Integration of genome-level data to allow identification of subtype-specific vulnerability genes as novel therapeutic targets

Schwalbe, Edward C., H, Lalchungnunga, Lafta, Fadhel, Barrow, Timothy M. and Strathdee, Gordon (2021) Integration of genome-level data to allow identification of subtype-specific vulnerability genes as novel therapeutic targets. Oncogene. ISSN 0950-9232 (In Press)

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Official URL: https://doi.org/10.1038/s41388-021-01923-1

Abstract

The identification of cancer-specific vulnerability genes is one of the most promising approaches for developing more effective and less toxic cancer treatments. Cancer genomes exhibit thousands of changes in DNA methylation and gene expression, with the vast majority likely to be passenger changes. We hypothesised that, through integration of genome-wide DNA methylation/expression data, we could exploit this inherent variability to identify cancer subtype-specific vulnerability genes that would represent novel therapeutic targets that could allow cancer-specific cell killing. We developed a bioinformatics pipeline integrating genome-wide DNA methylation/gene expression data to identify candidate subtype-specific vulnerability partner genes for the genetic drivers of individual genetic/molecular subtypes. Using acute lymphoblastic leukaemia as an initial model, 21 candidate subtype-specific vulnerability genes were identified across the five common genetic subtypes, with at least one per subtype. To confirm the approach was applicable across cancer types, we also assessed medulloblastoma, identifying 15 candidate subtype-specific vulnerability genes across three of four established subtypes. Almost all identified genes had not previously been implicated in these diseases. Functional analysis of seven candidate subtype-specific vulnerability genes across the two tumour types confirmed that siRNA-mediated knockdown induced significant inhibition of proliferation/induction of apoptosis, which was specific to the cancer subtype in which the gene was predicted to be specifically lethal. Thus, we present a novel approach that integrates genome-wide DNA methylation/expression data to identify cancer subtype-specific vulnerability genes as novel therapeutic targets. We demonstrate this approach is applicable to multiple cancer types and identifies true functional subtype-specific vulnerability genes with high efficiency.

Item Type: Article
Additional Information: Funding information: This work was supported by project grants from KidsCan (Grant number N/A) and Bloodwise (Grant number 14024).
Uncontrolled Keywords: Acute lymphocytic leukaemia, Cancer genomics, CNS cancer, Epigenomics, Target identification
Subjects: C700 Molecular Biology, Biophysics and Biochemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: John Coen
Date Deposited: 21 Jul 2021 08:18
Last Modified: 27 Jul 2021 14:45
URI: http://nrl.northumbria.ac.uk/id/eprint/46722

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