251
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Dong Z, Wang H, Chen H, Jiang H, Yuan J, Yang Z, Wang WJ, Xu F, Guo X, Cao Y, Zhu Z, Geng C, Cheung WC, Kwok YK, Yang H, Leung TY, Morton CC, Cheung SW, Choy KW. Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics. Genet Med 2017; 20:697-707. [PMID: 29095815 PMCID: PMC5932280 DOI: 10.1038/gim.2017.170] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/14/2017] [Indexed: 02/04/2023] Open
Abstract
Purpose Recent studies demonstrate that whole-genome sequencing (WGS) enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in The 1000 Genomes Project without knowing affected bands. Methods The 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparently BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories. We applied our analytical tool to 1,166 genomes from the 1000 Genomes Project with sufficient physical coverage (8.25-fold). Results Our approach detected four reciprocal balanced translocations and four inversions ranging in size from 57.9 kb to 13.3 Mb, all of which were confirmed by cytogenetic methods and PCR studies. One of DNAs has a subtle translocation that is not readily identified by chromosome analysis due to similar banding patterns and size of exchanged segments, and another results in disruption of all transcripts of an OMIM gene. Conclusions Our study demonstrates the extension of utilizing low-coverage WGS for unbiased detection of BCAs including translocations and inversions previously unknown in the 1000 Genomes Project.
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Affiliation(s)
- Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,BGI-Shenzhen, Shenzhen, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Huilin Wang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital, Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Haixiao Chen
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Jianying Yuan
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Zhenjun Yang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Ye Cao
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhenzhen Zhu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Chunyu Geng
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Wan Chee Cheung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Harvard Medical School, Boston, Massachusetts, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. .,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Center, Manchester, UK.
| | - Sau Wai Cheung
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
| | - Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China. .,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China.
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252
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Ahmad A, Strohbuecker S, Tufarelli C, Sottile V. Expression of a SOX1 overlapping transcript in neural differentiation and cancer models. Cell Mol Life Sci 2017; 74:4245-4258. [PMID: 28674729 PMCID: PMC5641280 DOI: 10.1007/s00018-017-2580-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 06/04/2017] [Accepted: 06/26/2017] [Indexed: 12/28/2022]
Abstract
SOX1 is a member of the SOXB1 subgroup of transcription factors involved in early embryogenesis, CNS development and maintenance of neural stem cells. The structure and regulation of the human SOX1 locus has been less studied than that of SOX2, another member of the SOXB1 subgroup for which an overlapping transcript has been reported. Here we report that the SOX1 locus harbours a SOX1 overlapping transcript (SOX1-OT), and describe expression, splicing variants and detection of SOX1-OT in different stem and cancer cells. RT-PCR and RACE experiments were performed to detect and characterise the structure of SOX1-OT in neuroprogenitor cultures and across different cancer cell lines. SOX1-OT was found to present a complex structure including several unannotated exons, different transcript variants and at least two potential transcription start sites. SOX1-OT was found to be highly expressed in differentiated neural stem cells across different time points of differentiation, and its expression correlated with SOX1 gene expression. Concomitant expression of SOX1 and SOX1-OT was further observed in several cancer cell models. While the function of this transcript is unknown, the regulatory role reported for other lncRNAs strongly suggests a possible role for SOX1-OT in regulating SOX1 expression, as previously observed for SOX2. The elucidation of the genetic and regulatory context governing SOX1 expression will contribute to clarifying its role in stem cell differentiation and tumorigenesis.
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Affiliation(s)
- Azaz Ahmad
- Wolfson STEM Centre, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Stephanie Strohbuecker
- Wolfson STEM Centre, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Cristina Tufarelli
- Division of Graduate Entry Medicine & Health, School of Medicine, University of Nottingham, Derby, UK.
| | - Virginie Sottile
- Wolfson STEM Centre, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK.
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253
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Yang F, Wang J, Pierce BL, Chen LS. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res 2017; 27:1859-1871. [PMID: 29021290 PMCID: PMC5668943 DOI: 10.1101/gr.216754.116] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
Abstract
The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their biological mechanisms. One common trans-eQTLs mechanism is "mediation" by a local (cis) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are "cis-mediators" of trans-eQTLs, including those "cis-hubs" involved in regulation of many trans-genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans-eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis-mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis-hubs and trans-eQTL regulation across tissue types.
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Affiliation(s)
- Fan Yang
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
- Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois 60637, USA
| | - Lin S Chen
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois 60637, USA
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254
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Hong S, Kim D. Computational characterization of chromatin domain boundary-associated genomic elements. Nucleic Acids Res 2017; 45:10403-10414. [PMID: 28977568 PMCID: PMC5737353 DOI: 10.1093/nar/gkx738] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/14/2017] [Indexed: 02/06/2023] Open
Abstract
Topologically associated domains (TADs) are 3D genomic structures with high internal interactions that play important roles in genome compaction and gene regulation. Their genomic locations and their association with CCCTC-binding factor (CTCF)-binding sites and transcription start sites (TSSs) were recently reported. However, the relationship between TADs and other genomic elements has not been systematically evaluated. This was addressed in the present study, with a focus on the enrichment of these genomic elements and their ability to predict the TAD boundary region. We found that consensus CTCF-binding sites were strongly associated with TAD boundaries as well as with the transcription factors (TFs) Zinc finger protein (ZNF)143 and Yin Yang (YY)1. TAD boundary-associated genomic elements include DNase I-hypersensitive sites, H3K36 trimethylation, TSSs, RNA polymerase II, and TFs such as Specificity protein 1, ZNF274 and SIX homeobox 5. Computational modeling with these genomic elements suggests that they have distinct roles in TAD boundary formation. We propose a structural model of TAD boundaries based on these findings that provides a basis for studying the mechanism of chromatin structure formation and gene regulation.
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Affiliation(s)
- Seungpyo Hong
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
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255
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A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers. Sci Rep 2017; 7:13347. [PMID: 29042628 PMCID: PMC5645309 DOI: 10.1038/s41598-017-13748-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 10/02/2017] [Indexed: 01/06/2023] Open
Abstract
The transcription factor Runx1 is essential for definitive haematopoiesis, and the RUNX1 gene is frequently translocated or mutated in leukaemia. Runx1 is transcribed from two promoters, P1 and P2, to give rise to different protein isoforms. Although the expression of Runx1 must be tightly regulated for normal blood development, the mechanisms that regulate Runx1 isoform expression during haematopoiesis remain poorly understood. Gene regulatory elements located in non-coding DNA are likely to be important for Runx1 transcription. Here we use circular chromosome conformation capture sequencing to identify DNA interactions with the P1 and P2 promoters of Runx1, and the previously identified +24 enhancer, in the mouse multipotent haematopoietic progenitor cell line HPC-7. The active promoter, P1, interacts with nine non-coding regions that are occupied by transcription factors within a 1 Mb topologically associated domain. Eight of nine regions function as blood-specific enhancers in zebrafish, of which two were previously shown to harbour blood-specific enhancer activity in mice. Interestingly, the +24 enhancer interacted with multiple distant regions on chromosome 16, suggesting it may regulate the expression of additional genes. The Runx1 DNA contact map identifies connections with multiple novel and known haematopoietic enhancers that are likely to be involved in regulating Runx1 expression in haematopoietic progenitor cells.
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256
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Glaser LV, Rieger S, Thumann S, Beer S, Kuklik-Roos C, Martin DE, Maier KC, Harth-Hertle ML, Grüning B, Backofen R, Krebs S, Blum H, Zimmer R, Erhard F, Kempkes B. EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells. PLoS Pathog 2017; 13:e1006664. [PMID: 28968461 PMCID: PMC5638620 DOI: 10.1371/journal.ppat.1006664] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 10/12/2017] [Accepted: 09/22/2017] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) infection converts resting human B cells into permanently proliferating lymphoblastoid cell lines (LCLs). The Epstein-Barr virus nuclear antigen 2 (EBNA2) plays a key role in this process. It preferentially binds to B cell enhancers and establishes a specific viral and cellular gene expression program in LCLs. The cellular DNA binding factor CBF1/CSL serves as a sequence specific chromatin anchor for EBNA2. The ubiquitous expression of this highly conserved protein raises the question whether additional cellular factors might determine EBNA2 chromatin binding selectively in B cells. Here we used CBF1 deficient B cells to identify cellular genes up or downregulated by EBNA2 as well as CBF1 independent EBNA2 chromatin binding sites. Apparently, CBF1 independent EBNA2 target genes and chromatin binding sites can be identified but are less frequent than CBF1 dependent EBNA2 functions. CBF1 independent EBNA2 binding sites are highly enriched for EBF1 binding motifs. We show that EBNA2 binds to EBF1 via its N-terminal domain. CBF1 proficient and deficient B cells require EBF1 to bind to CBF1 independent binding sites. Our results identify EBF1 as a co-factor of EBNA2 which conveys B cell specificity to EBNA2. Epstein-Barr virus (EBV) infection is closely linked to cancer development. At particular risk are immunocompromised individuals like post-transplant patients which can develop B cell lymphomas. In healthy individuals EBV preferentially infects B cells and establishes a latent infection without causing apparent clinical symptoms in most cases. Upon infection, Epstein-Barr virus nuclear antigen 2 (EBNA2) initiates a B cell specific gene expression program that causes activation and proliferation of the infected cells. EBNA2 is a transcription factor well known to use a cellular protein, CBF1/CSL, as a DNA adaptor. CBF1/CSL is a sequence specific DNA binding protein robustly expressed in all tissues. Here we show that EBNA2 can form complexes with early B cell factor 1 (EBF1), a B cell specific DNA binding transcription factor, and EBF1 stabilizes EBNA2 chromatin binding. This EBNA2/EBF1 complex might serve as a novel target to develop future small molecule strategies that act as antivirals in latent B cell infection.
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Affiliation(s)
- Laura V Glaser
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Simone Rieger
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Sybille Thumann
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | - Sophie Beer
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
| | | | | | | | | | - Björn Grüning
- Bioinformatics, Institute for Informatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics, Institute for Informatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Stefan Krebs
- Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Helmut Blum
- Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Ralf Zimmer
- Teaching and Research Unit Bioinformatics, Institute of Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Florian Erhard
- Teaching and Research Unit Bioinformatics, Institute of Informatics, Ludwig-Maximilians-University, Munich, Germany
| | - Bettina Kempkes
- Department of Gene Vectors, Helmholtz Center Munich, Munich, Germany
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257
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Konieczny P, Stepniak-Konieczna E, Taylor K, Sznajder LJ, Sobczak K. Autoregulation of MBNL1 function by exon 1 exclusion from MBNL1 transcript. Nucleic Acids Res 2017; 45:1760-1775. [PMID: 27903900 PMCID: PMC5389549 DOI: 10.1093/nar/gkw1158] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 11/07/2016] [Indexed: 01/14/2023] Open
Abstract
Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed that MBNL1 binds to MBNL1 exon 1 (e1) encoding both the major part of 5΄UTR and an amino-terminal region of MBNL1 protein. We tested several hypotheses regarding the possible autoregulatory function of MBNL1 binding to its own transcript. Our data indicate that MBNLs induce skipping of e1 from precursor MBNL1 mRNA and that e1 exclusion may impact transcript association with polysomes and translation. Furthermore, e1-deficient protein isoform lacking the first two zinc fingers is highly unstable and its EGFP fusion protein has severely compromised splicing activity. We also show that MBNL1 can be transcribed from three different promoters and that the transcription initiation site determines the mode of e1 regulation. Taken together, we demonstrate that MBNL proteins control steady-state levels of MBNL1 through an interaction with e1 in its precursor mRNA. Insights from our study open a new avenue in therapies against DM based on manipulation of the transcription initiation site and e1 splicing of MBNL1 mRNA.
