Integrative Analysis of lncRNA-mRNA Profile Reveals Potential Predictors for SAPHO Syndrome
Synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome is known as a rare disease characterized by inflammatory lesions on bones and skin. Polymorphism of clinical manifestation and lack of molecular biomarkers have both limited its diagnosis. Our study performed RNA sequencing (RN...
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doaj-7ca626d311d745fd8e3480587dde857d2021-06-21T07:25:31ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-06-011210.3389/fgene.2021.684520684520Integrative Analysis of lncRNA-mRNA Profile Reveals Potential Predictors for SAPHO SyndromeYuxiu Sun0Chen Li1Qingyi Lu2Haixu Jiang3Mengmeng Zhu4Guangrui Huang5Ting Wang6Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, ChinaDepartment of Traditional Chinese Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, ChinaSchool of Life Sciences, Beijing University of Chinese Medicine, Beijing, ChinaSchool of Life Sciences, Beijing University of Chinese Medicine, Beijing, ChinaSchool of Life Sciences, Beijing University of Chinese Medicine, Beijing, ChinaSchool of Life Sciences, Beijing University of Chinese Medicine, Beijing, ChinaBeijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, ChinaSynovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome is known as a rare disease characterized by inflammatory lesions on bones and skin. Polymorphism of clinical manifestation and lack of molecular biomarkers have both limited its diagnosis. Our study performed RNA sequencing (RNA-seq) and integrative bioinformatics analysis of long noncoding RNA (lncRNA)-messenger RNA (mRNA) profile in patients with SAPHO syndrome and healthy controls. A total of 4,419 differentially expressed (DE) mRNAs and 2,713 lncRNAs were identified (p < 0.05, fold change > 2) and a coexpression network was constructed to further investigate their regulatory interactions. The DE lncRNAs were predicted to interact with mRNAs in both cis and trans manners. Functional prediction found that the lncRNA-targeted genes may function in SAPHO syndrome by participating in biological process such as adipocytokine signaling pathway, ErbB signaling pathway, FoxO signaling pathway, as well as production and function of miRNAs. The expression levels of three pairs of coexpressed lncRNA-mRNAs were validated by qRT-PCR, and their relative expression levels were consistent with the RNA-seq data. The deregulated RNAs GAS7 and lnc-CLLU1.1-1:2 may serve as potential diagnostic biomarkers, and the combined receiver operating characteristic (ROC) curve of the two showed more reliable diagnostic ability with an AUC value of 0.871 in distinguishing SAPHO patients from healthy controls. In conclusion, this study provides a first insight into long noncoding RNA transcriptome profile changes associated with SAPHO syndrome and inspiration for further investigation on clinical biomarkers and molecular regulators of this inadequately understood clinical entity.https://www.frontiersin.org/articles/10.3389/fgene.2021.684520/fullSAPHO syndromeRNA-seqlncRNA-mRNA interactionneutrophilpredictor |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yuxiu Sun Chen Li Qingyi Lu Haixu Jiang Mengmeng Zhu Guangrui Huang Ting Wang |
spellingShingle |
Yuxiu Sun Chen Li Qingyi Lu Haixu Jiang Mengmeng Zhu Guangrui Huang Ting Wang Integrative Analysis of lncRNA-mRNA Profile Reveals Potential Predictors for SAPHO Syndrome Frontiers in Genetics SAPHO syndrome RNA-seq lncRNA-mRNA interaction neutrophil predictor |
author_facet |
Yuxiu Sun Chen Li Qingyi Lu Haixu Jiang Mengmeng Zhu Guangrui Huang Ting Wang |
author_sort |
Yuxiu Sun |
title |
Integrative Analysis of lncRNA-mRNA Profile Reveals Potential Predictors for SAPHO Syndrome |
title_short |
Integrative Analysis of lncRNA-mRNA Profile Reveals Potential Predictors for SAPHO Syndrome |
title_full |
Integrative Analysis of lncRNA-mRNA Profile Reveals Potential Predictors for SAPHO Syndrome |
title_fullStr |
Integrative Analysis of lncRNA-mRNA Profile Reveals Potential Predictors for SAPHO Syndrome |
title_full_unstemmed |
Integrative Analysis of lncRNA-mRNA Profile Reveals Potential Predictors for SAPHO Syndrome |
title_sort |
integrative analysis of lncrna-mrna profile reveals potential predictors for sapho syndrome |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2021-06-01 |
description |
Synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome is known as a rare disease characterized by inflammatory lesions on bones and skin. Polymorphism of clinical manifestation and lack of molecular biomarkers have both limited its diagnosis. Our study performed RNA sequencing (RNA-seq) and integrative bioinformatics analysis of long noncoding RNA (lncRNA)-messenger RNA (mRNA) profile in patients with SAPHO syndrome and healthy controls. A total of 4,419 differentially expressed (DE) mRNAs and 2,713 lncRNAs were identified (p < 0.05, fold change > 2) and a coexpression network was constructed to further investigate their regulatory interactions. The DE lncRNAs were predicted to interact with mRNAs in both cis and trans manners. Functional prediction found that the lncRNA-targeted genes may function in SAPHO syndrome by participating in biological process such as adipocytokine signaling pathway, ErbB signaling pathway, FoxO signaling pathway, as well as production and function of miRNAs. The expression levels of three pairs of coexpressed lncRNA-mRNAs were validated by qRT-PCR, and their relative expression levels were consistent with the RNA-seq data. The deregulated RNAs GAS7 and lnc-CLLU1.1-1:2 may serve as potential diagnostic biomarkers, and the combined receiver operating characteristic (ROC) curve of the two showed more reliable diagnostic ability with an AUC value of 0.871 in distinguishing SAPHO patients from healthy controls. In conclusion, this study provides a first insight into long noncoding RNA transcriptome profile changes associated with SAPHO syndrome and inspiration for further investigation on clinical biomarkers and molecular regulators of this inadequately understood clinical entity. |
topic |
SAPHO syndrome RNA-seq lncRNA-mRNA interaction neutrophil predictor |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2021.684520/full |
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