Skip to main content

Induced Pluripotent Stem Cells in Disease Modeling and Gene Identification

  • Protocol
  • First Online:
Disease Gene Identification

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1706))

Abstract

Experimental modeling of human inherited disorders provides insight into the cellular and molecular mechanisms involved, and the underlying genetic component influencing, the disease phenotype. The breakthrough development of induced pluripotent stem cell (iPSC) technology represents a quantum leap in experimental modeling of human diseases, providing investigators with a self-renewing and, thus, unlimited source of pluripotent cells for targeted differentiation. In principle, the entire range of cell types found in the human body can be interrogated using an iPSC approach. Therefore, iPSC technology, and the increasingly refined abilities to differentiate iPSCs into disease-relevant target cells, has far-reaching implications for understanding disease pathophysiology, identifying disease-causing genes, and developing more precise therapeutics, including advances in regenerative medicine. In this chapter, we discuss the technological perspectives and recent developments in the application of patient-derived iPSC lines for human disease modeling and disease gene identification.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

References

  1. Lander ES (2011) Initial impact of the sequencing of the human genome. Nature 470(7333):187–197. https://doi.org/10.1038/nature09792

    Article  CAS  PubMed  Google Scholar 

  2. Handley A, Schauer T, Ladurner AG et al (2015) Designing cell-type-specific genome-wide experiments. Mol Cell 58(4):621–631. https://doi.org/10.1016/j.molcel.2015.04.024

    Article  CAS  PubMed  Google Scholar 

  3. Phillips KA, Bales KL, Capitanio JP et al (2014) Why primate models matter. Am J Primatol 76(9):801–827. https://doi.org/10.1002/ajp.22281

    Article  PubMed  PubMed Central  Google Scholar 

  4. Seok J, Warren HS, Cuenca AG et al (2013) Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci U S A 110(9):3507–3512. https://doi.org/10.1073/pnas.1222878110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Springer MS, Murphy WJ, Eizirik E et al (2003) Placental mammal diversification and the cretaceous-tertiary boundary. Proc Natl Acad Sci U S A 100(3):1056–1061. https://doi.org/10.1073/pnas.0334222100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Masters JR, Stacey GN (2007) Changing medium and passaging cell lines. Nat Protoc 2(9):2276–2284

    Article  CAS  PubMed  Google Scholar 

  7. Min JL, Barrett A, Watts T et al (2010) Variability of gene expression profiles in human blood and lymphoblastoid cell lines. BMC Genomics 11:96. https://doi.org/10.1186/1471-2164-11-96

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Caliskan M, Cusanovich DA, Ober C et al (2011) The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet 20(8):1643–1652. https://doi.org/10.1093/hmg/ddr041

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Nestor CE, Ottaviano R, Reinhardt D et al (2015) Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems. Genome Biol 16:11. https://doi.org/10.1186/s13059-014-0576-y

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Horvath P, Aulner N, Bickle M et al (2016) Screening out irrelevant cell-based models of disease. Nat Rev Drug Discov 15(11):751–769. https://doi.org/10.1038/nrd.2016.175

    Article  CAS  PubMed  Google Scholar 

  11. Avior Y, Sagi I, Benvenisty N (2016) Pluripotent stem cells in disease modelling and drug discovery. Nat Rev Mol Cell Biol 17(3):170–182. https://doi.org/10.1038/nrm.2015.27

    Article  CAS  PubMed  Google Scholar 

  12. Evans MJ, Kaufman MH (1981) Establishment in culture of pluripotential cells from mouse embryos. Nature 292(5819):154–156

    Article  CAS  PubMed  Google Scholar 

  13. Thomson JA, Itskovitz-Eldor J, Shapiro SS et al (1998) Embryonic stem cell lines derived from human blastocysts. Science 282(5391):1145–1147

    Article  CAS  PubMed  Google Scholar 

  14. Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126(4):663–676

    Article  CAS  PubMed  Google Scholar 

  15. Takahashi K, Tanabe K, Ohnuki M et al (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131(5):861–872

    Article  CAS  PubMed  Google Scholar 

  16. Yu J, Vodyanik MA, Smuga-Otto K et al (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318(5858):1917–1920

    Article  CAS  PubMed  Google Scholar 

  17. Park IH, Zhao R, West JA et al (2008) Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451(7175):141–146

    Article  CAS  PubMed  Google Scholar 

  18. Aasen T, Raya A, Barrero MJ et al (2008) Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes. Nat Biotechnol 26(11):1276–1284. https://doi.org/10.1038/nbt.1503

    Article  CAS  PubMed  Google Scholar 

  19. Hanna J, Markoulaki S, Schorderet P et al (2008) Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell 133(2):250–264. https://doi.org/10.1016/j.cell.2008.03.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Utikal J, Maherali N, Kulalert W et al (2009) Sox2 is dispensable for the reprogramming of melanocytes and melanoma cells into induced pluripotent stem cells. J Cell Sci 122(Pt 19):3502–3510. https://doi.org/10.1242/jcs.054783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Carette JE, Pruszak J, Varadarajan M et al (2010) Generation of iPSCs from cultured human malignant cells. Blood 115(20):4039–4042. https://doi.org/10.1182/blood-2009-07-231845

