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Zhang Q, Ding L, Yan Y, Zhai Q, Guo Z, Li Y, Tang Z, Zang P, Ni C, Zhang S, Qian J, Han P, Li P, Shao P, Liang C, Li J. Decoding sunitinib resistance in ccRCC: Metabolic-reprogramming-induced ABAT and GABAergic system shifts. iScience 2024; 27:110415. [PMID: 39100925 PMCID: PMC11295714 DOI: 10.1016/j.isci.2024.110415] [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: 02/16/2024] [Revised: 05/13/2024] [Accepted: 06/27/2024] [Indexed: 08/06/2024] Open
Abstract
Sunitinib, a primary treatment for clear cell renal cell carcinoma (ccRCC), frequently encounters the challenge of resistance development. Metabolic reprogramming, a characteristic change in ccRCC, is likely linked to this resistance. Our research revealed a notable decrease in the expression of the key metabolic gene ABAT in ccRCC, which contributed to diminished sensitivity to sunitinib. Downregulation of ABAT led to an increase in the intracellular level of gamma-aminobutyric acid (GABA), triggering abnormal activation of the G-protein-coupled receptor GABA-B. This activation resulted in increased transactivation of the tyrosine kinase receptors SYK and LYN, thereby reducing the antitumor and antiangiogenic properties of sunitinib. However, the application of SYK and LYN inhibitors successfully inhibited this effect. The transactivation of SYK and LYN caused resistance to the antiangiogenic effects of sunitinib through the upregulation of PGF protein levels. Furthermore, the combined application of an LYN inhibitor with sunitinib has been shown to enhance therapeutic efficacy.
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Affiliation(s)
- Qian Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, Jiangsu Taizhou People’s Hospital, Taizhou 225300, China
| | - Lei Ding
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ye Yan
- Department of Urology, Peking University Third Hospital, Haidian District, Beijing, People’s Republic of China
| | - Qidi Zhai
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhisheng Guo
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yibo Li
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhentao Tang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pan Zang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chenbo Ni
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shaobo Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jian Qian
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Peng Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pu Li
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Shao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chao Liang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jie Li
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Davodabadi F, Farasati Far B, Sargazi S, Fatemeh Sajjadi S, Fathi-Karkan S, Mirinejad S, Ghotekar S, Sargazi S, Rahman MM. Nanomaterials-Based Targeting of Long Non-Coding RNAs in Cancer: A Cutting-Edge Review of Current Trends. ChemMedChem 2024; 19:e202300528. [PMID: 38267373 DOI: 10.1002/cmdc.202300528] [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: 09/30/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/26/2024]
Abstract
This review article spotlights the burgeoning potential of using nanotherapeutic strategies to target long non-coding RNAs (lncRNAs) in cancer cells. This updated discourse underlines the prominent role of lncRNAs in instigating cancer, facilitating its progression, and metastasis, validating lncRNAs' potential for being effective diagnostic biomarkers and therapeutic targets. The manuscript offers an in-depth examination of different strategies presently employed to modulate lncRNA expression and function for therapeutic purposes. Among these strategies, Antisense Oligonucleotides (ASOs), RNA interference (RNAi) technologies, and the innovative clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing tools garner noteworthy mention. A significant section of the review is dedicated to nanocarriers and their crucial role in drug delivery. These nanocarriers' efficiency in targeting lncRNAs in varied types of cancers is elaborated upon, validating the importance of targeted therapy. The manuscript culminates by reaffirming the promising prospects of targeting lncRNAs to enhance the accuracy of cancer diagnosis and improve treatment efficacy. Consequently, new paths are opened to more research and innovation in employing nanotherapeutic approaches against lncRNAs in cancer cells. Thus, this comprehensive manuscript serves as a valuable resource that underscores the vital role of lncRNAs and the various nano-strategies for targeting them in cancer treatment. Future research should also focus on unraveling the complex regulatory networks involving lncRNAs and identifying fundamental functional interactions to refine therapeutic strategies targeting lncRNAs in cancer.
