Molecular footprints of muscle-invasive bladder cancer in smoking and nonsmoking patients

Molecular Basis of Tumorigenesis of Bladder Cancer and Emerging Concepts in Developing Therapeutic Targets

BACKGROUND

Advanced urothelial carcinoma (UC) is an aggressive disease whose mutagenic processes are yet to be elucidated. Targeted therapies are urgently needed, but the road from bench to bedside is slowly progressing. In this review, we discuss urothelial carcinoma etiology, along with the most recent advances in UC candidate targeted therapies.

METHODOLOGY

A comprehensive database search was performed. We aimed to review the most recent updates on UC genomics and targeted therapies. Pre-clinical as well as clinical studies were included.

RESULTS

Our review highlights the advances in understanding the molecular basis of urothelial tumorigenesis, including smoking, chemical parasitic carcinogens, inheritance, and APOBEC3 editing enzymes. We discussed how these factors contributed to the current mutational landscape of UC. Therapeutic options for UC are still very limited. However, several promising therapeutic approaches are in development to leverage our knowledge of molecular targets, such as targeting fibroblast growth factor receptors (FGFR), DNA damage repair pathways, and HER2.

CONCLUSIONS

Blindly testing targeted therapies based on other cancer data is not sufficient. UC-specific biomarkers are needed to precisely use the appropriate drug for the appropriate population. More efforts to understand UC biology and evolution are urgently needed.

Analysis of Several Common APOBEC-type Mutations in Bladder Tumors Suggests Links to Viral Infection

FGFR3 and PIK3CA are among the most frequently mutated genes in bladder tumors. We hypothesized that recurrent mutations in these genes might be caused by common carcinogenic exposures such as smoking and other factors. We analyzed 2,816 bladder tumors with available data on FGFR3 and/or PIK3CA mutations, focusing on the most recurrent mutations detected in ≥10% of tumors. Compared to tumors with other FGFR3/PIK3CA mutations, FGFR3-Y375C was more common in tumors from smokers than never-smokers (P = 0.009), while several APOBEC-type driver mutations were enriched in never-smokers: FGFR3-S249C (P = 0.013) and PIK3CA-E542K/PIK3CA-E545K (P = 0.009). To explore possible causes of these APOBEC-type mutations, we analyzed RNA sequencing (RNA-seq) data from 798 bladder tumors and detected several viruses, with BK polyomavirus (BKPyV) being the most common. We then performed IHC staining for polyomavirus (PyV) Large T-antigen (LTAg) in an independent set of 211 bladder tumors. Overall, by RNA-seq or IHC-LTAg, we detected PyV in 26 out of 1,010 bladder tumors with significantly higher detection (P = 4.4 × 10-5), 25 of 554 (4.5%) in non-muscle-invasive bladder cancers (NMIBC) versus 1 of 456 (0.2%) of muscle-invasive bladder cancers (MIBC). In the NMIBC subset, the FGFR3/PIK3CA APOBEC-type driver mutations were detected in 94.7% (18/19) of PyV-positive versus 68.3% (259/379) of PyV-negative tumors (P = 0.011). BKPyV tumor positivity in the NMIBC subset with FGFR3- or PIK3CA-mutated tumors was also associated with a higher risk of progression to MIBC (P = 0.019). In conclusion, our results support smoking and BKPyV infection as risk factors contributing to bladder tumorigenesis in the general patient population through distinct molecular mechanisms.

PREVENTION RELEVANCE

Tobacco smoking likely causes one of the most common mutations in bladder tumors (FGFR3-Y375C), while viral infections might contribute to three others (FGFR3-S249C, PIK3CA-E542K, and PIK3CA-E545K). Understanding the causes of these mutations may lead to new prevention and treatment strategies, such as viral screening and vaccination.

Gender differences in smoking-induced changes in the tumor immune microenvironment

