Biomarker analysis for prostate cancer diagnosis using LC-MS and CE-MS

Liquid chromatography-tandem mass spectrometry analysis of eicosanoids and related compounds in cell models

Enzyme- and free radical-catalyzed oxidation of polyunsaturated fatty acids (PUFAs) produces the eicosanoids, docosanoids and octadecanoids. This large family of potent bioactive lipids is involved in many biochemical and signaling pathways which are implicated in physiological and pathophysiological processes and can be viable therapeutic targets. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) offers selectivity, sensitivity, robustness and high resolution and is able to analyze a large number of eicosanoids in biological samples in a short time. The present article reviews and discusses reported LC-MS/MS methods and the results obtained from their application in cell models. Reliable analytical outcomes are critically important for understanding physiological and pathophysiological cellular processes, such as inflammation, diseases with inflammatory components (e.g., cardiovascular disease, diabetes, metabolic syndrome), as well as cancer. Reported findings obtained by using the LC-MS/MS methodology in cell systems may have important predictive as well as nutritional and pharmacological implications. We conclude that the LC-MS/MS methodology is a versatile and reliable analytical tool for the simultaneous analysis of multiple PUFA-derived metabolites including the eicosanoids in cell culture samples at concentrations on the pM/nM threshold, i.e. at baseline and after stimulation.

Proteomics for breast cancer urine biomarkers

Although the survival of breast cancer (BC) patients has increased over the last two decades due to improved screening programs and postoperative adjuvant systemic therapies, many patients die from metastatic relapse. Current biomarkers used in the clinic are not useful for the early detection of BC, or monitoring its progression, and have limited value in predicting response to treatment. The development of proteomic techniques has sparked new searches for novel protein markers for many diseases including BC. Proteomic techniques allow for a high-throughput analysis of samples with the visualization and quantification of thousands of potential protein and peptide markers. Human urine is one of the most interesting and useful biofluids for routine testing and provides an excellent resource for the discovery of novel biomarkers, with the advantage over tissue biopsy samples due to the ease and less invasive nature of collection. In this review, we summarize the results from studies where urine was used as a source for BC biomarker research and discuss urine sample preparation, its advantage, challenges, and limitation. We focus on the gel-based proteomic approaches as well as the recent development of quantitative techniques in BC urine biomarker detection. Finally, the future use of modern proteomic techniques in BC biomarker identification will be discussed.

Ultrasensitive sample quantitation via selected reaction monitoring using CITP/CZE-ESI-triple quadrupole MS

We demonstrate the direct coupling of transient capillary isotachophoresis/capillary zone electrophoresis (CITP/CZE) with a high-sensitivity triple quadrupole mass spectrometer operating in selected reaction monitoring (SRM) mode for sample quantitation. The capability of CITP/CZE for in situ sample enrichment and separation has been shown to significantly improve the analytical figures of merit. A linear dynamic range spanning 4 orders of magnitude was observed. An average signal-to-noise ratio (S/N) of 49.6 was observed for 50 amol of targeted peptide in the presence of a complex and much more abundant bovine serum albumin (BSA) digest. Correlation of variation (CV) of <10% for peak area was measured from triplicate sample analyses at 50 pM peptide concentration, showing good reproducibility of this online CITP/CZE-SRM mass spectrometry (MS) platform, and with limit of quantitation (LOQ) demonstrated to be well below 50 pM.

Structure and function of noncanonical nucleobases

DNA and RNA contain, next to the four canonical nucleobases, a number of modified nucleosides that extend their chemical information content. RNA is particularly rich in modifications, which is obviously an adaptation to their highly complex and variable functions. In fact, the modified nucleosides and their chemical structures establish a second layer of information which is of central importance to the function of the RNA molecules. Also the chemical diversity of DNA is greater than originally thought. Next to the four canonical bases, the DNA of higher organisms contains a total of four epigenetic bases: m(5) dC, hm(5) dC, f(5) dC und ca(5) dC. While all cells of an organism contain the same genetic material, their vastly different function and properties inside complex higher organisms require the controlled silencing and activation of cell-type specific genes. The regulation of the underlying silencing and activation process requires an additional layer of epigenetic information, which is clearly linked to increased chemical diversity. This diversity is provided by the modified non-canonical nucleosides in both DNA and RNA.

Validation study of urinary metabolites as potential biomarkers for prostate cancer detection

Background: Urinary metabolomic profiles have recently drawn a lot of attention owing to a debate regarding their possible role as potential clinical markers for prostate cancer. In this study, levels of proline, kynurenine, uracil and glycerol-3-phosphate in 126 patients with genitourinary malignancies were analyzed using a validated method and compared with no evidence of malignancy. Results: The statistical results showed that these biomarkers cannot differentiate prostate cancer from no evidence of malignancy or from other related cancer types, such as bladder cancer. In addition, there was no significant difference in biomarker levels for T1 stages, T2 stages and Gleason scores <7, ≥7. From the correlation study, results showed/demonstrated that age or serum prostate-specific antigen levels do not influence these metabolite concentrations in urine. However, the strong correlation between these metabolites and urinary creatinine concentrations implies that their occurrence is mainly due to renal excretion. Conclusion: This detailed study shows that the aforementioned urinary metabolites are not reliable biomarkers for prostate cancer detection or for differentiating the aggressiveness of prostate cancer.