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| Status |
Public on Apr 06, 2021 |
| Title |
Identification of potential genes in upper tract urothelial carcinoma by using next-generation sequencing combined with bioinformatics analysis and in vitro study |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Prognostic biomarkers including microRNAs(miRNAs) and genes in upper tract urothelial carcinomas (UTUCs) originating from the renal pelvis and ureter account for only 5% to 10% of all UCs, but this figure is markedly higher in Taiwan, where it can reach up to 30%. By using next-generation sequencing (NGS), we analysed two pairs of renal pelvis tumours and adjacent normal urothelial tissues to screen miRNAs and messenger RNAs. By combining bioinformatics analysis from miRmap, Gene Expression Omnibus (GEO), and Oncomine and Ingenuity® Pathway Analysis databases, we identified candidate genes. To search upstream miRNAs with exact target binding sites, we used miRmap, TargetScan, and miRDB to enforce evidence. Then, we clarified gene and protein expression through an in vitro study. After interaction of the selected target genes obtained using the NGS and miRmap methods were analysed through a Venn diagram analysis, six potential genes—namely, PDE5A, RECK, ZEB2, NCALD, PLCXD3, CYBRD1—presenting significant differences were distinguished. Further analysis of gene expression indicated lower expression of that PDE5A, RECK, ZEB2, and CYBRD1 in bladder cancer tissue than in normal bladder mucosa, which indicated that PDE5A, RECK, ZEB2, and CYBRD1 may act as tumour suppressors in UTUC. In addition, we identified putative oncomiRs in miR-181c-5p target sites on PDE5A, miR-200c-3p target sites on RECK, and miR-200bc-3p/429 target sites on ZEB2. Compared with normal tissue, lower PDE5A expression in tumour specimens was demonstrated in paired UTUC tissues (normal and tumour) from 20 patients. Our findings suggest that both candidate miRNAs and regulated genes may play crucial roles in UTUC progression. We propose that these markers may be potential targets in both diagnostic and therapeutic strategies as clarified by in vitro and in vivo experiments. PDE5A also potentially presents tumour suppressor genes, as identified by comparing the expression between normal and tumour specimens from 10 patients.
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| Overall design |
We analysed two pairs of renal pelvis tumours and adjacent normal urothelial tissues to screen miRNAs and messenger RNAs.
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| Contributor(s) |
Lee H, Li C, Li W, Hsu Y, Yeh H, Ke H, Yeh B, Huang C, Li C, Kuo P, Wu W |
| Citation(s) |
33987019 |
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| Submission date |
Oct 22, 2020 |
| Last update date |
May 19, 2021 |
| Contact name |
Hsiang Ying Lee |
| E-mail(s) |
ashum1009@hotmail.com
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| Organization name |
Kaohsiung Municipal Ta-Tung Hospital
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| Street address |
Jhonghua 3rd Rd
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| City |
Kaohsiung |
| ZIP/Postal code |
80145 |
| Country |
Taiwan |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA670653 |
| SRA |
SRP288283 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE159824_UTUC_mRNA.xlsx |
4.4 Mb |
(ftp)(http) |
XLSX |
| GSE159824_UTUC_miRNA.xlsx |
167.3 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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