MicroRNA Dysregulation and Non-Muscle-Invasive Bladder Cancer Prognosis

The Role of miRNAs to Detect Progression, Stratify, and Predict Relevant Clinical Outcomes in Bladder Cancer

Bladder cancer (BC) is one of the most common types of cancer worldwide, with significant differences in survival depending on the degree of muscle and surrounding tissue invasion. For this reason, the timely detection and monitoring of the disease are important. Surveillance cystoscopy is an invasive, costly, and uncomfortable procedure to monitor BC, raising the need for new, less invasive alternatives. In this scenario, microRNAs (miRNAs) represent attractive prognostic tools given their role as gene regulators in different biological processes, tissue expression, and their ease of evaluation in liquid samples. In cancer, miRNA expression is dynamically modified depending on the tumor type and cancer staging, making them potential biomarkers. This review describes the most recent studies in the last five years exploring the utility of miRNA-based strategies to monitor progression, stratify, and predict relevant clinical outcomes of bladder cancer. Several studies have shown that multimarker miRNA models can better predict overall survival, recurrence, and progression in BC patients than traditional strategies, especially when combining miRNA expression with clinicopathological variables. Future studies should focus on validating their use in different cohorts and liquid samples.

An Updated Review of Contribution of Long Noncoding RNA-NEAT1 to the Progression of Human Cancers

Long non-coding RNAs (lncRNAs) present pivotal roles in cancer tumorigenesis and progression. Recently, nuclear paraspeckle assembly transcript 1 (NEAT1) as a lncRNA has been shown to mediate cell proliferation, migration, and EMT in tumor cells. NEAT1 by targeting several miRNAs/mRNA axes could regulate cancer cell behavior. Therefore, NEAT1 may function as a potent biomarker for the prediction and treatment of some human cancers. In this review, we summarized various NEAT1-related signaling pathways that are critical in cancer initiation and progression.

Prediction for recurrent non-muscle invasive bladder cancer

Non-muscle invasive bladder cancer (NMIBC) has a high recurrence rate, which places a significant burden on both patients and the healthcare system. Hence, it holds significant importance to predict the recurrence risk following treatment for individuals diagnosed with non-muscle invasive bladder cancer (NMIBC). As new generation technologies continue to emerge, an increasing number of recurrence risk prediction tools are being developed and discovered. This article provides an overview of the primary recurrence risk prediction tools currently available, including the liquid biopsy, tissue biopsy, and risk prediction tables. Each of these tools is described in detail and illustrated with relevant examples. Furthermore, we conduct an analysis of the advantages and disadvantages of these tools. This article aims to enhance the reader's understanding of the current progress in recurrence prediction tools and encourage their practical utilization in the fields of precision medicine and public health.

Progress in the development of tissue-based biomarkers for urothelial cancer

INTRODUCTION

As the understanding of molecular mechanisms of bladder cancer advances, molecularly-guided precision medicine becomes increasingly relevant. Biomarkers play a critical role in this setting, predicting treatment response and identifying candidates for targeted therapies.

AREAS COVERED

Current literature on biomarkers in their role in disease prognosis, and response to neoadjuvant and adjuvant therapies. In non-muscle invasive bladder cancer, particular focus is on markers of disease progression, and response to intravesical therapy. In muscle invasive and advanced bladder cancer, particular emphasis is on markers associated with neoadjuvant chemotherapy, as well as systemic immunotherapy. We discuss current shortcomings and pitfalls in contemporary markers, and future avenues of prospective research.

EXPERT OPINION

The focus on biomarkers has moved from immunohistochemical analysis and tumor-related phenotypic changes to examining genetic alterations. Single marker analysis has been shown to be insufficient in predicting both disease course and response to therapy, and studies have shifted towards examining marker combinations and genetic classifiers. Ultimately, significant progress in implementing biomarkers into clinical guidelines remains elusive, largely due to lack of prospective studies in well-defined patient cohorts and with clinically-meaningful endpoints. Until then, despite their promising value, tissue markers should be limited to experimental settings and clinical trials.

