- Research article
- Open Access
- Open Peer Review
LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients
BMC Medical Genomics volume 12, Article number: 57 (2019)
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.
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.
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.
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.
Urolithiasis is one of the most common diseases in department of urology with rising prevalence  of which kidney stones take up 6.4% prevalence in China . Kidney stones lead to recurrent urinary tract infection, urinary tract obstruction and even renal failure which have a severe impact on the health of the patients. Accounting for 80% of all stone compositions, calcium oxalate (CaOx) stone is the most common urinary stones that has a high recurrence rate of 40% within 5 years . However, the particular mechanisms of CaOx stone formation remain unclear. Renal tubular epithelial cell damage caused by hyperoxaluria, oxidative stress and inflammation are involved in the process of stone formation .
As a class of small endogenous non-protein-coding RNAs of 20–22 nucleotides, microRNAs (miRNA) lead to the target messenger RNA (mRNA) degradation or translation inhibition by combining with the 3′-untranslated region of target mRNA [5, 6]. 31% of the target gene expression involving in processes of cell proliferation, differentiation, development, aging, and apoptosis could be regulated by miRNA . Dysregulation of miRNAs in kidney might be associated with hypercalciuria which can lead to calcium urolithiasis . Long-non-coding RNA (lncRNA) is a kind of RNAs with a length greater than 200 nucleotides with many of the structural characteristics of mRNA, including a poly(A) tail, 50-capping, and a promoter structure, but not conserved open reading frames [9, 10]. LncRNAs have been demonstrated to interact with miRNAs, imposing an additional level of post-transcriptional regulation and forming a complex regulatory network . The expression profiles of lncRNAs and mRNAs in the CaOx-attached HK-2 cells, and bioinformatic analysis of lncRNA-related mRNA shown that these identified genes were involved in infectious system and signal transduction process .
Our previous study had investigated the miRNA and mRNA expression profile of kidney tissues in CaOx deposition rats and found that the biological functions of these reported miRNAs might be associated with the regulation of ion transport, inflammatory response, and response to wounding and metabolism of epithelial cells in pathogenesis of CaOx stone formation . Although the interaction among lncRNAs, miRNAs and mRNAs in the processes of CaOx stones formation has been paid little attention and has not been sufficiently investigated, lncRNA LINC00339 was found to promote cell pyroptosis and immune inflammation impairment in CaOx-treated HK-2 cells by sponging miR-22–3p to regulate NLRP3 expression . Other lncRNA-miRNA and mRNA interation in renal impairment include LOC105374325-miR-34c/miR-196a/b and Bax/Bak, and overexpression of LINC00520 -miR-27b-3p-OSMR [15, 16]. However, although previous studies have defined the expression profiles of miRNAs and lncRNAs in kidney tissue of CaOx animal model or in cells, the hyperoxaluria or hypercalciuria animal model and cell model treated with CaOx may not really consistent with pathological alterations in clinic CaOx patients [12, 17]. What’s more, as it is an ethical issue to study the kidney tissue of clinic patients and the urine of urolithiasis patients may also directly reflect the associated pathological alterations of human stone disease to some extent, we collected urine of urolithiasis patients and further investigated their alterations and interaction among miRNA, mRNA and lncRNA in this study. We also used the microarray technology and bioinformatics databases to integrally analyze the miRNA, mRNA and lncRNA expression network for the urine of CaOx stone patients.
This research was approved by the human ethics committee of the First Affiliated Hospital of Guangzhou Medical University (Guangzhou, Guangdong, China). All patients signed the informed consent prior to the study.
Patients and samples
The samples and clinical data were collected from the Minimally Invasive Surgery Center, Department of Urology, The First Affiliated Hospital of Guangzhou Medical University (Guangzhou, China) from October 2016 to December 2016. The inclusion criteria for the patients were: 1) male patients diagnosed as calcium oxalate renal stones; 2) aged 18–65 years. Exclusion criteria include urinary tract infection, diabetes mellitus, hypertension, dyslipidemia, dysfunction of liver and kidney, congenital dysplasia of urinary system, history of urinary tumor, renal transplantation and urinary diversion, ectopic kidney, polycystic kidney, horseshoe kidney, kidney malrotation, ureteral stenosis and other malformations. Five CaOx kidney stone patients were recruited in CaOx stone group, and six healthy people were included in control group. All participants were male, no significant difference in age, weight and height between the CaOx stone group and the control group was found. The detailed characteristics of study subjects are summarized in Table 1. Stone composition of CaOx was confirmed by infrared spectrum analysis method. Midstream morning urine was collected as specimen from all participants before patients were given any medicine on admission.
