201
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Salas LA, Wiencke JK, Koestler DC, Zhang Z, Christensen BC, Kelsey KT. Tracing human stem cell lineage during development using DNA methylation. Genome Res 2018; 28:1285-1295. [PMID: 30072366 PMCID: PMC6120629 DOI: 10.1101/gr.233213.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/27/2018] [Indexed: 12/22/2022]
Abstract
Stem cell maturation is a fundamental, yet poorly understood aspect of human development. We devised a DNA methylation signature deeply reminiscent of embryonic stem cells (a fetal cell origin signature, FCO) to interrogate the evolving character of multiple human tissues. The cell fraction displaying this FCO signature was highly dependent upon developmental stage (fetal versus adult), and in leukocytes, it described a dynamic transition during the first 5 yr of life. Significant individual variation in the FCO signature of leukocytes was evident at birth, in childhood, and throughout adult life. The genes characterizing the signature included transcription factors and proteins intimately involved in embryonic development. We defined and applied a DNA methylation signature common among human fetal hematopoietic progenitor cells and have shown that this signature traces the lineage of cells and informs the study of stem cell heterogeneity in humans under homeostatic conditions.
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Affiliation(s)
- Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
| | - John K Wiencke
- Department of Neurological Surgery, Institute for Human Genetics, University of California San Francisco, San Francisco, California 94158, USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Ze Zhang
- Department of Epidemiology, Brown University, Providence, Rhode Island 02912, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA.,Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island 02912, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
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202
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Aponte JL, Chiano MN, Yerges-Armstrong LM, Hinds DA, Tian C, Gupta A, Guo C, Fraser DJ, Freudenberg JM, Rajpal DK, Ehm MG, Waterworth DM. Assessment of rosacea symptom severity by genome-wide association study and expression analysis highlights immuno-inflammatory and skin pigmentation genes. Hum Mol Genet 2018; 27:2762-2772. [PMID: 29771307 PMCID: PMC6822543 DOI: 10.1093/hmg/ddy184] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 01/09/2023] Open
Abstract
Rosacea is a common, chronic skin disease of variable severity with limited treatment options. The cause of rosacea is unknown, but it is believed to be due to a combination of hereditary and environmental factors. Little is known about the genetics of the disease. We performed a genome-wide association study (GWAS) of rosacea symptom severity with data from 73 265 research participants of European ancestry from the 23andMe customer base. Seven loci had variants associated with rosacea at the genome-wide significance level (P < 5 × 10-8). Further analyses highlighted likely gene regions or effector genes including IRF4 (P = 1.5 × 10-17), a human leukocyte antigen (HLA) region flanked by PSMB9 and HLA-DMB (P = 2.2 × 10-15), HERC2-OCA2 (P = 4.2 × 10-12), SLC45A2 (P = 1.7 × 10-10), IL13 (P = 2.8 × 10-9), a region flanked by NRXN3 and DIO2 (P = 4.1 × 10-9), and a region flanked by OVOL1and SNX32 (P = 1.2 × 10-8). All associations with rosacea were novel except for the HLA locus. Two of these loci (HERC-OCA2 and SLC45A2) and another precedented variant (rs1805007 in melanocortin 1 receptor) with an association P value just below the significance threshold (P = 1.3 × 10-7) have been previously associated with skin phenotypes and pigmentation, two of these loci are linked to immuno-inflammation phenotypes (IL13 and PSMB9-HLA-DMA) and one has been associated with both categories (IRF4). Genes within three loci (PSMB9-HLA-DMA, HERC-OCA2 and NRX3-DIO2) were differentially expressed in a previously published clinical rosacea transcriptomics study that compared lesional to non-lesional samples. The identified loci provide specificity of inflammatory mechanisms in rosacea, and identify potential pathways for therapeutic intervention.
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Affiliation(s)
- Jennifer L Aponte
- Genomic Medicine, PAREXEL International, Research Triangle Park, NC, USA
| | | | | | | | - Chao Tian
- 23andMe Inc., Mountain View, CA, USA
| | - Akanksha Gupta
- Translational Science, Dermatology, GlaxoSmithKline, Research Triangle Park, NC, USA
| | - Cong Guo
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Dana J Fraser
- Genomic Medicine, PAREXEL International, Research Triangle Park, NC, USA
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203
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Quinn JP, Savage AL, Bubb VJ. Non-coding genetic variation shaping mental health. Curr Opin Psychol 2018; 27:18-24. [PMID: 30099302 PMCID: PMC6624474 DOI: 10.1016/j.copsyc.2018.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022]
Abstract
Gene expression determined by the genome mediating a response to cell environment. Genetic variation results in distinct individual response in gene expression. Non-coding DNA is an important site for such functional genetic variation. Gene expression is a major modulator of brain chemistry and thus behavior.
Over 98% of our genome is non-coding and is now recognised to have a major role in orchestrating the tissue specific and stimulus inducible gene expression pattern which underpins our wellbeing and mental health. The non-coding genome responds functionally to our environment at all levels, encompassing the span from psychological to physiological challenge. The gene expression pattern, termed the transcriptome, ultimately gives us our neurochemistry. Therefore a major modulator of mental wellbeing is how our genes are regulated in response to life experiences. Superimposed on the aforementioned non-coding DNA framework is a vast body of genetic variation in the elements that control response to challenges. These differences, termed polymorphisms, allow for a differential response from a specific DNA element to the same challenge thus potentially allowing ‘individuality’ in the modulation of our transcriptome. This review will focus on a fundamental mechanism defining our psychological and psychiatric wellbeing, namely how genetic variation can be correlated with differential gene expression in response to specific challenges, thus resulting in altered neurochemistry which consequently may shape behaviour.
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Affiliation(s)
- John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK.
| | - Abigail L Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
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204
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Klein RH, Tung PY, Somanath P, Fehling HJ, Knoepfler PS. Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer. Stem Cell Res 2018; 31:83-94. [PMID: 30031967 PMCID: PMC6133722 DOI: 10.1016/j.scr.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/20/2022] Open
Abstract
Developmental pluripotency associated factor 4 (Dppa4) is a highly specific marker of pluripotent cells, and is also overexpressed in certain cancers, but its function in either of these contexts is poorly understood. In this study, we use ChIP-Seq to identify Dppa4 binding genome-wide in three distinct cell types: mouse embryonic stem cells (mESC), embryonal carcinoma cells, and 3T3 fibroblasts ectopically expressing Dppa4. We find a core set of Dppa4 binding sites shared across cell types, and also a substantial number of sites unique to each cell type. Across cell types Dppa4 shows a preference for binding to regions with active chromatin signatures, and can influence chromatin modifications at target genes. In 3T3 fibroblasts with enforced Dppa4 expression, Dppa4 represses the cell cycle inhibitor Cdkn2c and activates Ets family transcription factor Etv4, leading to alterations in the cell cycle that likely contribute to the oncogenic phenotype. Dppa4 also directly regulates Etv4 in mESC but represses it in this context, and binds with Oct4 to a set of shared targets that are largely independent of Sox2 and Nanog, indicating that Dppa4 functions independently of the core pluripotency network in stem cells. Together these data provide novel insights into Dppa4 function in both pluripotent and oncogenic contexts.
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Affiliation(s)
- Rachel Herndon Klein
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Po-Yuan Tung
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Priyanka Somanath
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | | | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, 1 Shields Ave, Davis, CA 95616, United States.; Institute of Pediatric Regenerative Medicine, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States.
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205
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Szlachta K, Thys RG, Atkin ND, Pierce LCT, Bekiranov S, Wang YH. Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human. Genome Biol 2018; 19:89. [PMID: 30001206 PMCID: PMC6042338 DOI: 10.1186/s13059-018-1463-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/13/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the regulation or perturbation of these processes. We identify sites of high propensity to form stable DNA secondary structure across the human genome using Mfold and ViennaRNA programs with parameters for analyzing DNA. RESULTS The promoter-proximal regions of genes with paused transcription are significantly and energetically more favorable to form DNA secondary structure than non-paused genes or genes without RNA polymerase II (Pol II) binding. Using Pol II ChIP-seq, GRO-seq, NET-seq, and mNET-seq data, we arrive at a robust set of criteria for Pol II pausing, independent of annotation, and find that a highly stable secondary structure is likely to form about 10-50 nucleotides upstream of a Pol II pausing site. Structure probing data confirm the existence of DNA secondary structures enriched at the promoter-proximal regions of paused genes in human cells. Using an in vitro transcription assay, we demonstrate that Pol II pausing at HSPA1B, a human heat shock gene, is affected by manipulating DNA secondary structure upstream of the pausing site. CONCLUSIONS Our results indicate alternative DNA secondary structure formation as a mechanism for how GC-rich sequences regulate RNA Pol II promoter-proximal pausing genome-wide.
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Affiliation(s)
- Karol Szlachta
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | - Ryan G Thys
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA
| | | | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA.
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908-0733, USA.
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206
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Zhou Y, Xu Z, Quan D, Zhang F, Zhang H, Xiao T, Hou S, Qiao H, Harismendy O, Wang JYJ, Suo G. Nuclear respiratory factor 1 promotes spheroid survival and mesenchymal transition in mammary epithelial cells. Oncogene 2018; 37:6152-6165. [PMID: 29995872 DOI: 10.1038/s41388-018-0349-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 03/18/2018] [Accepted: 05/13/2018] [Indexed: 12/18/2022]
Abstract
Epithelial cells aggregate into spheroids when deprived of matrix, and the proclivity for spheroid formation and survival is a hallmark of normal and tumorigenic mammary stem cells. We show here that Nuclear Respiratory Factor 1 (NRF1) is a spheroid promoter by in silico identification of this transcription factor as highly connected to top shRNA-hits deduced from re-iterative selections for shRNAs enriched in MCF10A spheroids. NRF1-promoted spheroid survival is linked to its stimulation of mitochondrial OXPHOS, cell migration, invasion, and mesenchymal transition. Conversely, NRF1 knockdown in breast cancer MDA-MB-231 cells reduced spheroids, migration, invasion, and mesenchymal marker expression. NRF1 knockdown also reduced tumor burden in mammary fat pads and lungs of orthotopic- or tail vein-transplanted mice. With the Luminal A subtype of breast cancer, higher NRF1 expression is associated with lower survival. These results show that NRF1, an activator of mitochondrial metabolism, supports mammary spheroid survival and tumor development.
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Affiliation(s)
- Yuanshuai Zhou
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Jiangsu, 215123, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongjuan Xu
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Jiangsu, 215123, China
| | - Daniel Quan
- Division of Hematology/Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, School of Medicine, La Jolla, CA, 92093-0820, USA
| | - Fan Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Hai Zhang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Jiangsu, 215123, China
| | - Tongqian Xiao
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Jiangsu, 215123, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulan Hou
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Jiangsu, 215123, China
| | - Hong Qiao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Olivier Harismendy
- Division of Hematology/Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, School of Medicine, La Jolla, CA, 92093-0820, USA
| | - Jean Y J Wang
- Division of Hematology/Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, School of Medicine, La Jolla, CA, 92093-0820, USA
| | - Guangli Suo
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Jiangsu, 215123, China.
