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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] [Grants] [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.
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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.
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Ibrahim MB, Flanagan J, Ibrahim T, Rouleau E. Unraveling noncoding DNA variants and epimutations: a paradigm shift in hereditary cancer research. Future Oncol 2024; 20:1289-1298. [PMID: 38722139 PMCID: PMC11318707 DOI: 10.2217/fon-2023-0665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/11/2024] [Indexed: 06/12/2024] Open
Abstract
Exhaustive efforts have been dedicated to uncovering genomic aberrations linked to cancer susceptibility. Noncoding sequence variants and epigenetic alterations significantly influence gene regulation and could contribute to cancer development. However, exploring noncoding regions in hereditary cancer susceptibility demands cutting-edge methodologies for functionally characterizing genomic discoveries. Additionally, comprehending the impact on cancer development of variants in noncoding DNA and the epigenome necessitates integrating diverse data through bioinformatic analyses. As novel technologies and analytical methods continue to advance, this realm of research is rapidly gaining traction. Within this mini-review, we delve into future research domains concerning aberrations in noncoding DNA regions, such as pseudoexons, promoter variants and cis-epimutations.
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Affiliation(s)
- Maria Baz Ibrahim
- Department of Oncogenetics & Tumor Biology, Paul Brousse Hospital, Villejuif, France
| | - James Flanagan
- Department of Surgery & Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Tony Ibrahim
- International Department of Medical Oncology, Gustave Roussy, 94805, Villejuif, France
| | - Etienne Rouleau
- Department of Biology & Pathology-Cancer Genetics Laboratory, Gustave Roussy, 94805, Villejuif, France
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Frazer LC, Yamaguchi Y, Singh DK, Akopyants NS, Good M. DNA methylation in necrotizing enterocolitis. Expert Rev Mol Med 2024; 26:e16. [PMID: 38557638 PMCID: PMC11140546 DOI: 10.1017/erm.2024.16] [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: 07/26/2023] [Revised: 03/05/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Epigenetic modifications, such as DNA methylation, are enzymatically regulated processes that directly impact gene expression patterns. In early life, they are central to developmental programming and have also been implicated in regulating inflammatory responses. Research into the role of epigenetics in neonatal health is limited, but there is a growing body of literature related to the role of DNA methylation patterns and diseases of prematurity, such as the intestinal disease necrotizing enterocolitis (NEC). NEC is a severe intestinal inflammatory disease, but the key factors that precede disease development remain to be determined. This knowledge gap has led to a failure to design effective targeted therapies and identify specific biomarkers of disease. Recent literature has identified altered DNA methylation patterns in the stool and intestinal tissue of neonates with NEC. These findings provide the foundation for a new avenue in NEC research. In this review, we will provide a general overview of DNA methylation and then specifically discuss the recent literature related to methylation patterns in neonates with NEC. We will also discuss how DNA methylation is used as a biomarker for other disease states and how, with further research, methylation patterns may serve as potential biomarkers for NEC.
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Affiliation(s)
- Lauren C. Frazer
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yukihiro Yamaguchi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dhirendra K. Singh
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalia S. Akopyants
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Misty Good
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Sorroche BP, Miranda KC, Beltrami CM, Arantes LMRB, Kowalski LP, Marchi FA, Rogatto SR, Almeida JD. HOXA1 3'UTR Methylation Is a Potential Prognostic Biomarker in Oral Squamous cell Carcinoma. Cancers (Basel) 2024; 16:874. [PMID: 38473236 DOI: 10.3390/cancers16050874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND HOXA1 is a prognostic marker and a potential predictive biomarker for radioresistance in head and neck tumors. Its overexpression has been associated with promoter methylation and a worse prognosis in oral squamous cell carcinoma (OSCC) patients. However, opposite outcomes are also described. The effect of the methylation of this gene on different gene regions, other than the promoter, remains uncertain. We investigated the methylation profile at different genomic regions of HOXA1 in OSCC and correlated differentially methylated CpG sites with clinicopathological data. METHODS The HOXA1 DNA methylation status was evaluated by analyzing data from The Cancer Genome Atlas and three Gene Expression Omnibus datasets. Significant differentially methylated CpG sites were considered with a |∆β| ≥ 0.10 and a Bonferroni-corrected p-value < 0.01. Differentially methylated CpGs were validated by pyrosequencing using two independent cohorts of 15 and 47 OSCC patients, respectively. RESULTS Compared to normal tissues, we found significantly higher DNA methylation levels in the 3'UTR region of HOXA1 in OSCC. Higher methylation levels in tumor samples were positively correlated with smoking habits and patients' overall survival. CONCLUSIONS Our findings suggest that HOXA1 gene body methylation is a promising prognostic biomarker for OSCC with potential clinical applications in patient monitoring.
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Affiliation(s)
- Bruna Pereira Sorroche
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil
| | - Keila Cristina Miranda
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos 12224-300, Brazil
| | | | | | - Luiz Paulo Kowalski
- Head and Neck Surgery and Otorhinolaryngology Department, AC Camargo Cancer Center, Latin American Cooperative Oncology Group, São Paulo 01509-010, Brazil
- Head and Neck Surgery Department and LIM 28, University of São Paulo Medical School, São Paulo 01246-903, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo 01246-000, Brazil
- Clinical Hospital of the University of Sao Paulo Medical School (HCFMUSP), São Paulo 05403-010, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos 12224-300, Brazil
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Obata H, Ogawa M, Zalutsky MR. DNA Repair Inhibitors: Potential Targets and Partners for Targeted Radionuclide Therapy. Pharmaceutics 2023; 15:1926. [PMID: 37514113 PMCID: PMC10384049 DOI: 10.3390/pharmaceutics15071926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The present review aims to explore the potential targets/partners for future targeted radionuclide therapy (TRT) strategies, wherein cancer cells often are not killed effectively, despite receiving a high average tumor radiation dose. Here, we shall discuss the key factors in the cancer genome, especially those related to DNA damage response/repair and maintenance systems for escaping cell death in cancer cells. To overcome the current limitations of TRT effectiveness due to radiation/drug-tolerant cells and tumor heterogeneity, and to make TRT more effective, we propose that a promising strategy would be to target the DNA maintenance factors that are crucial for cancer survival. Considering their cancer-specific DNA damage response/repair ability and dysregulated transcription/epigenetic system, key factors such as PARP, ATM/ATR, amplified/overexpressed transcription factors, and DNA methyltransferases have the potential to be molecular targets for Auger electron therapy; moreover, their inhibition by non-radioactive molecules could be a partnering component for enhancing the therapeutic response of TRT.
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Affiliation(s)
- Honoka Obata
- Department of Advanced Nuclear Medicine Sciences, National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Department of Molecular Imaging and Theranostics, National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Departments of Radiology and Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
| | - Mikako Ogawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
| | - Michael R Zalutsky
- Departments of Radiology and Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
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Siri G, Mosallaei M, Ehtesham N, Rahimi H, Mazarei M, Nasrollahzadeh Sabet M, Behroozi J. TUSC3 Methylation in Peripheral Blood Cells as a Biomarker for Diagnosis of Colorectal Cancer. Adv Biomed Res 2023; 12:174. [PMID: 37564442 PMCID: PMC10410437 DOI: 10.4103/abr.abr_396_22] [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: 11/20/2022] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 08/12/2023] Open
Abstract
Background Several case-control studies have suggested that global and loci-specific deoxyribonucleic acid (DNA) methylation in peripheral blood mononuclear cells (PBMCs) of DNA might be potential biomarkers of cancer diagnosis and prognosis. In this study, for the first time, we intended to assess the diagnostic power of the methylation level of tumor suppressor candidate 3 (TUSC3) gene promoter in patients with colorectal cancer (CRC). Materials and Methods In the current study, we quantitatively assessed the promoter methylation level of TUSC3 in PBMCs of 70 CRC cases and 75 non-cancerous subjects via methylation quantification of endonuclease-resistant DNA (MethyQESD) method. Results The methylation level of the TUSC3 was meaningfully higher in CRC cases than in non-CRC subjects (43.55 ± 21.80% vs. 16.07 ± 13.63%, respectively; P < 0.001). The sensitivity and specificity of this gene for the detection of CRC were 88.6% and 76.0%, respectively. The receiver operating characteristic (ROC) curve examination discovered an area under the curve (AUC) of 0.880, representing a very high accuracy of the TUSC3 methylation marker in distinguishing CRC subjects from healthy individuals. However, there was no substantial diversity in methylation level between various CRC stages (P: 0.088). Conclusion For CRC screening, PBMCs are a reliable source for DNA methylation analysis and TUSC3 promoter methylation can be utilized as a hopeful biomarker for early and non-invasive diagnosis of CRC.
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Affiliation(s)
- Goli Siri
- Department of Internal Medicine, Amir-Alam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Meysam Mosallaei
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Naeim Ehtesham
- School of Medicine, Iranshahr University of Medical Sciences, Iranshahr, Iran
| | - Hasan Rahimi
- Faculty of Biostatistics, Tarbiat Modares University, Tehran, Iran
| | - Madineh Mazarei
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Science, Shahrekord, Iran
| | - Mehrdad Nasrollahzadeh Sabet
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Javad Behroozi
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, AJA University of Medical Sciences; Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran, Iran
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Chung FFL, Maldonado SG, Nemc A, Bouaoun L, Cahais V, Cuenin C, Salle A, Johnson T, Ergüner B, Laplana M, Datlinger P, Jeschke J, Weiderpass E, Kristensen V, Delaloge S, Fuks F, Risch A, Ghantous A, Plass C, Bock C, Kaaks R, Herceg Z. Buffy coat signatures of breast cancer risk in a prospective cohort study. Clin Epigenetics 2023; 15:102. [PMID: 37309009 PMCID: PMC10262593 DOI: 10.1186/s13148-023-01509-6] [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: 01/30/2023] [Accepted: 05/20/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Epigenetic alterations are a near-universal feature of human malignancy and have been detected in malignant cells as well as in easily accessible specimens such as blood and urine. These findings offer promising applications in cancer detection, subtyping, and treatment monitoring. However, much of the current evidence is based on findings in retrospective studies and may reflect epigenetic patterns that have already been influenced by the onset of the disease. METHODS Studying breast cancer, we established genome-scale DNA methylation profiles of prospectively collected buffy coat samples (n = 702) from a case-control study nested within the EPIC-Heidelberg cohort using reduced representation bisulphite sequencing (RRBS). RESULTS We observed cancer-specific DNA methylation events in buffy coat samples. Increased DNA methylation in genomic regions associated with SURF6 and REXO1/CTB31O20.3 was linked to the length of time to diagnosis in the prospectively collected buffy coat DNA from individuals who subsequently developed breast cancer. Using machine learning methods, we piloted a DNA methylation-based classifier that predicted case-control status in a held-out validation set with 76.5% accuracy, in some cases up to 15 years before clinical diagnosis of the disease. CONCLUSIONS Taken together, our findings suggest a model of gradual accumulation of cancer-associated DNA methylation patterns in peripheral blood, which may be detected long before clinical manifestation of cancer. Such changes may provide useful markers for risk stratification and, ultimately, personalized cancer prevention.
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Affiliation(s)
- Felicia Fei-Lei Chung
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France.
