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

doi:10.1186/s12864-023-09719-1

	Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks
	Li, Ying 1,2; Han, Liqin 1,2; Li, Peiluan 1,2; Ge, Jing 3; Xue, Yun 4; Chen, Luonan5,6,7,8
	2023-10-18
发表期刊	BMC GENOMICS (IF:3.5[JCR-2023],4.1[5-Year])
ISSN	1471-2164
卷号	24 期号:1
发表状态	已发表
DOI	10.1186/s12864-023-09719-1
摘要	To 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.
关键词	Single-cell RNA sequencing B cells Conditional cell-specific network Hub gene 'Dark' genes Pathway
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收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2022YFA1004800] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDB38040400] ; National Natural Science Foundation of China["31930022","12131020","T2350003","T2341007"] ; Special Fund for Science and Technology Innovation Strategy of Guangdong Province["2021B0909050004","2021B0909060002"] ; Young Backbone Teacher Funding Scheme of Henan[2019GGJS079] ; Key Research and Development and Promotion Special Program of Henan Province[212102310988] ; JST Moonshot RD[JPMJMS2021] ; Major projects of Henan Province[231100220100]
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:001095837600003
出版者	BMC
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/346496
专题	生命科学与技术学院生命科学与技术学院_特聘教授组_陈洛南组
通讯作者	Li, Peiluan; Chen, Luonan
作者单位	1.Henan Univ Sci & Technol, Sch Math & Stat, Luoyang 471023, Peoples R China 2.Longmen Lab, Luoyang 471003, Henan, Peoples R China 3.Shanghai Jiao Tong Univ, Shanghai Immune Therapy Inst, Sch Med, Renji Hosp, Shanghai, Peoples R China 4.Henan Univ Sci & Technol, Coll Med Technol & Engn, Luoyang 471023, Peoples R China 5.Chinese Acad Sci, Inst Biochem & Cell Biol, Ctr Excellence Mol Cell Sci, Key Lab Syst Biol, Shanghai 201100, Peoples R China 6.Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Key Lab Syst Hlth Sci Zhejiang Prov, Hangzhou 310013, Peoples R China 7.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201100, Peoples R China 8.Sichuan Univ, West China Hosp, West China Biomed Big Data Ctr, MedX Ctr Informat, Chengdu 610041, Peoples R China
通讯作者单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Li, Ying,Han, Liqin,Li, Peiluan,et al. Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks[J]. BMC GENOMICS,2023,24(1).
APA	Li, Ying,Han, Liqin,Li, Peiluan,Ge, Jing,Xue, Yun,&Chen, Luonan.(2023).Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks.BMC GENOMICS,24(1).
MLA	Li, Ying,et al."Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks".BMC GENOMICS 24.1(2023).