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Li J, Tang Y, Long F, Tian L, Tang A, Ding L, Chen J, Liu M. Integrating bulk RNA-seq and scRNA-seq analyses revealed the function and clinical value of thrombospondins in colon cancer. Comput Struct Biotechnol J 2024; 23:2251-2266. [PMID: 38827236 PMCID: PMC11140486 DOI: 10.1016/j.csbj.2024.05.021] [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: 12/14/2023] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
Background Acting as mediators in cell-matrix and cell-cell communication, matricellular proteins play a crucial role in cancer progression. Thrombospondins (TSPs), a type of matricellular glycoproteins, are key regulators in cancer biology with multifaceted roles. Although TSPs have been implicated in anti-tumor immunity and epithelial-mesenchymal transition (EMT) in several malignancies, their specific roles to colon cancer remain elusive. Addressing this knowledge gap is essential, as understanding the function of TSPs in colon cancer could identify new therapeutic targets and prognostic markers. Methods Analyzing 1981 samples from 10 high-throughput datasets, including six bulk RNA-seq, three scRNA-seq, and one spatial transcriptome dataset, our study investigated the prognostic relevance, risk stratification value, immune heterogeneity, and cellular origin of TSPs, as well as their influence on cancer-associated fibroblasts (CAFs). Utilizing survival analysis, unsupervised clustering, and functional enrichment, along with multiple correlation analyses of the tumor-microenvironment (TME) via Gene Set Variation Analysis (GSVA), spatial localization, Monocle2, and CellPhoneDB, we provided insights into the clinical and cellular implications of TSPs. Results First, we observed significant upregulation of THBS2 and COMP in colon cancer, both of which displayed significant prognostic value. Additionally, we detected a significant positive correlation between TSPs and immune cells, as well as marker genes of EMT. Second, based on TSPs expression, patients were divided into two clusters with distinct prognoses: the high TSPs expression group (TSPs-H) was characterized by pronounced immune and stromal cell infiltration, and notably elevated T-cell exhaustion scores. Subsequently, we found that THBS2 and COMP may be associated with the differentiation of CAFs into pan-iCAFs and pan-dCAFs, which are known for their heightened matrix remodeling activities. Moreover, THBS2 enhanced CAFs communication with vascular endothelial cells and monocyte-macrophages. CAFs expressing THBS2 (THBS2+ CAFs) demonstrated higher scores across multiple signaling pathways, including angiogenic, EMT, Hedgehog, Notch, Wnt, and TGF-β, when compared to THBS2- CAFs. These observations suggest that THBS2 may be associated with stronger pro-carcinogenic activity in CAFs. Conclusions This study revealed the crucial role of TSPs and the significant correlation between THBS2 and CAFs interactions in colon cancer progression, providing valuable insights for targeting TSPs to mitigate cancer progression.
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Affiliation(s)
- Jing Li
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Ying Tang
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
- Medical Laboratory, People's Hospital of Qingbaijiang District, Chengdu 61300, China
| | - Fei Long
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Luyao Tian
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Ao Tang
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - LiHui Ding
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Juan Chen
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Mingwei Liu
- Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
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Wang G, Zhuang T, Zhen F, Zhang C, Wang Q, Miao X, Qi N, Yao R. IGF2BP2 inhibits invasion and migration of clear cell renal cell carcinoma via targeting Netrin-4 in an m 6A-dependent manner. Mol Carcinog 2024; 63:1572-1587. [PMID: 38780170 DOI: 10.1002/mc.23746] [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: 01/30/2024] [Revised: 03/24/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC), the most common subtype of renal cell carcinoma, often leads to a poor prognosis due to metastasis. The investigation of N6-methyladenosine (m6A) methylation, a crucial RNA modification, and its role in ccRCC, particularly through the m6A reader insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), revealed significant insights. We found that IGF2BP2 was notably downregulated in ccRCC, which correlated with tumor aggressiveness and poor prognosis. Thus, IGFBP2 has emerged as an independent prognostic factor of ccRCC. Moreover, a strong positive correlation was observed between the expression of IGF2BP2 and Netrin-4. Netrin-4 was also downregulated in ccRCC, and its lower levels were associated with increased malignancy and poor prognosis. Overexpression of IGF2BP2 and Netrin-4 suppressed the invasion and migration of ccRCC cells, while Netrin-4 knockdown reversed these effects in ccRCC cell lines. RNA immunoprecipitation (RIP)-quantitative polymerase chain reaction validated the robust enrichment of Netrin-4 mRNA in anti-IGF2BP2 antibody immunoprecipitates. MeRlP showed significantly increased Netrin4 m6A levels after lGF2BP2 overexpression. Moreover, we found that IGF2BP2 recognized and bound to the m6A site within the coding sequence of Netrin-4, enhancing its mRNA stability. Collectively, these results showed that IGF2BP2 plays a suppressive role in the invasion and migration of ccRCC cells by targeting Netrin-4 in an m6A-dependent manner. These findings underscore the potential of IGF2BP2/Netrin-4 as a promising prognostic biomarker and therapeutic target in patients with ccRCC metastasis.
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Affiliation(s)
- Gui Wang
- Xuzhou Key Laboratory of Neurobiology, Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Tao Zhuang
- Xuzhou Key Laboratory of Neurobiology, Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Fei Zhen
- Department of Pathology, Hongze Huaian District People's Hospital, Hongze, China
| | - Chu Zhang
- Xuzhou Key Laboratory of Neurobiology, Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Qichao Wang
- Department of Urology, Xuzhou Cancer Hospital, Xuzhou, China
| | - Xu Miao
- Xuzhou Key Laboratory of Neurobiology, Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Nienie Qi
- Department of Urology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Ruiqin Yao
- Xuzhou Key Laboratory of Neurobiology, Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou, China
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Di SC, Chen WJ, Yang W, Zhang XM, Dong KQ, Tian YJ, Sun Y, Qian C, Chen JX, Liu ZC, Gong ZX, Chu J, Zhou W, Pan XW, Cui XG. DEPDC1 as a metabolic target regulates glycolysis in renal cell carcinoma through AKT/mTOR/HIF1α pathway. Cell Death Dis 2024; 15:533. [PMID: 39068164 PMCID: PMC11283501 DOI: 10.1038/s41419-024-06913-1] [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: 04/27/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
Renal cell carcinoma (RCC) is considered a "metabolic disease" characterized by elevated glycolysis in patients with advanced RCC. Tyrosine kinase inhibitor (TKI) therapy is currently an important treatment option for advanced RCC, but drug resistance may develop in some patients. Combining TKI with targeted metabolic therapy may provide a more effective approach for patients with advanced RCC. An analysis of 14 RCC patients (including three needle biopsy samples with TKI resistance) revealed by sing-cell RNA sequencing (scRNA-seq) that glycolysis played a crucial role in poor prognosis and drug resistance in RCC. TCGA-KIRC and glycolysis gene set analysis identified DEPDC1 as a target associated with malignant progression and drug resistance in KIRC. Subsequent experiments demonstrated that DEPDC1 promoted malignant progression and glycolysis of RCC, and knockdown DEPDC1 could reverse TKI resistance in RCC cell lines. Bulk RNA sequencing (RNA-seq) and non-targeted metabolomics sequencing suggested that DEPDC1 may regulate RCC glycolysis via AKT/mTOR/HIF1α pathway, a finding supported by protein-level analysis. Clinical tissue samples from 98 RCC patients demonstrated that DEPDC1 was associated with poor prognosis and predicted RCC metastasis. In conclusion, this multi-omics analysis suggests that DEPDC1 could serve as a novel target for TKI combined with targeted metabolic therapy in advanced RCC patients with TKI resistance.
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MESH Headings
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/drug therapy
- Humans
- Glycolysis/drug effects
- TOR Serine-Threonine Kinases/metabolism
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Kidney Neoplasms/drug therapy
- Kidney Neoplasms/genetics
- Proto-Oncogene Proteins c-akt/metabolism
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Cell Line, Tumor
- GTPase-Activating Proteins/metabolism
- GTPase-Activating Proteins/genetics
- Signal Transduction
- Mice
- Animals
- Male
- Female
- Mice, Nude
- Drug Resistance, Neoplasm/drug effects
- Gene Expression Regulation, Neoplastic
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Affiliation(s)
- Si-Chen Di
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Wen-Jin Chen
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, China
| | - Wei Yang
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xiang-Min Zhang
- Department of Urology, Shanghai Baoshan Luodian Hospital, Shanghai, China
| | - Ke-Qin Dong
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Department of Urology, Chinese PLA General Hospital of Central Theater Command, Wuhan, China
| | - Yi-Jun Tian
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ye Sun
- Department of Urology, Taian 88 Hospital, Taian, Shandong, China
| | - Cheng Qian
- Department of Urology, Shanghai Pudong New Area Gongli Hospital, Shanghai, China
| | - Jia-Xin Chen
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zi-Chang Liu
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zi-Xuan Gong
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jian Chu
- Department of Urology, Shanghai Baoshan Luodian Hospital, Shanghai, China.
| | - Wang Zhou
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
| | - Xiu-Wu Pan
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
| | - Xin-Gang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
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Lu L, Feng H, Dai G, Liu S, Feng Y, Tan H, Zhang X, Hong G, Lai X. A novel cancer-associated fibroblast signature for kidney renal clear cell carcinoma via integrated analysis of single-cell and bulk RNA-sequencing. Discov Oncol 2024; 15:309. [PMID: 39060620 PMCID: PMC11282037 DOI: 10.1007/s12672-024-01175-x] [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: 03/14/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer-associated fibroblasts (CAFs), integral components of the tumor microenvironment, play a pivotal role in tumor proliferation, metastasis, and clinical outcomes. However, its specific roles in Kidney Renal Clear Cell Carcinoma (KIRC) remain poorly understood. Employing the established Seurat single-cell analysis pipeline, we identified 21 CAFs marker genes. Subsequently, a prognostic signature consisting of 6 CAFs marker genes (RGS5, PGF, TPM2, GJA4, SEPT4, and PLXDC1) was developed in a cohort through univariate and LASSO Cox regression analyses. The model's efficacy was then validated in an external cohort, with a remarkable predictive performance in 1-, 3-, and 5-year. Patients in the high-risk group exhibited significantly inferior survival outcomes (p < 0.001), and the risk score was an independent prognostic factor (p < 0.05). Distinct differences in immune cell profiles and drug susceptibility were observed between the two risk groups. In KIRC, the PGF-VEGFR1 signaling pathway displayed a notable increase. PGF expression was significantly elevated in tumor tissues, as demonstrated by quantitative real-time polymerase chain reaction. In vitro, transwell assays and CCK8 revealed that recombinant-PGF could enhance the capability of cell proliferation, migration, and invasion in 769P and 786-O cells. This study firstly developed a novel predictive model based on 6 CAFs genes for KIRC. Additionally, PGF may present a potential therapeutic target to enhance KIRC treatment.
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Affiliation(s)
- Ling Lu
- Department of Renal Rheumatology Immunology, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Huaguo Feng
- Department of Hepatobiliary Surgery, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Guohua Dai
- Department of Hepatobiliary Surgery, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Shuangquan Liu
- Department of Hepatobiliary Surgery, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Yi Feng
- Department of Hepatobiliary Surgery, Jiangjin District Maternal and Child Health Hospital, Chongqing, China
| | - Haoyang Tan
- Department of Hepatobiliary Surgery, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Xian Zhang
- Department of Hepatobiliary Surgery, Tongnan District People's Hospital, No. 189, Jianshe Road, Dafo Street, Tongnan District, Chongqing, China
| | - Guoqing Hong
- Department of Hepatobiliary Surgery, Tongnan District People's Hospital, No. 189, Jianshe Road, Dafo Street, Tongnan District, Chongqing, China.
| | - Xing Lai
- Department of Hepatobiliary Surgery, Tongnan District People's Hospital, No. 189, Jianshe Road, Dafo Street, Tongnan District, Chongqing, China.
- Chongqing Traditional Chinese Medicine Hospital, Chongqing, China.
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Zheng J, Lu W, Wang C, Chen S, Zhang Q, Su C. Unfolding the mysteries of heterogeneity from a high-resolution perspective: integration analysis of single-cell multi-omics and spatial omics revealed functionally heterogeneous cancer cells in ccRCC. Aging (Albany NY) 2024; 16:10943-10971. [PMID: 38944814 PMCID: PMC11272124 DOI: 10.18632/aging.205974] [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: 09/19/2023] [Accepted: 05/16/2024] [Indexed: 07/01/2024]
Abstract
The genomic landscape of clear cell renal cell carcinoma (ccRCC) has a considerable intra-tumor heterogeneity, which is a significant obstacle in the field of precision oncology and plays a pivotal role in metastasis, recurrence, and therapeutic resistance of cancer. The mechanisms of intra-tumor heterogeneity in ccRCC have yet to be fully established. We integrated single-cell RNA sequencing (scRNA-seq) and transposase-accessible chromatin sequencing (scATAC-seq) data from a single-cell multi-omics perspective. Based on consensus non-negative matrix factorization (cNMF) algorithm, functionally heterogeneous cancer cells were classified into metabolism, inflammatory, and EMT meta programs, with spatial transcriptomics sequencing (stRNA-seq) providing spatial information of such disparate meta programs of cancer cells. The bulk RNA sequencing (RNA-seq) data revealed high clinical prognostic values of functionally heterogeneous cancer cells of three meta programs, with transcription factor regulatory network and motif activities revealing the key transcription factors that regulate functionally heterogeneous ccRCC cells. The interactions between varying meta programs and other cell subpopulations in the microenvironment were investigated. Finally, we assessed the sensitivity of cancer cells of disparate meta programs to different anti-cancer agents. Our findings inform on the intra-tumor heterogeneity of ccRCC and its regulatory networks and offers new perspectives to facilitate the designs of rational therapeutic strategies.