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Miyoshi N, Ishii H, Nagai K et al (2010) Defined factors induce reprogramming of gastrointestinal cancer cells. Proc Natl Acad Sci U S A 107(1):40–45. https://doi.org/10.1073/pnas.0912407107

    Article  CAS  PubMed  Google Scholar 

  23. Seki T, Yuasa S, Oda M et al (2010) Generation of induced pluripotent stem cells from human terminally differentiated circulating T cells. Cell Stem Cell 7(1):11–14. https://doi.org/10.1016/j.stem.2010.06.003

    Article  CAS  PubMed  Google Scholar 

  24. Tsai SY, Clavel C, Kim S et al (2010) Oct4 and klf4 reprogram dermal papilla cells into induced pluripotent stem cells. Stem Cells 28(2):221–228. https://doi.org/10.1002/stem.281

    CAS  PubMed  Google Scholar 

  25. Kim J, Lengner CJ, Kirak O et al (2011) Reprogramming of postnatal neurons into induced pluripotent stem cells by defined factors. Stem Cells 29(6):992–1000. https://doi.org/10.1002/stem.641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Kumar S, Curran JE, Glahn DC et al (2016) Utility of lymphoblastoid cell lines for induced pluripotent stem cell generation. Stem Cells Int 2016:2349261. https://doi.org/10.1155/2016/2349261

    Article  PubMed  PubMed Central  Google Scholar 

  27. Rubin LL (2008) Stem cells and drug discovery: the beginning of a new era? Cell 132(4):549–552. https://doi.org/10.1016/j.cell.2008.02.010

    Article  CAS  PubMed  Google Scholar 

  28. Maehr R, Chen S, Snitow M et al (2009) Generation of pluripotent stem cells from patients with type 1 diabetes. Proc Natl Acad Sci U S A 106(37):15768–15773. https://doi.org/10.1073/pnas.0906894106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Chun YS, Chaudhari P, Jang YY (2010) Applications of patient-specific induced pluripotent stem cells; focused on disease modeling, drug screening and therapeutic potentials for liver disease. Int J Biol Sci 6(7):796–805

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Ghodsizadeh A, Taei A, Totonchi M et al (2010) Generation of liver disease-specific induced pluripotent stem cells along with efficient differentiation to functional hepatocyte-like cells. Stem Cell Rev 6(4):622–632. https://doi.org/10.1007/s12015-010-9189-3

    Article  PubMed  Google Scholar 

  31. Rashid ST, Corbineau S, Hannan N et al (2010) Modeling inherited metabolic disorders of the liver using human induced pluripotent stem cells. J Clin Invest 120(9):3127–3136. https://doi.org/10.1172/JCI43122

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Rosenzweig A (2010) Illuminating the potential of pluripotent stem cells. N Engl J Med 363(15):1471–1472. https://doi.org/10.1056/NEJMe1007902

    Article  CAS  PubMed  Google Scholar 

  33. Yoshida Y, Yamanaka S (2010) Recent stem cell advances: induced pluripotent stem cells for disease modeling and stem cell-based regeneration. Circulation 122(1):80–87. https://doi.org/10.1161/CIRCULATIONAHA.109.881433

    Article  PubMed  Google Scholar 

  34. Zhang N, An MC, Montoro D et al (2010) Characterization of human Huntington’s disease cell model from induced pluripotent stem cells. PLoS Curr 2:RRN1193. https://doi.org/10.1371/currents.RRN1193

    Article  PubMed  PubMed Central  Google Scholar 

  35. Brennand KJ, Simone A, Jou J et al (2011) Modelling schizophrenia using human induced pluripotent stem cells. Nature 473(7346):221–225. https://doi.org/10.1038/nature09915

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Kondo T, Asai M, Tsukita K et al (2013) Modeling Alzheimer’s disease with iPSCs reveals stress phenotypes associated with intracellular Abeta and differential drug responsiveness. Cell Stem Cell 12(4):487–496. https://doi.org/10.1016/j.stem.2013.01.009

    Article  CAS  PubMed  Google Scholar 

  37. Liang P, Du J (2014) Human induced pluripotent stem cell for modeling cardiovascular diseases. Regen Med Res 2(1):4. https://doi.org/10.1186/2050-490X-2-4

    Article  PubMed  PubMed Central  Google Scholar 

  38. Brennand K, Savas JN, Kim Y et al (2015) Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Mol Psychiatry 20(3):361–368. https://doi.org/10.1038/mp.2014.22

