1
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Tjader NP, Beer AJ, Ramroop J, Tai MC, Ping J, Gandhi T, Dauch C, Neuhausen SL, Ziv E, Sotelo N, Ghanekar S, Meadows O, Paredes M, Gillespie J, Aeilts A, Hampel H, Zheng W, Jia G, Hu Q, Wei L, Liu S, Ambrosone CB, Palmer JR, Carpten JD, Yao S, Stevens P, Ho WK, Pan JW, Fadda P, Huo D, Teo SH, McElroy JP, Toland AE. Association of ESR1 germline variants with TP53 somatic variants in breast tumors in a genome-wide study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.06.23299442. [PMID: 38106140 PMCID: PMC10723566 DOI: 10.1101/2023.12.06.23299442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. HER2 positive and triple negative breast cancers (TNBC) have a higher frequency of TP53 somatic mutations than other subtypes. PIK3CA mutations are more frequently observed in hormone receptor positive tumors. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. Methods A genome-wide association study was conducted using breast cancer mutation status of TP53 and PIK3CA and functional mutation categories including TP53 gain of function (GOF) and loss of function mutations and PIK3CA activating/hotspot mutations. The discovery analysis consisted of 2850 European ancestry women from three datasets. Germline variants showing evidence of association with somatic mutations were selected for validation analyses based on predicted function, allele frequency, and proximity to known cancer genes or risk loci. Candidate variants were assessed for association with mutation status in a multi-ancestry validation study, a Malaysian study, and a study of African American/Black women with TNBC. Results The discovery Germline x Mutation (GxM) association study found five variants associated with one or more TP53 phenotypes with P values <1×10-6, 33 variants associated with one or more TP53 phenotypes with P values <1×10-5, and 44 variants associated with one or more PIK3CA phenotypes with P values <1×10-5. In the multi-ancestry and Malaysian validation studies, germline ESR1 locus variant, rs9383938, was associated with the presence of TP53 mutations overall (P values 6.8×10-5 and 9.8×10-8, respectively) and TP53 GOF mutations (P value 8.4×10-6). Multiple variants showed suggestive evidence of association with PIK3CA mutation status in the validation studies, but none were significant after correction for multiple comparisons. Conclusions We found evidence that germline variants were associated with TP53 and PIK3CA mutation status in breast cancers. Variants near the estrogen receptor alpha gene, ESR1, were significantly associated with overall TP53 mutations and GOF mutations. Larger multi-ancestry studies are needed to confirm these findings and determine if these variants contribute to ancestry-specific differences in mutation frequency.
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Affiliation(s)
- Nijole P. Tjader
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Abigail J. Beer
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Johnny Ramroop
- The City College of New York, City University of New York, New York, NY, USA
| | - Mei-Chee Tai
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Jie Ping
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Tanish Gandhi
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Medical School, Columbus, OH, 43210, USA
| | - Cara Dauch
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Wexner Medical Center, Clinical Trials Office, Columbus, OH 43210, USA
| | - Susan L. Neuhausen
- Beckman Research Institute of City of Hope, Department of Population Sciences, Duarte, CA, USA
| | - Elad Ziv
- University of California, Helen Diller Family Comprehensive Cancer Center, San Francisco, San Francisco, CA, USA
- University of California, Department of Medicine, San Francisco, San Francisco, CA, USA
- University of California San Francisco, Institute for Human Genetics, San Francisco, CA, USA
| | - Nereida Sotelo
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Shreya Ghanekar
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Owen Meadows
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Monica Paredes
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jessica Gillespie
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Amber Aeilts
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Heather Hampel
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Guochong Jia
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christine B. Ambrosone
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | - John D. Carpten
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Integrative Translational Sciences, City of Hope, Duarte, CA
| | - Song Yao
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Patrick Stevens
- The Ohio State University Comprehensive Cancer Center, Bioinformatics Shared Resource, Columbus, OH, USA
| | - Weang-Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Jia Wern Pan
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Paolo Fadda
- The Ohio State University Comprehensive Cancer Center, Genomics Shared Resource, Columbus, OH, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
- Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Joseph Paul McElroy
- The Ohio State University Center for Biostatistics, Department of Biomedical Informatics, Columbus, OH, USA
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA
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Pestana RMC, Silvino JPP, Oliveira AND, Soares CE, Sabino ADP, Simões R, Gomes KB. New Cardiovascular Biomarkers in Breast Cancer Patients Undergoing Doxorubicin-Based Chemotherapy. Arq Bras Cardiol 2023; 120:e20230167. [PMID: 38232245 DOI: 10.36660/abc.20230167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/04/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Central Illustration : New Cardiovascular Biomarkers in Breast Cancer Patients Undergoing Doxorubicin-Based Chemotherapy. Cardiovascular diseases (CVDs) are relevant to the management of breast cancer treatment since a substantial number of patients develop these complications after chemotherapy. OBJECTIVE This study aims to evaluate new cardiovascular biomarkers, namely CXCL-16 (C-X-C motif ligand 16), FABP3 (fatty acid binding protein 3), FABP4 (fatty acid binding protein 4), LIGHT (tumor necrosis factor superfamily member 14/TNFS14), GDF-15 (Growth/differentiation factor 15), sCD4 (soluble form of CD14), and ucMGP (uncarboxylated Matrix Gla-Protein) in breast cancer patients treated with doxorubicin (DOXO). METHODS This case-control study was conducted in an oncology clinic that included 34 women diagnosed with breast cancer and chemotherapy with DOXO and 34 control women without cancer and CVD. The markers were determined immediately after the last cycle of chemotherapy. The statistical significance level adopted was 5%. RESULTS The breast cancer group presented higher levels of GDF-15 (p<0.001), while control subjects had higher levels of FABP3 (p=0.038), FABP4 (p=0003), sCD14, and ucMGP (p<0.001 for both). Positive correlations were observed between FABPs and BMI in the cancer group. CONCLUSION GDF15 is an emerging biomarker with potential clinical applicability in this scenario. FABPs are proteins related to adiposity, which are potentially involved in breast cancer biology. sCD14 and ucMGP engage in inflammatory and vascular calcification. The evaluation of these novel cardiovascular biomarkers could be useful in the management of breast cancer chemotherapy with DOXO.
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Affiliation(s)
| | | | | | - Cintia Esteves Soares
- Fundação Hospitalar do Estado de Minas Gerais (FHEMIG), Belo Horizonte , MG - Brasil
| | | | - Ricardo Simões
- Instituto de Hipertensão , Belo Horizonte , MG - Brasil
- Fundação Hospitalar do Estado de Minas Gerais (FHEMIG), Belo Horizonte , MG - Brasil
- Faculdade de Farmácia - Universidade Federal de Minas Gerais , Belo Horizonte , MG - Brasil
| | - Karina Braga Gomes
- Faculdade de Medicina - Universidade Federal de Minas Gerais , Belo Horizonte , MG - Brasil
- Faculdade de Farmácia - Universidade Federal de Minas Gerais , Belo Horizonte , MG - Brasil
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Xiong Z, Yang L, Li N, Fu J, Liu P, Sun P, Wei W, Xie X. DAB2IP attenuates chemoresistance of triple-negative breast cancer through sequestration of RAC1 to prevent β-catenin nuclear accumulation. Clin Transl Med 2022; 12:e1133. [PMID: 36536485 PMCID: PMC9763535 DOI: 10.1002/ctm2.1133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/20/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Although chemotherapy, the most widely used systemic treatment in triple-negative breast cancer (TNBC), markedly improved the patients' outcome, chemoresistance always occurs. This study purposed to explore new therapeutic strategies for the treatment of chemoresistance. METHODS AND RESULTS The expression and prognostic value of DAB2IP were investigated in TNBC tissues and cell lines. Low DAB2IP expression predicted high mortality risk in TNBC. Inhibition of DAB2IP expression conferred cancer stem cell capacity and chemoresistance in TNBC cell lines. Using murine breast cancer (BC) xenograft models, we evaluated the association with DAB2IP and chemoresistance. DAB2IP inhibited TNBC tumourigenesis and chemoresistance in vivo. Further, we revealed that DAB2IP inhibited β-catenin nuclear transport through competitive interaction with RAC1 and decreased β-catenin accumulation in the cell nucleus. Finally, we found that the DNA methylation level was negatively associated with DAB2IP expression in TNBC. Inhibition of DNA methylation restored the DAB2IP expression and attenuated chemoresistance in TNBC. CONCLUSIONS We revealed that DAB2IP attenuates chemoresistance of TNBC via inhibition of RAC1-mediated β-catenin nuclear accumulation. Decitabine treatment results in re-expression of DAB2IP by inhibiting DNA methylation and could be a potential therapeutic strategy for chemoresistance in TNBC.
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Affiliation(s)
- Zhenchong Xiong
- Department of Breast OncologySun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Lin Yang
- Department of Radiation OncologyNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Ning Li
- Department of Breast OncologySun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Jianchang Fu
- Department of PathologySun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Peng Liu
- Department of Breast OncologySun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Peng Sun
- Department of PathologySun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Weidong Wei
- Department of Breast OncologySun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Xiaoming Xie
- Department of Breast OncologySun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangzhouChina
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Almutairi BO, Almutairi MH, Alrefaei AF, Ali D, Alkahtani S, Alarifi S. Cigarette Smoke Regulates the Expression of EYA4 via Alternation of DNA Methylation Status. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5032172. [PMID: 35607307 PMCID: PMC9124125 DOI: 10.1155/2022/5032172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022]
Abstract
Cigarette SMOKE (CS) considerably contributes to causing some diseases such as cancer, and it has a role in the alternation of gene expression through several mechanisms including epigenetics modification, particularly DNA methylation. EYA4 is one of the genes, that whose expression has been dysregulated in lung, colon, bladder, and breast cancer, leading to tumor progression. The alternation of DNA methylation levels has been implicated in regulating the expression of the EYA4 gene. Thus, in this study, we have shown the effect of CS on the DNA methylation level of the EYA4 promoter region as well as the methylation level on EYA4 expression. To determine the level of DNA methylation on the promoter region of the EYA4 gene, we have employed the bisulfite conversion treatment followed by the Sanger Sequence for 100 DNA samples taken from Saudi people (50 smokers and 50 nonsmokers). We found that 26% of DNA extracted from smoker samples is methylated, while there was no methylation identified in nonsmoker samples. Also, using the demethylating agents such as AZA on LoVo and Caco-2 cancer cell lines causes induction of transcription level of EYA4, implying the possible mechanism of DNA methylation in the upregulation of EYA4. These findings suggest the possible mechanism of CS in controlling the expression of EYA4 via changing the status of DNA methylation.
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Affiliation(s)
- Bader O. Almutairi
- Department of Zoology, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
| | - Mikhlid H. Almutairi
- Department of Zoology, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
| | - Abdulwahed F. Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
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5
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Yari H, Shabani S, Nafissi N, Majidzadeh T, Mahjoubi F. Investigation of promoter methylation patterns association with genes expression profile of ISL1, MGMT and DMNT3b in tissue of breast cancer patients. Mol Biol Rep 2022; 49:847-857. [PMID: 34997427 DOI: 10.1007/s11033-021-06546-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVES Cancer initiation and progression could influenced by both genetic and epigenetic events revealing of the overlap between epigenetic and genetic alteration can give important insights into cancer biology. METHODS AND RESULTS In this experiment ISL1, MGMT, DMNT3b genes were candidate to investigate both methylation status and expression profile by using methylation-specific PCR and real time PCR in 40 breast cancer patients, respectively, also we have assessed relation of the promoter methylation status and expression variation of the target genes. The mean level of methylation of ISL1 and MGMT in tumor tissues were significantly greater than normal tissues. In Contrast, DMNT3b gene was showed lower mean level of methylation in tumor tissue compared to normal tissues, however, this was not statistically significant. Relative expression analysis was displayed a significant reduction in expression level of ISL1 and MGMT in tumor tissues. Furthermore, there was a meaningful association between down expression of ISL1 with histological grade, Her2 and ER status. Moreover, MGMT down expression was significantly associated with tumor sizes. Any remarkable relation was not observed between DMNT3b expression level and clinic pathological features. At the end, significant relation between methylation status and expression level has been revealed. CONCLUSIONS In this study all observed results were exactly in line with the results were obtained from articles which were based on the methylation research and illustrate that the real-time PCR and methylation methods are in correlated with each other, furthermore, selected genes are capable to use as a potential biomarkers, however, more research on extended cases are needed.
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Affiliation(s)
- Hadi Yari
- Human Genetics Dept., Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Pajouhesh Blv, Tehran Karaj High Way, Tehran, Iran
| | - Samira Shabani
- Human Genetics Dept., Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Pajouhesh Blv, Tehran Karaj High Way, Tehran, Iran
| | - Nahid Nafissi
- Surgery Department of General Surgery, Iran University of Medical Science, Tehran, Iran
| | - Tayebeh Majidzadeh
- Human Genetics Dept., Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Pajouhesh Blv, Tehran Karaj High Way, Tehran, Iran
| | - Frouzandeh Mahjoubi
- Human Genetics Dept., Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Pajouhesh Blv, Tehran Karaj High Way, Tehran, Iran.