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Affiliation(s)
- Jie Zheng
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Wenhao Lu
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Chengbang Wang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Qingyun Zhang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Cheng Su
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
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Huang J, Wang Y, Xu F, Wang Z, Wu G, Kong W, Cheoklong NG, Tricard T, Wu X, Zhai W, Zhang W, Zhang J, Zhang D, Chen S, Lian Y, Chen Y, Zhang J, Huang Y, Xue W. Neoadjuvant toripalimab combined with axitinib in patients with locally advanced clear cell renal cell carcinoma: a single-arm, phase II trial. J Immunother Cancer 2024; 12:e008475. [PMID: 38862251 PMCID: PMC11168135 DOI: 10.1136/jitc-2023-008475] [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: 05/05/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND A combination of axitinib and immune checkpoint inhibitors (ICIs) demonstrated promising efficacy in the treatment of advanced renal cell carcinoma (RCC). This study aims to prospectively evaluate the safety, efficacy, and biomarkers of neoadjuvant toripalimab plus axitinib in non-metastatic clear cell RCC. METHODS This is a single-institution, single-arm phase II clinical trial. Patients with non-metastatic biopsy-proven clear cell RCC (T2-T3N0-1M0) are enrolled. Patients will receive axitinib 5 mg twice daily combined with toripalimab 240 mg every 3 weeks (three cycles) for up to 12 weeks. Patients then will receive partial (PN) or radical nephrectomy (RN) after neoadjuvant therapy. The primary endpoint is objective response rate (ORR). Secondary endpoints include disease-free survival, safety, and perioperative complication rate. Predictive biomarkers are involved in exploratory analysis. RESULTS A total of 20 patients were enrolled in the study, with 19 of them undergoing surgery. One patient declined surgery. The primary endpoint ORR was 45%. The posterior distribution of πORR had a mean of 0.44 (95% credible intervals: 0.24-0.64), meeting the predefined primary endpoint with an ORR of 32%. Tumor shrinkage was observed in 95% of patients prior to nephrectomy. Furthermore, four patients achieved a pathological complete response. Grade ≥3 adverse events occurred in 25% of patients, including hypertension, hyperglycemia, glutamic pyruvic transaminase/glutamic oxaloacetic transaminase (ALT/AST) increase, and proteinuria. Postoperatively, one grade 4a and eight grade 1-2 complications were noted. In comparison to patients with stable disease, responders exhibited significant differences in immune factors such as Arginase 1(ARG1), Melanoma antigen (MAGEs), Dendritic Cell (DC), TNF Superfamily Member 13 (TNFSF13), Apelin Receptor (APLNR), and C-C Motif Chemokine Ligand 3 Like 1 (CCL3-L1). The limitation of this trial was the small sample size. CONCLUSION Neoadjuvant toripalimab combined with axitinib shows encouraging activity and acceptable toxicity in locally advanced clear cell RCC and warrants further study. TRIAL REGISTRATION NUMBER clinicaltrials.gov, NCT04118855.
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Affiliation(s)
- Jiwei Huang
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yueming Wang
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Fan Xu
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Zaoyu Wang
- Department of Pathology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Guangyu Wu
- Department of Radiology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Wen Kong
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - N G Cheoklong
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Thibault Tricard
- Department of Urology, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Xiaorong Wu
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Wei Zhai
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | | | | | - Ding Zhang
- The Medical Department, 3D Medicines Inc, Shanghai, China
| | - Shuyin Chen
- Shanghai Junshi Biosciences Co Ltd, Shanghai, China
| | - Yuqing Lian
- Shanghai Junshi Biosciences Co Ltd, Shanghai, China
| | - Yonghui Chen
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jin Zhang
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yiran Huang
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Wei Xue
- Department of Urology, RenJi Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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Zhang Y, Huang X, Yu M, Zhang M, Zhao L, Yan Y, Zhang L, Wang X. The integrate profiling of single-cell and spatial transcriptome RNA-seq reveals tumor heterogeneity, therapeutic targets, and prognostic subtypes in ccRCC. Cancer Gene Ther 2024; 31:917-932. [PMID: 38480978 DOI: 10.1038/s41417-024-00755-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 06/23/2024]
Abstract
Clear-cell renal cell carcinoma (ccRCC) is the most common type of RCC; however, the intratumoral heterogeneity in ccRCC remains unclear. We first identified markers and biological features of each cell cluster using bioinformatics analysis based on single-cell and spatial transcriptome RNA-sequencing data. We found that gene copy number loss on chromosome 3p and amplification on chromosome 5q were common features in ccRCC cells. Meanwhile, NNMT and HILPDA, which are associated with the response to hypoxia and metabolism, are potential therapeutic targets for ccRCC. In addition, CD8+ exhausted T cells (LAG3+ HAVCR2+), CD8+ proliferated T cells (STMN+), and M2-like macrophages (CD68+ CD163+ APOC1+), which are closely associated with immunosuppression, played vital roles in ccRCC occurrence and development. These results were further verified by whole exome sequencing, cell line and xenograft experiments, and immunofluorescence staining. Finally, we divide patients with ccRCC into three subtypes using unsupervised cluster analysis. and generated a classifier to reproduce these subtypes using the eXtreme Gradient Boosting algorithm. Our classifier can help clinicians evaluate prognosis and design personalized treatment strategies for ccRCC. In summary, our work provides a new perspective for understanding tumor heterogeneity and will aid in the design of antitumor therapeutic strategies for ccRCC.
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Affiliation(s)
- Yanlong Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Shanxi Medical University, Shanxi Bethune Hospital, Taiyuan, Shanxi, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Department of Urology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xuefeng Huang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Minghang Yu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Menghan Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Li Zhao
- Shanxi Medical University, Shanxi Bethune Hospital, Taiyuan, Shanxi, China
| | - Yong Yan
- Department of Urology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
| | - Liyun Zhang
- Shanxi Medical University, Shanxi Bethune Hospital, Taiyuan, Shanxi, China.
| | - Xi Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Beijing Institute of Infectious Diseases, Beijing, 100015, China.
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
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Liu D, Wu G, Wang S, Zheng X, Che X. Evaluating the Role of Neddylation Modifications in Kidney Renal Clear Cell Carcinoma: An Integrated Approach Using Bioinformatics, MLN4924 Dosing Experiments, and RNA Sequencing. Pharmaceuticals (Basel) 2024; 17:635. [PMID: 38794205 PMCID: PMC11125012 DOI: 10.3390/ph17050635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Neddylation, a post-translational modification process, plays a crucial role in various human neoplasms. However, its connection with kidney renal clear cell carcinoma (KIRC) remains under-researched. METHODS We validated the Gene Set Cancer Analysis Lite (GSCALite) platform against The Cancer Genome Atlas (TCGA) database, analyzing 33 cancer types and their link with 17 neddylation-related genes. This included examining copy number variations (CNVs), single nucleotide variations (SNVs), mRNA expression, cellular pathway involvement, and methylation. Using Gene Set Variation Analysis (GSVA), we categorized these genes into three clusters and examined their impact on KIRC patient prognosis, drug responses, immune infiltration, and oncogenic pathways. Afterward, our objective is to identify genes that exhibit overexpression in KIRC and are associated with an adverse prognosis. After pinpointing the specific target gene, we used the specific inhibitor MLN4924 to inhibit the neddylation pathway to conduct RNA sequencing and related in vitro experiments to verify and study the specificity and potential mechanisms related to the target. This approach is geared towards enhancing our understanding of the prognostic importance of neddylation modification in KIRC. RESULTS We identified significant CNV, SNV, and methylation events in neddylation-related genes across various cancers, with notably higher expression levels observed in KIRC. Cluster analysis revealed a potential trade-off in the interactions among neddylation-related genes, where both high and low levels of gene expression are linked to adverse prognoses. This association is particularly pronounced concerning lymph node involvement, T stage classification, and Fustat score. Simultaneously, our research discovered that PSMB10 exhibits overexpression in KIRC when compared to normal tissues, negatively impacting patient prognosis. Through RNA sequencing and in vitro assays, we confirmed that the inhibition of neddylation modification could play a role in the regulation of various signaling pathways, thereby influencing the prognosis of KIRC. Moreover, our results underscore PSMB10 as a viable target for therapeutic intervention in KIRC, opening up novel pathways for the development of targeted treatment strategies. CONCLUSION This study underscores the regulatory function and potential mechanism of neddylation modification on the phenotype of KIRC, identifying PSMB10 as a key regulatory target with a significant role in influencing the prognosis of KIRC.
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Affiliation(s)
- Dequan Liu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (G.W.); (S.W.)
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (G.W.); (S.W.)
| | - Shijin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (G.W.); (S.W.)
| | - Xu Zheng
- Department of Cell Biology, College of Basic Medical Science, Dalian Medical University, Dalian 116011, China
| | - Xiangyu Che
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (G.W.); (S.W.)
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9
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Sjöberg E. Molecular mechanisms and clinical relevance of endothelial cell cross-talk in clear cell renal cell carcinoma. Ups J Med Sci 2024; 129:10632. [PMID: 38863726 PMCID: PMC11165252 DOI: 10.48101/ujms.v129.10632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/17/2024] [Accepted: 04/03/2024] [Indexed: 06/13/2024] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common renal cancer in adults and stands out as one of the most vascularized and immune-infiltrated solid tumors. Overproduction of vascular endothelial growth factor A promotes uncontrolled growth of abnormal vessels and immunosuppression, and the tumor microenvironment (TME) has a prominent role in disease progression, drug targeting and drug response, and for patient outcome. Methods Studies of experimental models, large-scale omics approaches, and patient prognosis and therapy prediction, using gene expression signatures and tissue biomarker analysis, have been reviewed for enhanced understanding of the endothelium in ccRCC and the interplay with the surrounding TME. Results Preclinical and clinical studies have discovered molecular mechanisms of endothelial cross-talk of relevance for disease progression, patient prognosis, and therapy prediction. There is, however, a lack of representative ccRCC experimental models. Omics approaches have identified clinically relevant subsets of angiogenic and immune-infiltrated tumors with distinct molecular signatures and distinct endothelial cell and immune cell populations in patients. Conclusions Recent genetically engineered ccRCC mouse models together with emerging evidence from single cell RNA sequencing data open up for future validation studies, including multiplex imaging of ccRCC patient cohorts. These studies are of importance for therapy benefit and personalized treatment of ccRCC patients.
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Affiliation(s)
- Elin Sjöberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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10
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Du Q, An Q, Zhang J, Liu C, Hu Q. Unravelling immune microenvironment features underlying tumor progression in the single-cell era. Cancer Cell Int 2024; 24:143. [PMID: 38649887 PMCID: PMC11036673 DOI: 10.1186/s12935-024-03335-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
The relationship between the immune cell and tumor occurrence and progression remains unclear. Profiling alterations in the tumor immune microenvironment (TIME) at high resolution is crucial to identify factors influencing cancer progression and enhance the effectiveness of immunotherapy. However, traditional sequencing methods, including bulk RNA sequencing, exhibit varying degrees of masking the cellular heterogeneity and immunophenotypic changes observed in early and late-stage tumors. Single-cell RNA sequencing (scRNA-seq) has provided significant and precise TIME landscapes. Consequently, this review has highlighted TIME cellular and molecular changes in tumorigenesis and progression elucidated through recent scRNA-seq studies. Specifically, we have summarized the cellular heterogeneity of TIME at different stages, including early, late, and metastatic stages. Moreover, we have outlined the related variations that may promote tumor occurrence and metastasis in the single-cell era. The widespread applications of scRNA-seq in TIME will comprehensively redefine the understanding of tumor biology and furnish more effective immunotherapy strategies.
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Affiliation(s)
- Qilian Du
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Qi An
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jiajun Zhang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Chao Liu
- Department of Radiation Oncology, Peking University First Hospital, Beijing, 100034, China.
| | - Qinyong Hu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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11
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Wang Y, Chen X, Tang N, Guo M, Ai D. Boosting Clear Cell Renal Carcinoma-Specific Drug Discovery Using a Deep Learning Algorithm and Single-Cell Analysis. Int J Mol Sci 2024; 25:4134. [PMID: 38612943 PMCID: PMC11012314 DOI: 10.3390/ijms25074134] [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: 02/17/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Clear cell renal carcinoma (ccRCC), the most common subtype of renal cell carcinoma, has the high heterogeneity of a highly complex tumor microenvironment. Existing clinical intervention strategies, such as target therapy and immunotherapy, have failed to achieve good therapeutic effects. In this article, single-cell transcriptome sequencing (scRNA-seq) data from six patients downloaded from the GEO database were adopted to describe the tumor microenvironment (TME) of ccRCC, including its T cells, tumor-associated macrophages (TAMs), endothelial cells (ECs), and cancer-associated fibroblasts (CAFs). Based on the differential typing of the TME, we identified tumor cell-specific regulatory programs that are mediated by three key transcription factors (TFs), whilst the TF EPAS1/HIF-2α was identified via drug virtual screening through our analysis of ccRCC's protein structure. Then, a combined deep graph neural network and machine learning algorithm were used to select anti-ccRCC compounds from bioactive compound libraries, including the FDA-approved drug library, natural product library, and human endogenous metabolite compound library. Finally, five compounds were obtained, including two FDA-approved drugs (flufenamic acid and fludarabine), one endogenous metabolite, one immunology/inflammation-related compound, and one inhibitor of DNA methyltransferase (N4-methylcytidine, a cytosine nucleoside analogue that, like zebularine, has the mechanism of inhibiting DNA methyltransferase). Based on the tumor microenvironment characteristics of ccRCC, five ccRCC-specific compounds were identified, which would give direction of the clinical treatment for ccRCC patients.
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Affiliation(s)
| | | | | | | | - Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; (Y.W.); (X.C.); (N.T.); (M.G.)
