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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.  ...  We have developed a scoring scheme for identification of immunological hot spots for HLA class I molecules, which is the sum of the highest four predictions within a window of 30 amino acids.  ...  1/55/20/282 (KNS, GZ, JTA, VB); and the National University of Singapore Graduate Scholarship (AMK).  ... 
doi:10.1093/bioinformatics/bth943 pmid:15262812 fatcat:ebmr7synkvedxavynpup6h4xcq

IgE-binding epitopes: a reappraisal

R. C. Aalberse, R. Crameri
2011 Allergy. European Journal of Allergy and Clinical Immunology  
Although the original definition of an epitope was coined for antigen-antibody interactions, it was later on applied also to describe the interactions between T cells and peptides recognized by the T-cell  ...  For a recent discussion on the effect of water exclusion from hot spots in protein-protein interactions, see Morena et al. (10) and Li and Li (11) .  ...  Conflicts of interest The authors have no conflict of interest to declare.  ... 
doi:10.1111/j.1398-9995.2011.02656.x pmid:21623828 fatcat:krntiqvxqfhizdlt4dkkwbnw6u

Variations in BK Polyomavirus Immunodominant Large Tumor Antigen-Specific 9mer CD8 T-Cell Epitopes Predict Altered HLA-Presentation and Immune Failure

Karoline Leuzinger, Amandeep Kaur, Maud Wilhelm, Hans Hirsch
2020 Viruses  
We investigated the variation of LTag-epitopes and their predicted effects on HLA-class 1 binding and T-cell activation.  ...  We focused on BKPyV-specific CD8 T-cells as key effectors and characterized immunodominant 9mer epitopes in the viral large tumor-antigen (LTag).  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/v12121476 pmid:33371492 pmcid:PMC7767524 fatcat:3peehnfdrvc4tf2mihvda4t3me

Discordant Brucella melitensis Antigens Yield Cognate CD8+ T Cells In Vivo

M. A. Durward, J. Harms, D. M. Magnani, L. Eskra, G. A. Splitter
2009 Infection and Immunity  
Two H-2 d CD8 ؉ T-cell epitopes have been characterized, and a group of immunogenic proteins have provoked gamma interferon production by CD8 ؉ T cells.  ...  Discovering the epitope containing antigens recognized by Brucella-specific CD8 ؉ T cells and correlating them with microarray data will aid in determining proteins critical for vaccine development that  ...  Sidney in the Division of Vaccine Discovery, La Jolla Institute of Allergy and Immunology (LIAI), for their critical review of the manuscript and access to their MHC binding lab.  ... 
doi:10.1128/iai.00994-09 pmid:19884330 pmcid:PMC2798188 fatcat:o3vrxjgnsng7hgic2dsyldzupe

Neoantigen Targeting—Dawn of a New Era in Cancer Immunotherapy?

Thomas C. Wirth, Florian Kühnel
2017 Frontiers in Immunology  
Also, it has to be taken into consideration that prediction of MHC class II epitopes is in general more error-prone than prediction of MHC class I epitopes.  ...  endogenous MHC class I and class II peptides that are already present on antigen-presenting cells.  ...  Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest  ... 
doi:10.3389/fimmu.2017.01848 pmid:29312332 pmcid:PMC5742119 fatcat:c4cns3xo2vee5fpp3hcrvfp2fq

Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1

Peter D. Kwong, Gwo-Yu Chuang, Brandon J. DeKosky, Tatyana Gindin, Ivelin S. Georgiev, Thomas Lemmin, Chaim A. Schramm, Zizhang Sheng, Cinque Soto, An-Suei Yang, John R. Mascola, Lawrence Shapiro
2017 Immunological Reviews  
To address this issue, we have undertaken an informatics-based approach to understand the genetic and immunologic processes controlling the development of HIV-1-neutralizing antibodies.  ...  As DNA sequencing comprises the fastest growing database of biological information, we focused on incorporating next-generation sequencing of B-cell transcripts to determine the origin, maturation pathway  ...  complex Free-energy perturbation calculations • Design of antibodies with superior neutralization potencies • Identification of functional 'hot spots' at the antibody- antigen interfaces  ... 
doi:10.1111/imr.12480 pmid:28133812 pmcid:PMC5516196 fatcat:ycalmvyminde7pineysmuzl5ne

