Abstract

BRCA1-associated protein 1 (BAP1) is a potent tumour suppressor gene that modulates environmental carcinogenesis1,2,3. All carriers of inherited heterozygous germline BAP1-inactivating mutations (BAP1+/−) developed one and often several BAP1−/− malignancies in their lifetime4, mostly malignant mesothelioma, uveal melanoma2,5, and so on6,7,8,9,10. Moreover, BAP1-acquired biallelic mutations are frequent in human cancers8,11,12,13,14. BAP1 tumour suppressor activity has been attributed to its nuclear localization, where it helps to maintain genome integrity15,16,17. The possible activity of BAP1 in the cytoplasm is unknown. Cells with reduced levels of BAP1 exhibit chromosomal abnormalities and decreased DNA repair by homologous recombination18, indicating that BAP1 dosage is critical. Cells with extensive DNA damage should die and not grow into malignancies. Here we discover that BAP1 localizes at the endoplasmic reticulum. Here, it binds, deubiquitylates, and stabilizes type 3 inositol-1,4,5-trisphosphate receptor (IP3R3), modulating calcium (Ca2+) release from the endoplasmic reticulum into the cytosol and mitochondria, promoting apoptosis. Reduced levels of BAP1 in BAP1+/− carriers cause reduction both of IP3R3 levels and of Ca2+ flux, preventing BAP1+/− cells that accumulate DNA damage from executing apoptosis. A higher fraction of cells exposed to either ionizing or ultraviolet radiation, or to asbestos, survive genotoxic stress, resulting in a higher rate of cellular transformation. We propose that the high incidence of cancers in BAP1+/− carriers results from the combined reduced nuclear and cytoplasmic activities of BAP1. Our data provide a mechanistic rationale for the powerful ability of BAP1 to regulate gene–environment interaction in human carcinogenesis.

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Acknowledgements

We are grateful to the members of the L and W families who donated their cells to our research. We acknowledge K. Dixon for advice on ultraviolet radiation studies, M. Pagano for advice on ubiquitylation assays, H. Yu for advice on DNA repair studies, I. Pagano for review of all statistical analyses, and G. Khan for technical support. This work was supported by grants National Cancer Institute (NCI) R01 CA198138 to M.C.; by NCI R01 CA160715, DOD CA120355 to H.Y.; by the University of Hawai’i Foundation, which received unrestricted donations to support mesothelioma research from Honeywell International, to M.C.; by The Riviera United 4-a Cure to M.C. and H.Y.; and by the Italian Association for Cancer Research (AIRC) (IG-18624, MFAG13521) and the Italian Ministry of Health to P.P. and C.G. P.P. thanks C. degli Scrovegni for support.

Author information

Affiliations

  1. University of Hawaii Cancer Center, University of Hawaii, Honolulu, Hawaii 96813 USA

    • Angela Bononi
    • , David Larson
    • , Kaitlyn Verbruggen
    • , Mika Tanji
    • , Laura Pellegrini
    • , Valentina Signorato
    • , Federica Olivetto
    • , Sandra Pastorino
    • , Masaki Nasu
    • , Andrea Napolitano
    • , Giovanni Gaudino
    • , Paul Morris
    • , Greg Sakamoto
    • , Haining Yang
    •  & Michele Carbone
  2. Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, 44121 Italy

    • Carlotta Giorgi
    • , Simone Patergnani
    • , Valentina Signorato
    • , Federica Olivetto
    • , Alberto Danese
    •  & Paolo Pinton
  3. Department of Dermatology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15213 USA

    • Laura K. Ferris
  4. Experimental Imaging Center, San Raffaele Scientific Institute Milano, 20132 Italy

    • Andrea Raimondi
    •  & Carlo Tacchetti
  5. Department of Experimental Medicine, University of Genova, Genova, 16132 Italy

    • Carlo Tacchetti
  6. Cancer Center, New York University, New York, New York 10016, USA

    • Shafi Kuchay
    •  & Harvey I. Pass
  7. Maisonneuve-Rosemont Hospital Research Center, Department of Medicine, University of Montréal, Montréal, Quebec H1T 2M4, Canada

    • El Bachir Affar

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Contributions

M.C. conceived the study. A.B. led the experiments and prepared the figures. M.C., S.Pas. and H.Y. built pedigrees. M.N. and M.T. genotyped patients and controls. P.M., G.S. and L.K.F. performed skin biopsies. A.B., C.G. and K.V. established fibroblast cell cultures. A.B., C.G., S.Pat. and V.S. independently conducted and reproduced cell death assays. D.L. performed flow cytometry experiments. A.R. and C.T. performed electron microscopy studies. A.B. and C.G. performed subcellular fractionation studies. A.B. performed western blot, co-immunoprecipitation, aequorin-based Ca2+ measurements, and in vitro cell transformation assays. C.G. and S.Pat. performed single-cell Ca2+ measurements. C.G., S.Pat. and F.O. performed immunofluorescence studies. A.D. performed proximity ligation assay studies. A.B., with the help of S.K., performed ubiquitylation assays. L.P. performed qRT–PCR studies. A.B., C.G. and S.Pat., with the help of E.B.A., performed ionizing radiation and ultraviolet radiation studies. A.N., S.Pas., G.G. and H.I.P. discussed the results. M.C., H.Y. and P.P. coordinated the study and oversaw the results. A.B. and M.C. wrote the manuscript with help from co-authors.

Competing interests

M.C. has pending patent applications on BAP1. M.C. provides consultation for mesothelioma diagnosis. The authors have no other potential competing financial interests.

Corresponding authors

Correspondence to Haining Yang or Paolo Pinton or Michele Carbone.

Reviewer Information Nature thanks M. Campanella, N. Hayward, K. D. Wilkinson and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

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  1. 1.

    Supplementary Figures

    This file contains Supplementary Figure 1 (Pedigrees of W and L family members), Supplementary Figure 2 (Uncropped scans with size marker indications) and Supplementary Figure 3 (Uncropped EM images).

  2. 2.

    Supplementary Tables

    This file contains Supplementary Tables 1 and 2.

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https://doi.org/10.1038/nature22798

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