Urine RNA extraction
Total RNA was extracted from urine using mirVana™ PARIS™ Kit (Ambion-1556, USA) according to the manufacturer’s protocol. The purity and concentration were assessed by NanoDrop ND-2000 (Thermo Fisher, USA) and the RNA integrity was confirmed by Agilent Bioanalyzer 2100 (Agilent Technologies). The concentrate of extracted RNA was about 200–2000 pg/μl, and the total extracted RNA over 2000 pg was used for next-step analysis. After the RNA was qualified, the samples were labeled, hybridized and eluted according to the standard procedure of microarray.
Both the samples from stone group and the samples from control group were selected for microarray analysis. LncRNA and mRNA expression profiles were analyzed by the Affymetrix® GeneChip® Whole Transcript Expression Arrays, and Agilent miRNA Microarrays 8x60K were applied to analyze miRNA expression profiles in the urine. Microarray analyses were performed by Oebiotech Corporation (Shanghai, China). Hierarchical clustering analysis and volcano maps were carried out using the gplots and heatmap packages in the R platform.
Construction of lncRNA-miRNA-mRNA and functional analysis
CeRNA network was built by the miRNAs, lncRNAs and mRNAs with significantly difference. First, the targets of differentially expressed miRNAs were predicted by miRanda and pearson correlation coefficient. MiRanda (www.microrna.org) was used to predict the miRNA responsive elements (MRE) of target genes and binding sites of detected miRNAs based on the sequences of lncRNAs and mRNAs . These predicted mRNAs and lncRNAs were compared with those detected from microarray, and then the overlap RNAs were determined. To reduce false positive of paired miRNA-mRNA and miRNA-lncRNA, Pearson correlation coefficient (PCC) was used to filtering the significant paired miRNA-mRNA and miRNA-lncRNA, and the P value of PCC in each pair was calculated by Fisher’s asymptotic distribution . Only the interactions ofnegative PCC with P value < 0.05 were included. Then shared pairs from the predicted paired miRNA-mRNA and miRNA-lncRNA by miRanda and PCC were selected for further analysis. Finally, a ceRNA network correlated with the CaOx stones was drawn by Cytoscape 2.8.0 (https://cytoscape.org/) according to predicted shared pairs of miRNA-mRNA and miRNA-lncRNA. In addition, ceRNA_scores were calculated according to the following formula for construction of ceRNA regulatory network , and the corresponding formula is showed below.
For the sake of determining the biological functions and pathways of these target mRNAs in ceRNA network, Gene ontology (GO, http://geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.kegg.jp/) annotations was carried out by DAVID Bioinformatics Resources.
Cell culture and cell exposure
Human Kidney Epithelial Cells, HK-2, were obtained from the American Type Culture Collection (Manassas, VA, USA) and maintained in a DMEM/F12 medium supplemented with 10% Fetal Bovine Serum and 1% penicillin/streptomycin. Confluent cells with 70–80% confluence were treated with 1 mM sodium oxalate (NaOx) for 24 h at 37 °C in a 6-well plate. Total RNA extracted from these cell was used forextraction and validation.
Cell RNA extraction and quantitative real-time PCR (qRT-PCR)
TRIzol reagent (Ambion, USA) was used to extract the total cell RNA according to the manufacturer’s instructions and the NanoPhotometer (Biotek, USA) was used to assess the purity and concentration of the extracted RNA. The extracted RNA concentration of all sample was higher than 400 μg/μl, and the A260/280 was in the range of 1.8–2.0.
