PTRF/CAVIN1, regulated by SHC1 through the EGFR pathway, is found in urine exosomes as a potential biomarker of ccRCC.

Polymerase I and transcript release factor (PTRF)/Cavin1 regulates RNA polymerase I during transcription and plays a critical role in endocytosis. Abnormal expressions of PTRF were detected in multiple cancers according to increasing research. PTRF has been showed to involve in the formation and secretion of exosomes and can be detected in the exosomes, which suggests that PTRF would be a potential biomarker for diagnosis of clear cell renal cell carcinoma (ccRCC) using urine samples. Approximately 50-90% of ccRCC cases suffered abnormal epidermal growth factor receptor (EGFR), which activates a variety of signaling pathways, including the mitogen-activated protein kinase/extracellular signal-regulated kinase and Phosphoinositide 3-Kinase/Akt pathway. According to bioinformatic analysis of gene expression arrays of kidney clear cell carcinoma from The Cancer Genome Atlas, we found SHC1 was significantly overexpressed in high-grade ccRCC and correlated to poor prognosis, and also SHC1 was annotated in extracellular matrix process, which was regulated by EGFR. Further studies showed that the expression of PTRF was regulated by SHC1 through EGFR-Phosphoinositide 3-Kinase/Akt pathway. PTRF was detected in the exosomes isolated from ccRCC patients' urine and ccRCC cancer cells culture medium. It suggested that the abnormal SHC1-increased PTRF, which is detected in exosomes from urine, would be a potential marker for ccRCC diagnose and treatment.

Comprehensive characterization of immune- and inflammation-associated biomarkers based on multi-omics integration in kidney renal clear cell carcinoma.

BACKGROUND: Kidney renal clear cell carcinoma (KIRC) is the most common type of kidney cancer in adults, and it is responsible for approximately 90-95% of cases. Although extensive evidence has suggested that many immune- and inflammation-related genes could serve as effective biomarkers in KIRC, the potential associations among immune-, inflammation- and KIRC-related genes has not been sufficiently understood. METHODS: Here, we integrated multiple levels of data to construct an immune-, inflammation- or KIRC-directed neighbour network (IIKDN network) and a KIRC-related gene-directed network (KIRCD network). RESULTS: Our analysis suggested that immune- and inflammation-related genes in the network have special topological characteristics and expression patterns related to KIRC. We further identified five core clusters that showed a tighter network structure and stronger correlation of expression from the KIRCD network. Specifically, multiple-level molecular characteristics were systematically portrayed, including somatic mutation, copy-number variant and DNA methylation for the genes in five core clusters. We discovered that the genes showed strong correlation with respect to the expression and methylation levels in these five core clusters. These five core clusters could become special prognostic biomarkers for KIRC, and functional analysis showed that they were associated with activation of the immune and inflammation systems and cancer progression. CONCLUSIONS: Our findings highlighted the novel role of the immune and inflammation genes in KIRC.

Downregulation of UBB potentiates SP1/VEGFA-dependent angiogenesis in clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) presents a unique profile characterized by high levels of angiogenesis and robust vascularization. Understanding the underlying mechanisms driving this heterogeneity is essential for developing effective therapeutic strategies. This study revealed that ubiquitin B (UBB) is downregulated in ccRCC, which adversely affects the survival of ccRCC patients. UBB exerts regulatory control over vascular endothelial growth factor A (VEGFA) by directly interacting with specificity protein 1 (SP1), consequently exerting significant influence on angiogenic processes. Subsequently, we validated that DNA methyltransferase 3 alpha (DNMT3A) is located in the promoter of UBB to epigenetically inhibit UBB transcription. Additionally, we found that an unharmonious UBB/VEGFA ratio mediates pazopanib resistance in ccRCC. These findings underscore the critical involvement of UBB in antiangiogenic therapy and unveil a novel therapeutic strategy for ccRCC.

Differential Expression Analysis Based on Ensemble Strategy on miRNA Profiles of Kidney Clear Cell Carcinoma.

