1.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;53(1):47-57
Objective:To classify bladder cancer based on immune cell infiltration score and to construct a prognosis assessment model of patients with bladder cancer.Methods:The transcriptome data and clinical data of breast cancer patients were obtained from the The Cancer Genome Atlas(TCGA)database.Single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells.The classification of breast cancer patients was achieved by unsupervised clustering,and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed.The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis(WGCNA),and the key genes in the modules were identified.A risk scoring model and a nomogram for prognosis assessment of bladder cancer patients were constructed and verified.Results:B cells,mast cells,neutrophils,T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer.The patients were clustered into two groups(Cluster 1′ and Custer 2)based on immune cell infiltration scores.Compared with patients with Cluster 1′,patients with Cluster 2 were more likely to benefit from immunotherapy(P<0.05),and patients with Cluster 2 were more sensitive to Enbeaten,Docetaxel,Cyclopamine,and Akadixin(P<0.05).35 genes related to key immune cells were screened out by WGCNA and 4 genes(GPR171,HOXB3,HOXB5 and HOXB6)related to the prognosis of bladder cancer were further screened by LASSO Cox regression.The areas under the ROC curve(AUC)of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-,3-and 5-year survival of patients were 0.735,0.765 and 0.799,respectively.The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-,3-,and 5-year overall survival of bladder cancer patients.Conclusions:According to the immune cell infiltration score,bladder cancer patients can be classified.Furthermore,bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.
2.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;53(1):47-57
Objective:To classify bladder cancer based on immune cell infiltration score and to construct a prognosis assessment model of patients with bladder cancer.Methods:The transcriptome data and clinical data of breast cancer patients were obtained from the The Cancer Genome Atlas(TCGA)database.Single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells.The classification of breast cancer patients was achieved by unsupervised clustering,and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed.The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis(WGCNA),and the key genes in the modules were identified.A risk scoring model and a nomogram for prognosis assessment of bladder cancer patients were constructed and verified.Results:B cells,mast cells,neutrophils,T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer.The patients were clustered into two groups(Cluster 1′ and Custer 2)based on immune cell infiltration scores.Compared with patients with Cluster 1′,patients with Cluster 2 were more likely to benefit from immunotherapy(P<0.05),and patients with Cluster 2 were more sensitive to Enbeaten,Docetaxel,Cyclopamine,and Akadixin(P<0.05).35 genes related to key immune cells were screened out by WGCNA and 4 genes(GPR171,HOXB3,HOXB5 and HOXB6)related to the prognosis of bladder cancer were further screened by LASSO Cox regression.The areas under the ROC curve(AUC)of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-,3-and 5-year survival of patients were 0.735,0.765 and 0.799,respectively.The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-,3-,and 5-year overall survival of bladder cancer patients.Conclusions:According to the immune cell infiltration score,bladder cancer patients can be classified.Furthermore,bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.
3.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;53(1):47-57
Objective:To classify bladder cancer based on immune cell infiltration score and to construct a prognosis assessment model of patients with bladder cancer.Methods:The transcriptome data and clinical data of breast cancer patients were obtained from the The Cancer Genome Atlas(TCGA)database.Single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells.The classification of breast cancer patients was achieved by unsupervised clustering,and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed.The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis(WGCNA),and the key genes in the modules were identified.A risk scoring model and a nomogram for prognosis assessment of bladder cancer patients were constructed and verified.Results:B cells,mast cells,neutrophils,T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer.The patients were clustered into two groups(Cluster 1′ and Custer 2)based on immune cell infiltration scores.Compared with patients with Cluster 1′,patients with Cluster 2 were more likely to benefit from immunotherapy(P<0.05),and patients with Cluster 2 were more sensitive to Enbeaten,Docetaxel,Cyclopamine,and Akadixin(P<0.05).35 genes related to key immune cells were screened out by WGCNA and 4 genes(GPR171,HOXB3,HOXB5 and HOXB6)related to the prognosis of bladder cancer were further screened by LASSO Cox regression.The areas under the ROC curve(AUC)of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-,3-and 5-year survival of patients were 0.735,0.765 and 0.799,respectively.The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-,3-,and 5-year overall survival of bladder cancer patients.Conclusions:According to the immune cell infiltration score,bladder cancer patients can be classified.Furthermore,bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.
