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Lee IH, Negron JA, Hernandez-Ferrer C, Alvarez WJ, Mandl KD, Kong SW. The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Hum Mutat 2020; 41:387-396. [PMID: 31691385 PMCID: PMC7180092 DOI: 10.1002/humu.23942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 11/08/2022]
Abstract
Genome sequencing is positioned as a routine clinical work-up for diverse clinical conditions. A commonly used approach to highlight candidate variants with potential clinical implication is to search over locus- and gene-centric knowledge databases. Most web-based applications allow a federated query across diverse databases for a single variant; however, sifting through a large number of genomic variants with combination of filtering criteria is a substantial challenge. Here we describe the Clinical Genome and Ancestry Report (CGAR), an interactive web application developed to follow clinical interpretation workflows by organizing variants into seven categories: (1) reported disease-associated variants, (2) rare- and high-impact variants in putative disease-associated genes, (3) secondary findings that the American College of Medical Genetics and Genomics recommends reporting back to patients, (4) actionable pharmacogenomic variants, (5) focused reports for candidate genes, (6) de novo variant candidates for trio analysis, and (7) germline and somatic variants implicated in cancer risk, diagnosis, treatment and prognosis. For each variant, a comprehensive list of external links to variant-centric and phenotype databases are provided. Furthermore, genotype-derived ancestral composition is used to highlight allele frequencies from a matched population since some disease-associated variants show a wide variation between populations. CGAR is an open-source software and is available at https://tom.tch.harvard.edu/apps/cgar/.
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Affiliation(s)
- In-Hee Lee
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115
| | - Jose A. Negron
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115
| | | | | | - Kenneth D. Mandl
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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152
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Wang J, Gaughan S, Lamer JT, Deng C, Hu W, Wachholtz M, Qin S, Nie H, Liao X, Ling Q, Li W, Zhu L, Bernatchez L, Wang C, Lu G. Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin. Evol Appl 2020; 13:263-277. [PMID: 31993075 PMCID: PMC6976960 DOI: 10.1111/eva.12863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/07/2019] [Accepted: 07/15/2019] [Indexed: 12/23/2022] Open
Abstract
The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate-to-high heterozygosity in bighead (0.0021) and silver (0.0036) carps, detected significantly higher dN/dS ratios of single-copy orthologous genes in bigheaded carps versus 10 other species of fish, and identified genes in both species potentially associated with environmental adaptation and other invasion-related traits. Additionally, we observed a high genomic similarity (96.3% in all syntenic blocks) between bighead and silver carps and over 90% embryonic viability in their experimentally induced hybrids. Our results suggest intrinsic genomic features of bigheaded carps, likely associated with life history traits that presumably evolved within their native ranges, might have facilitated their initial establishment of invasion, whereas ex-situ interspecific hybridization between the carps might have promoted their range expansion. This study reveals an alternative mechanism that could resolve one of the genetic paradoxes in biological invasions and provides invaluable genomic resources for applied research involving bigheaded carps.
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Affiliation(s)
- Jun Wang
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of AgricultureNational Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Sarah Gaughan
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
| | - James T. Lamer
- Department of Biological SciencesWestern Illinois UniversityMacombILUSA
| | - Cao Deng
- DNA Stories Bioinformatics CenterChengduChina
| | - Wanting Hu
- College of Life of SciencesNanjing Normal UniversityNanjingChina
| | | | | | - Hu Nie
- DNA Stories Bioinformatics CenterChengduChina
| | - Xiaolin Liao
- Institute of HydroecologyMinistry of Water Resources & Chinese Academy of SciencesWuhanChina
| | - Qufei Ling
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
- Aquaculture InstituteSchool of Biology and Basic Medical SciencesSoochow UniversitySuzhouChina
| | - Weitao Li
- Institute of HydroecologyMinistry of Water Resources & Chinese Academy of SciencesWuhanChina
| | - Lifeng Zhu
- College of Life of SciencesNanjing Normal UniversityNanjingChina
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes)Université LavalQuébecQCCanada
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of AgricultureNational Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Guoqing Lu
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
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153
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Pal LR, Kundu K, Yin Y, Moult J. Matching whole genomes to rare genetic disorders: Identification of potential causative variants using phenotype-weighted knowledge in the CAGI SickKids5 clinical genomes challenge. Hum Mutat 2020; 41:347-362. [PMID: 31680375 PMCID: PMC7182498 DOI: 10.1002/humu.23933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/26/2019] [Accepted: 10/13/2019] [Indexed: 02/06/2023]
Abstract
Precise identification of causative variants from whole-genome sequencing data, including both coding and noncoding variants, is challenging. The Critical Assessment of Genome Interpretation 5 SickKids clinical genome challenge provided an opportunity to assess our ability to extract such information. Participants in the challenge were required to match each of the 24 whole-genome sequences to the correct phenotypic profile and to identify the disease class of each genome. These are all rare disease cases that have resisted genetic diagnosis in a state-of-the-art pipeline. The patients have a range of eye, neurological, and connective-tissue disorders. We used a gene-centric approach to address this problem, assigning each gene a multiphenotype-matching score. Mutations in the top-scoring genes for each phenotype profile were ranked on a 6-point scale of pathogenicity probability, resulting in an approximately equal number of top-ranked coding and noncoding candidate variants overall. We were able to assign the correct disease class for 12 cases and the correct genome to a clinical profile for five cases. The challenge assessor found genes in three of these five cases as likely appropriate. In the postsubmission phase, after careful screening of the genes in the correct genome, we identified additional potential diagnostic variants, a high proportion of which are noncoding.
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Affiliation(s)
- Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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154
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Lavender CA, Shapiro AJ, Day FS, Fargo DC. ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets. PLoS Comput Biol 2020; 16:e1007571. [PMID: 31978042 PMCID: PMC7001987 DOI: 10.1371/journal.pcbi.1007571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/05/2020] [Accepted: 11/29/2019] [Indexed: 11/17/2022] Open
Abstract
High-throughput sequencing has become ubiquitous in biomedical sciences. As new technologies emerge and sequencing costs decline, the diversity and volume of available data increases exponentially, and successfully navigating the data becomes more challenging. Though datasets are often hosted by public repositories, scientists must rely on inconsistent annotation to identify and interpret meaningful data. Moreover, the experimental heterogeneity and wide-ranging quality of high-throughput biological data means that even data with desired cell lines, tissue types, or molecular targets may not be readily interpretable or integrated. We have developed ORSO (Online Resource for Social Omics) as an easy-to-use web application to connect life scientists with genomics data. In ORSO, users interact within a data-driven social network, where they can favorite datasets and follow other users. In addition to more than 30,000 datasets hosted from major biomedical consortia, users may contribute their own data to ORSO, facilitating its discovery by other users. Leveraging user interactions, ORSO provides a novel recommendation system to automatically connect users with hosted data. In addition to social interactions, the recommendation system considers primary read coverage information and annotated metadata. Similarities used by the recommendation system are presented by ORSO in a graph display, allowing exploration of dataset associations. The topology of the network graph reflects established biology, with samples from related systems grouped together. We tested the recommendation system using an RNA-seq time course dataset from differentiation of embryonic stem cells to cardiomyocytes. The ORSO recommendation system correctly predicted early data point sources as embryonic stem cells and late data point sources as heart and muscle samples, resulting in recommendation of related datasets. By connecting scientists with relevant data, ORSO provides a critical new service that facilitates wide-ranging research interests. New sequencing technologies have rapidly transformed biomedical research. Public data repositories now contain millions of datasets, which have the potential to accelerate and bolster research projects. However, the sheer magnitude of available data makes navigation difficult. We created ORSO (Online Resource for Social Omics) to address these challenges. ORSO is a social network where entries are not status updates or tweets, but biological datasets. Users may add their own data to ORSO, joining 30,000 validated datasets that are already hosted, and other users may find these data through intuitive search functions and informative analytics. Users can then favorite datasets relevant to their interests or follow contributing users. ORSO also uses a recommendation system like those used on commercial websites to automatically recommend data to users based on user interactions and dataset similarities. By making data more accessible and by connecting users to relevant data, we anticipate that ORSO will be an important resource for scientists. ORSO may be the first of many applications that use methods originating in social media and ecommerce to enhance and further research projects in the life sciences.
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Affiliation(s)
- Christopher A Lavender
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Andrew J Shapiro
- Program Operations Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Frank S Day
- Office of Scientific Computing, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - David C Fargo
- Office of Scientific Computing, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
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155
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Fachal L, Aschard H, Beesley J, Barnes DR, Allen J, Kar S, Pooley KA, Dennis J, Michailidou K, Turman C, Soucy P, Lemaçon A, Lush M, Tyrer JP, Ghoussaini M, Moradi Marjaneh M, Jiang X, Agata S, Aittomäki K, Alonso MR, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V, Aronson KJ, Arun BK, Auber B, Auer PL, Azzollini J, Balmaña J, Barkardottir RB, Barrowdale D, Beeghly-Fadiel A, Benitez J, Bermisheva M, Białkowska K, Blanco AM, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borg A, Bosse K, Brauch H, Brenner H, Briceno I, Brock IW, Brooks-Wilson A, Brüning T, Burwinkel B, Buys SS, Cai Q, Caldés T, Caligo MA, Camp NJ, Campbell I, Canzian F, Carroll JS, Carter BD, Castelao JE, Chiquette J, Christiansen H, Chung WK, Claes KBM, Clarke CL, Collée JM, Cornelissen S, Couch FJ, Cox A, Cross SS, Cybulski C, Czene K, Daly MB, de la Hoya M, Devilee P, Diez O, Ding YC, Dite GS, Domchek SM, Dörk T, Dos-Santos-Silva I, Droit A, Dubois S, Dumont M, Duran M, Durcan L, Dwek M, Eccles DM, Engel C, Eriksson M, Evans DG, Fasching PA, Fletcher O, Floris G, Flyger H, Foretova L, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gago-Dominguez M, Gambino G, Ganz PA, Gapstur SM, Garber J, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Tibiletti MG, Greene MH, Grip M, Gronwald J, Grundy A, Guénel P, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Harrington PA, Hartikainen JM, Hartman M, He W, Healey CS, Heemskerk-Gerritsen BAM, Heyworth J, Hillemanns P, Hogervorst FBL, Hollestelle A, Hooning MJ, Hopper JL, Howell A, Huang G, Hulick PJ, Imyanitov EN, Isaacs C, Iwasaki M, Jager A, Jakimovska M, Jakubowska A, James PA, Janavicius R, Jankowitz RC, John EM, Johnson N, Jones ME, Jukkola-Vuorinen A, Jung A, Kaaks R, Kang D, Kapoor PM, Karlan BY, Keeman R, Kerin MJ, Khusnutdinova E, Kiiski JI, Kirk J, Kitahara CM, Ko YD, Konstantopoulou I, Kosma VM, Koutros S, Kubelka-Sabit K, Kwong A, Kyriacou K, Laitman Y, Lambrechts D, Lee E, Leslie G, Lester J, Lesueur F, Lindblom A, Lo WY, Long J, Lophatananon A, Loud JT, Lubiński J, MacInnis RJ, Maishman T, Makalic E, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Matsuo K, Maurer T, Mavroudis D, Mayes R, McGuffog L, McLean C, Mebirouk N, Meindl A, Miller A, Miller N, Montagna M, Moreno F, Muir K, Mulligan AM, Muñoz-Garzon VM, Muranen TA, Narod SA, Nassir R, Nathanson KL, Neuhausen SL, Nevanlinna H, Neven P, Nielsen FC, Nikitina-Zake L, Norman A, Offit K, Olah E, Olopade OI, Olsson H, Orr N, Osorio A, Pankratz VS, Papp J, Park SK, Park-Simon TW, Parsons MT, Paul J, Pedersen IS, Peissel B, Peshkin B, Peterlongo P, Peto J, Plaseska-Karanfilska D, Prajzendanc K, Prentice R, Presneau N, Prokofyeva D, Pujana MA, Pylkäs K, Radice P, Ramus SJ, Rantala J, Rau-Murthy R, Rennert G, Risch HA, Robson M, Romero A, Rossing M, Saloustros E, Sánchez-Herrero E, Sandler DP, Santamariña M, Saunders C, Sawyer EJ, Scheuner MT, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schöttker B, Schürmann P, Scott C, Scott RJ, Senter L, Seynaeve CM, Shah M, Sharma P, Shen CY, Shu XO, Singer CF, Slavin TP, Smichkoska S, Southey MC, Spinelli JJ, Spurdle AB, Stone J, Stoppa-Lyonnet D, Sutter C, Swerdlow AJ, Tamimi RM, Tan YY, Tapper WJ, Taylor JA, Teixeira MR, Tengström M, Teo SH, Terry MB, Teulé A, Thomassen M, Thull DL, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Torres D, Torres-Mejía G, Troester MA, Truong T, Tung N, Tzardi M, Ulmer HU, Vachon CM, van Asperen CJ, van der Kolk LE, van Rensburg EJ, Vega A, Viel A, Vijai J, Vogel MJ, Wang Q, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wildiers H, Winqvist R, Wolk A, Wu AH, Yannoukakos D, Zhang Y, Zheng W, Hunter D, Pharoah PDP, Chang-Claude J, García-Closas M, Schmidt MK, Milne RL, Kristensen VN, French JD, Edwards SL, Antoniou AC, Chenevix-Trench G, Simard J, Easton DF, Kraft P, Dunning AM. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. Nat Genet 2020; 52:56-73. [PMID: 31911677 PMCID: PMC6974400 DOI: 10.1038/s41588-019-0537-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/24/2019] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes.
