US20140234963A1 - Efficient induction of definitive endoderm from pluripotent stem cells - Google Patents

Efficient induction of definitive endoderm from pluripotent stem cells Download PDF

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US20140234963A1
US20140234963A1 US14/127,296 US201214127296A US2014234963A1 US 20140234963 A1 US20140234963 A1 US 20140234963A1 US 201214127296 A US201214127296 A US 201214127296A US 2014234963 A1 US2014234963 A1 US 2014234963A1
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chir
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Nina Funa
Katja Hess
Jenny Ekberg
Henrik Semb
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Novo Nordisk AS
Takara Bio Europe AB
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Definitions

  • the present invention relates to a method to differentiate pluripotent stem cells to a primitive streak cell population, in a stepwise manner for further maturation to definitive endoderm.
  • DE cells from pluripotent embryonic stem (ES) cells has been reported for both mouse and human in, e.g., WO2005/116073, WO2005/063971, and US 2006/0148081.
  • the generation of pancreatic endoderm (PE) cells from DE cells is necessary for the generation of insulin-producing beta cells for the treatment of diabetes.
  • CHIR is a glycogen synthase kinase 3 beta (Gsk3b) inhibitor and a known component of a defined tissue culture medium to maintain mouse embryonic stem cells in the pluripotent state (Ying et al Nature 453, 519-523).
  • Gsk3b has multiple targets but is mainly known to regulate degradation and/or nuclear transfer of beta-catenin.
  • the role of stabilized beta-catenin in PS formation from human embryonic stem cells (hESC) has been described using other glycogen synthase kinase 3 beta (Gsk3b) inhibitors such as BIO and Wnt3a.
  • CHIR is the most selective Gsk3b-inhibitor reported to date.
  • the present invention relates to the utilization of CHIR without AA, at a defined concentration range to treat pluripotent stem cells prior to AA-mediated definitive endoderm induction compared to the conventional induction protocol for obtaining DE (D'Amour protocol, as described in Kroon et al. 2008).
  • This sequential exposure, first to CHIR and then to AA, is essential and reflects successive PS formation (induced by CHIR) followed by more efficient and rapid DE formation by AA.
  • the present invention relates to the discrete and successive control of induction of first PS then followed by DE leading to an overall more efficient, with earlier peak of SOX17 expression and robust DE protocol.
  • Ctrl No Chir treatment D1. Cells are left in RPMI during priming period, followed by AA D2 and AA+serum replacement (B27) from D3 onwards.
  • FIG. 1 shows the CHIR DE protocol nomenclature and overview. The protocol has been confirmed in 7 different pluripotent stem cell lines: SA121, SA181, SA461, SA167 (human ESCs) and chIPS2, chIPS3, chIPS4 (human iPSCs).
  • FIG. 2 shows transcriptional expression of PS markers Brachyury (T), MIXL1, EOMES and Goosecoid (GSC) after 24 h of CHIR treatment (D1) in hES SA121 ( FIG. 2A ) and chIPS4 ( FIG. 2B ), compared to non-treated cells. T protein levels were also confirmed with ICC ( FIG. 2C ). T fold inductions after 24 h CHIR treatment have spanned between 500-100000 compared to undifferentiated cells (n>60). Bars show Log 10 values relative to undifferentiated cells D0.
  • FIG. 3 shows gene expression of DE markers (SOX17, CXCR4, FOXA2, CER) one day after replacing CHIR with ActivinA (AA) compared to with cells that were not pretreated with CHIR. Expression is shown both in hESC SA121 ( FIG. 3A ) and iPSC chIPS4 ( FIG. 3B ). Bars show Log 10 values relative to undifferentiated cells D0.
  • FIG. 4 shows hESC SA121 ( 4 A-B) and iPSC chIPS4 ( 4 C) cells treated with either CHIR (3 ⁇ M), BIO (0.5 uM), Wnt3a (200 ng/ml) or AA alone (100 ng/ml) for 24 h (D1) prior to 2 d AA treatment (D3). Additionally, D'Amour (protocol as described in Kroon et al 2008) was analyzed. Expression of Brachyury and SOX17 was analyzed. hES cells treated with AA or BIO for the first 24 h did not survive until day 3.
