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Wang Q, Ma C, Mao H, Wang J. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates the ZNF334 gene to inhibit the growth of colorectal cancer. Int J Biol Macromol 2024; 277:134580. [PMID: 39122070 DOI: 10.1016/j.ijbiomac.2024.134580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Although therapeutic targets for colorectal cancer (CRC) treatment have been developed, the treatment outcomes are not ideal and survival rates for CRC patients remain low. It is critical to identify a specific target and develop an effective CRC treatment system. The ZNF334 gene is a newly identified member of Zinc-finger proteins (ZNFs), which is essential for key biological processes associated with tumorigenesis. Abnormal epigenetic reprogramming of the ZNF334 gene promoter region decreases its expression in CRC and further induces the occurrence of CRC. Here, we clarified that P300 in CRC can regulate the H3K9/27 ac in the ZNF334 promoter. Furthermore, histone acetylation of the ZNF334 promoter region was increased by dCas9-P300 to normalize the deficiency of ZNF334 expression, thereby inhibiting the growth of CRC. Collectively, our findings enable a facile way to affect gene expression using CRISPR/Cas9-based epigenome editing and further determine the causal link between histone acetylation and gene activation, providing a promising gene therapy strategy for the CRC treatment.
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Affiliation(s)
- Qin Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China; BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Chen Ma
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Huixian Mao
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jin Wang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China.
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2
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Rajalingam A, Ganjiwale A. Identification of common genetic factors and immune-related pathways associating more than two autoimmune disorders: implications on risk, diagnosis, and treatment. Genomics Inform 2024; 22:10. [PMID: 38956704 PMCID: PMC11221123 DOI: 10.1186/s44342-024-00004-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/22/2023] [Indexed: 07/04/2024] Open
Abstract
Autoimmune disorders (ADs) are chronic conditions resulting from failure or breakdown of immunological tolerance, resulting in the host immune system attacking its cells or tissues. Recent studies report shared effects, mechanisms, and evolutionary origins among ADs; however, the possible factors connecting them are unknown. This study attempts to identify gene signatures commonly shared between different autoimmune disorders and elucidate their molecular pathways linking the pathogenesis of these ADs using an integrated gene expression approach. We employed differential gene expression analysis across 19 datasets of whole blood/peripheral blood cell samples with five different autoimmune disorders (rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, Crohn's disease, and type 1 diabetes) to get nine key genes-EGR1, RUNX3, SMAD7, NAMPT, S100A9, S100A8, CYBB, GATA2, and MCEMP1 that were primarily involved in cell and leukocyte activation, leukocyte mediated immunity, IL-17, AGE-RAGE signaling in diabetic complications, prion disease, and NOD-like receptor signaling confirming its role in immune-related pathways. Combined with biological interpretations such as gene ontology (GO), pathway enrichment, and protein-protein interaction (PPI) network, our current study sheds light on the in-depth research on early detection, diagnosis, and prognosis of different ADs.
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Affiliation(s)
- Aruna Rajalingam
- Department of Life Science, Bangalore University, Bangalore, Karnataka, 560056, India
| | - Anjali Ganjiwale
- Department of Life Science, Bangalore University, Bangalore, Karnataka, 560056, India.
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3
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Yang B, Tang H, Wang N, Gu J, Wang Q. Targeted DNA demethylation of the ZNF334 promoter inhibits colorectal cancer growth. Cell Death Dis 2023; 14:210. [PMID: 36966142 PMCID: PMC10039945 DOI: 10.1038/s41419-023-05743-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/27/2023]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. Aberrant regulation of DNA methylation in promoters of tumor suppressor genes or proto-oncogenes is one of the fundamental processes driving the initiation and progression of CRC. Zinc-finger proteins (ZNFs) are one of the most abundant groups of proteins and function in many important biological processes related to tumorigenesis. Herein, we detected abnormal hypermethylation of the ZNF334 gene in CRC tissues compared with normal tissues, and this modification downregulated the expression of ZNF334. Furthermore, ten-eleven translocation 1 (TET1) was identified to be involved in regulating the methylation level of ZNF334. Next, a dCas9-multiGCN4/scFv-TET1CD-sgZNF334-targeted demethylation system was constructed to reverse the expression of ZNF334 through sgRNA targeting the ZNF334 promoter. Both in vitro and in vivo experiments demonstrated the targeted demethylation system upregulated ZNF334 expression and inhibited CRC growth. Collectively, targeted DNA demethylation of the ZNF334 promoter sheds light on the precise treatment of CRC.
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Affiliation(s)
- Bin Yang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Haiyu Tang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Nan Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Jian Gu
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Qin Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China.
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China.
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4
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Cheng Z, Yu R, Li L, Mu J, Gong Y, Wu F, Liu Y, Zhou X, Zeng X, Wu Y, Sun R, Xiang T. Disruption of ZNF334 promotes triple-negative breast carcinoma malignancy through the SFRP1/ Wnt/β-catenin signaling axis. Cell Mol Life Sci 2022; 79:280. [PMID: 35507080 PMCID: PMC11072843 DOI: 10.1007/s00018-022-04295-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/20/2022] [Accepted: 04/06/2022] [Indexed: 11/03/2022]
Abstract
Zinc-finger proteins (ZNFs) constitute the largest transcription factor family in the human genome. The family functions in many important biological processes involved in tumorigenesis. In our research, we identified ZNF334 as a novel tumor suppressor of triple-negative breast cancer (TNBC). ZNF334 expression was usually reduced in breast cancerv (BrCa) tissues and TNBC cell lines MDA-MB-231 (MB231) and YCCB1. We observed that promoter hypermethylation of ZNF334 was common in BrCa cell lines and tissues, which was likely responsible for its reduced expression. Ectopic expression of ZNF334 in TNBC cell lines MB231 and YCCB1 could suppress their growth and metastatic capacity both in vitro and in vivo, and as well induce cell cycle arrest at S phase and cell apoptosis. Moreover, re-expression of ZNF334 in TNBC cell lines could rescue Epithelial-Mesenchymal Transition (EMT) process and restrain stemness, due to up-regulation of SFRP1, which is an antagonist of Wnt/β-catenin signaling. In conclusion, we verified that ZNF334 had a suppressive function of TNBC cell lines by targeting the SFRP1/Wnt/β-catenin signaling axis, which might have the potentials to become a new biomarker for diagnosis and treatment of TNBC patients.
