TurboPutative: A web server for data handling and metabolite classification in untargeted metabolomics.

Untargeted metabolomics aims at measuring the entire set of metabolites in a wide range of biological samples. However, due to the high chemical diversity of metabolites that range from small to large and more complex molecules (i.e., amino acids/carbohydrates vs. phospholipids/gangliosides), the identification and characterization of the metabolome remain a major bottleneck. The first step of this process consists of searching the experimental monoisotopic mass against databases, thus resulting in a highly redundant/complex list of candidates. Despite the progress in this area, researchers are still forced to manually explore the resulting table in order to prioritize the most likely identifications for further biological interpretation or confirmation with standards. Here, we present TurboPutative (https://proteomics.cnic.es/TurboPutative/), a flexible and user-friendly web-based platform composed of four modules (Tagger, REname, RowMerger, and TPMetrics) that streamlines data handling, classification, and interpretability of untargeted LC-MS-based metabolomics data. Tagger classifies the different compounds and provides preliminary insights into the biological system studied. REname improves putative annotation handling and visualization, allowing the recognition of isomers and equivalent compounds and redundant data removal. RowMerger reduces the dataset size, facilitating the manual comparison among annotations. Finally, TPMetrics combines different datasets with feature intensity and relevant information for the researcher and calculates a score based on adduct probability and feature correlations, facilitating further identification, assessment, and interpretation of the results. The TurboPutative web application allows researchers in the metabolomics field that are dealing with massive datasets containing multiple putative annotations to reduce the number of these entries by 80%-90%, thus facilitating the extrapolation of biological knowledge and improving metabolite prioritization for subsequent pathway analysis. TurboPutative comprises a rapid, automated, and customizable workflow that can also be included in programmed bioinformatics pipelines through its RESTful API services. Users can explore the performance of each module through demo datasets supplied on the website. The platform will help the metabolomics community to speed up the arduous task of manual data curation that is required in the first steps of metabolite identification, improving the generation of biological knowledge.This research has been possible thanks to a Training of Research Staff (FPU) contract to carry out doctoral theses, granted to RB-R by the Ministry of Universities of Spain [FPU20/03365] and added to project [CSO2014-57826-P]. This study was also supported by competitive grants from the Spanish Ministry of Science, Innovation and Universities (BIO2015-67580-P and PGC2018-097019-B-I00), through the Carlos III Institute of Health-Fondo de Investigación Sanitaria grant PRB3 (IPT17/0019-ISCIII-SGEFI/ERDF, ProteoRed), the Fundació MaratóTV3 (grant 122/C/2015), “la Caixa” Banking Foundation (project code HR17-00247), and the European Research Council (ERC-2016- Consolidator Grant 725091). The CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Ministerio de Ciencia e Innovación (MCIN) and the Pro CNIC Foundation), and is a Severo Ochoa Center of Excellence (grant CEX2020-001041-S funded by MICIN/AEI/10.13039/ 501100011033).S

A highly pathogenic porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) strongly modulates cellular innate and adaptive immune subsets upon experimental infection

Highly pathogenic (HP) PRRSV isolates have been discovered within both PRRSV-1 and PRRSV-2 genotypes and investigated in recent years especially for their ability to cause extremely severe disease in conventional pig herds. The exacerbation of general and respiratory clinical signs has been attributed not only to an efficient replication (virulence) but also to the ability to dysregulate viral recognition and induce mechanisms of immune evasion or immune enhancement of humoral and cellular anti-viral responses differently from non-HP PRRSV isolates in terms of intensity and temporal onset. Thus, the understanding of the immunopathogenesis of HP PRRSV is a major concern for the study of virus biology and development of efficacious vaccines. The present study aims at addressing the modulation of relevant immune cell subsets by flow cytometry in the blood of 4- week-old pigs experimentally infected with the recently discovered PR40/2014 HP PRRSV-1.1 strain phenotypically characterized in Canelli et al. (2017) compared to pigs infected with a non-HP PRRSV isolate (PR11/ 2014) and uninfected controls. PR40 infected animals showed an early and marked reduction of pro-inflammatory CD172α+ CD14+CD16+ and CD14+CD163+ monocytes and TCRγδ+CD8α+/CD8α- lymphocytes when pigs were most infected, possibly due to a recruitment sustaining an acute inflammatory response in target tissues. The prolonged increased CD3+CD16+ NKT cell levels may sustain peripheral inflammation and/ or the anti-viral response. The late reduction (potential depletion) of γ/δ T lymphocytes and CD3+CD4+CD8α- naïve Th lymphocytes paralleled with the delayed increase of CD3+CD4+CD8α+ memory and CD3+CD4- CD8α/β+cytotoxic T lymphocytes. In addition, PR40 infection showed an early depletion of activated CD4+CD25+ T lymphocytes and Tregs together with an intense and lasting depletion of CD21+ B lymphocytes. Overall, these features demonstrate that the more severe clinical signs observed upon infection with the HP PR40 strain are sustained by remarkable changes in the peripheral blood distribution of immune cells and provide further insights into the immune regulation/immunopathogenesis induced by PRRSV-1 subtype 1 European isolates

