Genomic Subtyping in Bladder Cancer

Mutational signature and prognosis in adenocarcinoma of the bladder

Adenocarcinoma of the bladder is a rare urinary bladder carcinoma with limited therapy options due to lack of molecular characterization. Here, we aimed to reveal the mutational and transcriptomic landscapes of adenocarcinoma of the bladder and assess any relationship with prognosis. Between February 2015 and June 2021, a total of 23 patients with adenocarcinoma of the bladder were enrolled. These included 16 patients with primary bladder adenocarcinomas and seven patients with urachal adenocarcinoma. Whole exome sequencing (16 patients), whole genome sequencing (16 patients), bulk RNA sequencing (RNA-seq) (19 patients), and single-cell RNA-seq (5 patients) were conducted for the specimens. Correlation analysis, survival analysis, and t-tests were also performed. Prevalent T>A substitutions were observed among somatic mutations, and major trinucleotide contexts included 5'-CTC-3' and 5'-CTG-3'. This pattern was mainly contributed by COSMIC signature 22 related to chemical carcinogen exposure (probably aristolochic acid), which has not been reported in bladder adenocarcinoma. Moreover, genes with copy number changes were also enriched in the KEGG term 'chemical carcinogenesis'. Transcriptomic analysis suggested high immune cell infiltration and luminal-like features in the majority of samples. Interestingly, a small fraction of samples with an APOBEC-derived mutational signature exhibited a higher risk of disease progression compared with samples with only a chemical carcinogen-related signature, confirming the molecular and prognostic heterogeneity of bladder adenocarcinoma. This study presents mutational and transcriptomic landscapes of bladder adenocarcinoma, and indicates that a chemical carcinogen-related mutational signature may be related to a better prognosis compared with an APOBEC signature in adenocarcinoma of the bladder. © 2024 The Pathological Society of Great Britain and Ireland.

High risk of non-cancer mortality in bladder cancer patients: evidence from SEER-Medicaid

PURPOSE

The objective of this study was to investigate non-cancer causes of death and associated risk factors after bladder cancer (BC) diagnosis.

METHODS

Eligible BC patients were obtained from the SEER database. SEER*Stat software 8.3.9.2 was used to calculate the standardized mortality ratios (SMRs). The proportions of different non-cancer cause of death were calculated and analyzed in different follow-up periods. Multivariate competing risk model was used to analyze the risk factors for death of BC and non-cancer diseases.

RESULTS

In total, 240,954 BC patients were included and 106,092 patients experienced death, with 37,205 (35.07%), 13,208 (12.45%) and 55,679 (52.48%) patients experienced BC, other cancer and non-cancer disease-related deaths, respectively. Overall SMR for BC patients who died from non-cancer diseases was 2.42 (95% CI [2.40-2.44]). Cardiovascular diseases were the most common non-cancer cause of death, followed by respiratory diseases, diabetes mellitus, and infectious diseases. Multivariate competing risk analysis identified the following high-risk factors for non-cancer mortality: age > 60 years, male, whites, in situ stage, pathological type of transitional cell carcinoma, not receiving treatment (including surgery, chemotherapy, or radiation), and widowed.

CONCLUSIONS

Cardiovascular diseases are the leading non-cancer cause of death in BC patients, followed by respiratory disease, diabetes mellitus and infectious diseases. Physicians should pay attention to the risk of death from these non-cancer diseases. Also, physicians should encourage patients to engage in more proactive self-surveillance and follow up.

Optimizing identification of consensus molecular subtypes in muscle-invasive bladder cancer: a comparison of two sequencing methods and gene sets using FFPE specimens

BACKGROUND

Molecular subtypes predict prognosis in muscle-invasive bladder cancer (MIBC) and are explored as predictive markers. To provide a common base for molecular subtyping and facilitate clinical applications, a consensus classification has been developed. However, methods to determine consensus molecular subtypes require validation, particularly when FFPE specimens are used. Here, we aimed to evaluate two gene expression analysis methods on FFPE samples and to compare reduced gene sets to classify tumors into molecular subtypes.