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Affiliation(s)
- Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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258
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DeSmet ML, Fleet JC. Constitutively active RAS signaling reduces 1,25 dihydroxyvitamin D-mediated gene transcription in intestinal epithelial cells by reducing vitamin D receptor expression. J Steroid Biochem Mol Biol 2017; 173:194-201. [PMID: 28104492 PMCID: PMC5511787 DOI: 10.1016/j.jsbmb.2017.01.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 12/23/2016] [Accepted: 01/11/2017] [Indexed: 01/12/2023]
Abstract
High vitamin D status is associated with reduced colon cancer risk but these studies ignore the diversity in the molecular etiology of colon cancer. RAS activating mutations are common in colon cancer and they activate pro-proliferative signaling pathways. We examined the impact of RAS activating mutations on 1,25 dihydroxyvitamin D (1,25(OH)2D)-mediated gene expression in cultured colon and intestinal cell lines. Transient transfection of Caco-2 cells with a constitutively active mutant K-RAS (G12 V) significantly reduced 1,25(OH)2D-induced activity of both a human 25-hydroxyvitamin D, 24 hydroxyase (CYP24A1) promoter-luciferase and an artificial 3X vitamin D response element (VDRE) promoter-luciferase reporter gene. Young Adult Mouse Colon (YAMC) and Rat Intestinal Epithelial (RIE) cell lines with stable expression of mutant H-RAS had suppressed 1,25(OH)2D-mediated induction of CYP24A1 mRNA. The RAS effects were associated with lower Vitamin D receptor (VDR) mRNA and protein levels in YAMC and RIE cells and they could be partially reversed by VDR overexpression. RAS-mediated suppression of VDR levels was not due to either reduced VDR mRNA stability or increased VDR gene methylation. However, chromatin accessibility to the VDR gene at the proximal promoter (-300bp), an enhancer region at -6kb, and an enhancer region located in exon 3 was significantly reduced in RAS transformed YAMC cells (YAMC-RAS). These data show that constitutively active RAS signaling suppresses 1,25(OH)2D-mediated gene transcription in colon epithelial cells by reducing VDR gene transcription but the mechanism for this suppression is not yet known. These data suggest that cancers with RAS-activating mutations may be less responsive to vitamin D mediated treatment or chemoprevention.
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Affiliation(s)
- Marsha L DeSmet
- Purdue University Interdisciplinary Life Science Ph.D. Program, West Lafayette, IN, United States; Department of Nutrition Science, Purdue University, West Lafayette, IN, United States.
| | - James C Fleet
- Purdue University Interdisciplinary Life Science Ph.D. Program, West Lafayette, IN, United States; Purdue University Center for Cancer Research, West Lafayette, IN, United States; Department of Nutrition Science, Purdue University, West Lafayette, IN, United States.
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259
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miRNA-122 Protects Mice and Human Hepatocytes from Acetaminophen Toxicity by Regulating Cytochrome P450 Family 1 Subfamily A Member 2 and Family 2 Subfamily E Member 1 Expression. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2758-2774. [PMID: 28963035 DOI: 10.1016/j.ajpath.2017.08.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/26/2017] [Accepted: 08/17/2017] [Indexed: 12/18/2022]
Abstract
Acetaminophen toxicity is a leading cause of acute liver failure (ALF). We found that miRNA-122 (miR-122) is down-regulated in liver biopsy specimens of patients with ALF and in acetaminophen-treated mice. A marked decrease in the primary miR-122 expression occurs in mice on acetaminophen overdose because of suppression of its key transactivators, hepatocyte nuclear factor (HNF)-4α and HNF6. More importantly, the mortality rates of male and female liver-specific miR-122 knockout (LKO) mice were significantly higher than control mice when injected i.p. with an acetaminophen dose not lethal to the control. LKO livers exhibited higher basal expression of cytochrome P450 family 2 subfamily E member 1 (CYP2E1) and cytochrome P450 family 1 subfamily A member 2 (CYP1A2) that convert acetaminophen to highly reactive N-acetyl-p-benzoquinone imine. Upregulation of Cyp1a2 primary transcript and mRNA in LKO mice correlated with the elevation of aryl hydrocarbon receptor (AHR) and mediator 1 (MED1), two transactivators of Cyp1a2. Analysis of ChIP-seq data in the ENCODE (Encyclopedia of DNA Element) database identified association of CCCTC-binding factor (CTCF) with Ahr promoter in mouse livers. Both MED1 and CTCF are validated conserved miR-122 targets. Furthermore, depletion of Ahr, Med1, or Ctcf in Mir122-/- hepatocytes reduced Cyp1a2 expression. Pulse-chase studies found that CYP2E1 protein level is upregulated in LKO hepatocytes. Notably, miR-122 depletion sensitized differentiated human HepaRG cells to acetaminophen toxicity that correlated with upregulation of AHR, MED1, and CYP1A2 expression. Collectively, these results reveal a critical role of miR-122 in acetaminophen detoxification and implicate its therapeutic potential in patients with ALF.
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260
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Systems biology analysis of longitudinal functional response of endothelial cells to shear stress. Proc Natl Acad Sci U S A 2017; 114:10990-10995. [PMID: 28973892 DOI: 10.1073/pnas.1707517114] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Blood flow and vascular shear stress patterns play a significant role in inducing and modulating physiological responses of endothelial cells (ECs). Pulsatile shear (PS) is associated with an atheroprotective endothelial phenotype, while oscillatory shear (OS) is associated with an atheroprone endothelial phenotype. Although mechanisms of endothelial shear response have been extensively studied, most studies focus on characterization of single molecular pathways, mainly at fixed time points after stress application. Here, we carried out a longitudinal time-series study to measure the transcriptome after the application of PS and OS. We performed systems analyses of transcriptional data of cultured human vascular ECs to elucidate the dynamics of endothelial responses in several functional pathways such as cell cycle, oxidative stress, and inflammation. By combining the temporal data on differentially expressed transcription factors and their targets with existing knowledge on relevant functional pathways, we infer the causal relationships between disparate endothelial functions through common transcriptional regulation mechanisms. Our study presents a comprehensive temporally longitudinal experimental study and mechanistic model of shear stress response. By comparing the relative endothelial expressions of genes between OS and PS, we provide insights and an integrated perspective into EC function in response to differential shear. This study has significant implications for the pathogenesis of vascular diseases.
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261
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Robinson SC, Donaldson-Kabwe NS, Dvorkin-Gheva A, Longo J, He L, Daniel JM. The POZ-ZF transcription factor Znf131 is implicated as a regulator of Kaiso-mediated biological processes. Biochem Biophys Res Commun 2017; 493:416-421. [PMID: 28882591 DOI: 10.1016/j.bbrc.2017.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 09/03/2017] [Indexed: 12/14/2022]
Abstract
Znf131 belongs to the family of POZ-ZF transcription factors, but, in contrast to most other characterized POZ-ZF proteins that function as transcriptional repressors, Znf131 acts as a transcriptional activator. Znf131 heterodimerizes with the POZ-ZF protein Kaiso, which itself represses a subset of canonical Wnt target genes, including the cell cycle regulator Cyclin D1. Herein, we report a possible role for Znf131 in Kaiso-mediated processes. Notably, we found that Znf131 associates with several Kaiso target gene promoters, including that of CCND1. ChIP analysis revealed that Znf131 indirectly associates with the CCND1 promoter in HCT116 and MCF7 cells via a region that encompasses the previously characterized +69 Kaiso Binding Site, hinting that the Znf131/Kaiso heterodimer may co-regulate Cyclin D1 expression. We also demonstrate that Kaiso inhibits Znf131 expression, raising the possibility that Kaiso and Znf131 act to fine-tune target gene expression. Together, our findings implicate Znf131 as a co-regulator of Kaiso-mediated biological processes.
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Affiliation(s)
| | | | - Anna Dvorkin-Gheva
- Department of Pathology and Molecular Medicine, Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Joseph Longo
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Lloyd He
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Juliet M Daniel
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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Bustos MA, Ono S, Marzese DM, Oyama T, Iida Y, Cheung G, Nelson N, Hsu SC, Yu Q, Hoon DSB. MiR-200a Regulates CDK4/6 Inhibitor Effect by Targeting CDK6 in Metastatic Melanoma. J Invest Dermatol 2017; 137:1955-1964. [PMID: 28526299 DOI: 10.1016/j.jid.2017.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 03/03/2017] [Accepted: 03/19/2017] [Indexed: 12/29/2022]
Abstract
The CDK4/6 pathway is frequently dysregulated in cutaneous melanoma. Recently, CDK4/6 inhibitors have shown promising clinical activity against several cancer types, including melanoma. Here, we show that microRNA-200a decreases CDK6 expression and thus reduces the response of CDK4/6 inhibitor in highly proliferative metastatic melanoma. Down-regulation of microRNA-200a expression in melanoma cells is associated with disease progression and a higher number of lymph node metastases. Furthermore, microRNA-200a expression is epigenetically modulated by both DNA methylation at the promoter region and chromatin accessibility of an upstream genomic region with enhancer activity. Mechanistically, overexpression of miR-200a in metastatic melanoma cells induces cell cycle arrest by targeting CDK6 and decreases the levels of phosphorylated-Rb1 and E2F-downstream targets, diminishing cell proliferation; these effects are recovered by CDK6 overexpression. Conversely, low microRNA-200a expression in metastatic melanoma cells results in higher levels of CDK6 and a more significant response to CDK4/6 inhibitors. We propose that microRNA-200a functions as a "cell cycle brake" that is lost during melanoma progression to metastasis and provides the ability to identify melanomas that are highly proliferative and more prompted to respond to CDK4/6 inhibitors.
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Affiliation(s)
- Matias A Bustos
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Shigeshi Ono
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Diego M Marzese
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Takashi Oyama
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Yuuki Iida
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Garrett Cheung
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Nellie Nelson
- Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Sandy C Hsu
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA; Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Qiang Yu
- Cancer Biology and Pharmacology, Genome Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA; Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA.
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Liu Y, Reynolds LM, Ding J, Hou L, Lohman K, Young T, Cui W, Huang Z, Grenier C, Wan M, Stunnenberg HG, Siscovick D, Hou L, Psaty BM, Rich SS, Rotter JI, Kaufman JD, Burke GL, Murphy S, Jacobs DR, Post W, Hoeschele I, Bell DA, Herrington D, Parks JS, Tracy RP, McCall CE, Stein JH. Blood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosis. Nat Commun 2017; 8:393. [PMID: 28855511 PMCID: PMC5577184 DOI: 10.1038/s41467-017-00517-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/05/2017] [Indexed: 12/20/2022] Open
Abstract
Little is known regarding the epigenetic basis of atherosclerosis. Here we present the CD14+ blood monocyte transcriptome and epigenome signatures associated with human atherosclerosis. The transcriptome signature includes transcription coactivator, ARID5B, which is known to form a chromatin derepressor complex with a histone H3K9Me2-specific demethylase and promote adipogenesis and smooth muscle development. ARID5B CpG (cg25953130) methylation is inversely associated with both ARID5B expression and atherosclerosis, consistent with this CpG residing in an ARID5B enhancer region, based on chromatin capture and histone marks data. Mediation analysis supports assumptions that ARID5B expression mediates effects of cg25953130 methylation and several cardiovascular disease risk factors on atherosclerotic burden. In lipopolysaccharide-stimulated human THP1 monocytes, ARID5B knockdown reduced expression of genes involved in atherosclerosis-related inflammatory and lipid metabolism pathways, and inhibited cell migration and phagocytosis. These data suggest that ARID5B expression, possibly regulated by an epigenetically controlled enhancer, promotes atherosclerosis by dysregulating immunometabolism towards a chronic inflammatory phenotype.The molecular mechanisms mediating the impact of environmental factors in atherosclerosis are unclear. Here, the authors examine CD14+ blood monocyte's transcriptome and epigenome signatures to find differential methylation and expression of ARID5B to be associated with human atherosclerosis.
