The urothelial cancer proteome


Urothelial carcinoma, also termed transitional cell carcinoma or urinary bladder cancer, is a major cause of morbidity and mortality throughout the world. The highest frequency of cancer in the urinary bladder is found among urban Caucasians in Western Europe and in the United States of America. Urothelial cancer typically presents in patients over the age of 50 years and is approximately three times as common in males as in females. Smoking is considered as an important risk factor.

Urothelial cancer can be divided into papillary and non-papillary tumors depending on the morphological appearance. Approximately 25% of all urothelial tumors are non-invasive papillary tumors. However, 10-15% of these patients will subsequently develop an invasive tumor.

Here, we explore the urothelial cancer proteome using TCGA transcriptomics data and antibody based protein data. 1093 genes are suggested as prognostic based on transcriptomics data from 406 patients; 379 genes associated with unfavourable prognosis and 714 genes associated with favourable prognosis.

TCGA data analysis


In this metadata study we used data from TCGA where transcriptomics data was available from 406 patients in total. The dataset included 107 females and 299 males. 227 patients were still alive at the time of data collection. The stage distribution was stage i) 2 patients, stage ii) 129 patients, stage iii) 140 patients, stage iv) 133 patients and 2 patients with missing stage information.

Unfavourable prognostic genes in urothelial cancer


For unfavourable genes, higher relative expression levels at diagnosis gives significantly lower overall survival for the patients. There are 379 genes associated with unfavourable prognosis in urothelial cancer. In Table 1, the top 20 most significant genes related to unfavourable prognosis are listed.

EHBP1 is a gene associated with unfavourable prognosis in urothelial cancer. The best separation is achieved by an expression cutoff at 5.6 fpkm which divides the patients into two groups with 20% 5-year survival for patients with high expression versus 50% for patients with low expression, p-value: 1.95e-8. Immunohistochemical staining using an antibody targeting EHBP1 (HPA035469) shows differential expression pattern in urothelial cancer samples.

p<0.001
EHBP1 - survival analysis
EHBP1 - high expression
EHBP1 - low expression

ANXA1 is a gene associated with unfavourable prognosis in urothelial cancer. The best separation is achieved by an expression cutoff at 54.9 fpkm which divides the patients into two groups with 32% 5-year survival for patients with high expression versus 51% for patients with low expression, p-value: 6.19e-6. Immunohistochemical staining using an antibody targeting ANXA1 (HPA011271) shows differential expression pattern in urothelial cancer samples.

p<0.001
ANXA1 - survival analysis
ANXA1 - high expression
ANXA1 - low expression

Table 1. The 20 genes with highest significance associated with unfavourable prognosis in urothelial cancer.

Gene Description Predicted localization mRNA (cancer) p-value
EHBP1 EH domain binding protein 1 Intracellular,Secreted 4.9 1.95e-8
EMP1 epithelial membrane protein 1 Intracellular,Membrane 19.2 9.69e-8
HSPB6 heat shock protein family B (small) member 6 Intracellular 11.6 1.43e-6
TM4SF1 transmembrane 4 L six family member 1 Membrane 52.2 3.43e-6
AHNAK AHNAK nucleoprotein Intracellular 38.6 3.47e-6
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Favourable prognostic genes in urothelial cancer


For favourable genes, higher relative expression levels at diagnosis gives significantly higher overall survival for the patients. There are 714 genes associated with favourable prognosis in urothelial cancer. In Table 2, the top 20 most significant genes related to favourable prognosis are listed.

TRIM38 is a gene associated with favourable prognosis in urothelial cancer. The best separation is achieved by an expression cutoff at 6.0 fpkm which divides the patients into two groups with 65% 5-year survival for patients with high expression versus 29% for patients with low expression, p-value: 4.94e-9. Immunohistochemical staining using an antibody targeting TRIM38 (HPA031685) shows differential expression pattern in urothelial cancer samples.

p<0.001
TRIM38 - survival analysis
TRIM38 - high expression
TRIM38 - low expression

VAMP8 is another gene associated with favourable prognosis in urothelial cancer. The best separation is achieved by an expression cutoff at 124.6 fpkm which divides the patients into two groups with 47% 5-year survival for patients with high expression versus 20% for patients with low expression, p-value: 1.59e-6. Immunohistochemical staining using an antibody targeting VAMP8 (HPA006882) shows differential expression pattern in urothelial cancer samples.

p<0.001
VAMP8 - survival analysis
VAMP8 - high expression
VAMP8 - low expression

Table 2. The 20 genes with highest significance associated with favourable prognosis in urothelial cancer.

