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US-12618049-B2 - Reprogramming methods and cell culture platforms

US12618049B2US 12618049 B2US12618049 B2US 12618049B2US-12618049-B2

Abstract

The invention provides compositions and methods for manufacturing pluripotent cells. In particular, the invention provides improved culture platforms for manufacturing pluripotent cells with ground state pluripotency. In various embodiments, the invention contemplates, in part, a composition comprising: (a) a Wnt pathway agonist; (b) a MEK inhibitor; and (c) a ROCK inhibitor. In certain embodiments, the composition further comprises bFGF or LIF.

Inventors

  • Bahram Valamehr
  • Peter Flynn
  • Ramzey Abujarour
  • Megan ROBINSON

Assignees

  • FATE THERAPEUTICS, INC.

Dates

Publication Date
20260505
Application Date
20220119

Claims (15)

  1. 1 . A culture system comprising a cell culture platform for manufacturing induced pluripotent stem cells (iPSCs), the cell culture platform comprising a first composition and a second composition, wherein: (i) the first composition comprises non-pluripotent cells in a first culture medium comprising a Wnt pathway agonist, a MEK inhibitor, a ROCK inhibitor, and a TGFβR inhibitor; (ii) the second composition comprises iPSCs in a second culture medium comprising: (a) a Wnt pathway agonist; (b) a MEK inhibitor; and (c) a ROCK inhibitor; and (iii) the second composition does not comprise a TGFβR inhibitor.
  2. 2 . The culture system of claim 1 , wherein (i) the Wnt pathway agonist of the second composition is a GSK3 inhibitor; (ii) the Wnt pathway agonist of the second composition is CHIR99021 or BIO; (iii) the MEK inhibitor of the second composition is PD98059 or PD032901; 1v) the ROCK inhibitor of the second composition is thiazovivin or Y27632; or (v) the Wnt pathway agonist of the second composition is CHIR99021; the MEK inhibitor of the second composition is PD032901; and the ROCK inhibitor of the second composition is thiazovivin.
  3. 3 . The culture system of claim 1 , wherein the second composition further comprises (i) bFGF or LIF; or (ii) bFGF and LIF.
  4. 4 . The culture system of claim 1 , wherein the iPSCs are reprogrammed from non-pluripotent cells comprising (i) one or more exogenous polynucleotides that encode at least one, two or three polypeptides selected from the group consisting of an OCT4 polypeptide, an ECAT1 polypeptide, a UTF1 polypeptide, a NANOG polypeptide, and an ESRRB polypeptide, or (ii) at least one, two or three exogenous polypeptides selected from an OCT4 polypeptide, an ECAT1 polypeptide, a UTF1 polypeptide, a NANOG polypeptide, and an ESRRB polypeptide.
  5. 5 . The culture system of claim 4 , wherein the non-pluripotent cells from which the iPSCs are reprogrammed comprise: (i) one or more exogenous polynucleotides that encode an OCT4 polypeptide, an ECAT1 polypeptide, a UTF1 polypeptide, a NANOG polypeptide, and an ESRRB polypeptide, or (ii) one or more exogenous polynucleotides that encode an OCT4 polypeptide, an ECAT1 polypeptide, and a UTF1 polypeptide.
  6. 6 . The culture system of claim 4 , wherein the one or more exogenous polynucleotides were introduced to the non-pluripotent cells from which the iPSCs are reprogrammed by a retrovirus, a lentivirus, a Sendai virus, an adenovirus, an episome, mini-circle, vector system with expression cassette, or mRNA.
  7. 7 . The culture system of claim 4 , wherein the one or more exogenous polynucleotides are removable by CRE-mediated excision.
  8. 8 . The culture system of claim 4 , wherein the one or more exogenous polynucleotides comprise a polycistronic vector comprising a plurality of polynucleotides that are separated by at least one 2A peptide.
  9. 9 . The culture system of claim 8 , wherein the polycistronic vector comprises a plurality of polynucleotides each encoding an OCT4 polypeptide.
  10. 10 . The culture system of claim 4 , wherein the exogenous polynucleotide encoding an OCT4 polypeptide is linked to a selectable marker.
  11. 11 . The culture system of claim 4 , wherein the one or more exogenous polynucleotides comprise: (a) at least one OCT4 encoding polynucleotide, at least one ECAT1 encoding polynucleotide, at least one UTF1 encoding polynucleotide; (b) at least one OCT4 encoding polynucleotide, at least one ECAT1 encoding polynucleotide, at least one UTF1 encoding polynucleotide, and at least one NANOG encoding polynucleotide; (c) at least two OCT4 encoding polynucleotides, and at least one NANOG encoding polynucleotide; or (d) at least one OCT4 encoding polynucleotide, at least one DPPA2 encoding polynucleotide, and at least one ESRRB encoding polynucleotide.
  12. 12 . The culture system of claim 1 , wherein the iPSCs comprise ground state pluripotency.
  13. 13 . The culture system of claim 12 , wherein the iPSCs do not comprise an exogenously introduced polynucleotide encoding a reprogramming factor polypeptide.
  14. 14 . The culture system of claim 1 , wherein the iPSCs comprise single cell dissociated iPSCs.
  15. 15 . The culture system of claim 1 , wherein at least 70% of the iPSCs are positive for both SSEA4 and TRA1-81.

