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Wu G, Li T, Chen Y, Ye S, Zhou S, Tian X, Anwaier A, Zhu S, Xu W, Hao X, Ye D, Zhang H. Deciphering glutamine metabolism patterns for malignancy and tumor microenvironment in clear cell renal cell carcinoma. Clin Exp Med 2024; 24:152. [PMID: 38970690 PMCID: PMC11227463 DOI: 10.1007/s10238-024-01390-4] [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: 04/20/2024] [Accepted: 06/05/2024] [Indexed: 07/08/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer characterized by metabolic reprogramming. Glutamine metabolism is pivotal in metabolic reprogramming, contributing to the significant heterogeneity observed in ccRCC. Consequently, developing prognostic markers associated with glutamine metabolism could enhance personalized treatment strategies for ccRCC patients. This study obtained RNA sequencing and clinical data from 763 ccRCC cases sourced from multiple databases. Consensus clustering of 74 glutamine metabolism related genes (GMRGs)- profiles stratified the patients into three clusters, each of which exhibited distinct prognosis, tumor microenvironment, and biological characteristics. Then, six genes (SMTNL2, MIOX, TMEM27, SLC16A12, HRH2, and SAA1) were identified by machine-learning algorithms to develop a predictive signature related to glutamine metabolism, termed as GMRScore. The GMRScore showed significant differences in clinical prognosis, expression profile of immune checkpoints, abundance of immune cells, and immunotherapy response of ccRCC patients. Besides, the nomogram incorporating the GMRScore and clinical features showed strong predictive performance in prognosis of ccRCC patients. ALDH18A1, one of the GRMGs, exhibited elevated expression level in ccRCC and was related to markedly poorer prognosis in the integrated cohort, validated by proteomic profiling of 232 ccRCC samples from Fudan University Shanghai Cancer Center (FUSCC). Conducting western blotting, CCK-8, transwell, and flow cytometry assays, we found the knockdown of ALDH18A1 in ccRCC significantly promoted apoptosis and inhibited proliferation, invasion, and epithelial-mesenchymal transition (EMT) in two human ccRCC cell lines (786-O and 769-P). In conclusion, we developed a glutamine metabolism-related prognostic signature in ccRCC, which is tightly linked to the tumor immune microenvironment and immunotherapy response, potentially facilitating precision therapy for ccRCC patients. Additionally, this study revealed the key role of ALDH18A1 in promoting ccRCC progression for the first time.
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Affiliation(s)
- Gengrun Wu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China
| | - Teng Li
- Department of Urology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, People's Republic of China
| | - Yuanbiao Chen
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, People's Republic of China
| | - Shiqi Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China
| | - Siqi Zhou
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China
| | - Shuxuan Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China.
| | - Xiaohang Hao
- Department of Urology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, People's Republic of China.
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China.
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, People's Republic of China.
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Xu W, Lu J, Tian X, Ye S, Wei S, Wang J, Anwaier A, Qu Y, Liu W, Chang K, Zhang H, Ye D. Unveiling the impact of tertiary lymphoid structures on immunotherapeutic responses of clear cell renal cell carcinoma. MedComm (Beijing) 2024; 5:e461. [PMID: 38222314 PMCID: PMC10784869 DOI: 10.1002/mco2.461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 01/16/2024] Open
Abstract
Tertiary lymphoid structures (TLS) are organized aggregates of immune cells that form under pathological conditions. However, the predictive value of TLS in clear cell renal cell carcinoma (ccRCC) for immunotherapies remains unclear. We comprehensively assessed the implications for prognosis and immunological responses of the TLS spatial and maturation heterogeneity in 655 ccRCC patients. A higher proportion of early-TLS was found in peritumoral TLS, while intratumoral TLS mainly comprised secondary follicle-like TLS (SFL-TLS), indicating markedly better survival. Notably, presence of TLS, especially intratumoral TLS and SFL-TLS, significantly correlated with better survival and objective reflection rate for ccRCC patients receiving anti-Programmed Cell Death Protein-1 (PD-1)/Programmed Cell Death-Ligand-1 (PD-L1) immunotherapies. In peritumoral TLS cluster, primary follicle-like TLS, the proportion of tumor-associated macrophages, and Treg infiltration in the peritumoral regions increased prominently, suggesting an immunosuppressive tumor microenvironment. Interestingly, spatial transcriptome annotation and multispectral fluorescence showed that an abundance of mature plasma cells within mature TLS has the capacity to produce IgA and IgG, which demonstrate significantly higher objective response rates and a superior prognosis for ccRCC patients subjected to immunotherapy. In conclusion, this study revealed the implications of TLS spatial and maturation heterogeneity on the immunological status and clinical responses, allowing the improvement of precise immunotherapies of ccRCC.
