Validation of a Gene Expression Test for Mesothelioma Prognosis in Formalin-Fixed Paraffin-Embedded Tissues

Our plain-English summary of Validation of a Gene Expression Test for Mesothelioma Prognosis in Formalin-Fixed Paraffin-Embedded Tissues, by A. De Rienzo, R.W. Cook, J. Wilkinson, et al (The Journal of Molecular Diagnostics, 2017).

The study

• Authors: A. De Rienzo, R.W. Cook, J. Wilkinson, C.E. Gustafson, W. Amin, C.E. Johnson, K.M. Oelschlager, D.J. Maetzold, J.F. Stone, M.D. Feldman, M.J. Becich, B.Y. Yeap, W.G. Richards, R. Bueno
• Journal: The Journal of Molecular Diagnostics
• Published: 2017;19(1):65-71
• Cited by: 8 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

A molecular test performed using fresh-frozen tissue was proposed for use in the prognosis of patients with pleural mesothelioma. The accuracy of the test and its properties was assessed under Clinical Laboratory Improvement Amendments-approved guidelines using FFPE tissue from an independent multicenter patient cohort. Concordance studies were performed using matched frozen and FFPE mesothelioma samples. The prognostic value of the test was evaluated in an independent validation cohort of 73 mesothelioma patients who underwent surgical resection. FFPE-based classification demonstrated overall high concordance (83%) with the matched frozen specimens, on removal of cases with low confidence scores, showing sensitivity and specificity in predicting type B classification (poor outcome) of 43% and 98%, respectively. Concordance between research and clinical methods increased to 87% on removal of low confidence cases. Median survival times in the validation cohort were 18 and 7 months in type A and type B cases, respectively (P = 0.002). Multivariate classification adding pathologic staging information to the gene expression score resulted in significant stratification of risk groups. The median survival times were 52 and 14 months in the low-risk (class 1) and intermediate-risk (class 2) groups, respectively. The prognostic molecular test for mesothelioma can be performed on FFPE tissues to predict survival, and can provide an orthogonal tool, in combination with established pathologic parameters, for risk evaluation.

Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

In plain English

This study tested whether a four-gene test, previously developed on frozen tumor tissue to predict survival in pleural mesothelioma, works on formalin-fixed, paraffin-embedded (FFPE) tissue in a clinical laboratory. Asbestos exposure was not examined. The authors first compared 77 matched frozen and FFPE samples. The two methods agreed in 83% of cases (95% confidence interval 73% to 91%). The FFPE test identified 40% (16% to 68%) of poor-outlook (type B) cases and 94% (84% to 98%) of good-outlook (type A) cases, and most misclassified samples were type B. Among 73 surgically treated patients from the National Mesothelioma Virtual Bank, median survival was 18 months (14 to 42) for 64 type A patients and 7 months (1 to 14) for 9 type B patients. With tumor type and lymph node status added, median survival was 52 months (lower limit 21, upper limit not reached) for 21 low-risk patients and 14 months (10 to 17) for 50 intermediate-risk patients. Only 2 were high risk. The authors concluded there was sufficient rationale for clinical use on surgical specimens, noting the small high-risk group as a limitation.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory test validation study: comparison of the gene expression test on matched frozen and FFPE tumor samples, then testing of its survival prediction in a separate cohort of stored tumor samples with outcome data
• Who was studied: Patients with malignant pleural mesothelioma treated by surgery. The concordance study used 77 patients operated on at Brigham and Women's Hospital, Boston, between 1999 and 2010. The validation cohort was 73 patients with documented surgical resection, collected at the University of Pittsburgh and the University of Pennsylvania between 1996 and 2013 and supplied by the National Mesothelioma Virtual Bank. In the validation cohort the median age was 63.5 years and 86% were male.
• Exposure: No asbestos or other environmental exposure was studied. The study assessed a gene expression score based on four genes (TM4SF1, PKM2, ARHGDIA, COBLL1) measured in tumor tissue.
• Main results:
  • In the 77 matched pairs, frozen and FFPE classifications agreed in 83% of cases (95% CI 73% to 91%).
  • In all 77 pairs, the FFPE test's sensitivity for type B (poor prognosis) was 40% (95% CI 16% to 68%) and its specificity for type A (good prognosis) was 94% (95% CI 84% to 98%).
  • After excluding six cases with low-confidence scores, sensitivity was 43% (95% CI 18% to 71%) and specificity was 98% (95% CI 91% to 100%), P = 0.039.
  • Misclassified samples were mostly in the type B category, which the authors took to suggest that the FFPE test is more likely to underpredict poor prognosis.
  • In the 73-patient validation cohort, the test classified 64 patients (88%) as type A and 9 patients (12%) as type B.
  • In the validation cohort, median survival was 18 months (95% CI 14 to 42) for type A patients and 7 months (95% CI 1 to 14) for type B patients, P = 0.002.
  • In the validation cohort, 1-year and 3-year survival rates were 65% and 36% for type A patients, compared with 19% and 0% for type B patients.
  • The score was combined with tumor type and lymph node status. This placed 21 validation patients (29%) in class 1 (low risk), 50 (68%) in class 2 (intermediate risk) and 2 (3%) in class 3 (high risk).
  • Median survival was 52 months in class 1 (95% CI 21, upper limit not reached) and 14 months in class 2 (95% CI 10 to 17).
  • The gene expression score predicted survival risk with an unadjusted hazard ratio of 4.4 (P = 0.002). After adjustment for tumor type and lymph node status, the text gives a hazard ratio of 4.3 (P = 0.003), while Table 3 gives 4.4 (95% CI 1.7 to 11.1).
  • Unadjusted hazard ratios were 2.4 for tumor type (P = 0.018) and 1.9 for lymph node status (P = 0.088). Adjusted for the gene score, they were 2.1 (P = 0.043) and 1.7 (P = 0.162). The lymph node results were not statistically significant.
  • Tumor T status (T1-T2 versus T3-T4) was not an independent predictor of survival (P = 0.789 on univariate analysis).
• The authors' conclusion: The authors concluded that the test was successfully validated in paraffin-embedded tissue and in an independent cohort, and that there is sufficient rationale for its clinical use with surgical specimens.
• Limitations the authors state:
  • Few high-risk (class 3) patients were found in the validation cohort. The authors attributed this to some centers treating positive lymph nodes and non-epithelioid tumor type as reasons not to operate.
  • Lymph node status was not statistically significant in this cohort, which the authors attributed to modest statistical power.
  • Surgical samples were used, not the small diagnostic biopsies on which the test is intended to be used before surgery. The authors stated that future validation using biopsy will be required.

Topics

The National Library of Medicine indexes this study under subjects our site covers: Mesothelioma.

Medical terms in this study, explained in our Lexicon: Mesothelioma, Prognosis, Pleural Mesothelioma, Surgical Resection, Median Survival, Staging.

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