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Affiliation(s)
- Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hugues Aschard
- Centre de Bioinformatique Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Karen A Pooley
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology and The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Audrey Lemaçon
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mahdi Moradi Marjaneh
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- UK Dementia Research Institute, Imperial College London, London, UK
| | - Xia Jiang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology (IOV), IRCCS, Padua, Italy
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - M Rosario Alonso
- Human Genotyping-CEGEN Unit, Human Cancer Genetic Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, CA, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences and Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Banu K Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bernd Auber
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Paul L Auer
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Vall Hebron University Hospital, Barcelona, Spain
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Javier Benitez
- Centro de Investigación en Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Amie M Blanco
- Cancer Genetics and Prevention Program, University of California, San Francisco, San Francisco, CA, USA
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, Örebro University Hospital, Örebro, Sweden
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Kristin Bosse
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT Cluster of Excellence, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ignacio Briceno
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
- Medical Faculty, Universidad de La Sabana, Bogota, Colombia
| | - Ian W Brock
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Angela Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Trinidad Caldés
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Maria A Caligo
- SOD Genetica Molecolare, University Hospital, Pisa, Italy
| | - Nicola J Camp
- Department of Internal Medicine, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Ian Campbell
- Research Department, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Brian D Carter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Jocelyne Chiquette
- Axe Oncologie, Centre de Recherche, Centre Hospitalier Universitaire de Québec, Université Laval, Québec, Québec, Canada
| | - Hans Christiansen
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | | | - Christine L Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sten Cornelissen
- Division of Molecular Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Clinical and Molecular Genetics Area, Vall Hebron University Hospital, Barcelona, Spain
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Arnaud Droit
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, Centre de Recherche, Centre Hospitalier Universitaire de Québec, Laval University, Québec City, Québec, Canada
| | - Stéphane Dubois
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Martine Dumont
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Mercedes Duran
- Cáncer Hereditario, Instituto de Biología y Genética Molecular (IBGM), Universidad de Valladolid Centro Superior de Investigaciones Científicas (UVA-CSIC), Valladolid, Spain
| | - Lorraine Durcan
- Southampton Clinical Trials Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, UK
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter A Fasching
- David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Olivia Fletcher
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Giuseppe Floris
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - William D Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, Québec, Canada
| | - Eitan Friedman
- The Suzanne Levy-Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Lin Fritschi
- School of Public Health, Curtin University, Perth, Western Australia, Australia
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Patricia A Ganz
- Schools of Medicine and Public Health, Division of Cancer Prevention and Control Research, Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA, USA
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | | | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS, USA
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montréal, Québec, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montréal, Québec, Canada
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anne Grundy
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal, Montréal, Québec, Canada
| | - Pascal Guénel
- Cancer and Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Paris, France
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patricia A Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jaana M Hartikainen
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Surgery, National University Health System, Singapore, Singapore
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Catherine S Healey
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Jane Heyworth
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Peter Hillemanns
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Frans B L Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Guanmengqian Huang
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Agnes Jager
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Milena Jakimovska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Macedonian Academy of Sciences and Arts, Skopje, Republic of North Macedonia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
| | - Ramunas Janavicius
- Hematology, Oncology and Transfusion Medicine Center, Department of Molecular and Regenerative Medicine, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Rachel C Jankowitz
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Esther M John
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nichola Johnson
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Arja Jukkola-Vuorinen
- Department of Oncology, Tampere University Hospital, Tampere University and Tampere Cancer Center, Tampere, Finland
| | - Audrey Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daehee Kang
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Pooja Middha Kapoor
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Renske Keeman
- Division of Molecular Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Michael J Kerin
- Surgery, School of Medicine, National University of Ireland, Galway, Ireland
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia
| | - Johanna I Kiiski
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Judy Kirk
- Familial Cancer Service, Weatmead Hospital, Sydney, New South Wales, Australia
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn, Johanniter Krankenhaus, Bonn, Germany
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Veli-Matti Kosma
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katerina Kubelka-Sabit
- Department of Histopathology and Cytology, Clinical Hospital 'Acibadem Sistina', Skopje, Republic of North Macedonia
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Centre, Happy Valley, Hong Kong
- Department of Surgery, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Department of Surgery, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Pathology and The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Yael Laitman
- The Suzanne Levy-Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Institut Curie, Paris, France
- Mines ParisTech, Paris, France
- Genetic Epidemiology of Cancer Team, INSERM U900, Paris, France
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Jennifer T Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Tom Maishman
- Southampton Clinical Trials Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Maria Elena Martinez
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tabea Maurer
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Rebecca Mayes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Noura Mebirouk
- Institut Curie, Paris, France
- Mines ParisTech, Paris, France
- Department of Tumour Biology, INSERM U830, Paris, France
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, University of Munich, Munich, Germany
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Nicola Miller
- Surgery, School of Medicine, National University of Ireland, Galway, Ireland
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology (IOV), IRCCS, Padua, Italy
| | - Fernando Moreno
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | | | - Taru A Muranen
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Steven A Narod
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura University, Holy Makkah, Saudi Arabia
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Patrick Neven
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Finn C Nielsen
- Center for Genomic Medicine at Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Aaron Norman
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Kenneth Offit
- Clinical Genetics Research Laboratory, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Nick Orr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Ana Osorio
- Centro de Investigación en Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - V Shane Pankratz
- University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Janos Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | | | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - James Paul
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Beth Peshkin
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM-the FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Macedonian Academy of Sciences and Arts, Skopje, Republic of North Macedonia
| | - Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Ross Prentice
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nadege Presneau
- School of Life Sciences, University of Westminster, London, UK
| | - Darya Prokofyeva
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia
| | - Miquel Angel Pujana
- ProCURE, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan J Ramus
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Rohini Rau-Murthy
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gad Rennert
- Clalit National Israeli Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Harvey A Risch
- Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Maria Rossing
- Center for Genomic Medicine at Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Marta Santamariña
- Centro de Investigación en Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Christobel Saunders
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Maren T Scheuner
- Cancer Genetics and Prevention Program, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Schneeweiss
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Peter Schürmann
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Rodney J Scott
- Division of Molecular Medicine, Pathology North, John Hunter Hospital, Newcastle, New South Wales, Australia
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Leigha Senter
- Clinical Cancer Genetics Program, Division of Human Genetics, Department of Internal Medicine, The Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Caroline M Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, USA
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- School of Public Health, China Medical University, Taichung, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christian F Singer
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | | | - Snezhana Smichkoska
- University Clinic of Radiotherapy and Oncology, Medical Faculty, Ss. Cyril and Methodius University in Skopje, Skopje, Republic of North Macedonia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, Western Australia, Australia
| | - Dominique Stoppa-Lyonnet
- Department of Tumour Biology, INSERM U830, Paris, France
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rulla M Tamimi
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yen Yen Tan
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | | | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Maria Tengström
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, Kuopio, Finland
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Kuala Lumpur, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Alex Teulé
- Hereditary Cancer Program, ONCOBELL-IDIBELL-IDIBGI-IGTP, Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odence, Denmark
| | - Darcy L Thull
- Department of Medicine, Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, Québec, Canada
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Wellcome Trust Centre for Human Genetics and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Diana Torres
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriela Torres-Mejía
- Center for Population Health Research, National Institute of Public Health, Cuernavaca, Mexico
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Cancer and Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Paris, France
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Maria Tzardi
- Department of Pathology, University Hospital of Heraklion, Heraklion, Greece
| | | | - Celine M Vachon
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lizet E van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Alessandra Viel
- Division of Functional Onco-genomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Joseph Vijai
- Clinical Genetics Research Laboratory, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maartje J Vogel
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, USA
| | | | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Hans Wildiers
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON) Coordinating Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Australian Breast Cancer Tissue Bank, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Juliet D French
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stacey L Edwards
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec, Université Laval Research Center, Québec City, Québec, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.
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Timp W, Timp G. Beyond mass spectrometry, the next step in proteomics. SCIENCE ADVANCES 2020; 6:eaax8978. [PMID: 31950079 PMCID: PMC6954058 DOI: 10.1126/sciadv.aax8978] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
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Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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157
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Ke J, Peng X, Mei S, Tian J, Ying P, Yang N, Wang X, Zou D, Yang Y, Zhu Y, Gong Y, Gong J, Zhong R, Chang J, Fang Z, Miao X. Evaluation of polymorphisms in microRNA-binding sites and pancreatic cancer risk in Chinese population. J Cell Mol Med 2019; 24:2252-2259. [PMID: 31880394 PMCID: PMC7011162 DOI: 10.1111/jcmm.14906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/12/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
As promising biomarkers and therapy targets, microRNAs (miRNAs) are involved in various physiological and tumorigenic processes. Genetic variants in miRNA‐binding sites can lead to dysfunction of miRNAs and contribute to disease. However, systematic investigation of the miRNA‐related single nucleotide polymorphisms (SNPs) for pancreatic cancer (PC) risk remains elusive. We performed integrative bioinformatics analyses to select 31 SNPs located in miRNA‐target binding sites using the miRNASNP v2.0, a solid database providing miRNA‐related SNPs for genetic research, and investigated their associations with risk of PC in two large case‐control studies totally including 1847 cases and 5713 controls. We observed that the SNP rs3802266 is significantly associated with increased risk of PC (odds ratio (OR) = 1.21, 95% confidence intervals (CI) = 1.11‐1.31, P = 1.29E‐05). Following luciferase reporter gene assays show that rs3802266‐G creates a stronger binding site for miR‐181a‐2‐3p in 3′ untranslated region (3′UTR) of the gene ZHX2. Expression quantitative trait loci (eQTL) analysis suggests that ZHX2 expression is lower in individuals carrying rs3802266‐G with increased PC risk. In conclusion, our findings highlight the involvement of miRNA‐binding SNPs in PC susceptibility and provide new clues for PC carcinogenesis.