    Article  CAS  PubMed  Google Scholar 

  39. NIMH-RGR Data Explorer (2015) NIMH Repository and Genomics Resource, USA. https://explorer.nimhgenetics.org/. Accessed 14 Oct 2015

  40. Okita K, Yamakawa T, Matsumura Y et al (2013) An efficient nonviral method to generate integration-free human-induced pluripotent stem cells from cord blood and peripheral blood cells. Stem Cells 31(3):458–466. https://doi.org/10.1002/stem.1293

    Article  CAS  PubMed  Google Scholar 

  41. Rajesh D, Dickerson SJ, Yu J et al (2011) Human lymphoblastoid B-cell lines reprogrammed to EBV-free induced pluripotent stem cells. Blood 118(7):1797–1800. https://doi.org/10.1182/blood-2011-01-332064

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Choi SM, Liu H, Chaudhari P et al (2011) Reprogramming of EBV-immortalized B-lymphocyte cell lines into induced pluripotent stem cells. Blood 118(7):1801–1805. https://doi.org/10.1182/blood-2011-03-340620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Roe T, Reynolds TC, Yu G et al (1993) Integration of murine leukemia virus DNA depends on mitosis. EMBO J 12(5):2099–2108

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Bukrinsky MI, Sharova N, Dempsey MP et al (1992) Active nuclear import of human immunodeficiency virus type 1 preintegration complexes. Proc Natl Acad Sci U S A 89(14):6580–6584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Medvedev SP, Shevchenko AI, Zakian SM (2010) Induced pluripotent stem cells: problems and advantages when applying them in regenerative medicine. Acta Nat 2(2):18–28

    CAS  Google Scholar 

  46. Rao MS, Malik N (2012) Assessing iPSC reprogramming methods for their suitability in translational medicine. J Cell Biochem 113(10):3061–3068. https://doi.org/10.1002/jcb.24183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Chang CW, Lai YS, Pawlik KM et al (2009) Polycistronic lentiviral vector for “hit and run” reprogramming of adult skin fibroblasts to induced pluripotent stem cells. Stem Cells 27(5):1042–1049. https://doi.org/10.1002/stem.39

    Article  CAS  PubMed  Google Scholar 

  48. Soldner F, Hockemeyer D, Beard C et al (2009) Parkinson’s disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Cell 136(5):964–977. https://doi.org/10.1016/j.cell.2009.02.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Sommer CA, Stadtfeld M, Murphy GJ et al (2009) Induced pluripotent stem cell generation using a single lentiviral stem cell cassette. Stem Cells 27(3):543–549. https://doi.org/10.1634/stemcells.2008-1075

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Somers A, Jean JC, Sommer CA et al (2010) Generation of transgene-free lung disease-specific human induced pluripotent stem cells using a single excisable lentiviral stem cell cassette. Stem Cells 28(10):1728–1740. https://doi.org/10.1002/stem.495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. KUROYA M, ISHIDA N (1953) Newborn virus pneumonitis (type Sendai). II. The isolation of a new virus possessing hemagglutinin activity. Yokohama Med Bull 4(4):217–233

    CAS  PubMed  Google Scholar 

  52. Fusaki N, Ban H, Nishiyama A et al (2009) Efficient induction of transgene-free human pluripotent stem cells using a vector based on Sendai virus, an RNA virus that does not integrate into the host genome. Proc Jpn Acad Ser B Phys Biol Sci 85(8):348–362

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Ban H, Nishishita N, Fusaki N et al (2011) Efficient generation of transgene-free human induced pluripotent stem cells (iPSCs) by temperature-sensitive Sendai virus vectors. Proc Natl Acad Sci U S A 108(34):14234–14239. https://doi.org/10.1073/pnas.1103509108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Schlaeger TM, Daheron L, Brickler TR et al (2015) A comparison of non-integrating reprogramming methods. Nat Biotechnol 33(1):58–63. https://doi.org/10.1038/nbt.3070

    Article  CAS  PubMed  Google Scholar 

  55. Sun TQ, Fenstermacher DA, Vos JM (1994) Human artificial episomal chromosomes for cloning large DNA fragments in human cells. Nat Genet 8(1):33–41. https://doi.org/10.1038/ng0994-33

    Article  CAS  PubMed  Google Scholar 

  56. Simpson K, McGuigan A, Huxley C (1996) Stable episomal maintenance of yeast artificial chromosomes in human cells. Mol Cell Biol 16(9):5117–5126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Westphal EM, Sierakowska H, Livanos E et al (1998) A system for shuttling 200-kb BAC/PAC clones into human cells: stable extrachromosomal persistence and long-term ectopic gene activation. Hum Gene Ther 9(13):1863–1873. https://doi.org/10.1089/hum.1998.9.13-1863

    Article  CAS  PubMed  Google Scholar 

  58. Yu J, Hu K, Smuga-Otto K et al (2009) Human induced pluripotent stem cells free of vector and transgene sequences. Science 324(5928):797–801. https://doi.org/10.1126/science.1172482

