1
|
Xu L, Liddell B, Nesic K, Geissler F, Ashwood L, Wakefield M, Scott C, Waddell N, Kondrashova O. High-level tumour methylation of BRCA1 and RAD51C is required for homologous recombination deficiency in solid cancers. NAR Cancer 2024; 6:zcae033. [PMID: 39055334 PMCID: PMC11270467 DOI: 10.1093/narcan/zcae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
In ovarian and breast cancer, promoter methylation of BRCA1 or RAD51C is a promising biomarker for PARP inhibitor response, as high levels lead to homologous recombination deficiency (HRD). Yet the extent and role of such methylation in other cancers is not clear. This study comprehensively investigated promoter methylation of eight homologous recombination repair genes across 23 solid cancer types. Here, we showed that BRCA1 methylated cancers were associated with reduced gene expression, loss of heterozygosity (LOH), TP53 mutations and genomic features of HRD. We identified BRCA1 methylation in 3% of the copy-number high subtype of endometrial cancer, and as a rare event in six other cancer types, including lung squamous cell, pancreatic, bladder and stomach cancer. RAD51C promoter methylation was widespread across multiple cancer types, but HRD features were only observed for cases which contained high-level tumour methylation and LOH of RAD51C. While RAD51C methylation was frequent in stomach adenocarcinoma (6%) and low-grade glioma (2.5%), it was mostly detected at a low tumour level, suggestive of heterozygous methylation, and was associated with CpG island methylator phenotype. Our findings indicate that high-level tumour methylation of BRCA1 and RAD51C should be explored as a PARP inhibitor biomarker across multiple cancers.
Collapse
Affiliation(s)
- Lijun Xu
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- The University of Queensland, Brisbane, QLD, Australia
| | - Brett Liddell
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- The University of Queensland, Brisbane, QLD, Australia
| | - Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Franziska Geissler
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Lauren M Ashwood
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- The University of Queensland, Brisbane, QLD, Australia
| | - Matthew J Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia
| | - Nicola Waddell
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- The University of Queensland, Brisbane, QLD, Australia
| | - Olga Kondrashova
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- The University of Queensland, Brisbane, QLD, Australia
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| |
Collapse
|
2
|
Ruiz-De La Cruz M, Martínez-Gregorio H, Estela Díaz-Velásquez C, Ambriz-Barrera F, Resendiz-Flores NG, Gitler-Weingarten R, Rojo-Castillo MP, Pradda D, Oliver J, Perdomo S, Gómez-García EM, De La Cruz-Montoya AH, Terrazas LI, Torres-Mejía G, Hernández-Hernández FDLC, Vaca-Paniagua F. Methylation marks in blood DNA reveal breast cancer risk in patients fulfilling hereditary disease criteria. NPJ Precis Oncol 2024; 8:136. [PMID: 38898118 PMCID: PMC11187128 DOI: 10.1038/s41698-024-00611-z] [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: 08/25/2023] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
Less than 15-20% of patients who meet the criteria for hereditary breast and ovarian cancer (HBOC) carry pathogenic coding genetic mutations, implying that other molecular mechanisms may contribute to the increased risk of this condition. DNA methylation in peripheral blood has been suggested as a potential epigenetic marker for the risk of breast cancer (BC). We aimed to discover methylation marks in peripheral blood associated with BC in 231 pre-treatment BC patients meeting HBOC criteria, testing negative for coding pathogenic variants, and 156 healthy controls, through methylation analysis by targeted bisulfite sequencing on 18 tumor suppressor gene promoters (330 CpG sites). We found i) hypermethylation in EPCAM (17 CpG sites; p = 0.017) and RAD51C (27 CpG sites; p = 0.048); ii) hypermethylation in 36 CpG-specific sites (FDR q < 0.05) in the BC patients; iii) four specific CpG sites were associated with a higher risk of BC (FDR q < 0.01, Bonferroni p < 0.001): cg89786999-FANCI (OR = 1.65; 95% CI:1.2-2.2), cg23652916-PALB2 (OR = 2.83; 95% CI:1.7-4.7), cg47630224-MSH2 (OR = 4.17; 95% CI:2.1-8.5), and cg47596828-EPCAM (OR = 1.84; 95% CI:1.5-2.3). Validation of cg47630224-MSH2 methylation in one Australian cohort showed an association with 3-fold increased BC risk (AUC: 0.929; 95% CI: 0.904-0.955). Our findings suggest that four DNA methylation CpG sites may be associated with a higher risk of BC, potentially serving as biomarkers in patients without detectable coding mutations.
Collapse
Affiliation(s)
- Miguel Ruiz-De La Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
- Centro de Investigación y de Estudios Avanzados IPN (CINVESTAV). Avenida Instituto Politécnico Nacional #2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Departamento de Infectómica y Patogénesis Molecular, Ciudad de México, Mexico
| | - Héctor Martínez-Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | - Clara Estela Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
| | - Fernando Ambriz-Barrera
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | - Norma Gabriela Resendiz-Flores
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | | | | | - Didier Pradda
- Institute for Health Equity Research, Department of Health Science and Policy and Department of Environmental Medicine and Public Health at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Javier Oliver
- Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, CIMES, University of Málaga, 29010, Málaga, Spain
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), 150 Cours Albert Thomas, 69372, Lyon, France
| | | | | | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | | | - Fidel de la Cruz Hernández-Hernández
- Centro de Investigación y de Estudios Avanzados IPN (CINVESTAV). Avenida Instituto Politécnico Nacional #2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Departamento de Infectómica y Patogénesis Molecular, Ciudad de México, Mexico.
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico.
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico.
| |
Collapse
|
3
|
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 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.
Collapse
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
| |
Collapse
|
4
|
Schwartz M, Ibadioune S, Chansavang A, Vacher S, Caputo SM, Delhomelle H, Wong J, Abidallah K, Moncoutier V, Becette V, Popova T, Suybeng V, De Pauw A, Stern MH, Colas C, Mouret-Fourme E, Stoppa-Lyonnet D, Golmard L, Bieche I, Masliah-Planchon J. Mosaic BRCA1 promoter methylation contribution in hereditary breast/ovarian cancer pedigrees. J Med Genet 2024; 61:284-288. [PMID: 37748860 DOI: 10.1136/jmg-2023-109325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
PURPOSE Mosaic BRCA1 promoter methylation (BRCA1meth) increases the risk of early-onset breast cancer, triple-negative breast cancer and ovarian cancer. As mosaic BRCA1meth are believed to occur de novo, their role in family breast/ovarian cancer has not been assessed. PATIENTS Blood-derived DNA from 20 unrelated affected cases from families with aggregation of breast/ovarian cancer, but with no germline pathogenic variants in BRCA1/2, PALB2 or RAD51C/D, were screened by methylation-sensitive high-resolution melting. CpG analysis was performed by pyrosequencing on blood and buccal swab. Two probands carried a pathogenic variant in a moderate-penetrance gene (ATM and BARD1), and 8 of 18 others (44%) carried BRCA1meth (vs none of the 20 age-matched controls). Involvement of BRCA1 in tumourigenesis in methylated probands was demonstrated in most tested cases by detection of a loss of heterozygosity and a homologous recombination deficiency signature. Among the eight methylated probands, two had relatives with breast cancer with detectable BRCA1meth in blood, including one with high methylation levels in two non-tumour tissues. CONCLUSIONS The high prevalence of mosaic BRCA1meth in patients with breast/ovarian cancer with affected relatives, as well as this first description of a family aggregation of mosaic BRCA1meth, shows how this de novo event can contribute to hereditary breast/ovarian cancer pedigrees.
Collapse
Affiliation(s)
- Mathias Schwartz
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- UMR3244, Curie Institute, Paris, France
| | - Sabrina Ibadioune
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Albain Chansavang
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sophie Vacher
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sandrine M Caputo
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Hélène Delhomelle
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Jennifer Wong
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Khadija Abidallah
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Virginie Moncoutier
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Véronique Becette
- Paris Sciences & Lettres Research University, Paris, France
- Department of Pathology, Curie Institute, Saint-Cloud, France
| | - Tatiana Popova
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Voreak Suybeng
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Antoine De Pauw
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Marc-Henri Stern
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Chrystelle Colas
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Emmanuelle Mouret-Fourme
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Université de Paris Cité, Paris, France
| | - Lisa Golmard
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Ivan Bieche
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Université de Paris Cité, Paris, France
| | - Julien Masliah-Planchon
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Mandelker D, Marra A, Zheng-Lin B, Selenica P, Blanco-Heredia J, Zhu Y, Gazzo A, Wong D, Yelskaya Z, Rai V, Somar J, Ostafi S, Mehta N, Yang C, Li Y, Brown DN, da Silva EM, Pei X, Linkov I, Terraf P, Misyura M, Ceyhan-Birsoy O, Ladanyi M, Berger M, Pareja F, Stadler Z, Offit K, Riaz N, Park W, Chou J, Capanu M, Koehler M, Rosen E, O'Reilly EM, Reis-Filho JS. Genomic Profiling Reveals Germline Predisposition and Homologous Recombination Deficiency in Pancreatic Acinar Cell Carcinoma. J Clin Oncol 2023; 41:5151-5162. [PMID: 37607324 PMCID: PMC10667000 DOI: 10.1200/jco.23.00561] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 08/24/2023] Open
Abstract
PURPOSE To determine the genetic predisposition underlying pancreatic acinar cell carcinoma (PACC) and characterize its genomic features. METHODS Both somatic and germline analyses were performed using an Food and Drug Administration-authorized matched tumor/normal sequencing assay on a clinical cohort of 28,780 patients with cancer, 49 of whom were diagnosed with PACC. For a subset of PACCs, whole-genome sequencing (WGS; n = 12) and RNA sequencing (n = 6) were performed. RESULTS Eighteen of 49 (36.7%) PACCs harbored germline pathogenic variants in homologous recombination (HR) and DNA damage response (DDR) genes, including BRCA1 (n = 1), BRCA2 (n = 12), PALB2 (n = 2), ATM (n = 2), and CHEK2 (n = 1). Thirty-one PACCs displayed pure, and 18 PACCs harbored mixed acinar cell histology. Fifteen of 31 (48%) pure PACCs harbored a germline pathogenic variant affecting HR-/DDR-related genes. BRCA2 germline pathogenic variants (11 of 31, 35%) were significantly more frequent in pure PACCs than in pancreatic adenocarcinoma (86 of 2,739, 3.1%; P < .001), high-grade serous ovarian carcinoma (67 of 1,318, 5.1%; P < .001), prostate cancer (116 of 3,401, 3.4%; P < .001), and breast cancer (79 of 3,196, 2.5%; P < .001). Genomic features of HR deficiency (HRD) were detected in 7 of 12 PACCs undergoing WGS, including 100% (n = 6) of PACCs with germline HR-related pathogenic mutations and 1 of 6 PACCs lacking known pathogenic alterations in HR-related genes. Exploratory analyses revealed that in PACCs, the repertoire of somatic driver genetic alterations and the load of neoantigens with high binding affinity varied according to the presence of germline pathogenic alterations affecting HR-/DDR-related genes and/or HRD. CONCLUSION In a large pan-cancer cohort, PACC was identified as the cancer type with the highest prevalence of both BRCA2 germline pathogenic variants and genomic features of HRD, suggesting that PACC should be considered as part of the spectrum of BRCA-related malignancies.
Collapse
Affiliation(s)
- Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Binbin Zheng-Lin
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan Blanco-Heredia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yingjie Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrea Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Donna Wong
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zarina Yelskaya
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vikas Rai
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joshua Somar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Silvana Ostafi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ciyu Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yirong Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David N. Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Edaise M. da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xin Pei
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Irina Linkov
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Panieh Terraf
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maksym Misyura
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Ceyhan-Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wungki Park
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joanne Chou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ezra Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eileen M. O'Reilly
- Gastrointestinal Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY
- David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jorge S. Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
7
|
Muhammad N, Azeem A, Bakar MA, Prajzendanc K, Loya A, Jakubowska A, Hamann U, Rashid MU. Contribution of constitutional BRCA1 promoter methylation to early-onset and familial breast cancer patients from Pakistan. Breast Cancer Res Treat 2023; 202:377-387. [PMID: 37528266 DOI: 10.1007/s10549-023-07068-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023]
Abstract
PURPOSE Constitutional BRCA1 promoter methylation has been identified as a potential risk factor for breast cancer (BC) in the Caucasian population. However, this data is lacking for BC patients of Asian origin. Therefore, we assessed the contribution of constitutional BRCA1 promoter methylation in Pakistani BC patients. METHODS A total of 385 BRCA1/2-negative index BC patients (197 early-onset BC (≤ 30 years), 152 familial BC, 17 familial BC and ovarian cancer, 19 male BC) and 107 healthy controls were screened for the constitutional BRCA1 promoter methylation by methylation-sensitive high-resolution melting assay. Overall, 131 patients displayed triple-negative BC (TNBC) and 254 non-TNBC phenotypes. The prevalence of BRCA1 promoter methylation was calculated based on clinicopathological characteristics using univariable and multivariable logistic regression models. RESULTS Constitutional BRCA1 promoter methylation was identified in 19.5% (75/385) of BC patients and 13.1% (14/107) of controls. The frequency of methylation was higher in early-onset BC (23.4% vs. 13.1%, P = 0.035) and TNBC patients (29.0% vs. 13.1%, P = 0.004) compared to controls. Methylation was also more prevalent in patients with high-grade than low-grade tumors (21.7% vs. 12.2%, P = 0.034) and progesterone receptor (PR)-negative than PR-positive tumors (26.0% vs. 13.9%, P = 0.004). Constitutional BRCA1 promoter methylation remained independently associated with TNBC phenotype (odds ratio 1.99; 95% CI 1.12-3.54; P = 0.02) after adjusting for BC diagnosis age, tumor grade, ER, and PR status. CONCLUSION Constitutional BRCA1 promoter methylation is associated with TNBC and can serve as a non-invasive blood-based biomarker for Pakistani TNBC patients.
