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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] [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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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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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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Ruscito I, Gasparri ML, De Marco MP, Costanzi F, Besharat AR, Papadia A, Kuehn T, Gentilini OD, Bellati F, Caserta D. The Clinical and Pathological Profile of BRCA1 Gene Methylated Breast Cancer Women: A Meta-Analysis. Cancers (Basel) 2021; 13:cancers13061391. [PMID: 33808555 PMCID: PMC8003261 DOI: 10.3390/cancers13061391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/16/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND DNA aberrant hypermethylation is the major cause of transcriptional silencing of the breast cancer gene 1 (BRCA1) gene in sporadic breast cancer patients. The aim of the present meta-analysis was to analyze all available studies reporting clinical characteristics of BRCA1 gene hypermethylated breast cancer in women, and to pool the results to provide a unique clinical profile of this cancer population. METHODS On September 2020, a systematic literature search was performed. Data were retrieved from PubMed, MEDLINE, and Scopus by searching the terms: "BRCA*" AND "methyl*" AND "breast". All studies evaluating the association between BRCA1 methylation status and breast cancer patients' clinicopathological features were considered for inclusion. RESULTS 465 studies were retrieved. Thirty (6.4%) studies including 3985 patients met all selection criteria. The pooled analysis data revealed a significant correlation between BRCA1 gene hypermethylation and advanced breast cancer disease stage (OR = 0.75: 95% CI: 0.58-0.97; p = 0.03, fixed effects model), lymph nodes involvement (OR = 1.22: 95% CI: 1.01-1.48; p = 0.04, fixed effects model), and pre-menopausal status (OR = 1.34: 95% CI: 1.08-1.66; p = 0.008, fixed effects model). No association could be found between BRCA1 hypermethylation and tumor histology (OR = 0.78: 95% CI: 0.59-1.03; p = 0.08, fixed effects model), tumor grading (OR = 0.78: 95% CI :0.46-1.32; p = 0.36, fixed effects model), and breast cancer molecular classification (OR = 1.59: 95% CI: 0.68-3.72; p = 0.29, random effects model). CONCLUSIONS hypermethylation of the BRCA1 gene significantly correlates with advanced breast cancer disease, lymph nodes involvement, and pre-menopausal cancer onset.
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Affiliation(s)
- Ilary Ruscito
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
- Correspondence: ; Tel.: +39-06-3377-5696
| | - Maria Luisa Gasparri
- Department of Gynecology and Obstetrics, Ente Ospedaliere Cantonale (EOC), Via Tesserete 46, 6900 Lugano, Switzerland; (M.L.G.); (A.P.)
- University of the Italian Switzerland (USI), Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Maria Paola De Marco
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Flavia Costanzi
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Aris Raad Besharat
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Andrea Papadia
- Department of Gynecology and Obstetrics, Ente Ospedaliere Cantonale (EOC), Via Tesserete 46, 6900 Lugano, Switzerland; (M.L.G.); (A.P.)
- University of the Italian Switzerland (USI), Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Thorsten Kuehn
- Interdisciplinary Breast Center, Department of Gynecology and Obstetrics, Klinikum Esslingen, 73730 Neckar, Germany;
| | - Oreste Davide Gentilini
- Breast Surgery Unit, San Raffaele University Hospital, via Olgettina 60, 20132 Milan, Italy;
| | - Filippo Bellati
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Donatella Caserta
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
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Hu ZY, Liu L, Xie N, Lu J, Liu Z, Tang Y, Wang Y, Yang J, Ouyang Q. Germline PALB2 Mutations in Cancers and Its Distinction From Somatic PALB2 Mutations in Breast Cancers. Front Genet 2020; 11:829. [PMID: 33193564 PMCID: PMC7482549 DOI: 10.3389/fgene.2020.00829] [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: 12/30/2019] [Accepted: 07/09/2020] [Indexed: 12/27/2022] Open
Abstract
PALB2 is an important BRCAx candidate for familial breast cancers (FBC). PALB2 pathogenic variants (PVs) may not to conform to "two hit" paradigm. However, a recent study demonstrates that in the majority PALB2 germline mutant breast cancers, the loss of heterozygosity (LOH) and somatic point mutations are the "second hit." This study aimed to investigate the second hits in germline PALB2 mutations in breast cancers. We screened out 28 germline PALB2-mutation carriers among 480 familial cancer patients (including 143 FBC patients) in Geneplus database pool. Of the 143 patients with FBC, 10 had mono-allelic PALB2 germline mutations. All these germline PALB2 mutations were high-risk stop-gain, frameshift, or splicing mutations that concentrated in EX5-EX9 and might led to truncated proteins, severe functional defects and malignant phenotype. The hotspots were c.1057A[3 > 2] and c.3114-1G > A. Other mutations included c.389delA, c.2068C > T, c.2167_2168delAT, c.2629delT and c.2968G > T. Only one FBC patient has PALB2 somatic mutation and two patients had LOH of PALB2. All germline PALB2 mutations were high-risk mutations, whereas the somatic PALB2 mutations were moderate-risk missense mutations. We also distinguished PALB2 "novel mutations" from "reported mutations." In conclusion, germline PALB2 mutation should be put into the context of future screening.
