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Shen C, Jiang K, Zhang W, Su B, Wang Z, Chen X, Zheng B, He T. LASSO regression and WGCNA-based telomerase-associated lncRNA signaling predicts clear cell renal cell carcinoma prognosis and immunotherapy response. Aging (Albany NY) 2024; 16:9386-9409. [PMID: 38819232 PMCID: PMC11210217 DOI: 10.18632/aging.205871] [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: 01/08/2024] [Accepted: 04/16/2024] [Indexed: 06/01/2024]
Abstract
OBJECTIVE To investigate whether telomerase-associated lncRNA expression affects the prognosis and anti-tumor immunity of patients with renal clear cell carcinoma (ccRCC). METHODS A series of analyses were performed to establish a prognostic risk model and validate its accuracy. Immune-related analyses were performed to assess further the association between immune status, tumor microenvironment, and prognostic risk models. RESULTS Eight telomerase-associated lncRNAs associated with prognosis were identified and applied to establish a prognostic risk model. Overall survival was higher in the low-risk group. CONCLUSION The established prognostic risk model has a good predictive ability for the prognosis of ccRCC patients and provides a new possible therapeutic target for ccRCC.
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MESH Headings
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/mortality
- Carcinoma, Renal Cell/therapy
- Carcinoma, Renal Cell/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Humans
- Kidney Neoplasms/genetics
- Kidney Neoplasms/immunology
- Kidney Neoplasms/mortality
- Kidney Neoplasms/therapy
- Telomerase/genetics
- Telomerase/metabolism
- Prognosis
- Immunotherapy/methods
- Gene Expression Regulation, Neoplastic
- Tumor Microenvironment/immunology
- Tumor Microenvironment/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Signal Transduction/genetics
- Male
- Female
- Gene Regulatory Networks
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Affiliation(s)
- Cheng Shen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Kaiyao Jiang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Wei Zhang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Baohui Su
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Zhenyu Wang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinfeng Chen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Bing Zheng
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Tao He
- Party Committe and Hospital Administration Office, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
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2
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Li G, Wang Z, Gao B, Dai K, Niu X, Li X, Wang Y, Li L, Wu X, Li H, Yu Z, Wang Z, Chen G. ANKZF1 knockdown inhibits glioblastoma progression by promoting intramitochondrial protein aggregation through mitoRQC. Cancer Lett 2024; 591:216895. [PMID: 38670305 DOI: 10.1016/j.canlet.2024.216895] [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: 01/29/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Protein homeostasis is fundamental to the development of tumors. Ribosome-associated quality-control (RQC) is able to add alanine and threonine to the stagnant polypeptide chain C-terminal (CAT-tail) when protein translation is hindered, while Ankyrin repeat and zinc-finger domain-containing-protein 1 (ANKZF1) can counteract the formation of the CAT-tail, preventing the aggregation of polypeptide chains. In particular, ANKZF1 plays an important role in maintaining mitochondrial protein homeostasis by mitochondrial RQC (mitoRQC) after translation stagnation of precursor proteins targeting mitochondria. However, the role of ANKZF1 in glioblastoma is unclear. Therefore, the current study was aimed to investigate the effects of ANKZF1 in glioblastoma cells and a nude mouse glioblastoma xenograft model. Here, we reported that knockdown of ANKZF1 in glioblastoma cells resulted in the accumulation of CAT-tail in mitochondria, leading to the activated mitochondrial unfolded protein response (UPRmt) and inhibits glioblastoma malignant progression. Excessive CAT-tail sequestered mitochondrial chaperones HSP60, mtHSP70 and proteases LONP1 as well as mitochondrial respiratory chain subunits ND1, Cytb, mtCO2 and ATP6, leading to mitochondrial oxidative phosphorylation dysfunction, membrane potential impairment, and mitochondrial apoptotic pathway activation. Our study highlights ANKZF1 as a valuable target for glioblastoma intervention and provides an innovative insight for the treatment of glioblastoma through the regulating of mitochondrial protein homeostasis.
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Affiliation(s)
- Guangzhao Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China; Department of Neurosurgery, Hefei First People's Hospital, Hefei, 230031, China
| | - Zongqi Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Bixi Gao
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Kun Dai
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Xiaowang Niu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Yunjiang Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Longyuan Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Xin Wu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Zhengquan Yu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China
| | - Zhong Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China.
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215006, China; Institute of Stroke Research, Soochow University, Suzhou, 215006, China.
