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Janyasupab P, Singhanat K, Warnnissorn M, Thuwajit P, Suratanee A, Plaimas K, Thuwajit C. Identification of Tumor Budding-Associated Genes in Breast Cancer through Transcriptomic Profiling and Network Diffusion Analysis. Biomolecules 2024; 14:896. [PMID: 39199284 PMCID: PMC11352152 DOI: 10.3390/biom14080896] [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: 06/25/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 09/01/2024] Open
Abstract
Breast cancer has the highest diagnosis rate among all cancers. Tumor budding (TB) is recognized as a recent prognostic marker. Identifying genes specific to high-TB samples is crucial for hindering tumor progression and metastasis. In this study, we utilized an RNA sequencing technique, called TempO-Seq, to profile transcriptomic data from breast cancer samples, aiming to identify biomarkers for high-TB cases. Through differential expression analysis and mutual information, we identified seven genes (NOL4, STAR, C8G, NEIL1, SLC46A3, FRMD6, and SCARF2) that are potential biomarkers in breast cancer. To gain more relevant proteins, further investigation based on a protein-protein interaction network and the network diffusion technique revealed enrichment in the Hippo signaling and Wnt signaling pathways, promoting tumor initiation, invasion, and metastasis in several cancer types. In conclusion, these novel genes, recognized as overexpressed in high-TB samples, along with their associated pathways, offer promising therapeutic targets, thus advancing treatment and diagnosis for breast cancer.
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Affiliation(s)
- Panisa Janyasupab
- Advance Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Kodchanan Singhanat
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.S.); (P.T.)
| | - Malee Warnnissorn
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.S.); (P.T.)
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand;
- Intelligent and Nonlinear Dynamics Innovations Research Center, Science and Technology Research Institute, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand
| | - Kitiporn Plaimas
- Advance Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.S.); (P.T.)
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2
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Chen HW, Kuo WH, Lu YS, Chen IC, Hu FC, Wang MY, Zahid M, Rogan EG, Cheng AL, Lin CH. Interaction of base excision repair gene polymorphism and estrogen-DNA adducts in breast cancer risk among East Asian women. Breast Cancer Res Treat 2024:10.1007/s10549-024-07418-3. [PMID: 38969945 DOI: 10.1007/s10549-024-07418-3] [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: 04/23/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
PURPOSE In East Asia, the incidence of breast cancer has been increasing rapidly, particularly among premenopausal women. An elevated ratio of estrogen-DNA adducts was linked to a higher risk of breast cancer. The present study explored the influence of the interaction between base excision repair (BER) gene polymorphisms and estrogen-DNA adducts on breast cancer risk. METHODS We conducted a case-control study comprising healthy volunteers and individuals with benign breast disease (control arm, n = 176) and patients with invasive carcinoma or carcinoma in situ (case arm, n = 177). Genotyping for BER-related genes, including SMUG1, OGG1, ERCC5, and APEX1, was performed. A logistic regression model, incorporating interactions between gene polymorphisms, estrogen-DNA adduct ratio, and clinical variables, was used to identify the risk factors for breast cancer. RESULTS Univariate analysis indicated marginal associations between breast cancer risk and APEX1 rs1130409 T > G (P = 0.057) and APEX1 rs1760944 T > G (P = 0.065). Multivariate regression analysis revealed significant associations with increased breast cancer risk for APEX1_rs1130409 (GT/GG versus TT) combined with a natural logarithmic value of the estrogen-DNA adduct ratio (estimated OR 1.164, P = 0.023) and premenopausal status with an estrogen-DNA adduct ratio > 2.93 (estimated OR 2.433, P = 0.001). CONCLUSION APEX1_rs1130409 (GT/GG versus TT) polymorphisms, which are related to decreased BER activity, combined with an increased ratio of estrogen-DNA adducts, increase the risk of breast cancer in East Asian women.
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Affiliation(s)
- Hsing-Wu Chen
- Department of Oncology, National Taiwan University Hospital, Yun-Lin Branch, Yun-Lin, Taiwan
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University, Taipei, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Shen Lu
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University, Taipei, Taiwan
| | - I-Chun Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University, Taipei, Taiwan
- Department of Medical Oncology, National Taiwan University Hospital, Cancer Center Branch, Taipei, Taiwan
| | - Fu-Chang Hu
- Graduate Institute of Clinical Medicine and School of Nursing, College of Medicine, National Taiwan University, Taipei, Taiwan
- Statistical Consulting Clinic, International-Harvard Statistical Consulting Company, Taipei, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Muhammad Zahid
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Eleanor G Rogan
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ann-Lii Cheng
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Oncology, National Taiwan University Hospital, Cancer Center Branch, Taipei, Taiwan
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan.
- Department of Medical Oncology, National Taiwan University Hospital, Cancer Center Branch, Taipei, Taiwan.
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
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3
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Lirussi L, Ayyildiz D, Liu Y, Montaldo NP, Carracedo S, Aure MR, Jobert L, Tekpli X, Touma J, Sauer T, Dalla E, Kristensen VN, Geisler J, Piazza S, Tell G, Nilsen H. A regulatory network comprising let-7 miRNA and SMUG1 is associated with good prognosis in ER+ breast tumours. Nucleic Acids Res 2022; 50:10449-10468. [PMID: 36156150 PMCID: PMC9561369 DOI: 10.1093/nar/gkac807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/31/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Single-strand selective uracil-DNA glycosylase 1 (SMUG1) initiates base excision repair (BER) of uracil and oxidized pyrimidines. SMUG1 status has been associated with cancer risk and therapeutic response in breast carcinomas and other cancer types. However, SMUG1 is a multifunctional protein involved, not only, in BER but also in RNA quality control, and its function in cancer cells is unclear. Here we identify several novel SMUG1 interaction partners that functions in many biological processes relevant for cancer development and treatment response. Based on this, we hypothesized that the dominating function of SMUG1 in cancer might be ascribed to functions other than BER. We define a bad prognosis signature for SMUG1 by mapping out the SMUG1 interaction network and found that high expression of genes in the bad prognosis network correlated with lower survival probability in ER+ breast cancer. Interestingly, we identified hsa-let-7b-5p microRNA as an upstream regulator of the SMUG1 interactome. Expression of SMUG1 and hsa-let-7b-5p were negatively correlated in breast cancer and we found an inhibitory auto-regulatory loop between SMUG1 and hsa-let-7b-5p in the MCF7 breast cancer cells. We conclude that SMUG1 functions in a gene regulatory network that influence the survival and treatment response in several cancers.