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Affiliation(s)
- Zhe-Yu Hu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Liping Liu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Ning Xie
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Jun Lu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | | | - Yu Tang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Yikai Wang
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Jianbo Yang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Fujian Medical University Union Hospital, Fuzhou, China.,Department of Otolaryngology, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Quchang Ouyang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
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Kougioumtsidou N, Vavoulidis E, Nasioutziki M, Symeonidou M, Pratilas GC, Mareti E, Petousis S, Chatzikyriakidou A, Grimbizis G, Theodoridis T, Miliaras D, Dinas K, Zepiridis L. DNA methylation patterns of RAR-β2 and RASSF1A gene promoters in FNAB samples from Greek population with benign or malignant breast lesions. Diagn Cytopathol 2020; 49:153-164. [PMID: 32530576 DOI: 10.1002/dc.24513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/27/2020] [Accepted: 05/19/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Promoter hypermethylation is common in Breast Cancer (BC) with studies mainly in histological specimens showing frequent methylation of tumor suppressor genes (TSGs) compared with normal tissues. The aim of this study was to estimate the frequency of promoter methylation of RAR-β2 and RASSF1A genes in breast FNAB material aiming to evaluate the methylation status of these two genes as biomarker for detecting BC in Greek population. METHODS FNAB material from 104 patients was collected for cytological evaluation and epigenetic analysis. DNA was extracted and subjected to bisulfite conversion. A methylation-specific PCR was carried out and the final products were separated with electrophoresis in 2% agarose gels. RESULTS From 104 samples, RASSF1A hypermethylation was observed in 78 (75%) and RAR-β2 hypermethylation in 64 (61.6%). 84% and 78% of the cases diagnosed with breast malignancy (n = 50) were methylated for RASSF1A and RAR-β2, respectively. Methylated RASSF1A and RAR-β2 were also detected in 88.3% and 76.5% in samples diagnosed as suspicious for malignancy (n = 17) and in 57.2% of samples diagnosed with atypia (n = 14). The Odds Ratio for breast malignancy was 4.545 in patients with RASSF1A hypermethylation and 9.167 in patients with RAR-β2 hypermethylation underlying their promoter's methylation positive correlation with breast malignancy. CONCLUSION To optimize the sensitivity and specificity of this epigenetic setting, more TSGs related to BC should be gradually imported in our evaluated methylation panel and be validated in a larger study sample with the aim that the obtained epigenetic profiles will provide clinicians with valuable tools for management of BC patients in Greece.