  • FIG. 5 shows gene expression levels of DE markers SOX17, FOXA2 and CXCR4 ( FIG. 5A-C ) and OCT4 ( FIG. 5E ) after CHIR induction compared to D'Amour and quantified ICC protein levels of SOX17/OCT4 in chIPS4 cells ( FIG. 5D , F). Corresponding % of cells positively stained for OCT4 and SOX17 (D1-3) are also indicated in Table 2.
  • chIPS/SA121 DE cells using either of the two protocols, were further differentiated towards pancreatic endoderm (PE) using a previously published PE differentiation protocol (Amen et al 2010). Cells were analyzed after seven days of PE induction using ICC for PDX1 protein levels.
  • PE pancreatic endoderm
  • FIG. 6 shows gene expression of SOX17 D3 in hES SA121 ( FIG. 6A ) or chIPS4 ( FIG. 6C ) treated with either only RPMI, AA and Wnt3a or CHIR D1 followed by treatment with either AA or a combination of AA and Wnt3a D2 and AA D3 ( FIG. 6A ).
  • Cells were also treated with either CHIR D1 and AA D2 (“CHIR”), D'Amour, or CHIR on top of D'Amour and were analyzed for SOX17 expression ( FIG. 6B ) and morphology ( FIG. 6C ).
  • CHIR D1 and AA D2 (“CHIR”)
  • D'Amour D'Amour
  • CHIR CHIR on top of D'Amour
  • FIG. 7 shows that CHIR was titrated at concentrations between 1-7 uM and analysed after 24 h (D1) and after 2 d of following AA treatment (D3). CHIR 0.5-1 uM and CHIR 7 uM did not survive D3. Brachyury expression was analysed after 24 h treatment in SA121 ( FIG. 7A ) and chIPS cells ( FIG. 7C ). SOX17 expression was analysed D3 in SA121 ( FIG. 7B ) and chIPS cells ( FIG. 7D )).
  • FIG. 8 shows gene expression of SOX17 D3 after CHIR pre-treatment or after the D'Amour protocol in the mTeSR system ( FIG. 8 ).
  • FIG. 9 shows gene expression levels of markers Brachyury and SOX17 at D0, D2 and D3 when cultured on MEFfeeders.
  • the present invention also relates to a method for differentiation of stem cells into definitive endoderm comprising the steps of:
  • the present invention relates to a faster and more pronounced peak of SOX17 expression and a more robust method of differentiating human pluripotent stem cells to obtain definitive endoderm.
  • the present invention relates to a method for differentiation of stem cells into definitive endoderm comprising the steps of incubating pluripotent stem cells in a medium comprising at least 2 ⁇ M CHIR and subsequently incubating these cells in a medium comprising Activin A (AA).
  • the present inventors have found that using CHIR alone for 24 h prior to further addition of AA, induced a significant and dose dependent upregulation of PS markers such as Brachyury, Mixl1, Eomes and Goosecoid (GSC) during these 24 h.
  • PS markers such as Brachyury, Mixl1, Eomes and Goosecoid (GSC) during these 24 h.
  • the present inventors have surprisingly found that in the subsequent incubation with AA to induce DE, DE induction as measured by SOX17 expression, peaked at an earlier time point and with higher fold change when compared to cultures without CHIR pre-incubation or when compared to the conventional D'Amour protocol (Novocell, Nature Biotec 2006, 2008).
  • the present inventors surprisingly found that the method of the present invention was more efficient and showed a faster induction of Sox17 mRNA expression than other known protocols for DE Induction.
  • the CHIR-mediated effect has been reproduced both in other culture systems (mTeSR media and conventional ES media on mouse embryonic feeder (MEF) cells) and across different cell lines (SA121, SA181, SA461, SA167, chIPS2, chIPS3, chIPS4), showing that the effect is not dependent on the cell line or the DEF media culture system.
