Enterovirus A71 (EV-A71) is recognized as the primary causative agent of hand, foot, and mouth disease (HFMD) and is prevalent worldwide. However, the precise pathogenic mechanisms of EV-A71 remain unclear, and specific drugs targeting it have yet to be successfully developed. To explore the mechanisms underlying EV-A71 pathogenesis and to identify potential therapeutic opportunities, we performed a comprehensive proteogenomic characterization of muscle tissues from BALB/c mice infected with EV-A71, integrating transcriptomic, proteomic, and phosphoproteomic analyses. Our results showed that phagosome, complement, and coagulation cascade pathway-related molecules were activated, and the expression of cell growth-related molecules was downregulated. Concurrently, a rapid activation of the neutrophil extracellular trap pathway was observed at the protein level. Additionally, we mapped the global phosphorylation profiles to dysregulated kinases, predicting 32 drugs corresponding to 27 kinases. We found that kinase inhibitors have antiviral activity in vitro; vandetanib, nintedanib, dasatinib, avitinib, and nilotinib can inhibit virus replication in mice to some extent. Overall, this study provides a multi-omics resource for elucidating EV-A71-induced alterations in target tissues and for linking omics-based target discovery with drug screening and functional validation, providing new insights into both pathogenesis and therapeutic exploration.
| [1] |
L. Yi, J. Lu, H. F. Kung, and M. L. He, “The Virology and Developments Toward Control of Human Enterovirus 71,” Critical Reviews in Microbiology 37, no. 4 (2011): 313–327.
|
| [2] |
G. Zheng, J. Cao, J. Yu, et al., “Risk Factors for Death in Children With Critical and Severe Hand-Foot-and-Mouth Disease in Chongqing, China: An Observational Study,” Medicine 96, no. 49 (2017): e8934.
|
| [3] |
B. Liu, L. Luo, S. Yan, et al., “Clinical Features for Mild Hand, Foot and Mouth Disease in China,” PLoS ONE 10, no. 8 (2015): e0135503.
|
| [4] |
Y. He, J. Yang, G. Zeng, et al., “Risk Factors for Critical Disease and Death From Hand, Foot and Mouth Disease,” Pediatric Infectious Disease Journal 33, no. 9 (2014): 966–970.
|
| [5] |
J. Hong, F. Liu, H. Qi, et al., “Changing Epidemiology of Hand, Foot, and Mouth Disease in China, 2013–2019: A Population-Based Study,” Lancet Regional Health—Western Pacific 20 (2022): 100370.
|
| [6] |
T. T. Nguyen, C. H. Chiu, C. Y. Lin, et al., “Efficacy, Safety, and Immunogenicity of an Inactivated, Adjuvanted Enterovirus 71 Vaccine in Infants and Children: A Multiregion, Double-Blind, Randomised, Placebo-Controlled, Phase 3 Trial,” Lancet 399, no. 10336 (2022): 1708–1717.
|
| [7] |
R. L. Kuo, Y. H. Lin, R. Y. Wang, et al., “Proteomics Analysis of EV71-Infected Cells Reveals the Involvement of Host Protein NEDD4L in EV71 Replication,” Journal of Proteome Research 14, no. 4 (2015): 1818–1830.
|
| [8] |
H. Shi, S. Liu, Z. Tan, et al., “Proteomic and Metabonomic Analysis Uncovering Enterovirus A71 Reprogramming Host Cell Metabolic Pathway,” Proteomics 23, no. 2 (2023): e2200362.
|
| [9] |
M. Bouhaddou, D. Memon, B. Meyer, et al., “The Global Phosphorylation Landscape of SARS-CoV-2 Infection,” Cell 182, no. 3 (2020): 685–712. e19.
|
| [10] |
A. Stukalov, V. Girault, V. Grass, et al., “Multilevel Proteomics Reveals Host Perturbations by SARS-CoV-2 and SARS-CoV,” Nature 594, no. 7862 (2021): 246–252.
|
| [11] |
M. Wang, Z. Zhang, J. Liu, et al., “Gefitinib and Fostamatinib Target EGFR and SYK to Attenuate Silicosis: A Multi-Omics Study With Drug Exploration,” Signal Transduction and Targeted Therapy 7, no. 1 (2022): 157.
