Expression profiling by RNA-seq for identifying genes associated with prognosis in non-muscle-invasive bladder cancer.

Non-muscle-invasive bladder cancer (NMIBC) is clinically heterogeneous, and many NMIBC patients fail to respond to treatment and frequently experience disease relapse. We aim to identify a prognostic and predictive signature of the NMIBC heterogeneity. We constructed a transcriptomic data set by RNA-seq experiments from an independent NMIBC patient cohort (n=32). This cohort contains the patients stratified into three prognostic subgroups: Group 1 (patients with non-relapse; n=15), Group 2 (patients experiencing recurrence, n=9), and Group 3 (patients experiencing progression; n=8). We generated a RNA-seq dataset of 32 samples which were stratified into three prognostic subgroups: Group 1 (patients with non-relapse; n=15), Group 2 (patients experiencing recurrence, n=9), and Group 3 (patients experiencing progression; n=8). Total RNA was isolated using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. The sequencing library was prepared using the TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s instructions. In brief, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNA. Adapters were then ligated to the cDNA, and the fragments were amplified by PCR. Sequencing of paired-end reads (2×150 bp) was performed using the HiSeq 2500 platform (Illumina).