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Shen C, Zheng B, Chen Z, Zhang W, Chen X, Xu S, Ji J, Fang X, Shi C. Identification of prognostic models for glycosylation-related subtypes and tumor microenvironment infiltration characteristics in clear cell renal cell cancer. Heliyon 2024; 10:e27710. [PMID: 38515689 PMCID: PMC10955297 DOI: 10.1016/j.heliyon.2024.e27710] [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: 10/13/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Background One of the most fatal forms of cancer of the urinary system, renal cell carcinoma (RCC), significantly negatively impacts human health. Recent research reveals that abnormal glycosylation contributes to the growth and spread of tumors. However, there is no information on the function of genes related to glycosylation in RCC. Methods In this study, we created a technique that can be used to guide the choice of immunotherapy and chemotherapy regimens for RCC patients while predicting their survival prognosis. The Cancer Genome Atlas (TCGA) provided us with patient information, while the GeneCards database allowed us to collect genes involved in glycosylation. GSE29609 was used as external validation to assess the accuracy of prognostic models. The "ConsensusClusterPlus" program created molecular subtypes based on genes relevant to glycosylation discovered using differential expression analysis and univariate Cox analysis. We examined immune cell infiltration as measured by estimate, CIBERSORT, TIMER, and ssGSEA algorithms, Tumor Immune Dysfunction and Exclusion (TIDE) and exclusion of tumour stemness indices (TSIs) based on glycosylation-related molecular subtypes and risk profiles. Stratification, somatic mutation, nomogram creation, and chemotherapy response prediction were carried out based on risk factors. Results We built and verified 16 gene signatures associated with the prognosis of ccRCC patients, which are independent prognostic variables, and identified glycosylation-related genes by bioinformatics research. Cluster 2 is associated with lower human leukocyte antigen expression, worse overall survival, higher immunological checkpoints, and higher immune escape scores. In addition, cluster 2 had significantly better angiogenic activity, mesenchymal EMT, and stem ability scores. Higher immune checkpoint genes and human leukocyte antigens are associated with lower overall survival and a higher risk score. Higher estimated and immune scores, lesser tumor purity, lower mesenchymal EMT, and higher stem scores were all characteristics of the high-risk group. High amounts of tumor-infiltrating lymphocytes, a high mutation load, and a high copy number alteration frequency were present in the high-risk group.Discussion.According to our research, the 16-gene prognostic signature may be helpful in predicting prognosis and developing individualized treatments for patients with renal clear cell carcinoma, which may result in new personalized management options for these patients.
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Affiliation(s)
- Cheng Shen
- Department of Urology, Affiliated Hospital 2 of Nantong University, China
- Medical Research Center, Affiliated Hospital 2 of Nantong University, China
| | - Bing Zheng
- Department of Urology, Affiliated Hospital 2 of Nantong University, China
| | - Zhan Chen
- Department of Urology, Affiliated Hospital 2 of Nantong University, China
- Medical Research Center, Affiliated Hospital 2 of Nantong University, China
| | - Wei Zhang
- Department of Urology, Affiliated Hospital 2 of Nantong University, China
| | - Xinfeng Chen
- Department of Urology, Affiliated Hospital 2 of Nantong University, China
| | - Siyang Xu
- Clinical Medicine Specialty, Xinglin College of Nantong University, China
| | - Jianfeng Ji
- Department of Burn and plastic surgery, Affiliated Hospital 2 of Nantong University, China
| | - Xingxing Fang
- Nephrology Department, Affiliated Hospital 2 of Nantong University, China
| | - Chunmei Shi
- Department of Urology, Affiliated Hospital 2 of Nantong University, China
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Chen W, Li X, Jiang Y, Ni D, Yang L, Wu J, Gao M, Wang J, Song J, Shi W. Pancancer analysis of the correlations of HS6ST2 with prognosis, tumor immunity, and drug resistance. Sci Rep 2023; 13:19209. [PMID: 37932473 PMCID: PMC10628205 DOI: 10.1038/s41598-023-46525-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: 04/27/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023] Open
Abstract
HS6ST2 has ability to encodes a member of the heparan sulfate (HS) sulfotransferase gene family, which catalyze the transfer of sulfate to HS and a crucial regulator of cell growth, differentiation, adhesion, and migration. Although mounting evidence supports a vital role for HS6ST2 in tumorigenesis of some cancers, no pan-cancer analysis of HS6ST2 has been reported. Therefore, we aimed to explore the prognostic value of HS6ST2 in 33 cancer types and investigate its potential immune function. Based on data from The Cancer Genome Atlas, Cancer Cell Lines Encyclopedia, Genotype Tissue Expression, and GSCA, we used a range of bioinformatics approaches to explore the potential carcinogenic role of HS6ST2, analysis of HS6ST2 and prognosis, DNA methylation, RNA methylation, microsatellite instability (MSI), tumor mutation burden (TMB), and immune cell infiltration in different tumors. The results show that HS6ST2 was highly expressed in most cancers but lower in Breast invasive carcinoma, Kidney Chromophobe, Kidney renal clear cell carcinoma, Kidney renal papillary cell carcinoma, and Uterine Corpus Endometrial Carcinoma. Moreover, HS6ST2 is positively or negatively associated with prognosis in different cancers. HS6ST2 expression was not only associated with MSI in 5 cancer types and associated with TMB in 10 cancer types, and it's significantly correlated with DNA methylation in 13 types of cancer, but it's correlated with RNA methylation related genes in most cancer. HS6ST2 expression was correlated with immune cell infiltration, immune-related genes, tumor immune microenvironment, and drug resistance in various cancers. Eventually, HS6ST2 was validated in human lung adenocarcinoma tissues. Our study reveals that HS6ST2 can function as a prognostic marker in various malignant tumors because of its role in tumorigenesis and tumor immunity.
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Affiliation(s)
- Weiwei Chen
- Medical School of Nantong University, Nantong, 226007, China
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, 226001, China
- Department of Radiotherapy, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Xia Li
- Department of General Medicine, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Youqin Jiang
- Department of Radiotherapy, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Daguang Ni
- Department of Radiotherapy, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Longfei Yang
- Medical School of Nantong University, Nantong, 226007, China
| | - Jixiang Wu
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Mingcheng Gao
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China
| | - Jin Wang
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China.
| | - Jianxiang Song
- Department of Cardiothoracic Surgery, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng, 224002, China.
| | - Wenyu Shi
- Medical School of Nantong University, Nantong, 226007, China.
