PredIG: a predictor of T-cell immunogenicity

The identification of immunogenic epitopes (such as fragments of proteins, in particular peptides, that can trigger an immune response) is a fundamental need for immune-based therapies. A computational tool that could predict such immunogenic epitopes would have vast potential applications in biomedicine ranging, from vaccine design against viruses or bacteria to therapeutic vaccination of cancer patients. While there are several methods that predict whether a peptide will be shown to the immune system via the Human Leukocyte Antigen (HLA) proteins of a patient, most of them cannot predict whether such presentation will indeed trigger an immune response. Additionally, T-cell immunogenicity is determined by multiple cellular processes, some of which are often overlooked by the current state-of-the-art immunogenicity predictors. The aim of this project is to build PredIG, an immunogenicity predictor that discriminates immunogenic from non-immunogenic T-cell epitopes given the peptide sequence and the HLA typing. After a careful study of the drivers of antigen processing and presentation on HLA class I molecules and an assessment of the physicochemical factors influencing epitope recognition by T-cell receptors (TCRs), we have used a selection of publicly available tools and in-house developed algorithms to identify the most relevant features that determine epitope immunogenicity. We then used these features to build an immunogenicity predictor (PredIG) modelled by XGBoost against immunogenically validated epitopes by the ImmunoEpitope DataBase (IEDB)(1), the PRIME dataset(2) and the TANTIGEN database(3). Pondering the feature importance in the model, the in-house developed softwares, NOAH for HLA Binding Affinity and NetCleave for Proteasomal Processing were identified as the major contributors to the performance of the model. Once PredIG was developed, we benchmarked the capacity to predict the immunogenicity of validated T-cell epitopes versus a set of state-of-the-art methods (Fig.1). Relevantly, PredIG showed a greater performance than the Immunogenicity predictors from Prime(2) and IEDB(4). Additionally, our results confirm that predicting T-cell immunogenicity based on data from T-cell assays is more accurate than using HLA Binding assays, the method mostly used in the field. An AUC value of 0.67 and an enrichment factor in the TOP10 epitopes of 90% outperforms the predictive performance of the available methods. In the context of the immune response against cancers, Tcell immunogenicity of tumoral mutations has been described as a response biomarker for immunotherapies such as immune checkpoint inhibitors. Similarly, the presence of immune infiltrate in a tumor has been related to a better prognosis for many cancer types. What is missing is the link between T-cell immunogenicity of tumoral mutations and the capacity of a tumor to attract immune cells. For this reason, we correlated the PredIG immunogenicity score obtained in a dataset of the The Cancer Genome Atlas (TCGA) against the tumor infiltrate in such tumors demonstrating that rather the total number of mutations a tumor accumulates, the tumor mutation burden (TMB), it is the number of immunogenic mutations what should be accounted for as biomarker of response

Fichas de las especies

Sittasomus griseicapillus, Xiphorhynchus flavigaster, Myiopagis viridicata, Mitrephanes phaeocercus, Empidonax difficilis / occidentalis, Myiarchus tuberculifer, Myiarchus cinerascens, Myiarchus nuttingi, Myiarchus tyrannulus, Pitangus sulphuratus, Myiozetetes similis, Myiodynastes luteiventris, Pachyramphus aglaiae, Vireo brevipennis, Vireo bellii, Vireo nelsoni, Vireo hypochryseus, Vireo gilvus, Vireo flavoviridis, Thryothorus sinaloa, Thryothorus felix, Troglodytes brunneicollis, Troglodytes aedon, Henicorhina leucophrys, Polioptila caerulea, Myadestes occidentalis, Catharus aurantiirostris, Catharus occidentalis, Catharus frantzii, Catharus ustulatus, Turdus assimilis, Turdus rufopalliatus, Melanotis caerulescens, Vermivora celata, Vermivora ruficapilla, Vermivora crissalis, Parula superciliosa, Parula pitiayumi, Dendroica petechia, Dendroica coronata, Dendroica nigrescens, Dendroica townsendi, Dendroica graciae, Mniotilta varia, Seiurus aurocapilla, Seiurus noveboracensis, Seiurus motacilla, Oporornis tolmiei, Geothlypis trichas, Geothlypis poliocephala, Wilsonia pusilla, Cardellina rubrifrons, Myioborus miniatus, Basileuterus belli, Icteria virens, Granatellus venustus Piranga erythrocephala, Volatinia jacarina, Diglossa baritula, Atlapetes pileatus, Arremon virenticeps Arremonops rufivirgatus, Melozone kieneri, Pipilo ocai, Aimophila ruficauda, Melospiza lincolnii Saltator coerulescens, Pheucticus melanocephalus, Cyanocompsa parellina, Passerina leclancherii, Passerina versicolor, Passerina ciris, Icterus cucullatus, Icterus pustulatus, Icterus graduacauda Carduelis notat

