An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer

Characterisation of the tumour microenvironment and PD-L1 granularity reveals the prognostic value of cancer-associated myofibroblasts in non-invasive bladder cancer

High-risk non-muscle-invasive bladder cancer (NMIBC) presents high recurrence and progression rates. Despite the use of Bacillus Calmette-Guérin gold-standard immunotherapy and the recent irruption of anti-PD-1/PD-L1 drugs, we are missing a comprehensive understanding of the tumor microenvironment (TME) that may help us find biomarkers associated to treatment outcome. Here, we prospectively analyzed TME composition and PD-L1 expression of tumor and non-tumoral tissue biopsies from 73 NMIBC patients and used scRNA-seq, transcriptomic cohorts and tissue micro-array to validate the prognostic value of cell types of interest. Compared to non-tumoral tissue, NMIBC presented microvascular alterations, increased cancer-associated fibroblast (CAF) and myofibroblast (myoCAF) presence, and varied immune cell distribution, such as increased macrophage infiltration. Heterogeneous PD-L1 expression was observed across subsets, with macrophages showing the highest expression levels, but cancer cells as the primary potential anti-PD-L1 binding targets. Unbiased analysis revealed that myoCAF and M2-like macrophages are specifically enriched in high-grade NMIBC tumors. The topological distribution of these two cell types changed as NMIBC progresses, as shown by immunofluorescence. Only myoCAFs were associated with higher rates of progression and recurrence in three independent cohorts (888 total patients), reaching prediction values comparable to transcriptomic classes, which we further validated using tissue micro-array. Our study provides a roadmap to establish the landscape of the NMIBC TME, highlighting myoCAFs as potential prognostic markers.

A Systematic Review of Novel Intravesical Approaches for the Treatment of Patients with Non-muscle-invasive Bladder Cancer

BACKGROUND AND OBJECTIVE

Intravesical therapy is central to managing non-muscle-invasive bladder cancer (NMIBC); yet, recurrence and progression remain common, underscoring the need for new treatments. This systematic review evaluates clinical trials of novel intravesical therapies for all risk categories of NMIBC.

METHODS

A comprehensive literature search was conducted to identify the clinical trials assessing the effectiveness, safety, and tolerability of intravesical therapies for NMIBC. The search focused on studies published from 2020 to 2024, including trials on bacillus Calmette-Guérin (BCG)-unresponsive/refractory disease as well as on BCG-naïve and intermediate-risk patients. Mechanisms of action and drug delivery methods were summarized. No statistical syntheses were performed due to limited comparative data.

KEY FINDINGS AND LIMITATIONS

Out of 2998 studies identified, 36 reported on efficacy and safety, and six provided patient-reported outcomes (PROs). Intravesical therapies included BCG-based therapies, chemotherapy combinations, chemical-drug conjugates, thermogels, hyperthermic chemotherapy, osmotic pumps, and gene therapy. Initial response rates ranged from 42% to 85% for BCG-unresponsive/refractory patients and from 65% to 100% for treatment-naïve patients. The 12-mo recurrence-free survival rates ranged from 22% to 83% and 39% to 92%, respectively. Progression and severe toxicity (grade ≥3) were rare (0-17% and 0-20%, respectively). PROs were stable. The limitations included early-phase studies, heterogeneous outcome assessments, and a need for research on long-term durability, comparative effectiveness, quality of life, and cost.

CONCLUSIONS AND CLINICAL IMPLICATIONS

This systematic review highlights the promising efficacy and tolerability of novel intravesical therapies for NMIBC. However, further research is needed to refine treatment strategies and assess long-term outcomes, quality of life, and economic factors. Future studies should include multiarm, multistage designs with a focus on patient-centered outcomes.

Sex Disparity in Non-muscle-invasive Bladder Cancer: Pitfalls of Large Population-based Data Sets and Lessons from an Integrated Analysis

The impact of sex on non-muscle-invasive bladder cancer (NMIBC) remains uncertain and current evidence is conflicting. To address this uncertainty, we conducted an integrative analysis using Surveillance, Epidemiology and End Results (SEER)-Medicare and UROMOL data sets to explore sex disparities in NMIBC oncological outcomes. In the SEER-Medicare cohort, females had lower risks of recurrence and progression in comparison to males, but no significant difference in BC-specific mortality was observed. Analysis of the UROMOL cohort revealed no sex-specific differences in tumour biology across genomic, transcriptomic, and spatial proteomic domains. These findings highlight the limitations of relying on just SEER-Medicare data for NMIBC, for which identification of the true incidence of recurrence and progression is challenging, and emphasise the importance of combining population-based data and molecular biology results to gain a comprehensive understanding of NMIBC. PATIENT SUMMARY: The impact of sex on non-muscle-invasive bladder cancer (NMIBC) outcomes is unclear. Our analysis of a large population-based data set showed that the risks of recurrence and progression were lower for females. However, analysis of a separate molecular dataset showed no sex-specific differences. The results highlight the importance of combining population-based data and molecular biology results for a better understanding of NMIBC.

Study of urine-based mRNA biomarkers for early detection of nonmuscle invasive bladder cancer (NMIBC)

BACKGROUND AND OBJECTIVE

Research into new noninvasive diagnostic tools for bladder cancer (BCa) with superior sensitivity and specificity to cystoscopy and cytology is promising. The current study evaluated a diagnostic panel of tumor progression-related mRNAs in urine samples of NMIBC patients and controls.

METHODS

This study carefully selected 129 participants, including 67 NMIBC patients, 31 hematuria patients due to nonmalignant urological disorders, and 31 healthy individuals. Subsequently, ten significantly dysregulated mRNAs were identified in the urine specimens of these participants using RT-qPCR.

KEY FINDINGS

Expression levels of CA9, CDK1, CD24, TERT, CEP55, TOP2A, IQGAP3, UBE2C, and CRH in urine samples from NMIBC patients were higher than those in healthy individuals. Notably, CD24, TOP2A, IQGAP3, UBE2C, and CRH mRNA levels in NMIBC patients were significantly higher than in the hematuria group. In diagnosing low-grade from healthy and hematuria groups, analysis of the 5-gene profile yielded a sensitivity of 98 % and a specificity of 100 % and 90 %, respectively. For diagnosing high-grade tumors from healthy and hematuria groups, sensitivity was 96 % and 100 %, and specificity was 100 % and 83 %, respectively.

CONCLUSIONS AND CLINICAL IMPLICATIONS

These results emphasize the potential application of urine mRNA profiling in the early diagnosis of NMIBC and provide new insights into the molecular mechanisms involved.

Molecular feature-based classification of retroperitoneal liposarcoma: a prospective cohort study

Background

Retroperitoneal liposarcoma (RPLS) is a critical malignant disease with various clinical outcomes. However, the molecular heterogeneity of RPLS was poorly elucidated, and few biomarkers were proposed to monitor its progression.

Methods

RNA sequencing was performed on a training cohort of 88 RPLS patients to identify dysregulated genes and pathways using clusterProfiler. The GSVA algorithm was utilized to assess signaling pathway levels in each sample, and unsupervised clustering was employed to distinguish RPLS subtypes. Differentially expressed genes (DEGs) between RPLS subtypes were identified to construct a simplified dichotomous clustering via nonnegative matrix factorization. The feasibility of this classification was validated in a separate validation cohort (n=241) using immunohistochemistry (IHC) from the REtroperitoneal SArcoma Registry (RESAR). The study is registered with https://clinicaltrials.gov/ under number NCT03838718.

Results

Cell cycle, DNA damage and repair, and metabolism were identified as the most aberrant biological processes in RPLS, enabling the division of RPLS patients into two distinct subtypes with unique molecular signatures, tumor microenvironment, clinical features, and outcomes (overall survival [OS] and disease-free survival [DFS]). A simplified RPLS classification based on representative biomarkers (LEP and PTTG1) demonstrated high accuracy (area under the curve [AUC]>0.99), with patients classified as LEP+ and PTTG1-, showing lower aggressive pathological composition ratio and fewer surgery times, along with better OS (HR = 0.41, p<0.001) and DFS (HR = 0.60, p=0.005).

Conclusions

Our study provided an ever-largest gene expression landscape of RPLS and established an IHC-based molecular classification that was clinically relevant and cost-effective for guiding treatment decisions.

Funding

This work was supported by grants from the Beijing Municipal Science and Technology Project (Z191100006619081), National Natural Science Foundation of China (82073390), and Young Elite Scientists Sponsorship Program (2023QNRC001). The study sponsors had no role in the design and preparation of this manuscript.

Clinical trial number

NCT03838718.

Novel Gene expression-based Risk Stratification tool predicts recurrence in Non-muscle invasive Bladder cancer

BACKGROUND

Bladder cancer represents a heterogeneous disease with distinct clinical challenges. Non-muscle invasive bladder cancer (NMIBC) typically presents as indolent and slow-growing, yet a critical clinical challenge remains: identifying which patients will progress to muscle-invasive disease requiring radical interventions. Early detection of progression propensity is essential, as once muscle invasion occurs, the risk of distant metastasis increases substantially, and treatment shifts from conservative TURBT (Transurethral Resection of Bladder Tumor) to aggressive surgical interventions with significant morbidity. Current risk stratification methods fail to adequately predict this transition in approximately 30% of cases, highlighting the urgent need for more accurate prognostic tools.

OBJECTIVE

This retrospective study aimed to develop and validate a transcriptomics-based mRNA score for predicting early NMIBC recurrence, comparing its performance against traditional risk stratification methods.

