Coordinated inheritance of extrachromosomal DNAs in cancer cells.

Autor: Hung KL; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA., Jones MG; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA., Wong IT; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA., Curtis EJ; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA.; School of Medicine, University of California at San Diego, La Jolla, CA, USA., Lange JT; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA., He BJ; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA., Luebeck J; Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA., Schmargon R; Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.; Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany., Scanu E; Department of Mathematics, Queen Mary University of London, London, UK., Brückner L; Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.; Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany., Yan X; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA., Li R; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA., Gnanasekar A; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA., Chamorro González R; Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.; Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany., Belk JA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA., Liu Z; Department of Chemistry, Scripps Research, La Jolla, CA, USA., Melillo B; Department of Chemistry, Scripps Research, La Jolla, CA, USA.; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA., Bafna V; Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA., Dörr JR; Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.; Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany., Werner B; Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK., Huang W; Department of Mathematics, Queen Mary University of London, London, UK.; Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China., Cravatt BF; Department of Chemistry, Scripps Research, La Jolla, CA, USA.; Vividion Therapeutics, San Diego, CA, USA., Henssen AG; Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.; Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.; German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center DKFZ, Heidelberg, Germany.; Berlin Institute of Health, Berlin, Germany., Mischel PS; Sarafan ChEM-H, Stanford University, Stanford, CA, USA. pmischel@stanford.edu.; Department of Pathology, Stanford University, Stanford, CA, USA. pmischel@stanford.edu., Chang HY; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. howchang@stanford.edu.; Department of Genetics, Stanford University, Stanford, CA, USA. howchang@stanford.edu.; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.

Publikováno v: Nature [Nature] 2024 Nov; Vol. 635 (8037), pp. 201-209. Date of Electronic Publication: 2024 Nov 06.

Deciphering regulation of FOXP3 expression in human conventional T cells.

Autor: Umhoefer JM; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Biomedical Sciences graduate program, University of California, San Francisco, CA, USA., Arce MM; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Biomedical Sciences graduate program, University of California, San Francisco, CA, USA., Dajani R; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA., Belk JA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA., Mowery CT; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Biomedical Sciences graduate program, University of California, San Francisco, CA, USA., Nguyen V; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.; Department of Surgery, University of California, San Francisco, San Francisco, CA, USA.; UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA., Gowen BG; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA., Simeonov DR; Department of Medicine, University of California, San Francisco, CA, USA.; Biomedical Sciences graduate program, University of California, San Francisco, CA, USA., Curie GL; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA., Corn JE; Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Switzerland., Chang HY; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA., Marson A; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.; Department of Microbiology and Immunology, University of California, San Francisco, CA, USA.; Institute for Human Genetics, University of California, San Francisco, CA, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Sep 02. Date of Electronic Publication: 2024 Sep 02.

Clonal inactivation of TERT impairs stem cell competition.

Autor: Hasegawa K; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Zhao Y; Center for Personal Dynamic Regulomes, Stanford, CA, USA., Garbuzov A; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Corces MR; Center for Personal Dynamic Regulomes, Stanford, CA, USA., Neuhöfer P; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Gillespie VM; Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA., Cheung P; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Belk JA; Department of Computer Science, Stanford University, Stanford, CA, USA., Huang YH; Center for Personal Dynamic Regulomes, Stanford, CA, USA., Wei Y; Center for Personal Dynamic Regulomes, Stanford, CA, USA., Chen L; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.; Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA., Chang HY; Center for Personal Dynamic Regulomes, Stanford, CA, USA.; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA., Artandi SE; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. sartandi@stanford.edu.; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. sartandi@stanford.edu.; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA. sartandi@stanford.edu.

Publikováno v: Nature [Nature] 2024 Aug; Vol. 632 (8023), pp. 201-208. Date of Electronic Publication: 2024 Jul 17.

Xist ribonucleoproteins promote female sex-biased autoimmunity.

Autor: Dou DR; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Zhao Y; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Belk JA; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Zhao Y; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Casey KM; Department of Comparative Medicine, Stanford University, Stanford, CA, USA., Chen DC; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Li R; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Yu B; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Srinivasan S; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Abe BT; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Kraft K; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA., Hellström C; Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden., Sjöberg R; Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden., Chang S; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA., Feng A; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA., Goldman DW; Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Shah AA; Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Petri M; Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Chung LS; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA., Fiorentino DF; Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA., Lundberg EK; School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden; Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA., Wutz A; Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Zurich, Switzerland., Utz PJ; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA., Chang HY; Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA. Electronic address: howchang@stanford.edu.

Publikováno v: Cell [Cell] 2024 Feb 01; Vol. 187 (3), pp. 733-749.e16.

Clonal hematopoiesis is associated with protection from Alzheimer's disease.

Autor: Bouzid H; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Belk JA; Department of Computer Science, Stanford University, Stanford, CA, USA., Jan M; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA., Qi Y; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Sarnowski C; Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX, USA., Wirth S; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Ma L; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Chrostek MR; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Ahmad H; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.; Department of Cardiology, Charité Universitätsmedizin, Berlin, Germany., Nachun D; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Yao W; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Beiser A; Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA., Bick AG; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA., Bis JC; Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA., Fornage M; Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA., Longstreth WT Jr; Departments of Neurology and Epidemiology, University of Washington, Seattle, WA, USA., Lopez OL; Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA., Natarajan P; Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Psaty BM; Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA., Satizabal CL; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA.; Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA.; Department of Neurology, Boston University School of Medicine, Boston, MA, USA., Weinstock J; Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA., Larson EB; Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA., Crane PK; Department of Medicine, University of Washington, Seattle, WA, USA., Keene CD; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Seshadri S; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA., Satpathy AT; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Montine TJ; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Jaiswal S; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. sjaiswal@stanford.edu.; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA. sjaiswal@stanford.edu.; The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA. sjaiswal@stanford.edu.

Publikováno v: Nature medicine [Nat Med] 2023 Jul; Vol. 29 (7), pp. 1662-1670. Date of Electronic Publication: 2023 Jun 15.