In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue

Human Molecular Genetics

Volumn 22, Issue 17, 2013, Pages 3534-3546

  Hjelm, Brooke E ^a,b,c   Salhia, Bodour ^a   Kurdoglu, Ahmet ^a   Szelinger, Szabolcs ^a,b,c   Reiman, Rebecca A ^a   Sue, Lucia I ^b,d   Beach, Thomas G ^b,d   Huentelman, Matthew J ^a,b   Craig, David W ^a,b  

^a TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^b ARIZONA ALZHEIMER S CONSORTIUM   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

^d SUN HEALTH RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA;

AGED; ARTICLE; BRAIN TISSUE; CPG ISLAND; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; MALE; MICROARRAY ANALYSIS; NERVE CELL CULTURE; NERVE CELL DIFFERENTIATION; NEUROPATHOLOGY; NORMAL HUMAN; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; RNA METHYLATION; RNA SEQUENCE; TEMPORAL LOBE; TISSUE SPECIFICITY; TRANSCRIPTION INITIATION;

EID: 84881579993     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddt208     Document Type: Article

References (55)

1. Chaible, L.M., Corat, M.A., Abdelhay, E. and Dagli, M.L. (2010) Genetically modified animals for use in research and biotechnology. Genet. Mol. Res., 9, 1469-1482.
2. Pandey, U.B., Nichols, C.D. (2011)Humandisease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery. Pharmacol. Rev., 63, 411-436.
3. Li, Z.K., Zhou, Q. (2010) Cellular models for disease exploring and drug screening. Protein Cell, 1, 355-362.
4. Birney, E., Lieb, J.D., Furey, T.S., Crawford, G.E., Iyer, V.R. (2010) Allele-specific and heritable chromatin signatures in humans. Hum. Mol. Genet., 19, R204-R209.
5. Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., Yamanaka, S. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell, 131, 861-872.
6. Yu, J., Vodyanik, M.A., Smuga-Otto, K., Antosiewicz-Bourget, J., Frane, J.L., Tian, S., Nie, J., Jonsdottir, G.A., Ruotti, V., Stewart, R. et al. (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science, 318, 1917-1920.
7. Stadtfeld, M., Hochedlinger, K. (2010) Induced pluripotency: history, mechanisms, and applications. Genes Dev., 24, 2239-2263.
8. Park, I.H., Arora, N., Huo, H., Maherali, N., Ahfeldt, T., Shimamura, A., Lensch, M.W., Cowan, C., Hochedlinger, K., Daley, G.Q. (2008) Disease-specific induced pluripotent stem cells. Cell, 134, 877-886.
9. Allen, D.D., Caviedes, R., Cardenas, A.M., Shimahara, T., Segura-Aguilar, J., Caviedes, P.A. (2005) Cell lines as in vitro models for drug screening and toxicity studies. Drug Dev. Ind. Pharm., 31, 757-768.
10. Marchetto, M.C., Winner, B., Gage, F.H. (2010) Pluripotent stem cells in neurodegenerative and neurodevelopmental diseases. Hum. Mol. Genet., 19, R71-R76.
11. Han, S.S., Williams, L.A., Eggan, K.C. (2011) Constructing and deconstructing stem cell models of neurological disease. Neuron, 70, 626-644.
12. Murry, C.E., Keller, G. (2008) Differentiation of embryonic stem cells to clinically relevant populations: lessons from embryonic development. Cell, 132, 661-680.
13. Hanna, J.H., Saha, K., Jaenisch, R. (2010) Pluripotency and cellular reprogramming: facts, hypotheses, unresolved issues. Cell, 143, 508-525.
14. Wichterle, H., Przedborski, S. (2010) What can pluripotent stem cells teach us about neurodegenerative diseases. Nat. Neurosci., 13, 800-804.
15. Patterson, M., Chan, D.N., Ha, I., Case, D., Cui, Y.,VanHandel, B., Mikkola, H.K., Lowry, W.E. (2012) Defining the nature of human pluripotent stem cell progeny. Cell Res., 22, 178-193.