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, 226001, China.
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5
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Song L, Wang S, Zhang X, Song N, Lu Y, Qin C. Bridging the gap between clear cell renal cell carcinoma and cutaneous melanoma: the role of SCARB1 in dysregulated cholesterol metabolism. Aging (Albany NY) 2023; 15:10370-10388. [PMID: 37801479 PMCID: PMC10599744 DOI: 10.18632/aging.205083] [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: 04/26/2023] [Accepted: 08/22/2023] [Indexed: 10/08/2023]
Abstract
OBJECTIVE The metabolism of cholesterol has been found to be closely related to the proliferation, invasion, and metastasis of tumors. The purpose of this study was to investigate the correlation between cholesterol metabolic genes and the prognosis of clear cell renal cell carcinoma (ccRCC). METHODS Gene expression profiles and clinical information of individuals diagnosed with prevalent malignant tumors were obtained from the TCGA database. For survival analysis, Kaplan-Meier curves were used. Consensus clustering was utilized to identify distinct molecular clusters. LASSO regression analysis was utilized to construct a novel prognostic signature. Differential analysis was used to analyze the differences in gene expression and various evaluation indicators between different subgroups. RT-qPCR and Immunohistochemistry were performed to examine the gene expression. Small interfering RNA transfection, CCK-8, and clone formation assays were conducted to verify the function of the target gene in ccRCC cell lines. RESULTS Based on genes involved in cholesterol metabolism related to survival, two molecular ccRCC subtypes were identified with distinct clinical, immune, and biological features. A molecular signature which would be utilized to evaluate the prognosis and the immune status of the tumor microenvironment of ccRCC patients was also established. The SCARB1-mediated cholesterol-dependent metabolism occurred both in ccRCC and skin cutaneous melanoma. CONCLUSION A gene signature related to cholesterol metabolism was developed and validated to forecast the prognosis of ccRCC, demonstrating a correlation with immune infiltration. Cholesterol metabolic genes such as SCARB1, were expected to contribute to the diagnosis and precision treatment of both ccRCC and skin cutaneous melanoma.
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Affiliation(s)
- Lebin Song
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shuai Wang
- Department of Urology, The State Key Lab of Reproductive, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xi Zhang
- Department of Urology, The State Key Lab of Reproductive, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ninghong Song
- Department of Urology, The State Key Lab of Reproductive, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yan Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Chao Qin
- Department of Urology, The State Key Lab of Reproductive, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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Cotta BH, Choueiri TK, Cieslik M, Ghatalia P, Mehra R, Morgan TM, Palapattu GS, Shuch B, Vaishampayan U, Van Allen E, Ari Hakimi A, Salami SS. Current Landscape of Genomic Biomarkers in Clear Cell Renal Cell Carcinoma. Eur Urol 2023; 84:166-175. [PMID: 37085424 PMCID: PMC11175840 DOI: 10.1016/j.eururo.2023.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 03/16/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
CONTEXT Dramatic gains in our understanding of the molecular biology of clear cell renal cell carcinoma (ccRCC) have created a foundation for clinical translation to improve patient care. OBJECTIVE To review and contextualize clinically impactful data surrounding genomic biomarkers in ccRCC. EVIDENCE ACQUISITION A systematic literature search was conducted focusing on genomic-based biomarkers with an emphasis on studies assessing clinical outcomes. EVIDENCE SYNTHESIS The advancement of tumor sequencing techniques has led to a rapid increase in the knowledge of the molecular underpinnings of ccRCC and with that the discovery of multiple candidate genomic biomarkers. These include somatic gene mutations such as VHL, PBRM1, SETD2, and BAP1; copy number variations; transcriptomic multigene signatures; and specific immune cell populations. Many of these biomarkers have been assessed for their association with survival and a smaller number as potential predictors of a response to systemic therapy. In this scoping review, we discuss many of these biomarkers in detail. Further studies are needed to continue to refine and validate these molecular tools for risk stratification, with the ultimate goal of improving clinical decision-making and patient outcomes. CONCLUSIONS While no tissue or blood-based biomarkers for ccRCC have been incorporated into routine clinical practice to date, the field continues to expand rapidly. There remains a critical need to develop and validate these tools in order to improve the care for patients with kidney cancer. PATIENT SUMMARY Genomic biomarkers have the potential to better predict outcome and select the most appropriate treatment for patients with kidney cancer; however, further research is needed before any of these currently developed biomarkers are adopted into clinical practice.
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Affiliation(s)
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marcin Cieslik
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Pooja Ghatalia
- Department of Hematology and Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Rohit Mehra
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Todd M Morgan
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Ganesh S Palapattu
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Brian Shuch
- Department of Urology, University of California, Los Angeles, CA, USA
| | - Ulka Vaishampayan
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA
| | - Eliezer Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - A Ari Hakimi
- Division of Urology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simpa S Salami
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA.
