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Yang R, He J, Luo W, Xiang R, Zou G, Zhang X, Liu H, Deng J. Comprehensive analysis and prognostic assessment of senescence-associated genes in bladder cancer. Discov Oncol 2024; 15:130. [PMID: 38668876 PMCID: PMC11052743 DOI: 10.1007/s12672-024-00987-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND The prevalence and mortality of bladder cancer (BLCA) present a significant medical challenge. While the function of senescence-related genes in tumor development is recognized, their prognostic significance in BLCA has not been thoroughly explored. METHODS BLCA transcriptome datasets were sourced from the TCGA and GEO repositories. Gene groupings were determined through differential gene expression and non-negative matrix factorization (NMF) methodologies. Key senescence-linked genes were isolated using singular and multivariate Cox regression analyses, combined with lasso regression. Validation was undertaken with GEO database information. Predictive models, or nomograms, were developed by merging risk metrics with clinical records, and their efficacy was gauged using ROC curve methodologies. The immune response's dependency on the risk metric was assessed through the immune phenomenon score (IPS). Additionally, we estimated IC50 metrics for potential chemotherapeutic agents. RESULTS Reviewing 406 neoplastic and 19 standard tissue specimens from the TCGA repository facilitated the bifurcation of subjects into two unique clusters (C1 and C2) according to senescence-related gene expression. After a stringent statistical evaluation, a set of ten pivotal genes was discerned and applied for risk stratification. Validity tests for the devised nomograms in forecasting 1, 3, and 5-year survival probabilities for BLCA patients were executed via ROC and calibration plots. IC50 estimations highlighted a heightened responsiveness in the low-risk category to agents like cisplatin, cyclopamine, and sorafenib. CONCLUSIONS In summation, our research emphasizes the prospective utility of risk assessments rooted in senescence-related gene signatures for enhancing BLCA clinical oversight.
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Affiliation(s)
- Ruilin Yang
- Jinan University, 601 Huangpu Avenue West, Tianhe District, Guangzhou, 511400, China
- Andrology Clinic, The Affiliated Panyu Central Hospital of Guangzhou Medical University, 8 East Fuyu Road, Qiaonan Street, Panyu District, Guangzhou, 511400, China
| | - Jieling He
- Ultrasonography Department, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou, 511400, China
| | - Wenfeng Luo
- Central Laboratory, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou, 511400, China
| | - Renyang Xiang
- Department of Surgery, The University of HongKong-Shenzhen Hospital, Shenzhen, 518053, Guangdong, China
| | - Ge Zou
- Urology Department, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou, 511400, China
| | - Xintao Zhang
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 511400, China.
| | - Huang Liu
- National Health Commission (NHC) Key Laboratory of Male Reproduction and Genetics, Department of Andrology, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Human Sperm Bank of Guangdong Province, Guangzhou, China.
| | - Junhong Deng
- Department of Andrology, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China.
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Sannigrahi MK, Cao AC, Rajagopalan P, Sun L, Brody RM, Raghav L, Gimotty PA, Basu D. A novel pipeline for prioritizing cancer type-specific therapeutic vulnerabilities using DepMap identifies PAK2 as a target in head and neck squamous cell carcinomas. Mol Oncol 2024; 18:336-349. [PMID: 37997254 PMCID: PMC10850805 DOI: 10.1002/1878-0261.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/23/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
There is limited guidance on exploiting the genome-wide loss-of-function CRISPR screens in cancer Dependency Map (DepMap) to identify new targets for individual cancer types. This study integrated multiple tools to filter these data in order to seek new therapeutic targets specific to head and neck squamous cell carcinoma (HNSCC). The resulting pipeline prioritized 143 targetable dependencies that represented both well-studied targets and emerging target classes like mitochondrial carriers and RNA-binding proteins. In total, 14 targets had clinical inhibitors used for other cancers or nonmalignant diseases that hold near-term potential to repurpose for HNSCC therapy. Comparing inhibitor response data that were publicly available for 13 prioritized targets between the cell lines with high vs. low dependency on each target uncovered novel therapeutic potential for the PAK2 serine/threonine kinase. PAK2 gene dependency was found to be associated with wild-type p53, low PAK2 mRNA, and diploid status of the 3q amplicon containing PAK2. These findings establish a generalizable pipeline to prioritize clinically relevant targets for individual cancer types using DepMap. Its application to HNSCC highlights novel relevance for PAK2 inhibition and identifies biomarkers of PAK2 inhibitor response.