METHODS

We analyzed mRNA expression profiles from primary retrospective NMIBC tumor specimens (n = 25) collected between [2018-2022]. Traditional risk stratification tools, including EORTC scoring, were applied alongside our novel mRNA-based risk score to evaluate predictive accuracy for recurrence.

RESULTS

The transcriptomics-based mRNA score demonstrated a median prediction accuracy of 90% across 10,000 resampling iterations for predicting early NMIBC recurrence, significantly outperforming traditional EORTC risk scores. Our comprehensive gene set identified 435 differentially expressed genes associated with recurrence. Kaplan-Meier analysis showed significantly different recurrence-free survival between high and low mRNA risk score groups (Bonferroni corrected p-value < 0.0001).

CONCLUSIONS

This retrospective analysis confirms that mRNA expression-based risk stratification provides superior predictive accuracy compared to conventional clinicopathologic risk tools. Implementation of this gene signature could potentially reduce over-investigation and improve surveillance cost-effectiveness after TURBT in patients with primary high-risk NMIBC. These findings may transform the clinical management paradigm by enabling more personalized follow-up protocols based on molecular risk assessment.

Uncovering citron kinase as a key biomarker for predicting outcomes and therapy efficacy in non-muscle-invasive bladder cancer

Non-muscle-invasive bladder cancer (NMIBC) is highly heterogeneous, with frequent recurrence and progression. Identifying biomarkers can improve the prediction of therapeutic response and prognosis, guiding clinical decisions. In this study, public NMIBC databases were analyzed for differential expression, receiver operating characteristic (ROC), Cox regression, and Kaplan-Meier survival to identify and validate potential prognostic biomarkers of NMIBC. Functional enrichment analysis was conducted to reveal the potential molecular mechanisms of hub genes. Bioinformatics findings were validated through immunohistochemistry (IHC) and in vitro experiments. Immune cell infiltration and drug sensitivity analyses were performed to assess differences between low- and high-CIT expression groups. Citron kinase (CIT) was identified as a biomarker linked to aggressive tumors and poor prognosis in NMIBC patients. CIT overexpression predicts poor intravesical Bacillus Calmette-Guérin (BCG) efficacy in patients with NMIBC. Immunohistochemical staining demonstrated that the protein expression analysis of CIT was consistent with the mRNA analysis results. Functional enrichment analysis revealed that the function of CIT is associated with tumor development and progression. Furthermore, in vitro cell experiments demonstrated that CIT knockdown inhibited cell proliferation by inducing cell cycle arrest at the G2/M phase via downregulation of cyclin dependent kinase 1. Immune infiltration analysis revealed that high CIT expression contributed to BCG resistance by reducing CD8+ T cell infiltration in the NMIBC microenvironment. Additionally, drug sensitivity analysis further demonstrated that high CIT expression leads to resistance to common chemotherapy drugs, including epirubicin, gemcitabine, and cisplatin. This study identifies CIT as a promising biomarker, offering a foundation for prognostic evaluation and personalized therapeutic strategies for NMIBC patients.

Management Dilemma for Very High-risk Non-muscle-invasive Bladder Cancer: Real-World Data Challenge the Guideline Recommendation for Upfront Radical Cystectomy

We discuss real-world evidence that challenges the guideline recommendation of upfront radical cystectomy for all patients with very high-risk non-muscle-invasive bladder cancer. The evidence highlights the need for more accurate and dynamic tools to guide clinical decision-making. Until these are available, treatment decisions should be individualized and made in close consultation with the patient.

Patient-derived organoid co-culture systems as next-generation models for bladder cancer stem cell research

Three-dimensional patient-derived organoids (PDOs) have emerged as a powerful model for investigating the molecular and cellular mechanisms underlying bladder cancer, particularly in the context of cancer stem cells (CSCs) and drug screening. However, a significant limitation of conventional PDOs is the absence of tumor microenvironment (TME), which includes critical stromal, immune and microbial components that influence tumor behavior and treatment response. In this review, we provide a comprehensive overview of the recent advancements in PDO co-culture systems designed to integrate TME elements. Additionally, we emphasize the role of biomedical engineering technologies, such as 3D bioprinting and organoids-on-a-chip, in enhancing the physiological relevance of these models. Furthermore, we explore how bladder PDO co-culture systems are applied in research on bladder CSC characterization, evolution and treatment responses. Finally, we discuss future directions for improving PDO systems to achieve more accurate preclinical modeling and drug discovery.

Robust Consensus Molecular Subtyping of Muscle-Invasive Bladder Cancer Via 3' RNA Sequencing of Formalin-Fixed Paraffin-Embedded Tissues: Potential Impact for Clinical and Trial Settings

Transcriptome-based tumor classification has enhanced the molecular characterization of muscle-invasive bladder cancer (MIBC) subtypes. However, the degraded nature of formalin-fixed paraffin-embedded (FFPE) material and the expensive sequencing costs for routine use have limited the use of subtypes in clinical and trial settings. Here, we present an optimized analysis workflow for MIBC molecular subtype prediction from FFPE samples. FFPE material from 240 MIBC samples was sequenced using QuantSeq 3' mRNA sequencing with unique molecular identifiers (UMIs) and analyzed via a customized RNA-Seq pipeline. The association of consensus subtypes with histology and immunohistochemical expression of core basal/luminal protein markers was assessed. In addition, subtype robustness was explored by simulating scenarios at lower sequencing depths and without UMIs. Five MIBC consensus subtypes were identified in the cohort. The basal/squamous group showed higher expression of KRT14, KRT5, and CD44, and was mainly divergent squamous. Vice versa, luminal, and stroma-rich subtypes had conventional urothelial or urothelial subtype histology, with higher expression of KRT20, FOXA1, and GATA3. The neuroendocrine-like samples had small cell neuroendocrine histology and were negative for luminal/basal markers. Subtype calling from 24 matched fresh-frozen samples analyzed with full-length RNA-Seq showed 87.5% agreement. Furthermore, the subtypes were robust to decreasing sequencing depths and to the absence of UMIs. Taken together, we provide a robust and cost-effective workflow for MIBC consensus molecular subtyping from FFPE-derived RNA. This workflow can be easily implemented as a molecular pathological assay for patient care, clinical trials, and translational research.

Effective delivery of CRISPR/dCas9-SAM for multiplex gene activation based on mesoporous silica nanoparticles for bladder cancer therapy

The molecular complexity of bladder cancer restricts reliance on single-feature or single-gene targeted therapies, necessitating integrated individualized treatments and multi-gene interventions. In this study, we introduced the CRISPR/dCas9-SAM system to BCa treatment, known for its high specificity, low off-target effects, and reduced genetic toxicity, making it ideal for multiplexed gene activation at minimal cost-just 20 nucleotides per target. However, despite its potential in complex gene therapy and cellular engineering, challenges persist due to safety concerns associated with viral vectors and the risk of off-target effects during in vivo delivery, necessitating the development of new vectors. Herein, we reported pH-sensitive hollow mesoporous silica nanoparticles modified with PLZ4 ligands (PLZ4-Lip@AMSN/CRISPR/dCas9-SAM, PLACS NPs) for precise targeting of bladder tumors and co-delivery of CRISPR/dCas9-SAM system. With good stability and high plasmid loading capacity, they efficiently co-delivered dCas9-VP64, MS2-P65-HSF1, and sgRNA. Compared to Lipofectamine 3000, these nanoparticles exhibited superior lysosomal escape capability, significantly enhancing transfection efficiency in bladder cancer cells. Moreover, PLACS NPs simultaneously activated the expression of four target genes, inhibiting proliferation and migration, and promoting apoptosis in bladder cancer cells. In vivo, they achieved efficient gene editing at tumor sites, significantly inhibiting bladder tumor growth. Real-time imaging revealed their substantial accumulation and prolonged retention at bladder tumor sites without significant liver targeting and major organ damage, showcasing good specificity and biosafety. This study overcomes in vivo delivery challenges of multi-component CRISPR/dCas9 systems, enabling precise gene editing and anti-tumor effects, presenting an innovative strategy for targeted therapy in bladder cancer treatment. STATEMENT OF SIGNIFICANCE: This study introduces a newly-developed approach to address key challenges in bladder cancer gene therapy, namely low gene upregulation efficiency, limited targeting specificity, and inefficient nucleic acid delivery. By integrating the CRISPR/dCas9-SAM system, we achieve highly specific gene activation with minimal off-target effects, enabling the addition of treatment targets with just 20 nucleotides per target. To improve bladder cancer targeting, we developed PLACS NPs, a mesoporous silica nanoparticle system that enhances plasmid delivery, transfection efficiency, and endosomal escape. This system shows good tumor targeting and significant anti-tumor effects in bladder cancer, without significant liver targeting and major organ toxicity, offering promising therapeutic potential and broad clinical applications.

Interferon-γ/Janus Kinase 1/STAT1 Signaling Represses Forkhead Box A1 and Drives a Basal Transcriptional State in Muscle-Invasive Bladder Cancer

During progression, luminal muscle-invasive bladder cancer (MIBC) can transition to the aggressive basal-squamous (Ba/Sq) subtype. Reduced expression of forkhead box A1 (FOXA1) in the urothelium is a hallmark and driver of the Ba/Sq transcriptional state and squamous differentiation. Ba/Sq tumors are highly inflamed; however, the specific inflammatory pathways contributing to the Ba/Sq state are unknown. In this study, transcriptomic analyses of The Cancer Genome Atlas MIBC cohort were performed to determine whether immune response gene signatures were associated with MIBC molecular states. Results showed that Ba/Sq MIBCs were enriched for the interferon-γ (IFN-γ)-dominant signature. Ba/Sq MIBCs exhibited increased IFN-γ/Janus kinase (JAK)/STAT pathway activity, corresponding to reduced FOXA1 regulon activity. Immunohistochemistry of MIBC specimens demonstrated that JAK1 expression was significantly increased in tumor areas with squamous differentiation. IFN-γ treatment of luminal MIBC cell lines significantly decreased the expression of luminal transcriptional drivers, including FOXA1, and increased the expression of Ba/Sq markers in a STAT1-dependent manner. RNA-sequencing analyses identified IFN-γ as a driver of the Ba/Sq state. The ability of IFN-γ to repress FOXA1 in luminal cells was abrogated by ruxolitinib inhibition of JAK1/2 activity. Additionally, pharmacologic inhibition or genetic ablation of JAK1 restored FOXA1 expression in Ba/Sq MIBC cells. These findings are the first to identify IFN-γ as an epithelial cell-extrinsic mechanism to repress FOXA1 and drive the Ba/Sq state in MIBC.

Multi‑omics analysis identifies different molecular subtypes with unique outcomes in early-stage poorly differentiated lung adenocarcinoma

INTRODUCTION

Early-stage poorly differentiated lung adenocarcinoma (LUAD) is plagued by a high risk of postoperative recurrence, and its prognostic heterogeneity complicates treatment and surveillance planning. We conducted this integrative multi-omics study to identify those patients with a truly high risk of adverse outcomes.

METHODS

Whole-exome, RNA and whole methylome sequencing were carried out on 101 treatment-naïve early-stage poorly differentiated LUADs. Integrated analyses were conducted to disclose molecular characteristics and explore molecular subtyping. Functional validation of key molecules was carried out through in vitro and in vivo experiments.

RESULTS

Recurrent tumors exhibited significantly higher ploidy (p = 0.024), the fraction of the genome altered (FGA, p = 0.042), and aneuploidy (p < 0.05) compared to non-recurrent tumors, as well as a higher frequency of CNVs. Additionally, recurrent tumors showed hypomethylation at both the global level and in CpG island regions. Integrative transcriptomic and methylation analyses identified three molecular subtypes (C1, C2, and C3), with the C1 subtype presenting the worst prognosis (p = 0.024). Although frequently mutated genes showed similar mutation frequencies across the three subtypes, the C1 subtype exhibited the highest tumor mutation burden (TMB), mutant-allele tumor heterogeneity (MATH), aneuploidy, and HLA loss of heterozygosity (HLA-LOH), along with relatively lower immune cell infiltration. Furthermore, GINS1 and CPT1C were found to promote LUAD progression, and their high expression correlated with a poor prognosis.

CONCLUSIONS

This multi-omics study identified three integrative subtypes with distinct prognostic implications, paving the way for more precise management and postoperative monitoring of early-stage poorly differentiated LUAD.

Randomized Comparison of Magnetic Resonance Imaging Versus Transurethral Resection for Staging New Bladder Cancers: Results From the Prospective BladderPath Trial

PURPOSE

Transurethral resection of bladder tumor (TURBT) is the initial staging procedure for new bladder cancers (BCs). For muscle-invasive bladder cancers (MIBCs), TURBT may delay definitive treatment. We investigated whether definitive treatment can be expedited for MIBC using flexible cystoscopic biopsy and multiparametric magnetic resonance imaging (mpMRI) for initial staging.

PATIENTS AND METHODS

We conducted a prospective open-label, randomized study conducted within 17 UK hospitals (registered as ISRCTN 35296862). Participants with suspected new BC were randomly assigned 1:1 to TURBT-staged or mpMRI-staged care, with minimization factors of sex, age, and clinician visual assessment of stage. Blinding was not possible. Patients unable/unwilling to undergo mpMRI or with previous BC were ineligible. The study had two stages with separate primary outcomes of feasibility and time to correct treatment (TTCT) for MIBC, respectively.

RESULTS

Between May 31, 2018, and December 31, 2021, 638 patients were screened, and 143 participants randomly assigned to TURBT (n = 72; 55 males, 15 MIBCs) or initial mpMRI (n = 71; 53 males, 14 MIBCs). For feasibility, 36 of 39 (92% [95% CI, 79 to 98]) participants with suspected MIBC underwent mpMRI. The median TTCT for participants with MIBC was significantly shorter with initial mpMRI (n = 12, 53 days [95% CI, 20 to 89] v n = 14, 98 days [95% CI, 72 to 125] for TURBT, log-rank P .02). There was no detriment for participants with non-MIBC (median TTCT: n = 30, 17 days [95% CI, 8 to 25] for mpMRI v n = 28, 14 days [95% CI, 10 to 29] for TURBT, log-rank P = .67). No serious adverse events were reported.

CONCLUSION

The mpMRI-directed pathway led to a 45-day reduction in TTCT for MIBC. Incorporating mpMRI ahead of TURBT into the standard pathway was beneficial for all patients with suspected MIBC.

Glycosphingolipids as emerging attack points in bladder cancer

Bladder cancer is a prevalent malignancy associated with significant morbidity and mortality worldwide. Emerging research highlights the critical role of glycosphingolipids (GSLs) in bladder cancer progression. In this review, we examine GSL expression profiles in bladder cancer and explore their contributions to key cancer hallmarks, including invasion and metastasis, immune evasion, and resistance to cell death. We further discuss the potential of GSLs as therapeutic targets and non-invasive biomarkers, with an emphasis on recent advances in GSL-targeting strategies. Additionally, we highlight our recent discovery of a novel, patented biomarker for bladder cancer diagnosis, identified using cutting-edge glyco-analytical technologies.

Genomic subtypes of non-muscle-invasive bladder cancer: guiding immunotherapy decision-making for patients exposed to aristolochic acid

BACKGROUND

The limited genomic data on non-muscle-invasive bladder cancer (NMIBC) hampers our understanding of its carcinogenesis and development. Specifically, Aristolochic acid (AA), a potent human carcinogenic compound from aristolochia plants and commonly found in Chinese herbal medicine, has been extensively documented as being closely associated with the onset and progression of bladder cancer. However, the field of AA-induced NMIBC remains largely unexplored in terms of its genomic and molecular characteristics, as well as clinical therapeutic strategies.

METHODS

To bridge this knowledge gap, we conducted a comprehensive study using a cohort of 81 NMIBC samples. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) to obtain detailed genomic and transcriptomic data. We subjected these datasets to genomic analysis and subtype analysis to gain valuable insights into NMIBC.

RESULTS

By temporally dissecting mutations in NMIBC specimens, we identified a comprehensive mutational landscape of NMIBC and the associations of these mutations with recurrence-free survival. Additionally, we discerned four genomic subtypes of NMIBC: AA-like, FGFR3/HRAS, FGFR3 & chr9Del, and genome instability (GI). The AA-like subtype presented a high frequency of gene mutations along with a pronounced AA mutagenesis signature of SBS22 (Fisher test: P-value 3.5e-4, OR 25.25) even after temporal dissection. The FGFR3/HRAS subtype exhibited FGFR3 or HRAS mutations with few copy number alterations (CNAs). The FGFR3 & chr9Del subtype was characterized by the co-occurrence of chr9p and chr9q deletions as well as FGFR3 mutations, while the GI subtype showed a high frequency of CNAs. Notably, the AA-like and GI subtypes demonstrated better outcomes after immunotherapy, whereas the FGFR3/HRAS subtype showed poorer outcomes.

CONCLUSIONS

Our findings provide novel perspectives on the genomics of NMIBC, unveiling four prominent genomic subtypes, each showing different outcomes following immunotherapy.

TRIAL REGISTRATION

No. 2019PHB268-01 (retrospectively registered on February 14, 2020).

Liquid-liquid phase separation-related genes associated with prognosis, tumor microenvironment characteristics, and tumor cell features in bladder cancer

OBJECTIVE

This study aimed to explore the Liquid-liquid phase separation (LLPS)-related genes associated with the prognosis of bladder cancer (BCa) and assess the potential application of LLPS-related prognostic signature for predicting prognosis in BCa patients.

METHODS

Clinical information and transcriptome data of BCa patients were extracted from the Cancer Genome Atlas-BLCA (TCGA-BLCA) database and the GSE13507 database. Furthermore, 108 BCa patients who received treatment at our institution were subjected to a retrospective analysis. The least absolute shrinkage and selection operator (LASSO) analysis was performed to develop an LLPS-related prognostic signature for BCa. The CCK8, wound healing and Transwell assays were performed.

RESULTS

Based on 62 differentially expressed LLPS-related genes (DELRGs), three DELRGs were screened by LASSO analysis including kallikrein-related peptidase 5 (KLK5), monoacylglycerol O-acyltransferase 2 (MOGAT2) and S100 calcium-binding protein A7 (S100A7). Based on three DELRGs, a novel LLPS-related prognostic signature was constructed for individualized prognosis assessment. Kaplan-Meier curve analyses showed that LLPS-related prognostic signature was significantly correlated with overall survival (OS) of BCa. ROC analyses demonstrated the LLPS-related prognostic signature performed well in predicting the prognosis of BCa patients in the training group (the area under the curve (AUC) = 0.733), which was externally verified in the validation cohort 1 (AUC = 0.794) and validation cohort 2 (AUC = 0.766). Further experiments demonstrated that inhibiting KLK5 could affect the proliferation, migration, and invasion of BCa cells.