Collapse
Affiliation(s)
- Noor Muhammad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7-A, Block R-3, Johar Town, Lahore, 54770, Pakistan
| | - Ayesha Azeem
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7-A, Block R-3, Johar Town, Lahore, 54770, Pakistan
| | - Muhammad Abu Bakar
- Department of Cancer Registry and Clinical Data Management, SKMCH&RC, Lahore, Pakistan
| | - Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Asif Loya
- Department of Pathology, SKMCH&RC, Lahore, Pakistan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Muhammad Usman Rashid
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7-A, Block R-3, Johar Town, Lahore, 54770, Pakistan.
| |
Collapse
|
8
|
Machaj F, Sokolowska KE, Borowski K, Retfiński S, Strapagiel D, Sobalska-Kwapis M, Huzarski T, Lubiński J, Wojdacz TK. Analytical sensitivity of a method is critical in detection of low-level BRCA1 constitutional epimutation. Sci Rep 2023; 13:16102. [PMID: 37752189 PMCID: PMC10522570 DOI: 10.1038/s41598-023-43276-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
Recent reports based on a substantial number of cases, warrant need for population-based research to determine implications of constitutional methylation of tumor suppressor genes such as BRCA1 occurring in healthy tissue in the prediction of cancer. However, the detection of the constitutional methylation in DNA extracted from blood has already been shown to be technologically challenging, mainly because epimutations appear to be present in blood at a very low level. The analytical sensitivity required for low-level methylation detection can be provided by NGS, but this technique is still labor and cost-intensive. We assessed if PCR-based MS-HRM and BeadChip microarray technologies, which are standardized and cost-effective technologies for methylation changes screening, provide a sufficient level of analytical sensitivity for constitutional BRCA1 methylation detection in blood samples. The study included whole blood samples from 67 healthy women, 35 with previously confirmed and 32 with no detectable BRCA1 promoter methylation for which we performed both MS-HRM based BRCA1 gene methylation screening and genome wide methylation profiling with EPIC microarray. Our results shown, that low-level BRCA1 methylation can be effectively detected in DNA extracted from blood by PCR-based MS-HRM. At the same time, EPIC microarray does not provide conclusive results to unambiguously determine the presence of BRCA1 constitutional methylation in MS-HRM epimutation positive samples. The analytical sensitivity of MS-HRM is sufficient to detect low level BRCA1 constitutional epimutation in DNA extracted from blood and BeadChip technology-based microarrays appear not to provide that level of analytical sensitivity.
Collapse
Affiliation(s)
- Filip Machaj
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Katarzyna Ewa Sokolowska
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Konrad Borowski
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Szymon Retfiński
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Dominik Strapagiel
- Biobank Laboratory, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 139, 90-237, Lodz, Poland
| | - Marta Sobalska-Kwapis
- Biobank Laboratory, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 139, 90-237, Lodz, Poland
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Tomasz Kazimierz Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland.
| |
Collapse
|
9
|
Ghemrawi R, Al Qassem A, Ramadan A, Aldulaymi R, Sammani N, K Mousa W, Khair M. DNA and protein methyltransferases inhibition by adenosine dialdehyde reduces the proliferation and migration of breast and lung cancer cells by downregulating autophagy. PLoS One 2023; 18:e0288791. [PMID: 37506102 PMCID: PMC10381035 DOI: 10.1371/journal.pone.0288791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Protein and DNA methylation is involved in various biological functions such as signal transmission, DNA repair, and gene expression. Abnormal regulation of methyltransferases has been linked to multiple types of cancer, but its link to autophagy and carcinogenesis in breast and lung cancer is not fully understood. We utilized UALCAN, a web tool, to investigate breast and lung cancer database from The Cancer Genome Atlas. We found that 17 methyltransferases are upregulated in breast and/or lung cancer. We investigated the effect of methylation inhibition on two breast cancer cell lines (MDA-MB-231 and MCF-7) and two lung cancer cell lines (H292 and A549) by treating them with the indirect methyltransferase inhibitor adenosine dialdehyde (AdOx). We found that the migration ability of all cell lines was decreased, and the growth rate of MDA-MB-231, MCF-7 and H292 was also decreased after AdOx treatment. These results were correlated with an inhibition of the autophagy in MDA-MB-231, MCF-7 and H292 cell lines, since AdOx treatment induced a decreased expression of ATG7, a reduced ratio LC3-II/LC3-I and an increased p62 level. These findings suggest that inhibiting cells' methylation ability could be a potential target for breast and lung cancer treatment.
Collapse
Affiliation(s)
- Rose Ghemrawi
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Aya Al Qassem
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Azza Ramadan
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Raghad Aldulaymi
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Nour Sammani
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Walaa K Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mostafa Khair
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| |
Collapse
|
10
|
Joo JE, Mahmood K, Walker R, Georgeson P, Candiloro I, Clendenning M, Como J, Joseland S, Preston S, Graversen L, Wilding M, Field M, Lemon M, Wakeling J, Marfan H, Susman R, Isbister J, Edwards E, Bowman M, Kirk J, Ip E, McKay L, Antill Y, Hopper JL, Boussioutas A, Macrae FA, Dobrovic A, Jenkins MA, Rosty C, Winship IM, Buchanan DD. Identifying primary and secondary MLH1 epimutation carriers displaying low-level constitutional MLH1 methylation using droplet digital PCR and genome-wide DNA methylation profiling of colorectal cancers. Clin Epigenetics 2023; 15:95. [PMID: 37270516 PMCID: PMC10239107 DOI: 10.1186/s13148-023-01511-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND MLH1 epimutation is characterised by constitutional monoallelic MLH1 promoter hypermethylation, which can cause colorectal cancer (CRC). Tumour molecular profiles of MLH1 epimutation CRCs were used to classify germline MLH1 promoter variants of uncertain significance and MLH1 methylated early-onset CRCs (EOCRCs). Genome-wide DNA methylation and somatic mutational profiles of tumours from two germline MLH1: c.-11C > T and one MLH1: c.-[28A > G; 7C > T] carriers and three MLH1 methylated EOCRCs (< 45 years) were compared with 38 reference CRCs. Methylation-sensitive droplet digital PCR (ddPCR) was used to detect mosaic MLH1 methylation in blood, normal mucosa and buccal DNA. RESULTS Genome-wide methylation-based Consensus Clustering identified four clusters where the tumour methylation profiles of germline MLH1: c.-11C > T carriers and MLH1 methylated EOCRCs clustered with the constitutional MLH1 epimutation CRCs but not with the sporadic MLH1 methylated CRCs. Furthermore, monoallelic MLH1 methylation and APC promoter hypermethylation in tumour were observed in both MLH1 epimutation and germline MLH1: c.-11C > T carriers and MLH1 methylated EOCRCs. Mosaic constitutional MLH1 methylation in MLH1: c.-11C > T carriers and 1 of 3 MLH1 methylated EOCRCs was identified by methylation-sensitive ddPCR. CONCLUSIONS Mosaic MLH1 epimutation underlies the CRC aetiology in MLH1: c.-11C > T germline carriers and a subset of MLH1 methylated EOCRCs. Tumour profiling and ultra-sensitive ddPCR methylation testing can be used to identify mosaic MLH1 epimutation carriers.
Collapse
Affiliation(s)
- Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia.
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia.
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Ida Candiloro
- Beacon Biomarkers Lab, Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Lise Graversen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Mathilda Wilding
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Michael Field
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Michelle Lemon
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Janette Wakeling
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Tasman Health Care, Southport, QLD, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Joanne Isbister
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
| | - Emma Edwards
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Michelle Bowman
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Emilia Ip
- Department of Cancer Genetics, Liverpool Hospital, Liverpool, NSW, Australia
| | - Lynne McKay
- The Cabrini Family Cancer Clinic, Cabrini Health, Malvern, VIC, Australia
| | - Yoland Antill
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- The Cabrini Family Cancer Clinic, Cabrini Health, Malvern, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, VIC, Australia
| | - Alex Boussioutas
- Department of Gastroenterology, The Alfred Hospital, Melbourne, Parkville, VIC, 3010, Australia
- Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Finlay A Macrae
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Alexander Dobrovic
- Beacon Biomarkers Lab, Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Envoi Specialist Pathologists, Brisbane, Australia
- University of Queensland, Brisbane, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
| |
Collapse
|
11
|
Díaz-Velásquez CE, Gitler R, Antoniano A, Kershenovich Sefchovich R, De La Cruz-Montoya AH, Martínez-Gregorio H, Rojas-Jiménez EA, Cortez Cardoso Penha R, Terrazas LI, Wegman-Ostrosky T, Levi-Lahad E, Zabaleta J, Perdomo S, Vaca-Paniagua F. Evaluation of genetic alterations in hereditary cancer susceptibility genes in the Ashkenazi Jewish women community of Mexico. Front Genet 2023; 14:1094260. [PMID: 36845387 PMCID: PMC9950094 DOI: 10.3389/fgene.2023.1094260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Background: Individuals of Ashkenazi Jewish ancestry have been identified as having higher prevalence of specific pathogenic variants associated with susceptibility to specific rare and chronic diseases. In Mexico, the prevalence and composition of rare cancer predisposing germline variants in Ashkenazi Jewish individuals has not been evaluated. Aim and methods: We aimed to evaluate the prevalence of pathogenic variants by massive parallel sequencing in a panel of 143 cancer-predisposing genes in 341 women from the Ashkenazi Jewish community of Mexico, who were contacted and invited to participate in the study through the ALMA Foundation for Cancer Reconstruction. Pre- and posttest genetic counseling was given and a questionnaire on personal, gyneco-obstetric, demographic and lifestyle variables was conducted. From peripheral blood DNA, the complete coding region, and splicing sites of a panel of 143 cancer susceptibility genes, including 21 clinically relevant genes, were sequenced. The Mexican founder mutation BRCA1 ex9-12del [NC_000017.10(NM_007294):c. (825+1-826-1)_(4,589+1-4,590-1)del] was also evaluated. Results: Among study participants (mean age ±standard deviation: 47 ± 14) 15% reported a personal history of cancer (50/341). Fourteen percent of participants (48/341) were carriers of pathogenic and likely pathogenic variants distributed among seven high-risk genes (APC, CHEK2, MSH2, BMPR1A, MEN1, MLH1, and MSH6), whereas 18.2% (62/341) had variants of uncertain clinical significance in genes associated with breast and ovarian cancer susceptibility (list of genes with VUS). Pathogenic and likely pathogenic variants in 16 susceptibility genes with ambiguous or non-well-established risk association for cancer were detected in 17.6% (60/341) of participants. Sixty four percent of participants reported current alcohol consumption compared with the 39 percent prevalence of alcohol consumption in Mexican women. None of the participants carried the recurrent Ashkenazi and Mexican founder mutations in BRCA1 or BRCA2, but 2% (7/341) had pathogenic Ashkenazi Jewish founder variants in BLM. Conclusion: Our findings show a diverse pathogenic variant composition among the recruited individuals of Ashkenazi Jewish ancestry in Mexico consistent with being a high-risk population for genetic diseases, which warrants further investigation to adequately assess the burden of hereditary breast cancer in this group and implement appropriate preventative programs.
Collapse
Affiliation(s)
- Clara Estela Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado DeMéxico, Mexico
| | | | | | | | | | - Héctor Martínez-Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado DeMéxico, Mexico
| | - Ernesto Arturo Rojas-Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado DeMéxico, Mexico
| | | | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado DeMéxico, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, Estado DeMéxico, Mexico
| | - Talia Wegman-Ostrosky
- Subdirection of Basic Research, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Ephrat Levi-Lahad
- Department of Medical Genetics, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Jovanny Zabaleta
- Departament of Interdisciplinary Oncology, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
- Stanley S. Scott Cancer Center, LSU Health New Orleans, New Orleans, LA, United States
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado DeMéxico, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, Estado DeMéxico, Mexico
- Subdirection of Basic Research, Instituto Nacional de Cancerología, Mexico City, Mexico
| |
Collapse
|
12
|
Wang T, Meng Y, Tu Y, Zhang G, Wang K, Gong S, Zhang Y, Wang T, Li A, Christiani DC, Au W, Xia ZL. Associations between DNA methylation and genotoxicity among lead-exposed workers in China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120528. [PMID: 36341824 DOI: 10.1016/j.envpol.2022.120528] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Studies have shown that lead (Pb) exposure caused genotoxicity, however, the underlying mechanisms remain unclear. A mechanism may be via DNA methylation which is one of the most widely studied epigenetic regulations for cellular activities. Whether this is involved in Pb-induced genotoxicity has rarely been studied. Our study aimed to examine whether DNA methylation was associated with Pb exposure and genotoxicity, and to explore its potential mediating roles. A total of 250 Pb-exposed workers were enrolled. Blood lead levels (BLLs) and genotoxic biomarkers (Micronuclei and Comet) were analyzed. Methylation levels at CpG sites of LINE1 and Alu and promoter region of P53, BRCA1, TRIM36 and OGG1 were measured by pyrosequencing. Generalized linear model (GLM) combined with restricted cubic splines (RCS) were used to analyze relationships between Pb exposure, DNA methylation and genotoxicity. Mediation effect was used to explore mediating roles of DNA methylation. The distribution of BLLs was right-skewed and showed wide ranges from 23.7 to 636.2 μg/L with median (P25, P75) being 218.4 (106.1, 313.9) μg/L among all workers. Micronuclei frequencies showed Poisson distribution [1.94 ± 1.88‰] and Comet tail intensity showed normal distribution [1.69 ± 0.93%]. GLM combined with RCS showed that Alu methylation was negatively associated with BLLs, while P53 and OGG1 methylation were positively associated with BLLs. Micronuclei were negatively associated with Alu and TRIM36 methylation but positively with P53 methylation. Comet was positively associated with P53 and BRCA1 methylation. Mediation effect showed that Alu methylation mediated 7% effects on association between Pb exposure and micronuclei, whereas, P53 methylation mediated 14% and BRCA1 mediated 9% effects on association between Pb exposure and Comet. Our data show that Pb exposure induced changes of global and gene-specific DNA methylation which mediated Pb-induced genotoxicity.
