Collagen stiffness promoted non-muscle-invasive bladder cancer progression to muscle-invasive bladder cancer

Multi-omics characterization of esophageal squamous cell carcinoma identifies molecular subtypes and therapeutic targets

Esophageal squamous cell carcinoma (ESCC) is the predominant form of esophageal cancer and is characterized by an unfavorable prognosis. To elucidate the distinct molecular alterations in ESCC and investigate therapeutic targets, we performed a comprehensive analysis of transcriptomics, proteomics, and phosphoproteomics data derived from 60 paired treatment-naive ESCC and adjacent nontumor tissue samples. Additionally, we conducted a correlation analysis to describe the regulatory relationship between transcriptomic and proteomic processes, revealing alterations in key metabolic pathways. Unsupervised clustering analysis of the proteomics data stratified patients with ESCC into 3 subtypes with different molecular characteristics and clinical outcomes. Notably, subtype III exhibited the worst prognosis and enrichment in proteins associated with malignant processes, including glycolysis and DNA repair pathways. Furthermore, translocase of inner mitochondrial membrane domain containing 1 (TIMMDC1) was validated as a potential prognostic molecule for ESCC. Moreover, integrated kinase-substrate network analysis using the phosphoproteome nominated candidate kinases as potential targets. In vitro and in vivo experiments further confirmed casein kinase II subunit α (CSNK2A1) as a potential kinase target for ESCC. These underlying data represent a valuable resource for researchers that may provide better insights into the biology and treatment of ESCC.

A gene signature of cancer-associated fibroblasts predicts prognosis and treatment response in bladder cancer

OBJECTIVE

Due to the pivotal role cancer-associated fibroblasts (CAFs) play in tumor progression, our study aimed to develop a signature of CAFs-related gene (CRG) to predict the survival outcomes and treatment response of bladder cancer (BLCA).

METHODS

The transcriptome data and relevant clinical information about BLCA were collected from publicly available databases, including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Weighted gene co-expression network analysis was utilized to uncover CAFs-associated hub genes, and subsequently, a risk model for survival prognosis was constructed using LASSO-Cox regression. The immune microenvironment, immune infiltration, immunotherapy response, and drug sensitivity were explored using ESTIMATE, CIBERSORT, TIDE, and oncoPredict algorithms. To verify the expression of the CRGs, additional analyses were performed using online databases (HPA, CCLE, TIMER, cBioPortal, and TISCH).

RESULTS

Our study developed a CRG signature and constructed a prognostic model. Significant differences in overall survival were observed between the two risk stratifications. The risk score increased with the infiltration of CAFs and tumor staging progression, while closely correlating with immune checkpoint expression and infiltration of CD8 T cells, follicular helper T cells, regulatory T cells, activated dendritic cells, M0 macrophages, M2 macrophages, and resting mast cells. Furthermore, a higher proportion of patients in the low-risk stratification exhibited responsiveness to immunotherapy, and significant variances in sensitivity to multiple chemotherapy medications were observed between the two risk stratifications.

CONCLUSION

The construction of the risk model based on the CRG signature offers new avenues for the prognosis evaluation and development of personalized treatment strategies for BLCA.

COL6A1 expression as a potential prognostic biomarker for risk stratification of T1 high grade bladder cancer: Unveiling the aggressive nature of a distinct non-muscle invasive subtype

PURPOSE

T1 high grade (T1HG) bladder cancer (BC) is a type of non-muscle invasive BC (NMIBC) that is recognized as an aggressive subtype with a heightened propensity for progression. Current risk stratification methods for NMIBC rely on clinicopathological indicators; however, these approaches do not adequately capture the aggressive nature of T1HG BC. Thus, new, more accurate biomarkers for T1HG risk stratification are needed. Here, we enrolled three different patient cohorts and investigated expression of collagen type VI alpha 1 (COL6A1), a key component of the extracellular matrix, at different stages and grades of BC, with a specific focus on T1HG BC.

MATERIALS AND METHODS

Samples from 298 BC patients were subjected to RNA sequencing and real-time polymerase chain reaction.

RESULTS

We found that T1HG BC and muscle invasive BC (MIBC) exhibited comparable expression of COL6A1, which was significantly higher than that by other NMIBC subtypes. In particular, T1HG patients who later progressed to MIBC had considerably higher expression of COL6A1 than Ta, T1 low grade patients, and patients that did not progress, highlighting the aggressive nature and higher risk of progression associated with T1HG BC. Moreover, Cox and Kaplan-Meier survival analyses revealed a significant association between elevated expression of COL6A1 and poor progression-free survival of T1HG BC patients (multivariate Cox hazard ratio, 16.812; 95% confidence interval, 3.283-86.095; p=0.001 and p=0.0002 [log-rank test]).

CONCLUSIONS

These findings suggest that COL6A1 may be a promising biomarker for risk stratification of T1HG BC, offering valuable insight into disease prognosis and guidance of personalized treatment decisions.

A novel signature of aging-related genes associated with lymphatic metastasis for survival prediction in patients with bladder cancer

Background

The predominant and most prevalent form of metastatic bladder cancer (BCa) is lymphatic metastasis, which is associated with a highly dismal prognosis for patients. Aging-related genes (ARGs) are believed to contribute significantly to tumor development. However, the effect of ARGs on lymphatic metastasis of BCa is unclear. This research sought to establish a prognosis model based on ARGs associated with lymphatic metastasis in BCa.

Methods

We downloaded BCa data from the TCGA and GEO databases and ARGs from the Aging Atlas database. The least absolute shrinkage and selection operator (LASSO) approach was applied to obtain the characteristic ARGs of risk signature in the TCGA cohort. Verification was done using the GSE13507 dataset. The R package 'ConsensusClusterPlus' was employed to identify the molecular subtypes based on the characteristic ARGs. Protein-Protein interaction network, MCODE analysis, enrichment analysis (KEGG, GO, GSEA), and immune infiltration analysis were performed to investigate underlying mechanisms. EdU, migration and invasion assays, wound healing assays, immunofluorescence staining, and quantitative polymerase chain reaction were conducted to evaluate the impact of ELN on the proliferative, migratory, and invasive capacities of BCa cells.

Results

We identified 20 differently expressed ARGs. A four ARGs risk signature (EFEMP1, UCHL1, TP63, ELN) was constructed in the TCGA cohort. The high-risk group (category) recorded a reduced overall survival (OS) rate relative to the low-risk category (hazard ratio, 2.15; P <0.001). The risk score could predict lymphatic metastasis in TCGA cohort (AUC=0.67). The GSE13507 dataset was employed to verify the validity of this risk score. Based on the four ARGs, two distinct aging profiles (Cluster 1 and Cluster 2) were discovered utilizing the ConsensusClusterPlus, and Cluster 2 possessed a favorable OS in contrast with Cluster 1 (hazard ratio, 0.69; P =0.02). Classical tumor signaling pathways, ECM-associated signaling pathways, and immune-related signaling pathways participate in BCa progression. ELN recombinant protein affected the expression of collagen and increased migration and invasiveness in BCa cells.

Conclusion

We constructed a four-ARG risk signature and identified two aging molecular subtypes. This signature could serve as an effective survival predictor for patients with BCa.

Single-cell RNA sequencing reveals sexual diversity in the human bladder and its prospective impacts on bladder cancer and urinary tract infection

BACKGROUND

Some bladder-related diseases, such as bladder urinary tract infection (UTI) and bladder cancer (BCa), have significant six differences in incidence and prognosis. However, the molecular mechanisms underlying these sex differences are still not fully understood. Understanding the sex-biased differences in gene expression in normal bladder cells can help resolve these problems.

METHODS

We first collected published single-cell RNA sequencing (scRNA-seq) data of normal human bladders from females and males to map the bladder transcriptomic landscape. Then, Gene Ontology (GO) analysis and gene set enrichment analysis (GSEA) were used to determine the significant pathways that changed in the specific cell populations. The Monocle2 package was performed to reconstruct the differentiation trajectories of fibroblasts. In addition, the scMetabolism package was used to analyze the metabolic activity at the single-cell level, and the SCENIC package was used to analyze the regulatory network.

RESULTS

In total, 27,437 cells passed stringent quality control, and eight main cell types in human bladder were identified according to classical markers. Sex-based differential gene expression profiles were mainly observed in human bladder urothelial cells, fibroblasts, B cells, and T cells. We found that urothelial cells in males demonstrated a higher growth rate. Moreover, female fibroblasts produced more extracellular matrix, including seven collagen genes that may mediate BCa progression. Furthermore, the results showed that B cells in female bladders exhibited more B-cell activated signals and a higher expression of immunoglobulin genes. We also found that T cells in female bladders exhibited more T-cell activated signals. These different biological functions and properties of these cell populations may correlate with sex differences in UTI and BCa, and result in different disease processes and outcomes.