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207
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Holm LJ, Krogvold L, Hasselby JP, Kaur S, Claessens LA, Russell MA, Mathews CE, Hanssen KF, Morgan NG, Koeleman BPC, Roep BO, Gerling IC, Pociot F, Dahl-Jørgensen K, Buschard K. Abnormal islet sphingolipid metabolism in type 1 diabetes. Diabetologia 2018; 61:1650-1661. [PMID: 29671030 PMCID: PMC6445476 DOI: 10.1007/s00125-018-4614-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/15/2018] [Indexed: 12/17/2022]
Abstract
AIMS/HYPOTHESIS Sphingolipids play important roles in beta cell physiology, by regulating proinsulin folding and insulin secretion and in controlling apoptosis, as studied in animal models and cell cultures. Here we investigate whether sphingolipid metabolism may contribute to the pathogenesis of human type 1 diabetes and whether increasing the levels of the sphingolipid sulfatide would prevent models of diabetes in NOD mice. METHODS We examined the amount and distribution of sulfatide in human pancreatic islets by immunohistochemistry, immunofluorescence and electron microscopy. Transcriptional analysis was used to evaluate expression of sphingolipid-related genes in isolated human islets. Genome-wide association studies (GWAS) and a T cell proliferation assay were used to identify type 1 diabetes related polymorphisms and test how these affect cellular islet autoimmunity. Finally, we treated NOD mice with fenofibrate, a known activator of sulfatide biosynthesis, to evaluate the effect on experimental autoimmune diabetes development. RESULTS We found reduced amounts of sulfatide, 23% of the levels in control participants, in pancreatic islets of individuals with newly diagnosed type 1 diabetes, which were associated with reduced expression of enzymes involved in sphingolipid metabolism. Next, we discovered eight gene polymorphisms (ORMDL3, SPHK2, B4GALNT1, SLC1A5, GALC, PPARD, PPARG and B4GALT1) involved in sphingolipid metabolism that contribute to the genetic predisposition to type 1 diabetes. These gene polymorphisms correlated with the degree of cellular islet autoimmunity in a cohort of individuals with type 1 diabetes. Finally, using fenofibrate, which activates sulfatide biosynthesis, we completely prevented diabetes in NOD mice and even reversed the disease in half of otherwise diabetic animals. CONCLUSIONS/INTERPRETATION These results indicate that islet sphingolipid metabolism is abnormal in type 1 diabetes and suggest that modulation may represent a novel therapeutic approach. DATA AVAILABILITY The RNA expression data is available online at https://www.dropbox.com/s/93mk5tzl5fdyo6b/Abnormal%20islet%20sphingolipid%20metabolism%20in%20type%201%20diabetes%2C%20RNA%20expression.xlsx?dl=0 . A list of SNPs identified is available at https://www.dropbox.com/s/yfojma9xanpp2ju/Abnormal%20islet%20sphingolipid%20metabolism%20in%20type%201%20diabetes%20SNP.xlsx?dl=0 .
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Affiliation(s)
- Laurits J Holm
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen Biocenter, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Lars Krogvold
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Odontology, University of Oslo, Oslo, Norway
| | - Jane P Hasselby
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | - Laura A Claessens
- Department of Immunohaematology & Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
- Department of Medical Genetics, University Medical Center, Utrecht, the Netherlands
| | - Mark A Russell
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| | - Clayton E Mathews
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Kristian F Hanssen
- Faculty of Odontology, University of Oslo, Oslo, Norway
- Department of Endocrinology, Oslo University Hospital, Oslo, Norway
| | - Noel G Morgan
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| | - Bobby P C Koeleman
- Department of Medical Genetics, University Medical Center, Utrecht, the Netherlands
| | - Bart O Roep
- Department of Immunohaematology & Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
- Department of Diabetes Immunology, Diabetes & Metabolism Research Institute, Beckman Research Institute at the City of Hope, Duarte, CA, USA
| | - Ivan C Gerling
- Department of Medicine, University of Tennessee, Memphis, TN, USA
| | | | - Knut Dahl-Jørgensen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Karsten Buschard
- The Bartholin Institute, Department of Pathology, Rigshospitalet, Copenhagen Biocenter, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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208
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Dudek AM, Vermeulen SH, Kolev D, Grotenhuis AJ, Kiemeney LALM, Verhaegh GW. Identification of an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk. Cell Oncol (Dordr) 2018; 41:555-568. [PMID: 29956121 PMCID: PMC6153957 DOI: 10.1007/s13402-018-0393-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2018] [Indexed: 12/24/2022] Open
Abstract
Purpose Genome-wide association studies (GWAS) have led to the identification of a bladder cancer susceptibility variant (rs710521) in a non-coding intergenic region between the TP63 and LEPREL1 genes on chromosome 3q28, suggesting a role in the transcriptional regulation of these genes. In this study, we aimed to functionally characterize the 3q28 bladder cancer risk locus. Methods Fine-mapping was performed by focusing on the region surrounding rs710521, and variants were prioritized for further experiments using ENCODE regulatory data. The enhancer activity of the identified region was evaluated using dual-luciferase assays. CRISPR/Cas9-mediated deletion of the enhancer region was performed and the effect of this deletion on cell proliferation and gene expression levels was evaluated using CellTiter-Glo and RT-qPCR, respectively. Results Fine-mapping of the GWAS signal region led to the identification of twenty SNPs that showed a stronger association with bladder cancer risk than rs710521. Using publicly available data on regulatory elements and sequences, an enhancer region containing the bladder cancer risk variants was identified. Through reporter assays, we found that the presence of the enhancer region significantly increased ΔNTP63 promoter activity in bladder cancer-derived cell lines. CRISPR/Cas9-mediated deletion of the enhancer region reduced the viability of bladder cancer cells by decreasing the expression of ΔNTP63 and p63 target genes. Conclusions Taken together, our data show that bladder cancer risk-associated variants on chromosome 3q28 are located in an active enhancer region. Further characterization of the allele-specific activity of the identified enhancer and its target genes may lead to the identification of novel signaling pathways involved in bladder carcinogenesis. Electronic supplementary material The online version of this article (10.1007/s13402-018-0393-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleksandra M Dudek
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
| | - Sita H Vermeulen
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dimitar Kolev
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne J Grotenhuis
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lambertus A L M Kiemeney
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gerald W Verhaegh
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands.
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209
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Niu M, Tabari E, Ni P, Su Z. Towards a map of cis-regulatory sequences in the human genome. Nucleic Acids Res 2018; 46:5395-5409. [PMID: 29733395 PMCID: PMC6009671 DOI: 10.1093/nar/gky338] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/14/2018] [Accepted: 04/19/2018] [Indexed: 01/10/2023] Open
Abstract
Accumulating evidence indicates that transcription factor (TF) binding sites, or cis-regulatory elements (CREs), and their clusters termed cis-regulatory modules (CRMs) play a more important role than do gene-coding sequences in specifying complex traits in humans, including the susceptibility to common complex diseases. To fully characterize their roles in deriving the complex traits/diseases, it is necessary to annotate all CREs and CRMs encoded in the human genome. However, the current annotations of CREs and CRMs in the human genome are still very limited and mostly coarse-grained, as they often lack the detailed information of CREs in CRMs. Here, we integrated 620 TF ChIP-seq datasets produced by the ENCODE project for 168 TFs in 79 different cell/tissue types and predicted an unprecedentedly completely map of CREs in CRMs in the human genome at single nucleotide resolution. The map includes 305 912 CRMs containing a total of 1 178 913 CREs belonging to 736 unique TF binding motifs. The predicted CREs and CRMs tend to be subject to either purifying selection or positive selection, thus are likely to be functional. Based on the results, we also examined the status of available ChIP-seq datasets for predicting the entire regulatory genome of humans.
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Affiliation(s)
- Meng Niu
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Ehsan Tabari
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Pengyu Ni
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
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210
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De Leonibus C, Murray P, Garner T, Hanson D, Clayton P, Stevens A. The in vitro functional analysis of single-nucleotide polymorphisms associated with growth hormone (GH) response in children with GH deficiency. THE PHARMACOGENOMICS JOURNAL 2018; 19:200-210. [PMID: 29855605 DOI: 10.1038/s41397-018-0026-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 01/14/2018] [Accepted: 04/13/2018] [Indexed: 11/09/2022]
Abstract
Response to recombinant human growth hormone (r-hGH) in the first year of therapy has been associated with single-nucleotide polymorphisms (SNPs) in children with GH deficiency (GHD). Associated SNPs were screened for regulatory function using a combination of in silico techniques. Four SNPs in regulatory sequences were selected for the analysis of in vitro transcriptional activity (TA). There was an additive effect of the alleles in the four genes associated with good growth response. For rs3110697 within IGFBP3, rs1045992 in CYP19A1 and rs2888586 in SOS1, the variant associated with better growth response showed higher TA with r-hGH treatment. For rs1024531 in GRB10, a negative regulator of IGF-I signalling and growth, the variant associated with better growth response had a significantly lower TA on r-hGH stimulation. These results indicate that specific SNP variants have effects on TA that provide a rationale for their clinical impact on growth response to r-hGH therapy.
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Affiliation(s)
- Chiara De Leonibus
- Division of Developmental Biology & Medicine, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Philip Murray
- Division of Developmental Biology & Medicine, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK.,Royal Manchester Children's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Terence Garner
- Division of Developmental Biology & Medicine, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Daniel Hanson
- Division of Developmental Biology & Medicine, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Peter Clayton
- Division of Developmental Biology & Medicine, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK.,Royal Manchester Children's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Adam Stevens
- Division of Developmental Biology & Medicine, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK.
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211
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Guerrero-Ramirez GI, Valdez-Cordoba CM, Islas-Cisneros JF, Trevino V. Computational approaches for predicting key transcription factors in targeted cell reprogramming (Review). Mol Med Rep 2018; 18:1225-1237. [PMID: 29845286 PMCID: PMC6072137 DOI: 10.3892/mmr.2018.9092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/27/2018] [Indexed: 12/27/2022] Open
Abstract
There is a need for specific cell types in regenerative medicine and biological research. Frequently, specific cell types may not be easily obtained or the quantity obtained is insufficient for study. Therefore, reprogramming by the direct conversion (transdifferentiation) or re‑induction of induced pluripotent stem cells has been used to obtain cells expressing similar profiles to those of the desired types. Therefore, a specific cocktail of transcription factors (TFs) is required for induction. Nevertheless, identifying the correct combination of TFs is difficult. Although certain computational approaches have been proposed for this task, their methods are complex, and corresponding implementations are difficult to use and generalize for specific source or target cell types. In the present review four computational approaches that have been proposed to obtain likely TFs were compared and discussed. A simplified view of the computational complexity of these methods is provided that consists of three basic ideas: i) The definition of target and non‑target cell types; ii) the estimation of candidate TFs; and iii) filtering candidates. This simplified view was validated by analyzing a well‑documented cardiomyocyte differentiation. Subsequently, these reviewed methods were compared when applied to an unknown differentiation of corneal endothelial cells. The generated results may provide important insights for laboratory assays. Data and computer scripts that may assist with direct conversions in other cell types are also provided.
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Affiliation(s)
| | | | | | - Victor Trevino
- Tecnológico de Monterrey, Escuela de Medicina, Monterrey, Nuevo León 64710, México
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212
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Chen X, Gustafsson S, Whitington T, Borné Y, Lorentzen E, Sun J, Almgren P, Su J, Karlsson R, Song J, Lu Y, Zhan Y, Hägg S, Svensson P, Smedby KE, Slager SL, Ingelsson E, Lindgren CM, Morris AP, Melander O, Karlsson T, de Faire U, Caidahl K, Engström G, Lind L, Karlsson MCI, Pedersen NL, Frostegård J, Magnusson PKE. A genome-wide association study of IgM antibody against phosphorylcholine: shared genetics and phenotypic relationship to chronic lymphocytic leukemia. Hum Mol Genet 2018; 27:1809-1818. [PMID: 29547969 DOI: 10.1093/hmg/ddy094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/12/2018] [Indexed: 11/13/2022] Open
Abstract
Phosphorylcholine (PC) is an epitope on oxidized low-density lipoprotein (oxLDL), apoptotic cells and several pathogens like Streptococcus pneumoniae. Immunoglobulin M against PC (IgM anti-PC) has the ability to inhibit uptake of oxLDL by macrophages and increase clearance of apoptotic cells. From our genome-wide association studies (GWASs) in four European-ancestry cohorts, six single nucleotide polymorphisms (SNPs) in 11q24.1 were discovered (in 3002 individuals) and replicated (in 646 individuals) to be associated with serum level of IgM anti-PC (the leading SNP rs35923643-G, combined β = 0.19, 95% confidence interval 0.13-0.24, P = 4.3 × 10-11). The haplotype tagged by rs35923643-G (or its proxy SNP rs735665-A) is also known as the top risk allele for chronic lymphocytic leukemia (CLL), and a main increasing allele for general IgM. By using summary GWAS results of IgM anti-PC and CLL in the polygenic risk score (PRS) analysis, PRS on the basis of IgM anti-PC risk alleles positively associated with CLL risk (explained 0.6% of CLL variance, P = 1.2 × 10-15). Functional prediction suggested that rs35923643-G might impede the binding of Runt-related transcription factor 3, a tumor suppressor playing a central role in the immune regulation of cancers. Contrary to the expectations from the shared genetics between IgM anti-PC and CLL, an inverse relationship at the phenotypic level was found in a nested case-control study (30 CLL cases with 90 age- and sex-matched controls), potentially reflecting reverse causation. The suggested function of the top variant as well as the phenotypic association between IgM anti-PC and CLL risk needs replication and motivates further studies.
