A Tumor-Specific Neo-Antigen Caused by a Frameshift Mutation in BAP1 Is a Potential Personalized Biomarker in Malignant Peritoneal Mesothelioma

Our plain-English summary of A Tumor-Specific Neo-Antigen Caused by a Frameshift Mutation in BAP1 Is a Potential Personalized Biomarker in Malignant Peritoneal Mesothelioma, by J. Lai, Z. Zhou, X.J. Tang, et al (International Journal of Molecular Sciences, 2016).

The study

• Authors: J. Lai, Z. Zhou, X.J. Tang, Z.B. Gao, J. Zhou, S.Q. Chen
• Journal: International Journal of Molecular Sciences
• Published: 2016;17(5)
• Type of article: Case report
• Cited by: 18 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Malignant peritoneal mesothelioma (MPM) is an aggressive rare malignancy associated with asbestos exposure. A better understanding of the molecular pathogenesis of MPM will help develop a targeted therapy strategy. Oncogene targeted depth sequencing was performed on a tumor sample and paired peripheral blood DNA from a patient with malignant mesothelioma of the peritoneum. Four somatic base-substitutions in NOTCH2, NSD1, PDE4DIP, and ATP10B and 1 insert frameshift mutation in BAP1 were validated by the Sanger method at the transcriptional level. A 13-amino acids neo-peptide of the truncated Bap1 protein, which was produced as a result of this novel frameshift mutation, was predicted to be presented by this patient's HLA-B protein. The polyclonal antibody of the synthesized 13-mer neo-peptide was produced in rabbits. Western blotting results showed a good antibody-neoantigen specificity, and Immunohistochemistry (IHC) staining with the antibody of the neo-peptide clearly differentiated neoplastic cells from normal cells. A search of the Catalogue of Somatic Mutations in Cancer (COSMIC) database also revealed that 53.2% of mutations in BAP1 were frameshift indels with neo-peptide formation. An identified tumor-specific neo-antigen could be the potential molecular biomarker for personalized diagnosis to precisely subtype rare malignancies such as MPM.

In plain English

This laboratory study examined the tumor of one patient, a 68-year-old woman with a history of asbestos exposure and malignant peritoneal mesothelioma (mesothelioma of the abdominal lining). The authors sequenced 725 cancer-related genes in her tumor and her blood DNA. Five tumor-only mutations were confirmed, in NOTCH2, PDE4DIP, BAP1, ATP10B and NSD1. The BAP1 change, a 4-base insertion, shortened the Bap1 protein from 729 to 536 amino acids, adding a new 13-amino-acid tail matching no human protein in a database search. Computer prediction suggested that part of this tail could bind the patient's HLA-B immune molecule. A rabbit antibody against this fragment detected a shortened protein in tumor but not nearby tissue, and stained tumor cells intensely. COSMIC, a mutation database, had no BAP1 data for its 10 peritoneal samples; among pleural samples, the authors reported 47 amino-acid-changing BAP1 mutations, 53.2% of them small insertions and deletions. The authors concluded that such fragments could be ideal diagnostic biomarkers. They noted they had not shown the fragment on the cell surface and lacked a suitable cell model to confirm it.

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: Single-patient laboratory study: targeted gene sequencing of tumor and blood, computer prediction of immune binding, antibody production in rabbits, western blotting and immunohistochemistry, plus a search of the COSMIC mutation database
• Who was studied: One 68-year-old woman with a history of asbestos exposure, diagnosed with epithelial type peritoneal malignant mesothelioma. Ethical approval came from Zhejiang University School of Medicine, China. Dates are not given.
• Exposure: A history of asbestos exposure is stated for the patient. No fiber type, job, product or dose is given. The study itself examined genetic mutations in the tumor, not asbestos exposure.
• Main results:
  • In this patient's tumor, 5 somatic mutations were confirmed by Sanger sequencing, in NOTCH2, PDE4DIP, BAP1, ATP10B and NSD1.
  • The 4-base insertion in BAP1 produced a mutated Bap1 protein 536 amino acids long, compared with 729 amino acids for the normal protein.
  • The new 13-amino-acid tail of the mutated Bap1 protein was not similar to any human protein in a BLAST search.
  • Of 7 mutated peptides, 3 were predicted to bind strongly to the patient's HLA molecules. One was the 8-amino-acid LPHLQGAF fragment of mutated Bap1, with a predicted IC50 of 17.46 nM.
  • Of the three peptides injected into rabbits, only the Bap1 fragment provoked a strong immune response.
  • On western blotting, the antibody detected an estimated 60-kDa protein in tumor tissue. The same protein was not found in adjacent tissue.
  • On immunohistochemistry with the antibody, the mesothelial tumor cells were intensely stained.
  • In COSMIC version 76, the 10 peritoneal tissue samples had no BAP1 mutation information. In pleural tissue samples, the BAP1 mutation rate was 27.22% (89 of 327 tested).
  • Reported immediately after the pleural-sample figures, 47 BAP1 mutations were amino-acid-changing: 46.8% were missense mutations and 53.2% were small insertions and deletions. These figures do not come from peritoneal mesothelioma samples.
  • Across all BAP1 variants in COSMIC, regardless of tumor type, 134 of 532 (25.2%) were frameshift mutations.
• The authors' conclusion: The authors concluded that frameshift mutations in BAP1 are common events in malignant mesothelioma and that the resulting neo-antigens could be ideal biomarkers for diagnosis.
• Limitations the authors state:
  • Immunohistochemistry did not show that the neo-antigen is located on the cell surface.
  • Confirming the fragment as a true target is limited by the lack of a suitable cell model with the matching HLA genotype.
  • Sanger sequencing has limited sensitivity in mixed tumor DNA, so some mutations could not be confirmed.
  • Coverage depth was poor at two of the positions that could not be confirmed (MN1 and PRG4).

Topics

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

Medical terms in this study, explained in our Lexicon: BAP1, Biomarker, Peritoneal Mesothelioma, Asbestos Exposure, Targeted Therapy, Malignant Mesothelioma, Peritoneum, Immunohistochemistry.

Related studies

• BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas — N. Leblay, F. Leprêtre, et al. (2017)
• Loss of BAP1 expression is very rare in peritoneal and gynecologic serous adenocarcinomas and can be useful in the differential diagnosis with abdominal mesothelioma — J. Andrici, J. Jung, et al. (2016)
• Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma — S. Brich, F. Bozzi, et al. (2020)
• BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma — H. Alakus, S.E. Yost, et al. (2015)
• Detecting germline BAP1 mutations in patients with peritoneal mesothelioma: benefits to patient and family members — M. Kittaneh, C. Berkelhammer (2018)
• Molecular Analysis of a Patient With Neurofibromatosis 2 (NF2) and Peritoneal Malignant Mesothelioma — C. Glass, L.M. Sholl, et al. (2020)

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