{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:34:31Z","timestamp":1785429271978,"version":"3.56.0"},"posted":{"date-parts":[[2025,6,20]]},"group-title":"Genomics","reference-count":21,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T00:00:00Z","timestamp":1750377600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["R03AI159286"],"award-info":[{"award-number":["R03AI159286"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U24HG012674"],"award-info":[{"award-number":["U24HG012674"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R21CA280520"],"award-info":[{"award-number":["R21CA280520"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["3R21CA280520-01S1"],"award-info":[{"award-number":["3R21CA280520-01S1"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"name":"University of Washington Virginia and Prentice Bloedel Endowment"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,6,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Post-acute sequelae of SARS-CoV-2 infection (PASC) affects millions globally, yet the molecular mechanisms underlying acute COVID-19 and its chronic sequelae remain poorly understood.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We performed an integrative transcriptomic analysis of three independent RNA-seq datasets, capturing the complete COVID-19 pathophysiology from health through acute severe infection to post-acute sequelae and mortality (n=142 total samples). We implemented a containerized analytical pipeline from data download, quantification, differential gene expression to uniformly process these three RNA-seq datasets.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our analysis reveals striking molecular dichotomies contrasting disease phases with profound clinical implications. Acute severe\/critical COVID-19 reveals predominant enrichment of TNF-\u03b1 signaling via NF-\u03baB pathways (normalized enrichment score &gt;2.5, FDR &lt;0.001), reflecting a cytokine storm pathophysiology characterized by rapid inflammatory developments involving IL-6, TNF-\u03b1, and anti-apoptotic responses. In contrast, PASC patients exhibit dominant enrichment of Myc Targets V1 and Oxidative Phosphorylation pathways (NES &gt;2.2, FDR &lt;0.005), indicating important shifts toward cellular adaptation. Pathway signature analysis identifies core differentially expressed genes that reliably distinguish disease phases, thereby offering objective biomarkers for precision diagnosis and monitoring.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>These findings establish a comprehensive molecular framework distinguishing acute inflammatory from chronic metabolic COVID-19 phases, with potential clinical applicability. TNF-\u03b1\/NF-\u03baB pathway signatures identify patients at risk for severe disease progression, while Myc\/OXPHOS signatures allow objective PASC diagnosis, addressing current reliance on subjective and eliminative diagnosis. This integrative analytical framework has utility beyond COVID-19, offering an applicable approach for precision medicine implementation across other diseases processes.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Clinical Significance<\/jats:title>\n                  <jats:p>This study transforms COVID-19 from a symptom-based to a molecularly-defined disease spectrum, enabling precision diagnosis, prognostic monitoring, classification, and targeted therapeutic possibilities based on pathway-specific biomarkers rather than subjective clinical assessments.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.06.18.660454","type":"posted-content","created":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T23:40:11Z","timestamp":1750462811000},"source":"Crossref","is-referenced-by-count":0,"title":["Uncovering the Pathophysiological Pattern of Expression from Integrated Analysis across Uniformly Processed RNA Sequencing COVID-19 Datasets"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4159-3853","authenticated-orcid":false,"given":"Andrew","family":"Cole","sequence":"first","affiliation":[{"name":"Strathmore Institute of Mathematical Sciences, Strathmore University, Nairobi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-7203-5261","authenticated-orcid":false,"given":"Bryce","family":"Fukuda","sequence":"additional","affiliation":[{"name":"School of Engineering and Technology, University of Washington Tacoma, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4363-0697","authenticated-orcid":false,"given":"Thomas","family":"Dahlstrom","sequence":"additional","affiliation":[{"name":"School of Engineering and Technology, University of Washington Tacoma, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5209-2248","authenticated-orcid":false,"given":"Ling-Hong","family":"Hung","sequence":"additional","affiliation":[{"name":"School of Engineering and Technology, University of Washington Tacoma, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1754-7577","authenticated-orcid":false,"given":"Ka Yee","family":"Yeung","sequence":"additional","affiliation":[{"name":"School of Engineering and Technology, University of Washington Tacoma, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041204282847000_2025.06.18.660454v1.1","unstructured":"Post COVID-19 condition (long COVID). https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/post-covid-19-condition-(long-covid)."},{"key":"2026041204282847000_2025.06.18.660454v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-022-00846-2"},{"key":"2026041204282847000_2025.06.18.660454v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51893-7"},{"key":"2026041204282847000_2025.06.18.660454v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06651-y"},{"key":"2026041204282847000_2025.06.18.660454v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.01.014"},{"key":"2026041204282847000_2025.06.18.660454v1.6","doi-asserted-by":"crossref","unstructured":"Oliveira, T. T. , Freitas, J. F. , Medeiros, V. P. B. de , Xavier, T. J. da S. & Agnez-Lima, L. F. Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity. Life Science Alliance 7, (2024).","DOI":"10.26508\/lsa.202302358"},{"key":"2026041204282847000_2025.06.18.660454v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/J.TIBTECH.2017.02.012"},{"key":"2026041204282847000_2025.06.18.660454v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-021-01113x"},{"key":"2026041204282847000_2025.06.18.660454v1.9","doi-asserted-by":"crossref","unstructured":"Schulthei\u00df, C. et al. The IL-1\u03b2, IL-6, and TNF cytokine triad is associated with post-acute sequelae of COVID-19. CR Med 3, (2022).","DOI":"10.1016\/j.xcrm.2022.100663"},{"key":"2026041204282847000_2025.06.18.660454v1.10","doi-asserted-by":"crossref","unstructured":"Gardinassi, L. G. , Souza, C. O. S. , Sales-Campos, H. & Fonseca, S. G. Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse. Front. 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