# Investigating cohesin regulators to target Cornelia de Lange Syndrome

> **NIH NIH F30** · UNIVERSITY OF PENNSYLVANIA · 2021 · $51,036

## Abstract

PROJECT SUMMARY
Cornelia de Lange Syndrome (CdLS) is multi-system, dominant genetic disorder caused by mutations in the
structural or regulatory subunits of the cohesin complex. Cohesin regulates the 3D organization of chromatin,
especially at the level of chromatin looping and topologically associated domains (TAD). We recently showed
that cohesin depletion disrupts TAD boundaries and that differentially expressed genes in CdLS patient cells are
enriched at these boundaries, suggesting that 3D chromatin organization is key to disease pathogenesis. We
have additional preliminary evidence that co-depletion of WAPL, a negative regulator of cohesin, is able to rescue
the effects of cohesin loss of genome organization and gene expression. No drugs are known to target cohesin
or WAPL, however, and discovering novel cohesin regulators remains difficult with current approaches. To
discover genes that modulate the role of cohesin on TAD boundaries, I developed TAD high-throughput
fluorescence in situ hybridization (TAD Hi-FISH). TAD Hi-FISH uses Oligopaints and high-content imaging to
quantitatively identify genes that regulate TAD boundaries in a cohesin- or WAPL-like manner. To identify
potential drug targets for CdLS, I applied TAD Hi-FISH to the human “druggable genome,” i.e. 3,083 genes
targeted by known drugs. My primary screen uncovered 70 cohesin-like and 57 WAPL-like hits. GSK3A, a
multifunctional kinase, has been preliminarily validated as a lead WAPL-like hit that can suppress cohesin loss.
I propose to apply TAD Hi-FISH and other assays to further characterize the effects of GSK3A and all of my hits
on TAD boundaries and cohesin regulation. In aim 1, I will curate a set of druggable regulators of cohesin’s
chromatin architectural function. I will first use secondary TAD Hi-FISH screens to determine which hits regulate
TAD boundares in both a region non-specific and cohesin-dependent manner. Of these top secondary hits, I will
evaluate which affect cohesin chromatin binding by performing chromatin fractionation and western blot
experiments. Finally, I will evaluate the genome-wide effects of the strongest cohesin regulators using ChIP-seq
for cohesin. In aim 2, I will investigate the relationship of GSK3A to genome organization, cohesin, and
transcription. To study both GSK3A protein and its catalytic function, I will develop an inducible degron cell line
for GSK3A, and also optimize conditions in this cell line for a recently developed GSK3A chemical inhibitor. I will
then perform Hi-C after GSK3A depletion and inhibition to investigate the genome-wide effects of GSK3A on
chromatin architecture. Next, I will apply nascent transcriptomics using PRO-seq to determine whether GSK3A
co-depletion or inhibition can rescue the gene expression changes of cohesin loss. Together, these aims will
curate a novel set of cohesin regulators, including GSK3A, that will advance our understanding of 3D genome
organization and potential CdLS therapeutic developm...

## Key facts

- **NIH application ID:** 10139903
- **Project number:** 1F30HD104360-01
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Daniel Sungjoo Park
- **Activity code:** F30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $51,036
- **Award type:** 1
- **Project period:** 2021-02-01 → 2024-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10139903

## Citation

> US National Institutes of Health, RePORTER application 10139903, Investigating cohesin regulators to target Cornelia de Lange Syndrome (1F30HD104360-01). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10139903. Licensed CC0.

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