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Updated: Sep 15, 2025
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
Uncovering the Pathophysiological Pattern of Expression from Integrated Analysis across Uniformly Processed RNA
Andrew Cole1, Bryce Fukuda2, Thomas Dahlstrom2
1Strathmore Institute of Mathematical Sciences, Strathmore University, Nairobi, Kenya.
Background:
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.
Methods:
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.
Results:
Our analysis reveals striking molecular dichotomies contrasting disease phases with profound clinical implications. Acute severe/critical COVID-19 reveals predominant enrichment of TNF-α signaling via NF-κB pathways (normalized enrichment score >2.5, FDR <0.001), reflecting a cytokine storm pathophysiology characterized by rapid inflammatory developments involving IL-6, TNF-α, and anti-apoptotic responses. In contrast, PASC patients exhibit dominant enrichment of Myc Targets V1 and Oxidative Phosphorylation pathways (NES >2.2, FDR <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.
Conclusions:
These findings establish a comprehensive molecular framework distinguishing acute inflammatory from chronic metabolic COVID-19 phases, with potential clinical applicability. TNF-α/NF-κB 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.
Clinical Significance:
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.
