Abstract 614: Transcriptomic analysis of BCG-treated T1HG bladder cancer patients identifies an EMT-basal subgroup with immune suppressive characteristics at high risk of BCG-failure

Abstract

Abstract Intravesical instillations with Bacillus Calmette-Guérin (BCG) are the recommended treatment in T1 high-grade (HG) bladder cancer (BC) patients. However, even with BCG treatment, 50% of patients develop a HG recurrence or progression to advanced disease. Current risk stratification is insufficient to identify patients at risk of BCG failure. We aimed to identify molecular predictors of BCG failure in T1HG BC patients with the objective to improve clinical decision-making. Primary T1HG BC patients treated with ≥5/6 BCG induction instillations were retrospectively included. RNA-sequencing (50 million paired-end reads, ≥80% tumor) was performed on centrally reviewed tumors from: 1) BCG-naïve tumors and recurrent tumors from patients that failed BCG therapy (BCG non-responders), matched to an equal number of 2) patients who had an ongoing complete response until study inclusion (BCG responders). Endpoints were HG recurrence-free survival defined as BCG-failure (RFS) and progression-free survival (PFS), assessed by survival analyses. BCG-failure was defined as development of a biopsy-proven HG recurrence or progression to muscle-muscle invasion. Using RNA-seq, we sought to identify genes, pathways and signatures that stratified patients with respect to these endpoints. 132 BCG-naïve T1HG tumors were sequenced and 45 post-BCG tumors. Median follow-up for all patients was 75 months (IQR 48-106), 99 months for n=63 BCG-responders (IQR 74-120) and 49 months for n=69 BCG-non-responders (IQR 25-79). Three molecular subtypes were identified: BCG1 (32%), BCG2 (40%) and BCG3 (28%). BCG3 patients had a significantly worse RFS (HR 2.4 p<0.01) and PFS (HR 2.7; p<0.01) compared to BCG1 or BCG2 patients. BCG3 tumors expressed high EMT and basal markers and had an immune suppressive tumor microenvironment. Immune deconvolution revealed significantly increased immune cell infiltration (i.e. B cells, T regulatory cells and tumor associated macrophages), while CD14 and FOXP3 were identified as significant regulons in BCG3 patients. BCG1 patients showed a favorable PFS and overexpression of genes associated with BCG processing and antigen presentation. BCG2 patients overexpressed luminal BC markers, such as FGFR3, showed MYC pathway activity and were mostly luminal papillary (consensus muscle-invasive BC classifier). Interestingly, post-BCG tumor recurrences were strongly enriched for the BCG3 subtype; 30/45 (67%) of recurring tumors were classified as BCG3. Gene expression profiling of BCG-naïve primary T1HG BC patients identified three molecular subtypes that corresponded to clinical outcome and response to BCG therapy. The EMT-basal/immune suppressive BCG3 patients are not candidates for treatment with BCG given the poor RFS and PFS and might be candidates for early radical cystectomy or immune-modulating therapy. Citation Format: Florus C. De Jong, Teemu D. Laajala, Robert F. Hoedemaeker, Sébastien Rinaldetti, Jolien T. Mensink, Angelique C. Van der Made, Deric K. Van der Schoot, Egbert R. Boevé, Ellen C. Zwarthoff, Joost L. Boormans, Dan Theodorescu, James C. Costello, Tahlita C. Zuiverloon. Transcriptomic analysis of BCG-treated T1HG bladder cancer patients identifies an EMT-basal subgroup with immune suppressive characteristics at high risk of BCG-failure [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 614.