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Affiliation(s)
- Fatemeh Davodabadi
- Department of Biology, Faculty of Basic Science, Payame Noor University, Tehran, Iran
| | - Bahareh Farasati Far
- Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyedeh Fatemeh Sajjadi
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Sonia Fathi-Karkan
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, 9453155166, Iran
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, 9414974877, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Suresh Ghotekar
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India
| | - Sara Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohammed M Rahman
- Center of Excellence for Advanced Materials Research (CEAMR) & Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Meng J, Jiang A, Lu X, Gu D, Ge Q, Bai S, Zhou Y, Zhou J, Hao Z, Yan F, Wang L, Wang H, Du J, Liang C. Multiomics characterization and verification of clear cell renal cell carcinoma molecular subtypes to guide precise chemotherapy and immunotherapy. IMETA 2023; 2:e147. [PMID: 38868222 PMCID: PMC10989995 DOI: 10.1002/imt2.147] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/21/2023] [Indexed: 06/14/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a heterogeneous tumor with different genetic and molecular alterations. Schemes for ccRCC classification system based on multiomics are urgent, to promote further biological insights. Two hundred and fifty-five ccRCC patients with paired data of clinical information, transcriptome expression profiles, copy number alterations, DNA methylation, and somatic mutations were collected for identification. Bioinformatic analyses were performed based on our team's recently developed R package "MOVICS." With 10 state-of-the-art algorithms, we identified the multiomics subtypes (MoSs) for ccRCC patients. MoS1 is an immune exhausted subtype, presented the poorest prognosis, and might be caused by an exhausted immune microenvironment, activated hypoxia features, but can benefit from PI3K/AKT inhibitors. MoS2 is an immune "cold" subtype, which represented more mutation of VHL and PBRM1, favorable prognosis, and is more suitable for sunitinib therapy. MoS3 is the immune "hot" subtype, and can benefit from the anti-PD-1 immunotherapy. We successfully verified the different molecular features of the three MoSs in external cohorts GSE22541, GSE40435, and GSE53573. Patients that received Nivolumab therapy helped us to confirm that MoS3 is suitable for anti-PD-1 therapy. E-MTAB-3267 cohort also supported the fact that MoS2 patients can respond more to sunitinib treatment. We also confirm that SETD2 is a tumor suppressor in ccRCC, along with the decreased SETD2 protein level in advanced tumor stage, and knock-down of SETD2 leads to the promotion of cell proliferation, migration, and invasion. In summary, we provide novel insights into ccRCC molecular subtypes based on robust clustering algorithms via multiomics data, and encourage future precise treatment of ccRCC patients.
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Affiliation(s)
- Jialin Meng
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| | - Aimin Jiang
- Department of Urology, Changhai HospitalNaval Medical University (Second Military Medical University)ShanghaiChina
| | - Xiaofan Lu
- Department of Cancer and Functional GenomicsInstitute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRAIllkirchFrance
| | - Di Gu
- Department of Urology, Changhai HospitalNaval Medical University (Second Military Medical University)ShanghaiChina
| | - Qintao Ge
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| | - Suwen Bai
- The Second Affiliated Hospital, School of MedicineThe Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of ShenzhenShenzhenChina
| | - Yundong Zhou
- Department of Surgery, Ningbo Medical Center Lihuili HospitalNingbo UniversityNingboZhejiangChina
| | - Jun Zhou
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| | - Zongyao Hao
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| | - Fangrong Yan
- Research Center of Biostatistics and Computational PharmacyChina Pharmaceutical UniversityNanjingChina
| | - Linhui Wang
- Department of Urology, Changhai HospitalNaval Medical University (Second Military Medical University)ShanghaiChina
| | - Haitao Wang
- Cancer Center, Faculty of Health SciencesUniversity of MacauMacau SARChina
- Present address:
Center for Cancer ResearchBethesdaMarylandUSA
| | - Juan Du
- The Second Affiliated Hospital, School of MedicineThe Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of ShenzhenShenzhenChina
| | - Chaozhao Liang
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
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Lucerón-Lucas-Torres M, Cavero-Redondo I, Martínez-Vizcaíno V, Bizzozero-Peroni B, Pascual-Morena C, Álvarez-Bueno C. Association between wine consumption and cancer: a systematic review and meta-analysis. Front Nutr 2023; 10:1197745. [PMID: 37731399 PMCID: PMC10507274 DOI: 10.3389/fnut.2023.1197745] [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: 03/31/2023] [Accepted: 08/08/2023] [Indexed: 09/22/2023] Open
Abstract
Background Alcohol consumption is related to the risk of developing different types of cancer. However, unlike other alcoholic beverages, moderate wine drinking has demonstrated a protective effect on the risk of developing several types of cancer. Objective To analyze the association between wine consumption and the risk of developing cancer. Methods We searched the MEDLINE (through PubMed), Scopus, Cochrane, and Web of Science databases to conduct this systematic review and meta-analysis. Pooled relative risks (RRs) were calculated using the DerSimonian and Laird methods. I2 was used to evaluate inconsistency, the τ2 test was used to assess heterogeneity, and The Newcastle-Ottawa Quality Assessment Scale were applied to evaluate the risk of bias. This study was previously registered in PROSPERO, with the registration number CRD42022315864. Results Seventy-three studies were included in the systematic review, and 26 were included in the meta-analysis. The pooled RR for the effect of wine consumption on the risk of gynecological cancers was 1.03 (95% CI: 0.99, 1.08), that for colorectal cancer was 0.92 (95% CI: 0.82, 1.03), and that for renal cancer was 0.92 (95% CI: 0.81, 1.04). In general, the heterogeneity was substantial. Conclusion The study findings reveal no association between wine consumption and the risk of developing any type of cancer. Moreover, wine drinking demonstrated a protective trend regarding the risk of developing pancreatic, skin, lung, and brain cancer as well as cancer in general. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022315864, identifier CRD42022315864 (PROSPERO).
