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Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification

Nature communications 2025年第1期16卷 4852页

作者： Maria Zanti Denise G O'Mahony Michael T Parsons Leila Dorling Joe Dennis Nicholas J Boddicker Wenan Chen Chunling Hu Marc Naven Kristia Yiangou Thomas U Ahearn Christine B Ambrosone Irene L Andrulis Antonis C Antoniou Paul L Auer Caroline Baynes Clara Bodelon Natalia V Bogdanova Stig E Bojesen Manjeet K Bolla Kristen D Brantley Nicola J Camp Archie Campbell Jose E Castelao Melissa H Cessna Jenny Chang-Claude Fei Chen Georgia Chenevix-Trench Don M Conroy Kamila Czene Arcangela De Nicolo Susan M Domchek Thilo Dörk Alison M Dunning A Heather Eliassen D Gareth Evans Peter A Fasching Jonine D Figueroa Henrik Flyger Manuela Gago-Dominguez Montserrat García-Closas Gord Glendon Anna González-Neira Felix Grassmann Andreas Hadjisavvas Christopher A Haiman Ute Hamann Steven N Hart Mikael B A Hartman Weang-Kee Ho James M Hodge Reiner Hoppe Sacha J Howell Anna Jakubowska Elza K Khusnutdinova Yon-Dschun Ko Peter Kraft Vessela N Kristensen James V Lacey Jingmei Li Geok Hoon Lim Sara Lindström Artitaya Lophatananon Craig Luccarini Arto Mannermaa Maria Elena Martinez Dimitrios Mavroudis Roger L Milne Kenneth Muir Katherine L Nathanson Rocio Nuñez-Torres Nadia Obi Janet E Olson Julie R Palmer Mihalis I Panayiotidis Alpa V Patel Paul D P Pharoah Eric C Polley Muhammad U Rashid Kathryn J Ruddy Emmanouil Saloustros Elinor J Sawyer Marjanka K Schmidt Melissa C Southey Veronique Kiak-Mien Tan Soo Hwang Teo Lauren R Teras Diana Torres Amy Trentham-Dietz Thérèse Truong Celine M Vachon Qin Wang Jeffrey N Weitzel Siddhartha Yadav Song Yao Gary R Zirpoli Melissa S Cline Peter Devilee Sean V Tavtigian David E Goldgar Fergus J Couch Douglas F Easton Amanda B Spurdle Kyriaki Michailidou Biostatistics Unit The Cyprus Institute of Neurology & Genetics Nicosia Cyprus. Department of Medical Genetics Oslo University Hospital Oslo Norway. Population Health Program QIMR Berghofer Medical Research Institute Brisbane Queensland Australia. Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care University of Cambridge Cambridge UK. Department of Quantitative Health Sciences Division of Computational Biology Mayo Clinic Rochester MN USA. Department of Laboratory Medicine and Pathology Mayo Clinic Rochester MN USA. Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Department of Health and Human Services Bethesda MD USA. Department of Cancer Prevention and Control Roswell Park Comprehensive Cancer Institute Buffalo NY USA. Fred A. Litwin Center for Cancer Genetics Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Toronto Ontario Canada. Department of Molecular Genetics University of Toronto Toronto Ontario Canada. Division of Biostatistics Data Science Institute and Cancer Center Medical College of Wisconsin Milwaukee WI USA. Centre for Cancer Genetic Epidemiology Department of Oncology University of Cambridge Cambridge UK. Department of Population Science American Cancer Society Atlanta GA USA. Radiation Oncology Research Unit Hannover Medical School Hannover Germany. 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. Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA. Department of Internal Medicine and Huntsman Cancer Institute University of Utah Salt Lake City UT USA. Centre for Genomic and Experimental Medicine Institute of Genetics & Cancer The University of Ed

Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one evidence type used to classify VUS. As an initiative of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Analytical Working Group we analyze germline sequencing data of BRCA1 and BRCA2 from 96,691 female breast cancer cases and 302,116 controls from three studies: the BRIDGES study of the Breast cancer Association Consortium, the cancer Risk Estimates Related to Susceptibility consortium, and the UK Biobank. We observe 11,207 BRCA1 and BRCA2 variants, with 6909 being coding, covering 23.4% of BRCA1 and BRCA2 VUS in ClinVar and 19.2% of ClinVar curated (likely) benign or pathogenic variants. Case-control likelihood ratio (ccLR) evidence is highly consistent with ClinVar assertions for (likely) benign or pathogenic variants; exhibiting 99.1% sensitivity and 95.3% specificity for BRCA1 and 93.3% sensitivity and 86.6% specificity for BRCA2. This approach provides case-control evidence for 787 unclassified variants; these include 579 with strong or moderate benign evidence and 10 with strong pathogenic evidence for which ccLR evidence is sufficient to alter clinical classification.

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Genetic diversity of tumors with mismatch repair deficiency influences anti-PD-1 immunotherapy response

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Science 2019年第6439期364卷 485-491页

作者： Mandal, Rajarsi Samstein, Robert M. Lee, Ken-Wing Havel, Jonathan J. Wang, Hao Krishna, Chirag Sabio, Erich Y. Makarov, Vladimir Kuo, Fengshen Blecua, Pedro Ramaswamy, Apoorva T. Durham, Jennifer N. Bartlett, Bjarne Ma, Xiaoxiao Srivastava, Raghvendra Middha, Sumit Zehir, Ahmet Hechtman, Jaclyn F. Morris, Luc Gt Weinhold, Nils Riaz, Nadeem Le, Dung T. Diaz, Luis A. Chan, Timothy A. Department of Otolaryngology-Head and Neck Surgery Johns Hopkins University Baltimore 21287 MD United States Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins Baltimore 21287 MD United States Human Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer Center New York 10065 NY United States Department of Radiation Oncology Memorial Sloan Kettering Cancer Center New York 10065 NY United States Immunogenomics and Precision Oncology Platform Memorial Sloan Kettering Cancer Center New York 10065 NY United States Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Baltimore 21287 MD United States Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York 10065 NY United States Department of Otolaryngology-Head and Neck Surgery Weill Cornell New York Presbyterian Hospital New York 10065 NY United States Swim Across America Laboratory at Johns Hopkins Baltimore 21287 MD United States Department of Pathology Memorial Sloan Kettering Cancer Center New York 10065 NY United States Head and Neck Service Department of Surgery Memorial Sloan Kettering Cancer Center New York 10065 NY United States Division of Solid Tumor Oncology Department of Medicine Memorial Sloan Kettering Cancer Center New York 10065 NY United States Johns Hopkins Department of Otolaryngology-Head and Neck Surgery Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins Baltimore 21287 MD United States

Tumors with mismatch repair deficiency (MMR-d) are characterized by sequence alterations in microsatellites and can accumulate thousands of mutations. This high mutational burden renders tumors immunogenic and sensitive to programmed cell death-1 (PD-1) immune checkpoint inhibitors. Yet, despite their tumor immunogenicity, patients with MMR-deficient tumors experience highly variable responses, and roughly half are refractory to *** present experimental and clinical evidence showing that the degree of microsatellite instability (MSI) and resultant mutational load, in part, underlies the variable response to PD-1 blockade immunotherapy in MMR-d human and mouse tumors. The extent of response is particularly associated with the accumulation of insertion-deletion (indel) mutational load. This study provides a rationale for the genome-wide characterization of MSI intensity and mutational load to better profile responses to anti-PD-1 immunotherapy across MMR-deficient human cancers. © 2019 American Association for the Advancement of Science. All rights reserved.

关键词： Rajarsi Mandal[1] [2] [3] † Robert M. Samstein[3] [4] Ken-Wing Lee[3] Jonathan J. Havel[3] [5] Hao Wang[6] Chirag Krishna[7] Erich Y. Sabio[3] Vladimir Makarov[3] [5] Fengshen Kuo[5] Pedro Blecua[4] Apoorva T. Ramaswamy[8] Jennifer N. Durham[2] [6] [9] Bjarne Bartlett[9] Xiaoxiao Ma[3] Raghvendra Srivastava[5] Sumit Middha[10] Ahmet Zehir[10] Jaclyn F. Hechtman[10] Luc GT Morris[3] [5] [11] Nils Weinhold[4] Nadeem Riaz[3] [4] [5] Dung T. Le[2] [6] [9] Luis A. Diaz Jr.[5] [12] Timothy A. Chan[3] [4] [5] ‡

