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Single-cell analysis of human kidney biopsy tissue reveals epithelial and immune cell responses to BK polyomavirus infection

ABSTRACT: BK polyomavirus (BKV) infection is associated with injury and subsequent graft loss due to the extent of injury or rejection. However, the molecular mechanisms driving injury and subsequent adverse outcomes remain poorly understood. In a cross-sectional study, single-cell RNA sequencing from kidney allograft biopsies was used to assess cell type-specific responses between uninfected controls and two distinct phases of BKV infection: peaking (increasing viral blood titers) and resolving (decreasing viral titers following immunosuppression reduction). Genes upregulated in BK viral nephropathy (BKVN) were enriched for polyomavirus infection hallmarks, including ribosome biogenesis, translation, and energy restructuring. Additionally enriched pathways included wound healing, cellular stress, antigen presentation and immune signaling. Even without BKVN (peaking BK viremia alone), epithelial cells expressed signatures for wound healing, cellular stress, and extracellular matrix remodeling. In vivo tubular cell responses at single-cell resolution were validated against single cell transcriptomic data of BKV infected cells in a cell culture model. Despite similarities, in vivo tubular cells underwent metabolic adaptation favoring fatty acid oxidation and proinflammatory responses not observed in culture models likely from an absent innate and adaptive immune system. Despite lymphopenia and immunosuppressive therapies, the proportion of recipient derived intrarenal adaptive immune cells was expanded in biopsies associated with peaking viremia alongside activation of innate immune responses. Adaptive immune cells continued to have persistent inflammatory signaling and remodeling of energy metabolism during the resolving phase of infection. These novel insights into BKV-associated injury could have implications for clinical management and improved allograft outcomes

ORGANISM(S): Homo sapiens

PROVIDER: GSE317012 | GEO | 2026/02/10

REPOSITORIES: GEO

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Project description:Background: Although the clinical fingerprints of the BK virus (BKV) infection in kidney transplant recipients (KTRs) has been well documented, the systemic biological machinery involved in this complication is still poorly recognized. Proteomics analysis of urinary extracellular vesicles (EVs) can allow us to better address this knowledge gap. Methods: Twenty-nine adult KTRs with normal allograft function affected by BKV infection (15 with only viremia, 14 with viruria and viremia) and 15 controls (CTR) were enrolled and randomly divided in a training cohort (12 BKV and 6 CTR) used for the mass spectrometry analysis of the EVs protein content and a testing cohort(17 BKV and 9 CTR) used for the biological validation of the proteomic results by ELISA. Results: Mass spectrometry analysis revealed a large protein enrichment (more than 1500) in urinary EVs of BKV patients and controls. Pathway analysis by GSEA revealed that several biological gene ontologies (including immunity, complement activation, renal fibrosis, tubular diseases, epithelial to mesenchymal transition) were able to discriminate BKV versus CTR. Kinase was the only gene ontology annotation term negatively enriched in BKV (with SLK being the most down-regulated protein in BKV). Statistical analysis, then, identified a core panel of 70 proteins (including DNASE2, F12, AGT, CTSH, C4A, C7, FABP4 and BPNT1) able to discriminate the two study groups. Instead, although a set of proteins were able to differentiate patients with BKV viruria from those with both viremia-viruria, the urinary proteomic profile of these patients resulted quite similar between the two sub-groups. ELISA for SLK and ELISA for BPNT1 and DNASE2 validated proteomics results. Conclusions: Our study demonstrated that BK virus infection is able to significantly modify the urinary EVs proteomic profile of KTRs also in a very early stage of the disease (when patients still have normal allograft function and only BK viruria) suggesting, whether possible, to start an early preventive therapeutic approach to minimize the risk of the disease progression. Moreover, some 3 of our identified proteins could be employed in future as early urinary biomarkers and/or new therapeutic targets.

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Single-cell analysis of human kidney biopsy tissue reveals epithelial and immune cell responses to BK polyomavirus infection

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