Collapse
Affiliation(s)
- Tuanwei Wang
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China; Department of Environmental Health, School of Public Health, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Yu Meng
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yuting Tu
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Guanghui Zhang
- Department of Environmental Health, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Kan Wang
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Shiyang Gong
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yunxia Zhang
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Tongshuai Wang
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Anqi Li
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - David C Christiani
- Environmental Medicine and Epidemiology Program, Department of Environmental Health, Harvard University TH Chan School of Public Health, Boston, MA, USA
| | - William Au
- University of Medicine, Pharmacy, Science and Technology, Targu Mures, Romania, and University of Texas Medical Branch, Galveston, TX, USA
| | - Zhao-Lin Xia
- Department of Occupational Health & Toxicology, School of Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China; School of Public Health, Xinjiang Medical University, Urumqi 830011, China.
| |
Collapse
|
13
|
Lønning PE, Nikolaienko O, Pan K, Kurian AW, Eikesdal HP, Pettinger M, Anderson GL, Prentice RL, Chlebowski RT, Knappskog S. Constitutional BRCA1 Methylation and Risk of Incident Triple-Negative Breast Cancer and High-grade Serous Ovarian Cancer. JAMA Oncol 2022; 8:1579-1587. [PMID: 36074460 PMCID: PMC9459895 DOI: 10.1001/jamaoncol.2022.3846] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance About 25% of all triple-negative breast cancers (TNBCs) and 10% to 20% of high-grade serous ovarian cancers (HGSOCs) harbor BRCA1 promoter methylation. While constitutional BRCA1 promoter methylation has been observed in normal tissues of some individuals, the potential role of normal tissue methylation as a risk factor for incident TNBC or HGSOC is unknown. Objective To assess the potential association between white blood cell BRCA1 promoter methylation and subsequent risk of incident TNBC and HGSOC. Design, Setting, and Participants This case-control study included women who were participating in the Women's Health Initiative study who had not received a diagnosis of either breast or ovarian cancer before study entrance. A total of 637 women developing incident TNBC and 511 women developing incident HGSOC were matched with cancer-free controls (1841 and 2982, respectively) in a nested case-control design. Cancers were confirmed after central medical record review. Blood samples, which were collected at entry, were analyzed for BRCA1 promoter methylation by massive parallel sequencing. The study was performed in the Mohn Cancer Research Laboratory (Bergen, Norway) between 2019 and 2022. Main Outcomes and Measures Associations between BRCA1 methylation and incident TNBC and incident HGSOC were analyzed by Cox proportional hazards regression. Results Of 2478 cases and controls in the TNBC group and 3493 cases and controls in the HGSOC group, respectively, 7 (0.3%) and 3 (0.1%) were American Indian or Alaska Native, 46 (1.9%) and 30 (0.9%) were Asian, 1 (0.04%) and 1 (0.03%) was Native Hawaiian or Pacific Islander, 326 (13.2%) and 125 (3.6%) were Black or African, 56 (2.3%) and 116 (3.3%) were Hispanic, 2046 (82.6%) and 3257 (93.2%) were White, and 35 (1.4%) and 35 (1.0%) were multiracial. Median (range) age at entry was 62 (50-79) years, with a median interval to diagnosis of 9 (TNBC) and 10 (HGSOC) years. Methylated BRCA1 alleles were present in 194 controls (5.5%). Methylation was associated with risk of incident TNBC (12.4% methylated; HR, 2.35; 95% CI, 1.70-3.23; P < .001) and incident HGSOC (9.4% methylated; HR, 1.93; 95% CI, 1.36-2.73; P < .001). Restricting analyses to individuals with more than 5 years between sampling and cancer diagnosis yielded similar results (TNBC: HR, 2.52; 95% CI, 1.75-3.63; P < .001; HGSOC: HR, 1.82; 95% CI, 1.22-2.72; P = .003). Across individuals, methylation was not haplotype-specific, arguing against an underlying cis-acting factor. Within individuals, BRCA1 methylation was observed on the same allele, indicating clonal expansion from a single methylation event. There was no association found between BRCA1 methylation and germline pathogenic variant status. Conclusions and Relevance The results of this case-control suggest that constitutional normal tissue BRCA1 promoter methylation is significantly associated with risk of incident TNBC and HGSOC, with potential implications for prediction of these cancers. These findings warrant further research to determine if constitutional methylation of tumor suppressor genes are pancancer risk factors.
Collapse
Affiliation(s)
- Per E. Lønning
- K.G. Jebsen Centre for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Oleksii Nikolaienko
- K.G. Jebsen Centre for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Kathy Pan
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Allison W. Kurian
- Departments of Medicine and of Epidemiology and Population Health, Stanford University, Stanford, California
| | - Hans P. Eikesdal
- K.G. Jebsen Centre for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Mary Pettinger
- Division of Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Garnet L. Anderson
- Division of Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ross L. Prentice
- Division of Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Rowan T. Chlebowski
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Stian Knappskog
- K.G. Jebsen Centre for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| |
Collapse
|
14
|
Lobanova O, Medvedieva N, Fishchuk L, Dubitska O, Cheshuk V, Vereshchako R, Zakhartseva L, Rossokha Z, Gorovenko N. Methylation of promoter region of BRCA1 gene versus pathogenic variants of gene: risk factor or clinical marker of breast cancer. Breast Cancer Res Treat 2022; 196:505-515. [DOI: 10.1007/s10549-022-06774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
|
15
|
Leibowitz BD, Dougherty BV, Bell JSK, Kapilivsky J, Michuda J, Sedgewick AJ, Munson WA, Chandra TA, Dry JR, Beaubier N, Igartua C, Taxter T. Validation of genomic and transcriptomic models of homologous recombination deficiency in a real-world pan-cancer cohort. BMC Cancer 2022; 22:587. [PMID: 35643464 PMCID: PMC9148513 DOI: 10.1186/s12885-022-09669-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Background With the introduction of DNA-damaging therapies into standard of care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following the strong clinical evidence for the utility of DNA-sequencing-based HRD testing in ovarian cancer, and growing evidence in breast cancer, we present analytical validation of the Tempus HRD-DNA test. We further developed, validated, and explored the Tempus HRD-RNA model, which uses gene expression data from 16,750 RNA-seq samples to predict HRD status from formalin-fixed paraffin-embedded tumor samples across numerous cancer types. Methods Genomic and transcriptomic profiling was performed using next-generation sequencing from Tempus xT, Tempus xO, Tempus xE, Tempus RS, and Tempus RS.v2 assays on 48,843 samples. Samples were labeled based on their BRCA1, BRCA2 and selected Homologous Recombination Repair pathway gene (CDK12, PALB2, RAD51B, RAD51C, RAD51D) mutational status to train and validate HRD-DNA, a genome-wide loss-of-heterozygosity biomarker, and HRD-RNA, a logistic regression model trained on gene expression. Results In a sample of 2058 breast and 1216 ovarian tumors, BRCA status was predicted by HRD-DNA with F1-scores of 0.98 and 0.96, respectively. Across an independent set of 1363 samples across solid tumor types, the HRD-RNA model was predictive of BRCA status in prostate, pancreatic, and non-small cell lung cancer, with F1-scores of 0.88, 0.69, and 0.62, respectively. Conclusions We predict HRD-positive patients across many cancer types and believe both HRD models may generalize to other mechanisms of HRD outside of BRCA loss. HRD-RNA complements DNA-based HRD detection methods, especially for indications with low prevalence of BRCA alterations. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09669-z.
Collapse
|
16
|
Azzollini J, Vingiani A, Agnelli L, Tamborini E, Perrone F, Conca E, Capone I, Busico A, Peissel B, Rosina E, Ducceschi M, Mantiero M, Lopez S, Raspagliesi F, Niger M, Duca M, Damian S, Proto C, de Braud F, Pruneri G, Manoukian S. Management of BRCA Tumour Testing in an Integrated Molecular Tumour Board Multidisciplinary Model. Front Oncol 2022; 12:857515. [PMID: 35463374 PMCID: PMC9026437 DOI: 10.3389/fonc.2022.857515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Tumour testing of the BRCA1/2 genes is routinely performed in patients with different cancer histological subtypes. To accurately identify patients with tumour-detected germline pathogenic variants (PVs) is a relevant issue currently under investigation. This study aims at evaluating the performance of the tumour-to-germline diagnostic flowchart model defined at our Institutional Molecular Tumour Board (MTB). Results from tumour BRCA sequencing of 641 consecutive unselected cancer patients were discussed during weekly MTB meetings with the early involvement of clinical geneticists for appropriate referral to genetic counselling. The overall tumour detection rate of BRCA1/2 PVs was 8.7% (56/641), ranging from 24.4% (31/127) in high-grade ovarian cancer to 3.9% (12/304) in tumours not associated with germline BRCA1/2 PVs. Thirty-seven patients with PVs (66%) were evaluated by a clinical geneticist, and in 24 of them (64.9%), germline testing confirmed the presence of the PV in blood. Nine of these patients (37.5%) were not eligible for germline testing according to the criteria in use at our institution. Cascade testing was subsequently performed on 18 relatives. The tumour-to-germline diagnostic pipeline, developed in the framework of our institutional MTB, compared with guideline-based germline testing following genetic counselling, proved to be effective in identifying a higher number of germline BRCA PVs carriers.
Collapse
Affiliation(s)
- Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Vingiani
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
| | - Luca Agnelli
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Tamborini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Perrone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Conca
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Iolanda Capone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Adele Busico
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Erica Rosina
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monika Ducceschi
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mara Mantiero
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Lopez
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesco Raspagliesi
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Niger
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Duca
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvia Damian
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Claudia Proto
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo de Braud
- Oncology and Hemato-oncology Department, University of Milan, Milan, Italy.,Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
17
|
Galetzka D, Böck J, Wagner L, Dittrich M, Sinizyn O, Ludwig M, Rossmann H, Spix C, Radsak M, Scholz-Kreisel P, Mirsch J, Linke M, Brenner W, Marron M, Poplawski A, Haaf T, Schmidberger H, Prawitt D. Hypermethylation of RAD9A intron 2 in childhood cancer patients, leukemia and tumor cell lines suggest a role for oncogenic transformation. EXCLI JOURNAL 2022; 21:117-143. [PMID: 35221838 PMCID: PMC8859646 DOI: 10.17179/excli2021-4482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022]
Abstract
Most childhood cancers occur sporadically and cannot be explained by an inherited mutation or an unhealthy lifestyle. However, risk factors might trigger the oncogenic transformation of cells. Among other regulatory signals, hypermethylation of RAD9A intron 2 is responsible for the increased expression of RAD9A protein, which may play a role in oncogenic transformation. Here, we analyzed the RAD9A intron 2 methylation in primary fibroblasts of 20 patients with primary cancer in childhood and second primary cancer (2N) later in life, 20 matched patients with only one primary cancer in childhood (1N) and 20 matched cancer-free controls (0N), using bisulfite pyrosequencing and deep bisulfite sequencing (DBS). Four 1N patients and one 2N patient displayed elevated mean methylation levels (≥ 10 %) of RAD9A. DBS revealed ≥ 2 % hypermethylated alleles of RAD9A, indicative for constitutive mosaic epimutations. Bone marrow samples of NHL and AML tumor patients (n=74), EBV (Epstein Barr Virus) lymphoblasts (n=6), tumor cell lines (n=5) and FaDu subclones (n=13) were analyzed to substantiate our findings. We find a broad spectrum of tumor entities with an aberrant methylation of RAD9A. We detected a significant difference in mean methylation of RAD9A for NHL versus AML patients (p ≤0.025). Molecular karyotyping of AML samples during therapy with hypermethylated RAD9A showed an evolving duplication of 1.8 kb on Chr16p13.3 including the PKD1 gene. Radiation, colony formation assays, cell proliferation, PCR and molecular karyotyping SNP-array experiments using generated FaDu subclones suggest that hypermethylation of RAD9A intron 2 is associated with genomic imbalances in regions with tumor-relevant genes and survival of the cells. In conclusion, this is the very first study of RAD9A intron 2 methylation in childhood cancer and Leukemia. RAD9A epimutations may have an impact on leukemia and tumorigenesis and can potentially serve as a biomarker.
