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Liu M, Wang Z, Liu Q, Zhu H, Xu N. Expression of Micro-RNA-492 (MiR-492) in Human Cervical Cancer Cell Lines is Upregulated by Transfection with Wild-Type P53, Irradiation, and 5-Fluorouracil Treatment In Vitro. Med Sci Monit 2018; 24:7750-7758. [PMID: 30374014 PMCID: PMC6354641 DOI: 10.12659/msm.911585] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The status of p53 is critical to the chemoradiosensitivity of cervical cancer cells. Wild-type p53 is essential to orchestrate the cellular response to cytotoxic stimuli. Our previous data illustrated that cervical cancer patients whose specimens overexpressed microR-492 (miR-492) were highly sensitive to concurrent chemoradiation. Although p53 activation has been reported to upregulate miR-492 by a miRNA profiling assay in lung cancer cells, the transcriptional regulation of miR-492 in cervical cancer cells remains poorly understood. Therefore, we aimed to decipher the relationship between p53 and miR-492 in cervical cancer cells. Material/Methods The expression of p53 and miR-492 in cervical cancer cell lines was measured by western blot and real-time PCR. After cells were transfected with wild-type p53 plasmid or were treated by irradiation and 5-fluorouracil (5-FU), the expression changes of p53 as well as miR-492 were examined by western blot and real-time PCR. The putative p53 binding site of miR-492 was first analyzed by bioinformatics tools, then validated by chromatin immunoprecipitation and dual-luciferase reporter assays. Results We found that miR-492 was upregulated in cells with wild-type p53 compared to cells with mutant p53. Transfection of wild-type p53 plasmid or treatments with cytotoxic reagents including irradiation and 5-FU all induced miR-492 overexpression. Bioinformatics analysis and experimental validations further proved p53 interacted with miR-492 promoter directly. Conclusions In cervical cancer cells, p53 activated miR-492 expression transcriptionally.
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Affiliation(s)
- Mei Liu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Zaozao Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, China (mainland)
| | - Qiao Liu
- Key Laboratory of Experimental Teratology (Ministry of Education), Department of Molecular Medicine and Genetics, School of Basic Medicine Sciences, Shandong University, Jinan, Shandong, China (mainland)
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China (mainland)
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
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Gabdank I, Chan ET, Davidson JM, Hilton JA, Davis CA, Baymuradov UK, Narayanan A, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY, Hitz BC, Sloan CA, Cherry JM. Prevention of data duplication for high throughput sequencing repositories. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4913687. [PMID: 29688363 PMCID: PMC5829560 DOI: 10.1093/database/bay008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023]
Abstract
Database URL https://www.encodeproject.org/.
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Affiliation(s)
- Idan Gabdank
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Esther T Chan
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Jason A Hilton
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Carrie A Davis
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | | | - Aditi Narayanan
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Kathrina C Onate
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Keenan Graham
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Stuart R Miyasato
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Timothy R Dreszer
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Forrest Y Tanaka
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
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Cai Y, Wan J. Competing Endogenous RNA Regulations in Neurodegenerative Disorders: Current Challenges and Emerging Insights. Front Mol Neurosci 2018; 11:370. [PMID: 30344479 PMCID: PMC6182084 DOI: 10.3389/fnmol.2018.00370] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/18/2018] [Indexed: 12/14/2022] Open
Abstract
The past decade has witnessed exciting breakthroughs that have contributed to the richness and complexity of a burgeoning modern RNA world, and one particular breakthrough-the competing endogenous RNA (ceRNA) hypothesis-has been described as the "Rosetta Stone" for decoding the RNA language used in regulating RNA crosstalk and modulating biological functions. The proposed far-reaching mechanism unites diverse RNA species and provides new insights into previously unrecognized RNA-RNA interactions and RNA regulatory networks that perhaps determine gene expression in an organized, hierarchical manner. The recently uncovered ceRNA regulatory loops and networks have emphasized the power of ceRNA regulation in a wide range of developmental stages and pathological contexts, such as in tumorigenesis and neurodegenerative disorders. Although the ceRNA hypothesis drastically enhanced our understanding of RNA biology, shortly after the hypothesis was proposed, disputes arose in relation mainly to minor discrepancies in the reported effects of ceRNA regulation under physiological conditions, and this resulted in ceRNA regulation becoming an extensively studied and fast-growing research field. Here, we focus on the evidence supporting ceRNA regulation in neurodegenerative disorders and address three critical points related to the ceRNA regulatory mechanism: the microRNA (miRNA) and ceRNA hierarchies in cross-regulations; the balance between destabilization and stable binding in ceRNA-miRNA interactions; and the true extent to which ceRNA regulatory mechanisms are involved in both health and disease, and the experimental shortcomings in current ceRNA studies.
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Affiliation(s)
- Yifei Cai
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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54
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Sun W, Shi Y, Wang Z, Zhang J, Cai H, Zhang J, Huang D. Interaction of long-chain non-coding RNAs and important signaling pathways on human cancers (Review). Int J Oncol 2018; 53:2343-2355. [PMID: 30272345 DOI: 10.3892/ijo.2018.4575] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/24/2018] [Indexed: 11/05/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) usually refer to non-coding RNA transcripts >200 nucleotides in length. In terms of the full genomic transcript, the proportion of lncRNAs far exceeds that of coding RNA. Initially, lncRNAs were considered to be the transcriptional noise of genes, but it has since been demonstrated that lncRNAs serve an important role in the regulation of cellular activities through interaction with DNA, RNA and protein. Numerous studies have demonstrated that various intricate signaling pathways are closely related to lncRNAs. Here, we focus on a large number of studies regarding the interaction of lncRNAs with important signaling pathways. It is comprehensively illustrated that lncRNAs regulate key metabolic components and regulatory factors of signaling pathways to affect the biological activities of tumor cells. Evidence suggests that the abnormal expression or mutation of lncRNAs in human tumor cells, and their interaction with signaling pathways, may provide a basis and potential target for the diagnosis and treatment of human cancers.
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Affiliation(s)
- Wei Sun
- Department of Postgraduates, Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
| | - Ying Shi
- Department of Obstetrics, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Zhifei Wang
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Jiye Zhang
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Hanhui Cai
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Jungang Zhang
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Dongsheng Huang
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
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55
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Kober P, Boresowicz J, Rusetska N, Maksymowicz M, Goryca K, Kunicki J, Bonicki W, Siedlecki JA, Bujko M. DNA methylation profiling in nonfunctioning pituitary adenomas. Mol Cell Endocrinol 2018; 473:194-204. [PMID: 29410024 DOI: 10.1016/j.mce.2018.01.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/21/2017] [Accepted: 01/29/2018] [Indexed: 01/08/2023]
Abstract
Nonfunctioning pituitary adenomas (NFPAs) are among the most frequent intracranial tumors but their molecular background, including changes in epigenetic regulation, remains poorly understood. We performed genome-wide DNA methylation profiling of 34 NFPAs and normal pituitary samples. Methylation status of the selected genomic regions and expression level of corresponding genes were assessed in a group of 75 patients. NFPAs exhibited distinct global methylation profile as compared to normal pituitary. Aberrant DNA methylation appears to contribute to deregulation of the cancer-related pathways as shown by preliminary functional analysis. Promoter hypermethylation and decreased expression level of SFN, STAT5A, DUSP1, PTPRE and FGFR2 was confirmed in the enlarged group of NFPAs. Difference in the methylation profiles between invasive and non-invasive NFPAs is very slight. Nevertheless, invasiveness-related aberrant epigenetic deregulation of the particular genes was found including upregulation of ITPKB and downregulation CNKSR1 in invasive tumors.
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Affiliation(s)
- Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joanna Boresowicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland; Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Nataliia Rusetska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Maria Maksymowicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Wiesław Bonicki
- Department of Neurosurgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Janusz Aleksander Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
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56
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Godini R, Fallahi H. Shortening the list of essential genes in the human genome by network analysis. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Ross ME, Mason CE, Finnell RH. Genomic approaches to the assessment of human spina bifida risk. Birth Defects Res 2018; 109:120-128. [PMID: 27883265 DOI: 10.1002/bdra.23592] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/02/2016] [Accepted: 10/10/2016] [Indexed: 12/30/2022]
Abstract
Structural birth defects are a leading cause of mortality and morbidity in children world-wide, affecting as much as 6% of all live births. Among these conditions, neural tube defects (NTDs), including spina bifida and anencephaly, arise from a combination of complex gene and environment interactions that are as yet poorly understood within human populations. Rapid advances in massively parallel DNA sequencing and bioinformatics allow for analyses of the entire genome beyond the 2% of the genomic sequence covering protein coding regions. Efforts to collect and analyze these large datasets hold promise for illuminating gene network variations and eventually epigenetic events that increase individual risk for failure to close the neural tube. In this review, we discuss current challenges for DNA genome sequence analysis of NTD affected populations, and compare experience in the field with other complex genetic disorders for which large datasets are accumulating. The ultimate goal of this research is to find strategies for optimizing conditions that promote healthy birth outcomes for individual couples. Birth Defects Research 109:120-128, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- M Elizabeth Ross
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York
| | - Christopher E Mason
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Richard H Finnell
- Dell Pediatric Research Institute, Department of Nutritional Sciences, The University of Texas at Austin, Austin, Texas
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58
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Li JX, Fu WP, Zhang J, Zhang XH, Sun C, Dai LM, Zhong L, Yu L, Zhang YP. A functional SNP upstream of the ADRB2 gene is associated with COPD. Int J Chron Obstruct Pulmon Dis 2018; 13:917-925. [PMID: 29588580 PMCID: PMC5859892 DOI: 10.2147/copd.s151153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background Previous studies have suggested that β2-adrenergic receptor (ADRB2) is associated with COPD. However, the role of genetic polymorphisms in ADRB2 on COPD has not been evaluated yet. Methods In this study, SNaPshot genotyping, luciferase assay, chromatin immunoprecipitation and real-time polymerase chain reaction were adopted to investigate the association between ADRB2 genetic polymorphisms and COPD, comprehensively. Results One single nucleotide polymorphism (rs12654778), located upstream of ADRB2, showed a significant association with COPD by the logistic regression analysis after adjusting for age, sex and smoking history (p=0.04) in 200 COPD patients and 222 controls from southwest Chinese population. Furthermore, the luciferase assay indicated that rs12654778-A allele reduced the relative promoter activity by ~26% compared with rs12654778-G allele (p=0.0034). The chromatin immunoprecipitation analysis demonstrated that rs12654778 modulated the binding affinity of transcription factor neurofibromin 1. In addition, a significantly reduced expression of ADRB2 in COPD patients was observed, compared with normal controls (p=0.017). Conclusion Our findings suggest a previously unknown mechanism linking allele-specific effects of rs12654778 on ADRB2 expression to COPD onset, for the first time.
