Choosing Variant Interpretation Tools for Clinical Applications: Context Matters.

Pathogenicity predictors are computational tools that classify genetic variants as benign or pathogenic; this is currently a major challenge in genomic medicine. With more than fifty such predictors available, selecting the most suitable tool for clinical applications like genetic screening, molecular diagnostics, and companion diagnostics has become increasingly challenging. To address this issue, we have developed a cost-based framework that naturally considers the various components of the problem. This framework encodes clinical scenarios using a minimal set of parameters and treats pathogenicity predictors as rejection classifiers, a common practice in clinical applications where low-confidence predictions are routinely rejected. We illustrate our approach in four examples where we compare different numbers of pathogenicity predictors for missense variants. Our results show that no single predictor is optimal for all clinical scenarios and that considering rejection yields a different perspective on classifiers.

Increased dNTP pools rescue mtDNA depletion in human POLG-deficient fibroblasts.

Polymerase γ catalytic subunit (POLG) gene encodes the enzyme responsible for mitochondrial DNA (mtDNA) synthesis. Mutations affecting POLG are the most prevalent cause of mitochondrial disease because of defective mtDNA replication and lead to a wide spectrum of clinical phenotypes characterized by mtDNA deletions or depletion. Enhancing mitochondrial deoxyribonucleoside triphosphate (dNTP) synthesis effectively rescues mtDNA depletion in different models of defective mtDNA maintenance due to dNTP insufficiency. In this study, we studied mtDNA copy number recovery rates following ethidium bromide-forced depletion in quiescent fibroblasts from patients harboring mutations in different domains of POLG. Whereas control cells spontaneously recovered initial mtDNA levels, POLG-deficient cells experienced a more severe depletion and could not repopulate mtDNA. However, activation of deoxyribonucleoside (dN) salvage by supplementation with dNs plus erythro-9-(2-hydroxy-3-nonyl) adenine (inhibitor of deoxyadenosine degradation) led to increased mitochondrial dNTP pools and promoted mtDNA repopulation in all tested POLG-mutant cells independently of their specific genetic defect. The treatment did not compromise POLG fidelity because no increase in multiple deletions or point mutations was detected. Our study suggests that physiologic dNTP concentration limits the mtDNA replication rate. We thus propose that increasing mitochondrial dNTP availability could be of therapeutic interest for POLG deficiency and other conditions in which mtDNA maintenance is challenged.-Blázquez-Bermejo, C., Carreño-Gago, L., Molina-Granada, D., Aguirre, J., Ramón, J., Torres-Torronteras, J., Cabrera-Pérez, R., Martín, M. Á., Domínguez-González, C., de la Cruz, X., Lombès, A., García-Arumí, E., Martí, R., Cámara, Y. Increased dNTP pools rescue mtDNA depletion in human POLG-deficient fibroblasts.

Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces.

One of the known potential effects of disease-causing amino acid substitutions in proteins is to modulate protein-protein interactions (PPIs). To interpret such variants at the molecular level and to obtain useful information for prediction purposes, it is important to determine whether they are located at protein-protein interfaces, which are composed of two main regions, core and rim, with different evolutionary conservation and physicochemical properties. Here we have performed a structural, energetics and computational analysis of interactions between proteins hosting mutations related to diseases detected in newborn screening. Interface residues were classified as core or rim, showing that the core residues contribute the most to the binding free energy of the PPI. Disease-causing variants are more likely to occur at the interface core region rather than at the interface rim (p < 0.0001). In contrast, neutral variants are more often found at the interface rim or at the non-interacting surface rather than at the interface core region. We also found that arginine, tryptophan, and tyrosine are over-represented among mutated residues leading to disease. These results can enhance our understanding of disease at molecular level and thus contribute towards personalized medicine by helping clinicians to provide adequate diagnosis and treatments.

Screening for Polar Chemicals in Water by Trifunctional Mixed-Mode Liquid Chromatography-High Resolution Mass Spectrometry.

