Molecular profile of pure squamous cell carcinoma of the bladder identifies major roles for OSMR and YAP signalling

Pure squamous cell carcinoma (SCC) is the most common pure variant form of bladder cancer, found in 2–5% of cases. It often presents late and is unresponsive to cisplatin‐based chemotherapy. The molecular features of these tumours have not been elucidated in detail. We carried out whole‐exome sequencing (WES), copy number, and transcriptome analysis of bladder SCC. Muscle‐invasive bladder cancer (MIBC) samples with no evidence of squamous differentiation (non‐SD) were used for comparison. To assess commonality of features with urothelial carcinoma with SD, we examined data from SD samples in The Cancer Genome Atlas (TCGA) study of MIBC. TP53 was the most commonly mutated gene in SCC (64%) followed by FAT1 (45%). Copy number analysis revealed complex changes in SCC, many differing from those in samples with SD. Gain of 5p and 7p was the most common feature, and focal regions on 5p included OSMR and RICTOR. In addition to 9p deletions, we found some samples with focal gain of 9p24 containing CD274 (PD‐L1). Loss of 4q35 containing FAT1 was found in many samples such that all but one sample analysed by WES had FAT1 mutation or deletion. Expression features included upregulation of oncostatin M receptor (OSMR), metalloproteinases, metallothioneins, keratinisation genes, extracellular matrix components, inflammatory response genes, stem cell markers, and immune response modulators. Exploration of differentially expressed transcription factors identified BNC1 and TFAP2A, a gene repressed by PPARG, as the most upregulated factors. Known urothelial differentiation factors were downregulated along with 72 Kruppel‐associated (KRAB) domain‐containing zinc finger family protein (KZFP) genes. Novel therapies are urgently needed for these tumours. In addition to upregulated expression of EGFR, which has been suggested as a therapeutic target in basal/squamous bladder cancer, we identified expression signatures that indicate upregulated OSMR and YAP/TAZ signalling. Preclinical evaluation of the effects of inhibition of these pathways alone or in combination is merited.

Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight

Understanding the molecular determinants that underpin the clinical heterogeneity of non-muscle-invasive bladder cancer (NMIBC) is essential for prognostication and therapy development. Stage T1 disease in particular presents a high risk of progression and requires improved understanding. We present a detailed multi-omics study containing gene expression, copy number, and mutational profiles that show relationships to immune infiltration, disease recurrence, and progression to muscle invasion. We compare expression and genomic subtypes derived from all NMIBCs with those derived from the individual disease stages Ta and T1. We show that sufficient molecular heterogeneity exists within the separate stages to allow subclassification and that this is more clinically meaningful for stage T1 disease than that derived from all NMIBCs. This provides improved biological understanding and identifies subtypes of T1 tumors that may benefit from chemo- or immunotherapy.

Current Treatment and Outcomes Benchmark for Locally Advanced or Metastatic Urothelial Cancer From a Large UK-Based Single Centre

Objectives: To characterize treatment patterns and survival outcomes for patients with locally advanced or metastatic malignancy of the urothelial tract during a period immediately preceding the widespread use of immune checkpoint inhibitors in the UK.

Patients and Methods: We retrospectively examined the electronic case notes of patients attending the Leeds Cancer Center, UK with locally advanced or metastatic urothelial carcinoma, receiving chemotherapy between January 2003 and March 2017. Patient characteristics, treatment patterns, and outcomes were collected. Summary and descriptive statistics were calculated for categorical and continuous variables as appropriate. The Kaplan–Meier method was used to estimate median survival and Cox regression proportional hazards model was used to explore relationships between clinical variables and outcome.

Results: Two hundred and sixteen patients made up the study cohort, with a median age of 66 years (range: 35–83) and 72.7% being male. First-line treatment consisted of either a cisplatin- (44%) or carboplatin-based regimen (48%) in the majority of patients. Twenty seven percent of patients received a second-line of treatment (most commonly single-agent paclitaxel) following a first-line platinum containing regimen. Grade 4 neutropenia was observed in 19 and 27% of those treated with a first-line cisplatin- and carboplatin-based regimen, respectively. The median overall survival (mOS) of the study cohort was estimated to be 16.2 months (IQR: 10.6–28.3 months). Receipt by patients of cisplatin-based chemotherapy was associated with a longer mOS and this association persisted when survival analysis was adjusted for age, sex, performance status and presence of distant metastases.

Conclusions: This study provides a useful benchmark for outcomes achieved in a real-world setting for patients with locally advanced or metastatic UC treated with chemotherapy in the immediate pre-immunotherapy era.

Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency

Bladder cancer incurs a higher lifetime treatment cost than other cancers due to frequent recurrence of non-invasive disease. Improved prognostic biomarkers and localized therapy are needed for this large patient group. We defined two major genomic subtypes of primary stage Ta tumors. One of these was characterized by loss of 9q including TSC1, increased KI67 labeling index, upregulated glycolysis, DNA repair, mTORC1 signaling, features of the unfolded protein response, and altered cholesterol homeostasis. Comparison with muscle-invasive bladder cancer mutation profiles revealed lower overall mutation rates and more frequent mutations in RHOB and chromatin modifier genes. More mutations in the histone lysine demethylase KDM6A were present in non-invasive tumors from females than males.

The nuclear matrix protein CIZ1 facilitates localization of Xist RNA to the inactive X-chromosome territory

Here, Ridings-Figueroa et al. show that the nuclear matrix protein Cip1-interacting zinc finger protein 1 (CIZ1) is highly enriched on the inactive X chromosome (Xi) in mouse and human female cells and is retained by interaction with the RNA-dependent nuclear matrix. Their findings suggest that CIZ1 has an essential role in anchoring Xist to the nuclear matrix in specific somatic lineages.

The nuclear matrix protein Cip1-interacting zinc finger protein 1 (CIZ1) promotes DNA replication in association with cyclins and has been linked to adult and pediatric cancers. Here we show that CIZ1 is highly enriched on the inactive X chromosome (Xi) in mouse and human female cells and is retained by interaction with the RNA-dependent nuclear matrix. CIZ1 is recruited to Xi in response to expression of X inactive-specific transcript (Xist) RNA during the earliest stages of X inactivation in embryonic stem cells and is dependent on the C-terminal nuclear matrix anchor domain of CIZ1 and the E repeats of Xist. CIZ1-null mice, although viable, display fully penetrant female-specific lymphoproliferative disorder. Interestingly, in mouse embryonic fibroblast cells derived from CIZ1-null embryos, Xist RNA localization is disrupted, being highly dispersed through the nucleoplasm rather than focal. Focal localization is reinstated following re-expression of CIZ1. Focal localization of Xist RNA is also disrupted in activated B and T cells isolated from CIZ1-null animals, suggesting a possible explanation for female-specific lymphoproliferative disorder. Together, these findings suggest that CIZ1 has an essential role in anchoring Xist to the nuclear matrix in specific somatic lineages.

Abstract LB-323: The genomic landscape of non-muscle-invasive bladder cancer: implications for molecular classification and treatment

Non-muscle-invasive bladder cancers (NMIBC) and muscle-invasive bladder cancers (MIBC) show distinct molecular and clinical features and are considered to follow different pathogenesis pathways. MIBC commonly metastasise (>50%) and have poor prognosis whereas NMIBC, particularly low-stage low-grade tumors, rarely progress to invade muscle (<5%). Patients diagnosed with NMIBC frequently suffer disease recurrence, demanding long-term disease monitoring and repeated resection of recurrences. Large MIBC cohorts have been extensively interrogated on a genome-wide scale but relatively few NMIBC have been studied at this level. To address this we determined the mutational landscape of 82 non-muscle-invasive tumors (stage Ta grade 2) using whole-exome and targeted deep sequencing. Whole-exome sequencing identified an average of 124±79 synonymous and non-synonymous somatic mutations (single nucleotide substitutions and indels) per sample, giving mean and median somatic mutation rates of 2.41 and 1.64 per megabase, respectively. Overall, 47% of nucleotide substitutions were C>T transitions, followed by C>G transversions (24.8%). Similar to MIBC, APOBEC mutagenesis was the strongest source of mutation in NMIBC with 75% of samples showing up to 5-fold enrichment of the APOBEC mutation signature. Significantly mutated genes included genes implicated in epigenetic regulation and several genes that have not previously been reported as significantly mutated in bladder cancer. Comparison of mutation frequencies in NMIBC with those found in MIBC revealed both known differences (absence of TP53 mutations and high frequency of FGFR3, PIK3CA and STAG2 mutations in NMIBC) and novel findings including a higher frequency of mutations in chromatin-state regulators in NMIBC. Notably CDKN1A, RB1, ERCC2, ERBB3 and FBXW7, which are mutated in >10% of MIBC were not significantly mutated in TaG2 tumors, further delineating the distinct pathogenesis pathways of NMIBC and MIBC. Whole-genome expression array profiling and immunohistochemistry using a panel of markers were carried out to further examine the molecular features of NMIBC samples and define potentially clinically relevant subtypes. These data provide a detailed view of the genomic landscape of NMIBC that highlights chromatin modification as a key area for consideration in the development of potential future therapeutic approaches to the treatment of patients with non-muscle-invasive disease.

