scholarly journals Expression of lncRNAs in children with pancreaticobiliary maljunction: functional analysis and potential biomarkers

2022 ◽  
Author(s):  
Lian Zhao ◽  
San-li Shi ◽  
Wan-liang Guo
Keyword(s):  
Gene Ontology ◽  
Target Genes ◽  
Characteristic Curve ◽  
Pancreaticobiliary Maljunction ◽  
Differentially Expressed ◽  
Qrt Pcr ◽  
Extracellular Region ◽  
Potential Biomarker ◽  
The Difference ◽  
Cis And Trans

IntroductionPancreaticobiliary maljunction (PBM) leads to higher rates of complications, including cholangitis,pancreatitis, and malignancies. The present study was to investigat the expression profile of long non-coding RNAs (lncRNAs) and their potential role as biomarkers in children with pancreaticobiliary maljunction.Material and methodsThe differential expression of lncRNAs and mRNAs from 15 pediatric patients with pancreaticobiliary maljunction and 15 control subjects were analyzed using a commercial microarray and validated with qRT-PCR. The potential biological functions of differentially expressed genes were explored based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment. The ability of potential lncRNA biomarkers to predict pancreaticobiliary maljunction was assessed based on the area under the receiver operating characteristic curve (AUC).ResultsThere were 2915 mRNAs and 173 lncRNAs upregulated, and 2121 mRNAs and 316 lncRNAs downregulated in pancreaticobiliary maljunction cases compared to controls. The enriched Gene Ontology categories associated with differentially expressed mRNAs were extracellular matrix, extracellular region, and kinetochore. The most enriched Kyoto Encyclopedia pathway was protein digestion and absorption, which has been associated with cancer and PI3K-Akt signaling. Analysis of cis- and trans-target genes predicted that a single lncRNA was able to regulate several mRNAs. The qRT-PCR results for NR_110876, NR_132344, XR_946886, and XR_002956345 were consistent with the microarray results, and the difference was statistically significant for NR_132344, XR_946886, and XR_002956345 (p < 0.05). AUC was significant only for XR_946886 (0.837, p < 0.001).ConclusionsOur results implicate lncRNAs in common bile duct pathogenesis in pancreaticobiliary maljunction, and they identify XR_946886 as a potential biomarker for the disease.

scholarly journals LncRNA expression profile, functional analysis and potential biomarkers in children with pancreaticobiliary maljunction

2021 ◽  
Author(s):  
Lian Zhao ◽  
San-li Shi ◽  
Wan-liang Guo
Keyword(s):  
Expression Profile ◽  
Roc Curve ◽  
Messenger Rna ◽  
Pancreaticobiliary Maljunction ◽  
Extracellular Region ◽  
Non Coding Rnas ◽  
Polymerase Chain ◽  
The Difference ◽  
Differentially Expressed Mrna ◽  
Cis And Trans

Abstract Background The present study was aimed to investigate the expression profile of long non-coding RNAs (lncRNAs) and its potential as biomarker for pancreaticobiliary maljunction (PBM). Methods The differential expression of lncRNA and messenger RNA (mRNA) from 15 pediatric patients with PBM and 15 control subjects were analyzed with microArray and validated with quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Gene Ontology enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis were used to investigate the biological functions of these genes. The area under curve (AUC) of receiver operating characteristic (ROC) curve was used to predict the biomarker of lncRNA in PBM. Results There were 2915 mRNAs and 173 lncRNAs upregulated, 2121 mRNAs and 316 lncRNAs downregulated in PBM cases, respectively. The enriched GO associated with differentially expressed mRNA were extracellular matrix, extracellular region and kinetochore. The most enriched pathway of Protein digestion and absorption was associated with cancer and PI3K-Akt signaling. Cis- and Trans-target gene analysis indicated that mRNAs were predicted to be regulated by one lncRNA and one mRNA corresponded to several lncRNAs. The results showed that the expression trends of NR_110876, NR_132344, XR_946886 and XR_002956345 were consistent with the microarray results, and the difference was statistically significant NR_132344, XR_946886 and XR_002956345 (P < 0.05).The AUC of ROC curve was significant only for XR_946886 (0.837, P < 0.001). Conclusion The present study indicated that lncRNAs were involved the pathogenesis of common bile duct in PBM and XR_946886 would be biomarkers for PMB.

scholarly journals MiR-142-3p could serve as a potential biomarker for individualized treatment of solitary and multiple leiomyomas

