Single cell multiomic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients

Innate lymphoid cells (ILCs) are enriched at mucosal surfaces where they respond rapidly to environmental stimuli and contribute to both tissue inflammation and healing. To gain insight into the role of ILCs in the pathology and recovery from COVID-19 infection, we employed a multi-omic 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.  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 infection..., Study participants, blood draws and processing
Participants were recruited as described previously from adults who had a positive SARS-COV-2 RT-PCR test at Stanford Health Care (NCT04373148).  Collection of Covid samples occurred between May to December 2020. The cohort used in this study consisted of asymptomatic (n=2), mild (n=17), and moderate (n=3) COVID-19 infections, some of whom developed long term COVID-19 (n=15). The clinical case severities at the time of diagnosis were defined as asymptomatic, moderate or mild according to the guidelines released by NIH.  Long term (LT) COVID was defined as symptoms occurring 30 or more days after infection, consistent with CDC guidelines. Some participants in our study continued to have LT COVID symptoms 90 days after diagnosis (n=12).   Exclusion criteria for COVID sample study were NIH severity diagnosis of severe or critical at the time of positive covid test.  Samples selected for this study were obtained within 76 days of positive PCR C..., , # Single cell multiomics analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients

BD AbSeq allows simultaneous measurement of protein and RNA expression at the single-cell level, in combination with the BD Rhapsody high-throughput single-cell capture system. Cells were captured using D Rhapsody cell capture beads. Identity of proteins and mRNA was carried out as per protocol (see manuscript materials & method). We manually gated ILC1, ILC2 and ILCp single cells using FlowJo, enumerated the mRNA count in each cell.

More Information about BD rhapsody: [https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD-AbSeq-BD-Rhapsody-Simultaneous-mRNA-and-Protein-Quantification-DS.pdf](https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD-AbSeq-BD-Rhapsody-Simultaneous-mRNA-and-Protein-Quantification-DS.pdf)

## Description of the data and file structure

The processed dataset is available in Zip file (ReadCount.zip). ...