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Affiliation(s)
| | - Iván Cavero-Redondo
- Health and Social Research Center, Universidad de Castilla-La Mancha, Cuenca, Spain
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Vicente Martínez-Vizcaíno
- Health and Social Research Center, Universidad de Castilla-La Mancha, Cuenca, Spain
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Bruno Bizzozero-Peroni
- Health and Social Research Center, Universidad de Castilla-La Mancha, Cuenca, Spain
- Higher Institute of Physical Education, Universidad de la República, Rivera, Uruguay
| | | | - Celia Álvarez-Bueno
- Health and Social Research Center, Universidad de Castilla-La Mancha, Cuenca, Spain
- Universidad Politécnica y Artística del Paraguay, Asunción, Paraguay
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ANO4 Expression Is a Potential Prognostic Biomarker in Non-Metastasized Clear Cell Renal Cell Carcinoma. J Pers Med 2023; 13:jpm13020295. [PMID: 36836529 PMCID: PMC9965005 DOI: 10.3390/jpm13020295] [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: 01/02/2023] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Background: Over the past decade, transcriptome profiling has elucidated many pivotal pathways involved in oncogenesis. However, a detailed comprehensive map of tumorigenesis remains an enigma to solve. Propelled research has been devoted to investigating the molecular drivers of clear cell renal cell carcinoma (ccRCC). To add another piece to the puzzle, we evaluated the role of anoctamin 4 (ANO4) expression as a potential prognostic biomarker in non-metastasized ccRCC. Methods: A total of 422 ccRCC patients with the corresponding ANO4 expression and clinicopathological data were obtained from The Cancer Genome Atlas Program (TCGA). Differential expression across several clinicopathological variables was performed. The Kaplan-Meier method was used to assess the impact of ANO4 expression on the overall survival (OS), progression-free interval (PFI), disease-free interval (DFI), and disease-specific survival (DSS). Univariate and multivariate Cox logistic regression analyses were conducted to identify independent factors modulating the aforementioned outcomes. Gene set enrichment analysis (GSEA) was used to discern a set of molecular mechanisms involved in the prognostic signature. Tumor immune microenvironment was estimated using xCell. Results: ANO4 expression was upregulated in tumor samples compared to normal kidney tissue. Albeit the latter finding, low ANO4 expression is associated with advanced clinicopathological variables such as tumor grade, stage, and pT. In addition, low ANO4 expression is linked to shorter OS, PFI, and DSS. Multivariate Cox logistic regression analysis identified ANO4 expression as an independent prognostic variable in OS (HR: 1.686, 95% CI: 1.120-2.540, p = 0.012), PFI (HR: 1.727, 95% CI: 1.103-2.704, p = 0.017), and DSS (HR: 2.688, 95% CI: 1.465-4.934, p = 0.001). GSEA identified the following pathways to be enriched within the low ANO4 expression group: epithelial-mesenchymal transition, G2-M checkpoint, E2F targets, estrogen response, apical junction, glycolysis, hypoxia, coagulation, KRAS, complement, p53, myogenesis, and TNF-α signaling via NF-κB pathways. ANO4 expression correlates significantly with monocyte (ρ = -0.1429, p = 0.0033) and mast cell (ρ = 0.1598, p = 0.001) infiltration. Conclusions: In the presented work, low ANO4 expression is portrayed as a potential poor prognostic factor in non-metastasized ccRCC. Further experimental studies should be directed to shed new light on the exact molecular mechanisms involved.
