Integrated single-cell and bulk transcriptomic analyses reveal cDC1-centered ubiquitination dysregulation and identify UBE2F as a critical regulator in sepsis

BackgroundSepsis is a life-threatening syndrome with dysregulated immune responses and multiple organ dysfunction. However, precise diagnostic biomarkers and effective therapeutic targets for this syndrome are still lacking.

Protein ubiquitination modulates inflammatory regulation and immune cell function, but the specific immune cell subsets that drive ubiquitination-associated immune dysregulation in human sepsis have not been clearly identified.MethodsAn integrated analysis was performed using 315,220 single cells from two single-cell RNA sequencing (scRNA-seq) datasets in conjunction with independent bulk transcriptomic cohorts. We quantified cell-type responsiveness using Augur, inferred intercellular communication via CellChat, and identified ubiquitination-related gene networks through weighted gene co-expression network analysis (WGCNA) and subsequent multi-algorithm feature selection.

Functional validation was conducted with lipopolysaccharide (LPS)-stimulated murine dendritic cells (DCs) line - DC2.4 in vitro and a cecal ligation and puncture (CLP) mouse model in vivo.Resultsconventional Dendritic cells (cDCs) were identified as the most transcriptionally perturbed immune population in sepsis, with subsequent subclustering revealing that the type-1 conventional dendritic cells (cDC1) subset specifically exhibited pronounced activation of ubiquitination signatures.