IDEAS home Printed from https://ideas.repec.org/a/gam/jdataj/v9y2024i8p101-d1459709.html
   My bibliography  Save this article

Viral Targets in the Human Interactome with Comprehensive Centrality Analysis: SARS-CoV-2, a Case Study

Author

Listed:
  • Nilesh Kumar

    (Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA
    IRCP—Biological Data Sciences, University of Alabama at Birmingham, Birmingham, AL 35233, USA)

  • M. Shahid Mukhtar

    (Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA
    Department of Genetics & Biochemistry, Clemson University, 105 Collings St. Biosystems Research Complex, Clemson, SC 29634, USA)

Abstract

Network centrality analyses have proven to be successful in identifying important nodes in diverse host–pathogen interactomes. The current study presents a comprehensive investigation of the human interactome and SARS-CoV-2 host targets. We first constructed a comprehensive human interactome by compiling experimentally validated protein–protein interactions (PPIs) from eight distinct sources. Additionally, we compiled a comprehensive list of 1449 SARS-CoV-2 host proteins and analyzed their interactions within the human interactome, which identified enriched biological processes and pathways. Seven diverse topological features were employed to reveal the enrichment of the SARS-CoV-2 targets in the human interactome, with closeness centrality emerging as the most effective metric. Furthermore, a novel approach called CentralityCosDist was employed to predict SARS-CoV-2 targets, which proved to be effective in expanding the pool of predicted targets. Pathway enrichment analyses further elucidated the functional roles and potential mechanisms associated with predicted targets. Overall, this study provides valuable insights into the complex interplay between SARS-CoV-2 and the host’s cellular machinery, contributing to a deeper understanding of viral infection and immune response modulation.

