Multi-omics characterization of the monkeypox virus infection.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
08 Aug 2024
08 Aug 2024
Historique:
received:
19
12
2023
accepted:
26
07
2024
medline:
9
8
2024
pubmed:
9
8
2024
entrez:
8
8
2024
Statut:
epublish
Résumé
Multiple omics analyzes of Vaccinia virus (VACV) infection have defined molecular characteristics of poxvirus biology. However, little is known about the monkeypox (mpox) virus (MPXV) in humans, which has a different disease manifestation despite its high sequence similarity to VACV. Here, we perform an in-depth multi-omics analysis of the transcriptome, proteome, and phosphoproteome signatures of MPXV-infected primary human fibroblasts to gain insights into the virus-host interplay. In addition to expected perturbations of immune-related pathways, we uncover regulation of the HIPPO and TGF-β pathways. We identify dynamic phosphorylation of both host and viral proteins, which suggests that MAPKs are key regulators of differential phosphorylation in MPXV-infected cells. Among the viral proteins, we find dynamic phosphorylation of H5 that influenced the binding of H5 to dsDNA. Our extensive dataset highlights signaling events and hotspots perturbed by MPXV, extending the current knowledge on poxviruses. We use integrated pathway analysis and drug-target prediction approaches to identify potential drug targets that affect virus growth. Functionally, we exemplify the utility of this approach by identifying inhibitors of MTOR, CHUK/IKBKB, and splicing factor kinases with potent antiviral efficacy against MPXV and VACV.
Identifiants
pubmed: 39117661
doi: 10.1038/s41467-024-51074-6
pii: 10.1038/s41467-024-51074-6
doi:
Substances chimiques
Viral Proteins
0
Proteome
0
Antiviral Agents
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
6778Subventions
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : TRR179-272983813, TRR237-369799452, TRR353-471011418, INST 95/1650-1
Organisme : Helmholtz Association
ID : KA1-Co-02
Informations de copyright
© 2024. The Author(s).
Références
Breman, J. G. et al. Human monkeypox, 1970-79. Bull. World Health Organ 58, 165–182 (1980).
pubmed: 6249508
pmcid: 2395797
Wang, L. et al. Genomic annotation and molecular evolution of monkeypox virus outbreak in 2022. J. Med. Virol. https://doi.org/10.1002/jmv.28036 (2022).
Isidro, J. et al. Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nat. Med. 28, 1569–1572 (2022).
pubmed: 35750157
pmcid: 9388373
doi: 10.1038/s41591-022-01907-y
Otu, A., Ebenso, B., Walley, J., Barceló, J. M. & Ochu, C. L. Global human monkeypox outbreak: atypical presentation demanding urgent public health action. Lancet Microbe 3, e554–e555 (2022).
pubmed: 35688169
pmcid: 9550615
doi: 10.1016/S2666-5247(22)00153-7
Babkin, I. V., Babkina, I. N. & Tikunova, N. V. An update of orthopoxvirus molecular evolution. Viruses 14, 388 (2022).
pubmed: 35215981
pmcid: 8875945
doi: 10.3390/v14020388
Prieto-Granada, C. N., Lobo, A. Z. C. & Mihm, M. C. Chapter 19 - Skin Infections. in diagnostic Pathology of Infectious Disease (ed. Kradin, R. L.) 519–616 (W.B. Saunders, New York, 2010).
Tarín-Vicente, E. J. et al. Clinical presentation and virological assessment of confirmed human monkeypox virus cases in Spain: a prospective observational cohort study. Lancet 400, 661–669 (2022).
pubmed: 35952705
pmcid: 9533900
doi: 10.1016/S0140-6736(22)01436-2
Thornhill, J. P. et al. Monkeypox Virus Infection in Humans across 16 Countries - April-June 2022. N. Engl. J. Med. 387, 679–691 (2022).
pubmed: 35866746
doi: 10.1056/NEJMoa2207323
Wang, X. & Lun, W. Skin Manifestation of Human Monkeypox. J. Clin. Med. Res. 12, 914 (2023).