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, 5, Jalan Universiti, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia.
| | | | - Amelie Nemc
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Liacine Bouaoun
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Vincent Cahais
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Cyrille Cuenin
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Aurelie Salle
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Theron Johnson
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marina Laplana
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
- Department of Basic Medical Sciences, University of Lleida, IRBLleida, 25198, Lleida, Spain
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jana Jeschke
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Elisabete Weiderpass
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Vessela Kristensen
- Faculty of Medicine, Institute for Clinical Epidemiology and Molecular Biology, University of Oslo, Oslo, Norway
| | - Suzette Delaloge
- Department of Cancer Medicine, Institut Gustave Roussy, Villejuif, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Angela Risch
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, 5020, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Akram Ghantous
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zdenko Herceg
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France.
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DOK7 CpG hypermethylation in blood leukocytes as an epigenetic biomarker for acquired tamoxifen resistant in breast cancer. J Hum Genet 2023; 68:33-38. [PMID: 36372800 DOI: 10.1038/s10038-022-01092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Breast cancer (BC) is among the most common cause of cancer 10.4% and one of the leading causes of death among 20-50 years old women in the world. Tamoxifen drug is the first line therapy for BC however tamoxifen resistance (TR) has shown in 30-50% of cases that may face BC recurrence. Hence, TR early detection reduces BC recurrence and fatalities. The epigenetic alteration that happens by hypermethylation of tumor suppressor genes and hypomethylation of oncogenes has been suggested to be useful in early cancer or drug resistance diagnosis. METHODS This is the first study to investigate DOK7 CpG hypermethylation in blood leukocytes of 31 TR (ER+) BC compared to 29 tamoxifen sensitive BC to evaluate DOK7 as a potential TR biomarker. DNA was extracted from blood samples of all participants and MSRE-PCR and real-time PCR were used for quantification of CpG methylation alterations. RESULTS The means of DOK7 CpG hypermethylation were obtained as 85.03%, 29.1% and 57.34% in TR, TS and normal control respectively. Significant hypermethylation were found among TR vs. TS (p < 0.001), TS vs. normal (p < 0.001) and TR vs. normal controls (p < 0.03). Online databases expression and survival analysis of DOK7 showed increasing expression in TS groups vs. TR groups which have consistency with our methylation alteration results. The sensitivity and specificity of the TR epigenetic test were determined using ROC analysis showed 89.66% and 96.77% respectively and showed that 37.5% above hypermethylation is at risk for TR and breast cancer recurrence. CONCLUSION There is a significant difference in the methylation ratio of DOK7 between tamoxifen resistant and tamoxifen sensitive groups that may be useful in the early diagnosis of tamoxifen resistance in BC cases and cancer recurrence prevention.
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Dugué PA, Bodelon C, Chung FF, Brewer HR, Ambatipudi S, Sampson JN, Cuenin C, Chajès V, Romieu I, Fiorito G, Sacerdote C, Krogh V, Panico S, Tumino R, Vineis P, Polidoro S, Baglietto L, English D, Severi G, Giles GG, Milne RL, Herceg Z, Garcia-Closas M, Flanagan JM, Southey MC. Methylation-based markers of aging and lifestyle-related factors and risk of breast cancer: a pooled analysis of four prospective studies. Breast Cancer Res 2022; 24:59. [PMID: 36068634 PMCID: PMC9446544 DOI: 10.1186/s13058-022-01554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND DNA methylation in blood may reflect adverse exposures accumulated over the lifetime and could therefore provide potential improvements in the prediction of cancer risk. A substantial body of research has shown associations between epigenetic aging and risk of disease, including cancer. Here we aimed to study epigenetic measures of aging and lifestyle-related factors in association with risk of breast cancer. METHODS Using data from four prospective case-control studies nested in three cohorts of European ancestry participants, including a total of 1,655 breast cancer cases, we calculated three methylation-based measures of lifestyle factors (body mass index [BMI], tobacco smoking and alcohol consumption) and seven measures of epigenetic aging (Horvath-based, Hannum-based, PhenoAge and GrimAge). All measures were regression-adjusted for their respective risk factors and expressed per standard deviation (SD). Odds ratios (OR) and 95% confidence intervals (CI) were calculated using conditional or unconditional logistic regression and pooled using fixed-effects meta-analysis. Subgroup analyses were conducted by age at blood draw, time from blood sample to diagnosis, oestrogen receptor-positivity status and tumour stage. RESULTS None of the measures of epigenetic aging were associated with risk of breast cancer in the pooled analysis: Horvath 'age acceleration' (AA): OR per SD = 1.02, 95%CI: 0.95-1.10; AA-Hannum: OR = 1.03, 95%CI:0.95-1.12; PhenoAge: OR = 1.01, 95%CI: 0.94-1.09 and GrimAge: OR = 1.03, 95%CI: 0.94-1.12, in models adjusting for white blood cell proportions, body mass index, smoking and alcohol consumption. The BMI-adjusted predictor of BMI was associated with breast cancer risk, OR per SD = 1.09, 95%CI: 1.01-1.17. The results for the alcohol and smoking methylation-based predictors were consistent with a null association. Risk did not appear to substantially vary by age at blood draw, time to diagnosis or tumour characteristics. CONCLUSION We found no evidence that methylation-based measures of aging, smoking or alcohol consumption were associated with risk of breast cancer. A methylation-based marker of BMI was associated with risk and may provide insights into the underlying associations between BMI and breast cancer.
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Affiliation(s)
- Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia.
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia.
| | - Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Felicia F Chung
- International Agency for Research On Cancer (IARC), Lyon, France
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Hannah R Brewer
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Srikant Ambatipudi
- International Agency for Research On Cancer (IARC), Lyon, France
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | - Joshua N Sampson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Cyrille Cuenin
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Veronique Chajès
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Isabelle Romieu
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Giovanni Fiorito
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e Della Scienza University-Hospital, Turin, Italy
| | - Vittorio Krogh
- Department of Research, Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, MI, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia Federico II University, Naples, Italy
| | - Rosario Tumino
- Hyblean Association for Epidemiological Research AIRE-ONLUS, Ragusa, Italy
| | - Paolo Vineis
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | | | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, 56126, Pisa, Italy
| | - Dallas English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Gianluca Severi
- CESP UMR1018, Paris-Saclay University, UVSQ, Inserm, Gustave Roussy, Villejuif, France
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Zdenko Herceg
- International Agency for Research On Cancer (IARC), Lyon, France
| | | | - James M Flanagan
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia
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10
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Mekonnen N, Yang H, Shin YK. Homologous Recombination Deficiency in Ovarian, Breast, Colorectal, Pancreatic, Non-Small Cell Lung and Prostate Cancers, and the Mechanisms of Resistance to PARP Inhibitors. Front Oncol 2022; 12:880643. [PMID: 35785170 PMCID: PMC9247200 DOI: 10.3389/fonc.2022.880643] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Homologous recombination (HR) is a highly conserved DNA repair mechanism that protects cells from exogenous and endogenous DNA damage. Breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) play an important role in the HR repair pathway by interacting with other DNA repair proteins such as Fanconi anemia (FA) proteins, ATM, RAD51, PALB2, MRE11A, RAD50, and NBN. These pathways are frequently aberrant in cancer, leading to the accumulation of DNA damage and genomic instability known as homologous recombination deficiency (HRD). HRD can be caused by chromosomal and subchromosomal aberrations, as well as by epigenetic inactivation of tumor suppressor gene promoters. Deficiency in one or more HR genes increases the risk of many malignancies. Another conserved mechanism involved in the repair of DNA single-strand breaks (SSBs) is base excision repair, in which poly (ADP-ribose) polymerase (PARP) enzymes play an important role. PARP inhibitors (PARPIs) convert SSBs to more cytotoxic double-strand breaks, which are repaired in HR-proficient cells, but remain unrepaired in HRD. The blockade of both HR and base excision repair pathways is the basis of PARPI therapy. The use of PARPIs can be expanded to sporadic cancers displaying the “BRCAness” phenotype. Although PARPIs are effective in many cancers, their efficacy is limited by the development of resistance. In this review, we summarize the prevalence of HRD due to mutation, loss of heterozygosity, and promoter hypermethylation of 35 DNA repair genes in ovarian, breast, colorectal, pancreatic, non-small cell lung cancer, and prostate cancer. The underlying mechanisms and strategies to overcome PARPI resistance are also discussed.
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Affiliation(s)
- Negesse Mekonnen
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Department of Veterinary Science, School of Animal Science and Veterinary Medicine, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hobin Yang
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
| | - Young Kee Shin
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Graduate School of Convergence Science and Technology, Seoul, South Korea
- LOGONE Bio Convergence Research Foundation, Center for Companion Diagnostics, Seoul, South Korea
- *Correspondence: Young Kee Shin,
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11
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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.
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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
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12
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Rajkumar T, Amritha S, Sridevi V, Gopal G, Sabitha K, Shirley S, Swaminathan R. Identification and validation of plasma biomarkers for diagnosis of breast cancer in South Asian women. Sci Rep 2022; 12:100. [PMID: 34997107 PMCID: PMC8742108 DOI: 10.1038/s41598-021-04176-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/16/2021] [Indexed: 01/26/2023] Open
Abstract
Breast cancer is the most common malignancy among women globally. Development of a reliable plasma biomarker panel might serve as a non-invasive and cost-effective means for population-based screening of the disease. Transcriptomic profiling of breast tumour, paired normal and apparently normal tissues, followed by validation of the shortlisted genes using TaqMan® Low density arrays and Quantitative real-time PCR was performed in South Asian women. Fifteen candidate protein markers and 3 candidate epigenetic markers were validated first in primary breast tumours and then in plasma samples of cases [N = 202 invasive, 16 DCIS] and controls [N = 203 healthy, 37 benign] using antibody array and methylation specific PCR. Diagnostic efficiency of single and combined markers was assessed. Combination of 6 protein markers (Adipsin, Leptin, Syndecan-1, Basic fibroblast growth factor, Interleukin 17B and Dickopff-3) resulted in 65% sensitivity and 80% specificity in detecting breast cancer. Multivariate diagnostic analysis of methylation status of SOSTDC1, DACT2, WIF1 showed 100% sensitivity and up to 91% specificity in discriminating BC from benign and controls. Hence, combination of SOSTDC1, DACT2 and WIF1 was effective in differentiating breast cancer [non-invasive and invasive] from benign diseases of the breast and healthy individuals and could help as a complementary diagnostic tool for breast cancer.
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Affiliation(s)
- Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India.
| | - Sathyanarayanan Amritha
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Veluswami Sridevi
- Department of Surgical Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Gopisetty Gopal
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Kesavan Sabitha
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Sundersingh Shirley
- Department of Pathology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Rajaraman Swaminathan
- Department of Epidemiology and Biostatistics, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
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13
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Zhou C, Porter N, Borges M, Gauthier C, Ferguson L, Huang B, Nanda N, He J, Laheru D, Hruban RH, Goggins M, Klein AP, Roberts NJ. Examination of ATM, BRCA1, and BRCA2 promoter methylation in patients with pancreatic cancer. Pancreatology 2021; 21:938-941. [PMID: 33839031 PMCID: PMC8355034 DOI: 10.1016/j.pan.2021.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Pancreatic cancer is a lethal disease with a poor 5-year survival rate. Pathogenic germline variants in the coding regions of ATM, BRCA1, and BRCA2 are found in up to 4.8% of pancreatic cancer patients. Germline promoter methylation and gene silencing arising from a germline variant or through other mechanisms have been described as a cause of tumor suppressor gene inactivation. METHODS We measured the level of promoter methylation of the ATM, BRCA1, and BRCA2 genes in peripheral blood lymphocytes from 655 patients with pancreatic cancer using real-time PCR. RESULTS No evidence of germline promoter methylation of any of these genes was found. Promoter methylation levels were minimal with no patient having promoter methylation greater than 3.4%, 3.3%, and 7.6% for ATM, BRCA1 and BRCA2, respectively, well below levels found in patients who have inherited promoter methylation (∼50%). CONCLUSIONS We found no evidence of germline promoter methylation for the pancreatic susceptibility genes ATM, BRCA1 and BRCA2 in patients with pancreatic cancer. This study reveals that constitutive germline methylation of promoter CpG islands is rare in pancreatic cancer.
