neurogenetics

, Volume 9, Issue 3, pp 153–161 | Cite as

Heterogeneous dysregulation of microRNAs across the autism spectrum

  • Kawther Abu-Elneel
  • Tsunglin Liu
  • Francesca S. Gazzaniga
  • Yuhei Nishimura
  • Dennis P. Wall
  • Daniel H. Geschwind
  • Kaiqin Lao
  • Kenneth S. Kosik
Original Article

Abstract

microRNAs (miRNAs) are ~21 nt transcripts capable of regulating the expression of many mRNAs and are abundant in the brain. miRNAs have a role in several complex diseases including cancer as well as some neurological diseases such as Tourette’s syndrome and Fragile x syndrome. As a genetically complex disease, dysregulation of miRNA expression might be a feature of autism spectrum disorders (ASDs). Using multiplex quantitative polymerase chain reaction (PCR), we compared the expression of 466 human miRNAs from postmortem cerebellar cortex tissue of individuals with ASD (n = 13) and a control set of non-autistic cerebellar samples (n = 13). While most miRNAs levels showed little variation across all samples suggesting that autism does not induce global dysfunction of miRNA expression, some miRNAs among the autistic samples were expressed at significantly different levels compared to the mean control value. Twenty-eight miRNAs were expressed at significantly different levels compared to the non-autism control set in at least one of the autism samples. To validate the finding, we reversed the analysis and compared each non-autism control to a single mean value for each miRNA across all autism cases. In this analysis, the number of dysregulated miRNAs fell from 28 to 9 miRNAs. Among the predicted targets of dysregulated miRNAs are genes that are known genetic causes of autism such Neurexin and SHANK3. This study finds that altered miRNA expression levels are observed in postmortem cerebellar cortex from autism patients, a finding which suggests that dysregulation of miRNAs may contribute to autism spectrum phenotype.

Keywords

Autism spectrum disorder miRNA Postmortem tissue Cerebellum 

Notes

Acknowledgements

We thank the Autism Tissue Program, Harvard Brain Bank and The Maryland Tissue Bank for the tissue samples. We thank Dr. Margaret Bauman for tissue specimens. The National Alliance for Autism Research (NAAR-Autism Speaks) and the W.M. Keck Foundation supported this research. A Young Investigator grant from the Cure Autism Now Foundation supported Yuhei Nishimura.

