Molecular Subtype-Specific Immunocompetent Models of High-Grade Urothelial Carcinoma Reveal Differential Neoantigen Expression and Response to Immunotherapy

Saito, Ryoichi; Smith, Christof C.; Utsumi, Takanobu; Bixby, Lisa M.; Kardos, Jordan; Wobker, Sara E.; Stewart, Kyle G.; Chai, Shengjie; Manocha, Ujjawal; Byrd, Kevin M.; Damrauer, Jeffrey S.; Williams, Scott; Vincent, Benjamin G.; Kim, William Y.

doi:10.1158/0008-5472.can-18-0173

Cited by 90 publications

(118 citation statements)

References 34 publications

(53 reference statements)

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“…Tumors in the MB49 model develop rapidly, however MB49 cell lines vary considerably from lab to lab and in some cases, display a rapid aggressive growth rate that precludes studies of adaptive immunity (El Behi et al, 2013;Saito et al, 2018). In addition, the tumor that develops is homogeneous likely not accurately reflecting human bladder cancers (Saito et al, 2018). The induction of bladder cancer by BBN leads to more heterogeneous tumors, which reflect human disease (Fantini et al, 2018;Sfakianos et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Identification of sex differences in tumor-specific T cell infiltration in bladder tumor-bearing mice treated with BCG immunotherapy

Rousseau

O'Brien

Antequera

et al. 2020

Preprint

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Bladder cancer is the fourth most common cancer for men. However, women are often diagnosed with later stage disease and have poorer outcomes. Whether immune-based sex differences contribute to this discrepancy is unclear. In addition, models to investigate tumorspecific immunity in bladder cancer, in the context of tumor development or response to therapy, are lacking. To address this specific unmet need, we incorporated a commonly used model antigen, ovalbumin, into two well-established models of bladder cancer; the orthotopic MB49 cell line model and the carcinogenic BBN bladder cancer model. We tested the utility of these models to investigate tumor-specific immunity in the context of immunotherapy in both sexes. We found that BCG vaccination, prior to weekly BCG instillation does not impart an immune-specific benefit to tumor-bearing mice in the context of multiple BCG instillations.Furthermore, tumors developed in the testes in male mice, precluding the use of the MB49 model to directly investigate sex-based immune differences. In the BBN model, we observed that more tumor antigen-specific CD8 + T cells infiltrated male bladders compared to female bladders in the context of BCG immunotherapy and that these cells had the highest levels of the exhaustion marker PD-1. We propose our modified BBN model will contribute to our understanding of how tumor-specific immunity arises in bladder cancer. Additionally, the BBN bladder cancer model may help to uncover sex differences in tumor-specific immunity, which would provide valuable information for the development of new treatments or combination therapies for bladder cancer in women and men.

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Section: Discussionmentioning

confidence: 99%

Identification of sex differences in tumor-specific T cell infiltration in bladder tumor-bearing mice treated with BCG immunotherapy

Rousseau

O'Brien

Antequera

et al. 2020

Preprint

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“…The study we report here follows the analysis of a cohort of advanced stage MIBC. In this setting, understanding the molecular underpinnings of a sample is critical to better predicting how they will respond to therapy(10), especially ICIs (12,13). To better characterize the spatial arrangement of key molecular characteristics such as tumor-intrinsic subtype, TIL exclusion and composition, and tumor-stroma interaction we leveraged multiple traditional bulk and spatial platforms in conjunction highly multiplexed profiling by GeoMx within FFPE tissues.…”

Section: Discussionmentioning

confidence: 99%

“…Although responses can be durable, only 20-30% of patients with MIBC will respond to immune checkpoint inhibitors (ICIs), arguing for the identification of novel drug targets and need for a deeper understanding of predictive biomarkers to enrich for responses to current standard of care therapies (6,7). Multiple studies have identified distinct RNA expression subtypes within MIBC termed "luminal" and "basal-like" (8), each of which has unique gene expression patterns which have important implications for disease management with conventional chemotherapy (9)(10)(11) and immunotherapies (12). Response to immune checkpoint inhibitors in urothelial bladder cancer has been associated with several potential biomarkers including tumor mutation burden, tumor molecular subtype and PD-L1 expression on CD8+ tumor infiltrating lymphocytes (TILs) and other immune cells (7,(13)(14)(15).…”

Section: Introductionmentioning

confidence: 99%

Defining the microenvironment landscape of bladder cancer using highly multiplexed spatial genomic and proteomic analysis

