Methods for neural conversion of human embryonic stem cells

• US 10,260,041 B2
• Filed: 01/30/2014
• Issued: 04/16/2019
• Est. Priority Date: 02/17/2009
• Status: Active Grant

• Current Assignee: Memorial Sloan-Kettering Cancer Center
• Original Assignee: Memorial Sloan-Kettering Cancer Center
• Inventors: Chambers, Stuart, Studer, Lorenz
• Primary Examiner(s): Bertoglio, Valarie E
• Application Number:
  US14/168,835
• Publication Number:
  US 20170130199A1
• Time in Patent Office: 1,902 Days
• Field of Search: 435377, 435384, 435395, 435325
• CPC Class Codes: C12N 2500/90 Serum-free medium, which may still contain naturally-sourced components
• CPC Class Codes: C12N 2501/15 Transforming growth factor beta (TGF-β)
• CPC Class Codes: C12N 2501/155 Bone morphogenic proteins [BMP]; Osteogenins; Osteogenic factor; Bone inducing factor
• CPC Class Codes: C12N 2501/41 Hedgehog proteins; Cyclopamine (inhibitor)
• CPC Class Codes: C12N 2501/415 Wnt; Frizzeled
• CPC Class Codes: C12N 2501/60 Transcription factors
• CPC Class Codes: C12N 2501/998 Proteins not provided for elsewhere
• CPC Class Codes: C12N 2506/02 from embryonic cells
• CPC Class Codes: C12N 2506/45 from artificially induced pluripotent stem cells
• CPC Class Codes: C12N 5/0619 Neurons

Abstract

The present invention relates generally to the field of cell biology of stem cells, more specifically the directed differentiation of pluripotent or multipotent stem cells, including human embryonic stem cells (hESC), somatic stem cells, and induced human pluripotent stem cells (hiPSC) using novel culture conditions. Specifically, methods are provided for obtaining neural tissue, floor plate cells, and placode including induction of neural plate development in hESCs for obtaining midbrain dopamine (DA) neurons, motorneurons, and sensory neurons. Further, neural plate tissue obtained using methods of the present inventions are contemplated for use in co-cultures with other tissues as inducers for shifting differentiation pathways, i.e. patterning.

Claims

1. An in vitro method for differentiating pluripotent stem cells, comprising, exposing a plurality of pluripotent stem cells attached to a substrate to (a) a first inhibitor of Small Mothers Against Decapentaplegic (SMAD) protein signaling (first SMAD inhibitor) and (b) a second inhibitor of SMAD protein signaling (second SMAD inhibitor) to obtain a cell population comprising at least about 10% differentiated cells expressing paired box homeotic gene-6 (PAX6), wherein said first SMAD inhibitor comprises an inhibitor of bone morphogenetic protein (BMP) signaling, and said second SMAD inhibitor comprises an inhibitor of TGFβ

/Activin-Nodal signaling.

2. The method of claim 1, wherein said exposing is performed at least 72 hours after said plurality of pluripotent stem cells is contacted with said substrate.

3. The method of claim 1, wherein said pluripotent stem cells are human pluripotent stem cells.

4. The method of claim 3, wherein said human pluripotent stem cells are human embryonic stern cells (hESC) or human induced pluripotent stem cells (hiPSC).

5. The method of claim 1, wherein said cell population comprises at least about 80% of said differentiated cells expressing PAX6.

6. The method of claim 1, wherein said exposing comprises exposing said pluripotent stem cells to said first and second SMAD inhibitors for at least about 10 days.

7. The method of claim 6, wherein said exposing comprises exposing said pluripotent stem cells to said first and second SMAD inhibitors for about 10 days or about 11 days.

8. The method of claim 1, wherein said first SMAD inhibitor is selected from the group consisting of Noggin, a disulfide-linked homodimer of Noggin, Dorsomorphin, LDN-193189, and combinations thereof.