  • Human embryonic stem cells may be derived from single blastomeres without the destruction of the embryo (Klimanskaya et al. 2006; Chung et al. 2008; Geens et al. 2009).
  • Cell lines chIPS2, chIPS3, chIPS4 are iPS cell lines.
  • CHIR CHIR promotes high cell densities after AA is added. Dose dependency of CHIR in PS induction will allow future optimization of possible pre-patterning influences when initiating AA treatment. The subsequent order of added factors decreases the amount of signaling pathways that are activated in parallel. Minimizing the amount of factors that may influence the efficiency should promote robustness and reproducibility.
  • the present inventors have surprisingly found that the CHIR-priming step is unique for DE induction and was superior when compared to BIO or Wnt3a when it comes to efficiency peak of SOX17 expression and robustness.
  • hESCs Human embryonic stem cells
  • iPSCs human induced pluripotent stem cells
  • the present inventors have surprisingly found the CHIR-priming step resulted in a remarkably fast induction of SOX17 by AA peaking already after 1 day which is in contrast to AA alone where the peak is seen only after 3-4 days.
  • the sequential incubation with CHIR followed by AA is essential for DE formation to favourable levels.
  • the pancreatic endocrine cells obtainable by the method according to the invention are insulin producing cells, optionally together with cells differentiated towards glucagon, somatostatin, pancreatic polypeptide, and/or ghrelin producing cells.
  • insulin producing cells refers to cells that produce and store or secrete detectable amounts of insulin.
  • Insulin producing cells can be individual cells or collections of cells.
  • the cell population comprising pancreatic cells is obtained from a somatic cell population.
  • the somatic cell population has been induced to de-differentiate in to an embryonic-like stem (ES, e.g., a pluripotent) cell.
  • ES embryonic-like stem
  • IPS induced pluripotent stem cells
  • the cell population comprising pancreatic cells is obtained from embryonic stem (ES, e.g., pluripotent) cells.
  • ES embryonic stem
  • the cell population comprising pancreatic cells is pluripotent cells such as ES like-cells.
  • the cell population comprising pancreatic cells is embryonic differentiated stem (ES or pluripotent) cells. Differentiation takes place in embryoid bodies and/or in monolayer cell cultures or a combination thereof.
  • ES embryonic differentiated stem
  • the cell population is a population of stem cells.
  • the cell population is a population of stem cells differentiated to the pancreatic endocrine lineage.
  • Stem cells are undifferentiated cells defined by their ability at the single cell level to both self-renew and differentiate to produce progeny cells, including self-renewing progenitors, non-renewing progenitors, and terminally differentiated cells. Stem cells are also characterized by their ability to differentiate in vitro into functional cells of various cell lineages from multiple germ layers (endoderm, mesoderm and ectoderm), as well as to give rise to tissues of multiple germ layers following transplantation and to contribute substantially to most, if not all, tissues following injection into blastocysts.
  • Stem cells are classified by their developmental potential as: (1) totipotent, meaning able to give rise to all embryonic and extra embryonic cell types; (2) pluripotent, meaning able to give rise to all embryonic cell types; (3) multi-potent, meaning able to give rise to a subset of cell lineages, but all within a particular tissue, organ, or physiological system (for example, hematopoietic stem cells (HSC) can produce progeny that include HSC (self-renewal), blood cell restricted oligopotent progenitors and all cell types and elements (e.g., platelets) that are normal components of the blood); (4) oligopotent, meaning able to give rise to a more restricted subset of cell lineages than multi-potent stem cells; and (5) unipotent, meaning able to give rise to a single cell lineage (e.g., spermatogenic stem cells).
  • HSC hematopoietic stem cells
  • a protocol for obtaining pancreatic cells from stem cells is exemplified by, but not limited to, the protocols described in D'Amour, K. A. et al. (2006), Nat Biotechnol 24, 1392-401; Jiang, J. et al. (2007), Stem Cells 25, 1940-53; and Kroon, E. et al. (2008), Nat Biotechnol 26, 443-452.
  • a protocol for obtaining pancreatic cells from somatic cells or somatic cells induced to de-differentiate into pluripotent cells such as ES like-cells is exemplified by, but not limited to, the protocols described in Aoi, T. et al. (2008), Science 321 (no. 5889), 699-702; D'Amour, K. A. et al. (2006), Nat Biotechnol 24, 1392-401; Jiang, J. et al. (2007), Stem Cells 25, 1940-53; Kroon, E. et al. (2008), Nat Biotechnol 26, 443-452; Takahashi, K. et al. (2007), Cell 131, 861-72; Takahashi, K., and Yamanaka, S. (2006), Cell 126, 663-76; and Wernig, M. et al. (2007), Nature 448, 318-24.
  • differentiate refers to a process where cells progress from an undifferentiated state to a differentiated state, from an immature state to a less immature state or from an immature state to a mature state.
  • characteristics markers like Pdx1, Nkx6.1, and Ptf1a.
  • Mature or differentiated pancreatic cells do not proliferate and do secrete high levels of pancreatic endocrine hormones or digestive enzymes.
  • fully differentiated beta cells secrete insulin at high levels in response to glucose. Changes in cell interaction and maturation occur as cells lose markers of undifferentiated cells or gain markers of differentiated cells.
  • differentiation factor refers to a compound added to pancreatic cells to enhance their differentiation to mature endocrine cells also containing insulin producing beta cells.
  • exemplary differentiation factors include hepatocyte growth factor, keratinocyte growth factor, exendin-4, basic fibroblast growth factor, insulin-like growth factor-1, nerve growth factor, epidermal growth factor platelet-derived growth factor, and glucagon-like peptide 1.
  • differentiation of the cells comprises culturing the cells in a medium comprising one or more differentiation factors.
  • human pluripotent stem cells refers to cells that may be derived from any source and that are capable, under appropriate conditions, of producing human progeny of different cell types that are derivatives of all of the 3 germinal layers (endoderm, mesoderm, and ectoderm). hPS cells may have the ability to form a teratoma in 8-12 week old SCID mice and/or the ability to form identifiable cells of all three germ layers in tissue culture. Included in the definition of human pluripotent stem cells are embryonic cells of various types including human blastocyst derived stem (hBS) cells in 30 literature often denoted as human embryonic stem (hES) cells, (see, e.g., Thomson et al.
  • hBS human blastocyst derived stem
  • hES human embryonic stem
  • hPS cells suitable for use may be obtained from developing embryos.
  • suitable hPS cells may be obtained from established cell lines and/or human induced pluripotent stem (hiPS) cells.
  • hiPS cells refers to human induced pluripotent stem cells.
  • the term “blastocyst-derived stem cell” is denoted BS cell, and the human form is termed “hBS cells”.
  • BS cell the human form
  • the pluripotent stem cells used in the present invention can thus be embryonic stem cells prepared from blastocysts, as described in e.g. WO 03/055992 and WO 2007/042225, or be commercially available hBS cells or cell lines.
  • any human pluripotent stem cell can be used in the present invention, including differentiated adult cells which are reprogrammed to pluripotent cells by e.g. the treating adult cells with certain transcription factors, such as OCT4, SOX2, NANOG, and LIN28 as disclosed in Yu, et al., 2007, Takahashi et al. 2007 and Yu et al 2009.
  • feeder cells are intended to mean supporting cell types used alone or in combination.
  • the cell type may further be of human or other species origin.
  • the tissue from which the feeder cells may be derived include embryonic, fetal, neonatal, juvenile or adult tissue, and it further includes tissue derived from skin, including foreskin, umbilical chord, muscle, lung, epithelium, placenta, fallopian tube, glandula, stroma or breast.
  • the feeder cells may be derived from cell types pertaining to the group consisting of human fibroblasts, fibrocytes, myocytes, keratinocytes, endothelial cells and epithelial cells.