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Affiliation(s)
- Malay K. Sannigrahi
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Austin C. Cao
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Pavithra Rajagopalan
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lova Sun
- Department of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Robert M. Brody
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lovely Raghav
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Devraj Basu
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
- Ellen and Ronald Caplan Cancer CenterThe Wistar InstitutePhiladelphiaPAUSA
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Sun W, Yuan Y, Chen J, Bao Q, Shang M, Sun P, Peng H. Construction and validation of a novel senescence-related risk score can help predict the prognosis and tumor microenvironment of gastric cancer patients and determine that STK40 can affect the ROS accumulation and proliferation ability of gastric cancer cells. Front Immunol 2023; 14:1259231. [PMID: 37915566 PMCID: PMC10616298 DOI: 10.3389/fimmu.2023.1259231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
Background In recent years, significant molecules have been found in gastric cancer research. However, their precise roles in the disease's development and progression remain unclear. Given gastric cancer's heterogeneity, prognosis prediction is challenging. This study aims to assess patient prognosis and immune therapy efficacy using multiple key molecules. Method The WGCNA algorithm was employed to identify modules of genes closely related to immunity. A prognostic model was established using the Lasso-Cox method to predict patients' prognosis. Single-sample gene set enrichment analysis (ssGSEA) was conducted to quantify the relative abundance of 16 immune cell types and 13 immune functions. The relationship between risk score and TMB, MSI, immune checkpoints, and DNA repair genes was examined to predict the effectiveness of immune therapy. GO and KEGG analyses were performed to explore potential pathways and mechanisms associated with the genes of interest. Single-cell RNA sequencing was utilized to investigate the expression patterns of key genes in different cell types. Results Through the WGCNA algorithm and Lasso-Cox algorithm selected KL, SERPINE1, and STK40 as key genes for constructing the prognostic model. The SSGSEA algorithm was employed to evaluate the infiltration of immune cells and immune functions in different patients, and their association with the risk score was investigated. The high-risk group exhibited lower TMB and MSI compared to the low-risk group. MMR and immune checkpoint analysis revealed a significant correlation between the risk score and multiple molecules. Finally, we also believe that STK40 is the most critical senescence-related gene affecting the progression of gastric cancer. In vitro experiments showed that ROS accumulation and cell proliferation ability of gastric cancer cells were impaired when STK40 was knocked down. Conclusion In summary, we've constructed a prognostic model utilizing key genes for gastric cancer prognosis, while also showcasing its efficacy in predicting patient response to immunotherapy.