BACKGROUND: Kidney clear cell carcinoma (KIRC) is the most common type of kidney cancer, accounting for approximately 60-85% of all the kidney cancers. However, there are few options available for early treatment. Therefore, it is extremely important to identify biomarkers and study therapeutic targets for KIRC. METHODS: Since there are few studies on KIRC, we used a data-driven approach to identify differential genes. Here, we used miRNA gene expression profile data from the TCGA database species of KIRC and proposed a machine learning-based approach to quantify the importance score of each gene. Then, an ensemble method was utilized to find the optimal subset of genes used to predict KIRC by clustering. The most genetic subset was then used to classify and predict KIRC. RESULTS: Differential genes were screened by several traditional differential analysis methods, and the selected gene subset showed a better performance. Independent testing sets from the GEO database were used to verify the effectiveness of the optimal subset of genes. Besides, cross-validation was made to verify the effectiveness of the approach. CONCLUSIONS: Finally, important genes, such as miR-140 and miR-210, were found to be involved in the biochemical processes of KIRC, which also proved the effectiveness of our approach.

The categorizations of vasculogenic mimicry in clear cell renal cell carcinoma unveil inherent connections with clinical and immune features.

Background: Clear cell renal cell carcinoma (ccRCC) stands as the prevailing variant kidney cancer in humans. Unfortunately, patients with disseminated RCC at diagnosis often have a diminished prognosis. Rapid tumor growth necessitates efficient blood supply for oxygen and nutrients, involving the circulation of blood from vessels to tumor tissues, facilitating tumor cell entry into the extracellular matrix. Vasculogenic mimicry (VM) significantly contributes to tumor growth and metastasis. Within this investigation, we identified vasculogenic mimicry-related genes (VMRGs) by analyzing data from 607 cases of kidney renal clear cell carcinoma (KIRC) in The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). These findings offer insights into ccRCC progression and metastasis. Method: We identified VMRGs-related subtypes using consistent clustering methods. The signature of the VMRGs was created using univariate Cox regression and LASSO Cox regression analyses. To evaluate differences in immune cell infiltration, we employed ssGSEA. Afterwards, we created an innovative risk assessment model, known as the VM index, along with a nomogram to forecast the prognosis of ccRCC. Additionally, we verified the expression of an important gene related to VM, peroxiredoxin 2 (PRDX2), in tissue samples. Furthermore, we assessed the sensitivity to drugs in various groups by utilizing the pRRophetic R package. Results: Significant predictors of survival rates in both high- and low-risk groups of KIRC patients were identified as VMRGs. The independent prognostic factors for RCC were confirmed by both univariate and multivariate Cox regression analyses, validating VMRG risk signatures. Differences were observed in drug sensitivity, immune checkpoint expression, and responses to immune therapy between patients classified into high- and low-VMRG-risk groups. Our nomograms consistently demonstrated precise predictive capabilities. Finally, we experimentally verified PRDX2 expression levels and their impact on prognosis. Conclusion: The signature predicts patient prognosis and therapy response, laying the groundwork for future clinical strategies in treating ccRCC patients.

Molecular Characterization, Tumor Microenvironment Association, and Drug Susceptibility of DNA Methylation-Driven Genes in Renal Cell Carcinoma.

