Pesticide Exposure and Inherited Variants in Vitamin D Pathway Genes in Relation to Prostate Cancer
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Integrated Analysis of the Critical Region 5P15.3–P15.2 Associated with Cri-Du-Chat Syndrome
Genetics and Molecular Biology, 42, 1(suppl), 186-196 (2019) Copyright © 2019, Sociedade Brasileira de Genética. Printed in Brazil DOI: http://dx.doi.org/10.1590/1678-4685-GMB-2018-0173 Research Article Integrated analysis of the critical region 5p15.3–p15.2 associated with cri-du-chat syndrome Thiago Corrêa1, Bruno César Feltes2 and Mariluce Riegel1,3* 1Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. 2Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. 3Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil. Abstract Cri-du-chat syndrome (CdCs) is one of the most common contiguous gene syndromes, with an incidence of 1:15,000 to 1:50,000 live births. To better understand the etiology of CdCs at the molecular level, we investigated theprotein–protein interaction (PPI) network within the critical chromosomal region 5p15.3–p15.2 associated with CdCs using systemsbiology. Data were extracted from cytogenomic findings from patients with CdCs. Based on clin- ical findings, molecular characterization of chromosomal rearrangements, and systems biology data, we explored possible genotype–phenotype correlations involving biological processes connected with CdCs candidate genes. We identified biological processes involving genes previously found to be associated with CdCs, such as TERT, SLC6A3, and CTDNND2, as well as novel candidate proteins with potential contributions to CdCs phenotypes, in- cluding CCT5, TPPP, MED10, ADCY2, MTRR, CEP72, NDUFS6, and MRPL36. Although further functional analy- ses of these proteins are required, we identified candidate proteins for the development of new multi-target genetic editing tools to study CdCs. -
Estrogen Receptor Coregulators and Pioneer Factors: the Orchestrators of Mammary Gland Cell Fate and Development
REVIEW ARTICLE published: 12 August 2014 CELL AND DEVELOPMENTAL BIOLOGY doi: 10.3389/fcell.2014.00034 Estrogen receptor coregulators and pioneer factors: the orchestrators of mammary gland cell fate and development Bramanandam Manavathi*, Venkata S. K. Samanthapudi and Vijay Narasimha Reddy Gajulapalli Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India Edited by: The steroid hormone, 17β-estradiol (E2), plays critical role in various cellular processes Claude Beaudoin, Blaise Pascal such as cell proliferation, differentiation, migration and apoptosis, and is essential for University Clermont-Ferrand 2, reproduction and mammary gland development. E2 actions are mediated by two classical France nuclear hormone receptors, estrogen receptor α and β (ERs). The activity of ERs depends Reviewed by: Anne Hélène Duittoz, Université de on the coordinated activity of ligand binding, post-translational modifications (PTMs), and Tours, France importantly the interaction with their partner proteins called “coregulators.” Because Songhai Chen, University of Iowa, coregulators are proved to be crucial for ER transcriptional activity, and majority of breast USA cancers are ERα positive, an increased interest in the field has led to the identification of *Correspondence: a large number of coregulators. In the last decade, gene knockout studies using mouse Bramanandam Manavathi, Department of Biochemistry, School models provided impetus to our further understanding of the role of these coregulators of Life Sciences, University of in mammary gland development. Several coregulators appear to be critical for terminal Hyderabad, Gachibowli, end bud (TEB) formation, ductal branching and alveologenesis during mammary gland Hyderabad-500046, India development. The emerging studies support that, coregulators along with the other ER e-mail: [email protected] partner proteins called “pioneer factors” together contribute significantly to E2 signaling and mammary cell fate. -
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Systematic Evaluation of Genes and Genetic Variants Associated with Type 1 Diabetes Susceptibility This information is current as Ramesh Ram, Munish Mehta, Quang T. Nguyen, Irma of September 23, 2021. Larma, Bernhard O. Boehm, Flemming Pociot, Patrick Concannon and Grant Morahan J Immunol 2016; 196:3043-3053; Prepublished online 24 February 2016; doi: 10.4049/jimmunol.1502056 Downloaded from http://www.jimmunol.org/content/196/7/3043 Supplementary http://www.jimmunol.org/content/suppl/2016/02/19/jimmunol.150205 Material 6.DCSupplemental http://www.jimmunol.org/ References This article cites 44 articles, 5 of which you can access for free at: http://www.jimmunol.org/content/196/7/3043.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 23, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Systematic Evaluation of Genes and Genetic Variants Associated with Type 1 Diabetes Susceptibility Ramesh Ram,*,† Munish Mehta,*,† Quang T. -
