Transcriptome Profiling of a Multiple Recurrent Muscle-Invasive Urothelial Carcinoma of the Bladder by Deep Sequencing

Abstract

Urothelial carcinoma of the bladder (UCB) is one of the commonly diagnosed cancers in the world. The UCB has the highest rate of recurrence of any malignancy. A genome-wide screening of transcriptome dysregulation between cancer and normal tissue would provide insight into the molecular basis of UCB recurrence and is a key step to discovering biomarkers for diagnosis and therapeutic targets. Compared with microarray technology, which is commonly used to identify expression level changes, the recently developed RNA-seq technique has the ability to detect other abnormal regulations in the cancer transcriptome, such as alternative splicing. In this study, we performed high-throughput transcriptome sequencing at ∼50× coverage on a recurrent muscle-invasive cisplatin-resistance UCB tissue and the adjacent non-tumor tissue. The results revealed cancer-specific differentially expressed genes between the tumor and non-tumor tissue enriched in the cell adhesion molecules, focal adhesion and ECM-receptor interaction pathway. Five dysregulated genes, including CDH1, VEGFA, PTPRF, CLDN7, and MMP2 were confirmed by Real time qPCR in the sequencing samples and the additional eleven samples. Our data revealed that more than three hundred genes showed differential splicing patterns between tumor tissue and non-tumor tissue. Among these genes, we filtered 24 cancer-associated alternative splicing genes with differential exon usage. The findings from RNA-Seq were validated by Real time qPCR for CD44, PDGFA, NUMB, and LPHN2. This study provides a comprehensive survey of the UCB transcriptome, which provides better insight into the complexity of regulatory changes during recurrence and metastasis.

Adhesion GPCRs in Tumorigenesis

“…An invasion-associated four-gene signature including Latrophilin-1 obtained from the NCI-60 cell line panel has significant prediction in non-small cell lung cancer (NSCLC) [40]. A genome-wide screen between a recurrent muscle-invasive cis-platin-resistant urothelial bladder carcinoma and its adjacent non-tumor tissue found cancer-associated alternative splicing with differential exon usage for LPHN2 [153]. Linkage studies have revealed numerous Latrophilin-3 loss-of-function mutations in breast, lung, ovarian, and prostate cancers [21].…”

Alternative splicing of the cell fate determinant Numb in hepatocellular carcinoma

“…Thus, Numb PRR L promoted proliferation but not differentiation in murine embryonic carcinoma cells, whereas Numb PRR S promoted differentiation but not proliferation . Recently, global profiling identified Numb exon 12 inclusion as a frequent splicing event in human non‐small‐cell lung cancer and in invasive bladder cancer . Furthermore, expression of Numb PRR L was increased in tumors compared with normal tissues and correlated with poor prognosis.…”

An Osteopontin/CD44 Axis in RhoGDI2-Mediated Metastasis Suppression

“…CD44s is the major isoform expressed in UMUC3 cells, and was able to fully rescue CD44 knockdown. Interestingly, transcriptome analysis of recurrent muscle invasive bladder cancer patients compared to newly diagnosed patients revealed increased CD44 expression (Choi et al, 2014; Zhang et al, 2014). Moreover, we found that TIAM1, which binds the CD44s cytoplasmic domain and functions as a GEF for Rac1 (Terawaki et al, 2010), is the critical intracellular effector required for stimulation of invasion.…”