2020 ◽  
Author(s):  
Luqi Xue ◽  
E Yang ◽  
Zhengyu Li ◽  
Jinhai Gou ◽  
Dan Nie ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Microarray Analysis ◽  
Target Genes ◽  
Wnt Signaling Pathway ◽  
Individualized Treatment ◽  
Cell Counting ◽  
Aged Patients ◽  
Qrt Pcr ◽  
Potential Biomarker ◽  
The Difference

Abstract Background The pathogenesis and clinical behaviors between solitary leiomyoma (SL) and multiple leiomyomas (ML) vary, which lead to the difference in management for childbearing-aged patients. Herein, we aim to find the potential miRNA biomarkers for optimizing the individualized management between SL and ML. Methods A microarray analysis was conducted to screen out the potentially dysregulated miRNAs. Target genes and signaling pathway potentially involved in UL pathogenesis were predicted by bioinformatics. The effect of miRNA was examined by Cell Counting Kit-8 proliferation assay and qRT-PCR after transfection of miRNA mimics Results The top 5 differentially expressed miRNAs, Wnt signalling pathway and its two central molecules APC and CTNNB1 were screened out according to microarray analysis and bioinformatics. MiR-142-3p was selected for further exploration. In validation of qRT-PCR, MiR-142-3p was significantly upregulated in SL, while downregulated in ML, CTNNB1 and sequencing target AXIN-2 were expressed at higher level in ML than SL. Overexpression of MiR-142-3p resulted in lower transcription level of CTNNB1 and AXIN-2, and lower cell proliferation level. Conclusions MiR-142-3p may be involved in the development of SL and ML by interacting with CTNNB1 and AXIN-2 through Wnt signaling pathway. MiR-142-3p could serve as a potential biomarker for individualized treatment between SL and ML in the future.

scholarly journals MiR-142-3p could serve as a potential biomarker for individualized treatment of solitary and multiple leiomyomas

2020 ◽  
Author(s):  
Luqi Xue ◽  
E Yang ◽  
Zhengyu Li ◽  
Jinhai Gou ◽  
Dan Nie ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Microarray Analysis ◽  
Target Genes ◽  
Wnt Signaling Pathway ◽  
Individualized Treatment ◽  
Cell Counting ◽  
Aged Patients ◽  
Qrt Pcr ◽  
Potential Biomarker ◽  
The Difference

Abstract Background: The pathogenesis and clinical behaviors between solitary leiomyoma (SL) and multiple leiomyomas (ML) vary, which lead to the difference in management for childbearing-aged patients. Herein, we aim to find the potential miRNA biomarkers for optimizing the individualized management between SL and ML.Methods: A microarray analysis was conducted to screen out the potentially dysregulated miRNAs. Target genes and signaling pathway potentially involved in UL pathogenesis were predicted by bioinformatics. The effect of miRNA was examined by Cell Counting Kit-8 proliferation assay and qRT-PCR after transfection of miRNA mimicsResults: The top 5 differentially expressed miRNAs, Wnt signalling pathway and its two central molecules APC and CTNNB1 were screened out according to microarray analysis and bioinformatics. MiR-142-3p was selected for further exploration. In validation of qRT-PCR, MiR-142-3p was significantly upregulated in SL, while downregulated in ML, CTNNB1 and sequencing target AXIN-2 were expressed at higher level in ML than SL. Overexpression of MiR-142-3p resulted in lower transcription level of CTNNB1 and AXIN-2, and lower cell proliferation level.Conclusions: MiR-142-3p may be involved in the development of SL and ML by interacting with CTNNB1 and AXIN-2 through Wnt signaling pathway. MiR-142-3p could serve as a potential biomarker for individualized treatment between SL and ML in the future.

scholarly journals Profiling of Differentially Expressed MicroRNAs in Saliva of Parkinson's Disease Patients

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanyan Jiang ◽  
Jing Chen ◽  
Yunchuang Sun ◽  
Fan Li ◽  
Luhua Wei ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Microarray Analysis ◽  
Target Genes ◽  
Characteristic Curve ◽  
Differentially Expressed ◽  
Diagnostic Efficacy ◽  
Mirna Microarray ◽  
Candidate Mirnas ◽  
Diagnostic Potential

