Luminal Papillary Research Articles

Abstract A24: Establishment of a panel of patient-derived tumor xenograft models recapitulating molecular heterogeneity and drug response of muscle-invasive bladder tumors

Abstract Background: Muscle-invasive bladder cancers (MIBCs) constitute a heterogeneous group of tumors with poor outcome. Recently, MIBC molecular subtyping efforts from an international consortium led to the identification of six subtypes, improving prediction of clinical outcomes and treatment responses. FGFR3 alterations (mutations and translocations), observed in 20% of MIBCs, are found mainly in the luminal papillary subtype that respond poorly to chemo- and immunotherapy. Basal tumors represent 35% of MIBCs and were shown to be better responders to chemotherapy. Here, we describe the development and characterization of patient-derived primary MIBC xenografts (PDX) belonging to these main subtypes. Methods: Bladder tumors were obtained from patients at surgery. Tumor fragments were subcutaneously engrafted into immune-compromised mice. Primary tumors and matched PDX tumors at multiple passages were analyzed regarding growth characteristics, histopathology (H&E staining, CK5/6, FOXA1, and GATA3 immunohistochemistry), gene expression (Affymetrix U133 plus 2.0 microarray), and genetic stability (STR profiling). Hotspot oncogenic mutations for FGFR3, PIK3CA, HRAS, KRAS, NRAS, PPARG, and RXRA were also assessed. Additionally, pharmacologic responses to standard-of-care and targeted therapies were characterized. Findings: From 152 MIBC tumors at all stages and grades, 32 PDX models were successfully established (21.1% success rate). This take rate did not seem correlated to any classical tumor characteristics. Importantly, transcriptomic analysis allowed us to identify PDX models belonging to different molecular subtypes, notably the basal-like and luminal papillary subtypes, including PDXs with FGFR3 mutations. All histologic, genetic, and molecular features validated the stability of the PDX models compared to the parental tumors. Histologic analyses correlated with the molecular classification. These models reproduced the response to cisplatin-based therapies observed in the clinic. Basal models, except one harboring a FGFR3 mutation, were sensitive to anti-EGFR therapies but to a lesser extent than to chemotherapy. FGFR3-mutated PDX models, including a basal model, were highly responsive to FGFR3 inhibitors and less responsive to chemotherapy. Conclusion: We have developed and characterized highly relevant preclinical models for MIBCs, including basal and FGFR3-mutated tumors, recapitulating molecular heterogeneity and drug responses as observed in patients with MIBCs. They represent essential tools for developing new, efficient therapies against this deadly disease. Citation Format: Claire Béraud, Hervé Lang, Myriam Lassalle, Véronique Lindner, Aurélie Kamoun, Michel Soulié, Elodie Guillon, Clémentine Krucker, Xavier Gamé, Pascal Rischmann, Aurélien De Reynies, Yves Allory, François Radvanyi, Philippe Lluel, Thierry Massfelder, Isabelle Bernard-Pierrot. Establishment of a panel of patient-derived tumor xenograft models recapitulating molecular heterogeneity and drug response of muscle-invasive bladder tumors [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr A24.

Identification of Differential Tumor Subtypes of T1 Bladder Cancer

Stage T1 bladder cancers have the highest progression and recurrence rates of all non–muscle-invasive bladder cancers (NMIBCs). Most T1 cancers are treated with bacillus Calmette-Guérin (BCG), but many will progress or recur, and some T1 patients will die from bladder cancer. Particularly aggressive tumors could be treated with early cystectomy. To better understand the molecular heterogeneity of T1 cancers, we performed transcriptome profiling and unsupervised clustering, and identified five consensus subtypes of T1 tumors treated with repeat transurethral resection (reTUR) and induction and maintenance BCG. The T1-LumGU subtype was associated with carcinoma in situ (CIS; six/13, 46% of all CIS), had high E2F1 and EZH2 expression, and was enriched in E2F target and G2M checkpoint hallmarks. The T1-Inflam subtype was inflamed and infiltrated with immune cells. While most T1 tumors were classified as luminal papillary, the T1-TLum subtype had the highest median luminal papillary score and FGFR3 expression, no recurrence events, and the fewest copy number gains. T1-Myc and T1-Early subtypes had the most recurrences (14/30 within 24 mo), the highest median MYC expression, and, when combined, had significantly worse recurrence-free survival than the other three subtypes. T1-Early had five (38%) recurrences within the first 6 mo of BCG, and repressed IFN-α and IFN-γ hallmarks and inflammation. We developed a single-patient T1 classifier and validated our subtype biology in a second cohort of T1 tumors. Future research will be necessary to validate the proposed T1 subtypes and to determine if therapies can be individualized for each subtype. Patient summaryWe identified and characterized expression subtypes of high-grade stage T1 bladder cancer that are biologically heterogeneous and have variable responses to bacillus Calmette-Guérin treatment. We validated the subtypes and describe a single-patient classifier.

