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

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00931-w.

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, (iii) epigenetic and (iv) in the immune landscape of the tumor microenvironment. These results support the need for multi-sampling for the implementation of molecular-based precision medicine in MPM.

Citation Format: Clément Meiller, François Montagne, Théo Z. Hirsch, Stefano Caruso, Julien de Wolf, Quentin Bayard, Jean-Baptiste Assié, Léa Meunier, Yuna Blum, Lisa Quetel, Laure Gibault, Ecaterina Pintilie, Cécile Badoual, Marie-Christine Copin, Eric Letouzé, Arnaud Scherpereel, Jessica Zucman-Rossi, Françoise Le Pimpec-Barthes, Marie-Claude Jaurand, Didier Jean. Spatial intra-tumor molecular heterogeneity in malignant pleural mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3128.

Abstract B14: Discovery of YAP-TEAD protein-protein interaction inhibitors (PPI) for treating malignant pleural mesothelioma (MPM)

We have recently reported the development of YAP-TEAD interaction inhibitors that disrupt the YAP-TEAD complex and block proliferation of tumor cells. These compounds represent promising new treatment modalities for mesothelioma where the Hippo pathway is highly deregulated, with around 45% of MPM cases displaying a mutation of NF2 or LATS and predominantly nuclear YAP localization. MPM is an extremely aggressive disease with limited treatment options and no cure and is inherently chemoresistant, with only 50% of patients responding to the standard-of-care treatment; consequently, it has a very poor prognosis. The aim of this study was to support a multipronged approach to treat MPM. We have first established the in vitro proof of concept using siRNA experiments. Then, we have evaluated the effect of several Inventiva compounds (YAP-TEAD inhibitors) on the proliferation of a well-characterized YAP-dependent mesothelioma cell line (H2052) and on a large panel of MPM cells. We have further demonstrated the mechanism of action (MOA) of our compounds investigating the nuclear localization of YAP, the YAP-TEAD interactions, and the YAP protein expression levels in H2052 cancer cell line. To demonstrate the MOA, we have used immunofluorescence, proximity ligation assay, as well as Co-IP and Western blot experiments. Furthermore, we have examined the effect of IVA compounds in combination with the standard-of-care agent pemetrexed in a 3D spheroid model, and demonstrated the target engagement by looking at YAP-TEAD target gene expression. The effect of IVA compounds has been compared to this obtained with siRNA transfection. To assess the efficacy of pemetrexed +/- Inventiva compounds, we exposed H2052 cells to either each of the single agents or to their combination for 4 or 15 days in 2D or in 3D cultures. We used EdU incorporation assay or the measure of the spheroid area to access cell proliferation. We found a synergistic effect between YAP-TEAD inhibitors and pemetrexed, leading to a drastic inhibition of cancer cell proliferation and an increase of cytotoxicity. This suggests that YAP-TEAD inhibitors used in combination with existing chemotherapeutics could be used to attenuate multidrug resistance and resensitize chemoresistant cancer cells. We are currently exploring the effect of Inventiva compounds in H2052 mouse xenograft model. This study will be expanded to other indications and combination strategies where standard-of-care agents are ineffective and YAP is activated.

Citation Format: Anne Soudé, Martine Barth, Jean-Michel Luccarini, Séverine Delaporte, Florence Chirade, Christelle Valaire, Aude Boulay, Geneviève Cheret, Marie Dorchie, Céline Estivalet, Pascale Tuya-Boustugue, Robin Tranchand, Didier Jean, Lisa Quetel, Jean-Baptiste Assié, Irena Konstantinova, Jean-Louis Junien, Pierre Broqua. Discovery of YAP-TEAD protein-protein interaction inhibitors (PPI) for treating malignant pleural mesothelioma (MPM) [abstract]. In: Proceedings of the AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; 2019 May 8-11; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(8_Suppl):Abstract nr B14.

Genetic alterations of malignant pleural mesothelioma: association with tumor heterogeneity and overall survival

Development of precision medicine for malignant pleural mesothelioma (MPM) requires a deep knowledge of tumor heterogeneity. Histologic and molecular classifications and histo‐molecular gradients have been proposed to describe heterogeneity, but a deeper understanding of gene mutations in the context of MPM heterogeneity is required and the associations between mutations and clinical data need to be refined. We characterized genetic alterations on one of the largest MPM series (266 tumor samples), well annotated with histologic, molecular and clinical data of patients. Targeted next‐generation sequencing was performed focusing on the major MPM mutated genes and the TERT promoter. Molecular heterogeneity was characterized using predictors allowing classification of each tumor into the previously described molecular subtypes and the determination of the proportion of epithelioid‐like and sarcomatoid‐like components (E/S.scores). The mutation frequencies are consistent with literature data, but this study emphasized that TERT promoter, not considered by previous large sequencing studies, was the third locus most affected by mutations in MPM. Mutations in TERT promoter, NF2, and LATS2 were more frequent in nonepithelioid MPM and positively associated with the S.score. BAP1, NF2, TERT promoter, TP53, and SETD2 mutations were enriched in some molecular subtypes. NF2 mutation rate was higher in asbestos unexposed patient. TERT promoter, NF2, and TP53 mutations were associated with a poorer overall survival. Our findings lead to a better characterization of MPM heterogeneity by identifying new significant associations between mutational status and histologic and molecular heterogeneity. Strikingly, we highlight the strong association between new mutations and overall survival.

