# Assessing Genomic, Regulatory and Transcriptional Variation at Single Nuclei Resolution in the Brains of Individuals with Autism Spectrum Disorder

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2023 · $708,668

## Abstract

ABSTRACT
Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder of unknown etiology and with
limited effective therapeutic options that affects millions of individuals. Our research team has a longstanding
commitment to understanding the cause of ASD and the molecular processes underlying brain development,
function, and pathology. We will use this experience to apply the latest molecular techniques to samples from a
new repository of brain tissue from individuals with ASD to create the largest and most detailed analysis of the
molecular consequences of ASD. Genetic analyses of gene disrupting de novo mutations have identified over
one hundred genes associated with ASD with three main functional groups: regulation of gene expression,
neuronal communication, and cytoskeleton. Prior analyses of brain tissue from individuals with ASD have
identified a group of downregulated neuronal communication genes, that overlap with ASD-associated genes,
and a group of upregulated glial genes that do not overlap with ASD-associated genes or variants. It is unclear
if these changes reflect altered cell composition or cell function and how they relate to genetic factors. We
propose to analyze post-mortem brain samples from 40 individuals with ASD and 40 unaffected controls, sourced
from the Autism BrainNet BioBank, to assess the molecular changes that occur. We will use whole-genome
sequencing to identify gene disruptive variants in genes previously associated with ASD and to identify rare and
common variants that may alter gene expression or splicing. In tissue samples the prefrontal cortex and striatum
in from 40 cases and 40 controls, we will use recently developed single-nuclei methods to perform RNA-seq and
ATAC-seq at single-cell resolution to identify ASD-related changes in gene regulation and expression in specific
cell types and brain regions. For tissue samples from the prefrontal cortex of 20 cases and 20 controls we will
also use cutting-edge single nuclei long-read RNA-seq (Iso-seq), along with bulk tissue RNA-seq, for an in-depth
analysis of how gene isoforms differ between ASD cases and controls. Finally, we will assess how single-nuclei
gene expression varies in brain organoids grown from pluripotent stem cells edited to contain mutations in three
ASD-associated genes. Integrating these data, we will profile the molecular changes associated with ASD and
assess how these changes vary by cell type, brain region, age, sex, seizure status, and genotype. We will use
RNAscope in situ hybridization to validate the molecular and cell composition changes we observe and a
lentivirus-based massively parallel reporter assay to test the function of regulatory regions or variants in proximity
to genes with ASD-related differences in expression to validate these effects and assess causality. We hope that
these insights will provide a basis for understanding the heterogeneity of ASD and the neurobiological features
of this disorder and p...

## Key facts

- **NIH application ID:** 10657693
- **Project number:** 5R01MH125516-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** ARNOLD KRIEGSTEIN
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $708,668
- **Award type:** 5
- **Project period:** 2021-07-27 → 2027-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10657693

## Citation

> US National Institutes of Health, RePORTER application 10657693, Assessing Genomic, Regulatory and Transcriptional Variation at Single Nuclei Resolution in the Brains of Individuals with Autism Spectrum Disorder (5R01MH125516-03). Retrieved via AI Analytics 2026-06-12 from https://api.ai-analytics.org/grant/nih/10657693. Licensed CC0.

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