Polyamine-modulated factor-1 methylation predicts Bacillus Calmette-Guérin response in patients with high-grade non-muscle-invasive bladder carcinoma

Epigenetic changes associated with Bacillus Calmette-Guerin (BCG) treatment in bladder cancer

Bacillus Calmette-Guérin (BCG) treatment for non-muscle invasive bladder cancer (NMIBC) is an established immunotherapeutic, however, a significant portion of patients do not respond to treatment. Despite extensive research into the therapeutic mechanism of BCG, gaps remain in our understanding. This review specifically focuses on the epigenomic contributions in the immune microenvironment, in the context of BCG treatment for NMIBC. We also summarise the current understanding of NMIBC epigenetic characteristics, and discuss how future targeted strategies for BCG therapy should incorporate epigenomic biomarkers in conjunction with genomic biomarkers.

Epigenetic Regulation in Urothelial Carcinoma

Urothelial carcinoma (UC) is a common malignancy that remains a clinical challenge: Non-muscle-invasive urothelial carcinoma (NMIUC) has a high rate of recurrence and risk of progression, while muscle-invasive urothelial carcinoma (MIUC) has a high mortality. Although some new treatments, such as immunotherapies, have shown potential effects on some patients, most cases of advanced UC remain incurable. While treatments based on epigenetic mechanisms, whether combined with traditional platinum-based chemotherapy or emerging immunotherapy, show therapeutic advantages. With the advancement of sequencing and bioinformatics, the study of epigenomics, containing DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA, is increasingly linked with the occurrence and progression of UC. Since the epigenetics of UC is a constantly developing field of medicine, this review aims to summarize the latest research on epigenetic regulation of UC, generalize the mechanism of epigenetics in UC, and reveal the potential epigenetic therapies in the clinical setting, in order to provide some new clues on the discovery of new drugs based on the epigenetics.

Identifying novel biomarkers associated with bladder cancer treatment outcomes

Bladder cancer is a complex disease with variable prognosis. Recent investigations into the molecular landscape of bladder cancer have revealed frequent genetic alterations and molecular subtypes with therapeutic implications. Consequently, a shift toward personalized treatment of bladder cancer is underway. To this end, several biomarkers have been developed and tested in their ability to predict response to treatment in patients with bladder cancer and potentially help direct therapy. We performed a search of recently published PubMed articles using terms "biomarker," "bladder cancer," and the respective treatment discussed (i.e., "neoadjuvant" or "BCG"). In this review, we summarize the latest studies on novel biomarkers in bladder cancer with a focus on those intended to improve risk stratification and treatment selection.

Predictive biomarkers of response to bacillus Calmette‐Guérin immunotherapy and bacillus Calmette‐Guérin failure for non‐muscle invasive bladder cancer

Within the heterogeneous population of patients with bacillus Calmette‐Guérin failure, there are clear differences in prognosis and therapy with regard to the timeline when bacillus Calmette‐Guérin failure occurred. There are a variety of classifications which include bacillus Calmette‐Guérin refractory disease, relapsing, unresponsive, and intolerant. Further profiling of these patients may help to shed light on other forms of therapy that are less radical. We hereby summarize the different biomarkers that predicts for response to bacillus Calmette‐Guérin immunotherapy and bacillus Calmette‐Guérin failure for non‐muscle invasive bladder cancer.

Oncologic outcomes of Bacillus Calmette-Guérin therapy in elderly patients with non-muscle-invasive bladder cancer: A meta-analysis

Introduction

There is a challenge on the medical efficacy of intravesical Bacillus Calmette-Guérin (BCG) therapy and the power of the immune system boosting, which can be influenced by the age of the non-muscle-invasive bladder cancer (NMIBC) patients. This meta-analysis evaluates the efficacy of BCG therapy among aged (>70) and younger patients with non-muscle-invasive bladder cancer (NMIBC).

Methods

The central database of PubMed, Scopus, and Web of Science were queried until August 4, 2021, by using "BCG," "Bladder Cancer," "AGE," and "efficacy" keywords. After excluding duplicated results, titles and abstracts were evaluated by two independent reviewers. The exclusion criteria included non-English studies, conference abstracts, reviews, editorials, letters, and comments. Three main outcomes, disease-free survival (DFS), progression-free survival (PFS), and cancer-specific survival (CSS), were considered. The statistical analysis was performed using STATA (version 14; Stata Corp, College Station, Texas, USA).

