Transcriptome Comparison of Human Neurons Generated Using Induced Pluripotent Stem Cells Derived from Dental Pulp and Skin Fibroblasts

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Chen, Jian ^a   Lin, Mingyan ^a   Foxe, John J ^a   Pedrosa, Erika ^a   Hrabovsky, Anastasia ^a   Carroll, Reed ^a   Zheng, Deyou ^a   Lachman, Herbert M ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOXP2; TRANSCRIPTION FACTOR LHX2; TRANSCRIPTION FACTOR OTX1; UNCLASSIFIED DRUG;

ADULT; ARTICLE; ASCL1 GENE; BRAIN REGION; CONTROLLED STUDY; DECIDUOUS TOOTH; DOWN REGULATION; EMX1 GENE; EMX2 GENE; FEMALE; FOXG1 GENE; FOXP2 GENE; GENE; GENE EXPRESSION PROFILING; GENOME ANALYSIS; HOX GENE; HOXA AS3 GENE; HOXA4 GENE; HOXA5 GENE; HOXA7 GENE; HOXA9 GENE; HOXB AS4 GENE; HOXC8 GENE; HUMAN; HUMAN CELL; IRX1 GENE; IRX2 GENE; LHX2 GENE; MALE; MENTAL DISEASE; MULTIGENE FAMILY; MYT1L GENE; NERVE CELL DIFFERENTIATION; NEUROLOGIC DISEASE; NEUROPSYCHIATRIC DISORDER; OTX2 GENE; PHOX2A GENE; PLURIPOTENT STEM CELL; PROTEIN EXPRESSION; RBP4 GENE; RNA SEQUENCE; RORB GENE; SCHIZOPHRENIA; SCUBE2 GENE; SKIN FIBROBLAST; SLITRK2 GENE; SOMATIC CELL; TBR1 GENE; TOOTH PULP;

BIOLOGICAL MARKERS; CELL DIFFERENTIATION; DENTAL PULP; FIBROBLASTS; GENE EXPRESSION PROFILING; HUMANS; INDUCED PLURIPOTENT STEM CELLS; NEURONS; SEQUENCE ANALYSIS, RNA; SKIN;

EID: 84884826708     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0075682     Document Type: Article

References (45)

