Genetic Susceptibility in MAlignant Pleural Mesothelioma: Clinical Implication of GermliNE variaTionS

Plain-language summary

Malignant pleural mesothelioma (MPM) is a rare and aggressive neoplasm of the pleural mesothelium, mainly associated to asbestos exposure, still lacking effective therapies. Asbestos is a not-mutagenic agent: its nanosized fibres directly interact with tyrosine kinases (TKs) (e.g. EGFR) and may induce inappropriate receptor dimerization and activation, in absence of activating somatic mutations. TK receptor activation initiates cell signaling cascades and carcinogenesis. Asbestos, thus, induces the generation of an inflammatory immunosuppressive microenvironment that may support tumor growth in individuals with genetic predisposition (2). Consequently, the lack of actionable tumor targets together with the heterogeneous stroma, support the failure of modern drugs, both TK and immune-checkpoint inhibitors (TKIs, ICIs). In this complex context, the role of germline changes in MPM remains largely unexplored, except for changes in the BAP1 gene which are known to predispose to the disease (3). The main goal of the study is to look for germline changes of a panel of genes involved in microenvironment infiltration modulation, drug response and cancer predisposition. The study will be performed in parallel on blood samples obtained from asbestos-exposed subjects and on MPM patients. This approach will allow: detection of putative germline signatures associated with MPM onset predisposition (or even protection) with prognostic and predictive implications. The genetic characterization of MPM has not been fully clarified until now due to the significant inter-patient variability and to the scarcely reported somatic aberrations. Most of genetic alterations in MPM are loss of function of tumor suppressor genes or caretaker genes. Thus, the present project aimed at deeply investigate the germline variation in MPM and exposed population to determine host factors involved in MPM promotion. Pathogenic germline variants in MPM are often involved in DNA damage repair and chromatin remodeling pathways, and the most frequently identified germline mutations are in BAP1 which encodes for a tumor suppressor gene. Its protein is a nuclear deubiquitinating enzyme that plays an important role in chromatin modulation, transcriptional regulation, cell proliferation, DNA repair, cell death, and glucidic metabolism. Based on systematic literature review performed to identify all relevant data, a set of 30 genes involved in microenvironment infiltration modulation (e.g. RBL1), drug response (e.g. XRCC1) and cancer predisposition (e.g. BRAC1-2) has been defined. This phase will encompass a first step focused on deep mutational screening aimed at analyzing a custom panel of genes involved in microenvironment immune-inflammatory on peripheral blood mononuclear cell (PBMC)-derived DNA. A next-generation sequencing (NGS) approach will be applied by Illumina-iSeq 100 Sequencing System. From each subject enrolled in this study, total DNA will be extracted by automated purification system, then 20 ng of input DNA will be used for library construction and next generation sequencing of all coding exons from cancer related gene. The identified variants will be submitted to bioinformatics analysis by PolyPhen-2, SIFT and Ensembl Variant Effect Predictor (VEP), to assess the possible impact of the corresponding amino acid substitution on the structure and function of the encoded protein. In addition, clinically significant variants will be annotated by using ClinVar-NCBI, GnomAD and COSMIC databases. Recent clinical studies have associated high tumor mutational burden (TMB) with improved patient response rates and survival benefit from immune checkpoint inhibitors; hence, TMB is emerging as a biomarker of response for these immunotherapy agents. Moreover, it has been shown that germline variants can influence the molecular phenotypes of tumors and thus predict the checkpoint inhibitors efficacy. Staring from these considerations, in this study we will also analyze the germline tumor mutational burden (gTMB) by assessing the total number of nonsynonymous mutations in each selected gene.

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