{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:44:57Z","timestamp":1775609097615,"version":"3.50.1"},"reference-count":53,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2025,1,30]],"date-time":"2025-01-30T00:00:00Z","timestamp":1738195200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.mdpi.com"],"crossmark-restriction":true},"short-container-title":["IJMS"],"abstract":"<jats:p>The vaccinia virus (VV) is extensively utilized as a vaccine vector in the treatment of various infectious diseases, cardiovascular diseases, immunodeficiencies, and cancers. The vaccinia virus Tiantan strain (VVTT) has been instrumental as an irreplaceable vaccine strain in the eradication of smallpox in China; however, it still presents significant adverse toxic effects. After the WHO recommended that routine smallpox vaccination be discontinued, the Chinese government stopped the national smallpox vaccination program in 1981. The outbreak of monkeypox in 2022 has focused people\u2019s attention on the Orthopoxvirus. However, there are limited reports on the safety and toxic side effects of VVTT. In this study, we employed a combination of transcriptomic analysis and machine learning-based feature selection to identify key genes implicated in the VVTT infection process. We utilized four machine learning algorithms, including random forest (RF), minimum redundancy maximum relevance (MRMR), eXtreme Gradient Boosting (XGB), and least absolute shrinkage and selection operator cross-validation (LASSOCV), for feature selection. Among these, XGB was found to be the most effective and was used for further screening, resulting in an optimal model with an ROC curve of 0.98. Our analysis revealed the involvement of pathways such as spinocerebellar ataxia and the p53 signaling pathway. Additionally, we identified three critical targets during VVTT infection\u2014ARC, JUNB, and EGR2\u2014and further validated these targets using qPCR. Our research elucidates the mechanism by which VVTT infects cells, enhancing our understanding of the smallpox vaccine. This knowledge not only facilitates the development of new and more effective vaccines but also contributes to a deeper comprehension of viral pathogenesis. By advancing our understanding of the molecular mechanisms underlying VVTT infection, this study lays the foundation for the further development of VVTT. Such insights are crucial for strengthening global health security and ensuring a resilient response to future pandemics.<\/jats:p>","DOI":"10.3390\/ijms26031203","type":"journal-article","created":{"date-parts":[[2025,1,30]],"date-time":"2025-01-30T05:40:46Z","timestamp":1738215646000},"page":"1203","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Elucidating the Mechanism of VVTT Infection Through Machine Learning and Transcriptome Analysis"],"prefix":"10.3390","volume":"26","author":[{"given":"Zhili","family":"Chen","sequence":"first","affiliation":[{"name":"Academy of Military Medical Sciences, Beijing 100850, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongxin","family":"Jiang","sequence":"additional","affiliation":[{"name":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiazhen","family":"Cui","sequence":"additional","affiliation":[{"name":"Academy of Military Medical Sciences, Beijing 100850, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wannan","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1931-9316","authenticated-orcid":false,"given":"Weiwei","family":"Han","sequence":"additional","affiliation":[{"name":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2917-1693","authenticated-orcid":false,"given":"Gang","family":"Liu","sequence":"additional","affiliation":[{"name":"Academy of Military Medical Sciences, Beijing 100850, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1146\/annurev-virology-091919-104752","article-title":"The Life Cycle of the Vaccinia Virus Genome","volume":"9","author":"Greseth","year":"2022","journal-title":"Annu. Rev. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1128\/JVI.02797-14","article-title":"Evolution of and Evolutionary Relationships between Extant Vaccinia Virus Strains","volume":"89","author":"Qin","year":"2015","journal-title":"J. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1726","DOI":"10.3390\/v7041726","article-title":"The evolution of poxvirus vaccines","volume":"7","author":"Perdiguero","year":"2015","journal-title":"Viruses"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1126\/science.2047875","article-title":"Vaccinia virus: A tool for research and vaccine development","volume":"252","author":"Moss","year":"1991","journal-title":"Science"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1089\/vim.2012.0055","article-title":"Biological properties of H5 hemagglutinin expressed by vaccinia virus vector and its immunological reactivity with human sera","volume":"26","author":"Noisumdaeng","year":"2013","journal-title":"Viral Immunol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"11556","DOI":"10.1128\/JVI.00681-14","article-title":"Inducible gene expression in tumors colonized by modified oncolytic vaccinia virus strains","volume":"88","author":"Stritzker","year":"2014","journal-title":"J. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1128\/CVI.00678-13","article-title":"Immunological characterization of a modified vaccinia virus Ankara vector expressing the human papillomavirus 16 E1 protein","volume":"21","author":"Germain","year":"2014","journal-title":"Clin. Vaccine Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e00790-17","DOI":"10.1128\/mBio.00790-17","article-title":"Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins","volume":"8","author":"Wyatt","year":"2017","journal-title":"mBio"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/bs.aivir.2016.07.001","article-title":"Modified Vaccinia Virus Ankara: History, Value in Basic Research, and Current Perspectives for Vaccine Development","volume":"97","author":"Volz","year":"2017","journal-title":"Adv. Virus Res."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Yu, C., Wu, Q., Xin, J., Yu, Q., Ma, Z., Xue, M., Xu, Q., and Zheng, C. (2024). Designing a Smallpox B-Cell and T-Cell Multi-Epitope Subunit Vaccine Using a Comprehensive Immunoinformatics Approach. Microbiol. Spectr., 12.","DOI":"10.1128\/spectrum.00465-24"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2204151","DOI":"10.1080\/22221751.2023.2204151","article-title":"Mpox Multi-Antigen mRNA Vaccine Candidates by a Simplified Manufacturing Strategy Afford Efficient Protection Against Lethal Orthopoxvirus Challenge","volume":"12","author":"Zeng","year":"2023","journal-title":"Emerg. Microbes Infect."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"eadg3540","DOI":"10.1126\/scitranslmed.adg3540","article-title":"An Mpox Virus mRNA-Lipid Nanoparticle Vaccine Confers Protection Against Lethal Orthopoxviral Challenge","volume":"15","author":"Freyn","year":"2023","journal-title":"Sci. Transl. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.1016\/j.ymthe.2024.04.028","article-title":"Circular RNA Vaccines Against Monkeypox Virus Provide Potent Protection Against Vaccinia Virus Infection in Mice","volume":"32","author":"Zhou","year":"2024","journal-title":"Mol. Ther."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Miura, F., Kanzawa-Kiriyama, H., Hisano, O., Miura, M., Shibata, Y., Adachi, N., Kakuda, T., Shinoda, K.I., and Ito, T. (2023). A Highly Efficient Scheme for Library Preparation from Single-Stranded DNA. Sci. Rep., 13.","DOI":"10.1038\/s41598-023-40890-3"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e349","DOI":"10.1016\/S1473-3099(22)00574-6","article-title":"Prevention of Monkeypox with Vaccines: A Rapid Review","volume":"22","author":"Poland","year":"2022","journal-title":"Lancet Infect. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Noy-Porat, T., Tamir, H., Alcalay, R., Rosenfeld, R., Epstein, E., Cherry, L., Achdout, H., Erez, N., Politi, B., and Yahalom-Ronen, Y. (2023). Generation of Recombinant mAbs to Vaccinia Virus Displaying High Affinity and Potent Neutralization. Microbiol. Spectr., 11.","DOI":"10.1128\/spectrum.01598-23"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"638","DOI":"10.2471\/BLT.19.242347","article-title":"Modelling Human-to-Human Transmission of Monkeypox","volume":"98","author":"Grant","year":"2020","journal-title":"Bull. World Health Organ."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1093\/ije\/17.3.643","article-title":"The Transmission Potential of Monkeypox Virus in Human Populations","volume":"17","author":"Fine","year":"1988","journal-title":"Int. J. Epidemiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1007\/s40265-022-01742-y","article-title":"Prevention and Treatment of Monkeypox","volume":"82","author":"Rizk","year":"2022","journal-title":"Drugs"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1093\/oxfordjournals.bmb.a011720","article-title":"Re-Emergence of Monkeypox in Africa: A Review of the Past Six Years","volume":"54","author":"Heymann","year":"1998","journal-title":"Br. Med. Bull."