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Heterogeneous dysregulation of microRNAs across the autism spectrum

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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.

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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.

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Author notes

  1. Francesca S. Gazzaniga

    Present address: Biomedical Sciences, University of California San Francisco, San Francisco, CA, 94143, USA

Authors and Affiliations

  1. Neuroscience Research Institute, and Department of Molecular Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA

    Kawther Abu-Elneel, Tsunglin Liu, Francesca S. Gazzaniga & Kenneth S. Kosik

  2. Program in Neurogenetics and Neurobehavioral Genetics, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095-1769, USA

    Yuhei Nishimura & Daniel H. Geschwind

  3. The Center for Biomedical Informatics & Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA

    Dennis P. Wall

  4. Applied Biosystems, 850 Lincoln Centre Dr., Foster City, CA, 94404, USA

    Kaiqin Lao

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  1. Kawther Abu-Elneel
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Correspondence to Kenneth S. Kosik.

Additional information

Kawther Abu-Elneel and Tsunglin Liu contributed equally.

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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).

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 C t 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).

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).

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).

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).

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).

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).

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).

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Abu-Elneel, K., Liu, T., Gazzaniga, F.S. et al. Heterogeneous dysregulation of microRNAs across the autism spectrum. Neurogenetics 9, 153–161 (2008). https://doi.org/10.1007/s10048-008-0133-5

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