Kidney Renal Clear Cell Carcinoma(KIRC)is a malignant tumor that carries a substantial risk of morbidity and mortality.The MMP family assumes a crucial role in tumor invasion and metastasis.This study aimed to uncover...Kidney Renal Clear Cell Carcinoma(KIRC)is a malignant tumor that carries a substantial risk of morbidity and mortality.The MMP family assumes a crucial role in tumor invasion and metastasis.This study aimed to uncover the mechanistic relevance of the MMP gene family as a therapeutic target and diagnostic biomarker in Kidney Renal Clear Cell Carcinoma(KIRC)through a comprehensive approach encompassing both computational and molecular analyses.STRING,Cytoscape,UALCAN,GEPIA,OncoDB,HPA,cBioPortal,GSEA,TIMER,ENCORI,DrugBank,targeted bisulfite sequencing(bisulfite-seq),conventional PCR,Sanger sequencing,and RT-qPCR based analyses were used in the present study to analyze MMP gene family members to accurately determine a few hub genes that can be utilized as both therapeutic targets and diagnostic biomarkers for KIRC.By performing STRING and Cytohubba analyses of the 24 MMP gene family members,MMP2(matrix metallopeptidase 2),MMP9(matrix metallopeptidase 9),MMP12(matrix metallopeptidase 12),and MMP16(matrix metallopeptidase 16)genes were denoted as hub genes having highest degree scores.After analyzing MMP2,MMP9,MMP12,and MMP16 via various TCGA databases and RT-qPCR technique across clinical samples and KIRC cell lines,interestingly,all these hub genes were found significantly overexpressed at mRNA and protein levels in KIRC samples relative to controls.The notable effect of the up-regulated MMP2,MMP9,MMP12,and MMP16 was also documented on the overall survival(OS)of the KIRC patients.Moreover,targeted bisulfite-sequencing(bisulfite-seq)analysis revealed that promoter hypomethylation pattern was associated with up-regulation of hub genes(MMP2,MMP9,MMP12,and MMP16).In addition to this,hub genes were involved in various diverse oncogenic pathways.The MMP gene family members(MMP2,MMP9,MMP12,and MMP16)may serve as therapeutic targets and prognostic biomarkers in KIRC.展开更多
Background:Kidney renal clear cell carcinoma(KIRC),a prevalent urological malignancy,represents about 3%of all adult malignancies.KIRC,accounting for~75%of renal malignancies,has poor prognosis in metastatic stages.Id...Background:Kidney renal clear cell carcinoma(KIRC),a prevalent urological malignancy,represents about 3%of all adult malignancies.KIRC,accounting for~75%of renal malignancies,has poor prognosis in metastatic stages.Identifying robust prognostic markers remains urgent.Block of proliferation 1(BOP1),a WD40-repeat protein,is implicated in cancer pathogenesis,but its role in KIRC is unclear.This study aimed to characterize BOP1 expression in KIRC and evaluate its prognostic value.Methods:BOP1 transcriptional levels were assessed through TCGA-KIRC RNA sequencing datasets.ROC curve construction was implemented via R statistical packages for diagnostic evaluation.Patient survival outcomes were visualized through Kaplan-Meier plotting with log-rank testing.Multivariate logistic regression models quantified associations between BOP1 expression and clinicopathological parameters.TIMER algorithm analyzed immune microenvironment composition.Genomic alterations and epigenetic modifications were investigated using cBioPortal and MethSurv platforms respectively.BOP1 protein levels in 786-O clear cell renal cell carcinoma(ccRCC)versus HK-2(normal renal)cell lines were validated by immunoblotting.Results:Evaluation of the TCGA database demonstrated that BOP1 mRNA abundance was higher in tumor specimens than in corresponding adjacent tissues.Patients with KIRC who had high BOP1 expression had differential overall survival(OS),disease-specific survival(DSS),and disease-free interval(DFI).BOP1 expression accurately recognised tumour tissues versus normal tissues(AUC=0.858),and the area under the ROCs for survival at 1,3,and 5 years were all greater than 0.6.The BOP1 gene variant rate was<1%.Out of the 15 DNA methylation CpG sites examined,7 exhibited prognostic significance in KIRC.BOP1 displayed a distinct relationship with immune cell infiltration in KIRC.The 786-O experimental group exhibited substantially higher BOP1 expression,as confirmed by Western blot detection.Conclusion:This study indicates that heightened BOP1 expression is linked to an adverse prognosis in KIRC,establishing it as an independent risk factor for this disease.These findings establish BOP1 as a novel and independent prognostic biomarker for KIRC,offering potential clinical utility for risk stratification and personalized therapeutic strategies.展开更多