9. The method of claim 1, wherein said second SMAD inhibitor blocks phosphorylation of an anaplastic lymphoma kinase (ALK).

10. The method of claim 9, wherein said ALK is selected from the group consisting of ALK4, ALK5, and ALK7.

11. The method of claim 1, wherein said second SMAD inhibitor is 4-[4-(1,3-benzodioxo-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl] benzamide (SB431542).

12. The method of claim 1, wherein said substrate is selected from the group consisting of plates, flasks, tubes, coverslips, shell vials, roller bottles, and combinations thereof.

13. The method of claim 1, wherein one or both of said first and second SMAD inhibitors are comprised in a cell culture medium.

14. The method of claim 13, wherein said cell culture medium is selected from the group consisting of knock out serum replacement (KSR) media and N2 culture media.

15. The method of claim 13, wherein said first SMAD inhibitor is present in an amount of between about 125 ng/mL and about 500 ng/mL in said cell culture medium.

16. The method of claim 15, wherein said first SMAD inhibitor is present in an amount of about 500 ng/mL in said cell culture medium.

17. The method of claim 13, wherein said second SMAD inhibitor is present in an amount of between about 1 nM and about 1×

10³ μ

M in said cell culture medium.

18. The method of claim 17, wherein said second SMAD inhibitor is present in an amount of about 10 nM in said cell culture medium.

19. The method of claim 13, wherein said exposing comprises culturing said pluripotent stem cells in said cell culture medium.

20. The method of claim 1, wherein said differentiated cells expressing PAX6 are neuroectodermal cells.

21. An in vitro method for differentiating pluripotent stem cells, comprising:

exposing a plurality of pluripotent stem cells attached to a substrate to (a) a first SMAD inhibitor and (b) a second SMAD inhibitor to obtain a cell population comprising at least about 10% differentiated cells expressing SIX1,

wherein said exposing to said first SMAD inhibitor is discontinued after about two days or about three days from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor; and

wherein said first SMAD inhibitor comprises an inhibitor of BMP signaling, and said second SMAD inhibitor comprises an inhibitor of TGFβ

/Activin-Nodal signaling.

22. The method of claim 21, wherein said differentiated cells are placodal precursors.

33. The method of claim 21, wherein said pluripotent stem cells are human pluripotent stem cells.

34. The method of claim 33, wherein said human pluripotent stem cells are human embryonic stern cells (hESC) or human induced pluripotent stem cells (hiPSC).

35. The method of claim 21, wherein said cell population comprises at least about 70% of said differentiated cells expressing SIX1.

36. The method of claim 21, wherein said exposing comprises exposing said pluripotent stem cells to said second SMAD inhibitor for at least about 10 days.

37. The method of claim 21, wherein said exposing comprises exposing said pluripotent stem cells to said second SMAD inhibitor for about 10 days or about 11 days.

38. The method of claim 21, wherein said first SMAD inhibitor is selected from the group consisting of Noggin, a disulfide-linked homodimer of Noggin, Dorsomorphin, LDN-193189, and combinations thereof.

39. The method of claim 21, wherein said second SMAD inhibitor blocks phosphorylation of an ALK.

40. The method of claim 39, wherein said ALK is selected from the group consisting of ALK4, ALK5, and ALK7.

41. The method of claim 21, wherein said second SMAD inhibitor is SB431542.

42. The method of claim 21, wherein said substrate is selected from the group consisting of plates, flasks, tubes, coverslips, shell vials, roller bottles, and combinations thereof.

43. The method of claim 21, wherein one or both of said first and second SMAD inhibitors are comprised in a cell culture medium.

44. The method of claim 43, wherein said first SMAD inhibitor is present in an amount of between about 125 ng/mL and about 500 ng/mL in said cell culture medium.

45. The method of claim 44, wherein said first SMAD inhibitor is present in an amount of about 500 ng/mL in said cell culture medium.

