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Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes

Nature communications 2022年第1期13卷 7566页

作者： Matthew A Reyna David Haan Marta Paczkowska Lieven P C Verbeke Miguel Vazquez Abdullah Kahraman Sergio Pulido-Tamayo Jonathan Barenboim Lina Wadi Priyanka Dhingra Raunak Shrestha Gad Getz Michael S Lawrence Jakob Skou Pedersen Mark A Rubin David A Wheeler Søren Brunak Jose M G Izarzugaza Ekta Khurana Kathleen Marchal Christian von Mering S Cenk Sahinalp Alfonso Valencia Jüri Reimand Joshua M Stuart Benjamin J Raphael Department of Computer Science Princeton University Princeton NJ 08540 USA. Department of Biomedical Informatics Emory University Atlanta GA 30322 USA. Department of Biomolecular Engineering and UC Santa Cruz Genomics Institute University of California Santa Cruz Santa Cruz CA 95060 USA. Computational Biology Program Ontario Institute for Cancer Research Toronto Ontario Canada. Department of Information Technology IDLab Ghent University IMEC Ghent the Netherlands. Department of Plant Biotechnology and Bioinformatics Ghent University Ghent the Netherlands. Barcelona Supercomputing Center (BSC) Barcelona 08034 Spain. Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences Norwegian University of Science and Technology Trondheim Norway. Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics University of Zurich CH-8057 Zurich Switzerland. Department of Pathology and Molecular Pathology University Hospital Zurich CH-8091 Zurich Switzerland. Department of Physiology and Biophysics Weill Cornell Medicine New York NY 10065 USA. Vancouver Prostate Centre 2660 Oak Street Vancouver BC V6H 3Z6 Canada. The Broad Institute of MIT and Harvard Cambridge MA 02124 USA. Massachusetts General Hospital Center for Cancer Research Charlestown MA 02129 USA. Harvard Medical School 250 Longwood Avenue Boston MA 02115 USA. Massachusetts General Hospital Department of Pathology Boston MA 02114 USA. Department of Molecular Medicine (MOMA) Aarhus University Hospital Aarhus Denmark. Bioinformatics Research Centre (BiRC) Aarhus University Aarhus Denmark. Human Genome Sequencing Center Baylor College of Medicine Houston TX 77030 USA. DTU Bioinformatics Department of Bio and Health Informatics Technical University of Denmark Kemitorvet 2800 Kongens Lyngby Denmark. Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen 2200 Copenhagen Denmark. De

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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Evaluation of mobile health technology combining telemonitoring and teleintervention versus usual care in vulnerable-phase heart failure management (HERMeS): a multicentre, randomised controlled trial

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The Lancet Digital Health 2025年第5期7卷 100866页