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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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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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9
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Du R, Xiao Q, Huang J, Feng W, Zheng X, Yi T. A Seven-Autophagy-Related Long Non-Coding RNA Signature Can Accurately Predict the Prognosis of Patients with Renal Cell Carcinoma. Int J Gen Med 2022; 15:8143-8157. [DOI: 10.2147/ijgm.s381027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022] Open
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10
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Chi H, Peng G, Wang R, Yang F, Xie X, Zhang J, Xu K, Gu T, Yang X, Tian G. Cuprotosis Programmed-Cell-Death-Related lncRNA Signature Predicts Prognosis and Immune Landscape in PAAD Patients. Cells 2022; 11:cells11213436. [PMID: 36359832 PMCID: PMC9658590 DOI: 10.3390/cells11213436] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/22/2022] [Accepted: 10/28/2022] [Indexed: 12/03/2022] Open
Abstract
In terms of mortality and survival, pancreatic cancer is one of the worst malignancies. Known as a unique type of programmed cell death, cuprotosis contributes to tumor cell growth, angiogenesis, and metastasis. Cuprotosis programmed-cell-death-related lncRNAs (CRLs) have been linked to PAAD, although their functions in the tumor microenvironment and prognosis are not well understood. This study included data from the TCGA-PAAD cohort. Random sampling of PAAD data was conducted, splitting the data into two groups for use as a training set and test set (7:3). We searched for differentially expressed genes that were substantially linked to prognosis using univariate Cox and Lasso regression analysis. Through the use of multivariate Cox proportional risk regression, a risk-rating system for prognosis was developed. Correlations between the CRL signature and clinicopathological characteristics, tumor microenvironment, immunotherapy response, and chemotherapy sensitivity were further evaluated. Lastly, qRT-PCR was used to compare CRL expression in healthy tissues to that in tumors. Some CRLs are thought to have strong correlations with PAAD outcomes. These CRLs include AC005332.6, LINC02041, LINC00857, and AL117382.1. The CRL-based signature construction exhibited outstanding predictive performance and offers a fresh approach to evaluating pre-immune effectiveness, paving the way for future studies in precision immuno-oncology.
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Affiliation(s)
- Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Gaoge Peng
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Rui Wang
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou 646000, China
- Academician (Expert) Workstation of Sichuan Province, Luzhou 646000, China
| | - Fengyi Yang
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou 646000, China
- Academician (Expert) Workstation of Sichuan Province, Luzhou 646000, China
| | - Xixi Xie
- School of Stomatology, Southwest Medical University, Luzhou 646000, China
| | - Jinhao Zhang
- School of Stomatology, Southwest Medical University, Luzhou 646000, China
| | - Ke Xu
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Tao Gu
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Xiaoli Yang
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou 646000, China
- Academician (Expert) Workstation of Sichuan Province, Luzhou 646000, China
- Correspondence: (X.Y.); (G.T.); Tel.: +86-150-8687-8251 (X.Y.); +86-182-4436-2063 (G.T.)
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Correspondence: (X.Y.); (G.T.); Tel.: +86-150-8687-8251 (X.Y.); +86-182-4436-2063 (G.T.)
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11
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Construction and Characterization of n6-Methyladenosine-Related lncRNA Prognostic Signature and Immune Cell Infiltration in Kidney Renal Clear Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:7495183. [PMID: 36213821 PMCID: PMC9536954 DOI: 10.1155/2022/7495183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022]
Abstract
Background. Kidney renal clear cell carcinoma (KIRC) lacks effective prognostic biomarkers and the role and mechanism of N6-methyladenosine (m6A) modification of long noncoding RNAs (lncRNAs) in KIRC remain unclear. Methods. We extracted standard mRNA-sequencing and clinical data from the TCGA database. The prognostic risk model was obtained by Lasso regression and Cox regression. We randomly divided the samples into training and test sets, each taking half of the cases. Based on Lasso regression and Cox regression for training set, the prognostic risk signature was constructed; risk scores were calculated with the R package “glmnet.” Based on the median value of the prognostic risk score, risk scores were calculated for each patient and we divided all KIRC samples into high-risk and low-risk groups. Then, high- and low-risk subtypes were established and their prognosis, clinical features, and immune infiltration microenvironment were evaluated in test set and the entire sampled data set. The reliability of the prognostic model was confirmed by receiver operating characteristic curve analysis. Results. We found 28 prognostic m6A-related lncRNAs and established a m6A-related lncRNAs prognostic signature.
The signature showed a better predictive ability than other clinical indicators, including tumor node metastasis classification (TNM), histological, and pathological stages. In the high-risk group, M0 macrophages, CD8+ T cells, and regulatory T cells had significantly higher scores. Contrarily, in the low-risk group, activated dendritic cells, M1 macrophages, mast resting cells, and monocytes had significantly higher scores. In the high-risk group, LSECtin was overexpressed. In the low-risk group, PD-L1 was overexpressed. Moreover, high-risk patients may benefit more from AZ628. Conclusions. In conclusion, prognosis prediction of patients with KIRC and new insights for immunotherapy are provided by the m6A-related lncRNA prognostic signature.
