# Cell-type specific and activity-dependent characterization of non-coding autism de novo variants in human stem cell-derived neurons

> **NIH NIH F31** · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · 2024 · $48,974

## Abstract

PROJECT SUMMARY
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with a complex genetic
architecture. The development of effective therapeutics and diagnostic tools for ASD has been hindered by our
incomplete understanding of underlying genetic variation. De novo variants (DNVs), estimated to contribute to
30-40% of cases, have been primarily studied in protein-coding regions of the genome. Hundreds of thousands
of non-coding variants have been identified but deciphering their functional contribution to ASD etiology remains
challenging. Cis-regulatory elements such as promoters and enhancers represent one avenue to assay the
potential impact of non-coding DNVs, but their regulatory activity is dependent on cellular contexts such as cell
type and activation state. The two cell types primarily involved in ASD biology are excitatory (glutamatergic) and
inhibitory (GABAergic) neurons, both of which can be generated in vitro from human pluripotent stem cells and
depolarized to model the transcriptomic and epigenetic changes caused by neuronal activation. Our lab
annotated the enhancers present in both cell types at baseline and activated states and found 2495 enhancers
containing non-coding ASD DNVs, including several hundred that are cell-type specific or activity-dependent.
Using a massively parallel reporter assay (MPRA), this proposal will determine whether non-coding DNVs found
in individuals with autism alter cis-regulatory activity in glutamatergic or GABAergic human neurons in either
baseline or activated states. Further, gene-enhancer mapping has revealed that a subset of DNV-containing
enhancers is predicted to regulate genes previously implicated in ASD. To validate cis-regulatory activity and to
compare trans-effects on downstream gene networks, a CRISPR inhibition screen will be performed in both cell
types and activation states, targeting 25 ASD genes and their DNV-containing enhancers. If successful, this work
will demonstrate the potential functional contribution of non-coding de novo variants to ASD biology, which has
thus far remained an outstanding question in the field. Moreover, this will generate transcriptomic datasets for
top ASD risk genes in two clinically relevant cell types at both resting and active states to expand upon the
growing number of functional genomics ASD studies, emphasizing convergent regulatory gene networks. This
research will take place at the Icahn School of Medicine at Mount Sinai, containing the 2nd best NIH-funded
neuroscience department and home to the Seaver Autism Center, renowned for bridging basic science and
clinical trials for more effective ASD care. The scientific rigor, innovative techniques, sophisticated analyses,
multi-disciplinary collaborations, and ample mentorship opportunities outlined here would propel me towards a
successful career as an independent research professor studying the molecular mechanisms underlying
psychiatric disorders while mentoring futur...

## Key facts

- **NIH application ID:** 10918071
- **Project number:** 5F31MH133365-02
- **Recipient organization:** ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
- **Principal Investigator:** Sarah Elizabeth Williams
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $48,974
- **Award type:** 5
- **Project period:** 2023-04-24 → 2026-04-23

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10918071

## Citation

> US National Institutes of Health, RePORTER application 10918071, Cell-type specific and activity-dependent characterization of non-coding autism de novo variants in human stem cell-derived neurons (5F31MH133365-02). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10918071. Licensed CC0.

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