METHODS

RNA was isolated from FFPE blocks of 15 MIBC patients. Massive analysis of 3' cDNA ends (MACE) and the HTG transcriptome panel (HTP) were used to retrieve gene expression. We used normalized, log2-transformed data to call consensus and TCGA subtypes with the consensusMIBC package for R using all available genes, a 68-gene panel (ESSEN1), and a 48-gene panel (ESSEN2).

RESULTS

Fifteen MACE-samples and 14 HTP-samples were available for molecular subtyping. The 14 samples were classified as Ba/Sq in 7 (50%), LumP in 2 (14.3%), LumU in 1 (7.1%), LumNS in 1 (7.1%), stroma-rich in 2 (14.3%) and NE-like in 1 (7.1%) case based on MACE- or HTP-derived transcriptome data. Consensus subtypes were concordant in 71% (10/14) of cases when comparing MACE with HTP data. Four cases with aberrant subtypes had a stroma-rich molecular subtype with either method. The overlap of the molecular consensus subtypes with the reduced ESSEN1 and ESSEN2 panels were 86% and 100%, respectively, with HTP data and 86% with MACE data.

CONCLUSION

Determination of consensus molecular subtypes of MIBC from FFPE samples is feasible using various RNA sequencing methods. Inconsistent classification mainly involves the stroma-rich molecular subtype, which may be the consequence of sample heterogeneity with (stroma)-cell sampling bias and highlights the limitations of bulk RNA-based subclassification. Classification is still reliable when analysis is reduced to selected genes.

Therapeutic responses to chemotherapy or immunotherapy by molecular subtype in bladder cancer patients: A meta-analysis and systematic review

To systematically evaluate the differences in therapeutic response to chemotherapy or immunotherapy between different molecular subtypes of bladder cancer (BC). A comprehensive literature search was performed up to December 2021. Consensus clusters 1 (CC1), CC2 and CC3 molecular subtypes were used to perform meta-analysis. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the therapeutic response by fix-effect modeling. Eight studies involving 1,463 patients were included. For immunotherapy, CC3 showed the highest response rate (CC1 vs. CC3: OR=0.52, 95% CI=0.34-0.78, p=0.002; CC2 vs. CC3: OR=0.42, 95% CI=0.28-0.62, p<0.001), which was mainly reflected in the highest response rate to atezolizumab (CC1 vs. CC3: OR=0.47, 95% CI=0.29-0.75, p=0.002; CC2 vs. CC3: OR=0.38, 95% CI=0.24-0.59, p<0.001). For chemotherapy, CC3 had the lowest response rate to the overall chemotherapy (CC1 vs. CC3: OR=2.05, 95% CI=1.23-3.41, p=0.006; CC2 vs. CC3: OR=2.48, 95% CI=1.50-4.10, p<0.001). Compared with CC2, CC3 responded poorly to both neo-adjuvant chemotherapy (NAC) (OR=1.93, 95% CI=1.09-3.41, p=0.020) and chemoradiation therapy (CRT) (OR=6.07, 95% CI=1.87-19.71, p<0.001). Compared with CC1, CC3 only showed a poorer response to CRT (OR=4.53, 95% CI=1.26-16.27, p=0.020), and no difference in NAC. Our study suggested that molecular classifications are important predictors of cancer treatment outcomes of BC patients and could identify subgroup patients who are most likely to benefit from specific cancer treatments.

Precision Medicine in Bladder Cancer: Present Challenges and Future Directions

Bladder cancer (BC) is characterized by significant histopathologic and molecular heterogeneity. The discovery of molecular pathways and knowledge of cellular mechanisms have grown exponentially and may allow for better disease classification, prognostication, and development of novel and more efficacious noninvasive detection and surveillance strategies, as well as selection of therapeutic targets, which can be used in BC, particularly in a neoadjuvant or adjuvant setting. This article outlines recent advances in the molecular pathology of BC with a better understanding and deeper focus on the development and deployment of promising biomarkers and therapeutic avenues that may soon make a transition into the domain of precision medicine and clinical management for patients with BC.

