Systems-biology analysis of rheumatoid arthritis fibroblast-like synoviocytes implicates cell line-specific transcription factor function

Richard I. Ainsworth; Deepa Hammaker; Gyrid Nygaard; Cecilia Ansalone; Camilla Machado; Kai Zhang; Lina Zheng; Lucy Carrillo; Andre Wildberg; Amanda Kuhs; Mattias N. D. Svensson; David L. Boyle; Gary S. Firestein; Wei Wang

doi:10.1038/s41467-022-33785-w

Nature Communications (Oct 2022)

Systems-biology analysis of rheumatoid arthritis fibroblast-like synoviocytes implicates cell line-specific transcription factor function

Richard I. Ainsworth,
Deepa Hammaker,
Gyrid Nygaard,
Cecilia Ansalone,
Camilla Machado,
Kai Zhang,
Lina Zheng,
Lucy Carrillo,
Andre Wildberg,
Amanda Kuhs,
Mattias N. D. Svensson,
David L. Boyle,
Gary S. Firestein,
Wei Wang

Affiliations

Richard I. Ainsworth: Department of Chemistry and Biochemistry, University of California, San Diego
Deepa Hammaker: Department of Medicine, University of California, San Diego
Gyrid Nygaard: Department of Medicine, University of California, San Diego
Cecilia Ansalone: Department of Medicine, University of California, San Diego
Camilla Machado: Department of Medicine, University of California, San Diego
Kai Zhang: Department of Chemistry and Biochemistry, University of California, San Diego
Lina Zheng: Bioinformatics and Systems Biology Program, University of California, San Diego
Lucy Carrillo: Department of Medicine, University of California, San Diego
Andre Wildberg: Department of Chemistry and Biochemistry, University of California, San Diego
Amanda Kuhs: Department of Medicine, University of California, San Diego
Mattias N. D. Svensson: Department of Medicine, University of California, San Diego
David L. Boyle: Department of Medicine, University of California, San Diego
Gary S. Firestein: Department of Medicine, University of California, San Diego
Wei Wang: Department of Chemistry and Biochemistry, University of California, San Diego

DOI: https://doi.org/10.1038/s41467-022-33785-w
Journal volume & issue: Vol. 13, no. 1
pp. 1 – 11

Abstract

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Fibroblast-like synoviocytes (FLS) are used as a model of rheumatoid arthritis synoviocytes, although cell lines derived from individual patients can have heterogeneous biology. Here the authors use a Taiji computational approach to analyze gene expression, chromatin accessibility and functional differences between individual patient-derived RA FLS lines.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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