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Affiliation(s)
- Zhaobo Cheng
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Renjie Yu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Junhao Mu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yijia Gong
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fan Wu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yujia Liu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiangyi Zhou
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaohua Zeng
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yongzhong Wu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Ran Sun
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Tingxiu Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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5
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De Loma J, Gliga AR, Levi M, Ascui F, Gardon J, Tirado N, Broberg K. Arsenic Exposure and Cancer-Related Proteins in Urine of Indigenous Bolivian Women. Front Public Health 2020; 8:605123. [PMID: 33381488 PMCID: PMC7767847 DOI: 10.3389/fpubh.2020.605123] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022] Open
Abstract
Indigenous people living in the Bolivian Andes are exposed through their drinking water to inorganic arsenic, a potent carcinogen. However, the health consequences of arsenic exposure in this region are unknown. The aim of this study was to evaluate associations between arsenic exposure and changes in cancer-related proteins in indigenous women (n = 176) from communities around the Andean Lake Poopó, Bolivia. Arsenic exposure was assessed in whole blood (B-As) and urine (as the sum of arsenic metabolites, U-As) by inductively coupled plasma-mass spectrometry (ICP-MS). Cancer-related proteins (N = 92) were measured in urine using the proximity extension assay. The median B-As concentration was 2.1 (range 0.60-9.1) ng/g, and U-As concentration was 67 (12-399) μg/L. Using linear regression models adjusted for age, urinary osmolality, and urinary leukocytes, we identified associations between B-As and four putative cancer-related proteins: FASLG, SEZ6L, LYPD3, and TFPI2. Increasing B-As concentrations were associated with lower protein expression of SEZ6L, LYPD3, and TFPI2, and with higher expression of FASLG in urine (no association was statistically significant after correcting for multiple comparisons). The associations were similar across groups with different arsenic metabolism efficiency, a susceptibility factor for arsenic toxicity. In conclusion, arsenic exposure in this region was associated with changes in the expression of some cancer-related proteins in urine. Future research is warranted to understand if these proteins could serve as valid biomarkers for arsenic-related toxicity.
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Affiliation(s)
- Jessica De Loma
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anda R Gliga
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael Levi
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Franz Ascui
- Programa de Salud Familiar Comunitaria e Intercultural, Ministerio de Salud Bolivia, La Paz, Bolivia
| | - Jacques Gardon
- Hydrosciences Montpellier, Université de Montpellier, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Montpellier, France
| | - Noemi Tirado
- Genetics Institute, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Karin Broberg
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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6
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Ding W, Feng G, Hu Y, Chen G, Shi T. Co-occurrence and Mutual Exclusivity Analysis of DNA Methylation Reveals Distinct Subtypes in Multiple Cancers. Front Cell Dev Biol 2020; 8:20. [PMID: 32064261 PMCID: PMC7000380 DOI: 10.3389/fcell.2020.00020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Co-occurrence and mutual exclusivity (COME) of DNA methylation refer to two or more genes that tend to be positively or negatively correlated in DNA methylation among different samples. Although COME of gene mutations in pan-cancer have been well explored, little is known about the COME of DNA methylation in pan-cancer. Here, we systematically explored the COME of DNA methylation profile in diverse human cancer. A total of 5,128,332 COME events were identified in 14 main cancers types in The Cancer Genome Atlas (TCGA). We also identified functional epigenetic modules of the zinc finger gene family in six cancer types by integrating the gene expression and DNA methylation data and the frequently occurred COME network. Interestingly, most of the genes in those functional epigenetic modules are epigenetically repressed. Strikingly, those frequently occurred COME events could be used to classify the patients into several subtypes with significant different clinical outcomes in six cancers as well as pan-cancer (p-value ≤ = 0.05). Moreover, we observed significant associations between different COME subtypes and clinical features (e.g., age, gender, histological type, neoplasm histologic grade, and pathologic stage) in distinct cancers. Taken together, we identified millions of COME events of DNA methylation in pan-cancer and detected functional epigenetic COME events that could separate tumor patients into different subtypes, which may benefit the diagnosis and prognosis of pan-cancer.
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Affiliation(s)
- Wubin Ding
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Guoshuang Feng
- Big Data and Engineering Research Center, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yige Hu
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Big Data and Engineering Research Center, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.,Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, China
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7
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Lorenzo PM, Izquierdo AG, Diaz-Lagares A, Carreira MC, Macias-Gonzalez M, Sandoval J, Cueva J, Lopez-Lopez R, Casanueva FF, Crujeiras AB. ZNF577 Methylation Levels in Leukocytes From Women With Breast Cancer Is Modulated by Adiposity, Menopausal State, and the Mediterranean Diet. Front Endocrinol (Lausanne) 2020; 11:245. [PMID: 32390948 PMCID: PMC7191069 DOI: 10.3389/fendo.2020.00245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022] Open
Abstract
The methylation levels of ZNF577 in breast tumors has been previously identified as a possible epigenetic mark of breast cancer associated with obesity. The aim of the current study was to investigate differences in methylation levels of ZNF577 depending on obesity, menopausal state and dietary pattern in blood leukocytes, a non-invasive sample. The methylation levels of ZNF577 of two CpG sites (CpGs) located in promoter and island previously identified as differentially methylated according to adiposity and menopausal state by 450 k array (cg10635122, cg03562414) were evaluated by pyrosequencing in DNA from the blood leukocytes of breast cancer patients [n = 90; n = 64 (71.1%) overweight/obesity and n = 26 (28.9%) normal-weight] and paired tumor tissue biopsies (n = 8 breast cancer patients with obesity; n = 3/5 premenopausal/postmenopausal women). Differences in methylation levels were evaluated at each CpGs individually and at the mean of the two evaluated CpGs. Adherence to the Mediterranean diet was evaluated using the MEDAS-validated questionnaire, and the consumption of food groups of interest was also evaluated using the recommended intakes of the Sociedad Española de Nutricion Comunitaria. The methylation levels of ZNF577 were correlated between paired leukocytes and breast tumor biopsies (r = 0.62; p = 0.001). Moreover, higher methylation was found in leukocytes from patients with obesity (p = 0.002) and postmenopausal patients (p = 0.022) than patients with normal-weight or premenopausal, respectively. After adjusting for the body mass index and age, higher levels of ZNF577 methylation were also found in women with greater adherence to the Mediterranean diet (p = 0.017) or specific foods. Relevantly, the methylation levels of ZNF577 showed a good ability for fish consumption detection [area under the ROC curve (AUC) = 0.72; p = 0.016]. In conclusion, the association between methylation of ZNF577 and adiposity, menopausal state, and adherence to the Mediterranean diet can be detected in the blood leukocytes. The results guarantee the need of performing further studies in longer longitudinal cohorts in order to elucidate the role of ZNF577 methylation in the association between breast cancer, adiposity and dietary patterns.
