Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer

Our plain-English summary of Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer, by T. Hirosawa, M. Ishida, K. Ishii, et al (PloS One, 2018).

The study

• Authors: T. Hirosawa, M. Ishida, K. Ishii, K. Kanehara, K. Kudo, S. Ohnuma, T. Kamei, F. Motoi, T. Naitoh, F.M. Selaru, M. Unno
• Journal: PloS One
• Published: 2018;13(11):e0206643
• Cited by: 17 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Background: BRCA-1 associated protein (BAP1) is a de-ubiquitinating enzyme that regulates gene expression. Recently, the BAP1 mutation and its involvement in cancer survival have been reported in a range of tumor types, including uveal melanoma, mesothelioma, renal cancers, and biliary tract cancers. However, the frequency of BAP1 mutation and down-regulation varies among tumor types, and little is known about the function of BAP1 silencing in cancer cells. Gallbladder carcinoma (GBC) is a type of biliary tract cancer with a poor prognosis. Few mutational studies have investigated the role of BAP1 in GBC, and no functional study in vitro-, or clinical studies about cancer survival have been done.

Methods: GBC cells were studied by following the small interfering RNA mediated silencing of BAP1 with regard to proliferation, migration, invasion, and drug sensitivity. We carried out genomic, epigenomic and immunohistochemical analyses to detect somatic BAP1 alterations in 47 GBC patients undergoing surgical resection.

Results: BAP1 depletion resulted in increased migration and invasion, but not proliferation, and also resulted in decreased sensitivity to bortezomib, a proteasome inhibitor. Suppressed expression of BAP1 occurred in 22 GBC cases (46.8%) and showed a strong trend toward a worse median survival time of 13.3 months (95% CI, 17.6-62.6) (p = 0.0034). Sanger sequencing revealed a loss-of-function mutation of BAP1 in 11 out of these 22 GBC cases (50%) with low BAP1 expression, whereas 2 out of 25 GBC cases (8%) were detected in cases with high BAP1 expression. Partial changes in methylation were observed in 6 out of 47 cases, but methylation did not show a strong relationship to BAP1 expression or to the prognosis.

Conclusion: Our findings showed that genetic mutations are involved in BAP1 down-regulation, leading to promotion of the invasive character of cancer cells and poor prognosis in GBC.

In plain English

This study concerns gallbladder cancer. It examined no asbestos exposure. It focused on the BAP1 gene. When the authors lowered BAP1 in a gallbladder cancer cell line (G-415), cell growth did not change, but the cells migrated and invaded more and became less sensitive to the drug bortezomib. They also examined tumor tissue from 47 patients operated on at Tohoku University Hospital, Japan, between 2005 and 2016, and 22 tumors showed low BAP1. Among 41 patients included in the survival analysis, survival was poorer with low BAP1. Median survival was 13.3 months in that group and could not be calculated for the high-BAP1 group. Mutations altering the BAP1 protein were found in 11 of 22 low-BAP1 tumors (50%) and 2 of 25 high-BAP1 tumors (8%). Partial methylation, seen in 6 of 47 tumors, was not significantly related to BAP1 levels. The authors concluded that BAP1 loss, mainly from mutations, promotes invasiveness and correlates with poor prognosis. They noted that they used only one cell line and did not remove sequencing artifacts caused by preserved tissue.

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 (in vitro) cell-line experiments combined with an analysis of surgically removed tumor specimens and patient survival
• Who was studied: Two human gallbladder cancer cell lines (G-415 and OCUG-1), plus preserved tumor specimens from 47 patients who had surgery for gallbladder cancer at Tohoku University Hospital, Japan, between January 2005 and December 2016
• Exposure: No asbestos or fiber exposure was studied. The factor examined was BAP1: it was experimentally reduced in cells using small interfering RNA, and tumors were classified by BAP1 staining, mutation and methylation.
• Main results:
  • In the G-415 cell line, reducing BAP1 did not significantly change cell proliferation
  • Migration (scratch assay) changed 2.14-fold with siRNA1 and 2.27-fold with siRNA2 compared with control, both p less than 0.05
  • Invasion increased 2.16-fold with siRNA1 (p less than 0.05) and 1.85-fold with siRNA2 (p = 0.08) compared with control
  • BAP1-reduced cells were significantly less sensitive to bortezomib. Sensitivity to gemcitabine, cisplatin, fluorouracil, sodium valproate and 5-azacytidine did not change.
  • Of 47 tumors, 25 had high and 22 had low BAP1 staining
  • Among 41 patients analyzed, survival was significantly poorer in the low-BAP1 group (p less than 0.01). Median survival was 13.3 months for low-BAP1 patients and could not be calculated for the high-BAP1 group.
  • In the 28 patients with stage III or IV disease, median survival was 11.7 months for low-BAP1 patients and 85.8 months for high-BAP1 patients
  • In multivariate analysis, BAP1 expression was a significant prognostic factor (P less than 0.05), along with lymph node involvement, distant spread and residual disease
  • Protein-altering BAP1 mutations were found in 11 of 22 low-BAP1 tumors (50%) versus 2 of 25 high-BAP1 tumors (8%), p = 0.003
  • Homozygous deletion of BAP1 was suspected in 3 low-BAP1 tumors
  • Partial methylation was found in 6 of 47 tumors and was not significantly related to BAP1 expression (p = 0.40) or prognosis (P = 0.71)
• The authors' conclusion: The authors concluded that reduced BAP1, mainly due to genetic mutations, promotes migration and invasion of gallbladder cancer cells and correlates with poor prognosis
• Limitations the authors state:
  • The functional experiments used only one gallbladder cancer cell line
  • The authors did not apply a method to remove artificial sequence changes caused by formalin fixation of tissue
  • Mutations in non-coding (intron) regions and other epigenetic mechanisms were not examined
  • DNA sequencing may have missed a number of gene deletions

Topics

Medical terms in this study, explained in our Lexicon: BAP1, Mesothelioma, Carcinoma, Prognosis, Surgical Resection, Median Overall Survival.

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