The low survival rate of Kidney renal clear cell carcinoma(KIRC)patients is largely attributed to cisplatin resistance.Rather than focusing solely on individual proteins,exploring protein-protein interactions could of...The low survival rate of Kidney renal clear cell carcinoma(KIRC)patients is largely attributed to cisplatin resistance.Rather than focusing solely on individual proteins,exploring protein-protein interactions could offer greater insight into drug resistance.To this end,a series of in silico and in vitro experiments were conducted to identify hub genes in the intricate network of cisplatin resistance-related genes in KIRC chemotherapy.The genes involved in cisplatin resistance across KIRC were retrieved from the National Center for Biotechnology Information(NCBI)database using search terms as“Kidney renal clear cell carcinoma”and“Cisplatin resistance”.The genes retrieved were analyzed for hub gene identification using the STRING database and Cytoscape tool.Expression and promoter methylation profiling of the hub genes was done using UALCAN,GEPIA,OncoDB,and HPA databases.Mutational,survival,functional enrichment,immune cell infiltration,and drug prediction analyses of the hub genes were performed using the cBioPortal,GEPIA,GSEA,TIMER,and DrugBank databases.Lastly,expression and methylation levels of the hub genes were validated on two cisplatin-resistant RCC cell lines(786-O and A-498)and a normal renal tubular epithelial cell line(HK-2)using two high throughput techniques,including targeted bisulfite sequencing(bisulfite-seq)and RT-qPCR.A total of 124 genes were identified as being associated with cisplatin resistance in KIRC.Out of these genes,MCL1,IGF1R,CCND1,and PTEN were identified as hub genes and were found to have significant(p<0.05)variations in their mRNA and protein expressions and effects on the overall survival(OS)of the KIRC patients.Moreover,an aberrant promoter methylation pattern was found to be associated with the dysregulation of the hub genes.In addition to this,hub genes were also linked with different cisplatin resistance-causing pathways.Thus,hub genes can be targeted with Alvocidib,Estradiol,Tretinoin,Capsaicin,Dronabinol,Metribolone,Calcitriol,Acetaminophen,Acitretin,Cyclosporine,Azacitidine,Genistein,and Resveratrol drugs.As the pathogenesis of KIRC is complex,targeting hub genes and associated pathways involved in cisplatin resistance could bring a milestone change in the drug discovery and management of drug resistance,which might uplift overall survival among KIRC patients.展开更多
EVI2A has emerged as a significant biomarker in various diseases;however,its biological role and mechanism in kidney renal clear cell carcinoma(KIRC)remains unexplored.We used TCGA and GEO databases to analyze EVI2A g...EVI2A has emerged as a significant biomarker in various diseases;however,its biological role and mechanism in kidney renal clear cell carcinoma(KIRC)remains unexplored.We used TCGA and GEO databases to analyze EVI2A gene expression comprehensively and performed pan-cancer assessments.Clinical relevance was evaluated through Kaplan-Meier analysis and ROC curves.The gene’s immune relevance was explored through analyses of the tumor microenvironment(TME),Tumor Immune Single-cell Hub(TISCH),immune checkpoints,and immunotherapy sensitivity.Our results indicate that EVI2A expression is upregulated in KIRC,showing correlations with tumor grade and T/N/M stage.EVI2A demonstrates high diagnostic accuracy(AUC=0.906)and predicts poor overall and progression-free survival in KIRC patients.Furthermore,EVI2A expression exhibits significant associations with immunity,including TME scores and specific immune cell types such as Tfh cells,CD4 memory T cells,and CD8+T cells.Elevated EVI2A expression suggests increased sensitivity to PD-1/CTLA-4 and tyrosine kinase inhibitors.In vitro assays confirmed the impact of EVI2A on KIRC behavior,with its knockdown resulting in reduced cell proliferation and migration.In conclusion,our comprehensive analysis identifies EVI2A as a promising biomarker and a novel therapeutic target for intervening in KIRC.These findings hold significant implications for further research and potential clinical applications.展开更多
