{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T06:18:49Z","timestamp":1783491529401,"version":"3.55.0"},"reference-count":32,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"2020 Chest Foundation GlaxoSmithKline Distinguished Scholar in Respiratory Health"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Med."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Severe COVID-19\u2013related acute respiratory distress syndrome (ARDS) often progresses to respiratory failure requiring invasive mechanical ventilation (IMV). Although several biomarkers (e.g., CRP, suPAR, Ang-2) have been explored to predict COVID-19 disease severity, validated early-presentation biomarkers that specifically prognosticate the need for IMV and mechanistic pathways in ARDS remain limited.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Research question<\/jats:title>\n                    <jats:p>What transcriptomic and immune signatures distinguish IMV from non-IMV in patients with COVID-19 ARDS, and how do these molecular changes contribute to disease severity?<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Patients (\n                      <jats:italic>n<\/jats:italic>\n                      \u202f=\u202f36) with SARS-CoV-2 infection requiring oxygen support were enrolled in this prospective study. Blood samples were collected at baseline, day 4, and day 8 from patients on IMV (\n                      <jats:italic>n<\/jats:italic>\n                      \u202f=\u202f11) and non-IMV (\n                      <jats:italic>n<\/jats:italic>\n                      \u202f=\u202f25). Transcriptomic profiles of peripheral blood mononuclear cells were assessed using RNA-sequencing, followed by gene ontology and KEGG pathway enrichment. Plasma cytokines and chemokines were measured using multiplex immunoassays, peripheral immune cell endotypes were characterized by mass cytometry, and neutrophil extracellular trap (NET) formation was evaluated by kinetic live-cell imaging.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Clinically, IMV patients had significantly longer hospital (43.0 vs. 19.5\u202fdays,\n                      <jats:italic>p<\/jats:italic>\n                      \u202f=\u202f0.001) and ICU stays (39.6 vs. 9.1\u202fdays,\n                      <jats:italic>p<\/jats:italic>\n                      \u202f&amp;lt;\u202f0.01) and higher 28-day mortality (45.5% vs. 12.0%; aOR\u202f=\u202f8.78,\n                      <jats:italic>p<\/jats:italic>\n                      \u202f=\u202f0.04). Transcriptomic profiling identified 36 DEGs at day 4 and 21 at day 8 in patients on IMV, characterized by downregulation of mitochondrial gene MTARC2 and anticoagulant regulator TFPI, and upregulation of stress-response genes (RNF165, KCNMA1, and AC245014.3) (\n                      <jats:italic>p<\/jats:italic>\n                      \u202f&amp;lt;\u202f0.05). Plasma IL-6, IL-8, and IL-10 were elevated in IMV group, with IL-10 showing the strongest predictive value (AUC 0.74,\n                      <jats:italic>p<\/jats:italic>\n                      \u202f=\u202f0.0002). Immune profiling revealed higher percentage of CD57\n                      <jats:sup>\u2212<\/jats:sup>\n                      NK cells at baseline in non-IMV group. NET formation did not differ between groups.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Patients requiring IMV demonstrated distinct transcriptomic and immune profiles associated with severe COVID-19. These findings identify candidate biomarkers and pathways associated with disease severity; however, the results are exploratory and require validation in larger cohorts and functional studies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmed.2026.1856132","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:57:32Z","timestamp":1783490252000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated transcriptomic and immune analysis reveals distinct mitochondrial and immune signature in COVID-19 ARDS requiring invasive mechanical ventilation"],"prefix":"10.3389","volume":"13","author":[{"given":"Deepa B.","family":"Gotur","sequence":"first","affiliation":[{"name":"Division of Pulmonary, Critical Care, and Sleep Medicine, Houston Methodist Hospital","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diksha M.","family":"Gowda","sequence":"additional","affiliation":[{"name":"Charles W. Duncan Jr. Department of Medicine, Houston Methodist","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Decha","family":"Pinkaew","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Critical Care, and Sleep Medicine, Houston Methodist Hospital","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aijun","family":"Zhang","sequence":"additional","affiliation":[{"name":"Charles W. Duncan Jr. Department of Medicine, Houston Methodist","place":["Houston, TX, United States"]},{"name":"Center for Bioenergetics Research, Houston Methodist Research Institute","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Spencer","family":"Hankins","sequence":"additional","affiliation":[{"name":"Charles W. Duncan Jr. Department of Medicine, Houston Methodist","place":["Houston, TX, United States"]},{"name":"Center for Bioenergetics Research, Houston Methodist Research Institute","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaefali","family":"Rodgers","sequence":"additional","affiliation":[{"name":"Charles W. Duncan Jr. Department of Medicine, Houston Methodist","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yitian","family":"Xu","sequence":"additional","affiliation":[{"name":"Immunomonitoring Core, Houston Methodist Neal Cancer Center","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohi U.","family":"Syed","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Critical Care, and Sleep Medicine, Houston Methodist Hospital","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tejaswini","family":"Reddy","sequence":"additional","affiliation":[{"name":"Center for Inflammation and Infectious Disease, Houston Methodist Research Institute","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Systems Medicine and Bioengineering, Houston Methodist Cancer Center","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junjun","family":"Zheng","sequence":"additional","affiliation":[{"name":"Immunomonitoring Core, Houston Methodist Neal Cancer Center","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodney J.","family":"Folz","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Critical Care, and Sleep Medicine, Houston Methodist Hospital","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleftherios","family":"Mylonakis","sequence":"additional","affiliation":[{"name":"Charles W. 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Duncan Jr. Department of Medicine, Houston Methodist","place":["Houston, TX, United States"]},{"name":"Center for Bioenergetics Research, Houston Methodist Research Institute","place":["Houston, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,8]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"108427","DOI":"10.1016\/j.clim.2020.108427","article-title":"COVID-19 pathophysiology: a review","volume":"215","author":"Yuki","year":"2020","journal-title":"Clin Immunol"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1038\/s41572-019-0069-0","article-title":"Acute respiratory distress syndrome","volume":"5","author":"Matthay","year":"2019","journal-title":"Nat Rev Dis Primers"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.bbabio.2004.03.016","article-title":"Inhibition of mitochondrial respiratory complex I by nitric oxide, 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