Resultados generales

Aspecto externo Morfometría esquelética y masa Morfometría alar y caudal Tamaño Estructuras sexuales externas Determinación del sexo Neumatización craneal Muda Datación mediante variables semicuantitativas Ciclos vitale

The inflammatory potential of diet is related to incident frailty and slow walking in older adults

Background: Certain foods and dietary patterns have been associated with both inflammation and frailty. As chronic inflammation may play a role in frailty and disability, we examined the association of the inflammatory potential of diet with these outcomes. Methods: Data were taken from 1948 community-dwelling individuals =60 years old from the Seniors-ENRICA cohort, who were recruited in 2008–2010 and followed-up through 2012. Baseline diet data, obtained with a validated diet history, was used to calculate Shivappa's Dietary Inflammatory Index (DII), an “a priori” pattern score which is based on known associations of foods and nutrients with inflammation, and Tabung's Empirical Dietary Inflammatory Index (EDII), an “a posteriori” pattern score which was statistically derived from an epidemiological study. At follow-up, incident frailty was assessed with Fried's criteria, and incident limitation in instrumental activities of daily living (IADL) with the Lawton-Brody index. Statistical analyses were performed with logistic regression, and adjusted for the main confounders. Results: Compared with individuals in the lowest tertile of DII, those in the highest tertile showed higher risk of frailty (odds ratio [OR] 2.48; 95% confidence interval [CI]: 1.42, 4.44, p-trend = 0.001) and IADL disability (OR: 1.96; 95% CI: 1.03, 3.86, p-trend = 0.035). By contrast, EDII did not show an association with these outcomes. The DII score was associated with slow gait speed, both as a low score in the Short Physical Performance Battery test (OR: 1.82; 95% CI: 1.27, 2.62, p-trend = 0.001) and as a positive Fried's criterion (OR: 1.64; 95% CI: 1.08, 2.51, p-trend = 0.021), which use different thresholds. Conclusions: DII predicted frailty and IADL while EDII did not. DII is able to measure diet healthiness in terms of physical decline in addition to avoidance of inflammation

Sleep duration and subclinical atherosclerosis: The Aragon Workers' Health Study

Background and aims: Few studies have evaluated the association of sleep duration with subclinical atherosclerosis, and with heterogeneous findings. We evaluated the association of sleep duration with the presence of coronary, carotid, and femoral subclinical atherosclerosis in healthy middle-age men with low prevalence of clinical comorbidities. Methods: We performed a cross-sectional analysis of 1968 men, 40–60 years of age, participating in the Aragon Workers' Health Study (AWHS). Duration of sleep during a typical work week was assessed by questionnaire. Coronary artery calcium scores (CACS) was assessed by computed tomography and the presence of carotid plaque and femoral plaque by ultrasound. Results: In fully adjusted models, the odds ratios (95% CI) for CACS >0 comparing sleep durations of =5, 6, and =8 h with 7 h were 1.34 (0.98–1.85), 1.35 (1.08–1.69) and 1.21 (0.90–1.62), respectively (p = 0.04). A similar U-shaped association was observed for CACS =100 and for CACS. The corresponding odds ratios for the presence of at least one carotid plaque were =5, 6, and =8 h with 7 h were 1.23 (0.88–1.72), 1.09 (0.86–1.38), and 0.86 (0.63–1.17), respectively (p = 0.31), and for the presence of at least one femoral plaque were 1.25 (0.87–1.80), 1.19 (0.93–1.51) and 1.17 (0.86–1.61), respectively (p = 0.39). Conclusions: Middle-aged men reporting 7 h of sleep duration had the lowest prevalence of subclinical coronary atherosclerosis as assessed by CACs. Our results support that men with very short or very long sleep durations are at increased risk of atherosclerosis

