitotically inactivated mouse
embryonic fibroblasts (MEFs). Any of the other feeder cells
disclosed herein can be employed in the kit or article of
manufacture.
[0371] IV. Genetic Modification of Rat Embryonic Stem (ES)
Cells
[0372] The various rat ES cells and cell lines disclosed herein can
be modified to contain at least one targeted genetic modification.
Thus, various methods are provided for genetically modifying an
isolated rat embryonic stem (ES) cell as disclosed herein. The
method comprises introducing into the genome of an isolated rat ES
cell disclosed herein a targeted genetic modification to form a
genetically modified rat ES cell. The targeted genetic modification
can comprise any modification to the genome of rat ES including,
for example, an insertion, a deletion, a knockout, a knockin, a
mutation, or a combination thereof. In one embodiment, the targeted
genetic modification comprises insertion of a heterologous
polynucleotide into the genome of the rat ES cell. As used herein,
"heterologous" in reference to a sequence is a sequence that
originates from a foreign species, or, if from the same species, is
substantially modified from its native form in composition and/or
genomic locus by deliberate human intervention.
[0373] In one aspect, an isolated rat ES cell or rat ES cell line
is provided that is capable of sustaining pluripotency following
one or more genetic modifications in vitro and that is capable of
transmitting a genetically modified genome to a germline of an F1
generation. Thus, the rat ES cell maintains its pluripotency to
develop into a plurality of cell types following the one or more
serial genetic modifications in vitro (e.g., two, three, four,
five, or six or more serial genetic modifications). In other
embodiments, multiple targeted genetic modifications are made in a
given rat ES cell, including, for example, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13 14, 15 or more. As such, multiple heterologous
polynucleotides can also be integrated into the genome, including
for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 14, 15 or
more.
[0374] In one embodiment, following any one of the one to 15 serial
genetic modifications, the genetically modified rat ES cells upon
exposure to differentiation medium are capable of differentiation
into a plurality of cell types. In one embodiment, following any
one of the one to 15 serial genetic modifications, the genetically
modified rat ES cells are capable of being maintained in an
undifferentiated state in culture. In one embodiment, the
genetically modified and cultured rat ES cells in the
undifferentiated state, when employed as donor cells in a rat host
embryo, populate the embryo and form a blastocyst comprising the
one to fifteen genetic modifications. In one embodiment, the
blastocyst, when implanted into a surrogate mother under conditions
suitable for gestation, develops into an F0 rat progeny that
comprises the one to 15 genetic modifications.
[0375] Various methods for making targeted genetic modifications
within a genome of a rat ES cell can be used. For example, in one
instance, the targeted genetic modification employs a system that
will generate a targeted genetic modification via a homologous
recombination event. In other instances, the rat ES cells can be
modified using nuclease agents that generate a single or double
strand break at a targeted genomic location. The single or
double-strand break is then repaired by the non-homologous end
joining pathway (NHEJ). Such systems find use, for example, in
generating targeted loss of function genetic modifications. See,
for example, Tesson et al. (2011) Nature Biotechnology 29:695-696,
herein incorporated by reference. Such agents include,
Transcription Activator-Like Effector Nuclease (TALEN) (WO
2010/079430; Morbitzer et al. (2010) PNAS 10.1073/pnas.1013133107;
Scholze & Boch (2010) Virulence 1:428-432; Christian et al.
Genetics (2010) 186:757-761; Li et al. (2010) Nuc. Acids Res.
(2010) doi:10.1093/nar/gkq704; and Miller et al. (2011) Nature
Biotechnology 29:143-148; US Patent Application No. 2011/0239315
A1, 2011/0269234 A1, 2011/0145940 A1, 2003/0232410 A1, 2005/0208489
A1, 2005/0026157 A1, 2005/0064474 A1, 2006/0188987 A1, and
2006/0063231 A1 (each hereby incorporated by reference); a
zinc-finger nuclease (ZFN) (US20060246567; US20080182332;
US20020081614; US20030021776; WO/2002/057308A2; US20130123484;
US20100291048; and, WO/2011/017293A2, each of which is herein
incorporated by reference); a meganuclease (see, Epinat et al.,
(2003) Nucleic Acids Res 31:2952-62; Chevalier et al., (2002) Mol
Cell 10:895-905; Gimble et al., (2003) Mol Biol 334:993-1008;
Seligman et al., (2002) Nucleic Acids Res 30:3870-9; Sussman et
al., (2004) J Mol Biol 342:31-41; Rosen et al., (2006) Nucleic
Acids Res 34:4791-800; Chames et al., (2005) Nucleic Acids Res
33:e178; Smith et al., (2006) Nucleic Acids Res 34:e149; Gruen et
al., (2002) Nucleic Acids Res 30:e29; Chen and Zhao, (2005) Nucleic
Acids Res 33:e154; WO2005105989; WO2003078619; WO2006097854;
WO2006097853; WO2006097784; and WO2004031346); and a CAS/CRISPER
system (Mali P et al. (2013) Science 2013 Feb. 15; 339(6121):823-6;
Jinek M et al. Science 2012 Aug. 17; 337(6096):816-21; Hwang W Y et
al. Nat Biotechnol 2013 March; 31(3):227-9; Jiang W et al. Nat
Biotechnol 2013 March; 31(3):233-9; and, Cong L et al. Science 2013
Feb. 15; 339(6121):819-23, each of which is herein incorporated by
reference).
[0376] In other embodiments, the targeted genomic modification can
be made by employing a homologous recombination targeting vector.
In such instances, the targeting vector comprises the insert
polynucleotide and further comprises an upstream and a downstream
homology arm which flank the insert polynucleotide. The homology
arms which flank the insert polynucleotide correspond to genomic
regions within the targeted genomic locus. For ease of reference,
the corresponding genomic regions within the targeted genomic locus
are referred to herein as "target sites". Thus, in one example, a
targeting vector can comprise a first insert polynucleotide flanked
by a first and a second homology arm corresponding to a first and a
second target site located at the targeted genomic locus. The
targeting vector thereby aids in the integration of the insert
polynucleotide into the targeted genomic locus through a homologous
recombination event that occurs between the homology arms and the
corresponding target sites within the genome of the cell.
[0377] As used herein, a homology arm and a target site
"correspond" or are "corresponding" to one another when the two
regions share a sufficient level of sequence identity to one
another to act as substrates for a homologous recombination
reaction. By "homology" is meant DNA sequences that are either
identical or share sequence identity to a corresponding sequence.
The sequence identity between a given target site and the
corresponding homology arm found on the targeting vector can be any
degree of sequence identity that allows for homologous
recombination to occur. For example, the amount of sequence
identity shared by the homology arm of the targeting vector (or a
fragment thereof) and the target site (or a fragment thereof) can
be at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%,
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,
98%, 99%, 99.5%, 99.9% or 100% sequence identity, such that the
sequences undergo homologous recombination. Moreover, a
corresponding region of homology between the homology arm and the
corresponding target site can be of any length that is sufficient
to promote homologous recombination at the cleaved recognition
site.
[0378] In specific embodiments, the isolated rat ES cell, cell line
or cell population exhibits a homologous recombination efficiency
of at least 2%, at least 3%, at least 4%, at least 5%, at least 6%,
at least 7%, at least 8%, at least 9%, at least 10%, at least 11%,
at least 12%, at least 13%, at least 14%, at least 15%, at least
20%, at least 25%, at least 30%, at least 35%, at least 40%, at
least 45%, at least 50%, at least 55%, at least 60%, at least 65%,
at least 70%, at least 75%, or at least 80%. In one embodiment, the
homologous recombination efficiency employing the rat ES cell is
greater than 4%.
[0379] In specific embodiments, a selection marker is employed when
generating a targeted genetic modification in a rat ES cell. The
polynucleotide encoding the selection marker can be present on the
targeting vector which is designed to introduce the targeted
genetic modification into the genome, or it can be found on a
separate plasmid or vector. The polynucleotide encoding the
selection marker can be contained within in expression cassette.
The various components of such expression cassettes are discussed
in further detail elsewhere herein. Various selection markers can
be used in the methods and compositions disclosed herein. Such
selection markers can, for example, impart resistance to an
antibiotic such as G418, hygromycin, blastocidin, puromycin or
neomycin. Such selection markers include neomycin
phosphotransferase (neo.sup.r), hygromycin B phosphotransferase
(hyg.sup.r), puromycin N-acetyltransferase and blasticidin S
deaminase (bsr.sup.r). In still other embodiments, the selection
marker is operably linked to an inducible promoter and the
expression of the selection marker is toxic to the cell.
Non-limiting examples of such selection markers include
xanthine/guanine phosphoribosyl transferase (gpt),
hahypoxanthine-guanine phosphoribosyltransferase (HGPRT) or herpes
simplex virus thymidine kinase (HSV-TK). See, for example, Santerre
et al. (1984) Gene 30:147-56; Joyner (1999) The Practical Approach
Series, 293; Santerre et al. (1984) Gene 30:147-56; Bernard et al.
(1985) Exp Cell Res 158:237-43; Giordano and McAllister (1990)
Gene, 88:285-8; Izumi et al. (1991) Exp Cell Res 197:229-33), each
of which is herein incorporated by reference in their entirety. In
specific embodiments, the neoR selectable marker is the neomycin
phosphotransferase (neo) gene of Beck et al. (1982) Gene,
19:327-36, which is herein incorporated by reference. The neoR
selection maker is that used in U.S. Pat. No. 7,205,148 or
6,596,541, each of which are herein incorporated by reference.
[0380] In specific embodiments, the selection marker employed is a
non-attenuated selection marker. A "non-attenuated selection
marker" comprises a selection marker that retains the activity of
the native polypeptide or the selection marker has an increased
activity when compared to the native form of the polypeptide. An
increased in activity of a selection marker can comprise any
statistically significant increase in activity including, for
example, an increase of at least 5%, 10%, 20%, 30%, 40%, 50%, 60%,
70% 80% or higher. Thus, a non-attenuated selection marker when
expressed in a host cell will allow for a higher percentage of the
host cells to survive in the presence of a higher concentration of
the selection agent than when employing an attenuated selection
marker. Non-attenuated selection markers include, for example, a
neomycin non-attenuate selection marker. See, for example, Beck et
al. (1982) Gene, 19:327-36 or in U.S. Pat. No. 7,205,148 or
6,596,541, each of which are herein incorporated by reference.
[0381] In other instances, the increased activity of a selection
marker when compared to an attenuated selection marker and/or the
wild type (native) selection marker can result from increasing the
copy number of either the non-attenuated, attenuated or native
selection marker within the genome of the rat ES cell. As such, a
given rat ES cell can comprise within its genome at least 1, 2, 3,
4, 5, 6, 7, 8, 9, 10 or more copies of a given selection marker
(i.e., a non-attenuated selection marker, an attenuated selection
marker or a native (wildtype) selection marker).
[0382] The various selection markers employed are encoded by a
polynucleotide operably linked to a promoter active in the rat ES
cell. In specific embodiments, the increase in the activity of the
selection marker can result from an increase in expression of the
selection marker. Thus, a promoter can be employed to elevate the
expression levels of a given selection marker. Promoters of
interest include, but are not limited to, the CMV promoter, the PGK
promoter and the CAG promoter. In one embodiment, the human
Ubiquitin (hUb) promoter is used to express the selection marker.
See, Valenzuela et al. (2003) Nature Biotechnology 21:652-659,
herein incorporate by reference in its entirety.
[0383] In one embodiment, the rat ES cell maintains its
pluripotency to develop into a plurality of cell types following a
single round of electroporation with an exogenous nucleic acid. In
another embodiment, the rat ES cell maintains its pluripotency to
develop into a plurality of cell types following a second round of
electroporation with an exogenous nucleic acid, following a third
round of electroporation with an exogenous nucleic acid, following
a fourth round of electroporation with an exogenous nucleic acid,
following a fifth round of electroporation with an exogenous
nucleic acid, following a sixth round of electroporation with an
exogenous nucleic acid, following a seventh round of
electroporation with an exogenous nucleic acid, following an eighth
round of electroporation with an exogenous nucleic acid, following
a ninth round of electroporation with an exogenous nucleic acid,
following a tenth round of electroporation with an exogenous
nucleic acid, following an eleventh round of electroporation with
an exogenous nucleic acid, following a twelfth round of
electroporation with an exogenous nucleic acid, following a
thirteenth round of electroporation with an exogenous nucleic acid,
following a fourteenth round of electroporation with an exogenous
nucleic acid and/or following a fifteenth round of electroporation
with an exogenous nucleic acid. In other embodiments, the rat ES
cell is capable of transmitting a targeted genetic modification
into progeny following a successive round of electroporation (i.e.,
at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more rounds of
electroporation).