Objective: This study aims to identify differentially expressed salivary miRNAs and validate the diagnostic potential for idiopathic Parkinson's disease (PD). Also, the disease specificity of candidate miRNAs was evaluated between PD, multiple system atrophy (MSA), and essential tremor (ET).Methods: We collected salivary samples from 50 PD, 20 ET, and 20 MSA patients, as well as 30 healthy controls (HCs). In the discovery phase, salivary miRNA microarray analysis was performed. In-silico analysis was used to investigate the target genes of differentially expressed miRNAs and clustered pathways. In validation phase, RT-qPCR was performed with samples from 30 PD patients and 30 HCs. Subsequently, we investigated candidate miRNAs in all recruited subjects. Receiver operating characteristic curve and Spearman correlation analysis was performed to determine diagnostic usefulness.Results: We identified 43 miRNAs that were differentially expressed between 5 PD patients and 5 HCs by miRNA microarray analysis. Computational analysis revealed the target genes were clustered in the pathways associated with ubiquitin protein ligase activity. The result of RT-qPCR showed that the miR-29a-3p and miR-29c-3p were found to be significantly downregulated (p = 0.004, p = 0.027), whereas the miR-6756-5p was significantly upregulated in 30 PD patients compared with 30 HCs (p = 0.032). The miR-29a-3p expression level in PD patients was significantly lower than ET patients (p = 0.035), but higher than MSA patients (p &lt; 0.0001). The diagnostic efficacy reached a little higher when the combination of miR-29a-3p and miR-29c-3p.Conclusion: The miRNA combination of salivary miR-29a-3p and miR-29c-3p has potential to be a diagnostic biomarker for idiopathic PD.

MiR-142-3p May Be Involved in the Development of Solitary and Multiple Uterine Leiomyomasby Interacting with CTNNB1 and AXIN-2 Through Wnt Signaling Pathway

2020 ◽  
Author(s):  
Luqi xue ◽  
E Yang ◽  
Jinhai Gou ◽  
Dan Nie ◽  
Tao Yi ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Signaling Pathway ◽  
Uterine Leiomyoma ◽  
Wnt Signaling Pathway ◽  
Transcription Level ◽  
Aged Patients ◽  
Qrt Pcr ◽  
Potential Biomarker ◽  
Differentially Expressed Mirnas ◽  
The Difference

Abstract Background The pathogenesis and clinical behaviors between solitary uterine leiomyoma (SUL) and multiple uterine leiomyomas (MUL) vary, which lead to the difference in management for childbearing-aged patients. Herein, we aim to find the potential miRNAs involved in the development of SUL and MUL. Results The top 5 differentially expressed miRNAs, Wnt signalling pathway and its two central molecules APC and CTNNB1 were screened out according to microarray analysis and bioinformatics. MiR-142-3p was selected for further exploration. In validation of qRT-PCR, MiR-142-3p was significantly upregulated in SUL, while downregulated in MUL, CTNNB1 and sequencing target AXIN-2 were expressed at higher level in MUL than SUL. Overexpression of MiR-142-3p resulted in lower transcription level of CTNNB1 and AXIN-2, and lower cell proliferation level. Conclusions MiR-142-3p may be involved in the development of SUL and MUL by interacting with CTNNB1 and AXIN-2 through Wnt signaling pathway. MiR-142-3p could serve as a potential biomarker for individualized treatment between SUL and MUL in the future.

scholarly journals Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Candice P. Chu ◽  
Shiguang Liu ◽  
Wenping Song ◽  
Ethan Y. Xu ◽  
Mary B. Nabity
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Ckd Progression ◽  
Critical Pathways ◽  
Qrt Pcr ◽  
Hereditary Nephropathy ◽  
Differentially Expressed Mirnas

AbstractDogs with X-linked hereditary nephropathy (XLHN) are an animal model for Alport syndrome in humans and progressive chronic kidney disease (CKD). Using mRNA sequencing (mRNA-seq), we have characterized the gene expression profile affecting the progression of XLHN; however, the microRNA (miRNA, miR) expression remains unknown. With small RNA-seq and quantitative RT-PCR (qRT-PCR), we used 3 small RNA-seq analysis tools (QIAGEN OmicSoft Studio, miRDeep2, and CPSS 2.0) to profile differentially expressed renal miRNAs, top-ranked miRNA target genes, and enriched biological processes and pathways in CKD progression. Twenty-three kidney biopsies were collected from 5 dogs with XLHN and 4 age-matched, unaffected littermates at 3 clinical time points (T1: onset of proteinuria, T2: onset of azotemia, and T3: advanced azotemia). We identified up to 23 differentially expressed miRNAs at each clinical time point. Five miRNAs (miR-21, miR-146b, miR-802, miR-142, miR-147) were consistently upregulated in affected dogs. We identified miR-186 and miR-26b as effective reference miRNAs for qRT-PCR. This study applied small RNA-seq to identify differentially expressed miRNAs that might regulate critical pathways contributing to CKD progression in dogs with XLHN.

