# Analysis of epigenetic and neuronal circuit changes in autism on the single-cell level

> **NIH NIH R00** · DUKE UNIVERSITY · 2022 · $249,000

## Abstract

Project Summary/Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disease affecting almost 2% of children in the US
alone. Despite its genetic and clinical heterogeneity, recent systems biology and genomics studies demonstrated
that ASD converges on a specific set of cellular pathways. Epigenetic regulation and synaptic signaling emerged
as the two most prominent pathways in ASD, with many high-confidence genetic risk factors and dysregulated
genes involved in these processes. This observation prompted a hypothesis that epigenetic dysregulation leads
to improper neuronal circuit development and function, which has been demonstrated in mouse models of
epigenetic regulators recurrently mutated in ASD, such as CHD8 (Chromodomain Helicase DNA Binding Protein
8). However, the exact epigenetic changes, cell types they affect and the neuronal circuitry changes resulting
from epigenetic dysregulation in ASD are unknown. Recently, single-cell genomics approaches, including single-
cell RNA sequencing and single-cell ATAC sequinning, offered unprecedented new level of detail of cellular and
molecular composition of the brain, as well as processes underlying its development. In my postdoc, I applied
single-nucleus RNA sequencing to human post-mortem cortical tissue from ASD patients to gain insight into the
molecular changes associated with ASD in specific neuronal and glial subtypes. One of the most important
insights from this work is the implication of upper-layer cortical neurons as the cell type most affected by ASD-
associated transcriptional changes. This observation raises questions about the origin and functional effects of
such changes on specific neuronal circuits. As part of the Aim 1 of my K99 proposal, I will test the hypothesis
that gene expression changes in ASD are driven by changes in epigenetic states of specific cell types. To that
end, I will perform a joint RNA-seq and ATAC-seq profiling of neocortical tissue of ASD patients and controls to
identify cell type-specific epigenetic changes. Then, I will develop and test a high-throughput synaptic tracing
technique by combining barcoded rabies virus library with single-nucleus RNA sequencing (Aim 2 of K99 phase).
Finally, using the training, tools and preliminary data from the K99 phase of my proposal, I will launch an
independent research project that focuses on investigating cell-type specific epigenetic and neuronal circuitry
changes in the Chd8+/ mouse model during development (R00 phase). I will first apply the joint RNA-seq/ATAC-
seq protocol to study epigenetic changes in specific cell types during development caused by the loss of one of
Chd8 alleles. By crossing the Chd8+/ mouse with reporter lines expressing Cre recombinase in specific neuronal
subtypes, such as upper-layer cortical neurons (Cux2-Cre), I will be able to use the barcoded rabies virus library
and single-nucleus RNA-seq to identify changes in specific components of cortical circuitry as the result of C...

## Key facts

- **NIH application ID:** 10611017
- **Project number:** 4R00MH121534-03
- **Recipient organization:** DUKE UNIVERSITY
- **Principal Investigator:** Dmitry Velmeshev
- **Activity code:** R00 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $249,000
- **Award type:** 4N
- **Project period:** 2022-09-02 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10611017

## Citation

> US National Institutes of Health, RePORTER application 10611017, Analysis of epigenetic and neuronal circuit changes in autism on the single-cell level (4R00MH121534-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10611017. Licensed CC0.

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