46. The method of claim 43, wherein said second SMAD inhibitor is present in an amount of between about 1 nM and about 1×

10³ μ

M in said cell culture medium.

47. The method of claim 46, wherein said second SMAD inhibitor is present in an amount of about 10 nM in said cell culture medium.

48. The method of claim 21, further comprising subjecting said cell population to conditions suitable to obtain a second cell population comprising at least about 10% differentiated cells expressing at least one marker selected from the group consisting of Brn3A, Isl-1, and peripherin.

49. The method of claim 48, wherein said differentiated cells expressing said at least one marker are sensory neurons.

50. The method of claim 49, wherein said sensory neurons are peripheral sensory neurons.

23. An in vitro method for differentiating pluripotent stem cells, comprising:

exposing a plurality of pluripotent stem cells attached to a substrate to (a) a first SMAD inhibitor and (b) a second SMAD inhibitor to obtain a cell population comprising at least about 10% differentiated cells expressing CDX2,

wherein said exposing to said first SMAD inhibitor is discontinued after about one day from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor; and

wherein said first SMAD inhibitor comprises an inhibitor of BMP signaling, and said second SMAD inhibitor comprises an inhibitor of TGFβ

/Activin-Nodal signaling.

24. The method of claim 23, wherein said differentiated cells are trophectodermal precursors.

51. The method of claim 23, wherein said pluripotent stem cells are human pluripotent stem cells.

52. The method of claim 51, wherein said human pluripotent stem cells are human embryonic stern cells (hESC) or human induced pluripotent stem cells (hiPSC).

53. The method of claim 23, wherein said exposing comprises exposing said pluripotent stem cells to said second SMAD inhibitor for at least about 10 days.

54. The method of claim 23, wherein said exposing comprises exposing said pluripotent stem cells to said second SMAD inhibitor for about 10 days or about 11 days.

55. The method of claim 23, wherein said first SMAD inhibitor is selected from the group consisting of Noggin, a disulfide-linked homodimer of Noggin, Dorsomorphin, LDN-193189, and combinations thereof.

56. The method of claim 23, wherein said second SMAD inhibitor blocks phosphorylation of an ALK.

57. The method of claim 56, wherein said ALK is selected from the group consisting of ALK4, ALK5, and ALK7.

58. The method of claim 23, wherein said second SMAD inhibitor is SB431542.

59. The method of claim 23, wherein said substrate is selected from the group consisting of plates, flasks, tubes, coverslips, shell vials, roller bottles, and combinations thereof.

60. The method of claim 23, wherein one or both of said first and second SMAD inhibitors are comprised in a cell culture medium.

61. The method of claim 60, wherein said first SMAD inhibitor is present in an amount of between about 125 ng/mL and about 500 ng/mL in said cell culture medium.

62. The method of claim 61, wherein said first SMAD inhibitor is present in an amount of about 500 ng/mL in said cell culture medium.

63. The method of claim 62, wherein said second SMAD inhibitor is present in an amount of between about 1 nM and about 1×

10³ μ

M in said cell culture medium.

64. The method of claim 63, wherein said second SMAD inhibitor is present in an amount of about 10 nM in said cell culture medium.

25. An in vitro method for differentiating pluripotent stem cells, comprising:

exposing a plurality of pluripotent stem cells attached to a substrate to (a) a first SMAD inhibitor and (b) a second SMAD inhibitor; and

exposing said cells to (c) an activator of Sonic Hedgehog (SHH) signaling to obtain a cell population comprising at least about 10% differentiated cells expressing one or more marker selected from the group consisting of SHH, FOXA2, Netrin-1, and F-Spondin,

wherein said first SMAD inhibitor comprises an inhibitor of BMP signaling, and said second SMAD inhibitor comprises an inhibitor of TGFβ

/Activin-Nodal signaling.