Early occurrence of lung adenocarcinoma and breast cancer after radiotherapy of a chest wall sarcoma in a patient with a de novo germline mutation in TP53

We report a 26-year-old female patient who was diagnosed within 4years with chest sarcoma, lung adenocarcinoma, and breast cancer. While her family history was unremarkable, DNA sequencing of TP53 revealed a germline de novo non-sense mutation in exon 6 p.Arg213X. One year later, she further developed a contralateral ductal carcinoma in situ, and 18months later a jaw osteosarcoma. This case illustrates the therapeutic pitfalls in the care of a young cancer patient with TP53 de novo germline mutations and the complications related to her first-line therapy. Suggestion is made to use the less stringent Chompret criteria for germline TP53 mutation screening. Our observation underlines the possibly negative effect of radiotherapy in generating second tumors in patients with a TP53 mutation. We also present a review of six previously reported cases, comparing their cancer phenotypes with those generally produced by TP53 mutation

Biomass production and energy balance of herbaceous and woody crops on marginal soils in the Po valley

A wealth of data and information on the cultivation of perennial biomass crops has been collected, but direct comparisons between herbaceous and woody crops are rare. The main objective of this research was to compare the biomass yield, the energy balance and the biomass quality of six perennial bioenergy crops: Populus spp., Robinia pseudoacacia, Salix spp., Arundo donax, Miscanthus 9 giganteus, and Panicum virgatum, grown in two marginal environments. For giant reed and switchgrass, two levels of nitrogen fertilization were applied annually (0–100 kg ha 1). Nitrogen fertilization did not affect biomass or energy production of giant reed; thus, it significantly reduced the energy return on investment (EROI) (from 73 to 27). In switchgrass, nitrogen fertiliza- tion significantly increased biomass production and the capacity of this crop to respond to water availability, making it a favorable option when only biomass production is a target. Net energy gain (NEG) was higher for herbaceous crops than for woody crops. In Casale, EROI calculated for poplar and willow (7, on average) was significantly lower than that of the other crops (14, on average). In Gariga, the highest EROI was calculated for miscanthus (98), followed by nonfertilized giant reed and switchgrass (82 and 73, respectively). Growing degree days10 during the cropping season had no effect on biomass production in any of the studied species, although water availability from May to August was a major factor affecting biomass yield in herbaceous crops. Overall, herbaceous crops had the highest ranking for bioenergy production due to their high biomass yield, high net energy gain (NEG), and biomass quality that renders them suitable to both biochemical and thermochemical conversion. Miscanthus in particular had the highest EROI in both locations (16 and 98, in Casale and Gariga), while giant reed had the highest NEG on the silty-loam soil of Gariga

Eplerenone attenuated cardiac steatosis, apoptosis and diastolic dysfunction in experimental type-II diabetes