The presence of persistent and mobile organic contaminants (PMOC) in aquatic environments is a matter of high concern due to their capability of crossing through natural and anthropogenic barriers, even reaching drinking water. Most analytical methods rely on reversed-phase liquid chromatography (RPLC), which is quite limited for the detection of very polar chemicals. Thus, many of these PMOCs may have not been recognized as water pollutants yet, due to the lack of analytical methods capable to detect them. Mixed-mode LC (MMLC), providing the combination of RP and ion-exchange functionalities is explored in this work with a trifunctional column, combining RPLC, anion and cation exchange, which allows the simultaneous determination of analytes with extremely different properties. A nondiscriminant sample concentration step followed by a MMLC-high resolution mass spectrometry method was developed for a group of 37 very polar model chemicals with different acid/base functionalities. The overall method performance was satisfactory with a mean limit of detection of 50 ng/L, relative standard deviation lower than 20% and overall recoveries (including matrix effects) higher than 60% for 54% of model compounds. Then, the method was applied to 15 real water samples, by a suspect screening approach. For those detected PMOC with standard available, a preliminary estimation of concentrations was also performed. Thus, 22 compounds were unequivocally identified in a range of expected concentrations from 6 ng/L to 540 µg/L. Some of them are well-known PMOC, such as acesulfame, perfluorobutanoic acid or metformin, but other novel pollutants were also identified, as for example di-o-tolylguanidine or trifluoromethanesulfonic acid, which had not or were scarcely studied in water so far.

Simultaneous enzymatic hydrolysis and extraction of endocrine-disrupting chemicals in fish bile using polyethersulfone polymer.

This study describes a new method for the simultaneous extraction and enzymatic hydrolysis of alkylphenols, estrogens, bisphenol-A and phthalate metabolite (mono-2-ethylhexyl ester, MEHP) in fish bile using polyethersulfone (PES) polymer as sorptive material. Parameters affecting the hydrolysis (enzyme amount) and extraction (nature of polymeric material, PES desorption solvent nature and time, PES amount and time profile) were optimised. The optimum conditions were fixed as: 5 PES tubes (1.5 cm length × 0.7 mm o.d.) were added to a vessel with 100 µL of sample, 800 µL of ultrapure water, 1.5 mL phosphate buffer (0.1 mol L(-1), pH 6) and 200 µL of ß-glucuronidase (1000 U mL(-1)) enzyme and the mixture was stirred at 37 °C and 550 rpm for 3 h. Quantitative results were obtained after desorption of PES material using 500 µL of ethyl acetate. The extracts were reconstituted in 250 µL of methanol and analysed by liquid chromatography-tandem mass spectrometry, obtaining apparent recoveries in the range of 73-134 % using deuterated compounds surrogates corrections. Relative standard deviations below 27 % were obtained for all target analytes and the method detection limits (MDLs) were in low nanograms per mililliter level for all the studied compounds, except in the case of MEHP which was detected at higher concentration levels (ng µL(-1)) in bile samples that do not allow its MDL determination. Bisphenol A (MDL-10.8 ng mL(-1)), diethylstilbestrol (MDL-1.4 ng mL(-1)) and MEHP (975-2604 ng mL(-1)) were detected in grey mullets captured nearby the wastewater treatment plant of Gernika (Biosphere Reserve of Urdaibai).

Compensated pathogenic variants in coagulation factors VIII and IX present complex mapping between molecular impact and hemophilia severity.

Compensated pathogenic deviations (CPDs) are sequence variants that are pathogenic in humans but neutral in other species. In recent years, our molecular understanding of CPDs has advanced substantially. For example, it is known that their impact on human proteins is generally milder than that of average pathogenic mutations and that their impact is suppressed in non-human carriers by compensatory mutations. However, prior studies have ignored the evolutionarily relevant relationship between molecular impact and organismal phenotype. Here, we explore this topic using CPDs from FVIII and FIX and data concerning carriers' hemophilia severity. We find that, regardless of their molecular impact, these mutations can be associated with either mild or severe disease phenotypes. Only a weak relationship is found between protein stability changes and severity. We also characterize the population variability of hemostasis proteins, which constitute the genetic background of FVIII and FIX, using data from the 1000 Genome project. We observe that genetic background can vary substantially between individuals in terms of both the amount and nature of genetic variants. Finally, we discuss how these results highlight the need to include new terms in present models of protein evolution to explain the origin of CPDs.

