The role of antigen expression in shaping the repertoire of HLA presented ligands

Autores
García Álvarez, Heli Magalí; Kosaloglu Yalçin, Zeynep; Peters, Bjoern; Nielsen, Morten
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Human leukocyte antigen (HLA) presentation of peptides is a prerequisite of T cell immune activation. The understanding of the rules defining this event has large implications for our knowledge of basic immunology and for the rational design of immuno-therapeutics and vaccines. Historically, most of the available prediction methods have been solely focused on the information related to antigen processing and presentation. Recent work has, however, demonstrated that method performance can be boosted by integrating information related to antigen abundance. Here we expand on these later findings and develop an extended version of NetMHCpan, called NetMHCpanExp, integrating information on antigen abundance from RNA-Seq experiments. In line with earlier works, the model demonstrates improved performance for both HLA ligand and cancer neoantigen epitope prediction. Optimal results are obtained by use of sample-specific abundance information but also reference datasets can be applied with a limited performance drop. The developed tool is available at https://services.healthtech.dtu.dk/service.php?NetMHCpanExp-1.0
Fil: García Álvarez, Heli Magalí. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Biotecnológicas; Argentina
Fil: Kosaloglu Yalçin, Zeynep. La Jolla Institute for Allergy and Immunology; Estados Unidos
Fil: Peters, Bjoern. La Jolla Institute for Allergy and Immunology; Estados Unidos
Fil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
Materia
Immunology
Biocomputational method
Biological sciences tools
Transcriptomics
Antigen presentation
Antigen expression
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/267937
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/267937
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling The role of antigen expression in shaping the repertoire of HLA presented ligandsGarcía Álvarez, Heli MagalíKosaloglu Yalçin, ZeynepPeters, BjoernNielsen, MortenImmunologyBiocomputational methodBiological sciences toolsTranscriptomicsAntigen presentationAntigen expressionhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Human leukocyte antigen (HLA) presentation of peptides is a prerequisite of T cell immune activation. The understanding of the rules defining this event has large implications for our knowledge of basic immunology and for the rational design of immuno-therapeutics and vaccines. Historically, most of the available prediction methods have been solely focused on the information related to antigen processing and presentation. Recent work has, however, demonstrated that method performance can be boosted by integrating information related to antigen abundance. Here we expand on these later findings and develop an extended version of NetMHCpan, called NetMHCpanExp, integrating information on antigen abundance from RNA-Seq experiments. In line with earlier works, the model demonstrates improved performance for both HLA ligand and cancer neoantigen epitope prediction. Optimal results are obtained by use of sample-specific abundance information but also reference datasets can be applied with a limited performance drop. The developed tool is available at https://services.healthtech.dtu.dk/service.php?NetMHCpanExp-1.0Fil: García Álvarez, Heli Magalí. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Kosaloglu Yalçin, Zeynep. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Peters, Bjoern. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaCell Press2022-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/267937García Álvarez, Heli Magalí; Kosaloglu Yalçin, Zeynep; Peters, Bjoern; Nielsen, Morten; The role of antigen expression in shaping the repertoire of HLA presented ligands; Cell Press; iScience; 25; 9; 9-2022; 1-222589-0042CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S2589004222012470info:eu-repo/semantics/altIdentifier/doi/10.1016/j.isci.2022.104975info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T12:00:18Zoai:ri.conicet.gov.ar:11336/267937instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 12:00:19.002CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv The role of antigen expression in shaping the repertoire of HLA presented ligands
title The role of antigen expression in shaping the repertoire of HLA presented ligands
spellingShingle The role of antigen expression in shaping the repertoire of HLA presented ligands
García Álvarez, Heli Magalí
Immunology
Biocomputational method
Biological sciences tools
Transcriptomics
Antigen presentation
Antigen expression