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Affiliation(s)
- Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Whitington
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yan Borné
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Erik Lorentzen
- Department of Bioinformatics, Gothenburg University, Gothenburg, Sweden
| | - Jitong Sun
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Peter Almgren
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Jun Su
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jie Song
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yi Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Statistical Genetics, Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Yiqiang Zhan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Per Svensson
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Department of Cardiology, Södersjukhuset, Stockholm, Sweden
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Thomas Karlsson
- Health Metrics, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Ulf de Faire
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kenneth Caidahl
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Engström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Mikael C I Karlsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Frostegård
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Emergency Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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213
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Walker CJ, Rush CM, Dama P, O’Hern MJ, Cosgrove CM, Gillespie JL, Zingarelli RA, Smith B, Stein ME, Mutch DG, Shakya R, Chang CW, Selvendiran K, Song JW, Cohn DE, Goodfellow PJ. MAX Mutations in Endometrial Cancer: Clinicopathologic Associations and Recurrent MAX p.His28Arg Functional Characterization. J Natl Cancer Inst 2018; 110:517-526. [PMID: 29155953 PMCID: PMC6279289 DOI: 10.1093/jnci/djx238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/16/2017] [Accepted: 10/10/2017] [Indexed: 12/30/2022] Open
Abstract
Background Genomic studies have revealed that multiple genes are mutated at varying frequency in endometrial cancer (EC); however, the relevance of many of these mutations is poorly understood. An EC-specific recurrent mutation in the MAX transcription factor p.His28Arg was recently discovered. We sought to assess the functional consequences of this hotspot mutation and determine its association with cancer-relevant phenotypes. Methods MAX was sequenced in 509 endometrioid ECs, and associations between mutation status and clinicopathologic features were assessed. EC cell lines stably expressing MAXH28R were established and used for functional experiments. DNA binding was examined using electrophoretic mobility shift assays and chromatin immunoprecipitation. Transcriptional profiling was performed with microarrays. Murine flank (six to 11 mice per group) and intraperitoneal tumor models were used for in vivo studies. Vascularity of xenografts was assessed by MECA-32 immunohistochemistry. The paracrine pro-angiogenic nature of MAXH28R-expressing EC cells was tested using microfluidic HUVEC sprouting assays and VEGFA enzyme-linked immunosorbent assays. All statistical tests were two-sided. Results Twenty-two of 509 tumors harbored mutations in MAX, including 12 tumors with the p.His28Arg mutation. Patients with a MAX mutation had statistically significantly reduced recurrence-free survival (hazard ratio = 4.00, 95% confidence interval = 1.15 to 13.91, P = .03). MAXH28R increased affinity for canonical E-box sequences, and MAXH28R-expressing EC cells dramatically altered transcriptional profiles. MAXH28R-derived xenografts statistically significantly increased vascular area compared with MAXWT and empty vector tumors (P = .003 and P = .008, respectively). MAXH28R-expressing EC cells secreted nearly double the levels of VEGFA compared with MAXWT cells (P = .03, .005, and .005 at 24, 48, and 72 hours, respectively), and conditioned media from MAXH28R cells increased sprouting when applied to HUVECs. Conclusion These data highlight the importance of MAX mutations in EC and point to increased vascularity as one mechanism contributing to clinical aggressiveness of EC.
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MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Substitution/genetics
- Animals
- Animals, Outbred Strains
- Arginine/genetics
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics
- Carcinoma, Endometrioid/epidemiology
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/pathology
- Cells, Cultured
- Codon, Nonsense
- Endometrial Neoplasms/epidemiology
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/pathology
- Female
- Genetic Association Studies
- Genetic Predisposition to Disease
- HEK293 Cells
- Histidine/genetics
- Humans
- Mice
- Mice, Nude
- Middle Aged
- Neoplasm Invasiveness
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/pathology
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Affiliation(s)
| | - Craig M Rush
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
| | - Paola Dama
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
| | - Matthew J O’Hern
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
| | - Casey M Cosgrove
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
| | | | - Roman A Zingarelli
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
| | - Blair Smith
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
| | - Maggie E Stein
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
| | - David G Mutch
- Siteman Cancer Center and the Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO
| | | | | | | | - Jonathan W Song
- James Comprehensive Cancer Center
- Department of Mechanical and Aerospace Engineering The Ohio State University, Columbus, OH
| | - David E Cohn
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
| | - Paul J Goodfellow
- James Comprehensive Cancer Center
- Department of Obstetrics and Gynecology
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214
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Huiting LN, Samaha Y, Zhang GL, Roderick JE, Li B, Anderson NM, Wang YW, Wang L, Laroche F, Choi JW, Liu CT, Kelliher MA, Feng H. UFD1 contributes to MYC-mediated leukemia aggressiveness through suppression of the proapoptotic unfolded protein response. Leukemia 2018; 32:2339-2351. [PMID: 29743725 PMCID: PMC6202254 DOI: 10.1038/s41375-018-0141-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/11/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Despite the pivotal role of MYC in tumorigenesis, the mechanisms by which it promotes cancer aggressiveness remain incompletely understood. Here we show that MYC transcriptionally upregulates the ubiquitin fusion degradation 1 (UFD1) gene in T-cell acute lymphoblastic leukemia (T-ALL). Allelic loss of ufd1 in zebrafish induces tumor-cell apoptosis and impairs MYC-driven T-ALL progression but does not affect general health. As the E2 component of an endoplasmic reticulum (ER)-associated degradation (ERAD) complex, UFD1 facilitates the elimination of misfolded/unfolded proteins from the ER. We found that UFD1 inactivation in human T-ALL cells impairs ERAD, exacerbates ER stress, and induces apoptosis. Moreover, we show that UFD1 inactivation promotes the proapoptotic unfolded protein response (UPR) mediated by protein kinase RNA-like ER kinase (PERK). This effect is demonstrated by an upregulation of PERK and its downstream effector C/EBP homologous protein (CHOP), as well as a downregulation of BCL2 and BCLxL. Indeed, CHOP inactivation or BCL2 overexpression is sufficient to rescue tumor-cell apoptosis induced by UFD1 knockdown. Together, our studies identify UFD1 as a critical regulator of the ER stress response and a novel contributor to MYC-mediated leukemia aggressiveness, with implications for targeted therapy in T-ALL and likely other MYC-driven cancers.
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Affiliation(s)
- L N Huiting
- Departments of Pharmacology and Medicine, Cancer Research Center, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA
| | - Y Samaha
- Departments of Pharmacology and Medicine, Cancer Research Center, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA
| | - G L Zhang
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA.,Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - J E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - B Li
- Departments of Pharmacology and Medicine, Cancer Research Center, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA
| | - N M Anderson
- Departments of Pharmacology and Medicine, Cancer Research Center, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA
| | - Y W Wang
- Departments of Pharmacology and Medicine, Cancer Research Center, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA.,Department of Anatomy and Embryology, Wuhan University School of Basic Medical Sciences, Wuhan, Hubei, P. R. China
| | - L Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Fjf Laroche
- Departments of Pharmacology and Medicine, Cancer Research Center, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA
| | - J W Choi
- Departments of Pharmacology and Medicine, Cancer Research Center, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA
| | - C T Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - M A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - H Feng
- Departments of Pharmacology and Medicine, Cancer Research Center, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, USA.
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215
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Ali M, Ajore R, Wihlborg AK, Niroula A, Swaminathan B, Johnsson E, Stephens OW, Morgan G, Meissner T, Turesson I, Goldschmidt H, Mellqvist UH, Gullberg U, Hansson M, Hemminki K, Nahi H, Waage A, Weinhold N, Nilsson B. The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression. Nat Commun 2018; 9:1649. [PMID: 29695719 PMCID: PMC5917026 DOI: 10.1038/s41467-018-04082-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 03/26/2018] [Indexed: 02/06/2023] Open
Abstract
Recently, we identified ELL2 as a susceptibility gene for multiple myeloma (MM). To understand its mechanism of action, we performed expression quantitative trait locus analysis in CD138+ plasma cells from 1630 MM patients from four populations. We show that the MM risk allele lowers ELL2 expression in these cells (Pcombined = 2.5 × 10−27; βcombined = −0.24 SD), but not in peripheral blood or other tissues. Consistent with this, several variants representing the MM risk allele map to regulatory genomic regions, and three yield reduced transcriptional activity in plasmocytoma cell lines. One of these (rs3777189-C) co-locates with the best-supported lead variants for ELL2 expression and MM risk, and reduces binding of MAFF/G/K family transcription factors. Moreover, further analysis reveals that the MM risk allele associates with upregulation of gene sets related to ribosome biogenesis, and knockout/knockdown and rescue experiments in plasmocytoma cell lines support a cause–effect relationship. Our results provide mechanistic insight into MM predisposition. ELL2 was recently discovered as a susceptibility gene for multiple myeloma (MM). Here, they show that the MM risk allele lowers ELL2 expression in plasma cells, that it also upregulates gene sets related to ribosome biogenesis, and that one of the linked variants reduces binding of MAFF/G/K family transcription factors.
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Affiliation(s)
- Mina Ali
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Ram Ajore
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Anna-Karin Wihlborg
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Abhishek Niroula
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Bhairavi Swaminathan
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Ellinor Johnsson
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Owen W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Gareth Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Tobias Meissner
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD, 57105, USA
| | - Ingemar Turesson
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany.,National Center for Tumor Diseases, Ulm, 69120, Heidelberg, Germany
| | | | - Urban Gullberg
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden
| | - Markus Hansson
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden.,Hematology Clinic, Skåne University Hospital, SE 221 85, Lund, Sweden
| | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, SE 205 02, Malmö, Sweden
| | - Hareth Nahi
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, SE 171 77, Stockholm, Sweden
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Björn Nilsson
- Department of Laboratory Medicine, Hematology and Transfusion Medicine, SE 221 84, Lund, Sweden. .,Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA.
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216
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Guo J, Chen H, Yang P, Lee YT, Wu M, Przytycka TM, Kwoh CK, Zheng J. LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data. BMC Med Genomics 2018; 11:27. [PMID: 29697370 PMCID: PMC5918432 DOI: 10.1186/s12920-018-0351-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. Method To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. Conclusion To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system. Database URL http://histone.scse.ntu.edu.sg/LDSplitDB
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Affiliation(s)
- Jing Guo
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore
| | - Hao Chen
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore
| | - Peng Yang
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore.,Institute for Infocomm Research, Agency for Science, Technology & Research, 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Yew Ti Lee
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore
| | - Min Wu
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore.,Institute for Infocomm Research, Agency for Science, Technology & Research, 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Teresa M Przytycka
- NCBI, NLM, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland, 20894, USA
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore
| | - Jie Zheng
- School of Computer Science and Engineering, Nanyang Technological University, Nanyang Ave, Singapore, 639798, Singapore. .,Genome Institute of Singapore, Agency for Science, Technology, and Research, Biopolis, Singapore, 138672, Singapore.