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12
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Jiang A, Liu Y, Zhu B, Fang Y, Qu L, Yang Q, Luo P, Cai C, Wang L. SPCS, a Novel Classifier System Based on Senescence Axis Regulators Reveals Tumor Microenvironment Heterogeneity and Guides Frontline Therapy for Clear Cell Renal Carcinoma. Clin Genitourin Cancer 2024; 22:497-513. [PMID: 38245436 DOI: 10.1016/j.clgc.2024.01.005] [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: 07/09/2023] [Revised: 01/03/2024] [Accepted: 01/06/2024] [Indexed: 01/22/2024]
Abstract
RATIONALE The emerging evidence suggested that senescence regulator genes were involved in multi cancers, which may be utilized as new targets for cancers. However, the dysregulation and clinical impact of senescence regulator genes in clear cell renal cell cancer (ccRCC) were still in foggy. METHODS Using multiomics data from TCGA-KIRC and other datasets, we comprehensively investigated the function of senescence regulator genes in ccRCC. ccRCC patients could be remodeled into 2 significant different groups basing on senescence regulators expression: senescence-pattern cancer subtype1 (SPCS1) and subtype2 (SPCS2). We further explored clinical characteristics, functional analysis, tumor immune microenvironment, immunotherapy response, genomic mutation and drug sensitivity between the 2 subtypes. Besides, senescence-pattern related risk model was established to determine the patient's prognosis of ccRCC. Finally, the overview of MECP2 function was investigated in multi cancers. RESULTS ccRCC patients could be divided into SPCS1 (normal aging group) and SPCS2 (Aging disorder group). The 2 subtypes showed significant different clinical characteristics and biological process in ccRCC. SPCS2, an aggressive subtype, comprised higher clinical stage and worse prognosis of ccRCC patients. SPCS2 subtype indicated activated oncogenic signaling pathway and metabolic signatures to prompt cancer expansion. SPCS2 subgroup owned immunocompromised status, which induced immune dysfunction and low ICI therapy response. The genome-copy numbers of SPCS2, including arm-gain and arm-loss was significantly more frequent than SPCS1. In addition, the 2 subtypes argue contrasting drug sensitivity profiles in clinical specimens and matched cell lines. Finally, we constructed a prognostic risk model consisted of each subtype's leading biomarkers, which exerted a satisfied performance for ccRCC patients. CONCLUSION Senescence regulator-related signature could modify functional pathways and tumor immune microenvironment by genome mutation and pathway interaction. Senescence regulator-related molecular subtype strengthen the understanding of ccRCC' characterization and guide clinical treatment. Targeting senescence regulators may be regard as a proper way in ccRCC.
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Affiliation(s)
- Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Ying Liu
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Baohua Zhu
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yu Fang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Qiwei Yang
- Depanrtment of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China; Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Chen Cai
- Department of Special Clinic, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
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Hu J, Wang SG, Hou Y, Chen Z, Liu L, Li R, Li N, Zhou L, Yang Y, Wang L, Wang L, Yang X, Lei Y, Deng C, Li Y, Deng Z, Ding Y, Kuang Y, Yao Z, Xun Y, Li F, Li H, Hu J, Liu Z, Wang T, Hao Y, Jiao X, Guan W, Tao Z, Ren S, Chen K. Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression. Nat Genet 2024; 56:442-457. [PMID: 38361033 PMCID: PMC10937392 DOI: 10.1038/s41588-024-01662-5] [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: 02/20/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a complex disease with remarkable immune and metabolic heterogeneity. Here we perform genomic, transcriptomic, proteomic, metabolomic and spatial transcriptomic and metabolomic analyses on 100 patients with ccRCC from the Tongji Hospital RCC (TJ-RCC) cohort. Our analysis identifies four ccRCC subtypes including De-clear cell differentiated (DCCD)-ccRCC, a subtype with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, reduced metabolic activity, enhanced nutrient uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD is associated with worse outcomes and higher recurrence rate, suggesting that it cannot be cured by nephrectomy alone. Our study also suggests a treatment strategy based on subtype-specific immune cell infiltration that could guide the clinical management of ccRCC.
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Affiliation(s)
- Junyi Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaxin Hou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaohui Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lilong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruizhi Li
- Shanghai Luming Biotech, Shanghai, China
| | - Nisha Li
- Shanghai Luming Biotech, Shanghai, China
- Shanghai OE Biotech, Shanghai, China
| | - Lijie Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Yang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liping Wang
- Department of Pathology, Baylor Scott & White Medical Center, Temple, TX, USA
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Yang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yichen Lei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changqi Deng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyao Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhong Ding
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingchun Kuang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhipeng Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Xun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Hao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Philadelphia, PA, USA
| | - Wei Guan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhen Tao
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shancheng Ren
- Department of Urology, Second Affiliated Hospital of Naval Medical University, Shanghai, China.
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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López J, Hogan M, Sutton B, Church S, Angulo J, Nunes-Xavier C. Distinct spatial landscapes in clear-cell renal cell carcinoma as revealed by whole transcriptome analysis. IMMUNO-ONCOLOGY TECHNOLOGY 2024; 21:100690. [PMID: 38292905 PMCID: PMC10825646 DOI: 10.1016/j.iotech.2023.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive form of renal cancer and a paradigm of inter- and intratumor heterogeneity. We carried out an exploratory digital spatial profiling of the tumor interior and periphery of two ccRCC tumor specimens and mapped spatially the molecular and cellular composition of their tumor microenvironment and ecosystem. Materials and methods Digital spatial profiling of the whole transcriptome of 19 regions of interest (ROIs) was carried out from two selected highly immunogenic stage pT3a/grade 3 (G3) and stage pT3a/grade 4 (G4) ccRCC. A total of 9-10 ROIs were selected from distinct areas from each tumor, including tumor interior and tumor periphery, and differences in gene expression were analyzed by RNA sequencing, pathway enrichment analysis, and cell deconvolution. Results The distinct areas from the two locally advanced tumors displayed unique gene expression spatial patterns defining distinct biological pathways. Dimensional reduction analysis showed that the G3 ccRCC, compared to the G4 ccRCC, correlated with more variability between regions from the tumor interior and tumor periphery. Cell deconvolution analysis illustrated higher abundance of immune cells, including macrophages, myeloid dendritic cells, and CD4 T cells, and lower abundance of regulatory T cells in the tumor periphery compared to the tumor interior. Conclusions Transcriptome spatial profiling revealed high inter- and intratumor heterogeneity in the analyzed tumors and provided information with potential clinical utility. This included the finding of less intratumor heterogeneity and more tumor-infiltrated T cells in the ccRCC tumor specimen with a higher grade.
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Affiliation(s)
- J.I. López
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | | | - B. Sutton
- NanoString Technologies, Seattle, USA
| | | | - J.C. Angulo
- Service of Urology, University Hospital of Getafe, Getafe, Madrid
- Clinical Department, Faculty of Biomedical Sciences, European University of Madrid, Madrid, Spain
| | - C.E. Nunes-Xavier
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
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15
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Ruan H, Zhang J, Wang Y, Huang Y, Wu J, He C, Ke T, Luo J, Yang M. 27-Hydroxycholesterol/liver X receptor/apolipoprotein E mediates zearalenone-induced intestinal immunosuppression: A key target potentially linking zearalenone and cancer. J Pharm Anal 2024; 14:371-388. [PMID: 38618245 PMCID: PMC11010457 DOI: 10.1016/j.jpha.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/07/2023] [Accepted: 08/07/2023] [Indexed: 04/16/2024] Open
Abstract
Zearalenone (ZEN) is a mycotoxin that extensively contaminates food and feed, posing a significant threat to public health. However, the mechanisms behind ZEN-induced intestinal immunotoxicity remain unclear. In this study, Sprague-Dawley (SD) rats were exposed to ZEN at a dosage of 5 mg/kg/day b.w. for a duration of 14 days. The results demonstrated that ZEN exposure led to notable pathological alterations and immunosuppression within the intestine. Furthermore, ZEN exposure caused a significant reduction in the levels of apolipoprotein E (ApoE) and liver X receptor (LXR) (P < 0.05). Conversely, it upregulated the levels of myeloid-derived suppressor cells (MDSCs) markers (P < 0.05) and decreased the presence of 27-hydroxycholesterol (27-HC) in the intestine (P < 0.05). It was observed that ApoE or LXR agonists were able to mitigate the immunosuppressive effects induced by ZEN. Additionally, a bioinformatics analysis highlighted that the downregulation of ApoE might elevate the susceptibility to colorectal, breast, and lung cancers. These findings underscore the crucial role of the 27-HC/LXR/ApoE axis disruption in ZEN-induced MDSCs proliferation and subsequent inhibition of T lymphocyte activation within the rat intestine. Notably, ApoE may emerge as a pivotal target linking ZEN exposure to cancer development.
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Affiliation(s)
- Haonan Ruan
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jing Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Yunyun Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Ying Huang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jiashuo Wu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Chunjiao He
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Tongwei Ke
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jiaoyang Luo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Meihua Yang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
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16
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Yang G, Cheng J, Xu J, Shen C, Lu X, He C, Huang J, He M, Cheng J, Wang H. Metabolic heterogeneity in clear cell renal cell carcinoma revealed by single-cell RNA sequencing and spatial transcriptomics. J Transl Med 2024; 22:210. [PMID: 38414015 PMCID: PMC10900752 DOI: 10.1186/s12967-024-04848-x] [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: 09/06/2023] [Accepted: 12/31/2023] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma is a prototypical tumor characterized by metabolic reprogramming, which extends beyond tumor cells to encompass diverse cell types within the tumor microenvironment. Nonetheless, current research on metabolic reprogramming in renal cell carcinoma mostly focuses on either tumor cells alone or conducts analyses of all cells within the tumor microenvironment as a mixture, thereby failing to precisely identify metabolic changes in different cell types within the tumor microenvironment. METHODS Gathering 9 major single-cell RNA sequencing databases of clear cell renal cell carcinoma, encompassing 195 samples. Spatial transcriptomics data were selected to conduct metabolic activity analysis with spatial localization. Developing scMet program to convert RNA-seq data into scRNA-seq data for downstream analysis. RESULTS Diverse cellular entities within the tumor microenvironment exhibit distinct infiltration preferences across varying histological grades and tissue origins. Higher-grade tumors manifest pronounced immunosuppressive traits. The identification of tumor cells in the RNA splicing state reveals an association between the enrichment of this particular cellular population and an unfavorable prognostic outcome. The energy metabolism of CD8+ T cells is pivotal not only for their cytotoxic effector functions but also as a marker of impending cellular exhaustion. Sphingolipid metabolism evinces a correlation with diverse macrophage-specific traits, particularly M2 polarization. The tumor epicenter is characterized by heightened metabolic activity, prominently marked by elevated tricarboxylic acid cycle and glycolysis while the pericapsular milieu showcases a conspicuous enrichment of attributes associated with vasculogenesis, inflammatory responses, and epithelial-mesenchymal transition. The scMet facilitates the transformation of RNA sequencing datasets sourced from TCGA into scRNA sequencing data, maintaining a substantial degree of correlation. CONCLUSIONS The tumor microenvironment of clear cell renal cell carcinoma demonstrates significant metabolic heterogeneity across various cell types and spatial dimensions. scMet exhibits a notable capability to transform RNA sequencing data into scRNA sequencing data with a high degree of correlation.
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Affiliation(s)
- Guanwen Yang
- Department of Urology, Zhongshan Hospital, Fudan University, 180Th Fengling Rd, Xuhui District, Shanghai, 200032, China
| | - Jiangting Cheng
- Department of Urology, Zhongshan Hospital, Fudan University, 180Th Fengling Rd, Xuhui District, Shanghai, 200032, China
| | - Jiayi Xu
- Department of Urology, Zhongshan Hospital, Fudan University, 180Th Fengling Rd, Xuhui District, Shanghai, 200032, China
| | - Chenyang Shen
- Department of Urology, Zhongshan Hospital, Fudan University, 180Th Fengling Rd, Xuhui District, Shanghai, 200032, China
| | - Xuwei Lu
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Chang He
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Jiaqi Huang
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Minke He
- Department of Urology, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Jie Cheng
- Department of Urology, Xuhui Hospital, Fudan University, 966Th Huaihai Middle Rd, Xuhui District, Shanghai, 200031, China.
| | - Hang Wang
- Department of Urology, Zhongshan Hospital, Fudan University, 180Th Fengling Rd, Xuhui District, Shanghai, 200032, China.
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Yang W, Liu S, Mao M, Gong Y, Li X, Lei T, Liu C, Wu S, Hu Q. T-cell infiltration and its regulatory mechanisms in cancers: insights at single-cell resolution. J Exp Clin Cancer Res 2024; 43:38. [PMID: 38303018 PMCID: PMC10835979 DOI: 10.1186/s13046-024-02960-w] [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: 11/06/2023] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Tumor-infiltrating T cells recognize, attack, and clear tumor cells, playing a central role in antitumor immune response. However, certain immune cells can impair this response and help tumor immune escape. Therefore, exploring the factors that influence T-cell infiltration is crucial to understand tumor immunity and improve therapeutic effect of cancer immunotherapy. The use of single-cell RNA sequencing (scRNA-seq) allows the high-resolution analysis of the precise composition of immune cells with different phenotypes and other microenvironmental factors, including non-immune stromal cells and the related molecules in the tumor microenvironment of various cancer types. In this review, we summarized the research progress on T-cell infiltration and the crosstalk of other stromal cells and cytokines during T-cell infiltration using scRNA-seq to provide insights into the mechanisms regulating T-cell infiltration and contribute new perspectives on tumor immunotherapy.
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Affiliation(s)
- Wenhui Yang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Shimao Liu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Mengyun Mao
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Senior Department of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Xiaohui Li
- Department of Medical Oncology, Peking University First Hospital, Beijing, 100034, China
| | - Tianyu Lei
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Chao Liu
- Department of Radiation Oncology, Peking University First Hospital, Beijing, 100034, China.
| | - Shikai Wu
- Department of Medical Oncology, Peking University First Hospital, Beijing, 100034, China.
| | - Qinyong Hu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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Wang Z, Zhang Z. Single-cell analysis reveals ADGRL4+ renal tubule cells as a highly aggressive cell type in clear cell renal cell carcinoma. Sci Rep 2024; 14:2407. [PMID: 38287102 PMCID: PMC10824758 DOI: 10.1038/s41598-024-52928-1] [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: 10/25/2023] [Accepted: 01/25/2024] [Indexed: 01/31/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a highly heterogeneous cancer that poses great challenge to clinical treatment and prognostic prediction. Characterizing the cellular landscape of ccRCC in a single-cell dimension can help better understand the tumor heterogeneity and molecular mechanisms of ccRCC. This study analyzed single-cell profiles in ccRCC samples and para-tumor samples from Gene Expression Omnibus and identified a highly heterogeneous subcluster of renal tubule cells. Single-cell regulatory network inference and clustering analyses and cell communication analysis were performed to develop transcription factor-target gene regulatory networks and cell-cell interactions. Additionally, the distribution and prognostic risk of renal tubule cells from spatial transcriptome data (GSM6415706) and The Cancer Genome Atlas-Kidney Clear Cell Carcinoma data were analyzed. A total of 10 cell types were identified in ccRCC and para-tumor samples. The ccRCC renal tubule cells showed a high expression of the oncogene nicotinamide N-methyltransferase and a significantly high degree of tumor heterogeneity. We further identified 6 cell subclusters with specific expression of BEX2, PTHLH, SFRP2, KLRB1, ADGRL4, and HGF from the ccRCC renal tubule cells. ADGRL4+ renal tubule cells had highly metastatic and angiogenesis-inducing characteristics, with more ADGRL4+ renal tubule cells indicating a worse survival. ADGRL4+ renal tubule cells regulated the metastasis of other renal tubule cells through metastasis-related receptor-ligand communication. We also found that ADGRL4+ renal tubule cells clustered around the glomeruli but the rest of the renal tubule cell subclusters rarely localized in ccRCC tissues. ETS1 and ELK3 -dominant GRNs were remarkably activated in ADGRL4+ renal tubule cells, functionally, knockdown of ELK3 in A498 significantly disturbedaffected the cell migration and invasion. ADGRL4+ renal tubule cells, which were highly metastatic and invasive, might be an essential cell subcluster for ccRCC, and ADGRL4 could be used a novel therapeutic target.
