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

Clément Meiller (1) , François Montagne (1) , Theo Hirsch (1) , Stefano Caruso (1) , Julien de Wolf (1) , Quentin Bayard (1) , Jean-Baptiste Assié (1, 2, 3) , Léa Meunier (1) , Yuna Blum (4) , Lisa Quetel (1) , Laure Gibault (5, 6) , Ecaterina Pintilie (7) , Cécile Badoual (5, 6) , Sarah Humez (8, 9) , Françoise Galateau-Sallé (10) , Marie-Christine Copin (8) , Eric Letouzé (1) , Arnaud Scherpereel (11, 12) , Jessica Zucman-Rossi (1, 5) , Françoise Le Pimpec-Barthes (1, 5) , Marie-Claude Jaurand (1) , Didier Jean (1)

1 CRC (UMR_S_1138 / U1138) - Centre de Recherche des Cordeliers
2 CEpiA - Clinical Epidemiology and Ageing : Geriatrie Soins Primaires et Santé Publique
3 CHI Créteil
4 CIT - (le programme) Cartes d'identité des tumeurs
5 HEGP - Hôpital Européen Georges Pompidou [APHP]
6 UPCité - Université Paris Cité
7 Hôpital Albert Calmette
8 Institut de Pathologie [CHU Lille]
9 CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277
10 Centre Léon Bérard [Lyon]
11 ONCO-THAI - Thérapies Laser Assistées par l'Image pour l'Oncologie - U 1189
12 MESOCLIN - Réseau National Expert pour le Mésothéliome Pleural Malin [Lille]

Background : Malignant 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. Methods : Intra-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. Results : Sequencing 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. Conclusions : This 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.

Mots clés: Clonality; NF2 subclonal mutation; Spatial molecular intra-tumor heterogeneity; Thoracic tumor; Tumor microenvironment; Clonality

Domaines: Génomique, Transcriptomique et Protéomique [q-bio.GN]; Biologie cellulaire; Cancer; Génétique humaine; Biologie moléculaire

Clément Meiller, François Montagne, Theo Hirsch, Stefano Caruso, Julien de Wolf, et al.. Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma. Genome Medicine, 2021, 13 (1), pp.113. ⟨10.1186/s13073-021-00931-w⟩. ⟨inserm-03289952⟩