GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE326nnn/GSE326313/suppl/GSE326313_raw_counts.csv.gzftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE326nnn/GSE326313/primaryOK200TranscriptomicsHomo sapiensExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE326313GEOGSEfalseIntegrative analysis reveals ciliary dysfunction and compartmentalized LCN2 expression as distinct features of COVID-19 [PBMC]The unique pulmonary pathophysiology of COVID-19 compared with other respiratory viral infections remains poorly understood. We performed integrative bulk and single-cell RNA sequencing on bronchoalveolar lavage fluid (BALF) from patients with COVID-19 (n=24) or influenza (n=10) and healthy controls (n=10). While influenza primarily induced conventional inflammatory responses, COVID-19 triggered distinct microenvironmental remodeling characterized by a specific cilium-related gene signature (e.g., DNAH9, FOXJ1) and expansion of ciliated and airway epithelial cells. Cross-tissue comparison with peripheral blood mononuclear cells uncovered a compartmentalized immune response, particularly for Lipocalin-2 (LCN2), which showed opposite expression trends between the lung and systemic circulation. This study identifies ciliary dysfunction and epithelial-immune crosstalk as key features distinguishing COVID-19 from influenza and highlights epithelial-derived LCN2 as a robust, compartmentalized biomarker for disease severity.2026/04/03GSE326313GSM9628998GSM9628994GSM9628995GSM9628996GSM962899729480326313Homo sapiens