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412 Background: NMIBC has a highly variable clinical behavior not adequately predicted by histological grade or clinical parameters. Some are indolent; others quickly progress to MIBC. Discrepancies between phenotype and genotype is compounded further by interobserver variability in pathological grading. There is an unmet need to improve the prediction of NMIBC. Methods: Whole transcriptomic analysis of 178 bladder tumors (158 NMIBC, 20 MIBC/metastatic) was performed from FFPE tissue incorporating messenger RNA expression, splice variants, gene fusion, mutation detection and immune checkpoint inhibitor cascades. CTLA, PD-1, LAG3, TIM3, TIGIT and B7 were compiled as an index including all major cascade genes. Data were integrated and tested for correlations with pathological grading and clinical outcomes. Conventional pathological grading for WHO 1973 (Grade 1, 2, 3) and 2004 (LG vs HG) classifications was reviewed by 3 expert uro-pathologists. Kappa statistic for interobserver variability was calculated. For validation we used an independent RNA-seq dataset (n = 209, Hedegaard et al. 2016 Cancer Cell). Results: Unsupervised clustering of RNA-Seq data distinguished 3 molecular subtypes of NMIBC; Molecular Grade Related Index (MGRI) 1, MGRI2, MGRI3. MGRI1 comprised of almost exclusively LG tumors. MGRI3 clustered with HG MIBC. Kappa for interobserver variability of expert pathologists was 0.40 and 0.78 in 1973 and 2004 WHO classification, respectively. FGFR3 mutations, FGFR3::TACC3 fusion events and MGRI1 genes were associated with components of xenobiotic metabolism (p = 2.51x10-09) signalling systems, in particular, GTPase regulation (p = 0.002), respiratory cycle genes (p = 0.004), HOX cluster (p = 0.005). MGRI independently predicted progression to MIBC (n = 138, HR = 2.96, 95%CI = 1.70-5.13, p = 1.20x10-04). 5-year PFS in a combined data set (n = 347) differed significantly for MGRI1 (100%) vs MGRI2 (92.2%) vs MGRI3 (73.5%, p = 1.99x10-05, Gray’s test). PD-1 ICC independently predicted progression (OR = 2.85, p < 0.05). Conclusions: RNA-seq delineates 3 molecular classes of NMIBC with different risks of progression to MIBC compared to conventional histologic grading.

467 Background: There is an unmet need for a comprehensive genomic characterization of non muscle invasive bladder cancer (NMIBC). NMIBC comprise over 70% of all bladder cancers at presentation. They have highly variable clinical behavior that is not always adequately predicted on the basis of their histological grade (2004 World Health Organization low and high grade, LG-HG). The discrepancy between phenotype and genotype is compounded further by interobserver variability in pathological grading. We have previously established methods for whole transcriptome RNAseq from formalin fixed paraffin embedded tissues (FFPE). Methods: Whole transcriptomic analysis of 110 NMI FFPE BC both LG and HG was performed incorporating messenger RNA expression, splice variants, gene fusion, and pathway perturbation. We used a discovery (n = 40) and a validation cohort (n = 70). These data were integrated and tested for correlation with both pathological grading and clinical outcomes. Grade Risk Index (GRI) score quantifying how closely a patient's transcriptome is related to a reference set of LG NMIBC samples was established. Conventional pathological grading was reviewed by 3 different expert uro-pathologists and interobserver variability calculated. Results: Unsupervised clustering of data from RNA sequencing uncovered classification of three robust - - nonoverlapping, prognostically significant subtypes of NMIBC with distinct GRIs and signatures. When applied by expert pathologists, interobserver variability in histological grading was observed in 17.5%. In the intermediate group (GRI 0.13 to 0.19), pathologists disagreed in 37.5% whether BC was LG or HG. HG NMIBC clustered with MIBC. LG NMIBC in the intermediate GRI group included either very bulky tumors or extremely rare metastatic LG BC (n = 4). HG disease was associated with a shift in BMP signaling and a germ stem cell-like phenotype. Multiple components of the centromere complex and APOBEC3B were upregulated in HG BC. FGFR3::TACC3 fusion events were observed in LG NMIBC only (11.5%). Conclusions: Whole transcriptomic sequencing data delineated three molecular classes of NMIBC.