Urinary volatile organic compounds in prostate cancer biopsy pathologic risk stratification using logistic regression and multivariate analysis models.

Prostate cancer (PCa) is the second leading cause of cancer-related death in American men after lung cancer. The current PCa diagnostic method, the serum prostate-specific antigen (PSA) test, is not specific, thus, alternatives are needed to avoid unnecessary biopsies and over-diagnosis of clinically insignificant PCa. To explore the application of metabolomics in such effort, urine samples were collected from 386 male adults aged 44-93 years, including 247 patients with biopsy-proven PCa and 139 with biopsy-proven negative results. The PCa-positive group was further subdivided into two groups: low-grade (ISUP Grade Group = 1; n = 139) and intermediate/high-grade (ISUP Grade Group ≥ 2; n = 108). Volatile organic compounds (VOCs) in urine were extracted by stir bar sorptive extraction (SBSE) and analyzed using thermal desorption with gas chromatography and mass spectrometry (GC-MS). We used machine learning tools to develop and evaluate models for PCa diagnosis and prognosis. In total, 22,538 VOCs were identified in the urine samples. With regularized logistic regression, our model for PCa diagnosis yielded an area under the curve (AUC) of 0.99 and 0.88 for the training and testing sets respectively. Furthermore, the model for differentiating between low-grade and intermediate/high-grade PCa yielded an average AUC of 0.78 based on a repeated test-sample approach for cross-validation. These novel methods using urinary VOCs and logistic regression were developed to fill gaps in PCa screening and assessment of PCa grades prior to biopsy. Our study findings provide a promising alternative or adjunct to current PCa screening and diagnostic methods to better target patients for biopsy and mitigate the challenges associated with over-diagnosis and over-treatment of PCa.

Urinary fatty acid biomarkers for prostate cancer detection.

The lack of accuracy in the current prostate specific antigen (PSA) test for prostate cancer (PCa) screening causes around 60-75% of unnecessary prostate biopsies. Therefore, alternative diagnostic methods that have better accuracy and can prevent over-diagnosis of PCa are needed. Researchers have examined various potential biomarkers for PCa, and of those fatty acids (FAs) markers have received special attention due to their role in cancer metabolomics. It has been noted that PCa metabolism prefers FAs over glucose substrates for continued rapid proliferation. Hence, we proposed using a urinary FAs based model as a non-invasive alternative for PCa detection. Urine samples collected from 334 biopsy-designated PCa positive and 232 biopsy-designated PCa negative subjects were analyzed for FAs and lipid related compounds by stir bar sorptive extraction coupled with gas chromatography/mass spectrometry (SBSE-GC/MS). The dataset was split into the training (70%) and testing (30%) sets to develop and validate logit models and repeated for 100 runs of random data partitioning. Over the 100 runs, we confirmed the stability of the models and obtained optimal tuning parameters for developing the final FA based model. A PSA model using the values of the patients' PSA test results was constructed with the same cohort for the purpose of comparing the performances of the FA model against PSA test. The FA final model selected 20 FAs and rendered an AUC of 0.71 (95% CI = 0.67-0.75, sensitivity = 0.48, and specificity = 0.83). In comparison, the PSA model performed with an AUC of 0.51 (95% CI = 0.46-0.66, sensitivity = 0.44, and specificity = 0.71). The study supports the potential use of urinary FAs as a stable and non-invasive alternative test for PCa diagnosis.

Investigating the effects of storage conditions on urinary volatilomes for their reliability in disease diagnosis.

BACKGROUND: Cancer detection presents challenges regarding invasiveness, cost, and reliability. As a result, exploring alternative diagnostic methods holds significant clinical importance. Urinary metabolomic profiling has emerged as a promising avenue; however, its application for cancer diagnosis may be influenced by sample preparation or storage conditions. OBJECTIVE: This study aimed to assess the impact of sample storage and processing conditions on urinary volatile organic compounds (VOCs) profiles and establish a robust standard operating procedure (SOP) for such diagnostic applications. METHODS: Five key variables were investigated: storage temperatures, durations, freeze-thaw cycles, sample collection conditions, and sample amounts. The analysis of VOCs involved stir bar sorptive extraction coupled with thermal desorption-gas chromatography/mass spectrometry (SBSE-TD-GC-MS), with compound identification facilitated by the National Institute of Standards and Technology Library (NIST). Extensive statistical analysis, including combined scatterplot and response surface (CSRS) plots, partial least squares-discriminant analysis (PLS-DA), and probability density function plots (PDFs), were employed to study the effects of the factors. RESULTS: Our findings revealed that urine storage duration, sample amount, temperature, and fasting/non-fasting sample collection did not significantly impact urinary metabolite profiles. This suggests flexibility in urine sample collection conditions, enabling individuals to contribute samples under varying circumstances. However, the influence of freeze-thaw cycles was evident, as VOC profiles exhibited distinct clustering patterns based on the number of cycles. This emphasizes the effect of freeze-thaw cycles on the integrity of urinary profiles. CONCLUSIONS: The developed SOP integrating SBSE-TD-GC-MS and statistical analyses can serve as a valuable tool for analyzing urinary organic compounds with minimal preparation and sensitive detection. The findings also support that urinary VOCs for cancer screening and diagnosis could be a feasible alternative offering a robust, non-invasive, and sensitive approach for cancer screening.

Classification of Brazilian roasted coffees from different geographical origins and farming practices based on chlorogenic acid profiles.

Sixty-seven roasted coffee samples from different regions of Brazil cultivated using organic, conventional and biodynamic farming practices were analysed and quantified using high performance liquid chromatography coupled with mass spectrometry, and treated with supervised (PLS-DA) and unsupervised (PCA) multivariate statistical tools. The profile of the chlorogenic acids constituents were analysed by high resolution and tandem mass spectrometry, which allowed the identification of mono- caffeoyl-, feruloyl-, para-Coumaroylquinic acids and their respective regio-isomers. This study provides a comprehensive analysis of absolute quantitative data set of chlorogenic acids constituents (CQA, FQA and pCoQA isomers) in Brazilian coffee beans produced from different regions of the country. Variations in the chlorogenic acids compositions were observed if organic and conventional roasted coffee beans were compared. The use of multivariate statistical tools allowed the identification of suitable biomarkers for determining significant differences between the three coffee agricultural practices, while coffees produced from the diverse geographical regions showed no significant difference.

Comparison and quantification of chlorogenic acids for differentiation of green Robusta and Arabica coffee beans.

Coffea arabica and Coffea canephora (Robusta coffee) are the most commonly consumed coffee varieties globally. In this contribution, NMR was used to confirm the coffee authenticity and LC-ESI-MSn technique was employed to profile and quantify the most abundant chlorogenic acid in 54 different samples of the two coffee varieties from diverse origins. Significant variations were observed for feruloyl quinic acids, dicaffeoyl quinic acids and 5-sinapoylquinic acid while the mono-caffeoyl quinic acids showed no variation when the two coffee varieties were compared. Additionally isomer ratios were explored as a potential marker for coffee authenticity along with a thorough statistical evaluation of rather extensive data set. Robusta 5-CQA when compared with 3,4-DiCQA Robusta shows high positive correlation, similar high correlation coefficient was observed in 5-pCoQA Robusta when compared with 3-pCoQA as against the Arabica.