BAP1 is a novel regulator of HIF-1α

Our plain-English summary of BAP1 is a novel regulator of HIF-1α, by A. Bononi, Q. Wang, A.A. Zolondick, et al (Proceedings of the National Academy of Sciences of the United States of America, 2023).

The study

• Authors: A. Bononi, Q. Wang, A.A. Zolondick, F. Bai, M. Steele-Tanji, J.S. Suarez, S. Pastorino, A. Sipes, V. Signorato, A. Ferro, F. Novelli, J.H. Kim, M. Minaai, Y. Takinishi, L. Pellegrini, A. Napolitano, R. Xu, C. Farrar, C. Goparaju, C. Bassi, M. Negrini, I. Pagano, G. Sakamoto, G. Gaudino, H.I. Pass, J.N. Onuchic, H. Yang, M. Carbone
• Journal: Proceedings of the National Academy of Sciences of the United States of America
• Published: 2023;120(4):e2217840120
• Cited by: 28 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

BAP1 is a powerful tumor suppressor gene characterized by haplo insufficiency. Individuals carrying germline BAP1 mutations often develop mesothelioma, an aggressive malignancy of the serosal layers covering the lungs, pericardium, and abdominal cavity. Intriguingly, mesotheliomas developing in carriers of germline BAP1 mutations are less aggressive, and these patients have significantly improved survival. We investigated the apparent paradox of a tumor suppressor gene that, when mutated, causes less aggressive mesotheliomas. We discovered that mesothelioma biopsies with biallelic BAP1 mutations showed loss of nuclear HIF-1α staining. We demonstrated that during hypoxia, BAP1 binds, deubiquitylates, and stabilizes HIF-1α, the master regulator of the hypoxia response and tumor cell invasion. Moreover, primary cells from individuals carrying germline BAP1 mutations and primary cells in which BAP1 was silenced using siRNA had reduced HIF-1α protein levels in hypoxia. Computational modeling and co-immunoprecipitation experiments revealed that mutations of BAP1 residues I675, F678, I679, and L691 -encompassing the C-terminal domain-nuclear localization signal- to A, abolished the interaction with HIF-1α. We found that BAP1 binds to the N-terminal region of HIF-1α, where HIF-1α binds DNA and dimerizes with HIF-1β forming the heterodimeric transactivating complex HIF. Our data identify BAP1 as a key positive regulator of HIF-1α in hypoxia. We propose that the significant reduction of HIF-1α activity in mesothelioma cells carrying biallelic BAP1 mutations, accompanied by the significant reduction of HIF-1α activity in hypoxic tissues containing germline BAP1 mutations, contributes to the reduced aggressiveness and improved survival of mesotheliomas developing in carriers of germline BAP1 mutations.

In plain English

This laboratory study tested whether BAP1 regulates HIF-1α, a hypoxia-response factor, in mesothelioma. Of 49 mesothelioma biopsies from the National Mesothelioma Virtual Bank, 14 were BAP1 wild-type and 35 mutated; HIF-1α nuclear staining was present in 12 (86%) wild-type biopsies and absent in 26 (74%) mutated biopsies (chi-squared(1) = 14.7, P = 0.0001). Silencing BAP1 with siRNA reduced HIF-1α protein in primary human mesothelial cells held at 1% oxygen for 12 hours; under the same conditions, fibroblasts from six germline BAP1 mutation carriers in two families had significantly less HIF-1α protein than six age- and sex-matched wild-type relatives, with no significant changes detected in HIF1A messenger RNA. Co-immunoprecipitation, computational modelling and in vitro assays indicated that BAP1 binds the N-terminal region of HIF-1α and deubiquitylates it; mutating BAP1 residues I675, F678, I679 and L691 to alanine abolished binding. As a hypothesis, the authors proposed that reduced HIF-1α activity, from biallelic BAP1 mutations in tumour cells plus heterozygous mutations in surrounding cells, may contribute in part to the improved survival of carriers of germline BAP1 mutations with mesothelioma.