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Hu K, Yu J, Suknuntha K et al (2011) Efficient generation of transgene-free induced pluripotent stem cells from normal and neoplastic bone marrow and cord blood mononuclear cells. Blood 117(14):e109–e119. https://doi.org/10.1182/blood-2010-07-298331

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Lin T, Ambasudhan R, Yuan X et al (2009) A chemical platform for improved induction of human iPSCs. Nat Methods 6(11):805–808. https://doi.org/10.1038/nmeth.1393

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Yu J, Chau KF, Vodyanik MA et al (2011) Efficient feeder-free episomal reprogramming with small molecules. PLoS One 6(3):e17557. https://doi.org/10.1371/journal.pone.0017557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Chou BK, Mali P, Huang X et al (2011) Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures. Cell Res 21(3):518–529. https://doi.org/10.1038/cr.2011.12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Okita K, Matsumura Y, Sato Y et al (2011) A more efficient method to generate integration-free human iPS cells. Nat Methods 8(5):409–412. https://doi.org/10.1038/nmeth.1591

    Article  CAS  PubMed  Google Scholar 

  64. Warren L, Manos PD, Ahfeldt T et al (2010) Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 7(5):618–630. https://doi.org/10.1016/j.stem.2010.08.012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Goh PA, Caxaria S, Casper C et al (2013) A systematic evaluation of integration free reprogramming methods for deriving clinically relevant patient specific induced pluripotent stem (iPS) cells. PLoS One 8(11):e81622. https://doi.org/10.1371/journal.pone.0081622

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. Warren L, Ni Y, Wang J et al (2012) Feeder-free derivation of human induced pluripotent stem cells with messenger RNA. Sci Rep 2:657. https://doi.org/10.1038/srep00657

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  67. Merkle FT, Eggan K (2013) Modeling human disease with pluripotent stem cells: from genome association to function. Cell Stem Cell 12(6):656–668. https://doi.org/10.1016/j.stem.2013.05.016

    Article  CAS  PubMed  Google Scholar 

  68. Kajiwara M, Aoi T, Okita K et al (2012) Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells. Proc Natl Acad Sci U S A 109(31):12538–12543. https://doi.org/10.1073/pnas.1209979109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Mills JA, Wang K, Paluru P et al (2013) Clonal genetic and hematopoietic heterogeneity among human-induced pluripotent stem cell lines. Blood 122(12):2047–2051. https://doi.org/10.1182/blood-2013-02-484444

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Shao K, Koch C, Gupta MK et al (2013) Induced pluripotent mesenchymal stromal cell clones retain donor-derived differences in DNA methylation profiles. Mol Ther 21(1):240–250. https://doi.org/10.1038/mt.2012.207

    Article  CAS  PubMed  Google Scholar 

  71. Rouhani F, Kumasaka N, de Brito MC et al (2014) Genetic background drives transcriptional variation in human induced pluripotent stem cells. PLoS Genet 10(6):e1004432. https://doi.org/10.1371/journal.pgen.1004432

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  72. Kyttala A, Moraghebi R, Valensisi C et al (2016) Genetic variability overrides the impact of parental cell type and determines iPSC differentiation potential. Stem Cell Rep 6(2):200–212. https://doi.org/10.1016/j.stemcr.2015.12.009

    Article  Google Scholar 

  73. Bock C, Kiskinis E, Verstappen G et al (2011) Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 144(3):439–452. https://doi.org/10.1016/j.cell.2010.12.032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Boulting GL, Kiskinis E, Croft GF et al (2011) A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol 29(3):279–286. https://doi.org/10.1038/nbt.1783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. HD iPSC Consortium (2012) Induced pluripotent stem cells from patients with Huntington’s disease show CAG-repeat-expansion-associated phenotypes. Cell Stem Cell 11(2):264–278. https://doi.org/10.1016/j.stem.2012.04.027

    Article  CAS  Google Scholar 

  76. Cohen DE, Melton D (2011) Turning straw into gold: directing cell fate for regenerative medicine. Nat Rev Genet 12(4):243–252. https://doi.org/10.1038/nrg2938

    Article  CAS  PubMed  Google Scholar 

  77. Williams LA, Davis-Dusenbery BN, Eggan KC (2012) SnapShot: directed differentiation of pluripotent stem cells. Cell 149(5):1174–1174.e1. https://doi.org/10.1016/j.cell.2012.05.015

    Article  CAS  PubMed  Google Scholar 

  78. Lian X, Zhang J, Azarin SM et al (2013) Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/beta-catenin signaling under fully defined conditions. Nat Protoc 8(1):162–175. https://doi.org/10.1038/nprot.2012.150

