An analysis of natural T cell responses to predicted tumor neoepitopes

Personalization of cancer immunotherapies such as therapeutic vaccines and adoptive T-cell therapy may benefit from efficient identification and targeting of patient-specific neoepitopes. However, current neoepitope prediction methods based on sequencing and predictions of epitope processing and presentation result in a low rate of validation, suggesting that the determinants of peptide immunogenicity are not well understood. We gathered published data on human neopeptides originating from single amino acid substitutions for which T cell reactivity had been experimentally tested, including both immunogenic and non-immunogenic neopeptides. Out of 1,948 neopeptide-HLA (human leukocyte antigen) combinations from 13 publications, 53 were reported to elicit a T cell response. From these data, we found an enrichment for responses among peptides of length 9. Even though the peptides had been pre-selected based on presumed likelihood of being immunogenic, we found using NetMHCpan-4.0 that immunogenic neopeptides were predicted to bind significantly more strongly to HLA compared to non-immunogenic peptides. Investigation of the HLA binding strength of the immunogenic peptides revealed that the vast majority (96%) shared very strong predicted binding to HLA and that the binding strength was comparable to that observed for pathogen-derived epitopes. Finally, we found that neopeptide dissimilarity to self is a predictor of immunogenicity in situations where neo- and normal peptides share comparable predicted binding strength. In conclusion, these results suggest new strategies for prioritization of mutated peptides, but new data will be needed to confirm their value.Fil: Bjerregaard, Anne-Mette. Technical University of Denmark; DinamarcaFil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina. Technical University of Denmark; DinamarcaFil: Jurtz, Vanessa. Technical University of Denmark; DinamarcaFil: Barra, Carolina M.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Hadrup, Sine Reker. Technical University of Denmark; DinamarcaFil: Szallasi, Zoltan. Technical University of Denmark; Dinamarca. Harvard Medical School; Estados UnidosFil: Eklund, Aron Charles. Technical University of Denmark; Dinamarc

Innate lymphoid cells integrate stromal and immune signals to enhance antibody production by splenic marginal zone B cells

Innate lymphoid cells (ILCs) regulate stromal, epithelial and immune cells, but their impact on B cells remains unclear. We identified RORγt + ILCs nearby the marginal zone (MZ), a splenic compartment containing innate-like B cells that respond to circulating T cell-independent (TI) antigens. Spenic ILCs established a bidirectional crosstalk with MAdCAM-1 + marginal reticular cells by providing tumor necrosis factor (TNF) and lymphotoxin, and activated MZ B cells via BAFF, CD40 ligand and the Notch ligand, Delta-like 1. Splenic ILCs further helped MZ B cells and their plasma cell progeny by co-opting neutrophils through the release of GM-CSF. Consequently, ILC depletion impaired both pre- and post-immune TI antibody responses. Thus, ILCs integrate stromal and myeloid signals to orchestrate innate-like antibody production at the interface between the immune and circulatory systems

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

patrimonio intelectual

Actas de congresoLas VI Jornadas se realizaron con la exposición de ponencias que se incluyeron en cuatro ejes temáticos, que se desarrollaron de modo sucesivo para facilitar la asistencia, el intercambio y el debate, distribuidos en tres jornadas. Los ejes temáticos abordados fueron: 1. La enseñanza como proyecto de investigación. Recursos de enseñanza-aprendizaje como mejoras de la calidad educativa. 2. La experimentación como proyecto de investigación. Del ensayo a la aplicabilidad territorial, urbana, arquitectónica y de diseño industrial. 3. Tiempo y espacio como proyecto de investigación. Sentido, destino y usos del patrimonio construido y simbólico. 4. Idea constructiva, formulación y ejecución como proyecto de investigación. Búsqueda y elaboración de resultados que conforman los proyectos de la arquitectura y el diseño

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Sinusoid-lining cells are novel myeloid-endothelial innate cells that form splenic niches for marginal zone B cell activation and plasma cell survival

Los sinusoides del bazo humano promueven la lenta percolación de la sangre, favoreciendo la captura de antígeno por los fagocitos y linfocitos del sistema inmune local. Estratégicamente posicionadas delimitando los vasos, e históricamente conocidas como células retículo-endoteliales, las células que delinean los sinusoides (SLCs), tienen una biología enigmática y podrían ser vistas como un componente desconocido del sistema inmunológico. En esta tesis hemos observado que las SLCs poseían un fenotipo simil-endotelial, eran específicas de humano y expresaban moléculas típicamente asociadas al linaje endotelial como el factor de von Willenbrand, y las moléculas CD31, CD54, CD102, CD105 y CD141. Sin embargo, a diferencia de las células endoteliales, las SLCs también expresaban moléculas típicamente asociadas al linaje estromal como la vimentina y la actina de músculo liso, junto con varias moléculas del linaje mieloide como CD14, CD36, CD163, MR, DEC-205 y TLR4. A si mismo, las SLCs evidenciaron una huella genética típicamente macrofágica que incluía sensores microbianos, receptores de tipo “scavenger”, mediadores de la respuesta inmunitaria y reguladores de la fagocitosis y la presentación antigénica. Además de fagocitar antígenos a través de un mecanismo actina-dependiente, las SLCs secretaban BAFF, APRIL, IL-6 y CXCL10, induciendo el reclutamiento, la activación y la supervivencia de células B de la zona marginal, un subtipo celular especializado en la respuesta de anticuerpos frente a antígenos provenientes de la sangre. Por lo tanto, las SLCs son células endoteliomieloides que funcionan como centinelas dotados de funciones fagocíticas y que ayudan en la producción de anticuerpos.Sinusoid vessels promote the slow percolation of venous blood through the red pulp of the spleen, thereby favoring antigen capture by phagocytes and lymphocytes of the local immune system. Strategically positioned around sinusoids and historically known as reticulo-endothelial cells, sinusoid-lining cells (SLCs) have an enigmatic biology and thus can be viewed as an orphan component of our immune system. We found here that SLCs were a human-specific population of endothelial-like cells that expressed typical endothelial molecules such as von Willenbrand factor, CD31 (PECAM-1), CD54 (ICAM-1), CD102 (ICAM-2), CD105 (endoglin) and CD141 (thrombomodulin). However, unlike endothelial cells, SLCs also expressed the stromal molecules vimentin and smooth muscle actin along with several myeloid molecules such as CD14, CD36, CD163, MR, DEC-205 and TLR4. Accordingly, SLCs showed a prominent macrophage-like gene signature that included microbial sensors, scavanger receptors, immune mediators, and regulators of phagocytosis and antigen presentation. Besides phagocytosing particulate antigens through an actin-dependent mechanism, SLCs released BAFF, APRIL, IL-6 and CXCL10, which enhanced the recruitment, activation and survival of marginal zone (MZ) B cells, a splenic lymphocyte subset specialized in innate-like antibody responses to blood-borne antigens. Thus, SLCs are endothelialmyeloid cells that serve as sentinels endowed with phagocytic and antibody-enhancing functions