For miRNA, total RNA of 2 μg was used for cDNA synthesis and quantitative detection according to the protocol of the All-in-One™miRNA qRT-PCR Detection Kit (GeneCopoeia, Guangzhou, China). For mRNA and lncRNA, total RNA of 1 μg was reverse transcribed to cDNA by using Takara reverse transcription kit (Takara, Dalian, China) and PCR was performed based on standard protocol of SYBR Premix Ex Taq (Takara, Dalian, China). The primers were obtained and synthesized by Shanghai Generay Biotech Co., Ltd. U6 was chosen as the internal controls of miRNA, while GAPDH was used as the internal controls of lncRNA and mRNA. The expression of target miRNAs, mRNAs and lncRNAs were quantified by using 2-ΔΔCq method . To compare the relative expression of different groups, the control group were normalized as “1”. All reactions were performed in triplicate. The synthesized primer sequences of lncRNA, mRNA and lncRNA are list in Additional file 1: Table S1.
Continuous variables in Table 1 were shown in means ± standard deviation (SD), while experement results presented in Fig. 4 were expressed as means ± standard error (SEM). The student’s t-test was applied for statistical analysis by using SPSS 13.0. P < 0.05 was considered to be statistically significant.
Alteration of miRNA, mRNA and lncRNA expression profiles
The miRNA expression of the urine sample between the two groups was detected, and nine mature miRNAs which were significantly different between the two groups were identified. Compared to the control group (P < 0.05), the deferential expressions in the urine of CaOx stone group revealed 1.5-fold changes, including 4 upregulated miRNAs and 5 downregulated ones (Table 2).
To further investigate potential targets of the detected miRNAs, the mRNA and lncRNA expression profiles of the same urine samples were detected using Affymetrix expression arrays. A total of 883 mRNAs and 1002 lncRNAs were found to be differentially expressed. Among the differentially expressed mRNAs, a number of 467 mRNAs were upregulated and 416 mRNAs were downregulated in the stone group compared to control group, respectively (Table 3). Among the differentially expressed lncRNAs, 790 lncRNAs were significantly increased whereas 212 lncRNAs were significantly decreased in stone group (Table 4).
MiRNA (Fig. 1a), mRNA (Fig. 1c) and lncRNA (Fig. 1e) expression patterns between CaOx and normal urine sample were distinguished via hierarchical clustering heatmaps. Volcano plots were performed to assess the variation and reproducibility of miRNA (Fig. 1b), mRNA (Fig. 1d) and lncRNA (Fig. 1f) expression in urine between CaOx and normal group.
In line with our results, 131 mRNAs such as 5′ nucleotidase, ecto (NT5E), B-cell lymphoma 2 like 14 (BCL2L14), ubiquitin associated domain containing 1 (UBAC1), lamin A/C (LMNA), and chemokines chemokine ligand 3 (CCL3) and one miRNAs, miR-30d-5p, which were previously shown to be up-regulated or down-regulated in CaOx model were also found in this study (Fig. 2) . Although network analysis of the above signaling pathways are not constructed, the Venn diagram were constructed and those identified mRNAs and miRNA may provide a following reference for the corresponding biomarker research.
Construction and functional analysis of ceRNA network in urine sample
In order to figure out the relationships among these differentially expressed RNAs, the ceRNA network among differentially expressed miRNA, mRNA and lncRNA in urine were constructed. Regulatory relationship between differentially expressed miRNA and the targeted differentially expressed mRNA or lncRNA (miRNA-mRNA or miRNA-lncRNA) were predicted by miRanda and PCC. Then the predicted shared pairs of miRNA-mRNA and miRNA-lncRNA were selected for construction of ceRNA regulatory network. A ceRNA network correlated with the CaOx stones was drawn by Cytoscape after integrating the miRNA-mRNA interactions into lncRNA-miRNA interactions (Fig. 3). The ceRNA network was composed of nine miRNA nodes, 141 mRNA nodes and 65 lncRNA nodes. In the ceRNA network, hsa-miR-6776-3p targeted gene CDH4, a gene encoding retinal type I cadherin, which can activate c-Jun NH(2)-terminal kinase (JNK) signal pathways in osteosarcoma cells, leading to production of reactive oxygen species (ROS) [22, 23]. Several lncRNAs such as lnc-ABCA10–1:1, lnc-CANX-2:1, lnc-RDH8–4:1 and lnc-AC006156.1–12:1 were shown to share the common miRNA, hsa-miR-6776-3p, with CDH4, regulating production of ROS.