    Article  CAS  PubMed  Google Scholar 

  79. Yan Y, Shin S, Jha BS et al (2013) Efficient and rapid derivation of primitive neural stem cells and generation of brain subtype neurons from human pluripotent stem cells. Stem Cells Transl Med 2(11):862–870. https://doi.org/10.5966/sctm.2013-0080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Carlson C, Koonce C, Aoyama N et al (2013) Phenotypic screening with human iPS cell-derived cardiomyocytes: HTS-compatible assays for interrogating cardiac hypertrophy. J Biomol Screen 18(10):1203–1211. https://doi.org/10.1177/1087057113500812

    Article  PubMed  Google Scholar 

  81. Drawnel FM, Boccardo S, Prummer M et al (2014) Disease modeling and phenotypic drug screening for diabetic cardiomyopathy using human induced pluripotent stem cells. Cell Rep 9(3):810–821. https://doi.org/10.1016/j.celrep.2014.09.055

    Article  CAS  PubMed  Google Scholar 

  82. Slukvin II, Vodyanik MA, Thomson JA et al (2006) Directed differentiation of human embryonic stem cells into functional dendritic cells through the myeloid pathway. J Immunol 176(5):2924–2932

    Article  CAS  PubMed  Google Scholar 

  83. Erceg S, Lainez S, Ronaghi M et al (2008) Differentiation of human embryonic stem cells to regional specific neural precursors in chemically defined medium conditions. PLoS One 3(5):e2122. https://doi.org/10.1371/journal.pone.0002122

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  84. Prigodich AE, Seferos DS, Massich MD et al (2009) Nano-flares for mRNA regulation and detection. ACS Nano 3(8):2147–2152. https://doi.org/10.1021/nn9003814

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Larsson HM, Lee ST, Roccio M et al (2012) Sorting live stem cells based on Sox2 mRNA expression. PLoS One 7(11):e49874. https://doi.org/10.1371/journal.pone.0049874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Tohyama S, Hattori F, Sano M et al (2013) Distinct metabolic flow enables large-scale purification of mouse and human pluripotent stem cell-derived cardiomyocytes. Cell Stem Cell 12(1):127–137. https://doi.org/10.1016/j.stem.2012.09.013

    Article  CAS  PubMed  Google Scholar 

  87. Nguyen HN, Byers B, Cord B et al (2011) LRRK2 mutant iPSC-derived DA neurons demonstrate increased susceptibility to oxidative stress. Cell Stem Cell 8(3):267–280. https://doi.org/10.1016/j.stem.2011.01.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Israel MA, Yuan SH, Bardy C et al (2012) Probing sporadic and familial Alzheimer’s disease using induced pluripotent stem cells. Nature 482(7384):216–220. https://doi.org/10.1038/nature10821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Reinhardt P, Schmid B, Burbulla LF et al (2013) Genetic correction of a LRRK2 mutation in human iPSCs links parkinsonian neurodegeneration to ERK-dependent changes in gene expression. Cell Stem Cell 12(3):354–367. https://doi.org/10.1016/j.stem.2013.01.008

    Article  CAS  PubMed  Google Scholar 

  90. Ieda M, JD F, Delgado-Olguin P et al (2010) Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142(3):375–386. https://doi.org/10.1016/j.cell.2010.07.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Szabo E, Rampalli S, Risueno RM et al (2010) Direct conversion of human fibroblasts to multilineage blood progenitors. Nature 468(7323):521–526. https://doi.org/10.1038/nature09591

    Article  CAS  PubMed  Google Scholar 

  92. Vierbuchen T, Ostermeier A, Pang ZP et al (2010) Direct conversion of fibroblasts to functional neurons by defined factors. Nature 463(7284):1035–1041. https://doi.org/10.1038/nature08797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Sekiya S, Suzuki A (2011) Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors. Nature 475(7356):390–393. https://doi.org/10.1038/nature10263

    Article  CAS  PubMed  Google Scholar 

  94. Ring KL, Tong LM, Balestra ME et al (2012) Direct reprogramming of mouse and human fibroblasts into multipotent neural stem cells with a single factor. Cell Stem Cell 11(1):100–109. https://doi.org/10.1016/j.stem.2012.05.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Vierbuchen T, Wernig M (2011) Direct lineage conversions: unnatural but useful? Nat Biotechnol 29(10):892–907. https://doi.org/10.1038/nbt.1946

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Yang C, Al-Aama J, Stojkovic M et al (2015) Concise review: cardiac disease modeling using induced pluripotent stem cells. Stem Cells 33(9):2643–2651. https://doi.org/10.1002/stem.2070

    Article  PubMed  Google Scholar 

  97. Nishi M, Akutsu H, Kudoh A et al (2014) Induced cancer stem-like cells as a model for biological screening and discovery of agents targeting phenotypic traits of cancer stem cell. Oncotarget 5(18):8665–8680

    Article  PubMed  PubMed Central  Google Scholar 

  98. Curry EL, Moad M, Robson CN et al (2015) Using induced pluripotent stem cells as a tool for modelling carcinogenesis. World J Stem Cells 7(2):461–469. https://doi.org/10.4252/wjsc.v7.i2.461