mRNA-miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis

Bladder cancer (BC) is one of the most important cancers worldwide, and if it is diagnosed early, its progression in humans can be prevented and long-term survival will be achieved accordingly. This study aimed to identify novel micro-RNA (miRNA) and gene-based biomarkers for diagnosing BC. The microarray dataset of BC tissues (GSE13507) listed in the GEO database was analyzed for this purpose. The gene expression data from three BC tissues including 165 primary bladder cancer (PBC), 58 normal looking-bladder mucosae surrounding cancer (NBMSC), and 23 recurrent non-muscle invasive tumor tissues (RNIT) were used to reconstruct gene co-expression networks. After preprocessing and normalization, deferentially expressed genes (DEGs) were obtained and used to construct the weighted gene co-expression network (WGCNA). Gene co-expression modules and low-preserved modules were extracted among BC tissues using network clustering. Next, the experimentally validated mRNA-miRNA interaction information were used to reconstruct three mRNA-miRNA bipartite networks. Reactome pathway database and Gene ontology (GO) was subsequently performed for the extracted genes of three bipartite networks and miRNAs, respectively. To further analyze the data, ten hub miRNAs (miRNAs with the highest degree) were selected in each bipartite network to reconstruct three bipartite subnetworks. Finally, the obtained biomarkers were comprehensively investigated and discussed in authentic studies. The obtained results from our study indicated a group of genes including PPARD, CST4, CSNK1E, PTPN14, ETV6, and ADRM1 as well as novel miRNAs (e.g., miR-16-5p, miR-335-5p, miR-124-3p, and let-7b-5p) which might be potentially associated with BC and could be a potential biomarker. Afterward, three drug-gene interaction networks were reconstructed to explore candidate drugs for the treatment of BC. The hub miRNAs in the mRNA-miRNA bipartite network played a fundamental role in BC progression; however, these findings need further investigation.

Non-coding RNA-associated competitive endogenous RNA regulatory networks: Novel diagnostic and therapeutic opportunities for hepatocellular carcinoma

Hepatocellular carcinoma (HCC), as the most prevalent liver malignancy, is annually diagnosed in more than half a million people worldwide. HCC is strongly associated with hepatitis B and C viral infections as well as alcohol abuse. Obesity and nonalcoholic fatty liver disease (NAFLD) also significantly enhance the risk of liver cancer. Despite recent improvements in therapeutic approaches, patients diagnosed in advanced stages show poor prognosis. Accumulating evidence provides support for the regulatory role of non-coding RNAs (ncRNAs) in cancer. There are a variety of reports indicating the regulatory role of microRNAs (miRNAs) in different stages of HCC. Long non-coding RNAs (LncRNAs) exert their effects by sponging miRNAs and controlling the expression of miRNA-targeted genes. Circular RNAs (circRNAs) perform their biological functions by acting as transcriptional regulators, miRNA sponges and protein templates. Diverse studies have illustrated that dysregulation of competing endogenous RNA networks (ceRNETs) is remarkably correlated with HCC-causing diseases such as chronic viral infections, nonalcoholic steatohepatitis and liver fibrosis/cirrhosis. The aim of the current article was to provide an overview of the role and molecular mechanisms underlying the function of ceRNETs that modulate the characteristics of HCC such as uncontrolled cell proliferation, resistance to cell death, metabolic reprogramming, immune escape, angiogenesis and metastasis. The current knowledge highlights the potential of these regulatory RNA molecules as novel diagnostic biomarkers and therapeutic targets in HCC.

Lnc-STYK1-2 regulates bladder cancer cell proliferation, migration, and invasion by targeting miR-146b-5p expression and AKT/STAT3/NF-kB signaling

Background

Epigenetic modulation by noncoding RNAs substantially contributes to human cancer development, but noncoding RNAs involvement in bladder cancer remains poorly understood. This study investigated the role of long noncoding RNA (lncRNA) lnc-STYK1-2 in tumorigenesis in cancerous bladder cells.

Methods

Differential lncRNA and mRNA profiles were characterized by high-throughput RNA sequencing combined with validation via quantitative PCR. Bladder cancer cell proliferation was assessed through MTS, and bladder cancer cell migration and invasion were assessed through a Transwell system. The in vivo tumorigenesis of bladder cancer cells was evaluated using the cancer cell line-based xenograft model. The dual-luciferase reporter assay verified the association of miR-146b-5p with lnc-STYK1-2 and the target gene. Protein abundances and phosphorylation were detected by Western blotting.