Results

From 1115 found documents, the 24 research articles were recruited in the systematic review, and 10 were the candidate for meta-analysis. The overall estimate of H.R. revealed that BCG therapy in those over age 70 is significantly associated with an improved risk of progression and cancer-specific death in studied patients. However, this association was not statistically significant for DFS (1.04 (95% CI: 0.85,1.26)).

Conclusion

The BCG maintenance therapy improved CSS and PFS oncological outcomes in elderly patients with NMIBC. BCG therapy did not significantly change the DSF.

Tackling tumor microenvironment through epigenetic tools to improve cancer immunotherapy

BACKGROUND

Epigenetic alterations are known contributors to cancer development and aggressiveness. Additional to alterations in cancer cells, aberrant epigenetic marks are present in cells of the tumor microenvironment, including lymphocytes and tumor-associated macrophages, which are often overlooked but known to be a contributing factor to a favorable environment for tumor growth. Therefore, the main aim of this review is to give an overview of the epigenetic alterations affecting immune cells in the tumor microenvironment to provoke an immunosuppressive function and contribute to cancer development. Moreover, immunotherapy is briefly discussed in the context of epigenetics, describing both its combination with epigenetic drugs and the need for epigenetic biomarkers to predict response to immune checkpoint blockage.

MAIN BODY

Combining both topics, epigenetic machinery plays a central role in generating an immunosuppressive environment for cancer growth, which creates a barrier for immunotherapy to be successful. Furthermore, epigenetic-directed compounds may not only affect cancer cells but also immune cells in the tumor microenvironment, which could be beneficial for the clinical response to immunotherapy.

CONCLUSION

Thus, modulating epigenetics in combination with immunotherapy might be a promising therapeutic option to improve the success of this therapy. Further studies are necessary to (1) understand in depth the impact of the epigenetic machinery in the tumor microenvironment; (2) how the epigenetic machinery can be modulated according to tumor type to increase response to immunotherapy and (3) find reliable biomarkers for a better selection of patients eligible to immunotherapy.

Discovery of Molecular DNA Methylation-Based Biomarkers through Genome-Wide Analysis of Response Patterns to BCG for Bladder Cancer

Background: Bacillus Calmette-Guérin (BCG) immunotherapy, the standard adjuvant intravesical therapy for some intermediate and most high-risk non-muscle invasive bladder cancers (NMIBCs), suffers from a heterogenous response rate. Molecular markers to help guide responses are scarce and currently not used in the clinical setting. Methods: To identify novel biomarkers and pathways involved in response to BCG immunotherapy, we performed a genome-wide DNA methylation analysis of NMIBCs before BCG therapy. Genome-wide DNA methylation profiles of DNA isolated from tumors of 26 BCG responders and 27 failures were obtained using the Infinium MethylationEPIC BeadChip. Results: Distinct DNA methylation patterns were found by genome-wide analysis in the two groups. Differentially methylated CpG sites were predominantly located in gene promoters and gene bodies associated with bacterial invasion of epithelial cells, chemokine signaling, endocytosis, and focal adhesion. In total, 40 genomic regions with a significant difference in methylation between responders and failures were detected. The differential methylation state of six of these regions, localized in the promoters of the genes GPR158, KLF8, C12orf42, WDR44, FLT1, and CHST11, were internally validated by bisulfite-sequencing. GPR158 promoter hypermethylation was the best predictor of BCG failure with an AUC of 0.809 (p-value < 0.001). Conclusions: Tumors from BCG responders and BCG failures harbor distinct DNA methylation profiles. Differentially methylated DNA regions were detected in genes related to pathways involved in bacterial invasion of cells or focal adhesion. We identified candidate DNA methylation biomarkers that may help to predict patient prognosis after external validation in larger, well-designed cohorts.

