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Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic inflammatory disease with a high symptom burden, including nasal congestion and smell disorders. This study performed a detailed transcriptomic analysis in CRSwNP classified as eosinophilic CRS (ECRS), nonECRS according to the Japanese E...

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Autores principales: Ishino, Takashi, Takeno, Sachio, Takemoto, Kota, Yamato, Kensuke, Oda, Takashi, Nishida, Manabu, Horibe, Yuichiro, Chikuie, Nobuyuki, Kono, Takashi, Taruya, Takayuki, Hamamoto, Takao, Ueda, Tsutomu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9146754/
https://www.ncbi.nlm.nih.gov/pubmed/35628459
http://dx.doi.org/10.3390/ijms23105653
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author Ishino, Takashi
Takeno, Sachio
Takemoto, Kota
Yamato, Kensuke
Oda, Takashi
Nishida, Manabu
Horibe, Yuichiro
Chikuie, Nobuyuki
Kono, Takashi
Taruya, Takayuki
Hamamoto, Takao
Ueda, Tsutomu
author_facet Ishino, Takashi
Takeno, Sachio
Takemoto, Kota
Yamato, Kensuke
Oda, Takashi
Nishida, Manabu
Horibe, Yuichiro
Chikuie, Nobuyuki
Kono, Takashi
Taruya, Takayuki
Hamamoto, Takao
Ueda, Tsutomu
author_sort Ishino, Takashi
collection PubMed
description Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic inflammatory disease with a high symptom burden, including nasal congestion and smell disorders. This study performed a detailed transcriptomic analysis in CRSwNP classified as eosinophilic CRS (ECRS), nonECRS according to the Japanese Epidemiological Survey of Refractory Eosinophilic Chronic Rhinosinusitis (JESREC) criteria, and a group of ECRS with comorbid aspirin intolerant asthma (Asp). Gene expression profiles of nasal polyps and the uncinate process in CRSwNP patients and normal subjects (controls) were generated by bulk RNA barcoding and sequencing (BRB-seq). A differentially expressed genes (DEGs) analysis was performed using DESeq2 software in iDEP to clarify any relationship between gene expression and disease backgrounds. A total of 3004 genes were identified by DEGs analysis to be associated with ECRS vs control, nonECRS vs control, and Asp vs control. A pathway analysis showed distinct profiles between the groups. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) showed distinct phenotype-specific pathways of expressed genes. In the specific pathway of “cytokine–cytokine receptor interaction”, the differentially expressed genes were widely distributed. This study indicates that transcriptome analysis using BRB-seq may be a valuable tool to explore the pathogenesis of type 2 inflammation in CRSwNP.
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spelling pubmed-91467542022-05-29 Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing Ishino, Takashi Takeno, Sachio Takemoto, Kota Yamato, Kensuke Oda, Takashi Nishida, Manabu Horibe, Yuichiro Chikuie, Nobuyuki Kono, Takashi Taruya, Takayuki Hamamoto, Takao Ueda, Tsutomu Int J Mol Sci Article Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic inflammatory disease with a high symptom burden, including nasal congestion and smell disorders. This study performed a detailed transcriptomic analysis in CRSwNP classified as eosinophilic CRS (ECRS), nonECRS according to the Japanese Epidemiological Survey of Refractory Eosinophilic Chronic Rhinosinusitis (JESREC) criteria, and a group of ECRS with comorbid aspirin intolerant asthma (Asp). Gene expression profiles of nasal polyps and the uncinate process in CRSwNP patients and normal subjects (controls) were generated by bulk RNA barcoding and sequencing (BRB-seq). A differentially expressed genes (DEGs) analysis was performed using DESeq2 software in iDEP to clarify any relationship between gene expression and disease backgrounds. A total of 3004 genes were identified by DEGs analysis to be associated with ECRS vs control, nonECRS vs control, and Asp vs control. A pathway analysis showed distinct profiles between the groups. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) showed distinct phenotype-specific pathways of expressed genes. In the specific pathway of “cytokine–cytokine receptor interaction”, the differentially expressed genes were widely distributed. This study indicates that transcriptome analysis using BRB-seq may be a valuable tool to explore the pathogenesis of type 2 inflammation in CRSwNP. MDPI 2022-05-18 /pmc/articles/PMC9146754/ /pubmed/35628459 http://dx.doi.org/10.3390/ijms23105653 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ishino, Takashi
Takeno, Sachio
Takemoto, Kota
Yamato, Kensuke
Oda, Takashi
Nishida, Manabu
Horibe, Yuichiro
Chikuie, Nobuyuki
Kono, Takashi
Taruya, Takayuki
Hamamoto, Takao
Ueda, Tsutomu
Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing
title Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing
title_full Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing
title_fullStr Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing
title_full_unstemmed Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing
title_short Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing
title_sort distinct gene set enrichment profiles in eosinophilic and non-eosinophilic chronic rhinosinusitis with nasal polyps by bulk rna barcoding and sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9146754/
https://www.ncbi.nlm.nih.gov/pubmed/35628459
http://dx.doi.org/10.3390/ijms23105653
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