Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?

IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-...
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Autor*in:	Nikolas Dovrolis [verfasserIn] Eirini Filidou [verfasserIn] Gesthimani Tarapatzi [verfasserIn] Georgios Kokkotis [verfasserIn] Michail Spathakis [verfasserIn] Leonidas Kandilogiannakis [verfasserIn] Ioannis Drygiannakis [verfasserIn] Vassilis Valatas [verfasserIn] Konstantinos Arvanitidis [verfasserIn] Ioannis Karakasiliotis [verfasserIn] Stergios Vradelis [verfasserIn] Vangelis G. Manolopoulos [verfasserIn] Vasilis Paspaliaris [verfasserIn] Giorgos Bamias [verfasserIn] George Kolios [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	fibrosis IBD co-expression tissue localization transcriptomics

Übergeordnetes Werk:	In: Frontiers in Immunology - Frontiers Media S.A., 2011, 13(2022)
Übergeordnetes Werk:	volume:13 ; year:2022

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fimmu.2022.1058237

Katalog-ID:	DOAJ020759363

Internformat


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520			\|a IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies.
650		4	\|a fibrosis
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650		4	\|a tissue localization
650		4	\|a transcriptomics
653		0	\|a Immunologic diseases. Allergy
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700	0		\|a Eirini Filidou \|e verfasserin \|4 aut
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700	0		\|a Georgios Kokkotis \|e verfasserin \|4 aut
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allfields	10.3389/fimmu.2022.1058237 doi (DE-627)DOAJ020759363 (DE-599)DOAJb41850864da44ca39f0ec07673c3ce97 DE-627 ger DE-627 rakwb eng RC581-607 Nikolas Dovrolis verfasserin aut Co-expression of fibrotic genes in inflammatory bowel disease; A localized event? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies. fibrosis IBD co-expression tissue localization transcriptomics Immunologic diseases. Allergy Nikolas Dovrolis verfasserin aut Nikolas Dovrolis verfasserin aut Eirini Filidou verfasserin aut Eirini Filidou verfasserin aut Gesthimani Tarapatzi verfasserin aut Gesthimani Tarapatzi verfasserin aut Georgios Kokkotis verfasserin aut Michail Spathakis verfasserin aut Michail Spathakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Ioannis Drygiannakis verfasserin aut Vassilis Valatas verfasserin aut Vassilis Valatas verfasserin aut Konstantinos Arvanitidis verfasserin aut Konstantinos Arvanitidis verfasserin aut Ioannis Karakasiliotis verfasserin aut Stergios Vradelis verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vasilis Paspaliaris verfasserin aut Giorgos Bamias verfasserin aut George Kolios verfasserin aut George Kolios verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 13(2022) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:13 year:2022 https://doi.org/10.3389/fimmu.2022.1058237 kostenfrei https://doaj.org/article/b41850864da44ca39f0ec07673c3ce97 kostenfrei https://www.frontiersin.org/articles/10.3389/fimmu.2022.1058237/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
spelling	10.3389/fimmu.2022.1058237 doi (DE-627)DOAJ020759363 (DE-599)DOAJb41850864da44ca39f0ec07673c3ce97 DE-627 ger DE-627 rakwb eng RC581-607 Nikolas Dovrolis verfasserin aut Co-expression of fibrotic genes in inflammatory bowel disease; A localized event? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies. fibrosis IBD co-expression tissue localization transcriptomics Immunologic diseases. Allergy Nikolas Dovrolis verfasserin aut Nikolas Dovrolis verfasserin aut Eirini Filidou verfasserin aut Eirini Filidou verfasserin aut Gesthimani Tarapatzi verfasserin aut Gesthimani Tarapatzi verfasserin aut Georgios Kokkotis verfasserin aut Michail Spathakis verfasserin aut Michail Spathakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Ioannis Drygiannakis verfasserin aut Vassilis Valatas verfasserin aut Vassilis Valatas verfasserin aut Konstantinos Arvanitidis verfasserin aut Konstantinos Arvanitidis verfasserin aut Ioannis Karakasiliotis verfasserin aut Stergios Vradelis verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vasilis Paspaliaris verfasserin aut Giorgos Bamias verfasserin aut George Kolios verfasserin aut George Kolios verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 13(2022) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:13 year:2022 https://doi.org/10.3389/fimmu.2022.1058237 kostenfrei https://doaj.org/article/b41850864da44ca39f0ec07673c3ce97 kostenfrei https://www.frontiersin.org/articles/10.3389/fimmu.2022.1058237/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