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Affiliation(s)
- Lisa Lirussi
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway.,Section of Clinical Molecular Biology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway
| | - Dilara Ayyildiz
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, p.le M. Kolbe 4, 33100 Udine, Italy
| | - Yan Liu
- Section of Clinical Molecular Biology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway
| | - Nicola P Montaldo
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway
| | - Sergio Carracedo
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway.,Section of Clinical Molecular Biology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway
| | - Miriam R Aure
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo and Oslo University Hospital, 0450 Oslo, Norway
| | - Laure Jobert
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo and Oslo University Hospital, 0450 Oslo, Norway
| | - Joel Touma
- Department of Breast and Endocrine Surgery, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Campus AHUS, 1478 Lørenskog, Norway
| | - Torill Sauer
- Institute of Clinical Medicine, University of Oslo, Campus AHUS, 1478 Lørenskog, Norway.,Department of Pathology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, p.le M. Kolbe 4, 33100 Udine, Italy
| | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo and Oslo University Hospital, 0450 Oslo, Norway.,Department of Pathology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Jürgen Geisler
- Institute of Clinical Medicine, University of Oslo, Campus AHUS, 1478 Lørenskog, Norway.,Department of Oncology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway
| | - Silvano Piazza
- Bioinformatics Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, via Sommarive 18, 38123, Povo (Trento), Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, p.le M. Kolbe 4, 33100 Udine, Italy
| | - Hilde Nilsen
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, N-0318 Oslo, Norway.,Section of Clinical Molecular Biology, Akershus University Hospital (AHUS), 1478 Lørenskog, Norway.,Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
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4
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Li CL, Moi SH, Lin HS, Hou MF, Chen FM, Shih SL, Kan JY, Kao CN, Wu YC, Kao LC, Chen YH, Lee YC, Chiang CP. Comprehensive Transcriptomic and Proteomic Analyses Identify a Candidate Gene Set in Cross-Resistance for Endocrine Therapy in Breast Cancer. Int J Mol Sci 2022; 23:ijms231810539. [PMID: 36142451 PMCID: PMC9501051 DOI: 10.3390/ijms231810539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Endocrine therapy (ET) of selective estrogen receptor modulators (SERMs), selective estrogen receptor downregulators (SERDs), and aromatase inhibitors (AIs) has been used as the gold standard treatment for hormone-receptor-positive (HR+) breast cancer. Despite its clinical benefits, approximately 30% of patients develop ET resistance, which remains a major clinical challenge in patients with HR+ breast cancer. The mechanisms of ET resistance mainly focus on mutations in the ER and related pathways; however, other targets still exist from ligand-independent ER reactivation. Moreover, mutations in the ER that confer resistance to SERMs or AIs seldom appear in SERDs. To date, little research has been conducted to identify a critical target that appears in both SERMs/SERDs and AIs. In this study, we conducted comprehensive transcriptomic and proteomic analyses from two cohorts of The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) to identify the critical targets for both SERMs/SERDs and AIs of ET resistance. From a treatment response cohort with treatment response for the initial ET regimen and an endocrine therapy cohort with survival outcomes, we identified candidate gene sets that appeared in both SERMs/SERDs and AIs of ET resistance. The candidate gene sets successfully differentiated progress/resistant groups (PD) from complete response groups (CR) and were significantly correlated with survival outcomes in both cohorts. In summary, this study provides valuable clinical implications for the critical roles played by candidate gene sets in the diagnosis, mechanism, and therapeutic strategy for both SERMs/SERDs and AIs of ET resistance for the future.
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Affiliation(s)
- Chung-Liang Li
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Sin-Hua Moi
- Center of Cancer Program Development, E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan
| | - Huei-Shan Lin
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Ming-Feng Hou
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Fang-Ming Chen
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Shen-Liang Shih
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Jung-Yu Kan
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Chieh-Ni Kao
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Yi-Chia Wu
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Department of Surgery, Division of Plastic Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Li-Chun Kao
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Ying-Hsuan Chen
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Yi-Chen Lee
- Department of Anatomy, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Chih-Po Chiang
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
- Department of Medical Laboratory Sciences and Biotechnology, Fooyin University, Kaohsiung 83102, Taiwan
- Correspondence: or ; Tel.: +886-7-312-1101 (ext. 2260)
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5
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Mahmoodi A, Shoqafi A, Sun P, Giannakeas V, Cybulski C, Nofech-Mozes S, Masson JY, Sharma S, Samani AA, Madhusudan S, Narod SA, Akbari MR. High Expression of RECQL Protein in ER-Positive Breast Tumours Is Associated With a Better Survival. Front Oncol 2022; 12:877617. [PMID: 35712517 PMCID: PMC9195420 DOI: 10.3389/fonc.2022.877617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background RECQL (also known as RECQ1 and RECQL1) is a gene of recent interest in breast cancer and an association between high levels of RECQL protein in breast cancer tumour cells and good survival of patients has been reported. Methods To validate this association, we measured the RECQL protein levels in tumours of 933 breast cancer patients using immunohistochemistry analysis and followed the patients for death from breast cancer. Results Women with a level of RECQL protein above the 75th percentile had better 15-year disease-specific survival among ER-positive patients (62.5% vs. 48.7%, HR= 0.72, 95%CI= 0.52-0.98, p-value = 0.04), but not among ER- patients (48.9% vs. 48.0%, HR= 1.07, 95%CI= 0.67-1.69, p-value= 0.79). Among the ER-negative patients, high RECQL protein levels were associated with better survival among women who received tamoxifen treatment (67.0% vs. 51.5%, HR= 0.64, 95%CI= 0.41-0.99, p-value= 0.04). Conclusion RECQL might be a new predictive marker for tamoxifen treatment among ER-positive patients.
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Affiliation(s)
- Ardalan Mahmoodi
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Ahmed Shoqafi
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ping Sun
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON, Canada
| | - Vasily Giannakeas
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Sharon Nofech-Mozes
- Sunnybrook Health Science Centre, University of Toronto, Toronto, ON, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center, Oncology Axis, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC, United States
- National Human Genome Center, College of Medicine, Howard University, Washington, DC, United States
| | - Amir Abbas Samani
- Department of Laboratory Medicine and Pathology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Humber River Hospital, University of Toronto, Toronto, ON, Canada
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Steven A. Narod
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Mohammad R. Akbari
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohammad R. Akbari,
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Opattova A, Langie SAS, Milic M, Collins A, Brevik A, Coskun E, Dusinska M, Gaivão I, Kadioglu E, Laffon B, Marcos R, Pastor S, Slyskova J, Smolkova B, Szilágyi Z, Valdiglesias V, Vodicka P, Volkovova K, Bonassi S, Godschalk RWL. A pooled analysis of molecular epidemiological studies on modulation of DNA repair by host factors. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 876-877:503447. [PMID: 35483778 DOI: 10.1016/j.mrgentox.2022.503447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 12/06/2021] [Accepted: 01/10/2022] [Indexed: 02/09/2023]
Abstract
Levels of DNA damage represent the dynamics between damage formation and removal. Therefore, to better interpret human biomonitoring studies with DNA damage endpoints, an individual's ability to recognize and properly remove DNA damage should be characterized. Relatively few studies have included DNA repair as a biomarker and therefore, assembling and analyzing a pooled database of studies with data on base excision repair (BER) was one of the goals of hCOMET (EU-COST CA15132). A group of approximately 1911 individuals, was gathered from 8 laboratories which run population studies with the comet-based in vitro DNA repair assay. BER incision activity data were normalized and subsequently correlated with various host factors. BER was found to be significantly higher in women. Although it is generally accepted that age is inversely related to DNA repair, no overall effect of age was found, but sex differences were most pronounced in the oldest quartile (>61 years). No effect of smoking or occupational exposures was found. A body mass index (BMI) above 25 kg/m2 was related to higher levels of BER. However, when BMI exceeded 35 kg/m2, repair incision activity was significantly lower. Finally, higher BER incision activity was related to lower levels of DNA damage detected by the comet assay in combination with formamidopyrimidine DNA glycosylase (Fpg), which is in line with the fact that oxidatively damaged DNA is repaired by BER. These data indicate that BER plays a role in modulating the steady-state level of DNA damage that is detected in molecular epidemiological studies and should therefore be considered as a parallel endpoint in future studies.