Computer-aided laccase engineering: toward biological oxidation of arylamines

Oxidation of arylamines, such as aniline, is of high industrial interest and laccases have been proposed as biocata-lysts to replace harsh chemical oxidants. However, the reaction is hampered by the redox potential of the substrate at acid pH and enzyme engineering is required to improve the oxidation. In this work, instead of trying to improve the redox potential of the en-zyme, we aim towards the (transient) substrate’s one and propose this as a more reliable strategy. We have successfully combined a computational approach with experimental validation to rationally design an improved biocatalyst. The in silico protocol combines classical and quantum mechanics to deliver atomic and electronic level detail on the two main processes involved: substrate binding and electron transfer. After mutant expression and comparison to the parent type, kinetic results show that the protocol accurately predicts aniline’s improved oxidation (2-fold kcat increase) in the engineered variant for biocatalyzed polyaniline production.This study was supported by the INDOX (KBBE-2013-7-613549) EU-project, and the NOESIS (BI0201456388-R) and OxiDesign (CTQ2013-48287-R) Spanish project. GS thanks an FPI grant of the Spanish Ministry of Competitiveness.Peer ReviewedPostprint (author's final draft

Glycated hemoglobin, fasting insulin and the metabolic syndrome in males. Cross-sectional analyses of the aragon workers health study baseline

Background and aims: Glycated hemoglobin (HbA1c) is currently used to diagnose diabetes mellitus, while insulin has been relegated to research. Both, however, may help understanding the metabolic syndrome and profiling patients. We examined the association of HbA1c and fasting insulin with clustering of metabolic syndrome criteria and insulin resistance as two essential characteristics of the metabolic syndrome. Methods: We used baseline data from 3200 non-diabetic male participants in the Aragon Workers' Health Study. We conducted analysis to estimate age-adjusted odds ratios (ORs) across tertiles of HbA1c and insulin. Fasting glucose and Homeostatic model assessment - Insulin Resistance were used as reference. Here we report the uppermost-to-lowest tertile ORs (95%CI). Results: Mean age (SD) was 48.5 (8.8) years and 23% of participants had metabolic syndrome. The ORs for metabolic syndrome criteria tended to be higher across HbA1c than across glucose, except for high blood pressure. Insulin was associated with the criteria more strongly than HbA1c and similarly to Homeostatic model assessment - Insulin Resistance (HOMA-IR). For metabolic syndrome, the OR of HbA1c was 2.68, of insulin, 11.36, of glucose, 7.03, and of HOMA-IR, 14.40. For the clustering of 2 or more non-glycemic criteria, the OR of HbA1c was 2.10, of insulin, 8.94, of glucose, 1.73, and of HOMA-IR, 7.83. All ORs were statistically significant. The areas under the receiver operating characteristics curves for metabolic syndrome were 0.670 (across HbA1c values) and 0.770 (across insulin values), and, for insulin resistance, 0.647 (HbA1c) and 0.995 (insulin). Among non-metabolic syndrome patients, a small insulin elevation identified risk factor clustering. Conclusions: HbA1c and specially insulin levels were associated with metabolic syndrome criteria, their clustering, and insulin resistance. Insulin could provide early information in subjects prone to develop metabolic syndrome

High-quality intake of carbohydrates is associated with lower prevalence of subclinical atherosclerosis in femoral arteries: The AWHS study