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Ali A, Mahla SB, Reza V, Alireza F. Predicting the possible effect of miR-203a-3p and miR-29a-3p on DNMT3B and GAS7 genes expression. J Integr Bioinform 2021; 19:jib-2021-0016. [PMID: 34914337 PMCID: PMC9069646 DOI: 10.1515/jib-2021-0016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022] Open
Abstract
Aberrant expression of genes involved in methylation, including DNA methyltransferase 3 Beta (DNMT3B), can cause hypermethylation of various tumor suppressor genes. In this regard, various molecular factors such as microRNAs can play a critical role in regulating these methyltransferase enzymes and eventually downstream genes such as growth arrest specific 7 (GAS7). Accordingly, in the present study we aimed to predict regulatory effect of miRNAs on DNMT3B and GAS7 genes expression in melanoma cell line. hsa-miR-203a-3p and hsa-miR-29a-3p were predicted and selected using bioinformatics software. The Real-time PCR technique was performed to investigate the regulatory effect of these molecules on the DNMT3B and GAS7 genes expression. Expression analysis of DNMT3B gene in A375 cell line showed that there was a significant increase compared to control (p value = 0.0015). Analysis of hsa-miR-203a-3p and hsa-miR-29a-3p indicated the insignificant decreased expression in melanoma cell line compared to control (p value < 0.05). Compared to control, the expression of GAS7 gene in melanoma cells showed a significant decrease (p value = 0.0323). Finally, our findings showed that the decreased expression of hsa-miR-203a-3p and hsa-miR-29a-3p can hypothesize that their aberrant expression caused DNMT3B dysfunction, possible methylation of the GAS7 gene, and ultimately decreased its expression. However, complementary studies are necessary to definite comment.
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Affiliation(s)
- Afgar Ali
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Sattarzadeh Bardsiri Mahla
- Student Research Committee, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Vahidi Reza
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Farsinejad Alireza
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran
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Sharma M, Arora I, Chen M, Wu H, Crowley MR, Tollefsbol TO, Li Y. Therapeutic Effects of Dietary Soybean Genistein on Triple-Negative Breast Cancer via Regulation of Epigenetic Mechanisms. Nutrients 2021; 13:3944. [PMID: 34836197 PMCID: PMC8623013 DOI: 10.3390/nu13113944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
Consumption of dietary natural components such as genistein (GE) found in soy-rich sources is strongly associated with a lower risk of breast cancer. However, bioactive dietary component-based therapeutic strategies are largely understudied in breast cancer treatment. Our investigation sought to elucidate the potential mechanisms linking bioactive dietary GE to its breast cancer chemotherapeutic potential in a special subtype of aggressive breast cancer-triple-negative breast cancer (TNBC)-by utilizing two preclinical patient-derived xenograft (PDX) orthotopic mouse models: BCM-3204 and TM00091. Our study revealed that administration of GE resulted in a delay of tumor growth in both PDX models. With transcriptomics analyses in TNBC tumors isolated from BCM-3204 PDXs, we found that dietary soybean GE significantly influenced multiple tumor-regulated gene expressions. Further validation assessment of six candidate differentially expressed genes (DEGs)-Cd74, Lpl, Ifi44, Fzd9, Sat1 and Wwc1-demonstrated a similar trend at gene transcriptional and protein levels as observed in RNA-sequencing results. Mechanistically, GE treatment-induced Cd74 downregulation regulated the NF-κB/Bcl-xL/TAp63 signal pathway, which may contribute to soybean GE-mediated therapeutic effects on TNBC tumors. Additionally, our findings revealed that GE can modify expression levels of key epigenetic-associated genes such as DNA methyltransferases (Dnmt3b), ten-eleven translocation (Tet3) methylcytosine dioxygenases and histone deacetyltransferase (Hdac2), and their enzymatic activities as well as genomic DNA methylation and histone methylation (H3K9) levels. Collectively, our investigation shows high significance for potential development of a novel therapeutic approach by using bioactive soybean GE for TNBC patients who have few treatment options.
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Affiliation(s)
- Manvi Sharma
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.S.); (I.A.); (H.W.)
| | - Itika Arora
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.S.); (I.A.); (H.W.)
| | - Min Chen
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Huixin Wu
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.S.); (I.A.); (H.W.)
| | - Michael R. Crowley
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.S.); (I.A.); (H.W.)
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Integrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yuanyuan Li
- Department of Obstetrics, Gynecology & Women’s Heath, University of Missouri, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Columbia, MO 65211, USA
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8
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Tang H, Yang D, Han C, Mu P. Smoking, DNA Methylation, and Breast Cancer: A Mendelian Randomization Study. Front Oncol 2021; 11:745918. [PMID: 34650928 PMCID: PMC8507148 DOI: 10.3389/fonc.2021.745918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/01/2021] [Indexed: 01/24/2023] Open
Abstract
Background Smoking was strongly associated with breast cancer in previous studies. Whether smoking promotes breast cancer through DNA methylation remains unknown. Methods Two-sample Mendelian randomization (MR) analyses were conducted to assess the causal effect of smoking-related DNA methylation on breast cancer risk. We used 436 smoking-related CpG sites extracted from 846 middle-aged women in the ARIES project as exposure data. We collected summary data of breast cancer from one of the largest meta-analyses, including 69,501 cases for ER+ breast cancer and 21,468 cases for ER- breast cancer. A total of 485 single-nucleotide polymorphisms (SNPs) were selected as instrumental variables (IVs) for smoking-related DNA methylation. We further performed an MR Steiger test to estimate the likely direction of causal estimate between DNA methylation and breast cancer. We also conducted colocalization analysis to evaluate whether smoking-related CpG sites shared a common genetic causal SNP with breast cancer in a given region. Results We established four significant associations after multiple testing correction: the CpG sites of cg2583948 [OR = 0.94, 95% CI (0.91-0.97)], cg0760265 [OR = 1.07, 95% CI (1.03-1.11)], cg0420946 [OR = 0.95, 95% CI (0.93-0.98)], and cg2037583 [OR =1.09, 95% CI (1.04-1.15)] were associated with the risk of ER+ breast cancer. All the four smoking-related CpG sites had a larger variance than that in ER+ breast cancer (all p < 1.83 × 10-11) in the MR Steiger test. Further colocalization analysis showed that there was strong evidence (based on PPH4 > 0.8) supporting a common genetic causal SNP between the CpG site of cg2583948 [with IMP3 expression (PPH4 = 0.958)] and ER+ breast cancer. There were no causal associations between smoking-related DNA methylation and ER- breast cancer. Conclusions These findings highlight potential targets for the prevention of ER+ breast cancer. Tissue-specific epigenetic data are required to confirm these results.
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Affiliation(s)
- Haibo Tang
- Department of Metabolic and Bariatric Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Desong Yang
- Department of Thoracic Surgery II, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Chaofei Han
- Department of Burn and Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ping Mu
- Department of Physiology, Shenyang Medical College, Shenyang, China
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9
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Nomair AM, Ahmed SS, Mohammed AF, El Mansy H, Nomeir HM. SCGB3A1 gene DNA methylation status is associated with breast cancer in Egyptian female patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
In recent years, hypermethylation of gene promoters has emerged as one of the fundamental mechanisms for the inactivation of tumor suppressor genes and has a potential role in the early detection of breast cancer. The present study is a case-control study aimed to quantify the methylation levels in the promoters of secretoglobin 3A1 (SCGB3A1), and ataxia-telangiectasia mutated (ATM) genes and evaluate their relation to clinicopathological features of the tumor in a cohort of Egyptian female patients with breast cancer.
Methods
Genomic deoxyribonucleic acid (DNA) was extracted from 100 tissue samples, 50 breast cancer tissues and 50 adjacent non-cancerous breast tissues, then, it was subjected to bisulfite conversion. The converted DNA was amplified by real-time PCR; then, pyrosequencing was performed to quantify DNA methylation levels in four CpG sites in ATM and SCGB3A1 gene promoters. The methylation data were presented as the percentage of average methylation of all the observed CpG sites and were calculated for each sample and each gene.
Results
The percentage of DNA methylation of the SCGB3A1 promoter was significantly higher in the tumor group than in the normal group (P= 0.001). However, a non-statistical significance difference was found in the DNA methylation percentage of the ATM promoter in the tumor group compared to the normal group (P = 0.315). The SCGB3A1 promoter methylation frequency was significantly associated with estrogen receptors (ER) and progesterone receptors (PR) positive tumors, lymph node metastasis, and lymphovascular invasion. However, no association was found between ATM methylation status and the different clinicopathological features of the tumor.
Conclusions
The findings of this work showed that the SCGB3A1 promoter methylation was significantly higher in the tumor group and was significantly associated with different clinicopathologic features in breast cancer. It may be considered as a suitable biomarker for diagnosis and prognosis. However, the promoter methylation levels of the ATM gene in breast cancer cases were unable to distinguish between breast cancer tissues and adjacent normal tissues, and there is no evidence that epigenetic silencing by ATM methylation has a role in breast cancer pathogenesis.
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10
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Ramadan A, Hashim M, Abouzid A, Swellam M. Clinical impact of PTEN methylation status as a prognostic marker for breast cancer. J Genet Eng Biotechnol 2021; 19:66. [PMID: 33970384 PMCID: PMC8110663 DOI: 10.1186/s43141-021-00169-4] [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: 12/10/2020] [Accepted: 04/16/2021] [Indexed: 12/15/2022]
Abstract
Background Aberrant DNA methylation of phosphatase and tensin homolog (PTEN) gene has been found in many cancers. The object of this study was to evaluate the clinical impact of PTEN methylation as a prognostic marker in breast cancer. The study includes 153 newly diagnosed females, and they were divided according to their clinical diagnosis into breast cancer patients (n = 112) and females with benign breast lesion (n = 41). A group of healthy individuals (n = 25) were recruited as control individuals. Breast cancer patients were categorized into early stage (0–I, n = 48) and late stage (II–III, n = 64), and graded into low grade (I–II, n = 42) and high grade (III, n = 70). Their pathological types were invasive duct carcinoma (IDC) (n = 66) and duct carcinoma in situ (DCI) (n = 46). Tumor markers (CEA and CA15.3) were detected using ELISA. DNA was taken away from the blood, and the PTEN promoter methylation level was evaluated using the EpiTect Methyl II PCR method. Results The findings revealed the superiority of PTEN methylation status as a good discriminator of the cancer group from the other two groups (benign and control) with its highest AUC and increased sensitivity (96.4%) and specificity (100%) over tumor markers (50% and 84% for CEA and 49.1% and 86.4% for CA15.3), respectively. The frequency of PTEN methylation was 96.4% of breast cancer patients and none of the benign and controls showed PTEN methylation and the means of PTEN methylation (87 ± 0.6) were significantly increased in blood samples of breast cancer group as compared to both benign and control groups (25 ± 0.7 and 12.6 ± 0.3), respectively. Methylation levels of PTEN were higher in the blood of patients with ER-positive than in patients with ER-negative cancers (P = 0.007) and in HER2 positive vs. HER2 negative tumors (P = 0.001). The Kaplan-Meier analysis recognizes PTEN methylation status as a significant forecaster of bad progression-free survival (PFS) and overall survival (OS), after 40 months follow-up. Conclusions PETN methylation could be supposed as one of the epigenetic aspects influencing the breast cancer prognosis that might foretell more aggressive actions and worse results in breast cancer patients.
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Affiliation(s)
- Amal Ramadan
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt. .,High Throughput Molecular and Genetic Laboratory, Center for Excellence for Advanced Sciences, National Research Centre, Dokki, Giza, Egypt.
| | - Maha Hashim
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt.,High Throughput Molecular and Genetic Laboratory, Center for Excellence for Advanced Sciences, National Research Centre, Dokki, Giza, Egypt
| | - Amr Abouzid
- Surgical Oncology Department, Mansoura Oncology Centre, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Menha Swellam
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt.,High Throughput Molecular and Genetic Laboratory, Center for Excellence for Advanced Sciences, National Research Centre, Dokki, Giza, Egypt
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11
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Dong Z, Yeo KS, Lopez G, Zhang C, Dankert Eggum EN, Rokita JL, Ung CY, Levee TM, Her ZP, Howe CJ, Hou X, van Ree JH, Li S, He S, Tao T, Fritchie K, Torres-Mora J, Lehman JS, Meves A, Razidlo GL, Rathi KS, Weroha SJ, Look AT, van Deursen JM, Li H, Westendorf JJ, Maris JM, Zhu S. GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma. Cancer Res 2021; 81:2995-3007. [PMID: 33602789 DOI: 10.1158/0008-5472.can-20-1890] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/04/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022]
Abstract
One of the greatest barriers to curative treatment of neuroblastoma is its frequent metastatic outgrowth prior to diagnosis, especially in cases driven by amplification of the MYCN oncogene. However, only a limited number of regulatory proteins that contribute to this complex MYCN-mediated process have been elucidated. Here we show that the growth arrest-specific 7 (GAS7) gene, located at chromosome band 17p13.1, is preferentially deleted in high-risk MYCN-driven neuroblastoma. GAS7 expression was also suppressed in MYCN-amplified neuroblastoma lacking 17p deletion. GAS7 deficiency led to accelerated metastasis in both zebrafish and mammalian models of neuroblastoma with overexpression or amplification of MYCN. Analysis of expression profiles and the ultrastructure of zebrafish neuroblastoma tumors with MYCN overexpression identified that GAS7 deficiency led to (i) downregulation of genes involved in cell-cell interaction, (ii) loss of contact among tumor cells as critical determinants of accelerated metastasis, and (iii) increased levels of MYCN protein. These results provide the first genetic evidence that GAS7 depletion is a critical early step in the cascade of events culminating in neuroblastoma metastasis in the context of MYCN overexpression. SIGNIFICANCE: Heterozygous deletion or MYCN-mediated repression of GAS7 in neuroblastoma releases an important brake on tumor cell dispersion and migration to distant sites, providing a novel mechanism underlying tumor metastasis in MYCN-driven neuroblastoma.See related commentary by Menard, p. 2815.