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Yu W, Lu J, Wu C. Construction of a novel prognostic signature based on the composition of tumor-infiltrating immune cells in clear cell renal cell carcinoma. Front Genet 2022; 13:1024096. [PMID: 36313434 PMCID: PMC9606472 DOI: 10.3389/fgene.2022.1024096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/03/2022] [Indexed: 09/07/2024] Open
Abstract
Emerging evidence has uncovered that tumor-infiltrating immune cells (TIICs) play significant roles in regulating the tumorigenesis and progression of clear cell renal cell carcinoma (ccRCC). However, the exact composition of TIICs and their prognostic values in ccRCC have not been well defined. A total of 534 ccRCC samples with survival information and TIIC data from The Cancer Genome Atlas (TCGA) dataset were included in our research. The ImmuCellAI tool was employed to estimate the abundance of 24 TIICs and further survival analysis explored the prognostic values of TIICs in ccRCC. In addition, the expression levels of immunosuppressive molecules (PDL1, PD1, LAG3, and CTLA4) in the high- and low-risk groups were explored. Various subtypes of TIICs had distinct infiltrating features and most TIICs exhibited dysregulated abundance between normal and tumor tissues. Moreover, specific kinds of TIICs had encouraging prognostic values in ccRCC. Further analysis constructed a 4-TIICs signature to evaluate the prognosis of ccRCC patients. Cox regression analyses confirmed the independent prognostic role of the signature in ccRCC. Moreover, immunosuppressive molecules, including PD1, LAG3, and CTLA4, were significantly upregulated in the high-risk group and predicted poor prognosis. However, PDL1 was not changed between high- and low-risk groups and could not predict poor prognosis. To sum up, our research explored the landscape of TIICs in ccRCC and established a novel 4-TIIC prognostic signature, which could effectively predict the prognosis for patients with ccRCC. Based on this signature, we also concluded that PDL1 may not predict prognosis in ccRCC.
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Affiliation(s)
- Weiwei Yu
- Department of Oncology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Jiahui Lu
- Department of Oncology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Cen Wu
- Department of General Surgery, Rudong People’s Hospital, Nantong, Jiangsu, China
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Xu W, Liu W, Anwaier A, Tian X, Su J, Shi G, Wei S, Qu Y, Zhang H, Ye D. Deciphering the role of miR-187-3p/LRFN1 axis in modulating progression, aerobic glycolysis and immune microenvironment of clear cell renal cell carcinoma. Discov Oncol 2022; 13:59. [PMID: 35799072 PMCID: PMC9263027 DOI: 10.1007/s12672-022-00523-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common malignant genitourinary cancers with high recurrence risk worldwide. Recently, multi-omics data facilitate obtaining a molecular landscape of tumor development, and were implemented to affect pathogenesis, phenotype, and prognosis of ccRCC. In this study, after screening for differential expressed microRNAs based on multiply datasets, we tested expression levels and prognostic value of miR-187-3p in ccRCC samples, and transfected miR-187-3p mimics or negative controls into ccRCC cells. Up-regulation of miR-187-3p restrains proliferation, migration and promotes apoptosis ability in human ccRCC A498 and 786O cells. In addition, Luciferase reporter assay revealed that miR-187-3p directly targets LRFN1-3'-UTR and negatively modulates LRFN1 expression. LRFN1 rescues proliferation and invasion capacities after miR-187-3p mimic transfection in vitro and in subcutaneous xenograft models. We further performed deep-sequencing technology and bioinformatics analyses to evaluate the biological functions and potential clinical implications of LRFN1 expression in ccRCC. Interestingly, LRFN1 could serve as an independent and potential biomarker for prognosis in over 1000 patients with ccRCC from multiply independent cohorts. Besides, the up-regulated LRFN1 expression prominently promoted intra-tumoral heterogeneity and immune-infiltrating microenvironment, represented by elevated M2 macrophage infiltration, CD8+ T cells activity and PD-L1 expression. In conclusion, this study revealed the tumor-specific and immunological role of miR-187-3p/LRFN1 axis in the progression and reshaping of tumor immune microenvironment of ccRCC.