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Affiliation(s)
- Cancan Zhou
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nancy Porter
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Borges
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christian Gauthier
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lindsey Ferguson
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Bo Huang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Neha Nanda
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jin He
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel Laheru
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alison P Klein
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Nicholas J Roberts
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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14
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Nomair AM, Ahmed SS, Mohammed AF, El Mansy H, Nomeir HM. SCGB3A1 gene DNA methylation status is associated with breast cancer in Egyptian female patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
In recent years, hypermethylation of gene promoters has emerged as one of the fundamental mechanisms for the inactivation of tumor suppressor genes and has a potential role in the early detection of breast cancer. The present study is a case-control study aimed to quantify the methylation levels in the promoters of secretoglobin 3A1 (SCGB3A1), and ataxia-telangiectasia mutated (ATM) genes and evaluate their relation to clinicopathological features of the tumor in a cohort of Egyptian female patients with breast cancer.
Methods
Genomic deoxyribonucleic acid (DNA) was extracted from 100 tissue samples, 50 breast cancer tissues and 50 adjacent non-cancerous breast tissues, then, it was subjected to bisulfite conversion. The converted DNA was amplified by real-time PCR; then, pyrosequencing was performed to quantify DNA methylation levels in four CpG sites in ATM and SCGB3A1 gene promoters. The methylation data were presented as the percentage of average methylation of all the observed CpG sites and were calculated for each sample and each gene.
Results
The percentage of DNA methylation of the SCGB3A1 promoter was significantly higher in the tumor group than in the normal group (P= 0.001). However, a non-statistical significance difference was found in the DNA methylation percentage of the ATM promoter in the tumor group compared to the normal group (P = 0.315). The SCGB3A1 promoter methylation frequency was significantly associated with estrogen receptors (ER) and progesterone receptors (PR) positive tumors, lymph node metastasis, and lymphovascular invasion. However, no association was found between ATM methylation status and the different clinicopathological features of the tumor.
Conclusions
The findings of this work showed that the SCGB3A1 promoter methylation was significantly higher in the tumor group and was significantly associated with different clinicopathologic features in breast cancer. It may be considered as a suitable biomarker for diagnosis and prognosis. However, the promoter methylation levels of the ATM gene in breast cancer cases were unable to distinguish between breast cancer tissues and adjacent normal tissues, and there is no evidence that epigenetic silencing by ATM methylation has a role in breast cancer pathogenesis.
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15
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Ren C, Tang X, Lan H. Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer. PeerJ 2021; 9:e11377. [PMID: 33987034 PMCID: PMC8103922 DOI: 10.7717/peerj.11377] [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: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 11/20/2022] Open
Abstract
Background Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq. Methods We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset. Results We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using STITCH. Higher infiltration rates of CD8 T cells, plasma cells, and monocytes were found in the lower quartile WT1 group and the favorable 6-gene signature group. In conclusion, we demonstrated that WT1 is hypermethylated and up-regulated in the four BC molecular subtypes and a 6-gene signature may predict BC prognosis.
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Affiliation(s)
- Chongyang Ren
- Department of Breast Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaojiang Tang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Haitao Lan
- Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
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16
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Factors associated with breast cancer recurrence and survival at Sangre Grande Hospital, Trinidad. Cancer Causes Control 2021; 32:763-772. [PMID: 33835281 DOI: 10.1007/s10552-021-01427-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE The aim of this study is to determine the demographic, pathological, and treatment-related factors that predict recurrence and survival in a Trinidadian cohort of breast cancer patients. METHODS The inclusion criteria for this study were female, over 18 years, and with a primary breast cancer diagnosis confirmed by a biopsy report occurring between 2010 and 2015 at Sangre Grande Hospital, Trinidad. Univariate associations with 5-year recurrence-free survival and 5-year overall survival were calculated using the Kaplan-Meier method for categorical variables and Cox Proportional Hazards for continuous variables. A multivariate model for prediction of recurrence and survival was determined using Cox regression. RESULTS For the period 2010-2015, 202 records were abstracted. Five-year overall survival and recurrence-free survival rates were found to be 74.3% and 56.4%, respectively. Median times from first suspicious finding to date of biopsy report, date of surgery, and date of chemotherapy were 63 days, 125 days, and 189 days, respectively. In the univariate analysis, age (p = 0.038), stage (p < 0.001), recurrence (p = 0.035), surgery (p = 0.016), ER (p < 0.001) status, PR status (p < 0.001), and subtype (p < 0.001) were significantly associated with survival. Additionally, stage (p = 0.004), N score (p = 0.002), ER (p = 0.028) status, PR (p = 0.018) status, and subtype (p = 0.025) were significantly associated with recurrence. In the Cox multivariate model, Stage 4 was a significant predictor of survival (HR 6.77, 95% CI [0.09-2.49], p = 0.047) and N3 score was a significant predictor of recurrence (HR 4.47, 95% CI [1.29-15.54], p = 0.018). CONCLUSION This study reports a 5-year breast cancer survival rate of 74.3%, and a recurrence-free survival rate of 56.4% in Trinidad for the period 2010-2015.
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17
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Kuzmina NS, Luong TM, Rubanovich AV. Changes in DNA Methylation Induced by Dioxins and Dioxin-Like Compounds as Potential Predictor of Disease Risk. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420100063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Wielsøe M, Tarantini L, Bollati V, Long M, Bonefeld‐Jørgensen EC. DNA methylation level in blood and relations to breast cancer, risk factors and environmental exposure in Greenlandic Inuit women. Basic Clin Pharmacol Toxicol 2020; 127:338-350. [PMID: 32352194 PMCID: PMC7540549 DOI: 10.1111/bcpt.13424] [Citation(s) in RCA: 7] [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: 12/17/2019] [Revised: 03/23/2020] [Accepted: 04/24/2020] [Indexed: 01/22/2023]
Abstract
Several studies have found aberrant DNA methylation levels in breast cancer cases, but factors influencing DNA methylation patterns and the mechanisms are not well understood. This case-control study evaluated blood methylation level of two repetitive elements and selected breast cancer-related genes in relation to breast cancer risk, and the associations with serum level of persistent organic pollutants (POPs) and breast cancer risk factors in Greenlandic Inuit. DNA methylation was determined using bisulphite pyrosequencing in blood from 74 breast cancer cases and 80 controls. Using first tertile as reference, the following was observed. Positive associations for ATM in second tertile (OR: 2.33, 95% CI: 1.04; 5.23) and ESR2 in third tertile (OR: 2.22, 95% CI: 0.97; 5.05) suggest an increased breast cancer risk with high DNA methylation. LINE-1 methylation was lower in cases than controls. In third tertile (OR: 0.42, 95% CI: 0.18; 0.98), associations suggest in accordance with the literature an increased risk of breast cancer with LINE-1 hypomethylation. Among controls, significant associations between methylation levels and serum level of POPs and breast cancer risk factors (age, body mass index, cotinine level) were found. Thus, breast cancer risk factors and POPs may alter the risk through changes in methylation levels; further studies are needed to elucidate the mechanisms.
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Affiliation(s)
- Maria Wielsøe
- Department of Public HealthCentre for Arctic Health & Molecular EpidemiologyAarhus UniversityAarhus CDenmark
| | - Letizia Tarantini
- EPIGET – Epidemiology, Epigenetics and Toxicology LaboratoryDepartment of Clinical Sciences and Community HealthUniversità degli Studi di MilanoMilanItaly
| | - Valentina Bollati
- EPIGET – Epidemiology, Epigenetics and Toxicology LaboratoryDepartment of Clinical Sciences and Community HealthUniversità degli Studi di MilanoMilanItaly
| | - Manhai Long
- Department of Public HealthCentre for Arctic Health & Molecular EpidemiologyAarhus UniversityAarhus CDenmark
| | - Eva Cecilie Bonefeld‐Jørgensen
- Department of Public HealthCentre for Arctic Health & Molecular EpidemiologyAarhus UniversityAarhus CDenmark
- Greenland Center for Health ResearchUniversity of GreenlandNuukGreenland
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19
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Yin Q, Yang X, Li L, Xu T, Zhou W, Gu W, Ma F, Yang R. The Association Between Breast Cancer and Blood-Based Methylation of S100P and HYAL2 in the Chinese Population. Front Genet 2020; 11:977. [PMID: 33005177 PMCID: PMC7485126 DOI: 10.3389/fgene.2020.00977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 02/05/2023] Open
Abstract
Previous work has shown that DNA methylation in peripheral blood may be associated with malignancy; however, these studies have mainly been conducted within Caucasian populations. Here, we investigated the association between blood-based methylation of S100 calcium-binding protein P gene (S100P) and hyaluronoglucosaminidase 2 gene (HYAL2) and breast cancer (BC) via mass spectrometry in two independent case-control studies of the Chinese population with a total of 351 BC cases and 427 cancer-free female controls. In Study I, in which subjects had an average of 45 years, hypomethylation of S100P showed a protective effect for women ≤45 years (six out of nine CpG sites, p < 0.05) but not for women >45 years. In contrast, hypomethylation of HAYL2 was not correlated with BC in women ≤45 years but was a risk factor for women >45 years (three out of four CpG sites, p < 0.05). We proposed an age-dependent correlation between BC and methylation of S100P and HYAL2 and performed further validation in Study II with older subjects (average age = 52.5 years), where hypomethylation of both S100P and HYAL2 was a risk factor for BC (p < 0.05 for 10 CpG sites) as reported in Caucasians who develop BC around 55 years old. Together with the observation that Chinese cancer-free females having variant basal methylation levels comparing to Caucasians, we assumed that blood-based methylation might be modified by ethnic background, hormone status, and lifestyle. Here, we highlighted that the epigenetic biomarkers warrant validations when its application in variant ethnic groups is considered.
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Affiliation(s)
- Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaoqin Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wenjie Zhou
- Chengdu Shang Jin Nan Fu Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
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20
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Manoochehri M, Jones M, Tomczyk K, Fletcher O, Schoemaker MJ, Swerdlow AJ, Borhani N, Hamann U. DNA methylation of the long intergenic noncoding RNA 299 gene in triple-negative breast cancer: results from a prospective study. Sci Rep 2020; 10:11762. [PMID: 32678138 PMCID: PMC7367270 DOI: 10.1038/s41598-020-68506-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/27/2020] [Indexed: 02/08/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype associated with a high rate of recurrence and poor prognosis. Recently we identified a hypermethylation in the long noncoding RNA 299 (LINC00299) gene in blood-derived DNA from TNBC patients compared with healthy controls implying that LINC00299 hypermethylation may serve as a circulating biomarker for TNBC. In the present study, we investigated whether LINC00299 methylation is associated with TNBC in a prospective nested breast cancer case-control study within the Generations Study. Methylation at cg06588802 in LINC00299 was measured in 154 TNBC cases and 159 breast cancer-free matched controls using MethyLight droplet digital PCR. To assess the association between methylation level and TNBC risk, logistic regression was used to calculate odd ratios and 95% confidence intervals, adjusted for smoking status. We found no evidence for association between methylation levels and TNBC overall (P = 0.062). Subgroup analysis according to age at diagnosis and age at blood draw revealed increased methylation levels in TNBC cases compared with controls in the young age groups [age 26-52 (P = 0.0025) and age 22-46 (P = 0.001), respectively]. Our results suggest a potential association of LINC00299 hypermethylation with TNBC in young women.