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Affiliation(s)
- Yongmei Liu
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
| | - Lindsay M Reynolds
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Jingzhong Ding
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Li Hou
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Kurt Lohman
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Tracey Young
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Wei Cui
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | | | | | - Ma Wan
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences (NCMLS), 6525, GA, Nijmegen, The Netherlands
| | | | - Lifang Hou
- Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, 60208, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Joel D Kaufman
- Department of Environmental and Occupational Health Sciences, Medicine and Epidemiology, University of Washington, Seattle, WA, 98104, USA
| | - Gregory L Burke
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | | | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wendy Post
- Department of Pathology and Cardiology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Ina Hoeschele
- Biocomplexity Institute and Department of Statistics, Virginia Tech, VA, 24061, USA
| | - Douglas A Bell
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - David Herrington
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - John S Parks
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Russell P Tracy
- Department of Pathology, University of Vermont, Colchester, VT, 05446, USA
| | - Charles E McCall
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - James H Stein
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA
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264
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Mittal VK, McDonald JF. De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance. BMC Med Genomics 2017; 10:53. [PMID: 28851357 PMCID: PMC5575902 DOI: 10.1186/s12920-017-0289-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 08/17/2017] [Indexed: 11/10/2022] Open
Abstract
Background Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of the cellular transcriptome is a promising approach for the identification of chimeric transcripts of potential functional significance. We report here the development and use of an integrated computational pipeline for the de novo assembly and characterization of chimeric transcripts in 55 primary breast cancer and normal tissue samples. Methods An integrated computational pipeline was employed to screen the transcriptome of breast cancer and control tissues for high-quality RNA-sequencing reads. Reads were de novo assembled into contigs followed by reference genome mapping. Chimeric transcripts were detected, filtered and characterized using our R-SAP algorithm. The relative abundance of reads was used to estimate levels of gene expression. Results De novo assembly allowed for the accurate detection of 1959 chimeric transcripts to nucleotide level resolution and facilitated detailed molecular characterization and quantitative analysis. A number of the chimeric transcripts are of potential functional significance including 79 novel fusion-protein transcripts and many chimeric transcripts with alterations in their un-translated leader regions. A number of chimeric transcripts in the cancer samples mapped to genomic regions devoid of any known genes. Several ‘pro-neoplastic’ fusions comprised of genes previously implicated in cancer are expressed at low levels in normal tissues but at high levels in cancer tissues. Conclusions Collectively, our results underscore the utility of deep sequencing technologies and improved bioinformatics workflows to uncover novel and potentially significant chimeric transcripts in cancer and normal somatic tissues. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0289-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vinay K Mittal
- Integrated Cancer Research Center, School of Biological Sciences, and Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, 315 Ferst Dr, Atlanta, GA, 30332, USA
| | - John F McDonald
- Integrated Cancer Research Center, School of Biological Sciences, and Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, 315 Ferst Dr, Atlanta, GA, 30332, USA.
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265
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Persad PJ, Heid IM, Weeks DE, Baird PN, de Jong EK, Haines JL, Pericak-Vance MA, Scott WK. Joint Analysis of Nuclear and Mitochondrial Variants in Age-Related Macular Degeneration Identifies Novel Loci TRPM1 and ABHD2/RLBP1. Invest Ophthalmol Vis Sci 2017; 58:4027-4038. [PMID: 28813576 PMCID: PMC5559178 DOI: 10.1167/iovs.17-21734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Purpose Presently, 52 independent nuclear single nucleotide polymorphisms (nSNPs) have been associated with age-related macular degeneration (AMD) but their effects do not explain all its variance. Genetic interactions between the nuclear and mitochondrial (mt) genome may unearth additional genetic loci previously unassociated with AMD risk. Methods Joint effects of nSNPs and selected mtSNPs were analyzed by two degree of freedom (2df) joint tests of association in the International AMD Genomics Consortium (IAMDGC) dataset (17,832 controls and 16,144 advanced AMD cases of European ancestry). Subjects were genotyped on the Illumina HumanCoreExome array. After imputation using MINIMAC and the 1000 Genomes Project Phase I reference panel, pairwise linkage disequilibrium pruning, and quality control, 3.9 million nSNPs were analyzed for interaction with mtSNPs chosen based on association in this dataset or publications: A4917G, T5004C, G12771A, and C16069T. Results Novel locus TRPM1 was identified with genome-wide significant joint effects (P < 5.0 × 10−8) of two intronic TRPM1 nSNPs and AMD-associated nonsynonymous MT-ND2 mtSNP A4917G. Stratified analysis by mt allele identified an association only in 4917A (major allele) carriers (P = 4.4 × 10−9, odds ratio [OR] = 0.90, 95% confidence interval [CI] = 0.87–0.93). Intronic and intergenic ABHD2/RLBP1 nSNPs demonstrated genome-wide significant joint effects (2df joint test P values from 1.8 × 10−8 to 4.9 × 10−8) and nominally statistically significant interaction effects with MT-ND5 synonymous mtSNP G12771A. Although a positive association was detected in both strata, the association was stronger in 12771A subjects (P = 0.0020, OR = 2.17, 95% CI = 1.34–3.60). Conclusions These results show that joint tests of main effects and gene–gene interaction reveal associations at some novel loci that were missed when considering main effects alone.
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Affiliation(s)
- Patrice J Persad
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Daniel E Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States.,Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Paul N Baird
- Centre for Eye Research Australia, Department of Surgery (Ophthalmology) University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
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266
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Good CR, Madzo J, Patel B, Maegawa S, Engel N, Jelinek J, Issa JPJ. A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer. Nucleic Acids Res 2017; 45:8269-8281. [PMID: 28531272 PMCID: PMC5737541 DOI: 10.1093/nar/gkx435] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/14/2017] [Accepted: 05/03/2017] [Indexed: 02/07/2023] Open
Abstract
TET1 oxidizes methylated cytosine into 5-hydroxymethylcytosine (5hmC), resulting in regulation of DNA methylation and gene expression. Full length TET1 (TET1FL) has a CXXC domain that binds to unmethylated CpG islands (CGIs). This CXXC domain allows TET1 to protect CGIs from aberrant methylation, but it also limits its ability to regulate genes outside of CGIs. Here, we report a novel isoform of TET1 (TET1ALT) that has a unique transcription start site from an alternate promoter in intron 2, yielding a protein with a unique translation start site. Importantly, TET1ALT lacks the CXXC domain but retains the catalytic domain. TET1ALT is repressed in embryonic stem cells (ESCs) but becomes activated in embryonic and adult tissues while TET1FL is expressed in ESCs, but repressed in adult tissues. Overexpression of TET1ALT shows production of 5hmC with distinct (and weaker) effects on DNA methylation or gene expression when compared to TET1FL. TET1ALT is aberrantly activated in multiple cancer types including breast, uterine and glioblastoma, and TET1 activation is associated with a worse overall survival in breast, uterine and ovarian cancers. Our data suggest that the predominantly activated isoform of TET1 in cancer cells does not protect from CGI methylation and likely mediates dynamic site-specific demethylation outside of CGIs.
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Affiliation(s)
- Charly R. Good
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Bela Patel
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Shinji Maegawa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Nora Engel
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jean-Pierre J. Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
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267
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Sethi I, Gluck C, Zhou H, Buck MJ, Sinha S. Evolutionary re-wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species-specific gene expression and phenotypes. Nucleic Acids Res 2017; 45:8208-8224. [PMID: 28505376 PMCID: PMC5737389 DOI: 10.1093/nar/gkx416] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 04/26/2017] [Accepted: 05/11/2017] [Indexed: 02/06/2023] Open
Abstract
Although epidermal keratinocyte development and differentiation proceeds in similar fashion between humans and mice, evolutionary pressures have also wrought significant species-specific physiological differences. These differences between species could arise in part, by the rewiring of regulatory network due to changes in the global targets of lineage-specific transcriptional master regulators such as p63. Here we have performed a systematic and comparative analysis of the p63 target gene network within the integrated framework of the transcriptomic and epigenomic landscape of mouse and human keratinocytes. We determined that there exists a core set of ∼1600 genomic regions distributed among enhancers and super-enhancers, which are conserved and occupied by p63 in keratinocytes from both species. Notably, these DNA segments are typified by consensus p63 binding motifs under purifying selection and are associated with genes involved in key keratinocyte and skin-centric biological processes. However, the majority of the p63-bound mouse target regions consist of either murine-specific DNA elements that are not alignable to the human genome or exhibit no p63 binding in the orthologous syntenic regions, typifying an occupancy lost subset. Our results suggest that these evolutionarily divergent regions have undergone significant turnover of p63 binding sites and are associated with an underlying inactive and inaccessible chromatin state, indicative of their selective functional activity in the transcriptional regulatory network in mouse but not human. Furthermore, we demonstrate that this selective targeting of genes by p63 correlates with subtle, but measurable transcriptional differences in mouse and human keratinocytes that converges on major metabolic processes, which often exhibit species-specific trends. Collectively our study offers possible molecular explanation for the observable phenotypic differences between the mouse and human skin and broadly informs on the prevailing principles that govern the tug-of-war between evolutionary forces of rigidity and plasticity over transcriptional regulatory programs.
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Affiliation(s)
- Isha Sethi
- Department of Biochemistry, SUNY at Buffalo, Buffalo, NY 14203, USA
| | - Christian Gluck
- Department of Biochemistry, SUNY at Buffalo, Buffalo, NY 14203, USA
| | - Huiqing Zhou
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Michael J. Buck
- Department of Biochemistry, SUNY at Buffalo, Buffalo, NY 14203, USA
| | - Satrajit Sinha
- Department of Biochemistry, SUNY at Buffalo, Buffalo, NY 14203, USA
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Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells. Biol Sex Differ 2017; 8:28. [PMID: 28818098 PMCID: PMC5561606 DOI: 10.1186/s13293-017-0150-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/10/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Pre-implantation embryos exhibit sexual dimorphisms in both primates and rodents. To determine whether these differences reflected sex-biased expression patterns, we generated transcriptome profiles for six 40,XX, six 40,XY, and two 39,X mouse embryonic stem (ES) cells by RNA sequencing. RESULTS We found hundreds of coding and non-coding RNAs that were differentially expressed between male and female cells. Surprisingly, the majority of these were autosomal and included RNA encoding transcription and epigenetic and chromatin remodeling factors. We showed differential Prdm14-responsive enhancer activity in male and female cells, correlating with the sex-specific levels of Prdm14 expression. This is the first time sex-specific enhancer activity in ES cells has been reported. Evaluation of X-linked gene expression patterns between our XX and XY lines revealed four distinct categories: (1) genes showing 2-fold greater expression in the female cells; (2) a set of genes with expression levels well above 2-fold in female cells; (3) genes with equivalent RNA levels in male and female cells; and strikingly, (4) a small number of genes with higher expression in the XY lines. Further evaluation of autosomal gene expression revealed differential expression of imprinted loci, despite appropriate parent-of-origin patterns. The 39,X lines aligned closely with the XY cells and provided insights into potential regulation of genes associated with Turner syndrome in humans. Moreover, inclusion of the 39,X lines permitted three-way comparisons, delineating X and Y chromosome-dependent patterns. CONCLUSIONS Overall, our results support the role of the sex chromosomes in establishing sex-specific networks early in embryonic development and provide insights into effects of sex chromosome aneuploidies originating at those stages.