Brown, K. & Leggat, P. A. Human monkeypox: current state of knowledge and implications for the future. Trop Med Infect Dis 1, 8 (2016).
pubmed: 30270859
pmcid: 6082047
doi: 10.3390/tropicalmed1010008
Gross, E. Update on emerging infections: news from the Centers for Disease Control and prevention. Update: Multistate outbreak of monkeypox–Illinois, Indiana, Kansas, Missouri, Ohio, and Wisconsin, 2003. Annals of emergency medicine 42, 660–662 (2003).
pubmed: 14581919
pmcid: 9533866
doi: 10.1016/S0196-0644(03)00819-9
Alakunle, E. F. & Okeke, M. I. Monkeypox virus: a neglected zoonotic pathogen spreads globally. Nat. Rev. Microbiol. 20, 507–508 (2022).
pubmed: 35859005
pmcid: 9297671
doi: 10.1038/s41579-022-00776-z
Bertran, M. et al. Effectiveness of one dose of MVA–BN smallpox vaccine against mpox in England using the case-coverage method: an observational study. Lancet Infect. Dis. https://doi.org/10.1016/S1473-3099(23)00057-9 (2023).
Wolff Sagy, Y. et al. Real-world effectiveness of a single dose of mpox vaccine in males. Nat. Med. 29, 748–752 (2023).
pubmed: 36720271
pmcid: 9930701
doi: 10.1038/s41591-023-02229-3
Reynolds, M. G. & Damon, I. K. Outbreaks of human monkeypox after cessation of smallpox vaccination. Trends Microbiol 20, 80–87 (2012).
pubmed: 22239910
doi: 10.1016/j.tim.2011.12.001
Parker, S. et al. A human recombinant analogue to plasma-derived vaccinia immunoglobulin prophylactically and therapeutically protects against lethal orthopoxvirus challenge. Antiviral Res 195, 105179 (2021).
pubmed: 34530009
pmcid: 9628779
doi: 10.1016/j.antiviral.2021.105179
Grosenbach, D. W. et al. Oral tecovirimat for the treatment of smallpox. N. Engl. J. Med. 379, 44–53 (2018).
pubmed: 29972742
pmcid: 6086581
doi: 10.1056/NEJMoa1705688
Stittelaar, K. J. et al. Antiviral treatment is more effective than smallpox vaccination upon lethal monkeypox virus infection. Nature 439, 745–748 (2006).
pubmed: 16341204
doi: 10.1038/nature04295
Smee, D. F. Progress in the discovery of compounds inhibiting orthopoxviruses in animal models. Antivir. Chem. Chemother. 19, 115–124 (2008).
pubmed: 19024628
doi: 10.1177/095632020801900302
Rao, A. K. et al. Interim clinical treatment considerations for severe manifestations of mpox - united states, february 2023. MMWR Morb. Mortal. Wkly. Rep. 72, 232–243 (2023).
pubmed: 36862595
pmcid: 9997665
doi: 10.15585/mmwr.mm7209a4
Scaturro, P. et al. An orthogonal proteomic survey uncovers novel Zika virus host factors. Nature 561, 253–257 (2018).
pubmed: 30177828
doi: 10.1038/s41586-018-0484-5
Gordon, D. E. et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 370, eabe9403 (2020).
pubmed: 33060197
pmcid: 7808408
doi: 10.1126/science.abe9403
Stukalov, A. et al. Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 594, 246–252 (2021).
pubmed: 33845483
doi: 10.1038/s41586-021-03493-4
Barh, D. et al. Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19. Comput. Biol. Med. 126, 104051 (2020).
pubmed: 33131530
pmcid: 7547373
doi: 10.1016/j.compbiomed.2020.104051
Li, Y. et al. Multi-platform omics analysis reveals molecular signature for COVID-19 pathogenesis, prognosis and drug target discovery. Signal Transduct Target Ther 6, 155 (2021).
pubmed: 33859163
pmcid: 8047575
doi: 10.1038/s41392-021-00508-4
Rana, A., Sharma, M. & Kumar, G. Relevance of multi-omics approach for future pandemic preparedness and response. in Preparedness for Future Pandemics: Threats and Challenges (eds Varshney, R., Garg, I. & Srivastava, S.) 53–64 (Springer Nature Singapore, Singapore, 2023).