Cardiac steatosis and apoptosis are key processes in diabetic cardiomyopathy, but the underlying mechanisms have not been elucidated, leading to a lack of effective therapy. The mineralocorticoid receptor blocker, eplerenone, has demonstrated anti-fibrotic actions in the diabetic heart. However, its effects on the fatty-acid accumulation and apoptotic responses have not been revealed. Methods: Non-hypertensive Zucker Diabetic Fatty (ZDF) rats received eplerenone (25 mg/kg) or vehicle. Zucker Lean (ZL) rats were used as control (n = 10, each group). After 16 weeks, cardiac structure and function was examined, and plasma and hearts were isolated for biochemical and histological approaches. Cultured cardiomyocytes were used for in vitro assays to determine the direct effects of eplerenone on high fatty acid and high glucose exposed cells. Results: In contrast to ZL, ZDF rats exhibited hyperglycemia, hyperlipidemia, insulin-resistance, cardiac steatosis and diastolic dysfunction. The ZDF myocardium also showed increased mitochondrial oxidation and apoptosis. Importantly, eplerenone mitigated these events without altering hyperglycemia. In cultured cardiomyocytes, high-concentrations of palmitate stimulated the fatty-acid uptake (in detriment of glucose assimilation), accumulation of lipid metabolites, mitochondrial dysfunction, and apoptosis. Interestingly, fatty-acid uptake, ceramides formation and apoptosis were also significantly ameliorated by eplerenone. Conclusions: By blocking mineralocorticoid receptors, eplerenone may attenuate cardiac steatosis and apoptosis, and subsequent remodelling and diastolic dysfunction in obese/type-II diabetic ratsThis work was supported by national grants from Ministerio de Educación y Ciencia (SAF2009-08367), Comunidad de Madrid (CCG10-UAM/BIO-5289), FISS (PI10/00072), and a grant from by Pfizer (NY, USA), Spanish Ministry of Economy and Competitiveness (MINECO) CTQ2011-23562. These grants were used to provide consumables and animals required. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. AF received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under grant agreement nº 26486

ECM deposition is driven by caveolin-1-dependent regulation of exosomal biogenesis and cargo sorting.

The composition and physical properties of the extracellular matrix (ECM) critically influence tumor progression, but the molecular mechanisms underlying ECM layering are poorly understood. Tumor-stroma interaction critically depends on cell communication mediated by exosomes, small vesicles generated within multivesicular bodies (MVBs). We show that caveolin-1 (Cav1) centrally regulates exosome biogenesis and exosomal protein cargo sorting through the control of cholesterol content at the endosomal compartment/MVBs. Quantitative proteomics profiling revealed that Cav1 is required for exosomal sorting of ECM protein cargo subsets, including Tenascin-C (TnC), and for fibroblast-derived exosomes to efficiently deposit ECM and promote tumor invasion. Cav1-driven exosomal ECM deposition not only promotes local stromal remodeling but also the generation of distant ECM-enriched stromal niches in vivo. Cav1 acts as a cholesterol rheostat in MVBs, determining sorting of ECM components into specific exosome pools and thus ECM deposition. This supports a model by which Cav1 is a central regulatory hub for tumor-stroma interactions through a novel exosome-dependent ECM deposition mechanism.This study was supported by the Ministerio de Ciencia, Innovación y Universidades (CSD2009-0016, SAF2014-51876-R, SAF2017-83130-R, BFU2016-81912-REDC, and IGP-SO-MINSEV1512-07-2016); the Fundació La Marató de TV3 (385/C/2019); the Worldwide Cancer Research Foundation (AICR 15-0404); and Fondo Europeo de Desarrollo Regional “Una manera de hacer Europa” (to M.Á. del Pozo). M.Á. del Pozo’s group received funding from the European Union Horizon 2020 research and innovation program under Marie Sklodowska-Curie grant agreement no. 641639. M.Á. del Pozo is a member of the Tec4Bio consortium (ref. S2018/NMT4443; Actividades de I+D entre Grupos de Investigación en Tecnologías, Comunidad Autónoma de Madrid/FEDER, Spain). J. Balsinde was supported by Ministerio de Ciencia, Innovación y Universidades grants SAF2013-48201-R and SAF2016-80883-R, and G. Orend was supported by Institut National de la Santé et de la Recherche Médicale, the University of Strasbourg, the Ligue Contre le Cancer, and the Institut National du Cancer (ref. TENPLAMET). L. Albacete-Albacete was supported by a Ministerio de Ciencia, Innovación y Universidades predoctoral fellowship associated with the Severo Ochoa Excellence program (ref. SVP-2013-06789). I. Navarro-Lérida was supported by a postdoctoral fellowship from the Asociación Española Contra el Cáncer (ref. INVES191NAVA). The Centro Nacional de Investigaciones Cardiovasculares Carlos III is supported by the Ministerio de Ciencia e Innovación and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (SEV-2015-0505).S

Activation of amino acid metabolic program in cardiac HIF1-alpha-deficient mice.