Neoantigen-Specific Adoptive Cell Therapies for Cancer: Making T-Cell Products More Personal

Valentina Bianchi, Alexandre Harari, George Coukos
2020 Frontiers in Immunology  
The implementation of an isolation step, prior to T-cell in vitro expansion and reinfusion, may provide a way to improve the overall response rates achieved to date by adoptive T-cell therapies in metastatic  ...  The promising clinical outcomes of tumor-infiltrating lymphocyte (TIL) therapy have spurred interest in generating T-cell infusion products that have been selectively enriched in neoantigen (or autologous  ...  hot spots in solid tumors (127) (128) (129) (130) .  ... 
doi:10.3389/fimmu.2020.01215 pmid:32695101 pmcid:PMC7333784 fatcat:p6vl24lqfza5tcpb3zlv5w62by

Therapeutic Effectiveness of Recombinant Cancer Vaccines Is Associated with a Prevalent T-Cell Receptor α Usage by Melanoma-specific CD8+T Lymphocytes

Raffaele De Palma, Ilaria Marigo, Francesco Del Galdo, Carmela De Santo, Paolo Serafini, Sara Cingarlini, Thomas Tüting, Julia Lenz, Giuseppe Basso, Gabriella Milan, Paola Zanovello, Vincenzo Bronte
2004 Cancer Research  
Successful therapy correlated strictly with the skewing of the T-cell receptor repertoire of tetramersorted, TRP-2-specific CD8 ؉ T lymphocytes, which showed a preferential ␣ chain usage with a common  ...  To define surrogate end points predictive of the therapeutic efficacy of recombinant vaccines based on melanoma antigen tyrosinase-related protein (TRP)-2, we evaluated several properties of antigen-specific  ...  ACKNOWLEDGMENTS The authors would like to thank Susanna Mandruzzato and Jack Gorski for helpful discussions and critical reading of the manuscript, Pierantonio Gallo for assistance with graphics, Vito  ... 
doi:10.1158/0008-5472.can-04-0067 pmid:15520218 fatcat:624wvzuhqnhqhp57luayrfc65q

Endoplasmic reticulum chaperones stabilize ligand-receptive MR1 molecules for efficient presentation of metabolite antigens

Hamish E. G. McWilliam, Jeffrey Y. W. Mak, Wael Awad, Matthew Zorkau, Sebastian Cruz-Gomez, Hui Jing Lim, Yuting Yan, Sam Wormald, Laura F. Dagley, Sidonia B. G. Eckle, Alexandra J. Corbett, Haiyin Liu (+8 others)
2020 Proceedings of the National Academy of Sciences of the United States of America  
The antigen-presenting molecule MR1 (MHC class I-related protein 1) presents metabolite antigens derived from microbial vitamin B2 synthesis to activate mucosal-associated invariant T (MAIT) cells.  ...  This pool is the primary source of MR1 molecules for the presentation of exogenous metabolite antigens to MAIT cells.  ...  The antigen-presenting molecule MR1 (MHC class I-related protein 1) presents metabolite antigens derived from microbial vitamin B 2 synthesis to activate mucosal-associated invariant T (MAIT) cells.  ... 
doi:10.1073/pnas.2011260117 pmid:32958637 fatcat:5vkuh5fovjhd5ndi7hmhy5mxiy

Making a Cold Tumor Hot: The Role of Vaccines in the Treatment of Glioblastoma

Stephen C. Frederico, John C. Hancock, Emily E. S. Brettschneider, Nivedita M. Ratnam, Mark R. Gilbert, Masaki Terabe
2021 Frontiers in Oncology  
Several factors for this have been identified, one of which is that GBMs are immunologically "cold," implying that the cancer does not induce a strong T cell response.  ...  While it is well established that anti-cancer T cell responses can be facilitated by the presentation of tumor-specific antigens to the immune system, treatment-related death of GBM cells and subsequent  ...  ACKNOWLEDGMENTS This research was supported by the Intramural Research Program of the NIH, National Cancer Institute, the Center for Cancer Research, and the NIH Medical Research Scholars Program (a public-private  ... 
doi:10.3389/fonc.2021.672508 pmid:34041034 pmcid:PMC8141615 fatcat:w7imxanuebcjpekajnb4w4akpy