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Affiliation(s)
- Juntao Ke
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shufang Mei
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pingting Ying
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyang Wang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Rong Zhong
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zemin Fang
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Miao
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment & Health (Ministry of Education), Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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158
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Eigenbrod O, Debus KY, Reznick J, Bennett NC, Sánchez-Carranza O, Omerbašić D, Hart DW, Barker AJ, Zhong W, Lutermann H, Katandukila JV, Mgode G, Park TJ, Lewin GR. Rapid molecular evolution of pain insensitivity in multiple African rodents. Science 2019; 364:852-859. [PMID: 31147513 DOI: 10.1126/science.aau0236] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 04/25/2019] [Indexed: 12/19/2022]
Abstract
Noxious substances, called algogens, cause pain and are used as defensive weapons by plants and stinging insects. We identified four previously unknown instances of algogen-insensitivity by screening eight African rodent species related to the naked mole-rat with the painful substances capsaicin, acid (hydrogen chloride, pH 3.5), and allyl isothiocyanate (AITC). Using RNA sequencing, we traced the emergence of sequence variants in transduction channels, like transient receptor potential channel TRPA1 and voltage-gated sodium channel Nav1.7, that accompany algogen insensitivity. In addition, the AITC-insensitive highveld mole-rat exhibited overexpression of the leak channel NALCN (sodium leak channel, nonselective), ablating AITC detection by nociceptors. These molecular changes likely rendered highveld mole-rats immune to the stings of the Natal droptail ant. Our study reveals how evolution can be used as a discovery tool to find molecular mechanisms that shut down pain.
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Affiliation(s)
- Ole Eigenbrod
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Karlien Y Debus
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jane Reznick
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa
| | - Oscar Sánchez-Carranza
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Damir Omerbašić
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Daniel W Hart
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa
| | - Alison J Barker
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Wei Zhong
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Heike Lutermann
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa
| | - Jestina V Katandukila
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa.,University of Dar es Salaam, College of Natural and Applied Sciences, Department of Zoology and Wildlife Conservation, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Georgies Mgode
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Thomas J Park
- Laboratory of Integrative Neuroscience, Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Gary R Lewin
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany. .,NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
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159
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Luo J, Zhou T, You X, Zi Y, Li X, Wu Y, Lan Z, Zhi Q, Yi D, Xu L, Li A, Zhong Z, Zhu M, Sun G, Zhu T, Rao J, Lin L, Sang J, Shi Y. Assessing concordance among human, in silico predictions and functional assays on genetic variant classification. Bioinformatics 2019; 35:5163-5170. [PMID: 31141141 DOI: 10.1093/bioinformatics/btz442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/14/2019] [Accepted: 05/23/2019] [Indexed: 01/25/2023] Open
Abstract
MOTIVATION A variety of in silico tools have been developed and frequently used to aid high-throughput rapid variant classification, but their performances vary, and their ability to classify variants of uncertain significance were not systemically assessed previously due to lack of validation data. This has been changed recently by advances of functional assays, where functional impact of genetic changes can be measured in single-nucleotide resolution using saturation genome editing (SGE) assay. RESULTS We demonstrated the neural network model AIVAR (Artificial Intelligent VARiant classifier) was highly comparable to human experts on multiple verified datasets. Although highly accurate on known variants, AIVAR together with CADD and PhyloP showed non-significant concordance with SGE function scores. Moreover, our results indicated that neural network model trained from functional assay data may not produce accurate prediction on known variants. AVAILABILITY AND IMPLEMENTATION All source code of AIVAR is deposited and freely available at https://github.com/TopGene/AIvar. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiaqi Luo
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Tianliangwen Zhou
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Xiaobin You
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Yi Zi
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Xiaoting Li
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Yangming Wu
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Zhaoji Lan
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Qihuan Zhi
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Dandan Yi
- Department of General Surgery, Nanjing Drum Tower Hospital, Nanjing, Jiangsu, China
| | - Lei Xu
- Department of General Surgery, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ang Li
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Zaixuan Zhong
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Mei Zhu
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Gang Sun
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Tao Zhu
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Jianmei Rao
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Luhua Lin
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Jianfeng Sang
- Department of General Surgery, Nanjing Drum Tower Hospital, Nanjing, Jiangsu, China
| | - Yujian Shi
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
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160
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The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome. Cell Rep 2019; 24:1190-1202.e5. [PMID: 30067975 DOI: 10.1016/j.celrep.2018.06.109] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/25/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022] Open
Abstract
The skin functions as the primary interface between the human body and the external environment. To understand how the microbiome varies within urban mass transit and influences the skin microbiota, we profiled the human palm microbiome after contact with handrails within the Hong Kong Mass Transit Railway (MTR) system. Intraday sampling time was identified as the primary determinant of the variation and recurrence of the community composition, whereas human-associated species and clinically important antibiotic resistance genes (ARGs) were captured as p.m. signatures. Line-specific signatures were notably correlated with line-specific environmental exposures and city characteristics. The sole cross-border line appeared as an outlier in most analyses and showed high relative abundance and a significant intraday increment of clinically important ARGs (24.1%), suggesting potential cross-border ARG transmission, especially for tetracycline and vancomycin resistance. Our study provides an important reference for future public health strategies to mitigate intracity and cross-border pathogen and ARG transmission.
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161
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Miller JB, McKinnon LM, Whiting MF, Ridge PG. Codon use and aversion is largely phylogenetically conserved across the tree of life. Mol Phylogenet Evol 2019; 144:106697. [PMID: 31805345 DOI: 10.1016/j.ympev.2019.106697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 04/10/2019] [Accepted: 11/29/2019] [Indexed: 01/11/2023]
Abstract
Using parsimony, we analyzed codon usages across 12,337 species and 25,727 orthologous genes to rank specific genes and codons according to their phylogenetic signal. We examined each codon within each ortholog to determine the codon usage for each species. In total, 890,814 codons were parsimony informative. Next, we compared species that used a codon with species that did not use the codon. We assessed each codon's congruence with species relationships provided in the Open Tree of Life (OTL) and determined the statistical probability of observing these results by random chance. We determined that 25,771 codons had no parallelisms or reversals when mapped to the OTL. Codon usages from orthologous genes spanning many species were 1109× more likely to be congruent with species relationships in the OTL than would be expected by random chance. Using the OTL as a reference, we show that codon usage is phylogenetically conserved within orthologous genes in archaea, bacteria, plants, mammals, and other vertebrates. We also show how to use our provided framework to test different tree hypotheses by confirming the placement of turtles as sister taxa to archosaurs.
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Affiliation(s)
- Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Lauren M McKinnon
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; M.L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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162
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Jiang S, Cheng SJ, Ren LC, Wang Q, Kang YJ, Ding Y, Hou M, Yang XX, Lin Y, Liang N, Gao G. An expanded landscape of human long noncoding RNA. Nucleic Acids Res 2019; 47:7842-7856. [PMID: 31350901 PMCID: PMC6735957 DOI: 10.1093/nar/gkz621] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/18/2019] [Accepted: 07/11/2019] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as key regulators of multiple essential biological processes involved in physiology and pathology. By analyzing the largest compendium of 14,166 samples from normal and tumor tissues, we significantly expand the landscape of human long noncoding RNA with a high-quality atlas: RefLnc (Reference catalog of LncRNA). Powered by comprehensive annotation across multiple sources, RefLnc helps to pinpoint 275 novel intergenic lncRNAs correlated with sex, age or race as well as 369 novel ones associated with patient survival, clinical stage, tumor metastasis or recurrence. Integrated in a user-friendly online portal, the expanded catalog of human lncRNAs provides a valuable resource for investigating lncRNA function in both human biology and cancer development.
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Affiliation(s)
- Shuai Jiang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Si-Jin Cheng
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Chen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Qian Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Yu-Jian Kang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Yang Ding
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Mei Hou
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiao-Xu Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuan Lin
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Nan Liang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
| | - Ge Gao
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing 100871, China
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163
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Wilczynska A, Gillen SL, Schmidt T, Meijer HA, Jukes-Jones R, Langlais C, Kopra K, Lu WT, Godfrey JD, Hawley BR, Hodge K, Zanivan S, Cain K, Le Quesne J, Bushell M. eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5'UTR. Genome Biol 2019; 20:262. [PMID: 31791371 PMCID: PMC6886185 DOI: 10.1186/s13059-019-1857-2] [Citation(s) in RCA: 31] [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: 07/16/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Regulation of the mRNA life cycle is central to gene expression control and determination of cell fate. miRNAs represent a critical mRNA regulatory mechanism, but despite decades of research, their mode of action is still not fully understood. RESULTS Here, we show that eIF4A2 is a major effector of the repressive miRNA pathway functioning via the Ccr4-Not complex. We demonstrate that while DDX6 interacts with Ccr4-Not, its effects in the mechanism are not as pronounced. Through its interaction with the Ccr4-Not complex, eIF4A2 represses mRNAs at translation initiation. We show evidence that native eIF4A2 has similar RNA selectivity to chemically inhibited eIF4A1. eIF4A2 exerts its repressive effect by binding purine-rich motifs which are enriched in the 5'UTR of target mRNAs directly upstream of the AUG start codon. CONCLUSIONS Our data support a model whereby purine motifs towards the 3' end of the 5'UTR are associated with increased ribosome occupancy and possible uORF activation upon eIF4A2 binding.
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Affiliation(s)
- Ania Wilczynska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Sarah L Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Tobias Schmidt
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Hedda A Meijer
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
- Present Address: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | | | | | - Kari Kopra
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
- Present Address: Department of Chemistry, University of Turku, Vatselankatu 2, FI-20500, Turku, Finland
| | - Wei-Ting Lu
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Jack D Godfrey
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | | | - Kelly Hodge
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kelvin Cain
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - John Le Quesne
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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164
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Chen L, Pan X, Zeng T, Zhang YH, Zhang Y, Huang T, Cai YD. Immunosignature Screening for Multiple Cancer Subtypes Based on Expression Rule. Front Bioeng Biotechnol 2019; 7:370. [PMID: 31850330 PMCID: PMC6901955 DOI: 10.3389/fbioe.2019.00370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy (i.e., fluid biopsy) involves a series of clinical examination approaches. Monitoring of cancer immunological status by the “immunosignature” of patients presents a novel method for tumor-associated liquid biopsy. The major work content and the core technological difficulties for the monitoring of cancer immunosignature are the recognition of cancer-related immune-activating antigens by high-throughput screening approaches. Currently, one key task of immunosignature-based liquid biopsy is the qualitative and quantitative identification of typical tumor-specific antigens. In this study, we reused two sets of peptide microarray data that detected the expression level of potential antigenic peptides derived from tumor tissues to avoid the detection differences induced by chip platforms. Several machine learning algorithms were applied on these two sets. First, the Monte Carlo Feature Selection (MCFS) method was used to analyze features in two sets. A feature list was obtained according to the MCFS results on each set. Second, incremental feature selection method incorporating one classification algorithm (support vector machine or random forest) followed to extract optimal features and construct optimal classifiers. On the other hand, the repeated incremental pruning to produce error reduction, a rule learning algorithm, was applied on key features yielded by the MCFS method to extract quantitative rules for accurate cancer immune monitoring and pathologic diagnosis. Finally, obtained key features and quantitative rules were extensively analyzed.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, China.,College of Information Engineering, Shanghai Maritime University, Shanghai, China.,Shanghai Key Laboratory of Pure Mathematics and Mathematical Practice (PMMP), East China Normal University, Shanghai, China
| | - XiaoYong Pan
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China.,IDLab, Department for Electronics and Information Systems, Ghent University, Ghent, Belgium
| | - Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - YunHua Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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165
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An Overview of the Intrinsic Role of Citrullination in Autoimmune Disorders. J Immunol Res 2019; 2019:7592851. [PMID: 31886309 PMCID: PMC6899306 DOI: 10.1155/2019/7592851] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/03/2019] [Accepted: 09/28/2019] [Indexed: 02/07/2023] Open
Abstract
A protein undergoes many types of posttranslation modification. Citrullination is one of these modifications, where an arginine amino acid is converted to a citrulline amino acid. This process depends on catalytic enzymes such as peptidylarginine deiminase enzymes (PADs). This modification leads to a charge shift, which affects the protein structure, protein-protein interactions, and hydrogen bond formation, and it may cause protein denaturation. The irreversible citrullination reaction is not limited to a specific protein, cell, or tissue. It can target a wide range of proteins in the cell membrane, cytoplasm, nucleus, and mitochondria. Citrullination is a normal reaction during cell death. Apoptosis is normally accompanied with a clearance process via scavenger cells. A defect in the clearance system either in terms of efficiency or capacity may occur due to massive cell death, which may result in the accumulation and leakage of PAD enzymes and the citrullinated peptide from the necrotized cell which could be recognized by the immune system, where the immunological tolerance will be avoided and the autoimmune disorders will be subsequently triggered. The induction of autoimmune responses, autoantibody production, and cytokines involved in the major autoimmune diseases will be discussed.