CONCLUSIONS

Our study provides reasonable insights for further studies of sex-based physiological and pathological disparities in the human bladder, which will contribute to the understanding of epidemiological differences in UTI and BCa.

A prognostic model for bladder cancer based on cytoskeleton-related genes

BACKGROUND

A typical cancerous growth in the urinary tract, bladder cancer (BLCA) has a dismal survival rate and a poor chance of being cured. The cytoskeleton has been shown to be tightly related to tumor invasion and metastasis. Nevertheless, the expression of genes associated with the cytoskeleton and their prognostic significance in BLCA remain unknown.

METHODS

In our study, we performed differential expression analysis of cytoskeleton-related genes between BLCA versus normal bladder tissues. According to the outcomes of this analysis of differentially expressed genes, all BLCA cases doing nonnegative matrix decomposition clustering analysis be classified into different molecular subtypes and were subjected to Immune cell infiltration analysis. We then constructed a cytoskeleton-associated gene prediction model for BLCA, and performed risk score independent prognostic analysis and receiver operating characteristic curve analyses to evaluate and validate the prognostic value of the model. Furthermore, enrichment analysis, clinical correlation analysis of prognostic models, and immune cell correlation analysis were carried out.

RESULTS

We identified 546 differentially expressed genes that are linked to the cytoskeleton, including 314 up-regulated genes and 232 down-regulated genes. All BLCA cases doing nonnegative matrix decomposition clustering analysis could be classified into 2 molecular subtypes, and we observed differences (P < .05) in C1 and C2 immune scores about 9 cell types. Next, we obtained 129 significantly expressed cytoskeleton-related genes. A final optimized model was constructed consisting of 11 cytoskeleton-related genes. Survival curves and risk assessment predicted the prognostic risk in both groups of patients with BLCA. Survival curves and receiver operating characteristic curves were used to evaluate and validate the prognostic value of the model. Significant enrichment pathways for cytoskeleton-associated genes in bladder cancer samples were explored by Gene set enrichment analysis enrichment analysis. After we obtained the risk scores, a clinical correlation analysis was performed to examine which clinical traits were related to the risk scores. Finally, we demonstrated a correlation between different immune cells.

CONCLUSION

Cytoskeleton-related genes have an important predictive value for BLCA, and the prognostic model we constructed may enable personalized treatment of BLCA.

Association between Expression of Connective Tissue Genes and Prostate Cancer Growth and Progression

To find an association between genomic features of connective tissue and pejorative clinical outcomes on radical prostatectomy specimens. We performed a retrospective analysis of patients who underwent radical prostatectomy and underwent a Decipher transcriptomic test for localized prostate cancer in our institution (n = 695). The expression results of selected connective tissue genes were analyzed after multiple t tests, revealing significant differences in the transcriptomic expression (over- or under-expression). We investigated the association between transcript results and clinical features such as extra-capsular extension (ECE), clinically significant cancer, lymph node (LN) invasion and early biochemical recurrence (eBCR), defined as earlier than 3 years after surgery). The Cancer Genome Atlas (TCGA) was used to evaluate the prognostic role of genes on progression-free survival (PFS) and overall survival (OS). Out of 528 patients, we found that 189 had ECE and 27 had LN invasion. The Decipher score was higher in patients with ECE, LN invasion, and eBCR. Our gene selection microarray analysis showed an overexpression in both ECE and LN invasion, and in clinically significant cancer for COL1A1, COL1A2, COL3A1, LUM, VCAN, FN1, AEBP1, ASPN, TIMP1, TIMP3, BGN, and underexpression in FMOD and FLNA. In the TCGA population, overexpression of these genes was correlated with worse PFS. Significant co-occurrence of these genes was observed. When presenting overexpression of our gene selection, the 5-year PFS rate was 53% vs. 68% (p = 0.0315). Transcriptomic overexpression of connective tissue genes correlated to worse clinical features, such as ECE, clinically significant cancer and BCR, identifying the potential prognostic value of the gene signature of the connective tissue in prostate cancer. TCGAp cohort analysis showed a worse PFS in case of overexpression of the connective tissue genes.

Bladder Wall Stiffness after Cystectomy in Bladder Cancer Patients: A Preliminary Study

Bladder cancer (BlCa), specifically urothelial carcinomas, is a heterogeneous disease that derives from the urothelial lining. Two main classes of BlCa are acknowledged: the non-muscle invasive BlCa and the muscle-invasive BlCa; the latter constituting an aggressive disease which invades locally and metastasizes systemically. Distinguishing the specific microenvironment that cancer cells experience between mucosa and muscularis propria layers can help elucidate how these cells acquire invasive capacities. In this work, we propose to measure the micromechanical properties of both mucosa and muscularis propria layers of the bladder wall of BlCa patients, using atomic force microscopy (AFM). To do that, two cross-sections of both the macroscopically normal urinary bladder wall and the bladder wall adjacent to the tumor were collected and immediately frozen, prior to AFM samples analysis. The respective "twin" formalin-fixed paraffin-embedded tissue fragments were processed and later evaluated for histopathological examination. H&E staining suggested that tumors promoted the development of muscle-like structures in the mucosa surrounding the neoplastic region. The average Young's modulus (cell stiffness) in tumor-adjacent specimens was significantly higher in the muscularis propria than in the mucosa. Similarly, the tumor-free specimens had significantly higher Young's moduli in the muscularis propria than in the urothelium. Young's moduli were higher in all layers of tumor-adjacent tissues when compared with tumor-free samples. Here we provide insights into the stiffness of the bladder wall layers, and we show that the presence of tumor in the surrounding mucosa leads to an alteration of its smooth muscle content. The quantitative assessment of stiffness range here presented provides essential data for future research on BlCa and for understanding how the biomechanical stimuli can modulate cancer cells' capacity to invade through the different bladder layers.

The pro-invasive factor COL6A2 serves as a novel prognostic marker of glioma

Background

Glioma is an incurable malignant lesion with poor outcome characterized by easy recurrence after surgery with or without radiotherapy and chemotherapy. Studies have shown that COL6A2 is closely related to the tumorigenesis and development of a variety of tumors. However, the role of COL6A2 in glioma and the relationship between COL6A2 and tumor infiltrating immune cells remain unclear.

Methods

Western blot, real-time PCR, a tissue microarray and immunohistochemistry were applied to detect COL6A2 mRNA and protein amounts in glioma, and all experiments were repeated three times. A tissue microarray of glioma samples was used for prognostic analysis. Detection of COL6A2 co-expression with immune genes using immunohistochemical methods, and tumor modeling using nude mice for prevention and treatment studies. Based on the mRNA expression of COL6A2, patients with glioma in TCGA were divided into the low and high COL6A2 expression groups, and GO and KEGG pathway analyses were performed. A PPI network was constructed using STRING, and the associations of COL6A2 with tumor-infiltrating immune cells and immune genes were analyzed in the CIBERSORT and TISIDB databases. COL6A2 mRNA and protein amounts were increased in glioma.

Results

Multiple-database and tissue microarray analyses showed that COL6A2 expression in glioma was associated with poor prognosis, Tissue microarray showed that COL6A2 was the highest expressed in WHO IV and significantly higher in TCGA-GBM than in TCGA-LGG. Immunohistochemistry can well demonstrate the co-expression of COL6A2 with immune genes in a tumor model established in nude mice, showing that interference with COL6A2 expression may have an inhibitory effect on tumors. The mRNA expression of COL6A2 was involved in 22 KEGG pathways, and GSEA analysis showed that 28 and 57 gene sets were significantly enriched at nominal p values <0.01 and <0.05, respectively, protein network revealed a tight interaction between COL6A2 and SPARC. The CIBERSORT database indicated that COL6A2 was correlated with 15 types of tumor-infiltrating immune cells, including M2 macrophages, CD8 T cells, neutrophils, gamma delta T cells, activated CD4 memory T cells, follicular helper T cells, M0 macrophages, M1 macrophages, regulatory T cells (Tregs), activated NK cells, eosinophils, activated mast cells, monocytes, activated dendritic cells, and resting CD4 memory T cells. The TISIDB database indicated that COL6A2 was significantly correlated with lymphocytes such as regulatory T cell, Type 17 T helper cell, Type 1 T helper cell, and immunomodulatory genes. In addition, COL6A2-related immune regulatory genes show that most immune regulatorygenes have prognostic value for glioma, and high-risk immune genes are notconducive to the survival of glioma patients.