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Affiliation(s)
- Zhiwei Dong
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Kok Siong Yeo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Gonzalo Lopez
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Cheng Zhang
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Erin N Dankert Eggum
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Choong Yong Ung
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Taylor M Levee
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Zuag Paj Her
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Cassie J Howe
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Xiaonan Hou
- Departments of Oncology, Radiation Oncology, and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Janine H van Ree
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Shuai Li
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ting Tao
- Children's Hospital, Zhejiang University School of Medicine; National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, China
| | - Karen Fritchie
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jorge Torres-Mora
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Julia S Lehman
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
| | - Alexander Meves
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
| | - Gina L Razidlo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Komal S Rathi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - S John Weroha
- Departments of Oncology, Radiation Oncology, and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jan M van Deursen
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Hu Li
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Jennifer J Westendorf
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota.,Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - John M Maris
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota. .,Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
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12
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Cui J, Zhang Y, Ren X, Jin L, Zhang H. TBX1 Functions as a Tumor Activator in Prostate Cancer by Promoting Ribosome RNA Gene Transcription. Front Oncol 2021; 10:616173. [PMID: 33575219 PMCID: PMC7871003 DOI: 10.3389/fonc.2020.616173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/14/2020] [Indexed: 11/20/2022] Open
Abstract
TBX1 belongs to an evolutionarily conserved family of transcription factors involved in organ development. TBX1 has been reported to have a hypermethylated cytosine guanine dinucleotide island around its second exon, which was related to prostate cancer (PCa) progression. However, the role and exact mechanism of TBX1 in PCa remains unknown. Using human prostate samples, online data mining and multiple in vitro and in vivo models, we examined the biological role and underlying mechanisms of TBX1 in PCa. TBX1 was highly expressed in PCa tissues, and high TBX1 expression was positively associated with Gleason score, pathological tumor stage, pathological lymph node stage, extraprostatic extension and disease/progression-free survival. In vitro and in vivo data demonstrated that TBX1 silencing inhibits PCa cell proliferation and colony formation and increases the cell population at the G0/G1 phase. The exogenous expression of TBX1 rescued these phenotypes. Mechanistically, TBX1 silencing suppressed the expression of 45S ribosomal RNA (rRNA), which was rescued by the exogenous expression of TBX1. TBX1 silencing inhibited the monomethylation of histone 3 lysine 4 (H3K4me1) binding with the non-coding intergenic spacer (IGS) regions of ribosomal DNA (rDNA) and the recruitment of upstream binding factor to the promoter and IGS regions of rDNA. The drug-induced enhancement of H3K4me1 counteracted the effect of TBX1 silencing. These findings indicate that TBX1 exerts its tumor activator function in PCa cells via epigenetic control, thereby promoting rRNA gene transcription. Thus, TBX1 may represent a prognostic biomarker and therapeutic target for PCa patients.
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Affiliation(s)
- Jie Cui
- Department of Oncology, The First Affiliated Hospital, Xi'an Medical University, Xi'an, China.,School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Yamin Zhang
- Department of Oncology, The First Affiliated Hospital, Xi'an Medical University, Xi'an, China.,School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Xiaoyue Ren
- Department of Oncology, The First Affiliated Hospital, Xi'an Medical University, Xi'an, China.,School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Lei Jin
- School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Hongyi Zhang
- School of General Medicine, Xi'an Medical University, Xi'an, China.,Department of Urology, The First Affiliated Hospital, Xi'an Medical University, Xi'an, China
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13
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Chen X, Hu SL, Feng Y, Li P, Mao QS, Xue WJ. Expression of Fatty Acid-Binding Protein-3 in Gastrointestinal Stromal Tumors and Its Significance for Prognosis. J Surg Res 2020; 260:462-466. [PMID: 33272594 DOI: 10.1016/j.jss.2020.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 10/01/2020] [Accepted: 11/01/2020] [Indexed: 01/24/2023]
Abstract
BACKGROUND FABP3 is a member of the fatty acid-binding protein (FABP) family, whose role in various cancers has been reported in the past. However, little is known about the role that FABP3 plays in gastrointestinal stromal tumors (GISTs). METHODS FABP3 expression was analyzed in 119 patients with GISTs using immunohistochemistry and tissue microarrays to interrogate the relationship between expression and prognosis. Kaplan-Meier analysis was used to calculate patient survival rates using complete follow-up data and to evaluate the potential prognostic value of FABP3 using Cox regression analysis. RESULTS FABP3-positive signals were detected as brown particles located in the cytoplasm using immunohistochemistry. Among the 119 tissue samples, we observed high FABP3 expression in 64 and low or negative expression in 55. Immunohistochemical analyses suggested that FABP3 expression was significantly correlated with tumor size (P = 0.006), mitotic index (P = 0.016), gross classification (P = 0.048), and AFIP-Miettinen risk classification (P = 0.007). Multiple logistic regression analysis showed that the expression of FABP3 was significantly associated with tumor size (P = 0.021). Kaplan-Meier survival curves showed that patients with GISTs with low expression of FABP3 and classified with a very low to moderate AFIP-Miettinen risk had better prognosis. Multivariate analysis further showed that high expression of FABP3 (P = 0.017) was significantly associated with poor 5-year overall survival. CONCLUSIONS High FABP3 expression has a prognostic value for patients with GISTs.
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Affiliation(s)
- Xi Chen
- Department of Gastrointestinal Surgery, Affliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Shi-Liu Hu
- Department of Gastrointestinal Surgery, Affliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ying Feng
- Department of Gastrointestinal Surgery, Affliated Hospital of Nantong University, Nantong, Jiangsu, China; Research Center of Clinical Medicine, Affliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Peng Li
- Department of Gastrointestinal Surgery, Affliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Qin-Sheng Mao
- Department of Gastrointestinal Surgery, Affliated Hospital of Nantong University, Nantong, Jiangsu, China.
| | - Wan-Jiang Xue
- Department of Gastrointestinal Surgery, Affliated Hospital of Nantong University, Nantong, Jiangsu, China; Research Center of Clinical Medicine, Affliated Hospital of Nantong University, Nantong, Jiangsu, China.
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14
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Xu X, Zhang M, Xu F, Jiang S. Wnt signaling in breast cancer: biological mechanisms, challenges and opportunities. Mol Cancer 2020; 19:165. [PMID: 33234169 PMCID: PMC7686704 DOI: 10.1186/s12943-020-01276-5] [Citation(s) in RCA: 229] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Wnt signaling is a highly conserved signaling pathway that plays a critical role in controlling embryonic and organ development, as well as cancer progression. Genome-wide sequencing and gene expression profile analyses have demonstrated that Wnt signaling is involved mainly in the processes of breast cancer proliferation and metastasis. The most recent studies have indicated that Wnt signaling is also crucial in breast cancer immune microenvironment regulation, stemness maintenance, therapeutic resistance, phenotype shaping, etc. Wnt/β-Catenin, Wnt-planar cell polarity (PCP), and Wnt-Ca2+ signaling are three well-established Wnt signaling pathways that share overlapping components and play different roles in breast cancer progression. In this review, we summarize the main findings concerning the relationship between Wnt signaling and breast cancer and provide an overview of existing mechanisms, challenges, and potential opportunities for advancing the therapy and diagnosis of breast cancer.
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Affiliation(s)
- Xiufang Xu
- School of Medical Imaging, Hangzhou Medical College, Hangzhou, 310053 Zhejiang China
| | - Miaofeng Zhang
- Department of Orthopedic Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009 Zhejiang China
| | - Faying Xu
- School of Medical Imaging, Hangzhou Medical College, Hangzhou, 310053 Zhejiang China
| | - Shaojie Jiang
- School of Medical Imaging, Hangzhou Medical College, Hangzhou, 310053 Zhejiang China
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15
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Lee N, Park MJ, Song W, Jeon K, Jeong S. Currently Applied Molecular Assays for Identifying ESR1 Mutations in Patients with Advanced Breast Cancer. Int J Mol Sci 2020; 21:ijms21228807. [PMID: 33233830 PMCID: PMC7699999 DOI: 10.3390/ijms21228807] [Citation(s) in RCA: 2] [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: 10/27/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Approximately 70% of breast cancers, the leading cause of cancer-related mortality worldwide, are positive for the estrogen receptor (ER). Treatment of patients with luminal subtypes is mainly based on endocrine therapy. However, ER positivity is reduced and ESR1 mutations play an important role in resistance to endocrine therapy, leading to advanced breast cancer. Various methodologies for the detection of ESR1 mutations have been developed, and the most commonly used method is next-generation sequencing (NGS)-based assays (50.0%) followed by droplet digital PCR (ddPCR) (45.5%). Regarding the sample type, tissue (50.0%) was more frequently used than plasma (27.3%). However, plasma (46.2%) became the most used method in 2016-2019, in contrast to 2012-2015 (22.2%). In 2016-2019, ddPCR (61.5%), rather than NGS (30.8%), became a more popular method than it was in 2012-2015. The easy accessibility, non-invasiveness, and demonstrated usefulness with high sensitivity of ddPCR using plasma have changed the trends. When using these assays, there should be a comprehensive understanding of the principles, advantages, vulnerability, and precautions for interpretation. In the future, advanced NGS platforms and modified ddPCR will benefit patients by facilitating treatment decisions efficiently based on information regarding ESR1 mutations.
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Affiliation(s)
- Nuri Lee
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (N.L.); (M.-J.P.); (W.S.)
| | - Min-Jeong Park
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (N.L.); (M.-J.P.); (W.S.)
| | - Wonkeun Song
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (N.L.); (M.-J.P.); (W.S.)
| | - Kibum Jeon
- Department of Laboratory Medicine, Hangang Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea;
| | - Seri Jeong
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (N.L.); (M.-J.P.); (W.S.)
- Correspondence: ; Tel.: +82-845-5305
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16
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de Castro GS, Correia-Lima J, Simoes E, Orsso CE, Xiao J, Gama LR, Gomes SP, Gonçalves DC, Costa RGF, Radloff K, Lenz U, Taranko AE, Bin FC, Formiga FB, de Godoy LGL, de Souza RP, Nucci LHA, Feitoza M, de Castro CC, Tokeshi F, Alcantara PSM, Otoch JP, Ramos AF, Laviano A, Coletti D, Mazurak VC, Prado CM, Seelaender M. Myokines in treatment-naïve patients with cancer-associated cachexia. Clin Nutr 2020; 40:2443-2455. [PMID: 33190987 DOI: 10.1016/j.clnu.2020.10.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/10/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022]
Abstract
Cancer-associated cachexia is a complex metabolic syndrome characterized by weight loss and systemic inflammation. Muscle loss and fatty infiltration into muscle are associated with poor prognosis in cancer patients. Skeletal muscle secretes myokines, factors with autocrine, paracrine and/or endocrine action, which may be modified by or play a role in cachexia. This study examined myokine content in the plasma, skeletal muscle and tumor homogenates from treatment-naïve patients with gastric or colorectal stages I-IV cancer with cachexia (CC, N = 62), or not (weight stable cancer, WSC, N = 32). Myostatin, interleukin (IL) 15, follistatin-like protein 1 (FSTL-1), fatty acid binding protein 3 (FABP3), irisin and brain-derived neurotrophic factor (BDNF) protein content in samples was measured with Multiplex technology; body composition and muscle lipid infiltration were evaluated in computed tomography, and quantification of triacylglycerol (TAG) in the skeletal muscle. Cachectic patients presented lower muscle FSTL-1 expression (p = 0.047), higher FABP3 plasma content (p = 0.0301) and higher tumor tissue expression of FABP3 (p = 0.0182), IL-15 (p = 0.007) and irisin (p = 0.0110), compared to WSC. Neither muscle TAG content, nor muscle attenuation were different between weight stable and cachectic patients. Lumbar adipose tissue (AT) index, visceral AT index and subcutaneous AT index were lower in CC (p = 0.0149, p = 0.0455 and p = 0.0087, respectively), who also presented lower muscularity in the cohort (69.2% of patients; p = 0.0301), compared to WSC. The results indicate the myokine profile in skeletal muscle, plasma and tumor is impacted by cachexia. These findings show that myokines eventually affecting muscle wasting may not solely derive from the muscle itself (as the tumor also may contribute to the systemic scenario), and put forward new perspectives on cachexia treatment targeting myokines and associated receptors and pathways.
