Epitope-Evaluator: an interactive web application to study predicted T-cell epitopes

Multiple immunoinformatic tools have been developed to predict T-cell epitopes from protein amino acid sequences for different major histocompatibility complex (MHC) alleles. These prediction tools output hundreds of potential peptide candidates which require further processing; however, these tools are either not graphical or not friendly for non-programming users. We present Epitope-Evaluator, a web tool developed in the Shiny/R framework to interactively analyze predicted T-cell epitopes. Epitope-Evaluator contains six tools providing the distribution of epitopes across a selected set of MHC alleles, the promiscuity and conservation of epitopes, and their density and location within antigens. Epitope-Evaluator requires as input the fasta file of protein sequences and the output prediction file coming out from any predictor. By choosing different cutoffs and parameters, users can produce several interactive plots and tables that can be downloaded as JPG and text files, respectively. Using Epitope-Evaluator, we found the HLA-B*40, HLA-B*27:05 and HLA-B*07:02 recognized fewer epitopes from the SARS-CoV-2 proteome than other MHC Class I alleles. We also identified shared epitopes between Delta, Omicron, and Wuhan Spike variants as well as variant-specific epitopes. In summary, Epitope-Evaluator removes the programming barrier and provides intuitive tools, allowing a straightforward interpretation and graphical representations that facilitate the selection of candidate epitopes for experimental evaluation. The web server Epitope-Evaluator is available at https://fuxmanlab.shinyapps.io/Epitope-Evaluator/.R35 GM128625 - NIGMS NIH HHSPublished versio

Global landscape of mouse and human cytokine transcriptional regulation

Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through three decades of studies to generate a comprehensive database, CytReg, reporting 843 and 647 interactions between TFs and cytokine genes, in human and mouse respectively. By integrating CytReg with other functional datasets, we determined general principles governing the transcriptional regulation of cytokine genes. In particular, we show a correlation between TF connectivity and immune phenotype and disease, we discuss the balance between tissue-specific and pathogen-activated TFs regulating each cytokine gene, and cooperativity and plasticity in cytokine regulation. We also illustrate the use of our database as a blueprint to predict TF–disease associations and identify potential TF–cytokine regulatory axes in autoimmune diseases. Finally, we discuss research biases in cytokine regulation studies, and use CytReg to predict novel interactions based on co-expression and motif analyses which we further validated experimentally. Overall, this resource provides a framework for the rational design of future cytokine gene regulation studies.National Institutes of Health (NIH) [R00 GM114296 and R35 GM128625 to J.I.F.B., 5T32HL007501-34 to J.A.S.]; National Science Foundation [NSF-REU BIO-1659605 to M.M.]. Funding for open access charge: NIH [R35 GM128625]. (R00 GM114296 - National Institutes of Health (NIH); R35 GM128625 - National Institutes of Health (NIH); 5T32HL007501-34 - National Institutes of Health (NIH); NSF-REU BIO-1659605 - National Science Foundation; R35 GM128625 - NIH)Published versio

Widespread perturbation of ETS factor binding sites in cancer.

Although \u3e90% of somatic mutations reside in non-coding regions, few have been reported as cancer drivers. To predict driver non-coding variants (NCVs), we present a transcription factor (TF)-aware burden test based on a model of coherent TF function in promoters. We apply this test to NCVs from the Pan-Cancer Analysis of Whole Genomes cohort and predict 2555 driver NCVs in the promoters of 813 genes across 20 cancer types. These genes are enriched in cancer-related gene ontologies, essential genes, and genes associated with cancer prognosis. We find that 765 candidate driver NCVs alter transcriptional activity, 510 lead to differential binding of TF-cofactor regulatory complexes, and that they primarily impact the binding of ETS factors. Finally, we show that different NCVs within a promoter often affect transcriptional activity through shared mechanisms. Our integrated computational and experimental approach shows that cancer NCVs are widespread and that ETS factors are commonly disrupted

Extracellular bacterial DNA recognition by human neutrophils: it´s impact on the response to biofilms

