Reprogram or reboot: small molecule approaches for the production of induced pluripotent stem cells and direct cell reprogramming.

Stem cell transplantation is a potential therapy for regenerative medicine, which aims to restore tissues damaged by trauma, aging, and diseases. Since its conception in the late 1990s, chemical biology has provided powerful and diverse small molecule tools for modulating stem cell function. Embryonic stem cells could be an ideal source for transplantation, but ethical concerns restrict their development for cell therapy. The seminal advance of induced pluripotent stem cell (iPSC) technology provided an attractive alternative to human embryonic stem cells. However, iPSCs are not yet considered an ideal stem cell source, due to limitations associated with the reprogramming process and their potential tumorigenic behavior. This is an area of research where chemical biology has made a significant contribution to facilitate the efficient production of high quality iPSCs and elucidate the biological mechanisms governing their phenotype. In this review, we summarize these advances and discuss the latest progress in developing small molecule modulators. Moreover, we also review a new trend in stem cell research, which is the direct reprogramming of readily accessible cell types into clinically useful cells, such as neurons and cardiac cells. This is a research area where chemical biology is making a pivotal contribution and illustrates the many advantages of using small molecules in stem cell research.

[1]  E. Jho,et al.  Wnt/β-catenin signalling: from plasma membrane to nucleus. , 2013, The Biochemical journal.

[2]  Peter G. Schultz,et al.  A Chemical Genomic Analysis of Decoquinate, a Plasmodium falciparum Cytochrome b Inhibitor , 2011, ACS chemical biology.

[3]  Robert Zweigerdt,et al.  Scalable expansion of human pluripotent stem cells in suspension culture , 2011, Nature Protocols.

[4]  Lee E. Edsall,et al.  Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. , 2010, Cell stem cell.

[5]  J. Wrana,et al.  Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. , 2010, Cell stem cell.

[6]  Wenjun Guo,et al.  Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds , 2008, Nature Biotechnology.

[7]  J. Shay,et al.  A role for both RB and p53 in the regulation of human cellular senescence. , 1991, Experimental cell research.

[8]  K. Okkenhaug.  Signaling by the phosphoinositide 3-kinase family in immune cells. , 2013, Annual review of immunology.

[9]  Timothy J. Laurent,et al.  Conversion of Human Fibroblasts to Functional Endothelial Cells by Defined Factors , 2013, Arteriosclerosis, thrombosis, and vascular biology.

[10]  D. Beach,et al.  A high glycolytic flux supports the proliferative potential of murine embryonic stem cells. , 2006, Antioxidants & redox signaling.

[11]  Jeroen S. van Zon,et al.  Direct cell reprogramming is a stochastic process amenable to acceleration , 2009, Nature.

[12]  R. Cortese,et al.  The Aurora B kinase activity is required for the maintenance of the differentiated state of murine myoblasts , 2009, Cell Death and Differentiation.

[13]  E. Monti,et al.  Reversine-treated fibroblasts acquire myogenic competence in vitro and in regenerating skeletal muscle , 2006, Cell Death and Differentiation.

[14]  R. Pedersen,et al.  The role of E-cadherin and integrins in mesoderm differentiation and migration at the mammalian primitive streak. , 1993, Development.

[15]  Qi Zhou,et al.  Brief Report: Combined Chemical Treatment Enables Oct4‐Induced Reprogramming from Mouse Embryonic Fibroblasts , 2011, Stem cells.

[16]  F. López-Muñoz,et al.  Monoaminergic neurotransmission: the history of the discovery of antidepressants from 1950s until today. , 2009, Current pharmaceutical design.

[17]  H. Deng,et al.  Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small-Molecule Compounds , 2013, Science.

[18]  J. I. Izpisúa Belmonte,et al.  Mitochondrial regulation in pluripotent stem cells. , 2013, Cell metabolism.

[19]  Jialiang Liang,et al.  A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. , 2010, Cell stem cell.

[20]  Eric S. Lander,et al.  Dissecting direct reprogramming through integrative genomic analysis , 2008, Nature.

[21]  Thomas Scheper,et al.  Long term expansion of undifferentiated human iPS and ES cells in suspension culture using a defined medium. , 2010, Stem cell research.

[22]  Manuel Serrano,et al.  A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity , 2009, Nature.

[23]  R. Nusse,et al.  Towards an integrated view of Wnt signaling in development , 2009, Development.