Then, the differentially expressed mRNAs reflected in the network were utilized to reveal the gene functions of the dysregulated lncRNA-associated ceRNA network via GO and KEGG pathway analysis. In GO analysis, gene function enrichment in biological process, molecular function and cellular component were analyzed (P < 0.05) and the top five enriched GO terms of the three aspects are listed in Table 5. GO analysis of biological process revealed that differentially expressed mRNAs were primarily enriched in positive regulation of respiratory burst, cardiac ventricle morphogenesis and positive regulation of mitophagy. The cellular component results indicated that differentially expressed mRNAs were mainly enriched in MPP7-DLG1-LIN7 complex, GATOR2 complex and nuclear exosome (RNase complex). The molecular function results showed that differentially expressed mRNAs were mainly enriched in protein kinase regulator activity, chloride ion binding and transaminase activity. In KEGG pathway analysis, the top five enriched pathways included pentose phosphate pathway, pentose and glucuronate interconversions, glyoxylate and dicarboxylate metabolism, fructose and mannose metabolism and Janus kinase/signal transducer and activator of transcription (JAK-STAT) signaling pathways (Table 6).
Validation of differentially expressed miRNAs, mRNAs and lncRNAs in HK-2 cells treated with NaOx
To further screen out the differentially expression profiles of miRNAs, mRNA, and lncRNA, qRT-PCR were performed on HK-2 cells incubated by NaOx. All differentially expressed miRNAs, ten mRNAs and 10 lncRNAs with high fold change filtered from microarray were selected. Relative expression levels of the selected miRNA, mRNA and lncRNA were depicted in Fig. 4 (A-F). The genes that are consistent with the expression changes of microarray will be more convinced and more likely to be the biomarkers for kidney stones. The qRT-PCR results showed that hsa-miR-6796-3p, hsa-miR-30d-5p, hsa-miR-3192–3p, hsa-miR-518b and hsa-miR-6776-3p were found to be accord with the expression changes of microarray. For mRNAs, NT5E, CDH4, CLEC14A and CCNL1 were validated to be consistent with expression changes of microarray results. For lncRNAs, the expression of lnc-TIGD1L2–3 and lnc-KIN-1 were significantly increased, while lnc-FAM72B-4, lnc-EVI5L-1, lnc-SERPINI1–2 and lnc-MB-6 were shown to be downregulated in HK-2 cells incubated by NaOx. The variation tendency of o ther miRNAs, mRNAs and lncRNAs were not matched with the variations in NaOx induced HK-2 cells model, which may have lower possiblity for prediction of CaOx kidney stones formation.
Nephrolithiasis is a multifactorial disease with a rising prevalence. Numerous hypotheses have been investigated in previous research to clarify the mechanisms of CaOx stone formation [24,25,26,27]. Better understanding of the precise mechanisms of CaOx stones formation related to functional RNAs is critical for exploring potential new strategies for early diagnosis and therapy. In this study, we systematically analyzed the lncRNA-involved regulatory networks based on microarray data of urine from CaOx patients. This is our first attempt to explore a comprehensive molecular event leading to the pathogenesis of CaOx stones formation and discovered functional RNAs regulatory networks in the stones formation in urine sample from clinical CaOx patients.
Metabolite is highly correlated with CaOx kidney stone and the urine sample is one of the most direct and convenient body fluid for test. In the present study, we found nine miRNAs, 883 mRNAs and 1002 lncRNAs differentially expressed in urine between CaOx patients and the controls. In accordance with our previous study on integrative analysis miRNA and mRNA expression profiles, some previously identified differentially expressed mRNAs and miRNAs were also detected in this study . We also compared the results from our previous study in CaOx model and the present study in urine samples, and 131 mRNAs and one miRNAs, miR-30d-5p, were also found to be consistent in this study. This RNAs changing profiles consistent in different sources of samples may be taken as biomarkers for early diagnosis or prognosis of clinic CaOx stone patients. Most of these detected RNAs had been found to be associated with the stones formation. LMNA expression was increased in renal tubular cells adhered with calcium oxalate monohydrate (COM), and expression of LMNA in renal tubular cells is important for tissue repair, cell proliferation, and COM crystal adhesion . Inflammatory response and phagocytic mechanisms of macrophages exposed to COM crystal were also verified, and an inflammatory cascade including CCL3 was released by macrophages . Increase of miR-30d-5p resulted in reduction of autophagy , and autophagy has been proved to be significant for the regulation of oxidative stress-induced renal tubular injury in CaOx stones formation .
