Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks

Author:

Li Ying,Han Liqin,Li Peiluan,Ge Jing,Xue Yun,Chen Luonan

Abstract

AbstractTo explore the potential network markers and related signaling pathways of human B cells infected by COVID-19, we performed standardized integration and analysis of single-cell sequencing data to construct conditional cell-specific networks (CCSN) for each cell. Then the peripheral blood cells were clustered and annotated based on the conditional network degree matrix (CNDM) and gene expression matrix (GEM), respectively, and B cells were selected for further analysis. Besides, based on the CNDM of B cells, the hub genes and ‘dark’ genes (a gene has a significant difference between case and control samples not in a gene expression level but in a conditional network degree level) closely related to COVID-19 were revealed. Interestingly, some of the ‘dark’ genes and differential degree genes (DDGs) encoded key proteins in the JAK-STAT pathway, which had antiviral effects. The protein p21 encoded by the ‘dark’ gene CDKN1A was a key regulator for the COVID-19 infection-related signaling pathway. Elevated levels of proteins encoded by some DDGs were directly related to disease severity of patients with COVID-19. In short, the proteins encoded by ‘dark’ genes complement some missing links in COVID-19 and these signaling pathways played an important role in the growth and activation of B cells.

Funder

the Young Backbone Teacher Funding Scheme of Henan

Key Research and Development and Promotion Special Program of Henan Province

Major projects of Henan Province

the National Key R&D Program of China

Strategic Priority Research Program of the Chinese Academy of Sciences

National Natural Science Foundation of China

Special Fund for Science and Technology Innovation Strategy of Guangdong Province

JST Moonshot R&D

Publisher

Springer Science and Business Media LLC

Subject

Genetics,Biotechnology

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