Background and aims: High-quality of the carbohydrates consumed, apart from their total amount, appear to protect from cardiovascular disease (CVD). However, the relationship between the quality of carbohydrates and the early appearance of atherosclerosis has not yet been described. Our objective was to estimate the association between the quality of dietary carbohydrates and subclinical atherosclerosis in femoral and carotid arteries. Methods: Cross-sectional study of femoral and carotid atherosclerosis assessed using ultrasounds of 2074 middle-aged males, 50.9 (SD 3.9) years old, with no previous CVD, and pertaining to the Aragon Workers’ Health Study (AWHS) cohort. Food frequency questionnaires were used to calculate a carbohydrate quality index (CQI) defined as: consumption of dietary fiber, a lower glycemic index, the ratio of whole grains/total grains, and the ratio of solid carbohydrates/total carbohydrates. The presence of plaques across four CQI intervals was studied using adjusted logistic regression models. Results: The CQI showed a direct inverse association with subclinical atherosclerosis in femoral territories. Participants with a higher consumption of high-quality carbohydrates (13–15 points) were less likely to have femoral plaques when compared with participants in the lowest index interval (4–6 points) (OR = 0.59; 95% CI = 0.39, 0.89; p = 0.005). No association was found between the CQI and the presence of subclinical atherosclerosis in carotid territories. A lower consumption of high-quality carbohydrates tended to be associated with a greater atherosclerosis extension, considered as the odds for having more affected territories (p = 0.011). Conclusions: Among middle-aged males, a high-quality intake of carbohydrates is associated with a lower prevalence of femoral artery subclinical atherosclerosis when compared with a lower consumption. Thus, indicating an early relationship between the quality of carbohydrates and the development of CVD. © 2021 The Author(s

Harms in Systematic Reviews Paper 2: Methods used to assess harms are neglected in systematic reviews of gabapentin

Objective: We compared methods used with current recommendations for synthesizing harms in systematic reviews and meta-analyses (SRMAs) of gabapentin. Study Design & Setting: We followed recommended systematic review practices. We selected reliable SRMAs of gabapentin (i.e., met a pre-defined list of methodological criteria) that assessed at least one harm. We extracted and compared methods in four areas: pre-specification, searching, analysis, and reporting. Whereas our focus in this paper is on the methods used, Part 2 examines the results for harms across reviews. Results: We screened 4320 records and identified 157 SRMAs of gabapentin, 70 of which were reliable. Most reliable reviews (51/70; 73%) reported following a general guideline for SRMA conduct or reporting, but none reported following recommendations specifically for synthesizing harms. Across all domains assessed, review methods were designed to address questions of benefit and rarely included the additional methods that are recommended for evaluating harms. Conclusion: Approaches to assessing harms in SRMAs we examined are tokenistic and unlikely to produce valid summaries of harms to guide decisions. A paradigm shift is needed. At a minimal, reviewers should describe any limitations to their assessment of harms and provide clearer descriptions of methods for synthesizing harms

Harms in Systematic Reviews Paper 3: Given the same data sources, systematic reviews of gabapentin have different results for harms

Objective: In this methodologic study (Part 2 of 2), we examined the overlap in sources of evidence and the corresponding results for harms in systematic reviews for gabapentin. Study Design & Setting: We extracted all citations referenced as sources of evidence for harms of gabapentin from 70 systematic reviews, as well as the harms assessed and numerical results. We assessed consistency of harms between pairs of reviews with a high degree of overlap in sources of evidence (>50%) as determined by corrected covered area (CCA). Results: We found 514 reports cited across 70 included reviews. Most reports (244/514, 48%) were not cited in more than one review. Among 18 pairs of reviews, we found reviews had differences in which harms were assessed and their choice to meta-analyze estimates or present descriptive summaries. When a specific harm was meta-analyzed in a pair of reviews, we found similar effect estimates. Conclusion: Differences in harms results across reviews can occur because the choice of harms is driven by reviewer preferences, rather than standardized approaches to selecting harms for assessment. A paradigm shift is needed in the current approach to synthesizing harms