16. Hjelm, B.E., Rosenberg, J.B., Szelinger, S., Sue, L.I., Beach, T.G., Huentelman, M.J., Craig,D.W.(2011) Induction of pluripotent stem cells from autopsy donor-derived somatic cells. Neurosci. Lett., 502, 219-224.
17. Beach, T.G., Sue, L.I., Walker, D.G., Roher, A.E., Lue, L., Vedders, L., Connor, D.J., Sabbagh, M.N., Rogers, J. (2008) The Sun Health Research Institute Brain Donation Program: description and experience, 1987-2007. Cell Tissue Bank., 9, 229-245.
18. Nelson, P.T., Jicha, G.A., Kryscio, R.J., Abner, E.L., Schmitt, F.A., Cooper, G., Xu, L.O., Smith, C.D., Markesbery, W.R. (2010) Low sensitivity in clinical diagnoses of dementia with Lewy bodies. J Neurol., 257, 359-366.
19. Rohrer, J.D., Lashley, T., Schott, J.M., Warren, J.E., Mead, S., Isaacs, A.M., Beck, J., Hardy, J., de Silva, R., Warrington, E. et al. (2011) Clinical and neuroanatomical signatures of tissue pathology in frontotemporal lobar degeneration. Brain J. Neurol., 134, 2565-2581.
20. Beach, T.G., Monsell, S.E., Phillips, L.E., Kukull,W.(2012) Accuracy of the clinical diagnosis of Alzheimer disease at National Institute on Aging Alzheimer Disease Centers, 2005-2010. J. Neuropathol. Exp. Neurol., 71, 266-273.
21. Zeng, H., Guo, M., Martins-Taylor, K., Wang, X., Zhang, Z., Park, J.W., Zhan, S., Kronenberg, M.S., Lichtler, A., Liu, H.X. et al. (2010) Specification of region-specific neurons including forebrain glutamatergic neurons from human induced pluripotent stem cells. PloS One, 5, e11853.
22. Brennand, K.J., Simone, A., Jou, J., Gelboin-Burkhart, C., Tran, N., Sangar, S., Li, Y., Mu, Y., Chen, G., Yu, D. et al. (2011) Modelling schizophrenia using human induced pluripotent stem cells. Nature, 473, 221-225.
23. Shi, Y., Kirwan, P., Livesey, F.J. (2012) Directed differentiation of humanpluripotent stem cells to cerebral cortex neurons and neural networks. Nat. Protocol., 7, 1836-1846.
24. Mariani, J., Simonini, M.V., Palejev, D., Tomasini, L., Coppola, G., Szekely, A.M., Horvath, T.L., Vaccarino, F.M. (2012) Modeling human cortical development in vitro using induced pluripotent stem cells. Proc. Natl Acad. Sci. USA, 109, 12770-12775.
25. Scharfman, H.E. (2012) Alzheimer's disease and epilepsy: insight from animal models. Future Neurol., 7, 177-192.
26. Whalley, H.C., Papmeyer, M., Sprooten, E., Lawrie, S.M., Sussmann, J.E., McIntosh, A.M. (2012) Review of functional magnetic resonance imaging studies comparing bipolar disorder and schizophrenia. Bipolar Disorders, 14, 411-431.
27. Birdsill, A.C., Walker, D.G., Lue, L., Sue, L.I., Beach, T.G. (2011) Postmortem interval effect on RNA and gene expression in human brain tissue. Cell Tissue Bank., 12, 311-318.
28. Trapnell, C., Pachter, L., Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
29. Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., Pachter, L. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protocol., 7, 562-578.
30. Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
31. Krupp, M., Marquardt, J.U., Sahin, U., Galle, P.R., Castle, J., Teufel, A. (2012)RNA-SeqAtlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics, 28, 1184-1185.
32. Ponten, F., Schwenk, J.M., Asplund, A., Edqvist, P.H. (2011) TheHuman Protein Atlas as a proteomic resource for biomarker discovery. J. Int. Med., 270, 428-446.
33. Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A., Rinn, J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
34. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
35. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