    Article  PubMed  PubMed Central  Google Scholar 

  99. Wiley LA, Burnight ER, Songstad AE et al (2015) Patient-specific induced pluripotent stem cells (iPSCs) for the study and treatment of retinal degenerative diseases. Prog Retin Eye Res 44:15–35. https://doi.org/10.1016/j.preteyeres.2014.10.002

    Article  PubMed  Google Scholar 

  100. Zheng A, Li Y, Tsang SH (2015) Personalized therapeutic strategies for patients with retinitis pigmentosa. Expert Opin Biol Ther 15(3):391–402. https://doi.org/10.1517/14712598.2015.1006192

    Article  PubMed  PubMed Central  Google Scholar 

  101. Lysy PA, Weir GC, Bonner-Weir S (2012) Concise review: pancreas regeneration: recent advances and perspectives. Stem Cells Transl Med 1(2):150–159. https://doi.org/10.5966/sctm.2011-0025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Abdelalim EM, Bonnefond A, Bennaceur-Griscelli A et al (2014) Pluripotent stem cells as a potential tool for disease modelling and cell therapy in diabetes. Stem Cell Rev 10(3):327–337. https://doi.org/10.1007/s12015-014-9503-6

    Article  CAS  PubMed  Google Scholar 

  103. Peitz M, Jungverdorben J, Brustle O (2013) Disease-specific iPS cell models in neuroscience. Curr Mol Med 13(5):832–841

    Article  CAS  PubMed  Google Scholar 

  104. Crook JM, Wallace G, Tomaskovic-Crook E (2015) The potential of induced pluripotent stem cells in models of neurological disorders: implications on future therapy. Expert Rev Neurother 15(3):295–304. https://doi.org/10.1586/14737175.2015.1013096

    Article  CAS  PubMed  Google Scholar 

  105. Goring HH, Curran JE, Johnson MP et al (2007) Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 39(10):1208–1216. https://doi.org/10.1038/ng2119

    Article  PubMed  CAS  Google Scholar 

  106. Winnier DA, Fourcaudot M, Norton L et al (2015) Transcriptomic identification of ADH1B as a novel candidate gene for obesity and insulin resistance in human adipose tissue in Mexican Americans from the Veterans Administration Genetic Epidemiology Study (VAGES). PLoS One 10(4):e0119941. https://doi.org/10.1371/journal.pone.0119941

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  107. Pasca SP, Portmann T, Voineagu I et al (2011) Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome. Nat Med 17(12):1657–1662. https://doi.org/10.1038/nm.2576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Prilutsky D, Palmer NP, Smedemark-Margulies N et al (2014) iPSC-derived neurons as a higher-throughput readout for autism: promises and pitfalls. Trends Mol Med 20(2):91–104. https://doi.org/10.1016/j.molmed.2013.11.004

    Article  CAS  PubMed  Google Scholar 

  109. Wen Z, Nguyen HN, Guo Z et al (2014) Synaptic dysregulation in a human iPS cell model of mental disorders. Nature 515(7527):414–418. https://doi.org/10.1038/nature13716

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Farra N, Zhang WB, Pasceri P et al (2012) Rett syndrome induced pluripotent stem cell-derived neurons reveal novel neurophysiological alterations. Mol Psychiatry 17(12):1261–1271. https://doi.org/10.1038/mp.2011.180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Vaccarino FM, Urban AE, Stevens HE et al (2011) Annual research review: the promise of stem cell research for neuropsychiatric disorders. J Child Psychol Psychiatry 52(4):504–516. https://doi.org/10.1111/j.1469-7610.2010.02348.x

    Article  PubMed  PubMed Central  Google Scholar 

  112. Vaccarino FM, Stevens HE, Kocabas A et al (2011) Induced pluripotent stem cells: a new tool to confront the challenge of neuropsychiatric disorders. Neuropharmacology 60(7-8):1355–1363. https://doi.org/10.1016/j.neuropharm.2011.02.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Stevens HE, Mariani J, Coppola G et al (2012) Neurobiology meets genomic science: the promise of human-induced pluripotent stem cells. Dev Psychopathol 24(4):1443–1451. https://doi.org/10.1017/S095457941200082X

    Article  PubMed  PubMed Central  Google Scholar 

  114. Chae JI, Kim DW, Lee N et al (2012) Quantitative proteomic analysis of induced pluripotent stem cells derived from a human Huntington’s disease patient. Biochem J 446(3):359–371. https://doi.org/10.1042/BJ20111495

    Article  CAS  PubMed  Google Scholar 

  115. Szlachcic WJ, Switonski PM, Krzyzosiak WJ et al (2015) Huntington disease iPSCs show early molecular changes in intracellular signaling, the expression of oxidative stress proteins and the p53 pathway. Dis Model Mech 8(9):1047–1057. https://doi.org/10.1242/dmm.019406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Weinberger DR (1987) Implications of normal brain development for the pathogenesis of schizophrenia. Arch Gen Psychiatry 44(7):660–669