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Dong’an Road 270, Shanghai, 200032 People’s Republic of China
| | - Wangrui Liu
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 People’s Republic of China
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000 People’s Republic of China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Dong’an Road 270, Shanghai, 200032 People’s Republic of China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Dong’an Road 270, Shanghai, 200032 People’s Republic of China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Dong’an Road 270, Shanghai, 200032 People’s Republic of China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Dong’an Road 270, Shanghai, 200032 People’s Republic of China
| | - Shiyin Wei
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000 People’s Republic of China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Dong’an Road 270, Shanghai, 200032 People’s Republic of China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Dong’an Road 270, Shanghai, 200032 People’s Republic of China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Dong’an Road 270, Shanghai, 200032 People’s Republic of China
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Complementary roles of surgery and systemic treatment in clear cell renal cell carcinoma. Nat Rev Urol 2022; 19:391-418. [PMID: 35546184 DOI: 10.1038/s41585-022-00592-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
Abstract
Standard-of-care management of renal cell carcinoma (RCC) indisputably relies on surgery for low-risk localized tumours and systemic treatment for poor-prognosis metastatic disease, but a grey area remains, encompassing high-risk localized tumours and patients with metastatic disease with a good-to-intermediate prognosis. Over the past few years, results of major practice-changing trials for the management of metastatic RCC have completely transformed the therapeutic options for this disease. Treatments targeting vascular endothelial growth factor (VEGF) have been the mainstay of therapy for metastatic RCC in the past decade, but the advent of immune checkpoint inhibitors has revolutionized the therapeutic landscape in the metastatic setting. Results from several pivotal trials have shown a substantial benefit from the combination of VEGF-directed therapy and immune checkpoint inhibition, raising new hopes for the treatment of high-risk localized RCC. The potential of these therapeutics to facilitate the surgical extirpation of the tumour in the neoadjuvant setting or to improve disease-free survival in the adjuvant setting has been investigated. The role of surgery for metastatic RCC has been redefined, with results of large trials bringing into question the paradigm of upfront cytoreductive nephrectomy, inherited from the era of cytokine therapy, when initial extirpation of the primary tumour did show clinical benefits. The potential benefits and risks of deferred surgery for residual primary tumours or metastases after partial response to checkpoint inhibitor treatment are also gaining interest, considering the long-lasting effects of these new drugs, which encourages the complete removal of residual masses.
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Liu L, Du X, Fang J, Zhao J, Guo Y, Zhao Y, Zou C, Yan X, Li W. Development of an Interferon Gamma Response-Related Signature for Prediction of Survival in Clear Cell Renal Cell Carcinoma. J Inflamm Res 2021; 14:4969-4985. [PMID: 34611422 PMCID: PMC8485924 DOI: 10.2147/jir.s334041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022] Open
Abstract
Background Interferon plays a crucial role in the pathogenesis and progression of tumors. Clear cell renal cell carcinoma (ccRCC) represents a prevalent malignant urinary system tumor. An effective predictive model is required to evaluate the prognosis of patients to optimize treatment. Materials and Methods RNA-sequencing data and clinicopathological data from TCGA were involved in this retrospective study. The IFN-γ response genes with significantly different gene expression were screened out. Univariate Cox regression, LASSO regression and multivariate Cox regression were used to establish a new prognostic scoring model for the training group. Survival curves and ROC curves were drawn, and nomogram was constructed. At the same time, we conducted subgroup analysis and experimental verification using our own samples. Finally, we evaluated the relatedness between the prognostic signature and immune infiltration landscapes. In addition, the sensitivity of different risk groups to six drugs and immune checkpoint inhibitors was calculated. Results The IFN-γ response-related signature included 7 genes: C1S, IFI44, ST3GAL5, NUP93, TDRD7, DDX60, and ST8SIA4. The survival curves of the training and testing groups showed the model's effectiveness (P = 4.372e-11 and P = 1.08e-08, respectively), the ROC curves showed that the signature was stable, and subgroup analyses showed the wide applicability of the model (P<0.001). Multivariate Cox regression analysis showed that the risk model was an independent prognostic factor of ccRCC. A high-risk score may represent an immunosuppressive microenvironment, while the high-risk group exhibited poor sensitivity to drugs. Conclusion Our findings strongly indicate that the IFN-γ response-related signature can be used as an effective prognostic indicator of ccRCC.