Distribution of Molecular Subtypes in Muscle-invasive Bladder Cancer Is Driven by Sex-specific Differences

Muscle-invasive bladder cancer (MIBC) is a sex-biased cancer with a higher incidence in men but worse outcomes in women. The root cause behind these observations remains unclear. To investigate whether sex-specific tumor biology could explain the differences in clinical behavior of MIBC, we analyzed the transcriptome profiles from transurethral resected bladder tumors of 1000 patients. Female tumors expressed higher levels of basal- and immune-associated genes, while male tumors expressed higher levels of luminal markers. Using molecular subtyping, we found that the rates of the basal/squamous subtype were higher in females than in males. Males were enriched with tumors of the luminal papillary (LumP) and neuroendocrine-like subtypes. Male MIBC tumors had higher androgen response activity across all luminal subtypes and male patients with LumP tumors were younger. Taken together, these data confirm differences in molecular subtypes based on sex. The role of the androgen response pathway in explaining subtype differences between men and women should be studied further. Patient summaryWe explored the sex-specific biology of bladder cancer in 1000 patients and found that women had more aggressive cancer with higher immune activity. Men tended toward less aggressive tumors that showed male hormone signaling, suggesting that male hormones may influence the type of bladder cancer that a patient develops.

HOXB2 is a Putative Tumour Promotor in Human Bladder Cancer.

The present study aimed to investigate the role of Homebox B2 (HOXB2) in bladder cancer (BC). The Cancer Genome Atlas (TCGA) dataset was used to analyse HOXB2 expression in BC. The influence of HOXB2 on the cellular functions of BC cells was determined in both HOXB2 knockdown and HOXB2 overexpressed BC cell lines using in vitro assays. HOXB2 mRNA was significantly upregulated in luminal infiltrated and luminal papillary subtypes of BC. Drug Metabolism Cytochrome P450 was significantly enriched in BCs expressing high levels of HOXB2. Knockdown of HOXB2 from EJ138 cells reduced growth, adhesion and invasion. In contrast, overexpression of HOXB2 in RT112 cells induced growth and adhesion of bladder cancer cells. Increased HOXB2 expression in papillary BC can promote cell growth and adhesion of BC cells. Drug Metabolism Cytochrome P450 pathway was enriched in BCs overexpressing HOXB2.

Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis

BackgroundMuscle-invasive bladder cancer (MIBC) is a heterogeneous disease, and gene expression profiling has identified several molecular subtypes with distinct biological and clinicopathological characteristics. While MIBC subtyping has primarily been based on messenger RNA (mRNA), long non-coding RNAs (lncRNAs) may provide additional resolution.MethodsLncRNA expression was quantified from microarray data of a MIBC cohort treated with neoadjuvant chemotherapy (NAC) and radical cystectomy (RC) (n = 223). Unsupervised consensus clustering of highly variant lncRNAs identified a four-cluster solution, which was characterized using a panel of MIBC biomarkers, regulon activity profiles, gene signatures, and survival analysis. The four-cluster solution was confirmed in The Cancer Genome Atlas (TCGA) cohort (n = 405). A single-sample genomic classifier (GC) was trained using ridge-penalized logistic regression and validated in two independent cohorts (n = 255 and n = 94).ResultsNAC and TCGA cohorts both contained an lncRNA cluster (LC3) with favorable prognosis that was enriched with tumors of the luminal-papillary (LP) subtype. In both cohorts, patients with LP tumors in LC3 (LPL-C3) were younger and had organ-confined, node-negative disease. The LPL-C3 tumors had enhanced FGFR3, SHH, and wild-type p53 pathway activity. In the TCGA cohort, LPL-C3 tumors were enriched for FGFR3 mutations and depleted for TP53 and RB1 mutations. A GC trained to identify these LPL-C3 patients showed robust performance in two validation cohorts.ConclusionsUsing lncRNA expression profiles, we identified a biologically distinct subgroup of luminal-papillary MIBC with a favorable prognosis. These data suggest that lncRNAs provide additional information for higher-resolution subtyping, potentially improving precision patient management.