Accumulating evidence suggests that DNA methylation has essential roles in the development of renal cell carcinoma (RCC). Aberrant DNA methylation acts as a vital role in RCC progression through regulating the gene expression, yet little is known about the role of methylation and its association with prognosis in RCC. The purpose of this study is to explore the DNA methylation-driven genes for establishing prognostic-related molecular clusters and providing a basis for survival prediction. In this study, 5,198 differentially expressed genes (DEGs) and 270 DNA methylation-driven genes were selected to obtain 146 differentially expressed DNA methylation-driven genes (DEMDGs). Two clusters were distinguished by consensus clustering using 146 DEMDGs. We further evaluated the immune status of two clusters and selected 106 DEGs in cluster 1. Cluster-based immune status analysis and functional enrichment analysis of 106 DEGs provide new insights for the development of RCC. To predict the prognosis of patients with RCC, a prognostic model based on eight DEMDGs was constructed. The patients were divided into high-risk groups and low-risk groups based on their risk scores. The predictive nomogram and the web-based survival rate calculator (http://127.0.0.1:3496) were built to validate the predictive accuracy of the prognostic model. Gene set enrichment analysis was performed to annotate the signaling pathways in which the genes are enriched. The correlation of the risk score with clinical features, immune status, and drug susceptibility was also evaluated. These results suggested that the prognostic model might be a promising prognostic tool for RCC and might facilitate the management of patients with RCC.

Identification of a Five-miRNA Signature for Diagnosis of Kidney Renal Clear Cell Carcinoma.

Motivation: Kidney renal clear cell carcinoma, which is a common type and accounts for 70-80% of renal cell carcinoma, can easily lead to metastasis and even death. A reliable signature for diagnosis of this cancer is in need. Hence, we seek to select miRNAs for identifying kidney renal clear cell carcinoma. Method: A feature selection strategy is used and improved to identify microRNAs for diagnosis of kidney renal clear cell carcinoma. Samples representing kidney renal clear cell carcinoma and normal tissues are split into training and testing groups. Accumulated scores representing the variable importance of each miRNA are derived from an iteration of resampling, training, and scoring. Those miRNAs with higher scores are selected based on the Gaussian mixture model. The sample split is repeated ten times to get more central miRNAs. Results: A total of 611 samples are downloaded from TCGA, each of which contains 1,343 miRNAs. The improved feature selection method is implemented, and five miRNAs are identified as a biomarker for diagnosis of kidney renal clear cell carcinoma. GSE151419 and GSE151423 are selected as the independent testing sets. Experimental results indicate the effectiveness of the selected signature. Both data-driven measurements and knowledge-driven evidence are given to show the effectiveness of our selection results.

The clinical significance, immune infiltration, and tumor mutational burden of angiogenesis-associated lncRNAs in kidney renal clear cell carcinoma.

Background: Poor prognosis of kidney renal clear cell carcinoma (KIRC) is often related to angiogenesis. The lncRNAs that regulate angiogenesis could also affect the prognosis of KIRC. It is meaningful for us to use lncRNAs related to angiogenesis to construct a generic, individualized prognostic signature for patients with KIRC. Methods: We identified eight angiogenesis-associated genes (AAGs) by differential expression analysis and univariate Cox regression from The Cancer Genome Atlas dataset, including 537 KIRC samples and 72 normal samples. In total, 23 prognostic lncRNAs were screened out after Pearson correlation analysis and univariate Cox regression analysis. Then, we performed least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression to establish a four-AAG-related lncRNA prognostic signature. Results: The risk score was calculated for each KIRC patients by using a four-AAG-related lncRNA prognostic signature. We divided the KIRC patients into high- and low-risk groups by the median of the risk score. It was confirmed that the AAG-related lncRNA prognostic signature has good prognostic value for KIRC patients by time-dependent receiver operating characteristic and Kaplan-Meier survival analysis. We identified 3,399 differentially expressed genes between the high- and low-risk groups and performed their functional enrichment analyses. The AAG-related lncRNA prognostic signature was an independent prognostic predictor for KIRC patients and was used to perform a combined nomogram. We reevaluated them in terms of survival, clinic characteristics, tumor-infiltrating immune cells and tumor mutation burden. Conclusion: Our research indicates that the AAG-related lncRNA prognostic signature is a promising and potential independent prognostic indicator for KIRC patients. Then, it could offer new insights into the prognosis assessment and potential treatment strategies of KIRC patients.

Tumor-associated macrophage-derived exosomes transmitting miR-193a-5p promote the progression of renal cell carcinoma via TIMP2-dependent vasculogenic mimicry.