[24]  J. Adjaye,et al.  A Cyclic AMP Analog, 8-Br-cAMP, Enhances the Induction of Pluripotency in Human Fibroblast Cells , 2011, Stem Cell Reviews and Reports.

[25]  Hideyuki Okano,et al.  Steps Toward Safe Cell Therapy Using Induced Pluripotent Stem Cells , 2013, Circulation research.

[26]  H. Redl,et al.  Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. , 2010, Cell stem cell.

[27]  W. Reik,et al.  FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency , 2013, Clinical Epigenetics.

[28]  P. Ljungman,et al.  Improved survival after allogeneic hematopoietic stem cell transplantation in recent years. A single-center study. , 2011, Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation.

[29]  Christine Mummery,et al.  Human embryonic stem cells: research, ethics and policy. , 2003, Human reproduction.

[30]  D. Pei,et al.  MicroRNAs in somatic cell reprogramming. , 2013, Current opinion in cell biology.

[31]  Sheng Ding,et al.  Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. , 2008, Cell stem cell.

[32]  W. Reik.  Stability and flexibility of epigenetic gene regulation in mammalian development , 2007, Nature.

[33]  S. Dalton.  Signaling networks in human pluripotent stem cells. , 2013, Current opinion in cell biology.

[34]  Xiaolei Yin,et al.  Two supporting factors greatly improve the efficiency of human iPSC generation. , 2008, Cell stem cell.

[35]  Sheng Ding,et al.  Concise Review: A Chemical Approach to Control Cell Fate and Function , 2012, Stem cells.

[36]  Sheng Ding,et al.  Reprogramming of human primary somatic cells by OCT4 and chemical compounds. , 2010, Cell stem cell.

[37]  D. A. Gomes,et al.  Stem cells and calcium signaling. , 2012, Advances in experimental medicine and biology.

[38]  C. Prigent,et al.  Aurora/Ipl1p-related kinases, a new oncogenic family of mitotic serine-threonine kinases. , 1999, Journal of cell science.

[39]  Haibo Wu,et al.  Vitamin C Enhances Nanog Expression Via Activation of the JAK/STAT Signaling Pathway , 2014, Stem cells.

[40]  Da-Woon Jung,et al.  Small molecules that recapitulate the early steps of urodele amphibian limb regeneration and confer multipotency. , 2012, ACS chemical biology.

[41]  Peter A. Jones,et al.  Multiple new phenotypes induced in 10T 1 2 and 3T3 cells treated with 5-azacytidine , 1979, Cell.

[42]  L. Poellinger,et al.  Dual Inhibition of Src and GSK3 Maintains Mouse Embryonic Stem Cells, Whose Differentiation Is Mechanically Regulated by Src Signaling , 2012, Stem cells.

[43]  J. R. Smith,et al.  Mutant p53 rescues human diploid cells from senescence without inhibiting the induction of SDI1/WAF1. , 1995, Cancer research.

[44]  Roland Rad,et al.  Rapid and efficient reprogramming of somatic cells to induced pluripotent stem cells by retinoic acid receptor gamma and liver receptor homolog 1 , 2011, Proceedings of the National Academy of Sciences.

[45]  L. Cantley,et al.  Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation , 2009, Science.

[46]  S. Park,et al.  Lysophosphatidic acid and adenylyl cyclase inhibitor increase proliferation of senescent human diploid fibroblasts by inhibiting adenosine monophosphate-activated protein kinase. , 2008, Rejuvenation research.

[47]  Zhonghan Li,et al.  A kinase inhibitor screen identifies small-molecule enhancers of reprogramming and iPS cell generation , 2012, Nature Communications.

[48]  S. Ogawa,et al.  Cardiomyocytes can be generated from marrow stromal cells in vitro. , 1999, The Journal of clinical investigation.

[49]  Jie Na,et al.  Reprogramming to pluripotency and differentiation of cells with synthetic mRNA. , 2013, Methods in molecular biology.

[50]  Sheng Ding,et al.  A chemical platform for improved induction of human iPSCs , 2009, Nature Methods.

[51]  Y. Mu,et al.  Direct differentiation of hepatic stem-like WB cells into insulin-producing cells using small molecules , 2013, Scientific Reports.

[52]  Benjamin G. Bitler,et al.  A High-Content Screening Assay for Small-Molecule Modulators of Oncogene-Induced Senescence , 2013, Journal of biomolecular screening.

[53]  N. Schmitz,et al.  Autologous haematopoietic stem cell transplants for autoimmune disease – feasibility and transplant-related mortality , 1999, Bone Marrow Transplantation.