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Prognostic Gene Expression-Based Signature in Clear-Cell Renal Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14153754. [PMID: 35954418 PMCID: PMC9367562 DOI: 10.3390/cancers14153754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 02/01/2023] Open
Abstract
The inaccuracy of the current prognostic algorithms and the potential changes in the therapeutic management of localized ccRCC demands the development of an improved prognostic model for these patients. To this end, we analyzed whole-transcriptome profiling of 26 tissue samples from progressive and non-progressive ccRCCs using Illumina Hi-seq 4000. Differentially expressed genes (DEG) were intersected with the RNA-sequencing data from the TCGA. The overlapping genes were used for further analysis. A total of 132 genes were found to be prognosis-related genes. LASSO regression enabled the development of the best prognostic six-gene panel. Cox regression analyses were performed to identify independent clinical prognostic parameters to construct a combined nomogram which includes the expression of CERCAM, MIA2, HS6ST2, ONECUT2, SOX12, TMEM132A, pT stage, tumor size and ISUP grade. A risk score generated using this model effectively stratified patients at higher risk of disease progression (HR 10.79; p < 0.001) and cancer-specific death (HR 19.27; p < 0.001). It correlated with the clinicopathological variables, enabling us to discriminate a subset of patients at higher risk of progression within the Stage, Size, Grade and Necrosis score (SSIGN) risk groups, pT and ISUP grade. In summary, a gene expression-based prognostic signature was successfully developed providing a more precise assessment of the individual risk of progression.
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Huang S, Luo Q, Huang J, Wei J, Wang S, Hong C, Qiu P, Li C. A Cluster of Metabolic-Related Genes Serve as Potential Prognostic Biomarkers for Renal Cell Carcinoma. Front Genet 2022; 13:902064. [PMID: 35873461 PMCID: PMC9301649 DOI: 10.3389/fgene.2022.902064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most common type of renal cancer, characterized by the dysregulation of metabolic pathways. RCC is the second highest cause of death among patients with urologic cancers and those with cancer cell metastases have a 5-years survival rate of only 10–15%. Thus, reliable prognostic biomarkers are essential tools to predict RCC patient outcomes. This study identified differentially expressed genes (DEGs) in the gene expression omnibus (GEO) database that are associated with pre-and post-metastases in clear cell renal cell carcinoma (ccRCC) patients and intersected these with metabolism-related genes in the Kyoto encyclopedia of genes and genomes (KEGG) database to identify metabolism-related DEGs (DEMGs). GOplot and ggplot packages for gene ontology (GO) and KEGG pathway enrichment analysis of DEMGs with log (foldchange) (logFC) were used to identify metabolic pathways associated with DEMG. Upregulated risk genes and downregulated protective genes among the DEMGs and seven independent metabolic genes, RRM2, MTHFD2, AGXT2, ALDH6A1, GLDC, HOGA1, and ETNK2, were found using univariate and multivariate Cox regression analysis, intersection, and Lasso-Cox regression analysis to establish a metabolic risk score signature (MRSS). Kaplan-Meier survival curve of Overall Survival (OS) showed that the low-risk group had a significantly better prognosis than the high-risk group in both the training cohort (p < 0.001; HR = 2.73, 95% CI = 1.97–3.79) and the validation cohort (p = 0.001; HR = 2.84, 95% CI = 1.50–5.38). The nomogram combined with multiple clinical information and MRSS was more effective at predicting patient outcomes than a single independent prognostic factor. The impact of metabolism on ccRCC was also assessed, and seven metabolism-related genes were established and validated as biomarkers to predict patient outcomes effectively.
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14
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Liu F, Wang P, Sun W, Jiang Y, Gong Q. Identification of Ligand-Receptor Pairs Associated With Tumour Characteristics in Clear Cell Renal Cell Carcinoma. Front Immunol 2022; 13:874056. [PMID: 35734169 PMCID: PMC9207243 DOI: 10.3389/fimmu.2022.874056] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
The tumour microenvironment (TME) of clear cell renal cell carcinoma (ccRCC) comprises multiple cell types, which promote tumour progression and modulate drug resistance and immune cell infiltrations via ligand-receptor (LR) interactions. However, the interactions, expression patterns, and clinical relevance of LR in the TME in ccRCC are insufficiently characterised. This study characterises the complex composition of the TME in ccRCC by analysing the single-cell sequencing (scRNA-seq) data of patients with ccRCC from the Gene expression omnibus database. On analysing the scRNA-seq data combined with the cancer genome atlas kidney renal clear cell carcinoma (TCGA-KIRC) dataset, 46 LR-pairs were identified that were significantly correlated and had prognostic values. Furthermore, a new molecular subtyping model was proposed based on these 46 LR-pairs. Molecular subtyping was performed in two ccRCC cohorts, revealing significant differences in prognosis between the subtypes of the two ccRCC cohorts. Different molecular subtypes exhibited different clinicopathological features, mutational, pathway, and immune signatures. Finally, the LR.score model that was constructed using ten essential LR-pairs that were identified based on LASSO Cox regression analysis revealed that the model could accurately predict the prognosis of patients with ccRCC. In addition, the differential expression of ten LR-pairs in tumour and normal cell lines was identified. Further functional experiments showed that CX3CL1 can exert anti-tumorigenic role in ccRCC cell line. Altogether, the effects of immunotherapy were connected to LR.scores, indicating that potential medications targeting these LR-pairs could contribute to the clinical benefit of immunotherapy. Therefore, this study identifies LR-pairs that could be effective biomarkers and predictors for molecular subtyping and immunotherapy effects in ccRCC. Targeting LR-pairs provides a new direction for immunotherapy regimens and prognostic evaluations in ccRCC.