Scientific Opinion on the assessment of allergenicity of GM plants and microorganisms and derived food and feed

2010 EFSA Journal  
The weight-of-evidence, case-by-case approach is considered the most appropriate way of assessing the allergenicity of genetically modified (GM) food and feed.  ...  aspects of GM food and feed and in silico approaches, as well as IgE binding studies and cell-based methods, profiling techniques and animal models.  ...  T-cell epitope prediction algorithms There are several bioinformatics tools available for identification of T-cell epitopes to certain specific MHC alleles including those of MHC class II, such as MULTIPRED  ... 
doi:10.2903/j.efsa.2010.1700 fatcat:gikpgvgp3jgdrhacqv4d3nvyxu

Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy

Dinler A. Antunes, Maurício M. Rigo, Martiela V. Freitas, Marcus F. A. Mendes, Marialva Sinigaglia, Gregory Lizée, Lydia E. Kavraki, Liisa K. Selin, Markus Cornberg, Gustavo F. Vieira
2017 Frontiers in Immunology  
(29) , the implications of such "hot-spots" for cross-reactivity prediction are clear.  ...  Moreover, although we tend to think of these hot-spots as pMHC amino acid residues, we need to expand this concept to Structural Basis for T-Cell Cross-reactivity Frontiers in Immunology | www.frontiersin.org  ... 
doi:10.3389/fimmu.2017.01210 pmid:29046675 pmcid:PMC5632759 fatcat:e4y6gmbwxrhabbvq4j5o36lvxu

The major histocompatibility complex a la carte: are there analogies to plant disease resistance genes on the menu?

Jeffery L. Dangl
1992 The Plant Journal  
Indeed, recent evidence defines several recombinational hot spots in the mouse MHC.  ...  Jr, Marshall, G.R. and Unanue, E.R. (1987) identification of the T-cell and la contact residues of a T-cell antigenic epitope. Nature, 327, 713-715.  ... 
doi:10.1111/j.1365-313x.1992.00003.x fatcat:ufnfihhs7zcrnnilbvmheo4f4e

Nanomedicine and Onco-Immunotherapy: From the Bench to Bedside to Biomarkers

Vanessa Acebes-Fernández, Alicia Landeria-Viñuela, Pablo Juanes-Velasco, Angela-Patricia Hernández, Andrea Otazo-Perez, Raúl Manzano-Román, Rafael Gongora, Manuel Fuentes
2020 Nanomaterials  
Conflicts of Interest: The authors declare no conflict of interest  ...  These T cell auto-epitopes can be identified from MHC class I molecules [378] .  ...  Currently only peptides presented in MHC-I can be predicted, as prediction of CD4 T cell epitopes by algorithms is still limited [347] .  ... 
doi:10.3390/nano10071274 pmid:32610601 pmcid:PMC7407304 fatcat:7urjp2bjs5asxcfboaakb2qonm

Current Challenges in Vaccinology

Richard B. Kennedy, Inna G. Ovsyannikova, Peter Palese, Gregory A. Poland
2020 Frontiers in Immunology  
Informed by recent insights into pathogen biology, host genetic diversity, and immunology, the increasing use of genomic approaches is leading to new models and understanding of host immune system responses  ...  Several of these challenges include an incomplete understanding of how immunity develops, host and pathogen genetic variability, and an increased societal skepticism regarding vaccine safety.  ...  Likewise, synergistic effects of tapasin gene polymorphisms and specific HLA class I alleles to generate stronger anti-viral CD8+ T cell responses have been observed.  ... 
doi:10.3389/fimmu.2020.01181 pmid:32670279 pmcid:PMC7329983 fatcat:vbue2juffrfm5gqyfnihr7hfqm
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