  • Examples of specific cell types that may be used for deriving feeder cells include embryonic fibroblasts, extra embryonic endodermal cells, extra embryonic mesoderm cells, fetal fibroblasts and/or fibrocytes, fetal muscle cells, fetal skin cells, fetal lung cells, fetal endothelial cells, fetal epithelial cells, umbilical chord mesenchymal cells, placental fibroblasts and/or fibrocytes, placental endothelial cells,
  • MEF cells is intended to mean mouse embryonic fibroblasts.
  • CHIR glycogen synthase kinase 3 beta
  • bFGF basic fibroblast growth factor (FGF2)
  • Gsk3b glycogen synthase kinase 3 beta
  • hESC human embryonic stem cells
  • hIPSC human induced pluripotent cells
  • hPSC human pluripotent stem cells
  • RNA ribonucleic acid
  • SOX17 SRY (sex determining region Y)-box 17
  • the DE protocol was confirmed in two different feeder free (DEF, mTeSR) culture systems and one feeder dependent (MEF-ES) culture system.
  • hES cells SA121 and chIPS4 were grown on human fibronectin (Sigma) in DEF culture media (Cellartis) with 30 ng/ml bFGF (Invitrogen) and 10 ng/ml Noggin (Peprotech) in 6-96 well plates.
  • Cells were single cell passaged with Rock inhibitor Y-27632 (Calbiochem) and seeded at a density of 40000 cells/cm2 for experiments. Experiments were initiated 4 d after passage.
  • hES cells were cluster passaged from feeders (MEFs) to Matrigel (BD Biosciences) in mTeSR1 media (Cell Signaling Technologies) and passaged further with Dispase (BD Biosciences) according to the culture system protocol. DE was initiated once clusters started to touch each other
  • hES cells (SA121) were passaged on gelatine-coated plates pre-seeded with MEFs in hES media (KO-DMEM, PEST, Glutamax, NEAA, 2-mercaptoethanol, KO serum replacement, 10 ng/ml bFGF). DE was initiated at 80% confluency.
  • FIG. 1 Overview of the CHIR Definitive Endoderm protocol can be found in FIG. 1 .
  • the protocol has been confirmed in 7 different cell lines: SA121, SA181, SA461, SA167 (hESC) and chIPS2, chIPS3, chIPS4 (hiPSC).
  • Day 3&4 mediums were premixed (100 ng/ml Activin A and 2% B27 in prewarmed RPMI+0.1% PEST) and gently added to cell culture.
  • RNA samples were collected after 24 h pre-treatment (D1), after 1 day of AA treatment (D2) and after 1-2 d of AA+B27 treatment (D3-4). Total RNA was extracted with the Rneasy Plus Mini kit (Qiagen) and quantitative real-time PCR was performed using the StepOnePLus system (Applied Biosystems).
  • Undifferentiated SA121 hES and chIPS4 iPS cells in DEF media were cultured either in RPMI without CHIR (Ctrl D1) or treated for 24 h with CHIR in RPMI (CHIR D1). The cells were then washed to ensure absence of CHIR and then both conditions were treated with 1 d AA (Ctrl and CHIR d2). After 1 d CHIR treatment, PS markers such as Brachyury (T), MIXL1, EOMES and GSC were highly upregulated compared to non pre-treated cells ( FIG. 2A-C ). T fold inductions after 24 h CHIR treatment spanned between 500-100000 compared to undifferentiated cells (d0). T protein levels were also confirmed with ICC ( FIG. 2C ).
  • SOX17 expression peaked already after one day of AA treatment when cells were subjected to CHIR for 24 h before AA induction.
  • Cells in AA-containing media that were not pre-treated with CHIR (ctrl) did not show same speed or efficiency in Sox17 induction.
  • CHIR has a direct capacity to induce PS markers after 24 h treatment (D1) and resulted in a remarkably higher ability for AA to induce DE when added (D2). Brachyury was greatly repressed once AA was added indicating that the cells were differentiating in a highly stepwise order.