Galacto-Configured Aminocyclitol Phytoceramides Are Potent in Vivo Invariant Natural Killer T Cell Stimulators

A new class of α-galactosylceramide (αGC) nonglycosidic analogues bearing galacto-configured aminocyclitols as sugar surrogates have been obtained. The aminocyclohexane having a hydroxyl substitution pattern similar to an α-galactoside is efficiently obtained by a sequence involving Evans aldol reaction and ring-closing metathesis with a Grubbs catalyst to give a key intermediate cyclohexene, which has been converted in galacto-aminocyclohexanes that are linked through a secondary amine to a phytoceramide lipid having a cerotyl N-acyl group. Natural Killer T (NKT) cellular assays have resulted in the identification of an active compound, HS161, which has been found to promote NKT cell expansion in vitro in a similar fashion but more weakly than αGC. This compound stimulates the release of Interferon-γ (IFNγ) and Interleukin-4 (IL-4) in iNKT cell culture but with lower potency than αGC. The activation of Invariant Natural Killer T (iNKT) cells by this compound has been confirmed in flow cytometry experiments. Remarkably, when tested in mice, HS161 selectively induces a very strong production of IFN-γ indicative of a potent Th1 cytokine profile. Overall, these data confirm the agonist activity of αGC lipid analogues having charged amino-substituted polar heads and their capacity to modulate the response arising from iNKT cell activation in vivo.This work was supported by MICINN (Project CTQ2008–01426/BQU), Fondos Feder (EU), Generalitat de Catalunya (2005SGR01063), UAB (PRP2007–06), and CSIC (200480E561). The authors thank E. Dalmau for HRMS analysis and Dr, M. Egido-Gabas and Dr. Amaya Castro for analytical support. Y.H. thanks MICINN for a Juan de la Cierva fellowship.Peer reviewe

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes

Personalization of cancer immunotherapies such as therapeutic vaccines and adoptive T-cell therapy may benefit from efficient identification and targeting of patient-specific neoepitopes. However, current neoepitope prediction methods based on sequencing and predictions of epitope processing and presentation result in a low rate of validation, suggesting that the determinants of peptide immunogenicity are not well understood. We gathered published data on human neopeptides originating from single amino acid substitutions for which T cell reactivity had been experimentally tested, including both immunogenic and non-immunogenic neopeptides. Out of 1,948 neopeptide-HLA (human leukocyte antigen) combinations from 13 publications, 53 were reported to elicit a T cell response. From these data, we found an enrichment for responses among peptides of length 9. Even though the peptides had been pre-selected based on presumed likelihood of being immunogenic, we found using NetMHCpan-4.0 that immunogenic neopeptides were predicted to bind significantly more strongly to HLA compared to non-immunogenic peptides. Investigation of the HLA binding strength of the immunogenic peptides revealed that the vast majority (96%) shared very strong predicted binding to HLA and that the binding strength was comparable to that observed for pathogen-derived epitopes. Finally, we found that neopeptide dissimilarity to self is a predictor of immunogenicity in situations where neo- and normal peptides share comparable predicted binding strength. In conclusion, these results suggest new strategies for prioritization of mutated peptides, but new data will be needed to confirm their value

Study of Fatty Acids Profile in Biological Sample by Capillary Zone Electrophoresis Associate to Chemometric Approach

The determination of fatty acids (FA) in liver from three different groups of Wistar rats (six rats by group) submitted to diet (AIN-93G) by capillary zone electrophoresis (CZE) was proposed. Each group received the same diet. However, the soybean oil used to prepare the feed, whose amount was 7% w/w, had different origins. The first group was fed with feed containing soybean oil fresh; the second one was fed with soybean used during 7 days in deep frying process; finally, the third was fed with soybean used during 15 days in deep frying process. After 45 days the rats were submitted to euthanasia and the FA amount in liver was successful monitored by CZE in a simple, fast and efficient way. The results obtained were compared to gas chromatography official method and no significant differences were observed within 95% confidence interval. The electropherograms to FA analysis were submitted to principal component analysis (PCA) being possible to discriminate the final from the control and intermediate groups. In addition to PCA results, the low density lipoprotein (LDL) was evaluated indicating that the total time exposure of the oil submitted to deep frying processes can be considered relevant to evaluating the oil quality