References
- Abers, M.S., Delmonte, O.M., Ricotta, E.E., Fintzi, J., Fink, D.L., de Jesus, A.A.A., Zarember, K.A., Alehashemi, S., Oikonomou, V., Desai, J.V., et al. (2021). An immune-based biomarker signature is associated with mortality in COVID-19 patients. JCI Insight 6, e144455. https://doi.org/10.1172/jci.insight.144455
- Arunachalam, P.S., Wimmers, F., Mok, C.K.P., Perera, R., Scott, M., Hagan, T., Sigal, N., Feng, Y., Bristow, L., Tak-Yin Tsang, O., et al. (2020). Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science 369, 1210-1220. https://doi.org/10.1126/science.abc6261
- Bastard, P., Rosen, L.B., Zhang, Q., Michailidis, E., Hoffmann, H.H., Zhang, Y., Dorgham, K., Philippot, Q., Rosain, J., Beziat, V., et al. (2020). Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science 370, eabd4585. https://doi.org/10.1126/science.abd4585
- Bernardes, J.P., Mishra, N., Tran, F., Bahmer, T., Best, L., Blase, J.I., Bordoni, D., Franzenburg, J., Geisen, U., Josephs-Spaulding, J., et al. (2020). Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells, and plasmablasts as hallmarks of severe COVID-19. Immunity 53, 1296-1314.e9. https://doi.org/10.1016/j.immuni.2020.11.017
- Blanco-Melo, D., Nilsson-Payant, B.E., Liu, W.C., Uhl, S., Hoagland, D., Moller, R., Jordan, T.X., Oishi, K., Panis, M., Sachs, D., et al. (2020). Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181, 1036-1045.e9. https://doi.org/10.1016/j.cell.2020.04.026
- Bost, P., Giladi, A., Liu, Y., Bendjelal, Y., Xu, G., David, E., Blecher-Gonen, R., Cohen, M., Medaglia, C., Li, H., et al. (2020). Host-viral infection maps reveal signatures of severe COVID-19 patients. Cell 181, 1475-1488.e12. https://doi.org/10.1016/j.cell.2020.05.006
- Brodin, P. (2021). Immune determinants of COVID-19 disease presentation and severity. Nat. Med. 27, 28-33. https://doi.org/10.1038/s41591-020-01202-8
- Brunetta, E., Folci, M., Bottazzi, B., De Santis, M., Gritti, G., Protti, A., Mapelli, S.N., Bonovas, S., Piovani, D., Leone, R., et al. (2021). Macrophage expression and prognostic significance of the long pentraxin PTX3 in COVID-19. Nat. Immunol. 22, 19-24. https://doi.org/10.1038/s41590-020-00832-x
- Cameron, M.J., Ran, L., Xu, L., Danesh, A., Bermejo-Martin, J.F., Cameron, C.M., Muller, M.P., Gold, W.L., Richardson, S.E., Poutanen, S.M., et al. (2007). Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome. J. Virol. 81, 8692-8706. https://doi.org/10.1128/JVI.00527-07
- Carvelli, J., Demaria, O., Vely, F., Batista, L., Chouaki Benmansour, N., Fares, J., Carpentier, S., Thibult, M.L., Morel, A., Remark, R., et al. (2020). Association of COVID-19 inflammation with activation of the C5a-C5aR1 axis. Nature 588, 146-150. https://doi.org/10.1038/s41586-020-2600-6
- Channappanavar, R., Fehr, A.R., Zheng, J., Wohlford-Lenane, C., Abrahante, J.E., Mack, M., Sompallae, R., McCray, P.B., Jr., Meyerholz, D.K., and Perlman, S. (2019). IFN-I response timing relative to virus replication determines MERS coronavirus infection outcomes. J. Clin. Invest. 129, 3625-3639. https://doi.org/10.1172/JCI126363
- Chen, J. and Ivashkiv, L.B. (2010). IFN-gamma abrogates endotoxin tolerance by facilitating Toll-like receptor-induced chromatin remodeling. Proc. Natl. Acad. Sci. U. S. A. 107, 19438-19443. https://doi.org/10.1073/pnas.1007816107
- Cho, D.H., Kim, J.K., and Jo, E.K. (2020). Mitophagy and innate immunity in infection. Mol. Cells 43, 10-22. https://doi.org/10.14348/molcells.2020.2329
- Chua, R.L., Lukassen, S., Trump, S., Hennig, B.P., Wendisch, D., Pott, F., Debnath, O., Thurmann, L., Kurth, F., Volker, M.T., et al. (2020). COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis. Nat. Biotechnol. 38, 970-979. https://doi.org/10.1038/s41587-020-0602-4