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Affiliation(s)
- Alena Opattova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, 14200, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, the Netherlands
| | - Mirta Milic
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | | | - Asgeir Brevik
- Oslo Metropolitan University, Faculty of Health Sciences, PO Box 4, St. Olavs plass, 0130, Oslo, Norway
| | - Erdem Coskun
- Gazi University, Faculty of Pharmacy, Department of Toxicology, Etiler, Ankara, 06330, Turkey
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, Norwegian Institute for Air Research (NILU), 2002, Kjeller, Norway
| | - Isabel Gaivão
- Genetics and Biotechnology Department and Veterinary and Animal Research Centre (CECAV), Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Ela Kadioglu
- Gazi University, Faculty of Pharmacy, Department of Toxicology, Etiler, Ankara, 06330, Turkey
| | - Blanca Laffon
- Instituto de Investigación Biomédica de A Coruña (INIBIC), AE CICA-INIBIC. Oza, 15071, A Coruña, Spain; Universidade da Coruña, Grupo DICOMOSA, Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Psicología, Facultad de Ciencias de la Educación, Campus Elviña s/n, 15071, A Coruña, Spain
| | - Ricard Marcos
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Susana Pastor
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Jana Slyskova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, 14200, Czech Republic
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, 84505, Bratislava, Slovakia
| | - Zsófia Szilágyi
- Department of Non-ionizing Radiation, National Public Health Center, H-1221, Budapest, Hungary
| | - Vanessa Valdiglesias
- Instituto de Investigación Biomédica de A Coruña (INIBIC), AE CICA-INIBIC. Oza, 15071, A Coruña, Spain; Universidade da Coruña, Grupo DICOMOSA, Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Campus A Zapateira s/n, 15071, A Coruña, Spain
| | - Pavel Vodicka
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, 14200, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, 833 03, Bratislava, Slovakia
| | - Stefano Bonassi
- Unit of Clinical and Molecular Epidemiology, IRCCS, San Raffaele Pisana, Rome, Italy; Department of Human Sciences and Quality of Life Promotion, San Raffaele University, Rome, Italy
| | - Roger W L Godschalk
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, the Netherlands.
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7
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Jiménez-Salazar JE, Damian-Ferrara R, Arteaga M, Batina N, Damián-Matsumura P. Non-Genomic Actions of Estrogens on the DNA Repair Pathways Are Associated With Chemotherapy Resistance in Breast Cancer. Front Oncol 2021; 11:631007. [PMID: 33869016 PMCID: PMC8044931 DOI: 10.3389/fonc.2021.631007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Estrogens have been implicated in the etiology of breast cancer for a long time. It has been stated that long-term exposure to estrogens is associated with a higher incidence of breast cancer, since estradiol (E2) stimulates breast cell growth; however, its effect on DNA damage/repair is only starting to be investigated. Recent studies have documented that estrogens are able to modify the DNA damage response (DDR) and DNA repair mechanisms. On the other hand, it has been proposed that DDR machinery can be altered by estrogen signaling pathways, that can be related to cancer progression and chemoresistance. We have demonstrated that E2 promotes c-Src activation and breast cancer cell motility, through a non-genomic pathway. This review discusses scientific evidence supporting this non-genomic mechanism where estrogen modifies the DNA repair pathways, and its relationship to potential causes of chemoresistance.
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Affiliation(s)
- Javier E Jiménez-Salazar
- Department of Biology of Reproduction, Division of Biological Sciences and Health (DCBS), Autonomous Metropolitan University (UAM), Mexico City, Mexico.,School of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Rebeca Damian-Ferrara
- Monterrey Institute of Technology and Higher Education (ITESM), School of Engineering and Sciences, Monterrey, Mexico
| | - Marcela Arteaga
- Department of Biology of Reproduction, Division of Biological Sciences and Health (DCBS), Autonomous Metropolitan University (UAM), Mexico City, Mexico
| | - Nikola Batina
- Nanotechnology and Molecular Engineering Laboratory, Department of Chemistry, Division of Basic Science and Engineering (DCBI), Autonomous Metropolitan University (UAM), Mexico City, Mexico
| | - Pablo Damián-Matsumura
- Department of Biology of Reproduction, Division of Biological Sciences and Health (DCBS), Autonomous Metropolitan University (UAM), Mexico City, Mexico
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8
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Song D, He H, Sinha I, Hases L, Yan F, Archer A, Haldosen LA, Zhao C, Williams C. Blocking Fra-1 sensitizes triple-negative breast cancer to PARP inhibitor. Cancer Lett 2021; 506:23-34. [PMID: 33652085 DOI: 10.1016/j.canlet.2021.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]
Abstract
The AP-1 member Fra-1 is overexpressed in TNBC and plays crucial roles in tumor progression and treatment resistance. In a previous large-scale screen, we identified PARP1 to be among 118 proteins that interact with endogenous chromatin-bound Fra-1 in TNBC cells. PARP1 inhibitor (olaparib) is currently in clinical use for treatment of BRCA-mutated TNBC breast cancer. Here, we demonstrate that the Fra-1-PARP1 interaction impacts the efficacy of olaparib treatment. We show that PARP1 interacts with and downregulates Fra-1, thereby reducing AP-1 transcriptional activity. Olaparib treatment, or silencing of PARP1, consequently, increases Fra-1 levels and enhances its transcriptional activity. Increased Fra-1 can have adverse effect, including treatment resistance. We also found that a large fraction of PARP1-regulated genes was dependent on Fra-1. We show that by inhibiting Fra-1/AP-1, non-BRCA-mutated TNBC cells can become sensitized to olaparib treatment. We identify that high PARP1 expression is indicative of a poor clinical outcome in breast cancer patients overall (P = 0.01), but not for HER-2 positive patients. In conclusion, by exploring the functionality of the Fra-1 and PARP1 interaction, we propose that targeting Fra-1 could serve as a combinatory therapeutic approach to improve olaparib treatment outcome for TNBC patients.
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Affiliation(s)
- Dandan Song
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83 Huddinge, Sweden.
| | - Huan He
- School of Public Health, Jilin University, Changchun, 130021, China.
| | - Indranil Sinha
- Department of Women's and Children's Health, Karolinska Institutet, S-171 77 Stockholm, Sweden.
| | - Linnea Hases
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83 Huddinge, Sweden; Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Solna, Sweden.
| | - Feifei Yan
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83 Huddinge, Sweden.
| | - Amena Archer
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Solna, Sweden.
| | - Lars-Arne Haldosen
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83 Huddinge, Sweden.
| | - Chunyan Zhao
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83 Huddinge, Sweden.
| | - Cecilia Williams
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83 Huddinge, Sweden; Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Solna, Sweden.
