Recommendations for the classification of germline variants in the exonuclease domain of POLE and POLD1

BackgroundGermline variants affecting the proofreading activity of polymerases epsilon and delta cause a hereditary cancer and adenomatous polyposis syndrome characterized by tumors with a high mutational burden and a specific mutational spectrum. In addition to the implementation of multiple pieces of evidence for the classification of gene variants, POLE and POLD1 variant classification is particularly challenging given that non-disruptive variants affecting the proofreading activity of the corresponding polymerase are the ones associated with cancer. In response to an evident need in the field, we have developed gene-specific variant classification recommendations, based on the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology) criteria, for the assessment of non-disruptive variants located in the sequence coding for the exonuclease domain of the polymerases.MethodsA training set of 23 variants considered pathogenic or benign was used to define the usability and strength of the ACMG/AMP criteria. Population frequencies, computational predictions, co-segregation data, phenotypic and tumor data, and functional results, among other features, were considered.ResultsGene-specific variant classification recommendations for non-disruptive variants located in the exonuclease domain of POLE and POLD1 were defined. The resulting recommendations were applied to 128 exonuclease domain variants reported in the literature and/or public databases. A total of 17 variants were classified as pathogenic or likely pathogenic, and 17 as benign or likely benign.ConclusionsOur recommendations, with room for improvement in the coming years as more information become available on carrier families, tumor molecular characteristics and functional assays, are intended to serve the clinical and scientific communities and help improve diagnostic performance, avoiding variant misclassifications

Electrochemical Biosensor Based on Optimized Biocomposite for Organophosphorus and Carbamates Pesticides Detection

Altres ajuts: Universitat Autònoma de Barcelona (UAB) for the award of PIF studentshipThis paper presents the characterization and optimization of biosensors based on graphite-epoxy which incorporates the enzyme acetylcholinesterase (AChE). By means of advanced electrochemical techniques, such as electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV), the characterization and optimization of graphite-epoxy-AChE biosensors have been performed. In order to obtain sensitive electrodes, the optimal composition of the transducer material (graphite-epoxy-enzyme ratio) was studied. The optimization of the conductive particles distribution inside the biomaterial has allowed an improvement of the electrochemical properties. Optimal composition guarantees improving electrochemical properties required, such as high electron-transfer rate, high signal-to-noise ratio, and suitable sensitivity. The optimal biocomposite composition range was obtained between 16% and 17% of graphite and 0.12% of AChE. The biosensors were applied to the analysis of different pesticides, organophosphorus and carbamates, using indirect measurements based on enzymatic inhibition process. These optimized biosensors present detection limit one order of magnitude lower compared to the standard composition (nonoptimized) and allow achieving concentrations lower than the established ones by the pesticides regulation. Finally, spiked tap water samples with pesticides were analyzed with the optimized biosensors

Potential Involvement of NSD1, KRT24 and ACACA in the Genetic Predisposition to Colorectal Cancer

The ALFRED (Allelic Loss Featuring Rare Damaging) in silico method was developed to identify cancer predisposition genes through the identification of somatic second hits. By applying ALFRED to ~10,000 tumor exomes, 49 candidate genes were identified. We aimed to assess the causal association of the identified genes with colorectal cancer (CRC) predisposition. Of the 49 genes, NSD1, HDAC10, KRT24, ACACA and TP63 were selected based on specific criteria relevant for hereditary CRC genes. Gene sequencing was performed in 736 patients with familial/early onset CRC or polyposis without germline pathogenic variants in known genes. Twelve (predicted) damaging variants in 18 patients were identified. A gene-based burden test in 1596 familial/early-onset CRC patients, 271 polyposis patients, 543 TCGA CRC patients and >134,000 controls (gnomAD, non-cancer), revealed no clear association with CRC for any of the studied genes. Nevertheless, (non-significant) over-representation of disruptive variants in NSD1, KRT24 and ACACA in CRC patients compared to controls was observed. A somatic second hit was identified in one of 20 tumors tested, corresponding to an NSD1 carrier. In conclusion, most genes identified through the ALFRED in silico method were not relevant for CRC predisposition, although a possible association was detected for NSD1, KRT24 and ACACA

Rag1 immunodeficiency‐induced early aging and senescence in zebrafish are dependent on chronic inflammation and oxidative stress [Poster]

12th European Zebrafish Meeting, Krakow, 9-13 July 2023In mammals, recombination activating gene 1 (RAG1) plays a crucial role in adaptive immunity, generating a vast range of immunoglobulins. Rag1−/− zebrafish (Danio rerio) are viable and reach adulthood without obvious signs of infectious disease in standard nonsterile conditions, suggesting that innate immunity could be enhanced to compensate for the lack of adaptive immunity. By using microarray analysis, we confirmed that the expression of immunity- and apoptosis-related genes was increased in the rag1−/− fish. This tool also allows us to notice alterations of the DNA repair and cell cycle mechanisms in rag1−/− zebrafish. Several senescence and aging markers were analyzed. In addition to the lower lifespan of rag1−/− zebrafish compared to their wild-type (wt) siblings, rag1−/− showed a higher incidence of cell cycle arrest and apoptosis, a greater amount of phosphorylated histone H2AX, oxidative stress and decline of the antioxidant mechanisms, an upregulated expression and activity of senescence-related genes and senescence-associated β-galactosidase, respectively, diminished telomere length, and abnormal self-renewal and repair capacities in the retina and liver. Metabolomic analysis also demonstrated clear differences between wt and rag1−/− fish, as was the deficiency of the antioxidant metabolite L-acetylcarnitine (ALCAR) in rag1−/− fish. Therefore, Rag1 activity does not seem to be limited to V(D)J recombination but is also involved in senescence and aging. Furthermore, we confirmed the senolytic effect of ABT-263, a known senolytic compound and, for the first time, the potential in vivo senolytic activity of the antioxidant agent ALCAR, suggesting that this metabolite is essential to avoid premature agingN