Collapse
Affiliation(s)
- Danuta Galetzka
- Department of Radiation Oncology and Radiation Therapy, University Medical Centre, Mainz, Germany
| | - Julia Böck
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany.,Institute of Pathology, Julius Maximilians University, Würzburg, Germany
| | - Lukas Wagner
- Center for Pediatrics and Adolescent Medicine, University Medical Centre, Mainz, Germany
| | - Marcus Dittrich
- Bioinformatics Department, Julius Maximilians University, Würzburg, Germany
| | - Olesja Sinizyn
- Department of Radiation Oncology and Radiation Therapy, University Medical Centre, Mainz, Germany
| | | | - Heidi Rossmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Centre, Mainz, Germany
| | - Claudia Spix
- Division of Childhood Cancer Epidemiology, Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre, Mainz, Germany
| | - Markus Radsak
- Department of Hematology, University Medical Centre, Mainz, Germany
| | | | - Johanna Mirsch
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Germany
| | - Matthias Linke
- Institute of Human Genetics, University Medical Centre, Mainz, Germany
| | - Walburgis Brenner
- Department of Obstetrics and Women's Health, University Medical Centre, Mainz, Germany
| | - Manuela Marron
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany
| | - Alicia Poplawski
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre, Mainz, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Heinz Schmidberger
- Department of Radiation Oncology and Radiation Therapy, University Medical Centre, Mainz, Germany
| | - Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, University Medical Centre, Mainz, Germany
| |
Collapse
|
18
|
Toward More Comprehensive Homologous Recombination Deficiency Assays in Ovarian Cancer, Part 1: Technical Considerations. Cancers (Basel) 2022; 14:cancers14051132. [PMID: 35267439 PMCID: PMC8909526 DOI: 10.3390/cancers14051132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary High-grade serous ovarian cancer (HGSOC) is the most frequent and lethal form of ovarian cancer and is associated with homologous recombination deficiency (HRD) in 50% of cases. This specific alteration is associated with sensitivity to PARP inhibitors (PARPis). Despite vast prognostic improvements due to PARPis, current molecular assays assessing HRD status suffer from several limitations, and there is an urgent need for a more accurate evaluation. In these companion reviews (Part 1: Technical considerations; Part 2: Medical perspectives), we develop an integrative review to provide physicians and researchers involved in HGSOC management with a holistic perspective, from translational research to clinical applications. Abstract High-grade serous ovarian cancer (HGSOC), the most frequent and lethal form of ovarian cancer, exhibits homologous recombination deficiency (HRD) in 50% of cases. In addition to mutations in BRCA1 and BRCA2, which are the best known thus far, defects can also be caused by diverse alterations to homologous recombination-related genes or epigenetic patterns. HRD leads to genomic instability (genomic scars) and is associated with PARP inhibitor (PARPi) sensitivity. HRD is currently assessed through BRCA1/2 analysis, which produces a genomic instability score (GIS). However, despite substantial clinical achievements, FDA-approved companion diagnostics (CDx) based on GISs have important limitations. Indeed, despite the use of GIS in clinical practice, the relevance of such assays remains controversial. Although international guidelines include companion diagnostics as part of HGSOC frontline management, they also underscore the need for more powerful and alternative approaches for assessing patient eligibility to PARP inhibitors. In these companion reviews, we review and present evidence to date regarding HRD definitions, achievements and limitations in HGSOC. Part 1 is dedicated to technical considerations and proposed perspectives that could lead to a more comprehensive and dynamic assessment of HR, while Part 2 provides a more integrated approach for clinicians.
Collapse
|
19
|
Marino N, German R, Podicheti R, Rusch DB, Rockey P, Huang J, Sandusky GE, Temm CJ, Althouse S, Nephew KP, Nakshatri H, Liu J, Vode A, Cao S, Storniolo AMV. Aberrant epigenetic and transcriptional events associated with breast cancer risk. Clin Epigenetics 2022; 14:21. [PMID: 35139887 PMCID: PMC8830042 DOI: 10.1186/s13148-022-01239-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/25/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified several breast cancer susceptibility loci. However, biomarkers for risk assessment are still missing. Here, we investigated cancer-related molecular changes detected in tissues from women at high risk for breast cancer prior to disease manifestation. Disease-free breast tissue cores donated by healthy women (N = 146, median age = 39 years) were processed for both methylome (MethylCap) and transcriptome (Illumina's HiSeq4000) sequencing. Analysis of tissue microarray and primary breast epithelial cells was used to confirm gene expression dysregulation. RESULTS Transcriptomic analysis identified 69 differentially expressed genes between women at high and those at average risk of breast cancer (Tyrer-Cuzick model) at FDR < 0.05 and fold change ≥ 2. Majority of the identified genes were involved in DNA damage checkpoint, cell cycle, and cell adhesion. Two genes, FAM83A and NEK2, were overexpressed in tissue sections (FDR < 0.01) and primary epithelial cells (p < 0.05) from high-risk breasts. Moreover, 1698 DNA methylation changes were identified in high-risk breast tissues (FDR < 0.05), partially overlapped with cancer-related signatures, and correlated with transcriptional changes (p < 0.05, r ≤ 0.5). Finally, among the participants, 35 women donated breast biopsies at two time points, and age-related molecular alterations enhanced in high-risk subjects were identified. CONCLUSIONS Normal breast tissue from women at high risk of breast cancer bears molecular aberrations that may contribute to breast cancer susceptibility. This study is the first molecular characterization of the true normal breast tissues, and provides an opportunity to investigate molecular markers of breast cancer risk, which may lead to new preventive approaches.
Collapse
Affiliation(s)
- Natascia Marino
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA. .,Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Rana German
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Pam Rockey
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Jie Huang
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - George E Sandusky
- Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Constance J Temm
- Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sandra Althouse
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kenneth P Nephew
- Department of Anatomy, Cell Biology, & Physiology, Indiana University, Bloomington, IN, 47405, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jun Liu
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Ashley Vode
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Sha Cao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Anna Maria V Storniolo
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA.,Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| |
Collapse
|
20
|
Ganguly S, Arora I, Tollefsbol TO. Impact of Stilbenes as Epigenetic Modulators of Breast Cancer Risk and Associated Biomarkers. Int J Mol Sci 2021; 22:ijms221810033. [PMID: 34576196 PMCID: PMC8472542 DOI: 10.3390/ijms221810033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
With the recent advancement of genetic screening for testing susceptibility to mammary oncogenesis in women, the relevance of the gene−environment interaction has become progressively apparent in the context of aberrant gene expressions. Fetal exposure to external stressors, hormones, and nutrients, along with the inherited genome, impact its traits, including cancer susceptibility. Currently, there is increasing interest in the role of epigenetic biomarkers such as genomic methylation signatures, plasma microRNAs, and alterations in cell-signaling pathways in the diagnosis and primary prevention of breast cancer, as well as its prognosis. Polyphenols like natural stilbenes have been shown to be effective in chemoprevention by exerting cytotoxic effects that can stall cell proliferation. Besides possessing antioxidant properties against the DNA-damaging effects of reactive oxygen species, stilbenes have also been observed to modulate cell-signaling pathways. With the increasing trend of early-life screening for hereditary breast cancer risks, the potency of different phytochemicals in harnessing the epigenetic biomarkers of breast cancer risk demand more investigation. This review will explore means of exploiting the abilities of stilbenes in altering the underlying factors that influence breast cancer risk, as well as the appearance of associated biomarkers.
Collapse
Affiliation(s)
- Sebanti Ganguly
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (S.G.); (I.A.)
| | - Itika Arora
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (S.G.); (I.A.)
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (S.G.); (I.A.)
- Integrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Cell Senescence Culture Facility, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence: ; Tel.: +1-205-934-4573
| |
Collapse
|
21
|
Franchet C, Hoffmann JS, Dalenc F. Recent Advances in Enhancing the Therapeutic Index of PARP Inhibitors in Breast Cancer. Cancers (Basel) 2021; 13:cancers13164132. [PMID: 34439286 PMCID: PMC8392832 DOI: 10.3390/cancers13164132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Two to three percent of breast cancer patients harbor germline mutation of either BRCA1 or BRCA2 genes. Their tumor cells are deficient in homologous recombination, a BRCA-dependent DNA repair machinery. These deficient cells survive thanks to the PARP-mediated alternative pathway. Therefore, PARP inhibitors have already shown some level of efficiency in the treatment of metastatic breast cancer patients. Unfortunately, some tumor cells inevitably resist PARP inhibitors by different mechanisms. In this review, we (i) present the notion of homologous recombination deficiency and its evaluation methods, (ii) detail the PARP inhibitor clinical trials in breast cancer, (iii) briefly describe the mechanisms to PARP inhibitors resistance, and (iv) discuss some strategies currently under evaluation to enhance the therapeutic index of PARP inhibitors in breast cancer. Abstract As poly-(ADP)-ribose polymerase (PARP) inhibition is synthetic lethal with the deficiency of DNA double-strand (DSB) break repair by homologous recombination (HR), PARP inhibitors (PARPi) are currently used to treat breast cancers with mutated BRCA1/2 HR factors. Unfortunately, the increasingly high rate of PARPi resistance in clinical practice has dented initial hopes. Multiple resistance mechanisms and acquired vulnerabilities revealed in vitro might explain this setback. We describe the mechanisms and vulnerabilities involved, including newly identified modes of regulation of DSB repair that are now being tested in large cohorts of patients and discuss how they could lead to novel treatment strategies to improve the therapeutic index of PARPi.
Collapse
Affiliation(s)
- Camille Franchet
- Laboratoire de Pathologie and Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, 1 Av. Irène Joliot-Curie, 31100 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, 31037 Toulouse, France;
| | - Florence Dalenc
- Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, 1 Av. Irène Joliot-Curie, 31100 Toulouse, France
- Correspondence:
| |
Collapse
|
22
|
Li N, Zethoven M, McInerny S, Devereux L, Huang YK, Thio N, Cheasley D, Gutiérrez-Enríquez S, Moles-Fernández A, Diez O, Nguyen-Dumont T, Southey MC, Hopper JL, Simard J, Dumont M, Soucy P, Meindl A, Schmutzler R, Schmidt MK, Adank MA, Andrulis IL, Hahnen E, Engel C, Lesueur F, Girard E, Neuhausen SL, Ziv E, Allen J, Easton DF, Scott RJ, Gorringe KL, James PA, Campbell IG. Evaluation of the association of heterozygous germline variants in NTHL1 with breast cancer predisposition: an international multi-center study of 47,180 subjects. NPJ Breast Cancer 2021; 7:52. [PMID: 33980861 PMCID: PMC8115524 DOI: 10.1038/s41523-021-00255-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Abstract
Bi-allelic loss-of-function (LoF) variants in the base excision repair (BER) gene NTHL1 cause a high-risk hereditary multi-tumor syndrome that includes breast cancer, but the contribution of heterozygous variants to hereditary breast cancer is unknown. An analysis of 4985 women with breast cancer, enriched for familial features, and 4786 cancer-free women revealed significant enrichment for NTHL1 LoF variants. Immunohistochemistry confirmed reduced NTHL1 expression in tumors from heterozygous carriers but the NTHL1 bi-allelic loss characteristic mutational signature (SBS 30) was not present. The analysis was extended to 27,421 breast cancer cases and 19,759 controls from 10 international studies revealing 138 cases and 93 controls with a heterozygous LoF variant (OR 1.06, 95% CI: 0.82-1.39) and 316 cases and 179 controls with a missense variant (OR 1.31, 95% CI: 1.09-1.57). Missense variants selected for deleterious features by a number of in silico bioinformatic prediction tools or located within the endonuclease III functional domain showed a stronger association with breast cancer. Somatic sequencing of breast cancers from carriers indicated that the risk associated with NTHL1 appears to operate through haploinsufficiency, consistent with other described low-penetrance breast cancer genes. Data from this very large international multicenter study suggests that heterozygous pathogenic germline coding variants in NTHL1 may be associated with low- to moderate- increased risk of breast cancer.
Collapse
Affiliation(s)
- Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Magnus Zethoven
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Lisa Devereux
- Lifepool, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Yu-Kuan Huang
- Upper Gastrointestinal Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Melbourne, Vic, Australia
| | - Niko Thio
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Dane Cheasley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
| | - Sara Gutiérrez-Enríquez
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO); Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alejandro Moles-Fernández
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO); Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Orland Diez
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO); Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Area of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Quebec, Canada
| | - Martine Dumont
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Quebec, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Quebec, Canada
| | - Alfons Meindl
- University of Munich, Campus Großhadern, Department of Gynecology and Obstetrics, Munich, Germany
| | - Rita Schmutzler
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Integrated Oncology (CIO), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Muriel A Adank
- Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric Hahnen
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany
| | - Christoph Engel
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Elodie Girard
- Inserm, U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Discipline of Medical Genetics, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
- Division of Molecular Medicine, Pathology North, Newcastle, NSW, Australia
| | - Kylie L Gorringe
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia.
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia.
| |
Collapse
|
23
|
Reid BM, Fridley BL. DNA Methylation in Ovarian Cancer Susceptibility. Cancers (Basel) 2020; 13:E108. [PMID: 33396385 PMCID: PMC7795210 DOI: 10.3390/cancers13010108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic alterations are somatically acquired over the lifetime and during neoplastic transformation but may also be inherited as widespread 'constitutional' alterations in normal tissues that can cause cancer predisposition. Epithelial ovarian cancer (EOC) has an established genetic susceptibility and mounting epidemiological evidence demonstrates that DNA methylation (DNAm) intermediates as well as independently contributes to risk. Targeted studies of known EOC susceptibility genes (CSGs) indicate rare, constitutional BRCA1 promoter methylation increases familial and sporadic EOC risk. Blood-based epigenome-wide association studies (EWAS) for EOC have detected a total of 2846 differentially methylated probes (DMPs) with 71 genes replicated across studies despite significant heterogeneity. While EWAS detect both symptomatic and etiologic DMPs, adjustments and analytic techniques may enrich risk associations, as evidenced by the detection of dysregulated methylation of BNC2-a known CSG identified by genome-wide associations studies (GWAS). Integrative genetic-epigenetic approaches have mapped methylation quantitative trait loci (meQTL) to EOC risk, revealing DNAm variations that are associated with nine GWAS loci and, further, one novel risk locus. Increasing efforts to mapping epigenome variation across populations and cell types will be key to decoding both the genomic and epigenomic causal pathways to EOC.