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Affiliation(s)
- Gabriela S de Castro
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil.
| | - Joanna Correia-Lima
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil
| | - Estefania Simoes
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil
| | - Camila E Orsso
- University of Alberta, Department of Agricultural, Food and Nutritional Science, Canada
| | - Jingjie Xiao
- University of Alberta, Department of Agricultural, Food and Nutritional Science, Canada; Covenant Health Palliative Institute, Edmonton, Alberta, Canada
| | - Leonardo R Gama
- Departamento de Radiologia e Oncologia & Instituto do Câncer do Estado de São Paulo, Universidade de Sao Paulo, São Paulo, Brazil
| | - Silvio P Gomes
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil; Universidade de Sao Paulo Faculdade de Medicina Veterinaria, Departamento de Cirurgia, Brazil
| | - Daniela Caetano Gonçalves
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil; Universidade Federal de Sao Paulo, Instituto de Biociencias, Santos, Brazil
| | - Raquel G F Costa
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil
| | - Katrin Radloff
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil
| | - Ulrike Lenz
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil
| | - Anna E Taranko
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil
| | - Fang Chia Bin
- Santa Casa de Misericoria de Sao Paulo, São Paulo, Brazil
| | | | | | | | - Luis H A Nucci
- Instituto do Cancer Arnaldo Vieira de Carvalho, São Paulo, Brazil
| | - Mario Feitoza
- Instituto do Cancer Arnaldo Vieira de Carvalho, São Paulo, Brazil
| | - Claudio C de Castro
- Universidade de Sao Paulo Faculdade de Medicina, Departamento de Radiologia, São Paulo, Brazil; Universidade de Sao Paulo Hospital Universitario, São Paulo, Brazil
| | - Flavio Tokeshi
- Universidade de Sao Paulo Hospital Universitario, São Paulo, Brazil
| | | | - Jose P Otoch
- Universidade de Sao Paulo Hospital Universitario, São Paulo, Brazil
| | - Alexandre F Ramos
- Departamento de Radiologia e Oncologia & Instituto do Câncer do Estado de São Paulo, Universidade de Sao Paulo, São Paulo, Brazil; Escola de Artes, Ciencias e Humanidades, Universidade de Sao Paulo, São Paulo, Brazil
| | - Alessandro Laviano
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Dario Coletti
- Sorbonne Université, Department of Biological Adaptation and Aging, B2A, Paris, France; Department of AHFMO - Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Vera C Mazurak
- University of Alberta, Department of Agricultural, Food and Nutritional Science, Canada
| | - Carla M Prado
- University of Alberta, Department of Agricultural, Food and Nutritional Science, Canada
| | - Marilia Seelaender
- Cancer Metabolism Research Group, Universidade de Sao Paulo Instituto de Ciencias Biomedicas, Departamento de Biologia Celular e do Desenvolvimento and Faculdade de Medicina da Universidade de Sao Paulo, Departamento de Cirurgia, LIM 26-HC, São Paulo, Brazil
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17
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Ge A, Gao S, Liu Y, Zhang H, Wang X, Zhang L, Pang D, Zhao Y. Methylation of WT1, CA10 in peripheral blood leukocyte is associated with breast cancer risk: a case-control study. BMC Cancer 2020; 20:713. [PMID: 32736539 PMCID: PMC7393705 DOI: 10.1186/s12885-020-07183-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022] Open
Abstract
Background Studies have shown that abnormal changes of specific-gene DNA methylation in leukocytes may be associated with an elevated risk of cancer. However, associations between the methylation of the zinc-related genes, WT1 and CA10, and breast cancer risk remain unknown. Methods The methylation of WT1 and CA10 was analyzed by methylation-sensitive high-resolution-melting (MS-HRM) in a case-control study with female subjects (N = 959). Logistic regression was used to analyze the associations, and propensity score (PS) method was used to adjust confounders. Results The results showed that WT1 hypermethylation was associated with an increased risk of breast cancer, with an odds ratio (OR) of 3.07 [95% confidence interval (CI): 1.67–5.64, P < 0.01]. Subgroup analyses showed that WT1 hypermethylation was specifically associated with an elevated risk of luminal A subtype (OR = 2.62, 95% CI: 1.11–6.20, P = 0.03) and luminal B subtype (OR = 3.23, 95% CI: 1.34–7.80, P = 0.01). CA10 hypermethylation was associated with an increased risk of luminal B subtype (OR = 1.80, 95% CI: 1.09–2.98, P = 0.02). Conclusion The results of the present study suggest that the hypermethylation of WT1 methylation in leukocytes is significantly associated with an increased risk of breast cancer. The hypermethylation of WT1 is associated with an increased risk of luminal subtypes of breast cancer, and the hypermethylation of CA10 is associated with an increased risk of luminal B subtype of breast cancer.
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Affiliation(s)
- Anqi Ge
- Department of Epidemiology, School of Public Health, Harbin Medical University, 57 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Song Gao
- Department of Breast Surgery, the Tumor Hospital of Harbin Medical University, 150 Haping Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, School of Public Health, Harbin Medical University, 57 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Hui Zhang
- Department of Epidemiology, School of Public Health, Harbin Medical University, 57 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Xuan Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, 57 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Lei Zhang
- Department of Epidemiology, School of Public Health, Harbin Medical University, 57 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Da Pang
- Department of Breast Surgery, the Tumor Hospital of Harbin Medical University, 150 Haping Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China.
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, 57 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China.
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18
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Zhang Y, Bewerunge-Hudler M, Schick M, Burwinkel B, Herpel E, Hoffmeister M, Brenner H. Blood-derived DNA methylation predictors of mortality discriminate tumor and healthy tissue in multiple organs. Mol Oncol 2020; 14:2111-2123. [PMID: 32506842 PMCID: PMC7463320 DOI: 10.1002/1878-0261.12738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/14/2020] [Accepted: 06/02/2020] [Indexed: 12/27/2022] Open
Abstract
Evidence has shown that certain methylation markers derived from blood can mirror corresponding methylation signatures in internal tissues. In the current study, we aimed to investigate two strong epigenetic predictors for life span, derived from blood DNA methylation data, in tissue samples of solid cancer patients. Using data from the Cancer Genome Atlas (TCGA) and the German DACHS study, we compared a mortality risk score (MRscore) and DNAmPhenoAge in paired tumor and adjacent normal tissue samples of patients with lung (N = 69), colorectal (n = 299), breast (n = 90), head/neck (n = 50), prostate (n = 50), and liver (n = 50) cancer. To explore the concordance across tissue and blood, we additionally assessed the two markers in blood samples of colorectal cancer (CRC) cases and matched controls (n = 93) in the DACHS+ study. The MRscore was significantly elevated in tumor tissues compared to normal tissues of all cancers except prostate cancer, for which an opposite pattern was observed. DNAmPhenoAge was consistently higher in all tumor tissues. The MRscore discriminated lung, colorectal, and prostate tumor tissues from normal tissues with very high accuracy [AUCs of 0.87, 0.99 (TCGA) /0.94 (DACHS), and 0.92, respectively]. DNAmPhenoAge accurately discriminated five types of tumor tissues from normal tissues (except prostate cancer), with AUCs of 0.82–0.93. The MRscore was also significantly higher in blood samples of CRC cases than in controls, with areas under the curve (AUC) of 0.74, whereas DNAmPhenoAge did not distinguish cases from controls, with AUC of 0.54. This study provides compelling evidence that blood‐derived DNAm markers could reflect methylation changes in less accessible tissues. Further research should explore the potential use of these findings for cancer diagnosis and early detection.
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Affiliation(s)
- Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facilities, Microarray Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schick
- Genomics and Proteomics Core Facilities, Microarray Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology, German Cancer Research Center, Heidelberg, Germany.,Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Esther Herpel
- Department of General Pathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,NCT Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
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19
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Zeng WJ, Yang YL, Wen ZP, Chen P, Chen XP, Gong ZC. Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas. PeerJ 2020; 8:e9262. [PMID: 32547876 PMCID: PMC7275683 DOI: 10.7717/peerj.9262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 05/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background Lower-grade gliomas (LGGs) is characteristic with great difference in prognosis. Due to limited prognostic biomarkers, it is urgent to identify more molecular markers to provide a more objective and accurate tumor classification system for LGGs. Methods In the current study, we performed an integrated analysis of gene expression data and genome-wide methylation data to determine novel prognostic genes and methylation sites in LGGs. Results To determine genes that differentially expressed between 44 short-term survivors (<2 years) and 48 long-term survivors (≥2 years), we searched LGGs TCGA RNA-seq dataset and identified 106 differentially expressed genes. SERPINA5 and TIMP1 were selected for further study. Kaplan-Meier plots showed that SERPINA5 and TIMP1 expression were significantly correlated with overall survival (OS) and relapse-free survival (RFS) in TCGA LGGs patients. We next validated the correlation between the candidate genes expression and clinical outcome in CGGA LGGs patients. Multivariate analysis showed that TIMP1 mRNA expression had a significant prognostic value independent of other variables (HR = 4.825, 95% CI = 1.370-17.000, P = 0.014). Then, differential methylation sites were identified from differentially candidate gene expression groups, and all four methylation sites were significantly negatively correlated with gene expression (spearman r < - 0.5, P < 0.0001). Moreover, hyper-methylation of four methylation sites indicated better OS (P < 0.05), and three of them also shown statistical significantly association with better RFS, except for SERPINA5 cg15509705 (P = 0.0762). Conclusion Taken together, these findings indicated that the gene expression and methylation of SERPINA5 and TIMP1 may serve as prognostic predictors in LGGs and may help to precise the current histology-based tumors classification system and to provide better stratification for future clinical trials.
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Affiliation(s)
- Wen-Jing Zeng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan, China.,Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders (XIANGYA), Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yong-Long Yang
- Department of Clinical Pharmacology Research Center, Changsha Carnation Geriatrics Hospital, Changsha, Hunan, China
| | - Zhi-Peng Wen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan, China
| | - Peng Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan, China
| | - Xiao-Ping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan, China
| | - Zhi-Cheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders (XIANGYA), Xiangya Hospital, Central South University, Changsha, Hunan, China
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20
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Emerson MA, Reeder-Hayes KE, Tipaldos HJ, Bell ME, Sweeney MR, Carey LA, Earp HS, Olshan AF, Troester MA. Integrating biology and access to care in addressing breast cancer disparities: 25 years' research experience in the Carolina Breast Cancer Study. CURRENT BREAST CANCER REPORTS 2020; 12:149-160. [PMID: 33815665 DOI: 10.1007/s12609-020-00365-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Purpose of Review To review research on breast cancer mortality disparities, emphasizing research conducted in the Carolina Breast Cancer Study, with a focus on challenges and opportunities for integration of tumor biology and access characteristics across the cancer care continuum. Recent Findings Black women experience higher mortality following breast cancer diagnosis, despite lower incidence compared to white women. Biological factors, such as stage at diagnosis and breast cancer subtypes, play a role in these disparities. Simultaneously, social, behavioral, environmental, and access to care factors are important. However, integrated studies of biology and access are challenging and it is uncommon to have both data types available in the same study population. The central emphasis of Phase 3 of the Carolina Breast Cancer Study, initiated in 2008, was to collect rich data on biology (including germline and tumor genomics and pathology) and health care access in a diverse study population, with the long term goal of defining intervention opportunities to reduce disparities across the cancer care continuum. Summary Early and ongoing research from CBCS has identified important interactions between biology and access, leading to opportunities to build greater equity. However, sample size, population-specific relationships among variables, and complexities of treatment paths along the care continuum pose important research challenges. Interdisciplinary teams, including experts in novel data integration and causal inference, are needed to address gaps in our understanding of breast cancer disparities.
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Affiliation(s)
- Marc A Emerson
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine E Reeder-Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heather J Tipaldos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mary E Bell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marina R Sweeney
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC, USA
| | - Lisa A Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - H Shelton Earp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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21
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van Schie EH, van Amerongen R. Aberrant WNT/CTNNB1 Signaling as a Therapeutic Target in Human Breast Cancer: Weighing the Evidence. Front Cell Dev Biol 2020; 8:25. [PMID: 32083079 PMCID: PMC7005411 DOI: 10.3389/fcell.2020.00025] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/14/2020] [Indexed: 12/22/2022] Open
Abstract
WNT signaling is crucial for tissue morphogenesis during development in all multicellular animals. After birth, WNT/CTNNB1 responsive stem cells are responsible for tissue homeostasis in various organs and hyperactive WNT/CTNNB1 signaling is observed in many different human cancers. The first link between WNT signaling and breast cancer was established almost 40 years ago, when Wnt1 was identified as a proto-oncogene capable of driving mammary tumor formation in mice. Since that discovery, there has been a dedicated search for aberrant WNT signaling in human breast cancer. However, much debate and controversy persist regarding the importance of WNT signaling for the initiation, progression or maintenance of different breast cancer subtypes. As the first drugs designed to block functional WNT signaling have entered clinical trials, many questions about the role of aberrant WNT signaling in human breast cancer remain. Here, we discuss three major research gaps in this area. First, we still lack a basic understanding of the function of WNT signaling in normal human breast development and physiology. Second, the overall extent and precise effect of (epi)genetic changes affecting the WNT pathway in different breast cancer subtypes are still unknown. Which underlying molecular and cell biological mechanisms are disrupted as a result also awaits further scrutiny. Third, we survey the current status of targeted therapeutics that are aimed at interfering with the WNT pathway in breast cancer patients and highlight the importance and complexity of selecting the subset of patients that may benefit from treatment.