Gene Description Predicted localization mRNA (cancer) p-value
TRIM38 tripartite motif containing 38 Intracellular 5.4 4.94e-9
GSDMB gasdermin B Intracellular 9.3 5.91e-9
CXorf38 chromosome X open reading frame 38 Intracellular 5.1 1.44e-8
PTPN6 protein tyrosine phosphatase, non-receptor type 6 Intracellular 16.1 2.64e-8
ZNF524 zinc finger protein 524 Intracellular 17.0 4.98e-8
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The urothelial cancer transcriptome


The transcriptome analysis shows that 71% (n=13858) of all human genes (n=19479) are expressed in urothelial cancer. All genes were classified according to the urothelial cancer-specific expression into one of five different categories, based on the ratio between mRNA levels in urothelial cancer compared to the mRNA levels in the other 16 analyzed cancer tissues. 129 genes show some level of elevated expression in urothelial cancer compared to other cancers (Figure 1). The elevated category is further subdivided into three categories as shown in Table 3.

Figure 1. The distribution of all genes across the five categories based on transcript abundance in urothelial cancer as well as in all other cancer tissues.

Table 3. Number of genes in the subdivided categories of elevated expression in urothelial cancer.

Category Number of genes Description
Tissue enriched 15 At least five-fold higher mRNA levels in a particular cancer as compared to all other cancers
Group enriched 72 At least five-fold higher mRNA levels in a group of 2-7 cancers
Tissue enhanced 42 At least five-fold higher mRNA levels in a particular cancer as compared to average levels in all cancers
Total 129 Total number of elevated genes in urothelial cancer

Additional information


The majority of patients with urothelial cancer present symptoms of hematuria (blood in the urine) and/or dysuria (painful urination). Urothelial cancer most commonly arises in the urinary bladder, but can develop in the renal pelvis, ureters or urethra.

Papillary tumors appear in cystoscopy with variable size, ranging from minute excrescences to large, cauliflower like tumors protruding into the urinary bladder lumen. Histologically papillary tumors are characterized by tall and branched papillae that are usually covered by several layers of urothelial tumor cells.

Sarcomatoid (sarcoma and carcinoma features) variants of urothelial carcinoma exist and, furthermore, squamous cell carcinomas and adenocarcinomas can develop in the urinary bladder. Squamous cell carcinoma in the urinary bladder accounts for approximately 5% of all cancers in the urinary bladder. However, in areas where schistosomiasis is endemic, squamous cell carcinomas account for approximately 75% of all bladder carcinomas.

Urothelial cancer is classified with respect to surgical stage at time for diagnosis and tumor grade based on histology. Staging of urothelial cancer defines a tumor as cancer in situ, non-invasive, invasive in the lamina propria or invasive into muscular bladder wall. The TNM-based classification provides important prognostic information and guides further treatment. In addition, important prognostic information can also be obtained through grading of the tumor based on morphological features. Tumor cells vary in atypical appearance and are graded according to the degree of nuclear atypia into four different grades, including urothelial neoplasm of low malignant potential. The most malignant tumors are of grade 3, and exhibit at least focal areas of high-grade nuclear atypia and common mitotic figures. Urothelial carcinoma grade 3 represents a tumor with more aggressive behavior and increased risk for recurrence and metastatic spread.

Relevant links and publications


Uhlen M et al, 2017. A pathology atlas of the human cancer transcriptome. Science.
PubMed: 28818916 DOI: 10.1126/science.aan2507

Cancer Genome Atlas Research Network et al, 2013. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet.
PubMed: 24071849 DOI: 10.1038/ng.2764

Uhlén M et al, 2015. Tissue-based map of the human proteome. Science
PubMed: 25613900 DOI: 10.1126/science.1260419

Habuka M et al, 2015. The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling. PLoS One.
PubMed: 26694548 DOI: 10.1371/journal.pone.0145301

Histology dictionary - Urothelial cancer