Collapse
Affiliation(s)
- Brett M. Reid
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Brooke L. Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| |
Collapse
|
24
|
Abstract
Abstract
Genomic imprinting ensures the parent-specific expression of either the maternal or the paternal allele, by different epigenetic processes (DNA methylation and histone modifications) that confer parent-specific marks (imprints) in the paternal and maternal germline, respectively. Most protein-coding imprinted genes are involved in embryonic growth, development, and behavior. They are usually organized in genomic domains that are regulated by differentially methylated regions (DMRs). Genomic imprints are erased in the primordial germ cells and then reset in a gene-specific manner according to the sex of the germline. The imprinted genes regulate and interact with other genes, consistent with the existence of an imprinted gene network. Defects of genomic imprinting result in syndromal imprinting disorders. To date a dozen congenital imprinting disorders are known. Usually, a given imprinting disorder can be caused by different types of defects, including point mutations, deletions/duplications, uniparental disomy, and epimutations. Causative trans-acting factors in imprinting disorders, including ZFP57 and the subcortical maternal complex (SCMC), have the potential to affect multiple DMRs across the genome, resulting in a multi-locus imprinting disturbance. There is evidence that mutations in components of the SCMC can confer an increased risk for imprinting disorders.
Collapse
Affiliation(s)
- Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine , University Medical Centre Johannes Gutenberg University Mainz , Obere Zahlbacher Str. 63 , Mainz , Germany
| | - Thomas Haaf
- Institute of Human Genetics , Julius Maximilians University , Würzburg , Germany
| |
Collapse
|
25
|
Dey Bhowmik A, Podder S, Mondal P, Shaw P, Bandyopadhyay A, Das A, Bhattacharjee P, Chakraborty A, Sudarshan M, Chattopadhyay A. Chronic exposure to environmentally relevant concentration of fluoride alters Ogg1 and Rad51 expressions in mice: Involvement of epigenetic regulation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110962. [PMID: 32800233 DOI: 10.1016/j.ecoenv.2020.110962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Chronic exposure to fluoride (F) beyond the permissible limit (1.5 ppm) is known to cause detrimental health effects by induction of oxidative stress-mediated DNA damage overpowering the DNA repair machinery. In the present study, we assessed F induced oxidative stress through monitoring biochemical parameters and looked into the effect of chronic F exposure on two crucial DNA repair genes Ogg1 and Rad51 having important role against ROS induced DNA damages. To address this issue, we exposed Swiss albino mice to an environmentally relevant concentration of fluoride (15 ppm NaF) for 8 months. Results revealed histoarchitectural damages in liver, brain, kidney and spleen. Depletion of GSH, increase in lipid peroxidation and catalase activity in liver and brain confirmed the generation of oxidative stress. qRT-PCR result showed that expressions of Ogg1 and Rad51 were altered after F exposure in the affected organs. Promoter hypermethylation was associated with the downregulation of Rad51. F-induced DNA damage and the compromised DNA repair machinery triggered intrinsic pathway of apoptosis in liver and brain. The present study indicates the possible association of epigenetic regulation with F induced neurotoxicity.
Collapse
Affiliation(s)
- Arpan Dey Bhowmik
- Department of Zoology, Visva-Bharati, Santiniketan, 731235, West Bengal, India
| | - Santosh Podder
- Department of Zoology, Visva-Bharati, Santiniketan, 731235, West Bengal, India; Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India
| | - Paritosh Mondal
- Department of Zoology, Visva-Bharati, Santiniketan, 731235, West Bengal, India
| | - Pallab Shaw
- Department of Zoology, Visva-Bharati, Santiniketan, 731235, West Bengal, India
| | | | - Ankita Das
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Anindita Chakraborty
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, 3/LB-8, Bidhan Nagar, Kolkata, 700098, India
| | - Muthammal Sudarshan
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, 3/LB-8, Bidhan Nagar, Kolkata, 700098, India
| | | |
Collapse
|
26
|
Garg P, Jadhav B, Rodriguez OL, Patel N, Martin-Trujillo A, Jain M, Metsu S, Olsen H, Paten B, Ritz B, Kooy RF, Gecz J, Sharp AJ. A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions. Am J Hum Genet 2020; 107:654-669. [PMID: 32937144 PMCID: PMC7536611 DOI: 10.1016/j.ajhg.2020.08.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases. However, little information exists on the prevalence and distribution of rare epigenetic variation in the human population. In order to address this, we performed a survey of methylation profiles from 23,116 individuals using the Illumina 450k array. Using a robust outlier approach, we identified 4,452 unique autosomal epivariations, including potentially inactivating promoter methylation events at 384 genes linked to human disease. For example, we observed promoter hypermethylation of BRCA1 and LDLR at population frequencies of ∼1 in 3,000 and ∼1 in 6,000, respectively, suggesting that epivariations may underlie a fraction of human disease which would be missed by purely sequence-based approaches. Using expression data, we confirmed that many epivariations are associated with outlier gene expression. Analysis of variation data and monozygous twin pairs suggests that approximately two-thirds of epivariations segregate in the population secondary to underlying sequence mutations, while one-third are likely sporadic events that occur post-zygotically. We identified 25 loci where rare hypermethylation coincided with the presence of an unstable CGG tandem repeat, validated the presence of CGG expansions at several loci, and identified the putative molecular defect underlying most of the known folate-sensitive fragile sites in the genome. Our study provides a catalog of rare epigenetic changes in the human genome, gives insight into the underlying origins and consequences of epivariations, and identifies many hypermethylated CGG repeat expansions.
Collapse
Affiliation(s)
- Paras Garg
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY 10029, USA
| | - Bharati Jadhav
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY 10029, USA
| | - Oscar L Rodriguez
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY 10029, USA
| | - Nihir Patel
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY 10029, USA
| | - Alejandro Martin-Trujillo
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY 10029, USA
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Sofie Metsu
- Department of Medical Genetics, University of Antwerp, 2000 Antwerp, Belgium
| | - Hugh Olsen
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2000 Antwerp, Belgium
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5005, Australia; Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia; Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5006, Australia
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY 10029, USA.
| |
Collapse
|
27
|
Tolmacheva EN, Vasilyev SA, Lebedev IN. Aneuploidy and DNA Methylation as Mirrored Features of Early Human Embryo Development. Genes (Basel) 2020; 11:E1084. [PMID: 32957536 PMCID: PMC7564410 DOI: 10.3390/genes11091084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022] Open
Abstract
Genome stability is an integral feature of all living organisms. Aneuploidy is the most common cause of fetal death in humans. The timing of bursts in increased aneuploidy frequency coincides with the waves of global epigenetic reprogramming in mammals. During gametogenesis and early embryogenesis, parental genomes undergo two waves of DNA methylation reprogramming. Failure of these processes can critically affect genome stability, including chromosome segregation during cell division. Abnormal methylation due to errors in the reprogramming process can potentially lead to aneuploidy. On the other hand, the presence of an entire additional chromosome, or chromosome loss, can affect the global genome methylation level. The associations of these two phenomena are well studied in the context of carcinogenesis, but here, we consider the relationship of DNA methylation and aneuploidy in early human and mammalian ontogenesis. In this review, we link these two phenomena and highlight the critical ontogenesis periods and genome regions that play a significant role in human reproduction and in the formation of pathological phenotypes in newborns with chromosomal aneuploidy.
Collapse
Affiliation(s)
- Ekaterina N. Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, 634050 Tomsk, Russia; (S.A.V.); (I.N.L.)
| | | | | |
Collapse
|
28
|
Poduval DB, Ognedal E, Sichmanova Z, Valen E, Iversen GT, Minsaas L, Lønning PE, Knappskog S. Assessment of tumor suppressor promoter methylation in healthy individuals. Clin Epigenetics 2020; 12:131. [PMID: 32859265 PMCID: PMC7455917 DOI: 10.1186/s13148-020-00920-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background The number of tumor suppressor genes for which germline mutations have been linked to cancer risk is steadily increasing. However, while recent reports have linked constitutional normal tissue promoter methylation of BRCA1 and MLH1 to ovarian and colon cancer risk, the role of epigenetic alterations as cancer risk factors remains largely unknown, presenting an important area for future research. Currently, we lack fast and sensitive methods for assessment of promoter methylation status across known tumor suppressor genes. Results In this paper, we present a novel NGS-based approach assessing promoter methylation status across a large panel of defined tumor suppressor genes to base-pair resolution. The method omits the limitations related to commonly used array-approaches. Our panel includes 565 target regions covering the promoters of 283 defined tumor suppressors, selected by pre-specified criteria, and was applied for rapid targeted methylation-specific NGS. The feasibility of the method was assessed by analyzing normal tissue DNA (white blood cells, WBC) samples from 34 healthy postmenopausal women and by performing preliminary assessment of the methylation landscape of tumor suppressors in these individuals. The mean target coverage was 189.6x providing a sensitivity of 0.53%, sufficient for promoter methylation assessment of low-level methylated genes like BRCA1. Within this limited test-set, we detected 206 regions located in the promoters of 149 genes to be differentially methylated (hyper- or hypo-) at > 99% confidence level. Seven target regions in gene promoters (CIITA, RASSF1, CHN1, PDCD1LG2, GSTP1, XPA, and ZNF668) were found to be hyper-methylated in a minority of individuals, with a > 20 percent point difference in mean methylation across the region between individuals. In an exploratory hierarchical clustering analysis, we found that the individuals analyzed may be grouped into two main groups based on their WBC methylation profile across the 283 tumor suppressor gene promoters. Conclusions Methylation-specific NGS of our tumor suppressor panel, with detailed assessment of differential methylation in healthy individuals, presents a feasible method for identification of novel epigenetic risk factors for cancer.
Collapse
Affiliation(s)
- Deepak B Poduval
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, 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, Bergen, Norway.,Present address: Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Zuzana Sichmanova
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Gjertrud T Iversen
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, 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, 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, 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, Bergen, Norway.
| |
Collapse
|
29
|
Dámaso E, González-Acosta M, Vargas-Parra G, Navarro M, Balmaña J, Ramon y Cajal T, Tuset N, Thompson BA, Marín F, Fernández A, Gómez C, Velasco À, Solanes A, Iglesias S, Urgel G, López C, del Valle J, Campos O, Santacana M, Matias-Guiu X, Lázaro C, Valle L, Brunet J, Pineda M, Capellá G. Comprehensive Constitutional Genetic and Epigenetic Characterization of Lynch-Like Individuals. Cancers (Basel) 2020; 12:E1799. [PMID: 32635641 PMCID: PMC7408773 DOI: 10.3390/cancers12071799] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
The causal mechanism for cancer predisposition in Lynch-like syndrome (LLS) remains unknown. Our aim was to elucidate the constitutional basis of mismatch repair (MMR) deficiency in LLS patients throughout a comprehensive (epi)genetic analysis. One hundred and fifteen LLS patients harboring MMR-deficient tumors and no germline MMR mutations were included. Mutational analysis of 26 colorectal cancer (CRC)-associated genes was performed. Pathogenicity of MMR variants was assessed by splicing and multifactorial likelihood analyses. Genome-wide methylome analysis was performed by the Infinium Human Methylation 450K Bead Chip. The multigene panel analysis revealed the presence of two MMR gene truncating mutations not previously found. Of a total of 15 additional MMR variants identified, five -present in 6 unrelated individuals- were reclassified as pathogenic. In addition, 13 predicted deleterious variants in other CRC-predisposing genes were found in 12 probands. Methylome analysis detected one constitutional MLH1 epimutation, but no additional differentially methylated regions were identified in LLS compared to LS patients or cancer-free individuals. In conclusion, the use of an ad-hoc designed gene panel combined with pathogenicity assessment of variants allowed the identification of deleterious MMR mutations as well as new LLS candidate causal genes. Constitutional epimutations in non-LS-associated genes are not responsible for LLS.
Collapse
Affiliation(s)
- Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Gardenia Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d’Hebron Institute of Oncology (VHIO), Carrer de Natzaret 115-117, 08035 Barcelona, Spain;
| | - Teresa Ramon y Cajal
- Medical Oncology Department, Hospital de Santa Creu i Sant Pau, Carrer de Sant Quintí 89, 08041 Barcelona, Spain; (T.R.y.C.); (C.L.)
| | - Noemí Tuset
- Genetic Counseling Unit, Hospital Arnau de Vilanova, Avinguda Alcalde Rovira Roure 80, 25198 Lleida, Spain; (N.T.); (G.U.)
| | - Bryony A. Thompson
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Building 181 Grattan St, VIC 3010 Melbourne, Australia;
| | - Fátima Marín
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Àngela Velasco
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d’Investigació Biomèdica de Girona (IDIBGI), Carrer del Dr. Castany s/n, 17190 Salt, Girona, Spain
| | - Ares Solanes
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Sílvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Gisela Urgel
- Genetic Counseling Unit, Hospital Arnau de Vilanova, Avinguda Alcalde Rovira Roure 80, 25198 Lleida, Spain; (N.T.); (G.U.)
| | - Consol López
- Medical Oncology Department, Hospital de Santa Creu i Sant Pau, Carrer de Sant Quintí 89, 08041 Barcelona, Spain; (T.R.y.C.); (C.L.)
| | - Jesús del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Olga Campos
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
| | - Maria Santacana
- Pathology Department, Hospital Arnau de Vilanova, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Avinguda Alcalde Rovira Roure 80, 25198 Lleida, Spain;
| | - Xavier Matias-Guiu
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
- Pathology Department, Hospital Arnau de Vilanova, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Avinguda Alcalde Rovira Roure 80, 25198 Lleida, Spain;
- Pathology Department, Bellvitge University Hospital, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), Carrer de la Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d’Investigació Biomèdica de Girona (IDIBGI), Carrer del Dr. Castany s/n, 17190 Salt, Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Carrer Emili Grahit 77, 17003 Girona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d’Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Avinguda de la Gran Via de l’Hospitalet 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Spain; (E.D.); (M.G.-A.); (G.V.-P.); (M.N.); (F.M.); (A.F.); (C.G.); (A.S.); (S.I.); (J.d.V.); (O.C.); (C.L.); (L.V.); (J.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; (À.V.); (X.M.-G.)
| |
Collapse
|
30
|
Suszynska M, Ratajska M, Kozlowski P. BRIP1, RAD51C, and RAD51D mutations are associated with high susceptibility to ovarian cancer: mutation prevalence and precise risk estimates based on a pooled analysis of ~30,000 cases. J Ovarian Res 2020; 13:50. [PMID: 32359370 PMCID: PMC7196220 DOI: 10.1186/s13048-020-00654-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background It is estimated that more than 20% of ovarian cancer cases are associated with a genetic predisposition that is only partially explained by germline mutations in the BRCA1 and BRCA2 genes. Recently, several pieces of evidence showed that mutations in three genes involved in the homologous recombination DNA repair pathway, i.e., BRIP1, RAD51C, and RAD51D, are associated with a high risk of ovarian cancer. To more precisely estimate the ovarian cancer risk attributed to BRIP1, RAD51C, and RAD51D mutations, we performed a meta-analysis based on a comparison of a total of ~ 29,400 ovarian cancer patients from 63 studies and a total of ~ 116,000 controls from the gnomAD database. Results The analysis allowed precise estimation of ovarian cancer risks attributed to mutations in BRIP1, RAD51C, and RAD51D, confirming that all three genes are ovarian cancer high-risk genes (odds ratio (OR) = 4.94, 95%CIs:4.07–6.00, p < 0.0001; OR = 5.59, 95%CIs:4.42–7.07, p < 0.0001; and OR = 6.94, 95%CIs:5.10–9.44, p < 0.0001, respectively). In the present report, we show, for the first time, a mutation-specific risk analysis associated with distinct, recurrent, mutations in the genes. Conclusions The meta-analysis provides evidence supporting the pathogenicity of BRIP1, RAD51C, and RAD51D mutations in relation to ovarian cancer. The level of ovarian cancer risk conferred by these mutations is relatively high, indicating that after BRCA1 and BRCA2, the BRIP1, RAD51C, and RAD51D genes are the most important ovarian cancer risk genes, cumulatively contributing to ~ 2% of ovarian cancer cases. The inclusion of the genes into routine diagnostic tests may influence both the prevention and the potential treatment of ovarian cancer.