As the difference was existed among the urine of renal stone patients, animal model and cell models, it is true that some of the miRNAs, mRNAs and lncRNAs may not match in NaOx treated HK-2 cells compared to the urine sample. In this study, the expression of several miRNAs, mRNAs and lncRNAs were confirmed in renal cell injury model by NaOx via qRT-PCR and the outcomes were basically consistent with the microarray data. The genes, such as miR-30d-5p, CDH4 were in accord with the microarray variation, which is associated with pathological alteration in stone formation, and could serve as potential biomarker for diagnosis or therapeutic target of renal stone. The inconsistent results may be related to the differences of sample sources, as they were confirmed by cell models induced by NaOx instead of by urine samples from clinical patients.
To further explore the role of these differentially expressed RNAs in the formation of CaOx stones, ceRNA network was constructed and GO and KEGG pathway analysis were carried out. The positive regulation of respiratory burst, mitophagy and nitric-oxide synthase activity, which are related to the formation of CaOx stone were revealed. Strong up-regulation of respiratory burst involving nicotinamide adenine dinucleotide phosphate (NADPH) oxidase system has shown to be the key cause of oxalate- or CaOx- induced oxidative stress-mediated renal tubular cell injury, leading to the formation of stones [32,33,34,35]. In cellular component fold enrichment of GO analysis, MPP7-DLG1-LIN7 complex was the most enriched, which is a heterotrimeric protein complex formed by the union of membrane palmitoylated protein 7 (MPP7), discs large 1 (DLG) and protein lin-7 homolog (LIN7), regulating the stability of cell junction (http://www.geneontology.org). Cell junction always play important role in regulating reabsorption of calcium and maintaining polarity of cells . COM crystals would give rise to disruption of renal tubular epithelial cell tight junction, which triggered epithelial cell injury, inflammation and ultimately resulted in cell apoptosis or death by activating serine/threonine kinase (Akt), Protein Kinase B, signaling pathways or p38 mitogen-activated protein kinase (MAPK) pathways . In GO analysis of molecular function, the mostly highly enriched in molecular function are protein kinase regulator activity, chloride ion binding and MAPK kinase binding Growing evidences showed that protein phosphorylation played a vital role in the development of CaOx kidney stones. Increased phosphorylated Akt (p-Akt) expression contributed to the epithelial-mesenchymal transition (EMT) of renal epithelial cell treated by COM crystal . In another study, phosphorylation of MAPK was involved in COM crystal-induced damage, causing tight junction disruption .
According to the enriched KEGG pathway analysis, most of genes reflected in the ceRNA network were related to pentose phosphate pathway, pentose and glucuronate interconversions, glyoxylate and dicarboxylate metabolism, and JAK-STAT signaling pathway. The main function of pentose phosphate pathway is to generate NADPH, which serves as a coenzyme in a wide range of oxidation-reduction reactions. NADPH is essential for maintaining levels of reduced glutathione (GSH), which is a significant contributor to endogenous antioxidant processes [39,40,41,42]. ROS could promote the formation of kidney CaOx stone with signaling molecule changes, renal tubular cell injury and inflammation, and treatment with antioxidants significantly reduced the crystal deposition [33, 34].
Hyperoxaluria caused by excessive accumulation of glyoxylate was another factor participated in the process of CaOx stone formation . JAK/STAT signaling has emerged as key roles in EMT . While EMT induced by COM or oxalate was involved in renal fibrosis, contributing to CaOx stone formation [45, 46]. All functional analysis of this ceRNA network further indicated that the lncRNAs with ceRNA potential may play key roles in CaOx stone formation.
In the ceRNA network, hsa-miR-6776-3p targeted gene CDH4, and both hsa-miR-6776-3p and CDH4 were listed as top dysregulated RNA. In the process of urolithiasis, CaOx activated NADPH oxidase, producing ROS, via JNK pathway, which is activated by overexpression of CDH4 in osteosarcoma cells. Our qRT-PCR validation results of hsa-miR-6776-3p and CDH4 in NaOx treated HK-2 cells were also in accordance with microarray analysis. The ceRNA network showed that several lncRNAs such as lnc-ABCA10–1:1, lnc-CANX-2:1, lnc-RDH8–4:1 and lnc-AC006156.1–12:1 regulating the interaction between hsa-miR-6776-3p and CDH4. Among these lncRNAs, lnc-RDH8–4:1 has the highest fold change (3.0978) of deferential expressions, which may have the largest possibility to regulate hsa-miR-6776-3p-CDH4 interation and its downstream JNK pathway, finally with the production of ROS. These results indicated that lnc-RDH8–4:1, hsa-miR-6776-3p and CDH4 might serve as potential biomarker for diagnosis of renal stone by test of urine from CaOx patients.