4.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;53(1):47-57
Objective:To classify bladder cancer based on immune cell infiltration score and to construct a prognosis assessment model of patients with bladder cancer.Methods:The transcriptome data and clinical data of breast cancer patients were obtained from the The Cancer Genome Atlas(TCGA)database.Single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells.The classification of breast cancer patients was achieved by unsupervised clustering,and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed.The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis(WGCNA),and the key genes in the modules were identified.A risk scoring model and a nomogram for prognosis assessment of bladder cancer patients were constructed and verified.Results:B cells,mast cells,neutrophils,T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer.The patients were clustered into two groups(Cluster 1′ and Custer 2)based on immune cell infiltration scores.Compared with patients with Cluster 1′,patients with Cluster 2 were more likely to benefit from immunotherapy(P<0.05),and patients with Cluster 2 were more sensitive to Enbeaten,Docetaxel,Cyclopamine,and Akadixin(P<0.05).35 genes related to key immune cells were screened out by WGCNA and 4 genes(GPR171,HOXB3,HOXB5 and HOXB6)related to the prognosis of bladder cancer were further screened by LASSO Cox regression.The areas under the ROC curve(AUC)of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-,3-and 5-year survival of patients were 0.735,0.765 and 0.799,respectively.The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-,3-,and 5-year overall survival of bladder cancer patients.Conclusions:According to the immune cell infiltration score,bladder cancer patients can be classified.Furthermore,bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.
5.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;53(1):47-57
Objective:To classify bladder cancer based on immune cell infiltration score and to construct a prognosis assessment model of patients with bladder cancer.Methods:The transcriptome data and clinical data of breast cancer patients were obtained from the The Cancer Genome Atlas(TCGA)database.Single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells.The classification of breast cancer patients was achieved by unsupervised clustering,and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed.The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis(WGCNA),and the key genes in the modules were identified.A risk scoring model and a nomogram for prognosis assessment of bladder cancer patients were constructed and verified.Results:B cells,mast cells,neutrophils,T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer.The patients were clustered into two groups(Cluster 1′ and Custer 2)based on immune cell infiltration scores.Compared with patients with Cluster 1′,patients with Cluster 2 were more likely to benefit from immunotherapy(P<0.05),and patients with Cluster 2 were more sensitive to Enbeaten,Docetaxel,Cyclopamine,and Akadixin(P<0.05).35 genes related to key immune cells were screened out by WGCNA and 4 genes(GPR171,HOXB3,HOXB5 and HOXB6)related to the prognosis of bladder cancer were further screened by LASSO Cox regression.The areas under the ROC curve(AUC)of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-,3-and 5-year survival of patients were 0.735,0.765 and 0.799,respectively.The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-,3-,and 5-year overall survival of bladder cancer patients.Conclusions:According to the immune cell infiltration score,bladder cancer patients can be classified.Furthermore,bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.
6.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;53(1):47-57
Objective:To classify bladder cancer based on immune cell infiltration score and to construct a prognosis assessment model of patients with bladder cancer.Methods:The transcriptome data and clinical data of breast cancer patients were obtained from the The Cancer Genome Atlas(TCGA)database.Single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells.The classification of breast cancer patients was achieved by unsupervised clustering,and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed.The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis(WGCNA),and the key genes in the modules were identified.A risk scoring model and a nomogram for prognosis assessment of bladder cancer patients were constructed and verified.Results:B cells,mast cells,neutrophils,T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer.The patients were clustered into two groups(Cluster 1′ and Custer 2)based on immune cell infiltration scores.Compared with patients with Cluster 1′,patients with Cluster 2 were more likely to benefit from immunotherapy(P<0.05),and patients with Cluster 2 were more sensitive to Enbeaten,Docetaxel,Cyclopamine,and Akadixin(P<0.05).35 genes related to key immune cells were screened out by WGCNA and 4 genes(GPR171,HOXB3,HOXB5 and HOXB6)related to the prognosis of bladder cancer were further screened by LASSO Cox regression.The areas under the ROC curve(AUC)of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-,3-and 5-year survival of patients were 0.735,0.765 and 0.799,respectively.The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-,3-,and 5-year overall survival of bladder cancer patients.Conclusions:According to the immune cell infiltration score,bladder cancer patients can be classified.Furthermore,bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.