Conclusions

COL6A2-related immune regulatory genes show that most immune regulatory genes have prognostic value for glioma, and high-risk immune genes are not conducive to the survival of glioma patients. COL6A2 may be a novel potential prognostic biomarker of glioma and associated with tumor-infiltrating immune cells in the tumor microenvironment, and interference with COL6A2 expression can inhibit tumor growth, which suggests COL6A2 as a potential target for future treatment.

Promotion of Bladder Cancer Cell Metastasis by 2-Mercaptobenzothiazole via Its Activation of Aryl Hydrocarbon Receptor Transcription: Molecular Dynamics Simulations, Cell-Based Assays, and Machine Learning-Driven Prediction

2-Mercaptobenzothiazole (MBT) is an industrial chemical widely used for rubber products, corrosion inhibitors, and polymer materials with multiple environmental and exposure pathways. A growing body of evidence suggests its potential bladder cancer (BC) risk as a public health concern; however, the molecular mechanism remains poorly understood. Herein, we demonstrate the activation of the aryl hydrocarbon receptor (AhR) by MBT and reveal key events in carcinogenesis associated with BC. MBT alters conformational changes of AhR ligand binding domain (LBD) as revealed by 500 ns molecular dynamics simulations and activates AhR transcription with upregulation of AhR-target genes CYP1A1 and CYP1B1 to approximately 1.5-fold. MBT upregulates the expression of MMP1, the cancer cell metastasis biomarker, to 3.2-fold and promotes BC cell invasion through an AhR-mediated manner. MBT is further revealed to induce differentially expressed genes (DEGs) most enriched in cancer pathways by transcriptome profiling. The exposure of MBT at environmentally relevant concentrations induces BC risk via AhR signaling disruption, transcriptome aberration, and malignant cell metastasis. A machine learning-based model with an AUC value of 0.881 is constructed to successfully predict 31 MBT analogues. Overall, we provide molecular insight into the BC risk of MBT and develop an effective tool for rapid screening of AhR agonists.

Tyrosine kinase receptor RON activates MAPK/RSK/CREB signal pathway to enhance CXCR4 expression and promote cell migration and invasion in bladder cancer

Bladder cancer (BC) is one of the most lethal malignancies worldwide. The poor survival may be due to a high proportion of tumor metastasis. RON and CXCR4 are the key regulators of cell motility in BC, while the relationship between RON and CXCR4 remains elusive. In the present study, immunohistochemistry analysis of BC and adjacent normal tissues found that higher RON expression was positively correlated with CXCR4 expression. Inhibiting and replenishing RON level were used to regulate CXCR4 expression, observing the effects on migration and invasion of BC cells. Overexpression of RON reversed the inhibited cell migration and invasion following siCXCR4 treatment. Conversely, overexpression of CXCR4 restored the inhibition of cell migration and invasion caused by shRON. The activation of RON-MAPK/RSK/CREB pathway was demonstrated in BC cells under MSP treatment. Dual luciferase and CHIP assay showed that p-CREB targeted CXCR4 by binding to its CRE sequence. RON knockdown suppressed BC tumor growth in xenograft mouse tumors, accompanied by reduced expression of CXCR4. In conclusion, our data adds evidence that RON, a membrane tyrosine kinase receptor, promotes BC migration and invasion not only by itself, but also by activating MAPK/RSK/CREB signaling pathway to enhance CXCR4 expression.

The dynamic roles of the bladder tumour microenvironment

Bladder cancer is a prevalent but currently understudied cancer type and patient outcomes are poor when it progresses to the muscle-invasive stage. Current research in bladder cancer focuses on the genetic and epigenetic alterations occurring within the urothelial cell compartment; however, the stromal compartment receives less attention. Dynamic changes and intercellular communications occur in the tumour microenvironment (TME) of the bladder - a new concept and niche that we designate as the bladder TME (bTME) - during tumour evolution, metastatic progression and in the context of therapeutic response. Collagens and their cognate receptors, the discoidin domain receptors, have a role in various steps of the metastatic cascade and in immune checkpoint resistance. Furthermore, the presence of another TME niche, the metastatic TME (met-TME), is a novel concept that could support divergent progression of metastatic colonization in different organs, resulting in distant metastases with distinct characteristics and genetics from the primary tumour. The stroma has divergent roles in mediating therapeutic response to BCG immunotherapy and immune checkpoint inhibitors, as well as conventional chemotherapy or trimodality therapy (that is, maximal transurethral resection of bladder tumour, chemotherapy and radiotherapy). The local bTME and distant met-TME are currently conceptually and therapeutically unexploited niches that should be actively investigated. New biological insights from these TMEs will enable rational design of strategies that co-target the tumour and stroma, which are expected to improve the outcomes of patients with advanced bladder cancer.

Integrative transcriptional characterization of cell cycle checkpoint genes promotes clinical management and precision medicine in bladder carcinoma

Background

The aberrant regulation of cell cycle is significantly correlated with cancer carcinogenesis and progression, in which cell cycle checkpoints control phase transitions, cell cycle entry, progression, and exit. However, the integrative role of cell cycle checkpoint-related genes (CRGs) in bladder carcinoma (BC) remains unknown.

Methods

The transcriptomic data and clinical features of BC patients were downloaded from The Cancer Genome Atlas (TCGA), used to identify CRGs correlated with overall survival (OS) by univariate Cox regression analysis. Then, the multivariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses further developed a prognostic CRG signature, which was validated in three external datasets retrieved from Gene Expression Omnibus (GEO). The receiver operating characteristic curve (ROC) analysis was conducted for evaluating the performance of the CRG signature in prognosis prediction. RNA sequencing (RNA-Seq) was performed to explore the expression difference in the identified CRGs between tumor and normal tissue samples from 11 BC patients in the local cohort. Ultimately, genomic profiles and tumor microenvironment (TME), and the Genomics of Drug Sensitivity in Cancer (GDSC) were investigated to guide precision treatment for BC patients with different CRG features.

Results

The novel constructed 23-CRG prognostic signature could stratify BC patients into high-risk and low-risk groups with significantly different outcomes (median OS: 13.64 vs. 104.65 months). Notably, 19 CRGs were the first to be identified as being associated with BC progression. In three additional validation datasets (GSE13507, GSE31684, and GSE32548), higher CRG scores all indicated inferior survival, demonstrating the robust ability of the CRG signature in prognosis prediction. Moreover, the CRG signature as an independent prognostic factor had a robust and stable risk stratification for BC patients with different histological or clinical features. Then, a CRG signature-based nomogram with a better performance in prognostic prediction [concordance index (C-index): 0.76] was established. Functional enrichment analysis revealed that collagen-containing extracellular matrix (ECM), and ECM-related and MAPK signaling pathways were significantly associated with the signature. Further analysis showed that low-risk patients were characterized by particularly distinctive prevalence of FGFR3 (17.03% vs. 6.67%, p < 0.01) and POLE alterations (7.97% vs. 2.50%, p < 0.05), and enrichment of immune infiltrated cells (including CD8+ T cells, CD4+ naïve T cells, follicular helper T cells, Tregs, and myeloid dendritic cells). RNA-seq data in our local cohort supported the findings in the differentially expressed genes (DEGs) between tumor and normal tissue samples, and the difference in TME between high-risk and low-risk groups. Additionally, CRG signature score plus FGFR3 status divided BC patients into four molecular subtypes, with distinct prognosis, TME, and transcriptomic profiling of immune checkpoint genes. Of note, CRG signature score plus FGFR3 status could successfully distinguish BC patients who have a higher possibility of response to immunotherapy or chemotherapy drugs.

Conclusions

The CRG signature is a potent prognostic model for BC patients, and in combination with FGFR3 alterations, it had more practical capacity in the prediction of chemotherapy and immunotherapy response, helping guide clinical decision-making.

COL1A1: A novel oncogenic gene and therapeutic target in malignancies

Collagen type I alpha 1 (COL1A1), a member of the collagen family, is involved in epithelial-mesenchymal transition, which is closely linked to malignant tumorigenesis. COL1A1 is highly expressed in various cancers and regulates various cellular processes, including cell proliferation, metastasis, apoptosis, and cisplatin resistance. COL1A1 is also associated with cancer progression and prognosis; elevated COL1A1 expression is associated with poor prognosis in cancer patients. However, the main role of COL1A as a cancer-promoting factor in specific tumors has not been reported. Additionally, the protein levels and mechanisms of action of this protein differ among tumor types. This review discusses current research progress concerning COL1A1 in different tumor types, and then summarizes its contributions to cancer progression, thus providing a basis for follow-up research and potential targets for cancer treatment.