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166
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Byrne A, Cole C, Volden R, Vollmers C. Realizing the potential of full-length transcriptome sequencing. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190097. [PMID: 31587638 PMCID: PMC6792442 DOI: 10.1098/rstb.2019.0097] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
Long-read sequencing holds great potential for transcriptome analysis because it offers researchers an affordable method to annotate the transcriptomes of non-model organisms. This, in turn, will greatly benefit future work on less-researched organisms like unicellular eukaryotes that cannot rely on large consortia to generate these transcriptome annotations. However, to realize this potential, several remaining molecular and computational challenges will have to be overcome. In this review, we have outlined the limitations of short-read sequencing technology and how long-read sequencing technology overcomes these limitations. We have also highlighted the unique challenges still present for long-read sequencing technology and provided some suggestions on how to overcome these challenges going forward. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Ashley Byrne
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Charles Cole
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Roger Volden
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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167
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Chen G, Chen J, Liu H, Chen S, Zhang Y, Li P, Thierry-Mieg D, Thierry-Mieg J, Mattes W, Ning B, Shi T. Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. Front Cell Dev Biol 2019; 7:299. [PMID: 31824949 PMCID: PMC6881247 DOI: 10.3389/fcell.2019.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients’ survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.
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Affiliation(s)
- Geng Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwei Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Huanlong Liu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuangguan Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peng Li
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - William Mattes
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
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168
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van 't Hof FNG, Lai D, van Setten J, Bots ML, Vaartjes I, Broderick J, Woo D, Foroud T, Rinkel GJE, de Bakker PIW, Ruigrok YM. Exome-chip association analysis of intracranial aneurysms. Neurology 2019; 94:e481-e488. [PMID: 31732565 DOI: 10.1212/wnl.0000000000008665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/01/2019] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To investigate to what extent low-frequency genetic variants (with minor allele frequencies <5%) affect the risk of intracranial aneurysms (IAs). METHODS One thousand fifty-six patients with IA and 2,097 population-based controls from the Netherlands were genotyped with the Illumina HumanExome BeadChip. After quality control (QC) of samples and single nucleotide variants (SNVs), we conducted a single variant analysis using the Fisher exact test. We also performed the variable threshold (VT) test and the sequence kernel association test (SKAT) at different minor allele count (MAC) thresholds of >5 and >0 to test the hypothesis that multiple variants within the same gene are associated with IA risk. Significant results were tested in a replication cohort of 425 patients with IA and 311 controls, and results of the 2 cohorts were combined in a meta-analysis. RESULTS After QC, 995 patients with IA and 2,080 controls remained for further analysis. The single variant analysis comprising 46,534 SNVs did not identify significant loci at the genome-wide level. The gene-based tests showed a statistically significant association for fibulin 2 (FBLN2) (best p = 1 × 10-6 for the VT test, MAC >5). Associations were not statistically significant in the independent but smaller replication cohort (p > 0.57) but became slightly stronger in a meta-analysis of the 2 cohorts (best p = 4.8 × 10-7 for the SKAT, MAC ≥1). CONCLUSION Gene-based tests indicated an association for FBLN2, a gene encoding an extracellular matrix protein implicated in vascular wall remodeling, but independent validation in larger cohorts is warranted. We did not identify any significant associations for single low-frequency genetic variants.
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Affiliation(s)
- Femke N G van 't Hof
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH.
| | - Dongbing Lai
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Jessica van Setten
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Michiel L Bots
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Ilonca Vaartjes
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Joseph Broderick
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Daniel Woo
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Tatiana Foroud
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Gabriel J E Rinkel
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Paul I W de Bakker
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
| | - Ynte M Ruigrok
- From the Department of Neurology and Neurosurgery (F.N.G.v.H., G.J.E.R., Y.M.R.), Brain Center Rudolf Magnus, Department of Cardiology (J.v.S.), Department of Medical Genetics (P.I.W.d.B.), Centre for Molecular Medicine, and Department of Epidemiology (M.L.B., I.V., P.I.W.d.B.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, the Netherlands; Department of Medical and Molecular Genetics (D.L., T.F.), Indiana University School of Medicine, Indianapolis; and Department of Neurology and Rehabilitation Medicine (J.B., D.W.), University of Cincinnati School of Medicine, OH
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169
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Miller JB, Pickett BD, Ridge PG. JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. Bioinformatics 2019; 35:546-552. [PMID: 30084941 PMCID: PMC6378933 DOI: 10.1093/bioinformatics/bty669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/11/2018] [Accepted: 07/31/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation Orthologous gene identification is fundamental to all aspects of biology. For example, ortholog identification between species can provide functional insights for genes of unknown function and is a necessary step in phylogenetic inference. Currently, most ortholog identification algorithms require all-versus-all BLAST comparisons, which are time-consuming and memory intensive. Results In contrast to existing approaches, JustOrthologs exploits the conservation of gene structure by using the lengths of coding sequence regions and dinucleotide percentages to identify orthologs. In comparison to OrthoMCL, OMA and OrthoFinder, JustOrthologs decreases ortholog identification runtime by more than 96% and achieves comparable precision and recall scores. The computational speedup allowed us to conduct pairwise comparisons of 1197 complete genomes (780 eukaryotes and 417 archaea). We confirmed gene annotations for 384 120 genes, grouped 1 675 415 genes in previously unreported ortholog groups, and identified 51 429 potentially mislabeled genes across 622 843 ortholog groups. Availability and implementation JustOrthologs is an open source collaborative software package available in the GitHub repository: https://github.com/ridgelab/JustOrthologs/. All test FASTA files used for comparisons are freely available at https://github.com/ridgelab/JustOrthologs/comparisonFastaFiles/. Reference genomes used in this work are available for download from the NCBI repository: ftp://ftp.ncbi.nih.gov/genomes/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT, USA
| | | | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT, USA
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170
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Barton M, Santucci-Pereira J, Vaccaro OG, Nguyen T, Su Y, Russo J. BC200 overexpression contributes to luminal and triple negative breast cancer pathogenesis. BMC Cancer 2019; 19:994. [PMID: 31646972 PMCID: PMC6813071 DOI: 10.1186/s12885-019-6179-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 09/20/2019] [Indexed: 01/04/2023] Open
Abstract
Background Long non coding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that are not translated into proteins, but regulate the transcription of genes involved in different cellular processes, including cancer. Epidemiological analyses have demonstrated that parous women have a decreased risk of developing breast cancer in postmenopausal years if they went through a full term pregnancy in their early twenties. We here provide evidence of the role of BC200 in breast cancer and, potentially, in pregnancy’s preventive effect in reducing the lifetime risk of developing breast cancer. Methods Transcriptome analysis of normal breast of parous and nulliparous postmenopausal women revealed that several lncRNAs are differentially expressed in the parous breast. RNA sequencing of healthy postmenopausal breast tissue biopsies from eight parous and eight nulliparous women showed that there are 42 novel lncRNAs differentially expressed between these two groups. Screening of several of these 42 lncRNAs by RT-qPCR in different breast cancer cell lines, provided evidence that one in particular, lncEPCAM (more commonly known as BC200), was a strong candidate involved in cancer progression. Proliferation, migration, invasion and xerograph studies confirmed this hypothesis. Results The poorly studied oncogenic BC200 was selected to be tested in vitro and in vivo to determine its relevance in breast cancer and also to provide us with an understanding of its role in the increased susceptibility of the nulliparous women to cancer. Our results show that BC200 is upregulated in nulliparous women, and breast cancer cells and tissue. The role of BC200 is not completely understood in any of the breast cancer subtypes. We here provide evidence that BC200 has a role in luminal breast cancer as well as in the triple negative breast cancer subtype. Conclusion When overexpressed in luminal and triple negative breast cancer cell lines, BC200 shows increased proliferation, migration, and invasion in vitro. In vivo, overexpression of BC200 increased tumor size. Although treatment for cancer using lncRNAs as targets is in its infancy, the advancement in knowledge and technology to study their relevance in disease could lead to the development of novel treatment and preventive strategies for breast cancer.
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Affiliation(s)
- Maria Barton
- Biochemistry Department, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA. .,The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA.
| | - Julia Santucci-Pereira
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Olivia G Vaccaro
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Theresa Nguyen
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Yanrong Su
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Jose Russo
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
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171
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Roth SH, Levanon EY, Eisenberg E. Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity. Nat Methods 2019; 16:1131-1138. [PMID: 31636457 DOI: 10.1038/s41592-019-0610-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing by the adenosine deaminase that acts on RNA (ADAR) enzymes is a common RNA modification, preventing false activation of the innate immune system by endogenous double-stranded RNAs. Methods for quantification of ADAR activity are sought after, due to an increasing interest in the role of ADARs in cancer and autoimmune disorders, as well as attempts to harness the ADAR enzymes for RNA engineering. Here, we present the Alu editing index (AEI), a robust and simple-to-use computational tool devised for this purpose. We describe its properties and demonstrate its superiority to current quantification methods of ADAR activity. The AEI is used to map global editing across a large dataset of healthy human samples and identify putative regulators of ADAR, as well as previously unknown factors affecting the observed Alu editing levels. These should be taken into account in future comparative studies of ADAR activity. The AEI tool is available at https://github.com/a2iEditing/RNAEditingIndexer.
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Affiliation(s)
- Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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172
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Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res 2019; 47:e27. [PMID: 30624635 PMCID: PMC6411935 DOI: 10.1093/nar/gky1301] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.
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Affiliation(s)
- Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel Ardeljan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clarissa N Pacyna
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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173
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Xavier MJ, Nixon B, Roman SD, Scott RJ, Drevet JR, Aitken RJ. Paternal impacts on development: identification of genomic regions vulnerable to oxidative DNA damage in human spermatozoa. Hum Reprod 2019; 34:1876-1890. [DOI: 10.1093/humrep/dez153] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Abstract
STUDY QUESTION
Do all regions of the paternal genome within the gamete display equivalent vulnerability to oxidative DNA damage?
SUMMARY ANSWER
Oxidative DNA damage is not randomly distributed in mature human spermatozoa but is instead targeted, with particular chromosomes being especially vulnerable to oxidative stress.
WHAT IS KNOWN ALREADY
Oxidative DNA damage is frequently encountered in the spermatozoa of male infertility patients. Such lesions can influence the incidence of de novo mutations in children, yet it remains to be established whether all regions of the sperm genome display equivalent susceptibility to attack by reactive oxygen species.
STUDY DESIGN, SIZE, DURATION
Human spermatozoa obtained from normozoospermic males (n = 8) were split into equivalent samples and subjected to either hydrogen peroxide (H2O2) treatment or vehicle controls before extraction of oxidized DNA using a modified DNA immunoprecipitation (MoDIP) protocol. Specific regions of the genome susceptible to oxidative damage were identified by next-generation sequencing and validated in the spermatozoa of normozoospermic males (n = 18) and in patients undergoing infertility evaluation (n = 14).
PARTICIPANTS/MATERIALS, SETTING, METHODS
Human spermatozoa were obtained from normozoospermic males and divided into two identical samples prior to being incubated with either H2O2 (5 mm, 1 h) to elicit oxidative stress or an equal volume of vehicle (untreated controls). Alternatively, spermatozoa were obtained from fertility patients assessed as having high basal levels of oxidative stress within their spermatozoa. All semen samples were subjected to MoDIP to selectively isolate oxidized DNA, prior to sequencing of the resultant DNA fragments using a next-generation whole-genomic sequencing platform. Bioinformatic analysis was then employed to identify genomic regions vulnerable to oxidative damage, several of which were selected for real-time quantitative PCR (qPCR) validation.