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Affiliation(s)
- Zehua Wang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Zhongxiao Zhang
- Department of Urology, Qilu Hospital (Qingdao), Shandong University, Qingdao, 266035, China.
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Xu K, Li D, Qian J, Zhang Y, Zhang M, Zhou H, Hou X, Jiang J, Zhang Z, Sun H, Shi G, Dai H, Liu H. Single-cell disulfidptosis regulator patterns guide intercellular communication of tumor microenvironment that contribute to kidney renal clear cell carcinoma progression and immunotherapy. Front Immunol 2024; 15:1288240. [PMID: 38292868 PMCID: PMC10824999 DOI: 10.3389/fimmu.2024.1288240] [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: 09/04/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Background Disulfidptosis, an emerging type of programmed cell death, plays a pivotal role in various cancer types, notably impacting the progression of kidney renal clear cell carcinoma (KIRC) through the tumor microenvironment (TME). However, the specific involvement of disulfidptosis within the TME remains elusive. Methods Analyzing 41,784 single cells obtained from seven samples of KIRC through single-cell RNA sequencing (scRNA-seq), this study employed nonnegative matrix factorization (NMF) to assess 24 disulfidptosis regulators. Pseudotime analysis, intercellular communication mapping, determination of transcription factor activities (TFs), and metabolic profiling of the TME subgroup in KIRC were conducted using Monocle, CellChat, SCENIC, and scMetabolism. Additionally, public cohorts were utilized to predict prognosis and immune responses within the TME subgroup of KIRC. Results Through NMF clustering and differential expression marker genes, fibroblasts, macrophages, monocytes, T cells, and B cells were categorized into four to six distinct subgroups. Furthermore, this investigation revealed the correlation between disulfidptosis regulatory factors and the biological traits, as well as the pseudotime trajectories of TME subgroups. Notably, disulfidptosis-mediated TME subgroups (DSTN+CD4T-C1 and FLNA+CD4T-C2) demonstrated significant prognostic value and immune responses in patients with KIRC. Multiple immunohistochemistry (mIHC) assays identified marker expression within both cell clusters. Moreover, CellChat analysis unveiled diverse and extensive interactions between disulfidptosis-mediated TME subgroups and tumor epithelial cells, highlighting the TNFSF12-TNFRSF12A ligand-receptor pair as mediators between DSTN+CD4T-C1, FLNA+CD4T-C2, and epithelial cells. Conclusion Our study sheds light on the role of disulfidptosis-mediated intercellular communication in regulating the biological characteristics of the TME. These findings offer valuable insights for patients with KIRC, potentially guiding personalized immunotherapy approaches.
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Affiliation(s)
- Kangjie Xu
- Central Laboratory Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Dongling Li
- Nephrology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Jinke Qian
- Urology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Yanhua Zhang
- Obstetrics and Gynecology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Minglei Zhang
- Oncology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Hai Zhou
- Central Laboratory Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Xuefeng Hou
- Central Laboratory Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Jian Jiang
- Central Laboratory Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Zihang Zhang
- Pathology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Hang Sun
- Urology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Guodong Shi
- Medical Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Hua Dai
- Yangzhou University Clinical Medical College, Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yancheng, Jiangsu, China
| | - Hui Liu
- Urology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
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20
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Shi M, Huang K, Wei J, Wang S, Yang W, Wang H, Li Y. Identification and Validation of a Prognostic Signature Derived from the Cancer Stem Cells for Oral Squamous Cell Carcinoma. Int J Mol Sci 2024; 25:1031. [PMID: 38256104 PMCID: PMC10816075 DOI: 10.3390/ijms25021031] [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: 12/26/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
The progression and metastasis of oral squamous cell carcinoma (OSCC) are highly influenced by cancer stem cells (CSCs) due to their unique self-renewal and plasticity. In this study, data were obtained from a single-cell RNA-sequencing dataset (GSE172577) in the GEO database, and LASSO-Cox regression analysis was performed on 1344 CSCs-related genes to establish a six-gene prognostic signature (6-GPS) consisting of ADM, POLR1D, PTGR1, RPL35A, PGK1, and P4HA1. High-risk scores were significantly associated with unfavorable survival outcomes, and these features were thoroughly validated in the ICGC. The results of nomograms, calibration plots, and ROC curves confirmed the good prognostic accuracy of 6-GPS for OSCC. Additionally, the knockdown of ADM or POLR1D genes may significantly inhibit the proliferation, migration, and invasion of OSCC cells through the JAK/HIF-1 pathway. Furthermore, cell-cycle arrest occurred in the G1 phase by suppressing Cyclin D1. In summary, 6-GPS may play a crucial role in the occurrence and development of OSCC and has the potential to be developed further as a diagnostic, therapeutic, and prognostic tool for OSCC.
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Affiliation(s)
- Mingxuan Shi
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Ke Huang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730030, China
| | - Jiaqi Wei
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Shiqi Wang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Weijia Yang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Huihui Wang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Yi Li
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
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21
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Ma F, Wang S, Xu L, Huang W, Shi G, Sun Z, Cai W, Wu Z, Huang Y, Meng J, Sun Y, Fang M, Cheng M, Ji Y, Hu T, Zhang Y, Gu B, Zhang J, Song S, Sun Y, Yan W. Single-cell profiling of the microenvironment in human bone metastatic renal cell carcinoma. Commun Biol 2024; 7:91. [PMID: 38216635 PMCID: PMC10786927 DOI: 10.1038/s42003-024-05772-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: 12/10/2022] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
Bone metastasis is of common occurrence in renal cell carcinoma with poor prognosis, but no optimal treatment approach has been established for bone metastatic renal cell carcinoma. To explore the potential therapeutic targets for bone metastatic renal cell carcinoma, we profile single cell transcriptomes of 6 primary renal cell carcinoma and 9 bone metastatic renal cell carcinoma. We also include scRNA-seq data of early-stage renal cell carcinoma, late-stage renal cell carcinoma, normal kidneys and healthy bone marrow samples in the study to better understand the bone metastasis niche. The molecular properties and dynamic changes of major cell lineages in bone metastatic environment of renal cell carcinoma are characterized. Bone metastatic renal cell carcinoma is associated with multifaceted immune deficiency together with cancer-associated fibroblasts, specifically appearance of macrophages exhibiting malignant and pro-angiogenic features. We also reveal the dominance of immune inhibitory T cells in the bone metastatic renal cell carcinoma which can be partially restored by the treatment. Trajectory analysis showes that myeloid-derived suppressor cells are progenitors of macrophages in the bone metastatic renal cell carcinoma while monocytes are their progenitors in primary tumors and healthy bone marrows. Additionally, the infiltration of immune inhibitory CD47+ T cells is observed in bone metastatic tumors, which may be a result of reduced phagocytosis by SIRPA-expressing macrophages in the bone microenvironment. Together, our results provide a systematic view of various cell types in bone metastatic renal cell carcinoma and suggest avenues for therapeutic solutions.
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Affiliation(s)
- Fen Ma
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, 201203, Shanghai, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Shuoer Wang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Lun Xu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Wending Huang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Guohai Shi
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
- Department of Urology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
| | - Zhengwang Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Weiluo Cai
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Zhiqiang Wu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yiming Huang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Juan Meng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Yining Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
| | - Meng Fang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Mo Cheng
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yingzheng Ji
- Department of Orthopedic, Naval Medical Center of PLA, Second Military Medical University, 338 Huaihai West Road, Shanghai, China
| | - Tu Hu
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Yunkui Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
| | - Bingxin Gu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China
| | - Jiwei Zhang
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, 201203, Shanghai, China.
| | - Shaoli Song
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China.
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.
| | - Wangjun Yan
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, 138 Medical College Road, Shanghai, China.
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22
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Massenet-Regad L, Poirot J, Jackson M, Hoffmann C, Amblard E, Onodi F, Bouhidel F, Djouadou M, Ouzaid I, Xylinas E, Medvedovic J, Soumelis V. Large-scale analysis of cell-cell communication reveals angiogenin-dependent tumor progression in clear cell renal cell carcinoma. iScience 2023; 26:108367. [PMID: 38025776 PMCID: PMC10663819 DOI: 10.1016/j.isci.2023.108367] [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: 07/25/2023] [Revised: 09/25/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Cellular crosstalk in the tumor microenvironment (TME) is still largely uncharacterized, while it plays an essential role in shaping immunosuppression or anti-tumor response. Large-scale analyses are needed to better decipher cell-cell communication in cancer. In this work, we used original and publicly available single-cell RNA sequencing (scRNAseq) data to characterize in-depth the communication networks in human clear cell renal cell carcinoma (ccRCC). We identified 50 putative communication channels specifically used by cancer cells to interact with other cells, including two novel angiogenin-mediated interactions. Expression of angiogenin and its receptors was validated at the protein level in primary ccRCC. Mechanistically, angiogenin enhanced ccRCC cell line proliferation and down-regulated secretion of IL-6, IL-8, and MCP-1 proinflammatory molecules. This study provides novel biological insights into molecular mechanisms of ccRCC, and suggests angiogenin and its receptors as potential therapeutic targets in clear cell renal cancer.
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Affiliation(s)
- Lucile Massenet-Regad
- Université Paris Cité, INSERM, U976 HIPI, F-75010 Paris, France
- Université Paris-Saclay, F-91190 Saint Aubin, France
| | - Justine Poirot
- Université Paris Cité, INSERM, U976 HIPI, F-75010 Paris, France
- Université Paris-Saclay, F-91190 Saint Aubin, France
| | | | - Caroline Hoffmann
- INSERM U932, Department of Surgical Oncology, PSL University, Institut Curie, 75005 Paris, France
- Owkin France, 75010 Paris, France
| | - Elise Amblard
- Université Paris Cité, INSERM, U976 HIPI, F-75010 Paris, France
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble Alpes University, 38000 Grenoble, France
| | - Fanny Onodi
- Université Paris Cité, INSERM, U976 HIPI, F-75010 Paris, France
| | - Fatiha Bouhidel
- Department of Pathology, Saint-Louis Hospital, AP-HP.Nord, Université Paris Cité, 75010 Paris, France
| | - Malika Djouadou
- Department of Urology, Saint-Louis Hospital, AP-HP.Nord, Université Paris Cité, 75010 Paris, France
| | - Idir Ouzaid
- Department of Urology, Bichat-Claude Bernard Hospital, AP-HP.Nord, Université Paris Cité, 75018 Paris, France
| | - Evanguelos Xylinas
- Université Paris Cité, INSERM, U976 HIPI, F-75010 Paris, France
- Department of Urology, Bichat-Claude Bernard Hospital, AP-HP.Nord, Université Paris Cité, 75018 Paris, France
| | | | - Vassili Soumelis
- Université Paris Cité, INSERM, U976 HIPI, F-75010 Paris, France
- Owkin France, 75010 Paris, France
- Department of Immunology-Histocompatibility, Saint-Louis Hospital, AP-HP.Nord, Université Paris Cité, 75010 Paris, France
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23
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Schütz V, Lin H, Kaczorowski A, Zschäbitz S, Jäger D, Stenzinger A, Duensing A, Debus J, Hohenfellner M, Duensing S. Long-Term Survival of Patients with Stage T1N0M1 Renal Cell Carcinoma. Cancers (Basel) 2023; 15:5715. [PMID: 38136261 PMCID: PMC10741977 DOI: 10.3390/cancers15245715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Metastatic renal cell carcinoma (RCC) is among the most lethal urological malignancies. However, small, localized RCCs (≤7 cm, stage T1) have an excellent prognosis. There is a rare patient subgroup diagnosed with synchronous distant metastasis (T1N0M1), of which very little is known in terms of survival outcomes and underlying disease biology. Herein, we examined the long-term survival of 27 patients with clear cell RCC (ccRCC) stage T1N0M1 in comparison to 18 patients without metastases (T1N0M0). Tumor tissue was stained by immunohistochemistry for CD8+ tumor infiltrating lymphocytes (TILs). As expected, patients with stage T1N0M1 showed a significantly worse median cancer specific survival (CSS; 2.8 years) than patients with stage T1N0M0 (17.7 years; HR 0.077; 95% CI, 0.022-0.262). However, eight patients (29.6%) with ccRCC stage T1N0M1 survived over five years, and three of those patients (11.1%) survived over a decade. Some of these patients benefitted from an intensified, multimodal treatment including metastasis-directed therapy. The number of CD8+ TILs was substantially higher in stage T1N0M1 ccRCCs than in stage T1N0M0 ccRCCs, suggesting a more aggressive tumor biology. In conclusion, long-term survival is possible in patients with ccRCC stage T1N0M1, with some patients benefitting from an intensified, multimodal treatment approach.
