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Understanding Prediction Systems for HLA-Binding Peptides and T-Cell Epitope Identification [chapter]

Liwen You, Ping Zhang, Mikael Bodén, Vladimir Brusic
Lecture Notes in Computer Science  
The analysis of known T-cell epitopes of survivin and known HIV T-cell epitopes showed lack of correlation between binding affinity and immunogenicity of HLA-presented peptides.  ...  Peptide binding to HLA molecules is a critical step in induction and regulation of T-cell mediated immune responses.  ...  LY was supported by the National Research School in Genomics and Bioinformatics, Sweden. The authors acknowledge the support of the ImmunoGrid project, EC contract FP6-2004-IST-4, No. 028069.  ... 
doi:10.1007/978-3-540-75286-8_32 fatcat:zlv6qujpmnbjjbdr74qfj7ao4q

The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction

Amanda L. Creech, Ying S. Ting, Scott P. Goulding, John F.K. Sauld, Dominik Barthelme, Michael S. Rooney, Terri A. Addona, Jennifer G. Abelin
2018 Proteomics  
Currently, predictive algorithms are used to infer binding of peptides to human leukocyte antigen (HLA) heterodimers to aid in the selection of putative epitope targets.  ...  As such, these advances have enabled MS profiling of HLA-binding peptides to be a tractable, orthogonal approach to lower throughput biochemical assays for generating comprehensive datasets to train epitope  ...  ., and J.G.A. contributed equally to this work. The authors thank all the thought leaders for their work and contributions to the field of MHC epitope identification, specifically Donald F.  ... 
doi:10.1002/pmic.201700259 pmid:29314742 pmcid:PMC6033110 fatcat:didsinuuqrf2bojth7wvhbrtce

T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles

Luca Hensen, Patricia T. Illing, Louise C. Rowntree, Jane Davies, Adrian Miller, Steven Y. C. Tong, Jennifer R. Habel, Carolien E. van de Sandt, Katie L. Flanagan, Anthony W. Purcell, Katherine Kedzierska, E. Bridie Clemens
2022 Frontiers in Immunology  
Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different  ...  Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses.  ...  Nonetheless, the large majority of in silico SARS-CoV-2 studies have predicted T cell epitopes using existing peptide-HLA binding prediction methods, which benefit from years of peptide-HLA research.  ... 
doi:10.3389/fimmu.2022.812393 pmid:35603215 pmcid:PMC9121770 fatcat:h7hpc26htzhjlcmlsrzb4fob6e

Identification of CD8+ T Cell Epitopes Against Mycobacterium tuberculosis [chapter]

Fei Chen, Yanfeng Gao, Yuanming Qi
2012 Understanding Tuberculosis - Analyzing the Origin of Mycobacterium Tuberculosis Pathogenicity  
It includes: selection of the antigens; Prediction the CD8 + T cell epitopes; Synthesis and modification of the epitopes; Identification of epitopes by in vitro and in vivo assays; Development of CD8 +  ...  The MHC-I transfected cell line binding assay was utilized in many labs for its simplicity, repeatability and quantifiability for determining peptide and MHC-binding affinities [25, 32] .  ... 
doi:10.5772/30644 fatcat:w5uxydjv2jg5de2matvvjekilu

Immunoinformatics and Structural Analysis for Identification of Immunodominant Epitopes in SARS-CoV-2 as Potential Vaccine Targets

Sumit Mukherjee, Dmitry Tworowski, Rajesh Detroja, Sunanda Biswas Mukherjee, Milana Frenkel-Morgenstern
2020 Vaccines  
The identification of immunodominant epitopes for both B- and T-cells that induce protective responses in the host is crucial for effective vaccine design.  ...  Regions from SARS-CoV-2 protein sequences were defined as immunodominant, based on the following three criteria regarding B- and T-cell epitopes: (i) they were both mapped, (ii) they predicted protective  ...  Acknowledgments: We are thankful to Chaim Putterman and Karl Skorecki for critically reading the manuscript and all members of the Cancer Genomics and BioComputing of Complex Diseases Lab for discussions  ... 
doi:10.3390/vaccines8020290 pmid:32526960 fatcat:c66a4ciikbh2znedizo4zqky7q