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Affiliation(s)
- Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Katarzyna Tomczyk
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Anthony J Swerdlow
- The Institute of Cancer Research, London, UK.,Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Nasim Borhani
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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21
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Wang X, Liu Y, Sun H, Ge A, Li D, Fu J, Li Y, Pang D, Zhao Y. DNA Methylation in RARβ Gene as a Mediator of the Association Between Healthy Lifestyle and Breast Cancer: A Case-Control Study. Cancer Manag Res 2020; 12:4677-4684. [PMID: 32606959 PMCID: PMC7308131 DOI: 10.2147/cmar.s244606] [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: 01/03/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose Lifestyle factors and methylation in the retinoic acid receptor β (RARβ) gene are associated with breast cancer (BC). This study aims to examine the mediation effect of RARβ methylation on the association between healthy lifestyle and BC in Chinese women. Patients and Methods This case–control study consisted of 408 BC patients and 573 controls. A healthy lifestyle score (HLS) was constructed based on diet, alcohol use, physical activity, body mass index and smoking. The mediation effect of RARβ methylation in peripheral blood leukocytes was assessed in a causal mediation model using R package Lavaan. Results A higher HLS was significantly associated with lower risk of BC (P-value<0.001). In mediation analyses, the total effect of HLS on BC measured as a regression coefficient was significant (−0.237). The indirect effects of HLS on RARβ methylation (−0.153) and RARβ methylation on BC (0.220) were both significant. The significant mediation effect of RARβ methylation on the HLS-BC association was estimated at 14.3%. Conclusion The relationship between healthy lifestyle and BC is partly mediated by RARβ methylation, suggesting that epigenetic modifications play a role in the underlying mechanisms in response to lifestyles and contribute to the development of BC.
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Affiliation(s)
- Xuan Wang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Hongru Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Anqi Ge
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Dapeng Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Jinming Fu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Yan Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Da Pang
- Department of Breast Surgery, The Affiliated Cancer Hospital of Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
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22
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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.
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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
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23
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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.
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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.
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24
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Delmonico L, Silva Magalhães Costa MA, Gomes RJ, De Oliveira Vieira P, Da Silva ABP, Fournier MV, Scherrer LR, De Azevedo CM, Ornellas MHF, Alves G. Methylation profiling in promoter sequences of ATM and CDKN2A ( p14ARF/p16INK4a ) genes in blood and cfDNA from women with impalpable breast lesions. Oncol Lett 2020; 19:3003-3010. [PMID: 32218857 DOI: 10.3892/ol.2020.11382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The objective of the present study was to evaluate the epigenetic changes occurring in early stages of breast cancer. The present study investigated the methylation profile of the ATM, p14ARF and p16INK4a promoters in total blood and plasma cell-free DNA (cfDNA) from women with impalpable breast lesions compared with in total blood of a control cohort of women without breast lesions. The samples were evaluated using the methylation-specific PCR method. The Fisher's exact test was used to evaluate statistical significance between the methylation and clinical variables. A total of 111 women were evaluated, including 56 women with impalpable breast cancer (39/56 also had paired plasma cfDNA) and 55 women in the control cohort (55 blood DNA). For blood DNA from women with malignant impalpable breast lesions, p16INK4a exhibited the greatest percentage of methylation (48%), followed by ATM (37.5%) and p14ARF (27%) promoters, regardless of age variation. For plasma cfDNA, the methylation rates for ATM, p14ARF and p16INK4a were 26, 26 and 10%, respectively. The methylation rates for the blood DNA of controls were the lowest for ATM (9%), p14ARF (7%) and p16INK4a (7%). The women with impalpable breast lesions (benign and malignant lesions) exhibited the highest methylation rate, regardless of age, compared with the paired plasma cfDNA and controls. This epigenetic change was statistically significant for the promoters of ATM (P=0.009) and p16INK4a (P=0.001) (impalpable breast lesions vs. control). The present study demonstrated that epigenetic changes occurring in the ATM and CDKN2A genes detectable in liquid biopsy were associated with the development of impalpable breast lesions.
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Affiliation(s)
- Lucas Delmonico
- LaRBio-Radiation Laboratory in Biology, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | | | - Romario José Gomes
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Pâmella De Oliveira Vieira
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Ana Beatriz Passos Da Silva
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | | | | | | | - Maria Helena Faria Ornellas
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.,Postgraduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Gilda Alves
- Circulating Biomarkers Laboratory, Department of General Pathology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.,Postgraduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
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25
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Yan X, Wu T, Tang M, Chen D, Huang M, Zhou S, Zhang H, Yang X, Li G. Methylation of the ataxia telangiectasia mutated gene (ATM) promoter as a radiotherapy outcome biomarker in patients with hepatocellular carcinoma. Medicine (Baltimore) 2020; 99:e18823. [PMID: 31977876 PMCID: PMC7004781 DOI: 10.1097/md.0000000000018823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The goal of this study was to evaluate the contribution of ataxia telangiectasia mutated (ATM) gene promoter methylation to hepatocellular carcinoma (HCC) and the predictive value of radiotherapy outcome. ATM promoter methylation status was detected using methylation-specific PCR in 118 HCC, 50 adjacent liver, and 20 normal liver samples. PCR products were verified by bisulfite sequencing PCR. ATM expression was detected by quantitative PCR (qPCR) and immunohistochemistry (IHC) in 50 paired HCC and adjacent normal tissues and 68 locally advanced HCC biopsy tissues. Furthermore, radiotherapy outcomes in 68 locally advanced HCC patients were determined using European Association for the Study of Liver criteria and survival analysis. The results revealed that the methylation frequency of the ATM promoter was significantly higher in HCC tissues than in normal liver tissues (χ = 16.830, P < .001). Quantitative PCR (qPCR) and IHC results showed a significant association between ATM promoter methylation and ATM expression in HCC (χ = 10.510, P < .001), and methylated ATM was correlated with lower ATM expression compared with unmethylated ATM (r = 0.356, P < .001). Furthermore, methylation of the ATM promoter was significantly associated with superior outcomes in patients with locally advanced HCC who initially received radiotherapy. Together, these results indicate that ATM promoter methylation might increase the risk of HCC by regulating ATM expression, and thus may function as a potential biomarker for predicting radiotherapy outcomes in HCC patients.
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Affiliation(s)
- Xinjian Yan
- Department of Medical Oncology Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan
| | - Tianyu Wu
- Department of Medical Oncology Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan
| | - Mei Tang
- Department of Medical Oncology Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan
| | - Dongliang Chen
- Department of Medical Oncology Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan
| | - Meiyuan Huang
- Department of Medical Oncology Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan
| | - Sichun Zhou
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, Hunan, China
| | - Huihui Zhang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, Hunan, China
| | - Xiaoping Yang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, Hunan, China
| | - Gaofeng Li
- Department of Medical Oncology Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan
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26
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Prajzendanc K, Domagała P, Hybiak J, Ryś J, Huzarski T, Szwiec M, Tomiczek-Szwiec J, Redelbach W, Sejda A, Gronwald J, Kluz T, Wiśniowski R, Cybulski C, Łukomska A, Białkowska K, Sukiennicki G, Kulczycka K, Narod SA, Wojdacz TK, Lubiński J, Jakubowska A. BRCA1 promoter methylation in peripheral blood is associated with the risk of triple-negative breast cancer. Int J Cancer 2019; 146:1293-1298. [PMID: 31469414 DOI: 10.1002/ijc.32655] [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: 05/27/2019] [Revised: 07/19/2019] [Accepted: 08/16/2019] [Indexed: 12/16/2022]
Abstract
Methylation of the promoter of the BRCA1 gene in DNA derived from peripheral blood cells is a possible risk factor for breast cancer. It is not clear if this association is restricted to certain types of breast cancer or is a general phenomenon. We evaluated BRCA1 methylation status in peripheral blood cells from 942 breast cancer patients and from 500 controls. We also assessed methylation status in 262 paraffin-embedded breast cancer tissues. Methylation status was assessed using methylation-sensitive high-resolution melting and was categorized as positive or negative. BRCA1 methylation in peripheral blood cells was strongly associated with the risk of triple-negative breast cancer (TNBC) (odds ratio [OR] 4.70; 95% confidence interval [CI]: 3.13-7.07; p < 0.001), but not of estrogen-receptor positive breast cancer (OR 0.80; 95% CI: 0.46-1.42; p = 0.46). Methylation was also overrepresented among patients with high-grade cancers (OR 4.53; 95% CI: 2.91-7.05; p < 0.001) and medullary cancers (OR 3.08; 95% CI: 1.38-6.88; p = 0.006). Moreover, we detected a significant concordance of BRCA1 promoter methylation in peripheral blood and paired tumor tissue (p < 0.001). We found that BRCA1 promoter methylation in peripheral blood cells is associated with approximately five times greater risk of TNBC. We propose that BRCA1 methylation in blood-derived DNA could be a novel biomarker of increased breast cancer susceptibility, in particular for triple-negative tumors.
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Affiliation(s)
- Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Paweł Domagała
- Department of Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jolanta Hybiak
- Department of Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie Memorial Centre and Institute of Oncology, Cracow, Poland
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.,Department of Clinical Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Marek Szwiec
- Department of Surgery and Oncology, University of Zielona Góra, Zielona Góra, Poland.,Department of Clinical Oncology, University Hospital in Zielona Góra, Zielona Góra, Poland
| | - Joanna Tomiczek-Szwiec
- Department of Histology, Institute of Medicine, University of Opole, Opole, Poland.,Regional Oncology Centre, Opole, Poland
| | - Wojciech Redelbach
- Department of Anatomy, Institute of Medicine, University of Opole, Opole, Poland
| | - Aleksandra Sejda
- Department of Pathology, Provincial Specialist Hospital, Olsztyn, Poland.,Patomorphology Department, University of Warmia and Mazury, Olsztyn, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Kluz
- Institute of Obstetric and Emergency Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Rafał Wiśniowski
- Department of Clinical Oncology, Regional Oncology Centre, Bielsko-Biala, Poland
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Alicja Łukomska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Grzegorz Sukiennicki
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Kulczycka
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Steven A Narod
- Women's College Research Institute, Women's College Hospital, Toronto, ON, Canada
| | - Tomasz K Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - 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
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27
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Bodelon C, Ambatipudi S, Dugué PA, Johansson A, Sampson JN, Hicks B, Karlins E, Hutchinson A, Cuenin C, Chajès V, Southey MC, Romieu I, Giles GG, English D, Polidoro S, Assumma M, Baglietto L, Vineis P, Severi G, Herceg Z, Flanagan JM, Milne RL, Garcia-Closas M. Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies. Breast Cancer Res 2019; 21:62. [PMID: 31101124 PMCID: PMC6525390 DOI: 10.1186/s13058-019-1145-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Environmental and genetic factors play an important role in the etiology of breast cancer. Several small blood-based DNA methylation studies have reported risk associations with methylation at individual CpGs and average methylation levels; however, these findings require validation in larger prospective cohort studies. To investigate the role of blood DNA methylation on breast cancer risk, we conducted a meta-analysis of four prospective cohort studies, including a total of 1663 incident cases and 1885 controls, the largest study of blood DNA methylation and breast cancer risk to date. METHODS We assessed associations with methylation at 365,145 CpGs present in the HumanMethylation450 (HM450K) Beadchip, after excluding CpGs that did not pass quality controls in all studies. Each of the four cohorts estimated odds ratios (ORs) and 95% confidence intervals (CI) for the association between each individual CpG and breast cancer risk. In addition, each study assessed the association between average methylation measures and breast cancer risk, adjusted and unadjusted for cell-type composition. Study-specific ORs were combined using fixed-effect meta-analysis with inverse variance weights. Stratified analyses were conducted by age at diagnosis (< 50, ≥ 50), estrogen receptor (ER) status (+/-), and time since blood collection (< 5, 5-10, > 10 years). The false discovery rate (q value) was used to account for multiple testing. RESULTS The average age at blood draw ranged from 52.2 to 62.2 years across the four cohorts. Median follow-up time ranged from 6.6 to 8.4 years. The methylation measured at individual CpGs was not associated with breast cancer risk (q value > 0.59). In addition, higher average methylation level was not associated with risk of breast cancer (OR = 0.94, 95% CI = 0.85, 1.05; P = 0.26; P for study heterogeneity = 0.86). We found no evidence of modification of this association by age at diagnosis (P = 0.17), ER status (P = 0.88), time since blood collection (P = 0.98), or CpG location (P = 0.98). CONCLUSIONS Our data indicate that DNA methylation measured in the blood prior to breast cancer diagnosis in predominantly postmenopausal women is unlikely to be associated with substantial breast cancer risk on the HM450K array. Larger studies or with greater methylation coverage are needed to determine if associations exist between blood DNA methylation and breast cancer risk.