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AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets

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Immunoinformatics (Amsterdam, Netherlands) 2023年 10卷 100025页

作者： William D Lees Scott Christley Ayelet Peres Justin T Kos Brian Corrie Duncan Ralph Felix Breden Lindsay G Cowell Gur Yaari Martin Corcoran Gunilla B Karlsson Hedestam Mats Ohlin Andrew M Collins Corey T Watson Christian E Busse Institute of Structural and Molecular Biology Birkbeck College London England. Human-Centered Computing and Information Science Institute for Systems and Computer Engineering Technology and Science Porto Portugal. Peter O'Donnell Jr. School of Public Health UT Southwestern Medical Center Dallas TX USA. Bioengineering Program Faculty of Engineering Bar-Ilan University Ramat Gan Israel. Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville KY USA. Department of Biological Sciences Simon Fraser University Burnaby BC Canada. Fred Hutchinson Cancer Research Center Seattle WA USA. Peter O'Donnell Jr. School of Public Health Department of Immunology School of Biomedical Sciences UT Southwestern Medical Center Dallas TX USA. Department of Microbiology Tumor and Cell Biology Karolinska Institutet Stockholm Swede. Department of Immunotechnology and SciLifeLab Lund University Lund Sweden. School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia. Division of B Cell Immunology German Cancer Research Center Heidelberg Germany.

Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.

关键词： AIRR-seq Immune receptor Immune receptor germline Immune receptor repertoire Rep-seq

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Failure of human rhombic lip differentiation underlies medulloblastoma formation (vol 609, pg 1021, 2022)

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NATURE 2022年第7940期612卷 E12-E12页