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Affiliation(s)
| | - Renée van Amerongen
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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22
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Chen XQ, Zhang F, Su QC, Zeng C, Xiao FH, Peng Y. Methylome and transcriptome analyses reveal insights into the epigenetic basis for the good survival of hypomethylated ER-positive breast cancer subtype. Clin Epigenetics 2020; 12:16. [PMID: 31959227 PMCID: PMC6971951 DOI: 10.1186/s13148-020-0811-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 01/08/2020] [Indexed: 12/31/2022] Open
Abstract
Background Breast cancer (BRCA) is a heterogeneous disease, characterized by different histopathological and clinical features and responses to various therapeutic measures. Despite the research progress of DNA methylation in classification and diagnosis of BRCA and the close relationship between DNA methylation and hormone receptor status, especially estrogen receptor (ER), the epigenetic mechanisms in various BRCA subtypes and the biomarkers associated with diagnostic characteristics of patients under specific hormone receptor status remain elusive. Results In this study, we collected and analyzed methylation data from 785 invasive BRCA and 98 normal breast tissue samples from The Cancer Genome Atlas (TCGA) database. Consensus classification analysis revealed that ER-positive BRCA samples were constitutive of two distinct methylation subgroups; with the hypomethylated subgroup showing good survival probability. This finding was further supported by another cohort of ER-positive BRCA containing 30 subjects. Additionally, we identified 977 hypomethylated CpG loci showing significant associations with good survival probability in ER-positive BRCA. Genes with these loci were enriched in cancer-related pathways (e.g., Wnt signaling pathway). Among them, the upregulated 47 genes were also in line with good survival probability of ER-positive BRCA, while they showed significantly negative correlations between their expression and methylation level of certain hypomethylated loci. Functional assay in numerous literatures provided further evidences supporting that some of the loci have close links with the modulation of tumor-suppressive mechanisms via regulation gene transcription (e.g., SFRP1 and WIF1). Conclusions Our study identified a hypomethylated ER-positive BRCA subtype. Notably, this subgroup presented the best survival probability compared with the hypermethylated ER-positive and hypomethylated ER-negative BRCA subtypes. Specifically, we found that certain upregulated genes (e.g., SFRP1 and WIF1) have great potential to suppress the progression of ER-positive BRCA, concurrently exist negative correlations between their expression and methylation of corresponding hypomethylated CpG loci. Therefore, our study indicates that different epigenetic mechanisms likely exist in ER-positive BRCA and provides novel clinical biomarkers specific to ER-positive BRCA diagnosis and therapy.
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Affiliation(s)
- Xiao-Qiong Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Fan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Qi-Chen Su
- State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chi Zeng
- State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Yu Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering of China, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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23
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Qi L, Zhou B, Chen J, Hu W, Bai R, Ye C, Weng X, Zheng S. Significant prognostic values of differentially expressed-aberrantly methylated hub genes in breast cancer. J Cancer 2019; 10:6618-6634. [PMID: 31777591 PMCID: PMC6856906 DOI: 10.7150/jca.33433] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/31/2019] [Indexed: 12/24/2022] Open
Abstract
Introduction: Abnormal status of gene expression plays an important role in tumorigenesis, progression and metastasis of breast cancer. Mechanisms of gene silence or activation were varied. Methylation of genes may contribute to alteration of gene expression. This study aimed to identify differentially expressed hub genes which may be regulated by DNA methylation and evaluate their prognostic value in breast cancer by bioinformatic analysis. Methods: GEO2R was used to obtain expression microarray data from GSE54002, GSE65194 and methylation microarray data from GSE20713, GSE32393. Differentially expressed-aberrantly methylated genes were identified by FunRich. Biological function and pathway enrichment analysis were conducted by DAVID. PPI network was constructed by STRING and hub genes was sorted by Cytoscape. Expression and DNA methylation of hub genes was validated by UALCAN and MethHC. Clinical outcome analysis of hub genes was performed by Kaplan Meier-plotter database for breast cancer. IHC was performed to analyze protein levels of EXO1 and Kaplan-Meier was used for survival analysis. Results: 677 upregulated-hypomethylated and 361 downregulated-hypermethylated genes were obtained from GSE54002, GSE65194, GSE20713 and GSE32393 by GEO2R and FunRich. The most significant biological process, cellular component, molecular function enriched and pathway for upregulated-hypomethylated genes were viral process, cytoplasm, protein binding and cell cycle respectively. For downregulated-hypermethylated genes, the result was peptidyl-tyrosine phosphorylation, plasma membrane, transmembrane receptor protein tyrosine kinase activity and Rap1 signaling pathway (All p< 0.05). 12 hub genes (TOP2A, MAD2L1, FEN1, EPRS, EXO1, MCM4, PTTG1, RRM2, PSMD14, CDKN3, H2AFZ, CCNE2) were sorted from 677 upregulated-hypomethylated genes. 4 hub genes (EGFR, FGF2, BCL2, PIK3R1) were sorted from 361 downregulated-hypermethylated genes. Differential expression of 16 hub genes was validated in UALCAN database (p<0.05). 7 in 12 upregulated-hypomethylated and 2 in 4 downregulated-hypermethylated hub genes were confirmed to be significantly hypomethylated or hypermethylated in breast cancer using MethHC database (p<0.05). Finally, 12 upregulated hub genes (TOP2A, MAD2L1, FEN1, EPRS, EXO1, MCM4, PTTG1, RRM2, PSMD14, CDKN3, H2AFZ, CCNE2) and 3 downregulated genes (FGF2, BCL2, PIK3R1) contributed to significant unfavorable clinical outcome in breast cancer (p<0.05). High expression level of EXO1 protein was significantly associated with poor OS in breast cancer patients (p=0.03). Conclusion: Overexpression of TOP2A, MAD2L1, FEN1, EPRS, EXO1, MCM4, PTTG1, RRM2, PSMD14, CDKN3, H2AFZ, CCNE2 and downregulation of FGF2, BCL2, PIK3R1 might serve as diagnosis and poor prognosis biomarkers in breast cancer by more research validation. EXO1 was identified as an individual unfavorable prognostic factor. Methylation might be one of the major causes leading to abnormal expression of those genes. Functional analysis and pathway enrichment analysis of those genes would provide novel ideas for breast cancer research.
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Affiliation(s)
- Lina Qi
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Biting Zhou
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Jiani Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Rui Bai
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Chenyang Ye
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Xingyue Weng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
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Higashijima Y, Kanki Y. Molecular mechanistic insights: The emerging role of SOXF transcription factors in tumorigenesis and development. Semin Cancer Biol 2019; 67:39-48. [PMID: 31536760 DOI: 10.1016/j.semcancer.2019.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/31/2019] [Accepted: 09/15/2019] [Indexed: 01/22/2023]
Abstract
Over the last decade, the development and progress of next-generation sequencers incorporated with classical biochemical analyses have drastically produced novel insights into transcription factors, including Sry-like high-mobility group box (SOX) factors. In addition to their primary functions in binding to and activating specific downstream genes, transcription factors also participate in the dedifferentiation or direct reprogramming of somatic cells to undifferentiated cells or specific lineage cells. Since the discovery of SOX factors, members of the SOXF (SOX7, SOX17, and SOX18) family have been identified to play broad roles, especially with regard to cardiovascular development. More recently, SOXF factors have been recognized as crucial players in determining the cell fate and in the regulation of cancer cells. Here, we provide an overview of research on the mechanism by which SOXF factors regulate development and cancer, and discuss their potential as new targets for cancer drugs while offering insight into novel mechanistic transcriptional regulation during cell lineage commitment.
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Affiliation(s)
- Yoshiki Higashijima
- Department of Bioinformational Pharmacology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan.
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25
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McKillop IH, Girardi CA, Thompson KJ. Role of fatty acid binding proteins (FABPs) in cancer development and progression. Cell Signal 2019; 62:109336. [PMID: 31170472 DOI: 10.1016/j.cellsig.2019.06.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/31/2019] [Accepted: 06/01/2019] [Indexed: 01/06/2023]
Abstract
Fatty acid binding proteins (FABPs) are small, water soluble proteins that bind long chain fatty acids and other biologically active ligands to facilitate intracellular localization. Twelve FABP family members have been identified to date, with 10 isoforms expressed in humans. Functionally, FABPs are important in fatty acid metabolism and transport, with distinct family members having the capacity to influence gene transcription. Expression of FABPs is usually cell/tissue specific to one predominant FABP family member. Dysregulation of FABP expression can occur through genetic mutation and/or environmental-lifestyle influences. In addition to intracellular function, exogenous, circulating FABP expression can occur and is associated with specific disease states such as insulin resistance. A role for FABPs is increasingly being reported in tumor biology with elevated exogenous FABP expression being associated with tumor progression and invasiveness. However, a less clear role has been appreciated for dysregulated FABP expression during cell transformation and early expansion.
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Affiliation(s)
- Iain H McKillop
- Department of Surgery, Carolinas Medical Center, Atrium Health, Charlotte, NC 28203, USA
| | - Cara A Girardi
- Department of Surgery, Carolinas Medical Center, Atrium Health, Charlotte, NC 28203, USA
| | - Kyle J Thompson
- Department of Surgery, Carolinas Medical Center, Atrium Health, Charlotte, NC 28203, USA.
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Brinkman AB, Nik-Zainal S, Simmer F, Rodríguez-González FG, Smid M, Alexandrov LB, Butler A, Martin S, Davies H, Glodzik D, Zou X, Ramakrishna M, Staaf J, Ringnér M, Sieuwerts A, Ferrari A, Morganella S, Fleischer T, Kristensen V, Gut M, van de Vijver MJ, Børresen-Dale AL, Richardson AL, Thomas G, Gut IG, Martens JWM, Foekens JA, Stratton MR, Stunnenberg HG. Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation. Nat Commun 2019; 10:1749. [PMID: 30988298 PMCID: PMC6465362 DOI: 10.1038/s41467-019-09828-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. We comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of DNA methylation variation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). Repression effects on tumor suppressor genes are negligible as they are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin and may represent tissue-specific silent regions which tolerate instability at the epigenetic, transcriptomic and genetic level.
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Affiliation(s)
- Arie B Brinkman
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, PO Box 9101, Nijmegen, 6500 HB, The Netherlands.
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Femke Simmer
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
- Department of Pathology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - F Germán Rodríguez-González
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Marcel Smid
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Ludmil B Alexandrov
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Adam Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Dominik Glodzik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, SE-223 81, Sweden
| | - Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, SE-223 81, Sweden
| | - Anieta Sieuwerts
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Anthony Ferrari
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
| | - Sandro Morganella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310, Norway
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316, Norway
- Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, 1478, Norway
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, 08028, Spain
| | - Marc J van de Vijver
- Department of Pathology, Academic Medical Center, Meibergdreef 9, Amsterdam, AZ 1105, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316, Norway
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gilles Thomas
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, 08028, Spain
| | - John W M Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - John A Foekens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | | | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, PO Box 9101, Nijmegen, 6500 HB, The Netherlands.
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Yari K, Rahimi Z. Promoter Methylation Status of the Retinoic Acid Receptor-Beta 2 Gene in Breast Cancer Patients: A Case Control Study and Systematic Review. Breast Care (Basel) 2019; 14:117-123. [PMID: 31798384 DOI: 10.1159/000489874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background We aimed to determine the promoter methylation status of the retinoic acid receptor-beta 2 (RARβ2) gene among breast cancer patients and to review relevant studies in this field in various populations. Methods We analyzed 400 samples which comprised blood specimens from 102 breast cancer patients, 102 first-degree female relatives of patients, 100 cancer-free females, 48 breast cancer tissues, and 48 adjacent normal breast tissues from the same patients. The RARβ2 methylation status was determined using methylation-specific polymerase chain reaction (MSP) and DNA sequencing methods. Results The presence of combined partially methylated (MU) and fully methylated (MM) forms of the RARβ2 gene (MU+MM) in the blood of patients was associated with susceptibility to breast cancer (odds ratio = 4.7, p = 0.05). A significantly higher frequency of the MM genotype was observed in cancer tissue (10.4%) compared to matched adjacent normal breast tissue (0%) (p = 0.02). Conclusion We found a higher frequency of RARβ2 gene methylation in the blood and cancer tissues of patients compared to the blood of controls and adjacent normal breast tissues. The survey of studies on various populations demonstrated a higher RARβ2 methylation frequency in breast cancer patients compared to normal individuals, and many reports suggest a significant association between hypermethylation of the gene and susceptibility to breast cancer.
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Affiliation(s)
| | - Zohreh Rahimi
- Medical Biology Research Center.,Department of Clinical Biochemistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Lu JJ, Yuan Z. Application of DNA methylation in early diagnosis and treatment of pancreatic cancer. Shijie Huaren Xiaohua Zazhi 2019; 27:13-19. [DOI: 10.11569/wcjd.v27.i1.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PC) is one of the most malignant gastrointestinal tumors, characterized by a poor prognosis. Most of the patients have an advanced disease at the time of diagnosis and lose the opportunity of radical surgery, resulting in a 5-year survival rate of less than 5%. Circulating tumor DNA, whose concentration in plasma of patients with pancreatic adenocarcinoma is higher than that in health controls, carries specific gene mutation and aberrant DNA methylation. Epigenetic change is one of the important characteristics of cell carcinogenesis. DNA methylation is an early event in tumorigenesis, which is more helpful for early diagnosis than gene mutation and can be observed in each stage of PC. Therefore, the detection of aberrant DNA methylation in the promoter region in patients with PC may be a non-invasive method for early cancer detection, predicting prognosis, and monitoring recurrence. In the present review, we discuss the recent advances in the study of DNA methylation in the early diagnosis of PC, and the potential application value in the treatment of PC.
