Single cell multi-omic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients
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Updated: Jul 6, 2026
Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations
Published on: January 19, 2017
Abhinav Kaushik1, Iris Chang1, Xiaorui Han1
1Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States.
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.