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9
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FOXO3 Is Expressed in Ovarian Tissues and Acts as an Apoptosis Initiator in Granulosa Cells of Chickens. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6902906. [PMID: 31380433 PMCID: PMC6657628 DOI: 10.1155/2019/6902906] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/21/2019] [Accepted: 07/02/2019] [Indexed: 11/18/2022]
Abstract
FOXO3, which encodes the transcription factor forkhead box O-3 (FoxO3), is a member of the FOXO subfamily of the forkhead box (FOX) family. FOXO3 can be negatively regulated by its phosphorylation by the PI3K/Akt signaling pathway and ultimately drives apoptosis when activated. In mammalian ovaries, the FOXO3 protein regulates atresia and follicle growth by promoting apoptosis of ovarian granulosa cells. Nonetheless, the specific effects of the FOXO3 protein on granulosa apoptosis of avian ovaries have not been elucidated. Therefore, we studied FOXO3 expression in follicles with different organization and at all hierarchical levels of chicken follicles. Via an immunofluorescence assay, the chicken follicular theca at all hierarchical levels were found to be strongly stained with an anti-FOXO3 antibody. In chicken primary ovarian granulosa cells, mRNA levels of proapoptotic factors BNIP3 and BCL2L11 decreased in the absence of FOXO3, and so did PARP-1 and cleaved caspase 3 protein levels. After treatment with a recombinant FOXO3 protein, PARP-1 and caspase 3 protein levels increased, along with mRNA levels of Bnip3 and BCL2L11 (significantly, p<0.05). In addition, FOXO3 was downregulated in chicken granulosa cells when different estradiol or FSH concentrations were applied. In conclusion, FOXO3 is expressed in chicken reproductive tissues, including follicles and ovarian granulosa cells, and promotes apoptosis of chicken ovarian granulosa cells.
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10
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Ali R, Al-Kawaz A, Toss MS, Green AR, Miligy IM, Mesquita KA, Seedhouse C, Mirza S, Band V, Rakha EA, Madhusudan S. Targeting PARP1 in XRCC1-Deficient Sporadic Invasive Breast Cancer or Preinvasive Ductal Carcinoma In Situ Induces Synthetic Lethality and Chemoprevention. Cancer Res 2018; 78:6818-6827. [PMID: 30297533 DOI: 10.1158/0008-5472.can-18-0633] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/03/2018] [Accepted: 09/26/2018] [Indexed: 11/16/2022]
Abstract
: Targeting PARP1 for synthetic lethality is a new strategy for breast cancers harboring germline mutations in BRCA. However, these mutations are rare, and reactivation of BRCA-mediated pathways may result in eventual resistance to PARP1 inhibitor therapy. Alternative synthetic lethality approaches targeting more common sporadic breast cancers and preinvasive ductal carcinoma in situ (DCIS) are desirable. Here we show that downregulation of XRCC1, which interacts with PARP1 and coordinates base excision repair, is an early event in human breast cancer pathogenesis. XRCC1-deficient DCIS were aggressive and associated with increased risk of local recurrence. Human invasive breast cancers deficient in XRCC1 and expressing high PARP1 levels also manifested aggressive features and poor outcome. The PARP1 inhibitor olaparib was synthetically lethal in XRCC1-deficient DCIS and invasive breast cancer cells. We conclude that targeting PARP1 is an attractive strategy for synthetic lethality and chemoprevention in XRCC1-deficient breast cancers, including preinvasive DCIS. SIGNIFICANCE: These findings show that loss of XRCC1, which is associated with more malignant DCIS, can be exploited by PARP inhibition, suggesting its application as a promising therapeutic and chemoprevention strategy in XRCC1-deficient tumor cells.
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Affiliation(s)
- Reem Ali
- Translational Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Abdulbaqi Al-Kawaz
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Michael S Toss
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Andrew R Green
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Islam M Miligy
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Katia A Mesquita
- Translational Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Claire Seedhouse
- Academic Haematology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Centre, Nebraska Medical Centre, Omaha, Nebraska
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Centre, Nebraska Medical Centre, Omaha, Nebraska
| | - Emad A Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom.
| | - Srinivasan Madhusudan
- Translational Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, United Kingdom. .,Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham, United Kingdom
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11
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Anurag M, Punturi N, Hoog J, Bainbridge MN, Ellis MJ, Haricharan S. Comprehensive Profiling of DNA Repair Defects in Breast Cancer Identifies a Novel Class of Endocrine Therapy Resistance Drivers. Clin Cancer Res 2018; 24:4887-4899. [PMID: 29793947 PMCID: PMC6822623 DOI: 10.1158/1078-0432.ccr-17-3702] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/30/2018] [Accepted: 05/18/2018] [Indexed: 12/20/2022]
Abstract
Purpose: This study was undertaken to conduct a comprehensive investigation of the role of DNA damage repair (DDR) defects in poor outcome ER+ disease.Experimental Design: Expression and mutational status of DDR genes in ER+ breast tumors were correlated with proliferative response in neoadjuvant aromatase inhibitor therapy trials (discovery dataset), with outcomes in METABRIC, TCGA, and Loi datasets (validation datasets), and in patient-derived xenografts. A causal relationship between candidate DDR genes and endocrine treatment response, and the underlying mechanism, was then tested in ER+ breast cancer cell lines.Results: Correlations between loss of expression of three genes: CETN2 (P < 0.001) and ERCC1 (P = 0.01) from the nucleotide excision repair (NER) and NEIL2 (P = 0.04) from the base excision repair (BER) pathways were associated with endocrine treatment resistance in discovery dataset, and subsequently validated in independent patient cohorts. Complementary mutation analysis supported associations between mutations in NER and BER genes and reduced endocrine treatment response. A causal role for CETN2, NEIL2, and ERCC1 loss in intrinsic endocrine resistance was experimentally validated in ER+ breast cancer cell lines, and in ER+ patient-derived xenograft models. Loss of CETN2, NEIL2, or ERCC1 induced endocrine treatment resistance by dysregulating G1-S transition, and therefore, increased sensitivity to CDK4/6 inhibitors. A combined DDR signature score was developed that predicted poor outcome in multiple patient cohorts.Conclusions: This report identifies DDR defects as a new class of endocrine treatment resistance drivers and indicates new avenues for predicting efficacy of CDK4/6 inhibition in the adjuvant treatment setting. Clin Cancer Res; 24(19); 4887-99. ©2018 AACR.
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Affiliation(s)
- Meenakshi Anurag
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Nindo Punturi
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Jeremy Hoog
- Siteman Cancer Center Breast Cancer Program, Washington University School of Medicine, St. Louis, Missouri
| | - Matthew N Bainbridge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - Matthew J Ellis
- Department of Medicine, Baylor College of Medicine, Houston, Texas.
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Svasti Haricharan
- Department of Medicine, Baylor College of Medicine, Houston, Texas.
