Study Explores the Role of Sex-Biased Gene Expression in Autism Risk During Prenatal Development

By Dr. Chinta SidharthanReviewed by Lily Ramsey, LLMAug 7 2024

Although one in every 36 children in the United States is affected by autism spectrum disorder (ASD) — a neurodevelopmental disease that results in restrictive and repetitive behaviors and social deficits — the mechanisms underlying this complex disorder remain unclear, and there are no effective therapies for the disorder.

In a recent study published in Biological Psychiatry Global Open Science, researchers meta-analyzed two bulk ribonucleic acid (RNA) sequence datasets obtained from the cortex of prenatal donors to determine differentially expressed genes based on sex and potentially identify molecular and cellular mechanisms contributing to ASD.

​​​​​​​Study: Sex-Differential Gene Expression in Developing Human Cortex and Its Intersection With Autism Risk Pathways. Image Credit: Veja/Shutterstock.com

Background

Autism spectrum disorder is a highly prevalent neurodevelopmental disorder with a significant impact on the life of the child as well as on families due to the social communication deficits that characterize the disorder.

However, the underlying mechanisms of this complex disorder remain unclear, although a higher prevalence among male children has been observed.

Exome sequencing has identified over 100 genes associated with ASD, and studies have found that both rare and common inherited genetic variants are involved in ASD symptoms. The disorder is also diagnosed three to five times more often in male children than in female children.

This suggests that there are either protective mechanisms specific to the female sex or risk conditions particular to the male sex, and understanding these sex-based genetic differences might shed more light on the complex mechanisms of ASD.

About the Study

In the present study, the researchers used two large RNA sequence datasets obtained from the prenatal human cortex of 273 donors to quantify the sex-biased differential gene expressions and differences in co-expressions in the transcriptome.

Although limited by a small sample size, earlier studies that have attempted to delineate the sex-based differences in the transcriptome have reported a male-biased prenatal enrichment of genes involved in immune and glial function, which are similar to the transcriptomic changes observed in the brains of individuals with ASD.

Furthermore, analysis of whole brains from fetuses has shown differential expression of autosomal genes linked to the risk of ASD.

Here, the researchers analyzed RNA sequence data obtained from prenatal cortex donors between the ages of 14 and 21 weeks post-conception.

Single-nuclei RNA sequences and signatures specific to cell types were used to determine the proportion of neural cell types. This information was used to estimate the cell-specific gene expression in each sample.

Additionally, the assessment of differential gene expression was performed separately for each dataset, and the age-based differential gene expression was measured for males and females separately.

The sex-biased differentially expressed genes were then examined for enrichment of the common and rare variations of the ASD-risk genes identified through transcriptome-wide association studies, cell type markers, genes with dysregulated expression due to ASD, and those linked to neuropsychiatric phenotypes.

Co-expression analyses were also conducted to determine functional enrichment of the risk and dysregulated genes in ASD and the risk genes for neuropsychiatric phenotypes. The researchers also examined the contribution of individual genes to the sex-differential co-expression in ASD.

Major Findings

The study identified significant sex-biased differential gene expression in 101 genes, which included genes on the Y-chromosome that were affected due to the X-chromosome inactivation during development. Differential gene expression based on sex was also observed in autosomal genes.

The researchers observed a female-biased expression pattern in the genes that were not inactivated during X-chromosome inactivation, while those on the Y chromosome and the pseudo-autosomal regions showed a male-biased expression pattern.

Modest levels of sex-biased differential expression were also observed in other X-chromosome and autosomal genes.

However, the results also showed that the common and rare variants of the ASD risk genes were not enriched for sex-biased expression in the prenatal cortex, corroborating the findings from previous studies.

Furthermore, the male-biased differentially expressed genes did not exhibit enrichment for gene sets upregulated in ASD, and similarly, no ASD-related downregulation enrichment was observed in the female-biased differentially expressed genes.

Additionally, analysis of the co-expression modules also revealed that the male-specific modules showed enrichment for signaling, inflammatory, and immune pathways.

Conclusions

To summarize, the study examined the sex-biased differential gene expression and co-expression in two large RNA sequence datasets derived from prenatal cortex samples to understand the sex-based differences in the underlying mechanisms of ASD.

The findings reported significant levels of sex-differential gene expression in 101 genes, including autosomal genes and Y chromosome genes affected by X chromosome inactivation. However, the absence of overlap between the genes that were differentially expressed based on sex and the ASD risk genes in these prenatal cortex-derived datasets indicated that the differential changes in ASD-symptom may occur during other development stages or in other brain regions.

Further research on sex-differential gene expression during various developmental stages and from other cell types is needed to understand the mechanisms that determine the differential ASD risk based on sex.