Abstract

We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (2%; 4/216) and TRAF7 (2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.

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Acknowledgements

We acknowledge Genentech DNA Sequencing, Oligo and Bioinformatics groups for their help with the project. We also acknowledge the personnel of the tumor bank at the Brigham and Women's Hospital. We thank C.S. Rivers and C.J. Harris for the NGS library support. We thank Z. Zhang, P. George, K.V. Paul, P.M. Haverty, S. Jhunjhunwala, S. Sharma, B. Chow, J. Reeder and S. Lipscomb for the bioinformatics and computational support. This research was supported partly by grants to R.B. from the National Cancer Institute (2R01CA120528), The International Mesothelioma Program at Brigham and Women's Hospital and Genentech, Inc.

Author information

Author notes

    • Raphael Bueno
    • , Eric W Stawiski
    • , Leonard D Goldstein
    • , Steffen Durinck
    • , Assunta De Rienzo
    • , Zora Modrusan
    • , Florian Gnad
    • , Thong T Nguyen
    •  & Bijay S Jaiswal

    These authors contributed equally to this work.

Affiliations

  1. Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Raphael Bueno
    • , Assunta De Rienzo
    • , Daniele Sciaranghella
    • , Nhien Dao
    • , Corinne E Gustafson
    • , Kiara J Munir
    •  & William G Richards
  2. Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.

    • Eric W Stawiski
    • , Leonard D Goldstein
    • , Steffen Durinck
    • , Florian Gnad
    • , Jason A Hackney
    •  & Thomas D Wu
  3. Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA.

    • Eric W Stawiski
    • , Leonard D Goldstein
    • , Steffen Durinck
    • , Zora Modrusan
    • , Thong T Nguyen
    • , Bijay S Jaiswal
    • , Joseph Guillory
    • , Karen Toy
    • , Connie Ha
    • , Ying-Jiun Chen
    • , Jeremy Stinson
    • , Subhra Chaudhuri
    • , Na Zhang
    •  & Somasekar Seshagiri
  4. Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Lucian R Chirieac
  5. Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India.

    • Amitabha Chaudhuri
    •  & Ravi Gupta
  6. Division of Thoracic Surgery, Baylor College of Medicine, Houston, Texas, USA.

    • David J Sugarbaker
  7. Molecular Oncology Department, Genentech, Inc., South San Francisco, California, USA.

    • Frederic J de Sauvage

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Contributions

R.B. and S.S. conceived the study. R.B., E.W.S. and S.S. designed the experiments. E.W.S. oversaw the bioinformatics analysis and performed mutation and pathway analysis. L.D.G. performed splice variant analysis. S.D. performed gene expression and copy number analysis. F.G. performed whole-genome analysis. T.T.N. performed gene fusion analysis and neoantigen prediction. A.D.R., D.S. and N.D. were responsible for the samples and nucleic acid extractions. L.R.C. performed histological analysis. K.J.M. and W.G.R. managed the tissue repository and clinical annotation that supported the study. C.E.G. provided administrative, technical and material support. Z.M. oversaw collection of genomics data. Z.M. and Y.-J.C. performed validation of the fusions. T.D.W. supported gene fusion predictions. K.T. and C.H. prepared the sequencing libraries. B.S.J., S.C. and N.Z. performed biological validation studies. J.A.H. analyzed immune signatures. A.C. and R.G. were responsible for OncoMD. J.G. and J.S. collected sequencing data. D.J.S. and F.J.d.S. provided scientific and technical support. R.B., E.W.S., L.D.G., S.D., Z.M. and S.S. wrote the manuscript, which was reviewed and edited by the other coauthors.

Competing interests

E.W.S., L.D.G., S.D., Z.M., F.G., T.T.N., B.S.J., J.A.H., A.C., R.G., J.G., K.T., C.H., Y.-J.C., J.S., S.C., N.Z., T.D.W., F.J.d.S. and S.S. are employees of Genentech Inc. or MedGenome Labs Pvt. Ltd. E.W.S., S.D., Z.M., F.G., B.J.S., J.A.H., J.G., K.T., C.H., Y.-J.C., J.S., S.C., N.Z., T.D.W., F.J.d.S. and S.S. hold shares in Roche. A.C. and R.G. hold stock options in MedGenome.

Corresponding authors

Correspondence to Raphael Bueno or Eric W Stawiski or Somasekar Seshagiri.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–21

Excel files

  1. 1.

    Supplementary Table 1

    Sample summary and information.

  2. 2.

    Supplementary Table 2

    Differentially expressed genes in sarcomatoid versus epithelioid clusters.

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    Supplementary Table 3

    Sample-level exome coverage statistics.

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    Supplementary Table 4

    Targeted gene panel.

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    Supplementary Table 5

    Somatic mutations and germline variants of interest.

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    Supplementary Table 6

    Mutation consequences.

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    Supplementary Table 7

    Significantly mutated genes.

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    Supplementary Table 8

    Hotspot mutations.

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    Supplementary Table 9

    Meta-analysis–identified hotspot mutations.

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    Supplementary Table 10

    Gene fusions.

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    Supplementary Table 11

    Aberrant splice variants.

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    Supplementary Table 12

    Mutant SF3B1–associated splice variants.

  13. 13.

    Supplementary Table 13

    Tumor-infiltrating immune cell gene list and neoantigen prediction.

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    Supplementary Table 14

    Significantly mutated pathways and pathway gene mutation frequencies.

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DOI

https://doi.org/10.1038/ng.3520

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