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Affiliation(s)
- Paula M. Lorenzo
- Laboratory of Epigenomics in Endocrinology and Nutrition (EpiEndoNut), Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Andrea G. Izquierdo
- Laboratory of Epigenomics in Endocrinology and Nutrition (EpiEndoNut), Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenetics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- CIBER de Oncologia (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos C. Carreira
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
- Laboratory of Molecular and Cellular Endocrinology, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - Manuel Macias-Gonzalez
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA) and CIBEROBN, Málaga, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit and Epigenomics Core Facility, Health Research Institute La Fe, Valencia, Spain
| | - Juan Cueva
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rafael Lopez-Lopez
- CIBER de Oncologia (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Felipe F. Casanueva
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
- Laboratory of Molecular and Cellular Endocrinology, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - Ana B. Crujeiras
- Laboratory of Epigenomics in Endocrinology and Nutrition (EpiEndoNut), Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Ana B. Crujeiras
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Jiao L, Song J, Ding L, Liu T, Wu T, Zhang J, Bai H, Chen H, Zhao Z, Ying B. A Novel Genetic Variation in NCF2, the Core Component of NADPH Oxidase, Contributes to the Susceptibility of Tuberculosis in Western Chinese Han Population. DNA Cell Biol 2019; 39:57-62. [PMID: 31794672 DOI: 10.1089/dna.2019.5082] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of the disease tuberculosis (TB). Macrophages eliminate the Mtb, delivering it to the degradative, phagolysosomal compartment for degradation, in which reactive oxygen species generated by nicotinamide adenine dinucleotide phosphate oxidase (NADPHO) plays an important role. In our study, we aimed at investigating the association of polymorphisms in neutrophil cytosolic factor 2 (NCF2) gene, the core component of NADPHO, with susceptibility of TB in the Western Chinese Han population. We conducted a case-control study of 900 cases and 1534 controls and genotyped four single-nucleotide polymorphisms within the NCF2 gene. We found that the rs10911362 variants were associated with a decreased TB risk in this population (odds ratio [ORG] = 0.83 [0.72-0.95], ORadd = 0.83 [0.72-0.95], ORdom = 0.78 [0.66-0.93], p < 0.05). rs10911362 might fall in a transcriptional factor binding site associated with ZNF410 and may be the expression quantitative trait loci (eQTL) for the SMG7 gene according to the Ensembl data. Our study demonstrated for the first time that the G allele of NCF2 rs10911362 provided a protective role against TB risk in the Western Chinese Han population.
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Affiliation(s)
- Lin Jiao
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Jiajia Song
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Liu Ding
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Tangyuheng Liu
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Tao Wu
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Jingwei Zhang
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Hao Bai
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Hao Chen
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Binwu Ying
- Department of Laboratory Medicine, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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9
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He Y, de Witte LD, Houtepen LC, Nispeling DM, Xu Z, Yu Q, Yu Y, Hol EM, Kahn RS, Boks MP. DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data. Clin Epigenetics 2019; 11:80. [PMID: 31097004 PMCID: PMC6524251 DOI: 10.1186/s13148-019-0680-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 05/06/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND DNA methylation has recently been identified as a mediator between in utero famine exposure and a range of metabolic and psychiatric traits. However, genome-wide analyses are scarce and cross-sectional analyses are hampered by many potential confounding factors. Moreover, causal relations are hard to identify due to the lack of controlled experimental designs. In the current study, we therefore combined a comprehensive assessment of genome-wide DNA methylation differences in people exposed to the great Chinese famine in utero with an in vitro study in which we deprived fibroblasts of nutrition. METHODS We compared whole blood DNA methylation differences between 25 individuals in utero exposed to famine and 54 healthy control individuals using the HumanMethylation450 platform. In vitro, we analyzed DNA methylation changes in 10 fibroblast cultures that were nutritionally deprived for 72 h by withholding fetal bovine serum. RESULTS We identified three differentially methylated regions (DMRs) in four genes (ENO2, ZNF226, CCDC51, and TMA7) that were related to famine exposure in both analyses. Pathway analysis with data from both Chinese famine samples and fibroblasts highlighted the nervous system and neurogenesis pathways as the most affected by nutritional deprivation. CONCLUSIONS The combination of cross-sectional and experimental data provides indications that biological adaptation to famine leads to DNA methylation changes in genes involved in the central nervous system.
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Affiliation(s)
- Yujie He
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
- Brain Center University Medical Center Utrecht, Department of Translational Neuroscience, Utrecht University, Utrecht, The Netherlands
| | - Lot D de Witte
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, USA
| | - Lotte C Houtepen
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
| | - Danny M Nispeling
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
| | - Zhida Xu
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Yaqin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Elly M Hol
- Brain Center University Medical Center Utrecht, Department of Translational Neuroscience, Utrecht University, Utrecht, The Netherlands
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, an Institute of the Royal Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - René S Kahn
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, USA
| | - Marco P Boks
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands.
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10
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Merrick BA, Phadke DP, Bostrom MA, Shah RR, Wright GM, Wang X, Gordon O, Pelch KE, Auerbach SS, Paules RS, DeVito MJ, Waalkes MP, Tokar EJ. Arsenite malignantly transforms human prostate epithelial cells in vitro by gene amplification of mutated KRAS. PLoS One 2019; 14:e0215504. [PMID: 31009485 PMCID: PMC6476498 DOI: 10.1371/journal.pone.0215504] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
Inorganic arsenic is an environmental human carcinogen of several organs including the urinary tract. RWPE-1 cells are immortalized, non-tumorigenic, human prostate epithelia that become malignantly transformed into the CAsE-PE line after continuous in vitro exposure to 5μM arsenite over a period of months. For insight into in vitro arsenite transformation, we performed RNA-seq for differential gene expression and targeted sequencing of KRAS. We report >7,000 differentially expressed transcripts in CAsE-PE cells compared to RWPE-1 cells at >2-fold change, q<0.05 by RNA-seq. Notably, KRAS expression was highly elevated in CAsE-PE cells, with pathway analysis supporting increased cell proliferation, cell motility, survival and cancer pathways. Targeted DNA sequencing of KRAS revealed a mutant specific allelic imbalance, ‘MASI’, frequently found in primary clinical tumors. We found high expression of a mutated KRAS transcript carrying oncogenic mutations at codons 12 and 59 and many silent mutations, accompanied by lower expression of a wild-type allele. Parallel cultures of RWPE-1 cells retained a wild-type KRAS genotype. Copy number analysis and sequencing showed amplification of the mutant KRAS allele. KRAS is expressed as two splice variants, KRAS4a and KRAS4b, where variant 4b is more prevalent in normal cells compared to greater levels of variant 4a seen in tumor cells. 454 Roche sequencing measured KRAS variants in each cell type. We found KRAS4a as the predominant transcript variant in CAsE-PE cells compared to KRAS4b, the variant expressed primarily in RWPE-1 cells and in normal prostate, early passage, primary epithelial cells. Overall, gene expression data were consistent with KRAS-driven proliferation pathways found in spontaneous tumors and malignantly transformed cell lines. Arsenite is recognized as an important environmental carcinogen, but it is not a direct mutagen. Further investigations into this in vitro transformation model will focus on genomic events that cause arsenite-mediated mutation and overexpression of KRAS in CAsE-PE cells.
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Affiliation(s)
- B. Alex Merrick
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| | - Dhiral P. Phadke
- Sciome, LLC, Research Triangle Park, North Carolina, United States of America
| | - Meredith A. Bostrom
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States of America
| | - Ruchir R. Shah
- Sciome, LLC, Research Triangle Park, North Carolina, United States of America
| | - Garron M. Wright
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States of America
| | - Xinguo Wang
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States of America
| | - Oksana Gordon
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States of America
| | - Katherine E. Pelch
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Scott S. Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Richard S. Paules
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Michael J. DeVito
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Michael P. Waalkes
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Erik J. Tokar
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
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11
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Abstract
Post-translational modifications of histones are widely used to discriminate between different types of chromatin. In a recent issue of Molecular Cell, Becker et al. (2017) delineate chromatin states based on physical properties, thereby expanding our understanding of chromatin function.