Clinical potential of the Hippo-YAP pathway in bladder cancer

Bladder cancer (BC) is one of the world’s most frequent cancers. Surgery coupled with adjuvant platinum-based chemotherapy is the current standard of therapy for BC. However, a high proportion of patients progressed to chemotherapy-resistant or even neoplasm recurrence. Hence, identifying novel treatment targets is critical for clinical treatment. Current studies indicated that the Hippo-YAP pathway plays a crucial in regulating the survival of cancer stem cells (CSCs), which is related to the progression and reoccurrence of a variety of cancers. In this review, we summarize the evidence that Hippo-YAP mediates the occurrence, progression and chemotherapy resistance in BC, as well as the role of the Hippo-YAP pathway in regulating bladder cancer stem-like cells (BCSCs). Finally, the clinical potential of Hippo-YAP in the treatment of BC was prospected.

An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer

Simple Summary

Bladder cancer is evidently a challenge as far as its prognosis and treatment are concerned. The investigation of potential biomarkers and therapeutic targets is indispensable and still in progress. Most studies attempt to identify differential signatures between distinct molecular tumor subtypes. Therefore, keeping in mind the heterogeneity of urinary bladder tumors, we attempted to identify a consensus gene-related signature between the common expression profile of bladder cancer and control samples. In the quest for substantive features, we were able to identify key hub genes, whose signatures could hold diagnostic, prognostic, or therapeutic significance, but, primarily, could contribute to a better understanding of urinary bladder cancer biology.

Abstract

Bladder cancer (BCa) is one of the most prevalent cancers worldwide and accounts for high morbidity and mortality. This study intended to elucidate potential key biomarkers related to the occurrence, development, and prognosis of BCa through an integrated bioinformatics analysis. In this context, a systematic meta-analysis, integrating 18 microarray gene expression datasets from the GEO repository into a merged meta-dataset, identified 815 robust differentially expressed genes (DEGs). The key hub genes resulted from DEG-based protein–protein interaction and weighted gene co-expression network analyses were screened for their differential expression in urine and blood plasma samples of BCa patients. Subsequently, they were tested for their prognostic value, and a three-gene signature model, including COL3A1, FOXM1, and PLK4, was built. In addition, they were tested for their predictive value regarding muscle-invasive BCa patients’ response to neoadjuvant chemotherapy. A six-gene signature model, including ANXA5, CD44, NCAM1, SPP1, CDCA8, and KIF14, was developed. In conclusion, this study identified nine key biomarker genes, namely ANXA5, CDT1, COL3A1, SPP1, VEGFA, CDCA8, HJURP, TOP2A, and COL6A1, which were differentially expressed in urine or blood of BCa patients, held a prognostic or predictive value, and were immunohistochemically validated. These biomarkers may be of significance as prognostic and therapeutic targets for BCa.

COL8A1 Predicts the Clinical Prognosis of Gastric Cancer and Is Related to Epithelial-Mesenchymal Transition

Background

Gastric cancer (GC) is the fifth most common malignant tumor and the third leading cause of cancer-related deaths. Because GC has the characteristics of high heterogeneity, unclear mechanism, limited treatment methods, and low five-year survival rate, it is necessary to find the prognostic biomarkers of GC and explore the mechanism of GC.

Methods

We first identified differentially expressed genes (DEGs) between gastric cancer and normal gastric cells through expression analysis. A protein-protein interaction (PPI) network was constructed to find tightly connected modules. We performed survival analysis on the DEGs in the modules to identify genes with prognostic significance. Gene set enrichment analysis (GSEA) was used to identify gene enrichment pathways. Finally, we used our own collected clinical samples of 119 gastric adenocarcinoma (STAD) tissues and 40 normal gastric tissues to perform immunohistochemical (IHC) staining to verify the differential expression of COL8A1 in STAD tissues and normal gastric tissues and its correlation with epithelial-mesenchymal transition- (EMT-) related factors.

Results

We identified 356 DEGs through differential expression analysis. Through PPI analysis and survival analysis, we determined that the collagen type VII alpha-1 chain (COL8A1) gene has prognostic significance. GSEA analysis showed that COL8A1 was significantly enriched in the EMT. IHC results showed that COL8A1 was upregulated in STAD tissues and could be used as an independent prognostic factor and was related to EMT.

Conclusion

This study shows that COL8A1 is related to the prognosis of GC patients and might affect the progress of GC through the EMT pathway. Therefore, COL8A1 may be a biomarker for predicting the prognosis of GC.

The LINC01929/miR-6875-5p/ADAMTS12 Axis in the ceRNA Network Regulates the Development of Advanced Bladder Cancer

Considering its speedy development and extremely low 5-year overall survival rate worldwide, bladder cancer (BCa) is one of the most common and highly malignant tumors. Increasing evidence suggests that protein-coding mRNAs and non-coding RNAs, including long non-coding RNAs (lncRNAs) and micro RNAs (miRNAs), play an essential role in regulating the biological processes of cancer. To investigate the molecular regulation associated with poor prognosis during advanced BCa development, we constructed a competitive endogenous RNA (ceRNA) network. Using transcriptome profiles from The Cancer Genome Atlas and Gene Expression Omnibus databases, we performed differential expression (DE) analysis, weighted gene co-expression network analysis, functional enrichment analysis, survival analysis, prediction of miRNA targeting, and Pearson correlation analysis. Through layers of selection, 8 lncRNAs-28 mRNAs and 8 miRNAs-28 mRNAs pairs shared similar expression patterns, constituting a core ceRNA regulatory network related to the invasion, progression, and metastasis of advanced clinical stage (ACS) BCa. Subsequently, we conducted real time qPCR, western blotting, and immunohistochemistry to validate expression trend bioinformatics analysis on 3, 2, and 3 differentially expressed mRNAs, lncRNAs, and miRNAs, respectively. The most significantly differentially expressed LINC01929, miR-6875-5p and ADAMTS12 were selected for in vitro experiments to assess the functional role of the LINC01929/miR-6875-5p/ADAMTS12 axis. RNA pull-down, luciferase assays, and rescue assays were performed to examine the binding of LINC01929 and miR-6875-5p. Increasing trends in COL6A1, CDH11, ADAMTS12, LINC01705, and LINC01929 expression variation were verified as consistent with previous DE analysis results in ACS-BCa, compared with low clinical stage (LCS) BCa. Expression trends in parts of these RNAs, such as hsa-miR-6875-5p, hsa-miR-6784-5p, COL6A1, and CDH11, were measured in accordance with DE analysis in LCS-BCa, compared with normal bladder urothelium. Through experimental validation, the cancer-promoting molecule ADAMST12 was found to play a key role in the development of advanced BCa. Functionally, ADAMTS12 knockdown inhibited the progression of bladder cancer. Overexpression of LINC01929 promoted bladder cancer development, while overexpression of miR-6785-5p inhibited bladder cancer development. Mechanistically, LINC01929 acted as a sponge for miR-6785-5p and partially reversed the role of miR-6785-5p. Our findings provide an elucidation of the molecular mechanism by which advanced bladder cancer highly expressed LINC01929 upregulates ADAMTS12 expression through competitive adsorption of miR-6875-5p. It provides a new target for the prognosis and diagnosis of advanced bladder cancer.

A Multiomics Profiling Based on Online Database Revealed Prognostic Biomarkers of BLCA

Background

Bladder cancer (BLCA) is one of the most common urological malignancies globally, posing a severe threat to public health. In combination with protein-protein interaction (PPI) network analysis of proteomics, Gene Set Variation Analysis (GSVA) and “CancerSubtypes” package of R software for transcriptomics can help identify biomarkers related to BLCA prognosis. This will have significant implications for prevention and treatment.

Method

BLCA data were downloaded from The Cancer Genome Atlas (TCGA) database and GEO database (GSE13507). GSVA analysis converted the gene expression matrix to the gene set expression matrix. “CancerSubtypes” classified patients into three subtypes and established a prognostic model based on differentially expressed gene sets (DEGSs) among the three subtypes. For genes from prognosis-related DEGSs, functional and pathway enrichment analyses and PPI network analysis were carried out. The Human Protein Atlas (HPA) database was used for validation. Finally, the proportion of tumor-infiltrating immune cells (TIICs) was determined using the CIBERSORT algorithm.