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
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12
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Haricharan S, Punturi N, Singh P, Holloway KR, Anurag M, Schmelz J, Schmidt C, Lei JT, Suman V, Hunt K, Olson JA, Hoog J, Li S, Huang S, Edwards DP, Kavuri SM, Bainbridge MN, Ma CX, Ellis MJ. Loss of MutL Disrupts CHK2-Dependent Cell-Cycle Control through CDK4/6 to Promote Intrinsic Endocrine Therapy Resistance in Primary Breast Cancer. Cancer Discov 2017; 7:1168-1183. [PMID: 28801307 DOI: 10.1158/2159-8290.cd-16-1179] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 04/25/2017] [Accepted: 07/27/2017] [Indexed: 12/13/2022]
Abstract
Significant endocrine therapy-resistant tumor proliferation is present in ≥20% of estrogen receptor-positive (ER+) primary breast cancers and is associated with disease recurrence and death. Here, we uncover a link between intrinsic endocrine therapy resistance and dysregulation of the MutL mismatch repair (MMR) complex (MLH1/3, PMS1/2), and demonstrate a direct role for MutL complex loss in resistance to all classes of endocrine therapy. We find that MutL deficiency in ER+ breast cancer abrogates CHK2-mediated inhibition of CDK4, a prerequisite for endocrine therapy responsiveness. Consequently, CDK4/6 inhibitors (CDK4/6i) remain effective in MutL-defective ER+ breast cancer cells. These observations are supported by data from a clinical trial where a CDK4/6i was found to strongly inhibit aromatase inhibitor-resistant proliferation of MutL-defective tumors. These data suggest that diagnostic markers of MutL deficiency could be used to direct adjuvant CDK4/6i to a population of patients with breast cancer who exhibit marked resistance to the current standard of care.Significance: MutL deficiency in a subset of ER+ primary tumors explains why CDK4/6 inhibition is effective against some de novo endocrine therapy-resistant tumors. Therefore, markers of MutL dysregulation could guide CDK4/6 inhibitor use in the adjuvant setting, where the risk benefit ratio for untargeted therapeutic intervention is narrow. Cancer Discov; 7(10); 1168-83. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 1047.
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Affiliation(s)
- Svasti Haricharan
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Nindo Punturi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Purba Singh
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Kimberly R Holloway
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jacob Schmelz
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Cheryl Schmidt
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas.,Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas
| | - Vera Suman
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota
| | - Kelly Hunt
- Department of Breast Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John A Olson
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Jeremy Hoog
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, Missouri.,Siteman Cancer Center Breast Cancer Program, Washington University School of Medicine, Saint Louis, Missouri
| | - Shunqiang Li
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, Missouri.,Siteman Cancer Center Breast Cancer Program, Washington University School of Medicine, Saint Louis, Missouri
| | - Shixia Huang
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Dean P Edwards
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,Department of Immunology and Pathology, Baylor College of Medicine, Houston, Texas
| | - Shyam M Kavuri
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Matthew N Bainbridge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Rady's Children's Hospital, San Diego, California
| | - Cynthia X Ma
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, Missouri.,Siteman Cancer Center Breast Cancer Program, Washington University School of Medicine, Saint Louis, Missouri
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas. .,Department of Medicine, Baylor College of Medicine, Houston, Texas
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13
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Green AR, Aleskandarany MA, Ali R, Hodgson EG, Atabani S, De Souza K, Rakha EA, Ellis IO, Madhusudan S. Clinical Impact of Tumor DNA Repair Expression and T-cell Infiltration in Breast Cancers. Cancer Immunol Res 2017; 5:292-299. [PMID: 28254786 DOI: 10.1158/2326-6066.cir-16-0195] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/22/2016] [Accepted: 02/20/2017] [Indexed: 11/16/2022]
Abstract
Impaired DNA repair drives mutagenicity, which increases neoantigen load and immunogenicity. We investigated the expression of proteins involved in the DNA damage response (ATM, Chk2), double-strand break repair (BRCA1, BLM, WRN, RECQL4, RECQL5, TOPO2A, DNA-PKcs, Ku70/Ku80), nucleotide excision repair (ERCC1), base excision repair (XRCC1, pol β, FEN1, PARP1), and immune responses (CD8, PD-1, PD-L1, FOXP3) in 1,269 breast cancers and validated our findings in an independent estrogen receptor-negative (ER-) cohort (n = 279). Patients with tumors that expressed low XRCC1, low ATM, and low BRCA1 were not only associated with high numbers of CD8+ tumor-infiltrating lymphocytes, but were also linked to higher grades, high proliferation indexes, presence of dedifferentiated cells, ER- cells, and poor survival (all P ≤ 0.01). PD-1+ or PD-L1+ breast cancers with low XRCC1 were also linked to an aggressive phenotype that was high grade, had high proliferation indexes, contained dedifferentiated cells and ER- (all with P values ≤ 0.01), and poor survival (P = 0.00021 and P = 0.00022, for PD-1+ and PD-L1+ cancers, respectively) including in an independent ER- validation cohort (P = 0.007 and P = 0.047, respectively). We conclude that the interplay between DNA repair, CD8, PD-L1, and PD-1 can promote aggressive tumor phenotypes. XRCC1-directed personalization of immune checkpoint inhibitor therapy may be feasible and warrants further investigation in breast cancer. Cancer Immunol Res; 5(4); 292-9. ©2017 AACR.
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Affiliation(s)
- Andrew R Green
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Mohammed A Aleskandarany
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Reem Ali
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Eleanor Grace Hodgson
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Suha Atabani
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Karen De Souza
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Emad A Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ian O Ellis
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Srinivasan Madhusudan
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom. .,Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
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14
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DNA damage repair in breast cancer and its therapeutic implications. Pathology 2016; 49:156-165. [PMID: 28034453 DOI: 10.1016/j.pathol.2016.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/06/2016] [Accepted: 11/02/2016] [Indexed: 11/23/2022]
Abstract
The DNA damage response (DDR) involves the activation of numerous cellular activities that repair DNA lesions and maintain genomic integrity, and is critical in preventing tumorigenesis. Inherited or acquired mutations in specific genes involved in the DNA damage response, for example the breast cancer susceptibility genes 1/2 (BRCA1/2), phosphatase and tensin homolog (PTEN) and P53 are associated with various subtypes of breast cancer. Such changes can render breast cancer cells particularly sensitive to specific DNA damage response inhibitors, for example BRCA1/2 germline mutated cells are sensitive to poly (ADP-ribose) polymerase (PARP) inhibitors. The aims of this review are to discuss specific DNA damage response defects in breast cancer and to present the current stage of development of various DDR inhibitors (namely PARP, ATM/ATR, DNA-PK, PARG, RECQL5, FEN1 and APE1) for breast cancer mono- and combination therapy.