A Chromosome-Centric Human Proteome Project (C-HPP) To
computational proteomics Laboratory for Computational Proteomics www.FenyoLab.org E-mail: [email protected] Facebook: NYUMC Computational Proteomics Laboratory Twitter: @CompProteomics Perspective pubs.acs.org/jpr A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17 † ‡ § ∥ ‡ ⊥ Suli Liu, Hogune Im, Amos Bairoch, Massimo Cristofanilli, Rui Chen, Eric W. Deutsch, # ¶ △ ● § † Stephen Dalton, David Fenyo, Susan Fanayan,$ Chris Gates, , Pascale Gaudet, Marina Hincapie, ○ ■ △ ⬡ ‡ ⊥ ⬢ Samir Hanash, Hoguen Kim, Seul-Ki Jeong, Emma Lundberg, George Mias, Rajasree Menon, , ∥ □ △ # ⬡ ▲ † Zhaomei Mu, Edouard Nice, Young-Ki Paik, , Mathias Uhlen, Lance Wells, Shiaw-Lin Wu, † † † ‡ ⊥ ⬢ ⬡ Fangfei Yan, Fan Zhang, Yue Zhang, Michael Snyder, Gilbert S. Omenn, , Ronald C. Beavis, † # and William S. Hancock*, ,$, † Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States ‡ Stanford University, Palo Alto, California, United States § Swiss Institute of Bioinformatics (SIB) and University of Geneva, Geneva, Switzerland ∥ Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States ⊥ Institute for System Biology, Seattle, Washington, United States ¶ School of Medicine, New York University, New York, United States $Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia ○ MD Anderson Cancer Center, Houston, Texas, United States ■ Yonsei University College of Medicine, Yonsei University, -
Agricultural University of Athens
ΓΕΩΠΟΝΙΚΟ ΠΑΝΕΠΙΣΤΗΜΙΟ ΑΘΗΝΩΝ ΣΧΟΛΗ ΕΠΙΣΤΗΜΩΝ ΤΩΝ ΖΩΩΝ ΤΜΗΜΑ ΕΠΙΣΤΗΜΗΣ ΖΩΙΚΗΣ ΠΑΡΑΓΩΓΗΣ ΕΡΓΑΣΤΗΡΙΟ ΓΕΝΙΚΗΣ ΚΑΙ ΕΙΔΙΚΗΣ ΖΩΟΤΕΧΝΙΑΣ ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ ΑΘΗΝΑ 2020 ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Genome-wide association analysis and gene network analysis for (re)production traits in commercial broilers ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ Τριμελής Επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Επταμελής εξεταστική επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Πηνελόπη Μπεμπέλη (Καθ. ΓΠΑ) Δημήτριος Βλαχάκης (Επ. Καθ. ΓΠΑ) Ευάγγελος Ζωίδης (Επ.Καθ. ΓΠΑ) Γεώργιος Θεοδώρου (Επ.Καθ. ΓΠΑ) 2 Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Περίληψη Σκοπός της παρούσας διδακτορικής διατριβής ήταν ο εντοπισμός γενετικών δεικτών και υποψηφίων γονιδίων που εμπλέκονται στο γενετικό έλεγχο δύο τυπικών πολυγονιδιακών ιδιοτήτων σε κρεοπαραγωγικά ορνίθια. Μία ιδιότητα σχετίζεται με την ανάπτυξη (σωματικό βάρος στις 35 ημέρες, ΣΒ) και η άλλη με την αναπαραγωγική -
A Sequential Methodology for the Rapid Identification and Characterization of Breast Cancer-Associated Functional Snps
ARTICLE https://doi.org/10.1038/s41467-020-17159-8 OPEN A sequential methodology for the rapid identification and characterization of breast cancer-associated functional SNPs Yihan Zhao1,2,DiWu 3,4, Danli Jiang1, Xiaoyu Zhang 1, Ting Wu1,5, Jing Cui6, Min Qian2, Jean Zhao7, ✉ Steffi Oesterreich 8,9, Wei Sun10, Toren Finkel1,10 & Gang Li 1,10 1234567890():,; GWAS cannot identify functional SNPs (fSNP) from disease-associated SNPs in linkage disequilibrium (LD). Here, we report developing three sequential methodologies including Reel-seq (Regulatory element-sequencing) to identify fSNPs in a high-throughput fashion, SDCP-MS (SNP-specific DNA competition pulldown-mass spectrometry) to identify fSNP- bound proteins and AIDP-Wb (allele-imbalanced DNA pulldown-Western blot) to detect allele-specific protein:fSNP binding. We first apply Reel-seq to screen a library containing 4316 breast cancer-associated SNPs and identify 521 candidate fSNPs. As proof of principle, we verify candidate fSNPs on three well-characterized loci: FGFR2, MAP3K1 and BABAM1. Next, using SDCP-MS and AIDP-Wb, we rapidly identify multiple regulatory factors that specifically bind in an allele-imbalanced manner to the fSNPs on the FGFR2 locus. We finally demonstrate that the factors identified by SDCP-MS can regulate risk gene expression. These data suggest that the sequential application of Reel-seq, SDCP-MS, and AIDP-Wb can greatly help to translate large sets of GWAS data into biologically relevant information. 1 Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA. 2 School of Life Sciences, East China Normal University, Shanghai, China. 3 Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. -
Imputed Gene Associations Identify Replicable Trans-Acting Genes Enriched in Transcription Pathways and Complex Traits