  • OCT4 and SOX17 protein ICC quantifications in undifferentiated hES SA121/chIPS4 cells OCT4 SOX17 SA121 chIPS4 SA121 chIPS4 ICC % D'Amour CHIR D'Amour CHIR D'Amour CHIR D'Amour CHIR Undiff 97.5 98.3 0 0 D1 91.9 97.7 94.3 91.2 0 0 8.3 0.9 D2 55.2 2.4 14 3.1 61.6 72.1 75.2 68.8 D3 44.1 0.2 26.2 3.7 80.4 93.1 77.6 91.5
  • Table 2 shows D1-3 of DE induction according to D'Amour (protocol as described in Kroon et al 2008) and cells treated with 3 uM CHIR (CHIR D1) prior to addition of ActivinA (CHIR D2-3).
  • hES SA121 and ChIPS4 cells were treated with either CHIR (3 ⁇ M), BIO (0.5 uM), Wnt3a (200 ng/ml) or AA alone (100 ng/ml) for 24 h prior to AA addition to show CHIR specificity (d1). Additionally, D'Amour (protocol as described in Kroon et al 2008) was tested in parallel. CHIR treatment significantly upregulated Brachyury expression after 24 h (FIG. 4 A,C). After AA addition (D2), Brachyury was reduced and SOX17 was upregulated ( FIG. 4B ). hES cells treated with AA or BIO did not survive until day 3.
  • Undifferentiated ChIPS4 cells (d0) were either pre-treated for 24 h with CHIR (3 uM) or directly exposed to AA (100 ng/ml) and Wnta3a (25 ng/ml) according to Kroon et al 2008. The cells were then washed and AA was added for 1-4 d. See Table 1 for detailed setup.
  • CHIR treatment was superior in upregulating both T (mRNA D1) and SOX17 after CHIR pre-treatment (mRNA, ICC D3) compared to D'Amour ( FIG. 5 and Table 2).
  • mRNA D1 mRNA D1
  • SOX17 SOX17 after CHIR pre-treatment
  • ICC D3 D'Amour
  • the most striking difference between the protocols could be seen in terms of morphology with a much higher degree of cell death during D'Amour treatment.
  • chIPS4 cells treated with either the CHIR- or D'Amour-protocol were fixed and stained using a SOX17-specific ab and the images were quantified in respect of total amounts and the percentage of SOX17-positive cells. As shown in FIG.
  • chIPS4 cells differentiated to DE were further differentiated towards pancreatic endoderm (PE) by using a previously published PE differentiation protocol (Amen et al 2010). Seven days after the induction of PE differentiation the cells were fixed and analyzed by ICC using a PDX1 specific antibody. The results showed very modest PDX1-staining in the D'Amour-treated cells whereas the staining was evident in the CHIR pre-treated cells (data not shown). In parallel, mRNA was collected from the cells and the PDX1 expression was analyzed by real-time PCR.
  • Cells were pre-treated 1 d with either RPMI (ctrl), CHIR 3 uM, CHIR 3 uM+AA 100 ng/ml or 100 ng/ml AA+25 ng/ml Wnt3a (D'Amour) prior to addition of AA+/ ⁇ Wnt3a (25 ng/ml) d2 and AA d3 (Table 3).
  • B27 was added in Ctrl and CHIR d3 and FBS to D'Amour d2-3.
  • CHIR pretreatment replaces the requirement of both Wnt3a and AA during the first day of differentiation toward DE and also has a stabilizing effect leading to a more robust protocol.
  • CHIR and exogenous AA may have counteracting effects that reduce overall efficiency and/or target different cell populations differently, resulting in higher levels of heterogeneity within the cell culture and increased inter-experimental variability. This suggests that PS induction/transition before adding AA to the media is an important and novel step to enhance protocol efficiency and robustness.
  • Chir was titrated at concentrations between 1-7 uM and analyzed after 24 h Chir treatment (D1) and after 2 d of following AA treatment (D3). CHIR 0.5-1 uM and CHIR 7 uM did not survive d3.
  • the data indicates that PS formation is delayed at Chir concentrations under 1 uM, unabling further progression toward DE when AA is added.

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