[0384] i. Introducing Sequences into a Rat Embryonic Stem Cell
[0385] The methods provided herein comprise introducing into a cell
with one or more polynucleotides or polypeptide constructs
comprising the various components needed to make the targeted
genomic modification. "Introducing" means presenting to the cell
the sequence (polypeptide or polynucleotide) in such a manner that
the sequence gains access to the interior of the cell. The methods
provided herein do not depend on a particular method for
introducing any component of the targeted genomic integration
system into the cell, only that the polynucleotide gains access to
the interior of a least one cell. Methods for introducing
polynucleotides into various cell types are known in the art and
include, but are not limited to, stable transfection methods,
transient transfection methods, and virus-mediated methods. Such
method include, but are not limited to, electroporation,
intracytoplasmic injection, viral infection (including adenovirus,
lentivirus, and retrovirus vectors), transfection, lipid-mediated
transfection and/or Nucleofaction.TM.. See, for example, Stadtfeld
et al. (2009) Nature Methods 6(5):329-330; Yusa et al. (2009) Nat.
Methods 6:363-369; Woltjen et al. (2009) Nature 458, 766-770. Such
methods include, but are not limited to, direct delivery of DNA
such as by ex vivo transfection (Wilson et al., Science,
244:1344-1346, 1989, Nabel and Baltimore, Nature 326:711-713,
1987), optionally with Fugene6 (Roche) or Lipofectamine
(Invitrogen), by injection (U.S. Pat. Nos. 5,994,624, 5,981,274,
5,945,100, 5,780,448, 5,736,524, 5,702,932, 5,656,610, 5,589,466
and 5,580,859, each incorporated herein by reference), including
microinjection (Harland and Weintraub, J. Cell Biol.,
101:1094-1099, 1985; U.S. Pat. No. 5,789,215, incorporated herein
by reference); by electroporation (U.S. Pat. No. 5,384,253,
incorporated herein by reference; Tur-Kaspa et al., Mol. Cell
Biol., 6:716-718, 1986; Potter et al., Proc. Nat'l Acad. Sci. USA,
81:7161-7165, 1984); by calcium phosphate precipitation (Graham and
Van Der Eb, Virology, 52:456-467, 1973; Chen and Okayama, Mol. Cell
Biol., 7(8):2745-2752, 1987; Rippe et al., Mol. Cell Biol.,
10:689-695, 1990); by using DEAE-dextran followed by polyethylene
glycol (Gopal, Mol. Cell Biol., 5:1188-1190, 1985); by direct sonic
loading (Fechheimer et al., Proc. Nat'l Acad. Sci. USA,
84:8463-8467, 1987); by liposome mediated transfection (Nicolau and
Sene, Biochim. Biophys. Acta, 721:185-190, 1982; Fraley et al.,
Proc. Nat'l Acad. Sci. USA, 76:3348-3352, 1979; Nicolau et al.,
Methods Enzymol., 149:157-176, 1987; Wong et al., Gene, 10:87-94,
1980; Kaneda et al., Science, 243:375-378, 1989; Kato et al., Biol.
Chem., 266:3361-3364, 1991) and receptor-mediated transfection (Wu
and Wu, Biochemistry, 27:887-892, 1988; Wu and Wu, J. Biol. Chem.,
262:4429-4432, 1987); and any combination of such methods, each of
which is incorporated herein by reference.
[0386] In some embodiments, the cells employed in the methods and
compositions have a DNA construct stably incorporated into their
genome. "Stably incorporated" or "stably introduced" means the
introduction of a polynucleotide into the cell such that the
nucleotide sequence integrates into the genome of the cell and is
capable of being inherited by progeny thereof. Any protocol may be
used for the stable incorporation of the DNA constructs or the
various components employed to generate the targeted genomic
modification.
[0387] Transfection protocols as well as protocols for introducing
polypeptides or polynucleotide sequences into cells may vary.
Non-limiting transfection methods include chemical-based
transfection methods include the use of liposomes; nanoparticles;
calcium phosphate (Graham et al. (1973). Virology 52 (2): 456-67,
Bacchetti et al. (1977) Proc Natl Acad Sci USA 74 (4): 1590-4 and,
Kriegler, M (1991). Transfer and Expression: A Laboratory Manual.
New York: W. H. Freeman and Company. pp. 96-97); dendrimers; or
cationic polymers such as DEAE-dextran or polyethylenimine. Non
chemical methods include electroporation; Sono-poration; and
optical transfection. Particle-based transfection include the use
of a gene gun, magnet assisted transfection (Bertram, J. (2006)
Current Pharmaceutical Biotechnology 7, 277-28). Viral methods can
also be used for transfection.
[0388] A non-limiting example, of a method of introduction a
heterologous polynucleotide into a rat ES cell follows. The rat ES
cells, as described herein, are passaged for about 24 to about 48
prior to electroporation. About 24 hours prior to electroporation
the media is changed to RVG2i+ROCKi (10 .mu.M Y-27632). The rat ES
cells are trypsinized and the rat ES cells are isolated. The rat ES
cells are suspended to achieve a final cell concentration of about
2.times.10 6 to about 10.times.10 6 cells per 75 ul. About
75.lamda. of rat ES cells are added to about 50.lamda. DNA
comprising the heterologous polynucleotide and about 125.lamda. EP
buffer is added. In one non-limiting embodiment, the
electroporation is carried out with the following parameters: 400V;
400V; .OMEGA.; 100 .mu.F. The cells are then cultured in RVG2i and
10 .mu.M ROCKi and can be transferred onto feeder cells.
[0389] ii. Selecting Rat Embryonic Stem Cells Having a Targeted
Genomic Modification
[0390] Various method are provided for selecting and maintaining
rat ES cells having stably incorporated into their genome a
targeted genetic modification. In one non-limiting example, when
introducing a heterologous polynucleotide into a rat ES cell, the
method can comprise (a) providing an in vitro population of rat ES
cells; (b) introducing into at least one rat ES cell a heterologous
polynucleotide comprising a selection marker operably linked to a
promoter active the rat ES cell; and, (c) culturing in vitro the
rat ES cell population in an alternating first and second culture
media wherein the first culture media comprises an effective amount
of a selection agent for a first time period and the second culture
media do not comprise the selection agent, wherein the in vitro
culture conditions maintain pluripotency or totipotency; and
thereby selecting the rat ES cell having stably integrated into its
genome the heterologous polynucleotide. The various methods by
which the rat ES cell having the targeted genetic modification can
be selected in a given population can employ an in vitro culture
system which allows the rat ES cells to maintain pluripotency.
Thus, any of the in vitro culture media and feeder cells discussed
herein can be employed.
[0391] In specific embodiments, the first and the second culture
media are alternated about every 5, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40 hours or more. In a specific embodiment, the
first and second culture media are alternated every 24 hours.
[0392] Any appropriate selection marker can be used and the
corresponding selection agent will be present at an effective
concentration with the culture media. Such selection markers
include any of the native, attenuated or non-attenuated selection
marker discussed herein. In one embodiment, the selection marker
employed imparts resistance to an antibiotic, including for
example, G418. Non-limiting selection markers comprise neomycin
phosphotransferase II (nptII) or hygromycin phosphotransferase
(hpt).
[0393] The concentration of the selection agent is such as to allow
for the selection of a rat ES cell having the selection marker
while maintaining the pluipotency of the rat ES cells that are
present within the culture. When employing, for example, G418, the
concentration of the G418 in the selection media can range from
about 50 ug/ml to about 125 ug/ml, about 60 ug/ml to about 125
ug/ml, about 70 ug/ml to about 125 ug/ml, about 80 ug/ml to about
125 ug/ml, about 90 ug/ml to about 125 ug/ml, about 100 ug/ml to
about 125 ug/ml, about 110 ug/ml to about 125 ug/ml, about 80 ug/ml
to about 100 ug/ml, about 65 ug/ml to about 85 ug/ml, about 70
ug/ml to about 80 ug/ml. In one embodiment, the concentration of
G418 in the culture is 75 .mu.g/ml.
[0394] The media employed in the selection allows the rat embryonic
stem cells to retain pluripotency. Such media is described in
detail elsewhere herein.
[0395] The selection protocol can be initiated at any time
following the introduction of the polynucleotide encoding the
selection marker into the genome of the rat ES cell. In specific
embodiments, the selection protocol begins 10, 15, 20, 24, 30, 35,
40, 50, 60 or more hours after the introduction of the selection
marker into the rat ES cell. In one embodiment, the selection
protocol beings about 2 days following the introduction of the
polynucleotide encoding the selection marker.
[0396] A non-limiting selection protocol employing G418 is as
follows. Day 2, (2.sup.nd day after the introduction of the
polynucleotide encoding the selection marker) the population of rat
ES cells is incubated cells in 2i media and G418 at 75 .mu.g/ml. At
day 3, the population of rat ES cells are incubated cells in 2i
media without G418. At day 4, the population of rat ES cells are
incubated in 2i media and G418 at 75 .mu.g/ml. At day 5, the
population of rat ES cells are incubated cells in 2i media without
G418. At day 6, the population of rat ES cells are incubated in 2i
media and G418 at 75 .mu.g/ml. At day 7, the population of rat ES
cells is incubated in 2i media without G418. At day 8, the
population of rat ES cells is incubated in 2i media without G418
and 75 .mu.g/ml. At day 9, the population of rat ES cells is
incubated cells in 2i media without G418. At day 10, the population
of rat ES cells is incubated cells in 2i media and G418 at 75
.mu.g/ml. At day 11, the population of rat ES cells is incubated
cells in 2i media without G418. At day 12, colonies are picked for
expansion and screening.
[0397] Following the selection of the rat ES cells having the
selection marker, the colonies can be expanded. In specific
embodiments, the period for expansion can be about 1, 2, 3, 4, 5,
or more days in a culture condition that maintains the pluripotency
of the cells. In one non-limiting embodiment, the selected colonies
are expanded for 3 days. In a further embodiment, the media
employed is a 2i media. Each clone can then be passed and further
expanded.
