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Silva FFVE, Ballini A, Caponio VCA, Pérez-Sayáns M, Cortés MG, Rojo-Álvarez LI, García-García A, Suaréz-Peñaranda JM, Di Domenico M, Padín-Iruegas ME. Insights into MLH1 Methylation in Endometrial Adenocarcinoma through Pyrosequencing Analysis: A Retrospective Observational Study. Cancers (Basel) 2024; 16:2119. [PMID: 38893238 PMCID: PMC11171209 DOI: 10.3390/cancers16112119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Background: In cancer care, the MLH1 gene is crucial for DNA mismatch repair (MMR), serving as a vital tumor suppressor. Evaluating MLH1 protein expression status, followed by analysis of MLH1 promoter methylation, has become a key diagnostic and prognostic approach. Our study investigates the complex link between MLH1 methylation and prognosis in endometrial adenocarcinoma (EA) patients. Methodology: MLH1 methylation status was accessed by a Pyrosequencing (PSQ) assay. Qualitative positivity for methylation was established if it exceeded the 11% cut-off; as well, a quantitative methylation analysis was conducted to establish correlations with clinicopathological data, relapse-free survival, and disease-free survival. Results: Our study revealed that 33.3% of patients without MLH1 methylation experienced relapses, surpassing the 23.3% in patients with methylation. Furthermore, 16.7% of patients without methylation succumbed to death, with a slightly higher rate of 17.6% in methylated patients. Qualitative comparisons highlighted that the mean methylation rate in patients experiencing relapse was 35.8%, whereas in those without relapse, it was 42.2%. This pattern persisted in disease-specific survival (DSS), where deceased patients exhibited a higher mean methylation level of 49.1% compared to living patients with 38.8%. Conclusions: Our findings emphasize the efficacy of PSQ for evaluating MLH1 methylation. While unmethylation appears to be associated with a higher relapse rate, the survival rate does not seem to be influenced by methylation. Quantitative percentages suggest that elevated MLH1 methylation is linked to relapse and mortality, though a study with a larger sample size would be essential for statistically significant results.
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Affiliation(s)
- Fábio França Vieira e Silva
- Department of Medicine and Dentistry, University of Santiago de Compostela, San Francisco Street, s/n, 15782 Santiago de Compostela, Spain; (F.F.V.e.S.); (M.P.-S.); (A.G.-G.); (J.M.S.-P.)
- Health Research Institute of Santiago de Compostela (FIDIS), Santiago de Compostela University Clinical Hospital, University of Santiago de Compostela, Choupana Street, s/n, 15706 Santiago de Compostela, Spain; (M.G.C.); (L.I.R.-Á.); (M.E.P.-I.)
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Via L. De Crecchio, 7, 80138 Naples, Italy;
| | - Andrea Ballini
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Via L. De Crecchio, 7, 80138 Naples, Italy;
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli, 48, 71122, Foggia, Italy;
| | - Vito Carlo Alberto Caponio
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli, 48, 71122, Foggia, Italy;
| | - Mario Pérez-Sayáns
- Department of Medicine and Dentistry, University of Santiago de Compostela, San Francisco Street, s/n, 15782 Santiago de Compostela, Spain; (F.F.V.e.S.); (M.P.-S.); (A.G.-G.); (J.M.S.-P.)
- Health Research Institute of Santiago de Compostela (FIDIS), Santiago de Compostela University Clinical Hospital, University of Santiago de Compostela, Choupana Street, s/n, 15706 Santiago de Compostela, Spain; (M.G.C.); (L.I.R.-Á.); (M.E.P.-I.)
| | - Marina Gándara Cortés
- Health Research Institute of Santiago de Compostela (FIDIS), Santiago de Compostela University Clinical Hospital, University of Santiago de Compostela, Choupana Street, s/n, 15706 Santiago de Compostela, Spain; (M.G.C.); (L.I.R.-Á.); (M.E.P.-I.)