26. The method of claim 25, wherein said differentiated cells are neural floor plate cells.

65. The method of claim 25, wherein said pluripotent stem cells are human pluripotent stem cells.

66. The method of claim 65, wherein said human pluripotent stem cells are human embryonic stern cells (hESC) or human induced pluripotent stem cells (hiPSC).

67. The method of claim 25, wherein said cell population comprises at least about 60% of said differentiated cells expressing said one or more marker.

68. The method of claim 25, comprising initially exposing said cells to said activator of SHH signaling no later than about 5 days from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.

69. The method of claim 68, comprising initially exposing said cells to said activator of SHH signaling about 24 hours from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.

70. The method of claim 25, wherein said exposing comprises exposing said pluripotent stem cells to said first and second SMAD inhibitors for at least about 10 days.

71. The method of claim 70, wherein said exposing comprises exposing said pluripotent stem cells to said first and second SMAD inhibitors for about 10 days or about 11 days.

72. The method of claim 25, wherein said first SMAD inhibitor is selected from the group consisting of Noggin, a disulfide-linked homodimer of Noggin, Dorsomorphin, LDN-193189, and combinations thereof.

73. The method of claim 25, wherein said second SMAD inhibitor blocks phosphorylation of an ALK.

74. The method of claim 73, wherein said ALK is selected from the group consisting of ALK4, ALK5, and ALK7.

75. The method of claim 25, wherein said second SMAD inhibitor is SB431542.

76. The method of claim 25, wherein said activator of SHH signaling is a recombinant SHH.

77. The method of claim 76, wherein said recombinant N-terminal SHH.

78. The method of claim 77, wherein said recombinant N-terminal SHH is SHH C25II.

79. The method of claim 25, wherein said substrate is selected from the group consisting of plates, flasks, tubes, coverslips, shell vials, roller bottles, and combinations thereof.

80. The method of claim 25, wherein one, two or three of said first and second SMAD inhibitors and said activator of SHH signaling are comprised in a cell culture medium.

81. The method of claim 80, wherein said first SMAD inhibitor is present in an amount of between about 125 ng/mL and about 500 ng/mL in said cell culture medium.

82. The method of claim 81, wherein said first SMAD inhibitor is present in an amount of about 500 ng/mL in said cell culture medium.

83. The method of claim 80, wherein said second SMAD inhibitor is present in an amount of between about 1 nM and about 1×

10³ μ

M in said cell culture medium.

84. The method of claim 83, wherein said second SMAD inhibitor is present in an amount of about 10 nM in said cell culture medium.

85. The method of claim 80, wherein said activator of SHH signaling is present in an amount of between about 200 ng/mL and about 2000 ng/mL in said cell culture medium.

86. The method of claim 85, wherein said activator of SHH signaling is present in an amount of about 200 ng/mL in said cell culture medium.

87. The method of claim 25, further comprising exposing said cells to a DDK inhibitor.

88. The method of claim 87, wherein said DDK inhibitor is an anti-DDK antibody.

89. The method of claim 88, comprising initially exposing said cells to said DDK inhibitor no later than about 5 days from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.

90. The method of claim 26, wherein said neural floor plate cells are anterior floor plate cells.

27. An in vitro method for differentiating pluripotent stem cells, comprising:

exposing a plurality of pluripotent stem cells attached to a substrate to (a) a first SMAD inhibitor and (b) a second SMAD inhibitor; and

exposing said cells to (c) an activator of SHH signaling and (d) one or more caudalizing factor to obtain a cell population comprising at least about 10% differentiated cells expressing one or more marker selected from the group consisting of CORIN, LMX1B, EN1, NGN2, and NOV,

wherein said first SMAD inhibitor comprises an inhibitor of BMP signaling, and said second SMAD inhibitor comprises an inhibitor of TGFβ

/Activin-Nodal signaling.

28. The method of claim 27, wherein said differentiated cells are posterior floor plate cells, dopaminergic progenitors, or a combination thereof.