Novy, K. et al. Proteotype profiling unmasks a viral signalling network essential for poxvirus assembly and transcriptional competence. Nat Microbiol. 3, 588–599 (2018).
pubmed: 29632367
doi: 10.1038/s41564-018-0142-6
Soday, L. et al. Quantitative temporal proteomic analysis of vaccinia virus infection reveals regulation of histone deacetylases by an interferon antagonist. Cell Rep. 27, 1920–1933.e7 (2019).
pubmed: 31067474
pmcid: 6518873
doi: 10.1016/j.celrep.2019.04.042
Chou, W., Ngo, T. & Gershon, P. D. An overview of the vaccinia virus infectome: a survey of the proteins of the poxvirus-infected cell. J. Virol. 86, 1487–1499 (2012).
pubmed: 22090131
pmcid: 3264349
doi: 10.1128/JVI.06084-11
Albarnaz, J. D. et al. Quantitative temporal analysis of modified vaccinia Ankara, the monkeypox and smallpox vaccine. Res. Square https://doi.org/10.21203/rs.3.rs-1850393/v1 (2022).
Martin, C. K. et al. Vaccinia virus arrests and shifts the cell cycle. Viruses 14, 431 (2022).
pubmed: 35216024
pmcid: 8874441
doi: 10.3390/v14020431
Veyer, D. L., Carrara, G., Maluquer de Motes, C. & Smith, G. L. Vaccinia virus evasion of regulated cell death. Immunol. Lett. 186, 68–80 (2017).
pubmed: 28366525
doi: 10.1016/j.imlet.2017.03.015
Smith, G. L. et al. Vaccinia virus immune evasion: mechanisms, virulence and immunogenicity. J. Gen. Virol. 94, 2367–2392 (2013).
pubmed: 23999164
doi: 10.1099/vir.0.055921-0
Dhungel, P., Cantu, F. M., Molina, J. A. & Yang, Z. Vaccinia virus as a master of host shutoff induction: targeting processes of the central dogma and beyond. Pathogens 9, 400 (2020).
pubmed: 32455727
pmcid: 7281567
doi: 10.3390/pathogens9050400
Watanabe, Y. et al. Virological characterization of the 2022 outbreak-causing monkeypox virus using human keratinocytes and colon organoids. J. Med. Virol. 95, e28827 (2023).
pubmed: 37278443
doi: 10.1002/jmv.28827
Kakuk, B. et al. In-depth temporal transcriptome profiling of monkeypox and host cells using nanopore sequencing. Sci Data 10, 262 (2023).
pubmed: 37160911
pmcid: 10170163
doi: 10.1038/s41597-023-02149-4
Wang, Z. et al. The human host response to monkeypox infection: a proteomic case series study. EMBO Mol. Med. 14, e16643 (2022).
pubmed: 36169042
pmcid: 9641420
doi: 10.15252/emmm.202216643
Rubins, K. H., Hensley, L. E., Relman, D. A. & Brown, P. O. Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus. PLoS One 6, e15615 (2011).
pubmed: 21267444
pmcid: 3022624
doi: 10.1371/journal.pone.0015615
Ludwig, Holger et al. Role of viral factor e3l in modified vaccinia virus ankara infection of human hela cells: regulation of the virus life cycle and identification of differentially expressed host genes. J. Virol. 79, 2584–2596 (2005).
pubmed: 15681458
pmcid: 546556
doi: 10.1128/JVI.79.4.2584-2596.2005
Bourquain, D., Dabrowski, P. W. & Nitsche, A. Comparison of host cell gene expression in cowpox, monkeypox or vaccinia virus-infected cells reveals virus-specific regulation of immune response genes. Virol. J. 10, 61 (2013).
pubmed: 23425254
pmcid: 3599072
doi: 10.1186/1743-422X-10-61
Lu, C. & Bablanian, R. Characterization of small nontranslated polyadenylylated RNAs in vaccinia virus-infected cells. Proc. Natl. Acad. Sci. USA. 93, 2037–2042 (1996).
pubmed: 8700881
pmcid: 39905
doi: 10.1073/pnas.93.5.2037
Peng, C. et al. Identification of vaccinia virus inhibitors and cellular functions necessary for efficient viral replication by screening bioactives and FDA-approved drugs. Vaccines 8, 401 (2020).