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217
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Nguyen NPD, Deshpande V, Luebeck J, Mischel PS, Bafna V. ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res 2018; 46:3309-3325. [PMID: 29579309 PMCID: PMC6283451 DOI: 10.1093/nar/gky180] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/12/2018] [Accepted: 03/05/2018] [Indexed: 12/20/2022] Open
Abstract
The integration of viral sequences into the host genome is an important driver of tumorigenesis in many viral mediated cancers, notably cervical cancer and hepatocellular carcinoma. We present ViFi, a computational method that combines phylogenetic methods with reference-based read mapping to detect viral integrations. In contrast with read-based reference mapping approaches, ViFi is faster, and shows high precision and sensitivity on both simulated and biological data, even when the integrated virus is a novel strain or highly mutated. We applied ViFi to matched genomic and mRNA data from 68 cervical cancer samples from TCGA and found high concordance between the two. Surprisingly, viral integration resulted in a dramatic transcriptional upregulation in all proximal elements, including LINEs and LTRs that are not normally transcribed. This upregulation is highly correlated with the presence of a viral gene fused with a downstream human element. Moreover, genomic rearrangements suggest the formation of apparent circular extrachromosomal (ecDNA) human-viral structures. Our results suggest the presence of apparent small circular fusion viral/human ecDNA, which correlates with indiscriminate and unregulated expression of proximal genomic elements, potentially contributing to the pathogenesis of HPV-associated cervical cancers. ViFi is available at https://github.com/namphuon/ViFi.
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Affiliation(s)
- Nam-phuong D Nguyen
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Viraj Deshpande
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
- Department of Pathology, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Vineet Bafna
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
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218
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Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y. Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. eLife 2018; 7:33084. [PMID: 29648536 PMCID: PMC5943035 DOI: 10.7554/elife.33084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 04/11/2018] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) comprise almost half of primate genomes and their aberrant regulation can result in deleterious effects. In pluripotent stem cells, rapidly evolving KRAB-ZNF genes target TEs for silencing by H3K9me3. To investigate the evolution of TE silencing, we performed H3K9me3 ChIP-seq experiments in induced pluripotent stem cells from 10 human and 7 chimpanzee individuals. We identified four million orthologous TEs and found the SVA and ERV families to be marked most frequently by H3K9me3. We found little evidence of inter-species differences in TE silencing, with as many as 82% of putatively silenced TEs marked at similar levels in humans and chimpanzees. TEs that are preferentially silenced in one species are a similar age to those silenced in both species and are not more likely to be associated with expression divergence of nearby orthologous genes. Our data suggest limited species-specificity of TE silencing across 6 million years of primate evolution.
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Affiliation(s)
- Michelle C Ward
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Medicine, University of Chicago, Chicago, United States
| | - Siming Zhao
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan J Pavlovic
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Mohammad M Karimi
- MRC London Institute of Medical Sciences, Imperial College, London, United Kingdom
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Statistics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Medicine, University of Chicago, Chicago, United States
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219
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Li C, Lenhard B, Luscombe NM. Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. Genome Res 2018; 28:676-688. [PMID: 29618487 PMCID: PMC5932608 DOI: 10.1101/gr.231449.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/21/2018] [Indexed: 01/06/2023]
Abstract
Understanding the molecular mechanisms and evolution of the gene regulatory system remains a major challenge in biology. Transcription start sites (TSSs) are especially interesting because they are central to initiating gene expression. Previous studies revealed widespread transcription initiation and fast turnover of TSSs in mammalian genomes. Yet, how new TSSs originate and how they evolve over time remain poorly understood. To address these questions, we analyzed ∼200,000 human TSSs by integrating evolutionary (inter- and intra-species) and functional genomic data, particularly focusing on evolutionarily young TSSs that emerged in the primate lineage. TSSs were grouped according to their evolutionary age using sequence alignment information as a proxy. Comparisons of young and old TSSs revealed that (1) new TSSs emerge through a combination of intrinsic factors, like the sequence properties of transposable elements and tandem repeats, and extrinsic factors such as their proximity to existing regulatory modules; (2) new TSSs undergo rapid evolution that reduces the inherent instability of repeat sequences associated with a high propensity of TSS emergence; and (3) once established, the transcriptional competence of surviving TSSs is gradually enhanced, with evolutionary changes subject to temporal (fewer regulatory changes in younger TSSs) and spatial constraints (fewer regulatory changes in more isolated TSSs). These findings advance our understanding of how regulatory innovations arise in the genome throughout evolution and highlight the genomic robustness and evolvability in these processes.
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Affiliation(s)
- Cai Li
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
| | - Nicholas M Luscombe
- The Francis Crick Institute, London NW1 1AT, United Kingdom.,UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom.,Okinawa Institute of Science & Technology Graduate University, Okinawa, 904-0495, Japan
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220
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Reynolds LM, Howard TD, Ruczinski I, Kanchan K, Seeds MC, Mathias RA, Chilton FH. Tissue-specific impact of FADS cluster variants on FADS1 and FADS2 gene expression. PLoS One 2018; 13:e0194610. [PMID: 29590160 PMCID: PMC5874031 DOI: 10.1371/journal.pone.0194610] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/06/2018] [Indexed: 12/31/2022] Open
Abstract
Omega-6 (n-6) and omega-3 (n-3) long (≥ 20 carbon) chain polyunsaturated fatty acids (LC-PUFAs) play a critical role in human health and disease. Biosynthesis of LC-PUFAs from dietary 18 carbon PUFAs in tissues such as the liver is highly associated with genetic variation within the fatty acid desaturase (FADS) gene cluster, containing FADS1 and FADS2 that encode the rate-limiting desaturation enzymes in the LC-PUFA biosynthesis pathway. However, the molecular mechanisms by which FADS genetic variants affect LC-PUFA biosynthesis, and in which tissues, are unclear. The current study examined associations between common single nucleotide polymorphisms (SNPs) within the FADS gene cluster and FADS1 and FADS2 gene expression in 44 different human tissues (sample sizes ranging 70-361) from the Genotype-Tissue Expression (GTEx) Project. FADS1 and FADS2 expression were detected in all 44 tissues. Significant cis-eQTLs (within 1 megabase of each gene, False Discovery Rate, FDR<0.05, as defined by GTEx) were identified in 12 tissues for FADS1 gene expression and 23 tissues for FADS2 gene expression. Six tissues had significant (FDR< 0.05) eQTLs associated with both FADS1 and FADS2 (including artery, esophagus, heart, muscle, nerve, and thyroid). Interestingly, the identified eQTLs were consistently found to be associated in opposite directions for FADS1 and FADS2 expression. Taken together, findings from this study suggest common SNPs within the FADS gene cluster impact the transcription of FADS1 and FADS2 in numerous tissues and raise important questions about how the inverse expression of these two genes impact intermediate molecular (such a LC-PUFA and LC-PUFA-containing glycerolipid levels) and ultimately clinical phenotypes associated with inflammatory diseases and brain health.
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Affiliation(s)
- Lindsay M. Reynolds
- Department of Epidemiology & Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ingo Ruczinski
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kanika Kanchan
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Michael C. Seeds
- Department of Internal Medicine/Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Rasika A. Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Floyd H. Chilton
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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221
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Yadav DK, Shrestha S, Dadhwal G, Chandak GR. Identification and characterization of cis-regulatory elements 'insulator and repressor' in PPARD gene. Epigenomics 2018; 10:613-627. [PMID: 29583017 DOI: 10.2217/epi-2017-0139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
AIM Identification and functional characterization of cis-regulatory elements in human PPARD gene. METHODS We used various bioinformatic tools on the publicly available human genome and Encyclopedia of DNA Elements databases to explore potential cis-regulatory elements in PPARD gene region. RESULTS We predicted an insulator and an enhancer element in intron 2 of PPARD gene. Functional characterization using transient transfection, reporter assay and CTCF binding confirmed the insulator status. However, the predicted enhancer element showed repressor/silencer activity. Finally, we observed a potential interaction between these two cis-regulatory elements which is in agreement with 5C-Encyclopedia of DNA Elements data. CONCLUSION We report two functionally validated cis-regulatory elements in PPARD gene which will aid in understanding its regulation and role in metabolic functions.
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Affiliation(s)
- Dilip K Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500 007, India
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500 007, India.,Building No.7, School of Basic & Applied Sciences, Dayananda Sagar University, Shavige Malleshwara Hills, Kumaraswamy Layout, Bangalore 560 078, Karnataka, India
| | - Gunjan Dadhwal
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500 007, India.,Departement de Biochimie et Medecine Moleculaire, Universite de Montreal, Montreal, Quebec H3T 1J4, Canada
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500 007, India
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222
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Tang X, Srivastava A, Liu H, Machiraju R, Huang K, Leone G. annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq. Bioinformatics 2018; 33:1570-1571. [PMID: 28169395 DOI: 10.1093/bioinformatics/btx016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/27/2017] [Indexed: 11/12/2022] Open
Abstract
Summary We developed annoPeak, a web application to annotate, visualize and compare predicted protein-binding regions derived from ChIP-seq/ChIP-exo-seq experiments using human and mouse cells. Users can upload peak regions from multiple experiments onto the annoPeak server to annotate them with biological context, identify associated target genes and categorize binding sites with respect to gene structure. Users can also compare multiple binding profiles intuitively with the help of visualization tools and tables provided by annoPeak. In general, annoPeak will help users identify patterns of genome wide transcription factor binding profiles, assess binding profiles in different biological contexts and generate new hypotheses. Availability and Implementation The web service is freely accessible through URL: http://ccc-annopeak.osumc.edu/annoPeak . Source code is available at https://github.com/XingTang2014/annoPeak . Contact gustavo.leone@osumc.edu or kun.huang@osumc.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xing Tang
- Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Arunima Srivastava
- Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Huayang Liu
- Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Raghu Machiraju
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kun Huang
- Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - Gustavo Leone
- Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
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223
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Figueroa AA, Fasano JD, Martinez-Morilla S, Venkatesan S, Kupfer G, Hattangadi SM. miR-181a regulates erythroid enucleation via the regulation of Xpo7 expression. Haematologica 2018; 103:e341-e344. [PMID: 29567782 DOI: 10.3324/haematol.2017.171785] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Amalia Avila Figueroa
- Pediatric Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - James D Fasano
- Pediatric Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Srividhya Venkatesan
- Pediatric Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Gary Kupfer
- Pediatric Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Shilpa M Hattangadi
- Pediatric Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA
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224
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Potuijt JWP, Baas M, Sukenik-Halevy R, Douben H, Nguyen P, Venter DJ, Gallagher R, Swagemakers SM, Hovius SER, van Nieuwenhoven CA, Galjaard RJH, van der Spek PJ, Ahituv N, de Klein A. A point mutation in the pre-ZRS disrupts sonic hedgehog expression in the limb bud and results in triphalangeal thumb-polysyndactyly syndrome. Genet Med 2018. [PMID: 29543231 DOI: 10.1038/gim.2018.18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE The zone of polarizing activity regulatory sequence (ZRS) is an enhancer that regulates sonic hedgehog during embryonic limb development. Recently, mutations in a noncoding evolutionary conserved sequence 500 bp upstream of the ZRS, termed the pre-ZRS (pZRS), have been associated with polydactyly in dogs and humans. Here, we report the first case of triphalangeal thumb-polysyndactyly syndrome (TPT-PS) to be associated with mutations in this region and show via mouse enhancer assays how this mutation leads to ectopic expression throughout the developing limb bud. METHODS We used linkage analysis, whole-exome sequencing, Sanger sequencing, fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, single-nucleotide polymorphism array, and a mouse transgenic enhancer assay. RESULTS Ten members of a TPT-PS family were included in this study. The mutation was linked to chromosome 7q36 (LOD score 3.0). No aberrations in the ZRS could be identified. A point mutation in the pZRS (chr7:156585476G>C; GRCh37/hg19) was detected in all affected family members. Functional characterization using a mouse transgenic enhancer essay showed extended ectopic expression dispersed throughout the entire limb bud (E11.5). CONCLUSION Our work describes the first mutation in the pZRS to be associated with TPT-PS and provides functional evidence that this mutation leads to ectopic expression of this enhancer within the developing limb.
