利用次世代定序和生物資訊分析上尿路上皮癌的特定基因
李香瑩1,2,3、李經家2,3,4,5、李威明3,4,5,6、許雅玲5、葉信志2,3,4,5、柯宏龍3,4,5、黃俊農2,3,4,5、
李健逢7、吳文正2,3,4,5*、郭柏麟1*
高雄醫學大學臨醫所1; 高雄市立大同醫院泌尿科2; 高雄醫學大學附設中和紀念醫院泌尿部3; 高雄醫學大學醫學系泌尿學科4; 高雄醫學大學醫研所5; 衛生福利部屏東醫院泌尿科6; 奇美醫學中心病理部7
Identification of potential genes in upper tract urothelial carcinoma by using next-generation sequencing and bioinformatics analysis
Hsiang-Ying Lee MD, MS1,2,3, Ching-Chia Li MD, PhD 2,3,4,5, Wei-Ming Li MD, PhD 3,4,5,6, Ya-Ling Hsu PhD 5, Hsin-Chih Yeh MD, PhD 2,3,4,5, Hung-Lung Ke MD, PhD3,4,5, Chun-Nung Huang MD, PhD 2,3,4,5, Chien-Feng Li7, Wen-Jeng Wu MD, PhD 2,3,4,5*, Po-Lin Kuo PhD 1*
1Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
2Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
3Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
4 Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
5 Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
6 Department of Urology, Ministry of Health and Welfare Pingtung Hospital, Pingtung, Taiwan
7Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan
Objectives
To identify prognostic biomarkers including miRNAs and genes in upper tract urothelial carcinoma (UTUC) arising from renal pelvis and ureter accounts for only 5-10% of all UCs but about markedly increase up to 30% in Taiwan.
Material and Methods
By using next-generation sequencing (NGS), we analyzed two pairs of renal pelvis tumors and adjacent normal urothelial tissues to screen miRNAs and messenger RNAs. Combined with bioinformatics analysis from miRmap, Gene expression omnibus (GEO), Oncomine and Ingenuity® Pathway Analysis (IPA) databases, we identified candidate genes. For searching up-stream miRNAs with exactly target binding sites, we use miRmap, TargetScan and miRDB to enforce our evidence.
Results
After interaction with selected target genes between NGS and miRmap methods via Venn diagram analysis, 6 potential genes including PDE5A，RECK，ZEB2，NCALD，PLCXD3，CYBRD1 presenting significant difference were distinguished. Further analysis of gene expression, it showed that PDE5A、RECK、ZEB2、CYBRD1 present lower expression in bladder cancer tissue compared with normal bladder mucosa which indicated PDE5A、RECK、ZEB2、CYBRD1 may act as tumor suppressors in UTUC. In addition, we also identified putative oncomiRs in which target sites of miR-181c-5p on PDE5A, target sites of miR-200c-3p on RECK and target sites of miR-200bc-3p/429 on ZEB2.
Conclusions
Our findings suggest that both candidate miRNAs and regulated genes may play important roles in UTUC progression. We propose these markers may be potential targets in both diagnostic and therapeutic strategies after clarifying by vitro and vivo experiments.