CONCLUSIONS

In this study, a novel LLPS-related prognostic signature was successfully developed and validated, demonstrating strong performance in predicting the prognosis of BCa patients.

From Bench to Bladder: The Rise in Immune Checkpoint Inhibition in the Treatment of Non-Muscle Invasive Bladder Cancer

Non-muscle invasive bladder cancer (NMIBC) represents a significant clinical challenge due to its high recurrence rate and need for frequent monitoring. The current treatment modality is bacillus Calmette-Guérin (BCG) therapy combined with chemotherapy after transurethral resection of the bladder tumor (TURBT), which is highly effective in most patients. Yet, the cancer becomes resistant to these treatments in 30-40% of patients, necessitating the need for new treatment modalities. In the cancer world, the development of immune checkpoint inhibitors that target molecules, such as programmed cell death protein-1 (PD-1), its ligand, PD-L1, and Cytotoxic T-lymphocyte-associated protein-4 (CTLA-4), have revolutionized the treatment of many cancer types. PD-1/PD-L1 and CTLA-4 are shown to be upregulated in NMIBC in certain circumstances. PD-1/PD-L1 interactions play a role in immune evasion by suppressing T cell activity within the tumor microenvironment (TME), while the binding of CTLA-4 on T cells leads to downregulation of the immune response, making these pathways potential immunotherapeutic targets in NMIBC. This review seeks to understand the role of these therapies in treating NMIBC. We explore the cellular and non-cellular immune landscape in the TME of NMIBC, including Tregs, T effector cells, macrophages, B cells, and relevant cytokines. We also discuss the biological role of PD-1/PD-L1 and CTLA-4 while covering the rationale for these immunotherapies in NMIBC. Finally, we cover key clinical trials that have studied these treatments in NMIBC clinically. Such a study will be helpful for urologists and oncologists to manage patients with NMIBC more effectively.

Development of a Technique for Diagnosis and Screening of Superficial Bladder Cancer by Cell-Pellet DNA From Urine Sample

Bladder cancer (BCa) is the most common malignancy of the urinary system with high incidence and recurrence rates. There are several ways to detect BCa. However, different approaches have different accuracy, which essentially depends on the sensitivity and specificity of the technique. Alternative noninvasive diagnostic tools for BCa are needed. We isolated and compared urinary cell-pellet DNA (cpDNA), cell-free DNA, and exosomal DNA from patients with localized BCa. Consequently, we analyzed 12 tissues and cpDNA samples by next-generation sequencing and then used bioinformatic tools to analyze genomic and transcriptomic alterations in coding and noncoding sequences. Then, cpDNA and tissue DNA from 12 patients were analyzed using next-generation sequencing to verify that the genomic characteristics of cpDNA are concordant with those of tissue. We also detected somatic mutation patterns between tissues and their corresponding cpDNA samples. An overlapping variant analysis was performed based on somatic mutation data and a high similarity was observed. Moreover, we identified frequently mutated signaling pathways. In these results, several point mutations were analyzed in FGFR3, TTN, and LEPROTL1 from the cpDNA of patients with BCa. Tumor mutational burden analysis showed that cpDNA had no significant difference in tumor mutational burden compared with tumor tissue. These results provide that cpDNA is a potential diagnostic source for detecting and managing BCa using alternative noninvasive methods from patient urine. Our findings may serve as a clinical tool for early detection or recurrence screening of nonmuscle invasive BCa using urinary cpDNA.

Molecular Heterogeneity and Immune Infiltration Drive Clinical Outcomes in Upper Tract Urothelial Carcinoma

BACKGROUND AND OBJECTIVE

Molecular classification of upper tract urothelial carcinoma (UTUC) can provide insight into divergent clinical outcomes and provide a biological rationale for clinical decision-making. As such, we performed multi-omic analysis of UTUC tumors to identify molecular features associated with disease recurrence and response to immune checkpoint blockade (ICB).

METHODS

Targeted DNA and whole transcriptome RNA sequencing was performed on 100 UTUC tumors collected from patients undergoing nephroureterectomy. Consensus non-negative matrix factorization was used to identify molecular clusters associated with clinical outcomes. Gene set enrichment and immune deconvolution analyses were performed. Weighted gene co-expression network analysis was employed for unsupervised identification of gene networks in each cluster.

KEY FINDINGS AND LIMITATIONS

Five molecular clusters with distinct clinical outcomes were identified. Favorable subtypes (C1 and C2) were characterized by a luminal-like signature and an immunologically depleted tumor microenvironment (TME). Subtype C3 was characterized by FGFR3 alterations and a higher tumor mutational burden, and included all tumors with microsatellite instability. Despite higher rates of recurrence and inferior survival, subtypes C4 and C5 harbored an immunologically rich TME favoring response to ICB. Limitations include extrapolation of molecular features of tumors from the primary site to determine response to systemic immunotherapy and the limited resolution of bulk sequencing to distinguish gene expression in the tumor, stroma, and immune compartments.

CONCLUSIONS AND CLINICAL IMPLICATIONS

RNA sequencing identified previously underappreciated UTUC molecular heterogeneity and suggests that UTUC patients at the highest risk of metastatic recurrence following surgery include those most likely to benefit from perioperative ICB.

Mass spectrometry-based analysis of eccrine sweat supports predictive, preventive and personalised medicine in a cohort of breast cancer patients in Austria

Objective

Metabolomics measurements of eccrine sweat may provide novel and relevant biomedical information to support predictive, preventive and personalised medicine (3PM). However, only limited data is available regarding metabolic alterations accompanying chemotherapy of breast cancer patients related to residual cancer burden (RCB) or therapy response. Here, we have applied Metabo-Tip, a non-invasive metabolomics assay based on the analysis of eccrine sweat from the fingertips, to investigate the feasibility of such an approach, especially with respect to drug monitoring, assessing lifestyle parameters and stratification of breast cancer patients.

Methods

Eccrine sweat samples were collected from breast cancer patients (n = 9) during the first cycle of neoadjuvant chemotherapy at four time points in this proof-of-concept study at a Tertiary University Hospital. Metabolites in eccrine sweat were analysed using mass spectrometry. Blood plasma samples from the same timepoints were also collected and analysed using a validated targeted metabolomics kit, in addition to proteomics and fatty acids/oxylipin analysis.

Results

A total of 247 exogenous small molecules and endogenous metabolites were identified in eccrine sweat of the breast cancer patients. Cyclophosphamide and ondansetron were successfully detected and monitored in eccrine sweat of individual patients and accurately reflected the administration schedule. The non-essential amino acids asparagine, serine and proline, as well as ornithine were significantly regulated in eccrine sweat and blood plasma over the therapy cycle. However, their distinct time-dependent profiles indicated compartment-specific distributions. Indeed, the metabolite composition of eccrine sweat seems to largely resemble the composition of the interstitial fluid. Plasma proteins and fatty acids/oxylipins were not affected by the first treatment cycle. Individual smoking habit was revealed by the simultaneous detection of nicotine and its primary metabolite cotinine in eccrine sweat. Stratification according to RCB revealed pronounced differences in the metabolic composition of eccrine sweat in these patients at baseline, e.g., essential amino acids, possibly due to the systemic contribution of breast cancer and its impact on metabolic turnover.

Conclusion

Mass spectrometry-based analysis of metabolites from eccrine sweat of breast cancer patients successfully qualified lifestyle parameters for risk assessment and allowed us to monitor drug treatment and systemic response to therapy. Moreover, eccrine sweat revealed a potentially predictive metabolic pattern stratifying patients by the extent of the metabolic activity of breast cancer tissue at baseline. Eccrine sweat is derived from the otherwise hardly accessible interstitial fluid and, thus, opens up a new dimension for biomonitoring of breast cancer in secondary and tertiary care. The simple sample collection without the need for trained personnel could also enable decentralised long-term biomonitoring to assess stable disease or disease progression. Eccrine sweat analysis may indeed significantly advance 3PM for the benefit of breast cancer patients.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-025-00396-6.

Small non-coding RNA profiling in patients with non-muscle invasive bladder cancer

The intricate regulatory roles of small non-coding RNAs (sncRNAs), including PIWI-interacting RNAs (piRNAs) and microRNAs (miRNAs), have been increasingly recognized in the modulation of cellular functions and are associated with the pathogenesis of various diseases, notably cancer. However, the specific dysregulation patterns of sncRNAs in non-muscle-invasive bladder cancer (NMIBC) have yet to be fully delineated, highlighting a significant gap in our current understanding. To elucidate the expressional dynamics of sncRNAs for patients with NMIBC, we characterized the profile of piRNAs and miRNAs by next-generation sequencing. We identified the differentially expressed sncRNAs between tumor and paracancerous tissues and characterized their distribution along the genome. We further revealed a set of immune-related piRNAs and dysregulated miRNAs that might be associated with NMIBC pathogenesis. Differentially expressed piRNAs were predominantly localized at the long arms of chromosomes 13, 1, and 6. Notably, the targets of specific piRNAs, including piR-hsa-2215234, piR-hsa-105306, piR-hsa-102066, and piR-hsa-236465, show significant associated with antigen processing and presentation pathway. Additionally, differentially expressed miRNAs are mainly located on chromosome 14 and their target genes tend to be involved in cancer-related pathways, suggesting their potential regulatory roles in NMIBC. Collectively, this study revealed the global sncRNA dysregulation in NMIBC, and the identified sncRNAs are implicated in the modulation of both immune and cancer pathways, suggesting their contribution to the pathogenesis and potential targets for immunotherapy.