Background:Cuprotosis is a newly discovered Copper-dependence form of cell death.Cuprotosis-related genes(CRGs)regulating mitochondrial metabolism and protein lipoylation suggest the critical roles cuprotosis for in c...Background:Cuprotosis is a newly discovered Copper-dependence form of cell death.Cuprotosis-related genes(CRGs)regulating mitochondrial metabolism and protein lipoylation suggest the critical roles cuprotosis for in cancer.However,the prognostic value of CRGs in the highly immunogenic cancer type,kidney renal clear cell carcinoma(KIRC)needs to be further studied.Herein,we aim to identify novel prognostic genes and construct a CRGs prognostic signature for KIRC.Methods:We downloaded the mRNA sequencing data from the Cancer Genome Atlas,differentially expressed CRGs were screened out and their bio-function was elucidated.Then we used Cox regression analysis to establish a prediction model of CRGs.Subsequently,a prognostic scoring model based on the regression coefficients of the screened out CRGs and their corresponding mRNA expressions were constructed and validated.Results:Seven differentially expressed CRGs were screened.A two-gene model was built to separate samples into high-risk and low-risk groups.Overall survival was lower in the high-risk group than in the low-risk group(p<0.05).The receiver operating characteristic curve showed a good diagnostic efficiency of the signature.We verified this prognostic model in the Cancer Genome Atlas test cohorts.The risk score was identified as an independent prognostic factor via multivariate Cox regression.Moreover,the nomogram was used to predict 1-/3-/5-year OS of KIRC patients.Furthermore,risk score has a very significant effect on the infiltration of immune cells and the expression of immune checkpoints.Conclusions:To conclude,we constructed a novel prognostic signature based on CRGs.Targeting cuprotosis may represent a promising approach for the treatment of KIRC.展开更多
基金The authors would like to extend their sincere appreciation to the Researchers Supporting Project Number(RSP2023R457),King Saud University,Riyadh,Saudi Arabia.
文摘Kidney Renal Clear Cell Carcinoma(KIRC)is a malignant tumor that carries a substantial risk of morbidity and mortality.The MMP family assumes a crucial role in tumor invasion and metastasis.This study aimed to uncover the mechanistic relevance of the MMP gene family as a therapeutic target and diagnostic biomarker in Kidney Renal Clear Cell Carcinoma(KIRC)through a comprehensive approach encompassing both computational and molecular analyses.STRING,Cytoscape,UALCAN,GEPIA,OncoDB,HPA,cBioPortal,GSEA,TIMER,ENCORI,DrugBank,targeted bisulfite sequencing(bisulfite-seq),conventional PCR,Sanger sequencing,and RT-qPCR based analyses were used in the present study to analyze MMP gene family members to accurately determine a few hub genes that can be utilized as both therapeutic targets and diagnostic biomarkers for KIRC.By performing STRING and Cytohubba analyses of the 24 MMP gene family members,MMP2(matrix metallopeptidase 2),MMP9(matrix metallopeptidase 9),MMP12(matrix metallopeptidase 12),and MMP16(matrix metallopeptidase 16)genes were denoted as hub genes having highest degree scores.After analyzing MMP2,MMP9,MMP12,and MMP16 via various TCGA databases and RT-qPCR technique across clinical samples and KIRC cell lines,interestingly,all these hub genes were found significantly overexpressed at mRNA and protein levels in KIRC samples relative to controls.The notable effect of the up-regulated MMP2,MMP9,MMP12,and MMP16 was also documented on the overall survival(OS)of the KIRC patients.Moreover,targeted bisulfite-sequencing(bisulfite-seq)analysis revealed that promoter hypomethylation pattern was associated with up-regulation of hub genes(MMP2,MMP9,MMP12,and MMP16).In addition to this,hub genes were involved in various diverse oncogenic pathways.The MMP gene family members(MMP2,MMP9,MMP12,and MMP16)may serve as therapeutic targets and prognostic biomarkers in KIRC.