91. The method of claim 27, wherein said one or more caudalizing factor is selected from the group consisting of activators of wingless (Wnt) signaling, Fibroblast growth factors (FGF) and retinoic acid (RA).

92. The method of claim 91, wherein said activator of Wnt signaling is Wnt-1.

93. The method of claim 91, wherein said FGF is FGF8.

94. The method of claim 28, wherein said posterior floor plate cells are midbrain floor plate cells.

95. The method of claim 27, wherein said pluripotent stem cells are human pluripotent stem cells.

96. The method of claim 95, wherein said human pluripotent stem cells are human embryonic stern cells (hESC) or human induced pluripotent stem cells (hiPSC).

97. The method of claim 27, comprising initially exposing said cells to said activator of SHH signaling no later than about 5 days from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.

98. The method of claim 97, comprising initially exposing said cells to said activator of SHH signaling about 24 hours from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.

99. The method of claim 27, wherein said first SMAD inhibitor is selected from the group consisting of Noggin, a disulfide-linked homodimer of Noggin, Dorsomorphin, LDN-193189, and combinations thereof.

100. The method of claim 27, wherein said second SMAD inhibitor blocks phosphorylation of an ALK.

101. The method of claim 100, wherein said ALK is selected from the group consisting of ALK4, ALK5, and ALK7.

102. The method of claim 27, wherein said second SMAD inhibitor is SB431542.

103. The method of claim 27, wherein said activator of SHH signaling is a recombinant SHH.

104. The method of claim 103, wherein said recombinant N-terminal SHH.

105. The method of claim 104, wherein said recombinant N-terminal SHH is SHH C25II.

106. The method of claim 27, wherein said substrate is selected from the group consisting of plates, flasks, tubes, coverslips, shell vials, roller bottles, and combinations thereof.

107. The method of claim 27, wherein at least one of said first and second SMAD inhibitors, said activator of SHH signaling, and said one or more caudalizing factor are comprised in a cell culture medium.

108. The method of claim 107, wherein said first SMAD inhibitor is present in an amount of between about 125 ng/mL and about 500 ng/mL in said cell culture medium.

109. The method of claim 108, wherein said first SMAD inhibitor is present in an amount of about 500 ng/mL in said cell culture medium.

110. The method of claim 107, wherein said second SMAD inhibitor is present in an amount of between about 1 nM and about 1×

10³ μ

M in said cell culture medium.

111. The method of claim 110, wherein said second SMAD inhibitor is present in an amount of about 10 nM in said cell culture medium.

112. The method of claim 107, wherein said activator of SHH signaling is present in an amount of between about 200 ng/mL and about 2000 ng/mL in said cell culture medium.

113. The method of claim 112, wherein said activator of SHH signaling is present in an amount of about 200 ng/mL in said cell culture medium.

29. An in vitro method for differentiating pluripotent stem cells, comprising exposing a plurality of pluripotent stem cells attached to a substrate to (a) a first SMAD inhibitor and (b) a second SMAD inhibitor;

and exposing said cells to (c) an activator of SHH signaling to obtain a cell population comprising at least about 10% differentiated cells expressing Tyrosine hydroxylase (TH),

wherein said first SMAD inhibitor comprises an inhibitor of BMP signaling, and said second SMAD inhibitor comprises an inhibitor of TGFβ

/Activin-Nodal signaling.

30. The method of claim 29, wherein said differentiated cells are dopaminergic cells.

114. The method of claim 29, wherein said pluripotent stem cells are human pluripotent stem cells.

115. The method of claim 114, wherein said human pluripotent stem cells are human embryonic stern cells (hESC) or human induced pluripotent stem cells (hiPSC).

116. The method of claim 29, wherein said exposing comprises exposing said pluripotent stem cells to said first and second SMAD inhibitors for about 5 days or about 6 days.

117. The method of claim 29, wherein said exposing comprises exposing said cells to said activator of SHH signaling for about 7 days or about 8 days.