Previous studies have investigated whether tumor-associated macrophages (TAMs) play tumorigenic and immunosuppressive roles to encourage cancer development, but the role of TAMs in regulating vasculogenic mimicry (VM) in clear-cell renal cell carcinoma (ccRCC) cells has not been completely clarified. We conducted immunostaining of the tumor-associated macrophage biomarkers CD68/CD163 and double staining for PAS/CD31 in ccRCC human specimens to find that higher TAM infiltration was positively correlated with VM formation. Then we demonstrated that TAM-derived exosomes downregulate TIMP2 expression in RCC cells to promote VM and invasion by shuttling miR-193a-5p. Mechanistic analysis indicated that HIF-1α upregulation in macrophages could transcriptionally increase miR-193a-5p expression. Exosome-shuttled miR-193a-5p then targeted the 3' untranslated region (UTR) of TIMP2 mRNA to suppress its translation. A preclinical study using an in vivo orthotopic xenograft model of ccRCC in mice substantiated that TAM-derived exosomes enhance VM and enable tumor progression, which confirmed our in vitro data. Suppressing TAM-derived exosomal miR-193a-5p successfully inhibited tumor progression and metastasis. Overall, miR-193a-5p from TAM-derived exosomes downregulates the TIMP2 gene to facilitate the development of RCC, which provides a novel perspective for developing therapeutic strategies for RCC.

Intestinal dysbacteriosis leads to kidney stone disease.

The formation and physicochemical properties of kidney stones (KSs) are closely associated with diet. In view of the differences in ethnicity and dietary composition between Chinese and Western populations, the present study aimed to investigate the association between intestinal dysbacteriosis and KSs in China. The current study examined the differences in intestinal microbes between the KS disease (KSD) and the healthy control (HLT) groups, and statistically significant differences based on 16s rRNA gene amplicons were identified using a Student's t­test or one­way ANOVA. In addition, the calcium oxalate KS (COKS), uric acid KS (UAKS) and carbonate apatite KS(CCKS) groups were compared with a non­parametric statistical test. Determination of bacterial abundance was performed via the analysis of 16s rRNA marker gene sequences using next­generation sequencing. Firmicutes (F) and Bacteroides (B) levels were significantly higher in the KSD group compared with the HLT group (B/F=0.67 vs. 0.08; P<0.001), as were the overall levels of B (6.19­fold higher compared with the HLT group; 22.2 vs. 3.6%; P<0.001). The Prevotella­9 abundance levels in the KSD group were 4.65­fold higher compared with those in the HLT group (8.8 vs. 1.9%; P<0.001). The levels of Blautia and Lachnoclostridium were significantly decreased in the KSD group (13.3 vs. 6.0%; and 5.0 vs. 7.9%; both P<0.05). Moreover, Prevotella­9 levels were higher in non­calciferous KSs (UAKS) compared with calciferous KSs (COKS and CCKS). Therefore, the findings of the present study indicated a key association between specific KS components and intestinal flora, providing a theoretical basis for new treatment methods for KSs. Moreover, differences and interactions between these bacteria could initially predict specific types of urolithiasis.

Tumor Cell-Derived TGFß1 Attenuates Antitumor Immune Activity of T Cells via Regulation of PD-1 mRNA.

Dysfunction in T-cell antitumor activity contributes to the tumorigenesis, progression, and poor outcome of clear cell renal cell carcinoma (ccRCC), with this dysfunction resulting from high expression of programmed cell death-1 (PD-1) in T cells. However, the molecular mechanisms maintaining high PD-1 expression in T cells have not been fully investigated in ccRCC. Here, we describe a mechanism underlying the regulation of PD-1 at the mRNA level and demonstrated its impact on T-cell dysfunction. Transcriptomic analysis identified a correlation between TGFß1 and PD-1 mRNA levels in ccRCC samples. The mechanism underlying the regulation of PD-1 mRNA was then investigated in vitro and in vivo using syngeneic tumor models. We also observed that TGFß1 had prognostic significance in patients with ccRCC, and its expression was associated with PD-1 mRNA expression. CcRCC-derived TGFß1 activated P38 and induced the phosphorylation of Ser10 on H3, which recruited p65 to increase SRSF3 and SRSF5 expression in T cells. As a result, the half-life of PD-1 mRNA in T cells was prolonged. SRSF3 coordinated with NXF1 to induce PD-1 mRNA extranuclear transport in T cells. We then demonstrated that TGFß1 could induce SRSF3 expression to restrict the antitumor activity of T cells, which influenced immunotherapy outcomes in ccRCC mouse models. Our findings highlight that tumor-derived TGFß1 mediates immune evasion and has potential as a prognostic biomarker and therapeutic target in ccRCC.See related Spotlight on p. 1464.