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Affiliation(s)
- Niki Kougioumtsidou
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Eleftherios Vavoulidis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Maria Nasioutziki
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Marianthi Symeonidou
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Georgios Chrysostomos Pratilas
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Mareti
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Stamatios Petousis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Anthoula Chatzikyriakidou
- Faculty of Medicine, Laboratory of Medical Biology-Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Gregorios Grimbizis
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Theodoros Theodoridis
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Dimosthenis Miliaras
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Dinas
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Leonidas Zepiridis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
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Wu J, Mamidi TKK, Zhang L, Hicks C. Deconvolution of the Genomic and Epigenomic Interaction Landscape of Triple-Negative Breast Cancer. Cancers (Basel) 2019; 11:cancers11111692. [PMID: 31683572 PMCID: PMC6896043 DOI: 10.3390/cancers11111692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/07/2019] [Accepted: 10/19/2019] [Indexed: 12/26/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive form of breast cancer. Emerging evidenced suggests that both genetics and epigenetic factors play a role in the pathogenesis of TNBC. However, oncogenic interactions and cooperation between genomic and epigenomic variation have not been characterized. The objective of this study was to deconvolute the genomic and epigenomic interaction landscape in TNBC using an integrative genomics approach, which integrates information on germline, somatic, epigenomic and gene expression variation. We hypothesized that TNBC originates from a complex interplay between genomic (both germline and somatic variation) and epigenomic variation. We further hypothesized that these complex arrays of interacting genomic and epigenomic factors affect entire molecular networks and signaling pathways which, in turn, drive TNBC. We addressed these hypotheses using germline variation from genome-wide association studies and somatic, epigenomic and gene expression variation from The Cancer Genome Atlas (TCGA). The investigation revealed signatures of functionally related genes containing germline, somatic and epigenetic variations. DNA methylation had an effect on gene expression. Network and pathway analysis revealed molecule networks and signaling pathways enriched for germline, somatic and epigenomic variation, among them: Role of BRCA1 in DNA Damage Response, Hereditary Breast Cancer Signaling, Molecular Mechanisms of Cancer, Estrogen-Dependent Breast Cancer, p53, MYC Mediated Apoptosis, and PTEN Signaling pathways. The investigation revealed that integrative genomics is a powerful approach for deconvoluting the genomic-epigenomic interaction landscape in TNBC. Further studies are needed to understand the biological mechanisms underlying oncogenic interactions between genomic and epigenomic factors in TNBC.
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Affiliation(s)
- Jiande Wu
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
| | - Tarun Karthik Kumar Mamidi
- Graduate Biomedical Sciences, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35233, USA.
| | - Lu Zhang
- Department of Public Health Sciences, Clemson University, 513 Edwards Hall, Clemson, SC 29634, USA.
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA.
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Chen J, Haanpää MK, Gruber JJ, Jäger N, Ford JM, Snyder MP. High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients. Clin Cancer Res 2019; 25:5301-5314. [PMID: 31175093 DOI: 10.1158/1078-0432.ccr-18-2423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/11/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Understanding and explaining hereditary predisposition to cancer has focused on the genetic etiology of the disease. However, mutations in known genes associated with breast cancer, such as BRCA1 and BRCA2, account for less than 25% of familial cases of breast cancer. Recently, specific epigenetic modifications at BRCA1 have been shown to promote hereditary breast cancer, but the broader potential for epigenetic contribution to hereditary breast cancer is not yet well understood. EXPERIMENTAL DESIGN We examined DNA methylation through deep bisulfite sequencing of CpG islands and known promoter or regulatory regions in peripheral blood DNA from 99 patients with familial or early-onset breast or ovarian cancer, 6 unaffected BRCA mutation carriers, and 49 unaffected controls. RESULTS In 9% of patients, we observed altered methylation in the promoter regions of genes known to be involved in cancer, including hypermethylation at the tumor suppressor PTEN and hypomethylation at the proto-oncogene TEX14. These alterations occur in the form of allelic methylation that span up to hundreds of base pairs in length. CONCLUSIONS Our observations suggest a broader role for DNA methylation in early-onset, familial risk breast cancer. Further studies are warranted to clarify these mechanisms and the benefits of DNA methylation screening for early risk prediction of familial cancers.
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Affiliation(s)
- Justin Chen
- Department of Genetics, Stanford University, Stanford, California
| | - Maria K Haanpää
- Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Joshua J Gruber
- Department of Genetics, Stanford University, Stanford, California.,Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Natalie Jäger
- Department of Genetics, Stanford University, Stanford, California
| | - James M Ford
- Department of Genetics, Stanford University, Stanford, California. .,Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California.