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Affiliation(s)
- Lixiao Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xuedan Du
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Jintao Fang
- Department of Urinary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Jinduo Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Yong Guo
- Department of Urinary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Ye Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Chengyang Zou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xiaojian Yan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Wenfeng Li
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
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Dai L, Chen L, Wang W, Lin P. Resveratrol inhibits ACHN cells via regulation of histone acetylation. PHARMACEUTICAL BIOLOGY 2020; 58:231-238. [PMID: 32202448 PMCID: PMC7144206 DOI: 10.1080/13880209.2020.1738503] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 01/20/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
Context: The relationship between resveratrol and histone acetylation in renal cell carcinoma (RCC) has not yet been reported.Objective: To explore the functional role of resveratrol in RCC.Materials and methods: Functional experiments were performed to determine proliferatio n of ACHN cells with treatment of resveratrol (0, 7.8125, 15.625, 31.25 and 62.5 μg/mL, for 12, 24 and 48 h of culture) or 0.1 μM SAHA. The enzyme activities of MMP-2/-9 were measured by gelatine zymography and histone acetylation by Western blot.Results: When the cells were treated with 15.625, 31.25 and 62.5 μg/mL resveratrol, ACHN cells viability was 73.2 ± 3.5%, 61.4 ± 3.1%, 50.2 ± 4.7% for 12 h, 62.7 ± 4.5%, 52.4 ± 5.5%, 40.2 ± 3.8% for 24 h, and 60.8 ± 3.7%, 39.4 ± 5.1%, 37.6 ± 2.7% for 48 h, and the wound closure (%) of migration was increased from 0.6 to 0.7, 0.85, 0.9 for 12 h and from 0.23 to 0.3, 0.48, 0.59 for 24 h. The invasion rate was 8.5 ± 0.9%, 7.4 ± 0.3% and 5.8 ± 0.6%, and cell cycle was arrested at G1 from 42.5 ± 2.9% to 55.3 ± 5.7%, 59.8 ± 3.4%, 68.7 ± 4.6%. MMP-2/-9 expression (p < 0.05) was inhibited by resveratrol. The protein levels of histone acetylation (p < 0.01) was increased by resveratrol.Discussion and conclusions: Our results suggest that these effects might be related to a high level of histone acetylation, and resveratrol can be considered as an alternative treatment for RCC.
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Affiliation(s)
- Lili Dai
- Department of Science and Education, Jiujiang University Clinical Medical College, Jiujiang, China
| | - Lingyan Chen
- Department of Rehabilitation, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjing Wang
- TCM Basic Clinical Research Office, Guiyang University of Chinese Medicine, Guiyang, China
| | - Peizheng Lin
- Department of Encephalopathy, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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11
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Qian S, Sun S, Zhang L, Tian S, Xu K, Zhang G, Chen M. Integrative Analysis of DNA Methylation Identified 12 Signature Genes Specific to Metastatic ccRCC. Front Oncol 2020; 10:556018. [PMID: 33134164 PMCID: PMC7578385 DOI: 10.3389/fonc.2020.556018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Abnormal epigenetic alterations can contribute to the development of human malignancies. Identification of these alterations for early screening and prognosis of clear cell renal cell carcinoma (ccRCC) has been a highly sought-after goal. Bioinformatic analysis of DNA methylation data provides broad prospects for discovery of epigenetic biomarkers. However, there is short of exploration of methylation-driven genes of ccRCC. Methods: Gene expression data and DNA methylation data in metastatic ccRCC were sourced from the Gene Expression Omnibus (GEO) database. Differentially methylated genes (DMGs) at 5′-C-phosphate-G- 3′ (CpG) sites and differentially expressed genes (DEGs) were screened and the overlapping genes in DMGs and DEGs were then subject to gene set enrichment analysis. Next, the weighted gene co-expression network analysis (WGCNA) was used to search hub DMGs associated with ccRCC. Cox regression and ROC analyses were performed to screen potential biomarkers and develop a prognostic model based on the screened hub genes. Results: Three hundred and fourteen overlapping DMGs were obtained from two independent GEO datasets. The turquoise module contained 79 hub DMGs, which represent the most significant module screened by WGCNA. Furthermore, a total of 12 hub genes (CETN3, DCAF7, GPX4, HNRNPA0, NUP54, SERPINB1, STARD5, TRIM52, C4orf3, C12orf51, and C17orf65) were identified in the TCGA database by multivariate Cox regression analyses. All the 12 genes were then used to generate the model for diagnosis and prognosis of ccRCC. ROC analysis showed that these genes exhibited good diagnostic efficiency for metastatic and non-metastatic ccRCC. Furthermore, the prognostic model with the 12 methylation-driven genes demonstrated a good prediction of 5-year survival rates for ccRCC patients. Conclusion: Integrative analysis of DNA methylation data identified 12 signature genes, which could be used as epigenetic biomarkers for prognosis of metastatic ccRCC. This prognostic model has a good prediction of 5-year survival for ccRCC patients.
