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Proteome Sampling by the HLA Class I Antigen Processing Pathway

Ilka Hoof, Debbie van Baarle, William H. Hildebrand, Can Keşmir, Bjoern Peters
2012 PLoS Computational Biology  
The peptide repertoire that is presented by the set of HLA class I molecules of an individual is formed by the different players of the antigen processing pathway and the stringent binding environment  ...  of the HLA class I molecules.  ...  We thank Rob de Boer and Ronald Bontrop for critical review of the manuscript, and Hugo Meiring and Stefan Stevanovic for insightful discussions on peptide identification by mass spectrometry.  ... 
doi:10.1371/journal.pcbi.1002517 pmid:22615552 pmcid:PMC3355062 fatcat:7rdsr7duhreqhjq53chw3cb5aa

Alterations in HLA Class I-Presented Immunopeptidome and Class I-Interactome upon Osimertinib Resistance in EGFR Mutant Lung Adenocarcinoma

Yue A. Qi, Tapan K. Maity, Shaojian Gao, Tao Gong, Meriam Bahta, Abhilash Venugopalan, Xu Zhang, Udayan Guha
2021 Cancers  
resistant EGFR mutant lung adenocarcinoma by interrogating the alterations in the human leukocyte antigen (HLA) Class I-presented immunopeptidome, Class I-interactome, and the whole cell proteome between  ...  Our dataset also includes ~1000 novel HLA class I interaction partners and hundreds of Class I-presented immunopeptides in EGFR mutant lung adenocarcinoma.  ...  Acknowledgments: The authors thank Nitin Roper for providing assistance in in silico HLA typing.  ... 
doi:10.3390/cancers13194977 pmid:34638461 fatcat:ze6t54jawjaghk2z3dbmakmebi

Proteomics show antigen presentation processes in human immune cells after AS03-H5N1 vaccination

Allison C. Galassie, Johannes B. Goll, Parimal Samir, Travis L. Jensen, Kristen L. Hoek, Leigh M. Howard, Tara M. Allos, Xinnan Niu, Laura E. Gordy, C. Buddy Creech, Heather Hill, Sebastian Joyce (+2 others)
2017 Proteomics  
While comparison between temporal proteomic and transcriptomic results showed little overlap overall, enrichment of the MHC Class I antigen processing and presentation pathway in monocytes and neutrophils  ...  HLA Class I proteins was increased in the AS03 group.  ...  While HLA Class I protein encoding genes were slightly up-regulated but not significantly DE in the SV-AS03 group in monocytes, the Class I MHC-mediated antigen processing and presentation pathway was  ... 
doi:10.1002/pmic.201600453 pmid:28508465 pmcid:PMC5736144 fatcat:4kh2mhgjkzbodbzfgwv7tolz7u

Biogenesis of HLA Ligand Presentation in Immune Cells Upon Activation Reveals Changes in Peptide Length Preference

Fabio Marino, Aikaterini Semilietof, Justine Michaux, Hui-Song Pak, George Coukos, Markus Müller, Michal Bassani-Sternberg
2020 Frontiers in Immunology  
dendritic cells; DCs), the functionality of the antigen processing and presentation machinery (APPM), and the repertoire of HLA class I and II-bound peptides (termed immunopeptidome) presented to T cells  ...  So far, how molecular perturbations underlying DCs maturation and differentiation affect the in vivo cross-presented HLA class I and II immunopeptidomes is largely unknown.  ...  Supplementary Figure 6 | Proteomics expression of processing enzymes possibly involved in HLA class II pathway.  ... 
doi:10.3389/fimmu.2020.01981 pmid:32983136 pmcid:PMC7485268 fatcat:gkvgmp6v3farnbd6btask5df3i

Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome ProceedsViaHigh Specificity

Geert P. M. Mommen, Fabio Marino, Hugo D. Meiring, Martien C. M. Poelen, Jacqueline A. M. van Gaans-van den Brink, Shabaz Mohammed, Albert J. R. Heck, Cécile A. C. M. van Els
2016 Molecular & Cellular Proteomics  
displayed by the HLA-DR ligandome.  ...  Important selective sieving from the sampled proteome to the ligandome was evidenced by specificity in the sequences of the core regions both at their N-and C-termini, hence not only reflecting binding  ...  Therefore, most studies including ours substantiate the selective sampling of proteome cargo for both HLA class I and class II molecules on their way to the cell surface.  ... 
doi:10.1074/mcp.m115.055780 pmid:26764012 pmcid:PMC4824864 fatcat:vdpdv33x5jdcbmvvhe2c3ovt5q