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Affiliation(s)
- Wenhao Xu
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Jiahe Lu
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
- School of Cellular and Molecular MedicineUniversity of BristolBristolUK
| | - Xi Tian
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Shiqi Ye
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Shiyin Wei
- Affiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Jun Wang
- State Key Laboratory of Oncology in South ChinaCollaborativeInnovation Center for Cancer MedicineDepartment of UrologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Aihetaimujiang Anwaier
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Yuanyuan Qu
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Wangrui Liu
- Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Kun Chang
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Hailiang Zhang
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
| | - Dingwei Ye
- Department of UrologyFudan University Shanghai Cancer CenterShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteShanghaiChina
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Xu W, Lu J, Liu WR, Anwaier A, Wu Y, Tian X, Su JQ, Qu YY, Yang J, Zhang H, Ye D. Heterogeneity in tertiary lymphoid structures predicts distinct prognosis and immune microenvironment characterizations of clear cell renal cell carcinoma. J Immunother Cancer 2023; 11:e006667. [PMID: 38040418 PMCID: PMC10693897 DOI: 10.1136/jitc-2023-006667] [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] [Accepted: 07/17/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Tertiary lymphoid structures (TLS) are organized aggregates of immune cells that develop postnatally in non-lymphoid tissues and are associated with pathological conditions. TLS typically comprise B-cell follicles containing and are encompassed by T- cell zones and dendritic cells. The prognostic and predictive value of TLS in the tumor microenvironment (TME) as potential mediators of antitumor immunity have gained interest. However, the precise relationship between localization and maturation of TLS and the clinical outcome of their presence in clear cell renal cell carcinoma (ccRCC) is yet to be elucidated. METHODS Immunohistochemistry and multispectral fluorescence were used to evaluate the TLS heterogeneity along with TME cell-infiltrating characterizations. A thorough investigation of the prognostic implications of the TLS heterogeneity in 395 patients with ccRCC from two independent cohorts was conducted. Associations between TLS heterogeneity and immunologic activity were assessed by quantifying the immune cell infiltration. RESULTS Infiltrated TLS were identified in 34.2% of the ccRCC samples (N=395). These TLS were found to be tumor-proximal, tumor-distal, or both in 37.8%, 74.1%, and 11.9% of the TLS-positive cases, respectively. A higher proportion of early TLS was found in tumor-distal TLS (p=0.016), while tumor-proximal TLS primarily comprised secondary follicle-like structures (p=0.004). In the main study cohort (Fudan University Shanghai Cancer Center, N=290), Kaplan-Meier analyses revealed a significant correlation between the presence of tumor-proximal TLS and improved progression-free survival (PFS, p<0.001) and overall survival (OS, p=0.002). Conversely, the presence of tumor-distal TLS was associated with poor PFS (p=0.02) and OS (p=0.021). These findings were further validated in an external validation set of 105 patients with ccRCC. Notably, the presence of mature TLS (namely secondary follicle-like TLS, with CD23+ germinal center) was significantly associated with better clinical outcomes in patients with ccRCC. Furthermore, novel nomograms incorporating the presence of tumor-proximal TLS demonstrated remarkable predictability for the 8-year outcomes of resected ccRCC (area under the curve >0.80). Additionally, ccRCC samples with tumor-distal TLS enriched with primary follicle-like TLS exhibited higher programmed death-ligand 1 tumor-associated macrophages levels and regulatory T cells infiltration in the tumor-distal region, indicative of a suppressive TME. CONCLUSION This study for the first time elucidates the impact of TLS localization and maturation heterogeneities on the divergent clinical outcomes of ccRCC. The findings reveal that most TLS in ccRCC are located in the tumor-distal area and are associated with immature, immunosuppressive characterizations. Furthermore, our findings corroborate previous research demonstrating that tumor-proximal TLS were associated with favorable clinical outcomes.
