Gene Expression Profiles Identified Novel Urine Biomarkers for Diagnosis and Prognosis of High-Grade Bladder Urothelial Carcinoma

Impact of multi-parameter images obtained from dual-energy CT on radiomics to predict pathological grading of bladder urothelial carcinoma

OBJECTIVE

To investigate the effect of radiomics models obtained from dual-energy CT (DECT) material decomposition images and virtual monoenergetic images (VMIs) in predicting the pathological grading of bladder urothelial carcinoma (BUC).

MATERIALS AND METHODS

A retrospective analysis of preoperative DECT examination was conducted on 112 patients diagnosed with BUC. This cohort included 76 cases of high-grade urothelial carcinoma and 36 cases of low-grade urothelial carcinoma. DECT can provide material decomposition images of venous phase Iodine maps and Water maps based on the differences in attenuation of substances, as well as VMIs at 40 to 140 keV (interval 10 keV). A total of 13 image sets were obtained, and radiomics features were extracted and analyzed from each set to achieve preoperative prediction of BUC. The best features related to BUC were identified by recursive feature elimination (RFE), the Minimum Redundancy Maximum Relevance (mRMR), and the Least Absolute Shrinkage and Selection Operator (LASSO) in order. A five-fold cross-validation method was used to divide the samples into training and testing sets, and models for pathological prediction of BUC grading were constructed by a random forest (RF) classifier. Receiver operating curves (ROC) were plotted to evaluate the performance of 13 models obtained from each image set.

RESULTS

Despite the notable differences in the best radiomics features chosen from each image set, all the features selected from 40 to 100 keV VMIs included the Dependence Variance of the GLDM feature set. There were no statistically significant differences in the area under the curve (AUC) between the training set and the testing set for all 13 models. In the testing set, the AUCs of the models established through 40 keV to 140 keV (interval of 10 keV) image sets were 0.895, 0.874, 0.855, 0.889, 0.841, 0.868, 0.852, 0.847, 0.889, 0.887 and 0.863 respectively. The AUCs for the models established using the Iodine maps and Water maps image sets were 0.873 and 0.852, respectively.

CONCLUSION

Despite the differences in the selected radiomic features from DECT multi-parameter images, the performance of radiomics models in predicting the pathological grading of BUC was not affected by the variations in the types of images used for model training.

Integrated analysis of high‑throughput sequencing reveals the regulatory potential of hsa_circ_0035431 in HNSCC

Circular RNAs (circRNAs) are molecular sponges that are involved in regulation of multiple types of cancer. The present study aimed to screen and explore the key circRNA/microRNA (miRNA or miR)/mRNA interactions in head and neck squamous cell carcinoma (HNSCC) using bioinformatics. A total of six pairs of cancerous and adjacent healthy tissue were obtained from patients with HNSCC and genome-wide transcriptional sequencing was performed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed genes (DEGs). Moreover, expression levels of DEGs were verified in HNSCC cells and tissues using reverse transcription-quantitative (RT-q)PCR. A molecular regulatory network consisting of three circRNAs, seven miRNAs and seven mRNAs was constructed, resulting in identification of two signaling axes, hsa_circ_0035431/hsa-miR-940/fucosyltransferase 6 (FUT6) and hsa_circ_0035431/hsa-miR-940/cingulin-like 1 (CGNL1). FUT6 and CGNL1 were downregulated in HNSCC compared with adjacent healthy tissue and the expression levels of these genes were associated with tumor stage. Low FUT6 and CGNL1 expression levels were associated with lower overall survival rate and progression-free intervals in HNSCC. RT-qPCR demonstrated that hsa_circ_0035431, FUT6 and CGNL1 were downregulated in HNSCC cells and tissue and hsa-miR-940 was upregulated. Notably, these results were consistent with those obtained using high-throughput sequencing. In conclusion, hsa_circ_0035431 may participate in regulation of FUT6 and CGNL1 expression by sponging hsa-miR-940, thus, impacting the occurrence, development and prognosis of HNSCC.

