LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients
Abstract Background To explore long-non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression profiles and their biological functions in the urine samples in calcium oxalate (CaOx) patients. Methods Five CaOx kidney stone patients were recruited in CaOx stone group and six health...
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BMC
2019-04-01
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Series: | BMC Medical Genomics |
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Online Access: | http://link.springer.com/article/10.1186/s12920-019-0502-y |
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Article |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xiongfa Liang Yongchang Lai Weizhou Wu Dong Chen Fangling Zhong Jian Huang Tao Zeng Xiaolu Duan Yapeng Huang Shike Zhang Shujue Li Wenqi Wu |
spellingShingle |
Xiongfa Liang Yongchang Lai Weizhou Wu Dong Chen Fangling Zhong Jian Huang Tao Zeng Xiaolu Duan Yapeng Huang Shike Zhang Shujue Li Wenqi Wu LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients BMC Medical Genomics Calcium oxalate Kidney stone Competing endogenous RNA network Urine LncRNA MiRNA |
author_facet |
Xiongfa Liang Yongchang Lai Weizhou Wu Dong Chen Fangling Zhong Jian Huang Tao Zeng Xiaolu Duan Yapeng Huang Shike Zhang Shujue Li Wenqi Wu |
author_sort |
Xiongfa Liang |
title |
LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients |
title_short |
LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients |
title_full |
LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients |
title_fullStr |
LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients |
title_full_unstemmed |
LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients |
title_sort |
lncrna-mirna-mrna expression variation profile in the urine of calcium oxalate stone patients |
publisher |
BMC |
series |
BMC Medical Genomics |
issn |
1755-8794 |
publishDate |
2019-04-01 |
description |
Abstract Background To explore long-non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression profiles and their biological functions in the urine samples in calcium oxalate (CaOx) patients. Methods Five CaOx kidney stone patients were recruited in CaOx stone group and six healthy people were included as control group, whose midstream morning urine was collected before the patients were given any medicine on admission. After total RNA was extracted from urine, microarray of miRNA, mRNA and lncRNA were applied to explore their expression variation. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to reveal the gene functions of the dysregulated lncRNA-associated competing endogenous RNA (ceRNA) network. Quantitative real-time PCR were performed on HK-2 cells treated with sodium oxalate (NaOx) to further screen out the differentially expression profiles of these RNAs. Results A total of nine miRNAs, 883 mRNAs and 1002 lncRNAs were differentially expressed in urine of CaOx patients compared with normal population. GO analysis revealed that most of mRNAs from ceRNA network were enriched in terms of respiratory burst, regulation of mitophagy, and protein kinase regulator activity. KEGG pathway analysis of these genes related to ceRNA network highlight their critical role in pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, and Janus kinase/signal transducer and activator of transcription (JAK-STAT) signaling pathway. Five miRNAs (miR-6796-3p, miR-30d-5p, miR-3192–3p, miR-518b and miR-6776-3p), four mRNAs (NT5E, CDH4, CLEC14A, CCNL1) and six lncRNAs (lnc-TIGD1L2–3, lnc-KIN-1, lnc-FAM72B-4, lnc-EVI5L-1, lnc-SERPINI1–2, lnc-MB-6) from the HK-2 cells induced by NaOx were consistent with the expression changes of microarray results. Conclusion The differential expressed miRNAs, mRNAs and lncRNAs may be associated with numerous variations of the signaling pathways or regulation of metabolism and kinase activity, providing potential biomarkers for early diagnosis of urolithiasis and new basis for further research of urolithiasis mechanism. |
topic |
Calcium oxalate Kidney stone Competing endogenous RNA network Urine LncRNA MiRNA |
url |
http://link.springer.com/article/10.1186/s12920-019-0502-y |
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doaj-f21d73900e7d4b63878ed12d8c13f3532021-04-02T15:19:09ZengBMCBMC Medical Genomics1755-87942019-04-0112111110.1186/s12920-019-0502-yLncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patientsXiongfa Liang0Yongchang Lai1Weizhou Wu2Dong Chen3Fangling Zhong4Jian Huang5Tao Zeng6Xiaolu Duan7Yapeng Huang8Shike Zhang9Shujue Li10Wenqi Wu11Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyDepartment of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Urology Research Institute, Guangdong Key Laboratory of UrologyAbstract Background To explore long-non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression profiles and their biological functions in the urine samples in calcium oxalate (CaOx) patients. Methods Five CaOx kidney stone patients were recruited in CaOx stone group and six healthy people were included as control group, whose midstream morning urine was collected before the patients were given any medicine on admission. After total RNA was extracted from urine, microarray of miRNA, mRNA and lncRNA were applied to explore their expression variation. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to reveal the gene functions of the dysregulated lncRNA-associated competing endogenous RNA (ceRNA) network. Quantitative real-time PCR were performed on HK-2 cells treated with sodium oxalate (NaOx) to further screen out the differentially expression profiles of these RNAs. Results A total of nine miRNAs, 883 mRNAs and 1002 lncRNAs were differentially expressed in urine of CaOx patients compared with normal population. GO analysis revealed that most of mRNAs from ceRNA network were enriched in terms of respiratory burst, regulation of mitophagy, and protein kinase regulator activity. KEGG pathway analysis of these genes related to ceRNA network highlight their critical role in pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, and Janus kinase/signal transducer and activator of transcription (JAK-STAT) signaling pathway. Five miRNAs (miR-6796-3p, miR-30d-5p, miR-3192–3p, miR-518b and miR-6776-3p), four mRNAs (NT5E, CDH4, CLEC14A, CCNL1) and six lncRNAs (lnc-TIGD1L2–3, lnc-KIN-1, lnc-FAM72B-4, lnc-EVI5L-1, lnc-SERPINI1–2, lnc-MB-6) from the HK-2 cells induced by NaOx were consistent with the expression changes of microarray results. Conclusion The differential expressed miRNAs, mRNAs and lncRNAs may be associated with numerous variations of the signaling pathways or regulation of metabolism and kinase activity, providing potential biomarkers for early diagnosis of urolithiasis and new basis for further research of urolithiasis mechanism.http://link.springer.com/article/10.1186/s12920-019-0502-yCalcium oxalateKidney stoneCompeting endogenous RNA networkUrineLncRNAMiRNA |