Exploring the biological role of postzygotic and germinal de novo mutations in ASD

Abstract

De novo mutations (DNMs), including germinal and postzygotic mutations (PZMs), are a strong source of causality for Autism Spectrum Disorder (ASD). However, the biological processes involved behind them remain unexplored. Our aim was to detect DNMs (germinal and PZMs) in a Spanish ASD cohort (360 trios) and to explore their role across different biological hierarchies (gene, biological pathway, cell and brain areas) using bioinformatic approaches. For the majority of the analysis, a combined ASD cohort (N = 2171 trios) was created using previously published data by the Autism Sequencing Consortium (ASC). New plausible candidate genes for ASD such as FMR1 and NFIA were found. In addition, genes harboring PZMs were significantly enriched for miR-137 targets in comparison with germinal DNMs that were enriched in GO terms related to synaptic transmission. The expression pattern of genes with PZMs was restricted to early mid-fetal cortex. In contrast, the analysis of genes with germinal DNMs revealed a spatio-temporal window from early to mid-fetal development stages, with expression in the amygdala, cerebellum, cortex and striatum. These results provide evidence of the pathogenic role of PZMs and suggest the existence of distinct mechanisms between PZMs and germinal DNMs that are influencing ASD risk.

Figure 1

Manhattan plots depicting the ASD risk genes prioritized by TADA-Denovo (chromosome and log10 p value for each gene are represented in axis x and y). (a) p values were obtained from analysis of germinal mutations in the combined cohort using TADA-Denovo. Red line represents the p value < 1 × 10^–8 and blue line p value < 1 × 10⁻⁵. (b) p values were obtained from analysis of PZMs in the combined cohort using TADA-Denovo. Blue line represents p value < 1 × 10⁻⁵.

Figure 2

Gene-set enrichment analysis using germinal and PZM from the combined cohort. Gene-set enrichment analysis was done with DNENRICH. − log10 p value for each gene-set is shown for each type of mutation and tested gene-set.

Figure 3

Scatterplots representing the top 30 significant biological processes (combined cohort). (a) Top 30 biological processes enriched in genes harboring germinal DNM are shown. (b) Top 30 biological processes enriched in genes harboring PZMs DNMs are shown.

Figure 4

Visualization of the top 50 GO terms grouped by clusters of biological functions (DNMs obtained from the combined cohort) (a) GO terms clusters for genes harboring germinal mutations. (b) GO terms clusters for genes harboring PZMs.

Figure 5

Expression Weighted Cell type Enrichment for PZM and germinal genes.

Figure 6

Expression analysis across developmental stages and brain areas for germinal and PZMs genes from the combined cohort. Expression gene sets were obtained from BrainSpan. (a,c) Expression of germinal genes across different brain regions and developmental periods. (b,d) Expression of PZMs genes across different brain regions and developmental periods.