[0398] The rat ES cells and cell lines having one or more of the
targeted genetic modifications can have one or more any the
following properties:
[0399] (a) have germ-line competency following targeted genetic
modification, meaning when the rat ES cell is implanted into a rat
host embryo, the targeted genetic modification within the genome of
the rat ES cell line, is transmitted into an offspring;
[0400] (b) have pluripotency in vitro;
[0401] (c) have totipotency in vitro;
[0402] (d) when cultured in vitro loosely adhere to a feeder cell
layer;
[0403] (e) when cultured in vitro form sphere-like colonies when
plated on a feeder cell layer in vitro;
[0404] (f) maintain pluripotency when cultured in vitro under
conditions comprising a feeder cell layer that is not genetically
modified to express leukemia inhibitory factor (LIF), wherein the
culture media comprises a sufficient concentration of LIF;
[0405] (g) maintain pluripotency when cultured in vitro under
conditions comprising a feeder cell layer, wherein the culture
media comprises mouse LIF or an active variant or fragment
thereof;
[0406] (h) comprise a molecular signature characterized by [0407]
i) the expression of one or more of rat ES cell-specific genes
comprising Adherens Junctions Associate Protein 1 (Ajap1), Claudin
5 (Cldn5), Cdc42 guanine nucleotide exchange factor 9 (Arhgef9),
Calcium/calmodulin-dependent protein kinase IV (Camk4), ephrin-A1
(Efna1), EPH receptor A4 (Epha4), gap junction protein beta 5
(Gjb5), Insulin-like growth factor binding protein-like 1
(Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin 28 receptor,
alpha (1128ra), left-right determination factor 1 (Lefty1),
Leukemia inhibitory factor receptor alpha (Lifr), Lysophosphatidic
acid receptor 2 (Lpar2), Neuronal pentraxin receptor (Ntm), Protein
tyrosine phosphatase non-receptor type 18 (Ptpn18), Caudal type
homeobox 2 (Cdx2), Fibronectin type III and ankyrin repeat domains
1 (Fank1), Forkhead box E1 (thyroid transcription factor 2)
(Foxe1), Hairy/enhancer-of-split related with YRPW motif 2 (Hey2),
Forkhead box E1 (thyroid transcription factor 2) (Foxe1),
Hairy/enhancer-of-split related with YRPW motif 2 (Hey2), Lymphoid
enhancer-binding factor 1 (Lef1), Sal-like 3 (Drosophila) (Sall3),
SATB homeobox 1 (Satb1), miR-632, or a combination thereof; [0408]
ii) the expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more of the
rat ES cell-specific genes comprising Adherens Junctions Associate
Protein 1 (Ajap1), Claudin 5 (Cldn5), Cdc42 guanine nucleotide
exchange factor 9 (Arhgef9), Calcium/calmodulin-dependent protein
kinase IV (Camk4), ephrin-A1 (Efna1), EPH receptor A4 (Epha4), gap
junction protein beta 5 (Gjb5), Insulin-like growth factor binding
protein-like 1 (Igfbpl1), Interleukin 36 beta (Il1f8), Interleukin
28 receptor, alpha (1128ra), left-right determination factor 1
(Lefty1), Leukemia inhibitory factor receptor alpha (Lifr),
Lysophosphatidic acid receptor 2 (Lpar2), Neuronal pentraxin
receptor (Ntm), Protein tyrosine phosphatase non-receptor type 18
(Ptpn18), Caudal type homeobox 2 (Cdx2), Fibronectin type III and
ankyrin repeat domains 1 (Fank1), Forkhead box E1 (thyroid
transcription factor 2) (Foxe1), Hairy/enhancer-of-split related
with YRPW motif 2 (Hey2), Forkhead box E1 (thyroid transcription
factor 2) (Foxe1), Hairy/enhancer-of-split related with YRPW motif
2 (Hey2), Lymphoid enhancer-binding factor 1 (Lef1), Sal-like 3
(Drosophila) (Sall3), SATB homeobox 1 (Satb1), miR-632, or a
combination thereof; [0409] iii) at least a 20-fold increase in the
expression of one or more of the rat ES cell-specific genes as set
forth in Table 14 when compared to a F1H4 mouse ES cell; [0410] iv)
at least a 20-fold increase in the expression of at least 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25 or more of the rat ES cell-specific genes as set forth
in Table 14 when compared to a F1H4 mouse ES cell; [0411] v) the
expression of one or more of rat ES cell-specific genes as set
forth in Table 13; [0412] vi) the expression of at least 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 30, 35, 40, 45, 50 or more of the rat ES cell-specific
genes as set forth in Table 13; [0413] vii) at least a 20-fold
increase in the expression of one or more of the rat ES
cell-specific genes as set forth in Table 13 when compared to a
F1H4 mouse ES cell; [0414] viii) at least a 20-fold increase in the
expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or
more of the rat ES cell-specific genes as set forth in Table 13
when compared to a F1H4 mouse ES cell; [0415] ix) at least a
20-fold decrease in the expression of one or more of the rat ES
cell-specific genes as set forth in Table 12 when compared to a
F1H4 mouse ES cell; and/or [0416] x) at least a 20-fold decrease in
the expression of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50
or more of the rat ES cell-specific genes as set forth in Table 12
when compared to a F1H4 mouse ES cell; [0417] xi) any combination
of expression of the rat ES cell-specific genes of parts (i)-(x);
[0418] xii) a relative expression level of pluripotency markers as
shown in Table 15 for at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17 or 18 of the listed pluripotency markers. See,
pluripotency ranking column of Table 15 for relative expression
levels; [0419] xiii) a relative expression level of the mesodermal
markers as shown in Table 15 for at least 2, 3, or 4 of the listed
mesodermal markers. See, mesodermal ranking column in Table 15 for
relative expression levels; [0420] xiv) a relative expression level
of endodermal markers as shown in Table 15 for at least 2, 3, 4, 5,
or 6 of the listed endodermal markers. See, endodermal ranking
column in Table 15 for relative expression levels; [0421] xv) a
relative expression level of neural markers as shown in Table 15
for at least 2 and 3 of the listed neural markers. See, neural
ranking column in table 15 for relative expression levels; [0422]
xvi) a relative expression level of trophectoderm markers as shown
in Table 15 for the listed trophectoderm markers. See,
trophectoderm ranking column in table 15 for relative expression
levels; [0423] xvii) any relative expression level of one or more
(2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30) of the pluripotency
markers, mesodermal markers, endodermal markers, neural markers
and/or trophectoderm markers set forth in Table 15; [0424] xviii)
the relative expression level of each of the markers set forth in
table 15; [0425] xix) any combination of the signatures set forth
in xii-xiix; and/or [0426] xx) any combination of the signature set
forth in i-xiix.
[0427] (i) have the ability to produce a F0 rat;
[0428] (j) capable of being subcultured and maintaining the
undifferentiated state;
[0429] (k) having the same number of chromosomes a normal rat
cell;
[0430] (l) maintain pluripotency in vitro without requiring
paracrine LIF signaling; and/or
[0431] (m) have self renewal, meaning they divide indefinitely
while maintaining pluripotency.
[0432] iii. Expression Cassettes
[0433] The terms "polynucleotide," "polynucleotide sequence,"
"nucleic acid sequence," and "nucleic acid fragment" are used
interchangeably herein. These terms encompass nucleotide sequences
and the like. A polynucleotide may be a polymer of RNA or DNA that
is single- or double-stranded, that optionally contains synthetic,
non-natural or altered nucleotide bases. A polynucleotide in the
form of a polymer of DNA may be comprised of one or more segments
of cDNA, genomic DNA, synthetic DNA, or mixtures thereof.
Polynucleotides can comprise deoxyribonucleotides and
ribonucleotides include both naturally occurring molecules and
synthetic analogues, and any combination these. The polynucleotides
provided herein also encompass all forms of sequences including,
but not limited to, single-stranded forms, double-stranded forms,
hairpins, stem-and-loop structures, and the like.
[0434] Further provided are recombinant polynucleotides. The terms
"recombinant polynucleotide" and "recombinant DNA construct" are
used interchangeably herein. A recombinant construct comprises an
artificial or heterologous combination of nucleic acid sequences,
e.g., regulatory and coding sequences that are not found together
in nature. In other embodiments, a recombinant construct may
comprise regulatory sequences and coding sequences that are derived
from different sources, or regulatory sequences and coding
sequences derived from the same source, but arranged in a manner
different than that found in nature. Such a construct may be used
by itself or may be used in conjunction with a vector. If a vector
is used, then the choice of vector is dependent upon the method
that is used to transform the host cells as is well known to those
skilled in the art. For example, a plasmid vector can be used.
Genetic elements required to successfully transform, select and
propagate host cells and comprising any of the isolated nucleic
acid fragments provided herein. Screening may be accomplished by
Southern analysis of DNA, Northern analysis of mRNA expression,
immunoblotting analysis of protein expression, or phenotypic
analysis, among others.
[0435] In specific embodiments, one or more of the components
described herein can be provided in an expression cassette for
expression in a rat cell. The cassette can include 5' and 3'
regulatory sequences operably linked to a polynucleotide provided
herein. "Operably linked" means a functional linkage between two or
more elements. For example, an operable linkage between a
polynucleotide of interest and a regulatory sequence (i.e., a
promoter) is a functional link that allows for expression of the
polynucleotide of interest. Operably linked elements may be
contiguous or non-contiguous. When used to refer to the joining of
two protein coding regions, operably linked means that the coding
regions are in the same reading frame. In another instance, a
nucleic acid sequence encoding a protein may be operably linked to
regulatory sequences (e.g., promoter, enhancer, silencer sequence,
etc.) so as to retain proper transcriptional regulation. The
cassette may additionally contain at least one additional
polynucleotide of interest to be co-introduced into the rat ES
cell. Alternatively, the additional polynucleotide of interest can
be provided on multiple expression cassettes. Such an expression
cassette is provided with a plurality of restriction sites and/or
recombination sites for insertion of a recombinant polynucleotide
to be under the transcriptional regulation of the regulatory
regions. The expression cassette may additionally contain selection
marker genes.
[0436] The expression cassette can include in the 5'-3' direction
of transcription, a transcriptional and translational initiation
region (i.e., a promoter), a recombinant polynucleotide provided
herein, and a transcriptional and translational termination region
(i.e., termination region) functional in mammalian cell or a host
cell of interest. The regulatory regions (i.e., promoters,
transcriptional regulatory regions, and translational termination
regions) and/or a polynucleotide provided herein may be
native/analogous to the host cell or to each other. Alternatively,
the regulatory regions and/or a polynucleotide provided herein may
be heterologous to the host cell or to each other. For example, a
promoter operably linked to a heterologous polynucleotide is from a
species different from the species from which the polynucleotide
was derived, or, if from the same/analogous species, one or both
are substantially modified from their original form and/or genomic
locus, or the promoter is not the native promoter for the operably
linked polynucleotide. Alternatively, the regulatory regions and/or
a recombinant polynucleotide provided herein may be entirely
synthetic.
[0437] The termination region may be native with the
transcriptional initiation region, may be native with the operably
linked recombinant polynucleotide, may be native with the host
cell, or may be derived from another source (i.e., foreign or
heterologous) to the promoter, the recombinant polynucleotide, the
host cell, or any combination thereof.
[0438] In preparing the expression cassette, the various DNA
fragments may be manipulated, so as to provide for the DNA
sequences in the proper orientation. Toward this end, adapters or
linkers may be employed to join the DNA fragments or other
manipulations may be involved to provide for convenient restriction
sites, removal of superfluous DNA, removal of restriction sites, or
the like. For this purpose, in vitro mutagenesis, primer repair,
restriction, annealing, resubstitutions, e.g., transitions and
transversions, may be involved.
[0439] A number of promoters can be used in the expression
cassettes provided herein. The promoters can be selected based on
the desired outcome. It is recognized that different applications
can be enhanced by the use of different promoters in the expression
cassettes to modulate the timing, location and/or level of
expression of the polynucleotide of interest. Such expression
constructs may also contain, if desired, a promoter regulatory
region (e.g., one conferring inducible, constitutive,
environmentally- or developmentally-regulated, or cell- or
tissue-specific/selective expression), a transcription initiation
start site, a ribosome binding site, an RNA processing signal, a
transcription termination site, and/or a polyadenylation
signal.
[0440] iv. Generating F0 Rat Embryos and F1 Progeny Having the
Targeted Genetic Modification
[0441] The various methods and compositions provided herein can be
used to generate a genetically modified rat. Such methods generally
comprise (a) introducing into the genome of an isolated rat ES cell
disclosed herein a targeted genetic modification to form a rat ES
cell having a genetic modification; (b) implanting at least one of
the genetically modified rat ES cells having the genetic
modification into a rat host embryo to produce a F0 embryo; (c)
implanting the F0 embryo into a surrogate mother; (d) gestating the
F0 embryo in the surrogate mother to term; and, (e) identifying a
F0 rat having the genetic modification.
[0442] The genetically modified rat ES cells having the genetic
modification can be implanted into a rat host embryo that is from
the same rat strain or from a different rat strain. For example, a
genetically modified DA rat ES cell can be implanted into a DA rat
host embryo or it can be implanted into an SD host embryo, ACI host
embryo or other heterologous rat host embryo. Similarly, a
genetically modified ACI rat ES cell can be introduced into an ACI
rat host embryo or it can be introduced into an SD host embryo, DA
host embryo or other heterologous rat host embryo. Likewise, the
surrogate mother can be from the same rat strain as the genetically
modified rat cell and/or the rat host embryo or the surrogate
mother can be from a different rat strain as the genetically
modified rat cell and/or the rat host embryo. In one non-limiting
embodiment, the genetically modified rat cell is from a DA strain,
the host rat embryo is from an SD host embryo and the surrogate
mother is from a DA strain. In another non-limiting embodiment, the
genetically modified rat cell is from an ACI strain, the host rat
embryo is from an SD strain, and the surrogate mother is from a DA
strain.
[0443] In still further embodiments, the chimeric rat (F0) can be
breed to produce an F1 progeny that is heterozygous for the
targeted genetic modification. In addition, the male rat of the F1
progeny can be breed with a female rat of the F1 progeny to obtain
an F2 progeny that is homozygous for the genetic modification.
[0444] The methods and compositions provided herein allow for at
least 1%, 3%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,
60%, 65%, 70%, 75% or greater of the F0 F0 rats having the genetic
modification to transmit the genetic modification to the F1
progeny. In some embodiments, the rat ES cells having the targeted
genetic modification are introduced into a pre-morula stage embryo
from a corresponding organism, e.g., an 8-cell stage mouse embryo.
See, e.g., U.S. Pat. No. 7,576,259, U.S. Pat. No. 7,659,442, U.S.
Pat. No. 7,294,754, and US 2008-0078000 A1, all of which are
incorporated by reference herein in their entireties. In other
embodiments, the For, the donor rat ES cells may be implanted at 4
cell stage, 8 cell stage of the host embryo.
[0445] The rat embryos comprising the genetically modified rat ES
cells is incubated until the blastocyst stage and then implanted
into a surrogate mother to produce an F0. Rats bearing the
genetically modified genomic locus can be identified via
modification of allele (MOA) assay as described herein. The
resulting F0 generation derived from the genetically modified rat
ES cells is crossed to a wild-type rat to obtain F1 generation
offspring. Following genotyping with specific primers and/or
probes, F1 rats that are heterozygous for the genetically modified
genomic locus are crossed to each other to produce a rat that is
homozygous for the genetically modified genomic locus.