Both gender and smoking are correlated with prevalence and outcomes in many types of cancers. Tobacco smoke is a known carcinogen through its genotoxicity but can also affect cancer progression through its effect on the immune system. In this study, we aim to evaluate the hypothesis that the effects of smoking on the tumor immune microenvironment will be influenced differently by gender using large-scale analysis of publicly available cancer datasets. We used The Cancer Genomic Atlas (TCGA) datasets (n = 2724) to analyze effects of smoking on different cancer immune subtypes and the relative abundance of immune cell types between male and female cancer patients. We further validated our results by analyzing additional datasets, including Expression Project for Oncology (expO) bulk RNA-seq dataset (n = 1118) and single-cell RNA-seq dataset (n = 14). Results of our study indicate that in female patients, two immune subtypes, C1 and C2, are respectively over and under abundant in smokers vs. never smokers. In males, the only significant difference is underabundance of the C6 subtype in smokers. We identified gender-specific differences in the population of immune cell types between smokers and never smokers in all TCGA and expO cancer types. Increased plasma cell population was identified as the most consistent feature distinguishing smokers and never smokers, especially in current female smokers based on both TCGA and expO data. Our analysis of existing single-cell RNA-seq data further revealed that smoking differentially affects the gene expression profile of cancer patients based on the immune cell type and gender. In our analysis, female and male smokers show different smoking-induced patterns of immune cells in tumor microenvironment. Besides, our results suggest cancer tissues directly exposed to tobacco smoke undergo the most significant changes, but all other cancer types are affected as well. Findings of current study also indicate that changes in the populations of plasma cells and their correlations to survival outcomes are stronger in female current smokers, with implications for cancer immunotherapy of women smokers. In conclusion, results of this study can be used to develop personalized treatment plans for cancer patients who smoke, particularly women smokers, taking into account the unique immune cell profile of their tumors.

Tobacco Smoking and Survival Following a Diagnosis with Ovarian Cancer

BACKGROUND

Little is known about the influence of smoking on ovarian cancer survival. We investigated this relationship in a hospital-based study.

METHODS

Analyses included 519 women with ovarian cancer. We used multivariable adjusted Cox proportional hazards regression models to estimate HRs and 95% confidence intervals (CI).

RESULTS

Risk of all-cause mortality was increased for current smokers (HR = 1.70; 95% CI: 1.09-2.63) versus never smokers, especially for those with ≥15 cigarettes per day (HR = 1.92; 95% CI: 1.15-3.20). Results were largely similar after additional adjustment for debulking status (current vs. never smokers, HR = 2.96; 95% CI: 1.07-8.21) or neoadjuvant chemotherapy (comparable HR = 2.87; 95% CI: 1.02-8.06). Compared with never smokers, smoking duration ≥20 years (HR = 1.38; 95% CI: 0.94-2.03) and ≥20 pack-years (HR = 1.35; 95% CI: 0.92-1.99) were suggestively associated with worse outcomes. Current smoking was also positively associated with the risk of mortality among patients with ovarian cancer recurrence (current vs. never/past smokers, HR = 2.79; 95% CI: 1.44-5.41), despite the null association between smoking and recurrence (HR = 1.46; 95% CI: 0.86-2.48). Furthermore, no association was observed for smoking initiation before age 18 (HR = 1.22; 95% CI: 0.80-1.85), or either environmental smoke exposure at home (HR = 1.16; 95% CI: 0.76-1.78) or at work (HR = 1.10; 95% CI: 0.75-1.60).

CONCLUSIONS

Our results suggest active tobacco smoking is associated with worse ovarian cancer outcomes, particularly after a recurrence.

IMPACT

Our findings support structured smoking cessation programs for patients with ovarian cancer, especially in recurrent settings. Further research to confirm these findings and examine the interplay between smoking and the tumor immune microenvironment may help provide insight into ovarian cancer etiology.

Molecular Oncology of Bladder Cancer from Inception to Modern Perspective

Within the last forty years, seminal contributions have been made in the areas of bladder cancer (BC) biology, driver genes, molecular profiling, biomarkers, and therapeutic targets for improving personalized patient care. This overview includes seminal discoveries and advances in the molecular oncology of BC. Starting with the concept of divergent molecular pathways for the development of low- and high-grade bladder tumors, field cancerization versus clonality of bladder tumors, cancer driver genes/mutations, genetic polymorphisms, and bacillus Calmette-Guérin (BCG) as an early form of immunotherapy are some of the conceptual contributions towards improving patient care. Although beginning with a promise of predicting prognosis and individualizing treatments, "-omic" approaches and molecular subtypes have revealed the importance of BC stem cells, lineage plasticity, and intra-tumor heterogeneity as the next frontiers for realizing individualized patient care. Along with urine as the optimal non-invasive liquid biopsy, BC is at the forefront of the biomarker field. If the goal is to reduce the number of cystoscopies but not to replace them for monitoring recurrence and asymptomatic microscopic hematuria, a BC marker may reach clinical acceptance. As advances in the molecular oncology of BC continue, the next twenty-five years should significantly advance personalized care for BC patients.

Fighting the 'tobacco epidemic' - A call to action to identify Targeted Intervention Points (TIPs) for better counseling patients with urothelial cancer

The association between tobacco use and urothelial cancer of the bladder is well known. Given the worsening tobacco epidemic, here we make the case for systematic targeted points of intervention for urologists and other professionals to intervene against bladder cancer. Awareness of contemporary checkpoints where we can intervene for counseling patients may help medical education in a tobacco-pandemic difficult setting.