118. The method of claim 29, comprising initially exposing said cells to said activator of SHH signaling about 5 days from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.

119. The method of claim 29, wherein said first SMAD inhibitor is selected from the group consisting of Noggin, a disulfide-linked homodimer of Noggin, Dorsomorphin, LDN-193189, and combinations thereof.

120. The method of claim 29, wherein said second SMAD inhibitor blocks phosphorylation of an ALK.

121. The method of claim 120, wherein said ALK is selected from the group consisting of ALK4, ALK5, and ALK7.

122. The method of claim 29, wherein said second SMAD inhibitor is SB431542.

123. The method of claim 29, wherein said activator of SHH signaling is a recombinant SHH.

124. The method of claim 123, wherein said recombinant N-terminal SHH.

125. The method of claim 124, wherein said recombinant N-terminal SHH is SHH C25II.

126. The method of claim 29, wherein said substrate is selected from the group consisting of plates, flasks, tubes, coverslips, shell vials, roller bottles, and combinations thereof.

127. The method of claim 29, further comprising exposing said cells to at least one of a Brain-derived neurotrophic factor (BDNF), a FGF, and ascorbic acid.

128. The method of claim 29, wherein said cell population is detectable about 12 days from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.

129. The method of claim 29, further comprising subjecting said cell population to conditions for maturation.

130. The method of claim 129, wherein said conditions for maturation comprise exposing said cell population to at least one of BDNF, ascorbic acid, Glial cell-derived neurotrophic factor (GDNF), a Transforming Growth Factor, and cyclic-AMP.

31. An in vitro method for differentiating pluripotent stem cells, comprising:

exposing a plurality of pluripotent stem cells attached to a substrate to (a) a first SMAD inhibitor and (b) a second SMAD inhibitor and exposing said cells to a Brain-derived neurotrophic factor (BDNF), ascorbic acid, an activator of Sonic Hedgehog (SHH) signaling, and retinoic acid (RA) to obtain a cell population comprising at least about 10% differentiated cells expressing one or more marker selected from the group consisting of ISL1 and HB9,

wherein said first SMAD inhibitor comprises an inhibitor of BMP signaling, and said second SMAD inhibitor comprises an inhibitor of TGFβ

/Activin-Nodal signaling.

32. The method of claim 31, wherein said differentiated cells are motor neuronal cells.

131. The method of claim 31, wherein said pluripotent stem cells are human pluripotent stem cells.

132. The method of claim 131, wherein said human pluripotent stem cells are human embryonic stern cells (hESC) or human induced pluripotent stem cells (hiPSC).

133. The method of claim 31, wherein said exposing comprises exposing said pluripotent stem cells to said first and second SMAD inhibitors for about 5 days or about 6 days.

134. The method of claim 31, wherein said exposing comprises exposing said cells to said at least one molecule that induces initiation of motor neuronal patterning for about 6 days or about 7 days.

135. The method of claim 31, comprising initially exposing said cells to said at least one molecule that induces initiation of motor neuronal patterning about 5 days from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.

136. The method of claim 31, wherein said first SMAD inhibitor is selected from the group consisting of Noggin, a disulfide-linked homodimer of Noggin, Dorsomorphin, LDN-193189, and combinations thereof.

137. The method of claim 31, wherein said second SMAD inhibitor blocks phosphorylation of an ALK.

138. The method of claim 137, wherein said ALK is selected from the group consisting of ALK4, ALK5, and ALK7.

139. The method of claim 31, wherein said second SMAD inhibitor is SB431542.

140. The method of claim 31, wherein said substrate is selected from the group consisting of plates, flasks, tubes, coverslips, shell vials, roller bottles, and combinations thereof.

141. The method of claim 31, wherein said cell population is detectable about 19 days from the initial exposure of said pluripotent stem cells to said first SMAD inhibitor.