Reply to: Oncolytic Viral Therapy for Malignant Pleural Mesothelioma

Among the most frequent genomic alterations in malignant pleural mesothelioma (MPM) are the homozygous deletions (HDs) of the CDKN2A tumor suppressor gene. These alterations are found in 49% of patients with MPM according to a recent analysis of The Cancer Genome Atlas (TCGA).1Hmeljak J. Sanchez-Vega F. Hoadley K.A. et al.Integrative molecular characterization of malignant pleural mesothelioma.Cancer Discov. 2018; 8: 1548-1565Crossref PubMed Scopus (178) Google Scholar In our recent study performed on 78 short-term–cultured MPM cell lines and published in the Journal of Thoracic Oncology, we found CDKN2A HDs in 73% of patients.2Delaunay T. Achard C. Boisgerault N. et al.Frequent homozygous deletions of type I interferon genes in pleural mesothelioma confer sensitivity to oncolytic measles virus.J Thorac Oncol. 2020; 15: 827-842Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar We also reported that the CDKN2A HDs are accompanied in 30% of them by the HDs of all genes encoding IFN-I that are essential for cellular antiviral defense. Finally, we identified two MPM cell lines with constitutively activated IFN-I response characterized by the expression of numerous IFN-stimulated genes that resist the oncolytic activity of the vaccine Schwarz strain of measles virus (MV). Other frequent genomic alterations in MPM are the mutations and the HDs of the BAP1 gene.1Hmeljak J. Sanchez-Vega F. Hoadley K.A. et al.Integrative molecular characterization of malignant pleural mesothelioma.Cancer Discov. 2018; 8: 1548-1565Crossref PubMed Scopus (178) Google Scholar In their letter to the editor, Yang et al.3Yang H. Xu D. Gao Y. Schmid R.A. Peng R.-W. Oncolytic viral therapy for malignant pleural mesothelioma.J Thorac Oncol. 2020; Abstract Full Text Full Text PDF Scopus (3) Google Scholar focused on TCGA data and reported that BAP1 mutation and BAP1 HDs are found in 22% and 14% of patients, respectively. They performed a functional enrichment analysis using Gene Ontology and Reactome databases to identify the signal pathways that correlate to BAP1 expression. They found a strong negative correlation between BAP1 expression and a constitutively activated IFN-I response. They concluded that BAP1 loss-of-function may be used as a marker of tumors with constitutively activated IFN-I response, and thus, for resistance to oncolytic virotherapy. Hmeljak et al.1Hmeljak J. Sanchez-Vega F. Hoadley K.A. et al.Integrative molecular characterization of malignant pleural mesothelioma.Cancer Discov. 2018; 8: 1548-1565Crossref PubMed Scopus (178) Google Scholar earlier performed an analysis of TCGA on 74 patients with MPM, with a detailed focus on BAP1 alteration and its consequences. They reported an IFN-I signature in MPM tumors with an inactivated BAP1 gene (Supplementary Figs. 3H and 7D). Thus, the expression of BAP1 and its mutational status suggest a negative regulation of the IFN-I pathway in MPM by the BAP1 protein. Considering those results, we first analyzed BAP1 gene expression, as previously described,4Achard C. Boisgerault N. Delaunay T. et al.Sensitivity of pleural mesothelioma to oncolytic measles virus depends on defects of the type I interferon response.Oncotarget. 2015; 6: 44892-44904Crossref PubMed Scopus (27) Google Scholar in 19 MPM cell lines (from which we previously determined their MV-sensitivity5Blum Y. Meiller C. Quetel L. et al.Dissecting heterogeneity in malignant pleural mesothelioma through histo-molecular gradients for clinical applications.Nat Commun. 