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Affiliation(s)
- Jacob W P Potuijt
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Martijn Baas
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rivka Sukenik-Halevy
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California-San Francisco, San Francisco, California, USA.,Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Picard Nguyen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Deon J Venter
- Department of Pathology, Mater Health Services, South Brisbane, Queensland, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, Sydney, Australia.,School of Medicine, University of Wollongong, Wollongong, New South Wales, Australia
| | - Renée Gallagher
- Department of Pathology, Mater Health Services, South Brisbane, Queensland, Australia
| | - Sigrid M Swagemakers
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Steven E R Hovius
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christianne A van Nieuwenhoven
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert-Jan H Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter J van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California-San Francisco, San Francisco, California, USA
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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225
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Mitamura T, Pradeep S, McGuire M, Wu S, Ma S, Hatakeyama H, Lyons YA, Hisamatsu T, Noh K, Villar-Prados A, Chen X, Ivan C, Rodriguez-Aguayo C, Hu W, Lopez-Berestein G, Coleman RL, Sood AK. Induction of anti-VEGF therapy resistance by upregulated expression of microseminoprotein (MSMP). Oncogene 2018; 37:722-731. [PMID: 29059175 PMCID: PMC6040890 DOI: 10.1038/onc.2017.348] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 03/31/2017] [Accepted: 06/14/2017] [Indexed: 12/28/2022]
Abstract
Anti-vascular endothelial growth factor (VEGF) therapy has demonstrated efficacy in treating human metastatic cancers, but therapeutic resistance is a practical limitation and most tumors eventually become unresponsive. To identify microenvironmental factors underlying the resistance of cancer to antiangiogenesis therapy, we conducted genomic analyses of intraperitoneal ovarian tumors in which adaptive resistance to anti-VEGF therapy (B20 antibody) developed. We found that expression of the microseminoprotein, prostate-associated (MSMP) gene was substantially upregulated in resistant compared with control tumors. MSMP secretion from cancer cells was induced by hypoxia, triggering MAPK signaling in endothelial cells to promote tube formation in vitro. Recruitment of the transcriptional repressor CCCTC-binding factor (CTCF) to the MSMP enhancer region was decreased by histone acetylation under hypoxic conditions in cancer cells. MSMP siRNA, delivered in vivo using the DOPC nanoliposomes, restored tumor sensitivity to anti-VEGF therapy. In ovarian cancer patients treated with bevacizumab, serum MSMP concentration increased significantly only in non-responders. These findings imply that MSMP inhibition combined with the use of antiangiogenesis drugs may be a new strategy to overcome resistance to antiangiogenesis therapy.
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Affiliation(s)
- Takashi Mitamura
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Obstetrics and Gynecology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Sunila Pradeep
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael McGuire
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherry Wu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shaolin Ma
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hiroto Hatakeyama
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yasmin A. Lyons
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Takeshi Hisamatsu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyunghee Noh
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Gene Therapy Research Unit, Korea Research Institute of Bioscience and Biotechnology, Dajeon, Republic of Korea
| | - Alejandro Villar-Prados
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiuhui Chen
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Hu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert L. Coleman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil K. Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
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226
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Skorecki KL, Lee JH, Langefeld CD, Rosset S, Tzur S, Wasser WG, Shemer R, Hawkins GA, Divers J, Parekh RS, Li M, Sampson MG, Kretzler M, Pollak MR, Shah S, Blackler D, Nichols B, Wilmot M, Alper SL, Freedman BI, Friedman DJ. A null variant in the apolipoprotein L3 gene is associated with non-diabetic nephropathy. Nephrol Dial Transplant 2018; 33:323-330. [PMID: 28339911 PMCID: PMC5837424 DOI: 10.1093/ndt/gfw451] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/09/2016] [Indexed: 12/19/2022] Open
Abstract
Background Inheritance of apolipoprotein L1 gene (APOL1) renal-risk variants in a recessive pattern strongly associates with non-diabetic end-stage kidney disease (ESKD). Further evidence supports risk modifiers in APOL1-associated nephropathy; some studies demonstrate that heterozygotes possess excess risk for ESKD or show earlier age at ESKD, relative to those with zero risk alleles. Nearby loci are also associated with ESKD in non-African Americans. Methods We assessed the role of the APOL3 null allele rs11089781 on risk of non-diabetic ESKD. Four cohorts containing 2781 ESKD cases and 2474 controls were analyzed. Results Stratifying by APOL1 risk genotype (recessive) and adjusting for African ancestry identified a significant additive association between rs11089781 and ESKD in each stratum and in a meta-analysis [meta-analysis P = 0.0070; odds ratio (OR) = 1.29]; ORs were consistent across APOL1 risk strata. The biological significance of this association is supported by the finding that the APOL3 gene is co-regulated with APOL1, and that APOL3 protein was able to bind to APOL1 protein. Conclusions Taken together, the genetic and biological data support the concept that other APOL proteins besides APOL1 may also influence the risk of non-diabetic ESKD.
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Affiliation(s)
- Karl L Skorecki
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel
| | - Jessica H Lee
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Saharon Rosset
- School of Mathematical Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shay Tzur
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel
| | - Walter G Wasser
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel
- Mayanei HaYeshua Medical Center, Bnei Brak, Israel
| | - Revital Shemer
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
| | - Gregory A Hawkins
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jasmin Divers
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Rulan S Parekh
- Division of Pediatric Nephrology, Hospital for Sick Children, Toronto, Ontario, Canada
- Child Health Evaluative Sciences, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada
| | - Man Li
- Division of Nephrology, University of Utah, Salt Lake City, UT, USA
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew G Sampson
- Division of Nephrology, Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Matthias Kretzler
- Department of Internal Medicine - Nephrology, University of Michigan at Ann Arbor Medical School, Ann Arbor, MI, USA
| | - Martin R Pollak
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shrijal Shah
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Daniel Blackler
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Brendan Nichols
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Michael Wilmot
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Barry I Freedman
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - David J Friedman
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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227
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Boloc D, Rodríguez N, Gassó P, Abril JF, Bernardo M, Lafuente A, Mas S. SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling. Bioinformatics 2018; 34:303-305. [PMID: 28968821 DOI: 10.1093/bioinformatics/btx570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/21/2017] [Accepted: 09/13/2017] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION The selection of a single nucleotide polymorphism (SNP) using bibliographic methods can be a very time-consuming task. Moreover, a SNP selected in this way may not be easily visualized in its genomic context by a standard user hoping to correlate it with other valuable information. Here we propose a web form built on top of Circos that can assist SNP-centered screening, based on their location in the genome and the regulatory modules they can disrupt. Its use may allow researchers to prioritize SNPs in genotyping and disease studies. RESULTS SiNoPsis is bundled as a web portal. It focuses on the different structures involved in the genomic expression of a gene, especially those found in the core promoter upstream region. These structures include transcription factor binding sites (for promoter and enhancer signals), histones and promoter flanking regions. Additionally, the tool provides eQTL and linkage disequilibrium (LD) properties for a given SNP query, yielding further clues about other indirectly associated SNPs. Possible disruptions of the aforementioned structures affecting gene transcription are reported using multiple resource databases. SiNoPsis has a simple user-friendly interface, which allows single queries by gene symbol, genomic coordinates, Ensembl gene identifiers, RefSeq transcript identifiers and SNPs. It is the only portal providing useful SNP selection based on regulatory modules and LD with functional variants in both textual and graphic modes (by properly defining the arguments and parameters needed to run Circos). AVAILABILITY AND IMPLEMENTATION SiNoPsis is freely available at https://compgen.bio.ub.edu/SiNoPsis/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Boloc
- Dep. de Medicina, University of Barcelona, Barcelona, Spain
| | - Natalia Rodríguez
- Dep. Fonaments Clínics, Unitat de Farmacologia, University of Barcelona, Barcelona, Spain
| | - Patricia Gassó
- Dep. Fonaments Clínics, Unitat de Farmacologia, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Josep F Abril
- Dep. de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Miquel Bernardo
- Dep. de Medicina, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Unitat Esquizofrènia, Hospital Clínic de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
| | - Amalia Lafuente
- Dep. Fonaments Clínics, Unitat de Farmacologia, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
| | - Sergi Mas
- Dep. Fonaments Clínics, Unitat de Farmacologia, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
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228
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Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Hum Genomics 2018; 12:1. [PMID: 29335020 PMCID: PMC5769240 DOI: 10.1186/s40246-018-0132-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/02/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context. RESULTS We performed expression quantitative trait locus (eQTL) analysis using genome-wide SNP genotyping and gene expression profiling of lung tissue samples from 86 COPD cases and 31 controls, testing for SNPs associated with gene expression levels. These results were integrated with a prior COPD GWAS using an ensemble statistical and network methods approach to identify relevant genes and observe them in the context of overall genetic control of gene expression to highlight co-regulated genes and disease pathways. We identified 250,312 unique SNPs and 4997 genes in the cis(local)-eQTL analysis (5% false discovery rate). The top gene from the integrative analysis was MAPT, a gene recently identified in an independent GWAS of lung function. The genes HNRNPAB and PCBP2 with RNA binding activity and the gene ACVR1B were identified in network communities with validated disease relevance. CONCLUSIONS The integration of lung tissue gene expression with genome-wide SNP genotyping and subsequent intersection with prior GWAS and omics studies highlighted candidate genes within COPD loci and in communities harboring known COPD genes. This integration also identified novel disease genes in sub-threshold regions that would otherwise have been missed through GWAS.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - John Platig
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Bartholome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Gerard J Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
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229
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Glinsky GV. Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells. Chromosome Res 2018; 26:61-84. [PMID: 29335803 DOI: 10.1007/s10577-018-9571-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 11/28/2022]
Abstract
Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs. Here, the analysis of HSGRL, hESC-enriched enhancers, super-enhancers (SEs), and specific sub-TAD structures termed super-enhancer domains (SEDs) has been performed. In the hESC genome, 331 of 504 (66%) of SED-harboring TADs contain HSGRL and 68% of SEDs co-localize with HSGRL, suggesting that emergence of HSGRL may have rewired SED-associated GRNs within specific TADs by inserting novel and/or erasing existing non-coding regulatory sequences. Consequently, markedly distinct features of the principal regulatory structures of interphase chromatin evolved in the hESC genome compared to mouse: the SED quantity is 3-fold higher and the median SED size is significantly larger. Concomitantly, the overall TAD quantity is increased by 42% while the median TAD size is significantly decreased (p = 9.11E-37) in the hESC genome. Present analyses illustrate a putative global role for transposable elements and HSGRL in shaping the human-specific features of the interphase chromatin organization and functions, which are facilitated by accelerated creation of novel transcription factor binding sites and new enhancers driven by targeted placement of HSGRL at defined genomic coordinates. A trend toward the convergence of TAD and SED architectures of interphase chromatin in the hESC genome may reflect changes of 3D-folding patterns of linear chromatin fibers designed to enhance both regulatory complexity and functional precision of GRNs by creating predominantly a single gene (or a set of functionally linked genes) per regulatory domain structures. Collectively, present analyses reveal critical evolutionary contributions of transposable elements and distal enhancers to creation of thousands primate- and human-specific elements of a chromatin folding code, which defines the 3D context of interphase chromatin both restricting and facilitating biological functions of GRNs.
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Affiliation(s)
- Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Dr. MC 0435, La Jolla, CA, 92093-0435, USA.
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230
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Agopian AJ, Goldmuntz E, Hakonarson H, Sewda A, Taylor D, Mitchell LE. Genome-Wide Association Studies and Meta-Analyses for Congenital Heart Defects. ACTA ACUST UNITED AC 2018; 10:e001449. [PMID: 28468790 DOI: 10.1161/circgenetics.116.001449] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 02/01/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND Maternal and inherited (ie, case) genetic factors likely contribute to the pathogenesis of congenital heart defects, but it is unclear whether individual common variants confer a large risk. METHODS AND RESULTS To evaluate the relationship between individual common maternal/inherited genotypes and risk for heart defects, we conducted genome-wide association studies in 5 cohorts. Three cohorts were recruited at the Children's Hospital of Philadelphia: 670 conotruncal heart defect (CTD) case-parent trios, 317 left ventricular obstructive tract defect (LVOTD) case-parent trios, and 406 CTD cases (n=406) and 2976 pediatric controls. Two cohorts were recruited through the Pediatric Cardiac Genomics Consortium: 355 CTD trios and 192 LVOTD trios. We also conducted meta-analyses using the genome-wide association study results from the CTD cohorts, the LVOTD cohorts, and from the combined CTD and LVOTD cohorts. In the individual genome-wide association studies, several genome-wide significant associations (P≤5×10-8) were observed. In our meta-analyses, 1 genome-wide significant association was detected: the case genotype for rs72820264, an intragenetic single-nucleotide polymorphism associated with LVOTDs (P=2.1×10-8). CONCLUSIONS We identified 1 novel candidate region associated with LVOTDs and report on several additional regions with suggestive evidence for association with CTD and LVOTD. These studies were constrained by the relatively small samples sizes and thus have limited power to detect small to moderate associations. Approaches that minimize the multiple testing burden (eg, gene or pathway based) may, therefore, be required to uncover common variants contributing to the risk of these relatively rare conditions.