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, People's Republic of China
| | - Jiahe Lu
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, People's Republic of China
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Wang-Rui Liu
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, People's Republic of China
| | - Yuhao Wu
- Institute of Photomedicine, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, People's Republic of China
| | - Jia-Qi Su
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, People's Republic of China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, People's Republic of China
| | - Jianfeng Yang
- Department of Surgery, ShangNan Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, People's Republic of China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Shanghai Genitourinary Cancer Institute, Shanghai, People's Republic of China
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Gu Q, Zhou S, Chen C, Wang Z, Xu W, Zhang J, Wei S, Yang J, Chen H. CCL19: a novel prognostic chemokine modulates the tumor immune microenvironment and outcomes of cancers. Aging (Albany NY) 2023; 15:12369-12387. [PMID: 37944262 PMCID: PMC10683612 DOI: 10.18632/aging.205184] [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: 06/19/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND CCL19 is a chemokine involved in cancer research due to its important role in the tumor microenvironment (TME) and clinical relevance in cancers. This study aimed to analyze transcription expression, genomic alteration, association with tumor immune microenvironment of CCL19 expression and its prediction value for prognosis and responses to immunotherapy for patients with cancers. METHODS RNA sequencing data and corresponding clinicopathological information of a total of large-scale cancer patients were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. Multiplex immunofluorescence (mIF) was implemented to identify differential infiltration of Treg, CD8+ T cells, and tumor-associated macrophages, while CCL19 immunohistochemistry was conducted on 182 breast cancer samples from a real-world cohort. RESULTS Based on large-scale multi-center survival analysis of cancer patients, we found the prognosis of patients with high CCL19 expression was prominently better than those with low CCL19 expression. For patients from multiple independent cohorts, suppressed CCL19 expression exerts significant progressive phenotype and apoptosis activity of cancers, especially in breast and ovarian cancer. Interestingly, anti-tumor immune cells, specifically the CD8+ T cells and macrophages, were clustered from TME by elevated CCL19 expression. Additionally, higher CCL19 levels reflected heightened immune activity and substantial heterogeneity. CONCLUSIONS In conclusion, our findings support the notion that elevated CCL19 expression is linked to favorable outcomes and enhanced anti-tumor immunity, characterized by increased CD8+ T cells within the TME. This suggests the potential of CCL19 as a prognostic marker, predictive biomarker for immunotherapy, therapeutic target of cancers.
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Affiliation(s)
- Qiang Gu
- Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong 226000, China
| | - Shifang Zhou
- Department of Obstetrics and Gynecology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Cong Chen
- Department of Nursing, Fudan University Shanghai Cancer Center, Shanghai 201321, China
| | - Zhi Wang
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Wenhao Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jiarong Zhang
- Department of Obstetrics and Gynecology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shiyin Wei
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, China
| | - Jianfeng Yang
- Department of Surgery, Shangnan Branch of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Hongjing Chen
- Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong 226000, China
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Xiang J, Liu W, Liu S, Wang T, Tang H, Yang J. Deciphering the implications of mitophagy-related signatures in clinical outcomes and microenvironment heterogeneity of clear cell renal cell carcinoma. J Cancer Res Clin Oncol 2023; 149:16015-16030. [PMID: 37689589 DOI: 10.1007/s00432-023-05349-y] [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: 07/14/2023] [Accepted: 08/25/2023] [Indexed: 09/11/2023]
Abstract
BACKGROUND The role of mitophagy in various cancer-associated biological processes is well recognized. Nonetheless, the comprehensive implications of mitophagy in clear cell renal cell carcinoma (ccRCC) necessitate further exploration. METHODS Based on the transcriptomic data encompassing 25 mitophagy-related genes (MRGs), we identified the distinct mitophage patterns in 763 ccRCC samples. Subsequently, a mitophage-related predictive signature with machine learning algorithms was constructed, designated as RiskScore, to quantify the individual mitophagy status in ccRCC patients. Employing multispectral immunofluorescence (mIF) and immunohistochemistry (IHC) staining, we detected the effect of PTEN-induced putative kinase 1 (PINK1) in the prognosis and immune microenvironment of ccRCC. RESULTS Our analysis initially encompassed a comprehensive assessment of the expression profiling, genomic variations, and interactions among the 25 MRGs in ccRCC. Subsequently, the consensus clustering algorithm was applied to stratify ccRCC patients into three clusters with distinct prognostic outcomes, tumor microenvironment (TME) characteristics, and underlying biological pathways. We screened eight pivotal genes (CLIC4, PTPRB, SLC16A12, ENPP5, FLRT3, HRH2, PDK4, and SCD5) to construct a mitophagy-related predictive signature, which showed excellent prognostic value for ccRCC patients. Moreover, patient subgroups divided by the RiskScore showed contrasting expression levels of immune checkpoints (ICPs), abundance of immune cells, and immunotherapy response. Additionally, a nomogram was established with robust predictive power integrating the RiskScore and clinical features. Notably, we observed that PINK1 expression markedly correlated with favorable treatment response and advanced maturation stages of tertiary lymphoid structures, which potentially shed light on enhancing anti-tumor immunity of ccRCC. CONCLUSION Collectively, this study initially developed a signature associated with mitophagy, which demonstrated an excellent ability to predict the clinical prognosis, TME characterization, and responsiveness to targeted therapy and immunotherapy for ccRCC patients. Of particular note is the pivotal role of PINK1 in mediating the treatment response and immune microenvironment for ccRCC patients.