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Zheng M, Lin F, Hou F, Li G, Zhu C, Xu P, Xing C, Wang Q. Association between Promoter Methylation of Gene ERCC3 and Benzene Hematotoxicity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14080921. [PMID: 28813025 PMCID: PMC5580623 DOI: 10.3390/ijerph14080921] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/12/2022]
Abstract
Benzene is a primary industrial chemical and a ubiquitous environmental pollutant. ERCC3 is a key player in nucleotide excision repair. Recent studies suggested that site-specific methylation is a possible mechanism of the transcriptional dysregulation by blocking transcription factors binding. We previously found that the average promoter methylation level of ERCC3 was increased in benzene-exposed workers. In order to test whether specific CpG sites of ERCC3 play an important role in benzene-induced epigenetic changes and whether the specific methylation patterns are associated with benzene hematotoxicity, we analyzed the promoter methylation levels of individual CpG sites, transcription factor binding motif and the correlation between aberrant CpG methylation and hematotoxicity in 76 benzene-exposed workers and 24 unexposed controls in China. Out of all the CpGs analyzed, two CpG units located 43 bp upstream and 99 bp downstream of the transcription start site of ERCC3 (CpG 2–4 and CpG 17–18, respectively), showed the most pronounced increase in methylation levels in benzene-exposed workers, compared with unexposed controls (Mean ± SD: 5.86 ± 2.77% vs. 4.92 ± 1.53%, p = 0.032; 8.45 ± 4.09% vs. 6.79 ± 2.50%, p = 0.024, respectively). Using the JASPAR CORE Database, we found that CpG 2–4 and CpG 17–18 were bound by three putative transcription factors (TFAP2A, E2F4 and MZF1). Furthermore, the methylation levels for CpG 2–4 were correlated negatively with the percentage of neutrophils (β = −0.676, p = 0.005) in benzene-exposed workers. This study demonstrates that CpG-specific DNA methylation in the ERCC3 promoter region may be involved in benzene-induced epigenetic modification and it may contribute to benzene-induced hematotoxicity.
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Affiliation(s)
- Min Zheng
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Feiliang Lin
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
- Department of Nutrition, Food Safety and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China.
| | - Fenxia Hou
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Guilan Li
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Caiying Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital and Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
| | - Peiyu Xu
- Department of Nutrition, Food Safety and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China.
| | - Caihong Xing
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Qianfei Wang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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270
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Biogenesis of Pro-senescent Microparticles by Endothelial Colony Forming Cells from Premature Neonates is driven by SIRT1-Dependent Epigenetic Regulation of MKK6. Sci Rep 2017; 7:8277. [PMID: 28811647 PMCID: PMC5557933 DOI: 10.1038/s41598-017-08883-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/19/2017] [Indexed: 12/18/2022] Open
Abstract
Senescent cells may exert detrimental effect on microenvironment through the secretion of soluble factors and the release of extracellular vesicles, such as microparticles, key actors in ageing and cardiovascular diseases. We previously reported that sirtuin-1 (SIRT1) deficiency drives accelerated senescence and dysfunction of endothelial colony-forming cells (ECFC) in PT neonates. Because preterm birth (PT) increases the risk for cardiovascular diseases during neonatal period as well as at adulthood, we hypothesized that SIRT1 deficiency could control the biogenesis of microparticles as part of a senescence–associated secretory phenotype (SASP) of PT-ECFC and investigated the related molecular mechanisms. Compared to control ECFC, PT-ECFC displayed a SASP associated with increased release of endothelial microparticles (EMP), mediating a paracrine induction of senescence in naïve endothelial cells. SIRT1 level inversely correlated with EMP release and drives PT-ECFC vesiculation. Global transcriptomic analysis revealed changes in stress response pathways, specifically the MAPK pathway. We delineate a new epigenetic mechanism by which SIRT1 deficiency regulates MKK6/p38MAPK/Hsp27 pathway to promote EMP biogenesis in senescent ECFC. These findings deepen our understanding of the role of ECFC senescence in the disruption of endothelial homeostasis and provide potential new targets towards the control of cardiovascular risk in individuals born preterm.
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Mendes de Almeida R, Tavares J, Martins S, Carvalho T, Enguita FJ, Brito D, Carmo-Fonseca M, Lopes LR. Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PLoS One 2017; 12:e0182946. [PMID: 28797094 PMCID: PMC5552324 DOI: 10.1371/journal.pone.0182946] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/27/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High throughput sequencing technologies have revolutionized the identification of mutations responsible for genetic diseases such as hypertrophic cardiomyopathy (HCM). However, approximately 50% of individuals with a clinical diagnosis of HCM have no causal mutation identified. This may be due to the presence of pathogenic mutations located deep within the introns, which are not detected by conventional sequencing analysis restricted to exons and exon-intron boundaries. OBJECTIVE The aim of this study was to develop a whole-gene sequencing strategy to prioritize deep intronic variants that may play a role in HCM pathogenesis. METHODS AND RESULTS The full genomic DNA sequence of 26 genes previously associated with HCM was analysed in 16 unrelated patients. We identified likely pathogenic deep intronic variants in VCL, PRKAG2 and TTN genes. These variants, which are predicted to act through disruption of either splicing or transcription factor binding sites, are 3-fold more frequent in our cohort of probands than in normal European populations. Moreover, we found a patient that is compound heterozygous for a splice site mutation in MYBPC3 and the deep intronic VCL variant. Analysis of family members revealed that carriers of the MYBPC3 mutation alone do not manifest the disease, while family members that are compound heterozygous are clinically affected. CONCLUSION This study provides a framework for scrutinizing variation along the complete intronic sequence of HCM-associated genes and prioritizing candidates for mechanistic and functional analysis. Our data suggest that deep intronic variation contributes to HCM phenotype.
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Affiliation(s)
- Rita Mendes de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Tavares
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Dulce Brito
- Departamento de Cardiologia, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Luís Rocha Lopes
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
- Institute of Cardiovascular Science, University College London, London, United Kingdom
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272
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Satterfield L, Shuck R, Kurenbekova L, Allen-Rhoades W, Edwards D, Huang S, Rajapakshe K, Coarfa C, Donehower LA, Yustein JT. miR-130b directly targets ARHGAP1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. Int J Cancer 2017; 141:2062-2075. [PMID: 28748534 DOI: 10.1002/ijc.30909] [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: 02/24/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Ewing Sarcoma (ES) is a highly aggressive bone tumor with peak incidence in the adolescent population. It has a high propensity to metastasize, which is associated with dismal survival rates of approximately 25%. To further understand mechanisms of metastasis we investigated microRNA regulatory networks in ES. Our studies focused on miR-130b due to our analysis that enhanced expression of this microRNA has clinical relevance in multiple sarcomas, including ES. Our studies provide insights into a novel positive feedback network involving the direct regulation of miR-130b and activation of downstream signaling events contributing toward sarcoma metastasis. Specifically, we demonstrated miR-130b induces proliferation, invasion, and migration in vitro and increased metastatic potential in vivo. Using microarray analysis of ES cells with differential miR-130b expression we identified alterations in downstream signaling cascades including activation of the CDC42 pathway. We identified ARHGAP1, which is a negative regulator of CDC42, as a novel, direct target of miR-130b. In turn, downstream activation of PAK1 activated the JNK and AP-1 cascades and downstream transcriptional targets including IL-8, MMP1 and CCND1. Furthermore, chromatin immunoprecipitation of endogenous AP-1 in ES cells demonstrated direct binding to an upstream consensus binding site within the miR-130b promoter. Finally, small molecule inhibition of PAK1 blocked miR-130b activation of JNK and downstream AP-1 target genes, including primary miR-130b transcripts, and miR-130b oncogenic properties, thus identifying PAK1 as a novel therapeutic target for ES. Taken together, our findings identify and characterize a novel, targetable miR-130b regulatory network that promotes ES metastasis.
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Affiliation(s)
- Laura Satterfield
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX.,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX
| | - Ryan Shuck
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX
| | - Lyazat Kurenbekova
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX
| | - Wendy Allen-Rhoades
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX
| | - Dean Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Shixia Huang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Lawrence A Donehower
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX.,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX
| | - Jason T Yustein
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX.,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
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273
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Mullany LE, Herrick JS, Wolff RK, Stevens JR, Samowitz W, Slattery ML. Transcription factor-microRNA associations and their impact on colorectal cancer survival. Mol Carcinog 2017; 56:2512-2526. [PMID: 28667784 PMCID: PMC5633497 DOI: 10.1002/mc.22698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/06/2017] [Accepted: 06/29/2017] [Indexed: 01/16/2023]
Abstract
MicroRNAs (miRNAs) and Transcription Factors (TFs) both influence messenger RNA (mRNA) expression, disrupting biological pathways involved in carcinogenesis and prognosis. As many miRNAs target multiple mRNAs, thus influencing a multitude of biological pathways, deciphering which miRNAs are important for cancer development and survival is difficult. In this study, we (i) determine associations between TF and survival (N = 168 colon cancer cases); (ii) identify miRNAs associated with TFs related to survival; and (iii) determine if factors derived from TF-specific miRNA principal component analysis (PCA) influence survival. Cox Proportional hazard models were run for each PCA factor to determine Hazard Ratios (HR) and 95% Confidence Intervals (CI) adjusting for age, center, and AJCC stage. Thirty TFs improved survival when differential expression increased; 27 of these were associated significantly with normal colonic mucosa expression of 65 unique miRNAs when an FDR q-value of <0.05 was applied. Five factors, comprising 21 miRNAs, altered survival in rectal cancer subjects; four of these five factors improved survival and one factor reduced survival. One factor comprising four miRNAs reduced survival in colon cancer subjects. In summary, our data suggest that expression of TFs and their related miRNAs influence survival after diagnosis with colorectal cancer.
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Affiliation(s)
- Lila E Mullany
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Jennifer S Herrick
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Roger K Wolff
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, Utah
| | - Wade Samowitz
- Department of Pathology, University of Utah School, Salt Lake City, Utah
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
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274
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Stueve TR, Li WQ, Shi J, Marconett CN, Zhang T, Yang C, Mullen D, Yan C, Wheeler W, Hua X, Zhou B, Borok Z, Caporaso NE, Pesatori AC, Duan J, Laird-Offringa IA, Landi MT. Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers. Hum Mol Genet 2017; 26:3014-3027. [PMID: 28854564 PMCID: PMC5886283 DOI: 10.1093/hmg/ddx188] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/30/2017] [Accepted: 05/07/2017] [Indexed: 11/14/2022] Open
Abstract
Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. We identified seven smoking-associated hypomethylated CpGs (P < 1.0 × 10-7), which were replicated in NTL data from The Cancer Genome Atlas. Five of these loci were previously reported as hypomethylated in smokers' blood, suggesting that blood-based biomarkers can reflect changes in the target tissue for these loci. Four CpGs border sequences carrying aryl hydrocarbon receptor binding sites and enhancer-specific histone modifications in primary alveolar epithelium and A549 lung adenocarcinoma cells. A549 cell exposure to cigarette smoke condensate increased these enhancer marks significantly and stimulated expression of predicted target xenobiotic response-related genes AHRR (P = 1.13 × 10-62) and CYP1B1 (P < 2.49 × 10-61). Expression of both genes was linked to smoking-related transversion mutations in lung tumors. Thus, smoking-associated hypomethylation may be a consequence of enhancer activation, revealing environmentally-induced regulatory elements implicated in lung carcinogenesis.
