Feasibility and relevance of examining lymphoblastoid cell lines to study role of microRNAs in autism

Autism Research

Volumn 1, Issue 4, 2008, Pages 240-250

  Talebizadeh, Zohreh ^a   Butler, Merlin G ^a   Theodoro, Mariana F ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY SCHOOL OF MEDICINE   (United States)

Author keywords

Differential expression; Lymphoblastoid cell lines; microRNA; autism

Indexed keywords

MESSENGER RNA; MICRORNA;

AUTISM; FEASIBILITY STUDY; GENE EXPRESSION PROFILING; GENETIC LINKAGE; GENETICS; HUMAN; LYMPHATIC LEUKEMIA; PATHOLOGY; POLYMERASE CHAIN REACTION; REVIEW; TUMOR CELL LINE;

AUTISTIC DISORDER; CELL LINE, TUMOR; FEASIBILITY STUDIES; GENE EXPRESSION PROFILING; HUMANS; LEUKEMIA, LYMPHOID; LINKAGE (GENETICS); MICRORNAS; POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 66349107637     PISSN: 19393792     EISSN: 19393806     Source Type: Journal    
DOI: 10.1002/aur.33     Document Type: Article

References (59)

1. Abelson, J.F., Kwan, K.Y., O'Roak, B.J., Baek, D.Y., Stillman, A.A., et al. (2005). Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science, 310, 317-320.
2. Abu-Elneel, K., Liu, T., Gazzaniga, F.S., Nishimura, Y., Wall, D.P., et al. (2008). Heterogeneous dysregulation of microRNAs across the autism spectrum. Neurogenetics, 9, 153-161.
3. Aruga, J., Yokota, N., & Mikoshiba, K. (2003). Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. Gene, 315, 87-94.
4. Ashraf, S.I., & Kunes, S. (2006). A trace of silence: memory and microRNA at the synapse. Current Opinons in Neurobiology, 16, 535-539.
5. Ashraf, S.I., McLoon, A.L., Sclarsic, S.M., & Kunes, S. (2006). Synaptic protein synthesis associated with memory is regulated by the RISC pathway in Drosophila. Cell, 124, 191-205.
6. Baron, C.A., Tepper, C.G., Liu, S.Y., Davis, R.R., Wang, N.J., et al. (2006). Genomic and functional profiling of duplicated chromosome 15 cell lines reveal regulatory alterations in UBE3A-associated ubiquitin-proteasome pathway processes. Human Molecular Genetics, 15, 853-869.
7. Baskerville, S., & Bartel, D.P. (2005). Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11, 241-247.
8. Beitzinger, M., Peters, L., Zhu, J.Y., Kremmer, E., & Meister, G. (2007). Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biology, 4, 76-84.
9. Bittel, D.C., Kibiryeva, N., & Butler, M.G. (2006). Expression of 4 genes between chromosome 15 breakpoints 1 and 2 and behavioral outcomes in Prader-Willi syndrome. Pediatrics, 118, e1276-1283.
10. Blow, M.J., Grocock, R.J., van Dongen, S., Enright, A.J., Dicks, E., et al. (2006). RNA editing of human microRNAs. Genome Biology, 7, R27.
11. Bolstad, B.M., Irizarry, R.A., Astrand, M., & Speed, T.P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
12. Campbell, DB, Sutcliffe, JS, Ebert, PJ, Militerni, R, Bravaccio, C., et al. (2006). A genetic variant that disrupts MET transcription is associated with autism. Proceedings of the National Academy of Science USA, 103, 16834-16839.
13. Cao, X., Yeo, G., Muotri, A.R., Kuwabara, T., & Gage, F.H. (2006). Noncoding RNAs in the mammalian central nervous system. Annual Review of Neuroscience, 29, 77-103.
14. Chen, C., Ridzon, D.A., Broomer, A.J., Zhou, Z., Lee, D.H., et al. (2005). Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research, 33, e179.
15. Chen, J.F., Mandel, E.M., Thomson, J.M., Wu, Q., Callis, T.E., et al. (2006). The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nature Genetics, 38, 228-233.