[0446] Further provided is a F0 rat embryo comprising an inner cell
mass having at least one heterologous stem cell comprising any one
of the rat ES cells provided herein. In other embodiments, progeny
of a rat F0 embryo are provided wherein at least 50%, 60%, 70% or
more of the F0 progeny are derived from a genetically modified rat
ES cell of as disclosed herein.
[0447] In one aspect, a method for making a rat ES cell is
provided, comprising deriving from a morula-stage rat embryo, a
blastocyst-stage rat embryo, or a rat embryo at a developmental
stage between a morula-stage embryo and a blastocyst-stage embryo a
rat cell, and culturing the rat cell from the rat embryo under
conditions sufficient to maintain pluripotency and/or totipotency.
In on embodiment, the conditions sufficient to maintain
pluripotency and/or totipotency include 2i media.
[0448] In one aspect, a method for making a genetically modified
rat is provided, comprising a step of modifying a rat ES cell
genome with a nucleic acid sequence of interest to form a modified
rat ES cell, and employing the modified rat ES cell as a donor rat
ES cell, combining the rat donor ES cell with a rat host embryo,
culturing the donor ES cell and rat host embryo, and employing the
cultured host embryo to make a genetically modified rat.
[0449] In one aspect, a method for making genetically modified rat
F1 progeny is provided, comprising a step of modifying a rat ES
cell genome with a nucleic acid sequence of interest to form a
modified rat ES cell, and employing the modified rat ES cell as a
donor rat ES cell, combining the rat donor ES cell with a rat host
embryo, culturing the donor ES cell and rat host embryo, and
employing the cultured host embryo to make a genetically modified
rat, wherein the progeny are about 3%, about 10% or more, or about
63% or more derived from the genetically modified donor rat ES
cell.
[0450] In one embodiment, the cultured host embryo is implanted
into a surrogate rat mother, and the cultured host embryo is
gestated in the surrogate mother.
[0451] In one aspect, a method of transmitting a genetic
modification from a rat pluripotent cell to a rat progeny with high
frequency is provided, comprising genetically modifying a
pluripotent rat cell with a nucleic acid sequence of interest on a
bacterial artificial chromosome to form a genetically modified rat
pluripotent cell, and employing the genetically modified rat
pluripotent cell with a rat host embryo in a rat surrogate mother
to generate a progeny comprising the genetic modification and,
optionally, breeding the progeny.
[0452] In one aspect, a method for making a rat ES cell is
provided, wherein the method comprises culturing a frozen 8-cell
stage embryo to a blastocyst stage, and deriving from the cultured
blastocyst a rat cell, and culturing the rat cell under conditions
sufficient to maintain pluripotency and/or totipotency.
[0453] V. Variants, Fragments and Sequence Identity
[0454] Active variants and fragments of the disclosed LIF
polypeptide, particularly the mouse LIF polypeptide are provided
herein. "Variants" refer to substantially similar sequences. As
used herein, a "variant polypeptide" is intended to mean a
polypeptide derived from the native protein by deletion (so-called
truncation) of one or more amino acids at the N-terminal and/or
C-terminal end of the native protein; deletion and/or addition of
one or more amino acids at one or more internal sites in the native
protein; or substitution of one or more amino acids at one or more
sites in the native protein. Variant polypeptides continue to
possess the desired biological activity of the native polypeptide,
that is, they inhibit the differentiation of rat and/or mouse
embryonic stem cells and contribute to stem cell self-renewal. A
variant of a polypeptide or disclosed herein (i.e. SEQ ID NOS: 1 or
SwissProt Accession No. P09056) will typically have at least about
65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,
98%, 99% or more sequence identity with the reference sequence.
[0455] The term "fragment" refers to a portion of an amino acid
comprising a specified number of contiguous amino acid. In
particular embodiments, a fragment of a polypeptide disclosed
herein may retain the biological activity of the full-length
polypeptide and hence inhibit the differentiation of rat and/or
mouse embryonic stem cells and contribute to stem cell
self-renewal. Fragments of a polypeptide sequence disclosed herein
(i.e. SEQ ID NOS: 1 or SwissProt Accession No. P09056) may comprise
at least 10, 15, 25, 30, 50, 60, 70, 80, 90, 100, 110, 120, 130,
140, 150, 160, 170, 180, 190, 200, contiguous amino acids, or up to
the total number of amino acids present in a full-length
protein.
[0456] As used herein, "sequence identity" or "identity" in the
context of two polynucleotides or polypeptide sequences makes
reference to the residues in the two sequences that are the same
when aligned for maximum correspondence over a specified comparison
window. When percentage of sequence identity is used in reference
to proteins it is recognized that residue positions which are not
identical often differ by conservative amino acid substitutions,
where amino acid residues are substituted for other amino acid
residues with similar chemical properties (e.g., charge or
hydrophobicity) and therefore do not change the functional
properties of the molecule. When sequences differ in conservative
substitutions, the percent sequence identity may be adjusted
upwards to correct for the conservative nature of the substitution.
Sequences that differ by such conservative substitutions are said
to have "sequence similarity" or "similarity". Means for making
this adjustment are well known to those of skill in the art.
Typically this involves scoring a conservative substitution as a
partial rather than a full mismatch, thereby increasing the
percentage sequence identity. Thus, for example, where an identical
amino acid is given a score of 1 and a non-conservative
substitution is given a score of zero, a conservative substitution
is given a score between zero and 1. The scoring of conservative
substitutions is calculated, e.g., as implemented in the program
PC/GENE (Intelligenetics, Mountain View, Calif.).
[0457] As used herein, "percentage of sequence identity" means the
value determined by comparing two optimally aligned sequences over
a comparison window, wherein the portion of the polynucleotide
sequence in the comparison window may comprise additions or
deletions (i.e., gaps) as compared to the reference sequence (which
does not comprise additions or deletions) for optimal alignment of
the two sequences. The percentage is calculated by determining the
number of positions at which the identical nucleic acid base or
amino acid residue occurs in both sequences to yield the number of
matched positions, dividing the number of matched positions by the
total number of positions in the window of comparison, and
multiplying the result by 100 to yield the percentage of sequence
identity.
[0458] Unless otherwise stated, sequence identity/similarity values
provided herein refer to the value obtained using GAP Version 10
using the following parameters: % identity and % similarity for a
nucleotide sequence using GAP Weight of 50 and Length Weight of 3,
and the nwsgapdna.cmp scoring matrix; % identity and % similarity
for an amino acid sequence using GAP Weight of 8 and Length Weight
of 2, and the BLOSUM62 scoring matrix; or any equivalent program
thereof. "Equivalent program" means any sequence comparison program
that, for any two sequences in question, generates an alignment
having identical nucleotide or amino acid residue matches and an
identical percent sequence identity when compared to the
corresponding alignment generated by GAP Version 10.
[0459] The following examples are offered by way of illustration
and not by way of limitation.
EXAMPLES
Example 1
Rat ES Cell Derivation
[0460] rESC Characterization. As shown in FIG. 1, rESC grow as
compact spherical colonies which routinely detach and float in the
dish (close-up, FIG. 4). B, C, F, G: rESC express pluripotency
markers including Oct-4 (FIG. 2A) and Sox2 (FIG. 2B), and express
high levels of alkaline phosphatase (FIG. 3, left panel). Karyotype
for line DA.2B is 42X,Y (FIG. 4, right panel). rESC often become
tetraploid; thus, lines were pre-screened by counting metaphase
chromosome spreads; lines with mostly normal counts were then
formally karyotyped. ACI blastocysts were collected from
super-ovulated females obtained commercially; DA blasts were
cultured from frozen 8-cell embryos obtained commercially. Zona
pellucidae were removed with Acid Tyrodes and blasts were plated
onto mitotically inactivated MEFs. Outgrowths were picked and
expanded using standard methods. All blasts were plated, cultured
and expanded using 2i media (Li et al. (2008) Germline competent
embryonic stem cells derived from rat blastocysts, Cell
135:1299-1310; incorporated herein by reference).
TABLE-US-00003 TABLE 3 Rat ES Cell Derivation ACI DA Embryo source
Blastocysts Frozen 8-cell embryos (Superovulation) cultured to
blastocyst Blastocysts plated: 107 22 Outgrowths: 32 (30% of
blasts) 10 (45% of blasts) Lines: 16 (50% of 9 (90% of outgrowths)
outgrowths) Karyotyped: 3; all 42X, Y 6: 3 42X, X 3 42X, Y GLT
validated: 1 (ACI.G1) 1 42X, X (DA.2C) 1 42X, Y (DA.2B)
Example 2
Rat Production
[0461] Chimeric rats were produced by blastocyst injection and
transmission of the rESC genome through the germline. Chimeras
produced by blastocyst microinjection using parental ACI.G1 rESC
are shown in FIG. 5. F1 agouti pups with albino littermates, sired
by the ACI/SD chimera labeled with an asterisk (*) in FIG. 5 are
shown in FIG. 6.
[0462] Germline transmission of parental rESC. Three euploid rESC
lines were evaluated for pluripotency by microinjection into albino
SD blastocysts. Chimeras were identified by agouti coat color
indicating rESC contribution. For each line, a majority of chimeras
transmitted the rESC genome to F1 offspring (Table 4).
TABLE-US-00004 TABLE 4 Germline Transmission of Parental rESC Total
pups rESC- GLT Chimeras Germline from GLT derived efficiency Line
bred transmitters chimeras pups (%) ACI.G1 5 3 (60%) 103 11 11
DA.2B 5 4 (80%) 129 11 9 DA.2C 3 2 (66%) 45 7 16 (XX)
Example 3
rESC Targeting: The Rat Rosa 26 Locus
[0463] The rRosa26 locus lies between the Setd5 and Thumpd3 genes
as in mouse, with the same spacing. The rRosa 26 locus (FIG. 7,
Panel B) differs from the mRosa 26 locus (FIG. 7, Panel A). The
mRosa26 transcripts consist of 2 or 3 exons. The rat locus contains
a 2nd exon 1 (Ex1b) in addition to the homologous exon to mouse
exon1 (Ex1a). No 3rd exon has been identified in rat. Targeting of
a rRosa26 allele is depicted in FIG. 7 (bottom), where homology
arms of 5 kb each were cloned by PCR using genomic DNA from DA
rESC. The targeted allele contains a SA-lacZ-hUb-neo cassette
replacing a 117 bp deletion in the rRosa26 intron.
[0464] Targeting efficiency at the rRosa 26 locus was determined
(Table 5). Linearized vector was electroporated into DA or ACI
rESC, and transfected colonies were cultured in 2i media+G418,
using standard techniques. Individual colonies were picked and
screened using a Loss of Allele (LOA) assay (Valenzuela, D. et al.
(2003) High-throughput engineering of the mouse genome coupled with
high-resolution expression analysis, Nature Biotech. 21:652-660,
incorporated herein by reference).
TABLE-US-00005 TABLE 5 rRosa26 Targeting Efficiency Colonies
Reconfirmed Targeting efficiency Cell line picked positives (%)
DA.2B 192 4 2.1 ACI.G1 96 4 4.2
[0465] Chimera production and germline transmission using targeted
Rosa26 rESC. Reconfirmed targeted rRosa26 clones were microinjected
into SD blastocysts, which were then transferred to pseudopregnant
DS recipient females, using standard techniques. Chimeras were
identified by coat color; male F0 chimeras were bred to SD females.
Germline (agouti) F1 pups were genotyped for the presence of the
targeted Rosa26 allele; nine of 22 agouti pups genotyped as
heterozygous at the Rosa26 locus (Table 6).
TABLE-US-00006 TABLE 6 Germline Transmission Using Targeted Rosa26
rESC ESC- R26 Clones Germline rESC- derived Cell clones producing
Transmitting Total derived pups line injected Chimeras Clones Pups
Pups (%) DA.2B 4 3 2 AH7: AH7: AH7: 64 41 63 AE3: AE3: 6 AE3: 3 112
ACI.G1 4 4 1 DE9: 39 DE9: 4 10
Example 3
Derivation of Rat Embryonic Stem Cells
Superovulation Protocol, Rats
[0466] Day 0: injected with pregnant mare serum: IP, 20 U (0.4 ml).
Day 1: no action Day 2: (46 hr. later): injected with hCG, IP, 50 U
(1 ml). [0467] set up single female matings. Day 3: checked plugs.
Females were plugged. This is day 0.5. Day 6 (e3.5): Euthanized
females and flushed embryos.
ES Cell Derivation Protocol (Superovulation)
Day 0:
[0467] [0468] 1) Euthanized female rat with CO.sub.2. [0469] 2)
Swabbed ventral abdomen with 70% ethanol; using scissors, opened
the ventral body wall to expose the viscera. [0470] 3) Dissected
out the oviducts and uterine horns and placed them into a tissue
culture dish containing warm N2B27 media. Washed out as much blood
as possible and transferred to a new dish with N2B27. [0471] 4)
Using a 1 ml syringe and a blunt 27 g needle, flushed media through
the uterine horns and oviducts to eject blastocysts into the media.
