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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
Single cell multi-omic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19
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.
