Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines

Abstract

BackgroundAutism spectrum disorders (ASD) are neurodevelopmental disorders characterized by abnormalities in reciprocal social interactions and language development and/or usage, and by restricted interests and repetitive behaviors. Differential gene expression of neurologically relevant genes in lymphoblastoid cell lines from monozygotic twins discordant in diagnosis or severity of autism suggested that epigenetic factors such as DNA methylation or microRNAs (miRNAs) may be involved in ASD.MethodsGlobal miRNA expression profiling using lymphoblasts derived from these autistic twins and unaffected sibling controls was therefore performed using high-throughput miRNA microarray analysis. Selected differentially expressed miRNAs were confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis, and the putative target genes of two of the confirmed miRNA were validated by knockdown and overexpression of the respective miRNAs.ResultsDifferentially expressed miRNAs were found to target genes highly involved in neurological functions and disorders in addition to genes involved in gastrointestinal diseases, circadian rhythm signaling, as well as steroid hormone metabolism and receptor signaling. Novel network analyses of the putative target genes that were inversely expressed relative to the relevant miRNA in these same samples further revealed an association with ASD and other co-morbid disorders, including muscle and gastrointestinal diseases, as well as with biological functions implicated in ASD, such as memory and synaptic plasticity. Putative gene targets (ID3 and PLK2) of two RT-PCR-confirmed brain-specific miRNAs (hsa-miR-29b and hsa-miR-219-5p) were validated by miRNA overexpression or knockdown assays, respectively. Comparisons of these mRNA and miRNA expression levels between discordant twins and between case-control sib pairs show an inverse relationship, further suggesting that ID3 and PLK2 are in vivo targets of the respective miRNA. Interestingly, the up-regulation of miR-23a and down-regulation of miR-106b in this study reflected miRNA changes previously reported in post-mortem autistic cerebellum by Abu-Elneel et al. in 2008. This finding validates these differentially expressed miRNAs in neurological tissue from a different cohort as well as supports the use of the lymphoblasts as a surrogate to study miRNA expression in ASD.ConclusionsFindings from this study strongly suggest that dysregulation of miRNA expression contributes to the observed alterations in gene expression and, in turn, may lead to the pathophysiological conditions underlying autism.

Maternal immune activation alters brain microRNA expression in mouse offspring

“…Sarachana et al. reported downregulation of miR‐219‐5p and miR‐133b in lymphoblast cell lines from ASD patients 8. In particular, they confirmed that miR‐219‐5p targeted Polo like kinase 2 ( PLK2 ), whose activation in neurons is dependent on synaptic activity and is involved in homeostatic regulation of synaptic plasticity 41.…”

“…reported conflicting results; prenatal exposure to valproic acid upregulated miR‐132‐5p expression in the embryonic mouse brain 33. However, the effect of miR‐132‐5p upregulation was transient, lasting only 18–24 h after valproic acid exposure, which might explain the opposite direction of miR‐132‐5p dysregulation, compared to other studies in human cases 8, 9…”

“…microRNA (miRNA) is a well‐known epigenetic component that post‐transcriptionally regulates gene expression by binding to complementary nucleotide sequences in the 3′ untranslated region of target mRNAs 5. Altered miRNA expression has been associated with neurological disorders, including Alzheimer's disease,6 schizophrenia,7 and ASD 8, 9. Therefore, miRNAs may act as epigenetic factors in complex ASD etiologies, however, there have been substantial differences reported in miRNA expression profiles among different studies 10.…”

Profiling of Circulating Serum MicroRNAs in Children with Autism Spectrum Disorder using Stem-loop qRT-PCR Assay

“…Until now, studies have centered more on genetic factors, but only a few studies have investigated the role of miRNA as epigenetic factors involved in ASD. [2][3][4] Epigenetic factors regulate heritable modifi cations in gene function or activity without changes of the DNA sequence. МicroRNAs have recently became leading epigenetic regulators of various cellular processes.…”

Recent advances in nutrition, genes and brain health

“…These mechanisms are implicated in cognition, eating disorders, depression, autism and schizophrenia (25,(31)(32)(33) . Studies on other epigenetic mechanisms involving RNA methylation, non-coding microRNA, telomere control and chromosomal position effects should also provide new understanding of mechanisms linking nutrition and brain health (23,34,35) .…”