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15
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Casasent AK, Edgerton M, Navin NE. Genome evolution in ductal carcinoma in situ: invasion of the clones. J Pathol 2016; 241:208-218. [PMID: 27861897 DOI: 10.1002/path.4840] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/21/2016] [Accepted: 10/26/2016] [Indexed: 12/21/2022]
Abstract
Ductal carcinoma in situ (DCIS) is the most frequently diagnosed early-stage breast cancer. Only a subset of patients progress to invasive ductal carcinoma (IDC), and this presents a formidable clinical challenge for determining which patients to treat aggressively and which patients to monitor without therapeutic intervention. Understanding the molecular and genomic basis of invasion has been difficult to study in DCIS cancers due to several technical obstacles, including low tumour cellularity, lack of fresh-frozen tissues, and intratumour heterogeneity. In this review, we discuss the role of intratumour heterogeneity in the progression of DCIS to IDC in the context of three evolutionary models: independent lineages, evolutionary bottlenecks, and multiclonal invasion. We examine the evidence in support of these models and their relevance to the diagnosis and treatment of patients with DCIS. We also discuss how emerging technologies, such as single-cell sequencing, STAR-FISH, and imaging mass spectrometry, are likely to provide new insights into the evolution of this enigmatic disease. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Anna K Casasent
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mary Edgerton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas E Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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16
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Arora A, Parvathaneni S, Aleskandarany MA, Agarwal D, Ali R, Abdel-Fatah T, Green AR, Ball GR, Rakha EA, Ellis IO, Sharma S, Madhusudan S. Clinicopathological and Functional Significance of RECQL1 Helicase in Sporadic Breast Cancers. Mol Cancer Ther 2016; 16:239-250. [PMID: 27837030 DOI: 10.1158/1535-7163.mct-16-0290] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/14/2016] [Accepted: 11/01/2016] [Indexed: 01/16/2023]
Abstract
RECQL1, a key member of the RecQ family of DNA helicases, is required for DNA replication and DNA repair. Two recent studies have shown that germline RECQL1 mutations are associated with increased breast cancer susceptibility. Whether altered RECQL1 expression has clinicopathologic significance in sporadic breast cancers is unknown. We evaluated RECQL1 at the transcriptomic level (METABRIC cohort, n = 1,977) and at the protein level [cohort 1, n = 897; cohort 2, n = 252; cohort 3 (BRCA germline deficient), n = 74]. In RECQL1-depleted breast cancer cells, we investigated anthracycline sensitivity. High RECQL1 mRNA was associated with intClust.3 (P = 0.026), which is characterized by low genomic instability. On the other hand, low RECQL1 mRNA was linked to intClust.8 [luminal A estrogen receptor-positive (ER+) subgroup; P = 0.0455] and intClust.9 (luminal B ER+ subgroup; P = 0.0346) molecular phenotypes. Low RECQL1 expression was associated with shorter breast cancer-specific survival (P = 0.001). At the protein level, low nuclear RECQL1 level was associated with larger tumor size, lymph node positivity, high tumor grade, high mitotic index, pleomorphism, dedifferentiation, ER negativity, and HER-2 overexpression (P < 0.05). In ER+ tumors that received endocrine therapy, low RECQL1 was associated with poor survival (P = 0.008). However, in ER- tumors that received anthracycline-based chemotherapy, high RECQL1 was associated with poor survival (P = 0.048). In RECQL1-depleted breast cancer cell lines, we confirmed doxorubicin sensitivity, which was associated with DNA double-strand breaks accumulation, S-phase cell-cycle arrest, and apoptosis. We conclude that RECQL1 has prognostic and predictive significance in breast cancers. Mol Cancer Ther; 16(1); 239-50. ©2016 AACR.
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Affiliation(s)
- Arvind Arora
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Swetha Parvathaneni
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC
| | - Mohammed A Aleskandarany
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Devika Agarwal
- School of Science and Technology, Nottingham Trent University, Clifton campus, Nottingham, United Kingdom
| | - Reem Ali
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Tarek Abdel-Fatah
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Andrew R Green
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Graham R Ball
- School of Science and Technology, Nottingham Trent University, Clifton campus, Nottingham, United Kingdom
| | - Emad A Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ian O Ellis
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC.
| | - Srinivasan Madhusudan
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom. .,Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
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17
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Matta J, Morales L, Ortiz C, Adams D, Vargas W, Casbas P, Dutil J, Echenique M, Suárez E. Estrogen Receptor Expression Is Associated with DNA Repair Capacity in Breast Cancer. PLoS One 2016; 11:e0152422. [PMID: 27032101 PMCID: PMC4816515 DOI: 10.1371/journal.pone.0152422] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
Estrogen-receptor-positive (ER+) tumors employ complex signaling that engages in crosstalk with multiple pathways through genomic and non-genomic regulation. A greater understanding of these pathways is important for developing improved biomarkers that can better determine treatment choices, risk of recurrence and cancer progression. Deficiencies in DNA repair capacity (DRC) is a hallmark of breast cancer (BC); therefore, in this work we tested whether ER signaling influences DRC. We analyzed the association between ER positivity (% receptor activation) and DRC in 270 BC patients, then further stratified our analysis by HER2 receptor status. Our results show that among HER2 negative, the likelihood of having low DRC values among ER- women is 1.92 (95% CI: 1.03, 3.57) times the likelihood of having low DRC values among ER+ women, even adjusting for different potential confounders (p<0.05); however, a contrary pattern was observed among HER2 positives women. In conclusion, there is an association between DRC levels and ER status, and this association is modified by HER2 receptor status. Adding a DNA repair capacity test to hormone receptor testing may provide new information on defective DNA repair phenotypes, which could better stratify BC patients who have ER+ tumors. ER+/HER2- tumors are heterogeneous, incompletely defined, and clinically challenging to treat; the addition of a DRC test could better characterize and classify these patients as well as help clinicians select optimal therapies, which could improve outcomes and reduce recurrences.
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Affiliation(s)
- Jaime Matta
- Department of Basic Sciences, Division of Pharmacology & Toxicology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- * E-mail:
| | - Luisa Morales
- Public Health Program, Ponce Health Sciences University, Ponce, Puerto Rico, United States of America
| | - Carmen Ortiz
- Department of Basic Sciences, Division of Pharmacology & Toxicology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Damian Adams
- Department of Basic Sciences, Division of Pharmacology & Toxicology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Wanda Vargas
- Department of Basic Sciences, Division of Pharmacology & Toxicology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Patricia Casbas
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Biochemistry, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Julie Dutil
- Department of Basic Sciences, Division of Cancer Biology, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- Department of Basic Sciences, Division of Biochemistry, Ponce Health Sciences University-School of Medicine, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Miguel Echenique
- Auxilio Mutuo Hospital, San Juan, Puerto Rico, United States of America
| | - Erick Suárez
- Department of Biostatistics and Epidemiology, Graduate School of Public Health, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico, United States of America
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18
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Seibold P, Schmezer P, Behrens S, Michailidou K, Bolla MK, Wang Q, Flesch-Janys D, Nevanlinna H, Fagerholm R, Aittomäki K, Blomqvist C, Margolin S, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Lambrechts D, Wildiers H, Kristensen V, Alnæs GG, Nord S, Borresen-Dale AL, Hooning MJ, Hollestelle A, Jager A, Seynaeve C, Li J, Liu J, Humphreys K, Dunning AM, Rhenius V, Shah M, Kabisch M, Torres D, Ulmer HU, Hamann U, Schildkraut JM, Purrington KS, Couch FJ, Hall P, Pharoah P, Easton DF, Schmidt MK, Chang-Claude J, Popanda O. A polymorphism in the base excision repair gene PARP2 is associated with differential prognosis by chemotherapy among postmenopausal breast cancer patients. BMC Cancer 2015; 15:978. [PMID: 26674097 PMCID: PMC4682235 DOI: 10.1186/s12885-015-1957-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/27/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Personalized therapy considering clinical and genetic patient characteristics will further improve breast cancer survival. Two widely used treatments, chemotherapy and radiotherapy, can induce oxidative DNA damage and, if not repaired, cell death. Since base excision repair (BER) activity is specific for oxidative DNA damage, we hypothesized that germline genetic variation in this pathway will affect breast cancer-specific survival depending on treatment. METHODS We assessed in 1,408 postmenopausal breast cancer patients from the German MARIE study whether cancer specific survival after adjuvant chemotherapy, anthracycline chemotherapy, and radiotherapy is modulated by 127 Single Nucleotide Polymorphisms (SNPs) in 21 BER genes. For SNPs with interaction terms showing p<0.1 (likelihood ratio test) using multivariable Cox proportional hazard analyses, replication in 6,392 patients from nine studies of the Breast Cancer Association Consortium (BCAC) was performed. RESULTS rs878156 in PARP2 showed a differential effect by chemotherapy (p=0.093) and was replicated in BCAC studies (p=0.009; combined analysis p=0.002). Compared to non-carriers, carriers of the variant G allele (minor allele frequency=0.07) showed better survival after chemotherapy (combined allelic hazard ratio (HR)=0.75, 95% 0.53-1.07) and poorer survival when not treated with chemotherapy (HR=1.42, 95% 1.08-1.85). A similar effect modification by rs878156 was observed for anthracycline-based chemotherapy in both MARIE and BCAC, with improved survival in carriers (combined allelic HR=0.73, 95% CI 0.40-1.32). None of the SNPs showed significant differential effects by radiotherapy. CONCLUSIONS Our data suggest for the first time that a SNP in PARP2, rs878156, may together with other genetic variants modulate cancer specific survival in breast cancer patients depending on chemotherapy. These germline SNPs could contribute towards the design of predictive tests for breast cancer patients.