905PD - Multiple-cohort analysis investigating FGFR3 alteration as a predictor of non-response to neoadjuvant pembrolizumab (pembro) in muscle-invasive bladder cancer (MIBC)

BackgroundIn PURE01 study (NCT02736266), neoadjuvant pembro resulted in 42% pT0 in patients (pts) with MIBC. pT0 pts had features suggesting pre-existing immunity or higher tumor mutational burden (TMB) may promote response. In this study, we investigated potential mechanisms for resistance to pembro, including FGFR3 genomic alterations (GA). MethodsPts enrolled in the PURE-01, which is still recruiting pts in its amended design, had predominant urothelial carcinoma histology and stage cT≤4N0 MIBC. Biomarker analyses in the expanded cohort of 96 pts included PD-L1 combined positive score and comprehensive genomic profiling (FoundationCDx assay). In addition, TCGA MIBC (n=405) and a prospective commercial cohort (PCC) of 415 MIBC pts from the clinical use of the Decipher Bladder TURB test from the GRID registry (NCT02609269) were analyzed. A single-sample genomic classifier (GC) was trained to identify FGFR3-active tumors (FGFR3+). ResultsIn PURE01 cohort, despite a linear association of TMB with ypT0 in multivariable models (p=0.017), there was no association between FGFR3 GA and pathological response nor with PD-L1 expression. FGFR3 GA were found in 17.6% ypT0 vs 20.7% in ypT3-4 disease (corrected p=0.82). Applying the GC to the TCGA MIBC cohort, we found 45% of FGFR3+ cases had FGFR3 mutations vs 9% for the rest of the cohort. Applying the GC to the PCC, we found that the FGFR3+ tumors were Luminal (n=14), Luminal Infiltrated (n=10) or Luminal Papillary (n=30). FGFR3+ pts showed significantly lower PD-L1 (-0.03 vs. 0.109, p<0.001) and PD-L2 (0.184 vs. 0.389, p<0.001), but consistent PD-1 (0.175 vs. 0.163, p=0.48) gene expression. FGFR3+ pts had lower immune and stromal infiltration as measured by the immune190 (0.227 vs. 0.348, p<0.001) and Estimate (100.14 vs. 1099.2, p<0.001) gene expression signatures. ConclusionsIn our combined cohorts, FGFR3 GA did not correlate with response to pembro. FGFR3 GA are enriched in FGFR3+ tumors, which in turn tend to have lower immune activity, PD-L1 and PD-L2, suggesting FGFR3 activity may provide a potential tool for further discriminating the mechanisms underlying response and resistance to neoadjuvant pembro in MIBC. Clinical trial identificationNCT02736266 (PURE01) NCT02609269 (GRID Registry). Legal entity responsible for the studyThe authors. FundingDecipher Bioscience. DisclosureA. Necchi: Honoraria (institution), Advisory / Consultancy, Research grant / Funding (institution): Merck; Honoraria (institution), Advisory / Consultancy: Roche; Advisory / Consultancy: AstraZeneca; Advisory / Consultancy: BMS; Advisory / Consultancy, Research grant / Funding (institution): Incyte; Advisory / Consultancy: Clovis; Advisory / Consultancy: Janssen. R. Madison: Full / Part-time employment: Foundation Medicine. J. Chung: Full / Part-time employment: Foundation Medicine. Y. Liu: Full / Part-time employment: Decipher Bioscience. J. Chung: Full / Part-time employment: Foundation Medicine. J.S. Ross: Full / Part-time employment: Foundation Medicine. S.M. Ali: Full / Part-time employment: Foundation Medicine. E. Davicioni: Full / Part-time employment: Decipher Bioscience. E.A. Gibb: Full / Part-time employment: Decipher Bioscience. All other authors have declared no conflicts of interest.

A Consensus Molecular Classification of Muscle-invasive Bladder Cancer.