Targeted Deep Sequencing of Bladder Tumors Reveals Novel Associations between Cancer Gene Mutations and Mutational Signatures with Major Risk Factors

PURPOSE

Exome- and whole-genome sequencing of muscle-invasive bladder cancer has revealed important insights into the molecular landscape; however, there are few studies of non-muscle-invasive bladder cancer with detailed risk factor information.

EXPERIMENTAL DESIGN

We examined the relationship between smoking and other bladder cancer risk factors and somatic mutations and mutational signatures in bladder tumors. Targeted sequencing of frequently mutated genes in bladder cancer was conducted in 322 formalin-fixed paraffin-embedded bladder tumors from a population-based case-control study. Logistic regression was used to calculate odds ratios (OR) and 95% confidence intervals (CI), evaluating mutations and risk factors. We used SignatureEstimation to extract four known single base substitution mutational signatures and Poisson regression to calculate risk ratios (RR) and 95% CIs, evaluating signatures and risk factors.

RESULTS

Non-silent KDM6A mutations were more common in females than males (OR = 1.83; 95% CI, 1.05-3.19). There was striking heterogeneity in the relationship between smoking status and established single base substitution signatures: current smoking status was associated with greater ERCC2-Signature mutations compared with former (P = 0.024) and never smoking (RR = 1.40; 95% CI, 1.09-1.80; P = 0.008), former smoking was associated with greater APOBEC-Signature13 mutations (P = 0.05), and never smoking was associated with greater APOBEC-Signature2 mutations (RR = 1.54; 95% CI, 1.17-2.01; P = 0.002). There was evidence that smoking duration (the component most strongly associated with bladder cancer risk) was associated with ERCC2-Signature mutations and APOBEC-Signature13 mutations among current (P trend = 0.005) and former smokers (P = 0.0004), respectively.

CONCLUSIONS

These data quantify the contribution of bladder cancer risk factors to mutational burden and suggest different signature enrichments among never, former, and current smokers.

Educational Case: Bladder Urothelial Cell Carcinoma TNM Stage, Prognosis and Management

The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040. ¹.

Association of smoking status and recurrence of non-muscle invasive bladder cancer among patients managed with blue light cystoscopy

PURPOSE

Smoking has a strong causal association with bladder cancer but the relationship with recurrence is not well established. We sought to assess the association of smoking status on recurrence of non-muscle invasive bladder cancer (NMIBC) in a contemporary cohort of patients with predominantly high-risk, recurrent NMIBC managed with photodynamic enhanced cystoscopy.

MATERIALS AND METHODS

We performed a retrospective study of patients with NMIBC included in a multi-institutional registry. Our primary exposure of interest was smoking status. Our primary outcome was first recurrence of NMIBC. Kaplan-Meier analysis was used to calculate recurrence free probabilities and Cox proportional hazards regression was used to evaluate the impact of smoking status on recurrence free survival.

RESULTS

Our analytic cohort included 723 adults with bladder cancer, 11.5% with primary NMIBC and 88.5% with recurrent NMIBC. The majority of patients were white, male, and had high-risk NMIBC (72.6%). 52.6% of included patients were former smokers and 12.7% were current smokers. During the three-year study period, there was a NMIBC recurrence in 259 of the 723 patients (35.8%). The 1- and 3-year probability of recurrence was 19% and 44%, respectively. The grade and stage of recurrences were 28.9% LG Ta, 34.4% HG Ta, 15.8% pure CIS, 0.3% LG T1, 15.4% HG T1, and 5.4% unknown. After adjustment for a priori clinical and demographic factors, smoking status had no significant association with recurrence.

CONCLUSION

Smoking status was not significantly association with recurrence in a study of patients with predominantly high-risk recurrent NMIBC managed with photodynamic enhanced cystoscopy.