作者： Hendrikse, Liam D. Haldipur, Parthiv Saulnier, Olivier Millman, Jake Sjoboen, Alexandria H. Erickson, Anders W. Ong, Winnie Gordon, Victor Coudiere-Morrison, Ludivine Mercier, Audrey L. Shokouhian, Mohammad Suarez, Raul A. Ly, Michelle Borlase, Stephanie Scott, David S. Vladoiu, Maria C. Farooq, Hamza Sirbu, Olga Nakashima, Takuma Nambu, Shohei Funakoshi, Yusuke Bahcheli, Alec Diaz-Mejia, J. Javier Golser, Joseph Bach, Kathleen Phuong-Bao, Tram Skowron, Patryk Wang, Evan Y. Kumar, Sachin A. Balin, Polina Visvanathan, Abhirami Lee, John J. Y. Ayoub, Ramy Chen, Xin Chen, Xiaodi Mungall, Karen L. Luu, Betty Berube, Pierre Wang, Yu C. Pfister, Stefan M. Kim, Seung-Ki Delattre, Olivier Bourdeaut, Franck Doz, Francois Masliah-Planchon, Julien Grajkowska, Wieslawa A. Loukides, James Dirks, Peter Fevre-Montange, Michelle Jouvet, Anne French, Pim J. Kros, Johan M. Zitterbart, Karel Bailey, Swneke D. Eberhart, Charles G. Rao, Amulya A. N. Giannini, Caterina Olson, James M. Garami, Miklos Hauser, Peter Phillips, Joanna J. Ra, Young S. de Torres, Carmen Mora, Jaume Li, Kay K. W. Ng, Ho-Keung Poon, Wai S. Pollack, Ian F. Lopez-Aguilar, Enrique Gillespie, G. Yancey Van Meter, Timothy E. Shofuda, Tomoko Vibhakar, Rajeev Thompson, Reid C. Cooper, Michael K. Rubin, Joshua B. Kumabe, Toshihiro Jung, Shin Lach, Boleslaw Iolascon, Achille Ferrucci, Veronica de Antonellis, Pasqualino Zollo, Massimo Cinalli, Giuseppe Robinson, Shenandoah Stearns, Duncan S. Van Meir, Erwin G. Porrati, Paola Finocchiaro, Gaetano Massimino, Maura Carlotti, Carlos G. Faria, Claudia C. Roussel, Martine F. Boop, Frederick Chan, Jennifer A. Aldinger, Kimberly A. Razavi, Ferechte Silvestri, Evelina McLendon, Roger E. Thompson, Eric M. Ansari, Marc Garre, Maria L. Chico, Fernando Eguia, Pilar Perezpena, Mario Morrissy, A. Sorana Cavalli, Florence M. G. Wu, Xiaochong Daniels, Craig Rich, Jeremy N. Jones, Steven J. M. Moore, Richard A. Marra, Marco A. Huang, Xi Reimand, Juri Sorensen, Poul H. Wechsler-Reya, Robert J. Weiss, William A. Pugh, Trevor J. Garzia, Liv The Arthur and Sonia Labatt Brain Tumor Research Centre The Hospital for Sick Children Toronto Ontario Canada Developmental and Stem Cell Biology Program The Hospital for Sick Children Toronto Ontario Canada Department of Medical Biophysics University of Toronto Toronto Ontario Canada Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada Department of Molecular Genetics University of Toronto Toronto Ontario Canada Division of Neurosurgery The Hospital for Sick Children Toronto Ontario Canada Division of Haematology/Oncology Department of Pediatrics The Hospital for Sick Children Toronto Ontario Canada Computational Biology Program Ontario Institute for Cancer Research Toronto Ontario Canada Princess Margaret Cancer Centre University Health Network Toronto Ontario Canada Center for Integrative Brain Research Seattle Children’s Research Institute Seattle WA USA Brotman Baty Institute for Precision Medicine Seattle WA USA Department of Biochemistry and Medical Genetics University of Manitoba Winnipeg Manitoba Canada CancerCare Manitoba Research Institute Winnipeg Manitoba Canada PSL Research University Université Paris Sud Université Paris-Saclay CNRS UMR 3347 INSERM U1021 Institut Curie Orsay France Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics Rady Faculty of Health Sciences University of Manitoba Winnipeg Manitoba Canada Division of Brain Tumor Translational Research National Cancer Center Research Institute Tokyo Japan Adaptive Oncology Ontario Institute for Cancer Research Toronto Ontario Canada Canada’s Michael Smith Genome Sciences Centre BC Cancer Agency Vancouver British Columbia Canada Department of Medical Genetics University of British Columbia Vancouver British Columbia Canada Department of Molecular Biology and Biochemistry Simon Fraser University Burnaby British Columbia Canada McGill University Genome Centre McGill University Mon

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A molecular single-cell lung atlas of lethal COVID-19 (vol 595, pg 114, 2021)

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NATURE 2021年第7882期598卷 E2-E2页

作者： Melms, Johannes C. Biermann, Jana Huang, Huachao Wang, Yiping Nair, Ajay Tagore, Somnath Katsyv, Igor Rendeiro, Andre F. Amin, Amit Dipak Schapiro, Denis Frangieh, Chris J. Luoma, Adrienne M. Filliol, Aveline Fang, Yinshan Ravichandran, Hiranmayi Clausi, Mariano G. Alba, George A. Rogava, Meri Chen, Sean W. Ho, Patricia Montoro, Daniel T. Kornberg, Adam E. Han, Arnold S. Bakhoum, Mathieu F. Anandasabapathy, Niroshana Suarez-Farinas, Mayte Bakhoum, Samuel F. Bram, Yaron Borczuk, Alain Guo, Xinzheng V. Lefkowitch, Jay H. Marboe, Charles Lagana, Stephen M. Del Portillo, Armando Tsai, Emily J. Zorn, Emmanuel Markowitz, Glen S. Schwabe, Robert F. Schwartz, Robert E. Elemento, Olivier Saqi, Anjali Hibshoosh, Hanina Que, Jianwen Izar, Benjamin Department of Medicine Division of Hematology/Oncology Columbia University Irving Medical Center New York NY USA Columbia Center for Translational Immunology Columbia University Irving Medical Center New York NY USA Herbert Irving Comprehensive Cancer Center Columbia University Irving Medical Center New York NY USA Program for Mathematical Genomics Columbia University New York NY USA Columbia Center for Human Development Columbia University Irving Medical Center New York NY USA Division of Digestive and Liver Diseases Columbia University Irving Medical Center New York NY USA Department of Medicine Columbia University Irving Medical Center New York NY USA Institute of Human Nutrition Columbia University New York NY USA Department of Systems Biology Columbia University Irving Medical Center New York NY USA Department of Pathology and Cell Biology Columbia University Irving Medical Center New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Caryl and Israel Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA WorldQuant Initiative for Quantitative Prediction Weill Cornell Medicine New York NY USA Department of Physiology and Biophysics Weill Cornell Medical College New York NY USA Department of Dermatology Weill Cornell Medical College New York NY USA Meyer Cancer Center Weill Cornell Medical College New York NY USA Laboratory of Systems Pharmacology Harvard Medical School Boston MA USA Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Cancer Immunology and Virology Dana-Farber Cancer Center Boston MA USA Human Immune Monitoring Core Columbia University Irving Medical Center New York NY USA Department of Medicine Division of Pulmonary and Critical Care Massachusetts General Hospital Boston MA USA Cell Circu