scholarly journals Bioinformatic Analysis of Circular RNA-Associated ceRNA Network Associated with Hepatocellular Carcinoma

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Jiacheng Wu ◽  
Shui Liu ◽  
Yien Xiang ◽  
Xianzhi Qu ◽  
Yingjun Xie ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Pathway Analysis ◽  
Target Genes ◽  
Kegg Pathway ◽  
Interaction Network ◽  
Bioinformatic Analysis ◽  
Differentially Expressed ◽  
Qrt Pcr ◽  
Cerna Network ◽  
Kegg Pathway Analysis

Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and is associated with a high mortality rate and poor treatment efficacy. In an attempt to investigate the mechanisms involved in the pathogenesis of HCC, bioinformatic analysis and validation by qRT-PCR were performed. Three circRNA GEO datasets and one miRNA GEO dataset were selected for this purpose. Upon combined biological prediction, a total of 11 differentially expressed circRNAs, 15 differentially expressed miRNAs, and 560 target genes were screened to construct a circRNA-related ceRNA network. GO analysis and KEGG pathway analysis were performed for the 560 target genes. To further screen key genes, a protein-protein interaction network of the target genes was constructed using STRING, and the genes and modules with higher degree were identified by MCODE and CytoHubba plugins of Cytoscape. Subsequently, a module was screened out and subjected to GO enrichment analysis and KEGG pathway analysis. This module included eight genes, which were further screened using TCGA. Finally, UBE2L3 was selected as a key gene and the hsa_circ_0009910–miR-1261–UBE2L3 regulatory axis was established. The relative expression of the regulatory axis members was confirmed by qRT-PCR in 30 pairs of samples, including HCC tissues and adjacent nontumor tissues. The results suggested that hsa_circ_0009910, which was upregulated in HCC tissues, participates in the pathogenesis of HCC by acting as a sponge of miR-1261 to regulate the expression of UBE2L3. Overall, this study provides support for the possible mechanisms of progression in HCC.

scholarly journals Effect of miR-27b-5p on apoptosis of human vascular endothelial cells induced by simulated microgravity

APOPTOSIS ◽  
2019 ◽  
Vol 25 (1-2) ◽  
pp. 73-91 ◽  
Author(s):  
Yi-Kai Pan ◽  
Cheng-Fei Li ◽  
Yuan Gao ◽  
Yong-Chun Wang ◽  
Xi-Qing Sun
Keyword(s):  
Endothelial Cells ◽  
Western Blot ◽  
Target Gene ◽  
Simulated Microgravity ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Luciferase Assay ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas

AbstractWeightlessness-induced cardiovascular dysfunction can lead to physiological and pathological consequences. It has been shown that spaceflight or simulated microgravity can alter expression profiles of some microRNAs (miRNAs). Here, we attempt to identify the role of miRNAs in human umbilical vein endothelial cells (HUVECs) apoptosis under simulated microgravity. RNA-sequencing and quantitative real-time PCR (qRT-PCR) assays were used to identify differentially expressed miRNAs in HUVECs under simulated microgravity. Then we obtained the target genes of these miRNAs through target analysis software. Moreover, GO and KEGG enrichment analysis were performed. The effects of these miRNAs on HUVECs apoptosis were evaluated by flow cytometry, Western blot and Hoechst staining. Furthermore, we obtained the target gene of miR-27b-5p by luciferase assay, qRT-PCR and Western blot. Finally, we investigated the relationship between this target gene and miR-27b-5p in HUVECs apoptosis under normal gravity or simulated microgravity. We found 29 differentially expressed miRNAs in HUVECs under simulated microgravity. Of them, the expressions of 3 miRNAs were validated by qRT-PCR. We demonstrated that miR-27b-5p affected HUVECs apoptosis by inhibiting zinc fingers and homeoboxes 1 (ZHX1). Our results reported here demonstrate for the first time that simulated microgravity can alter the expression of some miRNAs in HUVECs and miR-27b-5p may protect HUVECs from apoptosis under simulated microgravity by targeting ZHX1.