Transmembrane Helices Are an Overlooked Source of Major Histocompatibility Complex Class I Epitopes

Frans Bianchi, Johannes Textor, Geert van den Bogaart
2017 Frontiers in Immunology  
This raises the question how membrane proteins are processed for MHC-I (cross-)presentation, with current research focusing on soluble antigens.  ...  About a fourth of the human proteome is anchored by transmembrane helices (TMHs) to lipid membranes.  ...  If and how these pathways contribute to MHC class I (MHC-I) presentation is unclear.  ... 
doi:10.3389/fimmu.2017.01118 pmid:28959259 pmcid:PMC5604083 fatcat:3cykznpo6vhl3phcppwstnzqdi

Novel identified aluminum hydroxide-induced pathways prove monocyte activation and pro-inflammatory preparedness

Sietske Kooijman, Jolanda Brummelman, Cécile A.C.M. van Els, Fabio Marino, Albert J.R. Heck, Geert P.M. Mommen, Bernard Metz, Gideon F.A. Kersten, Jeroen L.A. Pennings, Hugo D. Meiring
2018 Journal of Proteomics  
like TLR or NOD1 activation, and second the HLA class I antigen processing and presentation pathway.  ...  Class-I and Class-II antigen presenting pathways induced by IFNγ.  ...  We acknowledge Hilde Vrieling for performing the autofluorescent verification experiments for the flow cytometry data and for the THP-1 set up experiments.  ... 
doi:10.1016/j.jprot.2017.12.021 pmid:29317357 fatcat:h6zae2pcofd6dc4bzksxesiafa

Diversity of Natural Self-Derived Ligands Presented by Different HLA Class I Molecules in Transporter Antigen Processing-Deficient Cells

Elena Lorente, Susana Infantes, Eilon Barnea, Ilan Beer, Alejandro Barriga, Noel García-Medel, Fátima Lasala, Mercedes Jiménez, Arie Admon, Daniel López, Valli De Re
2013 PLoS ONE  
by four different HLA-A, -B, and -C class I molecules with very different TAP dependency from the same cell line.  ...  (HLA) class I molecules.  ...  David Yu (University of California, Los Angeles, CA) for the cell lines and Dr. B. De Andre ´s for critical reading of the manuscript.  ... 
doi:10.1371/journal.pone.0059118 pmid:23555621 pmcid:PMC3608615 fatcat:fyy33fvvgzcmtmasitshxmpdru

Carcinogenesis of renal cell carcinoma reflected in HLA ligands: A novel approach for synergistic peptide vaccination design

Martin G. Klatt, Daniel J. Kowalewski, Heiko Schuster, Moreno Di Marco, Jörg Hennenlotter, Arnulf Stenzl, Hans-Georg Rammensee, Stefan Stevanović
2016 Oncoimmunology  
By analyzing HLA-presented peptides for HLA class I and II of 11 malignant and 6 non-malignant kidney tissue samples, more than 2,700 peptides and 1,600 corresponding source proteins were identified.  ...  Subsequent biological function analysis of HLA ligands by the GeneMANIA online platform showed enrichment for well established, but also novel, pathways and biological processes involved in carcinogenesis  ...  Funding This work was supported by the Deutsche Forschungsgesellschaft (DFG, SFB 685 and GRK 794) and the German Cancer Consortium (DKTK).  ... 
doi:10.1080/2162402x.2016.1204504 pmid:27622074 pmcid:PMC5007970 fatcat:6ltcxjeh4bdghioakfmly5toau

Higher Throughput Methods of Identifying T Cell Epitopes for Studying Outcomes of Altered Antigen Processing and Presentation

Evan W. Newell
2013 Frontiers in Immunology  
Variation in the mechanisms that mediate antigen processing, MHC-loading, and presentation of peptides allows cells to significantly modulate the repertoire of peptides presented by both MHC class I or  ...  The importance of this analysis is highlighted by evidence that physiologically relevant variation in antigen processing and presentation as well as other factors can give rise to unpredictably different  ...  screening of both MHC class I and class II ligands identified by proteomics for the purposes of investigating the consequences of variable antigen processing and presentation pathways discussed here.  ... 
doi:10.3389/fimmu.2013.00430 pmid:24367368 pmcid:PMC3851853 fatcat:zsv7j5tetrdenpwzfdpsf5js5e