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9
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Vizcaino MA, Palsgrove DN, Yuan M, Giannini C, Cabrera-Aldana EE, Pallavajjala A, Burger PC, Rodriguez FJ. Granular cell astrocytoma: an aggressive IDH-wildtype diffuse glioma with molecular genetic features of primary glioblastoma. Brain Pathol 2018; 29:193-204. [PMID: 30222900 DOI: 10.1111/bpa.12657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
Granular cell astrocytoma (GCA) is a rare adult infiltrating glioma subtype. We studied a series of 39 GCAs. Median age of presentation was 57.8 years and most cases developed in the frontal or temporal lobes. Tumors included grade II (n = 14), grade III (n = 11), and grade IV (n = 14) by WHO criteria. Granular cell morphology was diffuse in 31 (79%) cases and partial in eight (21%). Immunohistochemistry showed frequent positivity for GFAP (28 of 31), OLIG2 (16 of 16), and CD68 (27 of 30), but HAM56, CD163, and IBA-1 histiocytic markers were all negative (22 of 22). IDH1(R132H) was negative in all the cases tested (16 of 16), while ATRX expression was retained (12 of 12). Cytogenetics demonstrated monosomy 10 (6 of 6) cases, +7 in 4 (of 6), -13q in 4 of 6, and -14 in 4 of 6. Next-generation sequencing demonstrated mutations in PTEN/PIK3 genes in 6/13 (46%), NF1 in 3 of 10 (30%), TP53 in 3 of 13 (23%), PALB2 in 3 of 10 (30%), STAG2 in 3 of 10 (30%), EGFR mutation/amplification in 3 of 13 (23%), and AR in 2 of 10 (20%). CDKN2A/B deletion was identified in 5 of 13 (30%) cases (homozygous deletion in 4). The TERT C228T mutation was identified in 9 of 13 (69%). No mutations were encountered in IDH1, IDH2, CIC, FUBP1, H3F3A, BRAF or ATRX genes. The mean overall survival was 11.3 months. Patients >60 years old at diagnosis had a worse survival than patients <60 years (P = 0.001). There were no statistically significant differences in survival by WHO grade, extent of granular cell change, sex or MIB-1 (P > 0.05). GCA is a variant of IDH-wildtype diffuse glioma with aggressive behavior irrespective of grade and extent of granular cell morphology, and with molecular genetic features corresponding to primary glioblastoma.
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Affiliation(s)
- M Adelita Vizcaino
- Department of Pathology, Johns Hopkins University, Baltimore, MD.,Faculty of Medicine, Department of Cellular and Tissue Biology, UNAM, Mexico City, Mexico
| | - Doreen N Palsgrove
- Department of Pathology, Johns Hopkins University, Baltimore, MD.,Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Ming Yuan
- Department of Pathology, Johns Hopkins University, Baltimore, MD
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Peter C Burger
- Department of Pathology, Johns Hopkins University, Baltimore, MD.,Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins University, Baltimore, MD.,Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
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10
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Kuzmina NS, Lapteva NS, Rusinova GG, Azizova TV, Vyazovskaya NS, Rubanovich AV. Gene hypermethylation in blood leukocytes in humans long term after radiation exposure - Validation set. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 234:935-942. [PMID: 29253833 DOI: 10.1016/j.envpol.2017.12.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 06/07/2023]
Abstract
UNLABELLED Hypermethylation of СpG islands in the promoter regions of several genes with basic protective function in blood leukocytes of individuals exposed to ionizing radiation long time ago (2-46 years), and differential effects of age and radiation exposure on hypermethylation was reported in our previous work. To validate these results, epigenetic modifications were assessed in an independent series of 49 nuclear industry workers from the "Mayak" facility (67-84 years old at sampling) with documented individual accumulated doses from the prolonged external γ-radiation exposure (95.9-409.5 cGy, end of work with radiation:0.3-39 years ago), and in 50 non-exposed persons matched by age. In addition to the genes analyzed before (RASSF1A, p16/INK4A, p14/ARF, GSTP1), four additional loci were analyzed: TP53, ATM, SOD3, ESR1. The frequency of individuals displaying promoter methylation of at least one of the 8 genes (71.4%) was significantly higher in exposed group as compared to the control group (40%), p = .002, OR = 3.75. A significantly elevated frequency of individuals with hypermethylated СpG islands in GSTP1, TP53, SOD3 promoters was revealed among exposed subjects as compared to the control group (p = .012, OR = 8.41; p = .041, OR = 4.02 and p = .009, OR = 3.42, respectively). A similar trend (p = .12, OR = 3.06) was observed for the p16/INK4A gene. As a whole, p16/INK4A and GSTP1 promoter hypermethylation in irradiated subjects from both previously and currently analyzed groups was pronounced. Thus, the direction of the effects was fully confirmed, suggesting the result reproducibility. No statistically significant correlation between promoter methylation and individual radiation dose was found. Further studies are required to create an array of blood epigenetic markers of radiation exposure associating with premature aging and age-related diseases and to accurately evaluate radiation-added effect across the range of doses. SYNTHESIS The results of studies of epigenetic changes in two independent samples of irradiated subjects indicated the significance of radiation factor in the induction of hypermethylation of CpG islands in gene promoters that is revealed in blood cells years and decades after exposure.