Establishment of Real-Time Multispectral Imaging for the Detection of Bladder Cancer Using a Preclinical in Vivo Model

BACKGROUND: Emerging imaging technologies such as real-time multispectral imaging (rMSI) hold great potential for simultaneous visualization of multiple target structures using fluorophores on various tumours including bladder cancer (BC). These technologies, however, require a multi-step preclinical evaluation process, including mouse models. OBJECTIVE: To demonstrate the suitability of the new rMSI technology for the detection of premalignant lesions and malignant BC in a preclinical mouse model using contrast agents. METHODS: Tumours were induced by N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN), which is known to induce BC in rodent models. In total, 30 mice (C57BL/6) were fed with 0.1% BBN ad libitum in drinking water for up to 5 months. Bladders were excised at 3 (n = 6) and 5 months (n = 24) of treatment and incubated ex vivo with Hexaminolevulinat (HAL, Hexvix®), CD47-FITC, CD90.2-FITC or a combination of CD90.2-FITC/CD47-FITC and HAL. The bladders were analyzed by an endoscopic rMSI prototype system equipped with a spectral filter (Chroma), a 4 mm endoscope (Karl Storz) with 30° optic, a LED light source and a PC with a microcontroller board. RESULTS: 5-month treatment of mice with 0.1% BBN led to the formation of squamous carcinoma (46%, n = 11) while urothelial carcinoma was observed only in one mouse (4%, n = 1). Carcinoma in situ (CIS) was detectable in twelve out of twenty-four mice (50%, n = 12) treated for 5 month and in three out of six mice (50%, n = 3) treated for 3 months.The metabolite of HAL, protoporphyrin IX (PpIX), could be reliably and specifically detected in all of mouse bladder tumours and CIS. However, detection of the CD90.2 surface marker was less reliable, potentially due to species- or tumour-subtype specificity. CONCLUSIONS: This model offers the potential for preclinical imaging studies with combined fluorescence targets, e.g. HAL, in combination with BC-specific antibodies.

Mutational Landscape and Environmental Effects in Bladder Cancer

Bladder cancer is the most common cancer of the urinary tract. Although nonmuscle-invasive bladder cancers have a good prognosis, muscle-invasive bladder cancers promote metastases and have a poor prognosis. Comprehensive analyses using RNA sequence of clinical tumor samples in bladder cancer have been reported. These reports implicated the candidate genes and pathways that play important roles in carcinogenesis and/or progression of bladder cancer. Further investigations for the function of each mutation are warranted. There is suggestive evidence for several environmental factors as risk factors of bladder cancer. Environmental factors such as cigarette smoking, exposure to chemicals and gases, bladder inflammation due to microbial and parasitic infections, diet, and nutrition could induce several genetic mutations and alter the tumor microenvironment, such as immune cells and fibroblasts. The detailed mechanism of how these environmental factors induce carcinogenesis and/or progression of bladder cancer remains unclear. To identify the relationship between the mutations and the lifestyle could be useful for prevention and treatment of bladder cancer.

Procarcinogen Activation and Mutational Signatures Model the Initiation of Carcinogenesis in Human Urothelial Tissues In Vitro

Disparity between genome-wide mutations in bladder and other cancers where smoking is a risk factor raises questions about carcinogenesis in different epithelia. To develop an experimental model of bladder carcinogenesis, we clonally expanded in vitro differentiated normal human urothelial (NHU) cells following exposure to an exemplar procarcinogen and used whole-genome DNA sequencing to derive mutational signatures. Benzo[a]pyrene (BaP) was activated by endogenous cytochrome P450 (cytochrome P450 family 1 subfamily A member 1 [CYP1A1]) to create genomically modified NHU cells. Comparison with the Catalogue of Somatic Mutations in Cancer (COSMIC) showed that mutations induced by BaP in NHU cells were similar to smoking-associated signatures in bladder and other cancers, including single- and doublet-base substitution signatures characterised by C > A transversions (COSMIC_SBS4 and COSMIC_DBS2, respectively), and an insertion/deletion signature of C deletions in homopolymer regions (COSMIC ID3). Our study provides the first direct evidence that BaP is activated locally in the urothelium, initiating the well-described smoking-associated mutational signatures. An absence of other common bladder cancer (BLCA)-associated genomic signatures points strongly to other primary causes of BLCA, which the new experimental approach described here is well placed to investigate. Mutational signatures ignore whether genes are affected, but tissue-specific drivers (KMT2D, KMT2C, and CDKN1A) were significantly overmutated in this model, providing insight on the emergent selection pressures.

Patient summary

In a carefully controlled laboratory setting, we exposed normal human urothelial tissues to a procarcinogen (benzo[a]pyrene) found in cigarette smoke. We show that the urothelial tissues activated the carcinogen and led to mutations forming across the genome in a characteristic pattern. This particular “mutational signature” is found in bladder tumours and other smoking-induced cancers (eg, lung); however, our study highlights that there are other unknown mutational processes in bladder cancer that is not the direct result of smoke carcinogens, and this will require further investigation.