Citation Format: Carolyn D. Hurst, Olivia Alder, Fiona M. Platt, Alastair Droop, Lucy F. Stead, Julie E. Burns, George J. Burghel, Sunjay Jain, Leszek J. Klimczak, Helen Lindsay, Jo-An Roulson, Claire F. Taylor, Helene Thygesen, Angus J. Cameron, Anne J. Ridley, Helene R. Mott, Dmitry A. Gordenin, Margaret A. Knowles. The genomic landscape of non-muscle-invasive bladder cancer: implications for molecular classification and treatment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-323.

Polycomb Repressor Complex 1 Member, BMI1 Contributes to Urothelial Tumorigenesis through p16-Independent Mechanisms

Urothelial carcinoma (UC) causes significant morbidity and remains the most expensive cancer to treat because of the need for repeated resections and lifelong monitoring for patients with non-muscle-invasive bladder cancer (NMIBC). Novel therapeutics and stratification approaches are needed to improve the outlook for both NMIBC and muscle-invasive bladder cancer. We investigated the expression and effects of B Lymphoma Mo-MLV Insertion Region 1 (BMI1) in UC. BMI1 was found to be overexpressed in most UC cell lines and primary tumors by quantitative real-time polymerase chain reaction and immunohistochemistry. In contrast to some previous reports, no association with tumor stage or grade was observed in two independent tumor panels. Furthermore, upregulation of BMI1 was detected in premalignant bladder lesions, suggesting a role early in tumorigenesis. BMI1 is not located within a common region of genomic amplification in UC. The CDKN2A locus (which encodes the p16 tumor suppressor gene) is a transcriptional target of BMI1 in some cellular contexts. In UC cell lines and primary tissues, no correlation between BMI1 and p16 expression was observed. Retroviral-mediated overexpression of BMI1 immortalized normal human urothelial cells (NHUC) in vitro and was associated with induction of telomerase activity, bypass of senescence, and repression of differentiation. The effects of BMI1 on gene expression were identified by expression microarray analysis of NHUC-BMI1. Metacore analysis of the gene expression profile implicated downstream effects of BMI1 on α4/β1 integrin-mediated adhesion, cytoskeleton remodeling, and CREB1-mediated transcription.

Abstract 5096: Quiescence induced checkpoint activation in the absence of CIZ1

The CIZ1 protein is required for timely entry to S phase following exit from quiescence (1). We show here that CIZ1 is also required for accurate entry into quiescence. Analysis of quiescence entry following contact inhibition in a CIZ1-deletion model has revealed a role in dampening a previously unreported quiescence checkpoint, evidenced by ubiquitous post-replicative phosphorylation of histone H2AX and activation of checkpoint kinases ATM and CHK1. Subsequent emergence of proliferating colonies indicates escape from checkpoint-mediated arrest, and begins to implicate inappropriate response to contact induced signaling as a novel endogenous driver of oncogenesis. Unscheduled checkpoint activation was also observed in bone marrow cells from juvenile CIZ1 null mice, and high frequency B-cell lymphoma in young adults in the absence of any additional oncogenic stimulation, supporting the idea that CIZ1 plays a very early role in tumorigenesis.

Analysis of cell cycle progression using immunofluorescence and flow cytometry of primary fibroblasts from post-natal CIZ1 null mice revealed cell cycle elongation, with extended expression of cyclins D2 and E1, increased cyclin A2, and altered p21, p27 and CDK2, but no checkpoint activation. Thus, CIZ1 null cells can tolerate altered expression, targeting and recruitment of multiple cell cycle regulators. Checkpoint activation occurs only after exit from the cell cycle, reflecting aberrant response to contact induced signaling and failure to accurately transition into a stable quiescent state.

Inappropriate expression of CIZ1 splice variants has been previously linked with both adult and pediatric cancers (2-4), and shown to play a proliferation-promoting role in lung (4) and breast (5) tumor models. Furthermore, CIZ1 b-variant has biomarker capability for the early detection of lung cancer (4). Despite these advances, the precise role of CIZ1 in the cell is not yet understood. The CIZ1 knock out mouse model described here, and a related model (6), indicate a tumor suppressor function, which is apparently at odds with the DNA replication- and proliferation-promoting roles reported previously. The current work helps to reconcile these observations by showing that CIZ1s established activity in the promotion of cyclin A-mediated initiation of DNA replication (1) is as a coordinator. This in fact, influences multiple cyclins and CDKis, however, impairment of this capability during cell cycle progression may not underlie CIZ1s role in tumorigenesis. Our central finding is that altered cell cycle homeostasis in CIZ1 null cells does not lead to checkpoint activation, until they are driven to contact induced quiescence.