Pharmacogenomics-based subtype decoded implications for risk stratification and immunotherapy in pancreatic adenocarcinoma

BACKGROUND

With fatal malignant peculiarities and poor survival rate, outcomes of pancreatic adenocarcinoma (PAAD) were frustrated by non-response and even resistance to therapy due to heterogeneity across clinical patients. Nevertheless, pharmacogenomics has been developed for individualized-treatment and still maintains obscure in PAAD.

METHODS

A total of 964 samples from 10 independent multi-center cohorts were enrolled in our study. With drug response data from the profiling of relative inhibition simultaneously in mixtures (PRISM) and genomics of drug sensitivity in cancer (GDSC) databases, we established and validated multidimensionally three pharmacogenomics-classified subtypes using non-negative matrix factorization (NMF) and nearest template prediction (NTP) algorithms, separately. The heterogenous biological characteristics and precision medicine strategies among subtypes were further investigated.

RESULTS

Three pharmacogenomics-classified subtypes after stable and reproducible validation, distinguished in six aspects of prognosis, biological peculiarities, immune landscapes, genomic variations, immunotherapy and individualized management strategies. Subtype 2 was close to immunocompetent phenotype and projected to immunotherapy; Subtype 3 held most favorable outcomes and metabolic pathways distinctively, promising to be treated with first-line agents. Subtype 1 with worst prognosis, was anticipated to chromosome instability (CIN) phenotype and resistant to chemotherapeutic agents. In addition, ITGB6 contributed to subtype 1 resistance to 5-fluorouracil, and knockdown of ITGB6 enhanced sensitivity to 5-fluorouracil in in vitro experiments. Ultimately, appropriate clinical stratified treatments were assigned to corresponding subtypes according to pharmacogenomic transcripts. Some limitations were not taken into account, thus needs to be supported by more research.

CONCLUSION

A span-new molecular subtype exploited for PAAD uncovered an insight into precise medication on ground of pharmacogenomics, and highly refined multiple clinical management strategies for specific patients.

Single Cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway

Non-muscle invasive bladder cancer (NMIBC) represents 70-80% patients with newly diagnosed bladder cancer, and Bacillus Calmette-Guérin (BCG) remains a cornerstone treatment for intermediate-and high-risk NMIBC to prevent disease recurrence and progression. However, many patients experience recurrence after induction BCG, posing significant challenges in the management of the disease. We conducted single cell RNA sequencing on freshly collected NMIBC samples, distinguishing between those naïve to BCG treatment and those that recurred post-BCG treatment. We observed a clear activation of inflammatory pathways across cell types during recurrence, but these were not associated with canonical immune checkpoint or T cell exhaustion phenotypes. Analysis of cell-to-cell communication revealed enhanced interactions between T cells and urothelial cells in BCG-recurrence, predominantly modulated by CD6 and ALCAM. Furthermore, we found CD6 hi T cells to be immunosuppressed and enriched in recurrent samples, suggesting a potential role for CD6 as an immune evasion signal in NMIBC.

SIGNIFICANCE

These findings uncover a novel mechanism responsible for bladder cancer recurrence after BCG treatment. Enhanced T cell-urothelial cell communication in recurrent tumors mediated by CD6 and ALCAM leads to an immunosuppressed state. Thus, CD6 may have potential as a therapeutic target to augment BCG response in non-muscle invasive bladder cancer.

Biological and therapeutic implications of FGFR alterations in urothelial cancer: A systematic review from non-muscle-invasive to metastatic disease

FGFR3 mutations are among the most frequent genomic alterations in urothelial cancer (UC) being mainly associated with the luminal papillary (LumP) subtype. With the establishment of fibroblast growth factor receptor (FGFR) inhibitors, the treatment of UC is now shifting more and more towards personalized medicine. A systematic review using Medline and scientific meeting records was carried out according to the Preferred Reporting Items for Systematic Review and Meta-analyses guidelines to assess the potential role of FGFR inhibitors in combination with additional therapies for the management of UC. Ongoing trials were identified via a systematic search on ClinicalTrials.gov. A total of eleven full-text papers, ten congress abstracts, and 5 trials on ClinicalTrials.gov were identified. Following the BLC2001 and THOR study, erdafitinib is the only approved FGFR1-4 inhibitor for metastatic UC with susceptible FGFR2/3 alterations following platinum-based chemotherapy. According to the THOR data of cohort 2, erdafitinib should not be recommended in patients who are eligible for and have not received prior immune checkpoint inhibitors (ICIs). One phase 3 trial is currently evaluating the intravesical device system (TAR210) in FGFR-altered intermediate non-muscle invasive bladder cancer (MoonRISe-1). Preclinical evidence suggests that combination-based approaches could be considered to improve the efficacy of FGFR inhibitors in patients with UC. Nine phase 1b/2 trials are focusing on the combination of FGFR inhibitors with ICIs, chemotherapy, or enfortumab vedotin. In metastatic disease, some preliminary analyses have reported promising results from these combinations (e.g. NORSE and FORT-2 trial). However, no phase 3 trial is terminated, so there is currently no level 1 evidence with long-term outcomes to support the combination of FGFR inhibitors with ICIs, chemotherapy, or targeted therapies. A better understanding of the different mechanisms of action to inhibit FGFR signaling pathways, optimal patient selection and treatment approaches is still needed.

The importance of data transformation in RNA-Seq preprocessing for bladder cancer subtyping

OBJECTIVE

RNA-Seq provides an accurate quantification of gene expression levels and it is widely used for molecular subtype classification in cancer, with special importance in prognosis. However, the reliability and validity of these analyses can significantly be influenced by how data are processed. In this study we evaluate how RNA-Seq preprocessing methods influence molecular subtype classification in bladder cancer. By benchmarking various aligners, quantifiers and methods of normalization and transformation, we stress the importance of preprocessing choices for accurate and consistent subtype classification.

RESULTS

Our findings highlight that log-transformation plays a crucial role in centroid-based classifiers such as consensusMIBC and TCGAclas, while distribution-free algorithms like LundTax offer robustness to preprocessing variations. Non log-transformed data resulted in low classification rates and poor agreement with reference classifications in consensusMIBC and TCGAclas classifiers. Additionally, LundTax consistently demonstrated better separation among subtypes, compared to consensusMIBC and TCGAclas, regardless of preprocessing methods. Nonetheless, the study is limited by the lack of a true reference for objective assessment of the accuracy of the assigned subtypes. Hence, future work will be necessary to determine the robustness and scalability of the obtained results.

Loss of YTHDC1 m6A reading function promotes invasiveness in urothelial carcinoma of the bladder

Bladder cancer poses significant clinical challenges due to its high metastatic potential and poor prognosis, especially when it progresses to muscle-invasive stages. Here, we show that the m6A reader YTHDC1 is downregulated in muscle-invasive bladder cancer and is negatively correlated with the expression of epithelial‒mesenchymal transition genes. The functional inhibition or depletion of YTHDC1 increased the migration and invasion of urothelial cells. Integrative analysis of multimodal sequencing datasets provided detailed insights into the molecular mechanisms mediating YTHDC1-dependent phenotypes and identified SMAD6 as a key transcript involved in the invasiveness of urothelial carcinoma of the bladder. Notably, SMAD6 mRNA colocalized less with YTHDC1 in tumoral tissues than in paratumoral tissues, indicating disrupted binding during cancer progression. Our findings establish YTHDC1-dependent m6A reading as a critical epitranscriptomic mechanism regulating bladder cancer invasiveness and provide a paradigm for the epitranscriptomic deregulation of cancer-associated networks.

Chemoresistance-motility signature of molecular evolution to chemotherapy in non-muscle-invasive bladder cancer and its clinical implications

Non-muscle-invasive bladder cancer (NMIBC) often recurs and can progress to MIBC due to resistance to treatments like intravesical chemotherapy or Bacillus Calmette-Guérin (BCG). Therefore, we established the Gemcitabine-Resistant Cells (GRCs) to study the molecular evolution under external pressure. A 63-gene Chemoresistance-Motility (CrM) signature was created to identify stage-specific traits of GRCs. This signature was tested on 1846 samples using log-rank tests and Cox regression to evaluate clinical utility. Early and intermediate resistance stages showed increased cell motility and metastatic potential. FAK, PI3K-AKT, and TGFβ pathways were activated first, followed by MAPK signaling. Single-cell analysis and experiments utilizing the CrM signature confirmed interaction with cancer-associated fibroblasts (CAFs). The high-CrM groups mainly included NMIBC patients with poor prognosis (progression-free survival analysis by log-rank test based on UROMOL cohort, p < 0.001), T1-high grade, high European Association of Urology (EAU) risk score, and also included MIBC patients with a history of metastases. Additionally, relative ineffectiveness was observed for BCG (the chi-square test based on BRS cohort, p = 0.02) and immune checkpoint inhibitors (ICIs) in patients with high-CrM. In addition, we identified five drugs that can be used with gemcitabine in these patients, including doxorubicin, docetaxel, paclitaxel, napabucacin, and valrubicin, and verified their efficacy. This study provides insights into NMIBC progression to MIBC via molecular evolution. The CrM signature can assess NMIBC prognosis and BCG treatment response, suggesting alternative treatments. Furthermore, these results need to be prospectively validated.