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Affiliation(s)
- Viktoria Schütz
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Huan Lin
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, 69120 Heidelberg, Germany
| | - Adam Kaczorowski
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, 69120 Heidelberg, Germany
| | - Stefanie Zschäbitz
- Department of Medical Oncology, National Center for Tumor Diseases Heidelberg, University Hospital Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases Heidelberg, University Hospital Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Anette Duensing
- Precision Oncology of Urological Malignancies, Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, 69120 Heidelberg, Germany
| | - Jürgen Debus
- Department of Radiation Oncology, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Markus Hohenfellner
- Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Im Neuenheimer Feld 517, 69120 Heidelberg, Germany
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24
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Tian L, Wang Y, Zhang Z, Feng X, Xiao F, Zong M. CD72, a new immune checkpoint molecule, is a novel prognostic biomarker for kidney renal clear cell carcinoma. Eur J Med Res 2023; 28:531. [PMID: 37980541 PMCID: PMC10656955 DOI: 10.1186/s40001-023-01487-8] [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: 09/20/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND The incidence and mortality of clear cell carcinoma of the kidney increases yearly. There are limited screening methods and advances in treating kidney renal clear cell carcinoma (KIRC). It is important to find new biomarkers to screen, diagnose and predict the prognosis of KIRC. Some studies have shown that CD72 influences the development and progression of colorectal cancer, nasopharyngeal cancer, and acute lymphoid leukemia. However, there is a lack of research on the role of CD72 in the pathogenesis of KIRC. This study aimed to determine whether CD72 is associated with the prognosis and immune infiltration of KIRC, providing an essential molecular basis for the early non-invasive diagnosis and immunotherapy of KIRC. METHODS Using TCGA, GTE, GEO, and ImmPort databases, we obtained the differentially expressed mRNA (DEmRNA) associated with the prognosis and immunity of KIRC patients. We used the Kruskal-Wallis test to identify clinicopathological parameters associated with target gene expression. We performed univariate and multivariate COX regression analyses to determine the effect of target gene expression and clinicopathological parameters on survival. We analyzed the target genes' relevant functions and signaling pathways through enrichment analysis. Finally, the correlation of target genes with tumor immune infiltration was explored by ssGSEA and Spearman correlation analysis. RESULTS The results revealed that patients with KIRC with higher expression of CD72 have a poorer prognosis. CD72 was associated with the Pathologic T stage, Pathologic stage, Pathologic M stage, Pathologic N stage, Histologic grade in KIRC patients, Laterality, and OS event. It was an independent predictor of the overall survival of KIRC patients. Functional enrichment analysis showed that CD72 was significantly enriched in oncogenic and immune-related pathways. According to ssGSEA and Spearman correlation analysis, CD72 expression was significantly associated with tumor immune cells and immune checkpoints. CONCLUSION Our study suggests that CD72 is associated with tumor immunity and may be a biomarker relevant to the diagnosis and prognosis of KIRC patients.
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Affiliation(s)
- Lv Tian
- Department of Rehabilitation, China-Japan Union Hospital of Jilin University, Changchun, 130033, China
- School of Nursing, Jilin University, Changchun, China
| | - Yiming Wang
- School of Nursing, Jilin University, Changchun, China
| | - Zhiyuan Zhang
- School of Nursing, Jilin University, Changchun, China
| | - Xuechao Feng
- School of Life Sciences, Northeast Normal University, Changchun, China
| | - Fengjun Xiao
- Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Minru Zong
- Department of Rehabilitation, China-Japan Union Hospital of Jilin University, Changchun, 130033, China.
- School of Nursing, Jilin University, Changchun, China.
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25
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Xiao Y, Jiang C, Li H, Xu D, Liu J, Huili Y, Nie S, Guan X, Cao F. Genes associated with inflammation for prognosis prediction for clear cell renal cell carcinoma: a multi-database analysis. Transl Cancer Res 2023; 12:2629-2645. [PMID: 37969384 PMCID: PMC10643973 DOI: 10.21037/tcr-23-1183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the largest subtype of kidney tumour, with inflammatory responses characterising all stages of the tumour. Establishing the relationship between the genes related to inflammatory responses and ccRCC may help the diagnosis and treatment of patients with ccRCC. Methods First, we obtained the data for this study from a public database. After differential analysis and Cox regression analysis, we obtained the genes for the establishment of a prognostic model for ccRCC. As we used data from multiple databases, we standardized all the data using the surrogate variable analysis (SVA) package to make the data from different sources comparable. Next, we used a least absolute shrinkage and selection operator (LASSO) regression to construct a prognostic model of genes related to inflammation. The data used for modelling and internal validation came from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) series (GSE29609) databases. ccRCC data from the International Cancer Genome Consortium (ICGC) database were used for external validation. Tumour data from the E-MTAB-1980 cohort were used for external validation. The GSE40453 and GSE53757 datasets were used to verify the differential expression of inflammation-related gene model signatures (IRGMS). The immunohistochemistry of IRGMS was queried through the Human Protein Atlas (HPA) database. After the adequate validation of the IRGM, we further explored its application by constructing nomograms, pathway enrichment analysis, immunocorrelation analysis, drug susceptibility analysis, and subtype identification. Results The IRGM can robustly predict the prognosis of samples from patients with ccRCC from different databases. The verification results show that nomogram can accurately predict the survival rate of patients. Pathway enrichment analysis showed that patients in the high-risk (HR) group were associated with a variety of tumorigenesis biological processes. Immune-related analysis and drug susceptibility analysis suggested that patients with higher IRGM scores had more treatment options. Conclusions The IRGMS can effectively predict the prognosis of ccRCC. Patients with higher IRGM scores may be better candidates for treatment with immune checkpoint inhibitors and have more chemotherapy options.
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Affiliation(s)
- Yonggui Xiao
- School of Clinical Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
| | - Chonghao Jiang
- Department of Urology, Affiliated Hospital of North China University of Science and Technology, Tangshan, China
| | - Hubo Li
- School of Clinical Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
| | - Danping Xu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jinzheng Liu
- School of Clinical Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
| | - Youlong Huili
- School of Clinical Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
| | - Shiwen Nie
- School of Clinical Medicine, Affiliated Hospital, North China University of Science and Technology, Tangshan, China
| | - Xiaohai Guan
- Department of Urology, Affiliated Hospital of North China University of Science and Technology, Tangshan, China
| | - Fenghong Cao
- Department of Urology, Affiliated Hospital of North China University of Science and Technology, Tangshan, China
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26
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Zhou S, Zheng J, Zhai W, Chen Y. Spatio-temporal heterogeneity in cancer evolution and tumor microenvironment of renal cell carcinoma with tumor thrombus. Cancer Lett 2023; 572:216350. [PMID: 37574183 DOI: 10.1016/j.canlet.2023.216350] [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: 06/12/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Metastasis is the most fatal aspect of cancer, often preceded by a tumor thrombus (TT) which forms within the vascular system. Renal cell carcinoma (RCC), the predominant form of kidney cancer, witnesses a venous system invasion in 4-10% of cases, resulting in venous tumor thrombus (RCC-TT). This variant represents a formidable clinical challenge due to its escalated surgical complexity, heightened risk of progression and metastasis, and an adverse prognosis. However, recent trials addressing RCC-TT face significant barriers stemming from the profound inter- and intra-tumoral heterogeneity, patient-specific treatment variations, and distinct therapeutic resistance patterns between the primary tumor (PT) and the TT. This review delves into the unique evolutionary pathway of RCC-TT, the relationship between the staging and grading of RCC-TT invasion patterns, and the spatial molecular profiling of RCC-TT. Additionally, we assess the temporal heterogeneity among TT, PT, and distant metastases, as well as the functional phenotypes of TME components. An outlook for future research on RCC-TT is also provided.
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Affiliation(s)
- Sian Zhou
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Junhua Zheng
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Wei Zhai
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China; Department of Urology, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Yonghui Chen
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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27
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Alchahin AM, Tsea I, Baryawno N. Recent Advances in Single-Cell RNA-Sequencing of Primary and Metastatic Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2023; 15:4734. [PMID: 37835428 PMCID: PMC10571653 DOI: 10.3390/cancers15194734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Over the past two decades, significant progress has been made in the treatment of clear cell renal cell carcinoma (ccRCC), with a shift towards adopting new treatment approaches ranging from monotherapy to triple-combination therapy. This progress has been spearheaded by fundamental technological advancements that have allowed a deeper understanding of the various biological components of this cancer. In particular, the rapid commercialization of transcriptomics technologies, such as single-cell RNA-sequencing (scRNA-seq) methodologies, has played a crucial role in accelerating this understanding. Through precise measurements facilitated by these technologies, the research community has successfully identified and characterized diverse tumor, immune, and stromal cell populations, uncovering their interactions and pathways involved in disease progression. In localized ccRCC, patients have shown impressive response rates to treatment. However, despite the emerging findings and new knowledge provided in the field, there are still patients that do not respond to treatment, especially in advanced disease stages. One of the key challenges lies in the limited study of ccRCC metastases compared to localized cases. This knowledge gap may contribute to the relatively low survival rates and response rates observed in patients with metastatic ccRCC. To bridge this gap, we here delve into recent research utilizing scRNA-seq technologies in both primary and metastatic ccRCC. The goal of this review is to shed light on the current state of knowledge in the field, present existing treatment options, and emphasize the crucial steps needed to improve survival rates, particularly in cases of metastatic ccRCC.
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Affiliation(s)
| | | | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 10000-19999 Stockholm, Sweden; (A.M.A.); (I.T.)
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Semenescu LE, Kamel A, Ciubotaru V, Baez-Rodriguez SM, Furtos M, Costachi A, Dricu A, Tătăranu LG. An Overview of Systemic Targeted Therapy in Renal Cell Carcinoma, with a Focus on Metastatic Renal Cell Carcinoma and Brain Metastases. Curr Issues Mol Biol 2023; 45:7680-7704. [PMID: 37754269 PMCID: PMC10528141 DOI: 10.3390/cimb45090485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
The most commonly diagnosed malignancy of the urinary system is represented by renal cell carcinoma. Various subvariants of RCC were described, with a clear-cell type prevailing in about 85% of all RCC tumors. Patients with metastases from renal cell carcinoma did not have many effective therapies until the end of the 1980s, as long as hormonal therapy and chemotherapy were the only options available. The outcomes were unsatisfactory due to the poor effectiveness of the available therapeutic options, but then interferon-alpha and interleukin-2 showed treatment effectiveness, providing benefits but only for less than half of the patients. However, it was not until 2004 that targeted therapies emerged, prolonging the survival rate. Currently, new technologies and strategies are being developed to improve the actual efficacy of available treatments and their prognostic aspects. This article summarizes the mechanisms of action, importance, benefits, adverse events of special interest, and efficacy of immunotherapy in metastatic renal cell carcinoma, with a focus on brain metastases.
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Affiliation(s)
- Liliana Eleonora Semenescu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, Str. Petru Rares nr. 2-4, 710204 Craiova, Romania; (L.E.S.); (A.C.)
| | - Amira Kamel
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, Soseaua Berceni 12, 041915 Bucharest, Romania; (A.K.); (V.C.); (S.M.B.-R.); (L.G.T.)
| | - Vasile Ciubotaru
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, Soseaua Berceni 12, 041915 Bucharest, Romania; (A.K.); (V.C.); (S.M.B.-R.); (L.G.T.)
| | - Silvia Mara Baez-Rodriguez
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, Soseaua Berceni 12, 041915 Bucharest, Romania; (A.K.); (V.C.); (S.M.B.-R.); (L.G.T.)
| | - Mircea Furtos
- Neurosurgical Department, University Emergency Hospital of Bucharest, 050098 Bucharest, Romania;
| | - Alexandra Costachi
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, Str. Petru Rares nr. 2-4, 710204 Craiova, Romania; (L.E.S.); (A.C.)
| | - Anica Dricu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, Str. Petru Rares nr. 2-4, 710204 Craiova, Romania; (L.E.S.); (A.C.)
| | - Ligia Gabriela Tătăranu
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, Soseaua Berceni 12, 041915 Bucharest, Romania; (A.K.); (V.C.); (S.M.B.-R.); (L.G.T.)
- Department of Neurosurgery, Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 020022 Bucharest, Romania
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Wang Y, Zhang X, Chen G, Xing Q, Zhu B, Wang X. Integrated analyses reveal the prognostic, immunological features and mechanisms of cuproptosis critical mediator gene FDX1 in KIRC. Genes Immun 2023; 24:171-182. [PMID: 37430022 DOI: 10.1038/s41435-023-00211-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023]
Abstract
The ferredoxin 1 (FDX1) gene had been recently reported as a critical mediator of cuproptosis, and without doubt, its roles in KIRC would be of importance. Hence, this paper was to explore the roles of FDX1 in kidney renal clear cell carcinoma (KIRC) and its potential molecular mechanisms via scRNA-sequencing and bulk RNA-sequencing analyses. FDX1 was lowly expressed in KIRC and validated both at the protein and mRNA levels (all p < 0.05). Moreover, its elevated expression was linked with a better overall survival (OS) prognosis in KIRC (p < 0.01). The independent impact of FDX1 on KIRC prognosis was demonstrated by univariate/multivariate regression analysis (p < 0.01). Gene set enrichment analysis (GSEA) identified seven pathways strongly associated with FDX1 in KIRC. Furthermore, FDX1 was also revealed to be significantly related with immunity (p < 0.05). In addition, patients with low expression of FDX1 might be more sensitive to immunotherapies. ScRNA-seq analysis found that FDX1 could be expressed in immune cells and was mainly differently expressed in Mono/Macro cells. Ultimately, we also identified several LncRNA/RBP/FDX1 mRNA networks to reveal its underlying mechanisms in KIRC. Taken together, FDX1 was closely related to prognosis and immunity in KIRC, and its RBP-involved mechanisms of LncRNA/RBP/FDX1 networks were also revealed by us.
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Affiliation(s)
- Yi Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Xinyu Zhang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Guihua Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Qianwei Xing
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Bingye Zhu
- Department of Urology, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, 226001, Jiangsu Province, China.
| | - Xiang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
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30
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Zhu M, Li Y, Wang Y, Lin P, Mi J, Zhong W. Multi-omics analysis uncovers clinical, immunological, and pharmacogenomic implications of cuproptosis in clear cell renal cell carcinoma. Eur J Med Res 2023; 28:248. [PMID: 37481601 PMCID: PMC10362584 DOI: 10.1186/s40001-023-01221-4] [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: 03/06/2023] [Accepted: 07/11/2023] [Indexed: 07/24/2023] Open
Abstract
OBJECTIVE The latest research proposed a novel copper-dependent programmed cell death named cuproptosis. We aimed to elucidate the influence of cuproptosis in clear cell renal cell carcinoma (ccRCC) from a multi-omic perspective. METHODS This study systematically assessed mRNA expression, methylation, and genetic alterations of cuproptosis genes in TCGA ccRCC samples. Through unsupervised clustering analysis, the samples were classified as different cuproptosis subtypes, which were verified through NTP method in the E-MTAB-1980 dataset. Next, the cuproptosis score (Cuscore) was computed based on cuproptosis-related genes via PCA. We also evaluated clinical and immunogenomic features, drug sensitivity, immunotherapeutic response, and post-transcriptional regulation. RESULTS Cuproptosis genes presented multi-layer alterations in ccRCC, and were linked with patients' survival and immune microenvironment. We defined three cuproptosis subtypes [C1 (moderate cuproptosis), C2 (low cuproptosis), and C3 (high cuproptosis)], and the robustness and reproducibility of this classification was further proven. Overall survival was best in C3, moderate in C1, and worst in C2. C1 had the highest sensitivity to pazopanib, and sorafenib, while C2 was most sensitive to sunitinib. Furthermore, C1 patients benefited more from anti-PD-1 immunotherapy. Patients with high Cuscore presented the notable survival advantage. Cuscore was highly linked with immunogenomic features, and post-transcriptional events that contributed to ccRCC development. Finally, several potential compounds and druggable targets (NMU, RARRES1) were selected for low Cuscore group. CONCLUSION Overall, our study revealed the non-negligible role of cuproptosis in ccRCC development. Evaluation of the cuproptosis subtypes improves our cognition of immunogenomic features and better guides personalized prognostication and precision therapy.
