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Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures.
Wang, Wenliang; Hariharan, Manoj; Bartlett, Anna; Barragan, Cesar; Castanon, Rosa; Rothenberg, Vince; Song, Haili; Nery, Joseph; Aldridge, Andrew; Altshul, Jordan; Kenworthy, Mia; Ding, Wubin; Liu, Hanqing; Tian, Wei; Zhou, Jingtian; Chen, Huaming; Wei, Bei; Gündüz, Irem B; Norell, Todd; Broderick, Timothy J; McClain, Micah T; Satterwhite, Lisa L; Burke, Thomas W; Petzold, Elizabeth A; Shen, Xiling; Woods, Christopher W; Fowler, Vance G; Ruffin, Felicia; Panuwet, Parinya; Barr, Dana B; Beare, Jennifer L; Smith, Anthony K; Spurbeck, Rachel R; Vangeti, Sindhu; Ramos, Irene; Nudelman, German; Sealfon, Stuart C; Castellino, Flora; Walley, Anna Maria; Evans, Thomas; Müller, Fabian; Greenleaf, William J; Ecker, Joseph R.
Afiliação
  • Wang W; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Hariharan M; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Bartlett A; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Barragan C; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Castanon R; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Rothenberg V; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Song H; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Nery J; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Aldridge A; Duke University School of Medicine, Bryan Research Building, 311 Research Drive, Durham, NC 27710, USA.
  • Altshul J; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Kenworthy M; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Ding W; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Liu H; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Tian W; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Zhou J; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Chen H; Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
  • Wei B; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
  • Gündüz IB; Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrücken, Germany.
  • Norell T; Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA.
  • Broderick TJ; Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA.
  • McClain MT; Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA.
  • Satterwhite LL; Durham Veterans Affairs Medical Center, Durham, NC 27705 USA.
  • Burke TW; Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA.
  • Petzold EA; Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA.
  • Shen X; Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA.
  • Woods CW; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA.
  • Fowler VG; Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA.
  • Ruffin F; Durham Veterans Affairs Medical Center, Durham, NC 27705 USA.
  • Panuwet P; Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA.
  • Barr DB; Duke Clinical Research Institute, Durham NC 27701 USA.
  • Beare JL; Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA.
  • Smith AK; Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA.
  • Spurbeck RR; Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA.
  • Vangeti S; Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA.
  • Ramos I; Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA.
  • Nudelman G; Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA.
  • Sealfon SC; Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA.
  • Castellino F; Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA.
  • Walley AM; Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA.
  • Evans T; Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA.
  • Müller F; U.S. Department of Health and Human Services, Administration for Strategic Preparedness and Response, Biomedical Advanced Research and Development Authority, Washington, DC, USA.
  • Greenleaf WJ; Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom.
  • Ecker JR; Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom.
bioRxiv ; 2023 Jun 30.
Article em En | MEDLINE | ID: mdl-37425926
ABSTRACT
Variations in DNA methylation patterns in human tissues have been linked to various environmental exposures and infections. Here, we identified the DNA methylation signatures associated with multiple exposures in nine major immune cell types derived from peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We performed methylome sequencing on 111,180 immune cells obtained from 112 individuals who were exposed to different viruses, bacteria, or chemicals. Our analysis revealed 790,662 differentially methylated regions (DMRs) associated with these exposures, which are mostly individual CpG sites. Additionally, we integrated methylation and ATAC-seq data from same samples and found strong correlations between the two modalities. However, the epigenomic remodeling in these two modalities are complementary. Finally, we identified the minimum set of DMRs that can predict exposures. Overall, our study provides the first comprehensive dataset of single immune cell methylation profiles, along with unique methylation biomarkers for various biological and chemical exposures.
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2023 Tipo de documento: Article
Texto completo
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XML
PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2023 Tipo de documento: Article