Targeting the Immune system and Epigenetic Landscape of Urological Tumors

In the last years, we have witnessed remarkable advances in targeted therapies for cancer patients. There is a growing effort to either replace or reduce the dose of unspecific, systemic (chemo)therapies, given the associated short- and long-term side effects, by introducing more specific targeted therapies as single or combination agents. Due to the well-known implications of the immune system and epigenetic landscape in modulating cancer development, both have been explored as potential targets in several malignancies, including those affecting the genitourinary tract. As the immune system function is also epigenetically regulated, there is rationale for combining both strategies. However, this is still rather underexplored, namely in urological tumors. We aim to briefly review the use of immune therapies in prostate, kidney, bladder, and testicular cancer, and further describe studies providing supporting evidence on their combination with epigenetic-based therapies.

Bladder cancer, a unique model to understand cancer immunity and develop immunotherapy approaches

With the mechanistic understanding of immune checkpoints and success in checkpoint blockade using antibodies for the treatment of certain cancers, immunotherapy has become one of the hottest areas in cancer research, with promise of long‐lasting therapeutic effect. Currently, however, only a proportion of cancers have a good response to checkpoint inhibition immunotherapy. Better understanding of the cancer response and resistance mechanisms is essential to fully explore the potential of immunotherapy to cure the majority of cancers. Bladder cancer, one of the most common and aggressive malignant diseases, has been successfully treated both at early and advanced stages by different immunotherapeutic approaches, bacillus Calmette–Guérin (BCG) intravesical instillation and anti‐PD‐1/PD‐L1 immune checkpoint blockade, respectively. Therefore, it provides a good model to investigate cancer immune response mechanisms and to improve the efficiency of immunotherapy. Here, we review bladder cancer immunotherapy with equal weight on BCG and anti‐PD‐1/PD‐L1 therapies and demonstrate why and how bladder cancer can be used as a model to study the predictors and mechanisms of cancer immune response and shine light on further development of immunotherapy approaches and response predictive biomarkers to improve immunotherapy of bladder cancer and other malignancies. We review the success of BCG and anti‐PD‐1/PD‐L1 treatment of bladder cancer, the underlying mechanisms and the therapeutic response predictors, including the limits to our knowledge. We then highlight briefly the adaptation of immunotherapy approaches and predictors developed in other cancers for bladder cancer therapy. Finally, we explore the potential of using bladder cancer as a model to investigate cancer immune response mechanisms and new therapeutic approaches, which may be translated into immunotherapy of other human cancers. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Predicting Response to Intravesical Therapy in Non-muscle-invasive Bladder Cancer

CONTEXT

The ability to predict response to intravesical therapy (IVT) following transurethral resection in non-muscle-invasive bladder cancer holds important prognostic information. However, few predictive tools are available to guide urologists.

OBJECTIVE

We reviewed the most recent studies investigating the predictors of response to IVT.

EVIDENCE ACQUISITION

A literature search was conducted using PubMed database from January 1, 2013 to April 1, 2018 following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) criteria. For our search strategy, we used the combination of the MeSH terms of "Administration, Intravesical" and "Urinary Bladder Neoplasms" with any of the following words: "Biomarkers," "Predictive Value of Tests," "response," "recurrence," and "progression." We limited our search to the English language.

EVIDENCE SYNTHESIS

Risk stratification models utilizing clinicopathological features are the most cost-effective and widely used tools currently available to predict response to IVT. Additionally, urinary fluorescence in situ hybridization testing and urinary cytokine-based nomograms (Cytokine Panel for Response to Intravesical Therapy) may enhance predictive ability. Protein-based biomarkers have been associated with predicting recurrence. Several gene-based biomarkers quantifying mutations in DNA damage repair genes may have predictive ability. However, genomic data are relatively new and lack validation.

CONCLUSIONS

Clinicopathological criteria remain the most widely utilized tool for predicting IVT response. Further research to validate protein- and genomic-based biomarkers are needed before adoption in clinical practice.

PATIENT SUMMARY

We reviewed contemporary studies that investigated how to predict response to medication instilled in the bladder (intravesical therapy) for bladder cancer. We found that most predictive tools use clinical data, such as tumor stage and grade, to determine the outcome. Newer biological (gene, protein, cytokines) marker tests are being studied. We concluded that the combination of clinical data with levels of certain experimental markers (fluorescence in situ hybridization test or urinary cytokines) may improve predictive ability. Genetic testing methods may also yield additional predictive markers in the future, but this needs more validation.