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Affiliation(s)
- Fahui Liu
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ping Wang
- Department of Dermatology, Fujian Provincial Geriatric Hospital, Fuzhou, China
| | - Wenjuan Sun
- Department of Internal Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Yan Jiang
- Guixi Key Laboratory for High Incidence Diseases, Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Qiming Gong, ; Yan Jiang,
| | - Qiming Gong
- Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Qiming Gong, ; Yan Jiang,
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15
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Li J, Gui C, Yao H, Luo C, Song H, Lin H, Xu Q, Chen X, Huang Y, Luo J, Chen W. An Aging and Senescence-Related Gene Signature for Prognosis Prediction in Clear Cell Renal Cell Carcinoma. Front Genet 2022; 13:871088. [PMID: 35646056 PMCID: PMC9136295 DOI: 10.3389/fgene.2022.871088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/05/2022] [Indexed: 12/04/2022] Open
Abstract
Background: Clear cell renal cell carcinoma (ccRCC) is the most common solid lesion in the kidney. This study aims to establish an aging and senescence-related mRNA model for risk assessment and prognosis prediction in ccRCC patients. Methods: ccRCC data were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets. By applying univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression, a new prognostic model based on aging and senescence-related genes (ASRGs) was established. Depending on the prognostic model, high- and low-risk groups were identified for further study. The reliability of the prediction was evaluated in the validation cohort. Pan-cancer analysis was conducted to explore the role of GNRH1 in tumors. Results: A novel prognostic model was established based on eight ASRGs. This model was an independent risk factor and significantly correlated with the prognosis and clinicopathological features of ccRCC patients. The high- and low-risk groups exhibited distinct modes in the principal component analysis and different patterns in immune infiltration. Moreover, the nomogram combining risk score and other clinical factors showed excellent predictive ability, with AUC values for predicting 1-, 3-, and 5-year overall survival in the TCGA cohort equal to 0.88, 0.82, and 0.81, respectively. Conclusion: The model and nomogram based on the eight ASRGs had a significant value for survival prediction and risk assessment for ccRCC patients, providing new insights into the roles of aging and senescence in ccRCC.
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Affiliation(s)
- Jiaying Li
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chengpeng Gui
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haohua Yao
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chenggong Luo
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongde Song
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haishan Lin
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Quanhui Xu
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xu Chen
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yong Huang
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Junhang Luo
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Junhang Luo, ; Wei Chen,
| | - Wei Chen
- Department of Urology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Junhang Luo, ; Wei Chen,
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Lee MG, Lee YK, Huang SC, Chang CL, Ko CY, Lee WC, Chen TY, Tzou SJ, Huang CY, Tai MH, Lin YW, Kung ML, Tsai MC, Chen YL, Chang YC, Wen ZH, Huang CC, Chu TH. DLK2 Acts as a Potential Prognostic Biomarker for Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis. Genes (Basel) 2022; 13:genes13040629. [PMID: 35456435 PMCID: PMC9030291 DOI: 10.3390/genes13040629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 02/07/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common RCC subtype with a high mortality. It has been reported that delta-like 1 homologue (DLK1) participates in the tumor microenvironmental remodeling of ccRCC, but the relationship between delta-like 2 homologue (DLK2, a DLK1 homologue) and ccRCC is still unclear. Thus, this study aims to investigate the role of DLK2 in the biological function and disease prognosis of ccRCC using bioinformatics analysis. The TNMplot database showed that DLK2 was upregulated in ccRCC tissues. From the UALCAN analysis, the overexpression of DLK2 was associated with advanced stage and high grade in ccRCC. Moreover, the Kaplan-Meier plotter (KM Plotter) database showed that DLK2 upregulation was associated with poor survival outcome in ccRCC. By the LinkedOmics analysis, DLK2 signaling may participated in the modulation of ccRCC extracellular matrix (ECM), cell metabolism, ribosome biogenesis, TGF-β signaling and Notch pathway. Besides, Tumor Immune Estimation Resource (TIMER) analysis showed that the macrophage and CD8+ T cell infiltrations were associated with good prognosis in ccRCC patients. Finally, DLK2 overexpression was associated with the reduced macrophage recruitments and the M1–M2 polarization of macrophage in ccRCC tissues. Together, DLK2 may acts as a novel biomarker, even therapeutic target in ccRCC. However, this study lacks experimental validation, and further studies are required to support this viewpoint.
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Affiliation(s)
- Man-Gang Lee
- Department of Surgery, Division of Urology, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
- Department of Surgery, Division of Urology, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung 81342, Taiwan
| | - Yung-Kuo Lee
- Medical Laboratory, Medical Education and Research Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
| | - Shih-Chung Huang
- Department of Internal Medicine, Division of Cardiology, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
- Department of Internal Medicine, Division of Cardiology, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (C.-L.C.); (C.-Y.K.); (S.-J.T.)
| | - Chen-Lin Chang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (C.-L.C.); (C.-Y.K.); (S.-J.T.)
- Department of Psychiatry, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan
| | - Chou-Yuan Ko
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (C.-L.C.); (C.-Y.K.); (S.-J.T.)
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Tri-Service General Hospital, National Defense Medical Center, Taipei 11490, Taiwan
| | - Wen-Chin Lee
- Department of Internal Medicine, Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan;
| | - Tung-Yuan Chen
- Department of Surgery, Division of Colorectal Surgery, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
| | - Shiow-Jyu Tzou
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (C.-L.C.); (C.-Y.K.); (S.-J.T.)
- Department of Nursing, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan
| | - Cheng-Yi Huang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (C.-Y.H.); (M.-H.T.)
- Department of Pathology, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan
| | - Ming-Hong Tai
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (C.-Y.H.); (M.-H.T.)