[0472] 5) Collected the blastocysts with a mouth pipet and transfer
to embryo culture dish containing KSOM+2i (1 .mu.MPD0325901, 3
.mu.M CHIR99021). KSOM is a culture medium produced by Millipore.
Catalog number is MR-106-D. [0473] 6) Cultured overnight at
37.degree.; 7.5% CO.sub.2.
ES Cell Derivation Protocol (Frozen Embryos)
Day 0:
[0473] [0474] 1) Thawed frozen 8-cell embryos (commercially
obtained) into M2 medium. Cultured 10 minutes at room temperature.
[0475] 2) Transferred to KSOM+2i and culture overnight.
ES Cell Derivation Protocol (Same for Both)
Day 1:
[0475] [0476] 1) Transferred cavitated embryos to 2i medium &
culture overnight. [0477] 2) Continued culturing un-cavitated
embryos in KSOM+2i
Day 2:
[0477] [0478] 1) Transferred all remaining embryos to 2i medium
(whether or not they've cavitated). [0479] 2) Cultured overnight;
continued culturing earlier embryos in 2i medium.
Day 3:
[0479] [0480] 1) Transferred embryos for 30-60 seconds with Acid
Tyrodes to remove the zona pellucida. [0481] 2) Washed embryos
3.times. in 2i medium to remove Acid Tyrodes. [0482] 3) Deposited
each embryo into a separate well of a 96-well feeder plate (the
well contains a monolayer of mitotically inactivated mouse
embryonic fibroblasts (MEFs). [0483] 4) Cultured overnight in 2i
medium.
Day 4-5:
[0483] [0484] 1) Monitored plated embryos for the presence of an
outgrowth (an amorphous undifferentiated mass of cells). Outgrowths
are ready for transfer when they are approximately twice the size
of the plated embryo. [0485] 2) Each day: remove spent media with a
mircropipet and replace with fresh 2i media. [0486] 3) Transferred
outgrowths to new feeder wells: [0487] a. Removed spent media and
gently wash well with PBS. [0488] b. Removed PBS and add 30 .mu.l
0.05% trypsin; incubate for 10 minutes. [0489] c. Stopped trypsin
reaction by adding 30 .mu.l 2i+10% FBS. [0490] d. Gently
dissociated the cells with a micropipettor and transferred entire
contents of the well to a new well in a 24-well feeder plate. This
was Passage 1 (P1). [0491] e. Cultured overnight in 2i medium. Day
5-8: (timing depends on how fast each line expands) [0492] 1)
Changed media each day (2i media) and monitored for the presence of
colonies with an ESC morphology. [0493] 2) When colonies appear,
continued culturing until colonies expand to .about.50% confluency.
[0494] 3) Tryspinzed and passaged colonies as before; plated on
feeders, 1 well per line, in a 6-well dish. This was Passage 2
(P2).
Ongoing:
[0494] [0495] 1) Continued feeding and monitoring each line until
approximately 50% confluent. [0496] 2) Trypsinized cells as usual.
[0497] 3) stopped trypsin with 2i+10% FBS; pelleted the cells by
centrifugation (5', 1200 rpm in Beckman-Coulter tabletop
centrifuge). [0498] 4) Aspirated the supernatant and gently
resuspend the cells in 400 .mu.l Freezing Medium (70% 2i, 20% FBS,
10% DMSO). [0499] 5) Distributed the cells into 2 vials and freeze
at -80.degree.. This was Passage 3 (P3). [0500] 6) For long-term
storage, transferred the vials to liquid N2 storage. The 2i media
was prepared as follows in Table 7.
TABLE-US-00007 [0500] Reagent Vendor Concentration DMEM/F12 basal
media Invitrogen/Life Technologies 1x Neurobasal media
Invitrogen/Life Technologies 1x Penicillin/streptomycin
Invitrogen/Life Technologies 1% L-Glutamine Invitrogen/Life
Technologies 4 mM 2-Mercaptoethanol Invitrogen/Life Technologies
0.1 mM N2 supplement Invitrogen/Life Technologies 1x B27 supplement
Invitrogen/Life Technologies 1x LIF Millipore 100 U/ml PD0325901
(MEK inhibitor). Stemgent 1 uM CHIR99021 (GSK inhibitor). Stemgent
3 uM
Materials:
[0501] Pregnant Mare's Serum Gonadotropin (PMSG) [0502] Human
Pregnancy Urine Chorionic Gonadotropin (HCG) [0503] Female Rats
(5-12 weeks old) [0504] Male rats (12 wks. to 8 mos. old), one per
cage [0505] Syringes/needles [0506] Animal room with lights on
6:00-18:00
Procedure:
[0507] Day 1: 8:00-10:00 AM [0508] Inject females with 20 IU PMSG
(0.4 ml), IP [0509] Discard unused PMSG.
[0510] Day 3: 8:00-10:00 AM (48 hours after PMSG injection) [0511]
Inject females with 50 IU HCG (1 ml), IP [0512] Place one female
per male in mating cage. [0513] Discard unused HCG.
[0514] Day 4: 8:00-10:00 AM (24 hrs. after HCG injection) [0515]
Check females for plugs.
Hormone Suppliers
[0516] PMSG: Sigma #G-4877 (1000 IU). Resuspend in PBS to a final H
of 50 IU/ml. Store at -20.degree. in 1 ml aliquots.
[0517] HCG: Sigma #CG-5 (5000 IU). Resuspend in PBS to a final H of
50 IU/ml. Store at -20.degree. in 1 ml aliquots.
Example 4
Karyotyping of Rat Embryonic Stem Cell Lines
[0518] The rat ES cell line generated herein were karyotyped, and
the results are summarized in Tables 8-11.
TABLE-US-00008 TABLE 8 ACI.G1 Karyotyping Results Number of cells
Number of cells karyotyped 7 Number of cells analyzed 20 Number of
42, XY cells 18 Number of abnormal cells 2 40, XY, -5, -9 1 41, XY,
-14 1 42, XY 18 Other notes: Two analyzed cells were missing
different autosomes, which may be a sporadic occurrence due to
technical artifact. 90% of analyzed cells had a normal male 42, XY
karyotype. FIG. 9 provides a photograph showing the analysis of the
chromosome number of the ACI.G1 rat ES cell line.
TABLE-US-00009 TABLE 9 DA.2B Karyotyping Results Number of cells
Number of cells karyotyped 6 Number of cells analyzed 20 Number of
42, XY cells 20 Number of abnormal cells 0 42, XY 20 Other notes:
All analyzed cells had a normal diploid 42, XY karyotype. FIG. 10
provides a photograph showing the analysis of the chromosome number
of the DA.2B rat ES cell line.
TABLE-US-00010 TABLE 10 DA.C2 Karyotyping Results Number of cells
Number of cells karyotyped 5 Number of cells analyzed 20 Number of
42, XY cells 20 Number of abnormal cells 0 42, XX Other notes: 100%
of analyzed cells had normal female XX rat karyotype. FIG. 11
provides a photograph showing the analysis of the chromosome number
of the DA.C2 rat ES cell line.
TABLE-US-00011 TABLE 11 Blastocysts Lines Lines Strain plated
established Karyotyped Karyotypes BN .times. SD 41 8 (20%) 5 all
lines were high % F1 complex polyploid ACI 27 16 (60%) 3 G1: 90% 42
XY; others were 70-85% euploid DA 20 9 (45%) 6 2B: 100% 42 XY; 2C:
100% 42 XX; others were 95-100% euploid F344 4 1 (25%) 0 Totals 92
34 (37%)
Example 5
Electroporation of Vector into Rat Embryonic Stem Cell
[0519] 1. Passaged rat ES cells 24-48 hrs prior to
electroporation.
[0520] 2. Changed media to RVG2i+ROCKi (10 .mu.M Y-27632) 24 hr.
prior to electroporation
[0521] 3. Changed media 30' prior to trypsinization.
[0522] 4. Aliquoted DNA to be electroporated.
[0523] 5. Allowed DNA to warm at RT for >10 min.
[0524] 6. Heated DNA for 5' @ 62.degree. C. Place DNA on ice.
[0525] 7. Trypsinized cells: [0526] a. Collected floating colonies.
Washed plate to collect as many floaters as possible. [0527] b.
Pelleted colonies: 3' @ 750 rpm. [0528] c. Washed pellet 1.times.
with 5-10 ml PBS and re-spin/pellet [0529] d. Aspirated
supernatant; add 500.lamda. trypsin, 0.05%+1% chicken serum. [0530]
i. Did not pool more than 1 10 cm plate of colonies per tube. If
there are too many colonies packed into the bottom of the tube
during trypsinization they will clump and most of the cells will be
lost. [0531] e. 4' @ 37.degree.. Pipeted colonies several times to
minimize clumping. [0532] f. Repeated steps 1-2 X: 4' @ 37.degree..
[0533] g. Stopped trypsin with 500.lamda. RVG2i+10% FBS.
[0534] 8. Pelleted cells: 5' @ 1200 rpm.
[0535] 9. Resuspend cells in 10 ml PBS. Count two 20.lamda.
aliquots to determine total cell number.
[0536] 10. Pelleted cells (5'/1200 rpm); calculate total cell
number and total resuspension volume to achieve correct cell
concentration (target #/75 .mu.l EP buffer).
[0537] 11. Resuspend in a minimal volume of EP buffer; measure
total volume and adjust to target volume with EP buffer.
Electroporation buffer is sold by Millipore. The catalog # is
ES-003-D. See, Valenzuela et al. (2003) Nature Biotechnology
21:652-659, which is herein incorporated by reference.
[0538] 12. Add 75.lamda. cells to 50.times.DNA; transfer the
125.lamda. cells/DNA solution to one well of a BTX 48-well cuvette.
[0539] a. Filled the empty wells in the same column with 125.lamda.
EP buffer.
[0540] 13. Pulsed the cuvette once in the BTX electroporator:
[0541] a. Settings: 400V; .OMEGA.; 100 .mu.F (settings may
vary)
[0542] 14. Placed cuvette on ice for 15' to recover.
[0543] 15. Removed cells into 5 ml RVG2i+10 .mu.M ROCKi.
[0544] 16. Added to 15 cm plate with 20 ml RVG2i+10 .mu.M ROCKi.
Plate has 2.times.neoR MEFs (or other MEFs depending on project).
The neoR selectable marker is the neomycin phosphotransferase (neo)
gene of Beck et al. (1982) Gene, 19:327-36 or in U.S. Pat. No.
7,205,148 or 6,596,541, each of which are herein incorporated by
reference.
[0545] 17. Incubated @ 37.degree.. Begin selection 48 hrs
later.
[0546] ROCK inhibitor used was Y-27632.
Example 6
Selecting Targeted Genetic Modification in a Rat Embryonic Stem
Cell
[0547] 1. Passaged cells for 24-48 hrs prior to
electroporation.
[0548] 2. Changed media to RVG2i+ROCKi (10 .mu.M Y-27632) 24 hr.
prior to electroporation
[0549] 3. Changed media 30' prior to trypsinization.
[0550] 4. Aliquoted DNA to be electroporated.
[0551] 5. Allowed DNA warm at RT for >10 min.
[0552] 6. Heated DNA for 5' @ 62.degree. C. Place DNA on ice.
[0553] 7. Trypsinized cells: [0554] h. Collected floating colonies.
Washed plate to collect as many floaters as possible. [0555] i.
Pelleted colonies: 3' @ 750 rpm. [0556] j. Washed pellet 1.times.
with 5-10 ml PBS and re-spin/pellet [0557] k. Aspirated
supernatant; add 500.lamda. trypsin, 0.05%+1% chicken serum. [0558]
i. Did not pool more than 1 10 cm plate of colonies per tube. If
there are too many colonies packed into the bottom of the tube
during trypsinization they will clump and most of the cells will be
lost. [0559] l. 4' @ 37.degree.. Pipeted colonies several times to
minimize clumping [0560] m. Repeated 1-2 X: 4' @ 37.degree.. [0561]
n. Stopped trypsin with 500.lamda. RVG2i+10% FBS.
[0562] 8. Pelleted cells: 5' @ 1200 rpm.
[0563] 9. Resuspended cells in 10 ml PBS. Count two 20.lamda.
aliquots to determine total cell number.
[0564] 10. Pelleted cells (5'/1200 rpm); calculate total cell
number and total resuspension volume to achieve correct cell
concentration (target #175 .mu.l EP buffer).
[0565] 11. Resuspend in a minimal volume of EP buffer; measured
total volume and adjusted to target volume with EP buffer.
[0566] 12. Added 75.lamda. cells to 50.times.DNA; transfer the
125.lamda. cells/DNA solution to one well of a BTX 48-well cuvette.