Supplementary material

10048_2008_133_MOESM1_ESM.doc (42 kb)
ESM-Figure 1 Scatter blot. Plotted 466-plex data versus 43 miRNAs corrected from the same RNA amplified used in the same experiment (DOC 43 KB).
10048_2008_133_MOESM2_ESM.xls (304 kb)
ESM-Table 1 The 466-multiplex miRNAs of original and normalized data of autism and control cases. Indicated miRNAs, snoRNAs and their sequences. First datasheet is multiplex Ct values of all tested miRNAs for autism and control cases. Second datasheet represents the normalized multiplex data. Third and fourth datasheets represent the 28 miRNAs dysregulated in the autism cases and the 9 miRNAs dysregulated in the control cases respectively. Indicated in bold, are the specific dysregulated miRNAs (XLS 311 KB).
10048_2008_133_MOESM3_ESM.doc (66 kb)
ESM-Table 2 List of the autism and control cases obtained from the different tissue banks. Indicated: age, sex, postmortem interval (PMI), cause of death, hemisphere, and source of tissues. N/A Not applicable. Source of tissue: Maryland, Brain and Tissue Bank University of Maryland; Harvard, Harvard Brain Tissue Resource Center (DOC 68 KB).
10048_2008_133_MOESM4_ESM.doc (38 kb)
ESM-Table 3 miRNA analysis of 13 autism and 13 control cases. A list of miRNAs for which Cts of all autism samples are different from those of the control with a significance p < 0.05 (Wilcoxon rank sum test). In this case, none of the miRNAs survived the Bonferroni correction for multiple hypotheses testing. Chr Chromosome (DOC 38 KB).
10048_2008_133_MOESM5_ESM.doc (194 kb)
ESM-Table 4 Overrepresented GO terms among the predicted targets of the 28 dysregulated miRNAs. The third/fourth column shows number of miRNAs (out of 28/453) that have an overrepresented GO term. The fifth column shows the ratio between the two percentages (DOC 198 KB).
10048_2008_133_MOESM6_ESM.doc (72 kb)
ESM-Table 5 A list of autism-associated markers and the corresponding regions. The list of the autism markers was complied as described under the “Material and Methods” section. Chr Chromosome (DOC 73 KB).
10048_2008_133_MOESM7_ESM.doc (50 kb)
ESM-Table 6 The probability for a miRNA to be in proximity to a marker peak. miRNAs (*, **) had a significance p < 0.05, and miRNAs (**) survived the correction for multiple comparisons by FDR set at 5%. Chr Chromosome. The following miRNAs were analyzed here but not tested in the 466-plex: hsa-miR-297; hsa-miR-668; hsa-miR-671; hsa-miR-675; hsa-miR-758; hsa-miR-765; hsa-miR-766; hsa-miR-767; hsa-miR-768; hsa-miR-769; hsa-miR-770; hsa-miR-801; hsa-miR-802 (DOC 51 KB).
10048_2008_133_MOESM8_ESM.xls (24 kb)
ESM-Table 7 Dysregulated miRNAs potentially targeting autism associated genes. TargetScan [45] context score (representing the possible correlation of repression of the gene by the specific miRNA) for the conserved and the nonconserved miRNA predicted target sites (left and right of “|”) in autism-associated genes. Listed 28 genes associated with ASD and 41 miRNAs found dysregulated in all statistical analysis (XLS 24 KB).