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Affiliation(s)
- Nina S Kuzmina
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia.
| | - Nellya Sh Lapteva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia.
| | | | | | | | - Alexander V Rubanovich
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia.
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11
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Nepomuceno TC, De Gregoriis G, de Oliveira FMB, Suarez-Kurtz G, Monteiro AN, Carvalho MA. The Role of PALB2 in the DNA Damage Response and Cancer Predisposition. Int J Mol Sci 2017; 18:ijms18091886. [PMID: 28858227 PMCID: PMC5618535 DOI: 10.3390/ijms18091886] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/21/2017] [Accepted: 08/26/2017] [Indexed: 01/01/2023] Open
Abstract
The deoxyribonucleic acid (DNA) damage response (DDR) is a major feature in the maintenance of genome integrity and in the suppression of tumorigenesis. PALB2 (Partner and Localizer of Breast Cancer 2 (BRCA2)) plays an important role in maintaining genome integrity through its role in the Fanconi anemia (FA) and homologous recombination (HR) DNA repair pathways. Since its identification as a BRCA2 interacting partner, PALB2 has emerged as a pivotal tumor suppressor protein associated to hereditary cancer susceptibility to breast and pancreatic cancers. In this review, we discuss how other DDR proteins (such as the kinases Ataxia Telangiectasia Mutated (ATM) and ATM- and Rad3-Related (ATR), mediators BRCA1 (Breast Cancer 1)/BRCA2 and effectors RAD51/DNA Polymerase η (Polη) interact with PALB2 to orchestrate DNA repair. We also examine the involvement of PALB2 mutations in the predisposition to cancer and the role of PALB2 in stimulating error-free DNA repair through the FA/HR pathway.
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Affiliation(s)
- Thales C Nepomuceno
- Programa de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Giuliana De Gregoriis
- Programa de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | | | - Guilherme Suarez-Kurtz
- Programa de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
| | - Marcelo A Carvalho
- Programa de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
- Instituto Federal do Rio de Janeiro-IFRJ, Rio de Janeiro 20270-021, Brazil.
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12
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Shen J, Liao Y, Hopper JL, Goldberg M, Santella RM, Terry MB. Dependence of cancer risk from environmental exposures on underlying genetic susceptibility: an illustration with polycyclic aromatic hydrocarbons and breast cancer. Br J Cancer 2017; 116:1229-1233. [PMID: 28350789 PMCID: PMC5418454 DOI: 10.1038/bjc.2017.81] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/16/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022] Open
Abstract
Background: Most studies of environmental risk factors and breast cancer are conducted using average risk cohorts. Methods: We examined the association between polycyclic aromatic hydrocarbon (PAH)-albumin adducts in bloods from baseline and breast cancer risk in a prospective nested case–control study (New York site of the BCFR, 80 cases and 156 controls). We estimated the 10-year absolute breast cancer risk by a risk model that uses pedigree information (BOADICEA) and evaluated whether the increased risk from PAH differed by absolute risk. Results: Women with detectable levels of PAH had a twofold association with breast cancer risk (odds ratio (OR)=2.04; 95% CI=1.06–3.93) relative to women with non-detectable levels. The association increased with higher levels of PAH (⩾median) and by a higher level of absolute breast cancer risk (10-year risk ⩾3.4%: OR=4.09, 95% CI=1.38–12.13). Conclusions: These results support that family-based cohorts can be an efficient way to examine gene–environment interactions.
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Affiliation(s)
- Jing Shen
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - Yuyan Liao
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, VIC 3010, Australia
| | - Mandy Goldberg
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, 1130 St Nicholas Avenue, New York, NY 10032, USA
| | - Mary Beth Terry
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA.,Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, 1130 St Nicholas Avenue, New York, NY 10032, USA
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