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CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional programs to Drive Prostate Tumorigenesis (vol 35, pg 603, 2019)

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cancer CELL 2019年第5期35卷 817-819页

作者： Augello, Michael A. Liu, Deli Deonarine, Lesa D. Robinson, Brian D. Huang, Dennis Stelloo, Suzan Blattner, Mirjam Doane, Ashley S. Wong, Elissa W. P. Chen, Yu Rubin, Mark A. Beltran, Himisha Elemento, Olivier Bergman, Andries M. Zwart, Wilbert Sboner, Andrea Dephoure, Noah Barbieri, Christopher E. Department of Urology Weill Cornell Medicine New York NY 10065 USA Sandra and Edward Meyer Cancer Center Weill Cornell Medicine New York NY 10065 USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medicine New York NY 10065 USA Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY 10065 USA Caryl and Israel Englander Institute for Precision Medicine Weill Cornell Medicine New York NY 10065 USA Division of Oncogenomics Oncode Institute The Netherlands Cancer Institute Amsterdam the Netherlands Human Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer Center New York NY 10065 USA Department of Medicine Memorial Sloan Kettering Cancer Center New York NY 10065 USA Department of Medicine Weill Cornell Medicine New York NY 10065 USA Division of Medical Oncology Netherlands Cancer Institute Amsterdam The Netherlands Laboratory of Chemical Biology and Institute for Complex Molecular Systems Department of Biomedical Engineering Eindhoven University of Technology Eindhoven The Netherlands Department of Biochemistry Weill Cornell Medicine New York NY 10065 USA

Summary Deletion of the gene encoding the chromatin remodeler CHD1 is among the most common alterations in prostate cancer (PCa); however, the tumor-suppressive functions of CHD1 and reasons for its tissue-specific loss remain undefined. We demonstrated that CHD1 occupied prostate-specific enhancers enriched for the androgen receptor (AR) and lineage-specific cofactors. Upon CHD1 loss, the AR cistrome was redistributed in patterns consistent with the oncogenic AR cistrome in PCa samples and drove tumor formation in the murine prostate. Notably, this cistrome shift was associated with a unique AR transcriptional signature enriched for pro-oncogenic pathways unique to this tumor subclass. Collectively, these data credential CHD1 as a tumor suppressor in the prostate that constrains AR binding/function to limit tumor progression.

关键词： prostate cancer androgen receptor prostate cancer subclass AR CHD1 epigenetics HOXB13 chromatin remodeling cistrome reprogramming interactome

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TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells (vol 50, pg 83, 2017)

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NATURE genetics 2018年第5期50卷 764-764页

