Gene expression in human brain implicates sexually dimorphic pathways in autism spectrum disorders

Abstract

Autism spectrum disorder (ASD) is more prevalent in males, and the mechanisms behind this sex-differential risk are not fully understood. Two competing, but not mutually exclusive, hypotheses are that ASD risk genes are sex-differentially regulated, or alternatively, that they interact with characteristic sexually dimorphic pathways. Here we characterized sexually dimorphic gene expression in multiple data sets from neurotypical adult and prenatal human neocortical tissue, and evaluated ASD risk genes for evidence of sex-biased expression. We find no evidence for systematic sex-differential expression of ASD risk genes. Instead, we observe that genes expressed at higher levels in males are significantly enriched for genes upregulated in post-mortem autistic brain, including astrocyte and microglia markers. This suggests that it is not sex-differential regulation of ASD risk genes, but rather naturally occurring sexually dimorphic processes, potentially including neuron-glial interactions, that modulate the impact of risk variants and contribute to the sex-skewed prevalence of ASD.

Figure 1. Microglia and astrocyte markers and genes upregulated in ASD brain tend toward higher expression in adult male brain.

(a) Volcano plot for the differential expression results from all 16,392 transcripts expressed in the adult BrainSpan sample (n male=29 samples from 5 subjects, n female=29 samples from 5 subjects). (b) Subset of the volcano plot in a for all 15,724 autosomal transcripts. (c) Enrichment for ASD risk genes and ASD-associated gene expression patterns, and (e) neural cell type markers, within male-DE (higher expression in males, FD⩾1.2, P⩽0.05; 439 genes) and female-DE (higher expression in females, FD⩾1.2, P⩽0.05; 427 genes) gene sets by Fisher's exact test; circle size and colour indicate the odds ratio of all significant overlaps (Bonferroni-adjusted P value <0.05); overlaid text displays the adjusted P value for each enrichment. (d) Shifts in the distribution of sex-differential expression direction for genes in each ASD risk or ASD expression sets, and (f) neural cell type markers. Blue and pink bars display the proportions of each gene set that have higher expression in males (FD>1) or females (FD<1); whiskers note 95% confidence intervals; horizontal black lines note the proportion of male- and female-higher genes in the corresponding background gene set. Overlaid text displays significant Bonferroni-adjusted P values from the binomial test. chr, chromosome; disr., disrupting; expr., expression; F, female; M, male.

Figure 2. Sex-differential expression parallels gene expression patterns in ASD brain.

Bar plots show FDs by sex and ASD status of sex-DE genes (FD≥1.2 and P<0.05) that also belong to ASD-associated co-expression modules. (a) Module asdM16_V, which is significantly upregulated in ASD and enriched for genes involved in the inflammatory response and immune system functions, and (b) module asdM12_V, which is significantly downregulated in ASD and enriched for genes with neuronal and synaptic functions. (c) FDs of sex-DE genes (FD≥1.2, P<0.05, 374 genes) by sex and status. Best-fit line and its 95% confidence interval are shown. CTL, control from ASD expression study; F, female; M, male.

Figure 3. Male-biased expression of astrocyte and asdM16_V module genes in an independent sample.

(a) FD for all sex-DE genes from the BrainSpan sample also tested in the replication set (BrainSpan FD≥1.2, P<0.05, 733 genes; grey points mark genes with FD<1.2 in the replication sample), and for (b) autosomal sex-DE genes from BrainSpan with FD≥1.2 in the replication sample (129 genes). Best-fit lines and 95% confidence intervals are shown on plots.

Figure 4. Microglia and astrocyte markers and genes upregulated in ASD brain tend toward higher expression in prenatal male brain.

(a) Volcano plot for all 9,889 transcripts expressed in the prenatal sample (n male=43 samples from 4 subjects, n female=43 samples from 4 subjects). (b) Subset of the plot in a for the 9,532 autosomal transcripts. (c) Enrichment for ASD risk genes and ASD-associated gene expression patterns, and (e) neural cell type markers, within male-DE (509 genes) and female-DE (528 genes) gene sets by Fisher's exact test; circle size and colour indicate the odds ratio of all significant overlaps (Bonferroni-adjusted P value <0.05); overlaid text displays the adjusted P value for each enrichment. (d) Shifts in the distribution of sex-differential expression direction for genes in each ASD risk or ASD expression sets, and (f) neural cell type markers. Blue and pink bars display the proportions of each gene set that have higher expression in males (FD>1) or females (FD<1); whiskers note 95% confidence intervals; horizontal black lines note the proportion of male- and female-higher genes in the corresponding background gene set. Overlaid text displays significant Bonferroni-adjusted P values from the binomial test. chr, chromosome; disr., disrupting; expr., expression; F, female; M, male.