The identification of potentially pathogenic and therapeutic epitopes from common human allergens

Véronique Schulten, Carla Oseroff, Rafeul Alam, David Broide, Pandurangan Vijayanand, Bjoern Peters, Alessandro Sette
2013 Annals of Allergy, Asthma & Immunology  
Acknowledgments Financial support: This work was supported by National Institutes of Allergy and Infectious diseases Contract HSN272200700048C (to A.S.) and Grant U19AI100275 (to A.S.)  ...  Validation of an approach for epitope identification based on bioinformatic prediction of promiscuous HLA binding Next, the restricting HLA locus was identified using anti-DR, DP or DQ antibodies.  ...  Next, the predictive strategy defined in the TG model system was utilized to identify promiscuous HLA class II binding peptides from the various allergen sources.  ... 
doi:10.1016/j.anai.2012.10.015 pmid:23244651 pmcid:PMC3547526 fatcat:ddekx43h6bawfo3u5xtj523u3u

Identification of T-cell epitopes for cancer immunotherapy

J H Kessler, C J M Melief
2007 Leukemia  
and T-helper cell epitopes within known antigens.  ...  Computer algorithms that in silico predict HLA class I and class II binding, proteasome cleavage patterns and transporter associated with antigen processing translocation are now available to expedite  ...  finding of MHC-specific peptide-binding motifs 3 and the identification of the first human leukocyte antigen (HLA) class I presented tumorspecific cytotoxic T lymphocyte (CTL) epitope, 4, 5 T-cell-mediated  ... 
doi:10.1038/sj.leu.2404787 pmid:17611570 fatcat:3nv7xaba2nd43h4p6zf5vmj3ru

Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?

Claus Lundegaard, Ole Lund, Morten Nielsen
2012 Expert Review of Vaccines  
Prediction methods as well as experimental methods for T-cell epitope discovery have developed significantly in recent years.  ...  MHC binding prediction methods are today of a very high quality and can predict MHC binding peptides with high accuracy.  ...  As data increase and prediction methods develop, a much greater understanding will emerge on what defines a dominant T-cell epitope.  ... 
doi:10.1586/erv.11.160 pmid:22149708 pmcid:PMC3297080 fatcat:tscymvsxafepvkcuifa4tg2iba

Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens

K.N. Srinivasan, G.L. Zhang, A.M. Khan, J.T. August, V. Brusic
2004 Bioinformatics  
We have developed a system that not only identifies high binding T-cell antigenic epitopes, but also class I T-cell antigenic clusters termed immunological hot spots.  ...  For illustration of its utility we applied MULTIPRED for prediction of promiscuous T-cell epitopes in all four SARS coronavirus structural proteins.  ...  The authors are also grateful to the Agency for Science, Technology and Research, Singapore.  ... 
doi:10.1093/bioinformatics/bth943 pmid:15262812 fatcat:ebmr7synkvedxavynpup6h4xcq

Potential T cell epitopes of Mycobacterium tuberculosis that can instigate molecular mimicry against host: implications in autoimmune pathogenesis

Sathi Babu Chodisetti, Pradeep K Rai, Uthaman Gowthaman, Susanta Pahari, Javed N Agrewala
2012 BMC Immunology  
Conclusions: The present study reveals many target proteins and their putative T cell epitopes that might have significant application in understanding the molecular basis of possible T cell autoimmune  ...  Results: Employing bioinformatics tools, we have identified potentially cross-reactive T cell epitopes restricted to predominant class I and II alleles of human leukocyte antigens (HLA).  ...  Acknowledgements The authors thank Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology (DBT), India, for financial support.  ... 
doi:10.1186/1471-2172-13-13 pmid:22435930 pmcid:PMC3359254 fatcat:xmhdagh3hjfbhkernbeixir5da

Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV

Yanbo Lv, Zhihua Ruan, Li Wang, Bing Ni, Yuzhang Wu
2009 BMC Immunology  
Results: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage.  ...  Four of eight candidate peptides were tested by HLA-A*0201 binding assays.  ...  The simultaneous prediction of MHC binding and proteasomal cleavage sites in an antigenic sequence leads to the identification of potential T-cell epitopes.  ... 
doi:10.1186/1471-2172-10-61 pmid:19958537 pmcid:PMC2792222 fatcat:r3ka2omkkrfkpj5cvzeb337g44

Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research

Hong Lin, Guang Zhang, Songsak Tongchusak, Ellis L Reinherz, Vladimir Brusic
2008 BMC Bioinformatics  
These peptides (HLA-II T-cell epitopes) are increasingly important as research targets for the development of vaccines and immunotherapies.  ...  Current predictive capabilities allow prediction of only 50% of actual T-cell epitopes using practical thresholds.  ...  Acknowledgements This work was supported by the ImmunoGrid project, under EC contract FP6-2004-IST-4, No. 028069, and NIH grant U19 A157330.  ... 
doi:10.1186/1471-2105-9-s12-s22 pmid:19091022 pmcid:PMC2638162 fatcat:sslcy6x4lbf4jhx2djzqb4edey

The ultimate mix and match: making sense of HLA alleles and peptide repertoires

David K Cole
2015 Immunology and Cell Biology  
and/or peptide-binding preferences. 7, 8 These methods have helped to predict potential peptide epitopes for different HLAI molecules and have contributed to our understanding of HLAI-mediated disease  ...  To conclude, classification of HLAI alleles and identification of peptide epitopes is a highly complex but important pursuit, with attendant implications for vaccine design, predicting tissue matches for  ... 
doi:10.1038/icb.2015.40 pmid:25823993 fatcat:rovbkz2zdvfsrglco4hw3md5wi

Bridging Computational Vaccinology and Vaccine Development Through Systematic Identification, Characterization, and Downselection of Conserved and Variable Circumsporozoite Protein CD4 T Cell Epitopes From Diverse Plasmodium falciparum Strains

Amy R. Noe, Frances E. Terry, Brian C. Schanen, Emily Sassano, Pooja Hindocha, Timothy W. Phares, Leonard Moise, Jayne M. Christen, Kenneth D. Tucker, Vinayaka Kotraiah, Donald R. Drake, William D. Martin (+2 others)
2021 Frontiers in Immunology  
A subset of these predicted class II epitope clusters was synthesized as peptides and assessed for HLA-DR binding in vitro.  ...  Specifically, we developed a systematic workflow to identify peptide sequences capable of binding HLA-DR in a context relevant to achieving broad human population coverage utilizing cognate T cell help  ...  ACKNOWLEDGMENTS The authors acknowledge Lorraine Soisson and Robin Miller for their critical review of the manuscript, and Jessica Smith for technical support.  ... 
doi:10.3389/fimmu.2021.689920 pmid:34168657 pmcid:PMC8217813 fatcat:4z5mpfj5ojapvl6ujht5rpiru4

T-cell epitope vaccine design by immunoinformatics

A. Patronov, I. Doytchinova
2013 Open Biology  
T-cell epitopes The epitope is recognizable by the immune system part of the antigen, and in particular by antibodies, B cells or T cells.  ...  One of the key issues in T-cell epitope prediction is the prediction of MHC binding, as it is considered a prerequisite for T cell recognition.  ... 
doi:10.1098/rsob.120139 pmid:23303307 pmcid:PMC3603454 fatcat:7jqqswcnafailh5r4p2wqnkgha
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