Abstract 3128: Spatial intra-tumor molecular heterogeneity in malignant pleural mesothelioma

Introduction: Malignant pleural mesothelioma (MPM) is a heterogeneous cancer characterized by a diffuse locoregional growth within the thoracic cavity. Better knowledge of molecular and cellular intra-tumor heterogeneity throughout the thoracic cavity is required to develop efficient therapies. Methods: Intra-tumor heterogeneity was investigated in 16 patients biopsied at distinct anatomic sites (apex, side wall, costo-diaphragmatic and highly metabolic site detected by PET scan when present). Paired biopsies and five derived primary cell lines were screened by targeted sequencing. Part of the cohort was also deeply characterized by whole exome sequencing, RNA-seq and DNA methylation profiling. Molecular classification and recently defined histo-molecular gradients were assessed, as were the cell populations infiltration of the tumor microenvironment. Results: Sequencing analysis showed that most of the protein-altering somatic variants were common between paired samples from a given patient. However, we identified heterogeneous variants notably in NF2, the well-known mesothelioma driver tumor suppressor gene. Furthermore, we highlighted subclonal tumor populations shared among paired biopsies, suggesting a polyclonal dissemination of the tumor. Chromosomal abnormalities profiles were similar between different regions within the same tumor suggesting that the main chromosomal alterations occurring in MPM are early events of mesothelial carcinogenesis. Transcriptomic analysis showed major differential gene expression between anatomic sites, leading to the dysregulation of specific pathways notably linked to cell adhesion and extracellular matrix. Accordingly, histo-molecular gradient determining the proportions of epithelioid-like and sarcomatoid-like cellular entities varied between these samples. These changes were linked to epigenetic mechanisms in two patients. Finally, we found consequent spatial intra-tumor heterogeneity of the immune microenvironment with differential expression of immune mediators and immune checkpoints, and differential infiltration of immune populations. These changes led to a switch from a hot to a cold immune profile in three patients. Conclusions: This study is the first to report on the multi-omics profiling of a substantial series of multi-site MPM tumor samples. Spatial intra-tumor heterogeneity is complex in MPM and varies among patients. We highlighted multiple types of heterogeneity, i.e. (i) genetic, (ii) transcriptomic,