Investigating regulatory chromatin landscapes in primary and metastatic gastro-oesophageal adenocarcinoma

Student thesis: Phd

Abstract

Oesophageal and gastric adenocarcinoma have poor prognoses with fewer than one in five patients surviving five years from their diagnosis. Patients cannot be cured of metastasis making this a milestone event in cancer progression which defines treatment options. Oesophageal and proximal gastric adenocarcinoma are anatomically adjacent entities and clinical treatment options differ little between them. We aimed to characterise features of oesophageal and proximal gastric adenocarcinoma, as well as of their metastases, primarily by defining their chromatin accessibility profiles. In order to achieve these aims we employed next generation bulk and single cell sequencing techniques including RNA-seq, ATAC-seq and spatial transcriptomics on cell lines, organoids and human tissue. Following bioinformatic analysis of the datasets generated, we manipulated action and expression of identified factors of interest, with the use of inhibitors as well as shRNAs and expression vectors delivered by lentiviral transduction. We identified overlap in the regions of chromatin opening on development of adenocarcinoma in the oesophagus and gastric cardia. We also found that depletion of multiple subunits of the SWI/SNF chromatin remodelling complexes resulted in altered chromatin accessibility in oesophageal epithelial cells. Open chromatin profiling in metastatic cell lines led to the identification of GRHL2 as a potential regulatory factor. Gene profiling and cellular assays demonstrated a role for GRHL2 in regulating metastatic properties. Similarly, the YAP-TEAD pathway was identified as potentially important in metastasis. We have provided further evidence for a degree of overlap in the entities of oesophageal and gastric adenocarcinoma through analysis of their chromatin accessibility profiles and resultant gene regulatory networks. Further to this we have advanced our understanding of the effects of depletion of commonly mutated SWI/SNF subunits in OAC and identified transcription factors of interest in controlling the metastasis of gastro-oesophageal adenocarcinoma.
Date of Award1 Aug 2023
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorAndrew Sharrocks (Supervisor) & Yeng Ang (Supervisor)

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