MAIN RESULTS AND THE ROLE OF CHANCE
Approximately 9000 genomic regions, 150–1000 bp in size, were identified as highly vulnerable to oxidative damage in human spermatozoa. Specific chromosomes showed differential susceptibility to damage, with chromosome 15 being particularly sensitive to oxidative attack while the sex chromosomes were protected. Susceptible regions generally lay outside protamine- and histone-packaged domains. Furthermore, we confirmed that these susceptible genomic sites experienced a dramatic (2–15-fold) increase in their burden of oxidative DNA damage in patients undergoing infertility evaluation compared to normal healthy donors.
LIMITATIONS, REASONS FOR CAUTION
The limited number of samples analysed in this study warrants external validation, as do the implications of our findings. Selection of male fertility patients was based on high basal levels of oxidative stress within their spermatozoa as opposed to specific sub-classes of male factor infertility.
WIDER IMPLICATIONS OF THE FINDINGS
The identification of genomic regions susceptible to oxidation in the male germ line will be of value in focusing future analyses into the mutational load carried by children in response to paternal factors such as age, the treatment of male infertility using ART and paternal exposure to environmental toxicants.
STUDY FUNDING/COMPETING INTEREST(S)
Project support was provided by the University of Newcastle’s (UoN) Priority Research Centre for Reproductive Science. M.J.X. was a recipient of a UoN International Postgraduate Research Scholarship. B.N. is the recipient of a National Health and Medical Research Council of Australia Senior Research Fellowship. Authors declare no conflict of interest.
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Affiliation(s)
- M J Xavier
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - B Nixon
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - S D Roman
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Drug Development, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - R J Scott
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Medical Genetics, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Division of Molecular Medicine, Pathology North, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - J R Drevet
- GReD Laboratory, CNRS UMR6293—INSERM U1103—Clermont Université, Clermont-Ferrand, France
| | - R J Aitken
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Medical Genetics, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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174
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Mirza M, Vainshtein A, DiRonza A, Chandrachud U, Haslett LJ, Palmieri M, Storch S, Groh J, Dobzinski N, Napolitano G, Schmidtke C, Kerkovich DM. The CLN3 gene and protein: What we know. Mol Genet Genomic Med 2019; 7:e859. [PMID: 31568712 PMCID: PMC6900386 DOI: 10.1002/mgg3.859] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/11/2022] Open
Abstract
Background One of the most important steps taken by Beyond Batten Disease Foundation in our quest to cure juvenile Batten (CLN3) disease is to understand the State of the Science. We believe that a strong understanding of where we are in our experimental understanding of the CLN3 gene, its regulation, gene product, protein structure, tissue distribution, biomarker use, and pathological responses to its deficiency, lays the groundwork for determining therapeutic action plans. Objectives To present an unbiased comprehensive reference tool of the experimental understanding of the CLN3 gene and gene product of the same name. Methods BBDF compiled all of the available CLN3 gene and protein data from biological databases, repositories of federally and privately funded projects, patent and trademark offices, science and technology journals, industrial drug and pipeline reports as well as clinical trial reports and with painstaking precision, validated the information together with experts in Batten disease, lysosomal storage disease, lysosome/endosome biology. Results The finished product is an indexed review of the CLN3 gene and protein which is not limited in page size or number of references, references all available primary experiments, and does not draw conclusions for the reader. Conclusions Revisiting the experimental history of a target gene and its product ensures that inaccuracies and contradictions come to light, long‐held beliefs and assumptions continue to be challenged, and information that was previously deemed inconsequential gets a second look. Compiling the information into one manuscript with all appropriate primary references provides quick clues to which studies have been completed under which conditions and what information has been reported. This compendium does not seek to replace original articles or subtopic reviews but provides an historical roadmap to completed works.
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Affiliation(s)
| | | | - Alberto DiRonza
- Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas
| | - Uma Chandrachud
- Center for Genomic Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | | | - Michela Palmieri
- Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas
| | - Stephan Storch
- Biochemistry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janos Groh
- Neurology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Niv Dobzinski
- Biochemistry and Biophysics, UCSF School of Medicine, San Francisco, California
| | | | - Carolin Schmidtke
- Biochemistry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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175
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Huan T, Joehanes R, Song C, Peng F, Guo Y, Mendelson M, Yao C, Liu C, Ma J, Richard M, Agha G, Guan W, Almli LM, Conneely KN, Keefe J, Hwang SJ, Johnson AD, Fornage M, Liang L, Levy D. Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease. Nat Commun 2019; 10:4267. [PMID: 31537805 PMCID: PMC6753136 DOI: 10.1038/s41467-019-12228-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/23/2019] [Indexed: 12/19/2022] Open
Abstract
Identifying methylation quantitative trait loci (meQTLs) and integrating them with disease-associated variants from genome-wide association studies (GWAS) may illuminate functional mechanisms underlying genetic variant-disease associations. Here, we perform GWAS of >415 thousand CpG methylation sites in whole blood from 4170 individuals and map 4.7 million cis- and 630 thousand trans-meQTL variants targeting >120 thousand CpGs. Independent replication is performed in 1347 participants from two studies. By linking cis-meQTL variants with GWAS results for cardiovascular disease (CVD) traits, we identify 92 putatively causal CpGs for CVD traits by Mendelian randomization analysis. Further integrating gene expression data reveals evidence of cis CpG-transcript pairs causally linked to CVD. In addition, we identify 22 trans-meQTL hotspots each targeting more than 30 CpGs and find that trans-meQTL hotspots appear to act in cis on expression of nearby transcriptional regulatory genes. Our findings provide a powerful meQTL resource and shed light on DNA methylation involvement in human diseases. Differentially methylated CpGs can inform on disease mechanisms and be useful as biomarkers. Here, the authors perform GWAS for DNA methylation in whole blood, cis- and trans-meQTL mapping, followed by Mendelian randomization analysis that links meQTLs with cardiovascular diseases.
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Affiliation(s)
- Tianxiao Huan
- The Framingham Heart Study, Framingham, MA, USA. .,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Roby Joehanes
- The Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ci Song
- The Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.,Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fen Peng
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yichen Guo
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Michael Mendelson
- The Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.,Department of Cardiology, Boston Children's Hospital, Harvard University, Boston, MA, USA
| | - Chen Yao
- The Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jiantao Ma
- The Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melissa Richard
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Golareh Agha
- Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Lynn M Almli
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua Keefe
- The Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shih-Jen Hwang
- The Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D Johnson
- The Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Liming Liang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA. .,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Daniel Levy
- The Framingham Heart Study, Framingham, MA, USA. .,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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176
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Tosoian JJ, Chinnaiyan AM. Translating Science to Medicine: When Will the Rubber Meet the Road? Eur Urol 2019; 76:560-561. [PMID: 31506226 DOI: 10.1016/j.eururo.2019.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 11/18/2022]
Affiliation(s)
- Jeffrey J Tosoian
- Department of Urology, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Arul M Chinnaiyan
- Department of Urology, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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177
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Carraro M, Monzon AM, Chiricosta L, Reggiani F, Aspromonte MC, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, Pal LR, Yin Y, Limongelli I, Andreoletti G, Moult J, Wilson SJ, Katsonis P, Lichtarge O, Chen J, Wang Y, Hu Z, Brenner SE, Ferrari C, Murgia A, Tosatto SC, Leonardi E. Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Hum Mutat 2019; 40:1330-1345. [PMID: 31144778 PMCID: PMC7341177 DOI: 10.1002/humu.23823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/07/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
The Critical Assessment of Genome Interpretation-5 intellectual disability challenge asked to use computational methods to predict patient clinical phenotypes and the causal variant(s) based on an analysis of their gene panel sequence data. Sequence data for 74 genes associated with intellectual disability (ID) and/or autism spectrum disorders (ASD) from a cohort of 150 patients with a range of neurodevelopmental manifestations (i.e. ID, autism, epilepsy, microcephaly, macrocephaly, hypotonia, ataxia) have been made available for this challenge. For each patient, predictors had to report the causative variants and which of the seven phenotypes were present. Since neurodevelopmental disorders are characterized by strong comorbidity, tested individuals often present more than one pathological condition. Considering the overall clinical manifestation of each patient, the correct phenotype has been predicted by at least one group for 93 individuals (62%). ID and ASD were the best predicted among the seven phenotypic traits. Also, causative or potentially pathogenic variants were predicted correctly by at least one group. However, the prediction of the correct causative variant seems to be insufficient to predict the correct phenotype. In some cases, the correct prediction has been supported by rare or common variants in genes different from the causative one.
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Affiliation(s)
- Marco Carraro
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | | | - Luigi Chiricosta
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Francesco Reggiani
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Department of Information Engineering, University of Padua, Padua, Italy
| | | | - Mariagrazia Bellini
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Kymberleigh Pagel
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Yuxiang Jiang
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Predrag Radivojac
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | | | - Gaia Andreoletti
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen J. Wilson
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Panagiotis Katsonis
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Jingqi Chen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yaqiong Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Carlo Ferrari
- Department of Information Engineering, University of Padua, Padua, Italy
| | - Alessandra Murgia
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Silvio C.E. Tosatto
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- CNR Institute of Neuroscience, Padua, Italy
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
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178
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Blackburn NB, Michael LF, Meikle PJ, Peralta JM, Mosior M, McAhren S, Bui HH, Bellinger MA, Giles C, Kumar S, Leandro AC, Almeida M, Weir JM, Mahaney MC, Dyer TD, Almasy L, VandeBerg JL, Williams-Blangero S, Glahn DC, Duggirala R, Kowala M, Blangero J, Curran JE. Rare DEGS1 variant significantly alters de novo ceramide synthesis pathway. J Lipid Res 2019; 60:1630-1639. [PMID: 31227640 PMCID: PMC6718439 DOI: 10.1194/jlr.p094433] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/13/2019] [Indexed: 02/06/2023] Open
Abstract
The de novo ceramide synthesis pathway is essential to human biology and health, but genetic influences remain unexplored. The core function of this pathway is the generation of biologically active ceramide from its precursor, dihydroceramide. Dihydroceramides have diverse, often protective, biological roles; conversely, increased ceramide levels are biomarkers of complex disease. To explore the genetics of the ceramide synthesis pathway, we searched for deleterious nonsynonymous variants in the genomes of 1,020 Mexican Americans from extended pedigrees. We identified a Hispanic ancestry-specific rare functional variant, L175Q, in delta 4-desaturase, sphingolipid 1 (DEGS1), a key enzyme in the pathway that converts dihydroceramide to ceramide. This amino acid change was significantly associated with large increases in plasma dihydroceramides. Indexes of DEGS1 enzymatic activity were dramatically reduced in heterozygotes. CRISPR/Cas9 genome editing of HepG2 cells confirmed that the L175Q variant results in a partial loss of function for the DEGS1 enzyme. Understanding the biological role of DEGS1 variants, such as L175Q, in ceramide synthesis may improve the understanding of metabolic-related disorders and spur ongoing research of drug targets along this pathway.
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Affiliation(s)
- Nicholas B Blackburn
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX.
| | - Laura F Michael
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Juan M Peralta
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Menzies Institute for Medical Research University of Tasmania, Hobart, TAS, Australia
| | - Marian Mosior
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | - Scott McAhren
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | - Hai H Bui
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | | | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Satish Kumar
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Ana C Leandro
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Marcio Almeida
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | | | - Michael C Mahaney
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Thomas D Dyer
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Laura Almasy
- Department of Biomedical and Health Informatics Children's Hospital of Philadelphia, Philadelphia, PA; Department of Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - John L VandeBerg
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - David C Glahn
- Department of Psychiatry Boston Children's Hospital and Harvard Medical School, Boston, MA; Olin Neuropsychiatry Research Center Institute of Living, Hartford Hospital, Hartford, CT
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Mark Kowala
- Lilly Research Laboratories,Eli Lilly and Company, Indianapolis, IN
| | - John Blangero
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute University of Texas Rio Grande Valley School of Medicine, Brownsville, TX; Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX.