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Affiliation(s)
- Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Srikant Ambatipudi
- International Agency for Research on Cancer (IARC), Lyon, France
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | | | - Joshua N. Sampson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Belynda Hicks
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Eric Karlins
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Amy Hutchinson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Veronique Chajès
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Australia
| | - Isabelle Romieu
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Graham G. Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Dallas English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Silvia Polidoro
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Manuela Assumma
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Gianluca Severi
- CESP (U1018 INSERM, Équipe Générations et Santé), Facultés de médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Roger L. Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
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Gurioli G, Martignano F, Salvi S, Costantini M, Gunelli R, Casadio V. GSTP1 methylation in cancer: a liquid biopsy biomarker? Clin Chem Lab Med 2019; 56:702-717. [PMID: 29305565 DOI: 10.1515/cclm-2017-0703] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/31/2017] [Indexed: 12/14/2022]
Abstract
The coding region of GSTP1 gene is preceded by a large CpG-rich region that is frequently affected by methylation. In many cancer types, GSTP1 is affected by hypermethylation and, as a consequence, it has a low expression. The aim of this review is to give an overview on GSTP1 methylation studies with a special focus on liquid biopsy, thus to summarize methods, results, sample types, different diseases, to have a complete information regarding this promising epigenetic biomarker. We used all the most valuable scientific search engines (PubMed, Medline, Scopus and Web of Science) searching the following keywords: GSTP1, methylation, cancer, urine, serum, plasma and blood. GSTP1 is a largely investigated tissue biomarker in several malignancies such as prostate, breast, lung and hepatocellular carcinoma with good performances especially for diagnostic purposes. As a liquid biopsy biomarker, it has been mainly investigated in prostate cancer (PCa) where it showed a high specificity but a low sensitivity; thus, it is recommended in combination with other biomarkers. Despite the large number of published papers and the promising results, GSTP1 has not yet entered the clinical practice even for PCa diagnosis. For this reason, further large and prospective studies are needed to validate this assay.
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Affiliation(s)
- Giorgia Gurioli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Filippo Martignano
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Samanta Salvi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Matteo Costantini
- Pathology Unit, Department of Medical Oncology, Morgagni Pierantoni Hospital, Forlì, Italy
| | - Roberta Gunelli
- Department of Urology, Morgagni Pierantoni Hospital, Forli, Italy
| | - Valentina Casadio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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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.
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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.
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Bermejo JL, Huang G, Manoochehri M, Mesa KG, Schick M, Silos RG, Ko YD, Brüning T, Brauch H, Lo WY, Hoheisel JD, Hamann U. Long intergenic noncoding RNA 299 methylation in peripheral blood is a biomarker for triple-negative breast cancer. Epigenomics 2019; 11:81-93. [DOI: 10.2217/epi-2018-0121] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: To identify DNA methylation biomarkers in peripheral blood samples from triple-negative breast cancer (TNBC) patients. Materials & methods: We conducted an epigenome-wide association study (EWAS): the most promising markers were identified in 233 TNBC case–control pairs (discovery set) and subsequently validated in an independent validation set (57 TNBC patients and 124 controls). Results: cg06588802 (LINC00299/ID2) showed a higher methylation in TNBC patients compared with controls (discovery set: 3% increase, p-value = 0.0009; validation set: 2% increase, p-value = 0.01). Consistent results at four neighboring methylation probes and the strong negative correlation (rho = -0.93) with LINC00299 expression add plausibility to this result. Conclusion: Hypermethylation of LINC00299 in peripheral blood may constitute a useful circulating biomarker for TNBC.
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Affiliation(s)
- Justo L Bermejo
- Statistical Genetics Group, Institute of Medical Biometry & Informatics, University of Heidelberg, Heidelberg, 69120, Germany
| | - Guanmengqian Huang
- Department of Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Mehdi Manoochehri
- Department of Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Karen G Mesa
- Statistical Genetics Group, Institute of Medical Biometry & Informatics, University of Heidelberg, Heidelberg, 69120, Germany
- Department of Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Matthias Schick
- Genomics & Proteomics Core Facility, Microarray Unit, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Rosa G Silos
- Statistical Genetics Group, Institute of Medical Biometry & Informatics, University of Heidelberg, Heidelberg, 69120, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, 53113, Germany
| | - Thomas Brüning
- Institute for Prevention & Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, 44789, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany
- Department of Clinical Pharmacology, University of Tübingen, Tübingen, 70376, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany
- Department of Clinical Pharmacology, University of Tübingen, Tübingen, 70376, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Ute Hamann
- Department of Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
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31
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Guan Z, Yu H, Cuk K, Zhang Y, Brenner H. Whole-Blood DNA Methylation Markers in Early Detection of Breast Cancer: A Systematic Literature Review. Cancer Epidemiol Biomarkers Prev 2018; 28:496-505. [DOI: 10.1158/1055-9965.epi-18-0378] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/09/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
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Maretina M, Egorova A, Baranov V, Kiselev A. DYNC1H1 gene methylation correlates with severity of spinal muscular atrophy. Ann Hum Genet 2018; 83:73-81. [PMID: 30246859 DOI: 10.1111/ahg.12288] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/20/2022]
Abstract
Methylation profiles of CpG islands within the SLC23A2, CDK2AP1, and DYNC1H1 genes and their association with spinal muscular atrophy (SMA) severity were studied. High clinical heterogeneity of SMA suggests the existence of different factors modifying SMA phenotype with gene methylation as a plausible one. The genes picked up in our earlier genome-wide methylation studies of SMA patients demonstrated obvious differences in their methylation patterns, thus suggesting the likely involvement of their protein products in SMA development. Significantly decreased methylation of CpG islands within exon 37 of the DYNC1H1 gene was observed in patients with a severe SMA manifestation (type I) compared to mildly affected SMA patients (types III-IV). This finding provides new information on peculiarities of methylation in clinically different types of SMA patients and gives a clue for identification of new SMA modifiers.
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Affiliation(s)
- Marianna Maretina
- Laboratory of Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia.,Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Anna Egorova
- Laboratory of Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia
| | - Vladislav Baranov
- Laboratory of Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia.,Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Anton Kiselev
- Laboratory of Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia
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Parashar S, Cheishvili D, Mahmood N, Arakelian A, Tanvir I, Khan HA, Kremer R, Mihalcioiu C, Szyf M, Rabbani SA. DNA methylation signatures of breast cancer in peripheral T-cells. BMC Cancer 2018; 18:574. [PMID: 29776342 PMCID: PMC5960123 DOI: 10.1186/s12885-018-4482-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 05/07/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Immune surveillance acts as a defense mechanism in cancer, and its disruption is involved in cancer progression. DNA methylation reflects the phenotypic identity of cells and recent data suggested that DNA methylation profiles of T cells and peripheral blood mononuclear cells (PBMC) are altered in cancer progression. METHODS We enrolled 19 females with stage 1 and 2, nine with stage 3 and 4 and 9 age matched healthy women. T cells were isolated from peripheral blood and extracted DNA was subjected to Illumina 450 K DNA methylation array analysis. Raw data was analyzed by BMIQ, ChAMP and ComBat followed by validation of identified genes by pyrosequencing. RESULTS Analysis of data revealed ~ 10,000 sites that correlated with breast cancer progression and established a list of 89 CG sites that were highly correlated (p < 0.01, r > 0.7, r < - 0.7) with breast cancer progression. The vast majority of these sites were hypomethylated and enriched in genes with functions in the immune system. CONCLUSIONS The study points to the possibility of using DNA methylation signatures as a noninvasive method for early detection of breast cancer and its progression which need to be tested in clinical studies.
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Affiliation(s)
- Surabhi Parashar
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - David Cheishvili
- Department of Pharmacology and Therapeutics, McGill University Health Center, Montreal, QC, Canada.,Present address: Montreal EpiTerapia Inc., Montreal, QC, Canada
| | - Niaz Mahmood
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Ani Arakelian
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | | | | | - Richard Kremer
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Catalin Mihalcioiu
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University Health Center, Montreal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada.
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Wu HC, Do C, Andrulis IL, John EM, Daly MB, Buys SS, Chung WK, Knight JA, Bradbury AR, Keegan THM, Schwartz L, Krupska I, Miller RL, Santella RM, Tycko B, Terry MB. Breast cancer family history and allele-specific DNA methylation in the legacy girls study. Epigenetics 2018; 13:240-250. [PMID: 29436922 DOI: 10.1080/15592294.2018.1435243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Family history, a well-established risk factor for breast cancer, can have both genetic and environmental contributions. Shared environment in families as well as epigenetic changes that also may be influenced by shared genetics and environment may also explain familial clustering of cancers. Epigenetic regulation, such as DNA methylation, can change the activity of a DNA segment without a change in the sequence; environmental exposures experienced across the life course can induce such changes. However, genetic-epigenetic interactions, detected as methylation quantitative trait loci (mQTLs; a.k.a. meQTLs) and haplotype-dependent allele-specific methylation (hap-ASM), can also contribute to inter-individual differences in DNA methylation patterns. To identify differentially methylated regions (DMRs) associated with breast cancer susceptibility, we examined differences in white blood cell DNA methylation in 29 candidate genes in 426 girls (ages 6-13 years) from the LEGACY Girls Study, 239 with and 187 without a breast cancer family history (BCFH). We measured methylation by targeted massively parallel bisulfite sequencing (bis-seq) and observed BCFH DMRs in two genes: ESR1 (Δ4.9%, P = 0.003) and SEC16B (Δ3.6%, P = 0.026), each of which has been previously implicated in breast cancer susceptibility and pubertal development. These DMRs showed high inter-individual variability in methylation, suggesting the presence of mQTLs/hap-ASM. Using single nucleotide polymorphisms data in the bis-seq amplicon, we found strong hap-ASM in SEC16B (with allele specific-differences ranging from 42% to 74%). These findings suggest that differential methylation in genes relevant to breast cancer susceptibility may be present early in life, and that inherited genetic factors underlie some of these epigenetic differences.