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Affiliation(s)
- Theresa Ryan Stueve
- Department of Preventive Medicine
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Wen-Qing Li
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
- Department of Dermatology, Warren Alpert Medical School
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI 02903, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
| | - Crystal N. Marconett
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
| | - Chenchen Yang
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel Mullen
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Chunli Yan
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - William Wheeler
- Information Management Services, Inc., Rockville, MD 20852, USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
| | - Beiyun Zhou
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90089, USA
| | - Zea Borok
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Will Rogers Institute Pulmonary Research Center and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90089, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
| | - Angela C. Pesatori
- Unit of Epidemiology, IRCCS Fondazione Ca’ Granda Ospedale Maggiore Policlinico and Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Jubao Duan
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, IL 60201, USA
| | - Ite A. Laird-Offringa
- USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Surgery
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, NCI, National Institute of Health, Bethesda, MD 20852, USA
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275
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Helling BA, Gerber AN, Kadiyala V, Sasse SK, Pedersen BS, Sparks L, Nakano Y, Okamoto T, Evans CM, Yang IV, Schwartz DA. Regulation of MUC5B Expression in Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2017; 57:91-99. [PMID: 28272906 DOI: 10.1165/rcmb.2017-0046oc] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The gain-of-function mucin 5B (MUC5B) promoter variant, rs35705950, confers the largest risk, genetic or otherwise, for the development of idiopathic pulmonary fibrosis; however, the mechanisms underlying the regulation of MUC5B expression have yet to be elucidated. Here, we identify a critical regulatory domain that contains the MUC5B promoter variant and has a highly conserved forkhead box protein A2 (FOXA2) binding motif. This region is differentially methylated in association with idiopathic pulmonary fibrosis, MUC5B expression, and rs35705950. In addition, we show that this locus binds FOXA2 dynamically, and that binding of FOXA2 is necessary for enhanced expression of MUC5B. In aggregate, our findings identify novel targets to regulate the expression of MUC5B.
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Affiliation(s)
- Britney A Helling
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Anthony N Gerber
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Vineela Kadiyala
- 2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Sarah K Sasse
- 2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Brent S Pedersen
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Lenore Sparks
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Yasushi Nakano
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Tsukasa Okamoto
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Christopher M Evans
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Ivana V Yang
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,3 University of Colorado-Denver, School of Public Health, Denver, Colorado
| | - David A Schwartz
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,2 Department of Medicine, National Jewish Health, Denver, Colorado; and
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276
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Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. Oncogene 2017; 36:6446-6461. [PMID: 28759043 PMCID: PMC5701091 DOI: 10.1038/onc.2017.246] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/05/2017] [Accepted: 06/08/2017] [Indexed: 12/14/2022]
Abstract
The majority of long noncoding RNAs (lncRNAs) is still poorly characterized with respect to function, interactions with protein-coding genes, and mechanisms that regulate their expression. As for protein-coding RNAs, epigenetic deregulation of lncRNA expression by alterations in DNA methylation might contribute to carcinogenesis. To provide genome-wide information on lncRNAs aberrantly methylated in breast cancer we profiled tumors of the C3(1) SV40TAg mouse model by MCIp-seq (Methylated CpG Immunoprecipitation followed by sequencing). This approach detected 69 lncRNAs differentially methylated between tumor tissue and normal mammary glands, with 26 located in antisense orientation of a protein-coding gene. One of the hypomethylated lncRNAs, 1810019D21Rik (now called Esrp2-antisense (as)) was identified in proximity to the epithelial splicing regulatory protein 2 (Esrp2) that is significantly elevated in C3(1) tumors. ESRPs were shown previously to have a dual role in carcinogenesis. Both gain and loss have been associated with poor prognosis in human cancers, but the mechanisms regulating expression are not known. In-depth analyses indicate that coordinate overexpression of Esrp2 and Esrp2-as inversely correlates with DNA methylation. Luciferase reporter gene assays support co-expression of Esrp2 and the major short Esrp2-as variant from a bidirectional promoter, and transcriptional regulation by methylation of a proximal enhancer. Ultimately, this enhancer-based regulatory mechanism provides a novel explanation for tissue-specific expression differences and upregulation of Esrp2 during carcinogenesis. Knockdown of Esrp2-as reduced Esrp2 protein levels without affecting mRNA expression and resulted in an altered transcriptional profile associated with extracellular matrix (ECM), cell motility and reduced proliferation, whereas overexpression enhanced proliferation. Our findings not only hold true for the murine tumor model, but led to the identification of an unannotated human homolog of Esrp2-as which is significantly upregulated in human breast cancer and associated with poor prognosis.
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277
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Liu S, Zibetti C, Wan J, Wang G, Blackshaw S, Qian J. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. BMC Bioinformatics 2017; 18:355. [PMID: 28750606 PMCID: PMC5530957 DOI: 10.1186/s12859-017-1769-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/19/2017] [Indexed: 12/04/2022] Open
Abstract
Background Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in various cellular and developmental contexts. The chromatin accessibility profiles provide useful information in prediction of TF binding events in various physiological conditions. Furthermore, ChIP-Seq analysis was used to determine genome-wide binding sites for a range of different TFs in multiple cell types. Integration of these two types of genomic information can improve the prediction of TF binding events. Results We assessed to what extent a model built upon on other TFs and/or other cell types could be used to predict the binding sites of TFs of interest. A random forest model was built using a set of cell type-independent features such as specific sequences recognized by the TFs and evolutionary conservation, as well as cell type-specific features derived from chromatin accessibility data. Our analysis suggested that the models learned from other TFs and/or cell lines performed almost as well as the model learned from the target TF in the cell type of interest. Interestingly, models based on multiple TFs performed better than single-TF models. Finally, we proposed a universal model, BPAC, which was generated using ChIP-Seq data from multiple TFs in various cell types. Conclusion Integrating chromatin accessibility information with sequence information improves prediction of TF binding.The prediction of TF binding is transferable across TFs and/or cell lines suggesting there are a set of universal “rules”. A computational tool was developed to predict TF binding sites based on the universal “rules”. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1769-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sheng Liu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Cristina Zibetti
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Jun Wan
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Guohua Wang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.,Centre for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.
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278
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Carlson JC, Taub MA, Feingold E, Beaty TH, Murray JC, Marazita ML, Leslie EJ. Identifying Genetic Sources of Phenotypic Heterogeneity in Orofacial Clefts by Targeted Sequencing. Birth Defects Res 2017; 109:1030-1038. [PMID: 28762674 PMCID: PMC5549861 DOI: 10.1002/bdr2.23605] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/09/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND Orofacial clefts (OFCs), including nonsyndromic cleft lip with or without cleft palate (NSCL/P), are common birth defects. NSCL/P is highly heterogeneous with multiple phenotypic presentations. Two common subtypes of NSCL/P are cleft lip (CL) and cleft lip with cleft palate (CLP) which have different population prevalence. Similarly, NSCL/P can be divided into bilateral and unilateral clefts, with unilateral being the most common. Individuals with unilateral NSCL/P are more likely to be affected on the left side of the upper lip, but right side affection also occurs. Moreover, NSCL/P is twice as common in males as in females. The goal of this study is to discover genetic variants that have different effects in case subgroups. METHODS We conducted both common variant and rare variant analyses in 1034 individuals of Asian ancestry with NSCL/P, examining four sources of heterogeneity within CL/P: cleft type, sex, laterality, and side. RESULTS We identified several regions associated with subtype differentiation: cleft type differences in 8q24 (p = 1.00 × 10-4 ), laterality differences in IRF6, a gene previously implicated with wound healing (p = 2.166 × 10-4 ), sex differences and side of unilateral CL differences in FGFR2 (p = 3.00 × 10-4 ; p = 6.00 × 10-4 ), and sex differences in VAX1 (p < 1.00 × 10-4 ) among others. CONCLUSION Many of the regions associated with phenotypic modification were either adjacent to or overlapping functional elements based on ENCODE chromatin marks and published craniofacial enhancers. We have identified multiple common and rare variants as potential phenotypic modifiers of NSCL/P, and suggest plausible elements responsible for phenotypic heterogeneity, further elucidating the complex genetic architecture of OFCs. Birth Defects Research 109:1030-1038, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Jenna C. Carlson
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eleanor Feingold
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Mary L. Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Elizabeth J. Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
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279
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She A, Kurtser I, Reis SA, Hennig K, Lai J, Lang A, Zhao WN, Mazitschek R, Dickerson BC, Herz J, Haggarty SJ. Selectivity and Kinetic Requirements of HDAC Inhibitors as Progranulin Enhancers for Treating Frontotemporal Dementia. Cell Chem Biol 2017; 24:892-906.e5. [PMID: 28712747 DOI: 10.1016/j.chembiol.2017.06.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 02/06/2017] [Accepted: 06/19/2017] [Indexed: 11/18/2022]
Abstract
Frontotemporal dementia (FTD) arises from neurodegeneration in the frontal, insular, and anterior temporal lobes. Autosomal dominant causes of FTD include heterozygous mutations in the GRN gene causing haploinsufficiency of progranulin (PGRN) protein. Recently, histone deacetylase (HDAC) inhibitors have been identified as enhancers of PGRN expression, although the mechanisms through which GRN is epigenetically regulated remain poorly understood. Using a chemogenomic toolkit, including optoepigenetic probes, we show that inhibition of class I HDACs is sufficient to upregulate PGRN in human neurons, and only inhibitors with apparent fast binding to their target HDAC complexes are capable of enhancing PGRN expression. Moreover, we identify regions in the GRN promoter in which elevated H3K27 acetylation and transcription factor EB (TFEB) occupancy correlate with HDAC-inhibitor-mediated upregulation of PGRN. These findings have implications for epigenetic and cis-regulatory mechanisms controlling human GRN expression and may advance translational efforts to develop targeted therapeutics for treating PGRN-deficient FTD.
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Affiliation(s)
- Angela She
- Chemical Neurobiology Laboratory, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Iren Kurtser
- Chemical Neurobiology Laboratory, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Surya A Reis
- Chemical Neurobiology Laboratory, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Krista Hennig
- Chemical Neurobiology Laboratory, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Jenny Lai
- Chemical Neurobiology Laboratory, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Audrey Lang
- Chemical Neurobiology Laboratory, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Bradford C Dickerson
- MGH Frontotemporal Disorders Unit, Gerontology Research Unit, Alzheimer's Disease Research Center, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Joachim Herz
- Departments of Molecular Genetics, Neuroscience, Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9046, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA.
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280
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Epstein-Barr Virus Rta-Mediated Accumulation of DNA Methylation Interferes with CTCF Binding in both Host and Viral Genomes. J Virol 2017; 91:JVI.00736-17. [PMID: 28490592 DOI: 10.1128/jvi.00736-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Rta, an Epstein-Barr virus (EBV) immediate-early protein, reactivates viral lytic replication that is closely associated with tumorigenesis. In previous studies, we demonstrated that in epithelial cells Rta efficiently induced cellular senescence, which is an irreversible G1 arrest likely to provide a favorable environment for productive replications of EBV and Kaposi's sarcoma-associated herpesvirus (KSHV). To restrict progression of the cell cycle, Rta simultaneously upregulates CDK inhibitors and downregulates MYC, CCND1, and JUN, among others. Rta has long been known as a potent transcriptional activator, thus its role in gene repression is unexpected. In silico analysis revealed that the promoter regions of MYC, CCND1, and JUN are common in (i) the presence of CpG islands, (ii) strong chromatin immunoprecipitation (ChIP) signals of CCCTC-binding factor (CTCF), and (iii) having at least one Rta binding site. By combining ChIP assays and DNA methylation analysis, here we provide evidence showing that Rta binding accumulated CpG methylation and decreased CTCF occupancy in the regulatory regions of MYC, CCND1, and JUN, which were associated with downregulated gene expression. Stable residence of CTCF in the viral latency and reactivation control regions is a hallmark of viral latency. Here, we observed that Rta-mediated decreased binding of CTCF in the viral genome is concurrent with virus reactivation. Via interfering with CTCF binding, in the host genome Rta can function as a transcriptional repressor for gene silencing, while in the viral genome Rta acts as an activator for lytic gene loci by removing a topological constraint established by CTCF.IMPORTANCE CTCF is a multifunctional protein that variously participates in gene expression and higher-order chromatin structure of the cellular and viral genomes. In certain loci of the genome, CTCF occupancy and DNA methylation are mutually exclusive. Here, we demonstrate that the Epstein-Barr virus (EBV) immediate-early protein, Rta, known to be a transcriptional activator, can also function as a transcriptional repressor. Via enriching CpG methylation and decreasing CTCF reloading, Rta binding efficiently shut down the expression of MYC, CCND1, and JUN, thus impeding cell cycle progression. Rta-mediated disruption of CTCF binding was also detected in the latency/reactivation control regions of the EBV genome, and this in turn led to viral lytic cycle progression. As emerging evidence indicates that a methylated EBV genome is a preferable substrate for EBV Zta, the other immediate-early protein, our results suggest a mechanistic link in understanding the molecular processes of viral latent-lytic switch.
