Research Project
10220099
PROJECT SUMMARY Over recent several decades, genomic analyses have elucidated etiologies for hundreds of disorders with syndromic and nonsyndromic intellectual disability (ID). However, this knowledge has not readily translated into treatment for patients, partly due to therapy development strategies that focus solely on single diseases. Many patients with ID have mutations in genes that encode chromatin-organizing proteins. Mutations in cohesin, a key chromatin-regulating protein, cause overlapping clinical findings with patients who have mutations in other chromatin regulatory complexes, including BAF/SWI-SNF and p160/NCOA. The long-term goal is to identify treatments to improve neurocognitive outcomes in children with chromatin-regulatory disorders. The overall objective of this R21 is to identify common informative target genes disrupted by chromatin regulatory gene mutations in experimentally approachable and patient-derived cell models. The central hypothesis is that mutations in cohesin, BAF/SWI-SNF and p160/NCOA complexes cause similar clinical features because they disrupt an overlapping set of target genes. The rationale is that identification of common, reproducible chromatin disruptions will enable breakthrough work to rapidly screen drugs in laboratory settings and enable confirmation of precision therapy in patient cells prior to treatment. This central hypothesis will be tested by the following two specific aims: 1) Identify common regions of chromatin disruption in HCT116 cells with heterozygous mutations in cohesin, BAF/SWI-SNF and p160/NCOA complex genes; and 2) Identify common regions of chromatin disruption in patient-derived lymphoblastoid cells. For the first aim, CRISPR-Cas9 will be used to create heterozygous loss-of-function mutations for each of six chromatin-regulatory genes in a monogenic lab cell line. RNA-seq and ATAC-seq will be used to identify resultant patterns of altered gene expression and chromatin accessibility. Under the second aim, the investigators' large collection of heterogenous patient lymphoblastoid cell lines with mutations in three chromatin-regulatory genes will be used to identify robust patterns of altered gene expression and chromatin accessibility to enable assessment of future precision therapy. This work is innovative, in the applicant's opinion, because it focuses on a novel approach to developing shared therapies for overlapping groups of rare ID disorders, and proposes a unique chromatin accessibility assay for future small molecule screening. This work is significant because it is expected to provide strong evidence to support widening the approach to additional chromatin disorders and pursing compounds that correct these chromatin disruptions. Ultimately, such knowledge has the potential to offer new opportunities for innovative treatments of intellectual disability.
