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Related Experiment Video

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In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

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Published on: October 21, 2022

Gene network inference from single-cell omics data and domain knowledge for constructing COVID-19-specific

Mitsuhiro Odaka^1,2,3,4, Morgan Magnin^2,3, Katsumi Inoue^1,2,3

¹The Graduate University for Advanced Studies, SOKENDAI, Tokyo, Japan.

Frontiers in Genetics

|September 18, 2023

Summary

This study identifies novel Intercellular Adhesion Molecule 1 (ICAM-1) signaling pathways involved in SARS-CoV-2 cell-to-cell transmission and COVID-19 severity. Discovering these ICAM-1 pathways enhances understanding of COVID-19 mechanisms.

Keywords:

COVID-19 ICAM-1 cell-to-cell transmission data-driven and knowledge-based approach model validation pathway enrichment analysis single-cell omics data analysis

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Published on: October 13, 2023

Area of Science:

Molecular Biology
Virology
Immunology

Background:

Intercellular Adhesion Molecule 1 (ICAM-1) is crucial for cell interactions and implicated in viral transmission (HIV-1, HTLV-1).
SARS-CoV-2 shares features with these viruses, and its cell-to-cell transmission correlates with COVID-19 severity.
ICAM-1 expression changes in COVID-19 patients, but its associated signaling pathways in this context remain unidentified.

Purpose of the Study:

To identify unknown ICAM-1-associated signaling pathways in COVID-19.
To elucidate the mechanism of SARS-CoV-2 cell-to-cell transmission and its link to COVID-19 severity.
To contribute to the completion of the COVID-19 Disease Map.

Main Methods:

Gene network inference using single-cell omics data.
Analysis of coexpressed genes, removing spurious correlations.
Validation of inferred models using multiple knowledge bases.

Main Results:

Construction of ICAM-1-associated pathways by integrating data-driven and knowledge-based approaches.
Identification of two novel pathways: an upstream pathway involving the non-canonical NF-κB pathway and a downstream pathway with integrins and cytoskeleton proteins.
Reproducibility of known pathways across different cell types and time points.

Conclusions:

The study successfully identified novel ICAM-1-associated pathways relevant to COVID-19.
These findings offer insights into SARS-CoV-2 transmission and disease mechanisms.
The results aid in refining the COVID-19 Disease Map for better understanding and potential therapeutic strategies.