Molecular Subtyping and Survival Analysis of Osteosarcoma Reveals Prognostic Biomarkers and Key Canonical Pathways

Osteosarcoma (OS) is a common bone malignancy in children and adolescents. Although histological subtyping followed by improved OS treatment regimens have helped achieve favorable outcomes, a lack of understanding of the molecular subtypes remains a challenge to characterize its genetic heterogeneity and subsequently to identify diagnostic and prognostic biomarkers for developing effective treatments. In the present study, global analysis of DNA methylation, and mRNA and miRNA gene expression in OS patient samples were correlated with their clinical characteristics. The mucin family of genes, MUC6, MUC12, and MUC4, were found to be highly mutated in the OS patients. Results revealed the enrichment of molecular pathways including Wnt signaling, Calcium signaling, and PI3K-Akt signaling in the OS tumors. Survival analyses showed that the expression levels of several genes such as RAMP1, CRIP1, CORT, CHST13, and DDX60L, miRNAs and lncRNAs were associated with survival of OS patients. Molecular subtyping using Cluster-Of-Clusters Analysis (COCA) for mRNA, lncRNA, and miRNA expression; DNA methylation; and mutation data from the TARGET dataset revealed two distinct molecular subtypes, each with a distinctive gene expression profile. Between the two subtypes, three upregulated genes, POP4, HEY1, CERKL, and seven downregulated genes, CEACAM1, ABLIM1, LTBP2, ISLR, LRRC32, PTPRF, and GPX3, associated with OS metastasis were found to be differentially regulated. Thus, the molecular subtyping results provide a strong basis for classification of OS patients that could be used to develop better prognostic treatment strategies.

Integrated risk scores from N6-methyladenosine-related lncRNAs are potential biomarkers for predicting the overall survival of bladder cancer patients

Background: N6-methyladenosine (m6A) is the most common form of mRNA- and long noncoding RNA (lncRNA)-specific internal modification encountered in eukaryotes, with important effects on mRNA stability, translation, and splicing. The role of m6A-modified lncRNAs (m6A-lncRNAs) in bladder cancer (BLCA) is rarely reported. This study aimed to evaluate an efficient prognostic model of BLCA in patients, based on m6A-lncRNAs, and to discover potential biological targets.

Methods: Differentially expressed lncRNAs were investigated in 433 BLCA samples derived from The Cancer Genome Atlas (TCGA) database. Kaplan–Meier and univariate Cox regression analyses were performed to screen for m6A-lncRNAs with prognostic roles in BLCA. We implemented Pearson correlation analysis to analyze 18 potentially prognostic lncRNAs and 20 known m6A-associated genes. Next, the data were imputed using least absolute shrinkage and selection operator (LASSO) Cox regression to establish an m6A-lncRNA prognostic signature.

Results: We established an integrated risk score (RS) containing five m6A-lncRNAs and constructed a nomogram that had the ability to forecast the overall survival (OS) of patients with BLCA. We showed that the predictive accuracy of the RS for BLCA prognosis was high, which was confirmed by the area under the receiver operating characteristic (ROC) curve. We analyzed the correlation between tumor immune infiltrating cells and RS in high- and low-risk patients with BLCA and used tumor immune dysfunction and exclusion to predict the effect of immunotherapy. We screened out the most relevant modules of RS through the weighted gene co-expression network analysis network and explored their potential biological functions using GO and KEGG analyses.

Conclusion: Our findings demonstrate that, compared with nomograms constructed using a single prognostic factor, the integrated RS represents a superior model for predicting survival in patients with BLCA, which may improve the clinical management of BLCA.

RalGPS2 Interacts with Akt and PDK1 Promoting Tunneling Nanotubes Formation in Bladder Cancer and Kidney Cells Microenvironment

Simple Summary

Cell-to-cell communication in the tumor microenvironment is a crucial process to orchestrate the different components of the tumoral infrastructure. Among the mechanisms of cellular interplay in cancer cells, tunneling nanotubes (TNTs) are dynamic connections that play an important role. The mechanism of the formation of TNTs among cells and the molecules involved in the process remain to be elucidated. In this study, we analyze several bladder cancer cell lines, representative of tumors at different stages and grades. We demonstrate that TNTs are formed only by mid or high-stage cell lines that show muscle-invasive properties and that they actively transport mitochondria and proteins. The formation of TNTs is triggered by stressful conditions and starts with the assembly of a specific multimolecular complex. In this study, we characterize some of the protein components of the TNTs complex, as they are potential novel molecular targets for future therapies aimed at counteracting tumor progression.