Description

CROSS REFERENCE TO RELATED APPLICATIONS This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 61/947,979, filed Mar. 4, 2014, which is incorporated by reference herein in its entirety. STATEMENT REGARDING SEQUENCE LISTING The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is FATE_122_01WO_ST25.txt. The text file is 8 KB, was created on Mar. 4, 2015, and is being submitted electronically via EFS-Web, concurrent with the filing of the specification. BACKGROUND Technical Field The invention relates generally to compositions and methods for manufacturing pluripotent cells. In particular, the invention relates to improved culture platforms for manufacturing pluripotent cells with ground state pluripotency. Description of the Related Art Today's pluripotent stem cell-based disease and toxicology screening efforts and tomorrow's auto/allogeneic pluripotent stem cell therapies will require robust, reproducible methods of cell line generation and expansion of human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs). hiPSCs have been generated by the ectopic expression of pluripotency factors introduced through genome-integrating retro- and lentiviral expression systems. Efforts to eliminate as many integrating events as possible have included substituting small molecule inhibitors for a number of reprogramming factors. In addition, non-integrative methods have proven to be inefficient and labor intensive, requiring additional reprogramming factors or not being effective in reprogramming all somatic cells (Lee et al., 2013). Several challenges associated with the culture of pluripotent stem cells have yet to be addressed to allow the cells to become suitable for future industrial and clinical applications. In the most commonly used conventional culture system, hESCs and hiPSCs are maintained on feeder cells while passaged as clumps to prevent extensive cell death and genomic aberrations (Thomson et al., 1998). The inability to single cell culture hiPSCs in a feeder-free (FF) environment severely limits potential industrial scale screening or cell therapy applications (Skottman et al., 2007; Valamehr et al., 2011). In addition, recent efforts on improving hiPSCs have focused on lentiviral derived hiPSC that were not transgene-free, limiting the therapeutic relevance of such efforts. Another challenge yet to be successfully addressed, short of genome modification, is the propensity for spontaneous differentiation of human pluripotent stem cells in culture (Pera and Trounson, 2004; Sathananthan and Trounson, 2005; Valamehr et al., 2011). Studies in hESCs and hiPSCs have been described, but continuous ectopic expression of pluripotency genes were necessary to maintain the ground state resulting in genome modified human pluripotent stem cells (Hanna et al., 2010a), which are unsuitable for industrial- and clinical-grade pluripotent cells. Accordingly, the absence of compositions and methods for high-throughput, transgene or footprint free generation of human pluripotent cell products has thus far proven to be a substantial hurdle in the development and commercialization of future pluripotent stem cell therapies. BRIEF SUMMARY The invention generally provides improved cell culture platforms. In various embodiments, the invention contemplates, in part, a composition comprising: (a) a Wnt pathway agonist; (b) a MEK inhibitor; and (c) a ROCK inhibitor, wherein the composition does not comprise a TGFβR inhibitor. In particular embodiments, the Wnt pathway agonist is a GSK3 inhibitor. In certain embodiments, the GSK3 inhibitor is CHIR99021 or BIO. In additional embodiments, the MEK inhibitor is PD98059 or PD032901. In further embodiments, the ROCK inhibitor is thiazovivin or Y27632. In some embodiments, the GSK3 inhibitor is CHIR99021; the MEK inhibitor is PD032901; and the ROCK inhibitor is thiazovivin. In certain embodiments, any of the foregoing compositions further comprises bFGF or LIF. In further embodiments, any of the foregoing compositions further comprises bFGF and LIF. In various embodiments, a culture medium is provided comprising any of the foregoing compositions, wherein the medium does not comprise a TGFβR inhibitor. In some embodiments, a method of culturing one or more pluripotent cells comprising culturing the one or more pluripotent cells in a cell culture medium according to any of the foregoing culture media. In additional embodiments, the one or more pluripotent cells are embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs). In particular embodiments, the one or more pluripotent cells are iPSCs. In certain embodiments, the composition comprises a population of pluripotent cells. In further embodiments, the population of pluripotent cells is a hom