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Affiliation(s)
- Hui-Chen Wu
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY
| | - Catherine Do
- c John Theurer Cancer Center , Hackensack University Medical Center , Hackensack NJ
| | - Irene L Andrulis
- d Lunenfeld-Tanenbaum Research Institute , Sinai Health System , Toronto , Ontario.,e Departments of Molecular Genetics and Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
| | - Esther M John
- f Cancer Prevention Institute of California , Fremont CA.,g Department of Health Research & Policy (Epidemiology) , and Stanford Cancer Institute, Stanford University School of Medicine , Stanford , CA
| | - Mary B Daly
- h Department of Clinical Genetics , Fox Chase Cancer Center , Philadelphia , PA
| | - Saundra S Buys
- i Department of Medicine and , Huntsman Cancer Institute, University of Utah Health Sciences Center , UT
| | - Wendy K Chung
- j Departments of Pediatrics ; Department of Medicine , Columbia University College of Physicians and Surgeons , New York , NY
| | - Julia A Knight
- d Lunenfeld-Tanenbaum Research Institute , Sinai Health System , Toronto , Ontario.,k Dalla Lana School of Public Health , University of Toronto , Toronto
| | - Angela R Bradbury
- l Departments of Medicine, Division of Hematology/Oncology, Department of Medical Ethics and Health Policy, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA
| | - Theresa H M Keegan
- m Center for Oncology Hematology Outcomes Research and Training (COHORT).,n Division of Hematology and Oncology , University of California Davis School of Medicine , Sacramento , CA
| | - Lisa Schwartz
- o Department of Pediatrics, Division of Oncology, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA.,p The Children's Hospital of Philadelphia , Philadelphia , PA
| | - Izabela Krupska
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY
| | - Rachel L Miller
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,j Departments of Pediatrics ; Department of Medicine , Columbia University College of Physicians and Surgeons , New York , NY
| | - Regina M Santella
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY
| | - Benjamin Tycko
- c John Theurer Cancer Center , Hackensack University Medical Center , Hackensack NJ.,q Lombardi Comprehensive Cancer Center , Georgetown University , Washington , DC
| | - Mary Beth Terry
- a Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York , NY.,b Department of Environmental Health Sciences , Mailman School of Public Health of Columbia University , New York , NY.,r Imprints Center , Columbia University Medical Center , New York , NY.,s Department of Epidemiology , Mailman School of Public Health of Columbia University , New York , NY
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35
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Cao X, Tang Q, Holland-Letz T, Gündert M, Cuk K, Schott S, Heil J, Golatta M, Sohn C, Schneeweiss A, Burwinkel B. Evaluation of Promoter Methylation of RASSF1A and ATM in Peripheral Blood of Breast Cancer Patients and Healthy Control Individuals. Int J Mol Sci 2018; 19:ijms19030900. [PMID: 29562656 PMCID: PMC5877761 DOI: 10.3390/ijms19030900] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 01/26/2023] Open
Abstract
Breast cancer (BC) is the most common cancer among women and has high mortality rates. Early detection is supposed to be critical for the patient’s prognosis. In recent years, several studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop putative screening markers for cancer. However, most of the studies have not yet been validated. In our study, we analyzed the promoter methylation of RASSF1A and ATM in peripheral blood DNA of 229 sporadic patients and 151 healthy controls by the MassARRAY EpiTYPER assay. There were no significant differences in DNA methylation levels of RASSF1A and ATM between the sporadic BC cases and the healthy controls. Furthermore, we performed the Infinium HumanMethylation450 BeadChip (450K) array analysis using 48 sporadic BC cases and 48 healthy controls (cases and controls are the same from those of the MassARRAY EpiTYPER assay) and made a comparison with the published data. No significant differences were presented in DNA methylation levels of RASSF1A and ATM between the sporadic BC cases and the healthy controls. So far, the evidence for powerful blood-based methylation markers is still limited and the identified markers need to be further validated.
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Affiliation(s)
- Xue Cao
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Tim Holland-Letz
- Division of Biostatistics (C060), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Melanie Gündert
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Katarina Cuk
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
| | - Jörg Heil
- Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg 69120, Germany.
| | - Michael Golatta
- Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg 69120, Germany.
| | - Christof Sohn
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
| | - Andreas Schneeweiss
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- National Centre for Tumor Diseases, Heidelberg 69120, Germany.
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
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36
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Widschwendter M, Jones A, Evans I, Reisel D, Dillner J, Sundström K, Steyerberg EW, Vergouwe Y, Wegwarth O, Rebitschek FG, Siebert U, Sroczynski G, de Beaufort ID, Bolt I, Cibula D, Zikan M, Bjørge L, Colombo N, Harbeck N, Dudbridge F, Tasse AM, Knoppers BM, Joly Y, Teschendorff AE, Pashayan N. Epigenome-based cancer risk prediction: rationale, opportunities and challenges. Nat Rev Clin Oncol 2018; 15:292-309. [PMID: 29485132 DOI: 10.1038/nrclinonc.2018.30] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The incidence of cancer is continuing to rise and risk-tailored early diagnostic and/or primary prevention strategies are urgently required. The ideal risk-predictive test should: integrate the effects of both genetic and nongenetic factors and aim to capture these effects using an approach that is both biologically stable and technically reproducible; derive a score from easily accessible biological samples that acts as a surrogate for the organ in question; and enable the effectiveness of risk-reducing measures to be monitored. Substantial evidence has accumulated suggesting that the epigenome and, in particular, DNA methylation-based tests meet all of these requirements. However, the development and implementation of DNA methylation-based risk-prediction tests poses considerable challenges. In particular, the cell type specificity of DNA methylation and the extensive cellular heterogeneity of the easily accessible surrogate cells that might contain information relevant to less accessible tissues necessitates the use of novel methods in order to account for these confounding issues. Furthermore, the engagement of the scientific community with health-care professionals, policymakers and the public is required in order to identify and address the organizational, ethical, legal, social and economic challenges associated with the routine use of epigenetic testing.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Allison Jones
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ewout W Steyerberg
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands.,Department of Biomedical Data Sciences, LUMC, Leiden, Netherlands
| | - Yvonne Vergouwe
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands
| | - Odette Wegwarth
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany.,Max Planck Institute for Human Development, Center for Adaptive Rationality, Berlin, Germany
| | - Felix G Rebitschek
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany
| | - Uwe Siebert
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria.,Harvard T. C. Chan School of Public Health, Center for Health Decision Science, Department of Health Policy and Management, Boston, MA, USA.,Oncotyrol: Center for Personalized Medicine, Innsbruck, Austria
| | - Gaby Sroczynski
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
| | - Inez D de Beaufort
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ineke Bolt
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - David Cibula
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Michal Zikan
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, and Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nicoletta Colombo
- European Institute of Oncology and University Milan-Bicocca, Milan, Italy
| | - Nadia Harbeck
- Breast Center, Department of Gynaecology and Obstetrics, University of Munich (LMU), Munich, Germany
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anne-Marie Tasse
- Public Population Project in Genomics and Society, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | | | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Andrew E Teschendorff
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Nora Pashayan
- Department of Applied Health Research, Institute of Epidemiology and Healthcare, University College London, UK
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37
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Yadav P, Masroor M, Nandi K, Kaza RCM, Jain SK, Khurana N, Saxena A. Promoter Methylation of BRCA1, DAPK1 and RASSF1A is
Associated with Increased Mortality among Indian Women
with Breast Cancer. Asian Pac J Cancer Prev 2018; 19:443-448. [PMID: 29480000 PMCID: PMC5980932 DOI: 10.22034/apjcp.2018.19.2.443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background: Promoter methylation has been observed for several genes in association with cancer development and
progression. Hypermethylation mediated-silencing of tumor suppressor genes (TSGs) may contribute to breast cancer
pathogenesis. The present study was conducted to investigate the promoter methylation status of BRCA1, DAPK1 and
RASSF1A genes in Indian women with breast cancer. Materials and Methods: Promoter methylation was evaluated
in DNA extracted from mononuclear cells (MNCs) in peripheral blood samples of 60 histopathologically confirmed
newly diagnosed, untreated cases of breast cancer as well as 60 age and sex matched healthy controls using MS-PCR.
Association of promoter methylation with breast cancer-specific mortality was analyzed with Cox proportional hazards
models. Kaplan-Meier survival analysis was performed for overall survival of the breast cancer patients. Results: We
observed a significant increase of BRCA1, DAPK1 and RASSF1A promoter methylation levels by 51.7% (P <0.001),
55.0% (P <0.001) and 46.6% (P <0.001), respectively, when compared to healthy controls. A strong correlation was
noted between hypermethylation of the tumor suppressor genes BRCA1 (P= 0.009), DAPK1 (P= 0.008) and RASSF1A
(P= 0.02)) with early and advanced stages of breast cancer patients. We also found that breast cancer-specific mortality
was significantly associated with promoter methylation of BRCA1 [HR and 95% CI: 3.25 (1.448-7.317)] and DAPK1
[HR and 95% CI: 2.32 (1.05-5.11)], whereas limited significant link was evident with RASSF1A [HR and 95% CI: 1.54
(0.697-3.413]. Conclusion: Our results suggest that promoter methylation of BRCA1, DAPK1 and RASSF1A genes
may be associated with disease progression and poor overall survival of Indian women with breast cancer.
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Affiliation(s)
- Prasant Yadav
- Department of Biochemistry, Maulana Azad Medical College, New Delhi, India.,Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India.
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38
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DNA methylation array analysis identifies breast cancer associated RPTOR, MGRN1 and RAPSN hypomethylation in peripheral blood DNA. Oncotarget 2018; 7:64191-64202. [PMID: 27577081 PMCID: PMC5325435 DOI: 10.18632/oncotarget.11640] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/13/2016] [Indexed: 11/30/2022] Open
Abstract
DNA methylation changes in peripheral blood DNA have been shown to be associated with solid tumors. We sought to identify methylation alterations in whole blood DNA that are associated with breast cancer (BC). Epigenome-wide DNA methylation profiling on blood DNA from BC cases and healthy controls was performed by applying Infinium HumanMethylation450K BeadChips. Promising CpG sites were selected and validated in three independent larger sample cohorts via MassARRAY EpiTyper assays. CpG sites located in three genes (cg06418238 in RPTOR, cg00736299 in MGRN1 and cg27466532 in RAPSN), which showed significant hypomethylation in BC patients compared to healthy controls in the discovery cohort (p < 1.00 × 10−6) were selected and successfully validated in three independent cohorts (validation I, n =211; validation II, n=378; validation III, n=520). The observed methylation differences are likely not cell-type specific, as the differences were only seen in whole blood, but not in specific sub cell-types of leucocytes. Moreover, we observed in quartile analysis that women in the lower methylation quartiles of these three loci had higher ORs than women in the higher quartiles. The combined AUC of three loci was 0.79 (95%CI 0.73-0.85) in validation cohort I, and was 0.60 (95%CI 0.54-0.66) and 0.62 (95%CI 0.57-0.67) in validation cohort II and III, respectively. Our study suggests that hypomethylation of CpG sites in RPTOR, MGRN1 and RAPSN in blood is associated with BC and might serve as blood-based marker supplements for BC if these could be verified in prospective studies.
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39
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Gao D, Herman JG, Guo M. The clinical value of aberrant epigenetic changes of DNA damage repair genes in human cancer. Oncotarget 2018; 7:37331-37346. [PMID: 26967246 PMCID: PMC5095080 DOI: 10.18632/oncotarget.7949] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/20/2016] [Indexed: 12/22/2022] Open
Abstract
The stability and integrity of the human genome are maintained by the DNA damage repair (DDR) system. Unrepaired DNA damage is a major source of potentially mutagenic lesions that drive carcinogenesis. In addition to gene mutation, DNA methylation occurs more frequently in DDR genes in human cancer. Thus, DNA methylation may play more important roles in DNA damage repair genes to drive carcinogenesis. Aberrant methylation patterns in DNA damage repair genes may serve as predictive, diagnostic, prognostic and chemosensitive markers of human cancer. MGMT methylation is a marker for poor prognosis in human glioma, while, MGMT methylation is a sensitive marker of glioma cells to alkylating agents. Aberrant epigenetic changes in DNA damage repair genes may serve as therapeutic targets. Treatment of MLH1-methylated colon cancer cell lines with the demethylating agent 5′-aza-2′-deoxycytidine induces the expression of MLH1 and sensitizes cancer cells to 5-fluorouracil. Synthetic lethality is a more exciting approach in patients with DDR defects. PARP inhibitors are the most effective anticancer reagents in BRCA-deficient cancer cells.