Reeves

Zhang²,

Norgaard

et al. 2019

Preprint

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One Sentence Summary:A new method for capturing tumor-immune signaling in FFPE tissues explores how the PPARG signaling axis is associated with immune cell exclusion in bladder cancer. Abstract:Muscle-invasive bladder cancer (MIBC) is an aggressive disease with limited therapeutic options. PD-1 pathway targeting immunotherapies have been approved to treat advanced bladder cancer, but most patients exhibit primary resistance, suggesting that immune evasion mechanisms exist. The PPARγ pathway has been identified as a potential therapeutic target in MIBC that is associated with reduced CD8+ T-cell infiltration and increased resistance to immunotherapies. We comprehensively profiled the tumor microenvironment (TME) in formalin-fixed, paraffin-embedded (FFPE) tissues from a cohort of PPARγ high (n=13) and PPRARγ low (n=12) MIBC, integrating bulk gene expression, targeted mutation sequencing, immunohistochemistry and multiplex spatial profiling of RNA and protein expression on the GeoMx™ Digital Spatial Profiling (DSP) platform. Molecular subtyping was consistent between traditional methods and GeoMx profiling, and, in this cohort, we observed little evidence of spatial heterogeneity in tumor subtyping. The previously characterized T-cell exclusion phenotype of PPARγ high MIBC was recapitulated on the GeoMx platform and was further extended to show that this is a general phenomenon across immune cell types, supporting potential combination of PPARγ inhibition with ICIs. Furthermore, we found that while immune cells were excluded from PPARγ high tumors, the stromal compartment from these tumors was not significantly different than those PPARγ low tumors. By preserving spatial relationships during the GeoMx analysis, we also identify a novel association between lower immune cell expression in the tumors and higher expression of β-catenin in the stroma, and differential expression of other WNT pathway members associated with PPARγ activity.Patients with the luminal I subtype rarely respond to ICIs(14,15), suggesting the existence of one or more immune escape mechanisms. We previously reported that the PPARγ/RxRa pathway constitutes a tumor-intrinsic mechanism underlying immune evasion in MIBC (6,16). In tumors with high PPARγ pathway activity, CD8+ T-cell infiltration appears to be impaired through chemokine suppression, though additional mechanisms may also impact Tcell infiltration. These findings suggest that pharmacological inhibition of PPARγ may induce sensitivity to immunotherapies. To further our understanding of tumor-immune escape mechanisms in MIBC, analysis of both the tumor and the surrounding microenvironment is necessary. Comprehensive interrogation of the interaction between these two compartments has proved challenging thus far because most of the foundational work in MIBC has relied on commonly available assays such as single-plex immunohistochemistry (IHC) assays or bulk RNA expression and mutation profiling. With limited availability of tumor tissues during clinical trials, highly multiplexed and quant...

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“…Many neoantigen prediction algorithms rely heavily on peptide/MHC binding affinity predictions to rank epitopes (7)(8)(9)(10)(11)(12)(13)(14). Unlike murine preclinical models, where in vivo/ex vivo methods to further screen for immunogenicity can be applied (3,15), no such benchtop prediction method for immunogenicity is currently available for humans. We have previously demonstrated in multiple murine models that the number of predicted neoantigens is much higher than the number of confirmed immunogenic neoantigens (15).…”

Section: Introductionmentioning

confidence: 99%

“…Unlike murine preclinical models, where in vivo/ex vivo methods to further screen for immunogenicity can be applied (3,15), no such benchtop prediction method for immunogenicity is currently available for humans. We have previously demonstrated in multiple murine models that the number of predicted neoantigens is much higher than the number of confirmed immunogenic neoantigens (15). Studies demonstrate that in some tumors, the number of predicted neoantigens is far greater than the number of immunogenic neoantigens that have been identified in mouse models (16,17).…”

Section: Introductionmentioning

confidence: 99%

Machine-Learning Prediction of Tumor Antigen Immunogenicity in the Selection of Therapeutic Epitopes

Smith

Chai

Washington

et al. 2019

Cancer Immunology Research

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Current tumor neoantigen calling algorithms primarily rely on epitope/major histocompatibility complex (MHC) binding affinity predictions to rank and select for potential epitope targets. These algorithms do not predict for epitope immunogenicity using approaches modeled from tumorspecific antigen data. Here, we describe peptide-intrinsic biochemical features associated with neoantigen and minor histocompatibility mismatch antigen immunogenicity and present a gradient boosting algorithm for predicting tumor antigen immunogenicity. This algorithm was validated in two murine tumor models and demonstrated the capacity to select for therapeutically active antigens. Immune correlates of neoantigen immunogenicity were studied in a pan-cancer data set from The Cancer Genome Atlas and demonstrated an association between expression of immunogenic neoantigens and immunity in colon and lung adenocarcinomas. Lastly, we present evidence for expression of an out-of-frame neoantigen that was capable of driving antitumor cytotoxic T-cell responses. With the growing clinical importance of tumor vaccine therapies, our approach may allow for better selection of therapeutically relevant tumor-specific antigens, including nonclassic out-of-frame antigens capable of driving antitumor immunity.

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Molecular Subtype-Specific Immunocompetent Models of High-Grade Urothelial Carcinoma Reveal Differential Neoantigen Expression and Response to Immunotherapy

Cited by 90 publications

References 34 publications

Identification of sex differences in tumor-specific T cell infiltration in bladder tumor-bearing mice treated with BCG immunotherapy

Identification of sex differences in tumor-specific T cell infiltration in bladder tumor-bearing mice treated with BCG immunotherapy

Defining the microenvironment landscape of bladder cancer using highly multiplexed spatial genomic and proteomic analysis

Machine-Learning Prediction of Tumor Antigen Immunogenicity in the Selection of Therapeutic Epitopes

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