Frequent Homozygous Deletions of Type I Interferon Genes in Pleural Mesothelioma Confer Sensitivity to Oncolytic Measles Virus

INTRODUCTION

Oncolytic immunotherapy is based on the use of nonpathogenic replicative oncolytic viruses that infect and kill tumor cells exclusively. Recently, we found that the spontaneous oncolytic activity of the Schwarz strain of measles virus (MV) against human malignant pleural mesothelioma (MPM) depends on defects in the antiviral type I interferon (IFN-I) response in tumor cells.

METHODS

In this study, we studied three independent human MPM bio-collections to identify the defects in the IFN-I responses in tumor cells.

RESULTS

We show that the most frequent defect is the homozygous deletions (HDs) of all the 14 IFN-I genes (IFN-α and IFN-β) that we found in more than half of MV-sensitive MPM cell lines. These HDs occur together with the HDs of the tumor suppressor gene CDKN2A also located in the 9p21.3 chromosome region. Therefore, the IFN-I^-/- MPM cell lines develop a partial and weak IFN-I response when they are exposed to the virus compared with that of normal cells and MV-resistant MPM cell lines. This response consists of the expression of a restricted number of IFN-stimulated genes that do not depend on the presence of IFN-I. In addition, the IFN-I^-/- MPM cell lines infected by MV also develop a pro-inflammatory response associated with stress of the endoplasmic reticulum.

CONCLUSION

Our study emphasizes the link between HDs of IFN-I encoding genes and the CDKN2A gene in MPM and sensitivity to MV oncolytic immunotherapy.

Dissecting heterogeneity in malignant pleural mesothelioma through histo-molecular gradients for clinical applications

Malignant pleural mesothelioma (MPM) is recognized as heterogeneous based both on histology and molecular profiling. Histology addresses inter-tumor and intra-tumor heterogeneity in MPM and describes three major types: epithelioid, sarcomatoid and biphasic, a combination of the former two types. Molecular profiling studies have not addressed intra-tumor heterogeneity in MPM to date. Here, we use a deconvolution approach and show that molecular gradients shed new light on the intra-tumor heterogeneity of MPM, leading to a reconsideration of MPM molecular classifications. We show that each tumor can be decomposed as a combination of epithelioid-like and sarcomatoid-like components whose proportions are highly associated with the prognosis. Moreover, we show that this more subtle way of characterizing MPM heterogeneity provides a better understanding of the underlying oncogenic pathways and the related epigenetic regulation and immune and stromal contexts. We discuss the implications of these findings for guiding therapeutic strategies, particularly immunotherapies and targeted therapies.

Assessment of signaling pathway inhibitors and identification of predictive biomarkers in malignant pleural mesothelioma

OBJECTIVES

Malignant pleural mesothelioma (MPM) is an aggressive tumor with limited therapeutic options, requiring the development of efficient targeted therapies based on molecular phenotype of the tumor and to identify predictive biomarkers of the response.

MATERIALS AND METHODS

The effect of inhibitors was investigated by cell viability assessment on primary MPM cell lines established in our laboratory from patient tumors, well characterized at the molecular level. Effects on apoptosis, cell proliferation and viability on MPM growing in multicellular spheroid were also assessed for verteporfin. Gene and protein expression, and gene knockdown by RNA interference were used to define mechanism of inhibition and specific predictive biomarkers.

RESULTS

Anti-tumor effect of eight major signaling pathways inhibitors involved in mesothelial carcinogenesis was investigated. Three inhibitors were more efficient than cisplatin, the drug used as first-line chemotherapy in patients with MPM: verteporfin, a putative YAP inhibitor, defactinib, a FAK inhibitor and NSC668394, an Ezrin inhibitor. Verteporfin, the most efficient inhibitor, induced cell proliferation arrest and cell death, and is effective on 3D spheroid multicellular model. Verteporfin sensitivity was YAP-independent and related to molecular classification of the tumors. Biomarkers based on gene expression were identified to predict accurately sensitivity to these three inhibitors.

CONCLUSION

Our study shows that drug screening on well-characterized MPM cells allows for the identification of novel potential therapeutic strategies and defining specific biomarkers predictive of the drug response.