    Article  CAS  PubMed  Google Scholar 

  117. White T, Anjum A, Schulz SC (2006) The schizophrenia prodrome. Am J Psychiatry 163(3):376–380

    Article  PubMed  Google Scholar 

  118. Gulsuner S, Walsh T, Watts AC et al (2013) Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell 154(3):518–529. https://doi.org/10.1016/j.cell.2013.06.049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Mariani J, Simonini MV, Palejev D et al (2012) Modeling human cortical development in vitro using induced pluripotent stem cells. Proc Natl Acad Sci U S A 109(31):12770–12775. https://doi.org/10.1073/pnas.1202944109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Nicholas CR, Chen J, Tang Y et al (2013) Functional maturation of hPSC-derived forebrain interneurons requires an extended timeline and mimics human neural development. Cell Stem Cell 12(5):573–586. https://doi.org/10.1016/j.stem.2013.04.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Espuny-Camacho I, Michelsen KA, Gall D et al (2013) Pyramidal neurons derived from human pluripotent stem cells integrate efficiently into mouse brain circuits in vivo. Neuron 77(3):440–456. https://doi.org/10.1016/j.neuron.2012.12.011

    Article  CAS  PubMed  Google Scholar 

  122. Maroof AM, Keros S, Tyson JA et al (2013) Directed differentiation and functional maturation of cortical interneurons from human embryonic stem cells. Cell Stem Cell 12(5):559–572. https://doi.org/10.1016/j.stem.2013.04.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Hu BY, Du ZW, Zhang SC (2009) Differentiation of human oligodendrocytes from pluripotent stem cells. Nat Protoc 4(11):1614–1622. https://doi.org/10.1038/nprot.2009.186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Wang S, Bates J, Li X et al (2013) Human iPSC-derived oligodendrocyte progenitor cells can myelinate and rescue a mouse model of congenital hypomyelination. Cell Stem Cell 12(2):252–264. https://doi.org/10.1016/j.stem.2012.12.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Kim C, Wong J, Wen J et al (2013) Studying arrhythmogenic right ventricular dysplasia with patient-specific iPSCs. Nature 494(7435):105–110. https://doi.org/10.1038/nature11799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Maher B (2008) Personal genomes: the case of the missing heritability. Nature 456(7218):18–21. https://doi.org/10.1038/456018a

    Article  CAS  PubMed  Google Scholar 

  127. Manolio TA, Collins FS, Cox NJ et al (2009) Finding the missing heritability of complex diseases. Nature 461(7265):747–753. https://doi.org/10.1038/nature08494; 10.1038/nature08494

  128. Franke A, McGovern DP, Barrett JC et al (2010) Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci. Nat Genet 42(12):1118–1125. https://doi.org/10.1038/ng.717

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Cardno AG, Gottesman II (2000) Twin studies of schizophrenia: from bow-and-arrow concordances to star wars Mx and functional genomics. Am J Med Genet 97(1):12–17. https://doi.org/10.1002/(SICI)1096-8628(200021)97:13.0.CO;2-U[pii]

  130. Sullivan PF, Kendler KS, Neale MC (2003) Schizophrenia as a complex trait: evidence from a meta-analysis of twin studies. Arch Gen Psychiatry 60(12):1187–1192. https://doi.org/10.1001/archpsyc.60.12.1187

    Article  PubMed  Google Scholar 

  131. Visscher PM, Goddard ME, Derks EM et al (2012) Evidence-based psychiatric genetics, AKA the false dichotomy between common and rare variant hypotheses. Mol Psychiatry 17(5):474–485. https://doi.org/10.1038/mp.2011.65

    Article  CAS  PubMed  Google Scholar 

  132. McGuire SE, McGuire AL (2008) Don’t throw the baby out with the bathwater: enabling a bottom-up approach in genome-wide association studies. Genome Res 18(11):1683–1685. https://doi.org/10.1101/gr.083584.108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Tracy RP (2008) ‘Deep phenotyping’: characterizing populations in the era of genomics and systems biology. Curr Opin Lipidol 19(2):151–157. https://doi.org/10.1097/MOL.0b013e3282f73893

    Article  CAS  PubMed  Google Scholar 

  134. Vogelstein B, Lane D, Levine AJ (2000) Surfing the p53 network. Nature 408(6810):307–310. https://doi.org/10.1038/35042675

    Article  CAS  PubMed  Google Scholar 

  135. Chao EC, Lipkin SM (2006) Molecular models for the tissue specificity of DNA mismatch repair-deficient carcinogenesis. Nucleic Acids Res 34(3):840–852

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Goh KI, Cusick ME, Valle D et al (2007) The human disease network. Proc Natl Acad Sci U S A 104(21):8685–8690