作者： Yun, Sergi Comín-Colet, Josep Calero-Molina, Esther Hidalgo, Encarnación José-Bazán, Núria Cobo Marcos, Marta Soria, Teresa Llàcer, Pau Fernández, Cristina García-Pinilla, José Manuel Cruzado, Concepción González-Franco, Álvaro García-Marina, Eva María Morales-Rull, José Luis Solé, Cristina García-Romero, Elena Núñez, Julio Civera, José Fernández, Coral Faraudo, Mercedes Moliner, Pedro Formiga, Francesc de-Juan Bagudá, Javier Zegri-Reiriz, Isabel Verdú-Rotellar, José María Vela, Emili Monterde, David Piera-Jiménez, Jordi Carot-Sans, Gerard Enjuanes, Cristina Faculty of Medicine and Health Sciences University of Barcelona Barcelona Spain Bio-Heart Cardiovascular Diseases Research Group Bellvitge Biomedical Research Institute L'Hospitalet de Llobregat Barcelona Spain Community Heart Failure Program Cardiology and Internal Medicine Department Bellvitge University Hospital L'Hospitalet de Llobregat Barcelona Spain Internal Medicine Department Bellvitge University Hospital L'Hospitalet de Llobregat Barcelona Spain Cardiology Department Bellvitge University Hospital L'Hospitalet de Llobregat Barcelona Spain Biomedical Research Networking Center on Cardiovascular Diseases Carlos III Health Institute Madrid Spain Department of Clinical Sciences School of Medicine University of Barcelona Barcelona Spain Cardiology Department Puerta de Hierro Majadahonda University Hospital Puerta de Hierro-Segovia de Arana Health Research Institute Madrid Spain Internal Medicine Department Hospital Universitario Ramón y Cajal IRYCIS Madrid Spain Department of Medicine and Medical Specialties Facultad de Medicina y Ciencias de la Salud Universidad de Alcalá Madrid Spain Cardiology Department Heart Failure and Familial Cardiomyopathy Unit Virgen de la Victoria University Hospital Instituto de Biomedicina de Málaga-IBIMA Plataforma BIONAND Málaga Spain Department of Medicine and Dermatology Universidad de Málaga Málaga Spain Internal Medicine Department Central de Asturias University Hospital Foundation for Health and Biomedicine Research and Innovation of Asturias Oviedo Spain Internal Medicine Department Heart Failure Unit Arnau de Vilanova University Hospital Lleida Biomedical Research Institute's Dr Pifarré Foundation Lleida Spain Advanced Heart Failure and Heart Transplant Program Cardiology Department Bellvitge University Hospital L'Hospitalet de Llobregat Barcelona Spain Cardiology Department Clinic of València University Hospital Biomedical Research Institute of València València Spain School of Medicine University of Valè

Background: The potential of mobile health (mHealth) technology combining telemonitoring and teleintervention as a non-invasive intervention to reduce the risk of cardiovascular events in patients with heart failure during the early post-discharge period (ie, the vulnerable phase) has not been evaluated to our knowledge. We investigated the efficacy of incorporating mHealth into routine heart failure management in vulnerable-phase patients. Methods: The Heart Failure Events Reduction with Remote Monitoring and eHealth Support (HERMeS) trial was a 24-week, randomised, controlled, open-label with masked endpoint adjudication, phase 3 trial conducted in ten centres (hospitals [n=9] and a primary care service [n=1]) experienced in heart failure management in Spain. We enrolled adults (aged ≥18 years) with heart failure diagnosed according to the 2016 European Society of Cardiology criteria (then-current clinical practice guidelines at the initiation of the trial) who had recently been discharged (within the preceding 30 days of enrolment) from a hospital admission that was due to heart failure decompensation, or who were in the process of discharge planning. After discharge, participants were centrally randomly assigned (1:1) via a web-based system to mHealth, comprising telemonitoring and preplanned structured health-care follow-up via videoconference, or usual care according to each centre's heart failure care framework including a nurse-led educational programme. The primary outcome was a composite of the occurrence of cardiovascular death or worsening heart failure events during the 6-month follow-up period, assessed by time-to-first-event analysis in the full analysis set by the intention-to-treat principle. No prospective systematic collection of harms information was planned. The HERMeS trial is registered with ***, NCT03663907, and is completed. Findings: From May 15, 2018, to April 4, 2022, 506 participants (207 [41%] women and 299 [59%] men) wer

关键词： mHealth

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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YY-1224, a terpene trilactone-strengthened Ginkgo biloba, attenuates neurodegenerative changes induced by β-amyloid (1-42) or double transgenic overexpression of APP and PS1 via inhibition of cyclooxygenase-2

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Journal of Neuroinflammation 2017年第1期14卷 1-22页

作者： Li, Zheng-Yi Chung, Yoon Hee Shin, Eun-Joo Dang, Duy-Khanh Jeong, Ji Hoon Ko, Sung Kwon Nah, Seung-Yeol Baik, Tae Gon Jhoo, Jin Hyeong Ong, Wei-Yi Nabeshima, Toshitaka Kim, Hyoung-Chun Kangwon National University Neuropsychopharmacology and Toxicology Program College of Pharmacy Chunchon 24341 South Korea Chung-Ang University Department of Anatomy College of Medicine Seoul 06974 South Korea Chung-Ang University Department of Pharmacology College of Medicine Seoul 06974 South Korea Semyung University Department of Oriental Medical Food and Nutrition Jecheon 27136 South Korea Konkuk University Ginsentology Research Laboratory and Department of Physiology College of Veterinary Medicine and Bio/Molecular Informatics Center Seoul 05029 South Korea R and D Center Yuyu Pharma Seoul 04598 South Korea Kangwon National University Department of Psychiatry Medical School Chunchon 24341 South Korea National University of Singapore Department of Anatomy Singapore 119260 Singapore Meijo University Nabeshima Laboratory Graduate School of Pharmaceutical Sciences Nagoya 468-8503 Japan

Background: Ginkgo biloba has been reported to possess free radical-scavenging antioxidant activity and anti-inflammatory properties. In our pilot study, YY-1224, a terpene trilactone-strengthened extract of G. biloba, showed anti-inflammatory, neurotrophic, and antioxidant effects. Results: We investigated the pharmacological potential of YY-1224 in β-amyloid (Aβ) (1-42)-induced memory impairment using cyclooxygenase-2 (COX-2) knockout (-/-) and APPswe/PS1dE9 transgenic (APP/PS1 Tg) mice. Repeated treatment with YY-1224 significantly attenuated Aβ (1-42)-induced memory impairment in COX-2 (+/+) mice, but not in COX-2 (-/-) mice. YY-1224 significantly attenuated Aβ (1-42)-induced upregulation of platelet-activating factor (PAF) receptor gene expression, reactive oxygen species, and pro-inflammatory factors. In addition, YY-1224 significantly inhibited Aβ (1-42)-induced downregulation of PAF-acetylhydrolase-1 (PAF-AH-1) and peroxisome proliferator-activated receptor γ (PPARγ) gene expression. These changes were more pronounced in COX-2 (+/+) mice than in COX-2 (-/-) mice. YY-1224 significantly attenuated learning impairment, Aβ deposition, and pro-inflammatory microglial activation in APP/PS1 Tg mice, whereas it significantly enhanced PAF-AH and PPARγ expression. A preferential COX-2 inhibitor, meloxicam, did not affect the pharmacological activity by YY-1224, suggesting that the COX-2 gene is a critical mediator of the neuroprotective effects of YY-1224. The protective activity of YY-1224 appeared to be more efficacious than a standard G. biloba extract (Gb) against Aβ insult. Conclusions: Our results suggest that the protective effects of YY-1224 against Aβ toxicity may be associated with its PAF antagonistic- and PPARγ agonistic-potential as well as inhibition of the Aβ-mediated pro-inflammatory switch of microglia phenotypes through suppression of COX-2 expression. © 2017 The Author(s).

关键词： APPswe/PS1dE9 transgenic mice Cyclooxygenase-2 knockout mice Microglia Peroxisome proliferators-activated receptor γ Platelet-activating factor Terpene trilactone-strengthened G. biloba

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Education for the future

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Science 2018年第6396期360卷 1409-1412页