|
| [12] |
M. J. Schnell, J. P. McGettigan, C. Wirblich, and A. Papaneri, “The Cell Biology of Rabies Virus: Using Stealth to Reach the Brain,” Nature Reviews Microbiology 8, no. 1 (2010): 51–61.
|
| [13] |
J. Liu, Y. Yang, Y. Xu, et al., “Lycorine Reduces Mortality of Human Enterovirus 71-Infected Mice by Inhibiting Virus Replication,” Virology Journal 8 (2011): 483.
|
| [14] |
V. Fensterl and G. C. Sen, “Interferon-Induced Ifit Proteins: Their Role in Viral Pathogenesis,” Journal of Virology 89, no. 5 (2015): 2462–2468.
|
| [15] |
T. A. Arvind and P. N. Rangarajan, “Mouse Apolipoprotein L9 Is a Phosphatidylethanolamine-Binding Protein,” Biochemical and Biophysical Research Communications 479, no. 4 (2016): 636–642.
|
| [16] |
Y. Chen, L. Graf, T. Chen, et al., “Rare Variant MX1 Alleles Increase Human Susceptibility to Zoonotic H7N9 Influenza Virus,” Science 373, no. 6557 (2021): 918–922.
|
| [17] |
X. Wang, S. Su, Y. Zhu, et al., “Metabolic Reprogramming via ACOD1 Depletion Enhances Function of Human Induced Pluripotent Stem Cell-Derived CAR-Macrophages in Solid Tumors,” Nature Communications 14, no. 1 (2023): 5778.
|
| [18] |
R. Wu, R. Kang, and D. Tang, “Mitochondrial ACOD1/IRG1 in Infection and Sterile Inflammation,” Journal of Intensive Care Medicine 2, no. 2 (2022): 78–88.
|
| [19] |
M. Gronbaek-Thygesen, C. Kampmeyer, K. Hofmann, and R. Hartmann-Petersen, “The Moonlighting of RAD23 in DNA Repair and Protein Degradation,” Biochimica et Biophysica Acta (BBA)—Gene Regulatory Mechanisms 1866, no. 2 (2023): 194925.
|
| [20] |
R. E. London, “XRCC1—Strategies for Coordinating and Assembling a Versatile DNA Damage Response,” DNA Repair 93 (2020): 102917.
|
| [21] |
Y. Gong, N. Handa, S. C. Kowalczykowski, and T. de Lange, “PHF11 Promotes DSB Resection, ATR Signaling, and HR,” Genes & Development 31, no. 1 (2017): 46–58.
|
| [22] |
R. Thakkar, G. R. Sareddy, Q. Zhang, et al., “PELP1: A Key Mediator of Oestrogen Signalling and Actions in the Brain,” Journal of Neuroendocrinology 30, no. 2 (2018): e12484.
|
| [23] |
S. Xu, S. K. Lai, D. Y. Sim, et al., “SRRM2 Organizes Splicing Condensates to Regulate Alternative Splicing,” Nucleic Acids Research 50, no. 15 (2022): 8599–8614.
|
| [24] |
Y. Onodera, K. Takagi, Y. Miki, et al., “TACC2 (Transforming Acidic Coiled-Coil Protein 2) in Breast Carcinoma as a Potent Prognostic Predictor Associated With Cell Proliferation,” Cancer Medicine 5, no. 8 (2016): 1973–1982.
|
| [25] |
R. Kaur, T. Tada, and N. R. Landau, “Restriction of SARS-CoV-2 Replication by Receptor Transporter Protein 4 (RTP4),” MBio 14, no. 4 (2023): e0109023.
|
| [26] |
I. N. Boys, E. Xu, K. B. Mar, et al., “RTP4 Is a Potent IFN-Inducible Anti-Flavivirus Effector Engaged in a Host-Virus Arms Race in Bats and Other Mammals,” Cell Host & Microbe 28, no. 5 (2020): 712–723. e9.
|
| [27] |
J. Li, J. Ma, R. Cao, et al., “A Skin Organoid-Based Infection Platform Identifies an Inhibitor Specific for HFMD,” Nature Communications 16, no. 1 (2025): 2513.