- Center for Neuroscience, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yu-Wei Lin
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung 813414, Taiwan;
| | - Mei-Lang Kung
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813414, Taiwan;
| | - Ming-Chao Tsai
- Department of Internal Medicine, Division of Hepato-Gastroenterology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan;
| | - Yung-Lung Chen
- Section of Cardiology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan;
| | - Yi-Chen Chang
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University and Academia Sinica, Kaohsiung 80424, Taiwan;
| | - Zhi-Hong Wen
- Department of Marine Biotechnology and Resources, Asia-Pacific Ocean Research Center, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
| | - Chao-Cheng Huang
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
- Biobank and Tissue Bank, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
- Correspondence: (C.-C.H.); (T.-H.C.); Tel.: +886-7-731-7123 (ext. 2557) (C.-C.H.); +886-7-749-6751 (ext. 726201) (T.-H.C.)
| | - Tian-Huei Chu
- Medical Laboratory, Medical Education and Research Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 80284, Taiwan;
- Correspondence: (C.-C.H.); (T.-H.C.); Tel.: +886-7-731-7123 (ext. 2557) (C.-C.H.); +886-7-749-6751 (ext. 726201) (T.-H.C.)
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Ning XH, Li NY, Qi YY, Li SC, Jia ZK, Yang JJ. Identification of a Hypoxia-Related Gene Model for Predicting the Prognosis and Formulating the Treatment Strategies in Kidney Renal Clear Cell Carcinoma. Front Oncol 2022; 11:806264. [PMID: 35141153 PMCID: PMC8818738 DOI: 10.3389/fonc.2021.806264] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose The present study aimed to establish a hypoxia related genes model to predict the prognosis of kidney clear cell carcinoma (KIRC) patients using data accessed from The Cancer Genome Atlas (TCGA) database and International Cancer Genome Consortium (ICGC) database. Methods Patients’ data were downloaded from the TCGA and ICGC databases, and hypoxia related genes were accessed from the Molecular Signatures Database. The differentially expressed genes were evaluated and then the differential expressions hypoxia genes were screened. The TCGA cohort was randomly divided into a discovery TCGA cohort and a validation TCGA cohort. The discovery TCGA cohort was used for constructing the hypoxia genes risk model through Lasso regression, univariate and multivariate Cox regression analysis. Receiver operating characteristic (ROC) curves were used to assess the reliability and sensitivity of our model. Then, we established a nomogram to predict the probable one-, three-, and five-year overall survival rates. Lastly, the Tumor Immune Dysfunction and Exclusion (TIDE) score of patients was calculated. Results We established a six hypoxia-related gene prognostic model of KIRC patients in the TCGA database and validated in the ICGC database. The patients with high riskscore present poorer prognosis than those with low riskscore in the three TCGA cohorts and ICGC cohort. ROC curves show our six-gene model with a robust predictive capability in these four cohorts. In addition, we constructed a nomogram for KIRC patients in the TCGA database. Finally, the high risk-group had a high TIDE score than the patients with low riskscore. Conclusions We established a six hypoxia-related gene risk model for independent prediction of the prognosis of KIRC patients was established and constructed a robust nomogram. The different riskscores might be a biomarker for immunotherapy strategy.
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Affiliation(s)
- Xiang-hui Ning
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Xiang-hui Ning, ; Jin-jian Yang,
| | - Ning-yang Li
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuan-yuan Qi
- Department of Nephrology, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Song-chao Li
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhan-kui Jia
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jin-jian Yang
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Xiang-hui Ning, ; Jin-jian Yang,
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Roldán FL, Lozano JJ, Ingelmo-Torres M, Carrasco R, Díaz E, Ramirez-Backhaus M, Rubio J, Reig O, Alcaraz A, Mengual L, Izquierdo L. Clinicopathological and Molecular Prognostic Classifier for Intermediate/High-Risk Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13246338. [PMID: 34944958 PMCID: PMC8699125 DOI: 10.3390/cancers13246338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary In this report, we identified biomarkers for tumor progression from tissue samples of intermediate/high-risk ccRCC. Using the molecular findings and the clinical data, we developed an improved prognostic model which could help to provide better individualized management recommendations. Abstract The probability of tumor progression in intermediate/high-risk clear cell renal cell carcinoma (ccRCC) is highly variable, underlining the lack of predictive accuracy of the current clinicopathological factors. To develop an accurate prognostic classifier for these patients, we analyzed global gene expression patterns in 13 tissue samples from progressive and non-progressive ccRCC using Illumina Hi-seq 4000. Expression levels of 22 selected differentially expressed genes (DEG) were assessed by nCounter analysis in an independent series of 71 ccRCCs. A clinicopathological-molecular model for predicting tumor progression was developed and in silico validated in a total of 202 ccRCC patients using the TCGA cohort. A total of 1202 DEGs were found between progressive and non-progressive intermediate/high-risk ccRCC in RNAseq analysis, and seven of the 22 DEGs selected were validated by nCounter. Expression of HS6ST2, pT stage, tumor size, and ISUP grade were found to be independent prognostic factors for tumor progression. A risk score generated using these variables was able to distinguish patients at higher risk of tumor progression (HR 7.27; p < 0.001), consistent with the results obtained from the TCGA cohort (HR 2.74; p < 0.002). In summary, a combined prognostic algorithm was successfully developed and validated. This model may aid physicians to select high-risk patients for adjuvant therapy.
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Affiliation(s)
- Fiorella L. Roldán
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Juan J. Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clinic, 08036 Barcelona, Spain;
| | - Mercedes Ingelmo-Torres
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Raquel Carrasco
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Esther Díaz
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Miguel Ramirez-Backhaus
- Department of Urology, Oncologic Institute of Valencia, 46009 Valencia, Spain; (M.R.-B.); (J.R.)
| | - José Rubio
- Department of Urology, Oncologic Institute of Valencia, 46009 Valencia, Spain; (M.R.-B.); (J.R.)
| | - Oscar Reig
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS) and Medical Oncology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain;
| | - Antonio Alcaraz
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
| | - Lourdes Mengual
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-93-227-54-00 (ext. 4820)
| | - Laura Izquierdo
- Department and Laboratory of Urology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036 Barcelona, Spain; (F.L.R.); (M.I.-T.); (R.C.); (E.D.); (A.A.); (L.I.)
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Li H, Chen L, Ke ZB, Chen SH, Xue XY, Zheng QS, Wei Y, Zeng K, Xu N. Angiogenesis-Related Molecular Subtypes and a Novel Prognostic Signature in Clear Cell Renal Cell Carcinoma Patients. Int J Gen Med 2021; 14:6325-6342. [PMID: 34629897 PMCID: PMC8497487 DOI: 10.2147/ijgm.s332732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/09/2021] [Indexed: 11/26/2022] Open
Abstract
Background This study aimed to develop and validate a novel angiogenesis-related gene (ARG) signature and molecular subtypes by bioinformatics analysis. Materials and Methods The transcriptome data and clinical data were obtained from TCGA and ICGC database. We performed consensus clustering analysis to identify angiogenesis molecular subtypes for ccRCC. Univariate and multivariate Cox regression analyses were used to develop a novel ARG-related signature as a prognostic biomarker for ccRCC. Internal and external validation were then performed in TCGA and ICGC cohort, respectively. Results We identified a total of two angiogenesis molecular subtypes of ccRCC. The overall survival (OS) of subtype 1 ccRCC was significantly decreased compared with that of subtype 2 ccRCC (P=0.001). These two molecular subtypes have significantly different tumor microenvironment and immune checkpoint inhibitor sensitivities (P<0.05). Besides, we developed a novel signature based on three ARGs (including MSX1, TIMP1 and JAG2) for subtype 1 ccRCC. The difference in OS between high- and low-risk group was statistically significant in training cohort (P=0.009), test cohort (P=0.024), the whole type 1 cohort (P<0.001), and validation cohort (P=0.041). The AUC for one-year OS prediction was 0.732, 0.710, 0.725, and 0.645 in training cohort, test cohort, the whole type 1 cohort, and validation cohort, respectively. Independent prognostic analysis showed that this signature was an independent predictor for OS of subtype 1 ccRCC (P=0.028914). The power of this prognostic signature was superior to other signatures reported in previous studies. Conclusion We developed and successfully validated a novel ARG signature for predicting prognosis of subtype 1 ccRCC, which was superior to several previous signatures.
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Affiliation(s)
- Hao Li
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Lu Chen
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Zhi-Bin Ke
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Shao-Hao Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Qing-Shui Zheng
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Yong Wei
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Kai Zeng
- Department of Anesthesiology, Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Department of Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Ning Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China.,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People's Republic of China
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Zhao H, Zhang J, Fu X, Mao D, Qi X, Liang S, Meng G, Song Z, Yang R, Guo Z, Tong B, Sun M, Zuo B, Li G. Integrated bioinformatics analysis of the NEDD4 family reveals a prognostic value of NEDD4L in clear-cell renal cell cancer. PeerJ 2021; 9:e11880. [PMID: 34458018 PMCID: PMC8378337 DOI: 10.7717/peerj.11880] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/07/2021] [Indexed: 12/20/2022] Open
Abstract
The members of the Nedd4-like E3 family participate in various biological processes. However, their role in clear cell renal cell carcinoma (ccRCC) is not clear. This study systematically analyzed the Nedd4-like E3 family members in ccRCC data sets from multiple publicly available databases. NEDD4L was identified as the only NEDD4 family member differentially expressed in ccRCC compared with normal samples. Bioinformatics tools were used to characterize the function of NEDD4L in ccRCC. It indicated that NEDD4L might regulate cellular energy metabolism by co-expression analysis, and subsequent gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. A prognostic model developed by the LASSO Cox regression method showed a relatively good predictive value in training and testing data sets. The result revealed that NEDD4L was associated with biosynthesis and metabolism of ccRCC. Since NEDD4L is downregulated and dysregulation of metabolism is involved in tumor progression, NEDD4L might be a potential therapeutic target in ccRCC.
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Affiliation(s)
- Hui Zhao
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China.,Department of Urology, China Rehabilitation Research Centre, Rehabilitation School of Capital Medical University, Beijing, China
| | - Junjun Zhang
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoliang Fu
- Department of Urology, The Second Affiliated Hospital of Air Force Medical University, Xian, China
| | - Dongdong Mao
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xuesen Qi
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Shuai Liang
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Gang Meng
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Ru Yang
- Henan Key Laboratory of Neurorestoratology, The First Affliated Hospital of Xinxiang Medical University, Weihui, China
| | - Zhenni Guo
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Binghua Tong
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Meiqing Sun
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Baile Zuo
- Tumor Molecular Immunology and Immunotherapy Laboratory, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.,Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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