Comprehensive Proteomic Quantification of Bladder Stone Progression in a Cystinuric Mouse Model Using Data-Independent Acquisitions

Abstract

Cystinuria is one of various disorders that cause biomineralization in the urinary system, including bladder stone formation in humans. It is most prevalent in children and adolescents and more aggressive in males. There is no cure, and only limited disease management techniques help to solubilize the stones. Recurrence, even after treatment, occurs frequently. Other than a buildup of cystine, little is known about factors involved in the formation, expansion, and recurrence of these stones. This study sought to define the growth of bladder stones, guided by micro-computed tomography imaging, and to profile dynamic stone proteome changes in a cystinuria mouse model. After bladder stones developed in vivo, they were harvested and separated into four developmental stages (sand, small, medium and large stone), based on their size. Data-dependent and data-independent acquisitions allowed deep profiling of stone proteomics. The proteomic signatures and pathways illustrated major changes as the stones grew. Stones initiate from a small nidus, grow outward, and show major enrichment in ribosomal proteins and factors related to coagulation and platelet degranulation, suggesting a major dysregulation in specific pathways that can be targeted for new therapeutic options.

Deep Coverage and Quantification of the Bone Proteome Provides Enhanced Opportunities for New Discoveries in Skeletal Biology and Disease

“…Deep protein coverage and quantification are achieved with our novel robust and reproducible proteomics protocol to efficiently extract proteins from the complex bone matrix and the subsequent combination with modern quantitative mass spectrometric strategies. We adapted and improved steps from a reported method that extracted proteins from bones (45), as well as from cystinuric bladder stones (46).…”

“…Deep protein coverage and quantification are achieved with our novel robust and reproducible proteomics protocol to efficiently extract proteins from the complex bone matrix and the subsequent combination with modern quantitative mass spectrometric strategies. We adapted and improved steps from a reported method that extracted proteins from bones (45), as well as from cystinuric bladder stones (46). When paired with data-independent acquisition (DIA) mass spectrometry (MS) (47–49), this novel workflow profiles and quantifies both dynamic changes in protein composition, as well as PTM signaling to investigate bone aging and diseases.…”