基金supported by Young Talents Cultivation Program of Xianning City,the Natural Science Foundation of Hubei Province,China(No.2024AFB502)Ph.D.Start-up Funding(No.BK202413)Medical Fund(No.2023YKY04)of Hubei University of Science and Technology.
文摘Background:Kidney renal clear cell carcinoma(KIRC),a prevalent urological malignancy,represents about 3%of all adult malignancies.KIRC,accounting for~75%of renal malignancies,has poor prognosis in metastatic stages.Identifying robust prognostic markers remains urgent.Block of proliferation 1(BOP1),a WD40-repeat protein,is implicated in cancer pathogenesis,but its role in KIRC is unclear.This study aimed to characterize BOP1 expression in KIRC and evaluate its prognostic value.Methods:BOP1 transcriptional levels were assessed through TCGA-KIRC RNA sequencing datasets.ROC curve construction was implemented via R statistical packages for diagnostic evaluation.Patient survival outcomes were visualized through Kaplan-Meier plotting with log-rank testing.Multivariate logistic regression models quantified associations between BOP1 expression and clinicopathological parameters.TIMER algorithm analyzed immune microenvironment composition.Genomic alterations and epigenetic modifications were investigated using cBioPortal and MethSurv platforms respectively.BOP1 protein levels in 786-O clear cell renal cell carcinoma(ccRCC)versus HK-2(normal renal)cell lines were validated by immunoblotting.Results:Evaluation of the TCGA database demonstrated that BOP1 mRNA abundance was higher in tumor specimens than in corresponding adjacent tissues.Patients with KIRC who had high BOP1 expression had differential overall survival(OS),disease-specific survival(DSS),and disease-free interval(DFI).BOP1 expression accurately recognised tumour tissues versus normal tissues(AUC=0.858),and the area under the ROCs for survival at 1,3,and 5 years were all greater than 0.6.The BOP1 gene variant rate was<1%.Out of the 15 DNA methylation CpG sites examined,7 exhibited prognostic significance in KIRC.BOP1 displayed a distinct relationship with immune cell infiltration in KIRC.The 786-O experimental group exhibited substantially higher BOP1 expression,as confirmed by Western blot detection.Conclusion:This study indicates that heightened BOP1 expression is linked to an adverse prognosis in KIRC,establishing it as an independent risk factor for this disease.These findings establish BOP1 as a novel and independent prognostic biomarker for KIRC,offering potential clinical utility for risk stratification and personalized therapeutic strategies.
基金The authors would like to extend their sincere appreciation to the Researchers Supporting Project Number(RSPD2023R986)King Saud University,Riyadh,Saudi Arabia.
文摘The low survival rate of Kidney renal clear cell carcinoma(KIRC)patients is largely attributed to cisplatin resistance.Rather than focusing solely on individual proteins,exploring protein-protein interactions could offer greater insight into drug resistance.To this end,a series of in silico and in vitro experiments were conducted to identify hub genes in the intricate network of cisplatin resistance-related genes in KIRC chemotherapy.The genes involved in cisplatin resistance across KIRC were retrieved from the National Center for Biotechnology Information(NCBI)database using search terms as“Kidney renal clear cell carcinoma”and“Cisplatin resistance”.The genes retrieved were analyzed for hub gene identification using the STRING database and Cytoscape tool.Expression and promoter methylation profiling of the hub genes was done using UALCAN,GEPIA,OncoDB,and HPA databases.Mutational,survival,functional enrichment,immune cell infiltration,and drug prediction analyses of the hub genes were performed using the cBioPortal,GEPIA,GSEA,TIMER,and DrugBank databases.Lastly,expression and methylation levels of the hub genes were validated on two cisplatin-resistant RCC cell lines(786-O and A-498)and a normal renal tubular epithelial cell line(HK-2)using two high throughput techniques,including targeted bisulfite sequencing(bisulfite-seq)and RT-qPCR.A total of 124 genes were identified as being associated with cisplatin resistance in KIRC.Out of these genes,MCL1,IGF1R,CCND1,and PTEN were identified as hub genes and were found to have significant(p<0.05)variations in their mRNA and protein expressions and effects on the overall survival(OS)of the KIRC patients.Moreover,an aberrant promoter methylation pattern was found to be associated with the dysregulation of the hub genes.In addition to this,hub genes were also linked with different cisplatin resistance-causing pathways.Thus,hub genes can be targeted with Alvocidib,Estradiol,Tretinoin,Capsaicin,Dronabinol,Metribolone,Calcitriol,Acetaminophen,Acitretin,Cyclosporine,Azacitidine,Genistein,and Resveratrol drugs.As the pathogenesis of KIRC is complex,targeting hub genes and associated pathways involved in cisplatin resistance could bring a milestone change in the drug discovery and management of drug resistance,which might uplift overall survival among KIRC patients.