36. Mercer, T.R., Dinger, M.E., Mattick, J.S. (2009) Long non-coding RNAs: insights into functions. Nat. Rev. Genet., 10, 155-159.
37. Bibikova, M., Barnes, B., Tsan, C., Ho, V., Klotzle, B., Le, J.M., Delano, D., Zhang, L., Schroth, G.P., Gunderson, K.L. et al. (2011) High density DNA methylation array with single CpG site resolution. Genomics, 98, 288-295.
38. Salhia, B., Baker, A., Ahmann, G., Auclair, D., Fonseca, R., Carpten, J. (2010) DNA methylation analysis determines the high frequency of genic hypomethylation and low frequency of hypermethylation events in plasma cell tumors. Cancer Res., 70, 6934-6944.
39. Irizarry, R.A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M. et al. (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.
40. Feinberg, A.P., Tycko, B. (2004) The history of cancer epigenetics. Nat. Rev. Cancer, 4, 143-153.
41. Deaton, A.M., Bird, A. (2011) CpG islands and the regulation of transcription. Genes Dev., 25, 1010-1022.
42. Doi, A., Park, I.H., Wen, B., Murakami, P., Aryee, M.J., Irizarry, R., Herb, B., Ladd-Acosta, C., Rho, J., Loewer, S. et al. (2009) Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet., 41, 1350-1353.
43. Ladd-Acosta, C., Pevsner, J., Sabunciyan, S., Yolken, R.H., Webster, M.J., Dinkins, T., Callinan, P.A., Fan, J.B., Potash, J.B., Feinberg, A.P. (2007) DNA methylation signatures within the human brain. Am. J. Hum. Genet., 81, 1304-1315.
44. Siegmund, K.D., Connor, C.M., Campan, M., Long, T.I., Weisenberger, D.J., Biniszkiewicz, D., Jaenisch, R., Laird, P.W., Akbarian, S. (2007) DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons. PloS One, 2, e895.
45. Sharma, R.P., Gavin, D.P., Grayson, D.R. (2010) CpG methylation in neurons: message, memory, or mask. Neuropsychopharmacology, 35, 2009-2020.
46. Ramskold, D., Wang, E.T., Burge, C.B., Sandberg, R. (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol., 5, e1000598.
47. Jongeneel, C.V., Delorenzi, M., Iseli, C., Zhou, D., Haudenschild, C.D., Khrebtukova, I., Kuznetsov, D., Stevenson, B.J., Strausberg, R.L., Simpson, A.J. et al. (2005) An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res., 15, 1007-1014.
48. Kang, H.J., Kawasawa, Y.I., Cheng, F., Zhu, Y., Xu, X., Li, M., Sousa, A.M., Pletikos, M., Meyer, K.A., Sedmak, G. et al. (2011) Spatio-temporal transcriptome of the human brain. Nature, 478, 483-489.
49. Sugiyama, Y., Kawabata, I., Sobue, K., Okabe, S. (2005) Determination of absolute protein numbers in single synapses by a GFP-based calibration technique. Nat. Methods, 2, 677-684.
50. Bayes, A., Grant, S.G. (2009) Neuroproteomics: understanding the molecular organization and complexity of the brain. Nat. Rev. Neurosci., 10, 635-646.
51. Johnson, M.B., Kawasawa, Y.I., Mason, C.E., Krsnik, Z., Coppola, G., Bogdanovic, D., Geschwind, D.H., Mane, S.M., State, M.W., Sestan, N. (2009) Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron, 62, 494-509.
52. Craig, D.W., O'Shaughnessy, J.A., Kiefer, J.A., Aldrich, J., Sinari, S., Moses, T.M., Wong, S., Dinh, J., Christoforides, A., Blum, J.L. et al. (2013) Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities. Mol. Cancer Therap., 12, 104-116.
53. Tariq, M.A., Kim, H.J., Jejelowo, O., Pourmand, N. (2011) Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res., 39, e120.
54. Craig, D.W., Pearson, J.V., Szelinger, S., Sekar, A., Redman, M., Corneveaux, J.J., Pawlowski, T.L., Laub, T., Nunn, G., Stephan, D.A. et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods, 5, 887-893.
55. Bennett, S. (2004) Solexa Ltd. Pharmacogenomics, 5, 433-438.