[0567] a. Filled the empty wells in the same column with 125.lamda.
EP buffer.
[0568] 13. Pulsed the cuvette once in the BTX electroporator:
[0569] a. Settings: 400V; 400V; .OMEGA.; 100 .mu.F (settings may
vary)
[0570] 14. Placed cuvette on ice for 15' to recover.
[0571] 15. Removed cells into 5 ml RVG2i+10 .mu.M ROCKi.
[0572] 16. Added to 15 cm plate with 20 ml RVG2i+10 .mu.M ROCKi.
Plate had 2.times.neoR MEFs (or other MEFs depending on
project).
[0573] 17. Incubated @ 37.degree.. Began selection 48 hrs
later.
[0574] 18. G418 selection protocol was as follows: [0575] a. Day 2
(2.sup.nd day after EP): incubated cells in 2i media+G418, 75
.mu.g/ml. [0576] b. Day 3: incubated cells in 2i media without G418
[0577] c. Day 4: incubated cells in 2i media+G418, 75 .mu.g/ml.
[0578] d. Day 5: incubated cells in 2i media without G418 [0579] e.
Day 6: incubated cells in 2i media+G418, 75 .mu.g/ml. [0580] f. Day
7: incubated cells in 2i media without G418 [0581] g. Day 8:
incubated cells in 2i media+G418, 75 .mu.g/ml. [0582] h. Day 9:
incubated cells in 2i media without G418 [0583] i. Day 10:
incubated cells in 2i media+G418, 75 .mu.g/ml. [0584] j. Day 11:
incubated cells in 2i media without G418 [0585] k. Day 12: picked
colonies to expand for screening. Each colony was dissociated in
0.05% trypsin+1% chicken serum for 10 minutes and then plated into
1 well of a 96-well feeder plate.
[0586] 19. Expanded colonies for 3 days in 2i media.
[0587] 20. Passaged clones 1:1 to new 96-well feeder plates.
[0588] 21. Expanded clones for 3 days in 2i media.
[0589] 22. For each clone, dissociated colonies in trypsin. Froze
2/3 of each clone and store at -80.degree.; plated the remaining
1/3 onto laminin plates (96-well plates coated with 10 .mu.g/ml
laminin).
[0590] 23. When the laminin plates were confluent, passed off to
the screening lab for genotyping of the clones.
Example 7
Molecular Signature of the Rat Embryonic Stem Cells
[0591] The genes listed in Table 13 were expressed at levels
20-fold higher in rat ES cells than the corresponding genes in
mouse ES cells. The genes listed in Table 12 were expressed at
20-fold lower in rat ES cells than the corresponding genes in mouse
ES cells.
[0592] The microarray data in Tables 12 and 13 was generated as
follows. Rat ES cells (ACI.G2 and DA.2B) and mouse ES cells (F1H4)
were cultured in 2i media for 3 passages until confluent. F1H4
cells were cultured on gelatin-coated plates in the absence of
feeders. F1H4 mouse ES cells were derived from 12956/SvEvTac and
C57BL/6NTac heterozygous embryos (see, e.g., U.S. Pat. No.
7,294,754 and Poueymirou, W. T., Auerbach, W., Frendewey, D.,
Hickey, J. F., Escaravage, J. M., Esau, L., Dore, A. T., Stevens,
S., Adams, N. C., Dominguez, M. G., Gale, N. W., Yancopoulos, G.
D., DeChiara, T. M., Valenzuela, D. M. (2007), incorporated by
reference herein in its entirety).
[0593] The following protocol was used for sample prep:
[0594] Materials included TRIzol Reagentp; RNA Lysis Buffer (Zymo
Kit); and 1.5 mL Eppendorf tubes.
[0595] The 1.5 mL Eppendorf tubes were labeled with the Sample ID.
Cells grown on a plate were rinsed in 37C PBS. PBS was removed and
300 ul of Trizol was added. A scraper was used to break the cells
in Trizol. The lysed cells were collected in Trizol in a 1.5 mL
Epperdorf tube. For cells grown on suspension, the cells were
rinsed in 37C PBS. The cells were collected in a 1.5 mL tube, the
cells were spun down, PBS was removed and 300 ul of Trizol was
added. The cells were pipeted up and down to break the cells.
Samples were sorted for FACS with 10.sup.1 to 10.sup.5 cells, the
volume was concentrated to less than 100 uL. 4 volumes of RNA Lysis
buffer was added and mix by pipetting. For sample, 320 uL RNA Lysis
buffer was added to 80 uL sample. Samples were stored at
-20.degree. C.
[0596] RNA-Seq was used to measure the expression level of mouse
and rat genes. Sequencing reads were mapped to mouse and rat
reference genome by Tophat, and RPKM (fragments per kilobase of
exon per million fragments mapped) were calculated for mouse and
rat genes. Homology genes based on gene symbol were selected, and
then used t-test to compare gene's expression level between mouse
and rat.
[0597] miR-632 is in the top 10 highest expressed in rat ESCs but
they were not expressed in mouse ES cells. There is therefore no
comparative data for these genes. Based on the levels of expression
compared to other genes and their known function in the embryonic
development, the expression of miR-632 were used as a marker for
rat ES cells.
TABLE-US-00012 TABLE 12 The genes listed were expressed at levels
20-fold lower in rat ES cells than the corresponding genes in mouse
ES cells. ID Notes Symbol Entrez Gene Name Location Type(s) Drug(s)
Abcb1b Abcb1b ATP-binding Plasma transporter cassette, sub-
Membrane family B (MDR/TAP), member 1B Acta2 ACTA2 actin, alpha 2,
Cytoplasm other smooth muscle, aorta Actg2 ACTG2 actin, gamma 2,
Cytoplasm other smooth muscle, enteric Aebp1 AEBP1 AE binding
protein 1 Nucleus peptidase Angptl2 ANGPTL2 angiopoietin-like 2
Extracellular other Space Ankrd1 ANKRD1 ankyrin repeat Cytoplasm
transcription domain 1 (cardiac regulator muscle) Anxa1 ANXA1
annexin A1 Plasma other hydrocortisone Membrane Anxa6 ANXA6 annexin
A6 Plasma other Membrane Anxa8 ANXA8L2 annexin A8-like 2 Plasma
other (includes Membrane others) Arhgef25 ARHGEF25 Rho guanine
Cytoplasm other nucleotide exchange factor (GEF) 25 Axl AXL AXL
receptor Plasma kinase cabozantinib tyrosine kinase Membrane Basp1
BASP1 brain abundant, Nucleus transcription membrane attached
regulator signal protein 1 Bgn BGN biglycan Extracellular other
Space Bst2 BST2 bone marrow Plasma other stromal cell antigen 2
Membrane Btf3 BTF3 basic transcription Nucleus transcription factor
3 regulator Btg2 BTG2 BTG family, Nucleus transcription member 2
regulator Capsl CAPSL calcyphosine-like Other other Cav1 CAV1
caveolin 1, Plasma transmembrane caveolae protein, Membrane
receptor 22 kDa Ccdc80 CCDC80 coiled-coil domain Nucleus other
containing 80 Ccnd2 CCND2 cyclin D2 Nucleus other Cd248 CD248 CD248
molecule, Plasma other endosialin Membrane Cd44 CD44 CD44 molecule
Plasma enzyme (Indian blood Membrane group) Cd97 CD97 CD97 molecule
Plasma G-protein Membrane coupled receptor Cdc42ep5 CDC42EP5 CDC42
effector Cytoplasm other protein (Rho GTPase binding) 5 Cdh11 CDH11
cadherin 11, type 2, Plasma other OB-cadherin Membrane (osteoblast)
Cdkn2a CDKN2A cyclin-dependent Nucleus transcription kinase
inhibitor 2A regulator Cdo1 CDO1 cysteine Cytoplasm enzyme
dioxygenase type 1 Clip3 CLIP3 CAP-GLY domain Cytoplasm other
containing linker protein 3 Cln5 CLN5 ceroid- Cytoplasm other
lipofuscinosis, neuronal 5 Cnn1 CNN1 calponin 1, basic, Cytoplasm
other smooth muscle Colla1 COL1A1 collagen, type I, Extracellular
other collagenase alpha 1 Space clostridium histolyticum Colla2
COL1A2 collagen, type I, Extracellular other collagenase alpha 2
Space clostridium histolyticum Col3a1 COL3A1 collagen, type III,
Extracellular other collagenase alpha 1 Space clostridium
histolyticum Col5a2 COL5A2 collagen, type V, Extracellular other
collagenase alpha 2 Space clostridium histolyticum Col6a2 COL6A2
collagen, type VI, Extracellular other collagenase alpha 2 Space
clostridium histolyticum Cryab CRYAB crystallin, alpha B Nucleus
other Csf1 CSF1 colony stimulating Extracellular cytokine factor 1
Space (macrophage) Cth CTH cystathionase Cytoplasm enzyme
(cystathionine gamma-lyase) Cthrc1 CTHRC1 collagen triple
Extracellular other helix repeat Space containing 1 Ctsc CTSC
cathepsin C Cytoplasm peptidase Cyr61 CYR61 cysteine-rich,
Extracellular other angiogenic inducer, Space 61 Ddx58 DDX58 DEAD
(Asp-Glu- Cytoplasm enzyme Ala-Asp) box polypeptide 58 Dkk3 DKK3
dickkopf WNT Extracellular cytokine signaling pathway Space
inhibitor 3 Dmc1 DMC1 DNA meiotic Nucleus enzyme recombinase 1
Dpysl3 DPYSL3 dihydropyrimidinase- Cytoplasm enzyme like 3 Dse DSE
dermatan sulfate Cytoplasm enzyme epimerase Dusp1 DUSP1 dual
specificity Nucleus phosphatase phosphatase 1 Dusp27 DUSP27 dual
specificity Other phosphatase phosphatase 27 (putative) Dusp9 DUSP9
dual specificity Nucleus phosphatase phosphatase 9 Ece2 ECE2
endothelin Plasma peptidase converting enzyme 2 Membrane Ecm1 ECM1
extracellular matrix Extracellular transporter protein 1 Space Egr1
EGR1 early growth Nucleus transcription response 1 regulator Emp1
EMP1 epithelial Plasma other membrane protein 1 Membrane Emp3 EMP3
epithelial Plasma other membrane protein 3 Membrane Ephx2 EPHX2
epoxide hydrolase Cytoplasm enzyme 2, cytoplasmic F3 F3 coagulation
factor Plasma transmembrane activated III (thromboplastin, Membrane
receptor recombinant tissue factor) human factor VII Fau FAU
Finkel-Biskis- Cytoplasm other Reilly murine sarcoma virus
(FBR-MuSV) ubiquitously expressed Fbn1 FBN1 fibrillin 1
Extracellular other Space Fbxo15 FBXO15 F-box protein 15 Other
transcription regulator Fhl2 FHL2 four and a half Nucleus
transcription LIM domains 2 regulator Flnc FLNC filamin C, gamma
Cytoplasm other Fos FOS FBJ murine Nucleus transcription
osteosarcoma viral regulator oncogene homolog Fundc2 FUNDC2 FUN14
domain Cytoplasm other containing 2 Gjb3 GJB3 gap junction Plasma
transporter protein, beta 3, Membrane 31 kDa Gpa33 GPA33
glycoprotein A33 Plasma other (transmembrane) Membrane Gpbp111
GPBP1L1 GC-rich promoter Other other binding protein 1- like 1 Gpc3
GPC3 glypican 3 Plasma other Membrane Grb10 GRB10 growth factor
Cytoplasm other receptor-bound protein 10 Gstm1 GSTM5 glutathione
S- Cytoplasm enzyme transferase mu 5 Hap1 HAP1 huntingtin-
Cytoplasm other associated protein 1 Hist1h2bc HIST2H2BE histone
cluster 2, Nucleus other (includes H2be others) Hmga2 HMGA2 high
mobility Nucleus enzyme group AT-hook 2 Hmgn3 Hmgn3 high mobility
Nucleus other group nucleosomal binding domain 3 Hormad1 HORMAD1
HORMA domain Nucleus other containing 1 Hsd17b14 HSD17B14
hydroxysteroid Cytoplasm enzyme (17-beta) dehydrogenase 14 Hspb1
HSPB1 heat shock 27 kDa Cytoplasm other protein 1 Hspb8 HSPB8 heat
shock 22 kDa Cytoplasm kinase protein 8 Htra1 HTRA1 HtrA serine
Extracellular peptidase peptidase 1 Space Ifi204 Ifi204 interferon