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Affiliation(s)
- Jia-Jun Lu
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Zhou Yuan
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
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Epigenetic Silencing of THY1 Tracks the Acquisition of the Notch1–EGFR Signaling in a Xenograft Model of CD44+/CD24low/CD90+ Myoepithelial Cells. Mol Cancer Res 2018; 17:628-641. [DOI: 10.1158/1541-7786.mcr-17-0324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/13/2017] [Accepted: 09/13/2018] [Indexed: 11/16/2022]
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30
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Williams KE, Jawale RM, Schneider SS, Otis CN, Pentecost BT, Arcaro KF. DNA methylation in breast cancers: Differences based on estrogen receptor status and recurrence. J Cell Biochem 2018; 120:738-755. [DOI: 10.1002/jcb.27431] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/12/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Kristin E. Williams
- Department of Molecular and Cellular Biology University of Massachusetts –Amherst Amherst Massachusetts
| | - Rahul M. Jawale
- Department of Pathology Baystate Medical Center Springfield Massachusetts
| | - Sallie S. Schneider
- Biospecimen Resource and Molecular Analysis Facility Baystate Medical Center Springfield Massachusetts
| | | | - Brian T. Pentecost
- Division of Translational Medicine Wadsworth Center, New York State Department of Health Albany New York
| | - Kathleen F. Arcaro
- Department of Veterinary and Animal Sciences University of Massachusetts – Amherst Amherst Massachusetts
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31
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Segaert P, Lopes MB, Casimiro S, Vinga S, Rousseeuw PJ. Robust identification of target genes and outliers in triple-negative breast cancer data. Stat Methods Med Res 2018; 28:3042-3056. [PMID: 30146936 PMCID: PMC6745616 DOI: 10.1177/0962280218794722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Correct classification of breast cancer subtypes is of high importance as it directly affects the therapeutic options. We focus on triple-negative breast cancer which has the worst prognosis among breast cancer types. Using cutting edge methods from the field of robust statistics, we analyze Breast Invasive Carcinoma transcriptomic data publicly available from The Cancer Genome Atlas data portal. Our analysis identifies statistical outliers that may correspond to misdiagnosed patients. Furthermore, it is illustrated that classical statistical methods may fail to identify outliers due to their heavy influence, prompting the need for robust statistics. Using robust sparse logistic regression we obtain 36 relevant genes, of which ca. 60% have been previously reported as biologically relevant to triple-negative breast cancer, reinforcing the validity of the method. The remaining 14 genes identified are new potential biomarkers for triple-negative breast cancer. Out of these, JAM3, SFT2D2, and PAPSS1 were previously associated to breast tumors or other types of cancer. The relevance of these genes is confirmed by the new DetectDeviatingCells outlier detection technique. A comparison of gene networks on the selected genes showed significant differences between triple-negative breast cancer and non-triple-negative breast cancer data. The individual role of FOXA1 in triple-negative breast cancer and non-triple-negative breast cancer, and the strong FOXA1-AGR2 connection in triple-negative breast cancer stand out. The goal of our paper is to contribute to the breast cancer/triple-negative breast cancer understanding and management. At the same time it demonstrates that robust regression and outlier detection constitute key strategies to cope with high-dimensional clinical data such as omics data.
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Affiliation(s)
| | - Marta B Lopes
- IDMEC, Instituto de Engenharia Mecânica, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Sandra Casimiro
- Luís Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Susana Vinga
- IDMEC, Instituto de Engenharia Mecânica, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,INESC-ID, Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento, Lisboa, Portugal
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32
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Abdallah MOE, Algizouli UK, Suliman MA, Abdulrahman RA, Koko M, Fessahaye G, Shakir JH, Fahal AH, Elhassan AM, Ibrahim ME, Mohamed HS. EBV Associated Breast Cancer Whole Methylome Analysis Reveals Viral and Developmental Enriched Pathways. Front Oncol 2018; 8:316. [PMID: 30151354 PMCID: PMC6099083 DOI: 10.3389/fonc.2018.00316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/24/2018] [Indexed: 01/18/2023] Open
Abstract
Background: Breast cancer (BC) ranks among the most common cancers in Sudan and worldwide with hefty toll on female health and human resources. Recent studies have uncovered a common BC signature characterized by low frequency of oncogenic mutations and high frequency of epigenetic silencing of major BC tumor suppressor genes. Therefore, we conducted a pilot genome-wide methylome study to characterize aberrant DNA methylation in breast cancer. Results: Differential methylation analysis between primary tumor samples and normal samples from healthy adjacent tissues yielded 20,188 differentially methylated positions (DMPs), which is further divided into 13,633 hypermethylated sites corresponding to 5339 genes and 6,555 hypomethylated sites corresponding to 2811 genes. Moreover, bioinformatics analysis revealed epigenetic dysregulation of major developmental pathways including hippo signaling pathway. We also uncovered many clues to a possible role for EBV infection in BC. Conclusion: Our results clearly show the utility of epigenetic assays in interrogating breast cancer tumorigenesis, and pinpointing specific developmental and viral pathways dysregulation that might serve as potential biomarkers or targets for therapeutic interventions.
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Affiliation(s)
- Mohammad O E Abdallah
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Ubai K Algizouli
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Maram A Suliman
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Rawya A Abdulrahman
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Mahmoud Koko
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Ghimja Fessahaye
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Jamal H Shakir
- Department of Surgery, Khartoum Teaching Hospital, Khartoum, Sudan
| | - Ahmed H Fahal
- Department of Surgery, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Ahmed M Elhassan
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Muntaser E Ibrahim
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan
| | - Hiba S Mohamed
- Department of Molecular Biology, Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan.,Department of Biology, Taibah University, Medina, Saudi Arabia
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Karpinski P, Patai AV, Hap W, Kielan W, Laczmanska I, Sasiadek MM. Multilevel omic data clustering reveals variable contribution of methylator phenotype to integrative cancer subtypes. Epigenomics 2018; 10:1289-1299. [PMID: 29896967 DOI: 10.2217/epi-2018-0057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM We aimed to assess to what extent CpG island methylator phenotype (CIMP) contributes to cancer subtypes obtained by multilevel omic data analysis. MATERIALS & METHODS 16 The Cancer Genome Atlas datasets encompassing three data layers in 4688 tumor samples were analyzed. We identified cancer integrative subtypes (ISs) by the use of similarity network fusion and consensus clustering. CIMP high (CIMP-H) associated ISs were profiled by gene sets and transcriptional regulators enrichment analysis. RESULTS & CONCLUSION In nine out of 16 cancer datasets CIMP-H clusters significantly overlaped with unique ISs. The contribution of CIMP-H on integrative molecular profiling is variable; therefore, only in a subset of cancer types does CIMP-H contribute to homogenous integrative subtype. CIMP-H associated ISs are heterogenous groups with regard to deregulated pathways and transcriptional regulators.
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Affiliation(s)
- Pawel Karpinski
- Department of Genetics; Wroclaw Medical University, Wroclaw, Poland
| | - Arpad V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Wojciech Hap
- 2nd Department of General & Oncological Surgery, Wroclaw Medical University, Wroclaw, Poland
| | - Wojciech Kielan
- 2nd Department of General & Oncological Surgery, Wroclaw Medical University, Wroclaw, Poland
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Zhang S, Wang Y, Gu Y, Zhu J, Ci C, Guo Z, Chen C, Wei Y, Lv W, Liu H, Zhang D, Zhang Y. Specific breast cancer prognosis-subtype distinctions based on DNA methylation patterns. Mol Oncol 2018; 12:1047-1060. [PMID: 29675884 PMCID: PMC6026876 DOI: 10.1002/1878-0261.12309] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/22/2018] [Accepted: 03/29/2018] [Indexed: 01/02/2023] Open
Abstract
Tumour heterogeneity is an obstacle to effective breast cancer diagnosis and therapy. DNA methylation is an important regulator of gene expression, thus characterizing tumour heterogeneity by epigenetic features can be clinically informative. In this study, we explored specific prognosis-subtypes based on DNA methylation status using 669 breast cancers from the TCGA database. Nine subgroups were distinguished by consensus clustering using 3869 CpGs that significantly influenced survival. The specific DNA methylation patterns were reflected by different races, ages, tumour stages, receptor status, histological types, metastasis status and prognosis. Compared with the PAM50 subtypes, which use gene expression clustering, DNA methylation subtypes were more elaborate and classified the Basal-like subtype into two different prognosis-subgroups. Additionally, 1252 CpGs (corresponding to 888 genes) were identified as specific hyper/hypomethylation sites for each specific subgroup. Finally, a prognosis model based on Bayesian network classification was constructed and used to classify the test set into DNA methylation subgroups, which corresponded to the classification results of the train set. These specific classifications by DNA methylation can explain the heterogeneity of previous molecular subgroups in breast cancer and will help in the development of personalized treatments for the new specific subtypes.
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Affiliation(s)
- Shumei Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yihan Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yue Gu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Jiang Zhu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Ce Ci
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Zhongfu Guo
- Department of General SurgeryThe Second Affiliated Hospital of Harbin Medical UniversityChina
| | - Chuangeng Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yanjun Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Wenhua Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Hongbo Liu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Dongwei Zhang
- Department of General SurgeryThe Second Affiliated Hospital of Harbin Medical UniversityChina
| | - Yan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
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Safo SE, Ahn J, Jeon Y, Jung S. Sparse generalized eigenvalue problem with application to canonical correlation analysis for integrative analysis of methylation and gene expression data. Biometrics 2018; 74:1362-1371. [DOI: 10.1111/biom.12886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 03/01/2018] [Accepted: 03/01/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Sandra E. Safo
- Division of BiostatisticsUniversity of MinnesotaMinneapolisMinnesotaU.S.A
| | - Jeongyoun Ahn
- Department of StatisticsUniversity of GeorgiaAthensGeorgiaU.S.A
| | - Yongho Jeon
- Department of Applied StatisticsYonsei UniversitySeoulSouth Korea
| | - Sungkyu Jung
- Department of StatisticsUniversity of PittsburghPittsburghPennsylvaniaU.S.A
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Homeobox A11 hypermethylation indicates unfavorable prognosis in breast cancer. Oncotarget 2018; 8:9794-9805. [PMID: 28038461 PMCID: PMC5354771 DOI: 10.18632/oncotarget.14216] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 12/05/2016] [Indexed: 01/17/2023] Open
Abstract
Homeobox A11 (HOXA11) is one of the hypermethylated genes in breast cancer and its function in breast tumorigenesis remains elusive. In this study, we analyzed the methylation status of HOXA11 in 264 paired breast cancer and normal tissue as well as in matched serum samples by MethyLight assay. Further, the function of HOXA11 in breast tumorigenesis was analyzed by cell proliferation and migration assays. We found that HOXA11 was hypermethylated in cancer tissues (45.08%), especially in invasive ductal carcinomas (P<0.001), patients with a family history of cancer (P=0.033), cases with metastatic lymph nodes (P=0.004) and P53 positive group (P=0.017). Kaplan-Meier survival analysis and Cox regression analysis revealed that HOXA11 hypermethylation is an independent predictor of poor outcomes. The over expression of HOXA11 suppressed cell growth in MDA-MB-231, MCF7, SKBR3 and BT474 cells. In conclusion, the hypermethylation of HOXA11 is an independent prognostic biomarker in breast cancer. Additionally, HOXA11 can be a potential tumor suppressor.
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Dumitrescu RG. Interplay Between Genetic and Epigenetic Changes in Breast Cancer Subtypes. Methods Mol Biol 2018; 1856:19-34. [PMID: 30178244 DOI: 10.1007/978-1-4939-8751-1_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Breast cancer is the most common cancer among women and represents one of the top five leading causes of cancer-related mortality. Inherited and acquired genetic mutations as well as epigenetic aberrations are known to be important contributors to the development and progression of breast cancer. Recent developments in high-throughput technologies have increased our understanding of the molecular changes in breast cancer, leading to the identification of distinctive genetic and epigenetic modifications in different breast cancer molecular subtypes. These genetic and epigenetic changes in luminal A, luminal B, ERBB2/HER2-enriched, basal-like, and normal-like breast cancer subtypes are discussed in this chapter. Furthermore, recent epigenome studies provided more information about further stratification of breast cancer subtypes, with essential role in the appropriate diagnosis and treatment of breast cancer. Thus, the inclusion of both genetic and epigenetic information in breast cancer clinical care could provide critical scientific base for precision medicine in breast cancer.