References

  1. 1.
    Centers for disease control (2007) Prevalence of autism spectrum disorders–autism and developmental disabilities monitoring network, 14 sites, United States, 2002. MMWR Surveill Summ 56(1):12–28Google Scholar
  2. 2.
    Comoletti D, De Jaco A, Jennings LL, Flynn RE, Gaietta G, Tsigelny I, Ellisman MH, Taylor P (2004) The Arg451Cys-neuroligin-3 mutation associated with autism reveals a defect in protein processing. J Neurosci 24(20):4889–4893CrossRefPubMedGoogle Scholar
  3. 3.
    Durand CM, Betancur C, Boeckers TM, Bockmann J, Chaste P, Fauchereau F, Nygren G, Rastam M, Gillberg IC, Anckarsater H et al (2007) Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are associated with autism spectrum disorders. Nat Genet 39(1):25–27CrossRefPubMedGoogle Scholar
  4. 4.
    Jamain S, Quach H, Betancur C, Rastam M, Colineaux C, Gillberg IC, Soderstrom H, Giros B, Leboyer M, Gillberg C et al (2003) Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. Nat Genet 34(1):27–29CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Laumonnier F, Bonnet-Brilhault F, Gomot M, Blanc R, David A, Moizard MP, Raynaud M, Ronce N, Lemonnier E, Calvas P et al (2004) X-linked mental retardation and autism are associated with a mutation in the NLGN4 gene, a member of the neuroligin family. Am J Hum Genet 74(3):552–557CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Moessner R, Marshall CR, Sutcliffe JS, Skaug J, Pinto D, Vincent J, Zwaigenbaum L, Fernandez B, Roberts W, Szatmari P et al (2007) Contribution of SHANK3 mutations to autism spectrum disorder. Am J Hum Genet 81(6):1289–1297CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Strauss KA, Puffenberger EG, Huentelman MJ, Gottlieb S, Dobrin SE, Parod JM, Stephan DA, Morton DH (2006) Recessive symptomatic focal epilepsy and mutant contactin-associated protein-like 2. N Engl J Med 354(13):1370–1377CrossRefPubMedGoogle Scholar
  8. 8.
    Gupta AR, State MW (2007) Recent advances in the genetics of autism. Biol Psychiatry 61(4):429–437CrossRefPubMedGoogle Scholar
  9. 9.
    Klauck SM (2006) Genetics of autism spectrum disorder. Eur J Hum Genet 14(6):714–720CrossRefPubMedGoogle Scholar
  10. 10.
    Szatmari P, Paterson AD, Zwaigenbaum L, Roberts W, Brian J, Liu XQ, Vincent JB, Skaug JL, Thompson AP, Senman L et al (2007) Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet 39(3):319–328CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Yang MS, Gill M (2007) A review of gene linkage, association and expression studies in autism and an assessment of convergent evidence. Int J Dev Neurosci 25(2):69–85CrossRefPubMedGoogle Scholar
  12. 12.
    Vorstman JA, Staal WG, van Daalen E, van Engeland H, Hochstenbach PF, Franke L (2006) Identification of novel autism candidate regions through analysis of reported cytogenetic abnormalities associated with autism. Mol Psychiatry 11(1):1, 18–28Google Scholar
  13. 13.
    Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y et al (2008) Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 82(2):477–488CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J et al (2007) Strong association of de novo copy number mutations with autism. Science 316(5823):445–449CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Cook EH Jr., Lindgren V, Leventhal BL, Courchesne R, Lincoln A, Shulman C, Lord C, Courchesne E (1997) Autism or atypical autism in maternally but not paternally derived proximal 15q duplication. Am J Hum Genet 60(4):928–934PubMedPubMedCentralGoogle Scholar
  16. 16.
    Percy AK, Lane JB (2004) Rett syndrome: clinical and molecular update. Curr Opin Pediatr 16(6):670–677CrossRefPubMedGoogle Scholar
  17. 17.
    Bolton PF, Griffiths PD (1997) Association of tuberous sclerosis of temporal lobes with autism and atypical autism. Lancet 349(9049):392–395CrossRefPubMedGoogle Scholar
  18. 18.
    Bolton PF, Park RJ, Higgins JN, Griffiths PD, Pickles A (2002) Neuro-epileptic determinants of autism spectrum disorders in tuberous sclerosis complex. Brain 125(Pt 6):1247–1255CrossRefPubMedGoogle Scholar
