Malignant pleural mesothelioma and mesothelial hyperplasia: A new molecular tool for the differential diagnosis

Abstract

Malignant pleural mesothelioma (MPM) is a rare asbestos related cancer, aggressive and unresponsive to therapies. Histological examination of pleural lesions is the gold standard of MPM diagnosis, although it is sometimes hard to discriminate the epithelioid type of MPM from benign mesothelial hyperplasia (MH).This work aims to define a new molecular tool for the differential diagnosis of MPM, using the expression profile of 117 genes deregulated in this tumour.The gene expression analysis was performed by nanoString System on tumour tissues from 36 epithelioid MPM and 17 MH patients, and on 14 mesothelial pleural samples analysed in a blind way. Data analysis included raw nanoString data normalization, unsupervised cluster analysis by Pearson correlation, non-parametric Mann Whitney U-test and molecular classification by the Uncorrelated Shrunken Centroid (USC) Algorithm.The Mann-Whitney U-test found 35 genes upregulated and 31 downregulated in MPM. The unsupervised cluster analysis revealed two clusters, one composed only of MPM and one only of MH samples, thus revealing class-specific gene profiles. The Uncorrelated Shrunken Centroid algorithm identified two classifiers, one including 22 genes and the other 40 genes, able to properly classify all the samples as benign or malignant using gene expression data; both classifiers were also able to correctly determine, in a blind analysis, the diagnostic categories of all the 14 unknown samples.In conclusion we delineated a diagnostic tool combining molecular data (gene expression) and computational analysis (USC algorithm), which can be applied in the clinical practice for the differential diagnosis of MPM.

Molecular markers and new diagnostic methods to differentiate malignant from benign mesothelial pleural proliferations: a literature review

“…In this context, we can mainly categorize the identification of reliable diagnostic biomarkers as the following: historical MPM biomarkers, including immunohistochemical ones (such as GLUT-1, p53, desmin, EMA, IMP-3) (5-13) and PE soluble ones analyzable by ELISA (such as mesothelin and fibulin-3) (41-47), which have been and are still extensively studied; emerging biomarkers recently introduced into clinical practice (BAP1 analyzable by IHC and p16 by FISH) (3); suggested MPM signatures based on miRNAs and mRNA expression panels (50-52); and new diagnostic tools based on molecular panels and classification algorithms (53,(55)(56)(57).…”

“…In the first part of our study, we analyzed mRNA from FFPE tissues of 36 (57). In the second part of our study, we utilized classification models to determine the diagnostic category of 14 pleural tissues (test samples) blindly analyzed, and all samples were correctly attributed to their diagnostic category (9 epithelioid MPM and 5 MH).…”

“…The main advantages of our approach include a low RNA input required to analyze 117 genes (as low as 150 ng), which is obtainable from FFPE tissues, and the fact that the USC algorithm does not require a priori assumption; therefore, normalized NanoString data from all genes could be directly utilized for computational classification without any further manipulation of data. On the other hand, our system requires further validation on a larger number of samples to determine the best classification model and its positive and negative predictive values, and our system should additionally be tested on cytological specimens before introduction in clinical practice (57).…”

Overexpressed genes in malignant pleural mesothelioma: implications in clinical management

“…The prognostic and diagnostic value of some of these genes (i.e., fibulin3) is still inconclusive due to the conflicting results observed; to overcome this problem it could be useful to analyze, with the same method and using the same patient stratification, the expression of these candidate markers in a larger sample size cohort. Due to the heterogeneity of the disease, it could be more effective the evaluation of a panel of markers instead of one independent marker, as recently suggested for the differential diagnosis of MPM (121). Moreover, the identification of reliable markers for early diagnosis of asymptomatic MPM is a very interesting research field because advances in therapy for patients with MPM may result in an improved outcome if they are applied to stage I disease.…”

Clinical diagnosis of malignant pleural mesothelioma

“…Molecular profiling technologies to assess DNA, RNA, protein and metabolites have led to better understanding of the molecular basis of cancer, with identification of new disease markers (28)(29)(30)(31)(32)(33)(34)(35)(36).…”