2019; 10: 1333Crossref PubMed Scopus (43) Google Scholar). We observed a significant enrichment of low BAP1-expressing MPM cell lines that are MV-resistant (p = 0.02) (Fig. 1A). We then screened BAP1 gene alterations in these cell lines by a targeted sequencing previously described.6Quetel L, Meiller C, Assié JB, et al. Genetic alterations of malignant pleural mesothelioma: association with tumor heterogeneity and overall survival [e-pub ahead of print]. Mol Oncol. https://doi.org/10.1002/1878-0261.12651, accessed May 6, 2020.Google Scholar Eight MPM cell lines harbored BAP1 alterations, three with HDs, and five with mutations (Fig. 1B). These data reveal that all MPM cell lines with IFNB1 deletion are sensitive to MV independently of the BAP1 mutation status. Interestingly, a slight enrichment of BAP1 genetic alterations was observed in MV-resistant compared with MV-sensitive MPM cell lines (p = 0.07), especially considering MPM cell lines without IFNB1 deletion (p = 0.06) (Fig. 1C). We, thus, analyzed the IFN-I signature of 36 short-term–cultured MPM cell lines in which IFNB1 and BAP1 genetic alteration status had been determined (61% with BAP1, 28% with IFNB1, 14% with both genes altered). We performed a pathway enrichment analysis using transcriptomic data previously generated from these cell lines7de Reyniès A. Jaurand M.C. Renier A. et al.Molecular classification of malignant pleural mesothelioma: identification of a poor prognosis subgroup linked to the epithelial-to-mesenchymal transition.Clin Cancer Res. 2014; 20: 1323-1334Crossref PubMed Scopus (73) Google Scholar and the online pathway analytic tool of the Reactome Knowledgebase (https://reactome.org/). We did not find any significant enrichment of IFN-I pathways on genes whose expression inversely correlated with BAP1 gene expression (Spearman’s r < −0.4, false discovery rate-adjusted p < 0.01), or on differentially expressed genes between MPM cell lines with or without BAP1 genetic alteration (data not shown). This lack of a link between BAP1 expression or alteration and IFN-I pathways was also observed in our previous study.2Delaunay T. Achard C. Boisgerault N. et al.Frequent homozygous deletions of type I interferon genes in pleural mesothelioma confer sensitivity to oncolytic measles virus.J Thorac Oncol. 2020; 15: 827-842Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar In the absence of a virus, the MV-resistant Meso61 cell line with a biallelic deletion and low expression of BAP1 harbors an inactivated IFN-I response, whereas the MV-resistant Meso45 with a high expression of wild-type BAP1 harbors a strong constitutively activated IFN-I. Altogether, our results suggest a correlation between BAP1 gene expression or alteration status and the resistance to MV; however, we cannot conclude on a link with the IFN-I response. This discrepancy of the results between tumor samples and cell lines may be explained by the microenvironment. It was reported that BAP1-altered MPM tumors reveal a different pattern of infiltration by immune cells than wild-type BAP1 tumors,8Ladanyi M. Sanchez Vega F. Zauderer M. Loss of BAP1 as a candidate predictive biomarker for immunotherapy of mesothelioma.Genome Med. 2019; 11: 18Crossref PubMed Scopus (12) Google Scholar and these infiltrations may play a role in the observed IFN-I signature. Furthermore, this IFN-I signature may be responsible for the presence of infiltrated immune cells as was reported for other cancers.9Cañadas I. Thummalapalli R. Kim J.W. et al.Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses.Nat Med. 2018; 24: 1143-1150Crossref PubMed Scopus (98) Google Scholar In conclusion, the negative correlation of BAP1 expression and the IFN-I signature in MPM observed by Yang H et al.3Yang H. Xu D. Gao Y. Schmid R.A. Peng R.-W. Oncolytic viral therapy for malignant pleural mesothelioma.J Thorac Oncol. 2020; Abstract Full Text Full Text PDF Scopus (3) Google Scholar could be of great interest in the context of the absence of IFNB1 deletion to identify patients with a lower chance of responding to oncolytic virotherapy using IFN-I–sensitive oncolytic viruses. It would, thus, be interesting to determine the mechanism of the IFN-I response modulation by the BAP1 protein.