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179
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ATG5 cancer mutations and alternative mRNA splicing reveal a conjugation switch that regulates ATG12-ATG5-ATG16L1 complex assembly and autophagy. Cell Discov 2019; 5:42. [PMID: 31636955 PMCID: PMC6796855 DOI: 10.1038/s41421-019-0110-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 06/26/2019] [Accepted: 06/30/2019] [Indexed: 02/08/2023] Open
Abstract
Autophagy is critical for maintaining cellular homeostasis during times of stress, and is thought to play important roles in both tumorigenesis and tumor cell survival. Formation of autophagosomes, which mediate delivery of cytoplasmic cargo to lysosomes, requires multiple autophagy-related (ATG) protein complexes, including the ATG12–ATG5-ATG16L1 complex. Herein, we report that a molecular ATG5 “conjugation switch”, comprised of competing ATG12 and ubiquitin conjugation reactions, integrates ATG12–ATG5-ATG16L1 complex assembly with protein quality control of its otherwise highly unstable subunits. This conjugation switch is tightly regulated by ATG16L1, which binds to free ATG5 and mutually protects both proteins from ubiquitin conjugation and proteasomal degradation, thereby instead promoting the irreversible conjugation of ATG12 to ATG5. The resulting ATG12–ATG5 conjugate, in turn, displays enhanced affinity for ATG16L1 and thus fully stabilizes the ATG12–ATG5-ATG16L1 complex. Most importantly, we find in multiple tumor types that ATG5 somatic mutations and alternative mRNA splicing specifically disrupt the ATG16L1-binding pocket in ATG5 and impair the essential ATG5-ATG16L1 interactions that are initially required for ATG12–ATG5 conjugation. Finally, we provide evidence that ATG16L2, which is overexpressed in several cancers relative to ATG16L1, hijacks the conjugation switch by competing with ATG16L1 for binding to ATG5. While ATG16L2 stabilizes ATG5 and enables ATG12–ATG5 conjugation, this endogenous dominant-negative inhibitor simultaneously displaces ATG16L1, resulting in its proteasomal degradation and a block in autophagy. Thus, collectively, our findings provide novel insights into ATG12–ATG5-ATG16L1 complex assembly and reveal multiple mechanisms wherein dysregulation of the ATG5 conjugation switch inhibits autophagy.
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180
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Liu Q, Borcherding N, Shao P, Cao H, Zhang W, Qi HH. Identification of novel TGF-β regulated genes with pro-migratory roles. Biochim Biophys Acta Mol Basis Dis 2019; 1865:165537. [PMID: 31449970 DOI: 10.1016/j.bbadis.2019.165537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/06/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022]
Abstract
Transforming growth factor-β (TGF-β) signaling plays fundamental roles in the development and homeostasis of somatic cells. Dysregulated TGF-β signaling contributes to cancer progression and relapse to therapies by inducing epithelial-to-mesenchymal transition (EMT), enriching cancer stem cells, and promoting immunosuppression. Although many TGF-β-regulated genes have been identified, only a few datasets were obtained by next-generation sequencing. In this study, we performed RNA-sequencing analysis of MCF10A cells and identified 1166 genes that were upregulated and 861 genes that were downregulated by TGF-β. Gene set enrichment analysis revealed that focal adhesion and metabolic pathways were the top enriched pathways of the up- and downregulated genes, respectively. Genes in these pathways also possess significant predictive value for renal cancers. Moreover, we confirmed that TGF-β induced expression of MICAL1 and 2, and the histone demethylase, KDM7A, and revealed their regulatory roles on TGF-β-induced cell migration. We also show a critical effect of KDM7A in regulating the acetylation of H3K27 on TGF-β-induced genes. In sum, this study identified novel effectors that mediate the pro-migratory role of TGF-β signaling, paving the way for future studies that investigate the function of MICAL family members in cancer and the novel epigenetic mechanisms downstream TGF-β signaling.
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Affiliation(s)
- Qi Liu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nicholas Borcherding
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Peng Shao
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Huojun Cao
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; School of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | - Weizhou Zhang
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Hank Heng Qi
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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181
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Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio MR, Takata Y, Lin K, Tomida MW, Shen J, Saha D, Gowher H, Zhao H, Chen T. DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res 2019; 47:152-167. [PMID: 30321403 PMCID: PMC6326784 DOI: 10.1093/nar/gky947] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/05/2018] [Indexed: 12/12/2022] Open
Abstract
DNMT3L (DNMT3-like), a member of the DNMT3 family, has no DNA methyltransferase activity but regulates de novo DNA methylation. While biochemical studies show that DNMT3L is capable of interacting with both DNMT3A and DNMT3B and stimulating their enzymatic activities, genetic evidence suggests that DNMT3L is essential for DNMT3A-mediated de novo methylation in germ cells but is dispensable for de novo methylation during embryogenesis, which is mainly mediated by DNMT3B. How DNMT3L regulates DNA methylation and what determines its functional specificity are not well understood. Here we show that DNMT3L-deficient mouse embryonic stem cells (mESCs) exhibit downregulation of DNMT3A, especially DNMT3A2, the predominant DNMT3A isoform in mESCs. DNA methylation analysis of DNMT3L-deficient mESCs reveals hypomethylation at many DNMT3A target regions. These results confirm that DNMT3L is a positive regulator of DNA methylation, contrary to a previous report that, in mESCs, DNMT3L regulates DNA methylation positively or negatively, depending on genomic regions. Mechanistically, DNMT3L forms a complex with DNMT3A2 and prevents DNMT3A2 from being degraded. Restoring the DNMT3A protein level in DNMT3L-deficient mESCs partially recovers DNA methylation. Thus, our work uncovers a role for DNMT3L in maintaining DNMT3A stability, which contributes to the effect of DNMT3L on DNMT3A-dependent DNA methylation.
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Affiliation(s)
- Nicolas Veland
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Sally Gaddis
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mary W Tomida
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Debapriya Saha
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Hongbo Zhao
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital and Institute of Obstetrics and Gynecology, Fudan University, Shanghai, People's Republic of China
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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182
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Miller JB, Brase LR, Ridge PG. ExtRamp: a novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or relative codon adaptiveness. Nucleic Acids Res 2019; 47:1123-1131. [PMID: 30649455 PMCID: PMC6379678 DOI: 10.1093/nar/gky1193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/16/2018] [Accepted: 11/12/2018] [Indexed: 11/21/2022] Open
Abstract
Different species, genes, and locations within genes use different codons to fine-tune gene expression. Within genes, the ramp sequence assists in ribosome spacing and decreases downstream collisions by incorporating slowly-translated codons at the beginning of a gene. Although previously reported as occurring in some species, no previous attempt at extracting the ramp sequence from specific genes has been published. We present ExtRamp, a software package that quickly extracts ramp sequences from any species using the tRNA adaptation index or relative codon adaptiveness. Different filters facilitate the analysis of codon efficiency and enable identification of genes with a ramp sequence. We validate the existence of a ramp sequence in most species by running ExtRamp on 229 742 339 genes across 23 428 species. We evaluate differences in reported ramp sequences when we use different parameters. Using the strictest ramp sequence cut-off, we show that across most taxonomic groups, ramp sequences are approximately 20–40 codons long and occur in about 10% of gene sequences. We also show that in Drosophila melanogaster as gene expression increases, a higher proportion of genes have ramp sequences. We provide a framework for performing this analysis on other species. ExtRamp is freely available at https://github.com/ridgelab/ExtRamp.
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Affiliation(s)
- Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Logan R Brase
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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183
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Transketolase and vitamin B1 influence on ROS-dependent neutrophil extracellular traps (NETs) formation. PLoS One 2019; 14:e0221016. [PMID: 31415630 PMCID: PMC6695114 DOI: 10.1371/journal.pone.0221016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Neutrophil extracellular traps (NETs) are a recently identified, web-like, extracellular structure composed of decondensed nuclear DNA and associated antimicrobial granules. NETs are extruded into the extracellular environment via the reactive oxygen species (ROS)-dependent cell death pathway participating in inflammation and autoimmune diseases. Transketolase (TKT) is a thiamine pyrophosphate (vitamin B1)-dependent enzyme that links the pentose phosphate pathway with the glycolytic pathway by feeding excess sugar phosphates into the main carbohydrate metabolic pathways to generate biosynthetic reducing capacity in the form of NADPH as a substrate for ROS generation. In this work, TKT was selected as a lead candidate from 24 NET-associated proteins obtained by literature screening and knowledge gap assessment. Consequently, we determined whether TKT influenced NET formation in vitro. We firstly established that the release of ROS-dependent NETs was significantly decreased after purified human PMNs were pretreated with oxythiamine, a TKT inhibitor, and in a concentration dependent manner. As a cofactor for TKT reaction, we evaluated the release of NET formation either in vitamin B1 treatment or in combined use of oxythiamine and vitamin B1, and found that those treatments also exerted a significant suppressive effect on the amount of NET-DNA and ROS production. The regulation of TKT by oxythiamine and/or vitamin B1 may therefore be associated with response to the modulation of NET formation by preventing generation of excessive NETs in inflammatory diseases.
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184
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Mathios D, Hwang T, Xia Y, Phallen J, Rui Y, See AP, Maxwell R, Belcaid Z, Casaos J, Burger PC, McDonald KL, Gallia GL, Cope L, Kai M, Brem H, Pardoll DM, Ha P, Green JJ, Velculescu VE, Bettegowda C, Park C, Lim M. Genome‐wide investigation of intragenic DNA methylation identifies
ZMIZ1
gene as a prognostic marker in glioblastoma and multiple cancer types. Int J Cancer 2019; 145:3425-3435. [DOI: 10.1002/ijc.32587] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/24/2019] [Accepted: 07/04/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Dimitrios Mathios
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
| | - Taeyoung Hwang
- Department of Biomedical EngineeringJohns Hopkins University School of Medicine Baltimore MD
- Lieber Institute for Brain Development Baltimore MD
| | - Yuanxuan Xia
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
| | - Jillian Phallen
- Department of Oncology and Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of Medicine Baltimore MD
| | - Yuan Rui
- Department of Biomedical EngineeringJohns Hopkins University School of Medicine Baltimore MD
- Lieber Institute for Brain Development Baltimore MD
| | - Alfred P. See
- Department of NeurosurgeryBrigham and Women's Hospital, Harvard School of Medicine Boston MA
| | - Russell Maxwell
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
- Department of Radiation Oncology and Molecular Radiation SciencesJohns Hopkins University School of Medicine Baltimore MD
| | - Zineb Belcaid
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
| | - Joshua Casaos
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
| | - Peter C. Burger
- Department of NeuropathologyJohns Hopkins University School of Medicine Baltimore MD
| | - Kerrie L. McDonald
- Cure for Life Neuro‐Oncology Group, Lowy Cancer Research CentrePrince of Wales Clinical School, University of New South Wales Sydney NSW Australia
| | - Gary L. Gallia
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
| | - Leslie Cope
- Department of Oncology and Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of Medicine Baltimore MD
| | - Mihoko Kai
- Department of Radiation Oncology and Molecular Radiation SciencesJohns Hopkins University School of Medicine Baltimore MD
| | - Henry Brem
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
| | - Drew M. Pardoll
- Department of Oncology and Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of Medicine Baltimore MD
- Department of MedicineJohns Hopkins University School of Medicine Baltimore MD
- Department of PathologyJohns Hopkins University School of Medicine Baltimore MD
| | - Patrick Ha
- Department of Otolaryngology‐Head and Neck SurgeryJohns Hopkins University School of Medicine Baltimore MD
| | - Jordan J. Green
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
- Department of Biomedical EngineeringJohns Hopkins University School of Medicine Baltimore MD
- Lieber Institute for Brain Development Baltimore MD
- Department of Oncology and Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of Medicine Baltimore MD
| | - Victor E. Velculescu
- Department of Oncology and Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of Medicine Baltimore MD
- Department of PathologyJohns Hopkins University School of Medicine Baltimore MD
| | - Chetan Bettegowda
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
- Department of Oncology and Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of Medicine Baltimore MD
| | - Chul‐Kee Park
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
- Department of NeurosurgerySeoul National University College of Medicine Seoul Republic of Korea
| | - Michael Lim
- Department of NeurosurgeryJohns Hopkins University School of Medicine Baltimore MD
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185
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Zhu Z, Ren J, Michail S, Sun F. MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations. Genome Biol 2019; 20:154. [PMID: 31387630 PMCID: PMC6683435 DOI: 10.1186/s13059-019-1773-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/24/2019] [Indexed: 12/15/2022] Open
Abstract
We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show that including reads from unknown organisms significantly increases the prediction accuracy of the disease status for three of the four datasets. We identify new microbial organisms associated with these diseases and show viruses play important prediction roles in colorectal cancer and liver cirrhosis, but not in type 2 diabetes. MicroPro is freely available at https://github.com/zifanzhu/MicroPro .
