Molecular and functional analysis of BRD4 isoforms in controlling gene expression and enhancer function

• Applicant: Privatdozentin Dr. Lena-Christin Conradi, since 3/2019
• Subject Area: General Genetics and Functional Genome Biology ; General and Visceral Surgery ; Gastroenterology
• Term: from 2013 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 242272040

Pancreatic ductal adenocarcinoma (PDAC) represents a major challenge in oncology with a dismal five-year survival rate of less than 7%. Recent high throughput genomic screening efforts have revealed that PDAC can be divided into various molecular subtypes based on their individual genetic and transcriptional profiles and display significant differences in patient survival. In particular, epigenetic regulation of cell phenotype and therapeutic responsiveness is emerging as a common theme in PDAC. One attractive target for the treatment of PDAC is the bromodomain and extra-terminal (BET) family of epigenetic readers. While a large number of studies have shown a potential therapeutic efficacy of small molecular BET inhibitors (BETi) in a range of solid tumors and hematological malignancies, PDAC tumor cell lines and patient-derived xenografts display significant variation in their responsiveness to BETi. Nevertheless, relatively little is known about the molecular determinants controlling tumor responsiveness to BETi treatment. In previous published and preliminary studies we have utilized various genome-wide approaches to uncover the molecular underpinnings and transcriptional networks that underlie the function of the major BET protein BRD4. We have displayed a particularly important role for BRD4 in controlling cell fate programming by controlling the activity of certain lineage-specific transcription factors at distal enhancer regions. However, BRD4 is not a single protein, but rather exists in two major isoforms produced via alternative splicing, each containing the amino-terminal tandem bromodomains followed by the extraterminal domain and therefore both targeted by BETi. While the short isoform (BRD4-S) ends shortly after the extraterminal domain, the long isoform (BRD4-L) also contains a C-terminal extension with unique interaction partners. In this project we aim to leverage our experience in examining transcriptional regulation and BRD4 function to gain further molecular insights into the individual functions of BRD4-S and BRD4-L in order to unravel their discrete contributions to gene activation. In order to do so, we will utilize state of the art transcriptomic and genome-wide occupancy methodology combined with genome-editing and genomic tethering approaches to not only decipher the genomic targets of BRD4-S and BRD4-L, but also determine whether individual BRD4-occupied enhancer regions are necessary and sufficient for target gene activation. Finally, we aim to further increase the repertoire of potential enhancer-associated therapeutic targets by identifying BRD4-S and BRD4-L-specific interaction partners and examine their importance in controlling BRD4 activity in PDAC cells. Thus, we expect to gain biological insights which will provide important information about the molecular mechanisms underlying BRD4 biology, while also yielding information likely to be directly relevant to the therapeutic targeting of pancreatic cancer.

• DFG Programme: Research Grants
• Ehemaliger Antragsteller: Professor Steven Johnsen, Ph.D., until 2/2019