scholarly journals Microarray Expression Profile of Circular RNAs in Plasma from Primary Biliary Cholangitis Patients

2017 ◽  
Vol 44 (4) ◽  
pp. 1271-1281 ◽  
Author(s):  
Jiajia Zheng ◽  
Zhenrong Li ◽  
Tiancheng Wang ◽  
Yang Zhao ◽  
Yongfeng Wang
Keyword(s):  
Expression Profile ◽  
Expression Profiles ◽  
Characteristic Curve ◽  
Group Versus ◽  
Target Prediction ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Primary Biliary Cholangitis ◽  
Healthy Controls ◽  
Qrt Pcr

Background/Aims: Circular RNAs (circRNAs) play a crucial role in the occurrence of several diseases, including autoimmune diseases. However, their role in primary biliary cholangitis (PBC) remains unclear. Here, we aimed to determine the circRNA expression profile in plasma from PBC patients and further explore the value of circRNA in diagnosing PBC. Methods: CircRNA microarrays were used to determine circRNA expression profiles in plasma samples from 6 PBC patients and 6 healthy controls. Statistical analyses identified differentially expressed circRNAs, and these circRNAs were verified by qRT-PCR in 29 PBC patients and 30 healthy controls. MicroRNA (miRNA) target prediction software identified putative miRNA response elements (MREs), which were used to construct a map of circRNA-miRNA interactions for the differentially expressed circRNAs. Results: Our results indicated that there were 18 up-regulated and 4 down-regulated circular RNAs in the plasma from PBC patients compared with that from healthy individuals. Among the differentially expressed circRNAs, hsa_circ_402458 (P=0.0033), hsa_circ_087631 and hsa_circ_406329 (P=0.0185) were up-regulated, and hsa_circ_407176 (P=0.0066) and hsa_circ_082319 were down-regulated in the PBC group versus the healthy group as demonstrated by qRT-PCR. In particular, hsa_circ_402458 was significantly higher in PBC patients not receiving UDCA treatment than in PBC patients receiving UDCA treatment (P=0.0338). The area under the receiver operating characteristic curve for hsa_circ_402458 for diagnosing PBC was 0.710 (P=0.005). For hsa_circ_402458, two putative miRNA targets, hsa-miR-522-3p and hsa-miR-943, were predicted. Conclusions: circRNA dysregulation may play a role in PBC pathogenesis, and hsa_circ_402458 shows promise as a candidate biomarker for PBC.

scholarly journals Global Transcriptome Analysis of Long Noncoding RNAs in Rice Seed Development

2021 ◽  
Vol 25 (04) ◽  
pp. 777-785
Author(s):  
Jingai Tan
Keyword(s):  
Seed Development ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
High Yield ◽  
Rice Seed ◽  
Extracellular Region ◽  
Dynamic Expression ◽  
Three Stages

Rice seed development involves an intricate regulatory network that directly determines seed size and weight. Long noncoding RNAs (lncRNAs) have been defined as key regulators of gene expression involved in diverse biological processes. However, the function of lncRNAs in rice seed development is still poorly understood. We performed paired-end RNA sequencing of Nipponbare rice at 5, 10 and 15 DPA (days post anthesis) in two different environments (early and middle-season rice). A total of 382 lncRNAs were detected as differentially expressed among these stages, including 344 and 307 lncRNAs in early and middle-season rice, respectively, and 70.42% (269 of 382) of the lncRNAs were found in both environments. The results showed that environment had little effect on the expression of lncRNAs. Furthermore, there were 127, 172, and 31 DElncs (differentially expressed lncRNAs) and 154, 140, and 59 DElncs in early and middle-season rice, respectively, in comparisons of 10_DPA vs 5_DPA, 15_DPA vs 5_DPA and 15_DPA vs 10_DPA. This result indicated that the number and expression level of lncRNAs at 5 DAP were significantly different from those at 10 DAP and 15 DAP. Furthermore, GO pathway analysis of cis target genes of DElncs in 10_DPA vs 5_DPA and 15_DPA vs 5_DPA revealed that the significant GO pathways were extracellular region, nutrient reservoir activity and cell wall macromolecule catabolic process. Our study revealed dynamic expression of lncRNAs in three stages and systematically explored the differences in lncRNAs between early and middle-season rice, which could provide a valuable resource for future high-yield breeding. © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers©

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