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Affiliation(s)
- Weijie Sun
- Digestive Endoscopy Center, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihang Yuan
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiaying Chen
- Digestive Endoscopy Center, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qun Bao
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengsi Shang
- Digestive Endoscopy Center, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Sun
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haixia Peng
- Digestive Endoscopy Center, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Lu Z, Lu Z, Lai Y, Zhou H, Li Z, Cai W, Xu Z, Luo H, Chen Y, Li J, Zhang J, He Z, Tang F. A comprehensive analysis of FBN2 in bladder cancer: A risk factor and the tumour microenvironment influencer. IET Syst Biol 2023; 17:162-173. [PMID: 37337404 PMCID: PMC10439492 DOI: 10.1049/syb2.12067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 04/15/2023] [Accepted: 05/28/2023] [Indexed: 06/21/2023] Open
Abstract
Bladder cancer (BLCA) is a common and difficult-to-manage disease worldwide. Most common type of BLCA is urothelial carcinoma (UC). Fibrillin 2 (FBN2) was first discovered while studying Marfan syndrome, and its encoded products are associated with elastin fibres. To date, the role of FBN2 in BLCA remains unclear. The authors first downloaded data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The patients were divided into high FBN2 expression and low FBN2 expression groups, and the survival curve, clinical characteristics, tumour microenvironment (TME), and immune cell differences were analysed between the two groups. Then, the differentially expressed genes (DEGs) were filtered, and functional enrichment for DEGs was performed. Finally, chemotherapy drug susceptibility analysis based on the high and low FBN2 groups was conducted. The authors found upregulated expression of FBN2 in BLCA and proved that FBN2 could be an independent prognostic factor for BLCA. TME analysis showed that the expression of FBN2 affects several aspects of the TME. The upregulated expression of FBN2 was associated with a high stromal score, which may lead to immunosuppression and be detrimental to immunotherapy. In addition, the authors found that NK cells resting, macrophage M0 infiltration, and other phenomena of immune cell infiltration appeared in the high expression group of FBN2. The high expression of FBN2 was related to the high sensitivity of some chemotherapy drugs. The authors systematically investigated the effects and mechanisms of FBN2 on BLCA and provided a new understanding of the role of FBN2 as a risk factor and TME influencer in BLCA.
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Affiliation(s)
- Zechao Lu
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Zeguang Lu
- The Second Clinical College of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Yongchang Lai
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Haobin Zhou
- The First Clinical College of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Zhibiao Li
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Wanyan Cai
- Department of Social and Behavioural SciencesCity University of Hong KongHong KongChina
| | - Zeyao Xu
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Hongcheng Luo
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Yushu Chen
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Jianyu Li
- The First Clinical College of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Jishen Zhang
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Zhaohui He
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Fucai Tang
- Department of UrologyThe Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhenGuangdongChina
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Pan T, Hu Z, Xu D, Zhou Y, Zhang S, Chen Y. A prognostic signature associated with cell senescence predicts survival outcomes and strongly associates with immunotherapy and chemotherapy response in breast cancer. Medicine (Baltimore) 2023; 102:e34018. [PMID: 37327286 PMCID: PMC10270517 DOI: 10.1097/md.0000000000034018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023] Open
Abstract
The objective of this study is to assess the predictive potency of cell senescence-related genes (CSRGs) in breast cancer (BC) and establish a risk signature. Trascriptome data of CSRGs were obtained from the TCGA and GEO databases. Consensus clustering was used to generate CSRGs-based molecular clusters for BC patients. A CSRGs-derived risk signature was built using multiple Cox regression analyses of differentially expressed genes (DEGs) between clusters. The prognosis, immune infiltration, chemotherapy and immunotherapy response between different risk groups were analyzed and compared. Two molecular clusters of BC patients were generated on the basis of 79 differentially expressed CSRGs, which showed distinct prognosis and immune infiltration. A total of 1403 DEGs between the CSRGs-derived clusters were found, and 10 of them were independent prognostic genes that used to construct a risk signature. The results demonstrated that patients with older age and advanced stage presented with a higher risk scores. In addition, the risk signature was found to be associated with outcomes, immune infiltration, chemotherapy and immunotherapy response. Patients in the low-risk group showed a favorable prognosis and higher immunotherapy response than those in the high-risk group. Finally, we developed a highly stable nomogram that incorporates risk signature, chemotherapy, radiotherapy, and stage variables, enabling accurate prediction of the overall survival (OS) of individual patients. To conclude, the signature derived from CSRGs holds great promise as a biomarker for prognostic assessment of BC and may serve as a valuable tool in guiding immunotherapy.