MiR-216a exerts tumor-suppressing functions in renal cell carcinoma by targeting TLR4.

MiR-216a, a tumor-related microRNA (miRNA), has been reported to be implicated in the tumorigenesis and progression of diverse types of human malignancies; however, its role in renal cell carcinoma (RCC) remains unclear. This study aimed to explore the biological role of miR-216a in RCC and clarify the potential mechanisms involved. In the present study, miR-216a was found to be significantly down-regulated in both RCC tissues and cell lines. Functional studies demonstrated that enhanced expression of miR-216a suppressed RCC cell proliferation, migration and invasion in vitro, inhibited tumor growth in vivo, and induced RCC cell cycle arrest and apoptosis. Moreover, the tumor-suppressing effects of miR-216a in RCC were abrogated by the miR-216a inhibitor treatment. Notably, toll-like receptor 4 (TLR4) was downregulated by miR-216a via direct binding to its 3' untranslated region in RCC cells. Furthermore, TLR4 expression was discovered to be markedly up-regulated and inversely correlated with miR-216a expression in RCC tissues. Mechanistic studies revealed that restoring the expression of TLR-4 alleviated miR-216a-induced inhibitory effects on proliferation, migration and invasion of RCC cells. Taken together, these findings suggest that miR-216a functions as a tumor suppressor in RCC by directly targeting TLR4 and that miR-216a might be a novel therapeutic target for RCC.

Study of the Changes of Acrosomal Enzyme, Nitric Oxide Synthase, and Superoxide Dismutase of Infertile Patients with Positive Antisperm Antibody in Seminal Plasma.

The purpose of this article is to study the effect of positive antisperm antibody (AsAb) in seminal plasma on acrosomal enzyme activity, nitric oxide synthase (NOS) activity, and superxide dismutase (SOD) activity of spermatozoa. A total of 40 infertility patients with positive AsAb in seminal plasma were selected as experimental group, and 40 fertile males were selected as control group. Based on the changes in absorbance, the acrosomal enzyme activity was detected by the BAEE/ADH method, the NOS activity was detected by the redoxreaction assay, and SOD level was measured with xanthine oxidase method. Compared with the control group, acrosomal enzyme activity of spermatozoa of the experimental group was significantly decreased (P < 0.01), NOS activity was apparently increased (P < 0.01), and the SOD level in seminal plasma was significantly decreased (P < 0.01). The infertility caused by positive AsAb in seminal plasma may be related to the changes in the acrosomal enzyme of spermatozoa and the SOD and NOS activities in seminal plasma.

The Change of Semen Superoxide Dismutase and Acrosin Activity in the Sterility of Male Patients with Positive Antisperm Antibody.

In this study, we report the change of semen superoxide dismutase (SOD) and acrosin activities in the male sterility patients with positive antisperm antibody (AsAb). The activity of SOD was measured by xanthine oxidase assay and sperm acrosin activity was calculated by BAEE/ADH. Our data show that compared with the normal fertility group, the semen SOD activity in AsAb-positive patients was significantly lower. Similarly, the sperm acrosin activity in AsAb-positive patients was also significantly lower. Our results suggest that the sterility resulting from positive AsAb may be related with the changes of semen SOD and sperm acrosin activities.