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Affiliation(s)
- Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Peter Schmezer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69124, Heidelberg, Germany.
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Cancer Center Hamburg (UCCH), Hamburg, Germany.
- Department of Medical Biometrics and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Rainer Fagerholm
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Kristiina Aittomäki
- Department of Clinical Genetics, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.
- Central Finland Health Care District, Jyväskylä Central Hospital, Jyväskylä, Finland.
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
| | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Leuven, Belgium.
- Department of Oncology, Laboratory for Translational Genetics, University of Leuven, Leuven, Belgium.
| | - Hans Wildiers
- Department of General Medical Oncology, Multidisciplinary Breast Center, University Hospitals Leuven, Leuven, Belgium.
| | - Vessela Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
- Institute of Clinical Medicine, K.G. Jebsen Center for Breast Cancer Research, Faculty of Medicine, University of Oslo (UiO), Oslo, Norway.
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, University of Oslo (UiO), Oslo, Norway.
| | - Grethe Grenaker Alnæs
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
| | - Anne-Lise Borresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
- Institute of Clinical Medicine, K.G. Jebsen Center for Breast Cancer Research, Faculty of Medicine, University of Oslo (UiO), Oslo, Norway.
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Caroline Seynaeve
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore.
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore.
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Alison M Dunning
- Department of Oncology, Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Valerie Rhenius
- Department of Oncology, Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Mitul Shah
- Department of Oncology, Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia.
| | | | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA.
| | - Kristen S Purrington
- Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, Michigan, USA.
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Michigan, USA.
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Paul Pharoah
- Department of Oncology, Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Doug F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Odilia Popanda
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69124, Heidelberg, Germany.
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19
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Arora A, Abdel-Fatah TMA, Agarwal D, Doherty R, Croteau DL, Moseley PM, Hameed K, Green A, Aleskandarany MA, Rakha EA, Patterson K, Ball G, Chan SYT, Ellis IO, Bohr VA, Bryant HE, Madhusudan S. Clinicopathological and prognostic significance of RECQL5 helicase expression in breast cancers. Carcinogenesis 2015; 37:63-71. [PMID: 26586793 DOI: 10.1093/carcin/bgv163] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/30/2015] [Indexed: 01/16/2023] Open
Abstract
RECQL5 is a member of the RecQ family of DNA helicases and has key roles in homologous recombination, base excision repair, replication and transcription. The clinicopathological significance of RECQL5 expression in breast cancer is unknown. In this study, we have evaluated RECQL5 mRNA expression in 1977 breast cancers, and RECQL5 protein level in 1902 breast cancers [Nottingham Tenovus series (n = 1650) and ER- cohort (n = 252)]. Expression levels were correlated to aggressive phenotypes and survival outcomes. High RECQL5 mRNA expression was significantly associated with high histological grade (P = 0.007), HER2 overexpression (P = 0.032), ER+/HER2-/high proliferation genefu subtype (P < 0.0001), integrative molecular clusters (intClust 1and 9) (P < 0.0001) and poor survival (P < 0.0001). In subgroup analysis, high RECQL5 mRNA level remains significantly associated with poor BCSS in ER+ cohort (P < 0.0001) but not in ER- cohort (P = 0.116). At the protein level, in tumours with low RAD51, high RECQL5 level was significantly associated with high histological grade (P < 0.0001), higher mitotic index (P = 0.008), dedifferentiation (P = 0.025), pleomorphism (P = 0.027) and poor survival (P = 0.003). In subgroup analysis, high RECQL5/low RAD51 remains significantly associated with poor BCSS in ER+ cohort (P = 0.010), but not in ER- cohort (P = 0.628). In multivariate analysis, high RECQL5 mRNA and high RECQL5/low RAD51 nuclear protein coexpression independently influenced survival (P = 0.022) in whole cohort and in the ER+ subgroup. Preclinically, we show that exogenous expression of RECQL5 in MCF10A cells can drive proliferation supporting an oncogenic function for RECQL5 in breast cancer. We conclude that RECQL5 is a promising biomarker in breast cancer.
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Affiliation(s)
- Arvind Arora
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG51PB, UK, Department of Oncology, Nottingham University Hospitals, Nottingham NG51PB, UK
| | | | - Devika Agarwal
- School of Science and Technology, Nottingham Trent University, Clifton campus, Nottingham NG11 8NS, UK
| | - Rachel Doherty
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG51PB, UK
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MA 21224-6825, USA
| | - Paul M Moseley
- Department of Oncology, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Khalid Hameed
- Department of Oncology, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Andrew Green
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham NG51PB, UK and
| | - Mohammed A Aleskandarany
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham NG51PB, UK and
| | - Emad A Rakha
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham NG51PB, UK and
| | - Karl Patterson
- Academic Unit of Molecular Oncology, Department of Oncology, Medical School Sheffield Cancer Research Centre, University of Sheffield, Sheffield S10 2RX, UK
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Clifton campus, Nottingham NG11 8NS, UK
| | - Stephen Y T Chan
- Department of Oncology, Nottingham University Hospitals, Nottingham NG51PB, UK
| | - Ian O Ellis
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MA 21224-6825, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MA 21224-6825, USA
| | - Helen E Bryant
- Academic Unit of Molecular Oncology, Department of Oncology, Medical School Sheffield Cancer Research Centre, University of Sheffield, Sheffield S10 2RX, UK
| | - Srinivasan Madhusudan
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG51PB, UK, Department of Oncology, Nottingham University Hospitals, Nottingham NG51PB, UK,
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20
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Doherty R, Madhusudan S. DNA Repair Endonucleases: Physiological Roles and Potential as Drug Targets. ACTA ACUST UNITED AC 2015; 20:829-41. [PMID: 25877151 DOI: 10.1177/1087057115581581] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/22/2015] [Indexed: 12/15/2022]
Abstract
Genomic DNA is constantly exposed to endogenous and exogenous damaging agents. To overcome these damaging effects and maintain genomic stability, cells have robust coping mechanisms in place, including repair of the damaged DNA. There are a number of DNA repair pathways available to cells dependent on the type of damage induced. The removal of damaged DNA is essential to allow successful repair. Removal of DNA strands is achieved by nucleases. Exonucleases are those that progressively cut from DNA ends, and endonucleases make single incisions within strands of DNA. This review focuses on the group of endonucleases involved in DNA repair pathways, their mechanistic functions, roles in cancer development, and how targeting these enzymes is proving to be an exciting new strategy for personalized therapy in cancer.