Torres, A. A., Albarnaz, J. D., Bonjardim, C. A. & Smith, G. L. Multiple Bcl-2 family immunomodulators from vaccinia virus regulate MAPK/AP-1 activation. J. Gen. Virol. 97, 2346–2351 (2016).
pubmed: 27312213
pmcid: 5042131
doi: 10.1099/jgv.0.000525
Liu, R., Olano, L. R., Mirzakhanyan, Y., Gershon, P. D. & Moss, B. Vaccinia virus ankyrin-repeat/f-box protein targets interferon-induced ifits for proteasomal degradation. Cell Rep 29, 816–828.e6 (2019).
pubmed: 31644906
pmcid: 6876622
doi: 10.1016/j.celrep.2019.09.039
Pollara, J. J., Spesock, A. H., Pickup, D. J., Laster, S. M. & Petty, I. T. D. Production of prostaglandin E
pubmed: 22534090
doi: 10.1016/j.virol.2012.03.019
Shi, J. et al. Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death. Nature 526, 660–665 (2015).
pubmed: 26375003
doi: 10.1038/nature15514
Imazu, T. et al. Bcl-2/E1B 19 kDa-interacting protein 3-like protein (Bnip3L) interacts with bcl-2/Bcl-xL and induces apoptosis by altering mitochondrial membrane permeability. Oncogene 18, 4523–4529 (1999).
pubmed: 10467396
doi: 10.1038/sj.onc.1202722
Vo, M. T., Smith, B. J., Nicholas, J. & Choi, Y. B. Activation of NIX-mediated mitophagy by an interferon regulatory factor homologue of human herpesvirus. Nat. Commun. 10, 3203 (2019).
pubmed: 31324791
pmcid: 6642096
doi: 10.1038/s41467-019-11164-2
Soares, J. A. P. et al. Activation of the PI3K/Akt pathway early during vaccinia and cowpox virus infections is required for both host survival and viral replication. J. Virol. 83, 6883–6899 (2009).
pubmed: 19386722
pmcid: 2698574
doi: 10.1128/JVI.00245-09
Huang, T.-S., Nilsson, C. E., Punga, T. & Akusjarvi, G. Functional inactivation of the SR family of splicing factors during a vaccinia virus infection. EMBO Rep 3, 1088–1093 (2002).
pubmed: 12393754
pmcid: 1307598
doi: 10.1093/embo-reports/kvf217
Hornbeck, P. V. et al. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res 43, D512–D520 (2015).
pubmed: 25514926
doi: 10.1093/nar/gku1267
Martin, J. C., Herbert, B.-S. & Hocevar, B. A. Disabled-2 downregulation promotes epithelial-to-mesenchymal transition. Br. J. Cancer 103, 1716–1723 (2010).
pubmed: 21063401
pmcid: 2994233
doi: 10.1038/sj.bjc.6605975
Jiang, Y., He, X. & Howe, P. H. Disabled-2 (Dab2) inhibits Wnt/β-catenin signalling by binding LRP6 and promoting its internalization through clathrin. EMBO J 31, 2336–2349 (2012).
pubmed: 22491013
pmcid: 3364753
doi: 10.1038/emboj.2012.83
Yang, Z. et al. Expression profiling of the intermediate and late stages of poxvirus replication. J. Virol. 85, 9899–9908 (2011).
pubmed: 21795349
pmcid: 3196450
doi: 10.1128/JVI.05446-11
Matson, J., Chou, W., Ngo, T. & Gershon, P. D. Static and dynamic protein phosphorylation in the Vaccinia virion. Virology 452-453, 310–323 (2014).
