Proteomic analysis of urinary extracellular vesicles from patients with ADTKD-HNF1β identifies roles for cilia-related proteins and serpins

Kahlman, E.J.E.M.
van Heugten, M.H.
Tholen, L.E.
Verploegen, M.F.A.
Spruijt, C.G.
Jansen, P.W.T.C.
Vermeulen, M.
Hoenderop, J.G.J.
Hoorn, E.J.
Nijenhuis, T.
de Baaij, J.H.F.

This collection contains the data for the study "Proteomic analysis of urinary extracellular vesicles from patients with ADTKD-HNF1B identifies roles for cilia-related proteins and serpins". This research article was published as a part of a thesis and in American Journal of Physiology Renal Physiology (PMID: 40013955). Autosomal dominant tubulointerstitial kidney disease-subtype hepatocyte nuclear factor 1β (ADTKD-HNF1β) is caused by pathogenic variants in or deletions of the gene encoding transcription factor HNF1β. Patients with the same mutation have variable renal and extrarenal phenotypes, including renal cysts, diabetes, and electrolyte disturbances. The aim of this exploratory study was to provide insight whether pathophysiological effects in the kidney of patients with ADTKD-HNF1β are visible by analyzing their urinary extracellular vesicle (uEV) proteome. We isolated uEVs collected from patients with ADTKD-HNF1β and included patients with autosomal dominant polycystic kidney disease (ADPKD) and patients with chronic kidney disease (CKD) as controls. Subsequent LC-MS/MS proteomics and differential and pathway enrichment analyses were performed. Transcriptional targets of HNF1β were selected with ChIP sequencing to study changes in protein abundance due to loss of HNF1β, and correlation analyses with clinical features were performed. We found differential enrichment of five proteins, enrichment of pathways involved in cilia and cell-cell adhesion, and depletion of several Serpins in patients with ADTKD-HNF1β and ADPKD, compared with patients with CKD. We identified differential enrichment of nine HNF1β transcriptional targets between patients with ADTKD-HNF1β and patients with CKD, and we demonstrated that Serpin abundance negatively correlated with estimated glomerular filtration rate (eGFR) in patients with ADTKD-HNF1β (R = -0.52). The uEV proteome of patients with ADTKD-HNF1β shows an enrichment in proteins involved in renal cysts development, with resemblance to ADPKD. These changes provide new insight into the pathophysiology of ADTKD-HNF1β. Their onset and association with cyst development and kidney function decline warrants further study. In this collection, you can find the processed mass spectrometry data, NTA data and data corresponding the ELISA assays. Raw mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD050720 (URL included in metadata). Supplemental material was also made available on figshare (DOI included in metadata).