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Affiliation(s)
- Zifan Zhu
- Quantitative and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA USA
| | - Jie Ren
- Quantitative and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA USA
| | - Sonia Michail
- Department of Pediatrics, Division of Gastroenterology, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Fengzhu Sun
- Quantitative and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA USA
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186
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Thormann V, Rothkegel MC, Schöpflin R, Glaser LV, Djuric P, Li N, Chung HR, Schwahn K, Vingron M, Meijsing SH. Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts. Nucleic Acids Res 2019; 46:2868-2882. [PMID: 29385519 PMCID: PMC5888794 DOI: 10.1093/nar/gky051] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/19/2018] [Indexed: 12/19/2022] Open
Abstract
Genomic binding of transcription factors, like the glucocorticoid receptor (GR), is linked to the regulation of genes. However, as we show here, GR binding is a poor predictor of GR-dependent gene regulation even when taking the 3D organization of the genome into account. To connect GR binding sites to the regulation of genes in the endogenous genomic context, we turned to genome editing. By deleting GR binding sites, individually or in combination, we uncovered how cooperative interactions between binding sites contribute to the regulation of genes. Specifically, for the GR target gene GILZ, we show that the simultaneous presence of a cluster of GR binding sites is required for the activity of an individual enhancer and that the GR-dependent regulation of GILZ depends on multiple GR-bound enhancers. Further, by deleting GR binding sites that are shared between different cell types, we show how cell type-specific genome organization and enhancer-blocking can result in cell type-specific wiring of promoter–enhancer contacts. This rewiring allows an individual GR binding site shared between different cell types to direct the expression of distinct transcripts and thereby contributes to the cell type-specific consequences of glucocorticoid signaling.
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Affiliation(s)
- Verena Thormann
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Maika C Rothkegel
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Laura V Glaser
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Petar Djuric
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Na Li
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Kevin Schwahn
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
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187
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Diaz de Arce AJ, Noderer WL, Wang CL. Complete motif analysis of sequence requirements for translation initiation at non-AUG start codons. Nucleic Acids Res 2019; 46:985-994. [PMID: 29228265 PMCID: PMC5778536 DOI: 10.1093/nar/gkx1114] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 12/06/2017] [Indexed: 01/23/2023] Open
Abstract
The initiation of mRNA translation from start codons other than AUG was previously believed to be rare and of relatively low impact. More recently, evidence has suggested that as much as half of all translation initiation utilizes non-AUG start codons, codons that deviate from AUG by a single base. Furthermore, non-AUG start codons have been shown to be involved in regulation of expression and disease etiology. Yet the ability to gauge expression based on the sequence of a translation initiation site (start codon and its flanking bases) has been limited. Here we have performed a comprehensive analysis of translation initiation sites that utilize non-AUG start codons. By combining genetic-reporter, cell-sorting, and high-throughput sequencing technologies, we have analyzed the expression associated with all possible variants of the -4 to +4 positions of non-AUG translation initiation site motifs. This complete motif analysis revealed that 1) with the right sequence context, certain non-AUG start codons can generate expression comparable to that of AUG start codons, 2) sequence context affects each non-AUG start codon differently, and 3) initiation at non-AUG start codons is highly sensitive to changes in the flanking sequences. Complete motif analysis has the potential to be a key tool for experimental and diagnostic genomics.
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Affiliation(s)
| | - William L Noderer
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Clifford L Wang
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
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188
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Byrne A, Supple MA, Volden R, Laidre KL, Shapiro B, Vollmers C. Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear ( Ursus maritimus). Front Genet 2019; 10:643. [PMID: 31379921 PMCID: PMC6658610 DOI: 10.3389/fgene.2019.00643] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/18/2019] [Indexed: 11/26/2022] Open
Abstract
Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result, long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9-based depletion method (depletion of abundant sequences by hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion, we discovered ∼6,000 high-confidence isoforms and a number of novel genes. This indicates that there is a high diversity of gene isoforms within U. maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.
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Affiliation(s)
- Ashley Byrne
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA, United States
- Genomics Institute, University of California, Santa Cruz, CA, United States
| | - Megan A. Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Roger Volden
- Genomics Institute, University of California, Santa Cruz, CA, United States
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Kristin L. Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, United States
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Christopher Vollmers
- Genomics Institute, University of California, Santa Cruz, CA, United States
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
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189
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Abstract
Gene maps, or annotations, enable us to navigate the functional landscape of our genome. They are a resource upon which virtually all studies depend, from single-gene to genome-wide scales and from basic molecular biology to medical genetics. Yet present-day annotations suffer from trade-offs between quality and size, with serious but often unappreciated consequences for downstream studies. This is particularly true for long non-coding RNAs (lncRNAs), which are poorly characterized compared to protein-coding genes. Long-read sequencing technologies promise to improve current annotations, paving the way towards a complete annotation of lncRNAs expressed throughout a human lifetime.
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190
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Frith MC, Khan S. A survey of localized sequence rearrangements in human DNA. Nucleic Acids Res 2019; 46:1661-1673. [PMID: 29272440 PMCID: PMC5829575 DOI: 10.1093/nar/gkx1266] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/07/2017] [Indexed: 01/29/2023] Open
Abstract
Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what types of complex mutation occur, and we cannot routinely characterize arbitrarily-complex mutations in a high-throughput, genome-wide manner. Long-read DNA sequencing methods (e.g. PacBio, nanopore) are promising for this task, because one read may encompass a whole complex mutation. We describe an analysis pipeline to characterize arbitrarily-complex 'local' mutations, i.e. intrachromosomal mutations encompassed by one DNA read. We apply it to nanopore and PacBio reads from one human cell line (NA12878), and survey sequence rearrangements, both real and artifactual. Almost all the real rearrangements belong to recurring patterns or motifs: the most common is tandem multiplication (e.g. heptuplication), but there are also complex patterns such as localized shattering, which resembles DNA damage by radiation. Gene conversions are identified, including one between hemoglobin gamma genes. This study demonstrates a way to find intricate rearrangements with any number of duplications, deletions, and repositionings. It demonstrates a probability-based method to resolve ambiguous rearrangements involving highly similar sequences, as occurs in gene conversion. We present a catalog of local rearrangements in one human cell line, and show which rearrangement patterns occur.
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Affiliation(s)
- Martin C Frith
- Artificial Intelligence Research Center, AIST, Tokyo 135-0064, Japan.,Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
| | - Sofia Khan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
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191
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Mourikis TP, Benedetti L, Foxall E, Temelkovski D, Nulsen J, Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald RC, Scaffidi P, Ciccarelli FD. Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. Nat Commun 2019; 10:3101. [PMID: 31308377 PMCID: PMC6629660 DOI: 10.1038/s41467-019-10898-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/04/2019] [Indexed: 12/25/2022] Open
Abstract
The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy.
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Affiliation(s)
- Thanos P Mourikis
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Elizabeth Foxall
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Damjan Temelkovski
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Juliane Perner
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Matteo Cereda
- Italian Institute for Genomic Medicine (IIGM), Turin, 10126, Italy
| | - Jesper Lagergren
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK.
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192
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Lyu X, Chastain M, Chai W. Genome-wide mapping and profiling of γH2AX binding hotspots in response to different replication stress inducers. BMC Genomics 2019; 20:579. [PMID: 31299901 PMCID: PMC6625122 DOI: 10.1186/s12864-019-5934-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Replication stress (RS) gives rise to DNA damage that threatens genome stability. RS can originate from different sources that stall replication by diverse mechanisms. However, the mechanism underlying how different types of RS contribute to genome instability is unclear, in part due to the poor understanding of the distribution and characteristics of damage sites induced by different RS mechanisms. RESULTS We use ChIP-seq to map γH2AX binding sites genome-wide caused by aphidicolin (APH), hydroxyurea (HU), and methyl methanesulfonate (MMS) treatments in human lymphocyte cells. Mapping of γH2AX ChIP-seq reveals that APH, HU, and MMS treatments induce non-random γH2AX chromatin binding at discrete regions, suggesting that there are γH2AX binding hotspots in the genome. Characterization of the distribution and sequence/epigenetic features of γH2AX binding sites reveals that the three treatments induce γH2AX binding at largely non-overlapping regions, suggesting that RS may cause damage at specific genomic loci in a manner dependent on the fork stalling mechanism. Nonetheless, γH2AX binding sites induced by the three treatments share common features including compact chromatin, coinciding with larger-than-average genes, and depletion of CpG islands and transcription start sites. Moreover, we observe significant enrichment of SINEs in γH2AX sites in all treatments, indicating that SINEs may be a common barrier for replication polymerases. CONCLUSIONS Our results identify the location and common features of genome instability hotspots induced by different types of RS, and help in deciphering the mechanisms underlying RS-induced genetic diseases and carcinogenesis.
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Affiliation(s)
- Xinxing Lyu
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Megan Chastain
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Weihang Chai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA.
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193
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Bim LV, Navarro FCP, Valente FOF, Lima-Junior JV, Delcelo R, Dias-da-Silva MR, Maciel RMB, Galante PAF, Cerutti JM. Retroposed copies of RET gene: a somatically acquired event in medullary thyroid carcinoma. BMC Med Genomics 2019; 12:104. [PMID: 31288802 PMCID: PMC6617568 DOI: 10.1186/s12920-019-0552-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Different pathogenic germline mutations in the RET oncogene are identified in MEN 2, a hereditary syndrome characterized by medullary thyroid carcinoma (MTC) and other endocrine tumors. Although genetic predisposition is recognized, not all RET mutation carriers will develop the disease during their lifetime or, likewise, RET mutation carriers belonging to the same family may present clinical heterogeneity. It has been suggested that a single germline mutation might not be sufficient for development of MEN 2-associated tumors and a somatic bi-allelic alteration might be required. Here we investigated the presence of somatic second hit mutation in the RET gene in MTC. METHODS We integrated Multiplex Ligation-dependent Probe Amplification (MLPA) and whole exome sequencing (WES) to search for copy number alteration (CNA) in the RET gene in MTC samples and medullary thyroid cell lines (TT and MZ-CR-1). We next found reads spanning exon-exon boundaries on RET, an indicative of retrocopy. We subsequently searched for RET retrocopies in the human reference genome (GRCh37) and in the 1000 Genomes Project data, by looking for reads reporting joined exons in the RET locus or distinct genomic regions. To determine RET retrocopy specificity and recurrence, DNA isolated from sporadic and MEN 2-associated MTC (n = 37), peripheral blood (n = 3) and papillary thyroid carcinomas with RET fusion (n = 10) samples were tested using PCR-sequencing methodology. RESULTS Through MLPA we have found evidence of CNA in the RET gene in MTC samples and MTC cell lines. WES analysis reinforced the presence of the CNA and hinted for a retroposed copy of RET not found in the human reference genome and 1.000 Genomes Project. Extended analysis confirmed the presence of a somatic MTC-related retrocopy of RET in both sporadic and hereditary tumors. We further unveiled a recurrent (28%) novel point mutation (p.G548 V) found exclusively in the retrocopy of RET. The mutation was also found in cDNA of mutated samples, suggesting it might be functional. CONCLUSION We here report a somatic specific RET retroposed copy in MTC samples and cell lines. Our results support the idea that generation of retrocopies in somatic cells is likely to contribute to MTC genesis and progression.