1 Copeland et al (2010) J Cell Sci 123, 1108-15

2 Warder & Keherly (2003) J Biomed Sci.10, 406-17

3 Rahman et al (2007) Human Mutation 28, 993-1004

4 Higgins et al (2012) Proc Natl Acad Sci U S A 109, E3128-35

5 den Hollander et al (2006) Cancer Research 66, 11021-30

6 Nishibe et al (2013) FEBS Lett 587, 1529-35

Citation Format: Rosemary H.C Wilson, Jo-An Roulson, Sumia Bageghni, Ghadeer Albadrani, Justin F-X Ainscough, Dawn Coverley. Quiescence induced checkpoint activation in the absence of CIZ1. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5096. doi:10.1158/1538-7445.AM2014-5096

Alteration of cell-cell and cell-matrix adhesion in urothelial cells: an oncogenic mechanism for mutant FGFR3

Activating mutations of FGFR3 are a common and early event in bladder cancer. Ectopic expression of mutant FGFR3 in normal urothelial cells has both pro-proliferative and antiapoptotic effects at confluence, suggesting that mutant cells are insensitive to cell-cell contact inhibition. Herein, detailed analysis revealed that these cells have reduced cell-cell adhesion, with large intercellular spaces observable at confluence, and diminished cell-substrate adhesion to collagen IV, collagen I, and fibronectin. These phenotypic alterations are accompanied by changes in the expression of genes involved in cell adhesion and extracellular matrix remodeling. Silencing of endogenous mutant FGFR3 in bladder cancer cells induced converse changes in transcript levels of CDH16, PLAU, MMP10, EPCAM, TNC, and HAS3, confirming them as downstream gene targets of mutant FGFR3. Overexpression of EPCAM, HAS3, and MMP10 transcripts was found in a large fraction of primary bladder tumors analyzed, supporting their key role in bladder tumorigenesis in vivo. However, no correlation was found between their protein and/or mRNA expression and FGFR3 mutation status in tumor specimens, indicating that these genes may be targeted by several converging oncogenic pathways. Overall, these results indicate that mutant FGFR3 favors the development and progression of premalignant bladder lesions by altering key genes regulating the cell-cell and cell-matrix adhesive properties of urothelial cells.

IMPLICATIONS

The ability of mutant FGFR3 to drive transcriptional expression profiles involved in tumor cell adhesion suggests a mechanism for expansion of premalignant urothelial lesions.

An integrated genomic, transcriptional and protein investigation of FGFRL1 as a putative 4p16.3 deletion target in bladder cancer

Loss of heterozygosity (LOH) of chromosome arm 4p is a common event in bladder and other malignancies. At least three distinct regions of deletion have been identified, but the deletion targets have so far remained elusive. In this study, we have identified a novel region of deletion mapping to 4p16.3 spanning 0-2.1 Mb, in 15% of bladder tumors and 24% of bladder cancer cell lines. FGFRL1, which maps within this region, was investigated as putative deletion target. The retained FGFRL1 allele was not mutated in cell lines and tumors with LOH, although in patients heterozygous for the rs4647930 functional polymorphism, the common allele was preferentially lost in tumor tissue. Epigenetic silencing of the retained allele was also excluded as levels of FGFRL1 mRNA and protein were similar in cell lines and tumors with and without 4p16.3 loss. However, while FGFRL1 protein was moderately expressed in all layers of the normal bladder epithelium, the majority of tumors showed areas of downregulation. Overall, average FGFRL1 protein expression was significantly lower in bladder tumors compared to normal tissue, but downregulation was independent from 4p16.3 LOH status, FGFR3 mutation, and tumor grade and stage. In conclusion, although we found no evidence supporting a "two-hit" inactivation of FGFRL1 in bladder carcinogenesis, the effect of heterozygous deletion coupled with functional polymorphisms, and the role of post-transcriptional downregulation deserves further investigation.

Littoral cell angioma of the spleen in a patient with severe aplastic anaemia

Littoral cell angioma (LCA) is a rare benign tumour of the spleen. We describe a patient with aplastic anaemia who, following multiple treatments with rabbit and horse Anti-Thymocyte Globulin and anabolic steroids developed marked splenomegaly and hypersplenism. LCA was diagnosed post splenectomy. This is the first case of LCA associated with aplastic anaemia and its treatment.

Littoral cell angioma of the spleen in a patient with severe aplastic anaemia

Littoral cell angioma (LCA) is a rare benign tumour of the spleen. We describe a patient with aplastic anaemia who, following multiple treatments with rabbit and horse Anti-Thymocyte Globulin and anabolic steroids developed marked splenomegaly and hypersplenism. LCA was diagnosed post splenectomy. This is the first case of LCA associated with aplastic anaemia and its treatment.