Collapse
Affiliation(s)
- Malwina Suszynska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Street, 61-704, Poznan, Poland
| | - Magdalena Ratajska
- Department of Pathology, Dunedin School of Medicine, University of Otago, 60 Hanover Street, Dunedin, 9016, New Zealand.,Department of Biology and Medical Genetics, Medical University of Gdansk, Debinki 1 St., 80-210, Gdansk, Poland
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Street, 61-704, Poznan, Poland.
| |
Collapse
|
31
|
Bao-Caamano A, Rodriguez-Casanova A, Diaz-Lagares A. Epigenetics of Circulating Tumor Cells in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1220:117-134. [PMID: 32304083 DOI: 10.1007/978-3-030-35805-1_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid biopsy based on the analysis of circulating tumor cells (CTCs) has emerged as an important field of research. Molecular characterization of CTCs can provide insights into cancer biology and biomarkers for the clinic, representing a non-invasive powerful tool for monitoring breast cancer metastasis and predict the therapeutic response. Epigenetic mechanisms play a key role in the control of gene expression and their alteration contributes to cancer development and progression. These epigenetic modifications in CTCs have been described mainly related to modifications of the DNA methylation pattern and changes in the expression profile of noncoding RNAs. Here we summarize the recent findings on the epigenetic characterization of CTCs in breast cancer and their clinical value as tumor biomarkers, and discuss challenges and opportunities in this field.
Collapse
Affiliation(s)
- Aida Bao-Caamano
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
| |
Collapse
|
32
|
Fiala EM, Ortiz MV, Kennedy JA, Glodzik D, Fleischut MH, Duffy KA, Hathaway ER, Heaton T, Gerstle JT, Steinherz P, Shukla N, McNeer N, Tkachuk K, Bouvier N, Cadoo K, Carlo MI, Latham A, Dubard Gault M, Joseph V, Kemel Y, Kentsis A, Stadler Z, La Quaglia M, Papaemmanuil E, Friedman D, Ganguly A, Kung A, Offit K, Kalish JM, Walsh MF. 11p15.5 epimutations in children with Wilms tumor and hepatoblastoma detected in peripheral blood. Cancer 2020; 126:3114-3121. [PMID: 32320050 PMCID: PMC7383476 DOI: 10.1002/cncr.32907] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/18/2020] [Accepted: 03/17/2020] [Indexed: 01/14/2023]
Abstract
Background Constitutional or somatic mosaic epimutations are increasingly recognized as a mechanism of gene dysregulation resulting in cancer susceptibility. Beckwith‐Wiedemann syndrome is the cancer predisposition syndrome most commonly associated with epimutation and is extremely variable in its phenotypic presentation, which can include isolated tumors. Because to the authors' knowledge large‐scale germline DNA sequencing studies have not included methylation analysis, the percentage of pediatric cancer predisposition that is due to epimutations is unknown. Methods Germline methylation testing at the 11p15.5 locus was performed in blood for 24 consecutive patients presenting with hepatoblastoma (3 patients) or Wilms tumor (21 patients). Results Six individuals with Wilms tumor and 1 patient with hepatoblastoma were found to have low‐level gain of methylation at imprinting control 1, and a child with hepatoblastoma was found to have loss of methylation at imprinting control 2. The loss of methylation at imprinting control 2 was found to be maternally inherited, despite not being associated with any detectable genomic alteration. Conclusions Overall, 33% of patients (8 of 24 patients) with Wilms tumor or hepatoblastoma were found to have an epigenetic susceptibility that was detectable in the blood. It is interesting to note that low‐level gain of methylation at imprinting control 1 predominantly was detected in females with bilateral Wilms tumors. Further studies in larger cohorts are needed to determine the efficacy of testing all patients with Wilms tumor or hepatoblastoma for 11p15.5 epimutations in the blood as part of DNA analysis because this hallmark of predisposition will not be detected by sequencing‐based approaches and detecting a cancer predisposition may modify treatment. In the current study, all patients presenting with Wilms tumor or hepatoblastoma undergo 11p15.5 methylation analysis. Approximately one‐third are found to have an epimutation at this locus that is detectable in peripheral blood.
Collapse
Affiliation(s)
- Elise M Fiala
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Jennifer A Kennedy
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dominik Glodzik
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Megan Harlan Fleischut
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kelly A Duffy
- Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Evan R Hathaway
- Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Todd Heaton
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justin T Gerstle
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter Steinherz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Nicole McNeer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaitlyn Tkachuk
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy Bouvier
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karen Cadoo
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria I Carlo
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alicia Latham
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Division of Long Term Follow-Up, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marianne Dubard Gault
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vijai Joseph
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Kemel
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alex Kentsis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia Stadler
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael La Quaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Danielle Friedman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Division of Long Term Follow-Up, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arupa Ganguly
- Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Kenneth Offit
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jennifer M Kalish
- Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael F Walsh
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
33
|
Analysis of BRCA1 and RAD51C Promoter Methylation in Italian Families at High-Risk of Breast and Ovarian Cancer. Cancers (Basel) 2020; 12:cancers12040910. [PMID: 32276467 PMCID: PMC7226593 DOI: 10.3390/cancers12040910] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/29/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Previous studies on breast and ovarian carcinoma (BC and OC) revealed constitutional BRCA1 and RAD51C promoter hypermethylation as epigenetic alterations leading to tumor predisposition. Nevertheless, the impact of epimutations at these genes is still debated. One hundred and eight women affected by BC, OC, or both and considered at very high risk of carrying BRCA1 germline mutations were studied. All samples were negative for pathogenic variants or variants of uncertain significance at BRCA testing. Quantitative BRCA1 and RAD51C promoter methylation analyses were performed by Epityper mass spectrometry on peripheral blood samples and results were compared with those in controls. All the 108 analyzed cases showed methylation levels at the BRCA1/RAD51C promoter comparable with controls. Mean methylation levels (± stdev) at the BRCA1 promoter were 4.3% (± 1.4%) and 4.4% (± 1.4%) in controls and patients, respectively (p > 0.05; t-test); mean methylation levels (± stdev) at the RAD51C promoter were 4.3% (± 0.9%) and 3.7% (± 0.9%) in controls and patients, respectively (p > 0.05; t-test). Based on these observations; the analysis of constitutional methylation at promoters of these genes does not seem to substantially improve the definition of cancer risks in patients. These data support the idea that epimutations represent a very rare event in high-risk BC/OC populations.
Collapse
|
34
|
Yang Y, Wu L, Shu XO, Cai Q, Shu X, Li B, Guo X, Ye F, Michailidou K, Bolla MK, Wang Q, Dennis J, Andrulis IL, Brenner H, Chenevix-Trench G, Campa D, Castelao JE, Gago-Dominguez M, Dörk T, Hollestelle A, Lophatananon A, Muir K, Neuhausen SL, Olsson H, Sandler DP, Simard J, Kraft P, Pharoah PDP, Easton DF, Zheng W, Long J. Genetically Predicted Levels of DNA Methylation Biomarkers and Breast Cancer Risk: Data From 228 951 Women of European Descent. J Natl Cancer Inst 2020; 112:295-304. [PMID: 31143935 PMCID: PMC7073907 DOI: 10.1093/jnci/djz109] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/08/2019] [Accepted: 05/22/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND DNA methylation plays a critical role in breast cancer development. Previous studies have identified DNA methylation marks in white blood cells as promising biomarkers for breast cancer. However, these studies were limited by low statistical power and potential biases. Using a new methodology, we investigated DNA methylation marks for their associations with breast cancer risk. METHODS Statistical models were built to predict levels of DNA methylation marks using genetic data and DNA methylation data from HumanMethylation450 BeadChip from the Framingham Heart Study (n = 1595). The prediction models were validated using data from the Women's Health Initiative (n = 883). We applied these models to genomewide association study (GWAS) data of 122 977 breast cancer patients and 105 974 controls to evaluate if the genetically predicted DNA methylation levels at CpG sites (CpGs) are associated with breast cancer risk. All statistical tests were two-sided. RESULTS Of the 62 938 CpG sites CpGs investigated, statistically significant associations with breast cancer risk were observed for 450 CpGs at a Bonferroni-corrected threshold of P less than 7.94 × 10-7, including 45 CpGs residing in 18 genomic regions, that have not previously been associated with breast cancer risk. Of the remaining 405 CpGs located within 500 kilobase flaking regions of 70 GWAS-identified breast cancer risk variants, the associations for 11 CpGs were independent of GWAS-identified variants. Integrative analyses of genetic, DNA methylation, and gene expression data found that 38 CpGs may affect breast cancer risk through regulating expression of 21 genes. CONCLUSION Our new methodology can identify novel DNA methylation biomarkers for breast cancer risk and can be applied to other diseases.
Collapse
Affiliation(s)
- Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Fei Ye
- Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Kyriaki Michailidou
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Irene L Andrulis
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research (HB) and German Cancer Consortium (HB), German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Biomedica Orense-Pontevedra-Vigo, Xerencia de Xestión Integrada de Vigo-SERGAS, Vigo, Spain
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago De Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, QC, Canada
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health (PK) and Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Paul D P Pharoah
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| |
Collapse
|
35
|
Wong EM, Southey MC, Terry MB. Integrating DNA methylation measures to improve clinical risk assessment: are we there yet? The case of BRCA1 methylation marks to improve clinical risk assessment of breast cancer. Br J Cancer 2020; 122:1133-1140. [PMID: 32066913 PMCID: PMC7156506 DOI: 10.1038/s41416-019-0720-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/11/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Current risk prediction models estimate the probability of developing breast cancer over a defined period based on information such as family history, non-genetic breast cancer risk factors, genetic information from high and moderate risk breast cancer susceptibility genes and, over the past several years, polygenic risk scores (PRS) from more than 300 common variants. The inclusion of additional data such as PRS improves risk stratification, but it is anticipated that the inclusion of epigenetic marks could further improve model performance accuracy. Here, we present the case for including information on DNA methylation marks to improve the accuracy of these risk prediction models, and consider how this approach contrasts genetic information, as identifying DNA methylation marks associated with breast cancer risk differs inherently according to the source of DNA, approaches to the measurement of DNA methylation, and the timing of measurement. We highlight several DNA-methylation-specific challenges that should be considered when incorporating information on DNA methylation marks into risk prediction models, using BRCA1, a highly penetrant breast cancer susceptibility gene, as an example. Only after careful consideration of study design and DNA methylation measurement will prospective performance of the incorporation of information regarding DNA methylation marks into risk prediction models be valid.
Collapse
Affiliation(s)
- Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
| |
Collapse
|
36
|
Dámaso E, Canet-Hermida J, Vargas-Parra G, Velasco À, Marín F, Darder E, Del Valle J, Fernández A, Izquierdo À, Mateu G, Oliveras G, Escribano C, Piñol V, Uchima HI, Soto JL, Hitchins M, Farrés R, Lázaro C, Queralt B, Brunet J, Capellá G, Pineda M. Highly sensitive MLH1 methylation analysis in blood identifies a cancer patient with low-level mosaic MLH1 epimutation. Clin Epigenetics 2019; 11:171. [PMID: 31779681 PMCID: PMC6883525 DOI: 10.1186/s13148-019-0762-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022] Open
Abstract
Constitutional MLH1 methylation (epimutation) is a rare cause of Lynch syndrome. Low-level methylation (≤ 10%) has occasionally been described. This study aimed to identify low-level constitutional MLH1 epimutations and determine its causal role in patients with MLH1-hypermethylated colorectal cancer. Eighteen patients with MLH1-hypermethylated colorectal tumors in whom MLH1 methylation was previously undetected in blood by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) were screened for MLH1 methylation using highly sensitive MS-melting curve analysis (MS-MCA). Constitutional methylation was characterized by different approaches. MS-MCA identified one patient (5.6%) with low-level MLH1 methylation (~ 1%) in blood and other normal tissues, which was confirmed by clonal bisulfite sequencing in blood. The patient had developed three clonally related gastrointestinal MLH1-methylated tumor lesions at 22, 24, and 25 years of age. The methylated region in normal tissues overlapped with that reported for other carriers of constitutional MLH1 epimutations. Low-level MLH1 methylation and reduced allelic expression were linked to the same genetic haplotype, whereas the opposite allele was lost in patient’s tumors. Mutation screening of MLH1 and other hereditary cancer genes was negative. Herein, a highly sensitive MS-MCA-based approach has demonstrated its utility for the identification of low-level constitutional MLH1 epigenetic mosaicism. The eventual identification and characterization of additional cases will be critical to ascertain the cancer risks associated with constitutional MLH1 epigenetic mosaicism.