- Combes, A.J., Courau, T., Kuhn, N.F., Hu, K.H., Ray, A., Chen, W.S., Chew, N.W., Cleary, S.J., Kushnoor, D., Reeder, G.C., et al. (2021). Global absence and targeting of protective immune states in severe COVID-19. Nature 591, 124-130. https://doi.org/10.1038/s41586-021-03234-7
- Consiglio, C.R., Cotugno, N., Sardh, F., Pou, C., Amodio, D., Rodriguez, L., Tan, Z., Zicari, S., Ruggiero, A., Pascucci, G.R., et al. (2020). The immunology of multisystem inflammatory syndrome in children with COVID-19. Cell 183, 968-981.e7. https://doi.org/10.1016/j.cell.2020.09.016
- Del Valle, D.M., Kim-Schulze, S., Huang, H.H., Beckmann, N.D., Nirenberg, S., Wang, B., Lavin, Y., Swartz, T.H., Madduri, D., Stock, A., et al. (2020). An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat. Med. 26, 1636-1643. https://doi.org/10.1038/s41591-020-1051-9
- Fajgenbaum, D.C. and June, C.H. (2020). Cytokine storm. N. Engl. J. Med. 383, 2255-2273. https://doi.org/10.1056/NEJMra2026131
- Galani, I.E., Rovina, N., Lampropoulou, V., Triantafyllia, V., Manioudaki, M., Pavlos, E., Koukaki, E., Fragkou, P.C., Panou, V., Rapti, V., et al. (2021). Untuned antiviral immunity in COVID-19 revealed by temporal type I/III interferon patterns and flu comparison. Nat. Immunol. 22, 32-40. https://doi.org/10.1038/s41590-020-00840-x
- Giamarellos-Bourboulis, E.J., Netea, M.G., Rovina, N., Akinosoglou, K., Antoniadou, A., Antonakos, N., Damoraki, G., Gkavogianni, T., Adami, M.E., Katsaounou, P., et al. (2020). Complex immune dysregulation in COVID-19 patients with severe respiratory failure. Cell Host Microbe 27, 992-1000. e3. https://doi.org/10.1016/j.chom.2020.04.009
- Giroux, N.S., Ding, S., McClain, M.T., Burke, T.W., Petzold, E., Chung, H.A., Palomino, G.R., Wang, E., Xi, R., Bose, S., et al. (2020). Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity. BioRxiv, https://doi.org/10.1101/2020.12.04.412155
- Grant, R.A., Morales-Nebreda, L., Markov, N.S., Swaminathan, S., Querrey, M., Guzman, E.R., Abbott, D.A., Donnelly, H.K., Donayre, A., Goldberg, I.A., et al. (2021). Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Nature 590, 635-641. https://doi.org/10.1038/s41586-020-03148-w
- Hadjadj, J., Yatim, N., Barnabei, L., Corneau, A., Boussier, J., Smith, N., Pere, H., Charbit, B., Bondet, V., Chenevier-Gobeaux, C., et al. (2020). Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients. Science 369, 718-724. https://doi.org/10.1126/science.abc6027
- Ivashkiv, L.B. (2018). IFNgamma: signalling, epigenetics and roles in immunity, metabolism, disease and cancer immunotherapy. Nat. Rev. Immunol. 18, 545-558. https://doi.org/10.1038/s41577-018-0029-z
- Ivashkiv, L.B. and Donlin, L.T. (2014). Regulation of type I interferon responses. Nat. Rev. Immunol. 14, 36-49. https://doi.org/10.1038/nri3581
- Kapellos, T.S., Bonaguro, L., Gemund, I., Reusch, N., Saglam, A., Hinkley, E.R., and Schultze, J.L. (2019). Human monocyte subsets and phenotypes in major chronic inflammatory diseases. Front. Immunol. 10, 2035. https://doi.org/10.3389/fimmu.2019.02035
- Karki, R., Sharma, B.R., Tuladhar, S., Williams, E.P., Zalduondo, L., Samir, P., Zheng, M., Sundaram, B., Banoth, B., Malireddi, R.K.S., et al. (2021). Synergism of TNF-alpha and IFN-gamma triggers inflammatory cell death, tissue damage, and mortality in SARS-CoV-2 infection and cytokine shock syndromes. Cell 184, 149-168.e17. https://doi.org/10.1016/j.cell.2020.11.025
- King, C. and Sprent, J. (2021). Dual nature of type I interferons in SARS-CoV-2-induced inflammation. Trends Immunol. 42, 312-322. https://doi.org/10.1016/j.it.2021.02.003