pubmed: 24606709
doi: 10.1016/j.virol.2014.01.012
Greseth, M. D., Carter, D. C., Terhune, S. S. & Traktman, P. Proteomic screen for cellular targets of the vaccinia virus f10 protein kinase reveals that phosphorylation of media regulates stress fiber formation. Mol. Cell. Proteomics 16, S124–S143 (2017).
pubmed: 28183815
pmcid: 5393388
doi: 10.1074/mcp.M116.065003
Leite, F. & Way, M. The role of signalling and the cytoskeleton during Vaccinia Virus egress. Virus Res. 209, 87–99 (2015).
pubmed: 25681743
doi: 10.1016/j.virusres.2015.01.024
Jha, S. et al. Trans-kingdom mimicry underlies ribosome customization by a poxvirus kinase. Nature 546, 651–655 (2017).
pubmed: 28636603
pmcid: 5526112
doi: 10.1038/nature22814
Boyle, K. A., Greseth, M. D. & Traktman, P. Genetic confirmation that the h5 protein is required for vaccinia virus DNA replication. J. Virol. 89, 6312–6327 (2015).
pubmed: 25855734
pmcid: 4474287
doi: 10.1128/JVI.00445-15
Kay, N. E. et al. Biochemical and biophysical properties of a putative hub protein expressed by vaccinia virus*. J. Biol. Chem. 288, 11470–11481 (2013).
pubmed: 23476017
pmcid: 3630899
doi: 10.1074/jbc.M112.442012
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844
pmcid: 8371605
doi: 10.1038/s41586-021-03819-2
Dai, A. et al. Ribosome profiling reveals translational upregulation of cellular oxidative phosphorylation mrnas during vaccinia virus-induced host shutoff. J. Virol. 91, e01858–16 (2017).
pubmed: 28003488
pmcid: 5309933
doi: 10.1128/JVI.01858-16
Van den Broeke, C., Jacob, T. & Favoreel, H. W. Rho’ing in and out of cells: viral interactions with Rho GTPase signaling. Small GTPases 5, e28318 (2014).
pubmed: 24691164
pmcid: 4114625
doi: 10.4161/sgtp.28318
Kotwal, G. J. Influence of glycosylation and oligomerization of vaccinia virus complement control protein on level and pattern of functional activity and immunogenicity. Protein Cell 1, 1084–1092 (2010).
pubmed: 21213103
doi: 10.1007/s13238-010-0139-2
Payne, L. G. & Kristensson, K. Effect of glycosylation inhibitors on the release of enveloped vaccinia virus. J. Virol. 41, 367–375 (1982).
pubmed: 7077747
pmcid: 256767
doi: 10.1128/jvi.41.2.367-375.1982
de Oliveira, L. C. et al. The host factor early growth response gene (egr-1) regulates vaccinia virus infectivity during infection of starved mouse cells. Viruses 10, 140 (2018).
pubmed: 29561772
pmcid: 5923434
doi: 10.3390/v10040140
Woodson, C. M. & Kehn-Hall, K. Examining the role of EGR1 during viral infections. Front. Microbiol. 13, 1020220 (2022).
pubmed: 36338037
pmcid: 9634628
doi: 10.3389/fmicb.2022.1020220
Bonjardim, C. A. Viral exploitation of the MEK/ERK pathway – A tale of vaccinia virus and other viruses. Virology 507, 267–275 (2017).
pubmed: 28526201
doi: 10.1016/j.virol.2016.12.011
Yang, S. H., Galanis, A. & Sharrocks, A. D. Targeting of p38 mitogen-activated protein kinases to MEF2 transcription factors. Mol. Cell. Biol. 19, 4028–4038 (1999).
pubmed: 10330143
pmcid: 104362
doi: 10.1128/MCB.19.6.4028
Ludwig, S. et al. Influenza virus-induced AP-1-dependent gene expression requires activation of the JNK signaling pathway. J. Biol. Chem. 276, 10990–10998 (2001).
pubmed: 11441823
doi: 10.1074/jbc.M009902200
Zachos, G., Clements, B. & Conner, J. Herpes simplex virus type 1 infection stimulates p38/c-Jun N-terminal mitogen-activated protein kinase pathways and activates transcription factor AP-1. J. Biol. Chem. 274, 5097–5103 (1999).