Suggested Citation

  • Nilesh Kumar & M. Shahid Mukhtar, 2024. "Viral Targets in the Human Interactome with Comprehensive Centrality Analysis: SARS-CoV-2, a Case Study," Data, MDPI, vol. 9(8), pages 1-12, August.
    • Handle: RePEc:gam:jdataj:v:9:y:2024:i:8:p:101-:d:1459709
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/2306-5729/9/8/101/pdf
    Download Restriction: no
    File URL: https://www.mdpi.com/2306-5729/9/8/101/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    1. Edward L. Huttlin & Raphael J. Bruckner & Joao A. Paulo & Joe R. Cannon & Lily Ting & Kurt Baltier & Greg Colby & Fana Gebreab & Melanie P. Gygi & Hannah Parzen & John Szpyt & Stanley Tam & Gabriela Z, 2017. "Architecture of the human interactome defines protein communities and disease networks," Nature, Nature, vol. 545(7655), pages 505-509, May.
    2. Katja Luck & Dae-Kyum Kim & Luke Lambourne & Kerstin Spirohn & Bridget E. Begg & Wenting Bian & Ruth Brignall & Tiziana Cafarelli & Francisco J. Campos-Laborie & Benoit Charloteaux & Dongsic Choi & At, 2020. "A reference map of the human binary protein interactome," Nature, Nature, vol. 580(7803), pages 402-408, April.
    3. Orit Rozenblatt-Rosen & Rahul C. Deo & Megha Padi & Guillaume Adelmant & Michael A. Calderwood & Thomas Rolland & Miranda Grace & Amélie Dricot & Manor Askenazi & Maria Tavares & Samuel J. Pevzner & F, 2012. "Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins," Nature, Nature, vol. 487(7408), pages 491-495, July.
    4. Cuihong Wan & Blake Borgeson & Sadhna Phanse & Fan Tu & Kevin Drew & Greg Clark & Xuejian Xiong & Olga Kagan & Julian Kwan & Alexandr Bezginov & Kyle Chessman & Swati Pal & Graham Cromar & Ophelia Pap, 2015. "Panorama of ancient metazoan macromolecular complexes," Nature, Nature, vol. 525(7569), pages 339-344, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Michael A. Skinnider & Mopelola O. Akinlaja & Leonard J. Foster, 2023. "Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Hong-Wen Tang & Kerstin Spirohn & Yanhui Hu & Tong Hao & István A. Kovács & Yue Gao & Richard Binari & Donghui Yang-Zhou & Kenneth H. Wan & Joel S. Bader & Dawit Balcha & Wenting Bian & Benjamin W. Bo, 2023. "Next-generation large-scale binary protein interaction network for Drosophila melanogaster," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Jiang, Xiongfei & Xiong, Long & Bai, Ling & Zhao, Na & Zhang, Jiu & Xia, Ke & Deng, Kai & Zheng, Bo, 2021. "Quantifying the social structure of elites in ancient China," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 573(C).
    4. Patrick Bryant & Gabriele Pozzati & Wensi Zhu & Aditi Shenoy & Petras Kundrotas & Arne Elofsson, 2022. "Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    5. Amika Singla & Daniel J. Boesch & Ho Yee Joyce Fung & Chigozie Ngoka & Avery S. Enriquez & Ran Song & Daniel A. Kramer & Yan Han & Esther Banarer & Andrew Lemoff & Puneet Juneja & Daniel D. Billadeau , 2024. "Structural basis for Retriever-SNX17 assembly and endosomal sorting," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    6. Yuwan Chen & Wen Zhou & Yufei Xia & Weijie Zhang & Qun Zhao & Xinwei Li & Hang Gao & Zhen Liang & Guanghui Ma & Kaiguang Yang & Lihua Zhang & Yukui Zhang, 2023. "Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    7. Krishna B. S. Swamy & Hsin-Yi Lee & Carmina Ladra & Chien-Fu Jeff Liu & Jung-Chi Chao & Yi-Yun Chen & Jun-Yi Leu, 2022. "Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility in yeast," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Ghulam Muhiuddin & Sovan Samanta & Abdulrahman F. Aljohani & Abeer M. Alkhaibari, 2023. "A Study on Graph Centrality Measures of Different Diseases Due to DNA Sequencing," Mathematics, MDPI, vol. 11(14), pages 1-18, July.
    9. Ann Schirin Mirsanaye & Saskia Hoffmann & Melanie Weisser & Andreas Mund & Blanca Lopez Mendez & Dimitris Typas & Johannes Boom & Bente Benedict & Ivo A. Hendriks & Michael Lund Nielsen & Hemmo Meyer , 2024. "VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    10. Paul T. Morse & Gonzalo Pérez-Mejías & Junmei Wan & Alice A. Turner & Inmaculada Márquez & Hasini A. Kalpage & Asmita Vaishnav & Matthew P. Zurek & Philipp P. Huettemann & Katherine Kim & Tasnim Arrou, 2023. "Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    11. Diego Esposito & Jane Dudley-Fraser & Acely Garza-Garcia & Katrin Rittinger, 2022. "Divergent self-association properties of paralogous proteins TRIM2 and TRIM3 regulate their E3 ligase activity," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    12. Bingjie Hao & István A. Kovács, 2023. "A positive statistical benchmark to assess network agreement," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    13. Pierre C. Havugimana & Raghuveera Kumar Goel & Sadhna Phanse & Ahmed Youssef & Dzmitry Padhorny & Sergei Kotelnikov & Dima Kozakov & Andrew Emili, 2022. "Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    14. Qian Jiang & Qijin Zhao & Yibing Chen & Chunxiao Ma & Xiaohong Peng & Xi Wu & Xingfeng Liu & Ruoran Wang & Shaocong Hou & Lijuan Kong & Yanjun Wan & Shusen Wang & Zhuo-Xian Meng & Bing Cui & Liangyi C, 2024. "Galectin-3 impairs calcium transients and β-cell function," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    15. Maik Müller & Fabienne Gräbnitz & Niculò Barandun & Yang Shen & Fabian Wendt & Sebastian N. Steiner & Yannik Severin & Stefan U. Vetterli & Milon Mondal & James R. Prudent & Raphael Hofmann & Marc Oos, 2021. "Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    16. Pisanu Buphamalai & Tomislav Kokotovic & Vanja Nagy & Jörg Menche, 2021. "Network analysis reveals rare disease signatures across multiple levels of biological organization," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    17. Xu-Wen Wang & Lorenzo Madeddu & Kerstin Spirohn & Leonardo Martini & Adriano Fazzone & Luca Becchetti & Thomas P. Wytock & István A. Kovács & Olivér M. Balogh & Bettina Benczik & Mátyás Pétervári & Be, 2023. "Assessment of community efforts to advance network-based prediction of protein–protein interactions," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    18. Jens S. Andersen & Aaran Vijayakumaran & Christopher Godbehere & Esben Lorentzen & Vito Mennella & Kenneth Bødtker Schou, 2024. "Uncovering structural themes across cilia microtubule inner proteins with implications for human cilia function," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    19. Cheoljun Choi & Yujin L. Jeong & Koung-Min Park & Minji Kim & Sangseob Kim & Honghyun Jo & Sumin Lee & Heeseong Kim & Garam Choi & Yoon Ha Choi & Je Kyung Seong & Sik Namgoong & Yeonseok Chung & Young, 2024. "TM4SF19-mediated control of lysosomal activity in macrophages contributes to obesity-induced inflammation and metabolic dysfunction," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    20. Yesheng Fu & Lei Li & Xin Zhang & Zhikang Deng & Ying Wu & Wenzhe Chen & Yuchen Liu & Shan He & Jian Wang & Yuping Xie & Zhiwei Tu & Yadi Lyu & Yange Wei & Shujie Wang & Chun-Ping Cui & Cui Hua Liu & , 2024. "Systematic HOIP interactome profiling reveals critical roles of linear ubiquitination in tissue homeostasis," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jdataj:v:9:y:2024:i:8:p:101-:d:1459709. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.