High-Throughput Remote Sensing of Vertical Green Living Walls (VGWs) in Workplaces

Vertical green living walls (VGWs)—growing plants on vertical walls inside or outside buildings—have been suggested as a nature-based solution to improve air quality and comfort in modern cities. However, as with other greenery systems (e.g., agriculture), managing VGW systems requires adequate temporal and spatial monitoring of the plants as well as the surrounding environment. Remote sensing cameras and small, low-cost sensors have become increasingly valuable for conventional vegetation monitoring; nevertheless, they have rarely been used in VGWs. In this descriptive paper, we present a first-of-its-kind remote sensing high-throughput monitoring system in a VGW workplace. The system includes low- and high-cost sensors, thermal and hyperspectral remote sensing cameras, and in situ gas-exchange measurements. In addition, air temperature, relative humidity, and carbon dioxide concentrations are constantly monitored in the operating workplace room (scientific computer lab) where the VGW is established, while data are continuously streamed online to an analytical and visualization web application. Artificial Intelligence is used to automatically monitor changes across the living wall. Preliminary results of our unique monitoring system are presented under actual working room conditions while discussing future directions and potential applications of such a high-throughput remote sensing VGW system

Spectral Estimation of <i>In Vivo</i> Wheat Chlorophyll a/b Ratio under Contrasting Water Availabilities

To meet the ever-growing global population necessities, integrating climate-change-relevant plant traits into breeding programs is required. Developing new tools for fast and accurate estimation of chlorophyll parameters, chlorophyll a (Chl-a) content, chlorophyll b (Chl-b) content, and their ratio (Chl-a/b), can promote breeding programs of wheat with enhanced climate adaptability. Spectral reflectance of leaves is affected by changes in pigment concentration and can be used to estimate chlorophyll parameters. The current study identified and validated the top known spectral indices and developed new vegetation indices (VIs) for Chl-a and Chl-b content estimation and used them to non-destructively estimate Chl-a/b values and compare them to hyperspectral estimations. Three wild emmer introgression lines, with contrasting drought stress responsiveness dynamics, were selected. Well-watered and water-limited irrigation regimes were applied. The wheat leaves were spectrally measured with a handheld spectrometer to acquire their reflectance in the 330 to 790 nm range. Regression models based on calculated VIs as well as all hyperspectral curves were calibrated and validated against chlorophyll extracted values. The developed normalized difference spectral indices (NDSIs) resulted in high accuracy of Chl-a (NDSI415,614) and Chl-b (NDSI406,525) estimation, allowing for indirect non-destructive estimation of Chl-a/b with root mean square error (RMSE) values that could fit 6 to 10 times in the range of the measured values. They also performed similarly to the hyperspectral models. Altogether, we present here a new tool for a non-destructive estimation of Chl-a/b, which can serve as a basis for future breeding efforts of climate-resilient wheat as well as other crops

A Model-based Approach to Realize Privacy and Data Protection by Design

International audienceTelecommunications and data are pervasive in almost each aspect of our every-day life and new concerns progressively arise as a result of stakes related to privacy and data protection. Indeed, systems development becomes data-centric leading to an ecosystem where a variety of players intervene (citizens, industry, regulators) and where the policies regarding data usage and utilization are far from consensual. The new General Data Protection Regulation (GDPR) enacted by the European Commission in 2018 has introduced new provisions including principles for lawfulness, fairness, transparency, etc. thus endorsing data subjects with new rights in regards to their personal data. In this context, a growing need for approaches that conceptualize and help engineers to integrate GDPR and privacy provisions at design time becomes paramount. This paper presents a comprehensive approach to support different phases of the design process with special attention to the integration of privacy and data protection principles. Among others, it is a generic model-based approach that can be specialized according to the specifics of different application domains

Electrochemical Biosensor Based on Optimized Biocomposite for Organophosphorus and Carbamates Pesticides Detection

Altres ajuts: Universitat Autònoma de Barcelona (UAB) for the award of PIF studentshipThis paper presents the characterization and optimization of biosensors based on graphite-epoxy which incorporates the enzyme acetylcholinesterase (AChE). By means of advanced electrochemical techniques, such as electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV), the characterization and optimization of graphite-epoxy-AChE biosensors have been performed. In order to obtain sensitive electrodes, the optimal composition of the transducer material (graphite-epoxy-enzyme ratio) was studied. The optimization of the conductive particles distribution inside the biomaterial has allowed an improvement of the electrochemical properties. Optimal composition guarantees improving electrochemical properties required, such as high electron-transfer rate, high signal-to-noise ratio, and suitable sensitivity. The optimal biocomposite composition range was obtained between 16% and 17% of graphite and 0.12% of AChE. The biosensors were applied to the analysis of different pesticides, organophosphorus and carbamates, using indirect measurements based on enzymatic inhibition process. These optimized biosensors present detection limit one order of magnitude lower compared to the standard composition (nonoptimized) and allow achieving concentrations lower than the established ones by the pesticides regulation. Finally, spiked tap water samples with pesticides were analyzed with the optimized biosensors