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Affiliation(s)
- Larissa V Bim
- Laboratório As Bases Genéticas dos Tumores da Tiroide, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fábio C P Navarro
- Centro de Oncologia Molecular, Hospital Sírio-libanês, São Paulo, SP, Brazil.,Departamento de Bioquímica, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Flávia O F Valente
- Laboratório de Endocrinologia Molecular e Translacional, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - José V Lima-Junior
- Laboratório As Bases Genéticas dos Tumores da Tiroide, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rosana Delcelo
- Departamento de Patologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Magnus R Dias-da-Silva
- Laboratório de Endocrinologia Molecular e Translacional, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rui M B Maciel
- Laboratório de Endocrinologia Molecular e Translacional, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-libanês, São Paulo, SP, Brazil
| | - Janete M Cerutti
- Laboratório As Bases Genéticas dos Tumores da Tiroide, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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194
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Karimzadeh M, Ernst C, Kundaje A, Hoffman MM. Umap and Bismap: quantifying genome and methylome mappability. Nucleic Acids Res 2019; 46:e120. [PMID: 30169659 PMCID: PMC6237805 DOI: 10.1093/nar/gky677] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/22/2018] [Indexed: 11/14/2022] Open
Abstract
Short-read sequencing enables assessment of genetic and biochemical traits of individual genomic regions, such as the location of genetic variation, protein binding and chemical modifications. Every region in a genome assembly has a property called 'mappability', which measures the extent to which it can be uniquely mapped by sequence reads. In regions of lower mappability, estimates of genomic and epigenomic characteristics from sequencing assays are less reliable. These regions have increased susceptibility to spurious mapping from reads from other regions of the genome with sequencing errors or unexpected genetic variation. Bisulfite sequencing approaches used to identify DNA methylation exacerbate these problems by introducing large numbers of reads that map to multiple regions. Both to correct assumptions of uniformity in downstream analysis and to identify regions where the analysis is less reliable, it is necessary to know the mappability of both ordinary and bisulfite-converted genomes. We introduce the Umap software for identifying uniquely mappable regions of any genome. Its Bismap extension identifies mappability of the bisulfite-converted genome. A Umap and Bismap track hub for human genome assemblies GRCh37/hg19 and GRCh38/hg38, and mouse assemblies GRCm37/mm9 and GRCm38/mm10 is available at https://bismap.hoffmanlab.org for use with genome browsers.
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Affiliation(s)
- Mehran Karimzadeh
- Princess Margaret Cancer Centre, M5G 1L7, Toronto, ON, Canada.,Department of Medical Biophysics, M5G 1L7, University of Toronto, Toronto, ON, Canada.,Vector Institute, M5G 1M1, Toronto, ON, Canada
| | - Carl Ernst
- Department of Human Genetics, McGill University, H3A 0C7, Montreal, QC, Canada
| | - Anshul Kundaje
- Department of Genetics, Stanford University, 94305-9025, Stanford, CA, USA.,Department of Computer Science, Stanford University, 94305-5120, Stanford, CA, USA
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, M5G 1L7, Toronto, ON, Canada.,Department of Medical Biophysics, M5G 1L7, University of Toronto, Toronto, ON, Canada.,Vector Institute, M5G 1M1, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, M5S 2E4, Toronto, ON, Canada
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195
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Marsh JW, Hayward RJ, Shetty AC, Mahurkar A, Humphrys MS, Myers GSA. Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments. Brief Bioinform 2019; 19:1115-1129. [PMID: 28535295 DOI: 10.1093/bib/bbx043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Indexed: 12/18/2022] Open
Abstract
Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA sequencing technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. Several laboratory protocols have been presented that outline the collection, extraction and sequencing of total RNA for dRNA-Seq experiments, but there is relatively little guidance available for the detailed bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic analyses with currently available software tools.
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Affiliation(s)
- James W Marsh
- The ithree institute, University of Technology Sydney
| | | | - Amol C Shetty
- Institute for Genome Sciences at the University of Maryland, Baltimore
| | - Anup Mahurkar
- Institute for Genome Sciences at the University of Maryland, Baltimore
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196
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Liu L, Kim MH, Hyeon C. Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C. Biophys J 2019; 117:613-625. [PMID: 31337548 DOI: 10.1016/j.bpj.2019.06.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/22/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
Abstract
Adapting a well-established formalism in polymer physics, we develop a minimalist approach to infer three-dimensional folding of chromatin from Hi-C data. The three-dimensional chromosome structures generated from our heterogeneous loop model (HLM) are used to visualize chromosome organizations that can substantiate the measurements from fluorescence in situ hybridization, chromatin interaction analysis by paired-end tag sequencing, and RNA-seq signals. We demonstrate the utility of the HLM with several case studies. Specifically, the HLM-generated chromosome structures, which reproduce the spatial distribution of topologically associated domains from fluorescence in situ hybridization measurement, show the phase segregation between two types of topologically associated domains explicitly. We discuss the origin of cell-type-dependent gene-expression level by modeling the chromatin globules of α-globin and SOX2 gene loci for two different cell lines. We also use the HLM to discuss how the chromatin folding and gene-expression level of Pax6 loci, associated with mouse neural development, are modulated by interactions with two enhancers. Finally, HLM-generated structures of chromosome 19 of mouse embryonic stem cells, based on single-cell Hi-C data collected over each cell-cycle phase, visualize changes in chromosome conformation along the cell-cycle. Given a contact frequency map between chromatic loci supplied from Hi-C, HLM is a computationally efficient and versatile modeling tool to generate chromosome structures that can complement interpreting other experimental data.
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Affiliation(s)
- Lei Liu
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Min Hyeok Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea.
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197
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Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276-W282. [PMID: 30997504 PMCID: PMC6602446 DOI: 10.1093/nar/gkz282] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/29/2019] [Accepted: 04/10/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding the evolutionary background of a bacterial isolate has applications for a wide range of research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA for species identification currently remains popular. Unfortunately, this widespread method suffers from low resolution at the species level due to high sequence conservation. Currently, there is now a wealth of genomic data that can be used to yield more accurate species designations via modern phylogenetic methods and multiple genetic loci. However, these often require extensive expertise and time. The Automated Multi-Locus Species Tree (autoMLST) was thus developed to provide a rapid 'one-click' pipeline to simplify this workflow at: https://automlst.ziemertlab.com. This server utilizes Multi-Locus Sequence Analysis (MLSA) to produce high-resolution species trees; this does not preform multi-locus sequence typing (MLST), a related classification method. The resulting phylogenetic tree also includes helpful annotations, such as species clade designations and secondary metabolite counts to aid natural product prospecting. Distinct from currently available web-interfaces, autoMLST can automate selection of reference genomes and out-group organisms based on one or more query genomes. This enables a wide range of researchers to perform rigorous phylogenetic analyses more rapidly compared to manual MLSA workflows.
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Affiliation(s)
- Mohammad Alanjary
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Katharina Steinke
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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198
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Wang C, Zhang S. Large-scale determination and characterization of cell type-specific regulatory elements in the human genome. J Mol Cell Biol 2019; 9:463-476. [PMID: 29281093 DOI: 10.1093/jmcb/mjx058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 12/19/2017] [Indexed: 01/05/2023] Open
Abstract
Histone modifications have been widely elucidated to play vital roles in gene regulation and cell identity. The Roadmap Epigenomics Consortium generated a reference catalog of several key histone modifications across >100s of human cell types and tissues. Decoding these epigenomes into functional regulatory elements is a challenging task in computational biology. To this end, we adopted a differential chromatin modification analysis framework to comprehensively determine and characterize cell type-specific regulatory elements (CSREs) and their histone modification codes in the human epigenomes of five histone modifications across 127 tissues or cell types. The CSREs show significant relevance with cell type-specific biological functions and diseases and cell identity. Clustering of CSREs with their specificity signals reveals distinct histone codes, demonstrating the diversity of functional roles of CSREs within the same cell or tissue. Last but not least, dynamics of CSREs from close cell types or tissues can give a detailed view of developmental processes such as normal tissue development and cancer occurrence.
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Affiliation(s)
- Can Wang
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.,School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihua Zhang
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.,School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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199
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Kwan HH, Culibrk L, Taylor GA, Leelakumari S, Tan R, Jackman SD, Tse K, MacLeod T, Cheng D, Chuah E, Kirk H, Pandoh P, Carlsen R, Zhao Y, Mungall AJ, Moore R, Birol I, Marra MA, Rosen DAS, Haulena M, Jones SJM. The Genome of the Steller Sea Lion ( Eumetopias jubatus). Genes (Basel) 2019; 10:genes10070486. [PMID: 31248052 PMCID: PMC6678222 DOI: 10.3390/genes10070486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 11/16/2022] Open
Abstract
The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770.
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Affiliation(s)
- Harwood H Kwan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T-1Z4, Canada
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
- Department of Graduate Studies, Bioinformatics, University of British Columbia, Vancouver, BC V6T-1Z4, Canada
| | - Gregory A Taylor
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Sreeja Leelakumari
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Ryan Tan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Shaun D Jackman
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Kane Tse
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Tina MacLeod
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Rebecca Carlsen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T-1Z4, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T-1Z4, Canada
| | - David A S Rosen
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T-1Z4, Canada
- Vancouver Aquarium, Vancouver, BC V6G 3E2, Canada
| | | | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC V5Z-4S6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T-1Z4, Canada.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A-1S6, Canada.
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200
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Richardson MF, Munyard K, Croft LJ, Allnutt TR, Jackling F, Alshanbari F, Jevit M, Wright GA, Cransberg R, Tibary A, Perelman P, Appleton B, Raudsepp T. Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids. Front Genet 2019; 10:586. [PMID: 31293619 PMCID: PMC6598621 DOI: 10.3389/fgene.2019.00586] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022] Open
Abstract
The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological significance. South American camelids serve people in extreme environments and are important fiber and companion animals worldwide. Despite this, the alpaca reference genome lags far behind those available for other domestic species. Here we produced a chromosome-level improved reference assembly for the alpaca genome using the DNA of the same female Huacaya alpaca as in previous assemblies. We generated 190X Illumina short-read, 8X Pacific Biosciences long-read and 60X Dovetail Chicago® chromatin interaction scaffolding data for the assembly, used testis and skin RNAseq data for annotation, and cytogenetic map data for chromosomal assignments. The new assembly VicPac3.1 contains 90% of the alpaca genome in just 103 scaffolds and 76% of all scaffolds are mapped to the 36 pairs of the alpaca autosomes and the X chromosome. Preliminary annotation of the assembly predicted 22,462 coding genes and 29,337 isoforms. Comparative analysis of selected regions of the alpaca genome, such as the major histocompatibility complex (MHC), the region involved in the Minute Chromosome Syndrome (MCS) and candidate genes for high-altitude adaptations, reveal unique features of the alpaca genome. The alpaca reference genome VicPac3.1 presents a significant improvement in completeness, contiguity and accuracy over VicPac2 and is an important tool for the advancement of genomics research in all New World camelids.
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Affiliation(s)
- Mark F Richardson
- Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
| | - Kylie Munyard
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Larry J Croft
- Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Theodore R Allnutt
- Bioinformatics Core Research Group, Deakin University, Geelong, VIC, Australia
| | - Felicity Jackling
- Department of Genetics, The University of Melbourne, Melbourne, VIC, Australia
| | - Fahad Alshanbari
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Matthew Jevit
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Gus A Wright
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Rhys Cransberg
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Ahmed Tibary
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Polina Perelman
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Belinda Appleton
- Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
| | - Terje Raudsepp
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
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