A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape

Abstract Background: Herpes simplex virus type 2 infects the body and becomes an incurable and recurring disease. The pathogenesis of HSV-2 infection is not completely clear.Methods: We analyze the GSE18527 dataset in the GEO database in this paper to obtain distinctively displayed genes(DDGs)in the total sequential RNA of the biopsies of normal and lesioned skin groups, healed skin and lesioned skin groups of genital herpes patients, respectively.The related data of 3 cases of normal skin group, 4 cases of lesioned group and 6 cases of healed group were analyzed.The histospecific gene analysis , functional enrichment and protein interaction network analysis of the differential genes were also performed, and the critical components were selected.Results: 40 up-regulated genes and 43 down-regulated genes were isolated by differential performance assay.Histospecific gene analysis of DDGs suggested that the most abundant system for gene expression was the skin, immune system and the nervous system.Through the construction of core gene combinations, protein interaction network analysis and selection of histospecific distribution genes, 17 associated genes were selected：CXCL10,MX1,ISG15,IFIT1,IFIT3,IFIT2,OASL,ISG20,RSAD2,GBP1,IFI44L,DDX58,USP18,CXCL11,GBP5,GBP4 and CXCL9.The above genes are mainly located in the skin, immune system, nervous system and reproductive system.Conclusion:This paper elucidates an effective approach for a new mechanism of HSV-2 infection, and the molecular mechanism of the selected core genes in the process of HSV-2 infection requires future experimental studies.

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Protein-protein interaction network clustering based on artificial immune system

Journal of Computer Applications ◽

10.3724/sp.j.1087.2013.03567 ◽

2013 ◽

Vol 33 (12) ◽

pp. 3567-3570

Author(s):

Chong WANG ◽

Xiujuan LEI

Keyword(s):

Immune System ◽

Protein Interaction ◽

Protein Interaction Network ◽

Artificial Immune System ◽

Interaction Network ◽

Network Clustering ◽

Artificial Immune ◽

Protein Protein Interaction ◽

Protein Protein Interaction Network

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In-Silico Analysis of Interacting Pathways Through Kim-1 Protein Interaction in Diabetic Nephropathy:

10.21203/rs.3.rs-738168/v1 ◽

2021 ◽

Author(s):

Fatima Abid ◽

Zil e Rubab Rubab ◽

Syeda Sadia Fatima ◽

Aijaz Ahmed Qureshi ◽

Arfa Azhar ◽

...

Keyword(s):

Diabetic Nephropathy ◽

Immune System ◽

Pathway Analysis ◽

Protein Interaction ◽

Innate Immune System ◽

Adaptive Immune System ◽

Innate Immune ◽

Cytokine Signaling ◽

Adaptive Immune ◽

Neutrophil Degranulation

Abstract Human Kidney Injury Molecule-1 also known as HAVCR-1 (Hepatitis A virus cellular receptor 1) belongs to cell-surface protein of immunoglobulin superfamily involved in phagocytosis by acting as scavenger receptor epithelial cells. The study focused to pinpoint the mechanisms and gene that interact with KIM-1.Methods: This in-silico study was done from March, 2019 to December 2019 .First the Enrichment and protein–protein interaction (PPI) network study of the carefully chosen proteins together with diagramed gene data sets was accomplished using FunRich version 3.1.3.it was done to unveil the proteins that may have an effect on the regulation of HAVCR1 or are may be regulated by this protein. These genes were then further considered in pathway analysis to discover the dysregulated pathways in diabetic nephropathy. The long list of differentially expressed genes is meaningless without pathway analysis. Results: Important pathways that are dysregulated in diabetic nephropathy patients are identified including Immune System (Total = 237, P<0.05), Innate Immune System (Total=140, P<0.05), Cytokine Signaling Immune system (Total = 116, P<0.05), Adaptive Immune System (Total =85) and Neutrophil degranulation (Total=78).Conclusion: The top 5 genes that are interacting directly with HIVCR1 include CASP3, CCL2, SPP1, B2M, and TIMP1 with degrees 161, 144, 108, 107, and 105 respectively for Immune system pathways (Innate Immune System, Cytokine Signaling Immune system, Adaptive Immune System and Neutrophil degranulation)

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Structure of the 5' untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune system via the human oligoadenylate synthase 1

10.1101/2021.12.10.472066 ◽

2021 ◽

Author(s):

Emmanuelle Bignon ◽

Tom Miclot ◽

Alessio Terenzi ◽

Giampaolo Barone ◽

Antonio Monari

Keyword(s):

Immune System ◽

Innate Immune System ◽

Viral Infections ◽

Interaction Network ◽

High Sensitivity ◽

Innate Immune ◽

System Response ◽

Oligoadenylate Synthetase ◽

Stem Loop ◽

Viral Maturation

The 2'-5'-oligoadenylate synthetase 1 (OAS1) have been identified as one of the key enzymes driving the innate immune system response to SARS-CoV-2 infection and has been related to COVID-19 severity. OAS1 is a sensor of endogenous RNA that triggers the 2'-5' oligoadenylate/RNase L pathway in response to viral infections, ultimately activating the RNA-Lyase which cleaves endogenous and exogenous RNA hence impeding the viral maturation. Upon SARS-CoV-2 infection, OAS1 is responsible for the recognition of viral RNA and has been shown to possess a particularly high sensitivity for the 5'-untranslated (5'-UTR) RNA region, which is organized in a double-strand stem loop motif (SL1). Yet the structure of the nucleic acid/protein complex has not been resolved. Here, we report the structure of the OAS1/SL1 complex generated by molecular modeling, including enhanced sampling approaches. We also pinpoint how SL1 region enhances the interaction network with the enzyme, promoting specific hydrogen bonds which are absent in normal double strand RNA fragments, hence rationalizing the high affinity shown by OAS1.

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