  19. 19.
    Lewis JC, Thomas HV, Murphy KC, Sampson JR (2004) Genotype and psychological phenotype in tuberous sclerosis. J Med Genet 41(3):203–207CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Cianchetti C, Sannio-Fancello G, Fratta AL, Manconi F, Orano A, Pischedda MP, Pruna D, Spinicci G, Archidiacono N, Filippi G (1991) Neuropsychological, psychiatric, and physical manifestations in 149 members from 18 fragile X families. Am J Med Genet 40(2):234–243CrossRefPubMedGoogle Scholar
  21. 21.
    Klauck SM, Munstermann E, Bieber-Martig B, Ruhl D, Lisch S, Schmotzer G, Poustka A, Poustka F (1997) Molecular genetic analysis of the FMR-1 gene in a large collection of autistic patients. Hum Genet 100(2):224–229CrossRefPubMedGoogle Scholar
  22. 22.
    Lombroso PJ (2003) Genetics of childhood disorders: XLVIII. Learning and memory, part 1: fragile X syndrome update. J Am Acad Child Adolesc Psychiatry 42(3):372–375CrossRefPubMedGoogle Scholar
  23. 23.
    Oostra BA, Chiurazzi P (2001) The fragile X gene and its function. Clin Genet 60(6):399–408CrossRefPubMedGoogle Scholar
  24. 24.
    Vincent JB, Thevarkunnel S, Kolozsvari D, Paterson AD, Roberts W, Scherer SW (2004) Association and transmission analysis of the FMR1 IVS10 + 14C-T variant in autism. Am J Med Genet B Neuropsychiatr Genet 125(1):54–56CrossRefGoogle Scholar
  25. 25.
    Sikora DM, Pettit-Kekel K, Penfield J, Merkens LS, Steiner RD (2006) The near universal presence of autism spectrum disorders in children with Smith–Lemli–Opitz syndrome. Am J Med Genet A 140(14):1511–1518CrossRefPubMedGoogle Scholar
  26. 26.
    Tierney E, Nwokoro NA, Porter FD, Freund LS, Ghuman JK, Kelley RI (2001) Behavior phenotype in the RSH/Smith–Lemli–Opitz syndrome. Am J Med Genet 98(2):191–200CrossRefPubMedGoogle Scholar
  27. 27.
    Freitag CM (2007) The genetics of autistic disorders and its clinical relevance: a review of the literature. Mol Psychiatry 12(1):2–22CrossRefPubMedGoogle Scholar
  28. 28.
    Bauman ML, Kemper TL (2005) Neuroanatomic observations of the brain in autism: a review and future directions. Int J Dev Neurosci 23(2–3):183–187CrossRefPubMedGoogle Scholar
  29. 29.
    Bailey A, Luthert P, Dean A, Harding B, Janota I, Montgomery M, Rutter M, Lantos P (1998) A clinicopathological study of autism. Brain 121(Pt 5):889–905CrossRefPubMedGoogle Scholar
  30. 30.
    Bauman ML, Kemper TL (2003) The neuropathology of the autism spectrum disorders: what have we learned? Novartis Found Symp 251:112–122 discussion 122–118, 281–197CrossRefPubMedGoogle Scholar
  31. 31.
    Courchesne E (1991) Neuroanatomic imaging in autism. Pediatrics 87(5 Pt 2):781–790PubMedGoogle Scholar
  32. 32.
    Kemper TL, Bauman ML (1993) The contribution of neuropathologic studies to the understanding of autism. Neurol Clin 11(1):175–187PubMedGoogle Scholar
  33. 33.
    Kern JK (2003) Purkinje cell vulnerability and autism: a possible etiological connection. Brain Dev 25(6):377–382CrossRefPubMedGoogle Scholar
  34. 34.
    Townsend J, Courchesne E, Covington J, Westerfield M, Harris NS, Lyden P, Lowry TP, Press GA (1999) Spatial attention deficits in patients with acquired or developmental cerebellar abnormality. J Neurosci 19(13):5632–5643PubMedGoogle Scholar
  35. 35.
    Sajdel-Sulkowska EM, Lipinski B, Windom H, Audhya T, Woody McGinnis W (2008) Oxidative stress in autism: elevated cerebellar 3-nitrotyrosine levels. American Journal of Biochemistry and Biotechnology 4(2):73–84CrossRefGoogle Scholar
  36. 36.
    Kosik KS (2006) The neuronal microRNA system. Nat Rev Neurosci 7(12):911–920CrossRefPubMedGoogle Scholar
  37. 37.
    Courchesne E (2004) Brain development in autism: early overgrowth followed by premature arrest of growth. Ment Retard Dev Disabil Res Rev 10(2):106–111CrossRefPubMedGoogle Scholar
  38. 38.
    Courchesne E, Pierce K (2005) Brain overgrowth in autism during a critical time in development: implications for frontal pyramidal neuron and interneuron development and connectivity. Int J Dev Neurosci 23(2–3):153–170CrossRefPubMedGoogle Scholar
