Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples

The study of transcriptomic interactions between host and pathogens in in vivo conditions is challenged by the low relative amounts of the pathogen RNA. Yeast opportunistic pathogens of the genus Candida can cause life-threatening systemic infections in immunocompromised patients, and are of growing...

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Autores: Hovhannisyan, Hrant, Rodriguez Sanchez, Antonio Jose, Saus, Ester, Vaneechoutte, Mario, Gabaldón, Toni
Tipo de recurso: artículo
Fecha de publicación:2023
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/383682
Acceso en línea:https://hdl.handle.net/2117/383682
https://dx.doi.org/10.3389/fcimb.2023.1093178
Access Level:acceso abierto
Palabra clave:Fungal infections
Non-coding RNA
Candida
Host-pathogen interactions in vivo
RNA-Seq
Probe-based enrichment
Long noncoding RNA (IncRNA)
Transcriptomes
Càndida
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
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spelling Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samplesHovhannisyan, HrantRodriguez Sanchez, Antonio JoseSaus, EsterVaneechoutte, MarioGabaldón, ToniFungal infectionsNon-coding RNACandidaHost-pathogen interactions in vivoRNA-SeqProbe-based enrichmentLong noncoding RNA (IncRNA)TranscriptomesCàndidaÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::BioinformàticaThe study of transcriptomic interactions between host and pathogens in in vivo conditions is challenged by the low relative amounts of the pathogen RNA. Yeast opportunistic pathogens of the genus Candida can cause life-threatening systemic infections in immunocompromised patients, and are of growing medical concern. Four phylogenetically diverse species account for over 90% of Candida infections, and their specific interactions with various human tissues are still poorly understood. To enable in vivo transcriptomic analysis in these species, we designed and validated pan-Candida target capture probes to enrich protein-coding and non-coding transcriptomes. The probe-based enrichment approach outperformed enrichment based on differential lysis of host cells, and showed similar enrichment performance as an existing capture design, yet achieving better fidelity of expression levels, enabling species multiplexing and capturing of lncRNAs. In addition, we show that our probe-based enrichment strategy allows robust genotype-based identification of the infecting strain present in the sample.TG group acknowledges support from the Spanish Ministry of Science and Innovation for grants ‘Centro de Excelencia Severo Ochoa’ and PGC2018-099921-B-I00, cofounded by European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR423, and grants from the European Union’s Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173, and the Marie Sklodowska-Curie grant agreement No. 642095. The group also receives support from an INB Grant (PT17/0009/0023 - ISCIII-SGEFI/ERDF). AR was also supported by the Marie Sklodowska-Curie grant agreement No. 642095.Peer ReviewedFrontiers Media20232023-01-0120232023-02-17journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/383682https://dx.doi.org/10.3389/fcimb.2023.1093178reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengEuropean Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 724173 Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes.open accesshttp://purl.org/coar/access_right/c_abf2Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3836822026-05-27T15:37:01Z
dc.title.none.fl_str_mv Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
title Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
spellingShingle Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
Hovhannisyan, Hrant
Fungal infections
Non-coding RNA
Candida
Host-pathogen interactions in vivo
RNA-Seq
Probe-based enrichment
Long noncoding RNA (IncRNA)
Transcriptomes
Càndida
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
title_short Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
title_full Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
title_fullStr Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
title_full_unstemmed Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
title_sort Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
dc.creator.none.fl_str_mv Hovhannisyan, Hrant
Rodriguez Sanchez, Antonio Jose
Saus, Ester
Vaneechoutte, Mario
Gabaldón, Toni
author Hovhannisyan, Hrant
author_facet Hovhannisyan, Hrant
Rodriguez Sanchez, Antonio Jose
Saus, Ester
Vaneechoutte, Mario
Gabaldón, Toni
author_role author
author2 Rodriguez Sanchez, Antonio Jose
Saus, Ester
Vaneechoutte, Mario
Gabaldón, Toni
author2_role author
author
author
author
dc.subject.none.fl_str_mv Fungal infections
Non-coding RNA
Candida
Host-pathogen interactions in vivo
RNA-Seq
Probe-based enrichment
Long noncoding RNA (IncRNA)
Transcriptomes
Càndida
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
topic Fungal infections
Non-coding RNA
Candida
Host-pathogen interactions in vivo
RNA-Seq
Probe-based enrichment
Long noncoding RNA (IncRNA)
Transcriptomes
Càndida
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
description The study of transcriptomic interactions between host and pathogens in in vivo conditions is challenged by the low relative amounts of the pathogen RNA. Yeast opportunistic pathogens of the genus Candida can cause life-threatening systemic infections in immunocompromised patients, and are of growing medical concern. Four phylogenetically diverse species account for over 90% of Candida infections, and their specific interactions with various human tissues are still poorly understood. To enable in vivo transcriptomic analysis in these species, we designed and validated pan-Candida target capture probes to enrich protein-coding and non-coding transcriptomes. The probe-based enrichment approach outperformed enrichment based on differential lysis of host cells, and showed similar enrichment performance as an existing capture design, yet achieving better fidelity of expression levels, enabling species multiplexing and capturing of lncRNAs. In addition, we show that our probe-based enrichment strategy allows robust genotype-based identification of the infecting strain present in the sample.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-01-01
2023
2023-02-17
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/383682
https://dx.doi.org/10.3389/fcimb.2023.1093178
url https://hdl.handle.net/2117/383682
https://dx.doi.org/10.3389/fcimb.2023.1093178
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv European Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 724173 Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes.
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,300719

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