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MESH Headings
- Adult
- Aged
- Binding Sites
- Case-Control Studies
- Cell Line
- Chi-Square Distribution
- China
- Female
- Forced Expiratory Volume
- Gene Frequency
- Genetic Association Studies
- Genetic Predisposition to Disease
- Humans
- Logistic Models
- Lung/metabolism
- Lung/physiopathology
- Male
- Middle Aged
- Neurofibromin 1/metabolism
- Odds Ratio
- Phenotype
- Polymorphism, Single Nucleotide
- Promoter Regions, Genetic
- Pulmonary Disease, Chronic Obstructive/diagnosis
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/physiopathology
- Receptors, Adrenergic, beta-2/genetics
- Receptors, Adrenergic, beta-2/metabolism
- Risk Factors
- Vital Capacity
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Affiliation(s)
- Jin-Xiu Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan
- Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University
| | - Wei-Ping Fu
- Department of Respiratory Critical Care Medicine
| | - Jing Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming
| | - Xiao-Hua Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan
- Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University
| | - Chang Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan
- College of Life Sciences
| | - Lu-Ming Dai
- Department of Respiratory Critical Care Medicine
| | - Li Zhong
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan
- College of Life Sciences
- Provincial Demonstration Center for Experimental Biology Education, Shaanxi Normal University, Xi’an
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan
- Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Non-coding RNAs in hepatocellular carcinoma: molecular functions and pathological implications. Nat Rev Gastroenterol Hepatol 2018; 15:137-151. [PMID: 29317776 DOI: 10.1038/nrgastro.2017.169] [Citation(s) in RCA: 314] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is a leading lethal malignancy worldwide. However, the molecular mechanisms underlying liver carcinogenesis remain poorly understood. Over the past two decades, overwhelming evidence has demonstrated the regulatory roles of different classes of non-coding RNAs (ncRNAs) in liver carcinogenesis related to a number of aetiologies, including HBV, HCV and NAFLD. Among the ncRNAs, microRNAs, which belong to a distinct class of small ncRNAs, have been proven to play a crucial role in the post-transcriptional regulation of gene expression. Deregulation of microRNAs has been broadly implicated in the inactivation of tumour-suppressor genes and activation of oncogenes in HCC. Modern high-throughput sequencing analyses have unprecedentedly identified a very large number of non-coding transcripts. Divergent groups of long ncRNAs have been implicated in liver carcinogenesis through interactions with DNA, RNA or proteins. Overall, ncRNAs represent a burgeoning field of cancer research, and we are only beginning to understand the importance and complicity of the ncRNAs in liver carcinogenesis. In this Review, we summarize the common deregulation of small and long ncRNAs in human HCC. We also comprehensively review the pathological roles of ncRNAs in liver carcinogenesis, epithelial-to-mesenchymal transition and HCC metastasis and discuss the potential applications of ncRNAs as diagnostic tools and therapeutic targets in human HCC.
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60
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Xi Y, Shi J, Li W, Tanaka K, Allton KL, Richardson D, Li J, Franco HL, Nagari A, Malladi VS, Coletta LD, Simper MS, Keyomarsi K, Shen J, Bedford MT, Shi X, Barton MC, Kraus WL, Li W, Dent SYR. Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. BMC Genomics 2018; 19:150. [PMID: 29458327 PMCID: PMC5819162 DOI: 10.1186/s12864-018-4533-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 02/05/2018] [Indexed: 12/19/2022] Open
Abstract
Background Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy. Results To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells. Discussion Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway. Conclusions Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment. Electronic supplementary material The online version of this article (10.1186/s12864-018-4533-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanxin Xi
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jiejun Shi
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Wenqian Li
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Kaori Tanaka
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Kendra L Allton
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Dana Richardson
- The Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Jing Li
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Hector L Franco
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Venkat S Malladi
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Luis Della Coletta
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Melissa S Simper
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Khandan Keyomarsi
- The Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Jianjun Shen
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Mark T Bedford
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Xiaobing Shi
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Michelle C Barton
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Wei Li
- Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Sharon Y R Dent
- The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
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Li J, Wang Y, Rao X, Wang Y, Feng W, Liang H, Liu Y. Roles of alternative splicing in modulating transcriptional regulation. BMC SYSTEMS BIOLOGY 2017; 11:89. [PMID: 28984199 PMCID: PMC5629561 DOI: 10.1186/s12918-017-0465-6] [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] [Indexed: 12/18/2022]
Abstract
Background The ability of a transcription factor to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms. Alternative splicing can modulate gene function by adding or removing certain protein domains, and therefore affect the activity of protein. Reverse engineering of gene regulatory networks using gene expression profiles has proven valuable in dissecting the logical relationships among multiple proteins during the transcriptional regulation. However, it is unclear whether alternative splicing of certain proteins affects the activity of other transcription factors. Results In order to investigate the roles of alternative splicing during transcriptional regulation, we constructed a statistical model to infer whether the alternative splicing events of modulator proteins can affect the ability of key transcription factors in regulating the expression levels of their transcriptional targets. We tested our strategy in KIRC (Kidney Renal Clear Cell Carcinoma) using the RNA-seq data downloaded from TCGA (the Cancer Genomic Atlas). We identified 828of modulation relationships between the splicing levels of modulator proteins and activity levels of transcription factors. For instance, we found that the activity levels of GR (glucocorticoid receptor) protein, a key transcription factor in kidney, can be influenced by the splicing status of multiple proteins, including TP53, MDM2 (mouse double minute 2 homolog), RBM14 (RNA-binding protein 14) and SLK (STE20 like kinase). The influenced GR-targets are enriched by key cancer-related pathways, including p53 signaling pathway, TR/RXR activation, CAR/RXR activation, G1/S checkpoint regulation pathway, and G2/M DNA damage checkpoint regulation pathway. Conclusions Our analysis suggests, for the first time, that exon inclusion levels of certain regulatory proteins can affect the activities of many transcription factors. Such analysis can potentially unravel a novel mechanism of how splicing variation influences the cellular function and provide important insights for how dysregulation of splicing outcome can lead to various diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0465-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jin Li
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, 150001, China
| | - Yang Wang
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, 150001, China.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Xi Rao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yue Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Weixing Feng
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, 150001, China
| | - Hong Liang
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, 150001, China.
| | - Yunlong Liu
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, 150001, China. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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62
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Ling H. Non-coding RNAs: Therapeutic Strategies and Delivery Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 937:229-37. [PMID: 27573903 DOI: 10.1007/978-3-319-42059-2_12] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The vast majority of the human genome is transcribed into RNA molecules that do not code for proteins, which could be small ones approximately 20 nucleotide in length, known as microRNAs, or transcripts longer than 200 bp, defined as long noncoding RNAs. The prevalent deregulation of microRNAs in human cancers prompted immediate interest on the therapeutic value of microRNAs as drugs and drug targets. Many features of microRNAs such as well-defined mechanisms, and straightforward oligonucleotide design further make them attractive candidates for therapeutic development. The intensive efforts of exploring microRNA therapeutics are reflected by the large body of preclinical studies using oligonucleotide-based mimicking and blocking, culminated by the recent entry of microRNA therapeutics in clinical trial for several human diseases including cancer. Meanwhile, microRNA therapeutics faces the challenge of effective and safe delivery of nucleic acid therapeutics into the target site. Various chemical modifications of nucleic acids and delivery systems have been developed to increase targeting specificity and efficacy, and reduce the associated side effects including activation of immune response. Recently, long noncoding RNAs become attractive targets for therapeutic intervention because of their association with complex and delicate phenotypes, and their unconventional pharmaceutical activities such as capacity of increasing output of proteins. Here I discuss the general therapeutic strategies targeting noncoding RNAs, review delivery systems developed to maximize noncoding RNA therapeutic efficacy, and offer perspectives on the future development of noncoding RNA targeting agents for colorectal cancer.
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Affiliation(s)
- Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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63
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Saelee P, Kearly A, Nutt SL, Garrett-Sinha LA. Genome-Wide Identification of Target Genes for the Key B Cell Transcription Factor Ets1. Front Immunol 2017; 8:383. [PMID: 28439269 PMCID: PMC5383717 DOI: 10.3389/fimmu.2017.00383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/17/2017] [Indexed: 12/16/2022] Open
Abstract
Background The transcription factor Ets1 is highly expressed in B lymphocytes. Loss of Ets1 leads to premature B cell differentiation into antibody-secreting cells (ASCs), secretion of autoantibodies, and development of autoimmune disease. Despite the importance of Ets1 in B cell biology, few Ets1 target genes are known in these cells. Results To obtain a more complete picture of the function of Ets1 in regulating B cell differentiation, we performed Ets1 ChIP-seq in primary mouse B cells to identify >10,000-binding sites, many of which were localized near genes that play important roles in B cell activation and differentiation. Although Ets1 bound to many sites in the genome, it was required for regulation of less than 5% of them as evidenced by gene expression changes in B cells lacking Ets1. The cohort of genes whose expression was altered included numerous genes that have been associated with autoimmune disease susceptibility. We focused our attention on four such Ets1 target genes Ptpn22, Stat4, Egr1, and Prdm1 to assess how they might contribute to Ets1 function in limiting ASC formation. We found that dysregulation of these particular targets cannot explain altered ASC differentiation in the absence of Ets1. Conclusion We have identified genome-wide binding targets for Ets1 in B cells and determined that a relatively small number of these putative target genes require Ets1 for their normal expression. Interestingly, a cohort of genes associated with autoimmune disease susceptibility is among those that are regulated by Ets1. Identification of the target genes of Ets1 in B cells will help provide a clearer picture of how Ets1 regulates B cell responses and how its loss promotes autoantibody secretion.