Collapse
Affiliation(s)
- Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Júlia Canet-Hermida
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Gardenia Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Àngela Velasco
- Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Fátima Marín
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Esther Darder
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Àngel Izquierdo
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Gemma Mateu
- Pathology Department, Dr Josep Trueta University Hospital, Girona, Spain
| | - Glòria Oliveras
- Pathology Department, Dr Josep Trueta University Hospital, Girona, Spain
| | | | - Virgínia Piñol
- Department of Gastroenterology, Dr Josep Trueta University Hospital, Girona, Spain
| | - Hugo-Ikuo Uchima
- Department of Gastroenterology, Dr Josep Trueta University Hospital, Girona, Spain
| | - José Luis Soto
- Hereditary Cancer Program Valencian Region, Molecular Genetics Laboratory, Elche University Hospital, Elche, Alicante, Spain
| | - Megan Hitchins
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, CA, Los Angeles, USA
| | - Ramon Farrés
- Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Bernat Queralt
- Department of Medical Oncology, Catalan Institute of Oncology, Girona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Sciences Department, School of Medicine, University of Girona, Girona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| |
Collapse
|
37
|
Kanakkanthara A, Huntoon CJ, Hou X, Zhang M, Heinzen EP, O'Brien DR, Oberg AL, John Weroha S, Kaufmann SH, Karnitz LM. ZC3H18 specifically binds and activates the BRCA1 promoter to facilitate homologous recombination in ovarian cancer. Nat Commun 2019; 10:4632. [PMID: 31604914 PMCID: PMC6789141 DOI: 10.1038/s41467-019-12610-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/18/2019] [Indexed: 01/27/2023] Open
Abstract
Reduced BRCA1 expression causes homologous recombination (HR) repair defects in high-grade serous ovarian cancers (HGSOCs). Here, we demonstrate that BRCA1 is transcriptionally activated by a previously unknown function of ZC3H18. We show that ZC3H18 is a DNA-binding protein that interacts with an E2F site in the BRCA1 promoter where it facilitates recruitment of E2F4 to an adjacent E2F site to promote BRCA1 transcription. Consistent with ZC3H18 role in activating BRCA1 expression, ZC3H18 depletion induces BRCA1 promoter methylation, reduces BRCA1 expression, disrupts HR, and sensitizes cells to DNA crosslinkers and poly(ADP-ribose) polymerase inhibitors. Moreover, in patient-derived xenografts and primary HGSOC tumors, ZC3H18 and E2F4 mRNA levels are positively correlated with BRCA1 mRNA levels, further supporting ZC3H18 role in regulating BRCA1. Given that ZC3H18 lies within 16q24.2, a region with frequent copy number loss in HGSOC, these findings suggest that ZC3H18 copy number losses could contribute to HR defects in HGSOC.
Collapse
Affiliation(s)
- Arun Kanakkanthara
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacology, Mayo Clinic, Rochester, MN, USA
| | | | - Xiaonan Hou
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Minzhi Zhang
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ethan P Heinzen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Daniel R O'Brien
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Ann L Oberg
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - S John Weroha
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
- Department of Pharmacology, Mayo Clinic, Rochester, MN, USA
| | - Larry M Karnitz
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA.
- Department of Pharmacology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
38
|
DNA Repair Deficiency in Breast Cancer: Opportunities for Immunotherapy. JOURNAL OF ONCOLOGY 2019; 2019:4325105. [PMID: 31320901 PMCID: PMC6607732 DOI: 10.1155/2019/4325105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/04/2019] [Accepted: 05/29/2019] [Indexed: 12/19/2022]
Abstract
Historically the development of anticancer treatments has been focused on their effect on tumor cells alone. However, newer treatments have shifted attention to targets on immune cells, resulting in dramatic responses. The effect of DNA repair deficiency on the microenvironment remains an area of key interest. Moreover, established therapies such as DNA damaging treatments such as chemotherapy and PARP inhibitors further modify the tumor microenvironment. Here we describe DNA repair pathways in breast cancer and activation of innate immune pathways in DNA repair deficiency, in particular, the STING (STimulator of INterferon Genes) pathway. Breast tumors with DNA repair deficiency are associated with upregulation of immune checkpoints including PD-L1 (Programmed Death Ligand-1) and may represent a target population for single agent or combination immunotherapy treatment.
Collapse
|
39
|
Chen J, Haanpää MK, Gruber JJ, Jäger N, Ford JM, Snyder MP. High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients. Clin Cancer Res 2019; 25:5301-5314. [PMID: 31175093 DOI: 10.1158/1078-0432.ccr-18-2423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/11/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Understanding and explaining hereditary predisposition to cancer has focused on the genetic etiology of the disease. However, mutations in known genes associated with breast cancer, such as BRCA1 and BRCA2, account for less than 25% of familial cases of breast cancer. Recently, specific epigenetic modifications at BRCA1 have been shown to promote hereditary breast cancer, but the broader potential for epigenetic contribution to hereditary breast cancer is not yet well understood. EXPERIMENTAL DESIGN We examined DNA methylation through deep bisulfite sequencing of CpG islands and known promoter or regulatory regions in peripheral blood DNA from 99 patients with familial or early-onset breast or ovarian cancer, 6 unaffected BRCA mutation carriers, and 49 unaffected controls. RESULTS In 9% of patients, we observed altered methylation in the promoter regions of genes known to be involved in cancer, including hypermethylation at the tumor suppressor PTEN and hypomethylation at the proto-oncogene TEX14. These alterations occur in the form of allelic methylation that span up to hundreds of base pairs in length. CONCLUSIONS Our observations suggest a broader role for DNA methylation in early-onset, familial risk breast cancer. Further studies are warranted to clarify these mechanisms and the benefits of DNA methylation screening for early risk prediction of familial cancers.
Collapse
Affiliation(s)
- Justin Chen
- Department of Genetics, Stanford University, Stanford, California
| | - Maria K Haanpää
- Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Joshua J Gruber
- Department of Genetics, Stanford University, Stanford, California.,Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Natalie Jäger
- Department of Genetics, Stanford University, Stanford, California
| | - James M Ford
- Department of Genetics, Stanford University, Stanford, California. .,Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California.
| |
Collapse
|
40
|
Hauke J, Hahnen E, Schneider S, Reuss A, Richters L, Kommoss S, Heimbach A, Marmé F, Schmidt S, Prieske K, Gevensleben H, Burges A, Borde J, De Gregorio N, Nürnberg P, El-Balat A, Thiele H, Hilpert F, Altmüller J, Meier W, Dietrich D, Kimmig R, Schoemig-Markiefka B, Kast K, Braicu E, Baumann K, Jackisch C, Park-Simon TW, Ernst C, Hanker L, Pfisterer J, Schnelzer A, du Bois A, Schmutzler RK, Harter P. Deleterious somatic variants in 473 consecutive individuals with ovarian cancer: results of the observational AGO-TR1 study (NCT02222883). J Med Genet 2019; 56:574-580. [PMID: 30979843 DOI: 10.1136/jmedgenet-2018-105930] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/26/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND For individuals with ovarian cancer (OC), therapy options mainly depend on BRCA1/2 germline status. What is the prevalence of deleterious somatic variants, that is, does genetic tumour testing identify subgroups of individuals who also might benefit from targeted therapy? METHODS Paired analysis of tumour-derived versus blood-derived DNA to determine the prevalence of deleterious somatic variants in OC predisposition genes (ATM, BRCA1/2, BRIP1, MSH2/6, PALB2, RAD51C/D and TP53) and the PIK3CA and PTEN genes in individuals with OC (AGO-TR1 study, NCT02222883). Results were complemented by BRCA1, PALB2 and RAD51C promoter methylation analyses and stratified by histological subtype; 473 individuals were included. RESULTS The combined analyses revealed that deleterious germline variants in established OC predisposition genes (all: 125/473, 26.4%; BRCA1/2: 97/473, 20.5%), deleterious somatic variants in established OC predisposition genes excluding TP53 (all: 39/473, 8.2%; BRCA1/2: 30/473, 6.3%) and promoter methylation (all: 67/473, 14.2%; BRCA1: 57/473, 12.1%; RAD51C: 10/473, 2.1%; PALB2: 0/473) were mutually exclusive, with a few exceptions. The same holds true for deleterious somatic PIK3CA and/or PTEN variants (33/473, 7.0%) found to be enriched in endometrioid and clear cell OC (16/35, 45.7%); 84.3 % of the deleterious single-nucleotide/indel germline variants in established OC predisposition genes showed significantly higher variant fractions (VFs) in the tumour-derived versus blood-derived DNA, indicating a loss of the wild-type alleles. CONCLUSION Tumour sequencing of the BRCA1, BRCA2, PIK3CA and PTEN genes along with BRCA1 and RAD51C promoter methylation analyses identified large subgroups of germline mutation-negative individuals who may be addressed in interventional studies using PARP or PI3K/AKT/mTOR inhibitors. TRIAL REGISTRATION NUMBER NCT02222883.
Collapse
Affiliation(s)
- Jan Hauke
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Stephanie Schneider
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Alexander Reuss
- Coordinating Center for Clinical Trials, Philipps-University of Marburg, Marburg, Germany
| | - Lisa Richters
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Stefan Kommoss
- Department of Women's Health, University Hospital Tuebingen, Tuebingen, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederik Marmé
- National Center for Tumor Disease, Department of Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Sandra Schmidt
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Katharina Prieske
- Department of Gynecology and Gynecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Alexander Burges
- Department of Gynecology, University Hospital Munich-Großhadern, Munich, Germany
| | - Julika Borde
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Nikolaus De Gregorio
- Department of Gynecology and Obstetrics, University Hospital, Universität Ulm, Ulm, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Ahmed El-Balat
- Department of Gynecology, University of Frankfurt, Frankfurt, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Felix Hilpert
- Department of Gynecology, University of Kiel, Kiel, Germany.,Onkologisches Therapiezentrum, Krankenhaus Jerusalem, Hamburg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Werner Meier
- Department of Gynecology and Obstetrics, University Hospital Duesseldorf, Duesseldorf, Germany
| | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Rainer Kimmig
- Department of Gynecology, University of Essen, Essen, Germany
| | | | - Karin Kast
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), Partner Site Dresden, Heidelberg, Germany
| | - Elena Braicu
- Department of Gynecology and Gynecological Oncology, Charité, Berlin, Germany
| | - Klaus Baumann
- Department of Gynecology, Gynecologic Endocrinology and Oncology, University of Gießen and Marburg GmbH, Marburg, Germany.,Department of Gynecology and Obstetrics, Klinikum Ludwigshafen, Ludwigshafen, Germany
| | - Christian Jackisch
- Department of Gynecology and Obstetrics, Sana Klinikum, Offenbach, Germany
| | | | - Corinna Ernst
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Lars Hanker
- Department of Gynecology & Obstetrics, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | | | - Andreas Schnelzer
- Department of Obstetrics and Gynecology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany.,Department of Obstetrics and Gynecology, RoMed Klinikum Rosenheim, Rosenheim, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| |
Collapse
|
41
|
Lønning PE, Eikesdal HP, Løes IM, Knappskog S. Constitutional Mosaic Epimutations - a hidden cause of cancer? Cell Stress 2019; 3:118-135. [PMID: 31225507 PMCID: PMC6551830 DOI: 10.15698/cst2019.04.183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Silencing of tumor suppressor genes by promoter hypermethylation is a key mechanism to facilitate cancer progression in many malignancies. While promoter hypermethylation can occur at later stages of the carcinogenesis process, constitutional methylation of key tumor suppressors may be an initiating event whereby cancer is started. Constitutional BRCA1 methylation due to cis-acting germline genetic variants is associated with a high risk of breast and ovarian cancer. However, this seems to be a rare event, restricted to a very limited number of families. In contrast, mosaic constitutional BRCA1 methylation is detected in 4-7% of newborn females without germline BRCA1 mutations. While the cause of such methylation is poorly understood, mosaic normal tissue BRCA1 methylation is associated with a 2-3 fold increased risk of high-grade serous ovarian cancer (HGSOC). As such, BRCA1 methylation may be the cause of a significant number of ovarian cancers. Given the molecular similarities between HGSOC and basal-like breast cancer, the findings with respect to HGSOC suggest that constitutional BRCA1 methylation could be a risk factor for basal-like breast cancer as well. Similar to BRCA1, some specific germline variants in MLH1 and MSH2 are associated with promoter methylation and a high risk of colorectal cancers in rare hereditary cases of the disease. However, as many as 15% of all colorectal cancers are of the microsatellite instability (MSI) "high" subtype, in which commonly the tumors harbor MLH1 hypermethylation. Constitutional mosaic methylation of MLH1 in normal tissues has been detected but not formally evaluated as a potential risk factor for incidental colorectal cancers. However, the findings with respect to BRCA1 in breast and ovarian cancer raises the question whether mosaic MLH1 methylation is a risk factor for MSI positive colorectal cancer as well. As for MGMT, a promoter variant is associated with elevated methylation across a panel of solid cancers, and MGMT promoter methylation may contribute to an elevated cancer risk in several of these malignancies. We hypothesize that constitutional mosaic promoter methylation of crucial tumor suppressors may trigger certain types of cancer, similar to germline mutations inactivating the same particular genes. Such constitutional methylation events may be a spark to ignite cancer development, and if associated with a significant cancer risk, screening for such epigenetic alterations could be part of cancer prevention programs to reduce cancer mortality in the future.
