Functional Impact of Chromatin Remodeling Gene Mutations and Predictive Signature for Therapeutic Response in Bladder Cancer

Abstract

Urothelial carcinoma accounts for most of the bladder cancer cases. Using next-generation sequencing (NGS) technology, we found that a significant percentage (83%) of tumors had mutations in chromatin-remodeling genes. Here, we examined the functional relevance of mutations in two chromatin-remodeling genes, EP300 and its paralog, CREBBP, which are mutated in almost one-third of patients. Interestingly, almost half of missense mutations cluster in the histone-acetyltransferase (HAT) domain of EP300/CREBBP. This domain catalyzes the transfer of an acetyl group to target molecules such as histones, thereby regulating chromatin dynamics. Thus, patients with EP300 or CREBBP mutations may have alterations in the ability of the corresponding proteins to modify histone proteins and control transcriptional profiles. In fact, it was determined that many of the missense HAT mutations in EP300 (64%) and CREBBP (78%) were HAT-inactivating. These inactivating mutations also correlated with invasive disease in patients. Strikingly, the prediction software Mutation Assessor accurately predicted the functional consequences of each HAT missense mutation. Finally, a gene expression signature was developed that associated with loss of HAT activity and that this signature was associated with more aggressive cancer in four patient datasets. Further supporting the notion that this score accurately reflects HAT activity, we found it is responsive to treatment of cancer cells to mocetinostat, a histone deacetylase (HDAC) inhibitor. Implication This study provides a rationale for targeted sequencing of EP300 and CREBBP and use of a gene profiling signature for predicting therapeutic response in patients.

Inhibition of urinary bladder cancer cell proliferation by silibinin

“…Moreover, histone acetylation and deacetylation are epigenetic events that also contribute to the tumorigenesis process in urinary bladder cancer. Histone acetyltransferases (HATs) relax the chromatin structure and may facilitate transcription of oncogenes (Duex et al ., 2018). Already, histone deacetylases (HDACs) may cause condensation of chromatin in suppressor genes, impeding its transcription (Yan et al ., 2013).…”

QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency

“…In the triple-negative breast cancer (TN) dataset, out of thirteen identified driver genes, eight are each mutated in only two out of 94 patients, and are analyzed below. A chromatin-remodeling gene CREBBP was found to be overexpressed in breast cancers [29], and is frequently mutated in bladder cancers [30]. DAPK1 is a potential tumor suppressor gene [31,32].…”

Mocetinostat for patients with previously treated, locally advanced/metastatic urothelial carcinoma and inactivating alterations of acetyltransferase genes

“…Inactivating alterations of CREBBP and EP300 are relatively frequent (approximately 13% and approximately 15%, respectively) in patients with urothelial carcinoma and are implicated in the dysregulation of key acetylation pathways and oncogenesis . Based on promising findings in urothelial carcinoma cell lines and tumor models (see Supporting Tables S1 and S2 and Supporting Fig.…”

“…10 Furthermore, a HAT inactivation signature associated with muscle-invasive bladder cancer was found to be inversely influenced by mocetinostat in breast cancer cells. 14 Mocetinostat also demonstrated preferential activity in CREB binding protein (CREBBP)-mutated and/or E1A binding protein p300 (EP300)-mutated (HAT genes) xenograft models and solid tumor cell lines, including urothelial cell carcinoma (see Supporting Tables S1 and S2 and Supporting Fig. S1).…”