  39. 39.
    Liu T, Papagiannakopoulos T, Puskar K, Qi S, Santiago F, Clay W, Lao K, Lee Y, Nelson SF, Kornblum HI et al (2007) Detection of a microRNA signal in an in vivo expression set of mRNAs. PLoS ONE 2(8):e804CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Schellenberg GD, Dawson G, Sung YJ, Estes A, Munson J, Rosenthal E, Rothstein J, Flodman P, Smith M, Coon H et al (2006) Evidence for multiple loci from a genome scan of autism kindreds. Mol Psychiatry 11(11):1049–1060, 1979CrossRefPubMedGoogle Scholar
  41. 41.
    Wellcome Trust Sanger Institute [http://microrna.sanger.ac.uk/sequences/]
  42. 42.
    Perkins DO, Jeffries CD, Jarskog LF, Thomson JM, Woods K, Newman MA, Parker JS, Jin J, Hammond SM (2007) microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder. Genome Biol 8(2):R27CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Bacchelli E, Maestrini E (2006) Autism spectrum disorders: molecular genetic advances. Am J Med Genet C Semin Med Genet 142(1):13–23CrossRefGoogle Scholar
  44. 44.
    Sykes NH, Lamb JA (2007) Autism: the quest for the genes. Expert Rev Mol Med 9(24):1–15CrossRefPubMedGoogle Scholar
  45. 45.
    TargetScan Prediction of microRNA Targets [http://www.targetscan.org/]
  46. 46.
    Pardo CA, Eberhart CG (2007) The neurobiology of autism. Brain Pathol 17(4):434–447CrossRefPubMedGoogle Scholar
  47. 47.
    Locke DP, Sharp AJ, McCarroll SA, McGrath SD, Newman TL, Cheng Z, Schwartz S, Albertson DG, Pinkel D, Altshuler DM et al (2006) Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am J Hum Genet 79(2):275–290CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W et al (2006) Global variation in copy number in the human genome. Nature 444(7118):444–454CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Autism Tissue Program [http://www.brainbank.org/]
  50. 50.
    Harvard Brain Tissue Resource Center [http://www.brainbank.mclean.org/]
  51. 51.
    Brain and Tissue Bank for Developmental Disorder University of Maryland [http://medschool.umaryland.edu/BTBank/]
  52. 52.
    Lao K, Xu NL, Yeung V, Chen C, Livak KJ, Straus NA (2006) Multiplexing RT-PCR for the detection of multiple miRNA species in small samples. Biochem Biophys Res Commun 343(1):85–89CrossRefPubMedGoogle Scholar
  53. 53.
    Li C, Hung Wong W (2001) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2(8):RESEARCH0032PubMedPubMedCentralGoogle Scholar
  54. 54.
    Chen GK, Kono N, Geschwind DH, Cantor RM (2006) Quantitative trait locus analysis of nonverbal communication in autism spectrum disorder. Mol Psychiatry 11(2):214–220CrossRefPubMedGoogle Scholar
  55. 55.
    Lauritsen MB, Als TD, Dahl HA, Flint TJ, Wang AG, Vang M, Kruse TA, Ewald H, Mors O (2006) A genome-wide search for alleles and haplotypes associated with autism and related pervasive developmental disorders on the Faroe Islands. Mol Psychiatry 11(1):37–46CrossRefPubMedGoogle Scholar
  56. 56.
    Broman KW, Murray JC, Sheffield VC, White RL, Weber JL (1998) Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet 63(3):861–869CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
  58. 58.
    The Gene Ontology [http://www.geneontology.org/]

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Kawther Abu-Elneel
    • 1
  • Tsunglin Liu
    • 1
  • Francesca S. Gazzaniga
    • 1
  • Yuhei Nishimura
    • 2
  • Dennis P. Wall
    • 3
  • Daniel H. Geschwind
    • 2
  • Kaiqin Lao
    • 4
  • Kenneth S. Kosik
    • 1
  1. 1.Neuroscience Research Institute, and Department of Molecular Cellular and Developmental BiologyUniversity of California Santa BarbaraSanta BarbaraUSA
  2. 2.Program in Neurogenetics and Neurobehavioral Genetics, Department of Neurology, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesUSA
  3. 3.The Center for Biomedical Informatics & Department of Systems BiologyHarvard Medical SchoolBostonUSA
  4. 4.Applied BiosystemsFoster CityUSA

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