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281
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Galperin MY, Fernández-Suárez XM, Rigden DJ. The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res 2017; 45:D1-D11. [PMID: 28053160 PMCID: PMC5210597 DOI: 10.1093/nar/gkw1188] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 12/23/2022] Open
Abstract
This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein-protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as 'breakthrough' contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the 'golden set' of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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282
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Coit P, Dozmorov MG, Merrill JT, McCune WJ, Maksimowicz-McKinnon K, Wren JD, Sawalha AH. Epigenetic Reprogramming in Naive CD4+ T Cells Favoring T Cell Activation and Non-Th1 Effector T Cell Immune Response as an Early Event in Lupus Flares. Arthritis Rheumatol 2017; 68:2200-9. [PMID: 27111767 DOI: 10.1002/art.39720] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/12/2016] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a relapsing autoimmune disease that affects multiple organ systems. T cells play an important role in the pathogenesis of lupus; however, early T cell events triggering disease flares are incompletely understood. This study was undertaken to examine DNA methylation in naive CD4+ T cells from lupus patients to determine if epigenetic remodeling in CD4+ T cells is an early event in lupus flares. METHODS A total of 74 lupus patients with an SLE Disease Activity Index score of 0-18 were included. Naive CD4+ T cells were isolated from peripheral blood samples, and DNA was extracted for genome-wide methylation assessment. RNA was also extracted from a subset of patients to determine the relationship between epigenetic changes and transcription activity using RNA sequencing and microRNA arrays. RESULTS We demonstrated that naive CD4+ T cells in lupus undergo an epigenetic proinflammatory shift, implicating effector T cell responses in lupus flare. This epigenetic landscape change occurs without changes in expression of the corresponding genes, poises naive CD4+ T cells for Th2, Th17, and follicular helper T cell immune responses, and opposes inhibitory transforming growth factor β signaling. Bioinformatics analyses indicate that the epigenetic modulator EZH2 might play an important role in shifting the epigenetic landscape, with increased disease activity in lupus naive CD4+ T cells. Further, the expression of microRNA-26a, which is sensitive to glucose availability and targets EZH2, was negatively correlated with disease activity in lupus patients. CONCLUSION An epigenetic landscape shift in naive CD4+ T cells that favors T cell activation and non-Th1 immune responses predates transcription activity and correlates with lupus activity. A role for EZH2 dysregulation in triggering lupus flares warrants further investigation.
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Affiliation(s)
| | | | | | | | | | - Jonathan D Wren
- Oklahoma Medical Research Foundation and University of Oklahoma, Oklahoma City
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283
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Song X, Li WQ, Hu N, Zhao XK, Wang Z, Hyland PL, Jiang T, Kong GQ, Su H, Wang C, Wang L, Sun L, Fan ZM, Meng H, Zhang TJ, Ji LF, Hu SJ, Han WL, Wu MJ, Zheng PY, Lv S, Li XM, Zhou FY, Burdett L, Ding T, Qiao YL, Fan JH, Han XY, Giffen C, Tucker MA, Dawsey SM, Freedman ND, Chanock SJ, Abnet CC, Taylor PR, Wang LD, Goldstein AM. GWAS follow-up study of esophageal squamous cell carcinoma identifies potential genetic loci associated with family history of upper gastrointestinal cancer. Sci Rep 2017; 7:4642. [PMID: 28680059 PMCID: PMC5498542 DOI: 10.1038/s41598-017-04822-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/22/2017] [Indexed: 01/01/2023] Open
Abstract
Based on our initial genome-wide association study (GWAS) on esophageal squamous cell carcinoma (ESCC) in Han Chinese, we conducted a follow-up study to examine the single nucleotide polymorphisms (SNPs) associated with family history (FH) of upper gastrointestinal cancer (UGI) cancer in cases with ESCC. We evaluated the association between SNPs and FH of UGI cancer among ESCC cases in a stage-1 case-only analysis of the National Cancer Institute (NCI, 541 cases with FH and 1399 without FH) and Henan GWAS (493 cases with FH and 869 without FH) data (discovery phase). The top SNPs (or their surrogates) from discovery were advanced to a stage-2 evaluation in additional Henan subjects (2801 cases with FH and 3136 without FH, replication phase). A total of 19 SNPs were associated with FH of UGI cancer in ESCC cases with P < 10-5 in the stage-1 meta-analysis of NCI and Henan GWAS data. In stage-2, the association for rs79747906 (located at 18p11.31, P = 5.79 × 10-6 in discovery) was replicated (P = 0.006), with a pooled-OR of 1.59 (95%CI: 1.11-2.28). We identified potential genetic variants associated with FH of UGI cancer. Our findings may provide important insights into new low-penetrance susceptibility regions involved in the susceptibility of families with multiple UGI cancer cases.
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Affiliation(s)
- Xin Song
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Wen-Qing Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.,Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, RI, USA.,Department of Epidemiology, School of Public Health, Brown University, Providence, RI, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Xue Ke Zhao
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Tao Jiang
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Guo Qiang Kong
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Hua Su
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Lemin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Li Sun
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Zong Min Fan
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Hui Meng
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Tang Juan Zhang
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Ling Fen Ji
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Shou Jia Hu
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Wei Li Han
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China
| | - Min Jie Wu
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan province, 450052, China
| | - Peng Yuan Zheng
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan province, 450052, China
| | - Shuang Lv
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan province, 450052, China
| | - Xue Min Li
- Department of Pathology, Cixian Hospital, Cixian, Hebei, 056500, P.R. China
| | - Fu You Zhou
- Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, Henan, 455000, P.R. China
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, P.R. China
| | - You-Lin Qiao
- Department of Epidemiology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Jin-Hu Fan
- Department of Epidemiology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xiao-You Han
- Shanxi Cancer Hospital, Taiyuan, Shanxi, P.R. China
| | - Carol Giffen
- Information Management Services, Inc., Silver Spring, MD, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Sanford M Dawsey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Li-Dong Wang
- Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, Henan, 450052, P.R. China.
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.
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284
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Moffett HF, Cartwright ANR, Kim HJ, Godec J, Pyrdol J, Äijö T, Martinez GJ, Rao A, Lu J, Golub TR, Cantor H, Sharpe AH, Novina CD, Wucherpfennig KW. The microRNA miR-31 inhibits CD8 + T cell function in chronic viral infection. Nat Immunol 2017; 18:791-799. [PMID: 28530712 PMCID: PMC5753758 DOI: 10.1038/ni.3755] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/27/2017] [Indexed: 12/13/2022]
Abstract
During infection, antigen-specific T cells undergo tightly regulated developmental transitions controlled by transcriptional and post-transcriptional regulation of gene expression. We found that the microRNA miR-31 was strongly induced by activation of the T cell antigen receptor (TCR) in a pathway involving calcium and activation of the transcription factor NFAT. During chronic infection with lymphocytic choriomeningitis virus (LCMV) clone 13, miR-31-deficent mice recovered from clinical disease, while wild-type mice continued to show signs of disease. This disease phenotype was explained by the presence of larger numbers of cytokine-secreting LCMV-specific CD8+ T cells in miR-31-deficent mice than in wild-type mice. Mechanistically, miR-31 increased the sensitivity of T cells to type I interferons, which interfered with effector T cell function and increased the expression of several proteins related to T cell dysfunction during chronic infection. These studies identify miR-31 as an important regulator of T cell exhaustion in chronic infection.
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Affiliation(s)
- Howell F Moffett
- Department of Cancer Immunology &Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Adam N R Cartwright
- Department of Cancer Immunology &Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Hye-Jung Kim
- Department of Cancer Immunology &Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jernej Godec
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason Pyrdol
- Department of Cancer Immunology &Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Tarmo Äijö
- Department of Information and Computer Science, Aalto University School of Science, Aalto, Finland
| | - Gustavo J Martinez
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Jun Lu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Harvey Cantor
- Department of Cancer Immunology &Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Arlene H Sharpe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Carl D Novina
- Department of Cancer Immunology &Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology &Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
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285
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Robinson SC, Klobucar K, Pierre CC, Ansari A, Zhenilo S, Prokhortchouk E, Daniel JM. Kaiso differentially regulates components of the Notch signaling pathway in intestinal cells. Cell Commun Signal 2017. [PMID: 28637464 PMCID: PMC5480165 DOI: 10.1186/s12964-017-0178-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background In mammalian intestines, Notch signaling plays a critical role in mediating cell fate decisions; it promotes the absorptive (or enterocyte) cell fate, while concomitantly inhibiting the secretory cell fate (i.e. goblet, Paneth and enteroendocrine cells). We recently reported that intestinal-specific Kaiso overexpressing mice (KaisoTg) exhibited chronic intestinal inflammation and had increased numbers of all three secretory cell types, hinting that Kaiso might regulate Notch signaling in the gut. However, Kaiso’s precise role in Notch signaling and whether the KaisoTg secretory cell fate phenotype was linked to Kaiso-induced inflammation had yet to be elucidated. Methods Intestines from 3-month old Non-transgenic and KaisoTg mice were “Swiss” rolled and analysed for the expression of Notch1, Dll-1, Jagged-1, and secretory cell markers by immunohistochemistry and immunofluorescence. To evaluate inflammation, morphological analyses and myeloperoxidase assays were performed on intestines from 3-month old KaisoTg and control mice. Notch1, Dll-1 and Jagged-1 expression were also assessed in stable Kaiso-depleted colon cancer cells and isolated intestinal epithelial cells using real time PCR and western blotting. To assess Kaiso binding to the DLL1, JAG1 and NOTCH1 promoter regions, chromatin immunoprecipitation was performed on three colon cancer cell lines. Results Here we demonstrate that Kaiso promotes secretory cell hyperplasia independently of Kaiso-induced inflammation. Moreover, Kaiso regulates several components of the Notch signaling pathway in intestinal cells, namely, Dll-1, Jagged-1 and Notch1. Notably, we found that in KaisoTg mice intestines, Notch1 and Dll-1 expression are significantly reduced while Jagged-1 expression is increased. Chromatin immunoprecipitation experiments revealed that Kaiso associates with the DLL1 and JAG1 promoter regions in a methylation-dependent manner in colon carcinoma cell lines, suggesting that these Notch ligands are putative Kaiso target genes. Conclusion Here, we provide evidence that Kaiso’s effects on intestinal secretory cell fates precede the development of intestinal inflammation in KaisoTg mice. We also demonstrate that Kaiso inhibits the expression of Dll-1, which likely contributes to the secretory cell phenotype observed in our transgenic mice. In contrast, Kaiso promotes Jagged-1 expression, which may have implications in Notch-mediated colon cancer progression. Electronic supplementary material The online version of this article (doi:10.1186/s12964-017-0178-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shaiya C Robinson
- Department of Biology, McMaster University, Hamilton, L8S 4K1, ON, Canada
| | - Kristina Klobucar
- Department of Biology, McMaster University, Hamilton, L8S 4K1, ON, Canada.,Current address: Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, L8N 3Z5, ON, Canada
| | - Christina C Pierre
- Department of Biology, McMaster University, Hamilton, L8S 4K1, ON, Canada.,Current address: Department of Life Science, University of the West Indies at St. Augustine, St. Augustine, Trinidad and Tobago
| | - Amna Ansari
- Department of Biology, McMaster University, Hamilton, L8S 4K1, ON, Canada
| | - Svetlana Zhenilo
- Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation, 117312
| | - Egor Prokhortchouk
- Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation, 117312
| | - Juliet M Daniel
- Department of Biology, McMaster University, Hamilton, L8S 4K1, ON, Canada.
