Evidence for differential alternative splicing in blood of young boys with autism spectrum disorders

Boryana S Stamova,Yingfang Tian,Christine W Nordahl,Sally Rogers,Mark D Shen,Frank R Sharp,David G Amaral

doi:10.1186/2040-2392-4-30

Boryana S Stamova, Yingfang Tian + Show 5 more

Open Access

https://doi.org/10.1186/2040-2392-4-30

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Abstract

BackgroundSince RNA expression differences have been reported in autism spectrum disorder (ASD) for blood and brain, and differential alternative splicing (DAS) has been reported in ASD brains, we determined if there was DAS in blood mRNA of ASD subjects compared to typically developing (TD) controls, as well as in ASD subgroups related to cerebral volume.MethodsRNA from blood was processed on whole genome exon arrays for 2-4–year-old ASD and TD boys. An ANCOVA with age and batch as covariates was used to predict DAS for ALL ASD (n=30), ASD with normal total cerebral volumes (NTCV), and ASD with large total cerebral volumes (LTCV) compared to TD controls (n=20).ResultsA total of 53 genes were predicted to have DAS for ALL ASD versus TD, 169 genes for ASD_NTCV versus TD, 1 gene for ASD_LTCV versus TD, and 27 genes for ASD_LTCV versus ASD_NTCV. These differences were significant at P <0.05 after false discovery rate corrections for multiple comparisons (FDR <5% false positives). A number of the genes predicted to have DAS in ASD are known to regulate DAS (SFPQ, SRPK1, SRSF11, SRSF2IP, FUS, LSM14A). In addition, a number of genes with predicted DAS are involved in pathways implicated in previous ASD studies, such as ROS monocyte/macrophage, Natural Killer Cell, mTOR, and NGF signaling. The only pathways significant after multiple comparison corrections (FDR <0.05) were the Nrf2-mediated reactive oxygen species (ROS) oxidative response (superoxide dismutase 2, catalase, peroxiredoxin 1, PIK3C3, DNAJC17, microsomal glutathione S-transferase 3) and superoxide radical degradation (SOD2, CAT).ConclusionsThese data support differences in alternative splicing of mRNA in blood of ASD subjects compared to TD controls that differ related to head size. The findings are preliminary, need to be replicated in independent cohorts, and predicted alternative splicing differences need to be confirmed using direct analytical methods.

Highlights

Since RNA expression differences have been reported in autism spectrum disorder (ASD) for blood and brain, and differential alternative splicing (DAS) has been reported in ASD brains, we determined if there was DAS in blood mRNA of ASD subjects compared to typically developing (TD) controls, as well as in ASD subgroups related to cerebral volume
Blood is useful to study in ASD for several reasons: (1) various factors - including genetics, toxicants, infections, immune and autoimmune factors implicated in ASD [6,7,8,9,10,11] - affect alternative splicing in leukocytes in blood [12,13,14,15,16,17,18,19]; (2) the monocyte transcriptome in blood is very similar to the microglia transcriptome [20,21], and microglia are activated in ASD brain [22]; (3) immune and autoimmune dysfunction that would be associated with alterations of gene expression and alternative splicing in blood has been reported in subgroups of ASD individuals [23,24,25,26]; (4) there is crosstalk between the immune system and the CNS [27,28]; (5) studies of blood allow us to investigate subjects at an early age when ASD becomes clinically evident
This study shows that differential alternative splicing may occur in selected genes in blood of 2-4-year-old boys with ASD compared to TD controls

Summary

Introduction

Since RNA expression differences have been reported in autism spectrum disorder (ASD) for blood and brain, and differential alternative splicing (DAS) has been reported in ASD brains, we determined if there was DAS in blood mRNA of ASD subjects compared to typically developing (TD) controls, as well as in ASD subgroups related to cerebral volume. For the present study, some genes showed evidence of altered differential alternative splicing (DAS) of specific FOX1 regulated mRNAs [5]. These data led us to consider in this study whether there might be altered DAS of mRNA in ASD blood. Blood is useful to study in ASD for several reasons: (1) various factors - including genetics, toxicants, infections, immune and autoimmune factors implicated in ASD [6,7,8,9,10,11] - affect alternative splicing in leukocytes in blood [12,13,14,15,16,17,18,19]; (2) the monocyte transcriptome in blood is very similar to the microglia (brain macrophage) transcriptome [20,21], and microglia are activated in ASD brain [22]; (3) immune and autoimmune dysfunction that would be associated with alterations of gene expression and alternative splicing in blood has been reported in subgroups of ASD individuals [23,24,25,26]; (4) there is crosstalk between the immune system and the CNS [27,28]; (5) studies of blood allow us to investigate subjects at an early age when ASD becomes clinically evident

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