pubmed: 9988758
doi: 10.1074/jbc.274.8.5097
Mirzaei, H., Khodadad, N., Karami, C., Pirmoradi, R. & Khanizadeh, S. The AP-1 pathway; A key regulator of cellular transformation modulated by oncogenic viruses. Rev. Med. Virol. 30, e2088 (2020).
pubmed: 31788897
doi: 10.1002/rmv.2088
Sanderson, C. M., Way, M. & Smith, G. L. Virus-Induced Cell Motility. J. Virol. 72, 1235–1243 (1998).
Beerli, C. et al. Vaccinia virus hijacks EGFR signalling to enhance virus spread through rapid and directed infected cell motility. Nat. Microbiol. 4, 216 (2019).
pubmed: 30420785
doi: 10.1038/s41564-018-0288-2
Park, C. & Walsh, D. RACK1 Regulates Poxvirus Protein Synthesis Independently of Its Role in Ribosome-Based Stress Signaling. J. Virol. 96, e0109322 (2022).
pubmed: 36098514
doi: 10.1128/jvi.01093-22
Sivan, G. et al. Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Proc. Natl. Acad. Sci. USA. 110, 3519–3524 (2013).
pubmed: 23401514
pmcid: 3587217
doi: 10.1073/pnas.1300708110
Hung, J.-J., Chung, C.-S. & Chang, W. Molecular chaperone Hsp90 is important for vaccinia virus growth in cells. J. Virol. 76, 1379–1390 (2002).
pubmed: 11773412
pmcid: 135870
doi: 10.1128/JVI.76.3.1379-1390.2002
Schild, H. & Rammensee, H. G. gp96–the immune system’s Swiss army knife. Nat. Immunol. 1, 100–101 (2000).
pubmed: 11248798
doi: 10.1038/77770
Griekspoor, A., Zwart, W., Neefjes, J. & Michalides, R. Visualizing the action of steroid hormone receptors in living cells. Nucl. Recept. Signal. 5, e003 (2007).
pubmed: 17464358
pmcid: 1853070
doi: 10.1621/nrs.05003
Reading, P. C., Moore, J. B. & Smith, G. L. Steroid hormone synthesis by vaccinia virus suppresses the inflammatory response to infection. J. Exp. Med. 197, 1269–1278 (2003).
pubmed: 12756265
pmcid: 2193778
doi: 10.1084/jem.20022201
Mo, M., Fleming, S. B. & Mercer, A. A. Cell cycle deregulation by a poxvirus partial mimic of anaphase-promoting complex subunit 11. Proc. Natl. Acad. Sci. USA. 106, 19527–19532 (2009).
pubmed: 19887645
pmcid: 2780751
doi: 10.1073/pnas.0905893106
Schweneker, M. et al. The vaccinia virus O1 protein is required for sustained activation of extracellular signal-regulated kinase 1/2 and promotes viral virulence. J. Virol. 86, 2323–2336 (2012).
pubmed: 22171261
pmcid: 3302380
doi: 10.1128/JVI.06166-11
Andrade, A. A. et al. The vaccinia virus-stimulated mitogen-activated protein kinase (MAPK) pathway is required for virus multiplication. Biochem. J 381, 437–446 (2004).
pubmed: 15025565
pmcid: 1133850
doi: 10.1042/BJ20031375
Johnson, J. L. et al. An atlas of substrate specificities for the human serine/threonine kinome. Nature 613, 759–766 (2023).
pubmed: 36631611
pmcid: 9876800
doi: 10.1038/s41586-022-05575-3
Dai, P. et al. Modified vaccinia virus Ankara triggers type I IFN production in murine conventional dendritic cells via a cGAS/STING-mediated cytosolic DNA-sensing pathway. PLoS Pathog 10, e1003989 (2014).
pubmed: 24743339
pmcid: 3990710
doi: 10.1371/journal.ppat.1003989
Waibler, Z. et al. Modified vaccinia virus Ankara induces Toll-like receptor-independent type I interferon responses. J. Virol. 81, 12102–12110 (2007).