Results

In total, 414 tumor samples and 19 adjacent-tumor samples were obtained from TCGA, with 145 samples belonging to subtype A, 126 samples belonging to subtype B, and 136 samples belonging to subtype C. Then, we identified 83 DEGSs and constituted a prognostic signature with two of them: “GSE1460_CD4_THYMOCYTE_VS_THYMIC_STROMAL_CELL_DN” and “MODULE_253.” Finally, five subnets of two PPI networks were established, and nine core proteins were obtained: CDH2, COL1A1, EIF2S2, PSMA3, NAA10, DNM1L, TUBA4A, KIF11, and KIF23. The HPA database confirmed the expression of the nine core proteins in BLCA tissues. Furthermore, EIF2S2, PSMA3, DNM1L, and TUBA4A could be novel BLCA prognostic biomarkers.

Conclusions

In this study, we discovered two gene sets linked to BLCA prognosis. PPI analysis confirmed the network's core proteins, and several newly discovered biomarkers of BLCA prognosis were identified.

High Stromal SFRP2 Expression in Urothelial Carcinoma Confers an Unfavorable Prognosis

Background

Urothelial carcinoma (UC) patients often bear clinical and genetic heterogeneity, which may differ in management and prognosis. Especially, patients with advanced/metastatic UC generally have a poor prognosis and survive for only few months. The Wnt/β-catenin signaling is found to be highly activated in several cancers, including UC. However, accumulated evidence has shown discordance between the Wnt/β-catenin signaling and UC carcinogenesis. Accordingly, we aim to get a better understanding of the molecular characterization of UC, focusing on the Wnt signaling, which may add value to guiding management more precisely.

Patients and Methods

Clinical data and pathological features were retrospectively surveyed. The correlations of secreted Frizzled-related protein 2 (SFRP2) immunoexpression with clinicopathological features were analyzed by Pearson's chi-square test. The Kaplan-Meier method with a log-rank test was employed to plot survival curves. All significant features from the univariate analysis were incorporated into the Cox regression model for multivariate analysis.

Results

Following data mining on a transcriptome dataset (GSE31684), we identified that 8 transcripts in relation to the Wnt signaling pathway (GO: 0016055) were significantly upregulated in advanced/metastatic bladder tumors. Among these transcripts, the SFRP2 level showed the most significant upregulation. Additionally, as SFRP2 is a putative Wnt inhibitor and may be expressed by stroma, we were interested in examining the immunoexpression and clinical relevance of stromal and tumoral SFRP2 in our urothelial carcinoma cohorts containing 295 urinary bladder UC (UBUC) and 340 upper urinary tract UC (UTUC) patients. We observed that high SFRP2 expression in stroma but not in tumors is significantly linked to aggressive UC features, including high tumor stage and histological grade, positive nodal metastasis, the presence of vascular and perineural invasion, and high mitotic activity in UBUC and UTUC. Moreover, high stromal SFRP2 expression significantly and independently predicted worse clinical outcomes in UBUC and UTUC. Utilizing bioinformatic analysis, we further noticed that stromal SFRP2 may link epithelial-mesenchymal transition (EMT) to UC progression.

Conclusion

Collectively, these results imply that stromal SFRP2 may exert oncogenic function beyond its Wnt antagonistic ability, and stromal SFRP2 expression can provide prognostic and therapeutic implications for UC patients.

Gemcitabine-Resistant Biomarkers in Bladder Cancer are Associated with Tumor-Immune Microenvironment

To identify key biomarkers in gemcitabine (GEM)-resistant bladder cancer (BCa) and investigate their associations with tumor-infiltrating immune cells in a tumor immune microenvironment, we performed the present study on the basis of large-scale sequencing data. Expression profiles from the Gene Expression Omnibus GSE77883 dataset and The Cancer Genome Atlas BLCA dataset were analyzed. Both BCa development and GEM-resistance were identified to be immune-related through evaluating tumor-infiltrating immune cells. Eighty-two DEGs were obtained to be related to GEM-resistance. Functional enrichment analysis demonstrated they were related to regulation of immune cells proliferation. Protein–protein interaction network selected six key genes (CAV1, COL6A2, FABP4, FBLN1, PCOLCE, and CSPG4). Immunohistochemistry confirmed the down-regulation of the six key genes in BCa. Survival analyses revealed the six key genes were significantly associated with BCa overall survival. Correlation analyses revealed the six key genes had high infiltration of most immune cells. Gene set enrichment analysis further detected the key genes might regulate GEM-resistance through immune response and drug metabolism of cytochrome P450. Next, microRNA-gene regulatory network identified three key microRNAs (hsa-miR-124-3p, hsa-miR-26b-5p, and hsa-miR-192-5p) involved in GEM-resistant BCa. Connectivity Map analysis identified histone deacetylase inhibitors might circumvent GEM-resistance. In conclusion, CAV1, COL6A2, FABP4, FBLN1, PCOLCE, and CSPG4 were identified to be critical biomarkers through regulating the immune cell infiltration in an immune microenvironment of GEM-resistance and could act as promising treatment targets for GEM-resistant muscle-invasive BCa.

USP3 promotes gastric cancer progression and metastasis by deubiquitination-dependent COL9A3/COL6A5 stabilisation

As an important regulator of intracellular protein degradation, the mechanism of the deubiquitinating enzyme family in tumour metastasis has received increasing attention. Our previous study revealed that USP3 promotes tumour progression and is highly expressed in gastric cancer (GC). Herein, we report two critical targets, COL9A3 and COL6A5, downstream of USP3, via the isobaric tags for relative and absolute quantification technique. Mechanistically, we observed that USP3 interacted with and stabilised COL9A3 and COL6A5 via deubiquitination in GC. Importantly, we found that COL9A3 and COL6A5 were essential mediators of USP3-modulated oncogenic activity in vitro and in vivo. Examination of clinical samples confirmed that elevated expression of USP3, concomitant with increased COL9A3 and COL6A5 abundance, correlates with human GC progression. These data suggest that USP3 promotes GC progression and metastasis by deubiquitinating COL9A3 and COL6A5. These findings identify a mechanism of GC metastasis regarding USP3-mediated deubiquitinating enzyme activity and suggest potential therapeutic targets for GC management.

Causal contributors to tissue stiffness and clinical relevance in urology

Mechanomedicine is an emerging field focused on characterizing mechanical changes in cells and tissues coupled with a specific disease. Understanding the mechanical cues that drive disease progression, and whether tissue stiffening can precede disease development, is crucial in order to define new mechanical biomarkers to improve and develop diagnostic and prognostic tools. Classically known stromal regulators, such as fibroblasts, and more recently acknowledged factors such as the microbiome and extracellular vesicles, play a crucial role in modifications to the stroma and extracellular matrix (ECM). These modifications ultimately lead to an alteration of the mechanical properties (stiffness) of the tissue, contributing to disease onset and progression. We describe here classic and emerging mediators of ECM remodeling, and discuss state-of-the-art studies characterizing mechanical fingerprints of urological diseases, showing a general trend between increased tissue stiffness and severity of disease. Finally, we point to the clinical potential of tissue stiffness as a diagnostic and prognostic factor in the urological field, as well as a possible target for new innovative drugs.

Prognostic Prediction, Immune Microenvironment, and Drug Resistance Value of Collagen Type I Alpha 1 Chain: From Gastrointestinal Cancers to Pan-Cancer Analysis

Background: Gastrointestinal cancers patients might experience multiple primary tumors in the digestive tract. Therefore, identifying potential biomarkers can help us better understand the underlying mechanism. From the GEO database, four profiles of gastrointestinal cancers were gathered for the screening process, and six hub genes were found by bioinformatics analysis. Collagen type I alpha 1 chain (COL1A1), one of the hub genes, is a component of the extracellular matrix and is critical for tumor microenvironment. However, the expression level, signaling pathway, prognostic prediction, and immunological value of COL1A1 in different cancers remain unclear.

Methods: We comprehensively analyzed gene expression and genetic alteration patterns of COL1A1 among 33 types of malignancies from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression projects. Besides, we explored the correlation of COL1A1 with cancer prognosis, immune infiltrates, PD-L1, tumor mutational burden (TMB)/microsatellite instability status (MSI), and the pathway and drug sensitivity of co-expressed genes.

Results: The results showed that COL1A1 was highly expressed and associated with poor prognosis in the majority of cancers. The most common alteration type of COL1A1 was missense mutation, and COL1A1 was associated with poor prognosis in KIRP, LGG, MESO, SKCM, and STAD. For the immunologic significance, COL1A1 expression was closely related to high TMB in THYM, LAML, ACC, KICH, PRAD, and LGG, and high MSI in TGCT, MESO, PRAD, COAD, SARC, and CESC. In addition, COL1A1 was positively correlated with the abundance of CAFs, macrophages, and tumor-infiltrating lymphocytes. However, it was negatively correlated with CD8⁺ T cells mainly in CESC, HNSC-HPV+, and SKCM. Besides, as a component of the extracellular matrix, COL1A1 was involved in the activation of epithelial-mesenchymal transition (EMT), and high expression of HTRA1 was resistant to multiple drugs.