GPX3 rs8177412 Polymorphism Modifies Risk of Upper Urothelial Tumors in Patients with Balkan Endemic Nephropathy

Current data suggest that aristolochic acid (AA) exposure is a putative cause of Balkan endemic nephropathy (BEN), a chronic kidney disease strongly associated with upper tract urothelial carcinoma. The cellular metabolism of AA is associated with the production of reactive oxygen species, resulting in oxidative distress. Purpose: Therefore, the aim of this study was to analyze individual, combined and cumulative effect of antioxidant gene polymorphisms (Nrf2 rs6721961, KEAP1 rs1048290, GSTP1AB rs1695, GSTP1CD rs1138272, GPX3 rs8177412 and MDR1 rs1045642), as well as GSTP1ABCD haplotypes with the risk for BEN development and associated urothelial cell carcinoma in 209 BEN patients and 140 controls from endemic areas. Experimental method: Genotyping was performed using polymerase chain reaction (PCR) and PCR with confronting two-pair primers (PCR-CTTP) methods. Results: We found that female patients carrying both variant GPX3 rs8177412 and MDR1 rs1045642 genotypes in combination exhibited significant risk towards BEN (OR 1 = 3.34, 95% CI = 1.16-9.60, p = 0.025; OR 2 = 3.79, 95% CI = 1.27-11.24, p = 0.016). Moreover, significant association was determined between GPX3rs8174412 polymorphism and risk for urothelial carcinoma. Carriers of variant GPX3*TC + CC genotype were at eight-fold increased risk of BEN-associated urothelial tumors development. There was no individual or combined impact on BEN development and BEN-associated tumors among all examined polymorphisms. The haplotype consisting of variant alleles for both polymorphisms G and T was associated with 1.6-fold increased risk although statistically insignificant (OR = 1.64; 95% CI = 0.75-3.58; p = 0.21). Conclusions: Regarding GPX3 rs8177412 polymorphism, the gene variant that confers lower expression is associated with significant increase in upper urothelial carcinoma risk. Therefore, BEN patients carrying variant GPX3 genotype should be more frequently monitored for possible upper tract urothelial carcinoma development.

GPx3 knockdown inhibits the proliferation and DNA synthesis and enhances the early apoptosis of human spermatogonial stem cells via mediating CXCL10 and cyclin B1

Spermatogenesis is regulated by genetic and epigenetic factors. However, the genes and signaling pathways mediating human spermatogenesis remain largely unknown. Here, we have for the first time explored the expression, function, and mechanism of glutathione peroxidase 3 (GPx3) in controlling the proliferation and apoptosis of human spermatogonial stem cells (SSCs). We found that GPx3 was expressed in human SSCs. Notably, we revealed that GPx3 knockdown resulted in the decrease in the proliferation, DNA synthesis, and cyclin B1 level in human SSC lines, which possessed the phenotypic features of human primary SSCs. Flow cytometry and TUNEL assays showed that GPx3 silencing led to enhancement of early apoptosis of human SSC line. RNA sequencing was utilized to identify CXCL10 as a target of GPx3 in human SSCs, and notably, both double immunostaining and co-immunoprecipitation (co-IP) demonstrated that there was an association between GPx3 and CXCL10 in these cells. CXCL10-shRNA resulted in the reduction in the proliferation and DNA synthesis of human SSC line and an increase in apoptosis of these cells. Taken together, these results implicate that GPx3 regulates the proliferation, DNA synthesis, and early apoptosis of human SSC line via mediating CXCL10 and cyclin B1. This study, thus, offers a novel insight into the molecular mechanism regulating the fate determinations of human SSCs and human spermatogenesis.

