Johanna Dahlqvist1,2, Charles P Fulco1,3,4, John P Ray1,5, Thomas Liechti6, Carl G de Boer7,8, David J Lieb1, Thomas M Eisenhaure1, Jesse M Engreitz1,9,10, Mario Roederer6, Nir Hacohen1,11. 1. Center for Cell Circuits, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA. 2. Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden. 3. Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. 4. Bristol Myers Squibb, Cambridge, MA 02142, USA. 5. Systems Immunology, Benaroya Research Institute, Seattle, WA 98101, USA. 6. ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20814, USA. 7. Klarman Cell Observatory, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA. 8. School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. 9. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. 10. BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA. 11. Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA.
Abstract
BACKGROUND: FCGR2A binds antibody-antigen complexes to regulate the abundance of circulating and deposited complexes along with downstream immune and autoimmune responses. Although the abundance of FCRG2A may be critical in immune-mediated diseases, little is known about whether its surface expression is regulated through cis genomic elements and non-coding variants. In the current study, we aimed to characterize the regulation of FCGR2A expression, the impact of genetic variation and its association with autoimmune disease. METHODS: We applied CRISPR-based interference and editing to scrutinize 1.7 Mb of open chromatin surrounding the FCGR2A gene to identify regulatory elements. Relevant transcription factors (TFs) binding to these regions were defined through public databases. Genetic variants affecting regulation were identified using luciferase reporter assays and were verified in a cohort of 1996 genotyped healthy individuals using flow cytometry. RESULTS: We identified a complex proximal region and five distal enhancers regulating FCGR2A. The proximal region split into subregions upstream and downstream of the transcription start site, was enriched in binding of inflammation-regulated TFs, and harbored a variant associated with FCGR2A expression in primary myeloid cells. One distal enhancer region was occupied by CCCTC-binding factor (CTCF) whose binding site was disrupted by a rare genetic variant, altering gene expression. CONCLUSIONS: The FCGR2A gene is regulated by multiple proximal and distal genomic regions, with links to autoimmune disease. These findings may open up novel therapeutic avenues where fine-tuning of FCGR2A levels may constitute a part of treatment strategies for immune-mediated diseases.
BACKGROUND: FCGR2A binds antibody-antigen complexes to regulate the abundance of circulating and deposited complexes along with downstream immune and autoimmune responses. Although the abundance of FCRG2A may be critical in immune-mediated diseases, little is known about whether its surface expression is regulated through cis genomic elements and non-coding variants. In the current study, we aimed to characterize the regulation of FCGR2A expression, the impact of genetic variation and its association with autoimmune disease. METHODS: We applied CRISPR-based interference and editing to scrutinize 1.7 Mb of open chromatin surrounding the FCGR2A gene to identify regulatory elements. Relevant transcription factors (TFs) binding to these regions were defined through public databases. Genetic variants affecting regulation were identified using luciferase reporter assays and were verified in a cohort of 1996 genotyped healthy individuals using flow cytometry. RESULTS: We identified a complex proximal region and five distal enhancers regulating FCGR2A. The proximal region split into subregions upstream and downstream of the transcription start site, was enriched in binding of inflammation-regulated TFs, and harbored a variant associated with FCGR2A expression in primary myeloid cells. One distal enhancer region was occupied by CCCTC-binding factor (CTCF) whose binding site was disrupted by a rare genetic variant, altering gene expression. CONCLUSIONS: The FCGR2A gene is regulated by multiple proximal and distal genomic regions, with links to autoimmune disease. These findings may open up novel therapeutic avenues where fine-tuning of FCGR2A levels may constitute a part of treatment strategies for immune-mediated diseases.
Authors: Pierre Bruhns; Bruno Iannascoli; Patrick England; David A Mancardi; Nadine Fernandez; Sylvie Jorieux; Marc Daëron Journal: Blood Date: 2008-11-18 Impact factor: 22.113
Authors: Arnon Arazi; Deepak A Rao; Celine C Berthier; Anne Davidson; Yanyan Liu; Paul J Hoover; Adam Chicoine; Thomas M Eisenhaure; A Helena Jonsson; Shuqiang Li; David J Lieb; Fan Zhang; Kamil Slowikowski; Edward P Browne; Akiko Noma; Danielle Sutherby; Scott Steelman; Dawn E Smilek; Patti Tosta; William Apruzzese; Elena Massarotti; Maria Dall'Era; Meyeon Park; Diane L Kamen; Richard A Furie; Fernanda Payan-Schober; William F Pendergraft; Elizabeth A McInnis; Jill P Buyon; Michelle A Petri; Chaim Putterman; Kenneth C Kalunian; E Steve Woodle; James A Lederer; David A Hildeman; Chad Nusbaum; Soumya Raychaudhuri; Matthias Kretzler; Jennifer H Anolik; Michael B Brenner; David Wofsy; Nir Hacohen; Betty Diamond Journal: Nat Immunol Date: 2019-06-17 Impact factor: 31.250
Authors: John P Ray; Carl G de Boer; Charles P Fulco; Caleb A Lareau; Masahiro Kanai; Jacob C Ulirsch; Ryan Tewhey; Leif S Ludwig; Steven K Reilly; Drew T Bergman; Jesse M Engreitz; Robbyn Issner; Hilary K Finucane; Eric S Lander; Aviv Regev; Nir Hacohen Journal: Nat Commun Date: 2020-03-06 Impact factor: 14.919