Results

Alterations in lncRNA profiles, including decreased lnc-STYK1-2 expression, were detected in bladder cancer tissues compared with adjacent noncancerous tissues. lnc-STYK1-2 silencing effectively promoted proliferation, migration, and invasion in two bladder cancer cell lines, 5637 and T24, and their tumorigenesis in nude mice. lnc-STYK1-2 siRNA promoted miR-146b-5p and reduced ITGA2 expression in bladder cancer cells. Moreover, miR-146b-5p suppressed ITGA2 expression in bladder cancer cells through direct association. Also, lnc-STYK1-2 directly associated with miR-146b-5p. Finally, miR-146b-5p inhibitors abrogated the alterations in bladder cell functions, ITGA2 expression, and phosphorylation of AKT, STAT3, and P65 proteins in 5637 and T24 cells induced by lnc-STYK1-2 silencing.

Conclusion

lnc-STYK1-2 inhibited bladder cancer cell proliferation, migration, and tumorigenesis by targeting miR-146b-5p to regulate ITGA2 expression and AKT/STAT3/NF-kB signaling.

Identification of Let-7f-5p as a novel biomarker of recurrence in non-muscle invasive bladder cancer

BACKGROUND

Among patients diagnosed with non-muscle invasive bladder cancer (NMIBC), 30% to 70% experience recurrences within 6 to 12 years of diagnosis. The need to screen for these events every 3 to 6 months and ultimately annually by cystoscopy makes bladder cancer one of the most expensive malignancies to manage.

OBJECTIVE

The purpose of this study was to identify reproducible prognostic microRNAs in resected non-muscle invasive bladder tumor tissue that are predictive of the recurrent tumor phenotype as potential biomarkers and molecular therapeutic targets.

METHODS

Two independent cohorts of NMIBC patients were analyzed using a biomarker discovery and validation approach, respectively.

RESULTS

miRNA Let-7f-5p showed the strongest association with recurrence across both cohorts. Let-7f-5p levels in urine and plasma were both found to be significantly correlated with levels in tumor tissue. We assessed the therapeutic potential of targeting Lin28, a negative regulator of Let-7f-5p, with small-molecule inhibitor C1632. Lin28 inhibition significantly increased levels of Let-7f-5p expression and led to significant inhibition of viability and migration of HTB-2 cells.

CONCLUSIONS

We have identified Let-7f-5p as a miRNA biomarker of recurrence in NMIBC tumors. We further demonstrate that targeting Lin28, a negative regulator of Let-7f-5p, represents a novel potential therapeutic opportunity in NMIBC.

Uncovering the expression patterns and the clinical significance of miR-182, miR-205, miR-27a and miR-369 in patients with urinary bladder cancer

BACKGROUND

Given the high recurrence and progression rates and the absence of reliable markers for early detection and prognosis prediction of patients with urothelial bladder cancer (BCa), the exploration of new biomarkers with high specificity is imperative. Mainly, microRNAs (miRNAs), which are involved in the initiation and the progression of BCa. Herein, the expression patterns of miR-182, miR-205, miR-27a and miR-369 were evaluated in patients with urothelial BCa.

METHODS AND RESULTS

The expression levels of the miRNAs were investigated in 90 FFPE tissue samples (23 LG NMIBC, 44 HG NMIBC, 23 MIBC) and 10 non tumoral bladder tissues using TaqMan based RT-qPCR. Data analysis was performed using 2^-ΔΔCT method. Correlation to clinical characteristics of the patients was performed using descriptive statistics and the receiver operating characteristic (ROC) curve was performed to evaluate the diagnostic value of all miRNAs. MiR-27a, miR-205 and miR-369 were down-regulated whereas miR-182 was up-regulated in patients compared to controls (p < 0.001). MiR-205 and miR-182 positively segregate between NMIBC and MIBC (p = 0.002 and p = 0.000 respectively) whereas the distribution of miR-27a's expression among these tumor groups was almost significant (p = 0.05) and that of miR-369's expression was irrelevant (p = 0.618). Interestingly, miR-182 was discriminative between LG NMIBC and HG NMIBC (p < 0.001) and Ta/T1 tumors (p = 0.000). Furthermore, high levels of miR-182 were potentially predictive of progression in NMIBC patients (p = 0.01).