pubmed: 17855554
pmcid: 2168990
doi: 10.1128/JVI.01190-07
Depierreux, D. M. et al. Selective modulation of cell surface proteins during vaccinia infection: A resource for identifying viral immune evasion strategies. PLoS Pathog 18, e1010612 (2022).
pubmed: 35727847
pmcid: 9307158
doi: 10.1371/journal.ppat.1010612
Izmailyan, R. et al. Integrin β1 mediates vaccinia virus entry through activation of PI3K/Akt signaling. J. Virol. 86, 6677–6687 (2012).
pubmed: 22496232
pmcid: 3393588
doi: 10.1128/JVI.06860-11
Ruiz, C., Zitnik, M. & Leskovec, J. Identification of disease treatment mechanisms through the multiscale interactome. Nat. Commun. https://doi.org/10.1038/s41467-021-21770-8 (2021).
Meade, N. et al. Poxviruses evade cytosolic sensing through disruption of an mtorc1-mtorc2 regulatory circuit. Cell 174, 1143–1157.e17 (2018).
pubmed: 30078703
pmcid: 6172959
doi: 10.1016/j.cell.2018.06.053
Duran-Frigola, M. et al. Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. Nat. Biotechnol. 38, 1087–1096 (2020).
pubmed: 32440005
doi: 10.1038/s41587-020-0502-7
Yang, G. et al. An orally bioavailable antipoxvirus compound (ST-246) inhibits extracellular virus formation and protects mice from lethal orthopoxvirus challenge. J. Virol. 79, 13139–13149 (2005).
pubmed: 16189015
pmcid: 1235851
doi: 10.1128/JVI.79.20.13139-13149.2005
Rosa, R. B. et al. In vitro and in vivo models for monkeypox. iScience 26, 105702 (2023).
pubmed: 36471873
doi: 10.1016/j.isci.2022.105702
Wei, Z.-K. et al. Animal models of mpox virus infection and disease. Infect. Med. 2, 153–166 (2023).
doi: 10.1016/j.imj.2023.05.004
Mucker, E. M. et al. Susceptibility of marmosets (callithrix jacchus) to monkeypox virus: a low dose prospective model for monkeypox and smallpox disease. PLoS One 10, e0131742 (2015).
pubmed: 26147658
pmcid: 4492619
doi: 10.1371/journal.pone.0131742
Mercer, J. et al. Vaccinia virus strains use distinct forms of macropinocytosis for host-cell entry. Proceedings of the National Academy of Sciences 107, 9346–9351 (2010).
doi: 10.1073/pnas.1004618107
Weisswange, I., Newsome, T. P., Schleich, S. & Way, M. The rate of N-WASP exchange limits the extent of ARP2/3-complex-dependent actin-based motility. Nature 458, 87–91 (2009).
pubmed: 19262673
doi: 10.1038/nature07773
Durkin, C. H. et al. RhoD inhibits RhoC-ROCK-dependent cell contraction via PAK6. Dev. Cell 41, 315–329.e7 (2017).
pubmed: 28486133
pmcid: 5425256
doi: 10.1016/j.devcel.2017.04.010
Handa, Y., Durkin, C. H., Dodding, M. P. & Way, M. Vaccinia virus F11 promotes viral spread by acting as a PDZ-containing scaffolding protein to bind myosin-9A and inhibit RhoA signaling. Cell Host Microbe 14, 51–62 (2013).
pubmed: 23870313
doi: 10.1016/j.chom.2013.06.006
Pfanzelter, J., Mostowy, S. & Way, M. Septins suppress the release of vaccinia virus from infected cells. J. Cell Biol. 217, 2911–2929 (2018).
pubmed: 29921601
pmcid: 6080921
doi: 10.1083/jcb.201708091
Xu, A., Basant, A., Schleich, S., Newsome, T. P. & Way, M. Kinesin-1 transports morphologically distinct intracellular virions during vaccinia infection. J. Cell Sci. 136, jcs260175 (2023).