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Affiliation(s)
- Dan Gao
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China.,Medical College of NanKai University, Tianjin, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
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40
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Ghosh M, Öner D, Poels K, Tabish AM, Vlaanderen J, Pronk A, Kuijpers E, Lan Q, Vermeulen R, Bekaert B, Hoet PH, Godderis L. Changes in DNA methylation induced by multi-walled carbon nanotube exposure in the workplace. Nanotoxicology 2017; 11:1195-1210. [PMID: 29191063 DOI: 10.1080/17435390.2017.1406169] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This study was designed to assess the epigenetic alterations in blood cells, induced by occupational exposure to multi-wall carbon nanotubes (MWCNT). The study population comprised of MWCNT-exposed workers (n=24) and unexposed controls (n=43) from the same workplace. We measured global DNA methylation/hydroxymethylation levels on the 5th cytosine residues using a validated liquid chromatography tandem-mass spectrometry (LC-MS/MS) method. Sequence-specific methylation of LINE1 retrotransposable element 1 (L1RE1) elements, and promoter regions of functionally important genes associated with epigenetic regulation [DNA methyltransferase-1 (DNMT1) and histone deacetylase 4 (HDAC4)], DNA damage/repair and cell cycle pathways [nuclear protein, coactivator of histone transcription/ATM serine/threonine kinase (NPAT/ATM)], and a potential transforming growth factor beta (TGF-β) repressor [SKI proto-oncogene (SKI)] were studied using bisulfite pyrosequencing. Analysis of global DNA methylation levels and hydroxymethylation did not reveal significant difference between the MWCNT-exposed and control groups. No significant changes in Cytosine-phosphate-Guanine (CpG) site methylation were observed for the LINE1 (L1RE1) elements. Further analysis of gene-specific DNA methylation showed a significant change in methylation for DNMT1, ATM, SKI, and HDAC4 promoter CpGs in MWCNT-exposed workers. Since DNA methylation plays an important role in silencing/regulation of the genes, and many of these genes have been associated with occupational and smoking-induced diseases and cancer (risk), aberrant methylation of these genes might have a potential effect in MWCNT-exposed workers.
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Affiliation(s)
- Manosij Ghosh
- a Department of Public Health and Primary Care, Centre Environment & Health , KU Leuven , Leuven , Belgium
| | - Deniz Öner
- a Department of Public Health and Primary Care, Centre Environment & Health , KU Leuven , Leuven , Belgium
| | - Katrien Poels
- a Department of Public Health and Primary Care, Centre Environment & Health , KU Leuven , Leuven , Belgium
| | - Ali M Tabish
- a Department of Public Health and Primary Care, Centre Environment & Health , KU Leuven , Leuven , Belgium
| | - Jelle Vlaanderen
- b Division of Environmental Epidemiology, Institute for Risk Assessment Sciences , Utrecht University , Utrecht , The Netherlands
| | - Anjoeka Pronk
- c TNO, Netherlands Organisation for Applied Scientific Research , Zeist , The Netherlands
| | - Eelco Kuijpers
- c TNO, Netherlands Organisation for Applied Scientific Research , Zeist , The Netherlands
| | - Qing Lan
- d Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics , National Cancer Institute , Bethesda , MD , USA
| | - Roel Vermeulen
- b Division of Environmental Epidemiology, Institute for Risk Assessment Sciences , Utrecht University , Utrecht , The Netherlands
| | - Bram Bekaert
- e Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archaeology , University Hospitals Leuven , Leuven , Belgium
| | - Peter Hm Hoet
- a Department of Public Health and Primary Care, Centre Environment & Health , KU Leuven , Leuven , Belgium
| | - Lode Godderis
- a Department of Public Health and Primary Care, Centre Environment & Health , KU Leuven , Leuven , Belgium.,f External Service for Prevention and Protection at Work , Idewe , Heverlee , Belgium
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41
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Begam N, Jamil K, Raju SG. Promoter Hypermethylation of the ATM Gene as a Novel Biomarker for Breast Cancer. Asian Pac J Cancer Prev 2017; 18:3003-3009. [PMID: 29172272 PMCID: PMC5773784 DOI: 10.22034/apjcp.2017.18.11.3003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background: Breast cancer may be induced by activation of protooncogenes to oncogenes and in many cases inactivation of tumor suppressor genes. Ataxia telangiectasia mutated (ATM) is an important tumor suppressor gene which plays central roles in the maintenance of genomic integrity by activating cell cycle checkpoints and promoting repair of double-strand breaks of DNA. In breast cancer, decrease ATM expression correlates with a poor outcome; however, the molecular mechanisms underlying downregulation are still unclear. Promoter hypermethylation may contribute in downregulation. Hence the present investigation was designed to evaluate promoter methylation and expression of the ATM gene in breast cancer cases, and to determine links with clinical and demographic manifestations, in a South Indian population. Methods: Tumor biopsy samples were collected from 50 pathologically confirmed sporadic breast cancer cases. DNA was isolated from tumor and adjacent non-tumorous regions, and sodium bisulfite conversion and methylation-specific PCR were performed using MS-PCR primers for the ATM promoter region. In addition, ATM mRNA expression was also analyzed for all samples using real-time PCR. Results: Fifty eight percent (58%) of cancer tissue samples showed promoter hypermethylation for the ATM gene, in contrast to only 4.44% of normal tissues (p= 0.0001). Furthermore, ATM promoter methylation was positively associated with age (p = 0.01), tumor size (p=0.045) and advanced stage of disease i.e. stages III and IV (p =0.019). An association between promoter hypermethylation and lower expression of ATM mRNA was also found (p=0.035). Conclusion: We report for the first time that promoter hypermethylation of ATM gene may be useful as a potential new biomarker for breast cancer, especially in the relatively young patients.
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Affiliation(s)
- Nasrin Begam
- Jawaharlal Nehru Institute of Advanced Studies (JNIAS), School of Life Sciences, Centre for Biotechnology and Bioinformatics,Secunderabad- 500003,Telangana, India.
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42
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Yang R, Stöcker S, Schott S, Heil J, Marme F, Cuk K, Chen B, Golatta M, Zhou Y, Sutter C, Wappenschmidt B, Schmutzler R, Bugert P, Qu B, Bartram CR, Sohn C, Schneeweiss A, Burwinkel B. The association between breast cancer and S100P methylation in peripheral blood by multicenter case-control studies. Carcinogenesis 2017; 38:312-320. [PMID: 28426874 DOI: 10.1093/carcin/bgx004] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 01/12/2017] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BC) is the leading cancer in women worldwide. Changes in DNA methylation in peripheral blood could be associated with malignant diseases. Making use of screening results by llumina 27K Methylation Assay, we validated demethylation of five CpG sites of S100P gene in blood cell DNA of BC patients by three independent retrospective studies with subjects from different centers (Validation I: 235 familial BC case and 206 controls, odds ratio per -1% methylation > 1.03, and P < 6.00 × 10-8 for all five CpG sites; Validation II: 189 sporadic BC case and 189 controls, odds ratio per -1% methylation > 1.03, P < 8.0 × 10-5 for four CpG sites; Validation III: 156 sporadic BC case and 151 controls, odds ratio per -1% methylation > 1.03, P < 6.0 × 10-4 for four CpG sites). In addition, the blood-based S100P methylation pattern was similar among BC patients with differential clinical characteristics regardless of stage, receptor status and menopause status. The observed BC-associated decreased S100P methylation in blood mainly originates from the leucocytes subpopulations but not B cells. The methylation levels of most S100P CpG sites were inversely correlated with the expression of S100P in leucocytes (P < 1.2 × 10-4) and in tissue (P < 1.1 × 10-4). This study reveals significant association between blood-based decreased S100P methylation and BC, and provides another proof for the application of altered DNA methylation signatures from blood cells as potential markers for the detection of BC, especially for the early stage.
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Affiliation(s)
- Rongxi Yang
- Molecular Biology of Breast Cancer.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Sarah Stöcker
- Molecular Biology of Breast Cancer.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Schott
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Jörg Heil
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Frederik Marme
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Katarina Cuk
- Molecular Biology of Breast Cancer.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Bowang Chen
- Division of Molecular Genetic Epidemiology (C050), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Department of Biology, South University of Science and Technology of China, 518055 Shenzhen, China
| | - Michael Golatta
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Yan Zhou
- Department of Biophysics, Saarland University, 66421 Homburg (Saar), Germany
| | - Christian Sutter
- Institute of Human Genetics, University of Heidelberg, 69120 Heidelberg, Germany
| | - Barbara Wappenschmidt
- Department of Gynecology and Obstetrics, Clinical Center of University of Cologne, 50931 Cologne, Germany
| | - Rita Schmutzler
- Department of Gynecology and Obstetrics, Clinical Center of University of Cologne, 50931 Cologne, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, German Red Cross Blood Service Baden-Württemberg - Hessen, 68167 Mannheim, Germany and
| | - Bin Qu
- Department of Biophysics, Saarland University, 66421 Homburg (Saar), Germany
| | - Claus R Bartram
- Institute of Human Genetics, University of Heidelberg, 69120 Heidelberg, Germany
| | - Christof Sohn
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Andreas Schneeweiss
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,Division Gynecologic Oncology, National Center for Tumor Diseases (NCT) 69120 Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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43
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White blood cell DNA methylation and risk of breast cancer in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). Breast Cancer Res 2017; 19:94. [PMID: 28821281 PMCID: PMC5563066 DOI: 10.1186/s13058-017-0886-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/25/2017] [Indexed: 01/24/2023] Open
Abstract
Background Several studies have suggested that global DNA methylation in circulating white blood cells (WBC) is associated with breast cancer risk. Methods To address conflicting results and concerns that the findings for WBC DNA methylation in some prior studies may reflect disease effects, we evaluated the relationship between global levels of WBC DNA methylation in white blood cells and breast cancer risk in a case-control study nested within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO) cohort. A total of 428 invasive breast cancer cases and 419 controls, frequency matched on age at entry (55–59, 60–64, 65–69, ≥70 years), year of entry (on/before September 30, 1997, on/after October 1, 1997) and period of DNA extraction (previously extracted, newly extracted) were included. The ratio of 5-methyl-2’ deoxycytidine [5-mdC] to 2’-deoxyguanine [dG], assuming [dG] = [5-mdC] + [2’-deoxycytidine [dC]] (%5-mdC), was determined by liquid chromatography-electrospray ionization-tandem mass spectrometry, an especially accurate method for assessing total genomic DNA methylation. Results Odds ratio (OR) estimates and 95% confidence intervals (CI) for breast cancer risk adjusted for age at entry, year of entry, and period of DNA extraction, were 1.0 (referent), 0.89 (95% CI, 0.6–1.3), 0.88 (95% CI, 0.6–1.3), and 0.84 (95% CI, 0.6–1.2) for women in the highest compared to lowest quartile levels of %5md-C (p for trend = .39). Effects did not meaningfully vary by time elapsed from WBC collection to diagnosis. Discussion These results do not support the hypothesis that global DNA hypomethylation in WBC DNA is associated with increased breast cancer risk prior to the appearance of clinical disease.