- Laing, A.G., Lorenc, A., Del Molino Del Barrio, I., Das, A., Fish, M., Monin, L., Munoz-Ruiz, M., McKenzie, D.R., Hayday, T.S., Francos-Quijorna, I., et al. (2020). A dynamic COVID-19 immune signature includes associations with poor prognosis. Nat. Med. 26, 1623-1635. https://doi.org/10.1038/s41591-020-1038-6
- Lee, J.S., Park, S., Jeong, H.W., Ahn, J.Y., Choi, S.J., Lee, H., Choi, B., Nam, S.K., Sa, M., Kwon, J.S., et al. (2020). Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19. Sci. Immunol. 5, eabd1554. https://doi.org/10.1126/sciimmunol.abd1554
- Liao, M., Liu, Y., Yuan, J., Wen, Y., Xu, G., Zhao, J., Cheng, L., Li, J., Wang, X., Wang, F., et al. (2020). Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat. Med. 26, 842-844. https://doi.org/10.1038/s41591-020-0901-9
- Lucas, C., Wong, P., Klein, J., Castro, T.B.R., Silva, J., Sundaram, M., Ellingson, M.K., Mao, T., Oh, J.E., Israelow, B., et al. (2020). Longitudinal analyses reveal immunological misfiring in severe COVID-19. Nature 584, 463-469. https://doi.org/10.1038/s41586-020-2588-y
- Mann, E.R., Menon, M., Knight, S.B., Konkel, J.E., Jagger, C., Shaw, T.N., Krishnan, S., Rattray, M., Ustianowski, A., Bakerly, N.D., et al. (2020). Longitudinal immune profiling reveals key myeloid signatures associated with COVID-19. Sci. Immunol. 5, eabd6197. https://doi.org/10.1126/sciimmunol.abd6197
- McNab, F., Mayer-Barber, K., Sher, A., Wack, A., and O'Garra, A. (2015). Type I interferons in infectious disease. Nat. Rev. Immunol. 15, 87-103. https://doi.org/10.1038/nri3787
- Merad, M. and Martin, J.C. (2020). Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages. Nat. Rev. Immunol. 20, 355-362. https://doi.org/10.1038/s41577-020-0331-4
- Middleton, E.A., He, X.Y., Denorme, F., Campbell, R.A., Ng, D., Salvatore, S.P., Mostyka, M., Baxter-Stoltzfus, A., Borczuk, A.C., Loda, M., et al. (2020). Neutrophil extracellular traps contribute to immunothrombosis in COVID-19 acute respiratory distress syndrome. Blood 136, 1169-1179. https://doi.org/10.1182/blood.2020007008
- Netea, M.G., Giamarellos-Bourboulis, E.J., Dominguez-Andres, J., Curtis, N., van Crevel, R., van de Veerdonk, F.L., and Bonten, M. (2020). Trained immunity: a tool for reducing susceptibility to and the severity of SARS-CoV-2 infection. Cell 181, 969-977. https://doi.org/10.1016/j.cell.2020.04.042
- Nie, X., Qian, L., Sun, R., Huang, B., Dong, X., Xiao, Q., Zhang, Q., Lu, T., Yue, L., Chen, S., et al. (2021). Multi-organ proteomic landscape of COVID-19 autopsies. Cell 184, 775-791.e14. https://doi.org/10.1016/j.cell.2021.01.004
- Park, A. and Iwasaki, A. (2020). Type I and type III interferons - induction, signaling, evasion, and application to combat COVID-19. Cell Host Microbe 27, 870-878. https://doi.org/10.1016/j.chom.2020.05.008
- Park, S.H., Kang, K., Giannopoulou, E., Qiao, Y., Kang, K., Kim, G., Park-Min, K.H., and Ivashkiv, L.B. (2017). Type I interferons and the cytokine TNF cooperatively reprogram the macrophage epigenome to promote inflammatory activation. Nat. Immunol. 18, 1104-1116. https://doi.org/10.1038/ni.3818
- Platanitis, E. and Decker, T. (2018). Regulatory networks involving STATs, IRFs, and NFkappaB in inflammation. Front. Immunol. 9, 2542. https://doi.org/10.3389/fimmu.2018.02542
- Radermecker, C., Detrembleur, N., Guiot, J., Cavalier, E., Henket, M., d'Emal, C., Vanwinge, C., Cataldo, D., Oury, C., Delvenne, P., et al. (2020). Neutrophil extracellular traps infiltrate the lung airway, interstitial, and vascular compartments in severe COVID-19. J. Exp. Med. 217, e20201012. https://doi.org/10.1084/jem.20201012