Proteomic profiling identifies muscle-invasive bladder cancers with distinct biology and responses to platinum-based chemotherapy

Platinum-based neoadjuvant chemotherapy prior to radical cystectomy is the preferred treatment for muscle-invasive bladder cancer despite modest survival benefit and significant associated toxicities. Here, we profile the global proteome of muscle-invasive bladder cancers pre- and post-neoadjuvant chemotherapy treatment using archival formalin-fixed paraffin-embedded tissue. We identify four pre-neoadjuvant chemotherapy proteomic clusters with distinct biology and response to therapy and integrate these with transcriptomic subtypes and immunohistochemistry. We observe proteomic plasticity post-neoadjuvant chemotherapy that is associated with increased extracellular matrix and reduced keratinisation compared to pre-neoadjuvant chemotherapy. Post-neoadjuvant chemotherapy clusters appear to be differentially enriched for druggable proteins. For example, MTOR and PARP are over-expressed at the protein level in tumours identified as neuronal-like. In addition, we determine that high intra-tumoural proteome heterogeneity in pre-neoadjuvant chemotherapy tissue is associated with worse prognosis. Our work highlights aspects of muscle-invasive bladder cancer biology associated with clinical outcomes and suggests biomarkers and therapeutic targets based on proteomic clusters.

FGFR Inhibition in Urothelial Carcinoma

BACKGROUND AND OBJECTIVE

The 2024 US Food and Drug Administration approval of erdafitinib for the treatment of metastatic urothelial carcinoma (mUC) with FGFR3 alterations ushered in the era of targeted therapy for bladder cancer. In this review, we summarize the effects of FGFR pathway alterations in oncogenesis, clinical data supporting FGFR inhibitors in the management of bladder cancer, and the challenges that remain.

METHODS

Original articles relevant to FGFR inhibitors in urothelial cancer between 1995 and 2024 were systematically identified in the PubMed and MEDLINE databases using the search terms "FGFR" and "bladder cancer". An international expert panel with extensive experience in FGFR inhibitor treatment was convened to synthesize a collaborative narrative review.

KEY FINDINGS AND LIMITATIONS

Somatic FGFR3 alterations are found in up to 70% of low-grade non-muscle-invasive bladder cancers; these activate downstream signaling cascades and culminate in cellular proliferation. Beyond a link to lower-grade/lower-stage tumors, there is little consistency regarding whether these alterations confer prognostic risks for cancer recurrence or progression. FGFR3-altered tumors have been linked to a non-inflamed tumor microenvironment, but paradoxically do not seem to impact the response to systemic immunotherapy. Several pan-FGFR inhibitors have been investigated in mUC. With the introduction of novel intravesical drug delivery systems, FGFR inhibitors are poised to transform the therapeutic landscape for early-stage UC.

CONCLUSIONS AND CLINICAL IMPLICATIONS

With deepening understanding of the biology of bladder cancer, novel diagnostics, and improved drug delivery methods, we posit that FGFR inhibition will lead the way in advancing precision treatment of bladder cancer.

Molecular profiling of bladder cancer xenografts defines relevant molecular subtypes and provides a resource for biomarker discovery

Bladder cancer (BLCA) genomic profiling has identified molecular subtypes with distinct clinical characteristics and variable sensitivities to frontline therapy. BLCAs can be categorized into luminal or basal subtypes based on their gene expression. We comprehensively characterized nine human BLCA cell lines (UC3, UC6, UC9, UC13, UC14, T24, SCaBER, RT4V6 and RT112) into molecular subtypes using orthotopic xenograft models. Patient-derived, luciferase-tagged BLCA cell lines were cultured in vitro and engrafted into bladders of NSG mice. Tumor growth was monitored using bioluminescence imaging and mRNA-based molecular classification was used to characterize xenografts into molecular subtypes. RNAseq analysis and basal, luminal, and epithelial-mesenchymal transition (EMT) marker expression revealed distinct patterns; certain cell lines expressed predominantly basal or luminal markers while others demonstrated mixed expression. SCaBER expressed high basal and EMT markers and low luminal markers, consistent with a true basal cell. RT4V6 was a true luminal cell line, displaying only high luminal makers. UC13, T24 and UC3 only showed increased expression of EMT markers. RT112, UC6, UC9 and UC14 expressed basal, luminal, and EMT markers. Immunohistochemical analysis validated our findings. Ki67 was assessed as a continuous percentage of positively stained cells. Morphological assessment of xenografts included H&E and α-SMA staining. These findings will allow for the rational use of appropriate models to develop targeted therapies to overcome or manipulate mechanisms of treatment resistance in BLCA.

Molecular biomarkers of progression in non-muscle-invasive bladder cancer - beyond conventional risk stratification

The global incidence of bladder cancer is more than half a million diagnoses each year. Bladder cancer can be categorized into non-muscle-invasive bladder cancer (NMIBC), which accounts for ~75% of diagnoses, and muscle-invasive bladder cancer (MIBC). Up to 45% of patients with NMIBC develop disease progression to MIBC, which is associated with a poor outcome, highlighting a clinical need to identify these patients. Current risk stratification has a prognostic value, but relies solely on clinicopathological parameters that might not fully capture the complexity of disease progression. Molecular research has led to identification of multiple crucial players involved in NMIBC progression. Identified biomarkers of progression are related to cell cycle, MAPK pathways, apoptosis, tumour microenvironment, chromatin stability and DNA-damage response. However, none of these biomarkers has been prospectively validated. Reported gene signatures of progression do not improve NMIBC risk stratification. Molecular subtypes of NMIBC have improved our understanding of NMIBC progression, but these subtypes are currently unsuitable for clinical implementation owing to a lack of prospective validation, limited predictive value as a result of intratumour subtype heterogeneity, technical challenges, costs and turnaround time. Future steps include the development of consensus molecular NMIBC subtypes that might improve conventional clinicopathological risk stratification. Prospective implementation studies of biomarkers and the design of biomarker-guided clinical trials are required for the integration of molecular biomarkers into clinical practice.

Integrative multi-omics and machine learning identify a robust signature for discriminating prognosis and therapeutic targets in bladder cancer

Background: Bladder cancer (BLCA) is a common malignant tumor whose pathogenesis has not yet been fully elucidated. This study analyzed prognostic genes in BLCA by integrating transcriptomics and proteomics data, and established prognostic models, aiming to offer novel insights for BLCA therapy. Methods: Transcriptomic, proteomic, and protein acetylation sequencing were conducted on six BLCA tumor tissues and six paraneoplastic tissue samples. Furthermore, data from TCGA-BLCA, GSE13507, and single-cell RNA sequencing (scRNA-seq) datasets were integrated. Initially, differential expression analysis identified candidate genes regulated by acetylation. These genes were further refined by intersecting with scRNA-DEG obtained from the scRNA-seq dataset, resulting in the identification of key genes. Subsequently, consistency clustering analysis was performed based on these key genes. Prognostic models were then developed utilizing Cox regression analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. Independent prognostic factors were determined through independent prognostic analysis, followed by the establishment of a nomogram model. Additionally, gene set enrichment analysis (GSEA), immune cell infiltration analysis, mutation analysis, and drug sensitivity analysis were conducted between the two risk groups to elucidate underlying mechanisms. Results: A total of 15 key genes were obtained by crossing 284 candidate genes with 510 scRNA-DEGs. Patients in the TCGA-BLCA dataset were categorized into two subtypes based on the 15 key genes. Next, a risk model was developed using five prognostic genes (CTSE, XAGE2, MAP1A, CASQ2, and FXYD6), and a nomogram model was developed using age, pathologic T, pathologic N, and risk score. A total of 1089 GO entries and 49 KEGG pathways, including cytokine-cytokine receptor interactions, ECM receptor interactions, etc., were involved in all genes in both risk groups. The immunization score, matrix score, and ESTIMATE score were significantly higher in the low-risk group than in the high-risk group. Conclusion: CTSE, XAGE2, MAP1A, CASQ2 and FXYD6 were selected as prognostic genes in BLCA, risk model and nomogram model predicting the prognosis of BLCA patients were constructed. These were helpful for prognostic assessment of BLCA.

Single-cell RNA sequencing and spatial transcriptome analysis in bladder cancer: Current status and future perspectives

Background

Bladder cancer is one of the most prevalent malignancies, and the mechanisms underlying its progression and the role of the tumor microenvironment (TME) are unclear. Recent advancements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) enable detailed analysis of the cellular heterogeneity, gene expression, and cell-cell interactions in bladder diseases.

Methodology

We conducted a comprehensive search for recent articles that have investigated bladder diseases using scRNA-seq and ST.

Results

scRNA-seq and ST have led to significant discoveries in bladder disease research. These technologies have enabled the identification of multiple molecular subtypes within individual tumors and of the mechanisms of treatment resistance. Additionally, molecular differences based on gender have been explored, explaining the heterogeneity of the incidence and progression of bladder cancer. These findings deepen our understanding of the pathology of bladder diseases and highlight the transformative potential of scRNA-seq and ST in identifying novel biomarkers and therapeutic targets.

Conclusions

Integrating scRNA-seq and ST has considerably enhanced our understanding of tumor heterogeneity and the tumor microenvironment within tissues. These insights may lead to the development of personalized therapies and the improvement of patient outcomes. Several challenges, such as technical limitations and access difficulties, need to be addressed for the future clinical application of these technologies.