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12
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Deyssenroth MA, Gennings C, Liu SH, Peng S, Hao K, Lambertini L, Jackson BP, Karagas MR, Marsit CJ, Chen J. Intrauterine multi-metal exposure is associated with reduced fetal growth through modulation of the placental gene network. ENVIRONMENT INTERNATIONAL 2018; 120:373-381. [PMID: 30125854 PMCID: PMC6288802 DOI: 10.1016/j.envint.2018.08.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Intrauterine metal exposures and aberrations in placental processes are known contributors to being born small for gestational age (SGA). However, studies to date have largely focused on independent effects, failing to account for potential interdependence among these markers. OBJECTIVES We evaluated the inter-relationship between multi-metal indices and placental gene network modules related to SGA status to highlight potential molecular pathways through which in utero multi-metal exposure impacts fetal growth. METHODS Weighted quantile sum (WQS) regression was performed using a panel of 16 trace metals measured in post-partum maternal toe nails collected from the Rhode Island Child Health Study (RICHS, n = 195), and confirmation of the derived SGA-related multi-metal index was conducted using Bayesian kernel machine regression (BKMR). We leveraged existing placental weighted gene coexpression network data to examine associations between the SGA multi-metal index and placental gene expression. Expression of select genes were assessed using RT-PCR in an independent birth cohort, the New Hampshire Birth Cohort Study (NHBCS, n = 237). RESULTS We identified a multi-metal index, predominated by arsenic (As) and cadmium (Cd), that was positively associated with SGA status (Odds ratio = 2.73 [1.04, 7.18]). This index was also associated with the expression of placental gene modules involved in "gene expression" (β = -0.02 [-0.04, -0.01]) and "metabolic hormone secretion" (β = 0.02 [0.00, 0.05]). We validated the association between cadmium exposure and the expression of GRHL1 and INHBA, genes in the "metabolic hormone secretion" module, in NHBCS. CONCLUSION We present a novel approach that integrates the application of advanced bioinformatics and biostatistics methods to delineate potential placental pathways through which trace metal exposures impact fetal growth.
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Affiliation(s)
- Maya A Deyssenroth
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chris Gennings
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shelley H Liu
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 20019, USA
| | - Shouneng Peng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Luca Lambertini
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian P Jackson
- Department of Earth Sciences, Dartmouth College, Hanover, NH 03755, USA
| | | | - Carmen J Marsit
- Department of Environmental Health, Emory University, Atlanta, GA 30322, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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13
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Pérez RF, Tejedor JR, Bayón GF, Fernández AF, Fraga MF. Distinct chromatin signatures of DNA hypomethylation in aging and cancer. Aging Cell 2018; 17:e12744. [PMID: 29504244 PMCID: PMC5946083 DOI: 10.1111/acel.12744] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2018] [Indexed: 12/21/2022] Open
Abstract
Cancer is an aging‐associated disease, but the underlying molecular links between these processes are still largely unknown. Gene promoters that become hypermethylated in aging and cancer share a common chromatin signature in ES cells. In addition, there is also global DNA hypomethylation in both processes. However, the similarity of the regions where this loss of DNA methylation occurs is currently not well characterized, and it is unknown if such regions also share a common chromatin signature in aging and cancer. To address this issue, we analyzed TCGA DNA methylation data from a total of 2,311 samples, including control and cancer cases from patients with breast, kidney, thyroid, skin, brain, and lung tumors and healthy blood, and integrated the results with histone, chromatin state, and transcription factor binding site data from the NIH Roadmap Epigenomics and ENCODE projects. We identified 98,857 CpG sites differentially methylated in aging and 286,746 in cancer. Hyper‐ and hypomethylated changes in both processes each had a similar genomic distribution across tissues and displayed tissue‐independent alterations. The identified hypermethylated regions in aging and cancer shared a similar bivalent chromatin signature. In contrast, hypomethylated DNA sequences occurred in very different chromatin contexts. DNA hypomethylated sequences were enriched at genomic regions marked with the activating histone posttranslational modification H3K4me1 in aging, while in cancer, loss of DNA methylation was primarily associated with the repressive H3K9me3 mark. Our results suggest that the role of DNA methylation as a molecular link between aging and cancer is more complex than previously thought.
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Affiliation(s)
- Raúl F. Pérez
- Nanomedicine Group; Nanomaterials and Nanotechnology Research Center (CINN-CSIC); Universidad de Oviedo; El Entrego, Asturias Spain
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias (HUCA); Universidad de Oviedo; Oviedo, Asturias Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias (HUCA); Universidad de Oviedo; Oviedo, Asturias Spain
- Cáncer Epigenetics Laboratory; Fundación para la Investigación Biosanitaria de Asturias (FINBA); Instituto de Investigación Sanitaria del Principado de Asturias (ISPA); Oviedo, Asturias Spain
| | - Gustavo F. Bayón
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias (HUCA); Universidad de Oviedo; Oviedo, Asturias Spain
| | - Agustín F. Fernández
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias (HUCA); Universidad de Oviedo; Oviedo, Asturias Spain
- Cáncer Epigenetics Laboratory; Fundación para la Investigación Biosanitaria de Asturias (FINBA); Instituto de Investigación Sanitaria del Principado de Asturias (ISPA); Oviedo, Asturias Spain
| | - Mario F. Fraga
- Nanomedicine Group; Nanomaterials and Nanotechnology Research Center (CINN-CSIC); Universidad de Oviedo; El Entrego, Asturias Spain
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14
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Identification of an episignature of human colorectal cancer associated with obesity by genome-wide DNA methylation analysis. Int J Obes (Lond) 2018; 43:176-188. [PMID: 29717273 DOI: 10.1038/s41366-018-0065-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/17/2018] [Accepted: 02/07/2018] [Indexed: 01/26/2023]
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15
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Minatel BC, Sage AP, Anderson C, Hubaux R, Marshall EA, Lam WL, Martinez VD. Environmental arsenic exposure: From genetic susceptibility to pathogenesis. ENVIRONMENT INTERNATIONAL 2018; 112:183-197. [PMID: 29275244 DOI: 10.1016/j.envint.2017.12.017] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/15/2017] [Accepted: 12/12/2017] [Indexed: 05/21/2023]
Abstract
More than 200 million people in 70 countries are exposed to arsenic through drinking water. Chronic exposure to this metalloid has been associated with the onset of many diseases, including cancer. Epidemiological evidence supports its carcinogenic potential, however, detailed molecular mechanisms remain to be elucidated. Despite the global magnitude of this problem, not all individuals face the same risk. Susceptibility to the toxic effects of arsenic is influenced by alterations in genes involved in arsenic metabolism, as well as biological factors, such as age, gender and nutrition. Moreover, chronic arsenic exposure results in several genotoxic and epigenetic alterations tightly associated with the arsenic biotransformation process, resulting in an increased cancer risk. In this review, we: 1) review the roles of inter-individual DNA-level variations influencing the susceptibility to arsenic-induced carcinogenesis; 2) discuss the contribution of arsenic biotransformation to cancer initiation; 3) provide insights into emerging research areas and the challenges in the field; and 4) compile a resource of publicly available arsenic-related DNA-level variations, transcriptome and methylation data. Understanding the molecular mechanisms of arsenic exposure and its subsequent health effects will support efforts to reduce the worldwide health burden and encourage the development of strategies for managing arsenic-related diseases in the era of personalized medicine.