| | - Laura Isabel Rojo-Álvarez
- Health Research Institute of Santiago de Compostela (FIDIS), Santiago de Compostela University Clinical Hospital, University of Santiago de Compostela, Choupana Street, s/n, 15706 Santiago de Compostela, Spain; (M.G.C.); (L.I.R.-Á.); (M.E.P.-I.)
| | - Abel García-García
- Department of Medicine and Dentistry, University of Santiago de Compostela, San Francisco Street, s/n, 15782 Santiago de Compostela, Spain; (F.F.V.e.S.); (M.P.-S.); (A.G.-G.); (J.M.S.-P.)
- Health Research Institute of Santiago de Compostela (FIDIS), Santiago de Compostela University Clinical Hospital, University of Santiago de Compostela, Choupana Street, s/n, 15706 Santiago de Compostela, Spain; (M.G.C.); (L.I.R.-Á.); (M.E.P.-I.)
| | - José Manuel Suaréz-Peñaranda
- Department of Medicine and Dentistry, University of Santiago de Compostela, San Francisco Street, s/n, 15782 Santiago de Compostela, Spain; (F.F.V.e.S.); (M.P.-S.); (A.G.-G.); (J.M.S.-P.)
- Health Research Institute of Santiago de Compostela (FIDIS), Santiago de Compostela University Clinical Hospital, University of Santiago de Compostela, Choupana Street, s/n, 15706 Santiago de Compostela, Spain; (M.G.C.); (L.I.R.-Á.); (M.E.P.-I.)
| | - Marina Di Domenico
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Via L. De Crecchio, 7, 80138 Naples, Italy;
| | - María Elena Padín-Iruegas
- Health Research Institute of Santiago de Compostela (FIDIS), Santiago de Compostela University Clinical Hospital, University of Santiago de Compostela, Choupana Street, s/n, 15706 Santiago de Compostela, Spain; (M.G.C.); (L.I.R.-Á.); (M.E.P.-I.)
- Human Anatomy and Embriology Area, Departament of Funcional Biology and Health Sciences, University of Vigo, Lagoas-Marcosende, s/n, 36310 Vigo, Spain
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2
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Ibrahim MB, Flanagan J, Ibrahim T, Rouleau E. Unraveling noncoding DNA variants and epimutations: a paradigm shift in hereditary cancer research. Future Oncol 2024; 20:1289-1298. [PMID: 38722139 PMCID: PMC11318707 DOI: 10.2217/fon-2023-0665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/11/2024] [Indexed: 06/12/2024] Open
Abstract
Exhaustive efforts have been dedicated to uncovering genomic aberrations linked to cancer susceptibility. Noncoding sequence variants and epigenetic alterations significantly influence gene regulation and could contribute to cancer development. However, exploring noncoding regions in hereditary cancer susceptibility demands cutting-edge methodologies for functionally characterizing genomic discoveries. Additionally, comprehending the impact on cancer development of variants in noncoding DNA and the epigenome necessitates integrating diverse data through bioinformatic analyses. As novel technologies and analytical methods continue to advance, this realm of research is rapidly gaining traction. Within this mini-review, we delve into future research domains concerning aberrations in noncoding DNA regions, such as pseudoexons, promoter variants and cis-epimutations.
