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- Title
Single cell multi-omic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients.
- Authors
Kaushik, Abhinav; Chang, Iris; Xiaorui Han; Ziyuan He; Komlosi, Zsolt I.; Xuhuai Ji; Shu Cao; Akdis, Cezmi A.; Boyd, Scott; Pulendran, Bali; Maecker, Holden T.; Davis, Mark M.; Chinthrajah, R. Sharon; DeKruyff, Rosemarie H.; Nadeau, Kari C.
- Abstract
Introduction: Innate lymphoid cells (ILCs) are enriched at mucosal surfaces where they respond rapidly to environmental stimuli and contribute to both tissue inflammation and healing. Methods: To gain insight into the role of ILCs in the pathology and recovery from COVID-19 infection, we employed a multi-omics approach consisting of Abseq and targeted mRNA sequencing to respectively probe the surface marker expression, transcriptional profile and heterogeneity of ILCs in peripheral blood of patients with COVID-19 compared with healthy controls. Results: We found that the frequency of ILC1 and ILC2 cells was significantly increased in COVID-19 patients. Moreover, all ILC subsets displayed a significantly higher frequency of CD69-expressing cells, indicating a heightened state of activation. ILC2s from COVID-19 patients had the highest number of significantly differentially expressed (DE) genes. The most notable genes DE in COVID-19 vs healthy participants included a) genes associated with responses to virus infections and b) genes that support ILC self-proliferation, activation and homeostasis. In addition, differential gene regulatory network analysis revealed ILC-specific regulons and their interactions driving the differential gene expression in each ILC. Discussion: Overall, this study provides mechanistic insights into the characteristics of ILC subsets activated during COVID-19 infection.
- Subjects
INNATE lymphoid cells; COVID-19; COVID-19 pandemic; CELL analysis; GENE regulatory networks
- Publication
Frontiers in Immunology, 2024, p1
- ISSN
1664-3224
- Publication type
Article
- DOI
10.3389/fimmu.2024.1374828