Production of antimicrobial peptides is associated with the reduction of severe kidney infections in human patients

Pyelonephritis (PN) is a common inflammatory disorder of the renal parenchyma, associated with severe morbidity, particularly among elderly and immunodeficient patients. While antibiotics are the most common treatment, the emergence of multi-drug-resistant strains of uropathogenic bacteria necessitates optimized treatment strategies. To unravel the molecular and cellular heterogeneity in PN patients, we analyzed the proteome profile of both the soluble and cellular components of the urine. The measurements were performed using a TimsTOF flex HT coupled with a nano-Elute2 (Bruker).

Gene Ontology Biological Process (GOBP)-based gene set enrichment analysis (GSEA) revealed a clear upregulation of biological processes involved in the immune and defense response, including significant upregulation of proteins with antimicrobial functions (AMPs) in PN patients compared to healthy donors. Monte Carlo reference-based consensus clustering of soluble urine proteins demonstrated a clear differentiation of PN patients into two groups, correlating with clinical characteristics. For the first group, showing a less severe and systemic infection, upregulation of reactive oxygen species, complement activation, leukocyte immune response, and positive regulation of AMP secretion were detected.

The other cohort with more severe infections showed alterations in extracellular matrix response to growth factors and renal system development.

Protein profiles of AMPs, serving as the first line defense of the innate immune system upon infection, along with recently described encrypted AMPs were the most significant factors in distinguishing the two groups of PN patients. Our data, for the first time, decrypts the AMP landscape of the urine in health and PN subgroups and highlights the high diagnostic potential of AMPs as potential alternate antibiotics and new biomarkers in a non-invasive approach for the early detection of tissue damage and the assessment of PN infection severity.