In summary, instead of kidney tissue from animal model or cells, the urine from stone patients was analyzed by microarray to determine miRNAs, mRNAs and lncRNAs expression profiles in this study, which may directly reflect the role of these RNA in the formation of CaOx stones, providing new biomarkers for early diagnosis and prognosis of urolithiasis. However, as there is a fundamental difference between urine and kidney, whether the miRNAs, mRNAs and lncRNAs observed in urine are consistent with the natural pathogenesis of CaOx stone in kidney are still under investigated. In addition, HK-2 cells treated with NaOx were used to validate the differentially expression profiles. The verification results on the cells did not fully match the results of the array, which may be related to the different sample sources. In fact, the urine samples from clinical patients may also vary in different patients and the large sample multi-centre study of this kind of urine samples is further needed in future. Moreover, whether the altered mRNAs could be translated into the similar proteins need further exploration.
Taken together, the different expression of miRNAs, mRNAs and lncRNAs in the urine between CaOx stone patients and normal population were well defined in this study, and GO and KEGG analysis were used to reveal the gene functions of the dysregulated lncRNA-associated ceRNA network, which included the respiratory burst, regulation of mitophagy, protein kinase regulator activity, pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, and JAK-STAT signaling pathway. This study may provide new diagnosis biomarkers or treament target for renal CaOx stone by test of urine from patients and new direction basis for further research on urolithiasis mechanism.
B-cell lymphoma 2 like 14
Chemokines chemokine ligand 3
competing endogenous RNA
Calcium oxalate monohydrate
Janus kinase/signal transducer and activator of transcription
C-Jun NH(2)-terminal kinase
Kyoto Encyclopedia of Genes and Genomes
Mitogen-activated protein kinase
MiRNA response elements
Nicotinamide adenine dinucleotide phosphate
5′ nucleotidase, ecto
Pearson correlation coefficient
Quantitative real-time PCR
Reactive oxygen species
Standard error of mean
Ubiquitin associated domain containing 1
Coe FL, Evan A, Worcester E. Kidney stone disease. J Clin Investig. 2005;115(10):2598.
Zeng G, Mai Z, Xia S, Wang Z, Zhang K, Wang L, et al. Prevalence of kidney stones in China: an ultrasonography based cross; ectional study. BJU Int. 2017;120(1):109–16.
Worcester EM, Coe FL. Clinical practice. Calcium kidney stones. N Engl J Med. 2010;363(10):954–63.
Khan SR. Crystal-induced inflammation of the kidneys: results from human studies, animal models, and tissue-culture studies. Clin Exp Nephrol. 2004;8(2):75–88.
Ambros V. microRNAs : tiny regulators with great potential. Cell. 2001;107(7):823–6.
Ambros V. The functions of animal microRNAs. Nature. 2004;431(7006):350–5.
Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian MicroRNA targets. Cell. 2003;115(7):787–98.
Lu Y, Qin B, Hu H, et al. Integrative microRNA-gene expression network analysis in genetic hypercalciuric stone-forming rat kidney. PeerJ. 2016;4(7):e1884.
Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, et al. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res. 2013;41(Database issue):D983–6.
Gutschner T, Diederichs S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol. 2012;9(6):703–19.
Juan L, Wang G, Radovich M, Schneider BP, Clare SE, Wang Y, et al. Potential roles of microRNAs in regulating long intergenic noncoding RNAs. BMC Med Genet. 2013;6(S1):S7.
Wang Z, Zhang JW, Zhang Y, Zhang SP, Hu QY, Liang H. Analyses of long non-coding RNA and mRNA profiling using RNA sequencing in calcium oxalate monohydrate-stimulated renal tubular epithelial cells. Urolithiasis. 2018. https://doi.org/10.1007/s00240-018-1065-7.
Lan C, Chen D, Liang X, Huang J, Zeng T, Duan X, et al. Integrative analysis of miRNA and mRNA expression profiles in calcium oxalate nephrolithiasis rat model. Biomed Res Int. 2017;2017(7):1–9.
Song Z, Zhang Y, Gong B, Xu H, Hao Z, Liang C. Long noncoding RNA LINC00339 promotes renal tubular epithelial pyroptosis by regulating the miR-22-3p/NLRP3 axis in calcium oxalate-induced kidney stone. J Cell Biochem. 2019. https://doi.org/10.1002/jcb.28330 [Epub ahead of print].
Hu S, Han R, Shi J, Zhu X, Qin W, Zeng C, et al. The long noncoding RNA LOC105374325 causes podocyte injury in individuals with focal segmental glomerulosclerosis[J]. J Biol Chem. 2018;293(52):20227–39.
Tian X, Ji Y, Liang Y, Zhang J, Guan L, Wang C. LINC00520 targeting miR-27b-3p regulates OSMR expression level to promote acute kidney injury development through the PI3K/AKT signaling pathway. J Cell Physiol. 2019. https://doi.org/10.1002/jcp.28118 [Epub ahead of print].
Cao Y, Gao X, Yang Y, Zhi Ye EW, Dong Z. Changing expression profiles of long non-coding RNAs, mRNAs and circular RNAs in ethylene glycol-induced kidney calculi rats[J]. BMC Genomics. 2018. https://doi.org/10.1186/s12864-018-5052-8.
Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell. 2011;146(3):353–8.
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009;458(7235):223–7.
Shaoli D, Suman G, Rituparno S, Jayprokas C, Sandro B. LnCeDB: database of human long noncoding RNA acting as competing endogenous RNA. PLoS One. 2014;9(6):e98965.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) method. Methods. 2001;25(4):402–8.
Tang Q, Lu J, Zou C, Shao Y, Chen Y, Narala S, et al. CDH4 is a novel determinant of osteosarcoma tumorigenesis and metastasis. Oncogene. 2018;37(27):3617–30.
Khan SR. Reactive oxygen species as the molecular modulators of calcium oxalate kidney stone formation: evidence from clinical and experimental investigations. J Urol. 2013;189(3):803–11.
Verkoelen CF, Verhulst A. Proposed mechanisms in renal tubular crystal retention. Kidney Int. 2007;72(1):13–8.
Evan AP, Lingeman JE, Coe FL, Parks JH, Bledsoe SB, Shao Y, et al. Randall’s plaque of patients with nephrolithiasis begins in basement membranes of thin loops of Henle. J Clin Investig. 2003;111(5):607–16.
Evan AP, Coe FL, Lingeman JE, Shao Y, Matlaga BR, Kim SC, et al. Renal crystal deposits and histopathology in patients with cystine stones. Kidney Int. 2006;69(12):2227–35.
Taylor ER, Stoller ML. Vascular theory of the formation of Randall plaques. Urolithiasis. 2015;43(1):41–5.
Pongsakul N, Vinaiphat A, Chanchaem P, Fong-Ngern K, Thongboonkerd V. Lamin a/C in renal tubular cells is important for tissue repair, cell proliferation, and calcium oxalate crystal adhesion, and is associated with potential crystal receptors. FASEB J. 2016;30(10):3368–77.
Kusmartsev S, Dominguez-Gutierrez PR, Canales BK, Bird VG, Vieweg J, Khan SR, et al. Calcium oxalate stone fragment and crystal phagocytosis by human macrophages. J Urol. 2016;195(4):1143–51.
Zhao F, Qu Y, Zhu J, L Z, L H, Liu H, et al. miR-30d-5p plays an important role in autophagy and apoptosis in developing rat brains after hypoxic-ischemic injury. J Neuropathol Exp Neurol. 2017;76(8):709–19.
Duan X, Kong Z, Mai X, Lan Y, Liu Y, Yang Z, et al. Autophagy inhibition attenuates hyperoxaluria-induced renal tubular oxidative injury and calcium oxalate crystal depositions in the rat kidney. Redox Biol. 2018;16:414–25.
Zuo J, Khan A, Glenton PA, Khan SR. Effect of NADPH oxidase inhibition on the expression of kidney injury molecule and calcium oxalate crystal deposition in hydroxy-L-proline-induced hyperoxaluria in the male Sprague–Dawley rats. Nephrol Dial Transplant. 2011;26(6):1785–96.