Conclusion:COL1A1 can serve as a prognostic and immunological biomarker in different cancers.

Blood-based protein biomarkers in bladder urothelial tumors

Bladder cancer (BC) is the fifth most common cancer with a high prevalence rate. It is classically classified in two groups, namely non-muscle invasive (NMIBC) and muscle invasive (MIBC). NMIBC accounts for 75% of cases and has a better prognosis than MIBC. However, 30-50% of the NMIBC patients will show recurrences throughout their lives, and about 10-20% of them will progress to MIBC, with frequent metastasis and a reduced survival rate. The diagnosis of bladder cancer is confirmed by direct visualization of the tumour and other mucosal abnormalities with endoscopic excision using cystoscopy and transurethral resection of the bladder (TURBT). An adequate TURBT requires complete resection of all visible tumour with appropriate sampling of the bladder to assess the depth of invasion. However, for many years, researchers have attempted to identify and utilise urinary markers for bladder cancer detection. Voided urine cytology has been the mainstay of urine-based diagnosis of bladder cancer since originally described by Papanicolau and Marshall. Nonetheless, urine cytology has several drawbacks, including a poor sensitivity for low-grade/stage tumours, a lack of interobserver consistency and a variable range of readings (e.g., atypical, atypical-suspicious, non-diagnostic). These shortcomings have inspired the search for more sensitive bladder cancer biomarkers. To bring precision medicine to genitourinary oncology, the analysis of the plasma/serum wide genome and proteome offers promising possibilities.

Extracellular matrix-related genes play an important role in the progression of NMIBC to MIBC: a bioinformatics analysis study

Bladder cancer is the 11th most common cancer in the world. Bladder cancer can be roughly divided into muscle invasive bladder cancer (MIBC) and non-muscle invasive bladder cancer (NMIBC). The aim of the present study was to identify the key genes and pathways associated with the progression of NMIBC to MIBC and to further analyze its molecular mechanism and prognostic significance. We analyzed microarray data of NMIBC and MIBC gene expression datasets (GSE31684) listed in the Gene Expression Omnibus (GEO) database. After the dataset was analyzed using R software, differentially expressed genes (DEGs) of NMIBC and MIBC were identified. These DEGs were analyzed using Gene Ontology (GO) enrichment, KOBAS-Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) analysis. The effect of these hub genes on the survival of bladder cancer patients was analyzed in The Cancer Genome Atlas (TCGA) database. A total of 389 DEGs were obtained, of which 270 were up-regulated and 119 down-regulated. GO and KEGG pathway enrichment analysis revealed that DEGs were mainly involved in the pathway of protein digestion and absorption, extracellular matrix (ECM) receiver interaction, phantom, toll-like receptor (TLR) signaling pathway, focal adhesion, NF-κB signaling pathway, PI3K/Akt signaling pathway, and other signaling pathways. Top five hub genes COL1A2, COL3A1, COL5A1, POSTN, and COL12A1 may be involved in the development of MIBC. These results may provide us with a further understanding of the occurrence and development of MIBC, as well as new targets for the diagnosis and treatment of MIBC in the future.

Tumor extracellular matrix: lessons from the second-harmonic generation microscopy

Extracellular matrix (ECM) represents more than a mere intercellular cement. It is physiologically active in cell communication, adhesion and proliferation. Collagen is the most abundant protein, making up to 90% of ECM, and 30% of total protein weight in humans. Second-harmonic generation (SHG) microscopy represents an important tool to study collagen organization of ECM in freshly unfixed tissues and paraffin-embedded tissue samples. This manuscript aims to review some of the applications of SHG microscopy in Oncologic Pathology, mainly in the study of ECM of epithelial tumors. It is shown how collagen parameters measured by this technique can aid in the differential diagnosis and in prognostic stratification. There is a tendency to associate higher amount, lower organization and higher linearity of collagen fibers with tumor progression and metastasizing. These represent complex processes, in which matrix remodeling plays a central role, together with cancer cell genetic modifications. Integration of studies on cancer cell biology and ECM are highly advantageous to give us a more complete picture of these processes. As microscopic techniques provide topographic information allied with biologic characteristics of tissue components, they represent important tools for a more complete understanding of cancer progression. In this context, SHG has provided significant insights in human tumor specimens, readily available for Pathologists.

Identification of vascular dementia and Alzheimer's disease hub genes expressed in the frontal lobe and temporal cortex by weighted co-expression network analysis and construction of a protein-protein interaction

Background: It is difficult to distinguish cognitive decline due to AD from that sustained by cerebrovascular disease in view of the great overlap. It is uncertain in the molecular biological pathway behind AD and VaD.Objective: Our study aimed to explore the hub molecules and their associations with each other to identify potential biomarkers and therapeutic targets for the AD and VaD.Methods: We screened the differentially expressed genes of AD and VaD, used weighted gene co-expression network analysis and then constructed a VaD-AD-specific protein-protein interaction network with functional annotation to their related metabolic pathways. Finally, we performed a ROC curve analysis of hub proteins to get an idea about their diagnostic value.Results: In the frontal lobe and temporal cortex, hub genes were identified. With regard to VaD, there were only three hub genes which encoded the neuropeptides, SST, NMU and TAC1. The AUC of these genes were 0.804, 0.768 and 0.779, respectively. One signature was established for these three hub genes with AUC of 0.990. For the identification of AD and VaD, all hub genes were receptors. These genes included SH3GL2, PROK2, TAC3, HTR2A, MET, TF, PTH2R CNR1, CHRM4, PTPN3 and CRH. The AUC of these genes were 0.853, 0.859, 0.796, 0.775, 0.706, 0.677, 0.696, 0.668 and 0.652, respectively. The other signature was built for eleven hub genes with AUC of 0.990.Conclusion: In the frontal lobe and temporal cortex regions, hub genes are used as diagnostic markers, which may provide insight into personalized potential biomarkers and therapeutic targets for patients with VaD and AD.

Identification of the potential biomarkers in patients with glioma: a weighted gene co-expression network analysis

Glioma is the most common brain tumor with high mortality. However, there are still challenges for the timely and accurate diagnosis and effective treatment of the tumor. One hundred and twenty-one samples with grades II, III and IV from the Gene Expression Omnibus database were used to construct gene co-expression networks to identify hub modules closely related to glioma grade, and performed pathway enrichment analysis on genes from significant modules. In gene co-expression network constructed by 2345 differentially expressed genes from 121 gene expression profiles for glioma, we identified the black and blue modules that associated with grading. The module preservation analysis based on 118 samples indicates that the two modules were replicable. Enrichment analysis showed that the extracellular matrix genes were enriched for blue module, while cell division genes were enriched for black module. According to survival analysis, 21 hub genes were significantly up-regulated and one gene was significantly down-regulated. What’s more, IKBIP, SEC24D, and FAM46A are the genes with little attention among the 22 hub genes. In this study, IKBIP, SEC24D, and FAM46A related to glioma were mentioned for the first time to the current knowledge, which might provide a new idea for us to study the disease in the future. IKBIP, SEC24D and FAM46A among the 22 hub genes identified that are related to the malignancy degree of glioma might be used as new biomarkers to improve the diagnosis, treatment and prognosis of glioma.

Reciprocal Interplay Between Fibrillar Collagens and Collagen-Binding Integrins: Implications in Cancer Progression and Metastasis

Cancers are complex ecosystems composed of malignant cells embedded in an intricate microenvironment made of different non-transformed cell types and extracellular matrix (ECM) components. The tumor microenvironment is governed by constantly evolving cell-cell and cell-ECM interactions, which are now recognized as key actors in the genesis, progression and treatment of cancer lesions. The ECM is composed of a multitude of fibrous proteins, matricellular-associated proteins, and proteoglycans. This complex structure plays critical roles in cancer progression: it functions as the scaffold for tissues organization and provides biochemical and biomechanical signals that regulate key cancer hallmarks including cell growth, survival, migration, differentiation, angiogenesis, and immune response. Cells sense the biochemical and mechanical properties of the ECM through specialized transmembrane receptors that include integrins, discoidin domain receptors, and syndecans. Advanced stages of several carcinomas are characterized by a desmoplastic reaction characterized by an extensive deposition of fibrillar collagens in the microenvironment. This compact network of fibrillar collagens promotes cancer progression and metastasis, and is associated with low survival rates for cancer patients. In this review, we highlight how fibrillar collagens and their corresponding integrin receptors are modulated during cancer progression. We describe how the deposition and alignment of collagen fibers influence the tumor microenvironment and how fibrillar collagen-binding integrins expressed by cancer and stromal cells critically contribute in cancer hallmarks.

miR-133b Suppresses Invasion and Migration of Gastric Cancer Cells via the COL1A1/TGF-β Axis

Objective

The study aimed to explore the mechanism of miR-133b regulating the invasion and migration of gastric cancer (GC) cells via the COL1A1/TGF-β axis.

