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Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants.
Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L. Gygi JP, et al. Among authors: fragiadakis gk. bioRxiv [Preprint]. 2023 Nov 6:2023.11.03.565292. doi: 10.1101/2023.11.03.565292. bioRxiv. 2023. PMID: 37986828 Free PMC article. Updated. Preprint.
Global Absence and Targeting of Protective Immune States in Severe COVID-19.
Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. Combes AJ, et al. Among authors: fragiadakis gk. bioRxiv [Preprint]. 2020 Oct 29:2020.10.28.359935. doi: 10.1101/2020.10.28.359935. bioRxiv. 2020. PMID: 33140050 Free PMC article. Updated. Preprint.
Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19: Anti-IFN antibodies in critical COVID-19 correlate with poor ISG response and upregulation of LAIR1 surface protein in PBMCs.
van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS; UCSF COMET consortium; Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. van der Wijst MGP, et al. Among authors: fragiadakis gk. bioRxiv [Preprint]. 2021 Mar 10:2021.03.09.434529. doi: 10.1101/2021.03.09.434529. bioRxiv. 2021. PMID: 33758859 Free PMC article. Preprint.
Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study.
Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LIR, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N; IMPACC study group members. Ozonoff A, et al. EBioMedicine. 2022 Sep;83:104208. doi: 10.1016/j.ebiom.2022.104208. Epub 2022 Aug 8. EBioMedicine. 2022. PMID: 35952496 Free PMC article.
Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients.
Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K; IMPACC Network; Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH. Diray-Arce J, et al. Cell Rep Med. 2023 Jun 20;4(6):101079. doi: 10.1016/j.xcrm.2023.101079. Epub 2023 May 23. Cell Rep Med. 2023. PMID: 37327781 Free PMC article.
Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study.
Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE; IMPACC Network; Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N. Ozonoff A, et al. Nat Commun. 2024 Jan 3;15(1):216. doi: 10.1038/s41467-023-44090-5. Nat Commun. 2024. PMID: 38172101 Free PMC article.
Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.
Phan HV, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns CB, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N; IMPACC Network; Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR. Phan HV, et al. Sci Transl Med. 2024 Apr 17;16(743):eadj5154. doi: 10.1126/scitranslmed.adj5154. Epub 2024 Apr 17. Sci Transl Med. 2024. PMID: 38630846
Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality.
Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Haddad EK; IMPACC Network; Reed EF, Kraft M, McComsey GA, Metcalf JP, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar WL, Maecker HT, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Sekaly RP, Ehrlich LI, Fourati S, Peters B, Kleinstein SH, Guan L. Gygi JP, et al. Among authors: fragiadakis gk. J Clin Invest. 2024 May 1;134(9):e176640. doi: 10.1172/JCI176640. J Clin Invest. 2024. PMID: 38690733 Free PMC article. Clinical Trial.
Mass cytometry reveals a conserved immune trajectory of recovery in hospitalized COVID-19 patients.
Burnett CE, Okholm TLH, Tenvooren I, Marquez DM, Tamaki S, Munoz Sandoval P, Willmore A; UCSF COMET Consortium; Hendrickson CM, Kangelaris KN, Langelier CR, Krummel MF, Woodruff PG, Calfee CS, Erle DJ, Ansel KM, Spitzer MH. Burnett CE, et al. Immunity. 2022 Jul 12;55(7):1284-1298.e3. doi: 10.1016/j.immuni.2022.06.004. Epub 2022 Jun 7. Immunity. 2022. PMID: 35779527 Free PMC article.
Plasma SARS-CoV-2 nucleocapsid antigen levels are associated with progression to severe disease in hospitalized COVID-19.
Wick KD, Leligdowicz A, Willmore A, Carrillo SA, Ghale R, Jauregui A, Chak SS, Nguyen V, Lee D, Jones C, Dewar R, Lane HC, Kangelaris KN, Hendrickson CM, Liu KD, Sinha P, Erle DJ, Langelier CR, Krummell MF, Woodruff PG, Calfee CS, Matthay MA; COMET Consortium. Wick KD, et al. Crit Care. 2022 Sep 14;26(1):278. doi: 10.1186/s13054-022-04153-3. Crit Care. 2022. PMID: 36104754 Free PMC article.
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