bioRxiv preprint doi: https://doi.org/10.1101/471748; this version posted November 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits Heather E. Wheeler1,2,3, , Sally Ploch1, Alvaro N. Barbeira4, Rodrigo Bonazzola4, Alireza Fotuhi Siahpirani5, Ashis Saha6, Alexis Battle6,7, Sushmita Roy8, and Hae Kyung Im4, 1Department of Biology, Loyola University Chicago, Chicago, IL 2Department of Computer Science, Loyola University Chicago, Chicago, IL 3Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 4Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 5Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 6Department of Computer Science, Johns Hopkins University, Baltimore, MD 7Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 8Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI Regulation of gene expression is an important mechanism SNPs associated with gene expression in cis, typically mean- through which genetic variation can affect complex traits. A ing SNPs within 1 Mb of the target gene. Because effect sizes substantial portion of gene expression variation can be ex- are large enough, around 100 samples in the early eQTL stud- plained by both local (cis) and distal (trans) genetic variation. ies could detect replicable associations in the reduced multi- Much progress has been made in uncovering cis-acting expres- ple testing space of cis-eQTLs (1–3). -
VULCAN: Network Analysis of ER-Α Activation Reveals Reprogramming of GRHL2
bioRxiv preprint doi: https://doi.org/10.1101/266908; this version posted March 13, 2018. The copyright holder for this preprint (which was1 not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. VULCAN: Network Analysis of ER-α activation reveals reprogramming of GRHL2 Andrew N. Holding1,3,*, Federico M. Giorgi1,3, Amanda Donnelly1, Amy E. Cullen1, Luke A. Selth2, and Florian Markowetz1 1 CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE 2 Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, SA, Australia 3 These authors contributed equally to this work. *Corresponding Author bioRxiv preprint doi: https://doi.org/10.1101/266908; this version posted March 13, 2018. The copyright holder for this preprint (which was2 not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract VULCAN utilises network analysis of genome-wide DNA binding data to predict regulatory interactions of transcription factors. We benchmarked our approach against alternative methods and found improved performance in all cases. VULCAN analysis of estrogen receptor (ER) activation in breast cancer highlighted key components of the ER signalling axis and identified a novel interaction with GRHL2, validated by ChIP-seq and quantitative proteomics. Mechanistically, we show E2-responsive GRHL2 binding occurs concurrently with increases in eRNA transcription and GRHL2 negatively regulates transcription at these sites. -
Pan-Cancer Molecular Subtypes Revealed by Mass-Spectrometry
ARTICLE https://doi.org/10.1038/s41467-019-13528-0 OPEN Pan-cancer molecular subtypes revealed by mass- spectrometry-based proteomic characterization of more than 500 human cancers Fengju Chen1, Darshan S. Chandrashekar2,3, Sooryanarayana Varambally2,3,4 & Chad J. Creighton 1,5,6,7* Mass-spectrometry-based proteomic profiling of human cancers has the potential for pan- cancer analyses to identify molecular subtypes and associated pathway features that might 1234567890():,; be otherwise missed using transcriptomics. Here, we classify 532 cancers, representing six tissue-based types (breast, colon, ovarian, renal, uterine), into ten proteome-based, pan- cancer subtypes that cut across tumor lineages. The proteome-based subtypes are obser- vable in external cancer proteomic datasets surveyed. Gene signatures of oncogenic or metabolic pathways can further distinguish between the subtypes. Two distinct subtypes both involve the immune system, one associated with the adaptive immune response and T-cell activation, and the other associated with the humoral immune response. Two addi- tional subtypes each involve the tumor stroma, one of these including the collagen VI interacting network. Three additional proteome-based subtypes—respectively involving proteins related to Golgi apparatus, hemoglobin complex, and endoplasmic reticulum—were not reflected in previous transcriptomics analyses. A data portal is available at UALCAN website. 1 Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA. 2 Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA. 3 Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA. 4 The Informatics Institute, University of Alabama at Birmingham, Birmingham, AL 35233, USA. -
Downloaded from the European Genotype Pared to Some Complex Trait GWAS), We Did Not Con- Archive (
