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Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing

A choledochal cyst (CC) is a common congenital biliary disease in children, yet the underlying molecular bases for the cystic and fusiform clinical subtypes are unknown. RNA sequencing (RNA-seq) has been performed on 22 high-quality CC samples, including 12 cystic CC and 10 fusiform CC samples, to s...

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Autores principales: Lv, Yong, Xie, Xiaolong, Pu, Lihui, Wang, Qi, Yang, Jiayin, Pu, Siyu, Ai, Chengbo, Liu, Yi, Chen, Jing, Xiang, Bo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369577/
https://www.ncbi.nlm.nih.gov/pubmed/34413880
http://dx.doi.org/10.3389/fgene.2021.709340
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author Lv, Yong
Xie, Xiaolong
Pu, Lihui
Wang, Qi
Yang, Jiayin
Pu, Siyu
Ai, Chengbo
Liu, Yi
Chen, Jing
Xiang, Bo
author_facet Lv, Yong
Xie, Xiaolong
Pu, Lihui
Wang, Qi
Yang, Jiayin
Pu, Siyu
Ai, Chengbo
Liu, Yi
Chen, Jing
Xiang, Bo
author_sort Lv, Yong
collection PubMed
description A choledochal cyst (CC) is a common congenital biliary disease in children, yet the underlying molecular bases for the cystic and fusiform clinical subtypes are unknown. RNA sequencing (RNA-seq) has been performed on 22 high-quality CC samples, including 12 cystic CC and 10 fusiform CC samples, to search for molecular features. Weighted gene co-expression network analysis (WGCNA) was performed to identify key modules associated with clinical subtypes. Bioinformatic analyses were conducted to elucidate potential mechanisms. Then, we constructed protein–protein interaction (PPI) networks to identify candidate hub genes related to CC. Finally, we used the support vector machine (SVM) to eliminate redundant features and screen out the hub genes. The selected gene expression was determined in CC patients through quantitative real-time polymerase chain reaction (PCR). A total of 6,463 genes were found to be aberrantly expressed between cystic CC and fusiform CC. Twelve co-expression modules that correlated with clinical subtypes of CC were identified and assigned representative colors. Among the 12 modules, the blue module was considered the key module. Two functionally distinct sets of dysregulated genes have been identified in two major subtypes, metabolism-related genes in cystic CC and immune-related genes in fusiform CC. A total of 20 candidate hub genes that were correlated with clinical subtypes were found in the blue module. In addition, we found ERBB2 and WNT11 that have not been studied in CC and verified their differential expression in CC through quantitative real-time PCR experiments. For the first time, we have described the transcriptome characteristics of CC. These results suggest that cystic CC and fusiform CC have different molecular mechanisms. The bi-omics-identified novel candidate genes and pathways might be helpful for personalized treatment and are of great clinical significance for CC.
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spelling pubmed-83695772021-08-18 Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing Lv, Yong Xie, Xiaolong Pu, Lihui Wang, Qi Yang, Jiayin Pu, Siyu Ai, Chengbo Liu, Yi Chen, Jing Xiang, Bo Front Genet Genetics A choledochal cyst (CC) is a common congenital biliary disease in children, yet the underlying molecular bases for the cystic and fusiform clinical subtypes are unknown. RNA sequencing (RNA-seq) has been performed on 22 high-quality CC samples, including 12 cystic CC and 10 fusiform CC samples, to search for molecular features. Weighted gene co-expression network analysis (WGCNA) was performed to identify key modules associated with clinical subtypes. Bioinformatic analyses were conducted to elucidate potential mechanisms. Then, we constructed protein–protein interaction (PPI) networks to identify candidate hub genes related to CC. Finally, we used the support vector machine (SVM) to eliminate redundant features and screen out the hub genes. The selected gene expression was determined in CC patients through quantitative real-time polymerase chain reaction (PCR). A total of 6,463 genes were found to be aberrantly expressed between cystic CC and fusiform CC. Twelve co-expression modules that correlated with clinical subtypes of CC were identified and assigned representative colors. Among the 12 modules, the blue module was considered the key module. Two functionally distinct sets of dysregulated genes have been identified in two major subtypes, metabolism-related genes in cystic CC and immune-related genes in fusiform CC. A total of 20 candidate hub genes that were correlated with clinical subtypes were found in the blue module. In addition, we found ERBB2 and WNT11 that have not been studied in CC and verified their differential expression in CC through quantitative real-time PCR experiments. For the first time, we have described the transcriptome characteristics of CC. These results suggest that cystic CC and fusiform CC have different molecular mechanisms. The bi-omics-identified novel candidate genes and pathways might be helpful for personalized treatment and are of great clinical significance for CC. Frontiers Media S.A. 2021-08-03 /pmc/articles/PMC8369577/ /pubmed/34413880 http://dx.doi.org/10.3389/fgene.2021.709340 Text en Copyright © 2021 Lv, Xie, Pu, Wang, Yang, Pu, Ai, Liu, Chen and Xiang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Lv, Yong
Xie, Xiaolong
Pu, Lihui
Wang, Qi
Yang, Jiayin
Pu, Siyu
Ai, Chengbo
Liu, Yi
Chen, Jing
Xiang, Bo
Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing
title Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing
title_full Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing
title_fullStr Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing
title_full_unstemmed Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing
title_short Molecular Characteristics of Choledochal Cysts in Children: Transcriptome Sequencing
title_sort molecular characteristics of choledochal cysts in children: transcriptome sequencing
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369577/
https://www.ncbi.nlm.nih.gov/pubmed/34413880
http://dx.doi.org/10.3389/fgene.2021.709340
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