title_short The role of antigen expression in shaping the repertoire of HLA presented ligands
title_full The role of antigen expression in shaping the repertoire of HLA presented ligands
title_fullStr The role of antigen expression in shaping the repertoire of HLA presented ligands
title_full_unstemmed The role of antigen expression in shaping the repertoire of HLA presented ligands
title_sort The role of antigen expression in shaping the repertoire of HLA presented ligands
dc.creator.none.fl_str_mv García Álvarez, Heli Magalí
Kosaloglu Yalçin, Zeynep
Peters, Bjoern
Nielsen, Morten
author García Álvarez, Heli Magalí
author_facet García Álvarez, Heli Magalí
Kosaloglu Yalçin, Zeynep
Peters, Bjoern
Nielsen, Morten
author_role author
author2 Kosaloglu Yalçin, Zeynep
Peters, Bjoern
Nielsen, Morten
author2_role author
author
author
dc.subject.none.fl_str_mv Immunology
Biocomputational method
Biological sciences tools
Transcriptomics
Antigen presentation
Antigen expression
topic Immunology
Biocomputational method
Biological sciences tools
Transcriptomics
Antigen presentation
Antigen expression
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Human leukocyte antigen (HLA) presentation of peptides is a prerequisite of T cell immune activation. The understanding of the rules defining this event has large implications for our knowledge of basic immunology and for the rational design of immuno-therapeutics and vaccines. Historically, most of the available prediction methods have been solely focused on the information related to antigen processing and presentation. Recent work has, however, demonstrated that method performance can be boosted by integrating information related to antigen abundance. Here we expand on these later findings and develop an extended version of NetMHCpan, called NetMHCpanExp, integrating information on antigen abundance from RNA-Seq experiments. In line with earlier works, the model demonstrates improved performance for both HLA ligand and cancer neoantigen epitope prediction. Optimal results are obtained by use of sample-specific abundance information but also reference datasets can be applied with a limited performance drop. The developed tool is available at https://services.healthtech.dtu.dk/service.php?NetMHCpanExp-1.0
Fil: García Álvarez, Heli Magalí. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Biotecnológicas; Argentina
Fil: Kosaloglu Yalçin, Zeynep. La Jolla Institute for Allergy and Immunology; Estados Unidos
Fil: Peters, Bjoern. La Jolla Institute for Allergy and Immunology; Estados Unidos
Fil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina
description Human leukocyte antigen (HLA) presentation of peptides is a prerequisite of T cell immune activation. The understanding of the rules defining this event has large implications for our knowledge of basic immunology and for the rational design of immuno-therapeutics and vaccines. Historically, most of the available prediction methods have been solely focused on the information related to antigen processing and presentation. Recent work has, however, demonstrated that method performance can be boosted by integrating information related to antigen abundance. Here we expand on these later findings and develop an extended version of NetMHCpan, called NetMHCpanExp, integrating information on antigen abundance from RNA-Seq experiments. In line with earlier works, the model demonstrates improved performance for both HLA ligand and cancer neoantigen epitope prediction. Optimal results are obtained by use of sample-specific abundance information but also reference datasets can be applied with a limited performance drop. The developed tool is available at https://services.healthtech.dtu.dk/service.php?NetMHCpanExp-1.0
publishDate 2022
dc.date.none.fl_str_mv 2022-09
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/267937
García Álvarez, Heli Magalí; Kosaloglu Yalçin, Zeynep; Peters, Bjoern; Nielsen, Morten; The role of antigen expression in shaping the repertoire of HLA presented ligands; Cell Press; iScience; 25; 9; 9-2022; 1-22
2589-0042
CONICET Digital
CONICET
url http://hdl.handle.net/11336/267937
identifier_str_mv García Álvarez, Heli Magalí; Kosaloglu Yalçin, Zeynep; Peters, Bjoern; Nielsen, Morten; The role of antigen expression in shaping the repertoire of HLA presented ligands; Cell Press; iScience; 25; 9; 9-2022; 1-22
2589-0042
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S2589004222012470
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.isci.2022.104975
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Cell Press
publisher.none.fl_str_mv Cell Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.982451

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