Identification of Circulating MicroRNAs in Biliary Atresia by Next-Generation Sequencing

Xiaofang Peng, Liyuan Yang, Haiying Liu, Shuyin Pang, Yihao Chen, Jie Fu, Y. Chen, Zhe Wen, Ruizhong Zhang, Bing Zhu, Jiakang Yu, Pietro Invernizzi

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

OBJECTIVES:: Biliary atresia (BA) is an idiopathic neonatal liver disease, characterized by inflammatory and fibrotic obliteration of extrahepatic bile ducts. Therefore, reliable methods for noninvasive diagnosis are needed. This study aimed to analyze circulating microRNAs (miRNAs) in patients with BA using next-generation sequencing (NGS) for identifying novel diagnostic biomarkers. METHODS:: An initial screening of miRNAs in plasma from patients with BA and healthy controls (HCs) was performed on an Illumina NGS platform. Differential miRNAs were validated by quantitative real-time PCR (qPCR). Target genes and related signal transduction pathways of differential miRNAs were predicted by online software. RESULTS:: In total, 146 differential miRNAs were identified by deep sequencing. Fifteen miRNAs with read counts more than 1000, that included 7 upregulated and 8 downregulated miRNAs, were predicted to be associated with liver fibrosis, biliary differentiation and bile duct development. Of these, six miRNAs with read counts more than 5000 were analyzed by qPCR on an independent sample set comprising 44 patients with BA, 20 cholestatic disease controls and 20 HCs. Two up-regulated miRNAs (miR-122–5p, miR-100–5p) and two down-regulated miRNAs (miR-140–3p, miR-126–3p) were confirmed by individual qPCR. Only miR-140–3p was significantly different from controls (P?<?0.05), yielding an area under receiver operating characteristic curve of 0.75 with sensitivity of 66.7% and specificity of 79.1% at optimal threshold. CONCLUSIONS:: Our findings indicate that patients with BA exhibit a distinct profile of circulating miRNAs and that plasma miR-140–3p may be a promising diagnostic biomarker for this disease.

Original languageEnglish (US)
JournalJournal of Pediatric Gastroenterology and Nutrition
DOIs
StateAccepted/In press - Mar 7 2016
Externally publishedYes

Fingerprint

Biliary Atresia
MicroRNAs
Infant, Newborn, Diseases
Biomarkers
Extrahepatic Bile Ducts
High-Throughput Nucleotide Sequencing
Bile Ducts
ROC Curve
Liver Cirrhosis
Liver Diseases
Real-Time Polymerase Chain Reaction
Signal Transduction
Down-Regulation
Software

ASJC Scopus subject areas

  • Gastroenterology
  • Pediatrics, Perinatology, and Child Health

Cite this

Identification of Circulating MicroRNAs in Biliary Atresia by Next-Generation Sequencing. / Peng, Xiaofang; Yang, Liyuan; Liu, Haiying; Pang, Shuyin; Chen, Yihao; Fu, Jie; Chen, Y.; Wen, Zhe; Zhang, Ruizhong; Zhu, Bing; Yu, Jiakang; Invernizzi, Pietro.

In: Journal of Pediatric Gastroenterology and Nutrition, 07.03.2016.

Research output: Contribution to journalArticle

Peng, Xiaofang ; Yang, Liyuan ; Liu, Haiying ; Pang, Shuyin ; Chen, Yihao ; Fu, Jie ; Chen, Y. ; Wen, Zhe ; Zhang, Ruizhong ; Zhu, Bing ; Yu, Jiakang ; Invernizzi, Pietro. / Identification of Circulating MicroRNAs in Biliary Atresia by Next-Generation Sequencing. In: Journal of Pediatric Gastroenterology and Nutrition. 2016.
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abstract = "OBJECTIVES:: Biliary atresia (BA) is an idiopathic neonatal liver disease, characterized by inflammatory and fibrotic obliteration of extrahepatic bile ducts. Therefore, reliable methods for noninvasive diagnosis are needed. This study aimed to analyze circulating microRNAs (miRNAs) in patients with BA using next-generation sequencing (NGS) for identifying novel diagnostic biomarkers. METHODS:: An initial screening of miRNAs in plasma from patients with BA and healthy controls (HCs) was performed on an Illumina NGS platform. Differential miRNAs were validated by quantitative real-time PCR (qPCR). Target genes and related signal transduction pathways of differential miRNAs were predicted by online software. RESULTS:: In total, 146 differential miRNAs were identified by deep sequencing. Fifteen miRNAs with read counts more than 1000, that included 7 upregulated and 8 downregulated miRNAs, were predicted to be associated with liver fibrosis, biliary differentiation and bile duct development. Of these, six miRNAs with read counts more than 5000 were analyzed by qPCR on an independent sample set comprising 44 patients with BA, 20 cholestatic disease controls and 20 HCs. Two up-regulated miRNAs (miR-122–5p, miR-100–5p) and two down-regulated miRNAs (miR-140–3p, miR-126–3p) were confirmed by individual qPCR. Only miR-140–3p was significantly different from controls (P?<?0.05), yielding an area under receiver operating characteristic curve of 0.75 with sensitivity of 66.7{\%} and specificity of 79.1{\%} at optimal threshold. CONCLUSIONS:: Our findings indicate that patients with BA exhibit a distinct profile of circulating miRNAs and that plasma miR-140–3p may be a promising diagnostic biomarker for this disease.",
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T1 - Identification of Circulating MicroRNAs in Biliary Atresia by Next-Generation Sequencing