作者： Cheung, Man Kit Schwendimann, Beat A. Ward, Adrian Pietrzak, Barbara Mollaoglu, Gurkan Duong, Michael Tran Allareddy, Veerasathpurush Ulltveit-Moe, Nils Dutton-Regester, Ken Zhang, Jian Scult, Matthew A. Singh, Poonam C. Yan, Hong Young Naz, Saima Isaacson, Kyle Dennis, Allison F. Beardsley, Felicia Rounds Al-Humaidan, Eyad Ibrahim Lo, Cody Jones, Tyler Sood, Prashant Nieuwenhuis, Rense Ali, Basant A. Yu, Kun-Hsing Arthur, Patrick Kobina Kumar, Brijesh Buschke, Falko Chen, Alexander Cingl, Lubomír O’Mullane, Anthony Peter Coetzee, Vinet Zaidi, Syed Shan-e-Ali Konstantinides, Nikos School of Life Sciences Chinese University of Hong Kong Shatin New Territories Hong Kong Graduate School of Education University of California Berkeley Berkeley 94720 CA United States University of Queensland St. Lucia 4072 QLD Australia Department of Hydrobiology Faculty of Biology Biological and Chemical Research Centre University of Warsaw Warsaw 02-089 Poland Department of Oncological Sciences University of Utah School of Medicine Salt Lake City 84112 UT United States Perelman School of Medicine University of Pennsylvania Philadelphia 19104 PA United States University of Illinois College of Dentistry Chicago 60612 IL United States Department of Information and Communication Technology University of Agder 4879 Grimstad Norway Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute Brisbane 4006 QLD Australia School of Safety and Environmental Engineering Hunan Institute of Technology Hengyang Hunan 421002 China Lahore 54000 Punjab Pakistan Department of Psychology and Neuroscience Duke University Durham 27708 NC United States National Museum of Marine Biology and Aquarium Chercheng Pingtung County 94450 Taiwan Division of Plant Microbe Interactions CSIR–National Botanical Research Institute Lucknow 226001 Uttar Pradesh India Program in Cell Molecular Developmental Biology and Biophysics (CMDB) Johns Hopkins University Baltimore 21218 MD United States Stem Cell and Tissue Re-Engineering Program King Faisal Specialist Hospital and Research Centre Riyadh Saudi Arabia Department of Sociology and Anthropology University of La Verne La Verne 91750 CA United States Department of Bioengineering University of Utah Salt Lake City 84112 UT United States MRC Centre for Medical Mycology University of Aberdeen Aberdeen AB25 2ZD United Kingdom Faculty of Medicine University of British Columbia Vancouver V6T 1Z2 BC Canada School of Engineering Brown University Providence 02912 RI United States

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Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

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Nature 2024年第8003期627卷 347-357页

作者： Ken Suzuki Konstantinos Hatzikotoulas Lorraine Southam Henry J Taylor Xianyong Yin Kim M Lorenz Ravi Mandla Alicia Huerta-Chagoya Giorgio E M Melloni Stavroula Kanoni Nigel W Rayner Ozvan Bocher Ana Luiza Arruda Kyuto Sonehara Shinichi Namba Simon S K Lee Michael H Preuss Lauren E Petty Philip Schroeder Brett Vanderwerff Mart Kals Fiona Bragg Kuang Lin Xiuqing Guo Weihua Zhang Jie Yao Young Jin Kim Mariaelisa Graff Fumihiko Takeuchi Jana Nano Amel Lamri Masahiro Nakatochi Sanghoon Moon Robert A Scott James P Cook Jung-Jin Lee Ian Pan Daniel Taliun Esteban J Parra Jin-Fang Chai Lawrence F Bielak Yasuharu Tabara Yang Hai Gudmar Thorleifsson Niels Grarup Tamar Sofer Matthias Wuttke Chloé Sarnowski Christian Gieger Darryl Nousome Stella Trompet Soo-Heon Kwak Jirong Long Meng Sun Lin Tong Wei-Min Chen Suraj S Nongmaithem Raymond Noordam Victor J Y Lim Claudia H T Tam Yoonjung Yoonie Joo Chien-Hsiun Chen Laura M Raffield Bram Peter Prins Aude Nicolas Lisa R Yanek Guanjie Chen Jennifer A Brody Edmond Kabagambe Ping An Anny H Xiang Hyeok Sun Choi Brian E Cade Jingyi Tan K Alaine Broadaway Alice Williamson Zoha Kamali Jinrui Cui Manonanthini Thangam Linda S Adair Adebowale Adeyemo Carlos A Aguilar-Salinas Tarunveer S Ahluwalia Sonia S Anand Alain Bertoni Jette Bork-Jensen Ivan Brandslund Thomas A Buchanan Charles F Burant Adam S Butterworth Mickaël Canouil Juliana C N Chan Li-Ching Chang Miao-Li Chee Ji Chen Shyh-Huei Chen Yuan-Tsong Chen Zhengming Chen Lee-Ming Chuang Mary Cushman John Danesh Swapan K Das H Janaka de Silva George Dedoussis Latchezar Dimitrov Ayo P Doumatey Shufa Du Qing Duan Kai-Uwe Eckardt Leslie S Emery Daniel S Evans Michele K Evans Krista Fischer James S Floyd Ian Ford Oscar H Franco Timothy M Frayling Barry I Freedman Pauline Genter Hertzel C Gerstein Vilmantas Giedraitis Clicerio González-Villalpando Maria Elena González-Villalpando Penny Gordon-Larsen Myron Gross Lindsay A Guare Sophie Hackinger Liisa Hakaste Sohee Han Andrew T Hattersley Christian Herder Momoko Horikoshi Annie-Green Howard Willa Centre for Genetics and Genomics Versus Arthritis Centre for Musculoskeletal Research Division of Musculoskeletal and Dermatological Sciences University of Manchester Manchester UK. Department of Diabetes and Metabolic Diseases Graduate School of Medicine University of Tokyo Tokyo Japan. Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan. Institute of Translational Genomics Helmholtz Zentrum München German Research Center for Environmental Health Neuherberg Germany. konstantinos.hatzikotoulas@helmholtz-munich.de. Institute of Translational Genomics Helmholtz Zentrum München German Research Center for Environmental Health Neuherberg Germany. Center for Precision Health Research National Human Genome Research Institute National Institutes of Health Bethesda MD USA. British Heart Foundation Cardiovascular Epidemiology Unit Department of Public Health and Primary Care University of Cambridge Cambridge UK. Heart and Lung Research Institute University of Cambridge Cambridge UK. Department of Epidemiology School of Public Health Nanjing Medical University Nanjing China. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor MI USA. Corporal Michael J. Crescenz VA Medical Center Philadelphia PA USA. Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania Perelman School of Medicine Philadelphia PA USA. Department of Genetics University of Pennsylvania Perelman School of Medicine Philadelphia PA USA. Programs in Metabolism and Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA. Diabetes Unit and Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. TIMI Study Group Division of Cardiovascular Medicine Brigham and Women's Hospital Harvard Medical School Boston MA USA. William Harvey Research Institute Barts and the London School of Medicine and Dentistry Queen Mary University of London L

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes and molecular mechanisms that are often specific to cell type. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.

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The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

NPJ Biodiversity

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NPJ biodiversity 2024年第1期3卷 1-17页

作者： Mc Cartney, Ann M. Formenti, Giulio Mouton, Alice De Panis, Diego Marins, Luísa S. Leitão, Henrique G. Diedericks, Genevieve Kirangwa, Joseph Morselli, Marco Salces-Ortiz, Judit Escudero, Nuria Iannucci, Alessio Natali, Chiara Svardal, Hannes Fernández, Rosa De Pooter, Tim Joris, Geert Strazisar, Mojca Wood, Jonathan M. D. Herron, Katie E. Seehausen, Ole Watts, Phillip C. Shaw, Felix Davey, Robert P. Minotto, Alice Fernández, José M. Böhne, Astrid Alegria, Carla Alioto, Tyler Alves, Paulo C. Amorim, Isabel R. Aury, Jean-Marc Backstrom, Niclas Baldrian, Petr Baltrunaite, Laima Barta, Endre Bedhom, Bertrand Belser, Caroline Bergsten, Johannes Bertrand, Laurie Bilandija, Helena Binzer-Panchal, Mahesh Bista, Iliana Blaxter, Mark Borges, Paulo A. V. Dias, Guilherme Borges Bosse, Mirte Brown, Tom Bruggmann, Rémy Buena-Atienza, Elena Burgin, Josephine Buzan, Elena Cariani, Alessia Casadei, Nicolas Chiara, Matteo Chozas, Sergio Jr, Fedor Čiampor Crottini, Angelica Cruaud, Corinne Cruz, Fernando Dalen, Love Biase, Alessiode Delcampo, Javier Delic, Teo Dennis, Aliceb. Derks, Martijn F. L. Diroma, Maria Angela Djan, Mihajla Duprat, Simone Eleftheriadi, Klara Feulner, Philine G. D. Flot, Jean-François Forni, Giobbe Fosso, Bruno Fournier, Pascal Fournier-Chambrillon, Christine Gabaldon, Toni Garg, Shilpa Gissi, Carmela Giupponi, Luca Gomez-Garrido, Jessica González, Josefa Grilo, Miguel L. Grüning, Björn Guerin, Thomas Guiglielmoni, Nadege Gut, Marta Haesler, Marcel P. Hahn, Christoph Halpern, Balint Harrison, Peter W. Heintz, Julia Hindrikson, Maris Höglund, Jacob Howe, Kerstin Hughes, Graham M. Istace, Benjamin Cock, Mark J. Janžekovič, Franc Jonsson, Zophonias O. Joye-Dind, Sagane Koskimäki, Janne J. Krystufek, Boris Kubacka, Justyna Kuhl, Heiner Kusza, Szilvia Labadie, Karine Lähteenaro, Meri Lantz, Henrik Lavrinienko, Anton Leclère, Lucas Lopes, Ricardo Jorge Madsen, Ole Magdelenat, Ghislaine Magoga, Giulia Manousaki, Tereza Mappes, Tapio Marques, Joao Pedro Redondo, Gemma I. Martinez Maumus, Florian McCarthy, Shane A. M Genomics Institute University of California SantaCruz CA United States TheVertebrate Genome Laboratory The Rockefeller University NewYork NY United States Department of Biology University of Florence Sesto Fiorentino Italy InBios-Conservation Genetics Laboratory University of Liege Liege Belgium Leibniz Institut für Zoo und Wildtierforschung Berlin Germany Berlin Center for Genomics in Biodiversity Research Berlin Germany Department of Biology University of Antwerp Antwerp Belgium Institute of Zoology University of Cologne Cologne Germany Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parma Italy Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra Barcelona Spain Naturalis Biodiversity Center Leiden Netherlands Neuromics Support Facility VIB Center for Molecular Neurology VIB Antwerp Belgium Neuromics Support Facility Department of Biomedical SciencesUniversity ofAntwerp Antwerp Belgium Tree of Life WellcomeSanger Institute Cambridge Hinxton United Kingdom School of Biology and Environmental Science University College Dublin Belfield Ireland Aquatic Ecology & Evolution Institute of Ecology & Evolution University of Bern Bern Switzerland Department of Fish Ecology & Evolution Eawag Kastanienbaum Switzerland Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland The EarlhamInstitute NorwichResearchPark Norwich United Kingdom Digital Science London United Kingdom Barcelona Supercomputing Center Spanish National Bioinformatics Institute ELIXIR Spain Getafe Spain Leibniz Institute for the Analysis of Biodiversity Change Museum Koenig Bonn Bonn Germany CE3C—Centre for Ecology Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute Faculdade de Ciências Universidade de Lisboa Campo Grande Lisboa Portugal Centro Nacional de Análisis Genómico (CNAG) Barcelona Spain Universitat de Barcelona (UB) Barcelona Spain CIBIO Cen

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries;however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth bioGenome Project (EBP), aiming to produce a database of highquality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP. © The Author(s) 2024, corrected publication 2024.

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Hitting two birds with one stone: The unforeseen consequences of nested gene knockouts in Caenorhabditis elegans

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Worm 2016年第2期5卷 e1156835页

作者： Richard Jovelin Asher D Cutter Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada Informatics and Bio-Computing Program Ontario Institute for Cancer Research Toronto Ontario Canada. Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada.

Nested genes represent an intriguing form of non-random genomic organization in which the boundaries of one gene are fully contained within another, longer host gene. The C. elegans genome contains over 10,000 nested genes, 92% of which are ncRNAs, which occur inside 16% of the protein coding gene complement. Host genes are longer than non-host coding genes, owing to their longer and more numerous introns. Indel alleles are available for nearly all of these host genes that simultaneously alter the nested gene, raising the possibility of nested gene disruption contributing to phenotypes that might be attributed to the host gene. Such dual-knockouts could represent a source of misinterpretation about host gene function. Dual-knockouts might also provide a novel source of synthetic phenotypes that reveal the functional effects of ncRNA genes, whereby the host gene disruption acts as a perturbed genetic background to help unmask ncRNA phenotypes.

关键词： gene knockout mutations nested genes non-coding RNAs polymorphism

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