Proteomic analysis of non-muscle invasive and muscle invasive bladder cancer highlights distinct subgroups with metabolic, matrisomal, and immune hallmarks and emphasizes importance of the stromal compartment

We present the proteomic profiling of 79 bladder cancers, including treatment-naïve non-muscle-invasive bladder cancer (NMIBC, n = 17), muscle-invasive bladder cancer (MIBC, n = 51), and neoadjuvant-treated MIBC (n = 11). Proteins were extracted from formalin-fixed, paraffin-embedded samples and analyzed using data-independent acquisition, yielding >8,000 quantified proteins. MIBC, compared to NMIBC, shows an extracellular matrix (ECM) and immune response signature as well as alteration of the metabolic proteome together with concomitant depletion of proteins involved in cell-cell adhesion and lipid metabolism. Neoadjuvant treatment did not consistently impact the proteome of the residual tumor mass. NMIBC presents two proteomic subgroups that correlate with histological grade and feature signatures of cell adhesion or lipid/DNA metabolism. Treatment-naïve MIBC presents three proteomic subgroups with resemblance to the basal-squamous, stroma-rich, or luminal subtypes and signatures of metabolism, immune functionality, or ECM. The metabolic subgroup presents an immune-depleted microenvironment, whereas the ECM and immune subgroups are enriched for markers of M2-like tumor-associated macrophages and dendritic cells. Markers for natural killer cells are exclusive for the ECM subgroup, and markers for cytotoxic T cells are a hallmark of the immune subgroup. Endogenous proteolysis is increased in MIBC alongside upregulation of matrix metalloproteases, including MMP-14. Genomic panel sequencing yielded the prototypical profile of prevalent FGRF3 alterations in NMIBC and TP53 alterations in MIBC. Tumor-stroma interactions of MIBC were investigated by proteomic analysis of patient-derived xenografts, highlighting specific tumor and stroma contributions to the matrisome and tumor-induced stromal proteome phenotypes. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Comprehensive genomic characterization of early-stage bladder cancer

Understanding the molecular landscape of nonmuscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and treatment regimens. We performed a comprehensive genomic analysis of patients with NMIBC using whole-exome sequencing (n = 438), shallow whole-genome sequencing (n = 362) and total RNA sequencing (n = 414). A large genomic variation within NMIBC was observed and correlated with different molecular subtypes. Frequent loss of heterozygosity in FGFR3 and 17p (affecting TP53) was found in tumors with mutations in FGFR3 and TP53, respectively. Whole-genome doubling (WGD) was observed in 15% of the tumors and was associated with worse outcomes. Tumors with WGD were genomically unstable, with alterations in cell-cycle-related genes and an altered immune composition. Finally, integrative clustering of multi-omics data highlighted the important role of genomic instability and immune cell exhaustion in disease aggressiveness. These findings advance our understanding of genomic differences associated with disease aggressiveness in NMIBC and may ultimately improve patient stratification.

Loss of NUMB drives aggressive bladder cancer via a RHOA/ROCK/YAP signaling axis

Advances in bladder cancer (BCa) treatment have been hampered by the lack of predictive biomarkers and targeted therapies. Here, we demonstrate that loss of the tumor suppressor NUMB promotes aggressive bladder tumorigenesis and worsens disease outcomes. Retrospective cohort studies show that NUMB-loss correlates with poor prognosis in post-cystectomy muscle-invasive BCa patients and increased risk of muscle invasion progression in non-muscle invasive BCa patients. In mouse models, targeted Numb ablation induces spontaneous tumorigenesis and sensitizes the urothelium to carcinogenic insults, accelerating tumor onset and progression. Integrative transcriptomic and functional analyses in mouse and human BCa models reveal that upregulation of YAP transcriptional activity via a RHOA/ROCK-dependent pathway is a hallmark of NUMB-deficient BCa. Pharmacological or genetic inhibition of this molecular pathway selectively inhibits proliferation and invasion of NUMB-deficient BCa cells in 3D-Matrigel organoids. Thus, NUMB-loss could serve as a biomarker for identifying high-risk patients who may benefit from targeted anti-RHOA/ROCK/YAP therapies.

A Versatile and Upgraded Version of the LundTax Classification Algorithm Applied to Independent Cohorts

Stratification of cancer into biologically and molecularly similar subgroups is a cornerstone of precision medicine. The Lund Taxonomy classification system for urothelial carcinoma aims to be applicable across the whole disease spectrum including both non-muscle-invasive and invasive bladder cancer. A successful classification system is one that can be robustly and reproducibly applied to new samples. However, transcriptomic methods used for subtype classification are affected by analytic platform, data preprocessing, cohort composition, and tumor purity. Furthermore, only limited data have been published evaluating the transferability of existing classification algorithms to external data sets. In this study, a single sample classifier was developed based on in-house microarray and RNA-sequencing data, intended to be broadly applicable across studies and platforms. The new classification algorithm was applied to 10 published external bladder cancer cohorts (n = 2560 cases) to evaluate its ability to capture characteristic subtype-associated gene expression signatures and complementary data such as mutations, clinical outcomes, treatment response, or histologic subtypes. The effect of sample purity on the classification results was evaluated by generating low-purity versions of samples in silico. The classifier was robustly applicable across different gene expression profiling platforms and preprocessing methods and was less sensitive to variations in sample purity.

The evolving role of multidisciplinary teams in optimizing non-muscle invasive bladder cancer care

INTRODUCTION

Non-muscle invasive bladder cancer (NMIBC) represents a significant portion of bladder cancer cases and imposes a substantial economic burden, stemming from both direct treatment costs and long-term surveillance. As the treatment landscape evolves with advances in immunotherapy and targeted therapies, a multidisciplinary approach to management is increasingly crucial for optimizing patient outcomes and resource utilization.

AREAS COVERED

A PubMed search from 2010 to 15 June 2024 was conducted. This review examines the evolving role of multidisciplinary team (MDT) care in NMIBC management. It explores the potential benefits of MDT care, including improved risk stratification and personalized treatment plans, while acknowledging the challenges to implementation and proposing strategies to overcome them.

EXPERT OPINION

With a growing understanding of NMIBC and expanding therapeutic options, MDT care is pivotal in navigating patient care and maximizing outcomes. Strategic planning and collaborative efforts will facilitate the broader adoption of MDT care, enhancing the value of NMIBC treatment. MDT care holds promise for personalized, effective, and cost-efficient care for patients with NMIBC in the future.

Prototol for the Prospective Sample Collection for Cancer of Bladder (ProCaB) Trial by the Cancer of the Bladder Leuven (CaBLe) Consortium

Non-muscle-invasive bladder cancer (NMIBC) is a heterogeneous disease categorized as low, intermediate, high, or very high risk, for which recurrence and progression rates and thus management strategies differ. Current molecular subclassification of bladder cancer (BC) is mainly based on data for muscle-invasive disease, with very few data for NMIBC. A more accurate classification system is needed for better stratification of NMIBC using multiomics and immunohistopathological molecular data alongside clinical data collected in a prospective cohort. ProCaB (Prospective Sample Collection for Cancer of Bladder) is a single-center non-interventional, prospective study recruiting all eligible patients diagnosed with BC in a tertiary center in the Flanders region of Belgium. Clinical data have been collected in a prospective registry since August 2013. Biosamples (blood, urine, and BC tissue) are collected from each patient at diagnosis and are stored at -80°C at BioBank UZ Leuven after appropriate processing according to the protocol. Multiomics (genomics, epigenetics, transcriptomics, proteomics, lipidomics, metabolomics) and immunohistopathology analyses will be performed on appropriate samples. The target is to enroll 300 patients over a 5-yr period, and all patients will be followed for 5 yr. The objective is to create a biobank of samples from patients diagnosed with BC for use in multiomics and immunohistopathological analyses. Results from these analyses, together with long-term clinical data, can be used for comprehensive multilayered molecular characterization of disease recurrence and progression in intermediate- and (very) high-risk NMIBC, identification of multibiomarker panels for better stratification, and identification of a patient subgroup that does not respond to bacillus Calmette-Guérin treatment. This trial is registered on ClinicalTrials.gov as NCT04167332.

Prognostic impact of EGFR expression and immunohistochemistry-based "molecular classification" in bladder cancer

Recent genomic studies emphasize the necessity of molecular classification to reflect diverse clinical and pathological characteristics of bladder cancer. Immunohistochemically bladder cancer can be classified into molecular subtypes, including basal, luminal, and p53-like subtypes. Epidermal growth factor receptor (EGFR) is frequently expressed in basal-type bladder cancers and is associated with poor prognosis. In our study, 88 urothelial carcinoma cases were retrospectively analyzed, molecularly subtyped using CK5/6, GATA3, p16 immunohistochemistry and examined for EGFR expressions as well as clinical and histopathological features. Tumor cell scores ≥20 % considered positive, classifying cases as luminal (GATA3-positive), basal (CK5/6-positive), double-positive (both-positive), or double-negative (both-negative). Further division of luminal and basal cases was based on p16 status: luminal-p53 or basal-p53 (p16-positive) and luminal-non-p53 or basal-non-p53 (p16-negative). Among the cases, 4 (4 %) were double-negative, 48 (55 %) luminal-non-p53, 21 (24 %) luminal-p53, 5 (6 %) basal-non-p53, 3 (3 %) basal-p53, and 7 (8 %) double-positive. Our findings revealed that basal-non-p53 type bladder cancer is associated with poor prognosis, muscle invasion, and high-grade cytology. Basal-p53 and double-negative types exhibited less aggressive features compared to basal-non-p53 types, with associations observed with lamina propria invasion and high-grade cytology. Luminal-p53 type demonstrated higher recurrence rates. Luminal-non-p53 type displayed the least aggressive characteristics, often associated with papillary histopathology. EGFR expression was found to be high in basal-non-p53 type and was further correlated with adverse prognostic indicators, lamina propria invasion, and high-grade cytology. The identification of molecular subtypes and EGFR expression through immunohistochemistry, alongside traditional bladder cancer classifications, enhances tumor behavior prediction and supports effective clinical management.