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Affiliation(s)
- Prontip Saelee
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Alyssa Kearly
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lee Ann Garrett-Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
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64
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Lee JJ, Kim M, Kim HP. Epigenetic regulation of long noncoding RNA UCA1 by SATB1 in breast cancer. BMB Rep 2017; 49:578-583. [PMID: 27697109 PMCID: PMC5227301 DOI: 10.5483/bmbrep.2016.49.10.156] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Indexed: 01/31/2023] Open
Abstract
Special AT-rich sequence binding protein 1 (SATB1) is a nuclear matrix-associated DNA-binding protein that functions as a chromatin organizer. SATB1 is highly expressed in aggressive breast cancer cells and promotes growth and metastasis by reprograming gene expression. Through genomewide cross-examination of gene expression and histone methylation, we identified SATB1 target genes for which expression is associated with altered epigenetic marks. Among the identified genes, long noncoding RNA urothelial carcinoma-associated 1 (UCA1) was upregulated by SATB1 depletion. Upregulation of UCA1 coincided with increased H3K4 trimethylation (H3K4me3) levels and decreased H3K27 trimethylation (H3K27me3) levels. Our study showed that SATB1 binds to the upstream region of UCA1 in vivo, and that its promoter activity increases with SATB1 depletion. Furthermore, simultaneous depletion of SATB1 and UCA1 potentiated suppression of tumor growth and cell survival. Thus, SATB1 repressed the expression of oncogenic UCA1, suppressing growth and survival of breast cancer cells. [BMB Reports 2016; 49(10): 578-583].
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Affiliation(s)
- Jong-Joo Lee
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Mikyoung Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hyoung-Pyo Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
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65
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López-García C, Sansregret L, Domingo E, McGranahan N, Hobor S, Birkbak NJ, Horswell S, Grönroos E, Favero F, Rowan AJ, Matthews N, Begum S, Phillimore B, Burrell R, Oukrif D, Spencer-Dene B, Kovac M, Stamp G, Stewart A, Danielsen H, Novelli M, Tomlinson I, Swanton C. BCL9L Dysfunction Impairs Caspase-2 Expression Permitting Aneuploidy Tolerance in Colorectal Cancer. Cancer Cell 2017; 31:79-93. [PMID: 28073006 PMCID: PMC5225404 DOI: 10.1016/j.ccell.2016.11.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 08/05/2016] [Accepted: 10/28/2016] [Indexed: 01/03/2023]
Abstract
Chromosomal instability (CIN) contributes to cancer evolution, intratumor heterogeneity, and drug resistance. CIN is driven by chromosome segregation errors and a tolerance phenotype that permits the propagation of aneuploid genomes. Through genomic analysis of colorectal cancers and cell lines, we find frequent loss of heterozygosity and mutations in BCL9L in aneuploid tumors. BCL9L deficiency promoted tolerance of chromosome missegregation events, propagation of aneuploidy, and genetic heterogeneity in xenograft models likely through modulation of Wnt signaling. We find that BCL9L dysfunction contributes to aneuploidy tolerance in both TP53-WT and mutant cells by reducing basal caspase-2 levels and preventing cleavage of MDM2 and BID. Efforts to exploit aneuploidy tolerance mechanisms and the BCL9L/caspase-2/BID axis may limit cancer diversity and evolution.
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Affiliation(s)
- Carlos López-García
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Laurent Sansregret
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Enric Domingo
- Oxford Centre for Cancer Gene Research, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK; Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Nicholas McGranahan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC2E 6DD, UK
| | - Sebastijan Hobor
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicolai Juul Birkbak
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC2E 6DD, UK
| | - Stuart Horswell
- Bioinformatics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francesco Favero
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer System Biology, Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Andrew J Rowan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicholas Matthews
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sharmin Begum
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin Phillimore
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rebecca Burrell
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dahmane Oukrif
- Research Department of Pathology, University College London Medical School, University Street, London WC1E 6JJ, UK
| | - Bradley Spencer-Dene
- Experimental Histopathology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michal Kovac
- Oxford Centre for Cancer Gene Research, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Gordon Stamp
- Experimental Histopathology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aengus Stewart
- Bioinformatics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Havard Danielsen
- Institute for Cancer Genetics and Informatics, Norwegian Radium Hospital, Oslo University Hospital, Ullernchausseen 70, 0379 Oslo, Norway
| | - Marco Novelli
- Research Department of Pathology, University College London Medical School, University Street, London WC1E 6JJ, UK
| | - Ian Tomlinson
- Oxford Centre for Cancer Gene Research, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC2E 6DD, UK.
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66
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A practical guide to filtering and prioritizing genetic variants. Biotechniques 2017; 62:18-30. [PMID: 28118812 DOI: 10.2144/000114492] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 10/11/2016] [Indexed: 11/23/2022] Open
Abstract
Next-generation sequencing (NGS) of whole genomes and exomes is a powerful tool in biomedical research and clinical diagnostics. However, the vast amount of data produced by NGS introduces new challenges and opportunities, many of which require novel computational and theoretical approaches when it comes to identifying the causal variant(s) for a disease of interest. While workflows and associated software to process raw data and produce high-confidence variant calls have significantly improved, filtering tens of thousands of candidates to identify a subset relevant to a specific study is still a complex exercise best left to bioinformaticists. However, as this prioritization procedure requires biological/biomedical reasoning, biologists and clinicians are increasingly motivated to handle the task themselves. Here, we describe a set of guidelines, tools, and online resources that can be used to identify functional variants from whole-genome and whole-exome variant calls and then prioritize these variants with potential associations to phenotypes of interest. Insights gained from a recently published analysis of protein-coding gene variation in >60,000 humans by the Exome Aggregation Consortium (ExAC) are also taken into account.
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67
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Chen CY, Shi W, Balaton BP, Matthews AM, Li Y, Arenillas DJ, Mathelier A, Itoh M, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Brown CJ, Wasserman WW. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. Sci Rep 2016; 6:37324. [PMID: 27857184 PMCID: PMC5114649 DOI: 10.1038/srep37324] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/24/2016] [Indexed: 12/27/2022] Open
Abstract
Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.
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Affiliation(s)
- Chih-Yu Chen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenqiang Shi
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradley P Balaton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Allison M Matthews
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yifeng Li
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - David J Arenillas
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Masayoshi Itoh
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Hideya Kawaji
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Timo Lassmann
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Piero Carninci
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan
| | - Alistair R R Forrest
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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68
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Azad P, Zhao HW, Cabrales PJ, Ronen R, Zhou D, Poulsen O, Appenzeller O, Hsiao YH, Bafna V, Haddad GG. Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease. J Exp Med 2016; 213:2729-2744. [PMID: 27821551 PMCID: PMC5110013 DOI: 10.1084/jem.20151920] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 06/02/2016] [Accepted: 10/06/2016] [Indexed: 01/17/2023] Open
Abstract
Azad and collaborators propose that Senp1 drives excessive erythropoiesis in high-altitude Andean dwellers suffering from chronic mountain sickness. In this study, because excessive polycythemia is a predominant trait in some high-altitude dwellers (chronic mountain sickness [CMS] or Monge’s disease) but not others living at the same altitude in the Andes, we took advantage of this human experiment of nature and used a combination of induced pluripotent stem cell technology, genomics, and molecular biology in this unique population to understand the molecular basis for hypoxia-induced excessive polycythemia. As compared with sea-level controls and non-CMS subjects who responded to hypoxia by increasing their RBCs modestly or not at all, respectively, CMS cells increased theirs remarkably (up to 60-fold). Although there was a switch from fetal to adult HgbA0 in all populations and a concomitant shift in oxygen binding, we found that CMS cells matured faster and had a higher efficiency and proliferative potential than non-CMS cells. We also established that SENP1 plays a critical role in the differential erythropoietic response of CMS and non-CMS subjects: we can convert the CMS phenotype into that of non-CMS and vice versa by altering SENP1 levels. We also demonstrated that GATA1 is an essential downstream target of SENP1 and that the differential expression and response of GATA1 and Bcl-xL are a key mechanism underlying CMS pathology.
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Affiliation(s)
- Priti Azad
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
| | - Huiwen W Zhao
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
| | - Pedro J Cabrales
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Roy Ronen
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093
| | - Dan Zhou
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
| | - Orit Poulsen
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
| | - Otto Appenzeller
- Department of Neurology, New Mexico Health Enhancement and Marathon Clinics Research Foundation, Albuquerque, NM 87122
| | - Yu Hsin Hsiao
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093
| | - Gabriel G Haddad
- Division of Respiratory Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093 .,Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093.,Rady Children's Hospital, San Diego, CA 92123
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69
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Polymorphisms in the prostaglandin receptor EP2 gene confers susceptibility to tuberculosis. INFECTION GENETICS AND EVOLUTION 2016; 46:23-27. [PMID: 27780787 DOI: 10.1016/j.meegid.2016.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/16/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Prostaglandin E2 (PGE2) is an important lipid mediator of the inflammatory immune response during acute and chronic infections. PGE2 modulates a variety of immune functions via four receptors (EP1-EP4), which mediate distinct PGE2 effects. Mice lacking EP2 are more susceptible to infection by Mycobacterium tuberculosis (M.tb), have a higher bacterial load, and increase size and number of granulomatous lesions. Our aim was to assess whether single nucleotide polymorphisms (SNPs) in EP2 increase the risk of tuberculosis. METHODS DNA re-sequencing revealed five common EP2 variants in the Chinese Han population. We sequenced the EP2 gene from 600 patients and 572 healthy controls to measure SNP frequencies in association with tuberculosis infections (TB) within the population. RESULTS The rs937337 polymorphism is associated with increased risk to tuberculosis (p=0.0044, odds ratio [OR], 1.67; 95% confidential interval,1.22-2.27). The rs937337 AA genotype and the rs1042618 CC genotype were significantly associated with TB. An estimation of the frequencies of haplotypes revealed a single protective haplotype GACGC for tuberculosis (p=0.00096, odds ratio [OR], 0.56; 95% confidential interval, 0.41-0.77). Furthermore, we determined that the remaining SNPs of EP2 were nominally associated with clinical patterns of disease. CONCLUSIONS We identified genetic polymorphisms in EP2 associated with susceptibility to tuberculosis within a Chinese population. Our data support that EP2 SNPs are genetic predispositions of increased susceptibility to TB and to different clinical patterns of disease.
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70
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Weinberg MS, Morris KV. Transcriptional gene silencing in humans. Nucleic Acids Res 2016; 44:6505-17. [PMID: 27060137 PMCID: PMC5001580 DOI: 10.1093/nar/gkw139] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 01/21/2023] Open
Abstract
It has been over a decade since the first observation that small non-coding RNAs can functionally modulate epigenetic states in human cells to achieve functional transcriptional gene silencing (TGS). TGS is mechanistically distinct from the RNA interference (RNAi) gene-silencing pathway. TGS can result in long-term stable epigenetic modifications to gene expression that can be passed on to daughter cells during cell division, whereas RNAi does not. Early studies of TGS have been largely overlooked, overshadowed by subsequent discoveries of small RNA-directed post-TGS and RNAi. A reappraisal of early work has been brought about by recent findings in human cells where endogenous long non-coding RNAs function to regulate the epigenome. There are distinct and common overlaps between the proteins involved in small and long non-coding RNA transcriptional regulatory mechanisms, suggesting that the early studies using small non-coding RNAs to modulate transcription were making use of a previously unrecognized endogenous mechanism of RNA-directed gene regulation. Here we review how non-coding RNA plays a role in regulation of transcription and epigenetic gene silencing in human cells by revisiting these earlier studies and the mechanistic insights gained to date. We also provide a list of mammalian genes that have been shown to be transcriptionally regulated by non-coding RNAs. Lastly, we explore how TGS may serve as the basis for development of future therapeutic agents.