Prognostic value of DNA methylation for bladder cancer

PURPOSE

A growing number of researches manifest that DNA methylation has been considered as biomarker for the prognosis of bladder cancer (BC). However, the results are still in a discrepancy.

MATERIALS AND METHODS

This meta-analysis was conducted in accordance with PRISMA guidelines. Studies evaluating the practicability of methylated DNA as a prognostic marker for BC were thoroughly searched via the PubMed, Web of science and the Cochrane Library databases from January 1st, 2000 to May 5th, 2018. The association between DNA methylation and overall survival (OS) and progression-free survival (PFS) was analyzed. Hazard ratios (HRs) or odds ratios (ORs) with 95% confidence intervals (95% CIs) were calculated to assess the correlation between methylated DNA and prognostic value in BC by using multivariate survival analysis.

RESULTS

Nineteen studies were included. Patients with methylated DNA had poorer OS, compared with those with unmethylated DNA, the combined HR was 2.766 (95%CI: 2.099-3.806). Simultaneously, methylated DNA was considerably associated with shorter PFS (HR = 2.872, 95%CI: 1.971-4.185). Furthermore, DNA methylation had a significant association with gender (male vs female: OR = 1.486, 95% CI = 1.090-2.025), grade (3 vs 1-2: OR = 3.153, 95% CI = 2.006-4.955), tumor diameter (≤3 cm vs >3 cm: OR = 0.408, 95% CI = 0.277-0.602), number of tumors (single vs multiple: OR = 0.683, 95% CI = 0.501-0.932), stage (Ta vs T1: OR = 0.472, 95% CI = 0.342-0.654), (Ta-T1 vs T2-T4: OR = 0.338, 95% CI =0.210-0.543).

CONCLUSIONS

DNA methylation was negatively correlated with the prognosis of BC patients and might become a promising biomarker.

Waiting in the wings: the emerging role of molecular biomarkers in bladder cancer

INTRODUCTION

Bladder cancer (BCa) is the fifth most frequently diagnosed cancer worldwide and is, in fact, the most expensive cancer on a per-patient to treat basis. There is a critical need to implement new tests into clinical practice to improve the quality of clinical care, decrease unnecessary invasive therapies and ultimately save costs. Currently, no molecular or genetic biomarker has been widely integrated into daily clinical practice. However, major milestones have been achieved in our understanding of the molecular alterations in BCa that will provide the basis for integrating molecular and genetic biomarkers into clinical decision making to guide management. Clinical implementation of such novel molecular and genetic concepts is the cornerstone in an effort to usher the age of precision medicine into patient care. Areas covered: In this review, the authors discuss the emerging role of molecular biomarkers in patients receiving BCG immunotherapy as well as neoadjuvant and adjuvant chemotherapy in BCa. Expert commentary: Molecular predictive and prognostic biomarkers in BCa are promising diagnostic options that will pave the way for molecular-based personalized medicine.

HumanMethylation450K Array-Identified Biomarkers Predict Tumour Recurrence/Progression at Initial Diagnosis of High-risk Non-muscle Invasive Bladder Cancer

Background:

High-risk non-muscle invasive bladder cancer (HR-NMIBC) is a clinically unpredictable disease. Despite clinical risk estimation tools, many patients are undertreated with intra-vesical therapies alone, whereas others may be over-treated with early radical surgery. Molecular biomarkers, particularly DNA methylation, have been reported as predictive of tumour/patient outcomes in numerous solid organ and haematologic malignancies; however, there are few reports in HR-NMIBC and none using genome-wide array assessment. We therefore sought to identify novel DNA methylation markers of HR-NMIBC clinical outcomes that might predict tumour behaviour at initial diagnosis and help guide patient management.

Patients and methods:

A total of 21 primary initial diagnosis HR-NMIBC tumours were analysed by Illumina HumanMethylation450 BeadChip arrays and subsequently bisulphite Pyrosequencing. In all, 7 had not recurred at 1 year after resection and 14 had recurred and/or progressed despite intra-vesical BCG. A further independent cohort of 32 HR-NMIBC tumours (17 no recurrence and 15 recurrence and/or progression despite BCG) were also assessed by bisulphite Pyrosequencing.