[54]  Jiuhong Kang,et al.  E‐Cadherin‐Mediated Cell–Cell Contact Is Critical for Induced Pluripotent Stem Cell Generation , 2010, Stem cells.

[55]  Peter G Schultz,et al.  Reprogramming of murine fibroblasts to induced pluripotent stem cells with chemical complementation of Klf4 , 2009, Proceedings of the National Academy of Sciences.

[56]  Timothy J. Laurent,et al.  Progress in the reprogramming of somatic cells. , 2013, Circulation research.

[57]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[58]  G. Daley,et al.  From fibroblasts to iPS cells: Induced pluripotency by defined factors , 2008, Journal of cellular biochemistry.

[59]  Jie Na,et al.  Mechanism and methods to induce pluripotency , 2011, Protein & Cell.

[60]  Martin J. Aryee,et al.  Epigenetic memory in induced pluripotent stem cells , 2010, Nature.

[61]  S. Yamanaka,et al.  Maturation, not initiation, is the major roadblock during reprogramming toward pluripotency from human fibroblasts , 2013, Proceedings of the National Academy of Sciences.

[62]  Thomas J. Dougherty,et al.  Antibiotic Discovery and Development , 2012, Springer US.

[63]  J. Utikal,et al.  Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. , 2007, Cell stem cell.

[64]  Qing-song Liu,et al.  Enhancing the efficiency of direct reprogramming of human mesenchymal stem cells into mature neuronal-like cells with the combination of small molecule modulators of chromatin modifying enzymes, SMAD signaling and cyclic adenosine monophosphate levels. , 2013, The international journal of biochemistry & cell biology.

[65]  J. Utikal,et al.  Immortalization eliminates a roadblock during cellular reprogramming into iPS cells , 2009, Nature.

[66]  Peter Wernet,et al.  Small molecules enable highly efficient neuronal conversion of human fibroblasts , 2012, Nature Methods.

[67]  Aaron M. Newman,et al.  Lab-specific gene expression signatures in pluripotent stem cells. , 2010, Cell stem cell.

[68]  G. Peters,et al.  Regulation of p16CDKN2 expression and its implications for cell immortalization and senescence , 1996, Molecular and cellular biology.

[69]  H. Clevers,et al.  Wnt signalling in stem cells and cancer , 2005, Nature.

[70]  Dongsup Kim,et al.  A novel small molecule facilitates the reprogramming of human somatic cells into a pluripotent state and supports the maintenance of an undifferentiated state of human pluripotent stem cells. , 2012, Angewandte Chemie.

[71]  S. Kuang,et al.  Hypoxia promotes satellite cell self-renewal and enhances the efficiency of myoblast transplantation , 2012, Development.

[72]  Susan S. Taylor,et al.  PKA: lessons learned after twenty years. , 2013, Biochimica et biophysica acta.

[73]  Akhilesh Pandey,et al.  Identification of c-Src Tyrosine Kinase Substrates Using Mass Spectrometry and Peptide Microarrays , 2008, Journal of proteome research.

[74]  Adrian Bird,et al.  Perceptions of epigenetics , 2007, Nature.

[75]  Hidenori Akutsu,et al.  A small-molecule inhibitor of tgf-Beta signaling replaces sox2 in reprogramming by inducing nanog. , 2009, Cell stem cell.

[76]  H. Schöler,et al.  A combined chemical and genetic approach for the generation of induced pluripotent stem cells. , 2008, Cell stem cell.

[77]  Shaohui Wang,et al.  Targeting disease through novel pathways of apoptosis and autophagy , 2012, Expert opinion on therapeutic targets.

[78]  Y. Tsunoda,et al.  Role of Histone Acetylation in Reprogramming of Somatic Nuclei Following Nuclear Transfer1 , 2006, Biology of reproduction.

[79]  T. Ichisaka,et al.  Hypoxia enhances the generation of induced pluripotent stem cells. , 2009, Cell stem cell.

[80]  Yuriy L Orlov,et al.  The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. , 2010, Cell stem cell.

[81]  C. Lipinski.  Lead- and drug-like compounds: the rule-of-five revolution. , 2004, Drug discovery today. Technologies.

[82]  V. Vedantham,et al.  Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors , 2010, Cell.

[83]  Hiroshi Ohta,et al.  Significant improvement of mouse cloning technique by treatment with trichostatin A after somatic nuclear transfer. , 2006, Biochemical and biophysical research communications.

