Guaifenesin stone matrix proteomics: a protocol for identifying proteins critical to stone formation

Comprehensive study of altered proteomic landscape in proximal renal tubular epithelial cells in response to calcium oxalate monohydrate crystals

Background

Calcium oxalate monohydrate (COM), the major crystalline composition of most kidney stones, induces inflammatory infiltration and injures in renal tubular cells. However, the mechanism of COM-induced toxic effects in renal tubular cells remain ambiguous. The present study aimed to investigate the potential changes in proteomic landscape of proximal renal tubular cells in response to the stimulation of COM crystals.

Methods

Clinical kidney stone samples were collected and characterized by a stone component analyzer. Three COM-enriched samples were applied to treat human proximal tubular epithelial cells HK-2. The proteomic landscape of COM-crystal treated HK-2 cells was screened by TMT-labeled quantitative proteomics analysis. The differentially expressed proteins (DEPs) were identified by pair-wise analysis. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEPs were performed. Protein interaction networks were identified by STRING database.

Results

The data of TMT-labeled quantitative proteomic analysis showed that a total of 1141 proteins were differentially expressed in HK-2 cells, of which 699 were up-regulated and 442 were down-regulated. Functional characterization by KEGG, along with GO enrichments, suggests that the DEPs are mainly involved in cellular components and cellular processes, including regulation of actin cytoskeleton, tight junction and focal adhesion. 3 high-degree hub nodes, CFL1, ACTN and MYH9 were identified by STRING analysis.

Conclusion

These results suggested that calcium oxalate crystal has a significant effect on protein expression profile in human proximal renal tubular epithelial cells.

Raman chemical imaging, a new tool in kidney stone structure analysis: Case-study and comparison to Fourier Transform Infrared spectroscopy

BACKGROUND AND OBJECTIVES

The kidney stone's structure might provide clinical information in addition to the stone composition. The Raman chemical imaging is a technology used for the production of two-dimension maps of the constituents' distribution in samples. We aimed at determining the use of Raman chemical imaging in urinary stone analysis.

MATERIAL AND METHODS

Fourteen calculi were analyzed by Raman chemical imaging using a confocal Raman microspectrophotometer. They were selected according to their heterogeneous composition and morphology. Raman chemical imaging was performed on the whole section of stones. Once acquired, the data were baseline corrected and analyzed by MCR-ALS. Results were then compared to the spectra obtained by Fourier Transform Infrared spectroscopy.

RESULTS

Raman chemical imaging succeeded in identifying almost all the chemical components of each sample, including monohydrate and dihydrate calcium oxalate, anhydrous and dihydrate uric acid, apatite, struvite, brushite, and rare chemicals like whitlockite, ammonium urate and drugs. However, proteins couldn't be detected because of the huge autofluorescence background and the small concentration of these poor Raman scatterers. Carbapatite and calcium oxalate were correctly detected even when they represented less than 5 percent of the whole stones. Moreover, Raman chemical imaging provided the distribution of components within the stones: nuclei were accurately identified, as well as thin layers of other components. Conversion of dihydrate to monohydrate calcium oxalate was correctly observed in the centre of one sample. The calcium oxalate monohydrate had different Raman spectra according to its localization.

CONCLUSION

Raman chemical imaging showed a good accuracy in comparison with infrared spectroscopy in identifying components of kidney stones. This analysis was also useful in determining the organization of components within stones, which help locating constituents in low quantity, such as nuclei. However, this analysis is time-consuming, making it more suitable for research studies rather than routine analysis.

Stone former urine proteome demonstrates a cationic shift in protein distribution compared to normal

Many urine proteins are found in calcium oxalate stones, yet decades of research have failed to define the role of urine proteins in stone formation. This urine proteomic study compares the relative amounts of abundant urine proteins between idiopathic calcium oxalate stone forming and non-stone forming (normal) cohorts to identify differences that might correlate with disease. Random mid-morning urine samples were collected following informed consent from 25 stone formers and 14 normal individuals. Proteins were isolated from urine using ultrafiltration. Urine proteomes for each sample were characterized using label-free spectral counting mass spectrometry, so that urine protein relative abundances could be compared between the two populations. A total of 407 unique proteins were identified with the 38 predominant proteins accounting for >82% of all sample spectral counts. The most highly abundant proteins were equivalent in stone formers and normals, though significant differences were observed in a few moderate abundance proteins (immunoglobulins, transferrin, and epidermal growth factor), accounting for 13 and 10% of the spectral counts, respectively. These proteins contributed to a cationic shift in protein distribution in stone formers compared to normals (22% vs. 18%, p = 0.04). Our data showing only small differences in moderate abundance proteins suggest that no single protein controls stone formation. Observed increases in immunoglobulins and transferrin suggest increased inflammatory activity in stone formers, but cannot distinguish cause from effect in stone formation. The observed cationic shift in protein distribution would diminish protein charge stabilization, which could lead to protein aggregation and increased risk for crystal aggregation.

Accurate stone analysis: the impact on disease diagnosis and treatment

This manuscript reviews the requirements for acceptable compositional analysis of kidney stones using various biophysical methods. High-resolution X-ray powder diffraction crystallography and Fourier transform infrared spectroscopy (FTIR) are the only acceptable methods in our labs for kidney stone analysis. The use of well-constructed spectral reference libraries is the basis for accurate and complete stone analysis. The literature included in this manuscript identify errors in most commercial laboratories and in some academic centers. We provide personal comments on why such errors are occurring at such high rates, and although the work load is rather large, it is very worthwhile in providing accurate stone compositions. We also provide the results of our almost 90,000 stone analyses and a breakdown of the number of components we have observed in the various stones. We also offer advice on determining the method used by the various FTIR equipment manufacturers who also provide a stone analysis library so that the FTIR users can feel comfortable in the accuracy of their reported results. Such an analysis on the accuracy of the individual reference libraries could positively influence the reduction in their respective error rates.