Advertisement

Optimization of Differentiation of Nonhuman Primate Pluripotent Cells Using a Combinatorial Approach

  • Steven L. Farnsworth
  • Zhifang Qiu
  • Anuja Mishra
  • Peter J. HornsbyEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1919)

Abstract

The directed differentiation of pluripotent stem cells to a desired lineage often involves complex and lengthy protocols. In order to study the requirements for differentiation in a systematic way, we present here methodology for an iterative approach using combinations of small molecules and biological factors. The factors are used in a cyclical process in which the best combination of factors and concentrations is selected in one round of testing, followed by a modification of the combination and subsequent rounds. While this may produce the desired differentiation in the cell population under study, it is also possible that other strategies may be needed to optimize the differentiation process. These strategies are described in this chapter.

Key words

Pluripotent stem cells Nonhuman primates Differentiation Algorithms Gene expression 

References

  1. 1.
    Farnsworth SL, Qiu Z, Mishra A, Hornsby PJ (2013) Directed neural differentiation of induced pluripotent stem cells from non-human primates. Exp Biol Med 238:276–284CrossRefGoogle Scholar
  2. 2.
    Tsutsui H, Valamehr B, Hindoyan A, Qiao R, Ding X, Guo S, Witte ON, Liu X, Ho CM, Wu H (2011) An optimized small molecule inhibitor cocktail supports long-term maintenance of human embryonic stem cells. Nat Commun 2:167CrossRefGoogle Scholar
  3. 3.
    Wu Y, Zhang Y, Mishra A, Tardif SD, Hornsby PJ (2010) Generation of induced pluripotent stem cells from newborn marmoset skin fibroblasts. Stem Cell Res 4:180–188CrossRefGoogle Scholar
  4. 4.
    Mishra A, Qiu Z, Farnsworth SL, Hemmi JJ, Li M, Pickering AV, Hornsby PJ (2016) Induced pluripotent stem cells from nonhuman primates. Methods Mol Biol 1357:183–193CrossRefGoogle Scholar
  5. 5.
    Hong CC, Yu PB (2009) Applications of small molecule BMP inhibitors in physiology and disease. Cytokine Growth Factor Rev 20:409–418CrossRefGoogle Scholar
  6. 6.
    Hollnagel A, Oehlmann V, Heymer J, Ruther U, Nordheim A (1999) Id genes are direct targets of bone morphogenetic protein induction in embryonic stem cells. J Biol Chem 274:19838–19845CrossRefGoogle Scholar
  7. 7.
    Ying QL, Nichols J, Chambers I, Smith A (2003) BMP induction of id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell 115:281–292CrossRefGoogle Scholar
  8. 8.
    Inman GJ, Nicolas FJ, Callahan JF, Harling JD, Gaster LM, Reith AD, Laping NJ, Hill CS (2002) SB-431542 is a potent and specific inhibitor of transforming growth factor-beta superfamily type I activin receptor-like kinase (ALK) receptors ALK4, ALK5, and ALK7. Mol Pharmacol 62:65–74CrossRefGoogle Scholar
  9. 9.
    Farberov S, Meidan R (2016) Thrombospondin-1 affects bovine luteal function via transforming growth factor-Beta1-dependent and independent actions. Biol Reprod 94:25CrossRefGoogle Scholar
  10. 10.
    Gudey SK, Sundar R, Heldin CH, Bergh A, Landstrom M (2017) Pro-invasive properties of Snail1 are regulated by sumoylation in response to TGFbeta stimulation in cancer. Oncotarget 8:97703–97726CrossRefGoogle Scholar
  11. 11.
    De Jaime-Soguero A, Aulicino F, Ertaylan G, Griego A, Cerrato A, Tallam A, Del Sol A, Cosma MP, Lluis F (2017) Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus. PLoS Genet 13:e1006682CrossRefGoogle Scholar