HIF1-alpha expression defines metabolic compartments in the developing heart, promoting glycolytic program in the compact myocardium and mitochondrial enrichment in the trabeculae. Nonetheless, its role in cardiogenesis is debated. To assess the importance of HIF1-alpha during heart development and the influence of glycolysis in ventricular chamber formation, herein we generated conditional knockout models of Hif1a in Nkx2.5 cardiac progenitors and cardiomyocytes. Deletion of Hif1a impairs embryonic glycolysis without influencing cardiomyocyte proliferation and results in increased mitochondrial number and transient activation of amino acid catabolism together with HIF2α and ATF4 upregulation by E12.5. Hif1a mutants display normal fatty acid oxidation program and do not show cardiac dysfunction in the adulthood. Our results demonstrate that cardiac HIF1 signaling and glycolysis are dispensable for mouse heart development and reveal the metabolic flexibility of the embryonic myocardium to consume amino acids, raising the potential use of alternative metabolic substrates as therapeutic interventions during ischemic events.This project has been supported by Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Spain and by grants to S.M.-P. from the European Research Council, European Union, FP7-PEOPLE-2010-RG_276891; Fundación TV3 La Marató, Spain, 201507.30.31; Comunidad de Madrid (CAM); Spain and European Union (EU), B2017/BMD-3875; Instituto de Salud Carlos III, Spain, PI17/01817; Universidad Francisco de Vitoria (UFV), Spain and LeDucq Foundation, France, 17CVD04. I.M.-M. was supported by La Caixa-CNIC and Fundacion Alfonso Martín Escudero fellowships, Spain. T.A.-G. was supported by a predoctoral award granted by CAM/EU and UFV, Spain, PEJD-2018-PRE/SAL-9529 and SM-P by a Contrato de Investigadores Miguel Servet (CPII16/00050) and UFV, Spain.S

ALDH4A1 is an atherosclerosis auto-antigen targeted by protective antibodies

Cardiovascular disease (CVD) is the leading cause of mortality in the world, with most CVD-related deaths resulting from myocardial infarction or stroke. The main underlying cause of thrombosis and cardiovascular events is atherosclerosis, an inflammatory disease that can remain asymptomatic for long periods. There is an urgent need for therapeutic and diagnostic options in this area. Atherosclerotic plaques contain autoantibodies, and there is a connection between atherosclerosis and autoimmunity. However, the immunogenic trigger and the effects of the autoantibody response during atherosclerosis are not well understood. Here we performed high-throughput single-cell analysis of the atherosclerosis-associated antibody repertoire. Antibody gene sequencing of more than 1,700 B cells from atherogenic Ldlr and control mice identified 56 antibodies expressed by in-vivo-expanded clones of B lymphocytes in the context of atherosclerosis. One-third of the expanded antibodies were reactive against atherosclerotic plaques, indicating that various antigens in the lesion can trigger antibody responses. Deep proteomics analysis identified ALDH4A1, a mitochondrial dehydrogenase involved in proline metabolism, as a target antigen of one of these autoantibodies, A12. ALDH4A1 distribution is altered during atherosclerosis, and circulating ALDH4A1 is increased in mice and humans with atherosclerosis, supporting the potential use of ALDH4A1 as a disease biomarker. Infusion of A12 antibodies into Ldlr mice delayed plaque formation and reduced circulating free cholesterol and LDL, suggesting that anti-ALDH4A1 antibodies can protect against atherosclerosis progression and might have therapeutic potential in CVD.Ministerio de Economía y Competitividad (SVP-2014-068289); P.D. was supported by an AECC grant (AIO 2012, Ayudas a Investigadores en Oncología 2012); A.S.-B. is a Juan de la Cierva researcher (IJC2018-035279-I); I.M.-F. was a fellow of the research training program funded by Ministerio de Economía y Competitividad (SVP-2014-068216); and A.R.R. and J.V. are supported by Centro Nacional de Investigaciones Cardiovasculares (CNIC). The project leading to these results has received funding from la Caixa Banking Foundation under the project code HR17-00247 and from SAF2016-75511-R and PID2019-106773RB-I00 grants to A.R.R. (Plan Estatal de Investigación Científica y Técnica y de Innovación 2013–201