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1038\/nm1273","article-title":"Multiple Diagnostic Techniques Identify Previously Vaccinated Individuals with Protective Immunity Against Monkeypox","volume":"11","author":"Hammarlund","year":"2005","journal-title":"Nat. Med."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2734","DOI":"10.1001\/jama.294.21.2734","article-title":"Adverse Events Associated with Smallpox Vaccination in the United States, January\u2013October 2003","volume":"294","author":"Casey","year":"2005","journal-title":"JAMA"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1016\/j.vaccine.2008.11.079","article-title":"Comparison of the Safety and Immunogenicity of ACAM1000, ACAM2000 and Dryvax in Healthy Vaccinia-Naive Adults","volume":"27","author":"Frey","year":"2009","journal-title":"Vaccine"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1056\/NEJMoa1817307","article-title":"Phase 3 Efficacy Trial of Modified Vaccinia Ankara as a Vaccine Against Smallpox","volume":"381","author":"Pittman","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref_25","unstructured":"Bipartisan Commission on Biodefense (2024). Box the Pox: Reducing the Risk of Smallpox and Other Orthopoxviruses, Bipartisan Commission on Biodefense."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"8134","DOI":"10.1038\/s41467-023-43299-8","article-title":"Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection","volume":"14","author":"Albarnaz","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Venu, V., Roth, C., Adikari, S.H., Small, E.M., Starkenburg, S.R., Sanbonmatsu, K.Y., and Steadman, C.R. (2024). Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection. Commun. Biol., 7.","DOI":"10.1038\/s42003-024-06389-x"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Maroti, Z., Tombacz, D., Prazsak, I., Moldovan, N., Csabai, Z., Torma, G., Balazs, Z., Kalmar, T., Denes, B., and Snyder, M. (2021). Time-course transcriptome analysis of host cell response to poxvirus infection using a dual long-read sequencing approach. BMC Res. Notes, 14.","DOI":"10.1186\/s13104-021-05657-x"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"giy139","DOI":"10.1093\/gigascience\/giy139","article-title":"Dynamic transcriptome profiling dataset of vaccinia virus obtained from long-read sequencing techniques","volume":"7","author":"Snyder","year":"2018","journal-title":"GigaScience"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1186\/s12967-023-04487-8","article-title":"Advancing polytrauma care: Developing and validating machine learning models for early mortality prediction","volume":"21","author":"He","year":"2023","journal-title":"J. Transl. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1007\/s10495-023-01923-4","article-title":"Significance of neutrophil extracellular traps-related gene in the diagnosis and classification of atherosclerosis","volume":"29","author":"Song","year":"2024","journal-title":"Apoptosis"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e13409","DOI":"10.1111\/cpr.13409","article-title":"An artificial intelligence network-guided signature for predicting outcome and immunotherapy response in lung adenocarcinoma patients based on 26 machine learning algorithms","volume":"56","author":"Zhang","year":"2023","journal-title":"Cell Prolif."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Atreya, M.R., Banerjee, S., Lautz, A.J., Alder, M.N., Varisco, B.M., Wong, H.R., Muszynski, J.A., Hall, M.W., Sanchez-Pinto, L.N., and Kamaleswaran, R. (2024). Machine learning-driven identification of the gene-expression signature associated with a persistent multiple organ dysfunction trajectory in critical illness. eBioMedicine, 99.","DOI":"10.1016\/j.ebiom.2023.104938"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Rychkov, D., Neely, J., Oskotsky, T., Yu, S., Perlmutter, N., Nititham, J., Carvidi, A., Krueger, M., Gross, A., and Criswell, L.A. (2021). Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.638066"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.virol.2013.03.025","article-title":"Genomic analysis of vaccinia virus strain TianTan provides new insights into the evolution and evolutionary relationships between Orthopoxviruses","volume":"442","author":"Qin","year":"2013","journal-title":"Virology"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1038\/s41392-023-01574-6","article-title":"Duration of humoral immunity from smallpox vaccination and its cross-reaction with Mpox virus","volume":"8","author":"Li","year":"2023","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"113609","DOI":"10.1016\/j.celrep.2023.113609","article-title":"Long-lasting humoral and cellular memory immunity to vaccinia virus Tiantan provides pre-existing immunity against mpox virus in Chinese population","volume":"43","author":"Li","year":"2024","journal-title":"Cell Rep."