Methods

The miRNA expression profiles of GC downloaded from TCGA database were subjected to differential analysis to determine the target miRNA of interest, and the target genes of the miRNA were predicted by bioinformatics. GSEA was used for gene enrichment analysis. qRT-PCR was carried out to detect gene expression in GC cells. The effect of miR-133b on GC cells was examined by CCK-8, wound healing and Transwell assays. Western blot was conducted to assess the protein expression of EMT-related proteins. The binding relationship between genes was verified by dual-luciferase reporter gene assay.

Results

The expression of miR-133b was markedly downregulated in GC tissue, while that of COL1A1 was upregulated. Overexpression of miR-133b decreased the migration and invasion of GC cells, and the EMT process was inhibited as well, while inverse results were observed when miR-133b was silenced. COL1A1 was a target gene of miR-133b and its overexpression had a significant impact on the prognosis of patients. GSEA pathway enrichment results showed that COL1A1 was markedly enriched in the TGF-β signaling pathway. In addition, COL1A1 overexpression induced the activation of the TGF-β signaling pathway to promote proliferation and migration of GC cells, whereas miR-133b overexpression suppressed the signaling pathway. Thus, overexpression of miR-133b and COL1A1 simultaneously would reverse the inhibitory effect of miR-133b on cell invasion and migration.

Conclusion

In this study, miR-133b was found to inhibit the invasion and migration of GC cells via the COL1A1/TGF-β axis, which provides a new research direction for the diagnosis and targeted therapy of GC.

Prognostic Value of Immune-Related Genes in the Tumor Microenvironment of Bladder Cancer

The tumor microenvironment (TME) is a complex system that plays an important role in tumor development and progression, but the current knowledge about its effect on bladder cancer (BC) is scarce. In this study, we performed a comprehensive analysis of the relationship between the TME and gene expression profiles to identify prognostic biomarkers for BC. The ESTIMATE algorithm was used to calculate immune and stromal scores of BC patients who were obtained from the Gene Expression Omnibus database. We found that the immune and stromal scores were associated with clinical characteristics and the prognosis of BC patients. Based on these scores, 104 immune-related differentially expressed genes were identified. Further, functional enrichment analysis revealed that these genes were mainly involved in the immune-related biological processes and signaling pathways. Three prognostic genes were then identified and used to establish a risk prediction model using Cox regression analyses. Kaplan–Meier survival analysis showed that the expression levels of COL1A1, COMP, and SERPINE2 significantly correlated with cancer-specific survival and overall survival of BC patients. Additionally, we validated the prognostic values of these genes using two independent cohorts from The Cancer Genome Atlas and Gene Expression Omnibus databases. Finally, the relationships between the three prognostic genes and several immune cells were evaluated using Tumor Immune Estimation Resource, indicating that the expression levels of COL1A1, COMP, and SERPINE2 correlated positively with the tumor infiltration levels of CD4⁺ T cells and macrophages. In conclusion, the current study comprehensively analyzed the TME and presented immune-related prognostic genes for BC, providing new insights into immunotherapeutic strategies for BC patients.

Comprehensive Transcriptomic Analysis and Experimental Validation Identify lncRNA HOXA-AS2/miR-184/COL6A2 as the Critical ceRNA Regulation Involved in Low-Grade Glioma Recurrence

Purpose

The recurrence and metastasis of glioma are closely related to complex regulatory networks among protein-coding genes, lncRNAs and microRNAs. The aim of this study was to investigate core genes, lncRNAs, miRNAs and critical ceRNA regulatory mechanisms, which are involved in lower-grade glioma (LGG) recurrence.

Materials and Methods

We employed multiple datasets from Chinese Glioma Genome Atlas (CGGA) database and The Cancer Genome Atlas (TCGA) to perform comprehensive transcriptomic analysis. Further in vitro experiments including cell proliferation assay, luciferase reporter assay, and Western blot were performed to validate our results.

Results

Recurrent LGG and glioblastoma (GBM) showed different transcriptome characteristics with less overlap of differentially expressed protein-coding genes (DEPs), lncRNAs (DELs) and miRNAs (DEMs) compared with primary samples. There were no overlapping gene in ontology (GO) terms related to GBM recurrence in the TCGA and CGGA databases, but there were overlaps associated with LGG recurrence. GO analysis and protein–protein interaction (PPI) network analysis identified three core genes: TIMP1, COL1A1 and COL6A2. By hierarchical cluster analysis of them, LGGs could be clustered as Low_risk and High_risk group. The High_risk group with high expression of TIMP1, COL1A1, and COL6A2 showed worse prognosis. By coexpression networks analysis, competing endogenous RNA (ceRNA) network analysis, cell proliferation assay and luciferase reporter assay, we confirmed that lncRNA HOXA-AS2 functioned as a ceRNA for miR-184 to regulate expression of COL6A2, which induced cell proliferation of low-grade glioma.

Conclusion

In this study, we revealed a 3-hub protein-coding gene signature to improve prognostic prediction in LGG, and identified a critical ceRNA regulation involved in LGG recurrence.

Pan-cancer analysis reveals the role of long non-coding RNA LINC01614 as a highly cancer-dependent oncogene and biomarker

Long intergenic non-coding RNA 1614 (LINC01614) is highly expressed in several malignant tumor types, suggesting that it may act as an oncogene. However, the specific roles of LINC01614 in malignant tumors have remained elusive. To examine the expression pattern of LINC01614 in various malignancies, a comprehensive pan-cancer analysis was performed using public databases, including 53 normal tissue types and 32 cancer datasets with samples from 9,091 patients. The results were validated using reverse transcription-quantitative PCR analysis of tissue specimens from patients. LINC01614 expression was upregulated in most malignant tumors, thus demonstrating diagnostic potential. Furthermore, upregulation of LINC01614 was associated with poor overall survival in the majority of cases. However, the association with clinical outcome was highly cancer-dependent; LINC01614 appeared to be an oncogene and diagnostic/prognostic biomarker in cancers of the digestive, respiratory, nervous and endocrine systems, as well as breast and head and neck cancer, but not in the cancers of the reproductive system or some of the urinary system. High LINC01614 expression was also markedly associated with the epithelial-mesenchymal transition (EMT) and associated signaling pathways. Overall, the present results suggest that LINC01614 is an EMT-associated oncogene that influences the metastasis and prognosis of several cancers, thus highlighting its potential as a novel diagnostic and prognostic marker.

Tissue stiffness contributes to YAP activation in bladder cancer patients undergoing transurethral resection

Changes in the cellular microenvironment play a critical role in the development of bladder cancer (BC). Yes-associated protein (YAP), a central mediator of the Hippo pathway, functions as a nuclear sensor of mechanotransduction that can be induced by stiffness of the extracellular matrix (ECM), including stiffness resulting from surgical manipulations. We aimed to clarify the possible association between surgically-related ECM stiffness and YAP activation in BC patients. We compared 30 bladder cancer tissues with grade II (n = 15 recurrent and n = 15 newly diagnosed) with 30 adjacent healthy tissues. Atomic force microscopy showed that patients with recurrent BC had stiffer ECM than newly diagnosed patients (P < 0.05). Gene expression profiles showed that β1 integrin (ITGB1), focal adhesion kinase (FAK), CDC42, and YAP were upregulated in cancerous tissues (P < 0.05); additionally, β1 integrin activation was confirmed using a specific antibody. Nuclear localization of YAP was higher in recurrent cancerous tissues compared with newly diagnosed and it was positively associated with higher stiffness (P < 0.05). Our results suggest that postsurgery-induced ECM stiffness can influence integrin-FAK-YAP activity and thereby YAP trafficking to the nucleus where it contributes to BC progression and relapse.