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Affiliation(s)
- Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Christine Anderson
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Roland Hubaux
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
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16
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van der Ven LT, Jelinek J, Hodemaekers HM, Zwart EP, Ruiter S, van den Brandhof EJ, Issa JPJ, Pennings JL, Luijten M. An Adverse Outcome Pathway Analysis Employing DNA Methylation Effects in Arsenic-Exposed Zebrafish Embryos Supports a Role of Epigenetic Events in Arsenic-Induced Chronic Disease. ACTA ACUST UNITED AC 2017. [DOI: 10.1089/aivt.2017.0018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Leo T.M. van der Ven
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Hennie M. Hodemaekers
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Edwin P. Zwart
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sander Ruiter
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Evert-Jan van den Brandhof
- Center for Environmental Quality, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jean-Pierre J. Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeroen L.A. Pennings
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Mirjam Luijten
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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17
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Zhang J, Wen X, Liu N, Li YQ, Tang XR, Wang YQ, He QM, Yang XJ, Zhang PP, Ma J, Sun Y. Epigenetic mediated zinc finger protein 671 downregulation promotes cell proliferation and tumorigenicity in nasopharyngeal carcinoma by inhibiting cell cycle arrest. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:147. [PMID: 29052525 PMCID: PMC5649082 DOI: 10.1186/s13046-017-0621-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/02/2017] [Indexed: 12/19/2022]
Abstract
Background Epigenetic abnormalities play important roles in nasopharyngeal cancer (NPC), however, the epigenetic changes associated with abnormal cell proliferation remain unclear. Methods We detected epigenetic change of ZNF671 in NPC tissues and cell lines by bisulfite pyrosequencing. We evaluated zinc finger protein 671 (ZNF671) expression in NPC cell lines and clinical tissues using real-time PCR and western blotting. Then, we established NPC cell lines that stably overexpressed ZNF671 and knocked down ZNF671 expression to explore its function in NPC in vitro and in vivo. Additionally, we investigated the potential mechanism of ZNF671 by identifying the mitotic spindle and G2/M checkpoint pathways pathway downstream genes using gene set enrichment analysis, flow cytometry and western blotting. Results ZNF671 was hypermethylated in NPC tissues and cell lines. The mRNA and protein expression of ZNF671 was down-regulated in NPC tissues and cell lines and the mRNA expression could be upregulated after the demethylation agent 5-aza-2′-deoxycytidine treatment. Overexpression of ZNF671 suppressed NPC cell proliferation and colony formation in vitro; silencing ZNF671 using a siRNA had the opposite effects. Additionally, overexpression of ZNF671 reduced the tumorigenicity of NPC cells in xenograft model in vivo. The mechanism study determined that overexpressing ZNF671 induced S phase arrest in NPC cells by upregulating p21 and downregulating cyclin D1 and c-myc. Conclusions Epigenetic mediated zinc finger protein 671 downregulation promotes cell proliferation and enhances tumorigenicity by inhibiting cell cycle arrest in NPC, which may represent a novel potential therapeutic target. Electronic supplementary material The online version of this article (10.1186/s13046-017-0621-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Zhang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Xin Wen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Na Liu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Ying-Qin Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Xin-Ran Tang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Ya-Qin Wang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Qing-Mei He
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Xiao-Jing Yang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Pan-Pan Zhang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China
| | - Jun Ma
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China.
| | - Ying Sun
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China.
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18
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Schlosberg CE, VanderKraats ND, Edwards JR. Modeling complex patterns of differential DNA methylation that associate with gene expression changes. Nucleic Acids Res 2017; 45:5100-5111. [PMID: 28168293 PMCID: PMC5435975 DOI: 10.1093/nar/gkx078] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/26/2017] [Indexed: 12/15/2022] Open
Abstract
Numerous genomic studies are underway to determine which genes are abnormally regulated by DNA methylation in disease. However, we have a poor understanding of how disease-specific methylation changes affect expression. We thus developed an integrative analysis tool, Methylation-based Gene Expression Classification (ME-Class), to explain specific variation in methylation that associates with expression change. This model captures the complexity of methylation changes around a gene promoter. Using 17 whole-genome bisulfite sequencing and RNA-seq datasets from different tissues from the Roadmap Epigenomics Project, ME-Class significantly outperforms standard methods using methylation to predict differential gene expression change. To demonstrate its utility, we used ME-Class to analyze 32 datasets from different hematopoietic cell types from the Blueprint Epigenome project. Expression-associated methylation changes were predominantly found when comparing cells from distantly related lineages, implying that changes in the cell's transcriptional program precede associated methylation changes. Training ME-Class on normal-tumor pairs from The Cancer Genome Atlas indicated that cancer-specific expression-associated methylation changes differ from tissue-specific changes. We further show that ME-Class can detect functionally relevant cancer-specific, expression-associated methylation changes that are reversed upon the removal of methylation. ME-Class is thus a powerful tool to identify genes that are dysregulated by DNA methylation in disease.
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Affiliation(s)
- Christopher E Schlosberg
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Nathan D VanderKraats
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - John R Edwards
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
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19
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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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20
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A Tox21 Approach to Altered Epigenetic Landscapes: Assessing Epigenetic Toxicity Pathways Leading to Altered Gene Expression and Oncogenic Transformation In Vitro. Int J Mol Sci 2017; 18:ijms18061179. [PMID: 28587163 PMCID: PMC5486002 DOI: 10.3390/ijms18061179] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 02/07/2023] Open
Abstract
An emerging vision for toxicity testing in the 21st century foresees in vitro assays assuming the leading role in testing for chemical hazards, including testing for carcinogenicity. Toxicity will be determined by monitoring key steps in functionally validated molecular pathways, using tests designed to reveal chemically-induced perturbations that lead to adverse phenotypic endpoints in cultured human cells. Risk assessments would subsequently be derived from the causal in vitro endpoints and concentration vs. effect data extrapolated to human in vivo concentrations. Much direct experimental evidence now shows that disruption of epigenetic processes by chemicals is a carcinogenic mode of action that leads to altered gene functions playing causal roles in cancer initiation and progression. In assessing chemical safety, it would therefore be advantageous to consider an emerging class of carcinogens, the epigenotoxicants, with the ability to change chromatin and/or DNA marks by direct or indirect effects on the activities of enzymes (writers, erasers/editors, remodelers and readers) that convey the epigenetic information. Evidence is reviewed supporting a strategy for in vitro hazard identification of carcinogens that induce toxicity through disturbance of functional epigenetic pathways in human somatic cells, leading to inactivated tumour suppressor genes and carcinogenesis. In the context of human cell transformation models, these in vitro pathway measurements ensure high biological relevance to the apical endpoint of cancer. Four causal mechanisms participating in pathways to persistent epigenetic gene silencing were considered: covalent histone modification, nucleosome remodeling, non-coding RNA interaction and DNA methylation. Within these four interacting mechanisms, 25 epigenetic toxicity pathway components (SET1, MLL1, KDM5, G9A, SUV39H1, SETDB1, EZH2, JMJD3, CBX7, CBX8, BMI, SUZ12, HP1, MPP8, DNMT1, DNMT3A, DNMT3B, TET1, MeCP2, SETDB2, BAZ2A, UHRF1, CTCF, HOTAIR and ANRIL) were found to have experimental evidence showing that functional perturbations played “driver” roles in human cellular transformation. Measurement of epigenotoxicants presents challenges for short-term carcinogenicity testing, especially in the high-throughput modes emphasized in the Tox21 chemicals testing approach. There is need to develop and validate in vitro tests to detect both, locus-specific, and genome-wide, epigenetic alterations with causal links to oncogenic cellular phenotypes. Some recent examples of cell-based high throughput chemical screening assays are presented that have been applied or have shown potential for application to epigenetic endpoints.
