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Renal cyst fluid proteomics in autosomal dominant polycystic kidney disease (ADPKD)

ADPKD is characterized by localized autonomous cellular proliferation, fluid accumulation within the cysts, and intraparenchymal fibrosis of the kidney. Little is known about the cyst fluid's protein composition. We hypothesized that the complex collection of cystic fluid proteins (cystic proteome) plabys a major role in cyst formation/maintenance and contains yet unknown diagnostic and mechanistic features that are common to all forms of PKD. We analyzed five kidney cyst fluids from four patients with ADPKD. Tryptic peptides from plasma‐protein immunodepleted (ProteoPrep®) and undepleted cyst fluid samples were analyzed by LC‐MS/MS. The proteins were identified by SEQUEST and validated via Trans‐Proteomic Pipeline. 391 proteins were identified with >90% confidence; 251 of them in undepleted and 362 in immunodepleted samples. Immunodepletion removed >98% of the cyst fluid protein. A surprisingly large and functionally diverse number of proteins common to all 5 cysts was identified. These proteins may be of mechanistic interest and include Ig γ κ and fragments; complement components; vitronectin; orosomucoid; prostaglandin D2 synthase; and vitamin D‐binding protein. Supported by AFOSR Grant FA9550‐06‐1‐0083.