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44
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Schott S, Yang R, Stöcker S, Canzian F, Giese N, Bugert P, Bergmann F, Strobel O, Hackert T, Sohn C, Burwinkel B. HYAL2 methylation in peripheral blood as a potential marker for the detection of pancreatic cancer: a case control study. Oncotarget 2017; 8:67614-67625. [PMID: 28978057 PMCID: PMC5620197 DOI: 10.18632/oncotarget.18757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy which is mostly diagnosed in advanced and inoperable stages though surgery remains the only curable therapeutic approach. Early detection markers are urgently needed to improve diagnosis. Altered hyaluronoglucosaminidase 2 gene (HYAL2) DNA methylation in peripheral blood is known to be associated with malignancy at early stage but has not been evaluated in PDAC patients. This study evaluates the association between blood-based HYAL2 methylation and PDAC by a case-control study with 191 controls and 82 PDAC patients. Decreased methylation of all four investigated HYAL2 methylation sites showed highly significant association with PDAC (odds ratio (ORs) per −10% methylation ranging from 2.03 to 12.74, depending on the specific CpG site, p < 0.0001 for all). HYAL2 methylation sites were also distinguishable between stage I&II PDAC (61 subjects) and controls (ORs per-10% methylation from 3.17 - 23.04, p < 0.0001 for all). Thus, HYAL2 methylation level enabled a very good discrimination of PDAC cases from healthy controls (area under curve (AUC) = 0.92, 95% Confidence interval (C.I.): 0.88 - 0.96), and was also powerful for the detection of PDAC at stage I&II (AUC = 0.93, 95% C.I.: 0.89 - 0.98). Moreover, the blood-based HYAL2 methylation pattern was similar among PDAC patients with differential clinical characteristics, and showed no correlation with the overall survival of PDAC patients. Our study reveals a strong association between decreased HYAL2 methylation in peripheral blood and PDAC, and provides a promising blood-based marker for the detection of PDAC.
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Affiliation(s)
- Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), NCT Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rongxi Yang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Stöcker
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Federico Canzian
- Genomic Epidemiology Group (C055), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, German Red Cross Blood Service Baden-Württemberg - Hessen, 68167 Mannheim, Germany
| | - Frank Bergmann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Christof Sohn
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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45
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Khakpour G, Noruzinia M, Izadi P, Karami F, Ahmadvand M, Heshmat R, Amoli MM, Tavakkoly-Bazzaz J. Methylomics of breast cancer: Seeking epimarkers in peripheral blood of young subjects. Tumour Biol 2017; 39:1010428317695040. [PMID: 28349825 DOI: 10.1177/1010428317695040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Critical roles of epigenomic alterations in the pathogenesis of breast cancer have recently seized great attentions toward finding epimarkers in either non-invasive or semi-non-invasive samples as well as peripheral blood. In this way, methylated DNA immunoprecipitation microarray (MeDIP-chip) was performed on DNA samples isolated from white blood cells of 30 breast cancer patients compared to 30 healthy controls. A total of 1799 differentially methylated regions were identified including SLC6A3, Rab40C, ZNF584, and FOXD3 whose significant methylation differences were confirmed in breast cancer patients through quantitative real-time polymerase chain reaction. Hypermethylation of APC, HDAC1, and GSK1 genes has been previously reported in more than one study on tissue samples of breast cancer. Methylation of those aforementioned genes in white blood cells of our young patients not only relies on their importance in breast cancer pathogenesis but also may highlight their potential as early epimarkers that makes further assessments necessary in large cohort studies.
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Affiliation(s)
- Golnaz Khakpour
- 1 Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Noruzinia
- 2 Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Pantea Izadi
- 1 Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Karami
- 3 Department of Medical Genetics, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Ahmadvand
- 4 Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Heshmat
- 5 Chronic Disease Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa M Amoli
- 6 Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Tavakkoly-Bazzaz
- 1 Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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46
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Schenkel LC, Rodenhiser D, Siu V, McCready E, Ainsworth P, Sadikovic B. Constitutional Epi/Genetic Conditions: Genetic, Epigenetic, and Environmental Factors. J Pediatr Genet 2017; 6:30-41. [PMID: 28180025 PMCID: PMC5288004 DOI: 10.1055/s-0036-1593849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
There are more than 4,000 phenotypes for which the molecular basis is at least partly known. Though defects in primary DNA structure constitute a major cause of these disorders, epigenetic disruption is emerging as an important alternative mechanism in the etiology of a broad range of congenital and developmental conditions. These include epigenetic defects caused by either localized (in cis) genetic alterations or more distant (in trans) genetic events but can also include environmental effects. Emerging evidence suggests interplay between genetic and environmental factors in the epigenetic etiology of several constitutional "epi/genetic" conditions. This review summarizes our broadening understanding of how epigenetics contributes to pediatric disease by exploring different classes of epigenomic disorders. It further challenges the simplistic dogma of "DNA encodes RNA encodes protein" to best understand the spectrum of factors that can influence genetic traits in a pediatric population.
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Affiliation(s)
- Laila C. Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
| | - David Rodenhiser
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Victoria Siu
- Children's Health Research Institute, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
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47
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Zhang Y, Xu YY, Yao CB, Li JT, Zhao XN, Yang HB, Zhang M, Yin M, Chen J, Lei QY. Acetylation targets HSD17B4 for degradation via the CMA pathway in response to estrone. Autophagy 2017; 13:538-553. [PMID: 28296597 DOI: 10.1080/15548627.2016.1268302] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dysregulation of hormone metabolism is implicated in human breast cancer. 17β-hydroxysteroid dehydrogenase type 4 (HSD17B4) catalyzes the conversion of estradiol (E2) to estrone (E1), and is associated with the pathogenesis and development of various cancers. Here we show that E1 upregulates HSD17B4 acetylation at lysine 669 (K669) and thereby promotes HSD17B4 degradation via chaperone-mediated autophagy (CMA), while a single mutation at K669 reverses the degradation and confers migratory and invasive properties to MCF7 cells upon E1 treatment. CREBBP and SIRT3 dynamically control K669 acetylation level of HSD17B4 in response to E1. More importantly, K669 acetylation is inversely correlated with HSD17B4 in human breast cancer tissues. Our study reveals a crosstalk between acetylation and CMA degradation in HSD17B4 regulation, and a critical role of the regulation in the malignant progression of breast cancer.
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Affiliation(s)
- Ye Zhang
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
| | - Ying-Ying Xu
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
| | - Chuan-Bo Yao
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
| | - Jin-Tao Li
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
| | - Xiang-Ning Zhao
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
| | - Hong-Bin Yang
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
| | - Min Zhang
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
| | - Miao Yin
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
| | - Jing Chen
- b Department of Hematology and Medical Oncology , Winship Cancer Institute of Emory, Emory University School of Medicine , Atlanta , GA , USA
| | - Qun-Ying Lei
- a Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology , School of Basic Medical Sciences, and Cancer Metabolism Laboratory, Institutes of Biomedical Sciences, and State Key Laboratory of Medical Neurobiology, Fudan University , Shanghai , China
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48
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Johansson A, Flanagan JM. Epigenome-wide association studies for breast cancer risk and risk factors. TRENDS IN CANCER RESEARCH 2017; 12:19-28. [PMID: 28955137 PMCID: PMC5612397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
There have been six epigenome-wide association studies (EWAS) for breast cancer risk using blood DNA from prospective cohorts published thus far, and the only consistent finding is a global loss of methylation observed in breast cancer cases compared with controls, with no individual CpG sites passing validation across studies. In contrast, a more successful approach has been the identification of EWAS signatures of cancer risk factors such as smoking, body mass index, age and alcohol use with numerous validated CpG sites. These signatures may be used as a molecular test to quantify cancer risk associated with these factors. It is clear from the larger EWAS of risk exposures that similar-sized large collaborative studies may be needed to robustly identify DNA methylation signatures of breast cancer risk.
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Affiliation(s)
- Annelie Johansson
- Epigenetics Unit, Division of Cancer, Department of Surgery and Cancer, Imperial College London, UK
| | - James M. Flanagan
- Epigenetics Unit, Division of Cancer, Department of Surgery and Cancer, Imperial College London, UK
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49
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WSB1 overcomes oncogene-induced senescence by targeting ATM for degradation. Cell Res 2016; 27:274-293. [PMID: 27958289 DOI: 10.1038/cr.2016.148] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/20/2022] Open
Abstract
Oncogene-induced senescence (OIS) or apoptosis through the DNA-damage response is an important barrier of tumorigenesis. Overcoming this barrier leads to abnormal cell proliferation, genomic instability, and cellular transformation, and finally allows cancers to develop. However, it remains unclear how the OIS barrier is overcome. Here, we show that the E3 ubiquitin ligase WD repeat and SOCS box-containing protein 1 (WSB1) plays a role in overcoming OIS. WSB1 expression in primary cells helps the bypass of OIS, leading to abnormal proliferation and cellular transformation. Mechanistically, WSB1 promotes ATM ubiquitination, resulting in ATM degradation and the escape from OIS. Furthermore, we identify CDKs as the upstream kinase of WSB1. CDK-mediated phosphorylation activates WSB1 by promoting its monomerization. In human cancer tissue and in vitro models, WSB1-induced ATM degradation is an early event during tumorigenic progression. We suggest that WSB1 is one of the key players of early oncogenic events through ATM degradation and destruction of the tumorigenesis barrier. Our work establishes an important mechanism of cancer development and progression in premalignant lesions.
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50
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Scott CM, Joo JE, O’Callaghan N, Buchanan DD, Clendenning M, Giles GG, Hopper JL, Wong EM, Southey MC. Methylation of Breast Cancer Predisposition Genes in Early-Onset Breast Cancer: Australian Breast Cancer Family Registry. PLoS One 2016; 11:e0165436. [PMID: 27902704 PMCID: PMC5130174 DOI: 10.1371/journal.pone.0165436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/11/2016] [Indexed: 12/31/2022] Open
Abstract
DNA methylation can mimic the effects of both germline and somatic mutations for cancer predisposition genes such as BRCA1 and p16INK4a. Constitutional DNA methylation of the BRCA1 promoter has been well described and is associated with an increased risk of early-onset breast cancers that have BRCA1-mutation associated histological features. The role of methylation in the context of other breast cancer predisposition genes has been less well studied and often with conflicting or ambiguous outcomes. We examined the role of methylation in known breast cancer susceptibility genes in breast cancer predisposition and tumor development. We applied the Infinium HumanMethylation450 Beadchip (HM450K) array to blood and tumor-derived DNA from 43 women diagnosed with breast cancer before the age of 40 years and measured the methylation profiles across promoter regions of BRCA1, BRCA2, ATM, PALB2, CDH1, TP53, FANCM, CHEK2, MLH1, MSH2, MSH6 and PMS2. Prior genetic testing had demonstrated that these women did not carry a germline mutation in BRCA1, ATM, CHEK2, PALB2, TP53, BRCA2, CDH1 or FANCM. In addition to the BRCA1 promoter region, this work identified regions with variable methylation at multiple breast cancer susceptibility genes including PALB2 and MLH1. Methylation at the region of MLH1 in these breast cancers was not associated with microsatellite instability. This work informs future studies of the role of methylation in breast cancer susceptibility gene silencing.
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Affiliation(s)
- Cameron M. Scott
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - JiHoon Eric Joo
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Neil O’Callaghan
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Graham G. Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Ee Ming Wong
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
- * E-mail:
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