Integrative Modeling Reveals Annexin A2-mediated Epigenetic Control of Mesenchymal Glioblastoma

Glioblastomas are characterized by transcriptionally distinct subtypes, but despite possible clinical relevance, their regulation remains poorly understood. The commonly used molecular classification systems for GBM all identify a subtype with high expression of mesenchymal marker transcripts, strongly associated with invasive growth. We used a comprehensive data-driven network modeling technique (augmented sparse inverse covariance selection, aSICS) to define separate genomic, epigenetic, and transcriptional regulators of glioblastoma subtypes. Our model identified Annexin A2 (ANXA2) as a novel methylation-controlled positive regulator of the mesenchymal subtype. Subsequent evaluation in two independent cohorts established ANXA2 expression as a prognostic factor that is dependent on ANXA2 promoter methylation. ANXA2 knockdown in primary glioblastoma stem cell-like cultures suppressed known mesenchymal master regulators, and abrogated cell proliferation and invasion. Our results place ANXA2 at the apex of a regulatory cascade that determines glioblastoma mesenchymal transformation and validate aSICS as a general methodology to uncover regulators of cancer subtypes.

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Glioblastoma, a form of brain cancer, is characterised by distinct molecular subtypes: proneural, classical and mesenchymal.

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We used a comprehensive data-driven strategy, aSICS, to elucidate the cellular mechanisms behind the subtypes.

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Epigenetic control of Annexin A2 (ANXA2) was predicted and confirmed to determine the invasive mesenchymal subtype.

Most cancers have distinct and clinically relevant transcriptional subtypes, but the underlying cellular mechanism behind such subtypes is often hard to resolve. We show that joint analysis across several layers of genomics data can uncover subtype regulators with good accuracy. Our method is applied to the brain cancer glioblastoma multiforme (GBM), revealing that the invasive mesenchymal subtype is driven by epigenetic modulation of the expression of Annexin A2 (ANXA2). Our analysis adds significantly to our understanding of brain cancer subtypes and open for new potential treatment options. The proposed computational technique can be applied to other cancers as well.