  12. 12.
    Kang Y, Hodges A, Ong E, Roberts W, Piermarocchi C, Paternostro G (2014) Identification of drug combinations containing imatinib for treatment of BCR-ABL+ leukemias. PLoS One 9:e102221CrossRefGoogle Scholar
  13. 13.
    Ding X, Matsuo K, Xu L, Yang J, Zheng L (2015) Optimized combinations of bortezomib, camptothecin, and doxorubicin show increased efficacy and reduced toxicity in treating oral cancer. Anti-Cancer Drugs 26:547–554CrossRefGoogle Scholar
  14. 14.
    Weiss A, Ding X, van Beijnum JR, Wong I, Wong TJ, Berndsen RH, Dormond O, Dallinga M, Shen L, Schlingemann RO, Pili R, Ho CM, Dyson PJ, van den Bergh H, Griffioen AW, Nowak-Sliwinska P (2015) Rapid optimization of drug combinations for the optimal angiostatic treatment of cancer. Angiogenesis 18:233–244CrossRefGoogle Scholar
  15. 15.
    Weiss A, Berndsen RH, Ding X, Ho CM, Dyson PJ, van den Bergh H, Griffioen AW, Nowak-Sliwinska P (2015) A streamlined search technology for identification of synergistic drug combinations. Sci Rep 5:14508CrossRefGoogle Scholar
  16. 16.
    Liu Q, Zhang C, Ding X, Deng H, Zhang D, Cui W, Xu H, Wang Y, Xu W, Lv L, Zhang H, He Y, Wu Q, Szyf M, Ho CM, Zhu J (2015) Preclinical optimization of a broad-spectrum anti-bladder cancer tri-drug regimen via the feedback system control (FSC) platform. Sci Rep 5:11464CrossRefGoogle Scholar
  17. 17.
    Ding X, Njus Z, Kong T, Su W, Ho CM, Pandey S (2017) Effective drug combination for Caenorhabditis elegans nematodes discovered by output-driven feedback system control technique. Sci Adv 3:eaao1254CrossRefGoogle Scholar
  18. 18.
    Chambers SM, Fasano CA, Papapetrou EP, Tomishima M, Sadelain M, Studer L (2009) Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat Biotechnol 27:275–280CrossRefGoogle Scholar
  19. 19.
    Eiraku M, Watanabe K, Matsuo-Takasaki M, Kawada M, Yonemura S, Matsumura M, Wataya T, Nishiyama A, Muguruma K, Sasai Y (2008) Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell 3:519–532CrossRefGoogle Scholar
  20. 20.
    Zhou J, Su P, Li D, Tsang S, Duan E, Wang F (2010) High-efficiency induction of neural conversion in human ESCs and human induced pluripotent stem cells with a single chemical inhibitor of transforming growth factor beta superfamily receptors. Stem Cells 28:1741–1750CrossRefGoogle Scholar
  21. 21.
    Morizane A, Doi D, Kikuchi T, Nishimura K, Takahashi J (2011) Small-molecule inhibitors of bone morphogenic protein and activin/nodal signals promote highly efficient neural induction from human pluripotent stem cells. J Neurosci Res 89:117–126CrossRefGoogle Scholar
  22. 22.
    Yu PB, Hong CC, Sachidanandan C, Babitt JL, Deng DY, Hoyng SA, Lin HY, Bloch KD, Peterson RT (2008) Dorsomorphin inhibits BMP signals required for embryogenesis and iron metabolism. Nat Chem Biol 4:33–41CrossRefGoogle Scholar
  23. 23.
    Vogt J, Traynor R, Sapkota GP (2011) The specificities of small molecule inhibitors of the TGF and BMP pathways. Cell Signal 23:1831–1842CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Steven L. Farnsworth
    • 1
  • Zhifang Qiu
    • 1
  • Anuja Mishra
    • 1
  • Peter J. Hornsby
    • 1
    Email author
  1. 1.Department of Cellular and Integrative Physiology and Barshop Institute for Longevity and Aging StudiesUniversity of Texas Health San AntonioSan AntonioUSA

Personalised recommendations