Targeted next-generation sequencing of cancer genes in advanced stage malignant pleural mesothelioma: a retrospective study

Our plain-English summary of Targeted next-generation sequencing of cancer genes in advanced stage malignant pleural mesothelioma: a retrospective study, by M. Lo Iacono, V. Monica, L. Righi, et al (Journal of Thoracic Oncology, 2015).

The study

• Authors: M. Lo Iacono, V. Monica, L. Righi, F. Grosso, R. Libener, S. Vatrano, P. Bironzo, S. Novello, L. Musmeci, M. Volante, M. Papotti, G.V. Scagliotti
• Journal: Journal of Thoracic Oncology
• Published: 2015;10(3):492-9
• Cited by: 119 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

Introduction: Malignant pleural mesothelioma (MPM) is a rare malignant disease, and the understanding of molecular pathogenesis has lagged behind other malignancies.

Methods: A series of 123 formalin-fixed, paraffin-embedded tissue samples with clinical annotations were retrospectively tested with a commercial library kit (Ion AmpliSeq Cancer Hotspot Panel v.2, Life Technologies, Grand Island, NY) to investigate 50 genes plus other two, BRCA1-associated protein-1 (BAP-1) and neurofibromatosis-2 (NF2), frequently altered in MPM. DNA was obtained from tissues after manual microdissection and enriched for at least 50% cancer cells. Variations affecting protein stability or previously correlated to cancer, more frequently identified (≥ 25 patients with at least 10% of allelic frequency), were subsequently evaluated by Sanger sequencing. Immunohistochemistry staining for BAP1 and NF2 proteins was also performed.

Results: The commonest genetic variations were clustered in two main pathways: the p53/DNA repair (TP53, SMACB1, and BAP1) and phosphatidylinositol 3-kinase-AKT pathways (PDGFRA, KIT, KDR, HRAS, PIK3CA, STK11, and NF2). PIK3CA:c.1173A>G mutation, STK11:rs2075606 (T>C), or TP53:rs1042522 (Pro/Pro) was significantly associated with time to progressive disease (TTPD; all p values < 0.01). Furthermore, the accumulation of genetic alterations correlated with shorter TTPD and reduced overall survival (TTPD p value = 0.02, overall survival p value = 0.04). BAP1 genetic variations identified were mainly located in exons 13 and 17, and BAP1 nonsynonymous variations were significantly correlated with BAP1 protein nuclear localization.

Conclusion: Next-generation sequencing was applied to a relatively large retrospective series of MPM using formalin-fixed, paraffin-embedded archival material. Our results indicate a complex mutational landscape with a higher number of genetic variations in the p53/DNA repair and phosphatidylinositol 3-kinase pathways, some of them with prognostic value.

In plain English

This retrospective study sequenced tumor DNA from 123 people with stage III or IV malignant pleural mesothelioma. They were diagnosed between 2003 and 2012 at two Italian hospitals and treated with platinum-based plus pemetrexed chemotherapy. The authors tested 50 cancer-related genes plus BAP1 and NF2. The article did not report the patients' asbestos exposure. BAP1 variations clustered in exons 13 and 17, and loss of nuclear BAP1 protein was significantly linked to protein-changing BAP1 variations. A TP53 genotype (Pro/Pro) was linked to earlier disease progression (median 8.1 months, versus 21.5 and 15.6 months for other genotypes), as was an STK11 variant. Patients carrying more of five tested variations progressed sooner and survived for shorter times: median time to progression was 22 months with none and 5 months in the highest group. The authors concluded that the tumors showed a complex mutational pattern, mainly in the p53/DNA repair and PI3K–AKT pathways, and called for prospective validation. They cautioned that links to outcome should be considered of borderline significance. They noted tissue was often unavailable because samples were requested in asbestos compensation cases.

