tetano
Editor, Senior Moderator
Front Immunol
. 2024 Jul 4:15:1374828.
doi: 10.3389/fimmu.2024.1374828. eCollection 2024. Single cell multi-omic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients
Abhinav Kaushik[SUP] 1 [/SUP], Iris Chang[SUP] 1 [/SUP], Xiaorui Han[SUP] 1 [/SUP], Ziyuan He[SUP] 1 [/SUP], Zsolt I Komlosi[SUP] 2 3 [/SUP], Xuhuai Ji[SUP] 4 [/SUP], Shu Cao[SUP] 1 [/SUP], Cezmi A Akdis[SUP] 3 5 [/SUP], Scott Boyd[SUP] 1 6 [/SUP], Bali Pulendran[SUP] 6 7 8 [/SUP], Holden T Maecker[SUP] 7 [/SUP], Mark M Davis[SUP] 7 8 9 [/SUP], R Sharon Chinthrajah[SUP] 1 [/SUP], Rosemarie H DeKruyff[SUP] #[/SUP][SUP] 1 [/SUP], Kari C Nadeau[SUP] #[/SUP][SUP] 1 [/SUP]
Affiliations
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.
Keywords: COVID - 19; SARSCoV- 2; innate lymphocyte cells (ILCs); single cell RNA analysis; single cell immunology.
. 2024 Jul 4:15:1374828.
doi: 10.3389/fimmu.2024.1374828. eCollection 2024. Single cell multi-omic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients
Abhinav Kaushik[SUP] 1 [/SUP], Iris Chang[SUP] 1 [/SUP], Xiaorui Han[SUP] 1 [/SUP], Ziyuan He[SUP] 1 [/SUP], Zsolt I Komlosi[SUP] 2 3 [/SUP], Xuhuai Ji[SUP] 4 [/SUP], Shu Cao[SUP] 1 [/SUP], Cezmi A Akdis[SUP] 3 5 [/SUP], Scott Boyd[SUP] 1 6 [/SUP], Bali Pulendran[SUP] 6 7 8 [/SUP], Holden T Maecker[SUP] 7 [/SUP], Mark M Davis[SUP] 7 8 9 [/SUP], R Sharon Chinthrajah[SUP] 1 [/SUP], Rosemarie H DeKruyff[SUP] #[/SUP][SUP] 1 [/SUP], Kari C Nadeau[SUP] #[/SUP][SUP] 1 [/SUP]
Affiliations
- PMID: 39026668
- PMCID: PMC11255397
- DOI: 10.3389/fimmu.2024.1374828
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.
Keywords: COVID - 19; SARSCoV- 2; innate lymphocyte cells (ILCs); single cell RNA analysis; single cell immunology.