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Affiliation(s)
- Tao Pan
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengfang Hu
- Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Dongyan Xu
- Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunxiang Zhou
- Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Suzhan Zhang
- Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiding Chen
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Gao L, Wang X, Wang X, Wang F, Tang J, Ji J. A prognostic model and immune regulation analysis of uterine corpus endometrial carcinoma based on cellular senescence. Front Oncol 2022; 12:1054564. [PMID: 36568182 PMCID: PMC9775865 DOI: 10.3389/fonc.2022.1054564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/28/2022] [Indexed: 12/13/2022] Open
Abstract
Background This study aimed to explore the clinical significance of cellular senescence in uterine corpus endometrial carcinoma (UCEC). Methods Cluster analysis was performed on GEO data and TCGA data based on cellular senescence related genes, and then performed subtype analysis on differentially expressed genes between subtypes. The prognostic model was constructed using Lasso regression. Survival analysis, microenvironment analysis, immune analysis, mutation analysis, and drug susceptibility analysis were performed to evaluate the practical relevance. Ultimately, a clinical nomogram was constructed and cellular senescence-related genes expression was investigated by qRT-PCR. Results We ultimately identified two subtypes. The prognostic model divides patients into high-risk and low-risk groups. There were notable discrepancies in prognosis, tumor microenvironment, immunity, and mutation between the two subtypes and groups. There was a notable connection between drug-sensitive and risk scores. The nomogram has good calibration with AUC values between 0.75-0.8. In addition, cellular senescence-related genes expression was investigated qRT-PCR. Conclusion Our model and nomogram may effectively forecast patient prognosis and serve as a reference for patient management.
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Affiliation(s)
- Lulu Gao
- Department of Obstetrics and Gynecology, Nantong Maternal and Child Health Hospital Affiliated to Nantong University, Nantong, China
| | - Xiangdong Wang
- Department of Integrated Traditional Chinese and Western Internal Medicine, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong, China,Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xuehai Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Fengxu Wang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Juan Tang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China,*Correspondence: Juan Tang, ; Jinfeng Ji,
| | - Jinfeng Ji
- Department of Integrated Traditional Chinese and Western Internal Medicine, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong, China,*Correspondence: Juan Tang, ; Jinfeng Ji,
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Luo L, Li F, Gong B, Xi P, Xie W. A novel prognostic model based on cellular senescence-related gene signature for bladder cancer. Front Oncol 2022; 12:937951. [PMID: 36505846 PMCID: PMC9727082 DOI: 10.3389/fonc.2022.937951] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/31/2022] [Indexed: 11/24/2022] Open
Abstract
Background Cellular senescence plays crucial role in the progression of tumors. However, the expression patterns and clinical significance of cellular senescence-related genes in bladder cancer (BCa) are still not clearly clarified. This study aimed to establish a prognosis model based on senescence-related genes in BCa. Methods The transcriptional profile data and clinical information of BCa were downloaded from TCGA and GEO databases. The least absolute shrinkage and selection operator (LASSO), univariate and multivariate Cox regression analyses were performed to develop a prognostic model in the TCGA cohort. The GSE13507 cohort were used for validation. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and single-sample gene set enrichment analysis (ssGSEA) were performed to investigate underlying mechanisms. Results A six-gene signature (CBX7, EPHA3, STK40, TGFB1I1, SREBF1, MYC) was constructed in the TCGA databases. Patients were classified into high risk and low risk group in terms of the median risk score. Survival analysis revealed that patients in the higher risk group presented significantly worse prognosis. Receiver operating characteristic (ROC) curve analysis verified the moderate predictive power of the risk model based on the six senescence-related genes signature. Further analysis indicated that the clinicopathological features analysis were significantly different between the two risk groups. As expected, the signature presented prognostic significance in the GSE13507 cohort. Functional analysis indicated that immune-related pathways activity, immune cell infiltration and immune-related function were different between two risk groups. In addition, risk score were positively correlated with multiple immunotherapy biomarkers. Conclusion Our study revealed that a novel model based on senescence-related genes could serve as a reliable predictor of survival for patients with BCa.
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Affiliation(s)
- Lianmin Luo
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Fenghua Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ping Xi
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Wenjie Xie
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China,*Correspondence: Wenjie Xie,
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