activated Nucleus transcription (includes gene 204 regulator
others) Ifi44 IFI44 interferon-induced Cytoplasm other protein 44
Ifit1 IFIT1B interferon-induced Cytoplasm other protein with
tetratricopeptide repeats 1B Ifitm3 IFITM2 interferon induced
Cytoplasm other transmembrane protein 2 Igf2 IGF2 insulin-like
growth Extracellular growth factor 2 Space factor (somatomedin A)
Igfbp7 IGFBP7 insulin-like growth Extracellular transporter factor
binding Space protein 7 Il1rl1 IL1RL1 interleukin 1 Plasma
transmembrane receptor-like 1 Membrane receptor Inhba INHBA
inhibin, beta A Extracellular growth Space factor Inhbb INHBB
inhibin, beta B Extracellular growth Space factor Irf7 IRF7
interferon Nucleus transcription regulatory factor 7 regulator
Isg15 ISG15 ISG15 ubiquitin- Extracellular other like modifier
Space Itga5 ITGA5 integrin, alpha 5 Plasma transmembrane
(fibronectin Membrane receptor receptor, alpha polypeptide) Jun JUN
jun proto-oncogene Nucleus transcription regulator Junb JUNB jun B
proto- Nucleus transcription oncogene regulator Lgals3bp LGALS3BP
lectin, galactoside- Plasma transmembrane binding, soluble, 3
Membrane receptor binding protein Lgals9 LGALS9 lectin,
galactoside- Extracellular other binding, soluble, 9 Space Lmna
LMNA lamin A/C Nucleus other Lox LOX lysyl oxidase Extracellular
enzyme Space Loxl2 LOXL2 lysyl oxidase-like 2 Extracellular enzyme
Space Loxl3 LOXL3 lysyl oxidase-like 3 Extracellular enzyme Space
Lrp1 LRP1 low density Plasma transmembrane lipoprotein Membrane
receptor receptor-related protein 1
Mageb16 MAGEB16 melanoma antigen Other other family B, 16 Mcam MCAM
melanoma cell Plasma other adhesion molecule Membrane Mgp MGP
matrix Gla protein Extracellular other Space Mmp2 MMP2 matrix
Extracellular peptidase marimastat metallopeptidase 2 Space
(gelatinase A, 72 kDa gelatinase, 72 kDa type IV collagenase) Mxra8
MXRA8 matrix-remodelling Other other associated 8 Myl9 MYL9 myosin,
light chain Cytoplasm other 9, regulatory Mylpf MYLPF myosin light
chain, Cytoplasm other phosphorylatable, fast skeletal muscle Nab2
NAB2 NGFI-A binding Nucleus transcription protein 2 (EGR1 regulator
binding protein 2) Ndufb4 NDUFB4 NADH Cytoplasm transporter
dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15 kDa Npm1 NPM1
nucleophosmin Nucleus transcription (nucleolar regulator
phosphoprotein B23, numatrin) Nr0b1 NR0B1 nuclear receptor Nucleus
ligand- subfamily 0, group dependent B, member 1 nuclear receptor
Nr4a1 NR4A1 nuclear receptor Nucleus ligand- subfamily 4, group
dependent A, member 1 nuclear receptor Nrp2 NRP2 neuropilin 2
Plasma kinase Membrane Oas1a OAS1 2'-5'-oligoadenylate Cytoplasm
enzyme synthetase 1, 40/46 kDa Oasl2 Oasl2 2'-5' oligoadenylate
Other enzyme synthetase-like 2 P4ha2 P4HA2 prolyl 4- Cytoplasm
enzyme hydroxylase, alpha polypeptide II Parp3 PARP3 poly
(ADP-ribose) Nucleus enzyme polymerase family, member 3 Pcolce
PCOLCE procollagen C- Extracellular other endopeptidase Space
enhancer Pcyt1b PCYT1B phosphate Cytoplasm enzyme
cytidylyltransferase 1, choline, beta Pdgfc PDGFC platelet derived
Extracellular growth growth factor C Space factor Phlda1 PHLDA1
pleckstrin Cytoplasm other homology-like domain, family A, member 1
Phlda2 PHLDA2 pleckstrin Cytoplasm other homology-like domain,
family A, member 2 Pla2g1b PLA2G1B phospholipase A2, Extracellular
enzyme niflumic acid group IB Space (pancreas) Pla2g4a PLA2G4A
phospholipase A2, Cytoplasm enzyme quinacrine group IVA (cytosolic,
calcium- dependent) Porcn PORCN porcupine homolog Cytoplasm other
(Drosophila) Postn POSTN periostin, Extracellular other osteoblast
specific Space factor Prrx1 PRRX1 paired related Nucleus
transcription homeobox 1 regulator Prss23 PRSS23 protease, serine,
23 Extracellular peptidase Space Psmb8 PSMB8 proteasome Cytoplasm
peptidase (prosome, macropain) subunit, beta type, 8 Ptgs2 PTGS2
prostaglandin- Cytoplasm enzyme acetaminophen/pentazocine,
endoperoxide acetaminophen/clemastine/ synthase 2 pseudoephedrine,
(prostaglandin G/H aspirin/butalbital/ synthase and caffeine,
cyclooxygenase) acetaminophen/caffeine/ dihydrocodeine,
aspirin/hydrocodone, aspirin/oxycodone, acetaminophen/aspirin/
caffeine, aspirin/pravastatin, acetaminophen/dexbrompheniramine/
pseudoephedrine, aspirin/meprobamate,
aspirin/caffeine/propoxyphene, aspirin/butalbital/
caffeine/codeine, aspirin/caffeine/dihydrocodeine,
chlorpheniramine/ ibuprofen/pseudoephedrine, licofelone,
menatetrenone, icosapent, suprofen, lornoxicam, tiaprofenic acid,
lumiracoxib, tenoxicam, naproxen/sumatriptan,
ibuprofen/phenylephrine, acetaminophen/aspirin/ codeine,
naproxen/esomeprazole, famotidine/ibuprofen,
ibuprofen/phenylephrine/ chlorpheniramine, diclofenac/misoprostol,
acetaminophen/butalbital/ caffeine, hydrocodone/ibuprofen,
acetaminophen/hydrocodone, acetaminophen/tramadol,
acetaminophen/codeine, acetaminophen/oxycodone,
acetaminophen/propoxyphene, niflumic acid, nitroaspirin,
ketoprofen, diclofenac, etoricoxib, naproxen, meclofenamic acid,
pomalidomide, meloxicam, celecoxib, dipyrone, nimesulide,
acetaminophen, mefenamic acid, diflunisal, ibuprofen, GW406381X,
phenylbutazone, indomethacin, sulfasalazine, piroxicam, valdecoxib,
aspirin, carprofen, zomepirac, rofecoxib, aspirin/methocarbamol,
aspirin/caffeine/orphenadrine, aspirin/carisoprodol,
aspirin/carisoprodol/ codeine, acetaminophen/butalbital,
balsalazide, aspirin/dipyridamole, acetaminophen/butalbital/
caffeine/codeine, racemic flurbiprofen, phenacetin, sulindac,
nabumetone, etodolac, tolmetin, ketorolac, oxaprozin, mesalamine,
salsalate, fenoprofen, salicylic acid,
acetaminophen/chlorpheniramine/ hydrocodone/ phenyl
ephrine/caffeine, bromfenac Ptn PTN pleiotrophin Extracellular
growth Space factor Ptrf PTRF polymerase I and Nucleus
transcription transcript release regulator factor Rarg RARG
retinoic acid Nucleus ligand- etretinate, receptor, gamma dependent
adapalene, nuclear isotretinoin, receptor tazarotene, acitretin,
tretinoin, alitretinoin, fenretinide Rgs16 RGS16 regulator of G-
Cytoplasm other protein signaling 16 Rn45s Rn45s 45S pre-ribosomal
Other other RNA Rpl10a RPL10A ribosomal protein Other other L10a
Rpl31 RPL31 ribosomal protein Other other L31 Rpl37a RPL37A
ribosomal protein Cytoplasm other L37a Rps10 RPS10- RPS10-NUDT3
Cytoplasm other NUDT3 readthrough Rps14 RPS14 ribosomal protein
Cytoplasm translation S14 regulator Rps20 Rps20 ribosomal protein
Cytoplasm other S20 Rps26 RPS26 ribosomal protein Cytoplasm other
S26 Rps9 RPS9 ribosomal protein Cytoplasm translation S9 regulator
S100a4 S100A4 S100 calcium Cytoplasm other binding protein A4
S100a6 S100A6 S100 calcium Cytoplasm transporter binding protein A6
Schip1 SCHIP1 schwannomin Cytoplasm other interacting protein 1
Sdc2 SDC2 syndecan 2 Plasma other Membrane Serpine1 SERPINE1 serpin
peptidase Extracellular other drotrecogin alfa inhibitor, clade E
Space (nexin, plasminogen activator inhibitor type 1), member 1
Serpine2 SERPINE2 serpin peptidase Extracellular other inhibitor,
clade E Space (nexin, plasminogen activator inhibitor type 1),
member 2 Serpinf1 SERPINF1 serpin peptidase Extracellular other
inhibitor, clade F Space (alpha-2 antiplasmin, pigment epithelium
derived factor), member 1 Sh3gl2 SH3GL2 SH3-domain Plasma enzyme
GRB2-like 2 Membrane
Slc19a2 SLC19A2 solute carrier Plasma transporter family 19
Membrane (thiamine transporter), member 2 Slc25a5 SLC25A5 solute
carrier Cytoplasm transporter clodronic acid family 25
(mitochondrial carrier; adenine nucleotide translocator), member 5
Slc29a1 SLC29A1 solute carrier Plasma transporter family 29
Membrane (equilibrative nucleoside transporter), member 1 Slc35f2
SLC35F2 solute carrier Other other family 35, member F2 Snrpn SNRPN
small nuclear Nucleus other ribonucleoprotein polypeptide N Snx22
SNX22 sorting nexin 22 Other transporter Sparc SPARC secreted
protein, Extracellular other acidic, cysteine- Space rich
(osteonectin) Spp1 SPP1 secreted Extracellular cytokine
phosphoprotein 1 Space Sult4a1 SULT4A1 sulfotransferase Cytoplasm
enzyme family 4A, member 1 Tagln TAGLN transgelin Cytoplasm other
Tcea3 TCEA3 transcription Nucleus transcription elongation factor A
regulator (SII), 3 Tgfb3 TGFB3 transforming Extracellular growth
growth factor, beta 3 Space factor Thbs1 THBS1 thrombospondin 1
Extracellular other Space Thbs2 THBS2 thrombospondin 2
Extracellular other Space Tm4sf1 TM4SF1 transmembrane 4 L Plasma
other six family member 1 Membrane Tmbim1 TMBIM1 transmembrane
Cytoplasm other BAX inhibitor motif containing 1 Tmem176b TMEM176B
transmembrane Other other protein 176B Tnc TNC tenascin C
Extracellular other Space Tpd52l1 TPD52L1 tumor protein D52-
Cytoplasm other like 1 Tpm2 TPM2 tropomyosin 2 Cytoplasm other
(beta) Usp18 USP18 ubiquitin specific Cytoplasm peptidase peptidase
18 Vim VIM vimentin Cytoplasm other Wfdc2 WFDC2 WAP four-
Extracellular other disulfide core Space domain 2 Wisp2 WISP2 WNT1
inducible Extracellular growth signaling pathway Space factor
protein 2 Ybx1 YBX1 Y box binding Nucleus transcription protein 1
regulator
TABLE-US-00013 TABLE 13 The genes listed were expressed at levels
20-fold higher in rat ES cells than the corresponding genes in
mouse ES cells. ID Notes Symbol Entrez Gene Name Location Type(s)
Drug(s) Ajap1 Ajap1 adherens junction Other other associated
protein 1 Amd1 AMD1 adenosylmethionine Cytoplasm enzyme
decarboxylase 1 Ankrd2 ANKRD2 ankyrin repeat Nucleus transcription
domain 2 (stretch regulator responsive muscle) Arhgef9 ARHGEF9
Cdc42 guanine Cytoplasm other nucleotide exchange factor (GEF) 9
Atp5h Atp5h ATP synthase, H+ Cytoplasm enzyme transporting,
mitochondrial F0 complex, subunit d Btg3 BTG3 BTG family, Nucleus
other member 3 Car6 CA6 carbonic anhydrase Extracellular enzyme
methazolamide, VI Space hydrochlorothiazide, acetazolamide,
trichloromethiazide, chlorothiazide, chlorthalidone, benzthiazide,
sulfacetamide, topiramate Camk4 CAMK4 calcium/calmodulin- Nucleus
kinase dependent protein kinase IV Capn12 CAPN12 calpain 12 Other
peptidase Cct6b CCT6B chaperonin Cytoplasm transporter containing
TCP1, subunit 6B (zeta 2) Cdx2 CDX2 caudal type Nucleus
transcription homeobox 2 regulator Cldn5 CLDN5 claudin 5 Plasma
