Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells

Introduction: Adherent-invasive Escherichia coli (AIEC) is strongly associated with the pathogenesis of Crohn’s disease (CD). However, no molecular markers currently exist for AIEC identification. This study aimed to identify differentially expressed genes (DEGs) between AIEC and non-AIEC strains th...

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Autores: Bonet-Rossinyol, Queralt, Camprubí Font, Carla, López Siles, Mireia, Martínez Medina, Margarita
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10256/25123
Acceso en línea:http://hdl.handle.net/10256/25123
Access Level:acceso abierto
Palabra clave:Escheríchia coli
Escherichia coli
Expressió gènica
Gene expression
Marcadors bioquímics
Biochemical markers
Crohn, Malaltia de -- Patogènesi
Crohn's disease -- Pathogenesis
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spelling Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cellsBonet-Rossinyol, QueraltCamprubí Font, CarlaLópez Siles, MireiaMartínez Medina, MargaritaEscheríchia coliEscherichia coliExpressió gènicaGene expressionMarcadors bioquímicsBiochemical markersCrohn, Malaltia de -- PatogènesiCrohn's disease -- PathogenesisIntroduction: Adherent-invasive Escherichia coli (AIEC) is strongly associated with the pathogenesis of Crohn’s disease (CD). However, no molecular markers currently exist for AIEC identification. This study aimed to identify differentially expressed genes (DEGs) between AIEC and non-AIEC strains that may contribute to AIEC pathogenicity and to evaluate their utility as molecular markers. Methods: Comparative transcriptomics was performed on two closely related AIEC/non-AIEC strain pairs during Intestine-407 cell infection. DEGs were quantified by RT-qPCR in the same RNA extracts, as well as in 14 AIEC and 23 non-AIEC strains to validate the results across a diverse strain collection. Binary logistical regression was performed to identify DEGs whose quantification could be used as AIEC biomarkers. Results: Comparative transcriptomics revealed 67 differences in expression between the two phenotypes in the strain pairs, 50 of which (81.97%) were corroborated by RT-qPCR. When explored in the whole strain collection, 29 DEGs were differentially expressed between AIEC and non-AIEC phenotypes (p-value < 0.042), and 42 genes between the supernatant fraction of infected cell cultures and the cellular fraction containing adhered and intracellular bacteria (p-value < 0.049). Notably, six DEGs detected in the strain collection were implicated in arginine biosynthesis and five in colanic acid synthesis. Furthermore, two biomarkers based on wzb and cueR gene expression were proposed with an accuracy of ≥ 85% in our strain collection. Discussion: This is the first transcriptomic study conducted using AIEC-infected cell cultures. We have identified several genes that may be involved in AIEC pathogenicity, two of which are putative biomarkers for identificationThis work was supported by the Universitat de Girona under Grants MPCUdG2016-009 and GdRCompetUdG2017; Spanish Ministry of Economy and Competitiveness (MINECO) under Grants PID2021-126699NB-I00/MCIN/AEI/10.13039/501100011033/FEDER, UE, SAF2017-82261-P and SAF2013-43284-P, being the last co-funded by the European Regional Development Fund. CC-F and QB-R were recipients of predoctoral fellowships (IF-UdG 2015 and IF-UdG 2019). ML-S was a Serra Húnter fellowFrontiers MediaAgencia Estatal de InvestigaciónMinisterio de Economía y Competitividad (Espanya)2023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionpeer-reviewedapplication/pdfhttp://hdl.handle.net/10256/25123http://hdl.handle.net/10256/25123Frontiers in Cellular and Infection Microbiology, 2023, vol. 13, art. núm. 1228159Articles publicats (D-B)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)Inglésinfo:eu-repo/semantics/altIdentifier/doi/10.3389/fcimb.2023.1228159info:eu-repo/semantics/altIdentifier/eissn/2235-2988PID2021-126699NB-I00SAF2017-82261-PSAF2013-43284-Pinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126699NB-I00info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/SAF2017-82261-Pinfo:eu-repo/grantAgreement/MINECO//SAF2013-43284-PAttribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10256/251232026-05-29T05:05:01Z
