Urine protein concentration estimation for biomarker discovery

Recent advances have been made in the study of urinary proteomics as a diagnostic tool for renal disease and pre-eclampsia which requires accurate measurement of urinary protein. We compared different protein assays (Bicinchoninic acid (BCA), Lowry and Bradford) against the ‘gold standard’ amino-acid assay in urine from 43 women (8 non-pregnant, 34 pregnant, including 8 with pre-eclampsia. BCA assay was superior to both Lowry and Bradford assays (Bland Altman bias: 0.08) compared to amino-acid assay, which performed particularly poorly at higher protein concentrations. These data highlight the need to use amino-acid or BCA assays for unprocessed urine protein estimation

Proteomics and peritoneal dialysis: early days but clear potential*

The application of proteomics (the study of protein products expressed by the genome) has become one of the leading post-genomic technologies given the increased understanding of the central role of proteins and protein–protein interactions in all aspects of cellular function [2]. Systematic global identification and quantification of proteins can, not only inform improved biomedical understanding of a particular system in healthy or diseased individuals, but also be used for protein biomarker discovery. The most popular of the many proteomic strategies available are summarized in Figure 1 and, whilst two-dimensional electrophoresis (2DE) gel-based approach remains popular, liquid chromatography–tandem mass spectrometry (LC-MS/MS) and gel electrophoresis then liquid chromatography mass spectrometry (geLC-MS) approaches are now preferred as state-of-the-art

The non-invasive biopsy: will urinary proteomics make the renal tissue biopsy redundant?

Proteomics is a rapidly advancing technique which gives a functional insight into gene expression in living organisms. Urine is an ideal medium for study as it is readily available, easily obtained and less complex than other bodily fluids. Considerable progress has been made over the last 5 years in the study of urinary proteomics as a diagnostic tool for renal disease. The advantages of this technique over the traditional renal biopsy include accessibility, safety, the possibility of serial sampling, and the potential for non-invasive prognostic and diagnostic monitoring of disease and an individual’s response to treatment. Urinary proteomics is now moving from a discovery phase in small studies to a validation phase in much larger numbers of patients with renal disease. Whilst there are still some limitations in methodology, which are assessed in this review, the possibility of urinary proteomics replacing the invasive tissue biopsy for diagnosis of renal disease is becoming increasingly realistic

Targeted Proteins Reveal Cathepsin D as a Novel Biomarker in Differentiating Hepatocellular Carcinoma from Cirrhosis and Other Liver Cancers

Objective: Hepatocellular carcinoma (HCC) represents a global health concern, particularly in Southeast Asia where hepatitis B virus (HBV) infection is common. In this study, we applied tissue-based proteomics to identify novel serological proteins for HCC and validated their performance in serum specimens. Methods: In a discovery set, liver tissue specimens of HBV-related HCC, intrahepatic cholangiocarcinoma (iCCA) and colorectal cancer with liver metastasis (CRLM) were analyzed using mass spectrometry (LTQ-Orbitrap-XL). A subset of proteins that showed highly expressed in HCC were then confirmed by Western blotting. Additionally, clinical significance of selected candidate proteins was tested in serum samples of 80 patients with HBV-related HCC, 50 patients with HBV-related liver cirrhosis and 30 healthy controls. Results: Based on LTQ-Orbitrap-XL mass spectrometer, various differentially expressed proteins (DEPs) between tumor and adjacent non-tumor tissues were identified. These included 77 DEPs for HCC, 77 DEPs for iCCA and 55 DEPs for CRLM. Among selected candidate proteins, annexin A2 and cathepsin D were confirmed to be overexpressed in HCC tissue by Western blot analysis. In a validate cohort, serum cathepsin D level, but not annexin A2, was significantly higher in HCC compared with the non-HCC groups. Serum cathepsin D level was also positively correlated with tumor size and tumor stage. Additionally, the combined assay of serum cathepsin D and alpha-fetoprotein had a high sensitivity in detecting early HCC (83%) and intermediate/advanced HCC (96%). Moreover, patients with low serum cathepsin D (<305 ng/mL) displayed significantly better overall survival than those whose serum levels were high (≥305 ng/mL). Conclusions: Proteomics and subsequent validation revealed cathepsin D as a novel biomarker for HCC. Apart from its diagnostic role, serum cathepsin D might also serve as a prognostic biomarker of HCC. Additional large-scale studies are needed to verify our finding

Urine Proteome Analysis May Allow Noninvasive Differential Diagnosis of Diabetic Nephropathy

AbstractObjective: Chronic renal insufficiency and/or proteinuria in type 2 diabetes may stem from chronic renal diseases (CKD) other than classic diabetic nephropathy (DN) in over one third of cases. We interrogated urine proteomic profiles generated by SELDI-TOF/MS with the aim to isolate a set of biomarkers able to reliably identify biopsy-proven DN and to establish a stringent correlation with the different patterns of renal injury. Research design and methods: Ten mug urine proteins from 190 subjects [20 healthy subjects (HS), 20 normoalbuminuric (NAD) and 18 microalbuminuric (MICRO) diabetic patients, and 132 patients with biopsy-proven nephropathy (65 DN, 10 diabetics with non-diabetic CKD (nd-CKD) and 57 non-diabetic patients with CKD)] were run by CM10 ProteinChip array and analysed by supervised learning methods (CART analysis). Results: The classification model correctly identified 75% NAD, 87.5% MICRO and 87.5% DN when applied to a blinded testing set. Most importantly, it was able to reliably differentiate DN from nd-CKD in both diabetic and non-diabetic patients. Among the best predictors of the classification model, we identified and validated 2 proteins, ubiquitin and ss2-microglobulin. Conclusions: Our data suggest the presence of a specific urine proteomic signature able to reliably identify type 2 diabetic patients with diabetic glomerulosclerosis

“Lossless” compression of high resolution mass spectra of small molecules

Fourier transform ion cyclotron resonance (FTICR) provides the highest resolving power of any commercially available mass spectrometer. This advantage is most significant for species of low mass-to-charge ratio (m/z), such as metabolites. Unfortunately, FTICR spectra contain a very large number of data points, most of which are noise. This is most pronounced at the low m/z end of spectra, where data point density is the highest but peak density low. We therefore developed a filter that offers lossless compression of FTICR mass spectra from singly charged metabolites. The filter relies on the high resolving power and mass measurement precision of FTICR and removes only those m/z channels that cannot contain signal from singly charged organic species. The resulting pseudospectra still contain the same signal as the original spectra but less uninformative background. The filter does not affect the outcome of standard downstream chemometric analysis methods, such as principal component analysis, but use of the filter significantly reduces memory requirements and CPU time for such analyses. We demonstrate the utility of the filter for urinary metabolite profiling using direct infusion electrospray ionization and a 15 tesla FTICR mass spectrometer