other Membrane Clec3a CLEC3A C-type lectin Other other domain
family 3, member A Clic6 CLIC6 chloride intracellular Plasma ion
channel channel 6 Membrane Dhrsx DHRSX dehydrogenase/reductase
Other enzyme (SDR family) X-linked Dpysl2 DPYSL2
dihydropyrimidinase- Cytoplasm enzyme like 2 Dusp26 DUSP26 dual
specificity Cytoplasm enzyme phosphatase 26 (putative) Eci3 Eci3
enoyl-Coenzyme A Other enzyme delta isomerase 3 Eef2k EEF2K
eukaryotic Cytoplasm kinase elongation factor-2 kinase Efna1 EFNA1
ephrin-A1 Plasma other Membrane Epha4 EPHA4 EPH receptor A4 Plasma
kinase Membrane Fank1 FANK1 fibronectin type III Nucleus
transcription and ankyrin repeat regulator domains 1 Fhit FHIT
fragile histidine Cytoplasm enzyme triad Filip1 FILIP1 filamin A
Cytoplasm other interacting protein 1 Fmod FMOD fibromodulin
Extracellular other Space Foxe1 FOXE1 forkhead box E1 Nucleus
transcription (thyroid regulator transcription factor 2) Fry FRY
furry homolog Extracellular other (Drosophila) Space Gjb5 GJB5 gap
junction protein, Plasma transporter beta 5, 31.1 kDa Membrane Gpx2
GPX2 glutathione Cytoplasm enzyme peroxidase 2 (gastrointestinal)
Grxcr2 GRXCR2 glutaredoxin, Other other cysteine rich 2 Hecw2 HECW2
HECT, C2 and WW Extracellular enzyme domain containing Space E3
ubiquitin protein ligase 2 Hey2 HEY2 hairy/enhancer-of- Nucleus
transcription split related with regulator YRPW motif 2 Icos Icos
inducible T-cell co- Plasma other stimulator Membrane Ifitm1 IFITM1
interferon induced Plasma transmembrane transmembrane Membrane
receptor protein 1 Il1f8 Interleukin 36 beta Il28ra Interleukin 28
receptor, alpha Igfbpl1 IGFBPL1 insulin-like growth Other other
factor binding protein-like 1 Ipcef1 IPCEF1 interaction protein
Cytoplasm enzyme for cytohesin exchange factors 1 Lctl Lctl
lactase-like Cytoplasm other Ldhd LDHD lactate Cytoplasm enzyme
dehydrogenase D Lef1 LEF1 lymphoid enhancer- Nucleus transcription
binding factor 1 regulator Lefty1 LEFTY1 left-right Extracellular
growth factor determination factor 1 Space Lifr LIFR leukemia
inhibitory Plasma transmembrane factor receptor alpha Membrane
receptor Lpar2 LPAR2 lysophosphatidic Plasma G-protein acid
receptor 2 Membrane coupled receptor Mog MOG myelin Extracellular
other oligodendrocyte Space glycoprotein Morn5 MORN5 MORN repeat
Other other containing 5 Pigz NCBP2 nuclear cap binding Nucleus
other protein subunit 2, 20 kDa Nptxr NPTXR neuronal pentraxin
Plasma transmembrane receptor Membrane receptor Ntm NTM neurotrimin
Plasma other Membrane Nutf2 NUTF2 nuclear transport Nucleus
transporter factor 2 Ocln OCLN occludin Plasma enzyme Membrane Olr1
OLR1 oxidized low density Plasma transmembrane lipoprotein (lectin-
Membrane receptor like) receptor 1 Pabpc4 PABPC4 poly(A) binding
Cytoplasm translation protein, cytoplasmic regulator 4 (inducible
form) Pde11a PDE11A phosphodiesterase Cytoplasm enzyme dyphylline,
11A nitroglycerin, aminophylline, dipyridamole, tolbutamide,
tadalafil, theophylline, pentoxifylline Pdyn PDYN prodynorphin
Extracellular transporter Space Per3 PER3 period circadian Nucleus
other clock 3 Pllp PLLP plasmolipin Plasma transporter Membrane
Ppp1r14c PPP1R14C protein phosphatase Cytoplasm other 1, regulatory
(inhibitor) subunit 14C Pramel6 Pramel6 preferentially Other other
expressed antigen in melanoma like 6 Ptpn18 PTPN18 protein tyrosine
Nucleus phosphatase phosphatase, non- receptor type 18
(brain-derived) Pycr1 PYCR1 pyrroline-5- Cytoplasm enzyme
carboxylate reductase 1 Rab26 RAB26 RAB26, member Plasma enzyme RAS
oncogene Membrane family Ramp2 RAMP2 receptor (G protein- Plasma
transporter pramlintide coupled) activity Membrane modifying
protein 2 Rbm24 RBM24 RNA binding motif Other other protein 24 Rhag
RHAG Rh-associated Plasma peptidase glycoprotein Membrane Rpl3 RPL3
ribosomal protein Cytoplasm other homoharringtonine L3 Sall3 SALL3
sal-like 3 Nucleus other (Drosophila) Satb1 SATB1 SATB homeobox 1
Nucleus transcription regulator Scg2 SCG2 secretogranin II
Extracellular cytokine Space Slc15a1 SLC15A1 solute carrier family
Plasma transporter 15 (oligopeptide Membrane transporter), member 1
Slc1a1 SLC1A1 solute carrier family 1 Plasma transporter riluzole
(neuronal/epithelial Membrane high affinity glutamate transporter,
system Xag), member 1 Slc24a5 Slc24a5 solute carrier family Other
other 24 (sodium/potassium/calcium exchanger), member 5 Slc37a2
SLC37A2 solute carrier family Other transporter 37 (glucose-6-
phosphate transporter), member 2 40424 SNTB1 syntrophin, beta 1
Plasma other (dystrophin- Membrane associated protein A1, 59 kDa,
basic component 1) St6galnac3 ST6GALNAC3 ST6 (alpha-N- Cytoplasm
enzyme acetyl-neuraminyl- 2,3-beta-galactosyl- 1,3)-N-
acetylgalactosaminide alpha-2,6- sialyltransferase 3 Tex12 TEX12
testis expressed 12 Nucleus other Tex15 TEX15 testis expressed 15
Extracellular other Space Tfap2a TFAP2A transcription factor
Nucleus transcription AP-2 alpha regulator (activating enhancer
binding protein 2 alpha) Tmc1 TMC1 transmembrane Plasma other
channel-like 1 Membrane Tmem130 TMEM130 transmembrane Other other
protein 130 Tmem30b TMEM30B transmembrane Other other protein 30B
Tomm20 TOMM20 translocase of outer Cytoplasm transporter
mitochondrial membrane 20 homolog (yeast) Tox3 TOX3 TOX high
mobility Other other group box family member 3 Ttc25 TTC25
tetratricopeptide Cytoplasm other repeat domain 25 Tymp TYMP
thymidine Extracellular growth factor phosphorylase Space Ubb Ubb
ubiquitin B Cytoplasm other
Vamp7 VAMP7 vesicle-associated Cytoplasm transporter membrane
protein 7 Wfdc12 Wfdc12 WAP four-disulfide Extracellular other core
domain 12 Space Wfdc15a Wfdc15a WAP four-disulfide Other other core
domain 15A Wfdc6a Wfdc6a WAP four-disulfide Other other core domain
6A
TABLE-US-00014 TABLE 14 A subset of genes from Table 13 which are
expressed at levels 20-fold higher in rat ES cells than the
corresponding genes in mouse ES cells. ID Entrez Gene Name Ajap1
Adherens Junctions Associate Protein 1 CldnS Claudin 5 Arhgef9
Cdc42 guanine nucleotide exchange facter 9 Camk4
Calcium/calmodulin- dependent protein kinase IV Efna1 ephrin-A1
Epha4 EPH receptor A4 GjbS gap junction protein beta 5 Igfbpl1
Insulin-like growth factor binding protein-like 1 Il1f8 Interleukin
36 beta Il28ra Interleukin 28 receptor, alpha Lefty1 left-right
determination factor 1 Lifr Leukemia inhibitory factor receptor
alpha Lpar2 Lysophosphatidic acid receptor 2 Ntm Neuronal pentraxin
receptor Ptpn18 Protein tyrosine phosphatase non-receptor type 18
Cdx2 Caudal type homeobox 2 Fank1 Fibronectin type III and ankyrin
repeat domains 1 Foxe1 Forkhead box E1 (thyroid transcription
factor 2) Hey2 Hairy/enhancer-of-split related with YRPW motif 2
Lef1 Lymphoid enhancer- binding factor 1 Sall3 Sal-like 3
(Drosophila) Satb1 SATB homeobox 1
[0598] An additional molecular signature employing the pluripotency
markers/genes for the rat ES cells has also been developed. Table
15 provides a gene list and their expression ranks from the RNA
profiling data. mRNA was isolated from rat ES cells and the
expression level of various pluripotency markers were compared
relative to each other. The "pluripotency genes" which are listed
are genes that other groups have used (mostly in mouse, but also in
rat) as markers of ES cells. Mesoderm endoderm and neural are
similarly defined. By "rank" is refers to the expression in our
experiment: the higher the rank (1 is highest) the higher the
expression. For example, Oct4's rank of 13 means that, of all the
genes assayed, it was expressed higher than all but 12 genes.
Background in this experiment was any expression value below 30;
6107 genes had expression values of 30 or higher.
TABLE-US-00015 TABLE 15 Rat ES cell molecular signature employing
the pluripotency, mesodermal, endodermal, neural and trophectoderm
markers/genes. Pluripotency Mesodermal Endodermal Neural
Trophectoderm Pluripotency Rank Mesodermal Rank Endodermal Rank
Neural Rank Trophectoderm Rank c-Myc 8248 Brachyury 7542 Gata6
11195 Nestin 7761 Cdx2 739 Dnmt3L 127 Flk1 Not Sox17 11418 Pax6
13570 tested Dppa2 Not tested Nodal 3050 Hhex1 4571 Sox2 681 Dppa5
Not tested Bmp4 3072 Nodal 3050 Ecat1 9714 Bmpr2 6382 Ext1 6091
Eras 2541 Sox7 10284 Err-beta 1368 Fbxo15 1369 Fgf4 3440 Fthl17 Not
tested Gdf3 2771 Rank >6107 = bkg expression Klf4 836 Lef1 1313
LIF receptor 724 Lin28 828 Nanog 774 Oct4 13 Rexo1 6119 Sox15 4524
Sox2 681 SSEA1 Not tested SSEA4 Not tested Stella Not tested Tcl1
Not tested Utf1 1501
[0599] All publications and patent applications mentioned in the
specification are indicative of the level of those skilled in the
art to which this invention pertains. All publications and patent
applications are herein incorporated by reference to the same
extent as if each individual publication or patent application was
specifically and individually indicated to be incorporated by
reference. Unless otherwise apparent from the context of any
embodiment, aspect, step or feature of the invention can be used in
combination with any other. Reference to a range includes any
integers within the range, any subrange within the range. Reference
to multiple ranges includes composites of such ranges.
Sequence CWU 1
1
11203PRTMus musculus 1Met Lys Val Leu Ala Ala Gly Ile Val Pro Leu
Leu Leu Leu Val Leu1 5 10 15 His Trp Lys His Gly Ala Gly Ser Pro
Leu Pro Ile Thr Pro Val Asn 20 25 30 Ala Thr Cys Ala Ile Arg His
Pro Cys His Gly Asn Leu Met Asn Gln 35 40 45 Ile Lys Asn Gln Leu
Ala Gln Leu Asn Gly Ser Ala Asn Ala Leu Phe 50 55 60 Ile Ser Tyr
Tyr Thr Ala Gln Gly Glu Pro Phe Pro Asn Asn Val Glu65 70 75 80 Lys
Leu Cys Ala Pro Asn Met Thr Asp Phe Pro Ser Phe His Gly Asn 85 90
95 Gly Thr Glu Lys Thr Lys Leu Val Glu Leu Tyr Arg Met Val Ala Tyr
100 105 110 Leu Ser Ala Ser Leu Thr Asn Ile Thr Arg Asp Gln Lys Val
Leu Asn 115 120 125 Pro Thr Ala Val Ser Leu Gln Val Lys Leu Asn Ala
Thr Ile Asp Val 130 135 140 Met Arg Gly Leu Leu Ser Asn Val Leu Cys
Arg Leu Cys Asn Lys Tyr145 150 155 160 Arg Val Gly His Val Asp Val
Pro Pro Val Pro Asp His Ser Asp Lys 165 170 175 Glu Ala Phe Gln Arg
Lys Lys Leu Gly Cys Gln Leu Leu Gly Thr Tyr 180 185 190 Lys Gln Val
Ile Ser Val Val Val Gln Ala Phe 195 200
* * * * *