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Affiliation(s)
- Siwei Qian
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Si Sun
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Lei Zhang
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China.,Institute of Urology, School of Medicine, Southeast University, Nanjing, China
| | - Shengwei Tian
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Kai Xu
- Department of Urology, Changzhou No. 2 People's Hospital, Changzhou, China
| | - Guangyuan Zhang
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China.,Institute of Urology, School of Medicine, Southeast University, Nanjing, China
| | - Ming Chen
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China.,Institute of Urology, School of Medicine, Southeast University, Nanjing, China
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12
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Xu Y, Li X, Han Y, Wang Z, Han C, Ruan N, Li J, Yu X, Xia Q, Wu G. A New Prognostic Risk Model Based on PPAR Pathway-Related Genes in Kidney Renal Clear Cell Carcinoma. PPAR Res 2020; 2020:6937475. [PMID: 33029112 PMCID: PMC7527891 DOI: 10.1155/2020/6937475] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE This study is aimed at using genes related to the peroxisome proliferator-activated receptor (PPAR) pathway to establish a prognostic risk model in kidney renal clear cell carcinoma (KIRC). METHODS For this study, we first found the PPAR pathway-related genes on the gene set enrichment analysis (GSEA) website and found the KIRC mRNA expression data and clinical data through TCGA database. Subsequently, we used R language and multiple R language expansion packages to analyze the expression, hazard ratio analysis, and coexpression analysis of PPAR pathway-related genes in KIRC. Afterward, using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) website, we established the protein-protein interaction (PPI) network of genes related to the PPAR pathway. After that, we used LASSO regression curve analysis to establish a prognostic survival model in KIRC. Finally, based on the model, we conducted correlation analysis of the clinicopathological characteristics, univariate analysis, and multivariate analysis. RESULTS We found that most of the genes related to the PPAR pathway had different degrees of expression differences in KIRC. Among them, the high expression of 27 genes is related to low survival rate of KIRC patients, and the high expression of 13 other genes is related to their high survival rate. Most importantly, we used 13 of these genes successfully to establish a risk model that could accurately predict patients' prognosis. There is a clear correlation between this model and metastasis, tumor, stage, grade, and fustat. CONCLUSIONS To the best of our knowledge, this is the first study to analyze the entire PPAR pathway in KIRC in detail and successfully establish a risk model for patient prognosis. We believe that our research can provide valuable data for future researchers and clinicians.
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Affiliation(s)
- Yingkun Xu
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Xiunan Li
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, China
| | - Yuqing Han
- Department of Radiology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Zilong Wang
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Chenglin Han
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Ningke Ruan
- The Nursing College of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jianyi Li
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Xiao Yu
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Qinghua Xia
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, China
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13
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Xu Y, Li X, Han Y, Wang Z, Han C, Ruan N, Li J, Yu X, Xia Q, Wu G. A New Prognostic Risk Model Based on PPAR Pathway-Related Genes in Kidney Renal Clear Cell Carcinoma. PPAR Res 2020; 2020:6937475. [PMID: 33029112 PMCID: PMC7527891 DOI: 10.1155/2020/6937475;] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 10/11/2024] Open
Abstract
Objective This study is aimed at using genes related to the peroxisome proliferator-activated receptor (PPAR) pathway to establish a prognostic risk model in kidney renal clear cell carcinoma (KIRC). Methods For this study, we first found the PPAR pathway-related genes on the gene set enrichment analysis (GSEA) website and found the KIRC mRNA expression data and clinical data through TCGA database. Subsequently, we used R language and multiple R language expansion packages to analyze the expression, hazard ratio analysis, and coexpression analysis of PPAR pathway-related genes in KIRC. Afterward, using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) website, we established the protein-protein interaction (PPI) network of genes related to the PPAR pathway. After that, we used LASSO regression curve analysis to establish a prognostic survival model in KIRC. Finally, based on the model, we conducted correlation analysis of the clinicopathological characteristics, univariate analysis, and multivariate analysis. Results We found that most of the genes related to the PPAR pathway had different degrees of expression differences in KIRC. Among them, the high expression of 27 genes is related to low survival rate of KIRC patients, and the high expression of 13 other genes is related to their high survival rate. Most importantly, we used 13 of these genes successfully to establish a risk model that could accurately predict patients' prognosis. There is a clear correlation between this model and metastasis, tumor, stage, grade, and fustat. Conclusions To the best of our knowledge, this is the first study to analyze the entire PPAR pathway in KIRC in detail and successfully establish a risk model for patient prognosis. We believe that our research can provide valuable data for future researchers and clinicians.
