{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Markov NS"],"funding":["NCATS NIH HHS","NIA NIH HHS","NIAID NIH HHS","U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","NIEHS NIH HHS","American Heart Association-American Stroke Association","NHLBI NIH HHS","U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)","NLM NIH HHS","NCI NIH HHS","NIH HHS","CSRD VA"],"pagination":["1607-1622"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11490290"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["25(9)"],"pubmed_abstract":["The evolution of T cell molecular signatures in the distal lung of patients with severe pneumonia is understudied. Here, we analyzed T cell subsets in longitudinal bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia, including unvaccinated patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or with respiratory failure not linked to pneumonia. In patients with SARS-CoV-2 pneumonia, activation of interferon signaling pathways, low activation of the NF-κB pathway and preferential targeting of spike and nucleocapsid proteins early after intubation were associated with favorable outcomes, whereas loss of interferon signaling, activation of NF-κB-driven programs and specificity for the ORF1ab complex late in disease were associated with mo"],"journal":["Nature immunology"],"pubmed_title":["Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia."],"pmcid":["PMC11490290"],"funding_grant_id":["R01 HL153122","R01 HL134800","F32 HL162377","R01 HL158139","R21 AG075423","F31 AG071225","R01 AI177498","R01 LM013337","UL1 TR001422","K23 HL169815","R01 HL149883","T32 AG020506","T32 AI007476","I01 CX001777","R01 HL094643","T32 HL076139","P30 CA060553","P01 AG049665","S10 OD032243","R01 HL147290","R01 HL153312","P01 HL154998","U19 AI135964","U01 TR003528","U19 AI181102","R01 ES034350","R01 HL147575","24PRE1196998","U19AI135964"],"pubmed_authors":["Fiala JA","Secunda K","Shen J","Mahmoud A","Pawlowski AE","Rasmussen L","Hartmann EM","Smith-Nunez A","Gottardi CJ","Laurenzo S","Grant RA","Kidd DA","Malsin ES","Pickens CO","Patel R","Go PD","Gao CA","Bolig T","Ridge KM","Olson EM","Simons LM","Clepp RK","Perez-Leonor XG","Rowe T","Budinger GRS","Borkowski N","Swaminathan S","Jain M","Wunderink RG","Simmons L","Leibenguth EM","Nwaezeapu J","Coleman J","Donnelly HK","Nunes Amaral LA","Liu GY","Sala MA","McQuattie-Pimentel AC","Ozer EA","Sznajder JI","Arnold JM","Ren Z","Chandel NS","Han S","Bartom ET","Cuttica MJ","Wolfe AR","Schroedl CJ","Schneider D","Kamp DW","Seed PC","Yu Z","Matias G","Hukamdad M","Gadhvi GT","White B","NU SCRIPT Study Investigators","Querrey M","Tran B","Rios-Guzman E","Vitale K","Meza D","Shanes ED","Hultquist J","Guzman ER","Gatesy SWM","Lomasney JW","Qi C","Kihshen H","Markov NS","Lu Z","Wagh AA","Yeldandi AV","Donayre A","Walter JM","Horvath CM","Stoeger T","Rosenbaum ML","Kandpal M","Mylvaganam RJ","Senkow KJ","Lombardo TA","Kang M","Sichizya L","Prickett MH","Wehbe F","Russell SR","Starren J","Green SJ","Helmin KA","Shilatifard A","Bharat A","Sporn PHS","Castellanos J","Hauser AR","Poor TA","Dematte JE","Misharin AV","Szabo A","Morales-Nebreda L","Hyder SM","Joudi AM","Nannapaneni P","Singer BD","Diaz E","Alisoltanidehkordi A","Sumner J","Thakkar S","Johnson L","Rosenberg SR","Textor LN","Lorenzo-Redondo R","Ludwig A","Cybulski TR","Rasmussen LV","Rowell J","Jonasson E","Tomic R","Abdala-Valencia H","Deters JS","Kruser JM","Jovisic M","Bailey JI","Levenson AR","Gradone LD","Hultquist JF","Politanska Y","Winter DR","Gusman E","Lawrence R","Kadar RB","Smith S","Kalhan R","Wolfe LF","Alexander MJ","Korth EA","Klug ZM","Gates KL","Nozick S"],"additional_accession":[]},"is_claimable":false,"name":"Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia.","description":"The evolution of T cell molecular signatures in the distal lung of patients with severe pneumonia is understudied. Here, we analyzed T cell subsets in longitudinal bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia, including unvaccinated patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or with respiratory failure not linked to pneumonia. In patients with SARS-CoV-2 pneumonia, activation of interferon signaling pathways, low activation of the NF-κB pathway and preferential targeting of spike and nucleocapsid proteins early after intubation were associated with favorable outcomes, whereas loss of interferon signaling, activation of NF-κB-driven programs and specificity for the ORF1ab complex late in disease were associated with mo","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Sep","modification":"2026-05-29T10:26:04.665Z","creation":"2026-04-08T04:27:40.111Z"},"accession":"S-EPMC11490290","cross_references":{"pubmed":["39138384"],"doi":["10.1038/s41590-024-01914-w"]}}