16. Conaco, C., Otto, S., Han, J.J., & Mandel, G. (2006). Reciprocal actions of REST and a microRNA promote neuronal identity. Proceedings of the National Academy of Science USA, 103, 2422-2427.
17. Dostie, J., Mourelatos, Z., Yang, M., Sharma, A., & Dreyfuss, G. (2003). Numerous microRNPs in neuronal cells containing novel microRNAs. RNA, 9, 180-186.
18. Duan, R., & Jin, P. (2006). Identification of messenger RNAs and microRNAs associated with fragile X mental retardation protein. Methods in Molecular Biology, 342, 267-276.
19. Easow, G., Teleman, A.A., & Cohen, S.M. (2007). Isolation of microRNA targets by miRNP immunopurification. RNA, 13, 1198-1204.
20. Farh, K.K., Grimson, A., Jan, C., Lewis, B.P., Johnston, W.K., et al. (2005). The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science, 310, 1817-1821.
21. Gao, X., Gulari, E., & Zhou, X. (2004). In situ synthesis of oligonucleotide microarrays. Biopolymers, 73, 579-596.
22. Hu, V.W., Frank, B.C., Heine, S., Lee, N.H., & Quackenbush, J. (2006). Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes. BMC Genomics, 7, 118.
23. Jin, P., Alisch, R.S., & Warren, S.T. (2004). RNA and microRNAs in fragile X mental retardation. Nature Cell Biology, 6, 1048-1053.
24. Jin, P., Zarnescu, D.C., Ceman, S., Nakamoto, M., Mowrey, J., et al. (2004). Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nature Neuroscience, 7, 113-117.
25. John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., & Marks, D.S. (2004). Human MicroRNA targets. PLoS Biology, 2, e363.
26. Kawahara, Y., Zinshteyn, B., Sethupathy, P., Iizasa, H., Hatzigeorgiou, A.G., & Nishikura, K. (2007). Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science, 315, 1137-1140.
27. Kishore, S., & Stamm, S. (2006). The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science, 311, 230-232.
28. Krichevsky, A.M., King, K.S., Donahue, C.P., Khrapko, K., & Kosik, K.S. (2003). A microRNA array reveals extensive regulation of microRNAs during brain development. RNA, 9, 1274-1281.
29. Kuhn, D.E., Martin, M.M., Feldman, D.S., Terry, Jr A.V., Nuovo, G.J., & Elton, T.S. (2008). Experimental validation of miRNA targets. Methods, 44, 47-54.
30. Lewis, B.P., Burge, C.B., & Bartel, D.P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
31. Liang, Y., Ridzon, D., Wong, L., & Chen, C. (2007). Characterization of microRNA expression profiles in normal human tissues. BMC Genomics, 8, 166.
32. Lord, C., Rutter, M., & Le Couteur, A. (1994). Autism Diagnostic Interview-Revised: a revised version of a diagnostic interview for caregivers of individuals with possible pervasive developmental disorders. Journal of Autism and Developmental Disorders, 24, 659-685.
33. Lukiw, W.J. (2007). Micro-RNA speciation in fetal, adult and Alzheimer's disease hippocampus. Neuroreport, 18, 297-300.
34. Lum, A.M., Wang, B.B., Li, L., Channa, N., Bartha, G., & Wabl, M. (2007). Retroviral activation of the mir-106a microRNA cistron in T lymphoma. Retrovirology, 4, 5.
35. Martin, K.C., & Kosik, K.S. (2002). Synaptic tagging-who's it? Nature reviews. Neuroscience, 3, 813-820.
36. Mattick, J.S., & Makunin, I.V. (2005). Small regulatory RNAs in mammals. Human Molecular Genetics, 14, R121-R132.
37. Mehler, M.F., & Mattick, J.S. (2006). Non-coding RNAs in the nervous system. The Journal of Physiology, 575, 333-341.
38. Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F., & Mattick, J.S. (2008). Specific expression of long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Science USA, 105, 716-721.
39. Miska, E.A., Alvarez-Saavedra, E., Townsend, M., Yoshii, A., Sestan, N., et al. (2004). Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biology, 5, R68.
