Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma

Clément Meiller,Léa Meunier,Jean-Baptiste Assié,Françoise Galateau-Sallé,Cécile Badoual,François Montagne,Françoise Le Pimpec‐Barthes ,Sarah Humez,Jessica Zucman–Rossi ,Arnaud Scherpereel,Marie-Claude Jaurand,Marie‐Christine Copin ,Éric Letouzé ,Théo Z Hirsch ,Ecaterina Pintilie,Lisa Quetel,Julien De Wolf,Quentin Bayard,Laure Gibault,Stefano Caruso,Yuna Blum,Didier Jean

doi:10.1186/s13073-021-00931-w

Abstract

BackgroundMalignant pleural mesothelioma (MPM) is a heterogeneous cancer. Better knowledge of molecular and cellular intra-tumor heterogeneity throughout the thoracic cavity is required to develop efficient therapies. This study focuses on molecular intra-tumor heterogeneity using the largest series to date in MPM and is the first to report on the multi-omics profiling of a substantial series of multi-site tumor samples.MethodsIntra-tumor heterogeneity was investigated in 16 patients from whom biopsies were taken at distinct anatomical sites. The paired biopsies collected from apex, side wall, costo-diaphragmatic, or highest metabolic sites as well as 5 derived cell lines were screened using targeted sequencing. Whole exome sequencing, RNA sequencing, and DNA methylation were performed on a subset of the cohort for deep characterization. Molecular classification, recently defined histo-molecular gradients, and cell populations of the tumor microenvironment were assessed.ResultsSequencing analysis identified heterogeneous variants notably in NF2, a key tumor suppressor gene of mesothelial carcinogenesis. Subclonal tumor populations were shared among paired biopsies, suggesting a polyclonal dissemination of the tumor. Transcriptome analysis highlighted dysregulation of cell adhesion and extracellular matrix pathways, linked to changes in histo-molecular gradient proportions between anatomic sites. Methylome analysis revealed the contribution of epigenetic mechanisms in two patients. Finally, significant changes in the expression of immune mediators and genes related to immunological synapse, as well as differential infiltration of immune populations in the tumor environment, were observed and led to a switch from a hot to a cold immune profile in three patients.ConclusionsThis comprehensive analysis reveals patient-dependent spatial intra-tumor heterogeneity at the genetic, transcriptomic, and epigenetic levels and in the immune landscape of the tumor microenvironment. Results support the need for multi-sampling for the implementation of molecular-based precision medicine.

Highlights

Malignant pleural mesothelioma (MPM) is a heterogeneous cancer
To compare with genes previously reported to be correlated to the E.score or the S.score [10], we only considered genes with expression changes in the expected sense according to the histo-molecular scores of the paired biopsies
Mutational intra-tumor heterogeneity Paired tumor samples collected prior to chemotherapy treatment at two distinct anatomical sites from 16 MPM patients and five MPM-derived primary cell lines were analyzed by different next-generation sequencing (NGS) and omics methods (Fig. 1a)

Summary

Introduction

Malignant pleural mesothelioma (MPM) is a heterogeneous cancer. Malignant pleural mesothelioma (MPM) is a rare and highly aggressive tumor arising in the thoracic cavity. Immunotherapy based on immune checkpoint inhibitors has shown survival benefits in particular in patients with non-epithelioid histology, without an accurate predictive biomarker for treatment response besides age and histology [2,3,4]. Despite this recent therapeutic progress, there is still an urgent need to develop a precision medicine approach taking into account MPM heterogeneity

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Conclusion