Temporal dynamics of immune cell patterns in bladder cancer patients receiving Bacillus Calmette-Guérin therapy

BACKGROUND

Bacillus Calmette-Guérin (BCG) is capable of enhancing the infiltration of immune cells into the tumour. However the temporal dynamics of immune cell patterns in patients receiving BCG instillation remains unclear.

METHODS

Ninety-six patients who underwent intravesical BCG therapy, comprising 46 responders and 50 non-responders, were retrospectively enroled to explore the evolving immune landscape. This study involved a detailed examination of sequential samples collected before, during, and after BCG treatment to assess BCG's influence on the immune microenvironment, employing techniques such as immunohistochemistry, fluorescent multiplex immunohistochemistry, and mass spectrometry techniques.

RESULTS

Our study found that initial BCG instillation leads to enhanced immune cell infiltration, correlating with treatment efficacy, with responders exhibiting more pronounced increases. Non-responders experience a rise in immune cell infiltration and PD-L1 expression during the first instillation, which returns to baseline after treatment. In non-responders, BCG re-challenge fail to further increase immune cell infiltration into the tumour or improve patient outcomes. Strikingly, proteomics data revealed that GBP1 expression was induced by BCG treatment in non-responders.

CONCLUSIONS

Our findings demonstrated the induction of tumour PD-L1 expression by BCG in non-responders, and therefore provide insights for the combination of BCG and anti-PD1/anti-PD-L1 therapy.

Relationship Between Loss of Y Chromosome and Urologic Cancers: New Future Perspectives

Background: The Y chromosome (ChrY) is essential for male sex determination and spermatogenesis. However, recent studies have revealed its broader role in various physiological processes and disease susceptibility, including cancer. Methods: A comprehensive literature review was conducted using databases like MEDLINE, Scopus, Web of Science, and Google Scholar. The review included clinical and preclinical studies in animals and humans focusing on the role of LoY in urological tumors. Data on the frequency of LoY, its clinical implications, and underlying mechanisms were extracted and analyzed. Results: The evidence suggests that LoY is associated with an increased risk of urologic neoplasms, potentially serving as an early marker of genomic instability. Studies reveal that LoY in urologic cancers correlates with worse survival outcomes and may contribute to tumor progression. LoY may interfere with chromatin structure and epigenetic regulation, suggesting its role as a contributor to early tumorigenesis. Conclusions: LoY appears to be a structural aberration with unique biological and clinical relevance in urologic cancers, possibly serving as a biomarker for genomic instability. Further research is necessary to identify specific Y-linked genes affected by LoY, potentially informing targeted therapies and early diagnostic strategies for these cancers.

Single-cell transcriptomics reveals IRF7 regulation of the tumor microenvironment in isocitrate dehydrogenase wild-type glioma

Mutations in isocitrate dehydrogenase (IDH) are important markers of glioma prognosis. However, few studies have examined the gene expression regulatory network (GRN) in IDH-mutant and wild-type gliomas. In this study, single-cell RNA sequencing and spatial transcriptome sequencing were used to analyze the GRN of cell subsets in patients with IDH-mutant and wild-type gliomas. Through gene transcriptional regulation analysis, we identified the M4 module, whose transcription factor activity is highly expressed in IDH wild-type gliomas compared to IDH-mutants. Enrichment analysis revealed that these genes were predominantly expressed in microglia and macrophages, with significant enrichment in interferon-related signaling pathways. Interferon regulatory factor 7 (IRF7), a transcription factor within this pathway, showed the highest percentage of enrichment and was primarily localized in the core region of wild-type IDH tumors. A machine-learning prognostic model identified novel subgroups within the wild-type IDH population. Additionally, IRF7 was shown to promote the proliferation and migration of T98G and U251 cells in vitro, and its knockdown affected glioma cell proliferation in vivo. This study systematically established the regulatory mechanism of IDH transcriptional activity in gliomas at the single-cell level and drew a corresponding cell map. The study presents a transcriptional regulatory activity map for IDH wild-type gliomas, involving single-cell RNA sequencing and spatial transcriptomics to identify gene regulatory networks, machine learning models for IDH subtyping, and experimental validation, highlighting the role of IRF7 in glioma progression.

French AFU Cancer Committee Guidelines - Update 2024-2026: Non-muscle invasive bladder cancer (NMIBC)

OBJECTIVE

To update the CCAFU recommendations for the management of non-muscle invasive bladder cancer (NMIBC).

METHODS

A systematic review (Medline) of the literature from 20222024 was performed, taking into account the elements of diagnosis, treatment options and monitoring of NMIBC and evaluating references with their level of evidence.

RESULTS

The diagnosis of NMIBC (Ta, T1, or CIS) is made after complete and deep tumour resection. The use of bladder photodynamic diagnosis and the indication for a second TURBT (4 to 6weeks later) help to improve the initial diagnosis. The risk of recurrence and/or tumour progression is assessed via the EORTC score. By stratifying patients into low-, intermediate- and high-risk groups, adjuvant treatment can be proposed, including endovesical instillations of chemotherapy (immediate postoperative regimen), BCG (induction and maintenance regimen), or even the indication of cystectomy for unresponsive patients.

CONCLUSION

Updating the CCAFU's recommendations should help improve patient management, as well as the diagnosis and treatment of NMIBC.

Deciphering the molecular heterogeneity of intermediate- and (very-)high-risk non-muscle-invasive bladder cancer using multi-layered -omics studies

Bladder cancer (BC) is the most common malignancy of the urinary tract. About 75% of all BC patients present with non-muscle-invasive BC (NMIBC), of which up to 70% will recur, and 15% will progress in stage and grade. As the recurrence and progression rates of NMIBC are strongly associated with some clinical and pathological factors, several risk stratification models have been developed to individually predict the short- and long-term risks of disease recurrence and progression. The NMIBC patients are stratified into four risk groups as low-, intermediate-, high-risk, and very high-risk by the European Association of Urology (EAU). Significant heterogeneity in terms of oncological outcomes and prognosis has been observed among NMIBC patients within the same EAU risk group, which has been partly attributed to the intrinsic heterogeneity of BC at the molecular level. Currently, we have a poor understanding of how to distinguish intermediate- and (very-)high-risk NMIBC with poor outcomes from those with a more benign disease course and lack predictive/prognostic tools that can specifically stratify them according to their pathologic and molecular properties. There is an unmet need for developing a more accurate scoring system that considers the treatment they receive after TURBT to enable their better stratification for further follow-up regimens and treatment selection, based also on a better response prediction to the treatment. Based on these facts, by employing a multi-layered -omics (namely, genomics, epigenetics, transcriptomics, proteomics, lipidomics, metabolomics) and immunohistopathology approach, we hypothesize to decipher molecular heterogeneity of intermediate- and (very-)high-risk NMIBC and to better stratify the patients with this disease. A combination of different -omics will provide a more detailed and multi-dimensional characterization of the tumor and represent the broad spectrum of NMIBC phenotypes, which will help to decipher the molecular heterogeneity of intermediate- and (very-)high-risk NMIBC. We think that this combinatorial multi-omics approach has the potential to improve the prediction of recurrence and progression with higher precision and to develop a molecular feature-based algorithm for stratifying the patients properly and guiding their therapeutic interventions in a personalized manner.

Molecular Landscape of Bladder Cancer: Key Genes, Transcription Factors, and Drug Interactions

Bladder cancer is among the most prevalent tumors in the urinary system and is known for its high malignancy. Although traditional diagnostic and treatment methods are established, recent research has focused on understanding the molecular mechanisms underlying bladder cancer. The primary objective of this study is to identify novel diagnostic markers and discover more effective targeted therapies for bladder cancer. This study identified differentially expressed genes (DEGs) between bladder cancer tissues and adjacent normal tissues using data from The Cancer Genome Atlas (TCGA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to explore the functional roles of these genes. A protein-protein interaction (PPI) network was also constructed to identify and analyze hub genes within this network. Gene set variation analysis (GSVA) was conducted to investigate the involvement of these genes in various biological processes and pathways. Ten key genes were found to be significantly associated with bladder cancer: IL6, CCNA2, CCNB1, CDK1, PLK1, TOP2A, AURKA, AURKB, FOXM1, and CALML5. GSVA analyses revealed that these genes are involved in a variety of biological processes and signaling pathways, including coagulation, UV-response-down, apoptosis, Notch signaling, and Wnt/beta-catenin signaling. The diagnostic relevance of these genes was validated through ROC curve analysis. Additionally, potential therapeutic drug interactions with these key genes were identified. This study provides valuable insights into key genes and their roles in bladder cancer. The identified genes and their interactions with therapeutic drugs could serve as potential biomarkers, presenting new opportunities for enhancing the diagnosis and prognosis of bladder cancer.