Fibroblast growth factor receptor 3 alterations and response to immune checkpoint inhibition in metastatic urothelial cancer: a real world experience

Abstract

Background: FGFR3-altered urothelial cancer (UC) correlates with a non-T cell-inflamed phenotype and has therefore been postulated to be less responsive to immune checkpoint blockade (ICB). Preclinical work suggests FGFR3 signalling may suppress pathways such as interferon signalling that alter immune microenvironment composition. However, correlative studies examining clinical trials have been conflicting as to whether FGFR altered tumours have equivalent response and survival to ICB in patients with metastatic UC. These findings have yet to be validated in real world data, therefore we evaluated clinical outcomes of patients with FGFR3-altered metastatic UC treated with ICB and investigate the underlying immunogenomic mechanisms of response and resistance.

Methods: 103 patients with metastatic UC treated with ICB at a single academic medical center from 2014 to 2018 were identified. Clinical annotation for demographics and cancer outcomes, as well as somatic DNA and RNA sequencing, were performed. Objective response rate to ICB, progression-free survival, and overall survival was compared between patients with FGFR3-alterations and those without. RNA expression, including molecular subtyping and T cell receptor clonality, was also compared between FGFR3-altered and non-altered patients.

Results: Our findings from this dataset confirm that FGFR3-altered (n = 17) and wild type (n = 86) bladder cancers are equally responsive to ICB (12 vs 19%, p = 0.73). Moreover, we demonstrate that despite being less inflamed, FGFR3-altered tumours have equivalent T cell receptor (TCR) diversity and that the balance of a CD8 T cell gene expression signature to immune suppressive features is an important determinant of ICB response.

Conclusions: Our work in a real world dataset validates prior observations from clinical trials but also extends this prior work to demonstrate that FGFR3-altered and wild type tumours have equivalent TCR diversity and that the balance of effector T cell to immune suppression signals are an important determinant of ICB response.

Fig. 1. FGFR3-altered patients treated with ICB have similar clinical benefit.

Patients with known FGFR3 status (n = 103) were classified as altered (n = 17) or wild-type (WT, n = 86) and compared for a OS (overall survival, Cox PH p = 0.38), b PFS (progression-free survival, Cox PH p = 0.95), and c Overall response rate. Response between FGFR3-altered and FGFR3 WT were compared by Responder (CR + PR) and Non-responder (SD + PD). Chi-square p = 0.73. d Interval estimates for coefficients in Cox PH model of OS for both univariate (black) and joint (blue) modelling. Variables significant at p < 0.05 marked with star. OS overall survival, CPH Cox-Proportional Hazards, PFS progression-free survival, WT wild type, TCC transitional cell carcinoma, LOT line of treatment, TMB tumour mutation burden, ECOG Eastern Cooperative Oncology Group, HR hazard ratio.

Fig. 2. FGFR3-altered tumours express higher FGFR3 and pathways associated with PPARG activation.

a Waterfall plot of relative expression of FGFR3 transcript from n = 89 tumours rank ordered by highest expression (right) to lowest expression (left). FGFR3-altered tumours are designated in dark red (mutations) and light red (fusions). b Violin plots of tumour mutational burden (TMB) by FGFR3 status (Mann–Whitney U test p = 0.055). c Volcano plot of differentially expressed genes identified by DEseq2 comparing FGFR3-altered and FGFR3 WT tumours. Significantly down (n = 802) or upregulated (n = 148) genes indicated in red. d Bar plot of −Log10 q-value of indicated pathways identified to be enriched in FGFR3-altered tumours relative to FGFR3 WT tumours. e Violin plot comparing levels of a previously published bladder cancer specific PPARG gene signature between FGFR3-altered and WT tumours. Dotted line = median. Solid lines = interquartile range (IQR).

Fig. 3. FGFR3-altered tumours are enriched in luminal and differentiated molecular subtypes.

a The indicated molecular subtyping schema were applied to tumours using the R package from Kamoun et. al. Bar plots indicated the percentage of tumours within that subtype with FGFR3-alterations. P values for Chi-square test are indicated. b Violin plots of FGFR3 transcript expression by indicated molecular subtype. c Violin plots of previously published FGFR3 activation signature by Sjödhal et al. by indicated molecular subtype.

Fig. 4. FGFR3-altered tumours have differential stromal and immunosuppression residuals.

a T cell receptor alpha (TRA) and T cell receptor beta (TRB) chain Shannon entropy was inferred from RNAseq data using MiXCR in both the current (UNC-108) and IMvigor210 datasets. All comparisons between FGFR3-altered and WT were not significant. b Fibroblast TGF beta Response Signature (FTBRS) from Mariathasan et al. [33] and the EMT_Stroma_core_18 from Wang et al. [32] signatures were evaluated in the UNC and IMvigor210 datasets comparing FGFR3-altered and WT tumours. c In FGFR3 wild type tumours from the UNC-108 dataset we tested whether the balance of effector (CD8 effector signature) to suppressor (FTBRS, EMT-Stroma or Immunosuppression signatures) gene signatures correlated with ICB response. A linear model was generated to determine the expected level of FTBRS, EMT-Stroma, and Immunosuppression signature for a given CD8 effector signature score (Supplementary Fig. 5). For each wild-type tumour we then used our model to calculate the ‘residual’ level of each suppressor signature versus its predicted level based upon its CD8 effector T cell signature. A higher stromal or immunosuppression residual score, therefore, represents a higher level of immune suppression than predicted. Non-responding patients had a higher level of all three of the EMT-stroma, FTBRS, and immunosuppression residuals than predicted.