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Affiliation(s)
- Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, WITS 2050, South Africa HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS 2050, South Africa
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA Center for Gene Therapy, City of Hope - BeckmanResearch Institute; Duarte, CA 91010, USA School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, 2033 Australia
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71
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Pesch R, Zimmer R. Cross-species Conservation of context-specific networks. BMC SYSTEMS BIOLOGY 2016; 10:76. [PMID: 27531214 PMCID: PMC4988053 DOI: 10.1186/s12918-016-0304-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/04/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND Many large data compendia on context-specific high-throughput genomic and regulatory data have been made available by international research consortia such as ENCODE, TCGA, and Epigenomics Roadmap. The use of these resources is impaired by the sheer size of the available big data and big metadata. Many of these context-specific data can be modeled as data derived regulatory networks (DDRNs) representing the complex and complicated interactions between transcription factors and target genes. These DDRNs are useful for the understanding of regulatory mechanisms and helpful for interpreting biomedical data. RESULTS The Cross-species Conservation framework (CroCo) provides a network-oriented view on the ENCODE regulatory data (CroCo network repository), convenient ways to access and browse networks and metadata, and a method to combine networks across compendia, experimental techniques, and species (CroCo tool suite). DDRNs can be combined with additional information and networks derived from the literature, curated resources, and computational predictions in order to enable detailed exploration and cross checking of regulatory interactions. Applications of the CroCo framework range from simple evidence look-up for user-defined regulatory interactions to the identification of conserved sub-networks in diverse cell-lines, conditions, and even species. CONCLUSION CroCo adds an intuitive unifying view on the data from the ENCODE projects via a comprehensive repository of derived context-specific regulatory networks and enables flexible cross-context, cross-species, and cross-compendia comparison via a basis set of analysis tools. The CroCo web-application and Cytoscape plug-in are freely available at: http://services.bio.ifi.lmu.de/croco-web . The web-page links to a detailed system description, a user guide, and tutorial videos presenting common use cases of the CroCo framework.
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Affiliation(s)
- Robert Pesch
- Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, München, Germany
| | - Ralf Zimmer
- Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 17, München, Germany
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Lerchenmüller C, Heißenberg J, Damilano F, Bezzeridis VJ, Krämer I, Bochaton-Piallat ML, Hirschberg K, Busch M, Katus HA, Peppel K, Rosenzweig A, Busch H, Boerries M, Most P. S100A6 Regulates Endothelial Cell Cycle Progression by Attenuating Antiproliferative Signal Transducers and Activators of Transcription 1 Signaling. Arterioscler Thromb Vasc Biol 2016; 36:1854-67. [PMID: 27386938 DOI: 10.1161/atvbaha.115.306415] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 06/27/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVE S100A6, a member of the S100 protein family, has been described as relevant for cell cycle entry and progression in endothelial cells. The molecular mechanism conferring S100A6's proliferative actions, however, remained elusive. APPROACH AND RESULTS Originating from the clinically relevant observation of enhanced S100A6 protein expression in proliferating endothelial cells in remodeling coronary and carotid arteries, our study unveiled S100A6 as a suppressor of antiproliferative signal transducers and activators of transcription 1 signaling. Discovery of the molecular liaison was enabled by combining gene expression time series analysis with bioinformatic pathway modeling in S100A6-silenced human endothelial cells stimulated with vascular endothelial growth factor A. This unbiased approach led to successful identification and experimental validation of interferon-inducible transmembrane protein 1 and protein inhibitors of activated signal transducers and activators of transcription as key components of the link between S100A6 and signal transducers and activators of transcription 1. CONCLUSIONS Given the important role of coordinated endothelial cell cycle activity for integrity and reconstitution of the inner lining of arterial blood vessels in health and disease, signal transducers and activators of transcription 1 suppression by S100A6 may represent a promising therapeutic target to facilitate reendothelialization in damaged vessels.
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Affiliation(s)
- Carolin Lerchenmüller
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries).
| | - Julian Heißenberg
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Federico Damilano
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Vassilios J Bezzeridis
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Isabel Krämer
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Marie-Luce Bochaton-Piallat
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Kristóf Hirschberg
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Martin Busch
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Hugo A Katus
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Karsten Peppel
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Anthony Rosenzweig
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Hauke Busch
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
| | - Melanie Boerries
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries).
| | - Patrick Most
- From the Cardiovascular Research Center, Massachusetts General Hospital (C.L., F.D., A.R.), Cardiovascular Institute, Beth Israel Deaconess Medical Center (F.D.), and Boston Children's Hospital (V.J.B.), Harvard Medical School, Boston, MA; Molecular and Translational Cardiology (MTC), Department of Internal Medicine III, University Hospital Heidelberg, Germany (C.L., J.H., I.K., M. Busch, P.M.); Department of Pathology and Immunology, University of Geneva, Switzerland (M.-L.B.-P.); DZHK (German Center for Cardiovascular Research), Partner site Heidelberg/Mannheim, University of Heidelberg, Germany (K.H., M. Busch, H.A.K., P.M.); Center for Translational Medicine, Jefferson Medical College, Philadelphia, PA (K.P., P.M.); Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany (H.B., M. Boerries); German Cancer Consortium (DKTK), Freiburg, Germany (H.B., M. Boerries); and German Cancer Research Center (DKFZ), Heidelberg, Germany (H.B., M. Boerries)
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73
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Miao Z, Wu L, Lu M, Meng X, Gao B, Qiao X, Zhang W, Xue D. Analysis of the transcriptional regulation of cancer-related genes by aberrant DNA methylation of the cis-regulation sites in the promoter region during hepatocyte carcinogenesis caused by arsenic. Oncotarget 2016; 6:21493-506. [PMID: 26046465 PMCID: PMC4673281 DOI: 10.18632/oncotarget.4085] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 05/11/2015] [Indexed: 12/12/2022] Open
Abstract
Liver is the major organ for arsenic methylation metabolism and may be the potential target of arsenic-induced cancer. In this study, normal human liver cell was treated with arsenic trioxide, and detected using DNA methylation microarray. Some oncogenes, tumor suppressor genes, transcription factors (TF), and tumor-associated genes (TAG) that have aberrant DNA methylation have been identified. However, simple functional studies of genes adjacent to aberrant methylation sites cannot well reflect the regulatory relationship between DNA methylation and gene transcription during the pathogenesis of arsenic-induced liver cancer, whereas a further analysis of the cis-regulatory elements and their trans-acting factors adjacent to DNA methylation can more precisely reflect the relationship between them. MYC and MAX (MYC associated factor X) were found to participating cell cycle through a bioinformatics analysis. Additionally, it was found that the hypomethylation of cis-regulatory sites in the MYC promoter region and the hypermethylation of cis-regulatory sites in the MAX promoter region result in the up-regulation of MYC mRNA expression and the down-regulation of MAX mRNA, which increased the hepatocyte carcinogenesis tendency.
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Affiliation(s)
- Zhuang Miao
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Lin Wu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Ming Lu
- Department of Surgery, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Xianzhi Meng
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Bo Gao
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Xin Qiao
- Department of Surgery, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Weihui Zhang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Dongbo Xue
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, PR China
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74
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Wiemerslage L, Gohel PA, Maestri G, Hilmarsson TG, Mickael M, Fredriksson R, Williams MJ, Schiöth HB. The Drosophila ortholog of TMEM18 regulates insulin and glucagon-like signaling. J Endocrinol 2016; 229:233-43. [PMID: 27029472 DOI: 10.1530/joe-16-0040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 03/29/2016] [Indexed: 12/19/2022]
Abstract
Transmembrane protein 18 (TMEM18) is an ill-described, obesity-related gene, but few studies have explored its molecular function. We found single-nucleotide polymorphism data, suggesting that TMEM18 may be involved in the regulation/physiology of metabolic syndrome based on associations with insulin, homeostatic model assessment-β (HOMAβ), triglycerides, and blood sugar. We then found an ortholog in the Drosophila genome, knocked down Drosophila Tmem18 specifically in insulin-producing cells, and tested for its effects on metabolic function. Our results suggest that TMEM18 affects substrate levels through insulin and glucagon signaling, and its downregulation induces a metabolic state resembling type 2 diabetes. This work is the first to experimentally describe the metabolic consequences of TMEM18 knockdown, and further supports its association with obesity.
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Affiliation(s)
- Lyle Wiemerslage
- Department of NeuroscienceFunctional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Priya A Gohel
- Department of NeuroscienceFunctional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Giulia Maestri
- Department of NeuroscienceFunctional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Torfi G Hilmarsson
- Department of NeuroscienceFunctional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Michel Mickael
- Department of NeuroscienceFunctional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Department of NeuroscienceFunctional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Michael J Williams
- Department of NeuroscienceFunctional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of NeuroscienceFunctional Pharmacology, Uppsala University, Uppsala, Sweden
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75
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Morgan DJ, Poolman TM, Williamson AJK, Wang Z, Clark NR, Ma'ayan A, Whetton AD, Brass A, Matthews LC, Ray DW. Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. Sci Rep 2016; 6:26419. [PMID: 27226058 PMCID: PMC4881047 DOI: 10.1038/srep26419] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/25/2016] [Indexed: 12/21/2022] Open
Abstract
The glucocorticoid receptor (GR), a nuclear receptor and major drug target, has a highly conserved minor splice variant, GRγ, which differs by a single arginine within the DNA binding domain. GRγ, which comprises 10% of all GR transcripts, is constitutively expressed and tightly conserved through mammalian evolution, suggesting an important non-redundant role. However, to date no specific role for GRγ has been reported. We discovered significant differences in subcellular localisation, and nuclear-cytoplasmic shuttling in response to ligand. In addition the GRγ transcriptome and protein interactome was distinct, and with a gene ontology signal for mitochondrial regulation which was confirmed using Seahorse technology. We propose that evolutionary conservation of the single additional arginine in GRγ is driven by a distinct, non-redundant functional profile, including regulation of mitochondrial function.