Identify Potential Urine Biomarkers for Bladder Cancer Prognosis Using NGS Data Analysis and Experimental Validation

Bladder cancer (BC) is one of the most often reported malignancies globally, with a high recurrence rate and associated morbidity and mortality, especially in advanced BC. There has been a surge in the number of molecular targets revealed for BC prognosis and treatment. However, there is still a great need to discover novel biomarkers. Consequently, the current study investigated biomarkers that might indicate the progression of bladder cancer. In this study, bioinformatics analysis was done on a single GEO dataset, and TCGA-BLCA information was connected with differentially expressed genes (DEGs). The levels of mRNA and protein expression were validated using qRT-PCR. According to our findings, CRYAB, ECM1, ALDOB, AOC, GPX3, IGFBP7, AQP2, LASS2, TMEM176A, GALNT1, and LASS2 were highly enriched in cell division, identical protein binding, and developmental process in bladder cancer patients. In addition, among the highly differentiated genes, ECM1, GALNT1, LASS2, and GPX3 showed significant molecular alterations in BC, which are crucial for marker identification. Moreover, the mRNA, CNVs, and protein levels of ECM1, GALNT1, LASS2, and GPX3 were significantly increased in BC patients. Our predictions and analysis studies stated that these four genes act as urine biomarkers and played a crucial role in disease prognosis and the therapeutic process of bladder cancer. Our outcomes showed that these four novel urine biomarkers have the potential to provide innovative diagnostics, early predictions, and disease targets, ultimately improving the BC patient's prognosis.

MTHFD2 is a potential oncogene for its strong association with poor prognosis and high level of immune infiltrates in urothelial carcinomas of bladder

BACKGROUND

The bifunctional methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase (MTHFD2) has been reported to play an oncogenic role in various types of cancers. However, the function of MTHFD2 in urothelial carcinomas of bladder (UCB) and its association with tumor immune infiltration remains unknown. We aim to examine the suitability of MTHFD2 to be a novel biomarker of bladder cancer and whether MTHFD2 is linked to immune infiltration.

METHODS

RNA sequencing data and clinical information (bladder cancer samples: normal samples = 414: 19) were downloaded from The Cancer Genome Atlas official website. Western blot analysis was performed to detect MTHFD2 expression in human bladder cancer (BLCA) cells and normal urothelial cell line SV-HUC-1. Associations between MTHFD2 expression and clinicopathological features were analyzed using Mann Whitney U test or Kruskal-Wallis H test. The "survival" and "survminer" packages were utilized to plot Kaplan-Meier survival curves. Moreover, the gene set enrichment analysis (GSEA) was conducted using a clusterProfiler package. The correlation of MTHFD2 expression with immune infiltration level was estimated using the single sample GSEA (ssGSEA) algorithm. Furthermore, associations between MTHFD2 and immune checkpoint genes were evaluated using the correlation analysis.

RESULTS

Transcriptome analysis manifested that MTHFD2 was highly expressed in UCB tissues than normal bladder tissues, which was further confirmed by western blot analysis in human BLCA cells and SV-HUC-1 cells. Moreover, MTHFD2 high expression was significantly associated with the advanced disease progression. Also, the high expression of MTHFD2 was correlated with poor prognosis, and MTHFD2 was considered as an independent prognostic factor for disease specific survival. Furthermore, a number of cancer-related pathways were enriched in MTHFD2 high group, including NF-κB activation, JAK/STAT, and cancer immunotherapy by PD1 blockade. Several immune checkpoint molecules were also strongly associated with MTHFD2 expression, including PDCD1, CD274, CTLA4, CD276, LAG3, HAVCR2, and TIGIT.

CONCLUSIONS

MTHFD2 expression was remarkably elevated in UCB, suggesting that MTHFD2 could be a promising biomarker for BLCA as well as novel target for anti-cancer immunotherapy since its close association with immune infiltration.

Omega-3 fatty acids decrease CRYAB, production of oncogenic prostaglandin E2 and suppress tumor growth in medulloblastoma

AIMS

Medulloblastoma (MB) is one of the most common malignant central nervous system tumors of childhood. Despite intensive treatments that often leads to severe neurological sequelae, the risk for resistant relapses remains significant. In this study we have evaluated the effects of the ω3-long chain polyunsaturated fatty acids (ω3-LCPUFA) docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) on MB cell lines and in a MB xenograft model.