Identification of potential key genes in gastric cancer using bioinformatics analysis

Gastric cancer (GC) is one of the most common types of cancer worldwide. Patients must be identified at an early stage of tumor progression for treatment to be effective. The aim of the present study was to identify potential biomarkers with diagnostic value in patients with GC. To examine potential therapeutic targets for GC, four Gene Expression Omnibus (GEO) datasets were downloaded and screened for differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were subsequently performed to study the function and pathway enrichment of the identified DEGs. A protein-protein interaction (PPI) network was constructed. The CytoHubba plugin of Cytoscape was used to calculate the degree of connectivity of proteins in the PPI network, and the two genes with the highest degree of connectivity were selected for further analysis. Additionally, the two DEGs with the largest and smallest log Fold Change values were selected. These six key genes were further examined using Oncomine and the Kaplan-Meier plotter platform. A total of 99 upregulated and 172 downregulated genes common to all four GEO datasets were screened. The DEGs were primarily enriched in the Biological Process terms: ‘extracellular matrix organization’, ‘collagen catabolic process’ and ‘cell adhesion’. These three KEGG pathways were significantly enriched in the categories: ‘ECM-receptor interaction’, ‘protein digestion and absorption’, and ‘focal adhesion’. Based on Oncomine, expression of ATP4A and ATP4B were downregulated in GC, whereas expression of the other genes were all upregulated. The Kaplan-Meier plotter platform confirmed that upregulated expression of the identified key genes was significantly associated with worse overall survival of patients with GC. The results of the present study suggest that FN1, COL1A1, INHBA and CST1 may be potential biomarkers and therapeutic targets for GC. Additional studies are required to explore the potential value of ATP4A and ATP4B in the treatment of GC.

The Clinical Significance of PPEF1 as a Promising Biomarker and Its Potential Mechanism in Breast Cancer

Background

Breast cancer (BC) is the leading cause of malignancy death in females worldwide. While intense efforts have been made to elucidate the pathogeny, the molecular mechanism of BC remains elusive. Thus, this study aimed to investigate the role of PPEF1 in the progression of BC and further explore the better clinical significance.

Methods

The diagnostic and prognostic values of elevated PPEF1 expression in BC were unveiled via public databases analysis. In addition, Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA) and Protein–protein interaction (PPI) analysis were performed to explore the potential functions and molecular mechanisms of PPEF1 in BC progression. Experimentally, transwell and CCK-8 assays were carried out to estimate the effects of PPEF1 on the BC metastasis. Meanwhile, the differential expressions of PPEF1 in paraffin-embedded tissues and serum samples were, respectively, analyzed by Immunohistochemical (IHC) analysis and enzyme-linked immunosorbent assay (ELISA) kit.

Results

The transcriptional levels of PPEF1 were higher in BC than in normal breast tissues or adjacent normal tissues. Moreover, survival analysis revealed that higher PPEF1 expression was negatively associated with overall survival (OS), all events-free (AE-free) and metastatic recurrence-free (MR-free) survival, and further was an independent risk factor of unfavorable prognosis in BC patients. Additionally, the present study provided the first evidence that PPEF1 participated in multiple biological processes and underly signaling pathways involving in tumorigenesis and development of BC. Furthermore, PPEF1 promotes the BC progression and can be used as a noninvasive diagnostic marker. Noteworthy, the combined determination of serum PPEF1 and traditional tumor markers can enhance diagnostic accuracy thus is of vital importance in the early diagnosis of BC.

Conclusion

PPEF1 exerted a tumorigenic role and involved in molecular mechanism of tumorigenesis in BC which served as a promising biomarker for prognosis and diagnosis.

Depletion of MLKL inhibits invasion of radioresistant nasopharyngeal carcinoma cells by suppressing epithelial-mesenchymal transition

BACKGROUND

To examine whether MLKL participated in the invasion of radiosensitive nasopharyngeal carcinoma (NPC) cell (CNE-2) and radioresistant NPC cell (CR) through regulating epithelial-mesenchymal transition (EMT).

METHODS

siRNA and CRISPR/Cas9 technique were used to decrease MLKL expression in NPC cell (CNE-2 and CR). Trans-well assay was conducted to evaluate invasion. Gene expression profiling was performed using Human U133 2.0 plus arrays (Affymetrix). Kyoto Encyclopedia of Genes and Genomes (KEGG) was adopted to analyze gene expression profiling. Hub genes at a functional level were accessed by protein-to-protein network (PPI). Quantitative real-time PCR and Western blot were used to access EMT markers.

RESULTS

Invasion of CR was about 3~fold change higher than that of CNE-2. Silencing MLKL by siRNA inhibited invasion of CR, not CNE-2. Further, depleting MLKL by CRISPR-Cas9 in CR (CR-MLKL KO) also inhibited its invasion. KEGG pathway analysis showed invasion-related pathways were altered, such as adherent junction, TGF-β signaling pathway. PPI demonstrated that compared with CNE-2, CR showed 9 elevated hub genes including EGFR, JUN, CD44, SPP1, VIM, IL-8, BCL2, WDFY2, PIK3CD and 1 downregulated hub gene CDH1. After MLKL depletion, 8 hub genes were downregulated (EGFR, JUN, CD44, SPP1, VIM, FGF13, PLAU, MMP1) and 2 hub genes were upregulated (MMP9, CDH1). Quantitative real-time PCR results showed that compared with CNE-2, CR displayed decreased epithelial markers significantly (E-Cadherin) and increased mesenchymal markers significantly (Vimentin, N-Cadherin, Zeb1), indicating irradiation-induced EMT. After depletion of MLKL in CR, the expression of E-Cadherin, Vimentin, N-Cadherin, Zeb1 was reversed to the level of CNE-2. Western blot confirmed the results from qRT-PCR.

CONCLUSIONS

Depletion of MLKL efficiently inhibits invasion of radioresistant NPC by suppressing EMT. MLKL may be an important target to suppress distant metastasis of NPC patients who relapsed after radiotherapy.

Agmatinase promotes the lung adenocarcinoma tumorigenesis by activating the NO-MAPKs-PI3K/Akt pathway

Lung adenocarcinoma (LUAD) is one of the leading causes of cancer-related death worldwide. There is an urgent need to uncover the pathogenic mechanism to develop new treatments. Agmatinase (AGMAT) expression and its association with clinicopathological characteristics were analyzed via GEO, Oncomine, and TCGA databases, and IHC staining in human LUAD specimens. An EdU cell proliferation kit, propidiumiodide staining, colony formation, cell migration, and invasion assays, and a xenograft tumor model were used to detect the biological function of AGMAT in LUAD. Furthermore, the expression level of nitric oxide (NO) was detected using a DAF-FMDA fluorescent probe or nitrite assay kit, and further validated with Carboxy-PTIO (a NO scavenger). The roles of three isoforms of nitric oxide synthases (nNOS, eNOS, and iNOS) were validated using L-NAME (eNOS inhibitor), SMT (iNOS inhibitor), and spermidine (nNOS inhibitor). AGMAT expression was up-regulated in LUAD tissues. LUAD patients with high AGMAT levels were associated with poorer prognoses. AGMAT promoted LUAD tumorigenesis in NO released by iNOS both in vitro and in vivo. Importantly, NO signaling up-regulated the expression of cyclin D1 via activating the MAPK and PI3K/Akt-dependent c-myc activity, ultimately promoting the malignant proliferation of tumor cells. On the whole, AGMAT promoted NO release via up-regulating the expression of iNOS. High levels of NO drove LUAD tumorigenesis via activating MAPK and PI3K/Akt cascades. AGMAT might be a potential diagnostic and therapeutic target for LUAD patients.

A Novel Drug Design Strategy: An Inspiration from Encaging Tumor by Metallofullerenol Gd@C82(OH)22

Cancer remains a major threat to human health worldwide. Cytotoxicity has imposed restrictions on the conventional cytotoxic drug-based chemotherapy. The rapidly-developing nanomedicine has shown great promise in revolutionizing chemotherapy with improved efficiency and reduced toxicity. Gd@C₈₂(OH)₂₂, a novel endohedral metallofullerenol, was first reported by our research group to suppress tumor growth and metastasis efficiently without obvious toxicity. Gd@C₈₂(OH)₂₂ imprisons tumors by facilitating the formation of surrounding fibrous layers which is different from chemotherapeutics that poison tumor cells. In this review, the authors first reported the antineoplastic activity of metallofullerenol Gd@C₈₂(OH)₂₂ followed by further discussions on its new anti-cancer molecular mechanism—tumor encaging. On this basis, the unparalleled advantages of nanomedicine in the future drug design are discussed. The unique interaction modes of Gd@C₈₂(OH)₂₂ with specific targeted biomolecules may shed light on a new avenue for drug design. Depending on the surface characteristics of target biomolecules, nanomedicine, just like a transformable and dynamic key, can self-assemble into suitable shapes to match several locks for the thermodynamic stability, suggesting the target-tailoring ability of nanomedicine.