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Affiliation(s)
- Rachel Doherty
- Laboratory of Molecular Oncology, Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, UK
| | - Srinivasan Madhusudan
- Laboratory of Molecular Oncology, Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, UK
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21
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Arora A, Abdel-Fatah TMA, Agarwal D, Doherty R, Moseley PM, Aleskandarany MA, Green AR, Ball G, Alshareeda AT, Rakha EA, Chan SYT, Ellis IO, Madhusudan S. Transcriptomic and Protein Expression Analysis Reveals Clinicopathological Significance of Bloom Syndrome Helicase (BLM) in Breast Cancer. Mol Cancer Ther 2015; 14:1057-65. [PMID: 25673821 DOI: 10.1158/1535-7163.mct-14-0939] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/04/2015] [Indexed: 11/16/2022]
Abstract
Bloom syndrome helicase (BLM) has key roles in homologous recombination repair, telomere maintenance, and DNA replication. Germ-line mutations in the BLM gene causes Bloom syndrome, a rare disorder characterized by premature aging and predisposition to multiple cancers, including breast cancer. The clinicopathologic significance of BLM in sporadic breast cancers is unknown. We investigated BLM mRNA expression in the Molecular Taxonomy of Breast Cancer International Consortium cohort (n = 1,950) and validated in an external dataset of 2,413 tumors. BLM protein level was evaluated in the Nottingham Tenovus series comprising 1,650 breast tumors. BLM mRNA overexpression was significantly associated with high histologic grade, larger tumor size, estrogen receptor-negative (ER(-)), progesterone receptor-negative (PR(-)), and triple-negative phenotypes (ps < 0.0001). BLM mRNA overexpression was also linked to aggressive molecular phenotypes, including PAM50.Her2 (P < 0.0001), PAM50.Basal (P < 0.0001), and PAM50.LumB (P < 0.0001) and Genufu subtype (ER(+)/Her2(-)/high proliferation; P < 0.0001). PAM50.LumA tumors and Genufu subtype (ER(+)/Her2(-)/low proliferation) were more likely to express low levels of BLM mRNA (ps < 0.0001). Integrative molecular clusters (intClust) intClust.1 (P < 0.0001), intClust.5 (P < 0.0001), intClust.9 (P < 0.0001), and intClust.10 (P < 0.0001) were also more likely in tumors with high BLM mRNA expression. BLM mRNA overexpression was associated with poor breast cancer-specific survival (BCSS; ps < 0.000001). At the protein level, altered subcellular localization with high cytoplasmic BLM and low nuclear BLM was linked to aggressive phenotypes. In multivariate analysis, BLM mRNA and BLM protein levels independently influenced BCSS. This is the first and the largest study to provide evidence that BLM is a promising biomarker in breast cancer.
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Affiliation(s)
- Arvind Arora
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom. Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | - Devika Agarwal
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham, United Kingdom
| | - Rachel Doherty
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Paul M Moseley
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Mohammed A Aleskandarany
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Andrew R Green
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham, United Kingdom
| | - Alaa T Alshareeda
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Emad A Rakha
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Stephen Y T Chan
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Ian O Ellis
- Department of Pathology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Srinivasan Madhusudan
- Department of Oncology, Nottingham University Hospitals, Nottingham, United Kingdom. Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom.
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22
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Abdel-Fatah TM, Arora A, Alsubhi N, Agarwal D, Moseley PM, Perry C, Doherty R, Chan SY, Green AR, Rakha E, Ball G, Ellis IO, Madhusudan S. Clinicopathological significance of ATM-Chk2 expression in sporadic breast cancers: a comprehensive analysis in large cohorts. Neoplasia 2014; 16:982-91. [PMID: 25425972 PMCID: PMC4240925 DOI: 10.1016/j.neo.2014.09.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 12/28/2022]
Abstract
ATM-Chk2 network is critical for genomic stability, and its deregulation may influence breast cancer pathogenesis. We investigated ATM and Chk2 protein levels in two cohorts [cohort 1 (n = 1650) and cohort 2 (n = 252)]. ATM and Chk2 mRNA expression was evaluated in the Molecular Taxonomy of Breast Cancer International Consortium cohort (n = 1950). Low nuclear ATM protein level was significantly associated with aggressive breast cancer including larger tumors, higher tumor grade, higher mitotic index, pleomorphism, tumor type, lymphovascular invasion, estrogen receptor (ER)-, PR -, AR -, triple-negative, and basal-like phenotypes (Ps < .05). Breast cancer 1, early onset negative, low XRCC1, low SMUG1, high FEN1, high MIB1, p53 mutants, low MDM2, low Bcl-2, low p21, low Bax, high CDK1, and low Chk2 were also more frequent in tumors with low nuclear ATM level (Ps < .05). Low ATM protein level was significantly associated with poor survival including in patients with ER-negative tumors who received adjuvant anthracycline or cyclophosphamide, methotrexate, and 5-fluorouracil-based adjuvant chemotherapy (Ps < .05). Low nuclear Chk2 protein was likely in ER -/PR -/AR -; HER-2 positive; breast cancer 1, early onset negative; low XRCC1; low SMUG1; low APE1; low polβ; low DNA-PKcs; low ATM; low Bcl-2; and low TOPO2A tumors (P < .05). In patients with ER + tumors who received endocrine therapy or ER-negative tumors who received chemotherapy, nuclear Chk2 levels did not significantly influence survival. In p53 mutant tumors, low ATM (P < .000001) or high Chk2 (P < .01) was associated with poor survival. When investigated together, low-ATM/high-Chk2 tumors have the worst survival (P = .0033). Our data suggest that ATM-Chk2 levels in sporadic breast cancer may have prognostic and predictive significance.
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Affiliation(s)
| | - Arvind Arora
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Nouf Alsubhi
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Devika Agarwal
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
| | - Paul M. Moseley
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Christina Perry
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Rachel Doherty
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Stephen Y.T. Chan
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Andrew R. Green
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Emad Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
| | - Ian O. Ellis
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
| | - Srinivasan Madhusudan
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
- Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1 PB, UK
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