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Expression, function, and regulation of the embryonic transcription factor TBX1 in parathyroid tumors. J Transl Med 2017; 97:1488-1499. [PMID: 28920943 DOI: 10.1038/labinvest.2017.88] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 07/16/2017] [Accepted: 07/19/2017] [Indexed: 01/11/2023] Open
Abstract
Transcription factors active in embryonic parathyroid cells can be maintained in adult parathyroids and be involved in tumorigenesis. TBX1, the candidate gene of 22q11.2-DiGeorge syndrome, which includes congenital hypoparathyroidism, is involved in parathyroid embryogenesis. The study aimed to investigate expression, function, and regulation of the parathyroid embryonic transcription factor TBX1 in human parathyroid adult normal and tumor tissues. TBX1 transcripts were detected in normal parathyroids and were deregulated in parathyroid tumors. Using immunohistochemistry, TBX1 protein was detected, mainly at the nuclear level, in a consistent proportion of cells in normal adult parathyroids, whereas TBX1 immunoreactivity was absent in fetal parathyroids. TBX1-expressing cells were markedly reduced in about a half of adenomas (PAds) and two-thirds of carcinomas and the proportion of TBX1-expressing cells negatively correlated with the serum albumin-corrected calcium levels in the analyzed tumors. Moreover, a subset of TBX1-expressing tumor cells coexpressed PTH. TBX1 silencing in HEK293 cells, expressing endogenous TBX1, increased the proportion of cells in the G0/G1 phase of cell cycle; concomitantly, CDKN1A/p21 and CDKN2A/p16 transcripts increased and ID1 mRNA levels decreased. TBX1 silencing exerted similar effects in PAd-derived cells, suggesting cell cycle arrest. Moreover, in PAd-derived cells GCM2 and PTH mRNA levels were unaffected by TBX1 deficiency, whereas it was associated with reduction of WNT5A, an antagonist of canonical WNT/β-catenin pathway. WNT/β-catenin activation by lithium chloride inhibited TBX1 expression levels both in HEK293 and PAd-derived cells. In conclusion, TBX1 is expressed in adult parathyroid cells and deregulated in parathyroid tumors, where TBX1 deficiency may potentially contribute to the low proliferative nature of parathyroid tumors.
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Reply to Joshua A. Linscott, Angela B. Smith, and Jesse D. Sammon's Letter to the Editor re: Woonyoung Choi, Andrea Ochoa, David J. McConkey, et al. Genetic Alterations in the Molecular Subtypes of Bladder Cancer: Illustration in the Cancer Genome Atlas Dataset. Eur Urol 2017;72:354-65. Eur Urol 2017; 73:e104-e105. [PMID: 29174465 DOI: 10.1016/j.eururo.2017.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 11/07/2017] [Indexed: 11/22/2022]
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40
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Deb S, Gorringe KL, Pang JMB, Byrne DJ, Takano EA, Dobrovic A, Fox SB. BRCA2 carriers with male breast cancer show elevated tumour methylation. BMC Cancer 2017; 17:641. [PMID: 28893223 PMCID: PMC5594583 DOI: 10.1186/s12885-017-3632-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/28/2017] [Indexed: 12/19/2022] Open
Abstract
Background Male breast cancer (MBC) represents a poorly characterised group of tumours, the management of which is largely based on practices established for female breast cancer. However, recent studies demonstrate biological and molecular differences likely to impact on tumour behaviour and therefore patient outcome. The aim of this study was to investigate methylation of a panel of commonly methylated breast cancer genes in familial MBCs. Methods 60 tumours from 3 BRCA1 and 25 BRCA2 male mutation carriers and 32 males from BRCAX families were assessed for promoter methylation by methylation-sensitive high resolution melting in a panel of 10 genes (RASSF1A, TWIST1, APC, WIF1, MAL, RARβ, CDH1, RUNX3, FOXC1 and GSTP1). An average methylation index (AMI) was calculated for each case comprising the average of the methylation of the 10 genes tested as an indicator of overall tumour promoter region methylation. Promoter hypermethylation and AMI were correlated with BRCA carrier mutation status and clinicopathological parameters including tumour stage, grade, histological subtype and disease specific survival. Results Tumours arising in BRCA2 mutation carriers showed significantly higher methylation of candidate genes, than those arising in non-BRCA2 familial MBCs (average AMI 23.6 vs 16.6, p = 0.01, 45% of genes hypermethylated vs 34%, p < 0.01). RARβ methylation and AMI-high status were significantly associated with tumour size (p = 0.01 and p = 0.02 respectively), RUNX3 methylation with invasive carcinoma of no special type (94% vs 69%, p = 0.046) and RASSF1A methylation with coexistence of high grade ductal carcinoma in situ (33% vs 6%, p = 0.02). Cluster analysis showed MBCs arising in BRCA2 mutation carriers were characterised by RASSF1A, WIF1, RARβ and GTSP1 methylation (p = 0.02) whereas methylation in BRCAX tumours showed no clear clustering to particular genes. TWIST1 methylation (p = 0.001) and AMI (p = 0.01) were prognostic for disease specific survival. Conclusions Increased methylation defines a subset of familial MBC and with AMI may be a useful prognostic marker. Methylation might be predictive of response to novel therapeutics that are currently under investigation in other cancer types. Electronic supplementary material The online version of this article (10.1186/s12885-017-3632-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siddhartha Deb
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Vic, Parkville, 3010, Australia
| | - Kylie L Gorringe
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Vic, Parkville, 3010, Australia.,Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Department of Pathology, University of Melbourne, Parkville, VIC, 3012, Australia
| | - Jia-Min B Pang
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - David J Byrne
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Elena A Takano
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
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- Kathleen Cuningham Foundation Consortium for research into Familial Breast Cancer, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Alexander Dobrovic
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Department of Pathology, University of Melbourne, Parkville, VIC, 3012, Australia.,Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3084, Australia
| | - Stephen B Fox
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Vic, Parkville, 3010, Australia. .,Department of Pathology, University of Melbourne, Parkville, VIC, 3012, Australia. .,School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3084, Australia.
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Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya, North East India reveals novel genes. Genomics 2017; 110:112-123. [PMID: 28890207 DOI: 10.1016/j.ygeno.2017.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/22/2022]
Abstract
Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.
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42
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Wang H, Yan W, Zhang S, Gu Y, Wang Y, Wei Y, Liu H, Wang F, Wu Q, Zhang Y. Survival differences of CIMP subtypes integrated with CNA information in human breast cancer. Oncotarget 2017; 8:48807-48819. [PMID: 28415743 PMCID: PMC5564726 DOI: 10.18632/oncotarget.16178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022] Open
Abstract
CpG island methylator phenotype of breast cancer is associated with widespread aberrant methylation at specified CpG islands and distinct patient outcomes. However, the influence of copy number contributing to the prognosis of tumors with different CpG island methylator phenotypes is still unclear. We analyzed both genetic (copy number) and epigenetic alterations in 765 breast cancers from The Cancer Genome Atlas data portal and got a panel of 15 biomarkers for copy number and methylation status evaluation. The gene panel identified two groups corresponding to distinct copy number profiles. In status of mere-loss copy number, patients were faced with a greater risk if they presented a higher CpG islands methylation pattern in biomarker panels. But for samples presenting merely-gained copy number, higher methylation level of CpG islands was associated with improved viability. In all, the integration of copy number alteration and methylation information enhanced the classification power on prognosis. Moreover, we found the molecular subtypes of breast cancer presented different distributions in two CpG island methylation phenotypes. Generated by the same set of human methylation 450K data, additional copy number information could provide insights into survival prediction of cancers with less heterogeneity and might help to determine the biomarkers for diagnosis and treatment for breast cancer patients in a more personalized approach.
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Affiliation(s)
- Huihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Weili Yan
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, China
| | - Shumei Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yue Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Fang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
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43
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Luo X, Xiong X, Shao Q, Xiang T, Li L, Yin X, Li X, Tao Q, Ren G. The tumor suppressor interferon regulatory factor 8 inhibits β-catenin signaling in breast cancers, but is frequently silenced by promoter methylation. Oncotarget 2017; 8:48875-48888. [PMID: 28388578 PMCID: PMC5564732 DOI: 10.18632/oncotarget.16511] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/13/2017] [Indexed: 12/21/2022] Open
Abstract
Interferon (IFN) regulatory factor 8 is encoded by a novel candidate tumor suppressor gene (IRF8), its promotor is frequently methylated in multiple cancers. However, the promoter methylation status, functions and underlying mechanisms of IRF8 in breast cancer remain unclear. We found that IRF8 was downregulated in breast cancer cell lines and primary tumors, compared with normal breast tissues, mainly because of aberrant promoter methylation. However, its expression was not associated with pathological characteristics. Restoration of IRF8 expression suppressed cell proliferation, colony formation, 5-ethynyl-2'-deoxyuridine incorporation, cell migration and invasion, and induced apoptosis and cell cycle arrest in vitro. IRF8 also inhibited xenograft growth in nude mice in vivo. Competition with IRF8 function by IRF8 mutant (K79E) enhanced cell migration and invasion in 4T1 murine cells in vitro. Importantly, IRF8, as both downstream target gene and regulator of IFN-γ/STAT1 signaling, inhibited canonical β-catenin signaling. These findings identify IRF8 as a novel tumor suppressor regulating IFN-γ/STAT1 signaling and β-catenin signaling in breast cancer.
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Affiliation(s)
- Xinrong Luo
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Xiong
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing Shao
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tingxiu Xiang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shine Institute of Health Sciences, The Chinese University of Hong Kong and CUHK Shenzhen Research Institute, Shatin, Hong Kong
| | - Xuedong Yin
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xia Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qian Tao
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shine Institute of Health Sciences, The Chinese University of Hong Kong and CUHK Shenzhen Research Institute, Shatin, Hong Kong
| | - Guosheng Ren
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Sheng X, Guo Y, Lu Y. Prognostic role of methylated GSTP1, p16, ESR1 and PITX2 in patients with breast cancer: A systematic meta-analysis under the guideline of PRISMA. Medicine (Baltimore) 2017; 96:e7476. [PMID: 28700487 PMCID: PMC5515759 DOI: 10.1097/md.0000000000007476] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/12/2017] [Accepted: 06/19/2017] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND BRCA1 and RASSF1A promoter methylation has been reported to be correlated with a worse survival in patients with breast cancer. However, the prognostic values of GSTP1, p16, ESR1, and PITX2 promoter methylation in breast cancer remain to be determined. Here, we performed this study to evaluate the prognostic significance of GSTP1, p16, ESR1, and PITX2 promoter methylation in breast cancer. METHODS A range of online databases was systematically searched to identify available studies based on the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guideline. The pooled hazard ratios (HRs) with their 95% confidence intervals (95% CIs) were applied to estimate the prognostic effect of GSTP1, p16, ESR1, and PITX2 promoter methylation in breast cancer for multivariate regression analysis. RESULTS 13 eligible articles involving 3915 patients with breast cancer were analyzed in this meta-analysis. In a large patient population, GSTP1 showed a trend toward a worse prognosis in overall survival (OS) (HR = 1.64, 95% CI = 0.93-2.87, P = .085). PITX2 promoter methylation was significantly correlated with a worse prognosis in OS (HR = 1.57, 95% CI = 1.15-2.14, P = .004), but no association between p16 promoter methylation and OS (HR = 0.92, 95% CI = 0.31-2.71, P = .884). PITX2 promoter methylation was significantly correlated with an unfavorable prognosis of patients with breast cancer in metastasis-free survival (MFS) (HR = 1.73, 95% CI = 1.33-2.26, P < .001). The result from 3 studies with 227 cases showed that ESR1 promoter methylation was linked to a worse prognosis in OS (HR = 1.55, 95% CI = 1.06-2.28, P = .025). CONCLUSIONS Our findings suggest ESR1 and PITX2 promoter methylation may be correlated with a worse survival of patients with breast cancer (ESR1: OS, PITX2: OS and MFS). The clinical utility of aberrantly methylated ESR1 and PITX2 could be a promising factor for the prognosis of breast cancer.
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Affiliation(s)
- Xianneng Sheng
- Department of Thyroid and Breast Surgery, Ningbo First Hospital
| | - Yu Guo
- Department of Thyroid and Breast Surgery, Ningbo First Hospital
| | - Yang Lu
- Medical School of Ningbo University, Ningbo, Zhejiang, China
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45
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Crujeiras AB, Diaz-Lagares A, Stefansson OA, Macias-Gonzalez M, Sandoval J, Cueva J, Lopez-Lopez R, Moran S, Jonasson JG, Tryggvadottir L, Olafsdottir E, Tinahones FJ, Carreira MC, Casanueva FF, Esteller M. Obesity and menopause modify the epigenomic profile of breast cancer. Endocr Relat Cancer 2017; 24:351-363. [PMID: 28442560 DOI: 10.1530/erc-16-0565] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
Abstract
Obesity is a high risk factor for breast cancer. This relationship could be marked by a specific methylome. The current work was aimed to explore the impact of obesity and menopausal status on variation in breast cancer methylomes. Data from Infinium 450K array-based methylomes of 64 breast tumors were coupled with information on BMI and menopausal status. Additionally, DNA methylation results were validated in 18 non-tumor and 81 tumor breast samples. Breast tumors arising in either pre- or postmenopausal women stratified by BMI or menopausal status alone were not associated with a specific DNA methylation pattern. Intriguingly, the DNA methylation pattern identified in association with the high-risk group (postmenopausal women with high BMI (>25) and premenopausal women with normal or low BMI < 25) exclusively characterized by hypermethylation of 1287 CpG sites as compared with the low-risk group. These CpG sites included the promoter region of fourteen protein-coding genes of which CpG methylation over the ZNF577 promoter region represents the top scoring associated event. In an independent cohort, the ZNF577 promoter methylation remained statistically significant in association with the high-risk group. Additionally, the impact of ZNF577 promoter methylation on mRNA expression levels was demonstrated in breast cancer cell lines after treatment with a demethylating agent (5-azacytidine). In conclusion, the epigenome of breast tumors is affected by a complex interaction between BMI and menopausal status. The ZNF577 methylation quantification is clearly relevant for the development of novel biomarkers of precision therapy in breast cancer.
