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. 2020 Jul 6;20(1):480.
doi: 10.1186/s12879-020-05214-0.

A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host

Qurat Ul Ain Farooq  1 , Zeeshan Shaukat  2 , Sara Aiman  1 , Tong Zhou  1 , Chunhua Li  3
Affiliations

A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host

Qurat Ul Ain Farooq et al. BMC Infect Dis. .

Abstract

Background: Influenza A virus (IAV) infection is a serious public health problem not only in South East Asia but also in European and African countries. Scientists are using network biology to dig deep into the essential host factors responsible for regulation of virus infections. Researchers can explore the virus invasion into the host cells by studying the virus-host relationship based on their protein-protein interaction network.

Methods: In this study, we present a comprehensive IAV-host protein-protein interaction network that is obtained based on the literature-curated protein interaction datasets and some important interaction databases. The network is constructed in Cytoscape and analyzed with its plugins including CytoHubba, CytoCluster, MCODE, ClusterViz and ClusterOne. In addition, Gene Ontology and KEGG enrichment analyses are performed on the highly IAV-associated human proteins. We also compare the current results with those from our previous study on Hepatitis C Virus (HCV)-host protein-protein interaction network in order to find out valuable information.

Results: We found out 1027 interactions among 829 proteins of which 14 are viral proteins and 815 belong to human proteins. The viral protein NS1 has the highest number of associations with human proteins followed by NP, PB2 and so on. Among human proteins, LNX2, MEOX2, TFCP2, PRKRA and DVL2 have the most interactions with viral proteins. Based on KEGG pathway enrichment analysis of the highly IAV-associated human proteins, we found out that they are enriched in the KEGG pathway of basal cell carcinoma. Similarly, the result of KEGG analysis of the common host factors involved in IAV and HCV infections shows that these factors are enriched in the infection pathways of Hepatitis B Virus (HBV), Viral Carcinoma, measles and certain other viruses.

Conclusion: It is concluded that the list of proteins we identified might be used as potential drug targets for the drug design against the infectious diseases caused by Influenza A Virus and other viruses.

Keywords: Cytoscape; Hepatitis C virus; Influenza a virus; KEGG; Protein-protein interaction networks.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Protein-protein interaction network of Influenza A virus with host Homo sapiens constructed in Cytoscape. The network contains 829 nodes (proteins) among which 14 are viral proteins while 815 are human proteins. Total number of edges (interactions) are 1051 and the highly connected nodes tend to make clusters and hubs in the network. Viral proteins NS1, NP and PB2 are shown in a bigger size due to their higher numbers of associations with human proteins. The average number of interactions for a node is 2.4, which means the network is not very dense
Fig. 2
Fig. 2
A pie chart of IAV proteins based on their numbers of interactions with human proteins
Fig. 3
Fig. 3
A highly connected subgraph formed between viral protein NS1 with human proteins
Fig. 4
Fig. 4
KEGG pathways in which the 13 highly IAV-interacting host factors are enriched. The color of the bar shows the intensity of the gene set enriched in a specific pathway. The lighter the color, the more enriched the genes are in that pathway
Fig. 5
Fig. 5
Node clusters made for IAV-human protein interaction network in Cytoscape with different clustering algorithms including MCODE a), CytoCluster b), ClusterViz c) and ClusterOne d)
Fig. 6
Fig. 6
KEGG pathways in which the common host genes are enriched involved in both infectious pathways of IAV and HCV viruses
See this image and copyright information in PMC

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