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Affiliation(s)
- A J Agopian
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Elizabeth Goldmuntz
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Hakon Hakonarson
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Anshuman Sewda
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Deanne Taylor
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Laura E Mitchell
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA.
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231
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Tiana M, Acosta-Iborra B, Puente-Santamaría L, Hernansanz-Agustin P, Worsley-Hunt R, Masson N, García-Rio F, Mole D, Ratcliffe P, Wasserman WW, Jimenez B, del Peso L. The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia. Nucleic Acids Res 2018; 46:120-133. [PMID: 29059365 PMCID: PMC5758878 DOI: 10.1093/nar/gkx951] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 10/02/2017] [Accepted: 10/06/2017] [Indexed: 01/02/2023] Open
Abstract
Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. To identify genes regulated by hypoxia at the transcriptional level, we pulse-labeled HUVEC cells with 4-thiouridine and sequenced nascent transcripts. Then, we searched genome-wide binding profiles from the ENCODE project for factors that correlated with changes in transcription and identified binding of several components of the Sin3A co-repressor complex, including SIN3A, SAP30 and HDAC1/2, proximal to genes repressed by hypoxia. SIN3A interference revealed that it participates in the downregulation of 75% of the hypoxia-repressed genes in endothelial cells. Unexpectedly, it also blunted the induction of 47% of the upregulated genes, suggesting a role for this corepressor in gene induction. In agreement, ChIP-seq experiments showed that SIN3A preferentially localizes to the promoter region of actively transcribed genes and that SIN3A signal was enriched in hypoxia-repressed genes, prior exposure to the stimulus. Importantly, SINA3 occupancy was not altered by hypoxia in spite of changes in H3K27ac signal. In summary, our results reveal a prominent role for SIN3A in the transcriptional response to hypoxia and suggest a model where modulation of the associated histone deacetylase activity, rather than its recruitment, determines the transcriptional output.
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Affiliation(s)
- Maria Tiana
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Barbara Acosta-Iborra
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
| | - Laura Puente-Santamaría
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
| | - Pablo Hernansanz-Agustin
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
- Servicio Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del hospital de La Princesa, 28006 Madrid, Spain
| | - Rebecca Worsley-Hunt
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada
| | - Norma Masson
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Francisco García-Rio
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Servicio de Neumología, Hospital Universitario La Paz, Instituto de Investigación Sanitaria del hospital de La Paz, 28029 Madrid, Spain
| | - David Mole
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford OX3 7BN, UK
| | - Peter Ratcliffe
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada
| | - Benilde Jimenez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Luis del Peso
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
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232
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Sikaria D, Tu YN, Fisler DA, Mauro JA, Blanck G. Identification of specific feed-forward apoptosis mechanisms and associated higher survival rates for low grade glioma and lung squamous cell carcinoma. J Cancer Res Clin Oncol 2018; 144:459-468. [PMID: 29305708 DOI: 10.1007/s00432-017-2569-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/27/2017] [Indexed: 01/10/2023]
Abstract
The mechanisms of cell proliferation due to the overexpression of certain transcription factors (TFs) have been well documented in the cancer setting. However, many of these same TFs have pro-apoptotic effects, particularly when expressed or activated at high levels, a process referred to as feed-forward apoptosis (FFA). To determine whether cancers could be stratified on the basis of specific FFA signatures, RNASeq data representing samples from the cancer genome atlas were analyzed, revealing that high expression of the pro-proliferative TFs, MYC and YY1, is associated with a favorable outcome in low-grade glioma (LGG) and lung squamous cell carcinoma (LUSC), respectively. Analysis of the RNASeq data also led to the identification of specific apoptosis-effector genes whose expression levels correlate with increased survival rates, for both LGG and LUSC. Although FFA has been demonstrated as a general effect in cancer, in this report, for the first time, results identify specific TFs and their responsive effector genes that distinguish subsets of cancer samples undergoing more or less of a FFA process in a way that is associated with distinct patient survival rates.
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Affiliation(s)
- Dhiraj Sikaria
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA
| | - Yaping N Tu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA
| | - Diana A Fisler
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA
| | - James A Mauro
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA. .,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA. .,, 12901 Bruce B. Downs. Bd. MDC7, Tampa, FL, 33612, USA.
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233
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Wang Z, Zhang Q, Zhang W, Lin JR, Cai Y, Mitra J, Zhang ZD. HEDD: Human Enhancer Disease Database. Nucleic Acids Res 2018; 46:D113-D120. [PMID: 29077884 PMCID: PMC5753236 DOI: 10.1093/nar/gkx988] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/26/2022] Open
Abstract
Enhancers, as specialized genomic cis-regulatory elements, activate transcription of their target genes and play an important role in pathogenesis of many human complex diseases. Despite recent systematic identification of them in the human genome, currently there is an urgent need for comprehensive annotation databases of human enhancers with a focus on their disease connections. In response, we built the Human Enhancer Disease Database (HEDD) to facilitate studies of enhancers and their potential roles in human complex diseases. HEDD currently provides comprehensive genomic information for ∼2.8 million human enhancers identified by ENCODE, FANTOM5 and RoadMap with disease association scores based on enhancer-gene and gene-disease connections. It also provides Web-based analytical tools to visualize enhancer networks and score enhancers given a set of selected genes in a specific gene network. HEDD is freely accessible at http://zdzlab.einstein.yu.edu/1/hedd.php.
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Affiliation(s)
- Zhen Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wen Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ying Cai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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234
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Dwight T, Flynn A, Amarasinghe K, Benn DE, Lupat R, Li J, Cameron DL, Hogg A, Balachander S, Candiloro ILM, Wong SQ, Robinson BG, Papenfuss AT, Gill AJ, Dobrovic A, Hicks RJ, Clifton-Bligh RJ, Tothill RW. TERT structural rearrangements in metastatic pheochromocytomas. Endocr Relat Cancer 2018; 25:1-9. [PMID: 28974544 DOI: 10.1530/erc-17-0306] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 10/03/2017] [Indexed: 12/21/2022]
Abstract
Pheochromocytomas (PC) and paragangliomas (PGL) are endocrine tumors for which the genetic and clinicopathological features of metastatic progression remain incompletely understood. As a result, the risk of metastasis from a primary tumor cannot be predicted. Early diagnosis of individuals at high risk of developing metastases is clinically important and the identification of new biomarkers that are predictive of metastatic potential is of high value. Activation of TERT has been associated with a number of malignant tumors, including PC/PGL. However, the mechanism of TERT activation in the majority of PC/PGL remains unclear. As TERT promoter mutations occur rarely in PC/PGL, we hypothesized that other mechanisms - such as structural variations - may underlie TERT activation in these tumors. From 35 PC and four PGL, we identified three primary PCs that developed metastases with elevated TERT expression, each of which lacked TERT promoter mutations and promoter DNA methylation. Using whole genome sequencing, we identified somatic structural alterations proximal to the TERT locus in two of these tumors. In both tumors, the genomic rearrangements led to the positioning of super-enhancers proximal to the TERT promoter, that are likely responsible for the activation of the normally tightly repressed TERT expression in chromaffin cells.
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Affiliation(s)
- Trisha Dwight
- Cancer GeneticsKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of SydneySydney, New South Wales, Australia
| | - Aidan Flynn
- The Finsen LaboratoryRigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC)University of Copenhagen, Copenhagen N, Denmark
| | | | - Diana E Benn
- Cancer GeneticsKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of SydneySydney, New South Wales, Australia
| | - Richard Lupat
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Jason Li
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Daniel L Cameron
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical BiologyUniversity of Melbourne, Melbourne, Victoria, Australia
| | - Annette Hogg
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Shiva Balachander
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Ida L M Candiloro
- Olivia Newton-John Cancer Research InstituteHeidelberg, Victoria, Australia
- The Department of PathologyUniversity of Melbourne, Parkville, Victoria, Australia
| | - Stephen Q Wong
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
| | - Bruce G Robinson
- Cancer GeneticsKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of SydneySydney, New South Wales, Australia
| | - Anthony T Papenfuss
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
- Bioinformatics DivisionThe Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical BiologyUniversity of Melbourne, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of OncologyThe University of Melbourne, Parkville, Victoria, Australia
- The Department of Mathematics and StatisticsUniversity of Melbourne, Parkville, Victoria, Australia
| | - Anthony J Gill
- The University of SydneySydney, New South Wales, Australia
- Cancer Diagnosis and Pathology GroupKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Alexander Dobrovic
- Olivia Newton-John Cancer Research InstituteHeidelberg, Victoria, Australia
- The Department of PathologyUniversity of Melbourne, Parkville, Victoria, Australia
- School of Cancer MedicineLa Trobe University, Bundoora, Victoria, Australia
| | - Rodney J Hicks
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of OncologyThe University of Melbourne, Parkville, Victoria, Australia
| | - Roderick J Clifton-Bligh
- Cancer GeneticsKolling Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
- The University of SydneySydney, New South Wales, Australia
| | - Richard W Tothill
- The Peter MacCallum Cancer CentreEast Melbourne, Victoria, Australia
- The Department of PathologyUniversity of Melbourne, Parkville, Victoria, Australia
- The Sir Peter MacCallum Department of OncologyThe University of Melbourne, Parkville, Victoria, Australia
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235
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McCormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers BD, McKinley B, Mattison A, Morishige DT, Grimwood J, Schmutz J, Mullet JE. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:338-354. [PMID: 29161754 DOI: 10.1111/tpj.13781] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 11/05/2017] [Accepted: 11/14/2017] [Indexed: 05/20/2023]
Abstract
Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.
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Affiliation(s)
- Ryan F McCormick
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Sandra K Truong
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shengqiang Shu
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - David Sims
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Megan Kennedy
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Brock D Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Ashley Mattison
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Daryl T Morishige
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - John E Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
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236
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Osanlou O, Pirmohamed M, Daly AK. Pharmacogenetics of Adverse Drug Reactions. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2018; 83:155-190. [PMID: 29801574 DOI: 10.1016/bs.apha.2018.03.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Adverse drug reactions (ADRs) are an important cause of morbidity and mortality. Genetic factors predispose to many ADRs, affecting susceptibility to both type A and type B reactions. The overall contribution of genetics will vary according to drug and ADR, and should be considered when attempting to predict and prevent ADRs. Genetic risk factors are considered in detail for a number of type A ADRs, especially those relating to warfarin and thiopurines, and type B ADRs affecting skin, the liver, and the heart. As the availability of whole genome sequencing increases, it is likely that prospective genotype for particular ADRs prior to drug prescription will become more common in the future. Current examples of genetic testing to prevent ADRs which have already been implemented and future prospects for developments in the field are discussed in detail.
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Affiliation(s)
- Orod Osanlou
- Department of Molecular and Clinical Pharmacology, The University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, The University of Liverpool, Liverpool, United Kingdom
| | - Ann K Daly
- Institute of Cellular Medicine, Newcastle University, Medical School, Newcastle upon Tyne, United Kingdom.