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Xia, A., Wang, X., He, J., Wu, W., Jiang, W., Xue, S., Zhang, Q., Gao, Y., Han, Y., and Li, Y. (2023). Cross-reactive antibody response to Monkeypox virus surface proteins in a small proportion of individuals with and without Chinese smallpox vaccination history. BMC Biol., 21.","DOI":"10.1186\/s12915-023-01699-8"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"114772","DOI":"10.1016\/j.jviromet.2023.114772","article-title":"Examination of the cross-reactivity between vaccinia virus Tiantan strain and monkeypox virus","volume":"320","author":"Huang","year":"2023","journal-title":"J. Virol. Methods"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"321","DOI":"10.3201\/eid3002.230542","article-title":"Residual Immunity from Smallpox Vaccination and Possible Protection from Mpox, China","volume":"30","author":"Huang","year":"2024","journal-title":"Emerg. Infect. Dis."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Hashemi, M., Zabihian, A., Hajsaeedi, M., and Hooshmand, M. (2024). Antivirals for monkeypox virus: Proposing an effective machine\/deep learning framework. PLoS ONE, 19.","DOI":"10.1101\/2024.02.11.579829"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e24972","DOI":"10.1016\/j.heliyon.2024.e24972","article-title":"Discovering conserved epitopes of Monkeypox: Novel immunoinformatic and machine learning approaches","volume":"10","author":"Izadi","year":"2024","journal-title":"Heliyon"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1007\/s12275-015-5041-4","article-title":"Replicating poxviruses for human cancer therapy","volume":"53","author":"Kim","year":"2015","journal-title":"J. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/1743-422X-10-61","article-title":"Comparison of host cell gene expression in cowpox, monkeypox or vaccinia virus-infected cells reveals virus-specific regulation of immune response genes","volume":"10","author":"Bourquain","year":"2013","journal-title":"Virol. J."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.antiviral.2016.01.013","article-title":"Seven major genomic deletions of vaccinia virus Tiantan strain are sufficient to decrease pathogenicity","volume":"129","author":"Li","year":"2016","journal-title":"Antivir. Res."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Dong, H.L., Chen, Z.L., He, M.J., Cui, J.Z., Cheng, H., Wang, Q.Y., Xiong, X.H., Liu, G., and Chen, H.P. (2024). The Chimeric Chaoyang-Zika Vaccine Candidate Is Safe and Protective in Mice. Vaccines, 12.","DOI":"10.3390\/vaccines12020215"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Li, Y., Zhu, Y., Chen, S., Li, W., Yin, X., Li, S., Xiao, P., Han, J., Li, X., and Sun, L. (2017). Generation of an Attenuated Tiantan Vaccinia Virus Strain by Deletion of Multiple Genes. Front. Cell Infect. Microbiol., 7.","DOI":"10.3389\/fcimb.2017.00462"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Liu, C., Liu, Y., Liang, L., Cui, S., and Zhang, Y. (2019). RNA-Seq based transcriptome analysis during bovine viral diarrhoea virus (BVDV) infection. BMC Genom., 20.","DOI":"10.1186\/s12864-019-6120-4"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: Protein\u2014Protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: Tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The Gene Ontology knowledgebase in 2023","volume":"224","author":"Consortium","year":"2023","journal-title":"Genetics"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res."}],"updated-by":[{"DOI":"10.3390\/ijms27073330","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2025,1,30]],"date-time":"2025-01-30T00:00:00Z","timestamp":1738195200000}}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/3\/1203\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T13:14:21Z","timestamp":1775567661000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/3\/1203"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,30]]},"references-count":53,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,2]]}},"alternative-id":["ijms26031203"],"URL":"https:\/\/doi.org\/10.3390\/ijms26031203","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,30]]}}}