Background:Muscle-invasive bladder cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, but the diversity of their subtype sets impedes their clinical application.Objective:To achieve an international consensus on MIBC molecular subtypes that reconciles the published classification schemes.Design, setting, and participants:We used 1750 MIBC transcriptomic profiles from 16 published datasets and two additional cohorts.Outcome measurements and statistical analysis:We performed a network-based analysis of six independent MIBC classification systems to identify a consensus set of molecular classes. Association with survival was assessed using multivariable Cox models.Results and limitations:We report the results of an international effort to reach a consensus on MIBC molecular subtypes. We identified a consensus set of six molecular classes: luminal papillary (24%), luminal nonspecified (8%), luminal unstable (15%), stroma-rich (15%), basal/squamous (35%), and neuroendocrine-like (3%). These consensus classes differ regarding underlying oncogenic mechanisms, infiltration by immune and stromal cells, and histological and clinical characteristics, including outcomes. We provide a single-sample classifier that assigns a consensus class label to a tumor sample’s transcriptome. Limitations of the work are retrospective clinical data collection and a lack of complete information regarding patient treatment.Conclusions:This consensus system offers a robust framework that will enable testing and validation of predictive biomarkers in future prospective clinical trials.Patient summary:Bladder cancers are heterogeneous at the molecular level, and scientists have proposed several classifications into sets of molecular classes. While these classifications may be useful to stratify patients for prognosis or response to treatment, a consensus classification would facilitate the clinical use of molecular classes. Conducted by multidisciplinary expert teams in the field, this study proposes such a consensus and provides a tool for applying the consensus classification in the clinical setting.

Abstract 1930: High specific characterization of patient-derived tumor xenograft models for accelerating drug development in muscle-invasive bladder cancers

Abstract Muscle-invasive bladder cancers (MIBCs) constitute a heterogeneous group of tumors with a poor outcome. Recently, MIBC molecular subtyping efforts from an international consortium led to the identification of six subtypes to improve prediction of clinical outcomes and treatment responses. These subtypes can be schematically divided into luminal (differentiated) and non-luminal subtypes. FGFR3 alterations (mutations and translocations) are among the most frequent genetic events in bladder carcinoma and are found mainly in one subtype, the luminal papillary that respond poorly to chemo- and immuno-therapy. Here we describe the development and characterization of patient-derived primary MIBC xenografts (PDX) belonging to these different subtypes. Bladder primary tumors and normal corresponding tissues were directly obtained from patients at surgery. Tumor fragments were subcutaneously xenografted into immune-compromised mice. After the first growth in mice, they were serially passaged. PDXs tumors at multiple passages and patients’ primary tumors from which they are derived were processed for analyses including growth characteristics, histopathology (H&amp;E, CK5/6, FOXA1 and GATA3), gene expression (Affymetrix U133 plus 2.0 microarray), genetic stability (STR profiling). Specifically, hotspot oncogenic mutations including FGFR3, PIK3CA, HRAS, KRAS, NRAS, and PPARG were also explored. Additionally, pharmacological responses to standards of care and targeted therapies were characterized. Since 10 years, we have collected 152 MIBC tumors at all stages and grades. Up to now, 32 PDX models have been successfully established (&amp;gt; P3 in mice), i.e. 21.1 % success rate. This take rate seems not to be correlated to any classical tumor characteristics. Importantly, transcriptomic analysis allowed us to identify PDX models belonging to the different molecular subtypes including the basal-like and the luminal papillary subtypes (which include several PDX with FGFR3 mutations). All histological, genetic and molecular features validated the stability of the PDX models compared to the parental tumors. Histological analyses were correlated with the molecular classification. These models reproduced the response to cisplatin-based therapies observed in the clinic and FGFR3-mutated PDX models were shown to be highly responder to FGFR3 inhibitors. We have developed highly relevant preclinical models for MIBCs corresponding to the main subtypes which have been described. They represent essential tools for developing adapted and efficient therapies against this deadly disease. Citation Format: Hervé Lang, Claire Beraud, Myriam Lassalle, Véronique Lindner, Michel Soulié, Xavier Gamé, Pascal Rischmann, Yves Allory, François Radvanyi, Isabelle Bernard-Pierrot, Philippe Lluel, Thierry Massfelder. High specific characterization of patient-derived tumor xenograft models for accelerating drug development in muscle-invasive bladder cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1930.

A Consensus Molecular Classification of Muscle-Invasive Bladder Cancer

Muscle-Invasive Bladder Cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, yielding diverse sets of subtypes. This diversity hampers the clinical application of such knowledge. Here, we report the results of a large international effort to reach a consensus on MIBC molecular subtypes. Using 1750 MIBC transcriptomes and a network-based analysis of six independent MIBC classification systems, we identified a consensus set of six molecular classes: Luminal Papillary (24%), Luminal Non-Specified (8%), Luminal Unstable (15%), Stroma-rich (15%), Basal/Squamous (35%), and Neuroendocrine-like (3%). These consensus classes differ regarding underlying oncogenic mechanisms, infiltration by immune and stromal cells, and histological and clinical characteristics. This consensus system offers a robust framework that will enable testing and validating predictive biomarkers in future clinical trials.