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 study combining immunohistochemistry of human mesothelioma biopsies, experiments in primary human cells and transfected HEK-293 cells, biochemical binding and deubiquitylation assays, and computational structural modelling
• Who was studied: 49 human mesothelioma biopsies from the National Mesothelioma Virtual Bank, plus two biopsies from patients with germline BAP1 mutations; primary human mesothelial cells; skin fibroblasts from 6 germline BAP1 mutation carriers and 6 age- and sex-matched wild-type relatives from two families (Wisconsin and Louisiana); HEK-293 cells
• Exposure: Not an asbestos exposure study: the variable studied was BAP1 status (germline heterozygous mutation, biallelic tumour mutation, or siRNA silencing) together with hypoxia (1% or 0.1% oxygen); the article states sporadic mesotheliomas are mostly caused by asbestos exposure
• Main results:
  • Among the 49 mesothelioma biopsies, HIF-1α nuclear staining was present in 12 (86%) of the 14 BAP1 wild-type biopsies and absent in 26 (74%) of the 35 BAP1-mutated biopsies
  • Primary human mesothelial cells transfected with siRNA against BAP1 had significantly less HIF-1α protein than scrambled-siRNA controls after 12 hours in 1% oxygen
  • When incubated in 1% oxygen for 12 hours, fibroblasts from the six carriers of germline BAP1 mutations had significantly less HIF-1α protein than matched wild-type family members
  • In time-course experiments, no significant changes were detected in HIF1A mRNA levels in the carrier fibroblasts compared with wild-type controls
  • BAP1 bound the N-terminal region of HIF-1α; the HIF-1α fragment lacking residues 1 to 73 did not bind BAP1
  • Mutating BAP1 residues I675, F678, I679 and L691 to alanine abolished binding to HIF-1α, while single point mutations only reduced it
  • In HEK-293 cells, overexpressed BAP1 reduced ubiquitylation of Flag-HIF-1α, whereas the catalytically inactive BAP1(C91S) did not
  • BAP1 also co-immunoprecipitated HIF-1β, binding its N-terminal DNA-binding and dimerization region; binding to both HIF-1α and HIF-1β persisted after benzonase degradation of DNA
• The authors' conclusion: The authors concluded that BAP1 deubiquitylates and stabilizes HIF-1α in hypoxia, so BAP1 mutations reduce HIF-1α protein, and they proposed this may contribute in part to the reduced aggressiveness and improved prognosis of mesothelioma in carriers of germline BAP1 mutations, through biallelic mutations in tumour cells combined with heterozygous mutations in the tumour microenvironment
• Limitations the authors state:
  • The authors noted that immunohistochemistry cannot precisely quantify protein expression and that the biopsy findings need validation by Western blot of frozen biopsies from carriers of germline BAP1 mutations, which were not available to them
  • Only two mesothelioma biopsies from patients carrying germline BAP1 mutations were available for staining
  • The authors stated that their findings may not apply to cancers in which VHL or other HIF-1α-suppressing genes are also mutated, and that further studies in renal cell carcinoma and uveal melanoma are necessary
  • The authors stated that future studies are needed to determine whether UCHL1 and BAP1 interact in regulating HIF-1α and whether effects are cell-type specific

Topics

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

Medical terms in this study, explained in our Lexicon: BAP1, Tumor Suppressor Gene, BAP1 Tumor Predisposition Syndrome, Mesothelioma, Pericardium, Hypoxia.

Related studies

• BAP1 forms a trimer with HMGB1 and HDAC1 that modulates gene × environment interaction with asbestos — F. Novelli, A. Bononi, et al. (2021)
• Germline BAP1 mutations induce a Warburg effect — A. Bononi, H. Yang, et al. (2017)
• BAP1 regulates IP3R3-mediated Ca2+ flux to mitochondria suppressing cell transformation — A. Bononi, C. Giorgi, et al. (2017)
• Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling — F. Novelli, Y. Yoshikawa, et al. (2024)
• Heterozygous germline BLM mutations increase susceptibility to asbestos and mesothelioma — A. Bononi, K. Goto, et al. (2020)
• Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s — M. Carbone, E.G. Flores, et al. (2015)

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