- Ramlall, V., Thangaraj, P.M., Meydan, C., Foox, J., Butler, D., Kim, J., May, B., De Freitas, J.K., Glicksberg, B.S., Mason, C.E., et al. (2020). Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection. Nat. Med. 26, 1609-1615. https://doi.org/10.1038/s41591-020-1021-2
- RECOVERY Collaborative Group, Horby, P., Lim, W.S., Emberson, J.R., Mafham, M., Bell, J.L., Linsell, L., Staplin, N., Brightling, C., Ustianowski, A., et al. (2021). Dexamethasone in hospitalized patients with Covid-19. N. Engl. J. Med. 384, 693-704. https://doi.org/10.1056/NEJMoa2021436
- Ren, X., Wen, W., Fan, X., Hou, W., Su, B., Cai, P., Li, J., Liu, Y., Tang, F., Zhang, F., et al. (2021). COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell 184, 1895-1913.e19. https://doi.org/10.1016/j.cell.2021.01.053
- Rodrigues, T.S., de Sa, K.S.G., Ishimoto, A.Y., Becerra, A., Oliveira, S., Almeida, L., Goncalves, A.V., Perucello, D.B., Andrade, W.A., Castro, R., et al. (2021). Inflammasomes are activated in response to SARS-CoV-2 infection and are associated with COVID-19 severity in patients. J. Exp. Med. 218, e20201707. https://doi.org/10.1084/jem.20201707
- Schoggins, J.W. and Rice, C.M. (2011). Interferon-stimulated genes and their antiviral effector functions. Curr. Opin. Virol. 1, 519-525. https://doi.org/10.1016/j.coviro.2011.10.008
- Schulte-Schrepping, J., Reusch, N., Paclik, D., Bassler, K., Schlickeiser, S., Zhang, B., Kramer, B., Krammer, T., Brumhard, S., Bonaguro, L., et al. (2020). Severe COVID-19 is marked by a dysregulated myeloid cell compartment. Cell 182, 1419-1440.e23. https://doi.org/10.1016/j.cell.2020.08.001
- Sheahan, T., Morrison, T.E., Funkhouser, W., Uematsu, S., Akira, S., Baric, R.S., and Heise, M.T. (2008). MyD88 is required for protection from lethal infection with a mouse-adapted SARS-CoV. PLoS Pathog. 4, e1000240. https://doi.org/10.1371/journal.ppat.1000240
- Shen, B., Yi, X., Sun, Y., Bi, X., Du, J., Zhang, C., Quan, S., Zhang, F., Sun, R., Qian, L., et al. (2020). Proteomic and metabolomic characterization of COVID-19 patient sera. Cell 182, 59-72.e15. https://doi.org/10.1016/j.cell.2020.05.032
- Shi, L., Zhang, Z., Yu, A.M., Wang, W., Wei, Z., Akhter, E., Maurer, K., Costa Reis, P., Song, L., Petri, M., et al. (2014). The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs. PLoS One 9, e93846. https://doi.org/10.1371/journal.pone.0093846
- Shin, D., Mukherjee, R., Grewe, D., Bojkova, D., Baek, K., Bhattacharya, A., Schulz, L., Widera, M., Mehdipour, A.R., Tascher, G., et al. (2020). Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587, 657-662. https://doi.org/10.1038/s41586-020-2601-5
- Silvin, A., Chapuis, N., Dunsmore, G., Goubet, A.G., Dubuisson, A., Derosa, L., Almire, C., Henon, C., Kosmider, O., Droin, N., et al. (2020). Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19. Cell 182, 1401-1418.e18. https://doi.org/10.1016/j.cell.2020.08.002
- Sokol, C.L. and Luster, A.D. (2015). The chemokine system in innate immunity. Cold Spring Harb. Perspect. Biol. 7, a016303. https://doi.org/10.1101/cshperspect.a016303
- Su, Y., Chen, D., Yuan, D., Lausted, C., Choi, J., Dai, C.L., Voillet, V., Duvvuri, V.R., Scherler, K., Troisch, P., et al. (2020). Multi-omics resolves a sharp disease-state shift between mild and moderate COVID-19. Cell 183, 1479-1495.e20. https://doi.org/10.1016/j.cell.2020.10.037
- Totura, A.L., Whitmore, A., Agnihothram, S., Schafer, A., Katze, M.G., Heise, M.T., and Baric, R.S. (2015). Toll-like receptor 3 signaling via TRIF contributes to a protective innate immune response to severe acute respiratory syndrome coronavirus infection. mBio 6, e00638-15.