pubmed: 36093836
doi: 10.1242/jcs.260175
Gowripalan, A. et al. Cell-to-cell spread of vaccinia virus is promoted by TGF-β-independent Smad4 signalling. Cell. Microbiol. 22, e13206 (2020).
pubmed: 32237038
doi: 10.1111/cmi.13206
Xu, W. et al. YAP manipulates proliferation via PTEN/AKT/mTOR-mediated autophagy in lung adenocarcinomas. Cancer Cell Int 21, 30 (2021).
pubmed: 33413409
pmcid: 7791871
doi: 10.1186/s12935-020-01688-9
Szajner, P., Weisberg, A. S. & Moss, B. Evidence for an essential catalytic role of the F10 protein kinase in vaccinia virus morphogenesis. J. Virol. 78, 257–265 (2004).
pubmed: 14671107
pmcid: 303407
doi: 10.1128/JVI.78.1.257-265.2004
Szajner, P., Jaffe, H., Weisberg, A. S. & Moss, B. A complex of seven vaccinia virus proteins conserved in all chordopoxviruses is required for the association of membranes and viroplasm to form immature virions. Virology 330, 447–459 (2004).
pubmed: 15567438
doi: 10.1016/j.virol.2004.10.008
Mercer, J. & Helenius, A. Vaccinia virus uses macropinocytosis and apoptotic mimicry to enter host cells. Science 320, 531–535 (2008).
pubmed: 18436786
doi: 10.1126/science.1155164
Humphrey, S. J., Karayel, O., James, D. E. & Mann, M. High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform. Nat. Protoc. 13, 1897–1916 (2018).
pubmed: 30190555
doi: 10.1038/s41596-018-0014-9
Corsello, S. M. et al. The drug repurposing Hub: a next-generation drug library and information resource. Nat. Med. 23, 405–408 (2017).
pubmed: 28388612
pmcid: 5568558
doi: 10.1038/nm.4306
Bhadra, A., Datta, J., Polson, N. G. & Willard, B. The horseshoe+ estimator of ultra-sparse signals. Bayesian Analysis 12, 1105–1131 (2017).
Goeminne, L. J. E., Gevaert, K. & Clement, L. Peptide-level robust ridge regression improves estimation, sensitivity, and specificity in data-dependent quantitative label-free shotgun proteomics. Mol. Cell. Proteomics 15, 657–668 (2016).
pubmed: 26566788
doi: 10.1074/mcp.M115.055897
Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).
pubmed: 26000488
pmcid: 4481139
doi: 10.1016/j.cell.2015.05.002
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014).
pubmed: 25516281
pmcid: 4302049
doi: 10.1186/s13059-014-0550-8
Stephens, M. False discovery rates: a new deal. Biostatistics 18, 275–294 (2017).
pubmed: 27756721
Keenan, A. B. et al. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res 47, W212–W224 (2019).
pubmed: 31114921
pmcid: 6602523
doi: 10.1093/nar/gkz446
Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22, 1813–1831 (2012).
pubmed: 22955991
pmcid: 3431496
doi: 10.1101/gr.136184.111
McInnes, L., Healy, J. & Melville, J. UMAP: Uniform manifold approximation and projection for dimension reduction. arXiv [stat.ML] (2018).
Yu, G. et al. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26, 976–978 (2010).
pubmed: 20179076
doi: 10.1093/bioinformatics/btq064
Resnik, P. Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. J. Artif. Intell. Res. (1999).
Bodenhofer, U., Kothmeier, A. & Hochreiter, S. APCluster: an R package for affinity propagation clustering. Bioinformatics 27, 2463–2464 (2011).
pubmed: 21737437
doi: 10.1093/bioinformatics/btr406
Stetson, D. B. & Medzhitov, R. Recognition of cytosolic DNA activates an IRF3-dependent innate immune response. Immunity 24, 93–103 (2006).
pubmed: 16413926
doi: 10.1016/j.immuni.2005.12.003
Pennemann, F. L. et al. Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators. Nat. Commun. 12, 7009 (2021).
pubmed: 34853303
pmcid: 8636641
doi: 10.1038/s41467-021-27192-w