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286
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Dave K, Sur I, Yan J, Zhang J, Kaasinen E, Zhong F, Blaas L, Li X, Kharazi S, Gustafsson C, De Paepe A, Månsson R, Taipale J. Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. eLife 2017; 6. [PMID: 28583252 PMCID: PMC5461110 DOI: 10.7554/elife.23382] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/18/2017] [Indexed: 12/18/2022] Open
Abstract
The gene desert upstream of the MYC oncogene on chromosome 8q24 contains susceptibility loci for several major forms of human cancer. The region shows high conservation between human and mouse and contains multiple MYC enhancers that are activated in tumor cells. However, the role of this region in normal development has not been addressed. Here we show that a 538 kb deletion of the entire MYC upstream super-enhancer region in mice results in 50% to 80% decrease in Myc expression in multiple tissues. The mice are viable and show no overt phenotype. However, they are resistant to tumorigenesis, and most normal cells isolated from them grow slowly in culture. These results reveal that only cells whose MYC activity is increased by serum or oncogenic driver mutations depend on the 8q24 super-enhancer region, and indicate that targeting the activity of this element is a promising strategy of cancer chemoprevention and therapy.
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Affiliation(s)
- Kashyap Dave
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Inderpreet Sur
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jian Yan
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jilin Zhang
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Eevi Kaasinen
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fan Zhong
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leander Blaas
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Xiaoze Li
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shabnam Kharazi
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Gustafsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ayla De Paepe
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
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287
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Yin J, Liu H, Liu Z, Owzar K, Han Y, Su L, Wei Y, Hung RJ, Brhane Y, McLaughlin J, Brennan P, Bickeboeller H, Rosenberger A, Houlston RS, Caporaso N, Landi MT, Heinrich J, Risch A, Christiani DC, Amos CI, Wei Q. Pathway-analysis of published genome-wide association studies of lung cancer: A potential role for the CYP4F3 locus. Mol Carcinog 2017; 56:1663-1672. [PMID: 28150878 PMCID: PMC5423820 DOI: 10.1002/mc.22622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 01/30/2017] [Indexed: 12/14/2022]
Abstract
The fatty acids (FAs) metabolism is suggested to play a pivotal role in the development of lung cancer, and we explored that by conducting a pathway-based analysis. We performed a meta-analysis of published datasets of six genome wide association studies (GWASs) from the Transdisciplinary Research in Cancer of the Lung (TRICL) consortium, which included 12 160 cases with lung cancer and 16 838 cancer-free controls. A total of 30 722 single-nucleotide polymorphisms (SNPs) from 317 genes relevant to FA metabolic pathways were identified. An additional dataset from the Harvard Lung Cancer Study with 984 cases and 970 healthy controls was also added to the final meta-analysis. In the initial meta-analysis, 26 of 28 SNPs that passed false discovery rate multiple tests were mapped to the CYP4F3 gene. Among the 26 top ranked hits was a proxy SNP, CYP4F3 rs4646904 (P = 8.65 × 10-6 , FDR = 0.018), which is suggested to change splicing pattern/efficiency and to be associated with gene expression levels. However, after adding data of rs4646904 from the Harvard GWAS, the significance in the combined analysis was reduced to P = 3.52 × 10-3 [odds ratio (OR) = 1.07, 95% confidence interval (95%CI) = 1.03-1.12]. Interestingly, the small Harvard dataset also pointed to the same direction of the association in subgroups of smokers (OR = 1.07) and contributed to a combined OR of 1.13 (95% CI = 1.06-1.20, P = 6.70 × 10-5 ). The results suggest that a potentially functional SNP in CYP4F3 (rs4646904) may contribute to the etiology of lung cancer, especially in smokers. Additional mechanistic studies are warranted to unravel the potential biological significance of the finding.
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Affiliation(s)
- Jieyun Yin
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Medical College of Soochow University, 199 Ren Ai Road, Suzhou, China
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC
| | - Younghun Han
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Li Su
- Massachusetts General Hospital, Boston, MA
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Yongyue Wei
- Massachusetts General Hospital, Boston, MA
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Heike Bickeboeller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Neil Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Maria Teresa Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joachim Heinrich
- Helmholtz Centre Munich, German Research Centre for Environmental Health, Institute of Epidemiology I, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital Munich, Ludwig Maximilian University Munich, Munich, Germany
| | - Angela Risch
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
- Department of Epigenomics and Cancer Risk Factors, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - David C. Christiani
- Massachusetts General Hospital, Boston, MA
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Christopher I. Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University School of Medicine, Durham, NC
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288
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Verbeeren J, Verma B, Niemelä EH, Yap K, Makeyev EV, Frilander MJ. Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA. PLoS Genet 2017; 13:e1006824. [PMID: 28549066 PMCID: PMC5473595 DOI: 10.1371/journal.pgen.1006824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/16/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3′ untranslated region (3′UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3′UTR to non-productive isoforms with a long 3′UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12- and U2-type 5′ splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3′UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm. The cellular homeostasis of many components of the eukaryotic RNA processing machinery is regulated via negative feed-back pathways that result in the formation of both productive and non-productive mRNA species. Typically, the formation of non-productive mRNAs species results from changes in alternative splicing that disrupt the reading frame of the protein coding region and leads to destabilization of the mRNA. Here, we have investigated the homeostasis regulation of the U11/U12-65K mRNA that encodes an essential protein component of the minor (U12-dependent) spliceosome intron recognition complex. We show that homeostasis is regulated at the level of nuclear mRNA export and mRNA 3′-end formation, and that it can be further regulated during neuronal differentiation. We describe a multilayered regulatory system utilizing alternative exon definition interactions that use the input from both spliceosomes and the polyadenylation machinery to decide between productive and non-productive mRNA formation. Because the 65K protein is an essential component of the minor spliceosome, this regulatory pathway can potentially affect the expression of ~700 genes containing U12-type introns.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Bhupendra Verma
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Elina H. Niemelä
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Karen Yap
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Eugene V. Makeyev
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Mikko J. Frilander
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
- * E-mail:
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289
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Loo LWM, Lemire M, Le Marchand L. In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants. BMC Genomics 2017; 18:381. [PMID: 28506205 PMCID: PMC5432975 DOI: 10.1186/s12864-017-3750-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/02/2017] [Indexed: 02/08/2023] Open
Abstract
Background Genome-wide association studies have identified 55 genetic variants associated with colorectal cancer risk to date. However, potential causal genes and pathways regulated by these risk variants remain to be characterized. Therefore, we performed gene ontology enrichment and pathway analyses to determine if there was an enrichment of genes in proximity to the colorectal cancer risk variants that could further elucidate the probable causal genes and pathways involved in colorectal cancer biology. Results For the 65 unique genes that either contained, or were immediately neighboring up- and downstream, of these variants there was a significant enrichment for the KEGG pathway, Pathways in Cancer (p-value = 2.67 × 10−5) and an enrichment for multiple biological processes (FDR < 0.05), such as cell junction organization, tissue morphogenesis, regulation of SMAD protein phosphorylation, and odontogenesis identified through Gene Ontology analysis. To identify potential causal genes, we conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using gene expression and genotype data from the Genotype-Tissue Expression (GTEx) Project portal in normal sigmoid (n = 124) and transverse (n = 169) colon tissue. In addition, we also did a cis-eQTL analysis on colorectal tumor tissue (n = 147) from The Cancer Genome Atlas (TCGA). We identified two risk alleles that were significant cis-eQTLs for FADS2 (rs1535) and COLCA1 and 2 (rs3802842) genes in the normal transverse colon tissue and two risk alleles that were significant cis-eQTLs for the CABLES2 (rs2427308) and LIPG (rs7229639) genes in the normal sigmoid colon tissue, but not tumor tissue. Conclusions Our data reaffirm the potential to identify an enrichment for biological processes and candidate causal genes based on expression profiles correlated with genetic risk alleles of colorectal cancer, however, the identification of these significant cis-eQTLs is context and tissue specific. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3750-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lenora W M Loo
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA.
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Loïc Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
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290
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Naderi A. C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. Oncotarget 2017; 8:57907-57933. [PMID: 28915724 PMCID: PMC5593696 DOI: 10.18632/oncotarget.17826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
This study investigated the network of genes that are co-expressed with androgen receptor (AR) to discover novel AR targets in breast cancer. Bioinformatics analysis of two datasets from breast cancer cell lines resulted in the identification of an AR-gene signature constituted of 98 genes that highly correlated with AR expression. Notably, C1orf64 showed the highest positive correlation with AR across the datasets with a correlation coefficient (CC) of 0.737. In addition, C1orf64 closely correlated with AR expression in primary and metastatic breast tumors and C1orf64 expression was relatively higher in breast tumors with a lower grade and lobular histology. Furthermore, there is a functional interplay between AR and C1orf64 in breast cancer. In this process, AR activation directly represses C1orf64 transcription and C1orf64, in turn, interacts with AR as a corepressor and negatively regulates the AR-mediated induction of prolactin-induced protein (PIP) and AR reporter activity. Moreover, the corepressor effect of C1orf64 results in a reduction of AR binding to PIP promoter. The other aspect of this interplay involves a cross-talk between AR and estrogen receptor (ER) signaling in which C1orf64 silencing intensifies the AR-mediated down-regulation of ER target gene, progesterone receptor. Therefore, the repression of C1orf64 by AR provides an underlying mechanism for the AR inhibitory effects on ER signaling. To elucidate the biochemical mechanisms of C1orf64 function, this study demonstrates that C1orf64 is a phosphothreonine protein that interacts with the chaperone protein 14-3-3. In summary, C1orf64 is a novel AR coregulator and a 14-3-3 binding partner in breast cancer.
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Affiliation(s)
- Ali Naderi
- University of Hawaii Cancer Center, Cancer Biology Program, Honolulu, Hawaii 96813, USA
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291
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Lund RJ, Huhtinen K, Salmi J, Rantala J, Nguyen EV, Moulder R, Goodlett DR, Lahesmaa R, Carpén O. DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer. Sci Rep 2017; 7:1469. [PMID: 28473707 PMCID: PMC5431431 DOI: 10.1038/s41598-017-01624-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/30/2017] [Indexed: 12/31/2022] Open
Abstract
High-grade serous ovarian cancer is the most common ovarian cancer type. Although the combination of surgery and platinum-taxane chemotherapy provide an effective treatment, drug resistance frequently occurs leading to poor outcome. In order to clarify the molecular mechanisms of drug resistance, the DNA methylation and transcriptomic changes, associated with the development of drug resistance in high-grade serous ovarian cancer, were examined from patient derived malignant ascites cells. In parallel with large-scale transcriptome changes, cisplatin resistance was associated with loss of hypermethylation at several CpG sites primarily localized in the intergenic regions of the genome. The transcriptome and CpG methylome changes in response to cisplatin treatment of both sensitive and resistant cells were minimal, indicating the importance of post-translational mechanisms in regulating death or survival of the cells. The response of resistant cells to high concentrations of cisplatin revealed transcriptomic changes in potential key drivers of drug resistance, such as KLF4. Among the strongest changes was also induction of IL6 in resistant cells and the expression was further increased in response to cisplatin. Also, several other components of IL6 signaling were affected, further supporting previous observations on its importance in malignant transformation and development of drug resistance in ovarian cancer.
