Mechanisms of action of ELF5 in breast cancer

Abstract

The ETS transcription factor ELF5 is a critical regulator of cell fate. In the mammary epithelium, ELF5 drives the development of the ER-negative milk-producing alveolar cells, and the balance between ER and ELF5 transcriptional activity is hypothesised to be a fundamental determinant of cell fate. ELF5-driven transcriptional programs may also function in breast cancer, with previous studies demonstrating roles in basal-like and endocrine-resistant disease. The aim of this thesis was to investigate the transcriptional functions of ELF5 in breast cancer, and the factors that regulate ELF5 activity.

A potential mechanism of ELF5 regulation is through alternative splicing, producing unique protein isoforms. There are four ELF5 isoforms; however little is known about their specific functions. ELF5 expression was comprehensively analysed at the isoform level, using RNA-sequencing data from 6,757 Cancer Genome Atlas samples. In breast cancer, ELF5 alterations were subtype-specific, with the basal subtype demonstrating unique isoform expression changes. Despite differences in protein domains, the in vitro functional effects of ELF5 isoforms were similar.

Genome-wide sequencing studies were also performed to investigate ELF5 DNA binding sites and transcriptional effects in ER-positive breast cancer cells. ELF5 regulated transcriptional signatures of long-term oestrogen deprivation, suppression of the interferon response, and MYC-regulated gene expression. Increased ELF5 also redistributed the genomic binding sites of the ER pioneer factor FOXA1, representing a novel mechanism by which ELF5 may modulate the oestrogen response.

Finally, interactions with other proteins are essential for specific transcriptional regulation. However, no ELF5-interacting proteins have previously been identified in human breast cancer cells. The protein interactions of chromatin-bound ELF5 were investigated using RIME, identifying DNA-PKcs. A transcriptional model involving ELF5, ER and DNA-PKcs was proposed, with important potential implications for the use of DNA-PKcs inhibitors in breast cancer treatment.

Effective therapeutic targeting of transcription factors depends on a detailed understanding of how transcription factors function, the mechanisms that regulate them, and how these processes are dysregulated in cancer. The new insights into ELF5 function provided by this thesis represent an important contribution towards realising the potential of ELF5 as a therapeutic target in cancer.