Circulating miR-320b and miR-483-5p levels are associated with COVID-19 in-hospital mortality

none28noThe stratification of mortality risk in COVID-19 patients remains extremely challenging for physicians, especially in older patients. Innovative minimally invasive molecular biomarkers are needed to improve the prediction of mortality risk and better customize patient management. In this study, aimed at identifying circulating miRNAs associated with the risk of COVID-19 in-hospital mortality, we analyzed serum samples of 12 COVID-19 patients by small RNA-seq and validated the findings in an independent cohort of 116 COVID-19 patients by qRT-PCR. Thirty-four significantly deregulated miRNAs, 25 downregulated and 9 upregulated in deceased COVID-19 patients compared to survivors, were identified in the discovery cohort. Based on the highest fold-changes and on the highest expression levels, 5 of these 34 miRNAs were selected for the analysis in the validation cohort. MiR-320b and miR-483-5p were confirmed to be significantly hyper-expressed in deceased patients compared to survived ones. Kaplan-Meier and Cox regression models, adjusted for relevant confounders, confirmed that patients with the 20% highest miR-320b and miR-483-5p serum levels had three-fold increased risk to die during in-hospital stay for COVID-19. In conclusion, high levels of circulating miR-320b and miR-483-5p can be useful as minimally invasive biomarkers to stratify older COVID-19 patients with an increased risk of in-hospital mortality.restrictedGiuliani, Angelica; Matacchione, Giulia; Ramini, Deborah; Di Rosa, Mirko; Bonfigli, Anna Rita; Sabbatinelli, Jacopo; Monsurrò, Vladia; Recchioni, Rina; Marcheselli, Fiorella; Marchegiani, Francesca; Piacenza, Francesco; Cardelli, Maurizio; Galeazzi, Roberta; Pomponio, Giovanni; Ferrarini, Alessia; Gabrielli, Armando; Baroni, Silvia Svegliati; Moretti, Marco; Sarzani, Riccardo; Giordano, Piero; Cherubini, Antonio; Corsonello, Andrea; Antonicelli, Roberto; Procopio, Antonio Domenico; Ferracin, Manuela; Bonafè, Massimiliano; Lattanzio, Fabrizia; Olivieri, FabiolaGiuliani, Angelica; Matacchione, Giulia; Ramini, Deborah; Di Rosa, Mirko; Bonfigli, Anna Rita; Sabbatinelli, Jacopo; Monsurrò, Vladia; Recchioni, Rina; Marcheselli, Fiorella; Marchegiani, Francesca; Piacenza, Francesco; Cardelli, Maurizio; Galeazzi, Roberta; Pomponio, Giovanni; Ferrarini, Alessia; Gabrielli, Armando; Baroni, Silvia Svegliati; Moretti, Marco; Sarzani, Riccardo; Giordano, Piero; Cherubini, Antonio; Corsonello, Andrea; Antonicelli, Roberto; Procopio, Antonio Domenico; Ferracin, Manuela; Bonafè, Massimiliano; Lattanzio, Fabrizia; Olivieri, Fabiol

Racial differences in systemic sclerosis disease presentation: a European Scleroderma Trials and Research group study

Objectives. Racial factors play a significant role in SSc. We evaluated differences in SSc presentations between white patients (WP), Asian patients (AP) and black patients (BP) and analysed the effects of geographical locations.Methods. SSc characteristics of patients from the EUSTAR cohort were cross-sectionally compared across racial groups using survival and multiple logistic regression analyses.Results. The study included 9162 WP, 341 AP and 181 BP. AP developed the first non-RP feature faster than WP but slower than BP. AP were less frequently anti-centromere (ACA; odds ratio (OR) = 0.4, P < 0.001) and more frequently anti-topoisomerase-I autoantibodies (ATA) positive (OR = 1.2, P = 0.068), while BP were less likely to be ACA and ATA positive than were WP [OR(ACA) = 0.3, P < 0.001; OR(ATA) = 0.5, P = 0.020]. AP had less often (OR = 0.7, P = 0.06) and BP more often (OR = 2.7, P < 0.001) diffuse skin involvement than had WP.AP and BP were more likely to have pulmonary hypertension [OR(AP) = 2.6, P < 0.001; OR(BP) = 2.7, P = 0.03 vs WP] and a reduced forced vital capacity [OR(AP) = 2.5, P < 0.001; OR(BP) = 2.4, P < 0.004] than were WP. AP more often had an impaired diffusing capacity of the lung than had BP and WP [OR(AP vs BP) = 1.9, P = 0.038; OR(AP vs WP) = 2.4, P < 0.001]. After RP onset, AP and BP had a higher hazard to die than had WP [hazard ratio (HR) (AP) = 1.6, P = 0.011; HR(BP) = 2.1, P < 0.001].Conclusion. Compared with WP, and mostly independent of geographical location, AP have a faster and earlier disease onset with high prevalences of ATA, pulmonary hypertension and forced vital capacity impairment and higher mortality. BP had the fastest disease onset, a high prevalence of diffuse skin involvement and nominally the highest mortality