CONCLUSION

Collectively, a selection of miRNAs was found to be aberrantly expressed in BCa suggesting a potential diagnostic value in BCa. In addition, the clinical value of miR-182 and miR-205 as potential prognosis biomarkers was highlighted. Indeed, our data provide additional insights into cancer biology. Further functional or target studies are mandatory to strengthen these findings.

MDEHT: a multivariate approach for detecting differential expression of microRNA isoform data in RNA-sequencing studies

Motivation

miRNA isoforms (isomiRs) are produced from the same arm as the archetype miRNA with a few nucleotides different at 5 and/or 3 termini. These well-conserved isomiRs are functionally important and have contributed to the evolution of miRNA genes. Accurate detection of differential expression of miRNAs can bring new insights into the cellular function of miRNA and a further improvement in miRNA-based diagnostic and prognostic applications. However, very few methods take isomiR variations into account in the analysis of miRNA differential expression.

Results

To overcome this challenge, we developed a novel approach to take advantage of the multidimensional structure of isomiR data from the same miRNAs, termed as a multivariate differential expression by Hotelling’s T² test (MDEHT). The utilization of the information hidden in isomiRs enables MDEHT to increase the power of identifying differentially expressed miRNAs that are not marginally detectable in univariate testing methods. We conducted rigorous and unbiased comparisons of MDEHT with seven commonly used tools in simulated and real datasets from The Cancer Genome Atlas. Our comprehensive evaluations demonstrated that the MDEHT method was robust among various datasets and outperformed other commonly used tools in terms of Type I error rate, true positive rate and reproducibility.

Availability and implementation

The source code for identifying and quantifying isomiRs and performing miRNA differential expression analysis is available at https://github.com/amanzju/MDEHT.

Supplementary information

Supplementary data are available at Bioinformatics online.

Expression profile of microRNAs in bladder cancer and their application as biomarkers

Bladder cancer (BC) comprises 3% of all cancers and is particularly common in the developed countries. Early diagnosis is an important necessity in improvement of BC prognosis, as patients' outcome is significantly different between muscle invasive BC (MIBC) and non-muscle invasive BC cases. This cancer is resulted from an intricate interaction between genetic and environmental factors. Recent studies have identified microRNAs (miRNAs) as potential modulators of carcinogenic potential of BC cells. These small transcripts regulate expression of target genes mostly through binding with their 3' untranslated regions. Expression of several oncomiRs has been increased in BC tissues, peripheral blood or urine samples of these patients. These miRNAs promote oncogenic potential of BC through modulation of epithelial-mesenchymal transition or PI3K/AKT, JAK/STAT and NF-κB/Snail signaling pathways. Besides, a number of tumor suppressive miRNAs have been down-regulated in BC samples leading to enhanced proliferation, invasiveness and metastasis of these cells. TGFβ1, Akt, MAPK, MET/SMAD3/SNAIL, MAPK1/Slug/vimentin and Wnt7a/β-catenin pathways and axes are among molecular targets of these miRNAs. Aberrant expressions of miRNAs in biofluids of patients with BC have potentiated them as molecular markers for prediction of disease course. In the current review, we provided a summary of studies which reported aberrant expression of miRNAs and their implications in the diagnosis or prognosis of patients with BC.

Oncogenic gene RGC-32 is a direct target of miR-26b and facilitates tongue squamous cell carcinoma aggressiveness through EMT and PI3K/AKT signalling