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21
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van den Dungen MW, Murk AJ, Kampman E, Steegenga WT, Kok DE. Association between DNA methylation profiles in leukocytes and serum levels of persistent organic pollutants in Dutch men. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx001. [PMID: 29492303 PMCID: PMC5804541 DOI: 10.1093/eep/dvx001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 01/07/2017] [Accepted: 01/17/2017] [Indexed: 05/18/2023]
Abstract
Consumption of polluted fish may lead to high levels of persistent organic pollutants (POPs) in humans, potentially causing adverse health effects. Altered DNA methylation has been suggested as a possible contributor to a variety of adverse health effects. The aim of this study was to evaluate the relationship between serum POP levels (dioxins, polychlorobiphenyls, and perfluoroctane sulphonate) and DNA methylation. We recruited a total of 80 Dutch men who regularly consumed eel from either low- or high-polluted areas, and subsequently had normal or elevated POP levels. Clinical parameters related to e.g. hormone levels and liver enzymes were measured as biomarkers for adverse health effects. The Infinium 450K BeadChip was used to assess DNA methylation in a representative subset of 34 men. We identified multiple genes with differentially methylated regions (DMRs; false discovery rate <0.05) related to POP levels. Several of these genes are involved in carcinogenesis (e.g. BRCA1, MAGEE2, HOXA5), the immune system (e.g. RNF39, HLA-DQB1), retinol homeostasis (DHRS4L2), or in metabolism (CYP1A1). The DMRs in these genes show mean methylation differences up to 7.4% when comparing low- and high-exposed men, with a mean difference up to 14.4% for single positions within a DMR. Clinical parameters were not significantly associated with serum POP levels. This is the first explorative study investigating extensive DNA methylation in relation to serum POP levels among men. We observed that elevated POP levels are associated with aberrant DNA methylation profiles in adult men who consumed high-polluted eel. These preliminary findings warrant further confirmation in other populations.
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Affiliation(s)
- Myrthe W. van den Dungen
- Division of Human Nutrition, Stippeneng 4, 6708 WE, Wageningen, Wageningen University, The Netherlands
- Marine Animal Ecology Group, De Elst 1, 6708 WD, Wageningen, Wageningen University, The Netherlands
| | - Albertinka J. Murk
- Marine Animal Ecology Group, De Elst 1, 6708 WD, Wageningen, Wageningen University, The Netherlands
| | - Ellen Kampman
- Division of Human Nutrition, Stippeneng 4, 6708 WE, Wageningen, Wageningen University, The Netherlands
| | - Wilma T. Steegenga
- Division of Human Nutrition, Stippeneng 4, 6708 WE, Wageningen, Wageningen University, The Netherlands
| | - Dieuwertje E. Kok
- Division of Human Nutrition, Stippeneng 4, 6708 WE, Wageningen, Wageningen University, The Netherlands
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22
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Yeh CM, Chen PC, Hsieh HY, Jou YC, Lin CT, Tsai MH, Huang WY, Wang YT, Lin RI, Chen SS, Tung CL, Wu SF, Chang DC, Shen CH, Hsu CD, Chan MWY. Methylomics analysis identifies ZNF671 as an epigenetically repressed novel tumor suppressor and a potential non-invasive biomarker for the detection of urothelial carcinoma. Oncotarget 2016; 6:29555-72. [PMID: 26320192 PMCID: PMC4745746 DOI: 10.18632/oncotarget.4986] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/16/2015] [Indexed: 11/25/2022] Open
Abstract
The molecular mechanism underlying the lethal phenomenon of urothelial carcinoma (UC) tumor recurrence remains unresolved. Here, by methylation microarray, we identified promoter methylation of the zinc-finger protein gene, ZNF671 in bladder UC tumor tissue samples, a finding that was independently validated by bisulphite pyrosequencing in cell lines and tissue samples. Subsequent assays including treatment with epigenetic depressive agents and in vitro methylation showed ZNF671 methylation to result in its transcriptional repression. ZNF671 re-expression in UC cell lines, via ectopic expression, inhibited tumor growth and invasion, in possible conjunction with downregulation of cancer stem cell markers (c-KIT, NANOG, OCT4). Clinically, high ZNF671 methylation in UC tumor tissues (n=96; 63 bladder, 33 upper urinary tract) associated with tumor grade and poor locoregional disease-free survival. Quantitative MSP analysis in a training (n=97) and test (n=61) sets of voided urine samples from bladder UC patients revealed a sensitivity and specificity of 42%-48% and 89%-92.8%, respectively, for UC cancer detection. Moreover, combining DNA methylation of ZNF671 and 2 other genes (IRF8 and sFRP1) further increased the sensitivity to 96.2%, suggesting a possible three-gene UC biomarker. In summary, ZNF671, an epigenetically silenced novel tumor suppressor, represents a potential predictor for UC relapse and non-invasive biomarker that could assist in UC clinical decision-making.
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Affiliation(s)
- Chia-Ming Yeh
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Pi-Che Chen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Hsiao-Yen Hsieh
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Yeong-Chin Jou
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Chang-Te Lin
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ming-Hsuan Tsai
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Wen-Yu Huang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Yi-Ting Wang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Ru-Inn Lin
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Departments of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Chia Yi, Taiwan
| | - Szu-Shan Chen
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Chun-Liang Tung
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Shu-Fen Wu
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - D Ching Chang
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Cheng-Da Hsu
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Michael W Y Chan
- Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan
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23
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Cho YJ, Kang W, Kim SH, Sa JK, Kim N, Paddison PJ, Kim M, Joo KM, Hwang YI, Nam DH. Involvement of DDX6 gene in radio- and chemoresistance in glioblastoma. Int J Oncol 2016; 48:1053-62. [PMID: 26783102 DOI: 10.3892/ijo.2016.3328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/06/2015] [Indexed: 11/05/2022] Open
Abstract
CCRT (concomitant chemotherapy and radiation therapy) is often used for glioblastoma multiforme (GBM) treatment after surgical therapy, however, patients treated with CCRT undergo poor prognosis due to development of treatment resistant recurrence. Many studies have been performed to overcome these problems and to discover genes influencing treatment resistance. To discover potential genes inducing CCRT resistance in GBM, we used whole genome screening by infecting shRNA pool in patient-derived cell. The cells infected ~8,000 shRNAs were implanted in mouse brain and treated RT/TMZ as in CCRT treated patients. We found DDX6 as the candidate gene for treatment resistance after screening and establishing DDX6 knock down cells for functional validation. Using these cells, we confirmed tumor associated ability of DDX6 in vitro and in vivo. Although proliferation improvement was not found, decreased DDX6 influenced upregulated clonogenic ability and resistant response against radiation treatment in vivo and in vitro. Taken together, we suggest that DDX6 discovered by using whole genome screening was responsible for radio- and chemoresistance in GBM.
