Defense Date


Document Type


Degree Name

Master of Science


Pharmaceutical Sciences

First Advisor

Joseph L. McClay Ph.D.

Second Advisor

Dayanjan Wijesinghe Ph.D.

Third Advisor

Mikhail Dozmorov Ph.D.


Purpose. We will evaluate the effects of drugging the epigenetic histone acetyltransferase (HAT) enzyme p300, encoded by the schizophrenia risk gene EP300, on genome-wide gene expression in neural cells. We hypothesize that drugging p300 will affect gene expression and alternative splicing of other schizophrenia risk genes. Our motivation is to identify potential new epigenetic treatment avenues for schizophrenia.

Methods. Prior to my joining the lab, an experiment was conducted using the novel p300 HAT inhibitor, A-485, to modulate genomic regulation in a neural cell line (SH-SY5Y). SH-SY5Y cells were exposed to 10μM of A-485 or vehicle (DMSO) for 24 hours. Changes to gene expression were assessed using standard mRNA sequencing (RNA-seq). Five replicates of 5x106 cells were used per condition (A485, DMSO) in RNA-seq. Polyadenylated RNAs were extracted and subjected to paired end 150 bp (PE150) sequencing using standard Illumina chemistry with a target of >20M reads per sample. I analyzed these data for differential exon usage, by first aligning reads to the human reference genome via STAR on the VCU High Performance Research Computing (HPRC) cluster, and then testing for genome-wide differential exon use with the DEXSeq package in R. Further interpretation of our findings used pathway analysis and data integration with chromatin-immunoprecipitation sequencing (ChIP-seq) data and schizophrenia risk gene data from the Psychiatric Genomics Consortium.

Results. We obtained an average of 33,376,816 reads per experiment with an average alignment of 87.75%. This indicated that the sequencing worked well. DEXSeq analysis revealed 1132 exons in 914 unique genes showing significantly different expression (FDR < 0.05) between the A-485 treated cells and DMSO vehicle controls. Then after further conversion and overlap analysis in RStudio, 34 genes were found to overlap between the DEXSeq results and the PGC schizophrenia risk genes.

Conclusions. The HAT inhibitor A-485 significantly affects gene expression in neural cells. Our study provides valuable insights into the effects of targeting the p300 histone acetyltransferase, which may have implications for the treatment of schizophrenia. The identification of 34 overlapping genes between our differential exon usage analysis and known PGC schizophrenia risk genes shows that p300 is involved in the regulation of other schizophrenia risk genes. Further investigation into the functional roles of these genes and their associated pathways may lead to the development of novel epigenetic-based treatments for schizophrenia and other related psychiatric disorders. Our study underscores the significance of integrative approaches combining epigenomic data with genetic risk factors to elucidate disease mechanisms and identify potential therapeutic targets.


© Shravani Malay

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