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Lage K, Hansen NT, Karlberg EO et al (2008) A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A 105(52):20870–20875. https://doi.org/10.1073/pnas.0810772105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Barshir R, Shwartz O, Smoly IY et al (2014) Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PLoS Comput Biol 10(6):e1003632. https://doi.org/10.1371/journal.pcbi.1003632

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  139. Jenkinson CP, Goring HH, Arya R et al (2015) Transcriptomics in type 2 diabetes: bridging the gap between genotype and phenotype. Genom Data 8:25–36. https://doi.org/10.1016/j.gdata.2015.12.001

    Article  PubMed  PubMed Central  Google Scholar 

  140. Kim H, Kim JS (2014) A guide to genome engineering with programmable nucleases. Nat Rev Genet 15(5):321–334. https://doi.org/10.1038/nrg3686

    Article  CAS  PubMed  Google Scholar 

  141. Boch J, Scholze H, Schornack S et al (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326(5959):1509–1512. https://doi.org/10.1126/science.1178811

    Article  CAS  PubMed  Google Scholar 

  142. Wood AJ, Lo TW, Zeitler B et al (2011) Targeted genome editing across species using ZFNs and TALENs. Science 333(6040):307. https://doi.org/10.1126/science.1207773

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Sanjana NE, Cong L, Zhou Y et al (2012) A transcription activator-like effector toolbox for genome engineering. Nat Protoc 7(1):171–192. https://doi.org/10.1038/nprot.2011.431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Cong L, Ran FA, Cox D et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819–823. https://doi.org/10.1126/science.1231143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Mali P, Yang L, Esvelt KM et al (2013) RNA-guided human genome engineering via Cas9. Science 339(6121):823–826. https://doi.org/10.1126/science.1232033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Carroll D, Morton JJ, Beumer KJ et al (2006) Design, construction and in vitro testing of zinc finger nucleases. Nat Protoc 1(3):1329–1341

    Article  CAS  PubMed  Google Scholar 

  147. Miller JC, Tan S, Qiao G et al (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29(2):143–148. https://doi.org/10.1038/nbt.1755

    Article  CAS  PubMed  Google Scholar 

  148. Jinek M, Chylinski K, Fonfara I et al (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821. https://doi.org/10.1126/science.1225829

    Article  CAS  PubMed  Google Scholar 

  149. Musunuru K (2013) Genome editing of human pluripotent stem cells to generate human cellular disease models. Dis Model Mech 6(4):896–904. https://doi.org/10.3824/stembook.1.94.1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Lombardo A, Genovese P, Beausejour CM et al (2007) Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol 25(11):1298–1306

    Article  CAS  PubMed  Google Scholar 

  151. Suzuki K, Mitsui K, Aizawa E et al (2008) Highly efficient transient gene expression and gene targeting in primate embryonic stem cells with helper-dependent adenoviral vectors. Proc Natl Acad Sci U S A 105(37):13781–13786. https://doi.org/10.1073/pnas.0806976105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Zou J, Maeder ML, Mali P et al (2009) Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell 5(1):97–110. https://doi.org/10.1016/j.stem.2009.05.023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Hockemeyer D, Wang H, Kiani S et al (2011) Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol 29(8):731–734. https://doi.org/10.1038/nbt.1927

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Li M, Suzuki K, Qu J et al (2011) Efficient correction of hemoglobinopathy-causing mutations by homologous recombination in integration-free patient iPSCs. Cell Res 21(12):1740–1744. https://doi.org/10.1038/cr.2011.186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Sebastiano V, Maeder ML, Angstman JF et al (2011) In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases. Stem Cells 29(11):1717–1726. https://doi.org/10.1002/stem.718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Soldner F, Laganiere J, Cheng AW et al (2011) Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell 146(2):318–331. https://doi.org/10.1016/j.cell.2011.06.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Yusa K, Rashid ST, Strick-Marchand H et al (2011) Targeted gene correction of alpha1-antitrypsin deficiency in induced pluripotent stem cells. Nature 478(7369):391–394. https://doi.org/10.1038/nature10424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Zou J, Mali P, Huang X et al (2011) Site-specific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease. Blood 118(17):4599–4608. https://doi.org/10.1182/blood-2011-02-335554

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Lan F, Lee AS, Liang P et al (2013) Abnormal calcium handling properties underlie familial hypertrophic cardiomyopathy pathology in patient-specific induced pluripotent stem cells. Cell Stem Cell 12(1):101–113. https://doi.org/10.1016/j.stem.2012.10.010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Satish Kumar .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Kumar, S., Blangero, J., Curran, J.E. (2018). Induced Pluripotent Stem Cells in Disease Modeling and Gene Identification. In: DiStefano, J. (eds) Disease Gene Identification. Methods in Molecular Biology, vol 1706. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7471-9_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7471-9_2

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7470-2

  • Online ISBN: 978-1-4939-7471-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics