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Predictable and precise template-free CRISPR editing of pathogenic variants (vol 563, pg 646, 2018)

NATURE 2019年第7746期567卷 E1-E2页

作者： Shen, Max W. Arbab, Mandana Hsu, Jonathan Y. Worstell, Daniel Culbertson, Sannie J. Krabbe, Olga Cassa, Christopher A. Liu, David R. Gifford, David K. Sherwood, Richard I. Computational and Systems Biology Program Massachusetts Institute of Technology Cambridge USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge USA Merkin Institute of Transformative Technologies in Healthcare Broad Institute of Harvard and MIT Cambridge USA Department of Chemistry and Chemical Biology Harvard University Cambridge USA Howard Hughes Medical Institute Harvard University Cambridge USA Department of Biological Engineering Massachusetts Institute of Technology Cambridge USA Molecular Pathology Unit Center for Cancer Research and Center for Computational and Integrative Biology Massachusetts General Hospital Charlestown USA Division of Genetics Department of Medicine Brigham and Women’s Hospital and Harvard Medical School Boston USA Hubrecht Institute for Developmental Biology and Stem Cell Research Royal Netherlands Academy of Arts and Sciences (KNAW) Utrecht The Netherlands Broad Institute of MIT and Harvard Cambridge USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge USA

In this Article, a data processing error affected Fig. 3e and Extended Data Table 2; these errors have been corrected online.

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Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals (vol 540, pg 428, 2016)

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NATURE 2019年第7769期572卷 E11-E15页

作者： Schworer, Simon Becker, Friedrich Feller, Christian Baig, Ali H. Kober, Ute Henze, Henriette Kraus, Johann M. Xin, Beibei Lechel, Andre Lipka, Daniel B. Varghese, Christy S. Schmidt, Manuel Rohs, Remo Aebersold, Ruedi Medina, Kay L. Kestler, Hans A. Neri, Francesco von Maltzahn, Julia Tumpel, Stefan Rudolph, K. Lenhard Leibniz-Institute on Aging – Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 Jena Germany Department of Biology Institute of Molecular Systems Biology ETH Zürich Auguste-Piccard-Hof 1 Zürich Switzerland Institute of Medical Systems Biology Ulm University James-Franck-Ring Ulm Germany Molecular and Computational Biology Program University of Southern California 1050 Childs Way Los Angeles USA Department of Internal Medicine I Ulm University Albert-Einstein-Allee 23 Ulm Germany Division of Epigenomics and Cancer Risk Factors DKFZ Im Neuenheimer Feld 280 Heidelberg Germany Faculty of Science University of Zürich Zürich Switzerland Department of Immunology Mayo Clinic 200 First Street SW Rochester USA Faculty of Medicine Friedrich-Schiller-University Jena Germany

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Antigen persistence and TLR stimulation contribute to induction of a durable HIV-1-specific neutralizing antibody response

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Nature communications 2025年第1期16卷 5162页

作者： Kenta Matsuda Mitra Harrison Eleanor Wettstein Jessica Pederson Alyssa A Pullano Lyuba Bolkhovitinov Breanna Kim Isabel Steinberg Trevor Griesman Sarah Stuccio Daniel Rogan Andy Patamawenu Tulley Shofner Nathaniel E Wright Jonathan D Webber Freya Van't Veer Rachel Roenicke Emma Koory Peyton M Roeder Ellison Ober Benjamin Leach Yaroslav Tsybovsky Tyler Stephens Ivan Del Moral-Sanchez Ilja Bontjer Lori W McGinnes-Cullen Eric Chu Jason Liang Jonathan L Torres Ryan N Lin Andy S Tran Gabrielle Dziubla Leonid Serebryannyy Sandeep Narpala Bob Lin Mike Castro Gabriel Ozorowski Andrew B Ward Rogier W Sanders Peter D Kwong Javier Guenaga Richard Wyatt Trudy Morrison Mark Connors HIV-Specific Immunity Section of the Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MD USA. Electron Microscopy Laboratory Cancer Research Technology Program Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research Frederick MD USA. Department of Medical Microbiology and Infection Prevention Amsterdam University Medical Centers Location AMC University of Amsterdam Amsterdam the Netherlands. Department of Microbiology and Physiological Systems Sherman Center University of Massachusetts Medical School Worcester MA USA. Division Of Clinical Research Biostatistics Research Branch National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MD USA. Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA USA. Vaccine Research Center National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MD USA. International AIDS Vaccine Initiative Neutralizing Antibody Center Department of Immunology and Microbiology The Scripps Research Institute San Diego CA USA. HIV-Specific Immunity Section of the Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MD USA. mconnors@nih.gov.

HIV-1 Env glycoprotein (Env) immunogenicity is limited in part by structural instability and extensive glycan shielding and is likely the greatest obstacle to an HIV-1 vaccine. Stabilized Env trimers can elicit serum neutralizing antibodies, but the response is short-lived. Here we use Newcastle Disease Virus-like particle (NDV-VLP) platform to present stabilized versions of HIV-1 Env at high valency and in the context of varied conformational stability, adjuvants, dose, and antigen persistence. Influenza virus hemagglutinin, or SARS-CoV2 Spike-bearing VLPs rapidly induce neutralizing antibodies, in contrast, they were not induced by those bearing Env. A replicating adenovirus type 4 expressing Env rapidly induces autologous neutralizing antibodies. However, durable neutralizing antibodies are induced only when multiple features of a replicating virus infection are combined, with the largest impact from dose and escalating dose. In summary, we show here immunogenicity of HIV-1 Env could be improved by reproducing features of virus infection.

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Towards decoding the coupled decision-making of metabolism and epithelial-mesenchymal transition in cancer

arXiv

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arXiv 2020年

作者： Jia, Dongya Park, Jun Hyoung Kaur, Harsimran Jung, Kwang Hwa Yang, Sukjin Tripathi, Shubham Galbraith, Madeline Deng, Youyuan Jolly, Mohit Kumar Kaipparettu, Benny Abraham Onuchic, José N. Levine, Herbert Center for Theoretical Biological Physics Rice University HoustonTX77005 United States Department of Molecular and Human Genetics Baylor College of Medicine HoustonTX77030 United States Centre for BioSystems Science and Engineering Indian Institute of Science BangaloreKarnataka560012 India PhD Program in Systems Synthetic and Physical Biology Rice University HoustonTX77005 United States Department of Physics Northeastern University BostonMA02115 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Rice University HoustonTX77005 United States Dan L. Duncan Comprehensive Cancer Center Baylor College of Medicine HoustonTX77030 United States Department of Chemistry Rice University HoustonTX77005 United States Department of Biosciences Rice University HoustonTX77005 United States Department of Bioengineering Northeastern University BostonMA02115 United States

cancer cells have the plasticity to adjust their metabolic phenotypes for survival and metastasis. During metastasis, a developmental program known as the epithelial-mesenchymal transition (EMT) plays a critical role. There is extensive cross-talk between metabolism and EMT, but how this leads to coordinated physiological changes is still uncertain. The elusive connection between metabolism and EMT compromises the efficacy of metabolic therapies targeting metastasis. In this review, we aim for clarifying causation between metabolism and EMT based on recent experimental studies and propose integrated theoretical-experimental efforts to better understand the coupled decision-making of metabolism and EMT. © 2020, CC-BY-NC-ND.

关键词： Metabolism

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Correction: A novel role of MNT as a negative regulator of REL and the NF-κB pathway

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Oncogenesis 2021年第8期10卷 57页

作者： Judit Liaño-Pons M Carmen Lafita-Navarro Lorena García-Gaipo Carlota Colomer Javier Rodríguez Alex von Kriegsheim Peter J Hurlin Fabiana Ourique M Dolores Delgado Anna Bigas Lluis Espinosa Javier León Departmento de Biología Molecular Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-Universidad de Cantabria Santander Spain. Department of Microbiology Tumor and Cell Biology (MTC) Biomedicum B7 Karolinska Institutet Stockholm Sweden. Department of Cell Biology UT Southwestern Medical Center Dallas TX USA. Cancer Research Program Institut Hospital del Mar d'Investigacions Mèdiques CIBERONC Hospital del Mar Barcelona Spain. Systems Biology Ireland University College Dublin Dublin Ireland. Edinburgh Cancer Research Center Institute of Genetics and Molecular Medicine University of Edinburgh Edinburgh UK. Shriners Hospitals for Children Research Center Department of Cell Developmental and Cancer Biology and Department of Orthopaedics and Rehabilitation Oregon Health and Science University Portland OR USA. Dept. of Biochemistry Universidade Federal de Santa Catarina (UFSC) Florianópolis Brazil. Departmento de Biología Molecular Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-Universidad de Cantabria Santander Spain. leonj@unican.es.

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Author Correction: Integrative pathway enrichment analysis of multivariate omics data

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Nature communications 2022年第1期13卷 7570页

作者： Marta Paczkowska Jonathan Barenboim Nardnisa Sintupisut Natalie S Fox Helen Zhu Diala Abd-Rabbo Miles W Mee Paul C Boutros Jüri Reimand Computational Biology Program Ontario Institute for Cancer Research 661 University Ave Suite 510 Toronto ON M5G 0A3 Canada. Department of Medical Biophysics University of Toronto 101 College Street Suite 15-701 Toronto ON M5G 1L7 Canada. Department of Pharmacology & Toxicology University of Toronto 1 King's College Circle Room 4207 Toronto ON M5S 1A8 Canada. Department of Human Genetics University of California Los Angeles 10833 Le Conte Avenue Los Angeles CA 90095 USA. Department of Urology University of California Los Angeles 200 Medical Plaza Driveway #140 Los Angeles CA 90024 USA. Institute of Precision Health University of California Los Angeles 10833 Le Conte Avenue Los Angeles CA 90024 USA. Broad Stem Cell Research Centre University of California Los Angeles 615 Charles E Young Drive S Los Angeles CA 90095 USA. Jonsson Comprehensive Cancer Centre University of California Los Angeles 10833 Le Conte Avenue Los Angeles CA 90024 USA. Computational Biology Program Ontario Institute for Cancer Research 661 University Ave Suite 510 Toronto ON M5G 0A3 Canada. Juri.Reimand@utoronto.ca. Department of Medical Biophysics University of Toronto 101 College Street Suite 15-701 Toronto ON M5G 1L7 Canada. Juri.Reimand@utoronto.ca.

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Author Correction: A co-clinical approach identifies mechanisms and potential therapies for androgen deprivation resistance in prostate cancer

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Nature genetics 2020年第10期52卷 1132页

作者： Andrea Lunardi Ugo Ala Mirjam T Epping Leonardo Salmena John G Clohessy Kaitlyn A Webster Guocan Wang Roberta Mazzucchelli Maristella Bianconi Edward C Stack Rosina Lis Akash Patnaik Lewis C Cantley Glenn Bubley Carlos Cordon-Cardo William L Gerald Rodolfo Montironi Sabina Signoretti Massimo Loda Caterina Nardella Pier Paolo Pandolfi Cancer Genetics Program Beth Israel Deaconess Cancer Center Department of Medicine and Pathology Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA. Department of Genetics Biology and Biochemistry Molecular Biotechnology Center University of Turin Turin Italy. Cancer Biology and Genetics Program Sloan-Kettering Institute Memorial Sloan-Kettering Cancer Center New York NY USA. Department of Pathology Human Oncology and Pathogenesis Program Memorial Sloan-Kettering Cancer Center New York NY USA. Biochemistry Cell & Molecular Biology Program Weill Graduate School of Medical Sciences Cornell University New York NY USA. Institute of Pathological Anatomy and Histopathology Polytechnic University of the Marche Region (Ancona) United Hospitals Ancona Italy. Clinic of Oncology Postgraduate School in Medical Oncology Polytechnic University of the Marche Region (Ancona) United Hospitals Ancona Italy. Center for Molecular Oncologic Pathology Dana-Farber Cancer Institute Boston MA USA. Department of Medical Oncology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA. Department of Pathology Brigham and Women's Hospital Harvard Medical School Boston MA USA. Division of Hematology/Oncology Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA. Department of Systems Biology Harvard Medical School Boston MA USA. Division of Signal Transduction Beth Israel Deaconess Medical Center Boston MA USA. Department of Genetics and Genomic Sciences The Mount Sinai School of Medicine New York NY USA. Broad Institute of Harvard and MIT Cambridge MA USA. Preclinical Murine Pharmacogenetics Facility Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA. Cancer Genetics Program Beth Israel Deaconess Cancer Center Department of Medicine and Pathology Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA. ppandolf@bidmc.harvard.edu. Cancer Biology and Genetics Program

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes

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Nature 2020年第7826期585卷 E20页

作者： Elizabeth J Adams Wouter R Karthaus Elizabeth Hoover Deli Liu Antoine Gruet Zeda Zhang Hyunwoo Cho Rose DiLoreto Sagar Chhangawala Yang Liu Philip A Watson Elai Davicioni Andrea Sboner Christopher E Barbieri Rohit Bose Christina S Leslie Charles L Sawyers Human Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer Center New York NY USA. Sandra and Edward Meyer Cancer Center Weill Cornell Medicine New York NY USA. Department of Urology Weill Cornell Medicine New York NY USA. HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medical College New York NY USA. Center for Epigenetics Research Memorial Sloan Kettering Cancer Center New York NY USA. Louis V. Gerstner Jr Graduate School of Biomedical Sciences Memorial Sloan Kettering Cancer Center New York NY USA. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA. Physiology Biophysics and Systems Biology Program Weill Cornell Graduate School New York NY USA. Tri-Institutional Training Program in Computational Biology & Medicine Weill Cornell Medicine New York NY USA. GenomeDx Bioscience Vancouver British Columbia Canada. Englander Institute for Precision Medicine of Weill Cornell Medicine and NewYork-Presbyterian Hospital New York NY USA. Departments of Anatomy Medicine and Urology University of California San Francisco San Francisco CA USA. Human Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer Center New York NY USA. sawyersc@***. Howard Hughes Medical Institute Chevy Chase MD USA. sawyersc@***.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

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Cell 2025年

作者： Pekar, Jonathan E. Lytras, Spyros Ghafari, Mahan Magee, Andrew F. Parker, Edyth Wang, Yu Ji, Xiang Havens, Jennifer L. Katzourakis, Aris Vasylyeva, Tetyana I. Suchard, Marc A. Hughes, Alice C. Hughes, Joseph Rambaut, Andrew Robertson, David L. Dellicour, Simon Worobey, Michael Wertheim, Joel O. Lemey, Philippe Institute of Ecology and Evolution University of Edinburgh Edinburgh United Kingdom Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla 92093 CA United States Department of Biomedical Informatics University of California San Diego La Jolla 92093 CA United States Department of Medicine University of California San Diego La Jolla 92093 CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Medical Research Council University of Glasgow Centre for Virus Research Glasgow United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States Department of Immunology and Microbiology The Scripps Research Institute La Jolla 92037 CA United States Institute of Genomics and Global Health Redeemer's University Osun State Ede Nigeria Department of Computer Science and Engineering University of California San Diego La Jolla 92093 CA United States Department of Mathematics School of Science and Engineering Tulane University New Orleans LA United States Department of Population Health and Disease Prevention University of California Irvine Irvine 92617 CA United States Department of Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles 90095 CA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States School of Biological Sciences University of Hong Kong Hong Kong Hong Kong China Biodiversity Green Development Foundation Beijing China Spatial Epidemiology Lab (SpELL) Université Libre de Bruxelles CP160/12 50 av. FD Roosevelt Bruxelles 1050 Belgium Department of Microbiology Immunology and Transplantation Rega Institute

The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses. © 2025 The Authors

关键词： molecular epidemiology phylogeography sarbecoviruses virus evolution

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Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

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npj Genomic Medicine 2024年第1期9卷 49页