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237
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Mullany LE, Herrick JS, Wolff RK, Stevens JR, Samowitz W, Slattery ML. MicroRNA-transcription factor interactions and their combined effect on target gene expression in colon cancer cases. Genes Chromosomes Cancer 2017; 57:192-202. [PMID: 29226599 PMCID: PMC5807123 DOI: 10.1002/gcc.22520] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/11/2022] Open
Abstract
Transcription factors (TFs) and microRNAs (miRNAs) regulate gene expression: TFs by influencing messenger RNA (mRNA) transcription and miRNAs by influencing mRNA translation and transcript degradation. Additionally, miRNAs and TFs alter each other's expression, making it difficult to ascertain the effect either one has on target gene (TG) expression. In this investigation, we use a two‐way interaction model with the TF and miRNA as independent variables to investigate whether miRNAs and TFs work together to influence TG expression levels in colon cancer subjects. We used known TF binding sites and validated miRNA targets to determine potential miRNA‐TF‐TG interactions, restricting interactions to those with a TF previously associated with altered risk of colorectal cancer death. We analyzed interactions using normal colonic mucosa expression as well as differential expression, which is measured as colonic carcinoma expression minus normal colonic mucosa expression. We analyzed 3518 miRNA‐TF‐TG triplets using normal mucosa expression and 617 triplets using differential expression. Normal colonic RNA‐Seq data were available for 168 individuals; of these, 159 also had carcinoma RNA‐Seq data. Thirteen unique miRNA‐TF‐TG interactions, comprising six miRNAs, four TFs, and 11 TGs, were statistically significant after adjustment for multiple comparisons in normal colonic mucosa, and 14 unique miRNA‐TF‐TG interactions, comprising two miRNAs, two TFs, and 13 TGs, were found for carcinoma‐normal differential expression. Our results show that TG expression is influenced by both miRNAs as well as TFs, and the influence of one regulator impacts the effect of the other on the shared TG expression.
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Affiliation(s)
- Lila E Mullany
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Division of Epidemiology, University of Utah, Salt Lake City, Utah
| | - Jennifer S Herrick
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Division of Epidemiology, University of Utah, Salt Lake City, Utah
| | - Roger K Wolff
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Division of Epidemiology, 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.,Division of Epidemiology, University of Utah, Salt Lake City, Utah
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238
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Stern JL, Paucek RD, Huang FW, Ghandi M, Nwumeh R, Costello JC, Cech TR. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes. Cell Rep 2017; 21:3700-3707. [PMID: 29281820 PMCID: PMC5747321 DOI: 10.1016/j.celrep.2017.12.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/29/2017] [Accepted: 11/30/2017] [Indexed: 01/18/2023] Open
Abstract
A mutation in the promoter of the Telomerase Reverse Transcriptase (TERT) gene is the most frequent noncoding mutation in cancer. The mutation drives unusual monoallelic expression of TERT, allowing immortalization. Here, we find that DNA methylation of the TERT CpG island (CGI) is also allele-specific in multiple cancers. The expressed allele is hypomethylated, which is opposite to cancers without TERT promoter mutations. The continued presence of Polycomb repressive complex 2 (PRC2) on the inactive allele suggests that histone marks of repressed chromatin may be causally linked to high DNA methylation. Consistent with this hypothesis, TERT promoter DNA containing 5-methyl-CpG has much increased affinity for PRC2 in vitro. Thus, CpG methylation and histone marks appear to collaborate to maintain the two TERT alleles in different epigenetic states in TERT promoter mutant cancers. Finally, in several cancers, DNA methylation levels at the TERT CGI correlate with altered patient survival.
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Affiliation(s)
- Josh Lewis Stern
- BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Richard D Paucek
- BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Franklin W Huang
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ronald Nwumeh
- BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - James C Costello
- Department of Pharmacology and University of Colorado Comprehensive Cancer Center, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas R Cech
- BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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239
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Iurato S, Carrillo-Roa T, Arloth J, Czamara D, Diener-Hölzl L, Lange J, Müller-Myhsok B, Binder EB, Erhardt A. "DNA Methylation signatures in panic disorder". Transl Psychiatry 2017; 7:1287. [PMID: 29249830 PMCID: PMC5802688 DOI: 10.1038/s41398-017-0026-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 01/15/2023] Open
Abstract
Panic disorder (PD) affects about four million Europeans, with women affected twice as likely as men, causing substantial suffering and high economic costs. The etiopathogenesis of PD remains largely unknown, but both genetic and environmental factors contribute to risk. An epigenome-wide association study (EWAS) was conducted to compare medication-free PD patients (n = 89) with healthy controls (n = 76) stratified by gender. Replication was sought in an independent sample (131 cases, 169 controls) and functional analyses were conducted in a third sample (N = 71). DNA methylation was assessed in whole blood using the Infinium HumanMethylation450 BeadChip. One genome-wide association surviving FDR of 5% (cg07308824, P = 1.094 × 10-7, P-adj = 0.046) was identified in female PD patients (N = 49) compared to controls (N = 48). The same locus, located in an enhancer region of the HECA gene, was also hypermethylated in female PD patients in the replication sample (P = 0.035) and the significance of the association improved in the meta-analysis (P-adj = 0.004). Methylation at this CpG site was associated with HECA mRNA expression in another independent female sample (N = 71) both at baseline (P = 0.046) and after induction by dexamethasone (P = 0.029). Of 15 candidates, 5 previously reported as associated with PD or anxiety traits also showed differences in DNA methylation after gene-wise correction and included SGK1, FHIT, ADCYAP1, HTR1A, HTR2A. Our study examines epigenome-wide differences in peripheral blood for PD patients. Our results point to possible sex-specific methylation changes in the HECA gene for PD but overall highlight that this disorder is not associated with extensive changes in DNA methylation in peripheral blood.
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Affiliation(s)
- Stella Iurato
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.
| | - Tania Carrillo-Roa
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Janine Arloth
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Laura Diener-Hölzl
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Jennifer Lange
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Bertram Müller-Myhsok
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B. Binder
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany ,0000 0001 0941 6502grid.189967.8Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - Angelika Erhardt
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.
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240
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Vohhodina J, Barros EM, Savage AL, Liberante FG, Manti L, Bankhead P, Cosgrove N, Madden AF, Harkin DP, Savage KI. The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export. Nucleic Acids Res 2017; 45:12816-12833. [PMID: 29112714 PMCID: PMC5728405 DOI: 10.1093/nar/gkx1046] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 10/03/2017] [Accepted: 10/19/2017] [Indexed: 12/18/2022] Open
Abstract
mRNA splicing and export plays a key role in the regulation of gene expression, with recent evidence suggesting an additional layer of regulation of gene expression and cellular function through the selective splicing and export of genes within specific pathways. Here we describe a role for the RNA processing factors THRAP3 and BCLAF1 in the regulation of the cellular DNA damage response (DDR) pathway, a key pathway involved in the maintenance of genomic stability and the prevention of oncogenic transformation. We show that loss of THRAP3 and/or BCLAF1 leads to sensitivity to DNA damaging agents, defective DNA repair and genomic instability. Additionally, we demonstrate that this phenotype can be at least partially explained by the role of THRAP3 and BCLAF1 in the selective mRNA splicing and export of transcripts encoding key DDR proteins, including the ATM kinase. Moreover, we show that cancer associated mutations within THRAP3 result in deregulated processing of THRAP3/BCLAF1-regulated transcripts and consequently defective DNA repair. Taken together, these results suggest that THRAP3 and BCLAF1 mutant tumors may be promising targets for DNA damaging chemotherapy.
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Affiliation(s)
- Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Eliana M. Barros
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Abigail L. Savage
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Fabio G. Liberante
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Lorenzo Manti
- Dipartimento di Fisica ‘E Pancini’, Università di Napoli Federico II, Monte S. Angelo, 80126 Napoli, Italy
| | - Peter Bankhead
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Nicola Cosgrove
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, D02 YN77, Ireland
| | - Angelina F. Madden
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - D. Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Kienan I. Savage
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
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241
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Wang Y, Wu W, Zhu M, Wang C, Shen W, Cheng Y, Geng L, Li Z, Zhang J, Dai J, Ma H, Chen L, Hu Z, Jin G, Shen H. Integrating expression-related SNPs into genome-wide gene- and pathway-based analyses identified novel lung cancer susceptibility genes. Int J Cancer 2017; 142:1602-1610. [DOI: 10.1002/ijc.31182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Yuzhuo Wang
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Weibing Wu
- Department of Thoracic Surgery; First Affiliated Hospital of Nanjing Medical University; Nanjing 210029 China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Wei Shen
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Yang Cheng
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Liguo Geng
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Zhihua Li
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Jiahui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
| | - Liang Chen
- Department of Thoracic Surgery; First Affiliated Hospital of Nanjing Medical University; Nanjing 210029 China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
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242
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Mnasri N, Mamarbachi M, Allen BG, Mayer G. 5-Azacytidine engages an IRE1α-EGFR-ERK1/2 signaling pathway that stabilizes the LDL receptor mRNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:29-40. [PMID: 29208426 DOI: 10.1016/j.bbagrm.2017.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/09/2017] [Accepted: 11/29/2017] [Indexed: 01/06/2023]
Abstract
Hepatic low-density lipoprotein receptor (LDLR) is the primary conduit for the clearance of plasma LDL-cholesterol and increasing its expression represents a central goal for treating cardiovascular disease. However, LDLR mRNA is unstable and undergoes rapid turnover mainly due to the three AU-rich elements (ARE) in its proximal 3'-untranslated region (3'-UTR). Herein, our data revealed that 5-azacytidine (5-AzaC), an antimetabolite used in the treatment of myelodysplastic syndrome, stabilizes the LDLR mRNA through a previously unrecognized signaling pathway resulting in a strong increase of its protein level in human hepatocytes in culture. 5-AzaC caused a sustained activation of the inositol-requiring enzyme 1α (IRE1α) kinase domain and c-Jun N-terminal kinase (JNK) independently of endoplasmic reticulum stress. This resulted in activation of the epidermal growth factor receptor (EGFR) and extracellular signal-regulated kinase1/2 (ERK1/2) that, in turn, stabilized LDLR mRNA. Systematic mutation of the AREs (ARE1-3) in the LDLR 3'UTR and expression of each mutant coupled to a luciferase reporter in Huh7 cells demonstrated that ARE1 is required for rapid LDLR mRNA decay and 5-AzaC-induced mRNA stabilization via the IRE1α-EGFR-ERK1/2 signaling cascade. The characterization of this pathway will help to reveal potential targets to enhance plasma LDL clearance and novel cholesterol-lowering therapeutic strategies.
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Affiliation(s)
- Nourhen Mnasri
- Laboratory of Molecular and Cellular Biology, Montreal Heart Institute, Montréal, QC, Canada; Department of Biomedical Sciences, Université de Montréal, Montréal, QC, Canada
| | - Maya Mamarbachi
- Molecular Biology Core Facility, Montreal Heart Institute, Montréal, QC, Canada
| | - Bruce G Allen
- Laboratory of Cell Biology, Montreal Heart Institute, Montréal, QC, Canada; Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Gaétan Mayer
- Laboratory of Molecular and Cellular Biology, Montreal Heart Institute, Montréal, QC, Canada; Faculty of Pharmacy, Université de Montréal, Montréal, QC, Canada.
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243
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Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A. Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. Genome Res 2017. [PMID: 29141961 DOI: 10.1101/088732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogeneous and simple systems, such as isolated cell populations or early-development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism Caenorhabditis elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development. We find that over 5000 distal noncoding regions exhibit dynamic changes in chromatin accessibility between developmental stages and could thereby represent putative enhancers. When tested in vivo, several of these putative enhancers indeed drive novel cell-type- and temporal-specific patterns of expression. Finally, by integrating transcription factor binding motifs in a machine learning framework, we identify EOR-1 as a unique transcription factor that may regulate chromatin dynamics during development. Our study provides a unique resource for C. elegans, a system in which the prevalence and importance of enhancers remains poorly characterized, and demonstrates the power of using whole organism chromatin accessibility to identify novel regulatory regions in complex systems.
