Volatile hypoxia signatures in oesophageal adenocarcinoma
File(s)
Author(s)
Das, Bibek
Type
Thesis
Abstract
The UK has one of the highest rates of oesophageal adenocarcinoma (OAC) in the world. Tumour hypoxia is an attractive therapeutic target, but clinically feasible and accurate biomarkers are needed to advance precision medicine trials of hypoxia-targeting therapy (HTT). Mass spectrometric analysis of exhaled volatile organic compounds (VOCs) is a promising approach to diagnose OAC and may also offer a unique opportunity to assess tumour hypoxia non-invasively.
Using experimental and bioinformatic approaches, a novel 12-gene OAC-specific hypoxia-associated gene expression signature (OAC-Hyp) was derived which was prognostic for overall survival in independent cohorts (HR 1.12 (95% CI 1.03-1.22) on meta-analysis). This signature out-performed existing literature gene signatures and identified OAC subgroups with aggressive molecular characteristics.
A pilot clinical phenotyping study was then performed in OAC patients (n = 30) stratified by hypoxic gene expression (OAC-Hyp). This utilised a laser capture microdissection-RNA-seq workflow and a TD-GC-ToF-MS breath analysis pipeline with stringent quality control. A multi-dimensional sequential re-collection pipeline was developed to improve compound identification. This identified eight candidate hypoxia-associated VOCs with good discriminatory performance (AUC 0.888 95% CI 0.770 – 0.975) suitable for future validation studies.
To explore the effects of hypoxia in vitro, a multi-omic phenotyping study was performed on OAC cells. A bespoke programming package was developed for the semi-automated pre-processing of biofluid VOC data for this purpose. Hypoxia was found to induce transcriptional metabolic reprogramming which generated distinct lipidomic and volatilomic signatures associated with redox dysfunction.
Finally, an in silico screening approach identified PARP inhibitors as candidate HTT in OAC. These findings were validated in vitro, providing the rationale for evaluating breath analysis in an active clinical trial.
These data offer insights into the potential of breath analysis to detect OAC tumour hypoxia non-invasively. Future research will explore the translational utility of exhaled VOCs in clinical trials of HTT.
Using experimental and bioinformatic approaches, a novel 12-gene OAC-specific hypoxia-associated gene expression signature (OAC-Hyp) was derived which was prognostic for overall survival in independent cohorts (HR 1.12 (95% CI 1.03-1.22) on meta-analysis). This signature out-performed existing literature gene signatures and identified OAC subgroups with aggressive molecular characteristics.
A pilot clinical phenotyping study was then performed in OAC patients (n = 30) stratified by hypoxic gene expression (OAC-Hyp). This utilised a laser capture microdissection-RNA-seq workflow and a TD-GC-ToF-MS breath analysis pipeline with stringent quality control. A multi-dimensional sequential re-collection pipeline was developed to improve compound identification. This identified eight candidate hypoxia-associated VOCs with good discriminatory performance (AUC 0.888 95% CI 0.770 – 0.975) suitable for future validation studies.
To explore the effects of hypoxia in vitro, a multi-omic phenotyping study was performed on OAC cells. A bespoke programming package was developed for the semi-automated pre-processing of biofluid VOC data for this purpose. Hypoxia was found to induce transcriptional metabolic reprogramming which generated distinct lipidomic and volatilomic signatures associated with redox dysfunction.
Finally, an in silico screening approach identified PARP inhibitors as candidate HTT in OAC. These findings were validated in vitro, providing the rationale for evaluating breath analysis in an active clinical trial.
These data offer insights into the potential of breath analysis to detect OAC tumour hypoxia non-invasively. Future research will explore the translational utility of exhaled VOCs in clinical trials of HTT.
Version
Open Access
Date Issued
2024-01-03
Date Awarded
2024-05-01
Copyright Statement
Creative Commons Attribution NonCommercial NoDerivatives Licence
Advisor
Hanna, George
Antonowicz, Stefan
Sponsor
Medical Research Council (Great Britain)
Grant Number
MR/V02955X/1
Publisher Department
Department of Surgery & Cancer
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)