MAIN METHODS

Effects of ω3-LCPUFA treatment of MB cells were assessed using the following: WST-1 assay, cell death probes, clonogenic assay, ELISA and western blot. MB cells were implanted into nude mice and the mice were randomized to DHA, or a combination of DHA and EPA treatment, or to control group. Treatment effects in tumor tissues were evaluated with: LC-MS/MS, RNA-sequencing and immunohistochemistry, and tumors, erythrocytes and brain tissues were analyzed with gas chromatography.

KEY FINDINGS

ω3-LCPUFA decreased prostaglandin E2 (PGE₂) secretion from MB cells, and impaired MB cell viability and colony forming ability and increased apoptosis in a dose-dependent manner. DHA reduced tumor growth in vivo, and both PGE₂ and prostacyclin were significantly decreased in tumor tissue from treated mice compared to control animals. All ω3-LCPUFA and dihomo-γ-linolenic acid increased in tumors from treated mice. RNA-sequencing revealed 10 downregulated genes in common among ω3-LCPUFA treated tumors. CRYAB was the most significantly altered gene and the downregulation was confirmed by immunohistochemistry.

SIGNIFICANCE

Our findings suggest that addition of DHA and EPA to the standard MB treatment regimen might be a novel approach to target inflammation in the tumor microenvironment.

Comprehensive analysis of circRNA expression pattern and circRNA-miRNA-mRNA network in oral squamous cell carcinoma

OBJECTIVE

CircRNAs are critical gene modulators in tumor initiation and progression. However, the expression pattern and molecular pathogenesis of circRNAs in oral squamous cell carcinoma (OSCC) are still poorly characterized.

METHODS

RNA sequencing with CIRCexplorer2 pipeline was performed to identify circRNAs in 46 tumor-normal paired tissues from OSCC patients. Another set of 48 head and neck squamous cell carcinoma samples from the MiOncoCirc database were utilized as an independent validation.

RESULTS

Of the 1276 identified high-confidence circRNAs, 154 were differentially expressed between tumor and normal tissues (log₂|Fold Change|≥1 and false discovery rate < 0.05). CircRNAs expression was globally down-regulated in tumors compared to normal tissues (P = 9.44 × 10^-14). Correlation analysis demonstrated that the global expression of circRNAs was positively related to tumor infiltrating lymphocyte (P = 1.10 × 10^-4) and stromal signature (P = 2.70 × 10^-3) whereas negatively associated with cell proliferation markers (P = 4.32 × 10^-2). CircRNAs-miRNAs-mRNAs regulatory network revealed 6574 interactions, and the target genes were enriched in extracellular matrix and immune-related pathways. Survival analysis were performed on target genes in immune-related pathways, and 20 genes were significantly associated with the prognostic status of OSCC in The Cancer Genome Atlas cohort. The risk model constructed with above 20 genes was associated with the prognosis status of OSCC (HR = 3.28, P = 5.06 × 10^-11), and the result was validated in an independent study (GSE41613) (HR = 2.06, P = 1.73 × 10^-2).

CONCLUSION

CircRNAs showed a global down-regulation pattern in OSCC tissues, and genes regulated by circRNAs primarily involved in immune and extracellular matrix pathways, which could also affect the OSCC prognosis, indicating that they may serve as potential prognostic biomarkers.

Expression and prognostic value of SULT1A2 in bladder cancer

Sulfotransferase Family 1A Member 2 (SULT1A2) is a protein coding gene. Several studies have reported that SULT1A2 may have a chemical carcinogenic effect if expressed as a functional protein. The present study aimed to investigate the expression and potential role of SULT1A2 in bladder cancer (BC). Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases were used to analyze SULT1A2 expression in BC. In addition, reverse transcription-quantitative PCR and western blot analyses were performed to detect SULT1A2 expression in BC cells and tissues. Immunohistochemistry analysis was performed on 100 formalin-fixed, paraffin-embedded BC tissues and corresponding adjacent normal bladder tissues (ANBTs) to verify SULT1A2 expression and determine the clinical significance of SULT1A2 in BC. Gene set enrichment analysis (GSEA) was performed to determine the potential biological processes and internal molecular mechanisms. The results demonstrated that SULT1A2 was highly expressed in BC tissues compared with ANBTs. Furthermore, high SULT1A2 expression was significantly associated with the staging of BC. Analyses of TCGA datasets and BC tissue microarray indicated that high SULT1A2 expression was significantly associated with a favorable overall survival in patients with BC. In addition, GSEA revealed pathways, diseases and biological processes associated with SULT1A2. Taken together, the results of the present study suggest that SULT1A2 acts as an oncogene in BC, and thus may serve as a biomarker for tumor staging and prognosis in patients with BC.