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Affiliation(s)
- Yu Jin Cho
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wonyoung Kang
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sung Heon Kim
- Department of Anatomy and Cell Biology, Sungkyunkwan University of Medicine, Suwon, Seoul, Republic of Korea
| | - Jason K Sa
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Nayoung Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Patrick J Paddison
- Department of Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Misuk Kim
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea
| | - Kyeung Min Joo
- Department of Anatomy and Cell Biology, Sungkyunkwan University of Medicine, Suwon, Seoul, Republic of Korea
| | - Young-Il Hwang
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Do-Hyun Nam
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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24
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Angulo JC, Andrés G, Ashour N, Sánchez-Chapado M, López JI, Ropero S. Development of Castration Resistant Prostate Cancer can be Predicted by a DNA Hypermethylation Profile. J Urol 2015; 195:619-26. [PMID: 26551297 DOI: 10.1016/j.juro.2015.10.172] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
Abstract
PURPOSE Detection of DNA hypermethylation has emerged as a novel molecular biomarker for prostate cancer diagnosis and evaluation of prognosis. We sought to define whether a hypermethylation profile of patients with prostate cancer on androgen deprivation would predict castrate resistant prostate cancer. MATERIALS AND METHODS Genome-wide methylation analysis was performed using a methylation cancer panel in 10 normal prostates and 45 tumor samples from patients placed on androgen deprivation who were followed until castrate resistant disease developed. Castrate resistant disease was defined according to EAU (European Association of Urology) guideline criteria. Two pathologists reviewed the Gleason score, Ki-67 index and neuroendocrine differentiation. Hierarchical clustering analysis was performed and relationships with outcome were investigated by Cox regression and log rank analysis. RESULTS We found 61 genes that were significantly hypermethylated in greater than 20% of tumors analyzed. Three clusters of patients were characterized by a DNA methylation profile, including 1 at risk for earlier castrate resistant disease (log rank p = 0.019) and specific mortality (log rank p = 0.002). Hypermethylation of ETV1 (HR 3.75) and ZNF215 (HR 2.89) predicted disease progression despite androgen deprivation. Hypermethylation of IRAK3 (HR 13.72), ZNF215 (HR 4.81) and SEPT9 (HR 7.64) were independent markers of prognosis. Prostate specific antigen greater than 25 ng/ml, Gleason pattern 5, Ki-67 index greater than 12% and metastasis at diagnosis also predicted a negative response to androgen deprivation. Study limitations included the retrospective design and limited number of cases. CONCLUSIONS Epigenetic silencing of the mentioned genes could be novel molecular markers for the prognosis of advanced prostate cancer. It might predict castrate resistance during hormone deprivation and, thus, disease specific mortality. Gene hypermethylation is associated with disease progression in patients who receive hormone therapy. It could serve as a marker of the treatment response.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Getafe, Spain.
| | - Guillermo Andrés
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Getafe, Spain
| | - Nadia Ashour
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Bilbao, Spain
| | - Manuel Sánchez-Chapado
- Servicio de Urología, Hospital Universitario Príncipe de Asturias, Universidad de Alcalá, Alcalá de Henares, Bilbao, Spain
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces, Universidad del País Vasco, Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Bilbao, Spain
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25
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Kiselev VY, Juvin V, Malek M, Luscombe N, Hawkins P, Le Novère N, Stephens L. Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop. Nucleic Acids Res 2015; 43:9663-79. [PMID: 26464442 PMCID: PMC4787766 DOI: 10.1093/nar/gkv1015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/24/2015] [Indexed: 01/10/2023] Open
Abstract
PIP3 is synthesized by the Class I PI3Ks and regulates complex cell responses, such as growth and migration. Signals that drive long-term reshaping of cell phenotypes are difficult to resolve because of complex feedback networks that operate over extended times. PIP3-dependent modulation of mRNA accumulation is clearly important in this process but is poorly understood. We have quantified the genome-wide mRNA-landscape of non-transformed, breast epithelium-derived MCF10a cells and its response to acute regulation by EGF, in the presence or absence of a PI3Kα inhibitor, compare it to chronic activation of PI3K signalling by cancer-relevant mutations (isogenic cells expressing an oncomutant PI3Kα allele or lacking the PIP3-phosphatase/tumour-suppressor, PTEN). Our results show that whilst many mRNAs are changed by long-term genetic perturbation of PIP3 signalling ('butterfly effect'), a much smaller number do so in a coherent fashion with the different PIP3 perturbations. This suggests a subset of more directly regulated mRNAs. We show that mRNAs respond differently to given aspects of PIP3 regulation. Some PIP3-sensitive mRNAs encode PI3K pathway components, thus suggesting a transcriptional feedback loop. We identify the transcription factor binding motifs SRF and PRDM1 as important regulators of PIP3-sensitive mRNAs involved in cell movement.
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Affiliation(s)
| | - Veronique Juvin
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Mouhannad Malek
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | | | - Phillip Hawkins
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Nicolas Le Novère
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK EMBL-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Len Stephens
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
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26
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Increased epigenetic alterations at the promoters of transcriptional regulators following inadequate maternal gestational weight gain. Sci Rep 2015; 5:14224. [PMID: 26415774 PMCID: PMC4586460 DOI: 10.1038/srep14224] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/20/2015] [Indexed: 01/01/2023] Open
Abstract
Epigenetic modifications are thought to serve as a memory of exposure to in utero environments. However, few human studies have investigated the associations between maternal nutritional conditions during pregnancy and epigenetic alterations in offspring. In this study, we report genome-wide methylation profiles for 33 postpartum placentas from pregnancies of normal and foetal growth restriction with various extents of maternal gestational weight gain. Epigenetic alterations accumulate in the placenta under adverse in utero environments, as shown by application of Smirnov-Grubbs’ outlier test. Moreover, hypermethylation occurs frequently at the promoter regions of transcriptional regulator genes, including polycomb targets and zinc-finger genes, as shown by annotations of the genomic and functional features of loci with altered DNA methylation. Aberrant epigenetic modifications at such developmental regulator loci, if occurring in foetuses as well, will elevate the risk of developing various diseases, including metabolic and mental disorders, later in life.
