Targeted next-generation sequencing of cancer genes in advanced stage malignant pleural mesothelioma: a retrospective study.

INTRODUCTION:: Malignant pleural mesothelioma (MPM) is a rare malignant disease and the understanding of molecular pathogenesis has lagged behind other malignancies. METHODS:: A series of 123 formalin-fixed, paraffin embedded (FFPE) tissue samples, with clinical annotations was retrospectively tested with a commercial library kit (Ion AmpliSeq Cancer Hotspot Panel v.2) to investigate 50 genes plus other two, BRCA1 associated protein-1 (BAP-1) and Neurofibromatosis-2 (NF2), frequently altered in MPM. DNA was obtained from tissues after manual microdissection and enriched for at least 50% cancer cells. Variations affecting protein stability or previously correlated to cancer, more frequently identified (≥25 patients with at least 10% of allelic frequency), were subsequently evaluated by Sanger sequencing. Immunohistochemistry staining for BAP1 and NF2 proteins was also performed. RESULTS:: The commonest genetic variations were clustered in two main pathways: the p53/DNA repair (TP53, SMACB1, and BAP1) and PI3K-AKT pathways (PDGFRA, KIT, KDR, HRAS, PIK3CA, STK11, and NF2). PIK3CA:c.1173A>G mutation, STK11:rs2075606 (T>C) or TP53:rs1042522 (Pro/Pro) were significantly associated to time to progressive disease (TTPD) (all p-values<0.01). Furthermore, the accumulation of genetic alterations correlated with shorter TTPD and reduced OS, respectively (TTPD p-value=0.02, OS p-value=0.04). BAP1 genetic variations identified were mainly located in exons 13 and 17 and BAP1 non-synonymous variations were significantly correlated with BAP1 protein nuclear localization. CONCLUSION: NGS was applied to a relatively large retrospective series of MPM using FFPE archival material. Our results indicate a complex mutational landscape with a higher number of genetic variations in the p53/DNA repair and Pi3K pathways, some of them with prognostic value.