Abstract

RalGPS2 is a Ras-independent Guanine Nucleotide Exchange Factor for RalA GTPase that is involved in several cellular processes, including cytoskeletal organization. Previously, we demonstrated that RalGPS2 also plays a role in the formation of tunneling nanotubes (TNTs) in bladder cancer 5637 cells. In particular, TNTs are a novel mechanism of cell–cell communication in the tumor microenvironment, playing a central role in cancer progression and metastasis formation. However, the molecular mechanisms involved in TNTs formation still need to be fully elucidated. Here we demonstrate that mid and high-stage bladder cancer cell lines have functional TNTs, which can transfer mitochondria. Moreover, using confocal fluorescence time-lapse microscopy, we show in 5637 cells that TNTs mediate the trafficking of RalA protein and transmembrane MHC class III protein leukocyte-specific transcript 1 (LST1). Furthermore, we show that RalGPS2 is essential for nanotubes generation, and stress conditions boost its expression both in 5637 and HEK293 cell lines. Finally, we prove that RalGPS2 interacts with Akt and PDK1, in addition to LST1 and RalA, leading to the formation of a complex that promotes nanotubes formation. In conclusion, our findings suggest that in the tumor microenvironment, RalGPS2 orchestrates the assembly of multimolecular complexes that drive the formation of TNTs.

Molecular Classification of Bladder Urothelial Carcinoma Using NanoString-Based Gene Expression Analysis

Simple Summary

Our study aimed to apply a quantitative method based on mRNA counting as nCounter (NanoString Technologies, Inc). This method can obtain precise and accurate measures of RNA expression compared to RT-PCR, and which might represent an alternative to the NGS-genomic/transcriptomic profiling frequently used to generate molecular data in bladder cancer and provide clinically meaningful datasets for the molecular classification of bladder cancer. The current study generated a four-gene classifier, incorporating GATA3 and KRT20 (typically related to luminal molecular subtype) and KRT5 and KRT14 (typically related to basal molecular subtype). This methodology allowed us to explore differences in clinicopathologic parameters and potential sensitivities to ICI immunotherapy in a cohort series of 91 urothelial carcinomas of the bladder.

Abstract

Molecular classification of bladder carcinoma is a relevant topic in modern bladder cancer oncology due to its potential to improve oncological outcomes. The available molecular classifications are generally based on transcriptomic profiles, generating highly diverse categories with limited correlation. Implementation of molecular classification in practice is typically limited due to the high complexity of the required technology, the elevated costs, and the limited availability of this technology worldwide. We have conducted a gene expression analysis using a four-gene panel related to luminal and basal subtypes in a series of 91 bladder cancer cases. NanoString-based gene expression analysis using typically luminal (GATA3+/KRT20+) and basal markers (KRT14+/KRT5+/GATA3low/-/KRT20low/-) classified urothelial bladder carcinoma samples as luminal, basal, and a third category (KRT14-/KRT5-/GATA3-/KRT20-), null/double negative (non-luminal/non-basal). These three categories were meaningful in terms of overall cancer-specific survival (p < 0.0001) or when classified as conventional urothelial carcinoma and variant histology urothelial carcinoma (p < 0.0001), NMIBC vs. MIBC (p < 0.001), or by AJCC stage category Ta (p = 0.0012) and T1 (p < 0.0001) but did not reach significance in T2-T4 (p = 0.563). PD-L1 expression (low vs. high) was also different according to molecular subtype, with high PD-L1 expression mostly seen in basal and null subtypes and carcinomas with variant histology (p = 0.002). Additionally, the luminal subtype was enriched in NMIBC with favorable cancer-specific survival (p < 0.0001). In contrast, basal and null subtypes resulted in aggressive MIBC tumors with shorter cancer-specific survival (p < 0.0001), some of which presented variant histology. In conclusion, a comprehensive evaluation of a gene classifier related to molecular taxonomy using NanoString technology is feasible. Therefore, it might represent an accessible and affordable tool in this rapidly expanding area of precision genomics.