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Affiliation(s)
- Riikka J Lund
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Kaisa Huhtinen
- Department of Pathology, Medicity Research Unit, University of Turku and Turku University Hospital, Turku, Finland
| | - Jussi Salmi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Juha Rantala
- Department of Pathology, Medicity Research Unit, University of Turku and Turku University Hospital, Turku, Finland
| | - Elizabeth V Nguyen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - David R Goodlett
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Olli Carpén
- Department of Pathology, Medicity Research Unit, University of Turku and Turku University Hospital, Turku, Finland.
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292
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LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes. Sci Rep 2017; 7:46440. [PMID: 28440307 PMCID: PMC5404328 DOI: 10.1038/srep46440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/20/2017] [Indexed: 11/09/2022] Open
Abstract
C/EBPε is a critical transcriptional factor for granulocyte differentiation and function. Individuals with germline mutations of C/EBPε fail to develop normal granulocytes and suffer from repeated infections. In order to gain a global view of the transcriptional machinery regulated by C/EBPε, we performed whole-genome ChIP-Seq using mouse bone marrow cells. To complement the C/EBPε DNA binding analyses, RNA-Sequencing was done in parallel using sorted mature and immature granulocytes from WT and C/EBPε KO bone marrow. This approach led to the identification of several direct targets of C/EBPε, which are potential effectors of its role in granulocytic differentiation and function. Interestingly, Trem1, a gene critical to granulocyte function, was identified as a direct C/EBPε target gene. Trem1 expression overlaps very closely with expression signature of C/EBPε during hematopoietic development. Luciferase reporter and EMSA assays revealed that C/EBPε binds to the regulatory elements of Trem1 and regulates its expression during granulocytic differentiation. In addition, we provide evidence that inflammatory stimuli (LPS) can also control the expression of Trem1 independent of C/EBPε. Overall, this study provides comprehensive profiling of the transcriptional network controlled by C/EBPε during granulopoiesis and identifies Trem1 as one of its downstream effectors involved in eliciting an immune response.
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293
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Lee K, Lee S, Bang H, Choi JK. Predictive long-range allele-specific mapping of regulatory variants and target transcripts. PLoS One 2017; 12:e0175768. [PMID: 28406955 PMCID: PMC5391085 DOI: 10.1371/journal.pone.0175768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/30/2017] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified a large number of noncoding associations, calling for systematic mapping to causal regulatory variants and their distal target genes. A widely used method, quantitative trait loci (QTL) mapping for chromatin or expression traits, suffers from sample-to-sample experimental variation and trans-acting or environmental effects. Instead, alleles at heterozygous loci can be compared within a sample, thereby controlling for those confounding factors. Here we introduce a method for chromatin structure-based allele-specific pairing of regulatory variants and target transcripts. With phased genotypes, much of allele-specific expression could be explained by paired allelic cis-regulation across a long range. This approach showed approximately two times greater sensitivity than QTL mapping. There are cases in which allele imbalance cannot be tested because heterozygotes are not available among reference samples. Therefore, we employed a machine learning method to predict missing positive cases based on various features shared by observed allele-specific pairs. We showed that only 10 reference samples are sufficient to achieve high prediction accuracy with a low sampling variation. In conclusion, our method enables highly sensitive fine mapping and target identification for trait-associated variants based on a small number of reference samples.
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Affiliation(s)
- Kibaick Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Seulkee Lee
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Hyoeun Bang
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
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294
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SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PLoS One 2017; 12:e0175310. [PMID: 28403240 PMCID: PMC5389787 DOI: 10.1371/journal.pone.0175310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/23/2017] [Indexed: 12/16/2022] Open
Abstract
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package.
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295
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Novel spliced variants of OCT4, OCT4C and OCT4C1, with distinct expression patterns and functions in pluripotent and tumor cell lines. Eur J Cell Biol 2017; 96:347-355. [PMID: 28476334 DOI: 10.1016/j.ejcb.2017.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/25/2017] [Accepted: 03/28/2017] [Indexed: 02/02/2023] Open
Abstract
OCT4 is a major regulator of pluripotency which has several spliced variants and expressed pseudogenes. Here, we are reporting the existence of two additional novel spliced variants of OCT4, OCT4C and OCT4C1, which lack Exon1 (E1) but start at a novel exon (E0) located ∼14kb upstream of E2. OCT4C/C1 is highly expressed in ES and iPS cells, and their expression was sharply turned off, upon the induction of neural differentiation. The long non-coding RNA (lncRNA) PSORS1C3, is located ∼9kb downstream of the E0 of OCT4C/C1. PSORS1C3 is vigorously spliced to generate nine novel variants, however, none of its exons incorporated in alternatively spliced variants of OCT4. Interestingly, the exons of OCT4 and PSORS1C3 are intertwined, with a novel exon (E0) of PSORS1C3 located ∼4kb upstream of OCT4 E0. This exon participates in generating some more variants of PSORS1C3 (variants 10-24). OCT4C/C1 knock-down in ES and iPS cell lines caused a slight downregulation of PSORS1C3 and OCT4A, a slight upregulation of OCT4B1, and a dramatic upregulation of OCT4B. Altogether, our data revisited the current view of OCT4 gene structure and regulation, and revealed its complex genomic features and expression regulation in stem and tumor cells.
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296
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Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol 2017; 18:57. [PMID: 28351423 PMCID: PMC5371228 DOI: 10.1186/s13059-017-1186-2] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammalian aging; however, epigenetic clocks have thus far been formulated only in humans. RESULTS We first examined whether mice and humans experience similar patterns of change in the methylome with age. We found moderate conservation of CpG sites for which methylation is altered with age, with both species showing an increase in methylome disorder during aging. Based on this analysis, we formulated an epigenetic-aging model in mice using the liver methylomes of 107 mice from 0.2 to 26.0 months old. To examine whether epigenetic aging signatures are slowed by longevity-promoting interventions, we analyzed 28 additional methylomes from mice subjected to lifespan-extending conditions, including Prop1df/df dwarfism, calorie restriction or dietary rapamycin. We found that mice treated with these lifespan-extending interventions were significantly younger in epigenetic age than their untreated, wild-type age-matched controls. CONCLUSIONS This study shows that lifespan-extending conditions can slow molecular changes associated with an epigenetic clock in mice livers.
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Affiliation(s)
- Tina Wang
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Brian Tsui
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Neil A Robertson
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Andrew M Gross
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael Ku Yu
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Holly M Brown-Borg
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Peter D Adams
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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297
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PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4. Sci Rep 2017; 7:45038. [PMID: 28332630 PMCID: PMC5362932 DOI: 10.1038/srep45038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/20/2017] [Indexed: 11/16/2022] Open
Abstract
The promyelocytic leukemia (PML) protein is an essential component of PML nuclear bodies (PML NBs) frequently lost in cancer. PML NBs coordinate chromosomal regions via modification of nuclear proteins that in turn may regulate genes in the vicinity of these bodies. However, few PML NB-associated genes have been identified. PML and PML NBs can also regulate mTOR and cell fate decisions in response to cellular stresses. We now demonstrate that PML depletion in U2OS cells or TERT-immortalized normal human diploid fibroblasts results in decreased expression of the mTOR inhibitor DDIT4 (REDD1). DNA and RNA immuno-FISH reveal that PML NBs are closely associated with actively transcribed DDIT4 loci, implicating these bodies in regulation of basal DDIT4 expression. Although PML silencing did reduce the sensitivity of U2OS cells to metabolic stress induced by metformin, PML loss did not inhibit the upregulation of DDIT4 in response to metformin, hypoxia-like (CoCl2) or genotoxic stress. Analysis of publicly available cancer data also revealed a significant correlation between PML and DDIT4 expression in several cancer types (e.g. lung, breast, prostate). Thus, these findings uncover a novel mechanism by which PML loss may contribute to mTOR activation and cancer progression via dysregulation of basal DDIT4 gene expression.
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298
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Dozmorov MG, Coit P, Maksimowicz-McKinnon K, Sawalha AH. Age-associated DNA methylation changes in naive CD4 + T cells suggest an evolving autoimmune epigenotype in aging T cells. Epigenomics 2017; 9:429-445. [PMID: 28322571 DOI: 10.2217/epi-2016-0143] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM We sought to define age-associated DNA methylation changes in naive CD4+ T cells. MATERIALS & METHODS Naive CD4+ T cells were collected from 74 healthy individuals (age 19-66 years), and age-related DNA methylation changes were characterized. RESULTS We identified 11,431 age-associated CpG sites, 57% of which were hypermethylated with age. Hypermethylated sites were enriched in CpG islands and repressive transcription factor binding sites, while hypomethylated sites showed T cell specific enrichment in active enhancers marked by H3K27ac and H3K4me1. Our data emphasize cancer-related DNA methylation changes with age, and also reveal age-associated hypomethylation in immune-related pathways, such as T cell receptor signaling, FCγR-mediated phagocytosis, apoptosis and the mammalian target of rapamycin signaling pathway. The MAPK signaling pathway was hypermethylated with age, consistent with a defective MAPK signaling in aging T cells. CONCLUSION Age-associated DNA methylation changes may alter regulatory mechanisms and signaling pathways that predispose to autoimmunity.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Patrick Coit
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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299
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Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. mSystems 2017; 2:mSystems00186-16. [PMID: 28317029 PMCID: PMC5350546 DOI: 10.1128/msystems.00186-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/02/2017] [Indexed: 12/19/2022] Open
Abstract
In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach. As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i.e., (i) an interactive genome viewer to display gene expression arrays, tiling arrays, and sequencing data sets along with proteomics and genomics data sets; (ii) an expression and protein atlas that connects every gene, small RNA, antisense RNA, or protein with the most relevant omics data; (iii) a specific tool for exploring protein conservation through the Listeria phylogenomic tree; and (iv) a coexpression network tool for the discovery of potential new regulations. Our platform integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. This website allows navigation among all these data sets with enriched metadata in a user-friendly format and can be used as a central database for systems biology analysis. IMPORTANCE In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach.
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Chen KW, Chen L. Epigenetic Regulation of BDNF Gene during Development and Diseases. Int J Mol Sci 2017; 18:ijms18030571. [PMID: 28272318 PMCID: PMC5372587 DOI: 10.3390/ijms18030571] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/01/2017] [Indexed: 12/14/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is required for the development of the nervous system, proper cognitive function and memory formation. While aberrant expression of BDNF has been implicated in neurological disorders, the transcriptional regulation of BDNF remains to be elucidated. In response to different stimuli, BDNF expression can be initiated from different promoters. Several studies have suggested that the expression of BDNF is regulated by promoter methylation. An emerging theme points to the possibility that histone modifications at the BDNF promoters may link to the neurological pathology. Thus, understanding the epigenetic regulation at the BDNF promoters will shed light on future therapies for neurological disorders. The present review summarizes the current knowledge of histone modifications of the BDNF gene in neuronal diseases, as well as the developmental regulation of the BDNF gene based on data from the Encyclopedia of DNA Elements (ENCODE).
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Affiliation(s)
- Kuan-Wei Chen
- Institute of Molecular Medicine and Department of Medical Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
| | - Linyi Chen
- Institute of Molecular Medicine and Department of Medical Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
- Department of Medical Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
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