dc.title.none.fl_str_mv Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells
title Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells
spellingShingle Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells
Bonet-Rossinyol, Queralt
Escheríchia coli
Escherichia coli
Expressió gènica
Gene expression
Marcadors bioquímics
Biochemical markers
Crohn, Malaltia de -- Patogènesi
Crohn's disease -- Pathogenesis
title_short Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells
title_full Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells
title_fullStr Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells
title_full_unstemmed Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells
title_sort Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells
dc.creator.none.fl_str_mv Bonet-Rossinyol, Queralt
Camprubí Font, Carla
López Siles, Mireia
Martínez Medina, Margarita
author Bonet-Rossinyol, Queralt
author_facet Bonet-Rossinyol, Queralt
Camprubí Font, Carla
López Siles, Mireia
Martínez Medina, Margarita
author_role author
author2 Camprubí Font, Carla
López Siles, Mireia
Martínez Medina, Margarita
author2_role author
author
author
dc.contributor.none.fl_str_mv Agencia Estatal de Investigación
Ministerio de Economía y Competitividad (Espanya)
dc.subject.none.fl_str_mv Escheríchia coli
Escherichia coli
Expressió gènica
Gene expression
Marcadors bioquímics
Biochemical markers
Crohn, Malaltia de -- Patogènesi
Crohn's disease -- Pathogenesis
topic Escheríchia coli
Escherichia coli
Expressió gènica
Gene expression
Marcadors bioquímics
Biochemical markers
Crohn, Malaltia de -- Patogènesi
Crohn's disease -- Pathogenesis
description Introduction: Adherent-invasive Escherichia coli (AIEC) is strongly associated with the pathogenesis of Crohn’s disease (CD). However, no molecular markers currently exist for AIEC identification. This study aimed to identify differentially expressed genes (DEGs) between AIEC and non-AIEC strains that may contribute to AIEC pathogenicity and to evaluate their utility as molecular markers. Methods: Comparative transcriptomics was performed on two closely related AIEC/non-AIEC strain pairs during Intestine-407 cell infection. DEGs were quantified by RT-qPCR in the same RNA extracts, as well as in 14 AIEC and 23 non-AIEC strains to validate the results across a diverse strain collection. Binary logistical regression was performed to identify DEGs whose quantification could be used as AIEC biomarkers. Results: Comparative transcriptomics revealed 67 differences in expression between the two phenotypes in the strain pairs, 50 of which (81.97%) were corroborated by RT-qPCR. When explored in the whole strain collection, 29 DEGs were differentially expressed between AIEC and non-AIEC phenotypes (p-value < 0.042), and 42 genes between the supernatant fraction of infected cell cultures and the cellular fraction containing adhered and intracellular bacteria (p-value < 0.049). Notably, six DEGs detected in the strain collection were implicated in arginine biosynthesis and five in colanic acid synthesis. Furthermore, two biomarkers based on wzb and cueR gene expression were proposed with an accuracy of ≥ 85% in our strain collection. Discussion: This is the first transcriptomic study conducted using AIEC-infected cell cultures. We have identified several genes that may be involved in AIEC pathogenicity, two of which are putative biomarkers for identification
publishDate 2023
dc.date.none.fl_str_mv 2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
peer-reviewed
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10256/25123
http://hdl.handle.net/10256/25123
url http://hdl.handle.net/10256/25123
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.3389/fcimb.2023.1228159
info:eu-repo/semantics/altIdentifier/eissn/2235-2988
PID2021-126699NB-I00
SAF2017-82261-P
SAF2013-43284-P
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126699NB-I00
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/SAF2017-82261-P
info:eu-repo/grantAgreement/MINECO//SAF2013-43284-P
dc.rights.none.fl_str_mv Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv 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 Frontiers in Cellular and Infection Microbiology, 2023, vol. 13, art. núm. 1228159
Articles publicats (D-B)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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