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Affiliation(s)
- Maoshu Zhu
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Yongsheng Li
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Yun Wang
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Pingli Lin
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Jun Mi
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China
| | - Weimin Zhong
- The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian, People's Republic of China.
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31
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Wang Y, Wang Y, Liu B, Gao X, Li Y, Li F, Zhou H. Mapping the tumor microenvironment in clear cell renal carcinoma by single-cell transcriptome analysis. Front Genet 2023; 14:1207233. [PMID: 37533434 PMCID: PMC10392130 DOI: 10.3389/fgene.2023.1207233] [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: 04/17/2023] [Accepted: 07/06/2023] [Indexed: 08/04/2023] Open
Abstract
Introduction: Clear cell renal cell carcinoma (ccRCC) is associated with unfavorable clinical outcomes. To identify viable therapeutic targets, a comprehensive understanding of intratumoral heterogeneity is crucial. In this study, we conducted bioinformatic analysis to scrutinize single-cell RNA sequencing data of ccRCC tumor and para-tumor samples, aiming to elucidate the intratumoral heterogeneity in the ccRCC tumor microenvironment (TME). Methods: A total of 51,780 single cells from seven ccRCC tumors and five para-tumor samples were identified and grouped into 11 cell lineages using bioinformatic analysis. These lineages included tumor cells, myeloid cells, T-cells, fibroblasts, and endothelial cells, indicating a high degree of heterogeneity in the TME. Copy number variation (CNV) analysis was performed to compare CNV frequencies between tumor and normal cells. The myeloid cell population was further re-clustered into three major subgroups: monocytes, macrophages, and dendritic cells. Differential expression analysis, gene ontology, and gene set enrichment analysis were employed to assess inter-cluster and intra-cluster functional heterogeneity within the ccRCC TME. Results: Our findings revealed that immune cells in the TME predominantly adopted an inflammatory suppression state, promoting tumor cell growth and immune evasion. Additionally, tumor cells exhibited higher CNV frequencies compared to normal cells. The myeloid cell subgroups demonstrated distinct functional properties, with monocytes, macrophages, and dendritic cells displaying diverse roles in the TME. Certain immune cells exhibited pro-tumor and immunosuppressive effects, while others demonstrated antitumor and immunostimulatory properties. Conclusion: This study contributes to the understanding of intratumoral heterogeneity in the ccRCC TME and provides potential therapeutic targets for ccRCC treatment. The findings emphasize the importance of considering the diverse functional roles of immune cells in the TME for effective therapeutic interventions.
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Affiliation(s)
- Yuxiong Wang
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Yishu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Jilin, China
| | - Bin Liu
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Xin Gao
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Yunkuo Li
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Faping Li
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Honglan Zhou
- Department of Urology, The First Hospital of Jilin University, Jilin, China
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Zhang J, Deng Y, Zhang H, Zhang Z, Jin X, Xuan Y, Zhang Z, Ma X. Single-Cell RNA-Seq Analysis Reveals Ferroptosis in the Tumor Microenvironment of Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2023; 24:ijms24109092. [PMID: 37240436 DOI: 10.3390/ijms24109092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
In this study, we investigated the role of ferroptosis in the tumor microenvironment (TME) of clear cell renal cell carcinoma (ccRCC), the leading cause of renal cancer-related death. We analyzed single-cell data from seven ccRCC cases to determine cell types most correlated with ferroptosis and performed pseudotime analysis on three myeloid subtypes. We identified 16 immune-related ferroptosis genes (IRFGs) by analyzing differentially expressed genes between cell subgroups and between high and low immune infiltration groups in the TCGA-KIRC dataset and the FerrDb V2 database. Using univariate and multivariate Cox regression, we identified two independent prognostic genes, AMN and PDK4, and constructed an IRFG score model immune-related ferroptosis genes risk score (IRFGRs) to evaluate its prognostic value in ccRCC. The IRFGRs demonstrated excellent and stable performance for predicting ccRCC patient survival in both the TCGA training set and the ArrayExpress validation set, with an AUC range of 0.690-0.754, outperforming other commonly used clinicopathological indicators. Our findings enhance the understanding of TME infiltration with ferroptosis and identify immune-mediated ferroptosis genes associated with prognosis in ccRCC.
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Affiliation(s)
- Jing Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Radiation Oncology, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Yun Deng
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Radiation Oncology, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Hui Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Radiation Oncology, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Zhiyuan Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Radiation Oncology, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Xin Jin
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Radiation Oncology, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Yan Xuan
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Radiation Oncology, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Zhen Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Radiation Oncology, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Xuejun Ma
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Radiation Oncology, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
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Saout JR, Lecuyer G, Léonard S, Evrard B, Kammerer-Jacquet SF, Noël L, Khene ZE, Mathieu R, Brunot A, Rolland AD, Bensalah K, Rioux-Leclercq N, Lardenois A, Chalmel F. Single-cell Deconvolution of a Specific Malignant Cell Population as a Poor Prognostic Biomarker in Low-risk Clear Cell Renal Cell Carcinoma Patients. Eur Urol 2023; 83:441-451. [PMID: 36801089 DOI: 10.1016/j.eururo.2023.02.008] [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: 09/12/2022] [Revised: 12/10/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Intratumor heterogeneity (ITH) is a key feature in clear cell renal cell carcinomas (ccRCCs) that impacts outcomes such as aggressiveness, response to treatments, or recurrence. In particular, it may explain tumor relapse after surgery in clinically low-risk patients who did not benefit from adjuvant therapy. Recently, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool to unravel expression ITH (eITH) and might enable better assessment of clinical outcomes in ccRCC. OBJECTIVE To explore eITH in ccRCC with a focus on malignant cells (MCs) and assess its relevance to improve prognosis for low-risk patients. DESIGN, SETTING, AND PARTICIPANTS We performed scRNA-seq on tumor samples from five untreated ccRCC patients ranging from pT1a to pT3b. Data were complemented with a published dataset composed of pairs of matched normal and ccRCC samples. INTERVENTION Radical or partial nephrectomy on untreated ccRCC patients. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Viability and cell type proportions were determined by flow cytometry. Following scRNA-seq, a functional analysis was performed and tumor progression trajectories were inferred. A deconvolution approach was applied on an external cohort, and Kaplan-Meier survival curves were estimated with respect to the prevalence of malignant clusters. RESULTS AND LIMITATIONS We analyzed 54 812 cells and identified 35 cell subpopulations. The eITH analysis revealed that each tumor contained various degrees of clonal diversity. The transcriptomic signatures of MCs in one particularly heterogeneous sample were used to design a deconvolution-based strategy that allowed the risk stratification of 310 low-risk ccRCC patients. CONCLUSIONS We described eITH in ccRCCs, and used this information to establish significant cell population-based prognostic signatures and better discriminate ccRCC patients. This approach has the potential to improve the stratification of clinically low-risk patients and their therapeutic management. PATIENT SUMMARY We sequenced the RNA content of individual cell subpopulations composed of clear cell renal cell carcinomas and identified specific malignant cells the genetic information of which can be used to predict tumor progression.
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Affiliation(s)
- Judikael R Saout
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Gwendoline Lecuyer
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Simon Léonard
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France; INSERM, EFS, UMR S1236, Univ Rennes, Rennes, France
| | - Bertrand Evrard
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Solène-Florence Kammerer-Jacquet
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Pathology Department, University Hospital of Rennes, Rennes, France
| | - Laurence Noël
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | | | - Romain Mathieu
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Urology Department, University Hospital of Rennes, Rennes, France
| | - Angélique Brunot
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Antoine D Rolland
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Karim Bensalah
- Urology Department, University Hospital of Rennes, Rennes, France
| | - Nathalie Rioux-Leclercq
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Pathology Department, University Hospital of Rennes, Rennes, France
| | - Aurélie Lardenois
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Frédéric Chalmel
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
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BAO WEI, HAN QIANGUANG, GUAN XIAO, WANG ZIJIE, GU MIN. Solute carrier-related signature for assessing prognosis and immunity in patients with clear-cell renal cell carcinoma. Oncol Res 2023; 31:181-192. [PMID: 37304236 PMCID: PMC10208045 DOI: 10.32604/or.2023.028051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/07/2023] [Indexed: 06/13/2023] Open
Abstract
Background Clear-cell renal cell carcinoma (ccRCC) is the most common malignant kidney cancer. However, the tumor microenvironment and crosstalk involved in metabolic reprogramming in ccRCC are not well-understood. Methods We used The Cancer Genome Atlas to obtain ccRCC transcriptome data and clinical information. The E-MTAB-1980 cohort was used for external validation. The GENECARDS database contains the first 100 solute carrier (SLC)-related genes. The predictive value of SLC-related genes for ccRCC prognosis and treatment was assessed using univariate Cox regression analysis. An SLC-related predictive signature was developed through Lasso regression analysis and used to determine the risk profiles of patients with ccRCC. Patients in each cohort were separated into high- and low-risk groups based on their risk scores. The clinical importance of the signature was assessed through survival, immune microenvironment, drug sensitivity, and nomogram analyses using R software. Results SLC25A23, SLC25A42, SLC5A1, SLC3A1, SLC25A37, SLC5A6, SLCO5A1, and SCP2 comprised the signatures of the eight SLC-related genes. Patients with ccRCC were separated into high- and low-risk groups based on the risk value in the training and validation cohorts; the high-risk group had a significantly worse prognosis (p < 0.001). The risk score was an independent predictive indicator of ccRCC in the two cohorts according to univariate and multivariate Cox regression (p < 0.05). Analysis of the immune microenvironment showed that immune cell infiltration and immune checkpoint gene expression differed between the two groups (p < 0.05). Drug sensitivity analysis showed that compared to the low-risk group, the high-risk group was more sensitive to sunitinib, nilotinib, JNK-inhibitor-VIII, dasatinib, bosutinib, and bortezomib (p < 0.001). Survival analysis and receiver operating characteristic curves were validated using the E-MTAB-1980 cohort. Conclusions SLC-related genes have predictive relevance in ccRCC and play roles in the immunological milieu. Our results provide insight into metabolic reprogramming in ccRCC and identify promising treatment targets for ccRCC.
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Affiliation(s)
- WEI BAO
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - QIANGUANG HAN
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - XIAO GUAN
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - ZIJIE WANG
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - MIN GU
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Liu X, Xie F, Ding J, Li S, Li J. Systematic pan-cancer analysis identifies gasdermin B as an immunological and prognostic biomarker for kidney renal clear cell carcinoma. Front Oncol 2023; 13:1164214. [PMID: 37064151 PMCID: PMC10101337 DOI: 10.3389/fonc.2023.1164214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
Gasdermin (GSDM)-mediated cell lytic death plays an essential role in immunity and tumorigenesis. Despite the association of gasdermin B (GSDMB) with the tumorigenesis of various cancers, whether GSDMB functions as a prognostic biomarker in renal cell carcinoma remains poorly understood. Here, we explored the potential immunological functions and the prognostic value of GSDMB across multiple tumors with The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, including analyzing the relationship between GSDMB expression and prognosis, tumor–immune system interactions, immunomodulators, and immune cell infiltration of different tumors. Importantly, elevated expression of GSDMB is an essential factor for the poor prognosis of kidney renal clear cell carcinoma (KIRC) patients, suggesting that it might be helpful to predict a survival benefit from a clinical therapy regimen. Furthermore, GSDMB expression promoted the level of CD4+ T-cell infiltration of the tumors but is significantly negatively associated with immature dendritic cells (iDCs) in KIRC. Additionally, we identified TNFRSF25 and TNFSF14 as immunostimulators highly correlated with GSDMB expression. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses showed that GSDMB and its interacting proteins might affect tumor growth through the serine metabolism pathway. Our current results demonstrate a promising therapeutic strategy targeting GSDMB and provide new insights into GSDMB as an immunological and prognostic biomarker for KIRC.
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Affiliation(s)
- Xuehe Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
| | - Feiyan Xie
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Suhua Li
- Division of Natural Science, Duke Kunshan University, Jiangsu, China
- *Correspondence: Jixi Li, ; Suhua Li,
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai, China
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
- *Correspondence: Jixi Li, ; Suhua Li,
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Xun Z, Ding X, Zhang Y, Zhang B, Lai S, Zou D, Zheng J, Chen G, Su B, Han L, Ye Y. Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis. Nat Commun 2023; 14:933. [PMID: 36806082 PMCID: PMC9941488 DOI: 10.1038/s41467-023-36560-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Although advances in spatial transcriptomics (ST) enlarge to unveil spatial landscape of tissues, it remains challenging to delineate pathology-relevant and cellular localizations, and interactions exclusive to a spatial niche (e.g., tumor boundary). Here, we develop Cottrazm, integrating ST with hematoxylin and eosin histological image, and single-cell transcriptomics to delineate the tumor boundary connecting malignant and non-malignant cell spots in tumor tissues, deconvolute cell-type composition at spatial location, and reconstruct cell type-specific gene expression profiles at sub-spot level. We validate the performance of Cottrazm along the malignant-boundary-nonmalignant spatial axis. We identify specific macrophage and fibroblast subtypes localized around tumor boundary that interacted with tumor cells to generate a structural boundary, which limits T cell infiltration and promotes immune exclusion in tumor microenvironment. In this work, Cottrazm provides an integrated tool framework to dissect the tumor spatial microenvironment and facilitates the discovery of functional biological insights, thereby identifying therapeutic targets in oncologic ST datasets.