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: Retrospective study using next-generation sequencing of archived tumor tissue, with Sanger sequencing to check selected findings and immunohistochemistry for BAP1 and NF2 proteins
• Who was studied: 123 consecutive malignant pleural mesothelioma cases diagnosed November 2003 to December 2012 at two institutions in Italy (Orbassano, 93; Alessandria, 30). All were stage III (T3) or IV, treated with platinum-based plus pemetrexed chemotherapy, with no surgery or radiation. There were 96 epithelioid, 22 biphasic and 5 sarcomatous tumors; 86 males and 37 females; median age 66.5 years.
• Exposure: Asbestos exposure was not reported. The study examined genetic variations in tumor tissue across 50 cancer-associated genes plus BAP1 and NF2.
• Main results:
  • BAP1 variations were mainly in exon 13 (54 variations in 47 patients, 38%) and exon 17 (44 variations in 31 patients, 25%).
  • BAP1 protein staining was assessed in 116 of 123 cases. 60 (52%) showed nuclear expression, 13 (11%) showed weak cytoplasmic staining only, and 43 (37%) were completely negative in tumor cells.
  • Lack of nuclear BAP1 protein was significantly correlated with nonsynonymous (protein-changing) BAP1 variations at allelic frequency of 10% or 25% (p less than 0.01 for both).
  • NF2 protein was present in the cytoplasm in 107 of 116 cases (92%). It was not correlated with NF2 gene variations or with clinical and pathological characteristics.
  • With sequencing (NGS) data, the TP53 rs1042522 G:G (Pro/Pro) genotype was associated with earlier progression than the C:C and C:G genotypes (median 8.1 vs 21.5 and 15.6 months; p less than 0.01). The link with overall survival was of borderline significance (p = 0.042).
  • In the 60 cases checked by Sanger sequencing, the TP53 association with time to progression remained (p = 0.042), with only a trend for overall survival (p = 0.087).
  • The STK11 intron polymorphism rs2075606 (T>C), found in 43% of samples, was significantly associated with early disease progression (p less than 0.01).
  • The PIK3CA mutation I391M was associated with disease progression after two chemotherapy cycles (p = 0.03). Median time to progression was not significantly different (p = 0.1). 27 of the 31 carriers had progressive disease as best response.
  • In multivariable analysis, STK11 rs2075606 and TP53 G:G were independent predictors of time to progression: STK11 HR 1.78 (95% CI 1.12 to 2.81; p = 0.01) and TP53 HR 3.9 (95% CI 1.54 to 9.79; p less than 0.01).
  • For overall survival, the multivariable results were STK11 HR 1.55 (95% CI 1.04 to 2.33; p = 0.03) and TP53 HR 2.65 (95% CI printed as 0.15 to 6.10; p = 0.02).
  • More of five validated variations (STK11, TP53, PIK3CA, KIT, KDR) went with shorter time to progression and survival (log-rank p = 0.02 and 0.04). Median time to progression was 22 months (none), 10.3 (one), 7.4 (two) and 5 months (highest group). Median survival was 20.8, 19.7, 16.6 and 12.8 months.
• The authors' conclusion: The authors concluded that the tumors showed a complex mutational pattern, mainly in the p53/DNA repair and PI3K–AKT pathways. Some variations, and their accumulation, were associated with early tumor progression. Future studies should prospectively validate their prognostic role.
• Limitations the authors state:
  • Selection bias from tissue availability: tissue blocks were often requested in asbestos workers' compensation litigation, leading to tissue exhaustion.
  • Apart from BAP1 and NF2, genes were tested only for the hotspot mutations included in the commercial panel.
  • Only gene mutations were assessed. Amplifications, large genetic losses and translocations could not be detected, which complicates comparison with other studies.
  • Any association between a gene variation and clinical outcome should be considered of borderline significance.

Topics

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

Medical terms in this study, explained in our Lexicon: Next-Generation Sequencing (NGS), Pleural Mesothelioma, Immunohistochemistry, BAP1, Overall Survival.

Related studies

• The use of a next-generation sequencing-derived machine-learning risk-prediction model (OncoCast-MPM) for malignant pleural mesothelioma: a retrospective study — M.G. Zauderer, A. Martin, et al. (2021)
• Next-generation sequencing informs diagnosis and identifies unexpected therapeutic targets in lung squamous cell carcinomas — J.M. Sands, T. Nguyen, et al. (2020)
• Whole exome and targeted deep sequencing identify genome-wide allelic loss and frequent SETDB1 mutations in malignant pleural mesotheliomas — H.C. Kang, H.K. Kim, et al. (2016)
• Molecular and Histopathological Characterization of the Tumor Immune Microenvironment in Advanced Stage of Malignant Pleural Mesothelioma — N.S. Patil, L. Righi, et al. (2018)
• miR-1254 and miR-574-5p: serum-based microRNA biomarkers for early-stage non-small cell lung cancer — K.M. Foss, C. Sima, et al. (2011)
• Differential expression of extracellular matrix constituents and cell adhesion molecules between malignant pleural mesothelioma and mesothelial hyperplasia — G. Alì, N. Borrelli, et al. (2013)

Browse more research in Journal of Thoracic Oncology, or return to medical research.