|
| [28] |
J. P. Kuppan, M. D. Mitrovich, and M. D. Vahey, “A Morphological Transformation in Respiratory Syncytial Virus Leads to Enhanced Complement Deposition,” Elife 10 (2021): e70575.
|
| [29] |
Y. Wu, X. Cui, W. Yang, et al., “Zika Virus Infection in Hypothalamus Causes Hormone Deficiencies and Leads to Irreversible Growth Delay and Memory Impairment in Mice,” Cell Reports 25, no. 6 (2018): 1537–1547. e4.
|
| [30] |
A. Hidalgo, P. Libby, O. Soehnlein, et al., “Neutrophil Extracellular Traps: From Physiology to Pathology,” Cardiovascular Research 118, no. 13 (2022): 2737–2753.
|
| [31] |
X. Li, Q. Gao, W. Wu, et al., “FGL2-MCOLN3-Autophagy Axis-Triggered Neutrophil Extracellular Traps Exacerbate Liver Injury in Fulminant Viral Hepatitis,” Cellular and Molecular Gastroenterology and Hepatology 14, no. 5 (2022): 1077–1101.
|
| [32] |
H. M. Al-Kuraishy, A. I. Al-Gareeb, H. A. Al-Hussaniy, et al., “Neutrophil Extracellular Traps (NETs) and Covid-19: A New Frontiers for Therapeutic Modality,” International Immunopharmacology 104 (2022): 108516.
|
| [33] |
Y. Wang, Q. Yang, Y. Dong, et al., “Piezo1-Directed Neutrophil Extracellular Traps Regulate Macrophage Differentiation During Influenza Virus Infection,” Cell Death & Disease 16, no. 1 (2025): 60.
|
| [34] |
N. Wang, X. Yang, J. Sun, et al., “Neutrophil Extracellular Traps Induced by VP1 Contribute to Pulmonary Edema During EV71 Infection,” Cell Death Discovery 5 (2019): 111.
|
| [35] |
O. Tatsiy, O. V. de Carvalho, H. T. Mosha, and P. P. McDonald, “Early and Late Processes Driving NET Formation, and the Autocrine/Paracrine Role of Endogenous RAGE Ligands,” Frontiers in Immunology 12 (2021): 675315.
|
| [36] |
Y. Zhang, S. Chen, T. Sun, et al., “Abundant Neutrophil-Initiated Acute Myocardial Injury Following Coxsackievirus A6 Infection,” Journal of Infectious Diseases 229, no. 5 (2024): 1440–1450.
|
| [37] |
E. J. Needham, B. L. Parker, T. Burykin, D. E. James, and S. J. Humphrey, “Illuminating the Dark Phosphoproteome,” Science Signaling 12, no. 565 (2019): eaau8645.
|
| [38] |
Y. Zhou, C. He, D. Yan, et al., “The Kinase CK1varepsilon Controls the Antiviral Immune Response by Phosphorylating the Signaling Adaptor TRAF3,” Nature Immunology 17, no. 4 (2016): 397–405.
|
| [39] |
J. K. Cheong and D. M. Virshup, “Casein Kinase 1: Complexity in the Family,” International Journal of Biochemistry & Cell Biology 43, no. 4 (2011): 465–469.
|
| [40] |
J. Zhang, Y. J. Wu, X. X. Hu, and W. Wei, “New Insights Into the Lck-NF-kappaB Signaling Pathway,” Frontiers in Cell and Developmental Biology 11 (2023): 1120747.
|
| [41] |
C. Brullo, C. Villa, B. Tasso, E. Russo, and A. Spallarossa, “Btk Inhibitors: A Medicinal Chemistry and Drug Delivery Perspective,” International Journal of Molecular Sciences 22, no. 14 (2021): 7641.
|
| [42] |
B. T. Brian and T. S. Freedman, “The Src-Family Kinase Lyn in Immunoreceptor Signaling,” Endocrinology 162, no. 10 (2021): bqab152.
|
| [43] |
W. Peng, J. Wu, B. Zhao, et al., “Pathogenicity and Transcriptomic Profiling Reveals Immunology Molecular Hallmarks After CA10 Virus Infection,” Animal Models and Experimental Medicine 7, no. 5 (2024): 717–731.
|
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