Sonic Hedgehog signaling pathway in gynecological and genitourinary cancer (Review)

Cancers of the urinary tract, as well as those of the female and male reproductive systems, account for a large percentage of malignancies worldwide. Mortality is frequently affected by late diagnosis or therapeutic difficulties. The Sonic Hedgehog (SHH) pathway is an evolutionary conserved molecular cascade, which is mainly associated with the development of the central nervous system in fetal life. The present review aimed to provide an in‑depth summary of the SHH signaling pathway, including the characterization of its major components, the mechanism of its upstream regulation and non‑canonical activation, as well as its interactions with other cellular pathways. In addition, the three possible mechanisms of the cellular SHH cascade in cancer tissue are discussed. The aim of the present review was to summarize significant findings with regards to the expression of the SHH pathway components in kidney, bladder, ovarian, cervical and prostate cancer. Reports associated with common deficits and de‑regulations of the SHH pathway were summarized, despite the differences in molecular and histological patterns among these malignancies. However, currently, neither are SHH pathway elements included in panels of prognostic/therapeutic molecular patterns in any of the discussed cancers, nor have the drugs targeting SMO or GLIs been approved for therapy. The findings of the present review may support future studies on the treatment of and/or molecular targets for gynecological and genitourinary cancers.

Adhesion GPR123 is an indicator for recurrence and prognosis in bladder cancer

BACKGROUND

Bladder cancer is a common urinary cancer, and most patients suffer tumor recurrence after surgery. Identifying more prognostic biomarkers is an essential task for precious treatment.

OBJECTIVE

To evaluate the expression and clinical significance of GPR123, Angiotensin-I a type of adhesion G protein-coupled receptors (aGPCRs), in bladder cancer.

METHODS

The expressions of GPR123 in two retrospective cohorts comprised of 150 and 56 patients with bladder cancer respectively, were detected with and immunohistochemistry (IHC). Moreover, GPR123 mRNAs in 11 non-muscle-invasive bladder cancers (NMIBCs) and 11 muscle-invasive bladder cancers (MIBCs) were detected with qRT-PCR. The correlation between GPR123 and the clinicopathological characters was estimated by Chi-square test. The significance of GPR123 and other clinicopathological characters in recurrence and prognosis of bladder cancer was evaluated by univariate and multivariate analyses.

RESULTS

GPR123 was mainly expressed in the cell membrane of bladder cancer. The percentages of high GPR123 expression in NMIBC and MIBC were 38.32 and 55.81 % in cohort 1, and 16.00 and 43.90 % in cohort 2. With qRT-PCR and IHC, we showed that GPR123 expression in MIBC was significantly higher than that in NMIBC. GPR123 was significantly associated with T and M stage of bladder cancer. GPR123 expression was all correlated with recurrence (disease-free survival rate), and prognosis (overall survival rate). High GPR123 expression was identified as independent biomarker indicating easier recurrence and poorer prognosis.

CONCLUSIONS

GPR123 was an independent biomarker of bladder cancer for recurrence and prognosis, indicating that GPR123 detection with IHC after operation could help find the high-risk patients and direct the post-operational surveillance.

Identification of a prognostic signature based on immune-related genes in bladder cancer

Bladder cancer (BLCA) has a high incidence and recurrence rate, and the effect of immunotherapy varies from person to person. Immune-related genes (IRGs) have been shown to be associated with immunotherapy and prognosis in many other cancers, but their role in immunogenic BLCA is less well defined. In this study, we constructed an eight-IRG risk model, which demonstrated strong prognostic and immunotherapeutic predictive power. The signature was significantly related to tumor clinicopathological characteristics, tumor class, immune cell infiltration and mutation status. Additionally, a nomogram containing the risk score and other potential risk factors could effectively predict the long-term overall survival probability of BLCA patients. The enriched mechanisms identified by gene set enrichment analysis suggested that the reason why this signature can accurately distinguish high- and low-risk populations may be closely related to the different degrees of innate immune response and T cell activation in different patients.