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Affiliation(s)
- Ana B Crujeiras
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Olafur A Stefansson
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Cancer Research LaboratoryFaculty of Medicine, University of Iceland, Reykjavic, Iceland
| | - Manuel Macias-Gonzalez
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
- Unidad de Gestión Clínica de Endocrinología y NutriciónInstituto de Investigación Biomédica de Málaga (IBIMA), Complejo Hospitalario de Málaga (Virgen de la Victoria), Universidad de Málaga, Málaga, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Juan Cueva
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Rafael Lopez-Lopez
- Translational Medical Oncology Group (Oncomet)Instituto de Investigación Sanitaria (IDIS); Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and CIBER de Cancer (CIBERONC), Santiago de Compostela, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Jon G Jonasson
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Laufey Tryggvadottir
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Elinborg Olafsdottir
- Department of Pathology and the Icelandic Cancer RegistryIcelandic Cancer society and Landspitali University Hospital, Reykjavik, Iceland
| | - Francisco J Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
- Unidad de Gestión Clínica de Endocrinología y NutriciónInstituto de Investigación Biomédica de Málaga (IBIMA), Complejo Hospitalario de Málaga (Virgen de la Victoria), Universidad de Málaga, Málaga, Spain
| | - Marcos C Carreira
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Felipe F Casanueva
- Laboratory of Molecular and Cellular EndocrinologyInstituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela University (USC), Santiago de Compostela, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn)Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Department of Physiological Sciences IISchool of Medicine, University of Barcelona and Instituto Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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vel Szic KS, Declerck K, Crans RA, Diddens J, Scherf DB, Gerhäuser C, Berghe WV. Epigenetic silencing of triple negative breast cancer hallmarks by Withaferin A. Oncotarget 2017; 8:40434-40453. [PMID: 28467815 PMCID: PMC5522326 DOI: 10.18632/oncotarget.17107] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/30/2017] [Indexed: 11/25/2022] Open
Abstract
Triple negative breast cancer (TNBC) is characterized by poor prognosis and a DNA hypomethylation profile. Withaferin A (WA) is a plant derived steroidal lactone which holds promise as a therapeutic agent for treatment of breast cancer (BC). We determined genome-wide DNA methylation changes in weakly-metastatic and aggressive, metastatic BC cell lines, following 72h treatment to a sub-cytotoxic concentration of WA. In contrast to the DNA demethylating agent 5-aza-2'-deoxycytidine (DAC), WA treatment of MDA-MB-231 cells rather tackles an epigenetic cancer network through gene-specific DNA hypermethylation of tumor promoting genes including ADAM metallopeptidase domain 8 (ADAM8), urokinase-type plasminogen activator (PLAU), tumor necrosis factor (ligand) superfamily, member 12 (TNFSF12), and genes related to detoxification (glutathione S-transferase mu 1, GSTM1), or mitochondrial metabolism (malic enzyme 3, ME3). Gene expression and pathway enrichment analysis further reveals epigenetic suppression of multiple cancer hallmarks associated with cell cycle regulation, cell death, cancer cell metabolism, cell motility and metastasis. Remarkably, DNA hypermethylation of corresponding CpG sites in PLAU, ADAM8, TNSF12, GSTM1 and ME3 genes correlates with receptor tyrosine-protein kinase erbB-2 amplification (HER2)/estrogen receptor (ESR)/progesterone receptor (PR) status in primary BC tumors. Moreover, upon comparing differentially methylated WA responsive target genes with DNA methylation changes in different clinical subtypes of breast cancer patients in the cancer genome atlas (TCGA), we found that WA silences HER2/PR/ESR-dependent gene expression programs to suppress aggressive TNBC characteristics in favor of luminal BC hallmarks, with an improved therapeutic sensitivity. In this respect, WA may represent a novel and attractive phyto-pharmaceutical for TNBC treatment.
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Affiliation(s)
- Katarzyna Szarc vel Szic
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Current address: Division of Hematology, Oncology and Stem Cell Transplantation, Center for Translational Cell Research, The University Medical Center Freiburg, Freiburg, Germany
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - René A.J Crans
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Current address: Laboratory for GPCR Expression and Signal Transduction (L-GEST), Department of Biochemistry and Microbiology, University of Ghent, Ghent, Belgium
| | - Jolien Diddens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - David B. Scherf
- Workgroup Cancer Chemoprevention and Epigenomics, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clarissa Gerhäuser
- Workgroup Cancer Chemoprevention and Epigenomics, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Lin X, Chen W, Wei F, Zhou BP, Hung MC, Xie X. POMC maintains tumor-initiating properties of tumor tissue-derived long-term-cultured breast cancer stem cells. Int J Cancer 2017; 140:2517-2525. [PMID: 28214331 DOI: 10.1002/ijc.30658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/11/2017] [Accepted: 02/13/2017] [Indexed: 12/22/2022]
Abstract
The identification and understanding of the molecular network of cancer stem cells (CSCs) have had a profound impact on our view of carcinogenesis and treatment strategy. Unfortunately, a major problem is that serial passages of CSCs from clinical solid tumor specimens currently are not available in any lab, and thus, reported data are difficult to confirm and intensively interrogated. Here, we have generated two tumor tissue-derived breast CSC (BCSC) lines that showed prolonged maintenance over 20 serial passages in vitro, while retaining their tumor-initiating biological properties. We then deciphered the intrinsic mechanism using analyses of mRNA expression array profiles. It has been determined that pro-opiomelanocortin (POMC) is closely related with protein phosphorylation mediated by G-protein-coupled estrogen receptor (GPER) in BCSC. Following, knockdown of POMC inhibits properties of mammosphere formation, CD44+ CD24- population, CD44 expression, and clonogenicity ability in BCSC. We found that inhibition of POMC attenuates phosphorylation of AKT2 and GSK3β in BCSC. Further in vivo investigations demonstrated that POMC interference regulates proliferation of BCSC-bearing tumors. Combination of the clinical results that POMC positive expression is frequently upregulated in human breast cancer and POMC positivity correlated with a poor prognosis, POMC is a potential therapeutic target for BCSC. In conclusion, we have successfully established two long-term-cultured BCSC from clinical specimens. We further indicated that POMC acts as a potential therapeutic target and prognostic marker for future treatment of BCSC.
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Affiliation(s)
- Xiaoti Lin
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China.,Department of Oncology, The Affiliated Xiang'an Hospital of Xiamen University, Medical College of Xiamen University, Xiamen, Fujian, 361003, China.,Department of Surgery, Fujian Provincial Tumor Hospital, Fuzhou, 350014, China
| | - Weiyu Chen
- Department of Physiology, Zhongshan medical school, Sun Yat-sen University, Guangzhou, 510060, China
| | - Fengqin Wei
- Department of Oncology, The Affiliated Xiang'an Hospital of Xiamen University, Medical College of Xiamen University, Xiamen, Fujian, 361003, China.,Department of Emergency, Fujian Provincial 2nd People's Hospital, Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350000, China
| | - Binhua P Zhou
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China.,Department of Molecular and Cellular Biochemistry, Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xiaoming Xie
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
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48
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Breast tumor DNA methylation patterns associated with smoking in the Carolina Breast Cancer Study. Breast Cancer Res Treat 2017; 163:349-361. [PMID: 28275920 DOI: 10.1007/s10549-017-4178-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/26/2017] [Indexed: 12/17/2022]
Abstract
PURPOSE Tobacco smoking is a risk factor in several cancers, yet its roles as a putative etiologic exposure or poor prognostic factor in breast cancer are less clear. Altered DNA methylation contributes to breast cancer development and may provide a mechanistic link between smoking and gene expression changes leading to cancer development or progression. METHODS Using a cancer-focused array, we examined methylation at 933 CpGs in 517 invasive breast tumors in the Carolina Breast Cancer Study to determine whether methylation patterns differ by exposure to tobacco smoke. Multivariable generalized linear regression models were used to compare tumor methylation profiles between smokers and never smokers, overall, or stratified on hormone receptor (HR) status. RESULTS Modest differences in CpG methylation were detected at p < 0.05 in breast tumors from current or ever smokers compared with never smokers. In stratified analyses, HR- tumors from smokers exhibited primarily hypomethylation compared with tumors from never smokers; hypomethylation was similarly detected within the more homogeneous basal-like subtype. Most current smoking-associated CpG loci exhibited methylation levels in former smokers that were intermediate between those in current and never smokers and exhibited progressive changes in methylation with increasing duration of smoking. Among former smokers, restoration of methylation toward baseline (never smoking) levels was observed with increasing time since quitting. Moreover, smoking-related hypermethylation was stronger in HR+ breast tumors from blacks than in whites. CONCLUSIONS Our results suggest that breast tumor methylation patterns differ with tobacco smoke exposure; however, additional studies are needed to confirm these findings.
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Zhou X, Guan T, Li S, Jiao Z, Lu X, Huang X, Ji Y, Ji Q. The association between HDAC9 gene polymorphisms and stroke risk in the Chinese population: A meta-analysis. Sci Rep 2017; 7:41538. [PMID: 28145521 PMCID: PMC5286403 DOI: 10.1038/srep41538] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023] Open
Abstract
Several recent genome-wide association studies (GWASs) have suggested that the histone deacetylase 9 (HDAC9) gene is associated with stroke, but the reliability of these findings remains controversial, particularly for the data derived from different ethnicities and geographical locations. Therefore, we performed a meta-analysis to explore the associations between HDAC9 polymorphisms and the risk of stroke in the Chinese population. All eligible case-control studies that met the search criteria were retrieved from multiple databases, and six case-control studies with a total of 2,356 stroke patients and 3,420 healthy controls were included. The pooled odds ratios (ORs) with 95% confidence intervals (95% CIs) were calculated to assess the strengths of the associations of 3 HDAC9 gene polymorphisms with stroke risk. Our results revealed statistically significant associations of the rs2107595 (T/C) polymorphism with an increased risk of stroke in the allele, codominant and dominant models. Additionally, the rs2389995 (G/A) polymorphism was found to be significantly associated with a decreased risk of stroke in all genetic models. In conclusion, this meta-analysis suggested that the T allele of rs2107595 in HDAC9 increases the risk of stroke but that the G allele of rs2389995 decreases the risk of stroke in the Chinese population.
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Affiliation(s)
- Xin Zhou
- Institute of Immunology, College of Life Science and Technology, Jinan University, Guangdong 510630, China
| | - Tangming Guan
- Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Shuyuan Li
- Institute of Immunology, College of Life Science and Technology, Jinan University, Guangdong 510630, China
| | - Zinan Jiao
- Institute of Immunology, College of Life Science and Technology, Jinan University, Guangdong 510630, China
| | - Xiaoshuang Lu
- Institute of Immunology, College of Life Science and Technology, Jinan University, Guangdong 510630, China
| | - Xiaodi Huang
- Institute of Immunology, College of Life Science and Technology, Jinan University, Guangdong 510630, China
| | - Yuhua Ji
- Institute of Immunology, College of Life Science and Technology, Jinan University, Guangdong 510630, China
| | - Qiuhong Ji
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong 226002, China
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Chae H, Lee S, Nephew KP, Kim S. Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. BMC SYSTEMS BIOLOGY 2016; 10:116. [PMID: 28155687 PMCID: PMC5259919 DOI: 10.1186/s12918-016-0356-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Aberrant epigenetic modifications, including DNA methylation, are key regulators of gene activity in tumorigenesis. Breast cancer is a heterogeneous disease, and large-scale analyses indicate that tumor from normal and benign tissues, as well as molecular subtypes of breast cancer, can be distinguished based on their distinct genomic, transcriptomic, and epigenomic profiles. In this study, we used affinity-based methylation sequencing data in 30 breast cancer cell lines representing functionally distinct cancer subtypes to investigate methylation and mutation patterns at the whole genome level. Results Our analysis revealed significant differences in CpG island (CpGI) shore methylation and mutation patterns among breast cancer subtypes. In particular, the basal-like B type, a highly aggressive form of the disease, displayed distinct CpGI shore hypomethylation patterns that were significantly associated with downstream gene regulation. We determined that mutation rates at CpG sites were highly correlated with DNA methylation status and observed distinct mutation rates among the breast cancer subtypes. These findings were validated by using targeted bisulfite sequencing of differentially expressed genes (n=85) among the cell lines. Conclusions Our results suggest that alterations in DNA methylation play critical roles in gene regulatory process as well as cytosine substitution rates at CpG sites in molecular subtypes of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0356-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Heejoon Chae
- School of Informatics and Computing, Indiana University Bloomington, IN 47405, USA, Waterloo Road, Bloomington, IN, 47405, USA
| | - Sangseon Lee
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kenneth P Nephew
- Indiana University School of Medicine, Department of Cellular and Integrative Physiology, Medical Sciences Program, Bloomington, USA
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.
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