[84]  Oliver Brüstle,et al.  Leveling Waddington: the emergence of direct programming and the loss of cell fate hierarchies , 2013, Nature Reviews Molecular Cell Biology.

[85]  S. Weissman,et al.  Cell engineering with synthetic messenger RNA. , 2013, Methods in molecular biology.

[86]  L. Meijer,et al.  Intracellular Targets of Paullones , 2002, The Journal of Biological Chemistry.

[87]  Hans Lehrach,et al.  The Senescence‐Related Mitochondrial/Oxidative Stress Pathway is Repressed in Human Induced Pluripotent Stem Cells , 2010, Stem cells.

[88]  H. Atkins,et al.  Hematopoietic Stem Cell Therapy for Multiple Sclerosis: Top 10 Lessons Learned , 2012, Neurotherapeutics.

[89]  E. Carver,et al.  The Mouse Snail Gene Encodes a Key Regulator of the Epithelial-Mesenchymal Transition , 2001, Molecular and Cellular Biology.

[90]  Andrea Musacchio,et al.  Dissecting the role of MPS1 in chromosome biorientation and the spindle checkpoint through the small molecule inhibitor reversine , 2010, The Journal of cell biology.

[91]  H. Weintraub,et al.  Expression of a single transfected cDNA converts fibroblasts to myoblasts , 1987, Cell.

[92]  A. Wolffe,et al.  Chromatin remodeling: why it is important in cancer , 2001, Oncogene.

[93]  R. Jaenisch,et al.  Pan-Src family kinase inhibitors replace Sox2 during the direct reprogramming of somatic cells. , 2011, Angewandte Chemie.

[94]  P. Schultz,et al.  Reversine increases the plasticity of lineage-committed mammalian cells , 2007, Proceedings of the National Academy of Sciences.

[95]  C. Pereira,et al.  Senescence impairs successful reprogramming to pluripotent stem cells. , 2009, Genes & development.

[96]  S. Moon,et al.  Inhibition of pluripotent stem cell-derived teratoma formation by small molecules , 2013, Proceedings of the National Academy of Sciences.

[97]  Gang Wang,et al.  Conversion of mouse fibroblasts into cardiomyocytes using a direct reprogramming strategy , 2011, Nature Cell Biology.

[98]  Jiannis Ragoussis,et al.  Direct reprogramming of fibroblasts into endothelial cells capable of angiogenesis and reendothelialization in tissue-engineered vessels , 2012, Proceedings of the National Academy of Sciences.

[99]  Yang Xu,et al.  Immunogenicity of induced pluripotent stem cells , 2011, Nature.

[100]  S. Patil,et al.  Natural killer cells – new understanding of basic biology may lead to more effective allogeneic haematopoietic stem cell transplantation , 2009, Internal medicine journal.

[101]  L. Quinlan,et al.  Self-renewal and differentiation of mouse embryonic stem cells as measured by Oct4 expression: the role of the cAMP/PKA pathway , 2007, In Vitro Cellular & Developmental Biology - Animal.

[102]  George Q. Daley,et al.  Reprogramming of human somatic cells to pluripotency with defined factors , 2008, Nature.

[103]  Sheng Ding,et al.  Small molecules that modulate embryonic stem cell fate and somatic cell reprogramming. , 2010, Trends in pharmacological sciences.

[104]  Sheng Ding,et al.  A chemical approach to stem-cell biology and regenerative medicine , 2008, Nature.

[105]  H. Niwa.  Wnt: What's Needed To maintain pluripotency? , 2011, Nature Cell Biology.

[106]  H. Schöler,et al.  Generation of Human‐Induced Pluripotent Stem Cells in the Absence of Exogenous Sox2 , 2009, Stem cells.

[107]  R. Jaenisch,et al.  Reprogramming Efficiency Following Somatic Cell Nuclear Transfer Is Influenced by the Differentiation and Methylation State of the Donor Nucleus , 2006, Stem cells.

[108]  J. Tischfield,et al.  Chromatin structure, pluripotency and differentiation , 2013, Experimental biology and medicine.

[109]  T. Ichisaka,et al.  Suppression of induced pluripotent stem cell generation by the p53–p21 pathway , 2009, Nature.

[110]  Chih-Ming Ho,et al.  An optimized small molecule inhibitor cocktail supports long-term maintenance of human embryonic stem cells. , 2011, Nature communications.