CXCL12 and CD3E as Indicators for Tumor Microenvironment Modulation in Bladder Cancer and Their Correlations With Immune Infiltration and Molecular Subtypes

Bladder cancer (BLCA) represents the ninth most common malignant tumor in the world and is characterized by high recurrence risk. Tumor microenvironment (TME) plays an important role in regulating the progression of BLCA. Immunotherapy, including Bacillus Calmette-Guerin (BCG) and programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1), is closely associated with TME and is widely used for treating BLCA. But parts of BLCA patients have no response to these treatment ways, thus a better understanding of the complex TME of BLCA is still needed. We downloaded the gene expression profile and corresponding clinical information of 414 BLCA patients from the TCGA database. Via the ESTIMATE and CIBERSORT algorithm, we identified the two hub genes (CXCL12 and CD3E) and explored their correlations with immune infiltration. We found that BLCA patients with higher expression of CXCL12 and lower expression of CD3E had prolonged survival. Gene set enrichment analysis (GSEA) revealed that both CXCL12 and CD3E were enriched in immune-related pathways. We also discovered that stromal score and the level of CXCL12 were higher in luminal subtype, and immune score and the level of CD3E were higher in the basal subtype. Furtherly, we found that CXCL12 was associated with naive B cells, resting mast cell, M2 macrophages, follicular helper T cells, and dendritic cells. CD8⁺ T cells, CD4⁺ T cells, regulatory T cells (Tregs), and macrophages were correlated with CD3E. In conclusions, we found that CXCL12 and CD3E might serve as indicators of TME modulation in BLCA. Therapy targeting CXCL12 and CD3E had the potential as novel therapeutic strategy.

A Comparative Meta-Analysis and in silico Analysis of Differentially Expressed Genes and Proteins in Canine and Human Bladder Cancer

Canine and human bladder cancer present similar anatomical, morphological, and molecular characteristics, and dogs can be considered a model for human bladder cancer. However, the veterinary literature lacks information regarding cross-validation analysis between human and canine large-scale data. Therefore, this research aimed to perform a meta-analysis of the canine literature on bladder cancer, identifying genes and proteins previously evaluated in these studies. In addition, we also performed a cross-validation of the canine transcriptome data and the human data from The Cancer Genome Atlas (TCGA) to identify potential markers for both species. The meta-analysis was performed using the following indexing terms: “bladder” AND “carcinoma” AND “dog” in different international databases, and 385 manuscripts were identified in our initial search. Then, several inclusion criteria were applied, and only 25 studies met these criteria. Among these studies, five presented transcriptome data, and 20 evaluated only isolated genes or proteins. Regarding the studies involving isolated protein analysis, the HER-2 protein was the most studied (3/20), followed by TAG-72 (2/20), COX-2 (2/20), survivin (2/20), and CK7 (2/20), and the remaining nine studies evaluated one isolated protein each. Regarding the cross-validation analysis of human and canine transcriptome data, we identified 35 dysregulated genes, including ERBB2, TP53, EGFR, and E2F2. Our results demonstrate that the canine literature on bladder cancer previously focused on the evaluation of isolated markers with no association with patient survival. This limitation may be related to the lack of a homogenous protocol for treating patients and the lack of follow-up during treatment. In addition, the lack of information regarding tumor muscle invasion can be considered an important limitation when comparing human and canine bladder tumors. Our in silico analysis involving canine and human transcriptome data provided several genes with the potential to be markers for both human and canine bladder tumors, and these genes should be considered for future studies on canine bladder cancer.

PTEN: What we know of the function and regulation of this onco-suppressor factor in bladder cancer?

Bladder cancer accounts for high morbidity and mortality around the world and its incidence rate is suggested to be higher in following years. A number of factors involve in bladder cancer development such as lifestyle and drugs. However, it appears that genetic factors play a significant role in bladder cancer development and progression. Phosphatase and tensin homolog (PTEN) is a cancer-related transcription factor that is corelated with reduced proliferation and invasion of cancer cells by negatively targeting PI3K/Akt/mTOR signaling pathway. In the present review, we aimed to explore the role of PTEN in bladder cancer cells and how upstream modulators affect PTEN in this life-threatening disorder. Down-regulation of PTEN is associated with poor prognosis, chemoresistance and progression of cancer cells. Besides, microRNAs, long non-coding RNAs, circular RNAs and other molecular pathways such as NF-kB are able to target PTEN in bladder cancer cells. Notably, anti-tumor drugs such as kaempferol, β-elemene and sorafenib upregulate the expression of PTEN to exert their inhibitory effects on bladder cancer cells.