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Affiliation(s)
- Jianfeng Xiang
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wangrui Liu
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shifan Liu
- Department of Medical Imaging, Medical School of Nantong University, Nantong, China
| | - Tao Wang
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Haidan Tang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.
| | - Jianfeng Yang
- Department of Surgery, Shangnan Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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Gu L, Ding D, Wei C, Zhou D. Cancer-associated fibroblasts refine the classifications of gastric cancer with distinct prognosis and tumor microenvironment characteristics. Front Oncol 2023; 13:1158863. [PMID: 37404754 PMCID: PMC10316023 DOI: 10.3389/fonc.2023.1158863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/21/2023] [Indexed: 07/06/2023] Open
Abstract
Background Cancer-associated fibroblasts (CAFs) are essential tumoral components of gastric cancer (GC), contributing to the development, therapeutic resistance and immune-suppressive tumor microenvironment (TME) of GC. This study aimed to explore the factors related to matrix CAFs and establish a CAF model to evaluate the prognosis and therapeutic effect of GC. Methods Sample information from the multiply public databases were retrieved. Weighted gene co-expression network analysis was used to identify CAF-related genes. EPIC algorithm was used to construct and verify the model. Machine-learning methods characterized CAF risk. Gene set enrichment analysis was employed to elucidate the underlying mechanism of CAF in the development of GC. Results A three-gene (GLT8D2, SPARC and VCAN) prognostic CAF model was established, and patients were markedly divided according to the riskscore of CAF model. The high-risk CAF clusters had significantly worse prognoses and less significant responses to immunotherapy than the low-risk group. Additionally, the CAF risk score was positively associated with CAF infiltration in GC. Moreover, the expression of the three model biomarkers were significantly associated with the CAF infiltration. GSEA revealed significant enrichment of cell adhesion molecules, extracellular matrix receptors and focal adhesions in patients at a high risk of CAF. Conclusion The CAF signature refines the classifications of GC with distinct prognosis and clinicopathological indicators. The three-gene model could effectively aid in determining the prognosis, drug resistance and immunotherapy efficacy of GC. Thus, this model has promising clinical significance for guiding precise GC anti-CAF therapy combined with immunotherapy.
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Affiliation(s)
- Lei Gu
- Department of General Surgery, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dan Ding
- Department of Gastroenterology, Changhai Hospital, Navy/Second Military Medical University, Shanghai, China
| | - Cuicui Wei
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Donglei Zhou
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Chang K, Su J, Li C, Anwaier A, Liu W, Xu W, Qu Y, Zhang H, Ye D. Multi-omics profiles refine L-dopa decarboxylase (DDC) as a reliable biomarker for prognosis and immune microenvironment of clear cell renal cell carcinoma. Front Oncol 2022; 12:1079446. [PMID: 36544704 PMCID: PMC9760914 DOI: 10.3389/fonc.2022.1079446] [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: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 12/07/2022] Open
Abstract
Background Increasing evidence indicates that L-dopa decarboxylase (DDC), which mediates aberrant amino acid metabolism, is significantly associated with tumor progression. However, the impacts of DDC are not elucidated clearly in clear cell renal cell carcinoma (ccRCC). This study aimed to evaluate DDC prognostic value and potential mechanisms for ccRCC patients. Methods Transcriptomic and proteomic expressions of and clinical data including 532 patients with ccRCC (The Cancer Genome Atlas RNA-seq data), 226 ccRCC samples (Gene Expression Omnibus), 101 ccRCC patients from the E-MTAB-1980 cohort, and 232 patients with ccRCC with proteogenomic data (Fudan University Shanghai Cancer Center) were downloaded and analyzed to investigate the prognostic implications of DDC expression. Cox regression analyses were implemented to explore the effect of DDC expression on the prognosis of pan-cancer. The "limma" package identified the differentially expressed genes (DEGs) between high DDC subgroups and low DDC groups. Functional enrichments were performed based DEGs between DDC subgroups. The differences of immune cell infiltrations and immune checkpoint genes between DDC subgroups were analyzed to identify potential influence on immune microenvironment. Results We found significantly decreased DDC expression in ccRCC tissues