List of the tumor specific mutations identified by whole-genome sequencing and validated in the 10 pairs of MPM tumor and germline DNA samples

XLSX file - 31K, PCR primers and genes. Sequences of the primers for the differential diagnosis of MPM. Selected genes for each diagnostic test.

Whole genome sequencing data analysis of 10 MPM tumor and matched DNA generated by Complete Genomics platform

List of the Tumor types having mutations in both MYH9 and RHOA genes in the cBioPortal for Cancer Genomics database

XLSX file - 240K, List of the differentially expressed probes for the analysis MPM vs. other tumor types.

XLSX file - 196K, List of the enriched functional terms for the analysis Epithelioid MPM vs. Sarcomatoid MPM.

Schematic representation of the SNVs and/or chromosomal aberrations identified in BAP1, NF2, TP53, MYH9, RHOA, MYH6, MYH10, PIK3C2A, TNFRSF1A, and 22q and 9p in a panel of 147 MPM tumors.

PDF file - 53K, Identification of Diagnostic Molecular Markers and Data Analysis, Real-Time Quantitative PCR Results, Hierarchical clustering analysis.

PDF file - 188K, Heat-map of the 26-gene signature used in the sequential combination of gene expression ratio tests in the 112 thoracic samples. Probes are annotated with gene symbol on the right. Relative gene expression levels are given by the scale at the top. The red asterisk indicates the mesothelioma samples.

XLSX file - 66K, List of the differentially expressed probes for the analysis Epithelioid MPM vs. Sarcomatoid MPM.

List of the 51 canonical pathways significantly enriched (p<0.05) for the mutated genes identify by Ingenuity Pathway Analysis

XLSX file - 34K, List of the enriched functional terms for for the analysis MPM vs. other tumor types.

XLSX file - 191K, Results of the binary diagnostic tests using microarray data and RT-PCR data in the original set of samples.

Expression levels of candidate genes in 151 patients by gender and histology

Expression levels for BAP1, NF2, TP53, MYH9, MYH6, MYH10, PIK3C2A, RHOA, and TNFRSF1A detected by Affymetrix® Human Gene 1.1 ST Array in 151 MPM

List of SNVs identified in the analyzed genes

XLSX file - 42K, Results of the binary diagnostic tests in a test set analyzed by RT-PCR.

Abstract Malignant pleural mesothelioma (MPM) is an aggressive cancer that occurs more frequently in men, but is associated with longer survival in women. Insight into the survival advantage of female patients may advance the molecular understanding of MPM and identify therapeutic interventions that will improve the prognosis for all MPM patients. In this study, we performed whole-genome sequencing of tumor specimens from 10 MPM patients and matched control samples to identify potential driver mutations underlying MPM. We identified molecular differences associated with gender and histology. Specifically, single-nucleotide variants of BAP1 were observed in 21% of cases, with lower mutation rates observed in sarcomatoid MPM (P < 0.001). Chromosome 22q loss was more frequently associated with the epithelioid than that nonepitheliod histology (P = 0.037), whereas CDKN2A deletions occurred more frequently in nonepithelioid subtypes among men (P = 0.021) and were correlated with shorter overall survival for the entire cohort (P = 0.002) and for men (P = 0.012). Furthermore, women were more likely to harbor TP53 mutations (P = 0.004). Novel mutations were found in genes associated with the integrin-linked kinase pathway, including MYH9 and RHOA. Moreover, expression levels of BAP1, MYH9, and RHOA were significantly higher in nonepithelioid tumors, and were associated with significant reduction in survival of the entire cohort and across gender subgroups. Collectively, our findings indicate that diverse mechanisms highly related to gender and histology appear to drive MPM. Cancer Res; 76(2); 319–28. ©2015 AACR.

Abstract Purpose: To develop a standardized approach for molecular diagnostics, we used the gene expression ratio bioinformatic technique to design a molecular signature to diagnose malignant pleural mesothelioma (MPM) from among other potentially confounding diagnoses and differentiate the epithelioid from the sarcomatoid histologic subtype of MPM. In addition, we searched for pathways relevant in MPM in comparison with other related cancers to identify unique molecular features in MPM. Experimental Design: We conducted microarray analysis on 113 specimens including MPMs and a spectrum of tumors and benign tissues comprising the differential diagnosis of MPM. We generated a sequential combination of binary gene expression ratio tests able to discriminate MPM from other thoracic malignancies. We compared this method with other bioinformatic tools and validated this signature in an independent set of 170 samples. Functional enrichment analysis was conducted to identify differentially expressed probes. Results: A sequential combination of gene expression ratio tests was the best molecular approach to distinguish MPM from all the other samples. Bioinformatic and molecular validations showed that the sequential gene ratio tests were able to identify the MPM samples with high sensitivity and specificity. In addition, the gene ratio technique was able to differentiate the epithelioid from the sarcomatoid type of MPM. Novel genes and pathways specifically activated in MPM were identified. Conclusions: New clinically relevant molecular tests have been generated using a small number of genes to accurately distinguish MPMs from other thoracic samples, supporting our hypothesis that the gene expression ratio approach could be a useful tool in the differential diagnosis of cancers. Clin Cancer Res; 19(9); 2493–502. ©2013 AACR.