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Zheng-Lin B, Rainone M, Varghese AM, Yu KH, Park W, Berger M, Mehine M, Chou J, Capanu M, Mandelker D, Stadler ZK, Birsoy O, Jairam S, Yang C, Li Y, Wong D, Benhamida JK, Ladanyi M, Zhang L, O’Reilly EM. Methylation Analyses Reveal Promoter Hypermethylation as a Rare Cause of "Second Hit" in Germline BRCA1-Associated Pancreatic Ductal Adenocarcinoma. Mol Diagn Ther 2022; 26:645-653. [PMID: 36178671 PMCID: PMC9626413 DOI: 10.1007/s40291-022-00614-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is characterized by the occurrence of pathogenic variants in BRCA1/2 in 5-6% of patients. Biallelic loss of BRCA1/2 enriches for response to platinum agents and poly (ADP-ribose) polymerase 1 inhibitors. There is a dearth of evidence on the mechanism of inactivation of the wild-type BRCA1 allele in PDAC tumors with a germline BRCA1 (gBRCA1) pathogenic or likely pathogenic variant (P/LPV). Herein, we examine promotor hypermethylation as a "second hit" mechanism in patients with gBRCA1-PDAC. METHODS We evaluated patients with PDAC who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) somatic and germline testing from an institutional database. DNA isolated from tumor tissue and matched normal peripheral blood were sequenced by MSK-IMPACT. In patients with gBRCA1-PDAC, we examined the somatic BRCA1 mutation status and promotor methylation status of the tumor BRCA1 allele via a methylation array analysis. In patients with sufficient remaining DNA, a second methylation analysis by pyrosequencing was performed. RESULTS Of 1012 patients with PDAC, 19 (1.9%) were identified to harbor a gBRCA1 P/LPV. Fifteen patients underwent a methylation array and the mean percentage of BRCA1 promotor methylation was 3.62%. In seven patients in whom sufficient DNA was available, subsequent pyrosequencing confirmed an unmethylated BRCA1 promotor. Loss of heterozygosity was detected in 12 of 19 (63%, 95% confidence interval 38-84) patients, demonstrating loss of heterozygosity is the major molecular mechanism of BRCA1 inactivation in PDAC. Two (10.5%) cases had a somatic BRCA1 mutation. CONCLUSIONS In patients with gBRCA1-P/LPV-PDAC, loss of heterozygosity is the main inactivating mechanism of the wild-type BRCA1 allele in the tumor, and methylation of the BRCA1 promoter is a distinctly uncommon occurrence.
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Affiliation(s)
- Binbin Zheng-Lin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Michael Rainone
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA USA
| | - Anna M. Varghese
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Office 1021, New York, NY 10065 USA
| | - Kenneth H. Yu
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Office 1021, New York, NY 10065 USA
| | - Wungki Park
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Office 1021, New York, NY 10065 USA ,Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY USA ,David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Michael Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Miika Mehine
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Joanne Chou
- Department of Epidemiology and Biostatistics, Weill Cornell Medical College, New York, NY USA
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Weill Cornell Medical College, New York, NY USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Zsofia K. Stadler
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Office 1021, New York, NY 10065 USA ,Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY USA ,David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ozge Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Sowmya Jairam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Donna Wong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles (UCLA), 10833 Le Conte Ave, Los Angeles, CA 90095 USA
| | - Eileen M. O’Reilly
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Office 1021, New York, NY 10065 USA ,Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY USA ,David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY USA
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