Antibody targeting of B7-H4 enhances the immune response in urothelial carcinoma

Patients with locally advanced and metastatic urothelial carcinoma have a low survival rate (median 15.7 months, 13.1-17.8), with only a 23% response rate to monotherapy treatment with anti-PDL1 checkpoint immunotherapy. To identify new therapeutic targets, we profiled the immune regulatory signatures during murine cancer development using the BBN carcinogen and identified an increase in the expression of the T cell inhibitory protein B7-H4 (VTCN1, B7S1, B7X). B7-H4 expression temporally correlated with decreased lymphocyte infiltration. While the increase in B7-H4 expression within the bladder by CD11b+ monocytes is shared with human cancers, B7-H4 expression has not been previously identified in other murine cancer models. Higher expression of B7-H4 was associated with worse survival in muscle-invasive bladder cancer in humans, and increased B7-H4 expression was identified in luminal and luminal-papillary subtypes of bladder cancer. Evaluation of B7-H4 by single-cell RNA-Seq and immune mass cytometry of human bladder tumors found that B7-H4 is expressed in both the epithelium of urothelial carcinoma and CD68+ macrophages within the tumor. To investigate the function of B7-H4, treatment of human monocyte and T cell co-cultures with a B7-H4 blocking antibody resulted in enhanced IFN-γ secretion by CD4+ and CD8+ T cells. Additionally, anti-B7-H4 antibody treatment of BBN-carcinogen bladder cancers resulted in decreased tumor size, increased CD8+ T cell infiltration within the bladder, and a complimentary decrease in tumor-infiltrating T regulatory cells (Tregs). Furthermore, treatment with a combination of anti-PD-1 and anti-B7-H4 antibodies resulted in a significant reduction in tumor stage, a reduction in tumor size, and an increased level of tumor necrosis. These findings suggest that antibodies targeting B7-H4 may be a viable strategy for bladder cancers unresponsive to PD-1 checkpoint inhibitors.

Cigarette and Cannabis Smoking Effects on GPR15+ Helper T Cell Levels in Peripheral Blood: Relationships with Epigenetic Biomarkers

Background: Smoking causes widespread epigenetic changes that have been linked with an increased risk of smoking-associated diseases and elevated mortality. Of particular interest are changes in the level of T cells expressing G-protein-coupled receptor 15 (GPR15), a chemokine receptor linked with multiple autoimmune diseases, including inflammatory bowel disease, multiple sclerosis and psoriasis. Accordingly, a better understanding of the mechanisms by which smoking influences variation in the GPR15+ helper T cell subpopulation is of potential interest. Methods: In the current study, we used flow cytometry and digital PCR assays to measure the GPR15+CD3+CD4+ populations in peripheral blood from a cohort of n = 62 primarily African American young adults (aged 27–35 years) with a high rate of tobacco and cannabis use. Results: We demonstrated that self-reported tobacco and cannabis smoking predict GPR15⁺CD3⁺CD4⁺ helper T cell levels using linear regression models. Further, we demonstrated that methylation of two candidate CpGs, cg19859270, located in GPR15, and cg05575921, located in the gene Aryl Hydrocarbon Receptor Repressor (AHRR), were both significant predictors of GPR15⁺CD3⁺CD4⁺ cell levels, mediating the relationship between smoking habits and increases in GPR15⁺CD3⁺CD4⁺ cells. As hypothesized, the interaction between cg05575921 and cg19859270 was also significant, indicating that low cg05575921 methylation was more strongly predictive of GPR15⁺CD3⁺CD4⁺ cell levels for those who also had lower cg19859270 methylation. Conclusions: Smoking leads changes in two CpGs, cg05575921 and cg19859270, that mediate 38.5% of the relationship between tobacco and cannabis smoking and increased GPR15⁺ T_h levels in this sample. The impact of cg19859270 in amplifying the association between cg05575921 and increased GPR15⁺ T_h levels is of potential theoretical interest given the possibility that it reflects a permissive interaction between different parts of the adaptive immune system.

Genomic classification and risk stratification of bladder cancer

Bladder cancer is the fourth most common cancer in men and fifth most common overall. The use of next-generation sequencing (NGS) approaches is crucial to precisely characterize the molecular defects of tumors, and this information could be combined with other clinical data, such as tumor histology and TNM staging, with the goal of precise tumor classification. In many settings, targeted NGS is evaluated in patients with first- and second-line metastatic cancer. Yet, in the decade to come we anticipate increased application of precision oncology at all stages of bladder cancer with the aim of customizing cancer treatment. Here, we review the genomic and transcriptomic features associated with risk stratification in bladder cancer and summarize the current efforts for precision oncology in localized urothelial carcinomas.