基金the Ethics Committee of the First Affiliated Hospital of Nanchang University(Approval:(2023)CDYFYYLK(03-013)).
文摘EVI2A has emerged as a significant biomarker in various diseases;however,its biological role and mechanism in kidney renal clear cell carcinoma(KIRC)remains unexplored.We used TCGA and GEO databases to analyze EVI2A gene expression comprehensively and performed pan-cancer assessments.Clinical relevance was evaluated through Kaplan-Meier analysis and ROC curves.The gene’s immune relevance was explored through analyses of the tumor microenvironment(TME),Tumor Immune Single-cell Hub(TISCH),immune checkpoints,and immunotherapy sensitivity.Our results indicate that EVI2A expression is upregulated in KIRC,showing correlations with tumor grade and T/N/M stage.EVI2A demonstrates high diagnostic accuracy(AUC=0.906)and predicts poor overall and progression-free survival in KIRC patients.Furthermore,EVI2A expression exhibits significant associations with immunity,including TME scores and specific immune cell types such as Tfh cells,CD4 memory T cells,and CD8+T cells.Elevated EVI2A expression suggests increased sensitivity to PD-1/CTLA-4 and tyrosine kinase inhibitors.In vitro assays confirmed the impact of EVI2A on KIRC behavior,with its knockdown resulting in reduced cell proliferation and migration.In conclusion,our comprehensive analysis identifies EVI2A as a promising biomarker and a novel therapeutic target for intervening in KIRC.These findings hold significant implications for further research and potential clinical applications.
基金financially supported by Hunan Provincial Natural Science Foundation of China 2022JJ40405(X.L).
文摘Background:Cuprotosis is a newly discovered Copper-dependence form of cell death.Cuprotosis-related genes(CRGs)regulating mitochondrial metabolism and protein lipoylation suggest the critical roles cuprotosis for in cancer.However,the prognostic value of CRGs in the highly immunogenic cancer type,kidney renal clear cell carcinoma(KIRC)needs to be further studied.Herein,we aim to identify novel prognostic genes and construct a CRGs prognostic signature for KIRC.Methods:We downloaded the mRNA sequencing data from the Cancer Genome Atlas,differentially expressed CRGs were screened out and their bio-function was elucidated.Then we used Cox regression analysis to establish a prediction model of CRGs.Subsequently,a prognostic scoring model based on the regression coefficients of the screened out CRGs and their corresponding mRNA expressions were constructed and validated.Results:Seven differentially expressed CRGs were screened.A two-gene model was built to separate samples into high-risk and low-risk groups.Overall survival was lower in the high-risk group than in the low-risk group(p<0.05).The receiver operating characteristic curve showed a good diagnostic efficiency of the signature.We verified this prognostic model in the Cancer Genome Atlas test cohorts.The risk score was identified as an independent prognostic factor via multivariate Cox regression.Moreover,the nomogram was used to predict 1-/3-/5-year OS of KIRC patients.Furthermore,risk score has a very significant effect on the infiltration of immune cells and the expression of immune checkpoints.Conclusions:To conclude,we constructed a novel prognostic signature based on CRGs.Targeting cuprotosis may represent a promising approach for the treatment of KIRC.
