# High-throughput functional analysis of autism risk genes

> **NIH NIH R01** · YALE UNIVERSITY · 2020 · $418,750

## Abstract

The central objective of this research is to elucidate the function of genes that are strongly associated
with autism spectrum disorders (ASD) in fundamental processes of vertebrate brain development. While
whole-exome sequencing has led to a growing list of “high confidence” ASD (hcASD) risk genes, which are
beginning to converge on common pathways, our understanding of the mechanisms by which hcASD gene
disruption alters the development of specific cell types and neural circuits, resulting in behavioral dysfunction,
remains limited. The long-term goal of this research is to illuminate the basic biological mechanisms underlying
ASD, which will provide a much-needed avenue for the discovery of targeted pharmacological treatments.
Here, we will capitalize on the unique advantages of zebrafish as an in vivo, biologically relevant system for the
rapid functional analysis of multiple hcASD genes in parallel, including: (i) the ability to directly visualize basic
neurodevelopmental processes and neural activity in a whole vertebrate brain through transparent embryos; (ii)
large progenies, which are ideal for conducting high-throughput in vivo screens to identify small molecule
suppressors of behavioral phenotypes; and (iii) ease of genetic manipulation, such that we have already
generated zebrafish mutants in 10 top hcASD genes, which we will analyze in the present study. Our central
hypothesis is that zebrafish mutants of hcASD genes will display quantifiable morphological, simple behavioral,
and circuit-level phenotypes that will converge on common pathways, providing new insights into the roles of
these genes in the developing vertebrate brain. This hypothesis is based on evidence from our study of
zebrafish mutants of the ASD risk gene, CNTNAP2, which revealed dysregulation of GABAergic and
glutamatergic signaling and identified a novel pharmacological suppressor of an ASD gene-associated mutant
behavioral phenotype. To test this hypothesis, we will pursue the following aims: 1) Identify quantifiable brain
phenotypes across 10 hcASD mutants using light-sheet imaging and automated deep phenotyping of CNS-
specific markers; 2) Conduct high-throughput pharmaco-behavioral profiling of hcASD mutants using a novel,
automated visual-startle assay and perform small molecule screens to identify suppressors of mutant startle
phenotypes; and 3) Characterize neural circuit deficits underlying altered sensory processing behaviors in
hcASD mutants and identify the circuit-level mechanisms of pharmacological suppressors using whole-brain in
vivo two-photon imaging. This approach is highly innovative and is the first to analyze the function of multiple
hcASD genes in parallel at the structural, behavioral, and circuit levels, allowing us to progress rapidly from risk
gene discovery to the elucidation of convergent pathways with relevance to ASD. Therefore, we expect that
this research will lead to critical advances in our understanding of the basic biology of ASD...

## Key facts

- **NIH application ID:** 9841445
- **Project number:** 5R01MH116002-03
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** ELLEN J HOFFMAN
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $418,750
- **Award type:** 5
- **Project period:** 2018-03-01 → 2022-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9841445

## Citation

> US National Institutes of Health, RePORTER application 9841445, High-throughput functional analysis of autism risk genes (5R01MH116002-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9841445. Licensed CC0.

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