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Affiliation(s)
- David J Morgan
- School of Computer Sciences, University of Manchester, Kilburn Building, Oxford Road, Manchester, Uk, M13 9PL.,Faculty of Medical and Human Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT
| | - Toryn M Poolman
- Faculty of Medical and Human Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT.,Manchester Centre for Nuclear Hormone Research in Disease, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT.,Manchester Academic Health Sciences Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT
| | - Andrew J K Williamson
- Faculty of Medical and Human Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT.,Manchester Academic Health Sciences Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Neil R Clark
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Anthony D Whetton
- Faculty of Medical and Human Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT.,Manchester Academic Health Sciences Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT.,Stoller Biomarker Discovery Centre, University of Manchester, Wolfson Molecular Imaging Centre, Palatine Road, Manchester, UK, M20 3LJ
| | - Andrew Brass
- School of Computer Sciences, University of Manchester, Kilburn Building, Oxford Road, Manchester, Uk, M13 9PL.,Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT
| | - Laura C Matthews
- Faculty of Medical and Human Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT.,Faculty of Medicine and Health, University of Leeds, Wellcome Trust Brenner Building, St James's University Hospital, Leeds, UK, LS9 7TF
| | - David W Ray
- Faculty of Medical and Human Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT.,Manchester Centre for Nuclear Hormone Research in Disease, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT.,Manchester Academic Health Sciences Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, UK, M13 9PT
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76
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de Leeuw CN, Korecki AJ, Berry GE, Hickmott JW, Lam SL, Lengyell TC, Bonaguro RJ, Borretta LJ, Chopra V, Chou AY, D'Souza CA, Kaspieva O, Laprise S, McInerny SC, Portales-Casamar E, Swanson-Newman MI, Wong K, Yang GS, Zhou M, Jones SJM, Holt RA, Asokan A, Goldowitz D, Wasserman WW, Simpson EM. rAAV-compatible MiniPromoters for restricted expression in the brain and eye. Mol Brain 2016; 9:52. [PMID: 27164903 PMCID: PMC4862195 DOI: 10.1186/s13041-016-0232-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/30/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Small promoters that recapitulate endogenous gene expression patterns are important for basic, preclinical, and now clinical research. Recently, there has been a promising revival of gene therapy for diseases with unmet therapeutic needs. To date, most gene therapies have used viral-based ubiquitous promoters-however, promoters that restrict expression to target cells will minimize off-target side effects, broaden the palette of deliverable therapeutics, and thereby improve safety and efficacy. Here, we take steps towards filling the need for such promoters by developing a high-throughput pipeline that goes from genome-based bioinformatic design to rapid testing in vivo. METHODS For much of this work, therapeutically interesting Pleiades MiniPromoters (MiniPs; ~4 kb human DNA regulatory elements), previously tested in knock-in mice, were "cut down" to ~2.5 kb and tested in recombinant adeno-associated virus (rAAV), the virus of choice for gene therapy of the central nervous system. To evaluate our methods, we generated 29 experimental rAAV2/9 viruses carrying 19 different MiniPs, which were injected intravenously into neonatal mice to allow broad unbiased distribution, and characterized in neural tissues by X-gal immunohistochemistry for icre, or immunofluorescent detection of GFP. RESULTS The data showed that 16 of the 19 (84 %) MiniPs recapitulated the expression pattern of their design source. This included expression of: Ple67 in brain raphe nuclei; Ple155 in Purkinje cells of the cerebellum, and retinal bipolar ON cells; Ple261 in endothelial cells of brain blood vessels; and Ple264 in retinal Müller glia. CONCLUSIONS Overall, the methodology and MiniPs presented here represent important advances for basic and preclinical research, and may enable a paradigm shift in gene therapy.
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Affiliation(s)
- Charles N de Leeuw
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Garrett E Berry
- Gene Therapy Centre, University of North Carolina, Chapel Hill, NC, 27599, U.S.A
| | - Jack W Hickmott
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Siu Ling Lam
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Tess C Lengyell
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Russell J Bonaguro
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Lisa J Borretta
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Vikramjit Chopra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Alice Y Chou
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Cletus A D'Souza
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Olga Kaspieva
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Stéphanie Laprise
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Simone C McInerny
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Elodie Portales-Casamar
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Magdalena I Swanson-Newman
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Kaelan Wong
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - George S Yang
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Michelle Zhou
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Robert A Holt
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2A1, Canada
| | - Aravind Asokan
- Gene Therapy Centre, University of North Carolina, Chapel Hill, NC, 27599, U.S.A
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada. .,Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2A1, Canada.
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Hong EL, Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe GR, Podduturi NR, Tanaka F, Hilton JA, Cherry JM. Principles of metadata organization at the ENCODE data coordination center. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw001. [PMID: 26980513 PMCID: PMC4792520 DOI: 10.1093/database/baw001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/04/2016] [Indexed: 12/20/2022]
Abstract
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects. In addition, we present how the data are validated and used by the ENCODE DCC in creating the ENCODE Portal (https://www.encodeproject.org/). Database URL:www.encodeproject.org
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Affiliation(s)
- Eurie L Hong
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Aditi K Narayanan
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Brian T Lee
- Center for Biomolecular Science and Engineering Santa Cruz, University of California, Santa Cruz, CA, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Timothy R Dreszer
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Greg R Roe
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - Jason A Hilton
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine Department of Genetics, Stanford, CA, USA
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78
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Olivo G, Wiemerslage L, Nilsson EK, Solstrand Dahlberg L, Larsen AL, Olaya Búcaro M, Gustafsson VP, Titova OE, Bandstein M, Larsson EM, Benedict C, Brooks SJ, Schiöth HB. Resting-State Brain and the FTO Obesity Risk Allele: Default Mode, Sensorimotor, and Salience Network Connectivity Underlying Different Somatosensory Integration and Reward Processing between Genotypes. Front Hum Neurosci 2016; 10:52. [PMID: 26924971 PMCID: PMC4756146 DOI: 10.3389/fnhum.2016.00052] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/01/2016] [Indexed: 11/17/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) of the fat mass and obesity associated (FTO) gene are linked to obesity, but how these SNPs influence resting-state neural activation is unknown. Few brain-imaging studies have investigated the influence of obesity-related SNPs on neural activity, and no study has investigated resting-state connectivity patterns. We tested connectivity within three, main resting-state networks: default mode (DMN), sensorimotor (SMN), and salience network (SN) in 30 male participants, grouped based on genotype for the rs9939609 FTO SNP, as well as punishment and reward sensitivity measured by the Behavioral Inhibition (BIS) and Behavioral Activation System (BAS) questionnaires. Because obesity is associated with anomalies in both systems, we calculated a BIS/BAS ratio (BBr) accounting for features of both scores. A prominence of BIS over BAS (higher BBr) resulted in increased connectivity in frontal and paralimbic regions. These alterations were more evident in the obesity-associated AA genotype, where a high BBr was also associated with increased SN connectivity in dopaminergic circuitries, and in a subnetwork involved in somatosensory integration regarding food. Participants with AA genotype and high BBr, compared to corresponding participants in the TT genotype, also showed greater DMN connectivity in regions involved in the processing of food cues, and in the SMN for regions involved in visceral perception and reward-based learning. These findings suggest that neural connectivity patterns influence the sensitivity toward punishment and reward more closely in the AA carriers, predisposing them to developing obesity. Our work explains a complex interaction between genetics, neural patterns, and behavioral measures in determining the risk for obesity and may help develop individually-tailored strategies for obesity prevention.
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Affiliation(s)
- Gaia Olivo
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Lyle Wiemerslage
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Emil K Nilsson
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | | | - Anna L Larsen
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Marcela Olaya Búcaro
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Veronica P Gustafsson
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Olga E Titova
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Marcus Bandstein
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Elna-Marie Larsson
- Section of Neuroradiology, Department of Radiology, Uppsala University Uppsala, Sweden
| | - Christian Benedict
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Samantha J Brooks
- Department of Psychiatry, University of Cape Town Cape Town, South Africa
| | - Helgi B Schiöth
- Functional Pharmacology, Department of Neuroscience, Uppsala University Uppsala, Sweden
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79
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Gee F, Rushton MD, Loughlin J, Reynard LN. Correlation of the osteoarthritis susceptibility variants that map to chromosome 20q13 with an expression quantitative trait locus operating on NCOA3 and with functional variation at the polymorphism rs116855380. Arthritis Rheumatol 2016. [PMID: 26211391 PMCID: PMC4832313 DOI: 10.1002/art.39278] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Objective To functionally characterize the osteoarthritis (OA) susceptibility variants that map to a region of high linkage disequilibrium (LD) on chromosome 20q13 marked by the single‐nucleotide polymorphism (SNP) rs6094710 and encompassing NCOA3 and SULF2. Methods Nucleic acids were extracted from the cartilage of OA patients. Overall and allelic expression of NCOA3 and SULF2 were measured by quantitative reverse transcription–polymerase chain reaction and pyrosequencing, respectively. The functional effect of SNPs within the 20q13 locus was assessed in vitro using luciferase reporter constructs and electrophoretic mobility shift assays (EMSAs). The in vivo effect of nuclear receptor coactivator 3 (NCOA3) protein depletion on primary human OA articular cartilage chondrocytes was assessed using RNA interference. Results Expression of NCOA3 correlated with the genotype at rs6094710 (P = 0.006), and the gene demonstrated allelic expression imbalance (AEI) in individuals heterozygous for the SNP (mean AEI 1.21; P < 0.0001). In both instances, expression of the OA‐associated allele was reduced. In addition, there was reduced enhancer activity of the OA‐associated allele of rs116855380, a SNP in perfect LD with rs6094710 in luciferase assays (P < 0.001). EMSAs demonstrated a protein complex binding with reduced affinity to this allele. Depletion of NCOA3 led to significant changes (all P < 0.05) in the expression of genes involved in cartilage homeostasis. Conclusion NCOA3 is subject to a cis‐acting expression quantitative trait locus in articular cartilage, which correlates with the OA association signal and with the OA‐associated allele of the functional SNP rs116855380, a SNP that is located only 10.3 kb upstream of NCOA3. These findings elucidate the effect of the association of the 20q13 region on OA cartilage and provide compelling evidence of a potentially causal candidate SNP.