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Affiliation(s)
- Zhenzhen Xun
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinyu Ding
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yao Zhang
- Department of Gastroenterology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Benyan Zhang
- Department of Pathology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shujing Lai
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Duowu Zou
- Department of Gastroenterology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Junke Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guoqiang Chen
- State Key Laboratory of Oncogenes and Related Genes, and Research Unit of Stress and Cancer, Chinese Academy of Medical Sciences, Shanghai Cancer Institute, Renji hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200127, China
| | - Bing Su
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA.
| | - Youqiong Ye
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Deciphering the Role of Melatonin-Related Signatures in Tumor Immunity and the Prognosis of Clear Cell Renal Cell Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:3077091. [PMID: 36825082 PMCID: PMC9943605 DOI: 10.1155/2023/3077091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 02/16/2023]
Abstract
Methods Adopting multiomics data from TCGA and other public datasets, we analysed the expression, mutation, and prognostic evaluation in multiple cancers. ccRCC patients were categorized into two subgroups by an unsupervised cluster algorithm: melatonin-pattern cancer subtype 1 (MPCS1) and subtype 2 (MPCS2). We then explored the immune microenvironment, immune therapy response, and tumor metabolic pathways between the two subtypes. The clinical characteristics, genomic mutation landscape, and molecular inhibitor response were further investigated. Finally, a melatonin regulator-related prognostic model was constructed to predict patient prognosis in ccRCC. Results We found that melatonin regulators were dysregulated depending on distinct cancer types, which were associated with genomic variation. The two subtypes indicated different clinical characteristics and biological processes in ccRCC. MPCS2, an aggressive subtype, led an advanced clinical stage and poorer survival of ccRCC patients. The activated oncogenic signaling pathway and metabolic signatures were responsible for cancer progression in the MPCS2 subtype. The MPCS2 subgroup suggested a higher tumor mutational burden and immune dysfunction state, resulting in a lower response to immunotherapy. The copy number variations of MPCS2 were significantly more frequent than those of MPCS1. In addition, the two subgroups exhibited distinct drug responsiveness, with MPCS2 being less responsive to multiple drugs. Finally, we established a subtype biomarker-based prognostic risk model that exhibited satisfactory performance in ccRCC patients. Conclusion Melatonin regulator-related features could remodel functional pathways and the tumor immune microenvironment through genomic mutations and pathway regulation. Melatonin regulator-associated molecular subtypes enhance the understanding of the molecular characteristics of renal cancer and can guide clinical treatment. Activating the melatonergic system axis may improve the effect of immunotherapy for ccRCC.
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Chen WJ, Dong KQ, Pan XW, Gan SS, Xu D, Chen JX, Chen WJ, Li WY, Wang YQ, Zhou W, Rini B, Cui XG. Single-cell RNA-seq integrated with multi-omics reveals SERPINE2 as a target for metastasis in advanced renal cell carcinoma. Cell Death Dis 2023; 14:30. [PMID: 36646679 PMCID: PMC9842647 DOI: 10.1038/s41419-023-05566-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023]
Abstract
Tumor growth, metastasis and therapeutic response are believed to be regulated by the tumor and its microenvironment (TME) in advanced renal cell carcinoma (RCC). However, the mechanisms underlying genomic, transcriptomic and epigenetic alternations in RCC progression have not been completely defined. In this study, single-cell RNA-sequencing (scRNA-seq) data were obtained from eight tissue samples of RCC patients, including two matched pairs of primary and metastatic sites (lymph nodes), along with Hi-C, transposable accessible chromatin by high-throughput (ATAC-seq) and RNA-sequencing (RNA-seq) between RCC (Caki-1) and human renal tubular epithelial cell line (HK-2). The identified target was verified in clinical tissue samples (microarray of 407 RCC patients, TMA-30 and TMA-2020), whose function was further validated by in vitro and in vivo experiments through knockdown or overexpression. We profiled transcriptomes of 30514 malignant cells, and 14762 non-malignant cells. Comprehensive multi-omics analysis revealed that malignant cells and TME played a key role in RCC. The expression programs of stromal cells and immune cells were consistent among the samples, whereas malignant cells expressed distinct programs associated with hypoxia, cell cycle, epithelial differentiation, and two different metastasis patterns. Comparison of the hierarchical structure showed that SERPINE2 was related to these NNMF expression programs, and at the same time targeted the switched compartment. SERPINE2 was highly expressed in RCC tissues and lowly expressed in para-tumor tissues or HK-2 cell line. SERPINE2 knockdown markedly suppressed RCC cell growth and invasion, while SERPINE2 overexpression dramatically promoted RCC cell metastasis both in vitro and in vivo. In addition, SERPINE2 could activate the epithelial-mesenchymal transition pathway. The above findings demonstrated that the role of distinct expression patterns of malignant cells and TME played a distinct role in RCC progression. SERPINE2 was identified as a potential therapeutic target for inhibiting metastasis in advanced RCC.
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Affiliation(s)
- Wen-Jin Chen
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Ke-Qin Dong
- Department of Urology, General Hospital of Central Theater Command of PLA, Wuhan, 430070, China
| | - Xiu-Wu Pan
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Si-Shun Gan
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Da Xu
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Jia-Xin Chen
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Wei-Jie Chen
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Wen-Yan Li
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Yu-Qi Wang
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Wang Zhou
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China.
| | - Brian Rini
- Division of Hematology Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Xin-Gang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China.
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China.
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Li Y, Lih TSM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJH, Clark DJ, Kołodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, Naser Al Deen N, Hosseini N, Newton CJ, Krug K, Xu Y, Cho KC, Hu Y, Zhang Y, Kumar-Sinha C, Ma W, Calinawan A, Wyczalkowski MA, Wendl MC, Wang Y, Guo S, Zhang C, Le A, Dagar A, Hopkins A, Cho H, Leprevost FDV, Jing X, Teo GC, Liu W, Reimers MA, Pachynski R, Lazar AJ, Chinnaiyan AM, Van Tine BA, Zhang B, Rodland KD, Getz G, Mani DR, Wang P, Chen F, Hostetter G, Thiagarajan M, Linehan WM, Fenyö D, Jewell SD, Omenn GS, Mehra R, Wiznerowicz M, Robles AI, Mesri M, Hiltke T, An E, Rodriguez H, Chan DW, Ricketts CJ, Nesvizhskii AI, Zhang H, Ding L. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness. Cancer Cell 2023; 41:139-163.e17. [PMID: 36563681 PMCID: PMC9839644 DOI: 10.1016/j.ccell.2022.12.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/18/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.
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Affiliation(s)
- Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Tung-Shing M Lih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rita Jiu-Hsien Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - David J Clark
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Iga Kołodziejczak
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yanyan Zhao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Seema Chugh
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Noshad Hosseini
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yuanwei Xu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Kyung-Cho Cho
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yuefan Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Shenghao Guo
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Aniket Dagar
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alex Hopkins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hanbyul Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Xiaojun Jing
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Melissa A Reimers
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Russell Pachynski
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Alexander J Lazar
- Departments of Pathology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian A Van Tine
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gilbert S Omenn
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Heliodor Swiecicki Clinical Hospital in Poznań, ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Mao ZH, Gao ZX, Liu Y, Liu DW, Liu ZS, Wu P. Single-cell transcriptomics: A new tool for studying diabetic kidney disease. Front Physiol 2023; 13:1053850. [PMID: 36685214 PMCID: PMC9846140 DOI: 10.3389/fphys.2022.1053850] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023] Open
Abstract
The kidney is a complex organ comprising various functional partitions and special cell types that play important roles in maintaining homeostasis in the body. Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease and is an independent risk factor for cardiovascular diseases. Owing to the complexity and heterogeneity of kidney structure and function, the mechanism of DKD development has not been fully elucidated. Single-cell sequencing, including transcriptomics, epigenetics, metabolomics, and proteomics etc., is a powerful technology that enables the analysis of specific cell types and states, specifically expressed genes or pathways, cell differentiation trajectories, intercellular communication, and regulation or co-expression of genes in various diseases. Compared with other omics, RNA sequencing is a more developed technique with higher utilization of tissues or samples. This article reviewed the application of single-cell transcriptomics in the field of DKD and highlighted the key signaling pathways in specific tissues or cell types involved in the occurrence and development of DKD. The comprehensive understanding of single-cell transcriptomics through single-cell RNA-seq and single-nucleus RNA-seq will provide us new insights into the pathogenesis and treatment strategy of various diseases including DKD.
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Affiliation(s)
- Zi-Hui Mao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zhong-Xiuzi Gao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Yong Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Dong-Wei Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zhang-Suo Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China,*Correspondence: Peng Wu, ; Zhang-Suo Liu,
| | - Peng Wu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China,*Correspondence: Peng Wu, ; Zhang-Suo Liu,
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Tian X, Wang Y, Xu W, Tang H, Zhu S, Anwaier A, Liu W, Wang W, Zhu W, Su J, Qu Y, Zhang H, Ye D. Special issue "The advance of solid tumor research in China": Multi-omics analysis based on 1311 clear cell renal cell carcinoma samples identifies a glycolysis signature associated with prognosis and treatment response. Int J Cancer 2023; 152:66-78. [PMID: 35579992 PMCID: PMC9796246 DOI: 10.1002/ijc.34121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/10/2022] [Accepted: 04/29/2022] [Indexed: 01/01/2023]
Abstract
In clear cell renal cell carcinoma (ccRCC), glycolysis is enhanced mainly because of the increased expression of key enzymes in glycolysis. Hence, the discovery of new molecular biomarkers for glycolysis may help guide and establish a precise system of diagnosis and treatment for ccRCC. Expression profiles of 1079 tumor samples of ccRCC patients (including 311 patients treated with everolimus or nivolumab) were downloaded from public databases. Proteomic profiles of 232 ccRCC samples were obtained from Fudan University Shanghai Cancer Center (FUSCC). Biological changes, tumor microenvironment and prognostic differences were explored between samples with various glycolysis characteristics. There were significant differences in CD8+ effector T cells, epithelial-to-mesenchymal transition and pan-fibroblast TGFb between the Low and High glyScore groups. The tumor mutation burden of the Low glyScore group was lower than that of the High glyScore group. And higher glyScore was significantly associated with worse overall survival (OS) in 768 ccRCC patients (P < .0001). External validation in FUSCC cohort also indicated that glyScore was of strong ability for predicting OS (P < .05). GlyScore may serve as a biomarker for predicting everolimus response in ccRCC patients due to its significant associations with progression-free survival (PFS). And glyScore may also predict overall survival in patients treated with nivolumab. We calculated the glyScore in ccRCC and the defined glyScore was of strong ability for predicting OS. In addition, glyScore may also serve as a biomarker for predicting PFS in patients treated with everolimus and could predict OS in patients treated with nivolumab.
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Affiliation(s)
- Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yue Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Haidan Tang
- Affiliated Hospital of Youjiang Medical University for NationalitiesGuangxiChina
| | - Shuxuan Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Wangrui Liu
- Affiliated Hospital of Youjiang Medical University for NationalitiesGuangxiChina,Department of Interventional Oncology, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Wenfeng Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Wenkai Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
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Wang X, Kong F, Lin Z. Cromolyn prevents cerebral vasospasm and dementia by targeting WDR43. Front Aging Neurosci 2023; 15:1132733. [PMID: 37122373 PMCID: PMC10133528 DOI: 10.3389/fnagi.2023.1132733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
Background Cerebral vasospasm (CV) can cause inflammation and damage to neuronal cells in the elderly, leading to dementia. Purpose This study aimed to investigate the genetic mechanisms underlying dementia caused by CV in the elderly, identify preventive and therapeutic drugs, and evaluate their efficacy in treating neurodegenerative diseases. Methods Genes associated with subarachnoid hemorrhage and CV were acquired and screened for differentially expressed miRNAs (DEmiRNAs) associated with aneurysm rupture. A regulatory network of DEmiRNAs and mRNAs was constructed, and virtual screening was performed to evaluate possible binding patterns between Food and Drug Administration (FDA)-approved drugs and core proteins. Molecular dynamics simulations were performed on the optimal docked complexes. Optimally docked drugs were evaluated for efficacy in the treatment of neurodegenerative diseases through cellular experiments. Results The study found upregulated genes (including WDR43 and THBS1) and one downregulated gene associated with aneurysm rupture. Differences in the expression of these genes indicate greater disease risk. DEmiRNAs associated with ruptured aortic aneurysm were identified, of which two could bind to THBS1 and WDR43. Cromolyn and lanoxin formed the best docking complexes with WDR43 and THBS1, respectively. Cellular experiments showed that cromolyn improved BV2 cell viability and enhanced Aβ42 uptake, suggesting its potential as a therapeutic agent for inflammation-related disorders. Conclusion The findings suggest that WDR43 and THBS1 are potential targets for preventing and treating CV-induced dementia in the elderly. Cromolyn may have therapeutic value in the treatment of Alzheimer's disease and dementia.
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Couto-Cunha A, Jerónimo C, Henrique R. Circulating Tumor Cells as Biomarkers for Renal Cell Carcinoma: Ready for Prime Time? Cancers (Basel) 2022; 15:cancers15010287. [PMID: 36612281 PMCID: PMC9818240 DOI: 10.3390/cancers15010287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
Renal cell carcinoma (RCC) is among the 15 most common cancers worldwide, with rising incidence. In most cases, this is a silent disease until it reaches advance stages, demanding new effective biomarkers in all domains, from detection to post-therapy monitoring. Circulating tumor cells (CTC) have the potential to provide minimally invasive information to guide assessment of the disease's aggressiveness and therapeutic strategy, representing a special pool of neoplastic cells which bear metastatic potential. In some tumor models, CTCs' enumeration has been associated with prognosis, but there is a largely unexplored potential for clinical applicability encompassing screening, diagnosis, early detection of metastases, prognosis, response to therapy and monitoring. Nonetheless, lack of standardization and high cost hinder the translation into clinical practice. Thus, new methods for collection and analysis (genomic, proteomic, transcriptomic, epigenomic and metabolomic) are needed to ascertain the role of CTC as a RCC biomarker. Herein, we provide a critical overview of the most recently published data on the role and clinical potential of CTCs in RCC, addressing their biology and the molecular characterization of this remarkable set of tumor cells. Furthermore, we highlight the existing and emerging techniques for CTC enrichment and detection, exploring clinical applications in RCC. Notwithstanding the notable progress in recent years, the use of CTCs in a routine clinical scenario of RCC patients requires further research and technological development, enabling multimodal analysis to take advantage of the wealth of information they provide.