Enrichment of perfluorinated alkyl substances on polyethersulfone using 1-methylpyperidine as ion-pair reagent for the clean-up of carrot and amended soil extracts.

The development of a simple, cheap and environment friendly analytical method for the simultaneous determination of different perfluoroalkyl substances (PFASs) including seven perfluoroalkyl carboxylic acids, three perfluoroalkane sulfonic acids and perfluorooctanesulfonamide in carrot and amended soil was carried out in the present work. The method was based on focused ultrasound solid-liquid extraction followed by extract clean-up through enrichment of the target compounds on a polymeric material using an ion-pair reagent and detection by liquid chromatography-tandem mass spectrometry. The following variables affecting the clean-up step were evaluated: the nature of the polymeric material (polyethersulfone, PES, versus silicone rod), the amount of the polymeric material (from 1 to 9 mg), the ion-pair reagent (1-methylpyperidine, 1-MP, versus tetrabutylammonium salts), the concentration of the ion-pair reagent (from 5 to 50 mM) and the extraction time (from 15 min to 24 h). Optimum clean-up conditions were obtained using preconcentration on 9 mg of PES polymeric material combined with 5 mM 1-MP as ion-pair reagent for 3h. The method was validated in terms of apparent recoveries in the range of 77-140% and 95-137% at the low concentration (50 ng g(-1)) and in the range of 70-136% and 79-132% at the high concentration (290 ng g(-1)) for amended soil and carrot, respectively, after correction with the corresponding labeled standards. Precision, as relative standard deviation, was within 2-23%, while method detection limits were 0.31-2.85 ng g(-1) for amended soil and 0.11-1.83 ng g(-1) for carrot. In the absence of a certified reference material for the target analytes in the matrices studied, inter-method comparison was carried out and the same samples were processed using two independent clean-up procedures, the one developed in the present work and a classical based on solid-phase extraction. Statistically comparable results were obtained according to the one-way analysis of variance for peel, core, leaves as well as amended soil (F(Calc)=2.59, 5.06, 5.82 and 2.34

Development of stir-bar sorptive extraction-thermal desorption-gas chromatography-mass spectrometry for the analysis of musks in vegetables and amended soils.

The aim of this study was to develop a sensitive and environment-friendly method based on stir-bar sorptive extraction (SBSE) followed by thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) to determine 8 synthetic musks (musk ambrette, musk ketone, celestolide, tonalide, galaxolide, phantolide, traseolide, and cashmeran) in vegetables (lettuce, carrot, and pepper) and amended soil samples. In a first step sorptive extraction was studied both in the headspace (HSSE) and in the immerse mode (SBSE). The best results were obtained in the immersion mode which was further studied. The influence of the main factors: methanol (20%) and NaCl addition (0%), extraction temperature (40°C) and time (180 min), extraction solvent volume (9 mL) and stirring rate (600 rpm) on the efficiency of SBSE was evaluated by means of experimental designs. In the case of TD, desorption time (10 min), desorption temperature (300°C), cryo-focusing temperature (-30°C), vent flow (75 mL/min) and vent pressure (7.2 psi) were studied using both a fractioned factorial design and a central composite design (CCD). The method was validated in terms of apparent recoveries (AR%), method detection limits (MDLs) and precision at two different concentration levels. Although quantification using instrumental calibration rendered odd results in most of the cases, satisfactory recoveries (74-126%) were obtained in the case of matrix-matched calibration approach for all of the analytes and matrices studied at the two concentration levels evaluated. MDLs in the range of 0.01-0.8 ng/g and 0.01-1.1 ng/g were obtained for vegetables and amended soil samples, respectively. RSD values within 1-23% were obtained for all the analytes and matrices. Finally, the method was applied to the determination of musks in vegetable and amended soil samples.