Guyatt et al. Human Genomics (2019) 13:6 https://doi.org/10.1186/s40246-018-0190-2 PRIMARY RESEARCH Open Access A genome-wide association study of mitochondrial DNA copy number in two population-based cohorts Anna L. Guyatt1,2, Rebecca R. Brennan3,5, Kimberley Burrows1,2, Philip A. I. Guthrie2, Raimondo Ascione4, Susan M. Ring1,2, Tom R. Gaunt1,2, Angela Pyle3, Heather J. Cordell5, Debbie A. Lawlor1,2, Patrick F. Chinnery6, Gavin Hudson3,5 and Santiago Rodriguez1,2* Abstract Background: Mitochondrial DNA copy number (mtDNA CN) exhibits interindividual and intercellular variation, but few genome-wide association studies (GWAS) of directly assayed mtDNA CN exist. We undertook a GWAS of qPCR-assayed mtDNA CN in the Avon Longitudinal Study of Parents and Children (ALSPAC) and the UK Blood Service (UKBS) cohort. After validating and harmonising data, 5461 ALSPAC mothers (16–43 years at mtDNA CN assay) and 1338 UKBS females (17–69 years) were included in a meta-analysis. Sensitivity analyses restricted to females with white cell-extracted DNA and adjusted for estimated or assayed cell proportions. Associations were also explored in ALSPAC children and UKBS males. Results: A neutrophil-associated locus approached genome-wide significance (rs709591 [MED24], β (change in SD units of mtDNA CN per allele) [SE] − 0.084 [0.016], p=1.54e−07) in the main meta-analysis of adult females. This association was concordant in magnitude and direction in UKBS males and ALSPAC neonates. SNPs in and around ABHD8 were associated with mtDNA CN in ALSPAC neonates (rs10424198, β [SE] 0.262 [0.034], p=1.40e−14), but not other study groups. -
Analysis of Haploinsufficiency in Women Carrying Germline Mutations in the BRCA1 Gene
AUTONOMOUS UNIVERSITY OF MADRID BIOCHEMISTRY DEPARTMENT Analysis of haploinsufficiency in women carrying germline mutations in the BRCA1 gene. Different mutations, different phenotypes? Tereza Vaclová MADRID, 2014 1 Cover design by Jiřina Vaclová Press financed by Human Cancer Genetics Programme (CNIO) 2 BIOCHEMISTRY DEPARTMENT FACULTY OF MEDICINE AUTONOMOUS UNIVERSITY OF MADRID Analysis of haploinsufficiency in women carrying germline mutations in the BRCA1 gene. Different mutations, different phenotypes? Doctoral thesis of M.Sc. in Molecular Biology and Genetics Tereza Vaclová Thesis directors Dr. Javier Benítez Ortiz Dr. Ana Osorio HUMAN GENETICS GROUP HUMAN CANCER GENETICS PROGRAMME SPANISH NATIONAL CANCER RESEARCH CENTRE 3 This thesis, submitted for the degree of Doctor of Philosophy at the Autonomous University of Madrid, has been elaborated in the Human Cancer Genetics laboratory at the Spanish National Cancer Research Center (CNIO), under the supervision of Dr. Ana Osorio and Dr. Javier Benítez Ortiz. This research was supported by following grants and fellowships: - La Caixa/CNIO International PhD Fellowship, 2010-2014: Tereza Vaclová - EMBO Short-Term Travel Fellowship, 2013: Tereza Vaclová - La Caixa/CNIO Short-Term Stay Fellowship, 2013: Tereza Vaclová - Spanish Ministry of Economy and Competitiveness (MINECO; SAF2010-20493) - Spanish Network on Rare Diseases (CIBERER) 9 This thesis is dedicated to my parents for their love, endless support and encouragement ♥ 11 12 ACKNOWLEDGEMENTS 14 This work would not be possible without a huge number of amazing people that I met during this four year roller coaster and it is my pleasure to have a chance to acknowledge them here. First of all, I would like to thank to my supervisors Javier and Ana, who modulated my scientific career the most and guided me throughout those four years. -
UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Dissecting Enhancer Functions in Signal Induced Transcription Programs Permalink https://escholarship.org/uc/item/0n31q74b Author Hu, Yiren Publication Date 2018 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Dissecting Enhancer Functions in Signal Induced Transcription Programs A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biology by Yiren Hu Committee in charge: Professor Michael Geoff Rosenfeld, Chair Professor Christopher K. Glass Professor Cornelis Murre Professor Amy Pasquinelli Professor Samuel Pfaff 2018 The Dissertation of Yiren Hu is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2018 iii Table of Contents Signature Page .................................................................................................................. iii Table of Contents ............................................................................................................... iv Acknowledgements .......................................................................................................... viii Vita .......................................................................................................................................x Publications ..........................................................................................................................x