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Affiliation(s)
- Anabela Couto-Cunha
- Integrated Master in Medicine, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Department of Pathology & Cancer Biology & Epigenetics Group—Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Centre Raquel Seruca (P.CCC Raquel Seruca), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Rui Henrique
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Department of Pathology & Cancer Biology & Epigenetics Group—Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Centre Raquel Seruca (P.CCC Raquel Seruca), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Correspondence: or
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Cancer stem/progenitor signatures refine the classification of clear cell renal cell carcinoma with stratified prognosis and decreased immunotherapy efficacy. Mol Ther Oncolytics 2022; 27:167-181. [DOI: 10.1016/j.omto.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
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Gong Q, Guo Z, Sun W, Du X, Jiang Y, Liu F. CX3CL1 promotes cell sensitivity to ferroptosis and is associated with the tumor microenvironment in clear cell renal cell carcinoma. BMC Cancer 2022; 22:1184. [PMCID: PMC9670481 DOI: 10.1186/s12885-022-10302-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
An increasing number of studies have demonstrated that CX3CL1 is involved in the development of tumors and may thus be considered a new potential therapeutic target for them. However, the function of CX3CL1 in clear cell renal cell carcinoma (ccRCC) remains poorly defined.
Methods
The pan-cancer expression pattern and prognostic value of CX3CL1 were evaluated in this study. Moreover, the relationship of CX3CL1 expression with the tumor microenvironment, especially the tumor immune microenvironment, was analyzed. Our analyses employed public repository data. Additionally, we generated stable CX3CL1-overexpressing 786-O cells to determine the role of CX3CL1 in vitro via cell viability and transwell assays. A xenograft tumor model was used to determine the role of CX3CL1 in vivo. The association between CX3CL1 and ferroptosis sensitivity of tumor cells was assessed using Ferrostatin-1.
Results
Our findings indicated the involvement of CX3CL1 in the occurrence and development of ccRCC by acting as a tumor suppressor. We also found that ccRCC patients with high CX3CL1 expression showed better clinical outcomes than those with low CX3CL1 expression. The findings of our epigenetic study suggested that the expression of CX3CL1 in ccRCC is correlated with its DNA methylation level. Furthermore, the CX3CL1 expression level was closely related to the infiltration level of CD8+ T cells into the tumor microenvironment (TME). CX3CL1 showed different predictive values in different immunotherapy cohorts. Finally, CX3CL1 overexpression inhibited tumor cell proliferation and metastasis and promoted tumor ferroptosis sensitivity in ccRCC.
Conclusions
This study revealed the role of CX3CL1 as a tumor suppressor in ccRCC. Our findings indicated that CX3CL1 plays a crucial role in regulating the ccRCC TME and is a potential predictor of immunotherapy outcomes in ccRCC. We also found that CX3CL1 can promote ferroptosis sensitivity in ccRCC cells.
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Liang Y, Tan Y, Guan B, Guo B, Xia M, Li J, Shi Y, Yu Z, Zhang Q, Liu D, Yang X, Hao J, Gong Y, Shakeel M, Zhou L, Ci W, Li X. Single-cell atlases link macrophages and CD8 + T-cell subpopulations to disease progression and immunotherapy response in urothelial carcinoma. Am J Cancer Res 2022; 12:7745-7759. [PMID: 36451860 PMCID: PMC9706581 DOI: 10.7150/thno.77281] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/30/2022] [Indexed: 12/03/2022] Open
Abstract
Rationale: Immune checkpoint inhibitors (ICIs) have revolutionized the management of locally advanced or metastatic urothelial carcinoma. Strikingly, compared to urothelial carcinoma of the bladder (UCB), upper tract urothelial carcinoma (UTUC) has a higher response rate to ICIs. The stratification of patients most likely to benefit from ICI therapy remains a major clinical challenge. Methods: In this study, we performed the first single-cell RNA sequencing (scRNA-seq) study of 13 surgical tissue specimens from 12 patients with UTUC. The key results were validated by the analysis of two independent cohorts with bulk RNA-seq data for UCB (n = 404) and UTUC (n = 158) and one cohort of patients with metastatic urothelial carcinoma (mUC) who were treated with atezolizumab (n = 348). Results: Using scRNA-seq, we observed a higher proportion of tumor-infiltrating immune cells in locally advanced UTUC. Similar prognostically relevant intrinsic basal and luminal-like epithelial subtypes were found in both UTUC and UCB, although UTUC is predominantly of the luminal subtype. We also discovered that immunosuppressive macrophages and exhausted T-cell subpopulations were enriched in the basal subtype and showed enhanced interactions. Furthermore, we developed a gene expression signature (Macro-C3 score) capturing the immunosuppressive macrophages that better predicts outcomes than the currently established subtypes. We also developed a computational method to model immune evasion, and the Macro-C3 score predicted therapeutic response of mUC treated with first-line anti-PD-L1 inhibitors in patients with lower basal scores. Conclusions: Overall, the distinct microenvironment and Macro-C3 score provide an explanation for ICI efficacy in urothelial carcinoma and reveal new candidate regulators of immune evasion, suggesting potential therapeutic targets for improving antitumor immunity in the basal subtype.
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Affiliation(s)
- Yuan Liang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yezhen Tan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao Guan
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
| | - Bin Guo
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mancheng Xia
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
| | - Juan Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zihui Yu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Liu
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Xiaopeng Yang
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Junfeng Hao
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China
| | - Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.,✉ Corresponding authors: Department of Urology, Peking University First Hospital; Institute of Urology, Peking University. No.8, Street Xishiku, District Xicheng, Beijing 100034, China. Tel: +86-10-8357-2211. E-mail addresses: (X. Li); (L. Zhou); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China. Tel. +86-10-8409-7318. E-mail address: (W. Ci)
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,✉ Corresponding authors: Department of Urology, Peking University First Hospital; Institute of Urology, Peking University. No.8, Street Xishiku, District Xicheng, Beijing 100034, China. Tel: +86-10-8357-2211. E-mail addresses: (X. Li); (L. Zhou); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China. Tel. +86-10-8409-7318. E-mail address: (W. Ci)
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.,✉ Corresponding authors: Department of Urology, Peking University First Hospital; Institute of Urology, Peking University. No.8, Street Xishiku, District Xicheng, Beijing 100034, China. Tel: +86-10-8357-2211. E-mail addresses: (X. Li); (L. Zhou); Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China. Tel. +86-10-8409-7318. E-mail address: (W. Ci)
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Xia ZA, Zhou Y, Li J, He J. Integrated Analysis of Single-Cell and Bulk RNA-Sequencing Reveals a Tissue-Resident Macrophage-Related Signature for Predicting Immunotherapy Response in Breast Cancer Patients. Cancers (Basel) 2022; 14:cancers14225506. [PMID: 36428599 PMCID: PMC9688720 DOI: 10.3390/cancers14225506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Immune checkpoint therapy (ICT) is among the widely used treatments for breast cancer (BC), but most patients do not respond to ICT and the availability of the predictive biomarkers is limited. Emerging evidence indicates that tissue-resident macrophages (RTMs) inhibit BC progression, suggesting that their presence may predict immunotherapy response. A single-cell RNA-sequencing analysis of BC samples was performed to identify five RTM clusters with a mixed phenotype of M1-M2 macrophages. The comprehensive results showed that a high score of each RTM cluster was associated with a high infiltration of CD8+ T cells, M1 macrophages, and dendritic cells, and improved overall survival. In addition, a low score of each RTM cluster was associated with a high infiltration of M0 macrophages, naïve B cells and Tregs, and poor overall survival. Gene signatures from each RTM cluster were significantly enriched in responders compared with nonresponders. Each RTM cluster expression was significantly higher in responders than in nonresponders. The analyses of bulk RNA-seq datasets of BC samples led to identification and validation of a gene expression signature, named RTM.Sig, which contained the related genes of RTM clusters for predicting response to immunotherapy. This study highlights RTM.Sig could provide a valuable tool for clinical decisions in administering ICT.
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Affiliation(s)
- Zi-An Xia
- Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - You Zhou
- Department of Pathology, Tongji Medical College Union Hospital, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jun Li
- Department of Nuclear Medicine, Peking University Shenzhen Hospital, Guangdong 518036, China
| | - Jiang He
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha 410008, China
- Correspondence: ; Tel.: +86-151-1135-7101
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Zheng D, Ning J, Xia Y, Ruan Y, Cheng F. Comprehensive analysis of a homeobox family gene signature in clear cell renal cell carcinoma with regard to prognosis and immune significance. Front Oncol 2022; 12:1008714. [PMID: 36387262 PMCID: PMC9660242 DOI: 10.3389/fonc.2022.1008714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/04/2022] [Indexed: 12/30/2022] Open
Abstract
The homeobox (HOX) family genes have been linked to multiple types of tumors, while their effect on malignant behaviors of clear cell renal cell carcinoma (ccRCC) and clinical significance remains largely unknown. Here, we comprehensively analyzed the expression profiles and prognostic value of HOX genes in ccRCC using datasets from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. We developed a prognostic signature comprising eight HOX genes (HOXB1, HOXA7, HOXB5, HOXD8, HOXD9, HOXB9, HOXA9, and HOXA11) for overall survival prediction in ccRCC and it allowed patients to be subdivided into high- and low-risk groups. Kaplan-Meier survival analysis in all the internal and external cohorts revealed significant difference in clinical outcome of patients in different risk groups, indicating the satisfactory predictive power of the signature. Additionally, we constructed a prognostic nomogram by integrating signature-derived risk score and clinical factors such as gender, age, T and M status, which might be helpful for clinical decision-making and designing tailored management schedules. Immunological analysis revealed that the regulatory T cells (Tregs) infiltrated differently between the two subgroups in both TCGA and ICGC cohorts. ssGSEA method showed that the enrichment scores for mast cells were significantly lower in high-risk group compared with the low-risk group, which was consistent in both TCGA and ICGC cohorts. As for the related immune function, the enrichment scores of APC co-inhibition, para-inflammation, and type II IFN response were consistently lower in high-risk group in both cohorts. Of the eight HOX genes, the mRNA and protein levels of HOXD8 were downregulated in ccRCC than that in normal tissues, and decreased expression of HOXD8 was associated with increased tumor grade and stage, and lymph node metastasis. Survival analysis revealed that lower expression of HOXD8 predicted worse overall survival in ccRCC. In conclusion, our HOX gene-based signature was a favorable indicator to predict the prognosis of ccRCC cases and associated with immune cell infiltration. HOXD8 might be a tumor suppressor gene in ccRCC and a potential predictor of tumor progression.
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Affiliation(s)
| | | | | | - Yuan Ruan
- *Correspondence: Fan Cheng, ; Yuan Ruan,
| | - Fan Cheng
- *Correspondence: Fan Cheng, ; Yuan Ruan,
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Sun M, Qi S, Wu M, Xia W, Xiong H. Calreticulin as a prognostic biomarker and correlated with immune infiltrate in kidney renal clear cell carcinoma. Front Genet 2022; 13:909556. [PMID: 36338983 PMCID: PMC9633671 DOI: 10.3389/fgene.2022.909556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/05/2022] [Indexed: 01/29/2024] Open
Abstract
Background: Calreticulin (CALR) has been investigated in several malignant diseases and is associated with immune-cell infiltration. However, the prognostic value of CALR in kidney renal clear cell carcinoma (KIRC) is still unknown. Methods: Based on the computational analysis, data from 530 KIRC cases and 72 normal kidney samples from The Cancer Genome Atlas (TGCA-KIRC) database were analyzed in this study. The expression of CALR mRNA in pan-cancer and immune infiltrates was analyzed using the Tumor Immune Estimation Resource (TIMER) database. The CALR protein expression was obtained from the UALCAN and Human Protein Atlas (HPA) databases. Survival, functional, and statistical analyses were conducted using R software. Results: The CALR expression was higher in KIRC cases than in normal kidneys. A high CALR expression was correlated with TNM stage, pathological stage, and histological grade. Kaplan-Meier survival analysis showed that a high CALR expression was associated with poor overall survival, disease-specific survival, and progression-free interval. Gene set enrichment analysis (GSEA) indicated that CALR was enriched in IL-6 and IL-2 signaling, interferon signaling, TNF signaling, inflammatory response, apoptosis, and the p53 pathway. CALR is correlated with immune-infiltrating cells. A significant correlation was observed between CALR expression and immunomodulators. Conclusion: We identified CALR as a prognostic biomarker of KIRC. Meanwhile, the CALR expression associated with immune infiltration indicated that CALR might be a potential immunotherapy target for patients with KIRC.
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Affiliation(s)
| | | | | | | | - Hao Xiong
- Department of Hematology and Oncology, Wuhan Children’s Hospital, Tongji Medical College, HUST, Wuhan, China
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Raghubar AM, Roberts MJ, Wood S, Healy HG, Kassianos AJ, Mallett AJ. Cellular milieu in clear cell renal cell carcinoma. Front Oncol 2022; 12:943583. [PMID: 36313721 PMCID: PMC9614096 DOI: 10.3389/fonc.2022.943583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is globally the most prevalent renal cancer. The cells of origin in ccRCC have been identified as proximal tubular epithelial cells (PTEC); however, the transcriptomic pathways resulting in the transition from normal to malignant PTEC state have remained unclear. Immunotherapy targeting checkpoints have revolutionized the management of ccRCC, but a sustained clinical response is achieved in only a minority of ccRCC patients. This indicates that our understanding of the mechanisms involved in the malignant transition and resistance to immune checkpoint therapy in ccRCC is unclear. This review examines recent single-cell transcriptomics studies of ccRCC to clarify the transition of PTEC in ccRCC development, and the immune cell types, states, and interactions that may limit the response to targeted immune therapy, and finally suggests stromal cells as key drivers in recurrent and locally invasive ccRCC. These and future single-cell transcriptomics studies will continue to clarify the cellular milieu in the ccRCC microenvironment, thus defining actional clinical, therapeutic, and prognostic characteristics of ccRCC.
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Affiliation(s)
- Arti M. Raghubar
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Matthew J. Roberts
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Department of Urology, Royal Brisbane and Women’s Hospital, Brisbane, QLD, Australia
- Department of Urology, Redcliffe Hospital, Redcliffe, QLD, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Simon Wood
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Department of Urology, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Helen G. Healy
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Andrew J. Kassianos
- Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Andrew J. Mallett
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- College of Medicine & Dentistry, James Cook University, Townsville, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- *Correspondence: Andrew J. Mallett,
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