AU - Peng, Xiaofang

AU - Yang, Liyuan

AU - Liu, Haiying

AU - Pang, Shuyin

AU - Chen, Yihao

AU - Fu, Jie

AU - Chen, Y.

AU - Wen, Zhe

AU - Zhang, Ruizhong

AU - Zhu, Bing

AU - Yu, Jiakang

AU - Invernizzi, Pietro

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N2 - OBJECTIVES:: Biliary atresia (BA) is an idiopathic neonatal liver disease, characterized by inflammatory and fibrotic obliteration of extrahepatic bile ducts. Therefore, reliable methods for noninvasive diagnosis are needed. This study aimed to analyze circulating microRNAs (miRNAs) in patients with BA using next-generation sequencing (NGS) for identifying novel diagnostic biomarkers. METHODS:: An initial screening of miRNAs in plasma from patients with BA and healthy controls (HCs) was performed on an Illumina NGS platform. Differential miRNAs were validated by quantitative real-time PCR (qPCR). Target genes and related signal transduction pathways of differential miRNAs were predicted by online software. RESULTS:: In total, 146 differential miRNAs were identified by deep sequencing. Fifteen miRNAs with read counts more than 1000, that included 7 upregulated and 8 downregulated miRNAs, were predicted to be associated with liver fibrosis, biliary differentiation and bile duct development. Of these, six miRNAs with read counts more than 5000 were analyzed by qPCR on an independent sample set comprising 44 patients with BA, 20 cholestatic disease controls and 20 HCs. Two up-regulated miRNAs (miR-122–5p, miR-100–5p) and two down-regulated miRNAs (miR-140–3p, miR-126–3p) were confirmed by individual qPCR. Only miR-140–3p was significantly different from controls (P?<?0.05), yielding an area under receiver operating characteristic curve of 0.75 with sensitivity of 66.7% and specificity of 79.1% at optimal threshold. CONCLUSIONS:: Our findings indicate that patients with BA exhibit a distinct profile of circulating miRNAs and that plasma miR-140–3p may be a promising diagnostic biomarker for this disease.

AB - OBJECTIVES:: Biliary atresia (BA) is an idiopathic neonatal liver disease, characterized by inflammatory and fibrotic obliteration of extrahepatic bile ducts. Therefore, reliable methods for noninvasive diagnosis are needed. This study aimed to analyze circulating microRNAs (miRNAs) in patients with BA using next-generation sequencing (NGS) for identifying novel diagnostic biomarkers. METHODS:: An initial screening of miRNAs in plasma from patients with BA and healthy controls (HCs) was performed on an Illumina NGS platform. Differential miRNAs were validated by quantitative real-time PCR (qPCR). Target genes and related signal transduction pathways of differential miRNAs were predicted by online software. RESULTS:: In total, 146 differential miRNAs were identified by deep sequencing. Fifteen miRNAs with read counts more than 1000, that included 7 upregulated and 8 downregulated miRNAs, were predicted to be associated with liver fibrosis, biliary differentiation and bile duct development. Of these, six miRNAs with read counts more than 5000 were analyzed by qPCR on an independent sample set comprising 44 patients with BA, 20 cholestatic disease controls and 20 HCs. Two up-regulated miRNAs (miR-122–5p, miR-100–5p) and two down-regulated miRNAs (miR-140–3p, miR-126–3p) were confirmed by individual qPCR. Only miR-140–3p was significantly different from controls (P?<?0.05), yielding an area under receiver operating characteristic curve of 0.75 with sensitivity of 66.7% and specificity of 79.1% at optimal threshold. CONCLUSIONS:: Our findings indicate that patients with BA exhibit a distinct profile of circulating miRNAs and that plasma miR-140–3p may be a promising diagnostic biomarker for this disease.

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