Epigenetic genes alterations in metastatic solid tumors: results from the prospective precision medicine MOSCATO and MATCH-R trials

Abstract Purpose: Although the role of epigenetic alterations in oncogenesis has been well studied, their prevalence in metastatic solid tumors is still poorly described. We therefore aimed at: (i) describing the presence of epigenetic gene alterations (EGA) - defined by an alteration in a gene encoding an epigenetic regulator; and (ii) evaluating their relationship with clinical characteristics and outcome in patients (pts) included in prospective molecular profiling trials.Patients and methods: On-purpose tumor biopsies from pts with metastatic solid tumors enrolled in the Gustave Roussy-sponsored MOSCATO (NCT01566019) and MATCHR (NCT02517892) trials were molecularly profiled using Whole Exome Sequencing (WES). Alterations in 176 epigenetic genes were assessed and classified as pathogenic variants (PV) or non-pathogenic variants by a molecular tumor board. Clinical characteristics and outcome were collected.Results: Between Dec 2011 and Oct 2016, WES was successfully performed in 292 pts presenting various solid tumors. We found 496 epigenetic gene alterations in 134 patients (49%), including 237 pathogenic variants in 86 patients; 63 tumor samples (47%) presented ≥3 EGAs. The median number of previous treatment lines was 3 (1 – 10). The most frequently altered genes were KMT2D and KMT2C (16% each), ARID1A and SETD2 (10% each) and KMT2A (8%).; 31% of EGA co-occurred with a driver gene alteration (p < 0.001). Outcome was not correlated with the presence of EGA.Conclusions: Epigenetic alterations occur frequently in metastatic solid tumors. With the current development of epigenetic modifiers, they increasingly represent actionable targets. Such genes should now be systematically analyzed in molecular profiling studies.