allfields_unstemmed	10.3389/fimmu.2022.1058237 doi (DE-627)DOAJ020759363 (DE-599)DOAJb41850864da44ca39f0ec07673c3ce97 DE-627 ger DE-627 rakwb eng RC581-607 Nikolas Dovrolis verfasserin aut Co-expression of fibrotic genes in inflammatory bowel disease; A localized event? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies. fibrosis IBD co-expression tissue localization transcriptomics Immunologic diseases. Allergy Nikolas Dovrolis verfasserin aut Nikolas Dovrolis verfasserin aut Eirini Filidou verfasserin aut Eirini Filidou verfasserin aut Gesthimani Tarapatzi verfasserin aut Gesthimani Tarapatzi verfasserin aut Georgios Kokkotis verfasserin aut Michail Spathakis verfasserin aut Michail Spathakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Ioannis Drygiannakis verfasserin aut Vassilis Valatas verfasserin aut Vassilis Valatas verfasserin aut Konstantinos Arvanitidis verfasserin aut Konstantinos Arvanitidis verfasserin aut Ioannis Karakasiliotis verfasserin aut Stergios Vradelis verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vasilis Paspaliaris verfasserin aut Giorgos Bamias verfasserin aut George Kolios verfasserin aut George Kolios verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 13(2022) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:13 year:2022 https://doi.org/10.3389/fimmu.2022.1058237 kostenfrei https://doaj.org/article/b41850864da44ca39f0ec07673c3ce97 kostenfrei https://www.frontiersin.org/articles/10.3389/fimmu.2022.1058237/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
allfieldsGer	10.3389/fimmu.2022.1058237 doi (DE-627)DOAJ020759363 (DE-599)DOAJb41850864da44ca39f0ec07673c3ce97 DE-627 ger DE-627 rakwb eng RC581-607 Nikolas Dovrolis verfasserin aut Co-expression of fibrotic genes in inflammatory bowel disease; A localized event? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies. fibrosis IBD co-expression tissue localization transcriptomics Immunologic diseases. Allergy Nikolas Dovrolis verfasserin aut Nikolas Dovrolis verfasserin aut Eirini Filidou verfasserin aut Eirini Filidou verfasserin aut Gesthimani Tarapatzi verfasserin aut Gesthimani Tarapatzi verfasserin aut Georgios Kokkotis verfasserin aut Michail Spathakis verfasserin aut Michail Spathakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Ioannis Drygiannakis verfasserin aut Vassilis Valatas verfasserin aut Vassilis Valatas verfasserin aut Konstantinos Arvanitidis verfasserin aut Konstantinos Arvanitidis verfasserin aut Ioannis Karakasiliotis verfasserin aut Stergios Vradelis verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vasilis Paspaliaris verfasserin aut Giorgos Bamias verfasserin aut George Kolios verfasserin aut George Kolios verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 13(2022) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:13 year:2022 https://doi.org/10.3389/fimmu.2022.1058237 kostenfrei https://doaj.org/article/b41850864da44ca39f0ec07673c3ce97 kostenfrei https://www.frontiersin.org/articles/10.3389/fimmu.2022.1058237/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
allfieldsSound	10.3389/fimmu.2022.1058237 doi (DE-627)DOAJ020759363 (DE-599)DOAJb41850864da44ca39f0ec07673c3ce97 DE-627 ger DE-627 rakwb eng RC581-607 Nikolas Dovrolis verfasserin aut Co-expression of fibrotic genes in inflammatory bowel disease; A localized event? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies. fibrosis IBD co-expression tissue localization transcriptomics Immunologic diseases. Allergy Nikolas Dovrolis verfasserin aut Nikolas Dovrolis verfasserin aut Eirini Filidou verfasserin aut Eirini Filidou verfasserin aut Gesthimani Tarapatzi verfasserin aut Gesthimani Tarapatzi verfasserin aut Georgios Kokkotis verfasserin aut Michail Spathakis verfasserin aut Michail Spathakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Leonidas Kandilogiannakis verfasserin aut Ioannis Drygiannakis verfasserin aut Vassilis Valatas verfasserin aut Vassilis Valatas verfasserin aut Konstantinos Arvanitidis verfasserin aut Konstantinos Arvanitidis verfasserin aut Ioannis Karakasiliotis verfasserin aut Stergios Vradelis verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vangelis G. Manolopoulos verfasserin aut Vasilis Paspaliaris verfasserin aut Giorgos Bamias verfasserin aut George Kolios verfasserin aut George Kolios verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 13(2022) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:13 year:2022 https://doi.org/10.3389/fimmu.2022.1058237 kostenfrei https://doaj.org/article/b41850864da44ca39f0ec07673c3ce97 kostenfrei https://www.frontiersin.org/articles/10.3389/fimmu.2022.1058237/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
language	English
source	In Frontiers in Immunology 13(2022) volume:13 year:2022
sourceStr	In Frontiers in Immunology 13(2022) volume:13 year:2022
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	fibrosis IBD co-expression tissue localization transcriptomics Immunologic diseases. Allergy
isfreeaccess_bool	true
container_title	Frontiers in Immunology
authorswithroles_txt_mv	Nikolas Dovrolis @@aut@@ Eirini Filidou @@aut@@ Gesthimani Tarapatzi @@aut@@ Georgios Kokkotis @@aut@@ Michail Spathakis @@aut@@ Leonidas Kandilogiannakis @@aut@@ Ioannis Drygiannakis @@aut@@ Vassilis Valatas @@aut@@ Konstantinos Arvanitidis @@aut@@ Ioannis Karakasiliotis @@aut@@ Stergios Vradelis @@aut@@ Vangelis G. Manolopoulos @@aut@@ Vasilis Paspaliaris @@aut@@ Giorgos Bamias @@aut@@ George Kolios @@aut@@
publishDateDaySort_date	2022-01-01T00:00:00Z
hierarchy_top_id	657998354
id	DOAJ020759363
language_de	englisch
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callnumber-first	R - Medicine
author	Nikolas Dovrolis
spellingShingle	Nikolas Dovrolis misc RC581-607 misc fibrosis misc IBD misc co-expression misc tissue localization misc transcriptomics misc Immunologic diseases. Allergy Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?
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topic_title	RC581-607 Co-expression of fibrotic genes in inflammatory bowel disease; A localized event? fibrosis IBD co-expression tissue localization transcriptomics
topic	misc RC581-607 misc fibrosis misc IBD misc co-expression misc tissue localization misc transcriptomics misc Immunologic diseases. Allergy
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title	Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?
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title_full	Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?
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author_browse	Nikolas Dovrolis Eirini Filidou Gesthimani Tarapatzi Georgios Kokkotis Michail Spathakis Leonidas Kandilogiannakis Ioannis Drygiannakis Vassilis Valatas Konstantinos Arvanitidis Ioannis Karakasiliotis Stergios Vradelis Vangelis G. Manolopoulos Vasilis Paspaliaris Giorgos Bamias George Kolios
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title_sort	co-expression of fibrotic genes in inflammatory bowel disease; a localized event?
callnumber	RC581-607
title_auth	Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?
abstract	IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies.
abstractGer	IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies.
abstract_unstemmed	IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies.
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title_short	Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?
url	https://doi.org/10.3389/fimmu.2022.1058237 https://doaj.org/article/b41850864da44ca39f0ec07673c3ce97 https://www.frontiersin.org/articles/10.3389/fimmu.2022.1058237/full https://doaj.org/toc/1664-3224
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author2	Nikolas Dovrolis Eirini Filidou Gesthimani Tarapatzi Georgios Kokkotis Michail Spathakis Leonidas Kandilogiannakis Ioannis Drygiannakis Vassilis Valatas Konstantinos Arvanitidis Ioannis Karakasiliotis Stergios Vradelis Vangelis G. Manolopoulos Vasilis Paspaliaris Giorgos Bamias George Kolios
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