From haystack to high precision: advanced sequencing methods to unraveling circulating tumor DNA mutations.

Identifying mutations in cancer-associated genes to guide patient treatments is essential for precision medicine. Circulating tumor DNA (ctDNA) offers valuable insights for early cancer detection, treatment assessment, and surveillance. However, a key issue in ctDNA analysis from the bloodstream is the choice of a technique with adequate sensitivity to identify low frequent molecular changes. Next-generation sequencing (NGS) technology, evolving from parallel to long-read capabilities, enhances ctDNA mutation analysis. In the present review, we describe different NGS approaches for identifying ctDNA mutation, discussing challenges to standardized methodologies, cost, specificity, clinical context, and bioinformatics expertise for optimal NGS application.

Non-Targeted Metabolomic Analysis of Arabidopsis thaliana (L.) Heynh: Metabolic Adaptive Responses to Stress Caused by N Starvation.

As sessile organisms, plants develop the ability to respond and survive in changing environments. Such adaptive responses maximize phenotypic and metabolic fitness, allowing plants to adjust their growth and development. In this study, we analyzed the metabolic plasticity of Arabidopsis thaliana in response to nitrate deprivation by untargeted metabolomic analysis and using wild-type (WT) genotypes and the loss-of-function nia1/nia2 double mutant. Secondary metabolites were identified using seedlings grown on a hydroponic system supplemented with optimal or limiting concentrations of N (4 or 0.2 mM, respectively) and harvested at 15 and 30 days of age. Then, spectral libraries generated from shoots and roots in both ionization modes (ESI +/-) were compared. Totals of 3407 and 4521 spectral signals (m/z_rt) were obtained in the ESI+ and ESI- modes, respectively. Of these, approximately 50 and 65% were identified as differentially synthetized/accumulated. This led to the presumptive identification of 735 KEGG codes (metabolites) belonging to 79 metabolic pathways. The metabolic responses in the shoots and roots of WT genotypes at 4 mM of N favor the synthesis/accumulation of metabolites strongly related to growth. In contrast, for the nia1/nia2 double mutant (similar as the WT genotype at 0.2 mM N), metabolites identified as differentially synthetized/accumulated help cope with stress, regulating oxidative stress and preventing programmed cell death, meaning that metabolic responses under N starvation compromise growth to prioritize a defensive response.

A novel strategy for the detection of boldenone undecylenate misuse in cattle using ultra-high performance liquid chromatography coupled to high resolution orbitrap mass spectrometry: From non-targeted to targeted.

In this work multivariate strategies were employed in order to highlight new potential biomarkers of interest to detect the exogenous treatment of steers intramuscularly treated with boldenone undecylenate. Serum samples collected from treated (n = 4) and control (n = 8) crossbred animals of varying ages and weights were extracted using a simple sample preparation procedure based on salt assisted liquid-liquid extraction. Data acquisition was performed using liquid chromatography and Q-Exactive™ Orbitrap mass spectrometry. Data processing and treatment were performed using two non-targeted workflows: (1) Compound Discoverer software and (2) XCMS package on the open-source R software combined with MetaboAnalyst. Three potential biomarkers were highlighted taking into account the chromatographic shapes, the feature location on the generated s-plots, the fold change, the adjusted p values, the coefficient of variation in the QC samples and the area under the ROC curves. Predicted formulas based on mass accuracy, structural composition and spectra similarity were proposed. A robust statistical model to predict the boldenone treatment was further developed based on the weighted abundances of the selected biomarkers. The requirements for screening methods were successfully fulfilled, together with a wider detection window in comparison with the monitoring of the deconjugated metabolite boldenone, although biomarker identification studies are still ongoing.

Improving Exposure Assessment Using Non-Targeted and Suspect Screening: The ISO/IEC 17025: 2017 Quality Standard as a Guideline.

The recent advances of novel methodologies such as non-targeted and suspect screening based on high-resolution mass spectrometry (HRMS) have paved the way to a new paradigm for exposure assessment. These methodologies allow to profile simultaneously thousands of small unknown molecules present in environmental and biological samples, and therefore hold great promises in order to identify more efficiently hazardous contaminants potentially associated with increased risks of developing adverse health outcomes. In order to further explore the potential of these methodologies and push the transition from research applications towards regulatory purposes, robust harmonized quality standards have to be implemented. Here, we discuss the feasibility of using ISO/IEC 17025: 2017 as a guideline to implement non-targeted and suspect screening methodologies in laboratories, whether it is for accreditation purposes or not. More specifically, we identified and then discussed how specificities of non-targeted HRMS methodology can be accounted for in order to comply with the specific items of ISO/IEC 17025: 2017. We also discussed other specificities of HRMS methodologies (e.g., need for digital storage capacity) that are so far not included in the ISO/IEC 17025 requirements but should be considered. This works aims to fuel and expand the discussion in order to subsidize new opportunities of harmonization for non-targeted and suspect screening.