Minimally Invasive Ways of Determining Circadian Rhythms in Humans

Circadian rhythm exerts a critical role in mammalian health and disease. A malfunctioning circadian clock can be a consequence, as well as the cause of several pathophysiologies. Clinical therapies and research may also be influenced by the clock. Since the most suitable manner of revealing this rhythm in humans is not yet established, we discuss existing methods and seek to determine the most feasible ones.

Insights into the role of GPX3, a highly efficient plasma antioxidant, in cancer

Glutathione peroxidases are well known antioxidant enzymes. They catalyze the reduction of hydrogen peroxide or organic hydroperoxides using glutathione. Among the reported 8 GPxs, GPx3, a highly conserved protein and a major ROS scavenger in plasma, has been well studied and confirmed to play a vital role as a tumor suppressor in most cancers. Additionally, this gene is known to be epigenetically regulated. It is downregulated either by hypermethylation or genomic deletion. In this review, we summarized the role of GPX3 in various cancers, its use as a prognostic biomarker, and a potential target for clinical intervention.

Extracellular Glutathione Peroxidase GPx3 and Its Role in Cancer

Mammalian cells possess a multifaceted antioxidant enzyme system, which includes superoxide dismutases, catalase, the peroxiredoxin/thioredoxin and the glutathione peroxidase systems. The dichotomous role of reactive oxygen species and antioxidant enzymes in tumorigenesis and cancer progression complicates the use of small molecule antioxidants, pro-oxidants, and targeting of antioxidant enzymes as therapeutic approaches for cancer treatment. It also highlights the need for additional studies to investigate the role and regulation of these antioxidant enzymes in cancer. The focus of this review is on glutathione peroxidase 3 (GPx3), a selenoprotein, and the only extracellular GPx of a family of oxidoreductases that catalyze the detoxification of hydro- and soluble lipid hydroperoxides by reduced glutathione. In addition to summarizing the biochemical function, regulation, and disease associations of GPx3, we specifically discuss the role and regulation of systemic and tumor cell expressed GPx3 in cancer. From this it is evident that GPx3 has a dichotomous role in different tumor types, acting as both a tumor suppressor and pro-survival protein. Further studies are needed to examine how loss or gain of GPx3 specifically affects oxidant scavenging and redox signaling in the extracellular tumor microenvironment, and how GPx3 might be targeted for therapeutic intervention.

FGF2-induced PI3K/Akt signaling evokes greater proliferation and adipogenic differentiation of human adipose stem cells from breast than from abdomen or thigh

In this study, human adipose stem cells were isolated from subcutaneous fat in the thigh (htASCs), abdomen (haASCs) and breast (hbASCs). Flow cytometry was used to detect cell surface markers, and an enzyme-linked immunosorbent assay was used to detect paracrine activity. Paracrine gene expression in the three cell types was examined using real-time qPCR, and adipogenic ability was assessed using Oil Red O staining. RNA from third-passage haASCs and hbASCs was sequenced. The results showed that the differentiation potential marker markers CD49d and CD54 were similar across hbASCs from 10 subjects. The hbASCs showed higher colony forming ability and expression of fibroblast growth factor-2, tissue inhibitor of metalloproteinase-1 and stromal cell derived factor-1 than htASCs and haASCs. Stimulating hbASCs with FGF2 promoted adipogenic differentiation, while treating the cells with the PI3K inhibitor LY294002 inhibited differentiation. These results suggest that the PI3K/Akt signaling pathway can promote proliferation and adipogenic differentiation of adipose stem cells, and that activation of this pathway by FGF2 may explain why hbASCs show greater proliferation and adipogenic differentiation than haASCs and htASCs.