40. Nishimura, Y., Martin, C.L., Vazquez-Lopez, A., Spence, S.J., Alvarez-Retuerto, A.I., et al. (2007). Genome-wide expression profiling of lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways. Human Molecular Genetics, 16, 1682-1698.
41. Perkins, D.O., Jeffries, C.D., Jarskog, L.F., Thomson, J.M., Woods, K., et al. (2007). MicroRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder. Genome Biology, 8, R27.
42. Pillai, R.S. (2005). MicroRNA function: multiple mechanisms for a tiny RNA? RNA, 11, 1753-1761.
43. Rodriguez, A., Vigorito, E., Clare, S., Warren, M.V., Couttet, P., et al. (2007). Requirement of bic/microRNA-155 for normal immune function. Science, 316, 608-611.
44. Rogaev, E.I. (2005). Small RNAs in human brain development and disorders. Biochemistry (Moscow), 70, 1404-1407.
45. Rogelj, B., & Giese, K.P. (2004). Expression and function of brain specific small RNAs. Reviews in the Neurosciences, 15, 185-198.
46. Schaefer, A., O'Carroll, D., Tan, C.L., Hillman, D., Sugimori, M., et al. (2007). Cerebellar neurodegeneration in the absence of microRNAs. The Journal of Experimental Medicine, 204, 1553-1558.
47. Schmittgen, T.D., Lee, E.J., Jiang, J., Sarkar, A., Yang, L., et al. (2008). Real-time PCR quantification of precursor and mature microRNA. Methods, 44, 31-38.
48. Schratt, G.M., Tuebing, F., Nigh, E.A., Kane, C.G., Sabatini, M.E., et al. (2006). A brain-specific microRNA regulates dendritic spine development. Nature, 439, 283-289.
49. Sempere, L.F., Freemantle, S., Pitha-Rowe, I., Moss, E., Dmitrovsky, E., & Ambros, V. (2004). Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biology, 5, R13.
50. Szatmari, P., Paterson, A.D., Zwaigenbaum, L., Roberts, W., Brian, J., et al. (2007). Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nature Genetics, 39, 319-328.
51. Talebizadeh, Z., Bittel, D.C., Veatch, O.J., Kibiryeva, N., & Butler, M.G. (2005). Brief report: non-random X chromosome inactivation in females with autism. Journal of Autism and Developmental Disorders, 35, 675-681.
52. Talebizadeh, Z., Lam, D.Y., Theodoro, M.F., Bittel, D.C., Lushington, G.H., & Butler, M.G. (2006). Novel splice isoforms for NLGN3 and NLGN4 with possible implications in autism. Journal of Medical Genetics, 43, e21.
53. Thai, T.H., Calado, D.P., Casola, S., Ansel, K.M., Xiao, C., et al. (2007). Regulation of the germinal center response by microRNA-155. Science, 316, 604-608.
54. Vasudevan, S., Tong, Y., & Steitz, J.A. (2007). Switching from repression to activation: microRNAs can up-regulate translation. Science, 318, 1931-1934.
55. Vitali, P., Royo, H., Seitz, H., Bachellerie, J.P., Huttenhofer, A., & Cavaille, J. (2003). Identification of 13 novel human modification guide RNAs. Nucleic Acids Research, 31, 6543-6551.
56. Wu, J., & Xie, X. (2006). Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression. Genome Biology, 7, R85.
57. Yonan, A.L., Alarcon, M., Cheng, R., Magnusson, P.K., Spence, S.J., et al. (2003). A genomewide screen of 345 families for autism-susceptibility loci. American Journal of Human Genetics, 73, 886-897.
58. Young, J.I., Hong, E.P., Castle, J.C., Crespo-Barreto, J., Bowman, A.B., et al. (2005). Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl- CpG binding protein 2. Proceedings of the National Academy of Science USA, 102, 17551-17558.
59. Zhu, Q., Hong, A., Sheng, N., Zhang, X., Matejko, A., et al. (2007). microParaflo biochip for nucleic acid and protein analysis. Methods in Molecular Biology, 382, 287-312.