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Affiliation(s)
- Maria Baz Ibrahim
- Department of Oncogenetics & Tumor Biology, Paul Brousse Hospital, Villejuif, France
| | - James Flanagan
- Department of Surgery & Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Tony Ibrahim
- International Department of Medical Oncology, Gustave Roussy, 94805, Villejuif, France
| | - Etienne Rouleau
- Department of Biology & Pathology-Cancer Genetics Laboratory, Gustave Roussy, 94805, Villejuif, France
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3
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Schwartz M, Ibadioune S, Vacher S, Villy MC, Trabelsi-Grati O, Le Gall J, Caputo SM, Delhomelle H, Warcoin M, Moncoutier V, Bourneix C, Boutry-Kryza N, De Pauw A, Stern MH, Buecher B, Mouret-Fourme E, Colas C, Stoppa-Lyonnet D, Masliah-Planchon J, Golmard L, Bieche I. Male breast cancer: No evidence for mosaic BRCA1 promoter methylation involvement. Breast 2024; 73:103620. [PMID: 38096711 PMCID: PMC10761895 DOI: 10.1016/j.breast.2023.103620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
Breast cancers (BC) are rare in men and are often caused by constitutional predisposing factors. In women, mosaic BRCA1 promoter methylations (MBPM) are frequent events, detected in 4-8% of healthy subjects. This constitutional epimutation increases risk of early-onset and triple-negative BC. However, the role of MBPM in male BC predisposition has never been assessed. We screened 40 blood samples from men affected by BC, and performed extensive tumour analysis on MBPM-positive patients. We detected two patients carrying MBPM. Surprisingly, tumour analysis revealed that neither of these two male BCs were caused by the constitutional BRCA1 epimutations carried by the patients.
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Affiliation(s)
- Mathias Schwartz
- Department of genetics, Curie Institute, Paris, France; UMR3244, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France.
| | - Sabrina Ibadioune
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Sophie Vacher
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Marie-Charlotte Villy
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France
| | - Olfa Trabelsi-Grati
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Jessica Le Gall
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Sandrine M Caputo
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Hélène Delhomelle
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Mathilde Warcoin
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Virginie Moncoutier
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Christine Bourneix
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | | | - Antoine De Pauw
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Marc-Henri Stern
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France; DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Paris, France
| | - Bruno Buecher
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Emmanuelle Mouret-Fourme
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Chrystelle Colas
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France; DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Paris, France
| | - Julien Masliah-Planchon
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Lisa Golmard
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Ivan Bieche
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France
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4
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Nikolaienko O, Eikesdal HP, Ognedal E, Gilje B, Lundgren S, Blix ES, Espelid H, Geisler J, Geisler S, Janssen EAM, Yndestad S, Minsaas L, Leirvaag B, Lillestøl R, Knappskog S, Lønning PE. Prenatal BRCA1 epimutations contribute significantly to triple-negative breast cancer development. Genome Med 2023; 15:104. [PMID: 38053165 PMCID: PMC10698991 DOI: 10.1186/s13073-023-01262-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Normal cell BRCA1 epimutations have been associated with increased risk of triple-negative breast cancer (TNBC). However, the fraction of TNBCs that may have BRCA1 epimutations as their underlying cause is unknown. Neither are the time of occurrence and the potential inheritance patterns of BRCA1 epimutations established. METHODS To address these questions, we analyzed BRCA1 methylation status in breast cancer tissue and matched white blood cells (WBC) from 408 patients with 411 primary breast cancers, including 66 TNBCs, applying a highly sensitive sequencing assay, allowing allele-resolved methylation assessment. Furthermore, to assess the time of origin and the characteristics of normal cell BRCA1 methylation, we analyzed umbilical cord blood of 1260 newborn girls and 200 newborn boys. Finally, we assessed BRCA1 methylation status among 575 mothers and 531 fathers of girls with (n = 102) and without (n = 473) BRCA1 methylation. RESULTS We found concordant tumor and mosaic WBC BRCA1 epimutations in 10 out of 66 patients with TNBC and in four out of six patients with estrogen receptor (ER)-low expression (< 10%) tumors (combined: 14 out of 72; 19.4%; 95% CI 11.1-30.5). In contrast, we found concordant WBC and tumor methylation in only three out of 220 patients with 221 ER ≥ 10% tumors and zero out of 114 patients with 116 HER2-positive tumors. Intraindividually, BRCA1 epimutations affected the same allele in normal and tumor cells. Assessing BRCA1 methylation in umbilical WBCs from girls, we found mosaic, predominantly monoallelic BRCA1 epimutations, with qualitative features similar to those in adults, in 113/1260 (9.0%) of individuals, but no correlation to BRCA1 methylation status either in mothers or fathers. A significantly lower fraction of newborn boys carried BRCA1 methylation (9/200; 4.5%) as compared to girls (p = 0.038). Similarly, WBC BRCA1 methylation was found less common among fathers (16/531; 3.0%), as compared to mothers (46/575; 8.0%; p = 0.0003). CONCLUSIONS Our findings suggest prenatal BRCA1 epimutations might be the underlying cause of around 20% of TNBC and low-ER expression breast cancers. Such constitutional mosaic BRCA1 methylation likely arise through gender-related mechanisms in utero, independent of Mendelian inheritance.
