Assessing the functions of autism risk genes in deep layer cortical neurons during primate midfetal development

  • Awarded: 2022
  • Award Type: Pilot
  • Award #: 971316

The prefrontal cortex (PFC) is critical for a myriad of higher-order brain functions, including working memory, planning, decision-making, language and creative intelligence. These functions are significantly altered in several conditions, including autism spectrum disorder (ASD) and schizophrenia.

Knowledge of the molecular and cellular processes that govern the development of human PFC has been largely extrapolated from rodent studies. However, comparative analyses have identified gene expression signatures that are unique to the PFC of humans and nonhuman primates. During development, neurons undergo dynamic morphological and functional maturation governed by intricate gene regulatory networks and signaling pathways. The co-expression of genes associated with ASD, especially those encoding chromatin modulators and synaptic proteins, in deep layer neurons during midfetal development1 underscores the importance of studying neuronal development in primates.

To date, no study has comprehensively characterized deep layer neurons in humans or nonhuman primates during development. Although primate pluripotent stem cells and their differentiated cells and organoids have been used to address functions of ASD risk genes, these cells do not form the same consistent and intricate cortical structure and circuitry.

Building upon the unique strengths and resources at the University of Wisconsin-Madison, Xinyu Zhao, Qiang Chang, André Sousa and Daifeng Wang have established a robust knockdown-multimodal analysis pipeline that combines whole-cell patch-clamp recording, morphological assessment and single-cell multi-omic analyses to assess the maturation of deep layer dorsolateral PFC (dlPFC) neurons in marmoset organotypic brain slices2.

The goal of the current project is to apply this innovative pipeline to assess the function of selected ASD risk genes in dlPFC neurons during midfetal development. The team aims to test the hypothesis that ASD risk genes are critical for the functional maturation of dlPFC neurons, which may underly their convergence during midfetal PFC development.

Zhao and colleagues plan to initially study three ASD risk genes (CHD8, POGZ and KDM3B). In addition to studying morphological and physiological changes in the knockdown brain slices compared to wild-type control slices, they also plan to perform integrative analysis of the data from all three knockdown models to potentially unveil convergent signatures of ASD risk genes and common regulatory networks that are affected across different cell types during midfetal development.

The group’s in vitro PFC organotypic slice culture and gene manipulation methods can be scaled-up, which would enable many ASD risk genes to be studied in parallel. Thus, results from this initial pilot study are expected to open doors for future collaborative projects that will provide new and in-depth knowledge about the function of ASD risk genes in primate brains.


  1. Willsey A.J. et al. Cell 155, 997-1007 (2013) PubMed
  2. Gao Y. et al. bioRxiv (2023) Preprint
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