作者： Verma, Nipun Pan, Heng Dore, Louis C. Shukla, Abhijit Li, Qing V. Pelham-Webb, Bobbie Teijeiro, Virginia Gonzalez, Federico Krivtsov, Andrei Chang, Chan-Jung Papapetrou, Eirini P. He, Chuan Elemento, Olivier Huangfu, Danwei Developmental Biology Program Sloan Kettering Institute New York NY USA Weill Graduate School of Medical Sciences at Cornell University/The Rockefeller University/Sloan Kettering Institute Tri-Institutional MD-PhD Program New York NY USA Department of Physiology and Biophysics Englander Institute for Precision Medicine Institute for Computational Biomedicine Weill Cornell Medical College New York NY USA Weill Cornell Graduate School of Medical Sciences Weill Cornell Medical College New York NY USA Department of Chemistry Department of Biochemistry and Molecular Biology Institute for Biophysical Dynamics Howard Hughes Medical Institute University of Chicago Chicago IL USA Louis V. Gerstner Jr. Graduate School of Biomedical Sciences Memorial Sloan Kettering Cancer Center New York NY USA Cancer Biology and Genetics Program Sloan Kettering Institute New York NY USA Department of Oncological Sciences and Black Family Stem Cell Institute Icahn School of Medicine at Mount Sinai New York NY USA

TET enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish owing to challenges in distinguishing global versus locus-specific effects. Here we show that TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit prominent bivalent promoter hypermethylation without an overall corresponding decrease in gene expression in the undifferentiated state. Focusing on the bivalent PAX6 locus, we find that increased DNMT3B binding is associated with promoter hypermethylation, which precipitates a neural differentiation defect and failure of PAX6 induction during differentiation. dCas9-mediated locus-specific demethylation and global inactivation of DNMT3B in TKO hESCs partially reverses the hypermethylation at the PAX6 promoter and improves differentiation to neuroectoderm. Taking these findings together with further genome-wide methylation and TET1 and DNMT3B ChIP-seq analyses, we conclude that TET proteins safeguard bivalent promoters from de novo methylation to ensure robust lineage-specific transcription upon differentiation.

关键词： Epigenetics Stem cells

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P417: A SINGLE AMINO ACID AT THE PNT DOMAIN OF ERG MEDIATES ITS LEUKEMOGENIC ACTIVITY THROUGH INTERACTION WITH THE NCOR-HDAC3 CO-REPRESSOR COMPLEX.

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HemaSphere 2022年第S3期6卷

作者： E. Kugler S. Madiwale D. Yong Y. Birger J. A. I. Thoms D. B. Sykes M. Yassin N. Aqaqe A. Rein H. Fishman I. Geron C.-W. Chen B. Raught Q. Liu M. Milyavsky J. Pimanda G. G. Privé S. Izraeli Institute of Hematology Davidoff Cancer Center Rabin medical center Petah Tikva Department of Human Molecular Genetics and Biochemistry Sackler Medical School Tel Aviv University Tel Aviv Israel Department of Biochemistry University of Toronto Toronto Canada The Rina Zaizov Pediatric Hematology and Oncology Division Schneider Children's Medical Center Petach Tikva Israel Adult Cancer Program Lowy Cancer Research Centre Sydney Australia Faculty of Medicine UNSW Sydney Sydney Australia Center for Regenerative Medicine Massachusetts General Hospital Boston Harvard Stem Cell Institute Cambridge United States of America Department of Pathology Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel Department of Systems Biology Beckman Research Institute City of Hope Duarte Department of Pediatric Oncology Dana-Farber Cancer Institute Harvard Medical School Boston City of Hope Comprehensive Cancer Center Duarte United States of America Princess Margaret Cancer Centre University Health Network Toronto Canada

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Correction to: Specific Susceptibility to COVID-19 in Adults with Down Syndrome

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Neuromolecular medicine 2021年第4期23卷 572-573页

