Metabolomics and Proteomics in Prostate Cancer Research: Overview, Analytical Techniques, Data Analysis, and Recent Clinical Applications

Prostate cancer (PCa) is a significant global contributor to mortality, predominantly affecting males aged 65 and above. The field of omics has recently gained traction due to its capacity to provide profound insights into the biochemical mechanisms underlying conditions like prostate cancer. This involves the identification and quantification of low-molecular-weight metabolites and proteins acting as crucial biochemical signals for early detection, therapy assessment, and target identification. A spectrum of analytical methods is employed to discern and measure these molecules, revealing their altered biological pathways within diseased contexts. Metabolomics and proteomics generate refined data subjected to detailed statistical analysis through sophisticated software, yielding substantive insights. This review aims to underscore the major contributions of multi-omics to PCa research, covering its core principles, its role in tumor biology characterization, biomarker discovery, prognostic studies, various analytical technologies such as mass spectrometry and Nuclear Magnetic Resonance, data processing, and recent clinical applications made possible by an integrative "omics" approach. This approach seeks to address the challenges associated with current PCa treatments. Hence, our research endeavors to demonstrate the valuable applications of these potent tools in investigations, offering significant potential for understanding the complex biochemical environment of prostate cancer and advancing tailored therapeutic approaches for further development.

Point-of-care diagnostics for rapid determination of prostate cancer biomarker sarcosine: application of disposable potentiometric sensor based on oxide-conductive polymer nanocomposite

One of the most important reasons for an increased mortality rate of cancer is late diagnosis. Point-of-care (POC) diagnostic sensors can provide rapid and cost-effective diagnosis and monitoring of cancer biomarkers. Portable, disposable, and sensitive sarcosine solid-contact ion-selective potentiometric sensors (SC-ISEs) were fabricated as POC analyzers for the rapid determination of the prostate cancer biomarker sarcosine. Tungsten trioxide nanoparticles (WO3 NPs), polyaniline nanoparticles (PANI NPs), and PANI-WO3 nanocomposite were used as ion-to-electron transducers on screen-printed sensors. WO3 NPs and PANI-WO3 nanocomposite have not been investigated before as ion-to-electron transducer layers in potentiometric SC sensors. The designated sensors were characterized using SEM, XRD, FTIR, UV-VIS spectroscopy, and EIS. The inclusion of WO3 and PANI in SC sensors enhanced the transduction at the interface between the screen-printed SC and the ion-selective membrane, offering lower potential drift, a longer lifetime, shorter response time, and better sensitivity. The proposed sarcosine sensors exhibited Nernstian slopes over linear response ranges 10-3-10-7 M, 10-3-10-8 M, 10-5-10-9 M, and 10-7-10-12 M for control, WO3 NPs, PANI NPs, and PANI-WO3 nanocomposite-based sensors, respectively. From a comparative point of view between the four sensors, PANI-WO3 nanocomposite inclusion offered the lowest potential drift (0.5 mV h-1), the longest lifetime (4 months), and the best LOD (9.95 × 10-13 M). The proposed sensors were successfully applied to determine sarcosine as a potential prostate cancer biomarker in urine without prior sample treatment steps. The WHO ASSURED criteria for point-of-care diagnostics are met by the proposed sensors.

12-Plex UHPLC-MS/MS analysis of sarcosine in human urine using integrated principle of multiplex tags chemical isotope labeling and selective imprint enriching

Urinary sarcosine was considered to be a potential biomarker for prostate cancer (Pca). In this work, an integrated strategy of multiplex tags chemical isotope labeling (MTCIL) combined with magnetic dispersive solid phase extraction (MDSPE), was proposed for specific extraction and high-throughput determination of sarcosine by ultra high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS). In the past three months, we have developed 8-plex MTCIL reagents with excellent qualitative and quantitative performance. In this work, the multiplexing capacity of MTCIL reagents (MTCIL360/361/362/363/364/365/366/375/376/378/379/381) was increased 1.5-fold from 8-plex to 12-plex. MTCIL359 was prepared and used to label sarcosine standard as internal standard (IS). The structural analogue derivative (MTCIL373-sarcosine) of all targeted MTCIL-sarcosine derivatives was synthesized and used as a novel dummy template to prepare dummy magnetic molecularly imprinted polymers (DMMIPs). The integration of MTCIL and DMMIPs procedures were extremely favorable to excellent chromatographic separation and efficient mass spectrometric detection. The labeling efficiency, chromatographic retention and mass spectrometry responses of MTCIL reagents were consistent for sarcosine. In a single UHPLC-MS/MS run (2.0 min), this method can simultaneously quantify sarcosine in 12-plex urine samples and achieve unbiased concentrations comparison between different urine samples. Analytical parameters including linearity (R² 0.989-0.997), detection limits (0.02 nM), precision (2.6-11.5%), accuracy (96.1-107.4%), matrix effect, labeling and extraction efficiency were carefully validated. The proposed method was successfully applied for urinary sarcosine determination of healthy male individuals and Pca patients. It was found that the sarcosine concentrations in these two groups were statistically extremely significantly different (P < 0.001). The developed method was a powerful analytical tool to substantially promote the analysis throughput and large-scale experiments about the potential biomarker research.

Endogenous formaldehyde is a memory-related molecule in mice and humans

Gaseous formaldehyde is an organic small molecule formed in the early stages of earth’s evolution. Although toxic in high concentrations, formaldehyde plays an important role in cellular metabolism and, unexpectedly, is found even in the healthy brain. However, its pathophysiological functions in the brain are unknown. Here, we report that under physiological conditions, spatial learning activity elicits rapid formaldehyde generation from mitochondrial sarcosine dehydrogenase (SARDH). We find that elevated formaldehyde levels facilitate spatial memory formation by enhancing N-methyl-D-aspartate (NMDA) currents via the C232 residue of the NMDA receptor, but that high formaldehyde concentrations gradually inactivate the receptor by cross-linking NR1 subunits to NR2B. We also report that in mice with aldehyde dehydrogenase-2 (ALDH2) knockout, formaldehyde accumulation due to hypofunctional ALDH2 impairs memory, consistent with observations of Alzheimerʼs disease patients. We also find that formaldehyde deficiency caused by mutation of the mitochondrial SARDH gene in children with sarcosinemia or in mice with Sardh deletion leads to cognitive deficits. Hence, we conclude that endogenous formaldehyde regulates learning and memory via the NMDA receptor.

Ai et al. report that endogenous formaldehyde bidirectionally modulates cognition via the NMDA-R receptor, with both insufficiency and overabundance resulting in cognitive defects. The target site of formaldehyde enhancing NMDA-currents is cysteine C232 residue in amino terminal domain sequence of the NR2B subunit of NMDA-R and excessive formaldehyde suppresses NMDA-R activity by cross-linking NR1 to NR2B residues.

Quantitative analysis of sarcosine with special emphasis on biosensors: a review

The quantitative determination of sarcosine is of great importance in clinical chemistry, food and fermentation industries. Elevated sarcosine levels are associated with Alzheimer, dementia, prostate cancer, colorectal cancer, stomach cancer and sarcosinemia. This review summarizes the various methods for quantitative analysis of sarcosine with special emphasis on various strategies of biosensors and their analytical performance. The current bio sensing methods have overcome the drawbacks of conventional methods. Sarcosine biosensors work optimally at pH 7.0 to 8.0 in the linear range of 0.1 to 100 μM within 2 to 17 s and between 25 and 37 °C, within a limit of detection (LOD) between 0.008 and 500 mM. The formulated biosensors can be reused within a stability period of 3-180 days. Future research could be focused to modify existing sarcosine biosensors, leading to simple, reliable, and economical sensors ideally suited for point-of-care treatment. Clinical significance Elevated sarcosine levels are associated with prostate and colorectal cancer, Alzheimer, dementia, stomach cancer and sarcosinemia. Quantitative determination of sarcosine is of great importance in clinical chemistry as well as food and fermentation industries. Attempts made in development of sarcosine biosensors have been reviewed with their advantages and disadvantages, so that scientist and clinicians can improvise the methods of developing more potent sarcosine biosensor applicable in multitudinous fields. This is the first comprehensive review which compares the various immobilization methods, sensing principles, strategies used in biosensors and their analytical performance in detail.

A highly sensitive DNA aptamer-based fluorescence assay for sarcosine detection down to picomolar levels

Sarcosine is an amino acid derivative, which is considered as a key metabolite in various metabolic processes. Therefore, simple and sensitive detection methods are needed for further understanding its metabolic role and diagnostic value. In this study, we developed a novel method that meets the need for practical and sensitive detection in a complex medium mimicking urine conditions. For this aim, we selected sarcosine-specific DNA aptamers using graphene oxide-assisted systemic evolution of ligands by exponential enrichment (GO-SELEX). The candidate aptamers were labeled with 6-carboxyfluorescein (6-FAM) at their 5' ends. Two aptamers, namely 9S and 13S produced a significant fluorescence signal upon sarcosine binding. Both aptamers enabled a sensitive analysis with a detection limit of 0.5 pM. The linear detection ranged between 5 pM and 50 μM for 9S aptamer, while 13S aptamer enabled a wider linear detection range between 5 pM and 500 μM. The aptamer-based assay allowed rapid detection with no need for chemical derivatization of sarcosine and sophisticated instruments. Moreover, the aptamer-based assay was free of interference from urea and human serum albumin.

A robust, single-injection method for targeted, broad-spectrum plasma metabolomics

BACKGROUND

Metabolomics is a powerful emerging technology for studying the systems biology and chemistry of health and disease. Current targeted methods are often limited by the number of analytes that can be measured, and/or require multiple injections.

METHODS

We developed a single-injection, targeted broad-spectrum plasma metabolomic method on a SCIEX Qtrap 5500 LC-ESI-MS/MS platform. Analytical validation was conducted for the reproducibility, linearity, carryover and blood collection tube effects. The method was also clinically validated for its potential utility in the diagnosis of chronic fatigue syndrome (CFS) using a cohort of 22 males CFS and 18 age- and sex-matched controls.

RESULTS

Optimization of LC conditions and MS/MS parameters enabled the measurement of 610 key metabolites from 63 biochemical pathways and 95 stable isotope standards in a 45-minute HILIC method using a single injection without sacrificing sensitivity. The total imprecision (CV_total) of peak area was 12% for both the control and CFS pools. The 8 metabolites selected in our previous study (PMID: 27573827) performed well in a clinical validation analysis even when the case and control samples were analyzed 1.5 years later on a different instrument by a different investigator, yielding a diagnostic accuracy of 95% (95% CI 85-100%) measured by the area under the ROC curve.

CONCLUSIONS

A reliable and reproducible, broad-spectrum, targeted metabolomic method was developed, capable of measuring over 600 metabolites in plasma in a single injection. The method might be a useful tool in helping the diagnosis of CFS or other complex diseases.