1. Lin M, Hrabovsky A, Pedrosa E, Wang T, Zheng D, et al. (2012) Allele-biased expression in differentiating human neurons: Implications for neuropsychiatric disorders. PLoS One 7: e44017 10.1371/journal.pone.0044017.
2. Lin M, Pedrosa E, Shah A, Hrabovsky A, Maqbool S, et al. (2011) RNA-seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PLoS One 6: e23356 10.1371/journal.pone.0023356.
3. DeRosa BA, Van Baaren JM, Dubey GK, Lee JM, Cuccaro ML, et al. (2012) Derivation of autism spectrum disorder-specific induced pluripotent stem cells from peripheral blood mononuclear cells. Neurosci Lett 516: 9-14 10.1016/j.neulet.2012.02.086.
4. Farra N, Zhang WB, Pasceri P, Eubanks JH, Salter MW, et al. (2012) Rett syndrome induced pluripotent stem cell-derived neurons reveal novel neurophysiological alterations. Mol Psychiatry. 10.1038/mp.2011.180; 10.1038/mp.2011.180.
5. Kim KY, Jung YW, Sullivan GJ, Chung L, Park IH. (2012) Cellular reprogramming: A novel tool for investigating autism spectrum disorders. Trends Mol Med. 10.1016/j.molmed.2012.06.002.
6. Brennand KJ, Simone A, Jou J, Gelboin-Burkhart C, Tran N, et al. (2011) Modelling schizophrenia using human induced pluripotent stem cells. Nature. 10.1038/nature09915.
7. Chiang CH, Su Y, Wen Z, Yoritomo N, Ross CA, et al. (2011) Integration-free induced pluripotent stem cells derived from schizophrenia patients with a DISC1 mutation. Mol Psychiatry. 10.1038/mp.2011.13.
8. Chamberlain SJ, Chen PF, Ng KY, Bourgois-Rocha F, Lemtiri-Chlieh F, et al. (2010) Induced pluripotent stem cell models of the genomic imprinting disorders angelman and prader-willi syndromes. Proc Natl Acad Sci U S A 107: 17668-17673 10.1073/pnas.1004487107.
9. Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, et al. (2010) A model for neural development and treatment of rett syndrome using human induced pluripotent stem cells. Cell 143: 527-539 10.1016/j.cell.2010.10.016.
10. Robicsek O, Karry R, Petit I, Salman-Kesner N, Muller FJ, et al. (2013) Abnormal neuronal differentiation and mitochondrial dysfunction in hair follicle-derived induced pluripotent stem cells of schizophrenia patients. Mol Psychiatry. 10.1038/mp.2013.67; 10.1038/mp.2013.67.
11. Tamaoki N, Takahashi K, Tanaka T, Ichisaka T, Aoki H, et al. (2010) Dental pulp cells for induced pluripotent stem cell banking. J Dent Res 89: 773-778 10.1177/0022034510366846.
12. Beltrao-Braga PI, Pignatari GC, Maiorka PC, Oliveira NA, Lizier NF, et al. (2011) Feeder-free derivation of induced pluripotent stem cells from human immature dental pulp stem cells. Cell Transplant. 10.3727/096368911X566235.
13. Yan X, Qin H, Qu C, Tuan RS, Shi S, et al. (2010) iPS cells reprogrammed from human mesenchymal-like stem/progenitor cells of dental tissue origin. Stem Cells Dev 19: 469-480 10.1089/scd.2009.0314.
14. Pedrosa E, Sandler V, Shah A, Carroll R, Chang C, et al. (2011) Development of patient-specific neurons in schizophrenia using induced pluripotent stem cells. J Neurogenet. 10.3109/01677063.2011.597908.
15. Okita K, Matsumura Y, Sato Y, Okada A, Morizane A, et al. (2011) A more efficient method to generate integration-free human iPS cells. Nat Methods 8: 409-412 10.1038/nmeth.1591.
16. Takahashi K, Yamanaka S, (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663-676 10.1016/j.cell.2006.07.024.
17. Muenthaisong S, Ujhelly O, Polgar Z, Varga E, Ivics Z, et al. (2012) Generation of mouse induced pluripotent stem cells from different genetic backgrounds using sleeping beauty transposon mediated gene transfer. Exp Cell Res 318: 2482-2489 10.1016/j.yexcr.2012.07.014; 10.1016/j.yexcr.2012.07.014.
18. Pal R, Mamidi MK, Das AK, Bhonde R. (2012) Comparative analysis of cardiomyocyte differentiation from human embryonic stem cells under 3-D and 2-D culture conditions. J Biosci Bioeng. 10.1016/j.jbiosc.2012.08.018; 10.1016/j.jbiosc.2012.08.018.
19. Davidkova G, Carroll RC, (2007) Characterization of the role of microtubule-associated protein 1B in metabotropic glutamate receptor-mediated endocytosis of AMPA receptors in hippocampus. J Neurosci 27: 13273-13278 -10.1523/JNEUROSCI.3334-07.2007.
20. Huangfu D, Osafune K, Maehr R, Guo W, Eijkelenboom A, et al. (2008) Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nat Biotechnol 26: 1269-1275 10.1038/nbt.1502.
21. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: Discovering splice junctions with RNA-seq. Bioinformatics 25: 1105-1111 10.1093/bioinformatics/btp120.
22. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, et al. (2012) GENCODE: The reference human genome annotation for the ENCODE project. Genome Res 22: 1760-1774 10.1101/gr.135350.111; 10.1101/gr.135350.111.