作者： Demidov, German Yaldiz, Burcu Garcia-Pelaez, José de Boer, Elke Schuermans, Nika Van de Vondel, Liedewei Paramonov, Ida Johansson, Lennart F. Musacchia, Francesco Benetti, Elisa Bullich, Gemma Sablauskas, Karolis Beltran, Sergi Gilissen, Christian Hoischen, Alexander Ossowski, Stephan de Voer, Richarda Lohmann, Katja Oliveira, Carla Topf, Ana Vissers, Lisenka E. L. M. Zguro, Kristina Zara, Federico Zaganas, Ioannis Yépez, Vicente A. Wirth, Brunhilde Webb, David Verdin, Hannah Van Nieuwenhove, Erika van Montfrans, Joris van Heurck, Roxane van der Veken, Lars Valle, Laura Uva, Paolo Udd, Bjarne Trimouille, Aurelien Thompson, Rachel Tartaglia, Marco Sznajer, Yves Striano, Pasquale Steinke-Lange, Verena Spilioti, Martha Scudieri, Paolo Schröck, Evelin Schon, Katherine Scala, Marcello Savarese, Marco Santen, Gijs W. E. Rump, Andreas Ruivenkamp, Claudia A. L. Roos, Andreas Rooryck, Caroline Riva, Antonella Renieri, Alessandra Ratnaike, Thiloka Radio, Francesca Clementina Privitera, Flavia De la Paz, Manuel Posada Poppe, Bruce Polavarapu, Kiran Platzer, Konrad Peterlin, Borut Pérez-Dueñas, Belén Pauly, Martje Parrini, Elena Olimpio, Catarina Reghan, Mary O. de Benito, Daniel Natera Osorio, Andrés Nascimento Munell, Francina Münchau, Alexander Moortgat, Stéphanie Monestier, Olivier Molnar, Maria Judit Meunier, Colombine Mertes, Christian Mei, Davide Maystadt, Isabelle May, Patrick Maver, Ales Mathioudakis, Lambros Masclaux, Frédéric Mary, Sandrine Delgado, Beatriz Martínez Marcé-Grau, Anna Malaichamy, Sivasankar Macaya, Alfons Luknárová, Rebeka Martín, Estrella López Lochmüller, Hanns Leitão, Elsa Lederer, Damien Leavis, Helen Laner, Andreas Lacombe, Didier Krass, Leon Korff, Christian Kokosali, Evgenia Karakaya, Mert Karadurmus, Deniz Kapaki, Elisabeth Johari, Mridul Iacomino, Michele Huibers, Manon Horvath, Rita Holinski-Feder, Elke Hoffer, Mariette J. V. Herzog, Rebecca Hemelsoet, Dimitri Bouveret, Eva Hammar Haimel, Matthias Hackman, Peter Guerrini, Renzo Grimbacher, Bodo Greally, Marie Ghani, Hamidah Gagneur, Julien Institute of Medical Genetics and Applied Genomics University of Tübingen Tübingen Germany Institute for Bioinformatics and Medical Informatics (IBMI) University of Tübingen Tübingen Germany Department of Human Genetics Radboud University Medical Center Nijmegen Netherlands Department of Clinical Genetics Maastricht University Medical Center Maastricht Netherlands i3S - Instituto de Investigação e Inovação em Saúde Rua Alfredo Allen 208 Porto 4200-135 Portugal IPATIMUP - Institute of Molecular Pathology and Immunology University of Porto Porto Portugal Faculty of Medicine University of Porto Porto Portugal Donders Institute for Brain Cognition and Behaviour Radboud University Nijmegen Netherlands Department of Clinical Genetics Erasmus MC University Medical Center Rotterdam Netherlands Center for Medical Genetics Ghent University Hospital Ghent Belgium Translational Neurosciences Faculty of Medicine and Health Sciences University of Antwerp Antwerp Belgium Laboratory of Neuromuscular Pathology Institute Born-Bunge University of Antwerp Antwerp Belgium Centro Nacional de Análisis Genómico (CNAG) C/Baldiri Reixac 4 Barcelona 08028 Spain Universitat de Barcelona (UB) Barcelona Spain University of Groningen University Medical Center Groningen Department of Genetics Groningen Netherlands Center for Human Technologies Italian Institute of Technology (IIT) Genova Italy Telethon Institute for Genetics and Medicine Pozzuoli (Napoli) 80078 Italy Department of Medical Biotechnologies Med Biotech Hub and Competence Center University of Siena Siena 53100 Italy Institute of Data Science and Digital Technologies Vilnius University Vilnius Lithuania Departament de Genètica Microbiologia i Estadística Facultat de Biologia Universitat de Barcelona (UB) Barcelona Spain Radboud Institute for Molecular Life Sciences Nijmegen Netherlands Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI) Radboud University Medical Center Nijmegen N

We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs. © The Author(s) 2024.

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