4.4 Bladder cancer classification
Bladder cancer was earlier annotated with mutation recurrence in 32 genes114 and characterized with signature genetic metabolism predispositions that includes; N-acetyl transferase editosome due to “apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like” (APOBEC)-cytidine deaminases.10Profiling of 58-genes and genes fusion of 784 genes have identified APOBEC signature mutations,115 that are highest in bladder cancer due to overexpression of APOBEC3B genes than in all solid tumours109 . However, cigarette smoking associated gene (GSTM1-null) has been found more susceptible in females andFGFR3 mutation which is more frequent in non-muscle invasive bladder cancer (NMIBC) types.10 Accurate association of bladder cancer histological variants pathological features and specific molecular mutational pattern might provide promising target for developing therapy.116  So far, the European Association of Urology has provided guidelines on identifying evidence-based prognosis and progression115 as different morphological subtype has different clinical course and response to treatment.117 Lin and colleagues102 recommend the use of radiomics and transcriptomics in further identification of prognostic signature markers for the different variants of bladder cancer.
The two main types of bladder cancer include the non-muscle-invasive bladder cancer (NMIBCs), which is a low-grade tumour,103,115 accounting for about 75% of all diagnosed cases10,103 and has been associated with a relative stable genomic FGFR mutation10,103 and homozygous deletion of CDKN2A .118 Gene expression profiling has identified 3 subtypes of NMIBCs from a luminal to basal type marker progression shift from class 1 to class 3.119 Other type of bladder cancer is the muscle-invasive bladder cancer (MIBC), although less frequently diagnosed, it is genetically predisposed as unstable and divergent type109,119. MIBC progress from a flat lesion and gradually acquire gene mutations that promote cell proliferation and survival120 and are associated with aneuploidyTP53 mutations.10,103 Other mutations observed with MIBCs include p53 expression stability, upregulated cytokeratin 20 (CK20 ) and HER2 /neu genes and downregulated PTENexpression that is associated with upregulation of phosphatidylinositol 3-kinase (PI3K) pathway.10 Additionally, the common RB1 deletion and 6P amplification are associated with MIBCs development118 with an unfortunate less than 50% 5-year survival.103,117 However, the NMIBCs exhibits a papillary growth pattern of low malignancy potential, however, they requires an expensive clinical management which includes local resection due to high tendency of recurrence.115,120
Nevertheless, the earlier anatomical based classification of bladder tumour (NMIBC; Tis, Ta &T1 and MIB; T2, T3 & T4) had limitation in the understanding of the diverse prognosis within same tumour type.121 Several studies have speculated that tumour heterogeneity might be associated with diagnosis, metastasis and pre-existing treatment resistance especially in the case of MIBCs.121 Therefore, for an optimized patient precision therapeutic management, identification of an accurate histopathological116,122 and specific transcriptomic biomarkers are encouraged to be adopted.123 Based on this, bladder cancer has been classified into urothelial carcinoma (UC), urothelial carcinoma with variant (UCV), squamous cell carcinoma (SCC), and adenocarcinoma (AD) subtypes.124,125Transcriptomics and other molecular techniques have led to the identification of urothelial carcinoma (UC) that account for 75%116 or even up to 90%126 of the bladder cancer. Whereas the remaining 25%, comprises of other histological variants known as the nonurothelial cancer.116 Invasive UC have a tendency to progress into divergent variants of nonurothelial tumours through progressive histological differentiation.126 Nonurothelial tumours are also known to consist of different range of rare variants based on the WHO 2016 classification that include the pure squamous, glandular, neuroendocrine, sarcomatoid, micropapillary, plasmacytoid, microcystic, clear cell and pure histological variants.116,117 The pasmacytoid variant has been reported to have the worst overall survival mean.116,124 In addition, other sub-populated tumours with either the pure squamous cell or glandular differentiation are shown not to be sensitive to adjuvant chemotherapy unlike their counterpart that are populated with small cell carcinoma which are however aggressive and sensitive to neo-adjuvant chemotherapy.124
Moreover, UC is more prevalent in developed countries like Japan, North America, Western countries,122 while squamous cell carcinoma (SCC) and adenocarcinoma have a higher prevalence in countries like Egypt.125 Zhang et al101 used high-throughput transcriptomic profiling in cisplatin resistant UCs, to unravel differential splicing in more than 300 genes with the specific dysregulation in five candidate genes were validated with real time PCR. These including upregulation of CDH1 , VEGFA , PTPRF ,CLDN7 genes and downregulation of MMP2 gene that are all together involved in cell adhesion molecules (CAMs), focal adhesion and bladder cancer progression pathways.101 In rare UC cases, fusion transcripts associated with chromosomal region rearrangements (17q25, 15q26.3 and 1p36.22) have been identified asSET9/CYHR, IGF1R/TTC23, SYT8/TNN12 and CASZ1/DFFA transcripts respectively.47 Similarly, about 25-30% of UC of the bladder possess histological variant which are predominantly populated with SCC known as the urothelial carcinoma with variant (UCV),125 which are associated with an enrichment ofMAPK signaling pathway121. Although SCC of the bladder represent a small fraction (2%-5% in the United State) of prevalence in the western countries based on the National Cancer Database (NCDB), it attributes the worse prognosis both in terms of stage-for-stage, grad, relapse and overall survival and to the UC.116,127 Both the UC and SCC are derived from UCV and have been demonstrated to have identical driving genes but completely different transcriptional profiles.128 On the other hand, SCC has also been attributed to be less responsive to chemotherapy, thus its standard pre-existing treatment is still radical cystectomy (RC) which might provide the maximal 5-year survival.129 Unlike UC, SCC is shown to have a negative expression of immune inhibitors biomarkers such as PD-L1, thus its higher grade and aggressive association. Owyong et al129 suggests the increase in the expression of PD-L1might improve the immune response associated with treatment outcome. Primary adenocarcinoma represents 0.5-2% of the all diagnosed bladder cancer, like SCC it has a poor prognosis and has a weak TM immunoexpression score than UC.130
On the other hand, small cell carcinoma (SmCC) is a rare bladder cancer variant (less than 1% of all bladder diagnosis) and belongs to the neuroendocrine carcinoma (NEBC) family, usually presented at a late stage.126 Neuroendocrine carcinoma is somewhat similar and sometimes intermingle with UC, although relatively rare (0.5-1.2% of new cases) it is highly lethal with a 1-year survival progression.126,131 Small cell carcinoma of the bladder is associated with a depletion of CCND1 and an amplification of CDKN2A genes whereas in UC, CDKN2A gene is depleted while CCND1 gene is amplified.131This variant has neuronal marker signatures including upregulation ofNESTIN , TUBB2B , PEG10 gene with low or no expression of basal or luminal biomarkers.131,132Another identified novel marker of SmCC is dysregulated PVT1-ERBB2 affecting ERBB2 gene expression which compliments the general MIBC signature markers; TP53 and RB1 depletion,126,133and are evident in their histological features.131Although SmCC/ NEBC may express basal or luminal biomarkers, a few of them have a basal molecular feature which might explain their positive response to chemotherapy126,132 or radiotherapy in improving survival.132 Study by Shen and others, shows that NEBC were sensitive to P13k inhibitor (GDC-0941) and FGFR inhibitor (NVP-BGJ398). While Wang et al126 recommended utilizing the common RB1 gene depletion as a potential therapeutic target.