Structural and Nonstructural Viral Proteins Are Targets of T-Helper Immune Response against Human Respiratory Syncytial Virus

Elena Lorente, Alejandro Barriga, Eilon Barnea, Carmen Mir, John A. Gebe, Arie Admon, Daniel López
2016 Molecular & Cellular Proteomics  
Molecular & Cellular Proteomics 15.6 * This work was supported by the Spanish Ministry of Economy grants BIO2011-25636 to D.L. and to A. A. from the ISF 916/05.  ...  The funding agencies had no role in the study design, data collection, analysis decision to publish, or preparation of the manuscript. We had no conflicting financial interests.  ...  Acknowledgments-The excellent technical assistance of M. Jime ´nez, F. Lasala and the Centro Nacional de Microbiología animal facility is gratefully acknowledged.  ... 
doi:10.1074/mcp.m115.057356 pmid:27090790 pmcid:PMC5083087 fatcat:lysthpz3cbhuxkbolqkg4hlkra

Proteomics special issue: Precision immunology and oncology

Sri H. Ramarathinam, Anthony W. Purcell
2021 Proteomics  
drugs analysed or predicted prior to treatment of the patient.  ...  Precision immunology aims to select targets from the host, the immune system, viral or tumour-specific factors for immunotherapy. While precision immunology was born out of  ...  These APCs take up exogenous antigen in their milieu, process and cleave the proteins in endosomal and lysosomal compartments, generating a pool of peptides some of which are loaded onto the HLA class  ... 
doi:10.1002/pmic.202000159 pmid:34510736 fatcat:4iseo72ylrdcvmh3b5cruzicpu

Computational characterization of the peptidome in transporter associated with antigen processing (TAP)-deficient cells

Antonio J. Martín-Galiano, Daniel López, Antony Nicodemus Antoniou
2019 PLoS ONE  
The transporter associated with antigen processing (TAP) is a key element of the major histocompatibility complex (MHC) class I antigen processing and presentation pathway.  ...  Antigen processing in TAP-deficient cells mainly focused on small, abundant or highly integral transmembrane proteins of the cellular proteome.  ...  No biological processes were significantly associated with TAP + ligands consistent with the fact that the proteasome evenly samples the whole proteome.  ... 
doi:10.1371/journal.pone.0210583 pmid:30645615 pmcid:PMC6333353 fatcat:2idhigg27fda5bdpoey4uwh2ma

Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue

Monique Ramos de Oliveira Trugilho, Eugenio Damaceno Hottz, Giselle Villa Flor Brunoro, André Teixeira-Ferreira, Paulo Costa Carvalho, Gustavo Adolfo Salazar, Guy A. Zimmerman, Fernando A. Bozza, Patrícia T. Bozza, Jonas Perales, Richard J. Kuhn
2017 PLoS Pathogens  
In addition, we found evidence that DENV infection triggers HLA class I synthesis and surface expression by a mechanism depending on functional proteasome activity.  ...  These findings are consistent with functional importance of HLA class I, PLOS Pathogens | https://doi.  ...  Acknowledgments The authors thank Juliana Freitas Lopes for virus production; Thiago Moreno L.  ... 
doi:10.1371/journal.ppat.1006385 pmid:28542641 pmcid:PMC5453622 fatcat:lvcj66znovhhtdn7r37tjgddkm

TMT-based quantitative proteomic profiling of human monocyte-derived macrophages and foam cells

Yali Zhang, Yu Fu, Linying Jia, Chenyang Zhang, Wenbin Cao, Naqash Alam, Rong Wang, Weirong Wang, Liang Bai, Sihai Zhao, Enqi Liu
2022 Proteome Science  
Discerning processes that participate in macrophage-to-foam cell formation are critical for understanding the basic mechanisms underlying atherosclerosis.  ...  Background Cardiovascular diseases remain the leading cause of morbidity and mortality worldwide, most of which are caused by atherosclerosis.  ...  dehydrogenase type 7 HSD3B7 1.992 O75911 Short-chain dehydrogenase/reductase 3 DHRS3 1.966 P30499 HLA class I histocompatibility antigen, Cw-1 alpha chain HLA-C 1.909 P01909 HLA class II histocompatibility  ... 
doi:10.1186/s12953-021-00183-x pmid:34980145 pmcid:PMC8725474 fatcat:mhosbses5zhkvbrvd3z7rdobdm
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