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Affiliation(s)
- Fiona Gee
- Newcastle University, Newcastle upon Tyne, UK
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80
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Di Giorgio E, Brancolini C. Regulation of class IIa HDAC activities: it is not only matter of subcellular localization. Epigenomics 2016; 8:251-69. [DOI: 10.2217/epi.15.106] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In response to environmental cues, enzymes that influence the functions of proteins, through reversible post-translational modifications supervise the coordination of cell behavior like orchestral conductors. Class IIa histone deacetylases (HDACs) belong to this category. Even though in vertebrates these deacetylases have discarded the core enzymatic activity, class IIa HDACs can assemble into multiprotein complexes devoted to transcriptional reprogramming, including but not limited to epigenetic changes. Class IIa HDACs are subjected to variegated and interconnected layers of regulation, which reflect the wide range of biological responses under the scrutiny of this gene family. Here, we discuss about the key mechanisms that fine tune class IIa HDACs activities.
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Affiliation(s)
- Eros Di Giorgio
- Department of Medical & Biological Sciences, Università degli Studi di Udine., P.le Kolbe 4 - 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medical & Biological Sciences, Università degli Studi di Udine., P.le Kolbe 4 - 33100 Udine, Italy
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81
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Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe G, Podduturi NR, Tanaka F, Hong EL, Cherry JM. ENCODE data at the ENCODE portal. Nucleic Acids Res 2016; 44:D726-32. [PMID: 26527727 PMCID: PMC4702836 DOI: 10.1093/nar/gkv1160] [Citation(s) in RCA: 326] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/07/2015] [Accepted: 10/19/2015] [Indexed: 01/20/2023] Open
Abstract
The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of creating a comprehensive catalog of functional elements in the human genome. This phase of the project includes an expansion of assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a wide range of cell and tissue types to identify putative regulatory elements. To date, results for almost 5000 experiments have been released for use by the scientific community. These data are available for searching, visualization and download at the new ENCODE Portal (www.encodeproject.org). The revamped ENCODE Portal provides new ways to browse and search the ENCODE data based on the metadata that describe the assays as well as summaries of the assays that focus on data provenance. In addition, it is a flexible platform that allows integration of genomic data from multiple projects. The portal experience was designed to improve access to ENCODE data by relying on metadata that allow reusability and reproducibility of the experiments.
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Affiliation(s)
- Cricket A Sloan
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Esther T Chan
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Jean M Davidson
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Venkat S Malladi
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - J Seth Strattan
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Benjamin C Hitz
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Idan Gabdank
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Aditi K Narayanan
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Marcus Ho
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Brian T Lee
- University of California at Santa Cruz, Center for Biomolecular Science and Engineering, Santa Cruz, CA, 95064, USA
| | - Laurence D Rowe
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Timothy R Dreszer
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Greg Roe
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Nikhil R Podduturi
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Forrest Tanaka
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - Eurie L Hong
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
| | - J Michael Cherry
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA
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Hazlewood RJ, Roos BR, Solivan-Timpe F, Honkanen RA, Jampol LM, Gieser SC, Meyer KJ, Mullins RF, Kuehn MH, Scheetz TE, Kwon YH, Alward WLM, Stone EM, Fingert JH. Heterozygous triplication of upstream regulatory sequences leads to dysregulation of matrix metalloproteinase 19 in patients with cavitary optic disc anomaly. Hum Mutat 2015; 36:369-78. [PMID: 25581579 DOI: 10.1002/humu.22754] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 12/23/2014] [Indexed: 11/06/2022]
Abstract
Patients with a congenital optic nerve disease, cavitary optic disc anomaly (CODA), are born with profound excavation of the optic nerve resembling glaucoma. We previously mapped the gene that causes autosomal-dominant CODA in a large pedigree to a chromosome 12q locus. Using comparative genomic hybridization and quantitative PCR analysis of this pedigree, we report identifying a 6-Kbp heterozygous triplication upstream of the matrix metalloproteinase 19 (MMP19) gene, present in all 17 affected family members and no normal members. Moreover, the triplication was not detected in 78 control subjects or in the Database of Genomic Variants. We further detected the same 6-Kbp triplication in one of 24 unrelated CODA patients and in none of 172 glaucoma patients. Analysis with a Luciferase assay showed that the 6-Kbp sequence has transcription enhancer activity. A 773-bp fragment of the 6-Kbp DNA segment increased downstream gene expression eightfold, suggesting that triplication of this sequence may lead to dysregulation of the downstream gene, MMP19, in CODA patients. Lastly, immunohistochemical analysis of human donor eyes revealed strong expression of MMP19 in optic nerve head. These data strongly suggest that triplication of an enhancer may lead to overexpression of MMP19 in the optic nerve that causes CODA.
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Affiliation(s)
- Ralph J Hazlewood
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
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Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. Genome Biol 2015; 16:263. [PMID: 26607552 PMCID: PMC4659173 DOI: 10.1186/s13059-015-0827-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0827-6) contains supplementary material, which is available to authorized users.
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84
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Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation. Genetics 2015; 202:733-50. [PMID: 26596347 DOI: 10.1534/genetics.115.178095] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/18/2015] [Indexed: 12/18/2022] Open
Abstract
A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called "3-population composite likelihood ratio" (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events.
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85
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Metagenomics: Retrospect and Prospects in High Throughput Age. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2015; 2015:121735. [PMID: 26664751 PMCID: PMC4664791 DOI: 10.1155/2015/121735] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/26/2015] [Indexed: 01/30/2023]
Abstract
In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.
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Taccioli C, Garofalo M, Chen H, Jiang Y, Tagliazucchi GM, Di Leva G, Alder H, Fadda P, Middleton J, Smalley KJ, Selmi T, Naidu S, Farber JL, Croce CM, Fong LY. Repression of Esophageal Neoplasia and Inflammatory Signaling by Anti-miR-31 Delivery In Vivo. J Natl Cancer Inst 2015; 107:djv220. [PMID: 26286729 PMCID: PMC4675101 DOI: 10.1093/jnci/djv220] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 01/31/2015] [Accepted: 07/20/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Overexpression of microRNA-31 (miR-31) is implicated in the pathogenesis of esophageal squamous cell carcinoma (ESCC), a deadly disease associated with dietary zinc deficiency. Using a rat model that recapitulates features of human ESCC, the mechanism whereby Zn regulates miR-31 expression to promote ESCC is examined. METHODS To inhibit in vivo esophageal miR-31 overexpression in Zn-deficient rats (n = 12-20 per group), locked nucleic acid-modified anti-miR-31 oligonucleotides were administered over five weeks. miR-31 expression was determined by northern blotting, quantitative polymerase chain reaction, and in situ hybridization. Physiological miR-31 targets were identified by microarray analysis and verified by luciferase reporter assay. Cellular proliferation, apoptosis, and expression of inflammation genes were determined by immunoblotting, caspase assays, and immunohistochemistry. The miR-31 promoter in Zn-deficient esophagus was identified by ChIP-seq using an antibody for histone mark H3K4me3. Data were analyzed with t test and analysis of variance. All statistical tests were two-sided. RESULTS In vivo, anti-miR-31 reduced miR-31 overexpression (P = .002) and suppressed the esophageal preneoplasia in Zn-deficient rats. At the same time, the miR-31 target Stk40 was derepressed, thereby inhibiting the STK40-NF-κΒ-controlled inflammatory pathway, with resultant decreased cellular proliferation and activated apoptosis (caspase 3/7 activities, fold change = 10.7, P = .005). This same connection between miR-31 overexpression and STK40/NF-κΒ expression was also documented in human ESCC cell lines. In Zn-deficient esophagus, the miR-31 promoter region and NF-κΒ binding site were activated. Zn replenishment restored the regulation of this genomic region and a normal esophageal phenotype. CONCLUSIONS The data define the in vivo signaling pathway underlying interaction of Zn deficiency and miR-31 overexpression in esophageal neoplasia and provide a mechanistic rationale for miR-31 as a therapeutic target for ESCC.
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Affiliation(s)
- Cristian Taccioli
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Michela Garofalo
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Hongping Chen
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Yubao Jiang
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Guidantonio Malagoli Tagliazucchi
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Gianpiero Di Leva
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Hansjuerg Alder
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Paolo Fadda
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Justin Middleton
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Karl J Smalley
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Tommaso Selmi
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Srivatsava Naidu
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - John L Farber
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Carlo M Croce
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN)
| | - Louise Y Fong
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (CT, MG, GDL, HA, PF, JM, CMC); Kimmel Cancer Center (HC, YJ, KJS, LYF) and Department of Pathology, Anatomy, and Cell Biology (YJ, JLF, LYF), Thomas Jefferson University, Philadelphia, PA; Center for Genome Research (CT, GMT), Department of Life Sciences (TS), University of Modena and Reggio Emilia, Modena, Italy (CT, GMT); Transcriptional Networks in Lung Cancer Group, Manchester Institute, University of Manchester, UK (MG, SN).
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Gloss BS, Dinger ME. The specificity of long noncoding RNA expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:16-22. [PMID: 26297315 DOI: 10.1016/j.bbagrm.2015.08.005] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/12/2015] [Accepted: 08/12/2015] [Indexed: 01/09/2023]
Abstract
Over the last decade, long noncoding RNAs (lncRNAs) have emerged as a fundamental molecular class whose members play pivotal roles in the regulation of the genome. The observation of pervasive transcription of mammalian genomes in the early 2000s sparked a revolution in the understanding of information flow in eukaryotic cells and the incredible flexibility and dynamic nature of the transcriptome. As a molecular class, distinct loci yielding lncRNAs are set to outnumber those yielding mRNAs. However, like many important discoveries, the road leading to uncovering this diverse class of molecules that act through a remarkable repertoire of mechanisms, was not a straight one. The same characteristic that most distinguishes lncRNAs from mRNAs, i.e. their developmental-stage, tissue-, and cell-specific expression, was one of the major impediments to their discovery and recognition as potentially functional regulatory molecules. With growing numbers of lncRNAs being assigned to biological functions, the specificity of lncRNA expression is now increasingly recognized as a characteristic that imbues lncRNAs with great potential as biomarkers and for the development of highly targeted therapeutics. Here we review the history of lncRNA research and how technological advances and insight into biological complexity have gone hand-in-hand in shaping this revolution. We anticipate that as increasing numbers of these molecules, often described as the dark matter of the genome, are characterized and the structure-function relationship of lncRNAs becomes better understood, it may ultimately be feasible to decipher what these non-(protein)-coding genes encode. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Brian S Gloss
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia
| | - Marcel E Dinger
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Australia.
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88
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Bomer N, den Hollander W, Ramos YFM, Bos SD, van der Breggen R, Lakenberg N, Pepers BA, van Eeden AE, Darvishan A, Tobi EW, Duijnisveld BJ, van den Akker EB, Heijmans BT, van Roon-Mom WMC, Verbeek FJ, van Osch GJVM, Nelissen RGHH, Slagboom PE, Meulenbelt I. Underlying molecular mechanisms of DIO2 susceptibility in symptomatic osteoarthritis. Ann Rheum Dis 2015; 74:1571-9. [PMID: 24695009 PMCID: PMC4516000 DOI: 10.1136/annrheumdis-2013-204739] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 03/14/2014] [Accepted: 03/15/2014] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To investigate how the genetic susceptibility gene DIO2 confers risk to osteoarthritis (OA) onset in humans and to explore whether counteracting the deleterious effect could contribute to novel therapeutic approaches. METHODS Epigenetically regulated expression of DIO2 was explored by assessing methylation of positional CpG-dinucleotides and the respective DIO2 expression in OA-affected and macroscopically preserved articular cartilage from end-stage OA patients. In a human in vitro chondrogenesis model, we measured the effects when thyroid signalling during culturing was either enhanced (excess T3 or lentiviral induced DIO2 overexpression) or decreased (iopanoic acid). RESULTS OA-related changes in methylation at a specific CpG dinucleotide upstream of DIO2 caused significant upregulation of its expression (β=4.96; p=0.0016). This effect was enhanced and appeared driven specifically by DIO2 rs225014 risk allele carriers (β=5.58, p=0.0006). During in vitro chondrogenesis, DIO2 overexpression resulted in a significant reduced capacity of chondrocytes to deposit extracellular matrix (ECM) components, concurrent with significant induction of ECM degrading enzymes (ADAMTS5, MMP13) and markers of mineralisation (ALPL, COL1A1). Given their concurrent and significant upregulation of expression, this process is likely mediated via HIF-2α/RUNX2 signalling. In contrast, we showed that inhibiting deiodinases during in vitro chondrogenesis contributed to prolonged cartilage homeostasis as reflected by significant increased deposition of ECM components and attenuated upregulation of matrix degrading enzymes. CONCLUSIONS Our findings show how genetic variation at DIO2 could confer risk to OA and raised the possibility that counteracting thyroid signalling may be a novel therapeutic approach.
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Affiliation(s)
- Nils Bomer
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands
- IDEAL, The Netherlands
| | | | | | - Steffan D Bos
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands
- Genomics Initiative, sponsored by the NCHA, Leiden, The Netherlands
| | | | - Nico Lakenberg
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands
| | - Barry A Pepers
- Department of Human Genetics, LUMC, Leiden, The Netherlands
| | | | - Arash Darvishan
- Department of Imaging & BioInformatics, LIACS, Leiden, The Netherlands
| | - Elmar W Tobi
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands
- IDEAL, The Netherlands
| | | | - Erik B van den Akker
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Bastiaan T Heijmans
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands
- Genomics Initiative, sponsored by the NCHA, Leiden, The Netherlands
| | | | - Fons J Verbeek
- Department of Imaging & BioInformatics, LIACS, Leiden, The Netherlands
| | - Gerjo J V M van Osch
- Department of Orthopaedics, Erasmus MC, Rotterdam, The Netherlands
- Deptartment of Otorhinolaryngology, Erasmus MC, Rotterdam, The Netherlands
| | | | - P Eline Slagboom
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands
- IDEAL, The Netherlands
- Genomics Initiative, sponsored by the NCHA, Leiden, The Netherlands
| | - Ingrid Meulenbelt
- Department of Molecular Epidemiology, LUMC, Leiden, The Netherlands
- Genomics Initiative, sponsored by the NCHA, Leiden, The Netherlands
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89
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Abstract
Strict control of tissue-specific gene expression plays a pivotal role during lineage commitment. The transcription factor c-Myb has an essential role in adult haematopoiesis and functions as an oncogene when rearranged in human cancers. Here we have exploited digital genomic footprinting analysis to obtain a global picture of c-Myb occupancy in the genome of six different haematopoietic cell-types. We have biologically validated several c-Myb footprints using c-Myb knockdown data, reporter assays and DamID analysis. We show that our predicted conserved c-Myb footprints are highly dependent on the haematopoietic cell type, but that there is a group of gene targets common to all cell-types analysed. Furthermore, we find that c-Myb footprints co-localise with active histone mark H3K4me3 and are significantly enriched at exons. We analysed co-localisation of c-Myb footprints with 104 chromatin regulatory factors in K562 cells, and identified nine proteins that are enriched together with c-Myb footprints on genes positively regulated by c-Myb and one protein enriched on negatively regulated genes. Our data suggest that c-Myb is a transcription factor with multifaceted target regulation depending on cell type.
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90
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Wang Z, Li X, Jiang Y, Shao Q, Liu Q, Chen B, Huang D. swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing. PLoS One 2015; 10:e0132866. [PMID: 26176536 PMCID: PMC4503785 DOI: 10.1371/journal.pone.0132866] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/18/2015] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a widespread epigenetic modification that plays an essential role in gene expression through transcriptional regulation and chromatin remodeling. The emergence of whole genome bisulfite sequencing (WGBS) represents an important milestone in the detection of DNA methylation. Characterization of differential methylated regions (DMRs) is fundamental as well for further functional analysis. In this study, we present swDMR (http://sourceforge.net/projects/swDMR/) for the comprehensive analysis of DMRs from whole genome methylation profiles by a sliding window approach. It is an integrated tool designed for WGBS data, which not only implements accessible statistical methods to perform hypothesis test adapted to two or more samples without replicates, but false discovery rate was also controlled by multiple test correction. Downstream analysis tools were also provided, including cluster, annotation and visualization modules. In summary, based on WGBS data, swDMR can produce abundant information of differential methylated regions. As a convenient and flexible tool, we believe swDMR will bring us closer to unveil the potential functional regions involved in epigenetic regulation.
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Affiliation(s)
- Zhen Wang
- Research Center of Blood Transfusion Medicine, Key Laboratory of Laboratory Medicine (Wenzhou Medical University), Ministry of Education, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Xianfeng Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qianzhi Shao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qi Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - BingYu Chen
- Research Center of Blood Transfusion Medicine, Key Laboratory of Laboratory Medicine (Wenzhou Medical University), Ministry of Education, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Dongsheng Huang
- Research Center of Blood Transfusion Medicine, Key Laboratory of Laboratory Medicine (Wenzhou Medical University), Ministry of Education, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
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91
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Tian X, Sun D, Zhao S, Xiong H, Fang J. Screening of potential diagnostic markers and therapeutic targets against colorectal cancer. Onco Targets Ther 2015; 8:1691-9. [PMID: 26185457 PMCID: PMC4501159 DOI: 10.2147/ott.s81621] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Objective To identify genes with aberrant promoter methylation for developing novel diagnostic markers and therapeutic targets against primary colorectal cancer (CRC). Methods Two paired CRC and adjacent normal tissues were collected from two CRC patients. A Resi: MBD2b protein-sepharose-4B column was used to enrich the methylated DNA fragments. Difference in the average methylation level of each DNA methylation region between the tumor and control samples was determined by log2 fold change (FC) in each patient to screen the differentially methylated DNA regions. Genes with log2FC value ≥4 or ≤−4 were identified to be hypermethylated and hypomethylated, respectively. Then, the underlying functions of methylated genes were speculated by Gene Ontology database and pathway enrichment analyses. Furthermore, a protein–protein interaction network was built using Search Tool for the Retrieval of Interacting Genes/Proteins database, and the transcription factor binding sites were screened via the Encyclopedia of DNA Elements (ENCODE) database. Results Totally, 2,284 and 1,142 genes were predicted to have aberrant promoter hypermethylation or hypomethylation, respectively. MAP3K5, MAP3K8, MAPK14, and MAPK9 with promoter hypermethylation functioned via MAPK signaling pathway, focal adhesion, or Wnt signaling pathway, whereas MAP2K1, MAPK3, MAPK11, and MAPK7 with promoter hypomethylation functioned via TGF-beta signaling pathway, neurotrophin signaling pathway, and chemokine signaling pathway. CREBBP, PIK3R1, MAPK14, APP, ESR1, MAPK3, and HRAS were the seven hubs in the constructed protein–protein interaction network. RPL22, RPL36, RPLP2, RPS7, and RPS9 were commonly regulated by transcription factors, and YY1 and IRF4 were hypermethylated. Conclusion MAPK14, MAPK3, HRAS, YY1, and IRF4 may be considered as potential biomarkers for early diagnosis and therapy of CRC.
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Affiliation(s)
- XiaoQing Tian
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - DanFeng Sun
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - ShuLiang Zhao
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hua Xiong
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - JingYuan Fang
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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92
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Cardiac gene expression data and in silico analysis provide novel insights into human and mouse taste receptor gene regulation. Naunyn Schmiedebergs Arch Pharmacol 2015; 388:1009-27. [PMID: 25986534 DOI: 10.1007/s00210-015-1118-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/24/2015] [Indexed: 12/21/2022]
Abstract
G protein-coupled receptors are the principal mediators of the sweet, umami, bitter, and fat taste qualities in mammals. Intriguingly, the taste receptors are also expressed outside of the oral cavity, including in the gut, airways, brain, and heart, where they have additional functions and contribute to disease. However, there is little known about the mechanisms governing the transcriptional regulation of taste receptor genes. Following our recent delineation of taste receptors in the heart, we investigated the genomic loci encoding for taste receptors to gain insight into the regulatory mechanisms that drive their expression in the heart. Gene expression analyses of healthy and diseased human and mouse hearts showed coordinated expression for a subset of chromosomally clustered taste receptors. This chromosomal clustering mirrored the cardiac expression profile, suggesting that a common gene regulatory block may control the taste receptor locus. We identified unique domains with strong regulatory potential in the vicinity of taste receptor genes. We also performed de novo motif enrichment in the proximal promoter regions and found several overrepresented DNA motifs in cardiac taste receptor gene promoters corresponding to ubiquitous and cardiac-specific transcription factor binding sites. Thus, combining cardiac gene expression data with bioinformatic analyses, this study has provided insights into the noncoding regulatory landscape for taste GPCRs. These findings also have broader relevance for the study of taste GPCRs outside of the classical gustatory system, where understanding the mechanisms controlling the expression of these receptors may have implications for future therapeutic development.
