Summary
A study using human neural progenitor cells and cerebral organoids found that disruptions to different autism-linked genes can produce overlapping changes in gene expression. Its network analysis points to the X-linked regulator ZFX as a possible contributor to lower autism risk in females.
A study of human neural progenitor cells and lab-grown cerebral organoids found that disrupting different autism-linked genes can lead to overlapping changes in gene activity. The researchers also identified the X-linked transcription factor ZFX as a possible contributor to the lower prevalence of autism in females. The proposed protective role is based on gene-regulation analyses and cell models, rather than a direct test of autism risk in people.
Autism is diagnosed three to four times more often in males than in females, and previous studies have found that autistic females tend to carry more autosomal genetic risk variants. This pattern is known as the female protective effect: it describes a difference in the genetic burden associated with autism, while its biological basis remains under investigation.
Different gene disruptions converge on shared changes
The researchers used CasRx, an RNA-targeting tool, to reduce the activity of 20 autism-associated genes individually in human neural progenitor cells. The cells came from one control male induced pluripotent stem-cell line. Eighteen of the 20 perturbations produced enough differentially expressed genes for the main analysis. RNA sequencing was performed 24 hours after gene knockdown, with three independent cell samples per condition.
The changes overlapped: 15 of the 18 perturbations altered genes in the SFARI autism-gene database more often than expected, and many of the shared changes involved reduced expression. In particular, 27 high-confidence autism-associated genes were differentially expressed in at least 10 of the 18 perturbations, and all 27 were downregulated. CHD8, a well-established autism risk gene, was also reduced in most of the perturbation conditions.
The team extended the work to cerebral organoids, three-dimensional cell models that develop several brain cell types. Single-cell RNA sequencing showed overlapping gene-expression changes across different perturbations and cell types. Some long-term knockdowns also changed the balance of progenitor cells and neurons in the organoids. Together, the cell and organoid results suggest that genetically diverse disruptions can affect shared gene-regulatory networks during neural development.
Why ZFX is a candidate
To identify regulators that might connect these changes, the researchers reconstructed a gene regulatory network from their cell data. The analysis highlighted several regulators, including CHD8 and REST. It also pointed to ZFX, a transcription factor encoded on the X chromosome, as a regulator of many autism-associated genes.
ZFX is expressed from both the active and inactive X chromosomes in females, and the study notes that it is more highly expressed in the female brain. The authors propose that this higher baseline expression could help maintain the activity of autism-associated genes when other genes in the network are disrupted. In this model, ZFX could partly buffer the effects of risk variants and contribute to the female protective effect.
The study’s experiments used a male cell line, while the proposed role for ZFX draws on its known expression pattern and analyses of regulatory relationships. The findings therefore identify a possible mechanism for the sex difference in autism risk, not a demonstrated effect of ZFX on autism rates. Testing the model directly in female neural cells will be important for establishing how sex-specific ZFX activity affects the response to autism-associated variants.