Co-occurring Mutations of Tumor Suppressor Genes, LATS2 and NF2, in Malignant Pleural Mesothelioma

Purpose: To better define malignant pleural mesothelioma (MPM) heterogeneity and identify molecular subtypes of MPM, we focus on the tumor suppressor gene LATS2, a member of the Hippo signaling pathway, which plays a key role in mesothelial carcinogenesis.Experimental Design: Sixty-one MPM primary cultures established in our laboratory were screened for mutations in LATS2 Gene inactivation was modeled using siRNAs. Gene and protein expressions were analyzed by quantitative RT-PCR, Western blot analysis, and reverse phase protein array. Cell proliferation, viability, apoptosis, mobility, and invasion were determined after siRNA knockdown or YAP (verteporfin), mTOR (rapamycin), and mTOR/PI3K/AKT (PF-04691502) inhibitor treatment.Results: The LATS2 gene was altered in 11% of MPM by point mutations and large exon deletions. Genetic data coupled with transcriptomic data allowed the identification of a new MPM molecular subgroup, C2^LN, characterized by a co-occurring mutation in the LATS2 and NF2 genes in the same MPM. MPM patients of this subgroup presented a poor prognosis. Coinactivation of LATS2 and NF2 leads to loss of cell contact inhibition between MPM cells. Hippo signaling pathway activity, mTOR expression, and phosphorylation were altered in the C2^LN MPM subgroup. MPMs of this new subgroup show higher sensitivity to PF-04691502 inhibitor. The MOK gene was identified as a potential biomarker of the C2^LN MPM subgroup and PF-04691502 sensitivity.Conclusions: We identified a new MPM molecular subgroup that shares common genetic and transcriptomic characteristics. Our results made it possible to highlight a greater sensitivity to an anticancer compound for this MPM subgroup and to identify a specific potential biomarker. Clin Cancer Res; 23(12); 3191-202. ©2016 AACR.

Abstract 112: Genetic alterations in molecular tumor subgroups of malignant pleural mesothelioma

Background: Malignant pleural mesothelioma (MPM) is a very aggressive neoplasm linked to asbestos exposure. In spite of research efforts to develop more effective therapeutic approaches, its prognosis remains poor, because of the absence of curative treatment. The identification of molecular profiles by omic analyses is a powerful approach to better define MPM subclasses and new targeted therapies. A recent transcriptomic analysis allowed to define a robust MPM classification and to identify two subgroups, C1 and C2, linked to histology and survival. The main finding was to separate epitheloid MPM, the most frequent histologic subtype, within these two subgroups. Epitheloid MPM with a worse survival prognosis were classified in the C2 subgroup. To better define the heterogeneity of MPM and establish a more precise classification, we determined genetic alterations in C1 and C2 MPM.

Material and Methods: Using a gene candidate approach, we performed Next-Generation Sequencing (Miseq, Illumina) in 84 MPM including 49 MPM primary cultures and 35 frozen tumors to identify genetic alterations in specific genes with a 200X depth. We selected 22 genes including key altered genes in mesothelial carcinogenesis (NF2, CDKN2A, CDKN2B BAP1, TP53 and LATS2) previously sequenced by Sanger method, genes mutated at low frequency in MPM (KRAS, HRAS, EGFR⋯) and genes recently suggested as altered in MPM (CUL1, KMT2D, SETD2⋯).

Results: Previous mutations identified by Sanger sequencing in our collection have been confirmed. The results showed an enrichment in C>T transitions, which was already observed in an exome sequencing study in MPM. We identified 93 variants inducing protein structure modification. Among them, 70% were deleterious to the function of the protein (deletion/insertion, splice-site mutation, substitutions nonsense and damaging missense predicted by SIFT or Polyphen). For most of the genes, the mutation frequency was consistent with literature data. The highest alteration frequency was found in CDKN2A, CDKN2B, NF2 and BAP1 genes (over 25%), lower frequencies were found in TP53, LATS2, KMT2D and SETD2 genes (5% to 20%). The alteration frequency of four genes was different between C1 and C2 tumor subgroups. BAP1 mutations were more frequent in C1 MPM, as we showed previously. We also identified new relevant mutations notably in the methyltransferases SETD2 and KMT2D that are also associated to C1 MPM. Mutations in TP53 were significantly associated with C2 MPM.

Conclusion: We defined the genetic alterations signatures of C1 and C2 tumor subgroups. Mutations in enzymes involved in chromatin organization seem to be characteristic of the C1 subgroup. Interestingly, TP53 mutations, which are known to provide tumor aggressiveness, are found in the C2 subgroup gathering patients with the worse prognosis. Ongoing analysis of 83 additional MPM would allow to confirm statistically all the associations we observed.

Citation Format: Lisa Quetel, Robin Tranchant, Clément Meiller, Sandrine Imbeaud, Annie Renier, Françoise Le Pimpec-Barthes, Jessica Zucman-Rossi, Marie-Claude Jaurand, Didier Jean. Genetic alterations in molecular tumor subgroups of malignant pleural mesothelioma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 112.