作者： Tomer Illouz Arya Biragyn Milana Frenkel-Morgenstern Orly Weissberg Alessandro Gorohovski Eugene Merzon Ilan Green Florencia Iulita Lisi Flores-Aguilar Mara Dierssen Ilario De Toma Hefziba Lifshitz Stylianos E Antonarakis Eugene Yu Yann Herault Marie-Claude Potier Alexandra Botté Randall Roper Benjamin Sredni Ronit Sarid Jacqueline London William Mobley Andre Strydom Eitan Okun The Leslie and Susan Gonda Multidisciplinary Brain Research Center Bar-Ilan University 5290002 Ramat-Gan Israel. The Paul Feder Laboratory On Alzheimer's Disease Research Bar-Ilan University 5290002 Ramat-Gan Israel. Laboratory of Molecular Biology and Immunology NIA Baltimore MD 21224 USA. Cancer Genomics and BioComputing of Complex Diseases Lab Azrieli Faculty of Medicine Bar-Ilan University Safed Israel. Leumit Health Services Department of Family Medicine Sackler School of Medicine Tel Aviv University Tel Aviv-Yafo Israel. Sant Pau Memory Unit Department of Neurology Hospital de La Santa Creu I Sant Pau Barcelona Spain. Biomedical Research Institute Sant Pau Universitat Autònoma de Barcelona Barcelona Spain. Center of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED) Madrid Spain. Alzheimer-Down Unit Fundación Catalana Síndrome de Down Barcelona Spain. Department of Anatomy and Cell Biology McGill University Montreal Canada. Center for Genomic Regulation The Barcelona Institute for Science and Technology Barcelona Spain. University Pompeu Fabra Barcelona Spain. Biomedical Research Networking Center for Rare Diseases (CIBERER) Barcelona Spain. Cellular & Systems Neurobiology Systems Biology Program The Barcelona Institute of Science and Technology Centre for Genomic Regulation (CRG) Dr. Aiguader 88 08003 Barcelona Spain. Universitat Pompeu Fabra (UPF) Barcelona Spain. Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Madrid Spain. School of Education Bar-Ilan University 5290002 Ramat-Gan Israel. Department of Genetic Medicine and Development University of Geneva 1211 Geneva Switzerland. Medigenome Swiss Institute of Genomic Medicine 1207 Geneva Switzerland. iGE3 Institute of Genetics and Genomics of Geneva 1211 Geneva Switzerland. The Children's Guild Foundation Down Syndrome Research Program Genetics and Genomics Program and Department of Cancer Genetics and Genomics Roswell Park Comprehensi

A correction to this paper has been published: https://***/10.1007/s12017-021-08657-z

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Author Correction: The lactate receptor HCAR1 drives the recruitment of immunosuppressive PMN-MDSCs in colorectal cancer

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Nature immunology 2025年第4期26卷 635页

作者： Jiacheng He Xiaolei Chai Qiansen Zhang Yang Wang Yijie Wang Xinyu Yang Jingbo Wu Bo Feng Jing Sun Weiwei Rui Shuyin Ze Yuanyuan Fu Yumiao Zhao Ying Zhang Yao Zhang Meizhen Liu Chuang Liu Meifu She Xiangfei Hu Xueyun Ma Huaiyu Yang Dawei Li Senlin Zhao Guichao Li Zhen Zhang Zhonghui Tian Yanlin Ma Lingyan Cao Bo Yi Dali Li Ruth Nussinov Charis Eng Timothy A Chan Eytan Ruppin J Silvio Gutkind Feixiong Cheng Mingyao Liu Weiqiang Lu Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences East China Normal University Shanghai China. Department of Urology and Department of Pathology The Fifth People's Hospital of Shanghai Fudan University Shanghai China. Department of General Surgery and Department of Pathology Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China. Research Center for Complexity Sciences Hangzhou Normal University Hangzhou China. Department of Colorectal Surgery Department of Radiation Oncology Fudan University Shanghai Cancer Center Shanghai China. School of Life Sciences Fudan University Shanghai China. Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research Hainan Provincial Clinical Research Center for Thalassemia Department of Reproductive Medicine Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University) Ministry of Education The First Affiliated Hospital of Hainan Medical University Haikou China. Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine College of Stomatology Shanghai Jiao Tong University Shanghai China. Department of Gastrointestinal Surgery The Third Xiangya Hospital Central South University Changsha China. Computational Structural Biology Section Basic Science Program Frederick National Laboratory for Cancer Research National Cancer Institute at Frederick Frederick MD USA. Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine Tel Aviv University Tel Aviv Israel. Genomic Medicine Institute Lerner Research Institute Cleveland Clinic Cleveland OH USA. Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine Case Western Reserve University Cleveland OH USA. Case Comprehensive Cancer Center Case Western Reserve University School of Medicine Cleveland OH USA. Center for Immunotherapy and Precision Immuno-Oncology Cleveland Clini

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