7.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;53(1):47-57
Objective:To classify bladder cancer based on immune cell infiltration score and to construct a prognosis assessment model of patients with bladder cancer.Methods:The transcriptome data and clinical data of breast cancer patients were obtained from the The Cancer Genome Atlas(TCGA)database.Single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells.The classification of breast cancer patients was achieved by unsupervised clustering,and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed.The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis(WGCNA),and the key genes in the modules were identified.A risk scoring model and a nomogram for prognosis assessment of bladder cancer patients were constructed and verified.Results:B cells,mast cells,neutrophils,T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer.The patients were clustered into two groups(Cluster 1′ and Custer 2)based on immune cell infiltration scores.Compared with patients with Cluster 1′,patients with Cluster 2 were more likely to benefit from immunotherapy(P<0.05),and patients with Cluster 2 were more sensitive to Enbeaten,Docetaxel,Cyclopamine,and Akadixin(P<0.05).35 genes related to key immune cells were screened out by WGCNA and 4 genes(GPR171,HOXB3,HOXB5 and HOXB6)related to the prognosis of bladder cancer were further screened by LASSO Cox regression.The areas under the ROC curve(AUC)of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-,3-and 5-year survival of patients were 0.735,0.765 and 0.799,respectively.The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-,3-,and 5-year overall survival of bladder cancer patients.Conclusions:According to the immune cell infiltration score,bladder cancer patients can be classified.Furthermore,bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.
8.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;53(1):47-57
Objective:To classify bladder cancer based on immune cell infiltration score and to construct a prognosis assessment model of patients with bladder cancer.Methods:The transcriptome data and clinical data of breast cancer patients were obtained from the The Cancer Genome Atlas(TCGA)database.Single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells.The classification of breast cancer patients was achieved by unsupervised clustering,and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed.The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis(WGCNA),and the key genes in the modules were identified.A risk scoring model and a nomogram for prognosis assessment of bladder cancer patients were constructed and verified.Results:B cells,mast cells,neutrophils,T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer.The patients were clustered into two groups(Cluster 1′ and Custer 2)based on immune cell infiltration scores.Compared with patients with Cluster 1′,patients with Cluster 2 were more likely to benefit from immunotherapy(P<0.05),and patients with Cluster 2 were more sensitive to Enbeaten,Docetaxel,Cyclopamine,and Akadixin(P<0.05).35 genes related to key immune cells were screened out by WGCNA and 4 genes(GPR171,HOXB3,HOXB5 and HOXB6)related to the prognosis of bladder cancer were further screened by LASSO Cox regression.The areas under the ROC curve(AUC)of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-,3-and 5-year survival of patients were 0.735,0.765 and 0.799,respectively.The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-,3-,and 5-year overall survival of bladder cancer patients.Conclusions:According to the immune cell infiltration score,bladder cancer patients can be classified.Furthermore,bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.
9.Classification of bladder cancer based on immune cell infiltration and construction of a risk prediction model for prognosis.
Guicao YIN ; Shengqi ZHENG ; Wei ZHANG ; Xin DONG ; Lezhong QI ; Yifan LI
Journal of Zhejiang University. Medical sciences 2024;():1-11
OBJECTIVES:
To classify bladder cancer based on immune cell infiltration score and to construct a risk assessment model for prognosis of patients.
METHODS:
The transcriptome data and data of breast cancer patients were obtained from the TCGA database. The single sample gene set enrichment analysis was used to calculate the infiltration scores of 16 immune cells. The classification of breast cancer patients was realized by unsupervised clustering, and the sensitivity of patients with different types to immunotherapy and chemotherapy was analyzed. The key modules significantly related to the infiltration of key immune cells were identified by weighted correlation network analysis (WGCNA), and the key genes in the modules were extracted. A risk scoring model and a nomogram for risk assessment of prognosis for bladder cancer patients were constructed and verified.
RESULTS:
The immune cell infiltration scores of normal tissues and tumor tissues were calculated, and B cells, mast cells, neutrophils, T helper cells and tumor infiltrating lymphocytes were determined to be the key immune cells of bladder cancer. Breast cancer patients were clustered into two groups (Cluster 1 and Custer 2) based on immune cell infiltration scores. Compared with patients with Cluster 1, patients with Cluster 2 were more likely to benefit from immunotherapy (P<0.05), and patients with Cluster 2 were more sensitive to Enbeaten, Docetaxel, Cyclopamine, and Akadixin (P<0.05). WGCNA screened out 35 genes related to key immune cells, and 4 genes (GPR171, HOXB3, HOXB5 and HOXB6) related to the prognosis of bladder cancer were further screened by LASSO Cox regression. The areas under the ROC curve (AUC) of the bladder cancer prognosis risk scoring model based on these 4 genes to predict the 1-, 3- and 5-year survival of patients were 0.735, 0.765 and 0.799, respectively. The nomogram constructed by combining risk score and clinical parameters has high accuracy in predicting the 1-, 3-, and 5-year overall survival of bladder cancer patients.
CONCLUSIONS
According to the immune cell infiltration score, bladder cancer patients can be classified. And the bladder cancer prognosis risk scoring model and nomogram based on key immune cell-related genes have high accuracy in predicting the prognosis of bladder cancer patients.