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27
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Riedmann C, Ma Y, Melikishvili M, Godfrey SG, Zhang Z, Chen KC, Rouchka EC, Fondufe-Mittendorf YN. Inorganic Arsenic-induced cellular transformation is coupled with genome wide changes in chromatin structure, transcriptome and splicing patterns. BMC Genomics 2015; 16:212. [PMID: 25879800 PMCID: PMC4371809 DOI: 10.1186/s12864-015-1295-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/29/2015] [Indexed: 12/29/2022] Open
Abstract
Background Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with a higher than normal risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. While arsenic-induced biological changes play a role in disease pathology, little is known about the dynamic cellular changes resulting from arsenic exposure and withdrawal. Results In these studies, we sought to understand the molecular mechanisms behind the biological changes induced by arsenic exposure. A comprehensive global approach was employed to determine genome-wide changes to chromatin structure, transcriptome patterns and splicing patterns in response to chronic low dose arsenic and its subsequent withdrawal. Our results show that cells exposed to chronic low doses of sodium arsenite have distinct temporal and coordinated chromatin, gene expression, and miRNA changes consistent with differentiation and activation of multiple biochemical pathways. Most of these temporal patterns in gene expression are reversed when arsenic is withdrawn. However, some gene expression patterns remained altered, plausibly as a result of an adaptive response by cells. Additionally, the correlation of changes to gene expression and chromatin structure solidify the role of chromatin structure in gene regulatory changes due to arsenite exposure. Lastly, we show that arsenite exposure influences gene regulation both at the initiation of transcription as well as at the level of splicing. Conclusions Our results show that adaptation of cells to iAs-mediated EMT is coupled to changes in chromatin structure effecting differential transcriptional and splicing patterns of genes. These studies provide new insights into the mechanism of iAs-mediated pathology, which includes epigenetic chromatin changes coupled with changes to the transcriptome and splicing patterns of key genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1295-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caitlyn Riedmann
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.
| | - Ye Ma
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.
| | - Manana Melikishvili
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.
| | - Steven Grason Godfrey
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.
| | - Zhou Zhang
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY, 40536, USA.
| | - Kuey Chu Chen
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40536, USA.
| | - Eric C Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40292, USA.
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28
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Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nat Commun 2015; 6:5899. [PMID: 25641231 DOI: 10.1038/ncomms6899] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 11/17/2014] [Indexed: 01/09/2023] Open
Abstract
Epigenetic alterations in the cancer methylome are common in breast cancer and provide novel options for tumour stratification. Here, we perform whole-genome methylation capture sequencing on small amounts of DNA isolated from formalin-fixed, paraffin-embedded tissue from triple-negative breast cancer (TNBC) and matched normal samples. We identify differentially methylated regions (DMRs) enriched with promoters associated with transcription factor binding sites and DNA hypersensitive sites. Importantly, we stratify TNBCs into three distinct methylation clusters associated with better or worse prognosis and identify 17 DMRs that show a strong association with overall survival, including DMRs located in the Wilms tumour 1 (WT1) gene, bi-directional-promoter and antisense WT1-AS. Our data reveal that coordinated hypermethylation can occur in oestrogen receptor-negative disease, and that characterizing the epigenetic framework provides a potential signature to stratify TNBCs. Together, our findings demonstrate the feasibility of profiling the cancer methylome with limited archival tissue to identify regulatory regions associated with cancer.
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29
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Tao YF, Hu SY, Lu J, Cao L, Zhao WL, Xiao PF, Xu LX, Li ZH, Wang NN, Du XJ, Sun LC, Zhao H, Fang F, Su GH, Li YH, Li YP, Xu YY, Ni J, Wang J, Feng X, Pan J. Zinc finger protein 382 is downregulated by promoter hypermethylation in pediatric acute myeloid leukemia patients. Int J Mol Med 2014; 34:1505-15. [PMID: 25319049 PMCID: PMC4214337 DOI: 10.3892/ijmm.2014.1966] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 10/03/2014] [Indexed: 11/06/2022] Open
Abstract
Acute myeloid leukemia (AML) is the second-most common form of leukemia in children. Aberrant DNA methylation patterns are characteristic of AML. Zinc finger protein 382 (ZNF382) has been suggested to be a tumor suppressor gene possibly regulated by promoter hypermethylation in various types of human cancer. However, ZNF382 expression and methylation status in pediatric AML is unknown. In the present study, ZNF382 transcription levels were evaluated by quantitative reverse-transcription PCR. Methylation status was investigated by methylation-specific (MSP) PCR and bisulfate genomic sequencing (BGS). The prognostic significance of ZNF382 expression and promoter methylation was assessed in 105 cases of pediatric AML. The array data suggested that the ZNF382 promoter was hypermethylated in the AML cases examined. MSP PCR and BGS analysis revealed that ZNF382 was hypermethylated in leukemia cell lines. Furthermore, treatment with 5-aza-2'-deoxycytidine (5-Aza) upregulated ZNF382 expression in the selected leukemia cell lines. The aberrant methylation of ZNF382 was observed in 10% (2/20) of the control samples compared with 26.7% (28/105) of the AML samples. ZNF382 expression was significantly decreased in the 105 AML patients compared with the controls. Patients with ZNF382 methylation showed lower ZNF382 transcript levels compared with patients exhibiting no methylation. There were no significant differences in clinical characteristics or cytogenetic analysis between the patients with or without ZNF382 methylation. ZNF382 methylation correlated with minimal residual disease (MRD). Kaplan-Meier survival analysis revealed similar survival times in the samples with ZNF382 methylation, and multivariate analysis revealed that ZNF382 methylation was not an independent prognostic factor in pediatric AML. The epigenetic inactivation of ZNF382 by promoter hypermethylation can be observed in AML cell lines and pediatric AML samples. Therefore, our study suggests that ZNF382 may be considered a putative tumor suppressor gene in pediatric AML. However, further studies focusing on the mechanisms responsible for ZNF382 downregulation in pediatric leukemia are required.
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Affiliation(s)
- Yan-Fang Tao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Shao-Yan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Lan Cao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Wen-Li Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Pei-Fang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Li-Xiao Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Zhi-Heng Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Na-Na Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Xiao-Juan Du
- Department of Gastroenterology, The 5th Hospital of Chinese PLA, Yinchuan, Ningxia, P.R. China
| | - Li-Chao Sun
- Department of Cell and Molecular Biology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - He Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Fang Fang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Guang-Hao Su
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Yan-Hong Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Yi-Ping Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Yun-Yun Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Jian Ni
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Jian Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Xing Feng
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Jian Pan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
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Suv39h1 mediates AP-2α-dependent inhibition of C/EBPα expression during adipogenesis. Mol Cell Biol 2014; 34:2330-8. [PMID: 24732798 DOI: 10.1128/mcb.00070-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have shown that CCAAT/enhancer-binding protein α (C/EBPα) plays a very important role during adipocyte terminal differentiation and that AP-2α (activator protein 2α) acts as a repressor to delay the expression of C/EBPα. However, the mechanisms by which AP-2α prevents the expression of C/EBPα are not fully understood. Here, we present evidence that Suv39h1, a histone H3 lysine 9 (H3K9)-specific trimethyltransferase, and G9a, a euchromatic methyltransferase, both interact with AP-2α and enhance AP-2α-mediated transcriptional repression of C/EBPα. Interestingly, we discovered that G9a mediates dimethylation of H3K9, thus providing the substrate, which is methylated by Suv39h1, to H3K9me3 on the C/EBPα promoter. The expression level of AP-2α was consistent with enrichment of H3K9me2 and H3K9me3 on the C/EBPα promoter in 3T3-L1 preadipocytes. Knockdown of Suv39h markedly increased C/EBPα expression and promoted adipogenesis. Conversely, ectopic expression of Suv39h1 delayed C/EBPα expression and impaired the accumulation of triglyceride, while simultaneous knockdown of AP-2α or G9a partially rescued this process. These findings indicate that Suv39h1 enhances AP-2α-mediated transcriptional repression of C/EBPα in an epigenetic manner and further inhibits adipocyte differentiation.
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