Khan SR. Hyperoxaluria-induced oxidative stress and antioxidants for renal protection. Urol Res. 2005;33(5):349–57.
Umekawa T, Tsuji H, Uemura H, Khan SR. Superoxide from NADPH oxidase as second messenger for the expression of osteopontin and monocyte chemoattractant protein-1 in renal epithelial cells exposed to calcium oxalate crystals. BJU Int. 2009;104(1):115–20.
Khan SR, Khan A, Byer KJ. Temporal changes in the expression of mRNA of NADPH oxidase subunits in renal epithelial cells exposed to oxalate or calcium oxalate crystals. Nephrol Dial Transplant. 2011;26(6):1778–85.
Gong Y, Hou J. Claudins in barrier and transport function-the kidney. Pflugers Arch - Eur J Physiol. 2017;469(1):105–13.
Yu L, Gan X, Liu X, An R. Calcium oxalate crystals induces tight junction disruption in distal renal tubular epithelial cells by activating ROS/Akt/p38 MAPK signaling pathway. Ren Fail. 2017;39(1):440–51.
Wang XF, et al. Gastrin-releasing peptide receptor gene silencing inhibits the development of the epithelial-mesenchymal transition and formation of a calcium oxalate crystal in renal tubular epithelial cells in mice with kidney stones via the PI3K/Akt signaling pathway. J Cell Physiol. 2019;234(2):1567–77.
Jeon SM, Chandel NS, Hay N. AMPK regulates NADPH homeostasis to promote tumour cell survival during energy stress. Nature. 2012;485(7400):661–5.
Tan SX, Teo M, Lam YT, Dawes IW, Perrone GG. Cu, Zn superoxide dismutase and NADP(H) homeostasis are required for tolerance of endoplasmic reticulum stress in Saccharomyces cerevisiae. Mol Biol Cell. 2009;20(5):1493–508.
Cao L, Chen J, Li M, Qin YY, Sun M, Sheng R, et al. Endogenous level of TIGAR in brain is associated with vulnerability of neurons to ischemic injury. Neurosci Bull. 2015;31(5):527–40.
Li M, Zhou ZP, Sun M, Cao L, Chen J, Qin YY, et al. Reduced nicotinamide adenine dinucleotide phosphate, a pentose phosphate pathway product, might be a novel drug candidate for ischemic stroke. Stroke. 2016;47(1):187–95.
Cochat P, Rumsby G. Primary hyperoxaluria. N Engl J Med. 2013;369(7):649–58.
Yu L, Zhang Y, Zhang H, Li Y. SOCS3 overexpression inhibits advanced glycation end product-induced EMT in proximal tubule epithelial cells. Exp Ther Med. 2017;13(6):3109–15.
Convento MB, Pessoa EA, Cruz E, da Glória MA, Schor N, Borges FT. Calcium oxalate crystals and oxalate induce an epithelial-to-mesenchymal transition in the proximal tubular epithelial cells: contribution to oxalate kidney injury. Sci Rep. 2017;7:45740.
Kanlaya R, Sintiprungrat K, Thongboonkerd V. Secreted products of macrophages exposed to calcium oxalate crystals induce epithelial mesenchymal transition of renal tubular cells via RhoA-dependent TGF-beta1 pathway. Cell Biochem Biophys. 2013;67(3):1207–15.
This work was financially supported in part by research grants from Science and Technology Project of Guangzhou (201604020001), Guangzhou Science Technology and Innovation Commission (201607010162) and National Natural Science Foundation of China (81570633). The fund was mainly used for microarray analysis and examinations of subjects in study such as CT scan and chemical composition of urinary stones.
Availability of data and materials
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.
Ethics approval and consent to participate
This research was approved by the human ethics committee of the First Affiliated Hospital of Guangzhou Medical University (Guangzhou, Guangdong, China). All patients signed the informed consent prior to the study.
Consent for publication
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Liang, X., Lai, Y., Wu, W. et al. LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients. BMC Med Genomics 12, 57 (2019). https://doi.org/10.1186/s12920-019-0502-y
- Calcium oxalate
- Kidney stone
- Competing endogenous RNA network