Non-muscle Invasive Bladder Cancer Molecular Subtypes Predict Differential Response to Intravesical Bacillus Calmette-Guérin

Abstract

SummaryThe recommended treatment for patients with high-risk non-muscle invasive bladder cancer (HR-NMIBC) is tumor resection followed by adjuvant Bacillus Calmette-Guérin (BCG) bladder instillations. However, only 50% of patients benefit from this therapy. In case of progression to advanced disease, patients must undergo a radical cystectomy with significant morbidity and have a poor clinical outcome. Identifying tumors least likely to respond to BCG can translate into alternative treatments, such as early radical cystectomy or novel targeted or immunotherapies. Here we present molecular profiling of 132 BCG-naive, HR-NMIBC patients, and 44 post-BCG recurrences (34 matched), which uncovered three distinct BCG Response Subtypes (BRS1-3). Patients with BRS3 tumors have reduced recurrence and progression-free survival compared to BRS1-2. BRS3 tumors expressed high EMT-basal markers and had an immunosuppresive profile, which was confirmed with spatial proteomics. Tumors which recurred post-BCG were enriched for BRS3. BRS stratification was validated in a second cohort of 151 BCG-naive HR-NMIBC patients and the molecular subtypes outperformed guideline recommended risk stratification based on clinicopathological variables. For clinical application, we validated that a commercially approved assay was able to accurately predict BRS3 tumors (AUROC 0.86). Our findings provide a potential clinical tool for improved identification of HR-NMIBC patients at the highest risk of progression, which can be used to select patients for early radical cystectomy or novel subtype-directed therapies.One Sentence SummaryMolecular subtypes are predictive of response to intravesical Bacillus Calmette-Guérin immunotherapy in non-muscle invasive bladder cancer.

Increased stromal densities of B cells, CD103+ cells, and CD163+ M2-like macrophages associate with poor clinical outcomes in BCG treated non-muscle invasive bladder cancer

“…Our findings demonstrate a robust association between CD79a+ B cell infiltration in both stromal and epithelial compartments, which is more pronounced in high-grade tumors from female patients who experienced early recurrence and disease progression following BCG therapy. These observations align with current literature highlighting the importance of CD79a+ B cells in driving tumor progression and fostering resistance to BCG therapy, particularly within the stromal milieu [21].…”

“…The patients in this cohort were stratified into different quartiles according to their CD79a and CD163 gene expression levels. Patient clinical demographics and outcome data was extracted from the supplementary information provided by de Jong et al ., [21] These clinical attributes were then combined with the gene expression profiles of the primary tumors. Subsequently, an analysis was conducted using the time to disease progression and the progression status in R version 4.2.0.…”

“…In silico analysis of CD79A, CD103 and CD163 gene expression profiles in transcriptomic profiles of tumors from BCG naïve high-risk patients Based on our previous findings [18] on the associations between tumor infiltrating CD79a+ B cells and M2-like macrophage densities and overall poor clinical outcomes in patients with NMIBC, irrespective of the treatment type, we first evaluated the publicly available normalized bulk RNA-sequencing based tumor whole transcriptome profiles of 283 patients with NMIBC that was recently generated by Jong et al, [21]. The patients in this cohort were stratified into different quartiles according to their CD79a and CD163 gene expression levels.…”

Identifying novel biomarkers associated with bladder cancer treatment outcomes

“…The molecular subtype associated with the worst PFS and recurrence, termed BCG response subtype 3 (BRS3), was found to have overexpression of immunosuppressive genes, including PD-1/PD-L1 and chemokines, as well as overexpression of basal and epithelial-to-mesenchymal transition (EMT) activation markers. PFS in this cohort was 61%, compared to 78% and 83% in the other two molecular subtypes (20). Kim et al similarly identified three molecular subtypes exhibiting distinct prognostic features (21).…”

Prognostic Role of RNA Expression Molecular Biomarkers in Prostate and Bladder Cancers

“…2). Three molecular subtypes with a distinct response to Bacillus Calmette-Guérin (BCG) were recently introduced [16]. These subtypes are currently being investigated in a prospective trial assessing their ability to predict response to BCG therapy.…”