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93
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Montes M, Nielsen MM, Maglieri G, Jacobsen A, Højfeldt J, Agrawal-Singh S, Hansen K, Helin K, van de Werken HJG, Pedersen JS, Lund AH. The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence. Nat Commun 2015; 6:6967. [PMID: 25908244 DOI: 10.1038/ncomms7967] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 03/20/2015] [Indexed: 12/31/2022] Open
Abstract
Oncogene-induced senescence (OIS) can occur in response to oncogenic insults and is considered an important tumour suppressor mechanism. Here we identify the lncRNA MIR31HG as upregulated in OIS and find that knockdown of MIR31HG promotes a strong p16(INK4A)-dependent senescence phenotype. Under normal conditions, MIR31HG is found in both nucleus and cytoplasm, but following B-RAF expression MIR31HG is located mainly in the cytoplasm. We show that MIR31HG interacts with both INK4A and MIR31HG genomic regions and with Polycomb group (PcG) proteins, and that MIR31HG is required for PcG-mediated repression of the INK4A locus. We further identify a functional enhancer, located between MIR31HG and INK4A, which becomes activated during OIS and interacts with the MIR31HG promoter. Data from melanoma patients show a negative correlation between MIR31HG and p16(INK4A) expression levels, suggesting a role for this transcript in cancer. Hence, our data provide a new lncRNA-mediated regulatory mechanism for the tumour suppressor p16(INK4A).
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Affiliation(s)
- Marta Montes
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark
| | - Morten M Nielsen
- Department of Molecular Medicine, Århus University Hospital, Skejby, Århus N 8200, Denmark
| | - Giulia Maglieri
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark
| | - Anders Jacobsen
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jonas Højfeldt
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Shuchi Agrawal-Singh
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Klaus Hansen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Jakob S Pedersen
- Department of Molecular Medicine, Århus University Hospital, Skejby, Århus N 8200, Denmark.,Bioinformatics Research Center, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark
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Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SYR. Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev 2015; 29:803-16. [PMID: 25877919 PMCID: PMC4403257 DOI: 10.1101/gad.255109.114] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/20/2015] [Indexed: 11/29/2022]
Abstract
Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Hirsch et al. performed a functional RNAi screen and identified components of the SAGA histone acetyltransferase complex, in particular Gcn5, as critical regulators of reprogramming initiation. In mouse pluripotent stem cells, Gcn5 strongly associates with Myc, and, upon initiation of somatic reprogramming, Gcn5 and Myc form a positive feed-forward loop that activates a distinct alternative splicing network and the early acquisition of pluripotency-associated splicing events. Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we performed a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. We identified components of the SAGA histone acetyltransferase complex, in particular Gcn5, as critical regulators of reprogramming initiation. Furthermore, we showed in mouse pluripotent stem cells that Gcn5 strongly associates with Myc and that, upon initiation of somatic reprogramming, Gcn5 and Myc form a positive feed-forward loop that activates a distinct alternative splicing network and the early acquisition of pluripotency-associated splicing events. These studies expose a Myc–SAGA pathway that drives expression of an essential alternative splicing regulatory network during somatic cell reprogramming.
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Affiliation(s)
- Calley L Hirsch
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Zeynep Coban Akdemir
- Program in Genes and Development, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Li Wang
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA; Program in Molecular Carcinogenesis, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Gowtham Jayakumaran
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Dan Trcka
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Alexander Weiss
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - J Javier Hernandez
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Hong Han
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Xueping Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zheng Xia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Andrew P Salinger
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Marenda Wilson
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Frederick Vizeacoumar
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Alessandro Datti
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Wei Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Austin J Cooney
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michelle C Barton
- Program in Genes and Development, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Benjamin J Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Jeffrey L Wrana
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada;
| | - Sharon Y R Dent
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA;
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95
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Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene. BIOMED RESEARCH INTERNATIONAL 2015; 2015:514709. [PMID: 25918715 PMCID: PMC4396065 DOI: 10.1155/2015/514709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/12/2015] [Accepted: 02/26/2015] [Indexed: 01/05/2023]
Abstract
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has emerged as a powerful customizable artificial nuclease to facilitate precise genetic correction for tissue regeneration and isogenic disease modeling. However, previous studies reported substantial off-target activities of CRISPR system in human cells, and the enormous putative off-target sites are labor-intensive to be validated experimentally, thus motivating bioinformatics methods for rational design of CRISPR system and prediction of its potential off-target effects. Here, we describe an integrative analytical process to identify specific CRISPR target sites in the human β-globin gene (HBB) and predict their off-target effects. Our method includes off-target analysis in both coding and noncoding regions, which was neglected by previous studies. It was found that the CRISPR target sites in the introns have fewer off-target sites in the coding regions than those in the exons. Remarkably, target sites containing certain transcriptional factor motif have enriched binding sites of relevant transcriptional factor in their off-target sets. We also found that the intron sites have fewer SNPs, which leads to less variation of CRISPR efficiency in different individuals during clinical applications. Our studies provide a standard analytical procedure to select specific CRISPR targets for genetic correction.
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96
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Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL. Ontology application and use at the ENCODE DCC. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav010. [PMID: 25776021 PMCID: PMC4360730 DOI: 10.1093/database/bav010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a catalog of genomic annotations. To date, the project has generated over 4000 experiments across more than 350 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory network and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All ENCODE experimental data, metadata and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage and distribution to community resources and the scientific community. As the volume of data increases, the organization of experimental details becomes increasingly complicated and demands careful curation to identify related experiments. Here, we describe the ENCODE DCC’s use of ontologies to standardize experimental metadata. We discuss how ontologies, when used to annotate metadata, provide improved searching capabilities and facilitate the ability to find connections within a set of experiments. Additionally, we provide examples of how ontologies are used to annotate ENCODE metadata and how the annotations can be identified via ontology-driven searches at the ENCODE portal. As genomic datasets grow larger and more interconnected, standardization of metadata becomes increasingly vital to allow for exploration and comparison of data between different scientific projects. Database URL: https://www.encodeproject.org/
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Affiliation(s)
- Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Drew T Erickson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gregory R Roe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matt Simison
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - W James Kent
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eurie L Hong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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97
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Salvi A, Bongarzone I, Ferrari L, Abeni E, Arici B, De Bortoli M, Scuri S, Bonini D, Grossi I, Benetti A, Baiocchi G, Portolani N, De Petro G. Molecular characterization of LASP-1 expression reveals vimentin as its new partner in human hepatocellular carcinoma cells. Int J Oncol 2015; 46:1901-12. [PMID: 25760690 PMCID: PMC4383023 DOI: 10.3892/ijo.2015.2923] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/03/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related mortality worldwide. We have previously reported that LASP-1 is a downstream protein of the urokinase type plasminogen activator (uPA). Here we investigated the role of LASP-1 in HCC by a molecular and biological characterization of LASP-1 expression in human HCC specimens and in cultured HCC cells. We determined the LASP-1 mRNA expression levels in 55 HCC cases with different hepatic background disease. We identified 3 groups of patients with high, equal or low LASP-1 mRNA levels in HCC tissues compared to the peritumoral (PT) tissues. In particular we found that i) the HCCs displayed a higher LASP-1 mRNA level in HCC compared to PT tissues; ii) the expression levels of LASP-1 mRNA in female HCCs were significantly higher compared to male HCCs; iii) the cirrhotic HCCs displayed a higher LASP-1 mRNA. Further, the biological characterization of the ectopic LASP-1 overexpression in HCC cells, using MALDI-TOF mass spectrometer on the LASP-1 co-immunoprecipitated fractions, displayed vimentin as a novel putative partner of LASP-1. Our results suggest that LASP-1 mRNA overexpression may be mainly implicated in female HCCs and cirrhotic HCCs; and that LASP1 may play its role with vimentin in HCC cells.
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Affiliation(s)
- Alessandro Salvi
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Italia Bongarzone
- Department of Experimental Oncology and Molecular Medicine, Proteomics Laboratory, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lia Ferrari
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Edoardo Abeni
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Bruna Arici
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Maida De Bortoli
- Department of Experimental Oncology and Molecular Medicine, Proteomics Laboratory, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sabrina Scuri
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Daniela Bonini
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Ilaria Grossi
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Anna Benetti
- Department of Clinical and Experimental Sciences, Division of Morbid Anatomy, University of Brescia, Brescia, Italy
| | - Gianluca Baiocchi
- Department of Clinical and Experimental Sciences, Surgical Clinic, University of Brescia, Brescia, Italy
| | - Nazario Portolani
- Department of Clinical and Experimental Sciences, Surgical Clinic, University of Brescia, Brescia, Italy
| | - Giuseppina De Petro
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
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98
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Abstract
When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking.
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Affiliation(s)
- Avazeh T Ghanbarian
- Department of Biology and Biochemisty, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- Department of Biology and Biochemisty, University of Bath, Bath, United Kingdom
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99
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Abstract
Observations over the last decade suggest that some RNA transcripts, such as non-coding RNAs, function in regulating the transcriptional and epigenetic state of gene expression. DNA methylation appears to be operative in non-coding RNA regulation of gene expression. Interestingly, methylated cytosines undergo deamination to remove the methylation, which if not properly repaired results in the methylated cytosine being recognized by the cell as a thymine. This observation suggests that the process of non-coding RNA-directed epigenetic targeting also has the potential to alter the genomic landscape of the cell by changing cytosines to thymines and ultimately influence the evolution of the cell. This proposed theory of "RNA-mediated gene evolution" might be one possible mechanism of action whereby RNA participates in the natural selective process to drive cellular and possibly organismal evolution.
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Affiliation(s)
- Kevin V Morris
- a The University of New South Wales; Biotechnology and Biomedical Sciences ; Sydney , NSW Australia
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100
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Taher L, Narlikar L, Ovcharenko I. Identification and computational analysis of gene regulatory elements. Cold Spring Harb Protoc 2015; 2015:pdb.top083642. [PMID: 25561628 PMCID: PMC5885252 DOI: 10.1101/pdb.top083642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the last two decades, advances in experimental and computational technologies have greatly facilitated genomic research. Next-generation sequencing technologies have made de novo sequencing of large genomes affordable, and powerful computational approaches have enabled accurate annotations of genomic DNA sequences. Charting functional regions in genomes must account for not only the coding sequences, but also noncoding RNAs, repetitive elements, chromatin states, epigenetic modifications, and gene regulatory elements. A mix of comparative genomics, high-throughput biological experiments, and machine learning approaches has played a major role in this truly global effort. Here we describe some of these approaches and provide an account of our current understanding of the complex landscape of the human genome. We also present overviews of different publicly available, large-scale experimental data sets and computational tools, which we hope will prove beneficial for researchers working with large and complex genomes.
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Affiliation(s)
- Leila Taher
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, 18051 Rostock, Germany
| | - Leelavati Narlikar
- Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
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