- Vabret, N., Britton, G.J., Gruber, C., Hegde, S., Kim, J., Kuksin, M., Levantovsky, R., Malle, L., Moreira, A., Park, M.D., et al. (2020). Immunology of COVID-19: current state of the science. Immunity 52, 910-941. https://doi.org/10.1016/j.immuni.2020.05.002
- van der Poll, T., van de Veerdonk, F.L., Scicluna, B.P., and Netea, M.G. (2017). The immunopathology of sepsis and potential therapeutic targets. Nat. Rev. Immunol. 17, 407-420. https://doi.org/10.1038/nri.2017.36
- Venkatesh, D., Ernandez, T., Rosetti, F., Batal, I., Cullere, X., Luscinskas, F.W., Zhang, Y., Stavrakis, G., Garcia-Cardena, G., Horwitz, B.H., et al. (2013). Endothelial TNF receptor 2 induces IRF1 transcription factor-dependent interferon-beta autocrine signaling to promote monocyte recruitment. Immunity 38, 1025-1037. https://doi.org/10.1016/j.immuni.2013.01.012
- Wang, N., Zhan, Y., Zhu, L., Hou, Z., Liu, F., Song, P., Qiu, F., Wang, X., Zou, X., Wan, D., et al. (2020). Retrospective multicenter cohort study shows early interferon therapy is associated with favorable clinical responses in COVID-19 patients. Cell Host Microbe 28, 455-464.e2. https://doi.org/10.1016/j.chom.2020.07.005
- Wei, J., Alfajaro, M.M., DeWeirdt, P.C., Hanna, R.E., Lu-Culligan, W.J., Cai, W.L., Strine, M.S., Zhang, S.M., Graziano, V.R., Schmitz, C.O., et al. (2021). Genome-wide CRISPR screens reveal host factors critical for SARS-CoV-2 infection. Cell 184, 76-91.e13. https://doi.org/10.1016/j.cell.2020.10.028
- Wilk, A.J., Rustagi, A., Zhao, N.Q., Roque, J., Martinez-Colon, G.J., McKechnie, J.L., Ivison, G.T., Ranganath, T., Vergara, R., Hollis, T., et al. (2020). A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat. Med. 26, 1070-1076. https://doi.org/10.1038/s41591-020-0944-y
- Yarilina, A., Park-Min, K.H., Antoniv, T., Hu, X., and Ivashkiv, L.B. (2008). TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon-response genes. Nat. Immunol. 9, 378-387. https://doi.org/10.1038/ni1576
- Zhang, Q., Bastard, P., Liu, Z., Le Pen, J., Moncada-Velez, M., Chen, J., Ogishi, M., Sabli, I.K.D., Hodeib, S., Korol, C., et al. (2020). Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science 370, eabd4570. https://doi.org/10.1126/science.abd4570
- Zhou, R., To, K.K., Wong, Y.C., Liu, L., Zhou, B., Li, X., Huang, H., Mo, Y., Luk, T.Y., Lau, T.T., et al. (2020a). Acute SARS-CoV-2 infection impairs dendritic cell and T cell responses. Immunity 53, 864-877.e5. https://doi.org/10.1016/j.immuni.2020.07.026
- Zhou, Z., Ren, L., Zhang, L., Zhong, J., Xiao, Y., Jia, Z., Guo, L., Yang, J., Wang, C., Jiang, S., et al. (2020b). Heightened innate immune responses in the respiratory tract of COVID-19 patients. Cell Host Microbe 27, 883-890.e2. https://doi.org/10.1016/j.chom.2020.04.017
- Zhu, L., Yang, P., Zhao, Y., Zhuang, Z., Wang, Z., Song, R., Zhang, J., Liu, C., Gao, Q., Xu, Q., et al. (2020). Single-cell sequencing of peripheral mononuclear cells reveals distinct immune response landscapes of COVID-19 and influenza patients. Immunity 53, 685-696.e3. https://doi.org/10.1016/j.immuni.2020.07.009
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