Collapse
Affiliation(s)
- Per E. Lønning
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Hans P. Eikesdal
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Inger M. Løes
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| |
Collapse
|
42
|
Azzollini J, Pesenti C, Pizzamiglio S, Fontana L, Guarino C, Peissel B, Plebani M, Tabano S, Sirchia SM, Colapietro P, Villa R, Paolini B, Verderio P, Miozzo M, Manoukian S. Constitutive BRCA1 Promoter Hypermethylation Can Be a Predisposing Event in Isolated Early-Onset Breast Cancer. Cancers (Basel) 2019; 11:cancers11010058. [PMID: 30634417 PMCID: PMC6356733 DOI: 10.3390/cancers11010058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022] Open
Abstract
Early age at onset of breast cancer (eoBC) is suggestive of an increased genetic risk. Although genetic testing is offered to all eoBC-affected women, in isolated cases the detection rate of pathogenic variants is <10%. This study aimed at assessing the role of constitutive promoter methylation at BC-associated loci as an underlying predisposing event in women with eoBC and negative family history. Promoter methylation at 12 loci was assessed by the MassARRAY technology in blood from 154 BRCA1/2 negative patients with eoBC and negative family history, and 60 healthy controls. Hypermethylation was determined, within each promoter, by comparing the patient’s mean methylation value with thresholds based on one-sided 95% bootstrap confidence interval of the controls’ mean. Three patients had hypermethylated results, two at BRCA1 and one at RAD51C. Analyses on tumor tissue from the patient exceeding the highest threshold at BRCA1 revealed a mean methylation >60% and loss of heterozygosity at chromosome 17q. The patient hypermethylated at RAD51C showed low methylation in the tumor sample, ruling out a role for methylation-induced silencing in tumor development. In isolated eoBC patients, BRCA1 constitutive promoter methylation may be a predisposing event. Further studies are required to define the impact of methylation changes occurring at BC-predisposing genes and their role in tumorigenesis.
Collapse
Affiliation(s)
- Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Chiara Pesenti
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano; Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy.
| | - Sara Pizzamiglio
- Unit of Bioinformatics and Biostatistics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Laura Fontana
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano; Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy.
| | - Carmela Guarino
- Immunohematology & Transfusion Medicine Service, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy.
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Maddalena Plebani
- Unit of Bioinformatics and Biostatistics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Silvia Tabano
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano; Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy.
| | - Silvia Maria Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy.
| | - Patrizia Colapietro
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano; Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy.
| | - Roberta Villa
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Biagio Paolini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Paolo Verderio
- Unit of Bioinformatics and Biostatistics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Monica Miozzo
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano; Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy.
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| |
Collapse
|
43
|
The Clinical Utility of Epigenetics: A Case Study. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
44
|
Evans DGR, van Veen EM, Byers HJ, Wallace AJ, Ellingford JM, Beaman G, Santoyo-Lopez J, Aitman TJ, Eccles DM, Lalloo FI, Smith MJ, Newman WG. A Dominantly Inherited 5' UTR Variant Causing Methylation-Associated Silencing of BRCA1 as a Cause of Breast and Ovarian Cancer. Am J Hum Genet 2018; 103:213-220. [PMID: 30075112 PMCID: PMC6080768 DOI: 10.1016/j.ajhg.2018.07.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/29/2018] [Indexed: 12/20/2022] Open
Abstract
Pathogenic variants in BRCA1 or BRCA2 are identified in ∼20% of families with multiple individuals affected by early-onset breast and/or ovarian cancer. Extensive searches for additional highly penetrant genes or alternative mutational mechanisms altering BRCA1 or BRCA2 have not explained the missing heritability. Here, we report a dominantly inherited 5' UTR variant associated with epigenetic BRCA1 silencing due to promoter hypermethylation in two families affected by breast and ovarian cancer. BRCA1 promoter methylation of ten CpG dinucleotides in families who are affected by breast and/or ovarian cancer but do not have germline BRCA1 or BRCA2 pathogenic variants was assessed by pyrosequencing and clonal bisulfite sequencing. RNA and DNA sequencing of BRCA1 from lymphocytes was undertaken to establish allelic expression and the presence of germline variants. BRCA1 promoter hypermethylation was identified in 2 of 49 families in which multiple women are affected by grade 3 breast cancer or high-grade serous ovarian cancer. Soma-wide BRCA1 promoter hypermethylation was confirmed in blood, buccal mucosa, and hair follicles. Pyrosequencing showed that DNA was ∼50% methylated, consistent with the silencing of one allele, which was confirmed by clonal bisulfite sequencing. RNA sequencing revealed the allelic loss of BRCA1 expression in both families and that this loss of expression segregated with the heterozygous variant c.-107A>T in the BRCA1 5' UTR. Our results establish a mechanism whereby familial breast and ovarian cancer is caused by an in cis 5' UTR variant associated with epigenetic silencing of the BRCA1 promoter in two independent families. We propose that methylation analyses be undertaken to establish the frequency of this mechanism in families affected by early-onset breast and/or ovarian cancer without a BRCA1 or BRCA2 pathogenic variant.
Collapse
Affiliation(s)
- D Gareth R Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; Prevention Breast Cancer Centre and Nightingale Breast Screening Centre, University Hospital of South Manchester, Manchester M23 9LT, UK; Christie NHS Foundation Trust, Manchester M20 4BX, UK; Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester M20 4BX, UK.
| | - Elke M van Veen
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Helen J Byers
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Jamie M Ellingford
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Glenda Beaman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Javier Santoyo-Lopez
- Centre for Genomic and Experimental Medicine and Edinburgh Genomics, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Timothy J Aitman
- Centre for Genomic and Experimental Medicine and Edinburgh Genomics, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Diana M Eccles
- Cancer Sciences Academic Unit and Southampton Clinical Trials Unit, Faculty of Medicine, University of Southampton and University Hospital Southampton Foundation Trust, Southampton S016 6YD, UK
| | - Fiona I Lalloo
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Miriam J Smith
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester M20 4BX, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK.
| |
Collapse
|
45
|
Al-Moghrabi N, Al-Showimi M, Al-Yousef N, Al-Shahrani B, Karakas B, Alghofaili L, Almubarak H, Madkhali S, Al Humaidan H. Methylation of BRCA1 and MGMT genes in white blood cells are transmitted from mothers to daughters. Clin Epigenetics 2018; 10:99. [PMID: 30049288 PMCID: PMC6062990 DOI: 10.1186/s13148-018-0529-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/08/2018] [Indexed: 12/31/2022] Open
Abstract
Background Constitutive methylation of tumor suppressor genes are associated with increased cancer risk. However, to date, the question of epimutational transmission of these genes remains unresolved. Here, we studied the potential transmission of BRCA1 and MGMT promoter methylations in mother-newborn pairs. Methods A total of 1014 female subjects (cancer-free women, n = 268; delivering women, n = 295; newborn females, n = 302; breast cancer patients, n = 67; ovarian cancer patients, n = 82) were screened for methylation status in white blood cells (WBC) using methylation-specific PCR and bisulfite pyrosequencing assays. In addition, BRCA1 gene expression levels were analyzed by quantitative real-time PCR. Results We found similar methylation frequencies in newborn and adults for both BRCA1 (9.9 and 9.3%) and MGMT (12.3 and 13.1%). Of the 290 mother-newborn pairs analyzed for promoter methylation, 20 mothers were found to be positive for BRCA1 and 29 for MGMT. Four mother-newborn pairs were positive for methylated BRCA1 (20%) and nine pairs were positive for methylated MGMT (31%). Intriguingly, the delivering women had 26% lower BRCA1 and MGMT methylation frequencies than those of the cancer-free female subjects. BRCA1 was downregulated in both cancer-free woman carriers and breast cancer patients but not in newborn carriers. There was a statistically significant association between the MGMT promoter methylation and late-onset breast cancers. Conclusions Our study demonstrates that BRCA1and MGMT epimutations are present from the early life of the carriers. We show the transmission of BRCA1 and MGMT epimutations from mother to daughter. Our data also point at the possible demethylation of BRCA1and MGMT during pregnancy.
Collapse
Affiliation(s)
- Nisreen Al-Moghrabi
- Head of Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia.
| | - Maram Al-Showimi
- Cancer Epigenetic section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Nujoud Al-Yousef
- Head of Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Bushra Al-Shahrani
- Cancer Epigenetic section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Bedri Karakas
- Head of Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Lamyaa Alghofaili
- Al Faisal University College of Medicine, PO BOX 50927, Riyadh, 11533, Kingdom of Saudi Arabia
| | - Hannah Almubarak
- Head of Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Safia Madkhali
- King Saud bin Abdulaziz University for Health Sciences, PO BOX 22490, Riyadh, 3130, Kingdom of Saudi Arabia
| | - Hind Al Humaidan
- Department of pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, PO BOX 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| |
Collapse
|
46
|
Abstract
Epigenetic alterations such as DNA methylation defects and aberrant covalent histone modifications occur within all cancers and are selected for throughout the natural history of tumor formation, with changes being detectable in early onset, progression, and ultimately recurrence and metastasis. The ascertainment and use of these marks to identify at-risk patient populations, refine diagnostic criteria, and provide prognostic and predictive factors to guide treatment decisions are of growing clinical relevance. Furthermore, the targetable nature of epigenetic modifications provides a unique opportunity to alter treatment paradigms and provide new therapeutic options for patients whose malignancies possess these aberrant epigenetic modifications, paving the way for new and personalized medicine. DNA methylation has proven to be of significant clinical utility for its stability and relative ease of testing. The intent of this review is to elaborate upon well-supported examples of epigenetic precision medicine and how the field is moving forward, primarily in the context of aberrant DNA methylation.
Collapse
Affiliation(s)
- Rachael J Werner
- From the *Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | | | | |
Collapse
|
47
|
Abstract
PURPOSE OF REVIEW Prostate cancer is a disease of the elderly but a clinically relevant subset occurs early in life. In the current review, we discuss recent findings and the current understanding of the molecular underpinnings associated with early-onset prostate cancer (PCa) and the evidence supporting age-specific differences in the cancer genomes. RECENT FINDINGS Recent surveys of PCa patient cohorts have provided novel age-dependent links between germline and somatic aberrations which points to differences in the molecular cause and treatment options. SUMMARY Identifying the earliest molecular alterations in PCa can provide insight into the cause of the disease and biomarkers for patient risk stratification. Genomic aberrations of early-onset PCas display several patterns distinct from late-onset PCa genomes, suggesting age-dependent pathomechanisms involving alterations in the androgen receptor pathway.
Collapse
|
48
|
Böck J, Appenzeller S, Haertle L, Schneider T, Gehrig A, Schröder J, Rost S, Wolf B, Bartram CR, Sutter C, Haaf T. Single CpG hypermethylation, allele methylation errors, and decreased expression of multiple tumor suppressor genes in normal body cells of mutation-negative early-onset and high-risk breast cancer patients. Int J Cancer 2018; 143:1416-1425. [PMID: 29659014 PMCID: PMC6099327 DOI: 10.1002/ijc.31526] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/28/2018] [Indexed: 01/01/2023]
Abstract
To evaluate the role of constitutive epigenetic changes in normal body cells of BRCA1/BRCA2-mutation negative patients, we have developed a deep bisulfite sequencing assay targeting the promoter regions of 8 tumor suppressor (TS) genes (BRCA1, BRCA2, RAD51C, ATM, PTEN, TP53, MLH1, RB1) and the estrogene receptor gene (ESR1), which plays a role in tumor progression. We analyzed blood samples of two breast cancer (BC) cohorts with early onset (EO) and high risk (HR) for a heterozygous mutation, respectively, along with age-matched controls. Methylation analysis of up to 50,000 individual DNA molecules per gene and sample allowed quantification of epimutations (alleles with >50% methylated CpGs), which are associated with epigenetic silencing. Compared to ESR1, which is representative for an average promoter, TS genes were characterized by a very low (< 1%) average methylation level and a very low mean epimutation rate (EMR; < 0.0001% to 0.1%). With exception of BRCA1, which showed an increased EMR in BC (0.31% vs. 0.06%), there was no significant difference between patients and controls. One of 36 HR BC patients exhibited a dramatically increased EMR (14.7%) in BRCA1, consistent with a disease-causing epimutation. Approximately one third (15 of 44) EO BC patients exhibited increased rates of single CpG methylation errors in multiple TS genes. Both EO and HR BC patients exhibited global underexpression of blood TS genes. We propose that epigenetic abnormalities in normal body cells are indicative of disturbed mechanisms for maintaining low methylation and appropriate expression levels and may be associated with an increased BC risk.
Collapse
Affiliation(s)
- Julia Böck
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | | | - Larissa Haertle
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Tamara Schneider
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Andrea Gehrig
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Jörg Schröder
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Beat Wolf
- University of Applied Sciences Western Switzerland, Fribourg, Switzerland.,Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Claus R Bartram
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| |
Collapse
|
49
|
Diversity of genetic events associated with MLH1 promoter methylation in Lynch syndrome families with heritable constitutional epimutation. Genet Med 2018; 20:1589-1599. [DOI: 10.1038/gim.2018.47] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 02/20/2018] [Indexed: 02/07/2023] Open
|
50
|
Saif I, Kasmi Y, Allali K, Ennaji MM. Prediction of DNA methylation in the promoter of gene suppressor tumor. Gene 2018; 651:166-173. [DOI: 10.1016/j.gene.2018.01.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 12/23/2017] [Accepted: 01/25/2018] [Indexed: 10/18/2022]
|