Identification of novel therapeutic strategies for immune-active oesophageal adenocarcinoma

  • Éilis Sutton

Student thesis: Doctoral ThesisDoctor of Philosophy


Introduction: Oesophageal adenocarcinoma (OAC) is a lethal cancer where incidence in high-income countries continues to rise. Conventional treatment elicits poor response rates and novel therapies are urgently required. Previous work to select molecular targets has failed to address the highly heterogeneous nature of this cancer. By focusing on an immune-mediated subgroup of patients defined by a gene expression assay we aim to exploit the underlying biology in order to re-position existing drugs or discover novel drug targets that will enhance chemosensitivity.

Materials and Methods: A 44-gene DNA damage immune response (DDIR) assay was applied to 273 pre-treatment OAC biopsies transcriptionally profiled using Almac Diagnostics Xcel array™. Using software from the Broad Institute, a gene set enrichment analysis (GSEA) was employed, to obtain a list of genes, within enriched biological pathways, differentially regulated between DDIR-positive and DDIR-negative phenotypes. Based on pre-determined criteria, suitable candidates for a small interfering RNA (siRNA) gene-silencing screen were chosen from the enriched genes.

A panel of OAC cell lines was scored using the DDIR assay. Four cell lines (OE33, OE19, FLO1 and SKGT4) were selected to represent a range of scores. An siRNA screen was performed in the cell line with the highest DDIR score (OE33) followed by mechanistic analyses to determine the effect of combination treatment of novel or existing targets with chemotherapy. Inhibition of the ATR-mediated DNA damage response was also explored alone and in combination with chemotherapy.

Results: Inhibition of ATR increased chemosensitivity to cisplatin and epirubicin in three OAC cell lines (OE33, OE19, SKGT4). GSEA revealed 1063 genes within 80 enriched pathways, differently regulated between DDIR-positive (24%) and DDIR-negative tumours (76%). Using pre-determined criteria, 84 genes were selected for siRNA gene silencing in the OE33 cell line identifying two novel DNA repair targets, Vav2 and USP7, with the potential to enhance chemosensitivity in DDIR-positive tumours.

Conclusion: Novel therapies for OAC patients are vital to improve the poor response rates to current treatments. Using a pathways biology approach, two new molecular targets were identified, and one existing target was repositioned, all with the potential to enhance the effect of current chemotherapeutic treatment in OAC patients with deficiencies in their DNA repair pathways and immune activation.

Date of AwardJul 2023
Original languageEnglish
Awarding Institution
  • Queen's University Belfast
SponsorsMarie Sklodowska Curie COFUND & OGCancer NI
SupervisorRichard Turkington (Supervisor) & Richard Kennedy (Supervisor)

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