Urothelial Bladder Cancer (UBC) subtypes characterization

Resumen

Bladder cancer (BC) is the fourth most common cancer in men in Europe. Spain presents one of the highest incidences among men with a men:women ratio of 7 in comparison to 3 in the rest of European countries. In contrast, the relatively low mortality of BC points to the chronicity of the disease. Urothelial bladder cancer (UBC) morphology represents 90% of BC. Subsequently, it can be subdivided into non-muscle invasive (NMIBC) and muscle-invasive BC (MIBC). In addition to this microscopic classification system, molecular subtypes exist within and between NMIBC and MIBC that better predicts the clinical evolution of UBC patients. In this regard, transcriptome profiling facilitates the identification of molecular subtypes with a more precise patient stratification according to prognosis and therapeutic response prediction which might have highly relevant patient management implications. UBC is an immunogenic tumor due to its relatively high tumor mutational burden and its responsiveness to immune therapies. Cisplatin-based neoadjuvant chemotherapy (NAC) is the recommended treatment for locally-advanced MIBC. However, not all patients benefit from this therapy. In this regard, this thesis investigated the role of the molecular MIBC subtypes in NAC response prediction. Paraffin-embedded tissue slices were immunostained with CK5/6, CK14, FOXA1, and GATA3. The UBC subtypes were identified using hierarchical clustering of the four markers in 126 tumors. The association analysis was done using multinomial association. Univariable and multivariate Cox regression models were applied for the survival analyses. Patients with BASQ-like tumors had a higher likelihood (OR=4.06, 95%CI=1.18-13.99) of undergoing a pathological complete response to NAC in comparison to the luminal-like subtype (OR=1.34, 95%CI=0.34-5.26). The different UBC subtypes may present different genetic and environmental factors participating and interacting in their development. To assess this hypothesis, slices from 904 paraffin-embedded UBC included in the SBC/EPICURO study were immunostained with the above-mentioned four markers, and the same clustering analysis was applied to identify UBC subtypes. Furthermore, 1270 controls were considered to assess the association of each UBC subtype with candidate risk factors and GWAS-variants. The genetic susceptibility patterns across the different subtypes were evaluated by applying a binomial ENET approach. Tobacco smoking risk was slightly higher for Luminal-like subtypes (LumC1: OR=6.72 CI95% 4.4-10.24, LumC2: OR=6.02 CI95% 3.81-9.51, LumI: OR=5.10 CI95% 2.65-9.81, LumM: OR=4.3 CI95% 1.66-11.12) than the risk for BASQ-like tumours (OR=3.51 CI95% 0.93-13.22). A higher risk of LumC1 tumours was associated with a lower intake of fruits and vegetables (OR=1.53 CI95% 1.06-2.21). Locus rs8102137 was significantly associated with the BASQ-like subtype (OR=2.07 CI95% 1.09-3.94). In addition, different genetic susceptibility patterns were observed for each of the subtypes. This study provided evidence of different genetic and non-genetic risk factors profiles associated with UBC taxonomic subtypes, pointing to the need to stratify UBC into molecular subtypes to further characterize its etiology. It has been suggested that MIBC-subtypes present different immune cells infiltration patterns, including T and B lymphocytes. Therefore, the tumor-infiltrating B and T cell receptor repertoire was characterized in 396 MIBC according to the different molecular subtypes. To do so, the immune-related information was extracted from the TCGA RNA-seq data. The MIBC international consensus classification was considered for UBC subtyping. Different statistical classical analyses and a network approach were used to evaluate the immune-repertoire differences across the subtypes. Overall, we observed that each subtype presented its own tumor immune-microenvironment pattern. Stroma-rich and Ba/Sq tumors showed the highest BCR and TCR infiltration while LumP showed the lowest. In addition, we observed that the Ba/Sq and Stroma-rich tumors were more clonally expanded than the Luminal subtypes. Moreover, higher TCR richness and diversity was significantly associated with better survival in the Stroma-rich and Ba/Sq subtypes (p.value<0.01) only.Determining the causes of these different patterns will help to improve our understanding of the disease and the distinct rate of response to immunotherapy of MIBC. Overall, this thesis provides strong evidence that UBC molecular subtypes differ from each other in terms of treatment response, genetic and non-genetic risk factors, as well as the tumor microenvironment. Altogether, the molecular classification of UBC can improve the specific etiological knowledge of each subtype, as well as it can provide diagnostic, prognostic, and therapeutic options for the treatment of this disease and, therefore, improved patient management depending on an adequate characterization of these subtypes.