Growing data have recognized the significance of Response Gene to Complement (RGC)-32 in numerous tumour developments. Notwithstanding, the functional role and underlying mechanism of it in tongue squamous cell carcinoma (TSCC) remain enigmatic. Here, to identify the impact of RGC-32 in TSCC, its expression in multiple TSCC cells was measured and loss-of-function experiments in cell lines were performed to illuminate the function of it induced TSCC progression, via si-RNA knockdown, CCK-8, colony formation, wound-healing, transwell, flow cytometry and western blot assays. To clarify potential mechanism, expressions of hallmarks in epithelial-mesenchymal transition (EMT) process and PI3K/AKT signalling were assessed, and the upstream miR regulator of RGC-32 was predicted and verified by applying bioinformatic approaches and dual-luciferase reporter assay, respectively. Finally, the rescue experiments were applied to better elucidate the effect of miR-26b/RGC-32 axis in TSCC behaviours. As a result, RGC-32 was upregulated in TSCC cells and knocking down of it abrogated cell proliferation, trans-migration and invasion, whilst promoted apoptosis in TSCC, which was regulated through repressing EMT and inactivation of PI3K/AKT signalling. Subsequently, miR-26b was predicted and identified as an upstream regulator of RGC-32, and the pro-tumorigenic effect of RGC-32 was reversed by miR-26b overexpression. Collectively, our results demonstrated that RGC-32 facilitated TSCC progression, which was modulated by activations of PI3K/AKT pathway and EMT process, and reduction of its negative regulator of miR-26b. These findings highlight a novel role of miR-26b/RGC-32 axis in TSCC and underlying mechanism, encouraging a potent usage in TSCC treatment. SIGNIFICANCE OF THE STUDY: We first uncovered that Response Gene to Complement-32 played a significantly pro-tumorigenic role in tongue squamous cell carcinoma (TSCC), which was closely regulated by downregulation of miR-26b and activations of epithelial-mesenchymal transition process and PI3K/AKT signalling. These findings contribute to better understand the molecular mechanism in carcinogenesis of TSCC, and shed some light on promising strategy for TSCC therapeutics.

MiRNA-217 accelerates the proliferation and migration of bladder cancer via inhibiting KMT2D

To uncover the biological function of miRNA-217 in the progression of bladder cancer and the underlying mechanism. Potential miRNAs binding KMT2D were predicted through online bioinformatics. Their expression levels in bladder cancer tissues and adjacent ones were determined. Through Pearson correlation analysis and survival analysis, the most potential miRNA candidate (miRNA-217) that targets and regulates KMT2D in bladder cancer was selected. Subsequently, expression levels of miRNA-217 and KMT2D in non-muscle invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC) were detected. MiRNA-217 level in bladder cancer cell lines was determined as well. The interaction between KMT2D and miRNA-217 was verified by dual-luciferase reporter gene assay. Finally, regulatory effect of miRNA-217 on viability and migration in T24 and UMUC-3 cells were investigated. Five potential candidates that were upstream genes binding KMT2D were searched by bioinformatics. Among them, miRNA-217 was remarkably upregulated in bladder cancer tissues and closely linked to poor prognosis of affected patients. Moreover, dual-luciferase reporter gene assay verified the interaction between miRNA-217 and KMT2D. MiRNA-217 was able to downregulate mRNA and protein levels of KMT2D. Furthermore, knockdown of miRNA-217 attenuated viability and migration in bladder cancer cells. MiRNA-217 accelerates proliferative and migratory abilities in bladder cancer via inhibiting the level of tumor suppressor KMT2D, thereafter leading to the poor prognosis in bladder cancer patients.

Multi-Walled Carbon Nanotube-Induced Gene Expression Biomarkers for Medical and Occupational Surveillance

As the demand for multi-walled carbon nanotube (MWCNT) incorporation into industrial and biomedical applications increases, so does the potential for unintentional pulmonary MWCNT exposure, particularly among workers during manufacturing. Pulmonary exposure to MWCNTs raises the potential for development of lung inflammation, fibrosis, and cancer among those exposed; however, there are currently no effective biomarkers for detecting lung fibrosis or predicting the risk of lung cancer resulting from MWCNT exposure. To uncover potential mRNAs and miRNAs that could be used as markers of exposure, this study compared in vivo mRNA and miRNA expression in lung tissue and blood of mice exposed to MWCNTs with in vitro mRNA and miRNA expression from a co-culture model of human lung epithelial and microvascular cells, a system previously shown to have a higher overall genome-scale correlation with mRNA expression in mouse lungs than either cell type grown separately. Concordant mRNAs and miRNAs identified by this study could be used to drive future studies confirming human biomarkers of MWCNT exposure. These potential biomarkers could be used to assess overall worker health and predict the occurrence of MWCNT-induced diseases.