23. Anders S, Huber W. (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106-2010-11-10-r106. Epub 2010 Oct 27. 10.1186/gb-2010-11-10-r106; 10.1186/gb-2010-11-10-r106.
24. van den Berg DL, Snoek T, Mullin NP, Yates A, Bezstarosti K, et al. (2010) An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6: 369-381 10.1016/j.stem.2010.02.014.
25. Larimore J, Ryder PV, Kim KY, Ambrose LA, Chapleau C, et al. (2013) MeCP2 regulates the synaptic expression of a dysbindin-BLOC-1 network component in mouse brain and human induced pluripotent stem cell-derived neurons. PLoS One 8: e65069 10.1371/journal.pone.0065069; 10.1371/journal.pone.0065069.
26. Juhasz G, Dunham JS, McKie S, Thomas E, Downey D, et al. (2011) The CREB1-BDNF-NTRK2 pathway in depression: Multiple gene-cognition-environment interactions. Biol Psychiatry 69: 762-771 10.1016/j.biopsych.2010.11.019.
27. Di Lieto A, Rantamaki T, Vesa L, Yanpallewar S, Antila H, et al. (2012) The responsiveness of TrkB to BDNF and antidepressant drugs is differentially regulated during mouse development. PLoS One 7: e32869 10.1371/journal.pone.0032869.
28. Thompson Ray M, Weickert CS, Wyatt E, Webster MJ, (2011) Decreased BDNF, trkB-TK+ and GAD(67) mRNA expression in the hippocampus of individuals with schizophrenia and mood disorders. J Psychiatry Neurosci 36: 195-203 10.1503/jpn.100048.
29. Grande I, Fries GR, Kunz M, Kapczinski F, (2010) The role of BDNF as a mediator of neuroplasticity in bipolar disorder. Psychiatry Investig 7: 243-250 10.4306/pi.2010.7.4.243.
30. Li W, Pozzo-Miller L. (2013) BDNF deregulation in rett syndrome. Neuropharmacology. 10.1016/j.neuropharm.2013.03.024; 10.1016/j.neuropharm.2013.03.024.
31. Vierbuchen T, Ostermeier A, Pang ZP, Kokubu Y, Sudhof TC, et al. (2010) Direct conversion of fibroblasts to functional neurons by defined factors. Nature 463: 1035-1041 10.1038/nature08797.
32. Lei JX, Cassone CG, Luebbert C, Liu QY, (2011) A novel neuron-enriched protein SDIM1 is down regulated in alzheimer's brains and attenuates cell death induced by DNAJB4 over-expression in neuro-progenitor cells. Mol Neurodegener 6: 9-1326-6-9 10.1186/1750-1326-6-9; 10.1186/1750-1326-6-9.
33. Katoh Y, Katoh M, (2005) Hedgehog signaling pathway and gastric cancer. Cancer Biol Ther 4: 1050-1054.
34. Smith EN, Bloss CS, Badner JA, Barrett T, Belmonte PL, et al. (2009) Genome-wide association study of bipolar disorder in european american and african american individuals. Mol Psychiatry 14: 755-763 10.1038/mp.2009.43.
35. Piton A, Gauthier J, Hamdan FF, Lafreniere RG, Yang Y, et al. (2011) Systematic resequencing of X-chromosome synaptic genes in autism spectrum disorder and schizophrenia. Mol Psychiatry 16: 867-880 10.1038/mp.2010.54; 10.1038/mp.2010.54.
36. Johnson JL, Hall TE, Dyson JM, Sonntag C, Ayers K, et al. (2012) Scube activity is necessary for hedgehog signal transduction in vivo. Dev Biol 368: 193-202 10.1016/j.ydbio.2012.05.007; 10.1016/j.ydbio.2012.05.007.
37. Xavier GM, Cobourne MT, (2011) Scube2 expression extends beyond the central nervous system during mouse development. J Mol Histol 42: 383-391 10.1007/s10735-011-9341-7.
38. Petit I, Kesner NS, Karry R, Robicsek O, Aberdam E, et al. (2012) Induced pluripotent stem cells from hair follicles as a cellular model for neurodevelopmental disorders. Stem Cell Res 8: 134-140 10.1016/j.scr.2011.09.003; 10.1016/j.scr.2011.09.003.
39. Ruiz S, Diep D, Gore A, Panopoulos AD, Montserrat N, et al. (2012) Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Proc Natl Acad Sci U S A 109: 16196-16201 10.1073/pnas.1202352109; 10.1073/pnas.1202352109.
40. Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, et al. (2011) Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 29: 1117-1119 10.1038/nbt.2052; 10.1038/nbt.2052.
41. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, et al. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131: 861-872 10.1016/j.cell.2007.11.019.
42. Miletich I, Sharpe PT, (2003) Normal and abnormal dental development. Hum Mol Genet 12 Spec No 1: R69-73.
43. Patthey C, Gunhaga L, (2011) Specification and regionalisation of the neural plate border. Eur J Neurosci 34: 1516-1528 -10.1111/j.1460-9568.2011.07871.x; -10.1111/j.1460-9568.2011.07871.x.
44. Casey JP, Magalhaes T, Conroy JM, Regan R, Shah N, et al. (2012) A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. Hum Genet 131: 565-579 10.1007/s00439-011-1094-6.
45. Toma C, Hervas A, Torrico B, Balmana N, Salgado M, et al. (2013) Analysis of two language-related genes in autism: A case-control association study of FOXP2 and CNTNAP2. Psychiatr Genet 23: 82-85 10.1097/YPG.0b013e32835d6fc6; 10.1097/YPG.0b013e32835d6fc6.