Results:

Array analyses identified 206 CpG loci that segregated non-recurrent HR-NMIBC tumours from clinically more aggressive recurrence/progression tumours. Hypermethylation of CpG cg11850659 and hypomethylation of CpG cg01149192 in combination predicted HR-NMIBC recurrence and/or progression within 1 year of diagnosis with 83% sensitivity, 79% specificity, and 83% positive and 79% negative predictive values.

Conclusions:

This is the first genome-wide DNA methylation analysis of a unique HR-NMIBC tumour cohort encompassing known 1-year clinical outcomes. Our analyses identified potential novel epigenetic markers that could help guide individual patient management in this clinically unpredictable disease.

The prognostic role of epigenetic dysregulation in bladder cancer: A systematic review

BACKGROUND

Despite adequate treatment and follow-up, around one fifth of patients with localized bladder cancer will present with disease progression. Adequate prognostic biomarkers are lacking to define patients who are at risk. Mutations in chromatin remodeling genes are more frequently found in bladder cancer than in any other solid tumor. However, the prognostic relevance of epigenetic dysregulation has not been established and may offer an opportunity for biomarker discovery.

METHODS

Looking for prognostic epigenetic factors, we performed a comprehensive PubMed search using keywords such as "bladder cancer", "chromatin remodeling", "gene methylation" and "epigenetics". We only included studies reporting on the association of epigenetic markers with prognostic outcomes such as recurrence, progression or survival.

RESULTS

Of 1113 results, 87 studies met the inclusion criteria, which represented a total of 85 epigenetic markers with potential prognostic relevance. No prospective studies were identified. Seventy-three percent (64/87) of the studies involved mixed cohorts of muscle invasive and non-muscle invasive bladder cancer. Promoter methylation of genes with putative prognostic value affected cellular processes such as cell cycle, apoptosis, cell-adhesion or migration, as well as critical pathways such as MAP-kinase or Wnt. Alteration of chromatin regulatory elements suggest a prognostic relevance alterations leading to a predominantly silenced chromatin state.

CONCLUSIONS

The prognostic impact of epigenetic alterations in bladder cancer is still unclear. Prospective evaluation of methylation marks and chromatin remodeling gene alterations using consistent methods and criteria is warranted.

Prediction of Bacillus Calmette-Guerin Response in Patients with Bladder Cancer after Transurethral Resection of Bladder Tumor by Using Genetic Variation Based on Genomic Studies

Purpose. We aimed to comprehensively review contemporary literature on genetic and epigenetic biomarkers associated with the prediction of Bacillus Calmette-Guerin (BCG) response after the transurethral resection of a bladder tumor and to discuss the application of these biomarkers in precision cancer care for bladder cancer. Method. We performed a systematic review of published literatures in the databases PubMed and Embase by using the following key words: bladder cancer, BCG, gene, and methylation. Studies associated with cell lines, animal models, and muscle invasive bladder cancer were excluded. Results. The genetic variations associated with BCG response can be classified into three categories: germline variations, somatic variations, and epigenetic alterations. Genes related to BCG response were mainly involved in single-nucleotide polymorphisms, copy number variations, and gene methylations. Conclusions. Although these gene alterations are currently the most promising predictive markers of BCG response, most studies about bladder cancer DNA biomarkers are related to germline variations in candidate genes, and the results are not consistent. Only one study is related to somatic variation, and further evaluation in large-scale validation studies should be conducted to assess the potential clinical application of these findings. In addition, other biomarkers based on different “–omics” technologies should be considered in future studies.

Can we use methylation markers as diagnostic and prognostic indicators for bladder cancer?

Urothelial carcinomas of the urinary bladder have diverse biological and functional characteristics, and numerous factors are likely to be involved in recurrence, progression, and patient survival. While several molecular markers used to evaluate the development and prognosis of bladder cancer have been studied, they are of limited value; therefore, new molecular parameters useful for predicting the prognosis of bladder cancer patients (particularly patients at high risk of progression and recurrence) are required. Recent progress in the understanding of epigenetic modification and gene silencing has provided new opportunities for the detection, treatment, and prevention of cancer. Methylation is an important molecular mechanism in bladder cancer and may have utility as a prognostic and/or diagnostic marker. This review discusses the epigenetic issues involved in the detection and prediction of bladder cancer.