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Affiliation(s)
- Oleksii Nikolaienko
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway
| | - Hans P Eikesdal
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway
| | - Elisabet Ognedal
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway
| | - Bjørnar Gilje
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Steinar Lundgren
- Cancer Clinic, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Egil S Blix
- Department of Oncology, University Hospital of North Norway, Tromsø, Norway
| | - Helge Espelid
- Department of Surgery, Haugesund Hospital, Haugesund, Norway
| | - Jürgen Geisler
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Stephanie Geisler
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
| | - Emiel A M Janssen
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, Stavanger University, Stavanger, Norway
| | - Synnøve Yndestad
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway
| | - Laura Minsaas
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway
| | - Beryl Leirvaag
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway
| | - Reidun Lillestøl
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway
| | - Stian Knappskog
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway
| | - Per E Lønning
- K.G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Oncology, Haukeland University Hospital, Jonas Lies Vei 65, N5021, Bergen, Norway.
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5
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Plotkin A, Olkhov-Mitsel E, Nofech-Mozes S. MLH1 Methylation Testing as an Integral Component of Universal Endometrial Cancer Screening-A Critical Appraisal. Cancers (Basel) 2023; 15:5188. [PMID: 37958361 PMCID: PMC10650699 DOI: 10.3390/cancers15215188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
MLH1/PMS2 loss due to MLH1 promoter hypermethylation (MLH1-PHM) is the most common cause of mismatch repair (MMR) deficiency in endometrial cancer (EC). This study aimed to determine the proportion of MLH1-deficient EC with PHM, assess the impact of the reflex MLH1-PHM testing strategy, and evaluate the associated costs within the publicly funded Canadian healthcare system. In a cohort of 2504 EC samples, 534 (21.4%) exhibited dual MLH1/PMS2 loss, prompting MLH1-PHM testing. Among 418 cases with available testing results, 404 (96.7%) were MLH1-hypermethylated, while 14 (3.3%) were non-methylated. The incidence of MLH1 non-methylated cases in our cohort was 14/2504 (0.56%) of all ECs, underscoring the prevalence of hypermethylation-driven MLH1/PMS2 loss in ECs universally screened for MMR deficiency. Reflex MLH1-PHM testing incurs substantial costs and resource utilization. Assay cost is CAD 231.90 per case, amounting to CAD 123,834.60 for 534 cases, with 30 tests needed per additional candidate for MLH1 germline analysis (CAD 6957.00 per candidate). This raises a provocative question: can we assume that the majority of the MLH1-deficient ECs are due to PHM and forgo further testing in healthcare systems with finite resources? It is imperative to assess resource utilization efficiency and explore optimized approaches that encompass clinical correlation, family history and judicious utilization of methylation testing to ensure it is provided only to those who stand to benefit from it.
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Affiliation(s)
- Anna Plotkin
- Department of Laboratory Medicine and Molecular Diagnostics, Division of Anatomic Pathology, Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ekaterina Olkhov-Mitsel
- Department of Laboratory Medicine and Molecular Diagnostics, Division of Anatomic Pathology, Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Sharon Nofech-Mozes
- Department of Laboratory Medicine and Molecular Diagnostics, Division of Anatomic Pathology, Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
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