compared with normal tissues from multiple independent cohorts based on multi-omics data. We also found that DDC expression was correlated with tumor grades and stages.The following findings revealed that lower DDC expression levels significantly correlated with shorter overall survival (P <0.001) of patients with ccRCC. Moreover, we found that DDC expression significantly correlated with an immunosuppressive tumor microenvironment, higher intra-tumoral heterogeneity, elevated expression of immune checkpoint CD274, and possibly mediated malignant behaviors of ccRCC cells via the PI3k/Akt signaling pathway. Conclusion The present study is the first to our knowledge to indicate that decreased DDC expression is significantly associated with poor survival and an immune-suppressive tumor microenvironment in ccRCC. These findings suggest that DDC could serve as a biomarker for guiding molecular diagnosis and facilitating the development of novel individual therapeutic strategies for patients with advanced ccRCC.
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Affiliation(s)
- Kun Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Chuanyu Li
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
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Yang J, Xu J, Gao Q, Wu F, Han W, Yu C, Shi Y, Qiu Y, Chen Y, Zhou X. Identification of adenylate cyclase 2 methylation in bladder cancer with implications for prognosis and immunosuppressive microenvironment. Front Oncol 2022; 12:1025195. [PMID: 36313639 PMCID: PMC9614257 DOI: 10.3389/fonc.2022.1025195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
Background The incidence and mortality of bladder cancer (BCa) are increasing, while the existing diagnostic methods have limitations. Therefore, for early detection and response prediction, it is crucial to improve the prognosis and treatment strategies. However, with existing diagnostic methods, detecting BCa in the early stage is challenging. Hence, novel biomarkers are urgently needed to improve early diagnosis and treatment efficiency. Methods The gene expression profile and gene methylation profile dataset were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs), differentially methylated genes (DMGs), and methylation-regulated differentially expressed genes (MeDEGs) were gradually identified. A cancer genome map was obtained using online gene expression profile interaction analysis, and survival implications were produced using Kaplan-Meier survival analysis. GSEA was employed to predict the marker pathways where DEGs were significantly involved. The study used bisulfite PCR amplification combined with bisulfite amplicon sequencing (BSAS) to screen for methylation analysis of multiple candidate regions of the adenylate cyclase 2 (ADCY2) based on the sequence design of specific gene regions and CpG islands. Results In this study, DEGs and DMGs with significantly up- or down-regulated expression were selected. The intersection method was used to screen the MeDEGs. The interaction network group in STRING was then visualized using Cytoscape, and the PPI network was constructed to identify the key genes. The key genes were then analyzed using functional enrichment. To compare the relationship between key genes and the prognosis of BCa patients, we further investigated ADCY2 and found that ADCY2 can be a potential clinical biomarker in BCa prognosis and immunotherapy response prediction. In human BCa 5637 and MGH1 cells, we developed and verified the effectiveness of ADCY2 primers using BSAS technology. The findings revealed that the expression of ADCY2 is highly regulated by the methylation of the promoter regions. Conclusion This study revealed that increased expression of ADCY2 was significantly correlated with increased tumor heterogeneity, predicting worse survival and immunotherapy response in BCa patients.
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Affiliation(s)
- Jianfeng Yang
- Department of Surgery, Shangnan Branch of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jin Xu
- Institute of Regenerative Biology and Medicine, Helmholtz Zentrum München, Munich, Germany
| | - Qian Gao
- Wound Treatment Center Affiliated Xinhua Hospital of Medicine College of Shanghai Jiaotong University, Shanghai, China
| | - Fan Wu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Han
- Institute of Regenerative Biology and Medicine, Helmholtz Zentrum München, Munich, Germany
| | - Chao Yu
- Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Youyang Shi
- Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yunhua Qiu
- Department of Surgery, Shangnan Branch of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanbiao Chen
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xiqiu Zhou
- Department of Surgery, Shangnan Branch of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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