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Affiliation(s)
- Aaron C Daugherty
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Robin W Yeo
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Jason D Buenrostro
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, California 94305, USA
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244
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Man J, Yu X, Huang H, Zhou W, Xiang C, Huang H, Miele L, Liu Z, Bebek G, Bao S, Yu JS. Hypoxic Induction of Vasorin Regulates Notch1 Turnover to Maintain Glioma Stem-like Cells. Cell Stem Cell 2017; 22:104-118.e6. [PMID: 29198941 DOI: 10.1016/j.stem.2017.10.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/11/2017] [Accepted: 10/13/2017] [Indexed: 12/16/2022]
Abstract
Tumor hypoxia is associated with poor patient survival and is a characteristic of glioblastoma. Notch signaling is implicated in maintaining glioma stem-like cells (GSCs) within the hypoxic niche, although the molecular mechanisms linking hypoxia to Notch activation have not been clearly delineated. Here we show that Vasorin is a critical link between hypoxia and Notch signaling in GSCs. Vasorin is preferentially induced in GSCs by a HIF1α/STAT3 co-activator complex and stabilizes Notch1 protein at the cell membrane. This interaction prevents Numb from binding Notch1, rescuing it from Numb-mediated lysosomal degradation. Thus, Vasorin acts as a switch to augment Notch signaling under hypoxic conditions. Vasorin promotes tumor growth and reduces survival in mouse models of glioblastoma, and its expression correlates with increased aggression of human gliomas. These findings provide mechanistic insights into how hypoxia promotes Notch signaling in glioma and identify Vasorin as a potential therapeutic target.
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Affiliation(s)
- Jianghong Man
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NE30, Cleveland, OH 44195, USA; National Center of Biomedical Analysis, Beijing 100850, China
| | - Xingjiang Yu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NE30, Cleveland, OH 44195, USA
| | - Haidong Huang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NE30, Cleveland, OH 44195, USA
| | - Wenchao Zhou
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NE30, Cleveland, OH 44195, USA
| | - Chaomei Xiang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NE30, Cleveland, OH 44195, USA
| | - Haohao Huang
- National Center of Biomedical Analysis, Beijing 100850, China
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center, Clinical Sciences Research Building, Room 657, 533 Bolivar Street, New Orleans, LA 70112, USA
| | - Zhenggang Liu
- Cell and Cancer Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Gurkan Bebek
- Department of Nutrition, Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, BRB 921, Cleveland, OH 44106, USA
| | - Shideng Bao
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NE30, Cleveland, OH 44195, USA; Burkhardt Brain Tumor and Neuro-Oncology Center, Neurological Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Jennifer S Yu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NE30, Cleveland, OH 44195, USA; Burkhardt Brain Tumor and Neuro-Oncology Center, Neurological Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, 9500 Euclid Avenue, CA50, Cleveland, OH 44195, USA.
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245
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Jylhävä J, Kananen L, Raitanen J, Marttila S, Nevalainen T, Hervonen A, Jylhä M, Hurme M. Methylomic predictors demonstrate the role of NF-κB in old-age mortality and are unrelated to the aging-associated epigenetic drift. Oncotarget 2017; 7:19228-41. [PMID: 27015559 PMCID: PMC4991378 DOI: 10.18632/oncotarget.8278] [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: 11/06/2015] [Accepted: 03/10/2016] [Indexed: 01/24/2023] Open
Abstract
Changes in the DNA methylation (DNAm) landscape have been implicated in aging and cellular senescence. To unravel the role of specific DNAm patterns in late-life survival, we performed genome-wide methylation profiling in nonagenarians (n=111) and determined the performance of the methylomic predictors and conventional risk markers in a longitudinal setting. The survival model containing only the methylomic markers was superior in terms of predictive accuracy compared with the model containing only the conventional predictors or the model containing conventional predictors combined with the methylomic markers. At the 2.55-year follow-up, we identified 19 mortality-associated (false-discovery rate <0.5) CpG sites that mapped to genes functionally clustering around the nuclear factor kappa B (NF-κB) complex. Interestingly, none of the mortality-associated CpG sites overlapped with the established aging-associated DNAm sites. Our results are in line with previous findings on the role of NF-κB in controlling animal life spans and demonstrate the role of this complex in human longevity.
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Affiliation(s)
- Juulia Jylhävä
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland
| | - Laura Kananen
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland
| | - Jani Raitanen
- School of Health Sciences, University of Tampere, Tampere, Finland.,UKK Institute for Health Promotion Research, Tampere, Finland
| | - Saara Marttila
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland
| | - Tapio Nevalainen
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland
| | - Antti Hervonen
- Gerontology Research Center, University of Tampere, Tampere, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Marja Jylhä
- Gerontology Research Center, University of Tampere, Tampere, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Mikko Hurme
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
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246
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Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. Genome Res 2017; 27:2096-2107. [PMID: 29141961 PMCID: PMC5741055 DOI: 10.1101/gr.226233.117] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022]
Abstract
Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogeneous and simple systems, such as isolated cell populations or early-development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism Caenorhabditis elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development. We find that over 5000 distal noncoding regions exhibit dynamic changes in chromatin accessibility between developmental stages and could thereby represent putative enhancers. When tested in vivo, several of these putative enhancers indeed drive novel cell-type- and temporal-specific patterns of expression. Finally, by integrating transcription factor binding motifs in a machine learning framework, we identify EOR-1 as a unique transcription factor that may regulate chromatin dynamics during development. Our study provides a unique resource for C. elegans, a system in which the prevalence and importance of enhancers remains poorly characterized, and demonstrates the power of using whole organism chromatin accessibility to identify novel regulatory regions in complex systems.
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247
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Baena-Del Valle JA, Zheng Q, Esopi DM, Rubenstein M, Hubbard GK, Moncaliano MC, Hruszkewycz A, Vaghasia A, Yegnasubramanian S, Wheelan SJ, Meeker AK, Heaphy CM, Graham MK, De Marzo AM. MYC drives overexpression of telomerase RNA (hTR/TERC) in prostate cancer. J Pathol 2017; 244:11-24. [PMID: 28888037 DOI: 10.1002/path.4980] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 08/07/2017] [Accepted: 08/24/2017] [Indexed: 01/21/2023]
Abstract
Telomerase consists of at least two essential elements, an RNA component hTR or TERC that contains the template for telomere DNA addition and a catalytic reverse transcriptase (TERT). While expression of TERT has been considered the key rate-limiting component for telomerase activity, increasing evidence suggests an important role for the regulation of TERC in telomere maintenance and perhaps other functions in human cancer. By using three orthogonal methods including RNAseq, RT-qPCR, and an analytically validated chromogenic RNA in situ hybridization assay, we report consistent overexpression of TERC in prostate cancer. This overexpression occurs at the precursor stage (e.g. high-grade prostatic intraepithelial neoplasia or PIN) and persists throughout all stages of disease progression. Levels of TERC correlate with levels of MYC (a known driver of prostate cancer) in clinical samples and we also show the following: forced reductions of MYC result in decreased TERC levels in eight cancer cell lines (prostate, lung, breast, and colorectal); forced overexpression of MYC in PCa cell lines, and in the mouse prostate, results in increased TERC levels; human TERC promoter activity is decreased after MYC silencing; and MYC occupies the TERC locus as assessed by chromatin immunoprecipitation (ChIP). Finally, we show that knockdown of TERC by siRNA results in reduced proliferation of prostate cancer cell lines. These studies indicate that TERC is consistently overexpressed in all stages of prostatic adenocarcinoma and that its expression is regulated by MYC. These findings nominate TERC as a novel prostate cancer biomarker and therapeutic target. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Javier A Baena-Del Valle
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pathology and Laboratory Medicine, Fundacion Santa Fe De Bogota University Hospital, Bogota, DC, Colombia
| | - Qizhi Zheng
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David M Esopi
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Rubenstein
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Gretchen K Hubbard
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Maria C Moncaliano
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Hruszkewycz
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
| | - Ajay Vaghasia
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Departments of Urology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sarah J Wheelan
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Departments of Urology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alan K Meeker
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher M Heaphy
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mindy K Graham
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Angelo M De Marzo
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Departments of Urology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,The Brady Urological Research Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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248
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Abstract
Noncoding DNA regions have central roles in human biology, evolution, and disease. ChromHMM helps to annotate the noncoding genome using epigenomic information across one or multiple cell types. It combines multiple genome-wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer a complete annotation for each cell type. ChromHMM learns chromatin-state signatures using a multivariate hidden Markov model (HMM) that explicitly models the combinatorial presence or absence of each mark. ChromHMM uses these signatures to generate a genome-wide annotation for each cell type by calculating the most probable state for each genomic segment. ChromHMM provides an automated enrichment analysis of the resulting annotations to facilitate the functional interpretations of each chromatin state. ChromHMM is distinguished by its modeling emphasis on combinations of marks, its tight integration with downstream functional enrichment analyses, its speed, and its ease of use. Chromatin states are learned, annotations are produced, and enrichments are computed within 1 d.
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249
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Beyond genome-wide scan: Association of a cis-regulatory NCR3 variant with mild malaria in a population living in the Republic of Congo. PLoS One 2017; 12:e0187818. [PMID: 29121672 PMCID: PMC5679660 DOI: 10.1371/journal.pone.0187818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/26/2017] [Indexed: 12/15/2022] Open
Abstract
Linkage studies have revealed a linkage of mild malaria to chromosome 6p21 that contains the NCR3 gene encoding a natural killer cell receptor, whereas NCR3-412G>C (rs2736191) located in its promoter region was found to be associated with malaria in Burkina Faso. Here we confirmed the association of rs2736191 with mild malaria in a Congolese cohort and investigated its potential cis-regulatory effect. Luciferase assay results indicated that rs2736191-G allele had a significantly increased promoter activity compared to rs2736191-C allele. Furthermore, EMSAs demonstrated an altered binding of two nuclear protein complexes to the rs2736191-C allele in comparison to rs2736191-G allele. Finally, after in silico identification of transcription factor candidates, pull-down western blot experiments confirmed that both STAT4 and RUNX3 bind the region encompassing rs2736191 with a higher affinity for the G allele. To our knowledge, this is the first report that explored the functional role of rs2736191. These results support the hypothesis that genetic variation within natural killer cell receptors alters malaria resistance in humans.
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250
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Buxboim A, Irianto J, Swift J, Athirasala A, Shin JW, Rehfeldt F, Discher DE. Coordinated increase of nuclear tension and lamin-A with matrix stiffness outcompetes lamin-B receptor that favors soft tissue phenotypes. Mol Biol Cell 2017; 28:3333-3348. [PMID: 28931598 PMCID: PMC5687034 DOI: 10.1091/mbc.e17-06-0393] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/06/2017] [Accepted: 09/13/2017] [Indexed: 12/31/2022] Open
Abstract
Matrix stiffness that is sensed by a cell or measured by a purely physical probe reflects the intrinsic elasticity of the matrix and also how thick or thin the matrix is. Here, mesenchymal stem cells (MSCs) and their nuclei spread in response to thickness-corrected matrix microelasticity, with increases in nuclear tension and nuclear stiffness resulting from increases in myosin-II and lamin-A,C. Linearity between the widely varying projected area of a cell and its nucleus across many matrices, timescales, and myosin-II activity levels indicates a constant ratio of nucleus-to-cell volume, despite MSCs' lineage plasticity. Nuclear envelope fluctuations are suppressed on the stiffest matrices, and fluctuation spectra reveal a high nuclear tension that matches trends from traction force microscopy and from increased lamin-A,C. Transcriptomes of many diverse tissues and MSCs further show that lamin-A,C's increase with tissue or matrix stiffness anti-correlates with lamin-B receptor (LBR), which contributes to lipid/sterol biosynthesis. Adipogenesis (a soft lineage) indeed increases LBR:lamin-A,C protein stoichiometry in MSCs versus osteogenesis (stiff). The two factors compete for lamin-B in response to matrix elasticity, knockdown, myosin-II inhibition, and even constricted migration that disrupts and segregates lamins in situ. Matrix stiffness-driven contractility thus tenses the nucleus to favor lamin-A,C accumulation and suppress soft tissue phenotypes.
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Affiliation(s)
- Amnon Buxboim
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
- Department/Graduate Group of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Jerome Irianto
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Joe Swift
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Avathamsa Athirasala
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Jae-Won Shin
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Florian Rehfeldt
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E Discher
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
- Department/Graduate Group of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
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