Previamente demostramos que el ADN bacteriano extracelular activa a los neutrófilos a través de un mecanismo diferente al canónico CpG-dependiente. El ADN extracelular es un componente central en la formación y estructura de los biofilms bacterianos, comunidades responsables de más del 60% de las infecciones ocasionadas por estos microorganismos. La presente tesis tuvo como objetivos centrales determinar el impacto del ADN de la matriz de los biofilms en la activación de los neutrófilos humanos y la identificaron del receptor involucrado en el reconocimiento de ADN. Los estudios realizados indicaron que la degradación con DNAsa I del ADN de la matriz extracelular de los biofilms de P. aeruginosa redujo marcadamente su capacidad de inducir la activación de los neutrófilos, determinada en función de su habilidad para producir citoquinas proinflamatorias, incrementar marcadores de activación fisiológicamente relevantes, de mediar la fagocitosis y de liberar trampas extracelulares de los neutrófilos (NET). La aplicación de técnicas de MALDI-TOF nos permitió identificar, en el neutrófilo, 16 proteínas con capacidad de unir ADN bacteriano. A pesar de que ninguna de ellas resultó ser el receptor de la superficie celular para ADN, es posible que dos de las proteínas encontradas constituyan sensores intracelulares de ADN, cuya relevancia queda por ser explorada. Los hallazgos realizados en la presente Tesis confirman la existencia de una proteína de la superficie del neutrófilo capaz de mediar el reconocimiento de ADN y la activación celular por esta molécula. Además, indican que el ADN de la matriz extracelular representa un componente proinflamatorio relevante de los biofilms de P. aeruginosa. Los mismos permiten especular que el reconocimiento del ADN de la matriz de biofilms podría representar un mecanismo seleccionado evolutivamente para permitir al huésped incrementar su capacidad de responder a este tipo de infecciones bacterianas persistentesWe have previously demonstrated that extracellular bacterial DNA activates neutrophils through a non-canonical mechanism. Extracelular DNA is a key component in the formation and composition of bacterial biofilms, that are communities responsible for more than 60% of the infections caused by these microorganisms. The aims of this Thesis were to determine the impact of DNA present in the biofilm matrix in triggering human neutrophil activation and to identify the receptor involved in DNA recognition. We found that extracelluar DNA degradation of P. aeruginosa biofilm matrix with DNase I markedly reduced its ability to induce neutrophil activation, determined by evaluating proinflammatoy cytokines production, the increase of physiologically relevant activation markers, phagocytosis and neutrophil extracelullar traps (NET) release. By application of MALDI-TOF techniques we identified 16 neutrophil proteins that bind bacterial DNA. Although none of them proved to be the DNA surface receptor, it is possible that two of these proteins correspond to intracellular DNA sensors whose relevance remains to be explored. The findings presented in this Thesis confirm the existence of a neutrophil surface protein capable of mediating DNA recognition and cell activation. Additionaly, they indicate that extracellular matrix DNA represents a relevant proinflammatory component of P. aeruginosa biofilms. Thus, it is possible to speculate that recognition of extracellular DNA of the biofilm matrix represents an evolutionary selected mechanism that increases the ability of the host to respond to these types of persistent bacterial infections.Fil:Fuxman Bass, Juan Ignacio. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

Flagellin delays spontaneous human neutrophil apoptosis

Neutrophils are short-lived cells that rapidly undergo apoptosis. However, their survival can be regulated by signals from the environment. Flagellin, the primary component of the bacterial flagella, is known to induce neutrophil activation. In this study we examined the ability of flagellin to modulate neutrophil apoptosis. Neutrophils cultured for 12 and 24 h in the presence of flagellin from Salmonella thyphimurim at concentrations found in pathological situations underwent a marked prevention of apoptosis. In contrast, Helicobacter pylori flagellin did not affect neutrophil survival, suggesting that Salmonella flagellin exerts the antiapoptotic effect by interacting with TLR5. The delaying in apoptosis mediated by Salmonella flagellin was coupled to higher expression levels of the antiapoptotic protein Mcl-1 and lower levels of activated caspase-3. Analysis of the signaling pathways indicated that Salmonella flagellin induced the activation of the p38 and ERK1/2 MAPK pathways as well as the PI3K/Akt pathway. Furthermore, it also stimulated IBα degradation and the phosphorylation of the p65 subunit, suggesting that Salmonella flagellin also triggers NF-B activation. Moreover, the pharmacological inhibition of ERK1/2 pathway and NF-B activation partially prevented the antiapoptotic effects exerted by flagellin. Finally, the apoptotic delaying effect exerted by flagellin was also evidenced when neutrophils were cultured with whole heat-killed S. thyphimurim. Both a wild-type and an aflagellate mutant S. thyphimurim strain promoted neutrophil survival; however, when cultured in low bacteria/neutrophil ratios, the flagellate bacteria showed a higher capacity to inhibit neutrophil apoptosis, although both strains showed a similar ability to induce neutrophil activation. Taken together, our results indicate that flagellin delays neutrophil apoptosis by a mechanism partially dependent on the activation of ERK1/2 MAPK and NF-B. The ability of flagellin to delay neutrophil apoptosis could contribute to perpetuate the inflammation during infections with flagellated bacteria.Fil: Salamone, Gabriela Veronica. Academia Nacional de Medicina de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Petracca, Yanina Luján. Academia Nacional de Medicina de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fuxman Bass, Juan Ignacio. Academia Nacional de Medicina de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rumbo, Martín. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biológicas. Laboratorio de Investigaciones del Sistema Inmune; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Nahmod, Karen Amelia. Academia Nacional de Medicina de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Gabelloni, María Laura. Academia Nacional de Medicina de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Vermeulen, Elba Monica. Academia Nacional de Medicina de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Matteo, Mario José. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Geffner, Jorge Raúl. Academia Nacional de Medicina de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Trevani, Analía Silvina. Academia Nacional de Medicina de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentin