Abstract
The COVID-19 pandemic has highlighted the need to come out with quick interventional solutions that can now be obtained through the application of different bioinformatics software to ...actively improve the success rate. Technological advances in fields such as computer modeling and simulation are enriching the discovery, development, assessment and monitoring for better prevention, diagnosis, treatment and scientific evidence generation of specific therapeutic strategies. The combined use of both molecular prediction tools and computer simulation in the development or regulatory evaluation of a medical intervention, are making the difference to better predict the efficacy and safety of new vaccines. An integrated bioinformatics pipeline that merges the prediction power of different software that act at different scales for evaluating the elicited response of human immune system against every pathogen is proposed. As a working example, we applied this problem solving protocol to predict the cross-reactivity of pre-existing vaccination interventions against SARS-CoV-2.
Many pathogenic organisms have an inherent ability to rapidly evolve into new variants, which enables them to escape previously existing immune responses. Vaccine design strategies should be aimed to ...counteract such variability, targeting the conserved antigen regions of the pathogen. Sequence variability analysis allows the identification of conserved regions upon multiple sequence alignments of the relevant antigens. In this chapter, we describe a detailed protocol and provide software to build variability-free proteomes for epitope-vaccine design. The procedure, which will be illustrated for human herpesvirus 1 (HHV1), involves the identification of protein clusters, followed by multiple sequence alignments and Shannon variability calculations. The software required to build variability-free proteomes is available at http://imed.med.ucm.es/software/mmb2019 .
There has recently been an increase in quantification and objective analysis of soccer performance due to improvements in technology using load indexes such as Player Load (PL) and Metabolic Power ...(MP). The objectives of this study were: (1) to describe the performance of PL and MP in competition according to the specific role, match‐to‐ match variation, periods of play, game location and match status according to game periods, and (2) to analyze the relationship between both indexes. Twenty‐one national‐level soccer players were distributed in the following specific positional roles: external defenders (ED) (n = 4), central defenders (CD) (n = 4), midfielders (M) (n = 5), external midfielders (EM) (n = 4) and attackers (A) (n = 4). A total of 12 matches played by a Spanish Third Division team during the 2016/2017 season were analyzed. WIMU PRO
inertial devices (RealTrack System, Almeria, Spain) were used for recording the data. The main results were: (1) a performance reduction in both variables over the course of match time, (2) significant differences in both variables based on the specific position, (3) differences in physical demands during the season matches, (4) winning during a game period and the condition of being the visitor team provoked higher demands, and (5) a high correlation between both variables in soccer. In conclusion, different contextual variables influence the external load demands; both indexes are related so they could be used for external load quantification, and it is necessary to analyze physical demands of the competition for a specific and individualized load design in training sessions.
Epstein-Barr virus is a very common human virus that infects 90% of human adults. EBV replicates in epithelial and B cells and causes infectious mononucleosis. EBV infection is also linked to various ...cancers, including Burkitt’s lymphoma and nasopharyngeal carcinomas, and autoimmune diseases such as multiple sclerosis. Currently, there are no effective drugs or vaccines to treat or prevent EBV infection. Herein, we applied a computer-aided strategy to design a prophylactic epitope vaccine ensemble from experimentally defined T and B cell epitopes. Such strategy relies on identifying conserved epitopes in conjunction with predictions of HLA presentation for T cell epitope selection and calculations of accessibility and flexibility for B cell epitope selection. The T cell component includes 14 CD8 T cell epitopes from early antigens and 4 CD4 T cell epitopes, targeted during the course of a natural infection and providing a population protection coverage of over 95% and 81.8%, respectively. The B cell component consists of 3 experimentally defined B cell epitopes from gp350 plus 4 predicted B cell epitopes from other EBV envelope glycoproteins, all mapping in flexible and solvent accessible regions. We discuss the rationale for the formulation and possible deployment of this epitope vaccine ensemble.
Distinguishing T cell epitope distribution patterns is relevant for epitope-vaccine design. To that end, we invest0069gated the distribution of known CD8 T cell epitopes from Hepatitis C Virus, Human ...Immunodeficiency Virus-1 and Influenza A Virus using χ(2) statistics. We found that epitopes are not distributed in the viral proteomes proportionally to the size of the source proteins. Specifically, capsid and matrix proteins pack significantly more epitopes than those expected by their size. Such non-homogeneous distribution cannot be accounted by underlying MHC I-peptide binding preferences nor it is related to sequence variability. Instead, we propose that it might be related to preferential protein translation/biosynthesis. Overall, these results support the prioritization of structural antigens for epitope identification and vaccine design.
T cell immunity is traditionally assessed through functional recall assays, which detect the consequences of the T cells' antigen encounter, or via fluorescently labeled multimers that selectively ...bind peptide-specific T cell receptors. Using either approach, if the wrong antigen or peptide of a complex antigenic system, such as a virus, is used for immune monitoring, either false negative data will be obtained, or the magnitude of the antigen-specific T cell compartment will go largely underestimated. In this work, we show how selection of the "right" antigen or antigenic peptides is critical for successful T cell immune monitoring against human cytomegalovirus (HCMV). Specifically, we demonstrate that individual HCMV antigens, along with previously reported epitopes, frequently failed to detect CD8+ T cell immunity in test subjects. Through systematic assessment of T cell reactivity against individual nonamer peptides derived from the HCMVpp65 protein, our data clearly establish that (i) systematic testing against all potential epitopes encoded by the genome of the antigen of interest is required to reliably detect CD8+ T cell immunity, and (ii) genome-wide, large scale systematic testing of peptides has become feasible through high-throughput ELISPOT-based "brute force" epitope mapping.
CD8+ T cell immune monitoring aims at measuring the size and functions of antigen-specific CD8+ T cell populations, thereby providing insights into cell-mediated immunity operational in a test ...subject. The selection of peptides for
CD8+ T cell detection is critical because within a complex antigen exists a multitude of potential epitopes that can be presented by HLA class I molecules. Further complicating this task, there is HLA class I polygenism and polymorphism which predisposes CD8+ T cell responses towards individualized epitope recognition profiles. In this study, we compare the actual CD8+ T cell recognition of a well-characterized model antigen, human cytomegalovirus (HCMV) pp65 protein, with its anticipated epitope coverage. Due to the abundance of experimentally defined HLA-A
02:01-restricted pp65 epitopes, and because
epitope predictions are most advanced for HLA-A
02:01, we elected to focus on subjects expressing this allele. In each test subject, every possible CD8+ T cell epitope was systematically covered testing 553 individual peptides that walk the sequence of pp65 in steps of single amino acids. Highly individualized CD8+ T cell response profiles with aleatory epitope recognition patterns were observed. No correlation was found between epitopes' ranking on the prediction scale and their actual immune dominance. Collectively, these data suggest that accurate CD8+ T cell immune monitoring may necessitate reliance on agnostic mega peptide pools, or brute force mapping, rather than electing individual peptides as representative epitopes for tetramer and other multimer labeling of surface antigen receptors.
West Nile Virus (WNV) causes a debilitating and life-threatening neurological disease in humans. Since its emergence in Africa 50 years ago, new strains of WNV and an expanding geographical ...distribution have increased public health concerns. There are no licensed therapeutics against WNV, limiting effective infection control. Vaccines represent the most efficacious and efficient medical intervention known. Epitope-based vaccines against WNV remain significantly underexploited. Here, we use a selection protocol to identify a set of conserved prevalidated immunogenic T cell epitopes comprising a putative WNV vaccine. Experimentally validated immunogenic WNV epitopes and WNV sequences were retrieved from the IEDB and West Nile Virus Variation Database. Clustering and multiple sequence alignment identified a smaller subset of representative sequences. Protein variability analysis identified evolutionarily conserved sequences, which were used to select a diverse set of immunogenic candidate T cell epitopes. Cross-reactivity and human leukocyte antigen-binding affinities were assessed to eliminate unsuitable epitope candidates. Population protection coverage (PPC) quantified individual epitopes and epitope combinations against the world population. 3 CD8+ T cell epitopes (ITYTDVLRY, TLARGFPFV, and SYHDRRWCF) and 1 CD4+ epitope (VTVNPFVSVATANAKVLI) were selected as a putative WNV vaccine, with an estimated PPC of 97.14%.
PDF