Placenta, Pericarp, and Seeds of Tabasco Chili Pepper Fruits Show a Contrasting Diversity of Bioactive Metabolites.

Chili pepper (Capsicum spp.) is one of the most important horticultural crops worldwide, and its unique organoleptic properties and health benefits have been established for centuries. However, there is little knowledge about how metabolites are distributed throughout fruit parts. This work focuses on the use of liquid chromatography coupled with high resolution mass spectrometry (UHPLC-ESI-HRMS) to estimate the global metabolite profiles of the pericarp, placenta, and seeds of Tabasco pepper fruits (Capsicum frutescens L.) at the red mature stage of ripening. Our main results putatively identified 60 differential compounds between these tissues and seeds. Firstly, we found that pericarp has a higher content of glycosides, showing on average a fold change of 5 and a fold change of 14 for terpenoids when compared with other parts of the fruit. While placenta was the richest tissue in capsaicinoid-related compounds, alkaloids, and tocopherols, with a 35, 3, and 7 fold change, respectively. However, the seeds were richer in fatty acids and saponins with fold changes of 86 and 224, respectively. Therefore, our study demonstrates that a non-targeted metabolomic approach may help to improve our understanding of unexplored areas of plant metabolism and also may be the starting point for a detailed analysis in complex plant parts, such as fruits.

Non-targeted acquisition strategy for screening doping compounds based on GC-EI-hybrid quadrupole-Orbitrap mass spectrometry: A focus on exogenous anabolic steroids.

This is a first look at a non-targeted screening method based on Orbitrap gas chromatography-mass spectrometry (GC-MS) technology for a large number of banned compounds in sports found in urine, including exogenous anabolic steroids, ß-agonists, narcotics, stimulants, hormone modulators, and diuretics. A simple sample preparation was processed in four steps: an enzymatic hydrolysis, liquid-liquid extraction, evaporation, and trimethylsilylation. All compounds were able to meet the World Anti-Doping Agency's sensitivity criteria with mass accuracies less than 1 ppm and with sufficient points across the peak by running the Orbitrap GC-MS in full-scan mode. In addition, we discuss our initial findings of using a full-scan selected ion monitoring-tandem mass spectrometry (SIM-MS/MS) approach as a way to obtain lower detection limits and reach desirable selectivity for some exogenous anabolic steroids.

Non-targeted analyses of organic compounds in urban wastewater.

A large number of organic pollutants that cause damage to the ecosystem and threaten human health are transported to wastewater treatment plants (WWTPs). The problems regarding water pollution in Latin America have been well documented, and there is no evidence of substantive efforts to change the situation. In the present work, two methods to study wastewater samples are employed: non-targeted 1D ((13)C and (1)H) and 2D NMR spectroscopic analysis to characterize the largest possible number of compounds from urban wastewater and analysis by HPLC-(UV/MS)-SPE-ASS-NMR to detect non-specific recalcitrant organic compounds in treated wastewater without the use of common standards. The set of data is composed of several compounds with the concentration ranging considerably with treatment and seasonality. An anomalous discharge, the influence of stormwater on the wastewater composition and the presence of recalcitrant compounds (linear alkylbenzene sulfonate surfactant homologs) in the effluent were further identified. The seasonal variations and abnormality in the composition of organic compounds in sewage indicated that the procedure that was employed can be useful in the identification of the pollution source and to enhance the effectiveness of WWTPs in designing preventive action to protect the equipment and preserve the environment.

Big Data Analysis on Puerto Rico Testsite for Exploring Contamination Threats.

In this paper, we present the use of Principal Component Analysis and customized software, to accelerate the spectral analysis of biological samples. The work is part of the mission of the National Institute of Environmental Health Sciences sponsored Puerto Rico Testsite for Exploring Contamination Threats Center, establishing linkages between environmental pollutants and preterm birth. This paper provides an overview of the data repository developed for the Center, and presents a use case analysis of biological sample data maintained in the database system.