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Affiliation(s)
- Yingkun Xu
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Xiunan Li
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, China
| | - Yuqing Han
- Department of Radiology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Zilong Wang
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Chenglin Han
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Ningke Ruan
- The Nursing College of Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jianyi Li
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Xiao Yu
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
| | - Qinghua Xia
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, China
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14
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Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma. Aging (Albany NY) 2020; 12:9205-9223. [PMID: 32420905 PMCID: PMC7288970 DOI: 10.18632/aging.103192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/17/2020] [Indexed: 02/07/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) remains one of the most common cancer types globally, and while it has been extensively studied, the molecular basis for its pathology remains incompletely understood. Herein, we profiled three previously published datasets (GSE66272, GSE100666, and GSE105261) in a single integrated analysis aimed at identifying disease-associated patterns of gene expression that may offer mechanistic insight into the drivers of this disease. We pooled expression data from 39 normal kidney samples and 39 kidney tumors, leading us to identify 310 differentially expressed genes (DEGs) that were linked to kidney cancer in all three analyzed datasets. Of these genes, 133 and 177 were up- and down-regulated, respectively, in cancer samples. We then incorporated these DEGs into a protein-protein interaction network with the STRING and Cytoscape tools, and we were able to identify signaling pathways significantly enriched for these DEGs. The relationship between DEG expression and ccRCC patient survival was further evaluated using a Kaplan-Meier approach, leading us to identify TIMP1 as an independent prognostic factor in ccRCC patients. When TIMP1 expression was disrupted in ccRCC cell lines, this impaired their migratory and invasive capabilities. In summary, we employed an integrative bioinformatics approach to identify ccRCC-related DEGs and associated signaling pathways. Together these findings offer novel insight into the mechanistic basis for ccRCC, potentially helping to identify novel therapeutic targets for the treatment of this deadly disease.
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15
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Identification of Four Pathological Stage-Relevant Genes in Association with Progression and Prognosis in Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2137319. [PMID: 32309427 PMCID: PMC7142335 DOI: 10.1155/2020/2137319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/09/2020] [Indexed: 12/13/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a major histological subtype of renal cell carcinoma and can be clinically divided into four stages according to the TNM criteria. Identifying clinical stage-related genes is beneficial for improving the early diagnosis and prognosis of ccRCC. By using bioinformatics analysis, we aim to identify clinical stage-relevant genes that are significantly associated with the development of ccRCC. First, we analyzed the gene expression microarray data sets: GSE53757 and GSE73731. We divided these data into five groups by staging information-normal tissue and ccRCC stages I, II, III, and IV-and eventually identified 500 differentially expressed genes (DEGs). To obtain precise stage-relevant genes, we subsequently applied weighted gene coexpression network analysis (WGCNA) to the GSE73731 dataset and KIRC data from The Cancer Genome Atlas (TCGA). Two modules from each dataset were identified to be related to the tumor TNM stage. Several genes with high inner connection inside the modules were considered hub genes. The intersection results between hub genes of key modules and 500 DEGs revealed UBE2C, BUB1B, RRM2, and TPX2 as highly associated with the stage of ccRCC. In addition, the candidate genes were validated at both the RNA expression level and the protein level. Survival analysis also showed that 4 genes were significantly correlated with overall survival. In conclusion, our study affords a deeper understanding of the molecular mechanisms associated with the development of ccRCC and provides potential biomarkers for early diagnosis and individualized treatment for patients at different stages of ccRCC.
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16
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Xu H, Xu WH, Ren F, Wang J, Wang HK, Cao DL, Shi GH, Qu YY, Zhang HL, Ye DW. Prognostic value of epithelial-mesenchymal transition markers in clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12:866-883. [PMID: 31915310 PMCID: PMC6977664 DOI: 10.18632/aging.102660] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/24/2019] [Indexed: 04/13/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) is important in tumor invasiveness and metastasis. We aimed to determine prognostic value of six key EMT markers (CDH1, CDH2, SNAI1, SNAI2, VIM, TWIST1) in clear cell renal cell carcinoma (ccRCC). A total of 533 ccRCC patients with RNASeq data from The Cancer Genome Atlas (TCGA) cohort were included for analysis. Gene expression of these EMT markers was compared between tumor and normal tissues based on Oncomine database and TCGA cohort. Their correlations with progression-free survival (PFS) and overall survival (OS) were also examined in both TCGA cohort and FUSCC (Fudan University Shanghai Cancer Center) cohort. Cox proportional hazards regression model and Kaplan-Meier plot were used to assess the relative factors. Functional enrichment analyses were utilized to describe biologic function annotations and significantly involved hallmarks pathways of each gene. We found that Epithelial marker, CDH1 expression was lower, while mesenchymal markers (CDH2, SNAI1, VIM, TWIST1) expression was higher in ccRCC primary tumors. In the TCGA cohort, we found that patients with higher expression of VIM, TWIST1 or lower expression of CDH1 had worse prognosis. Further, in the FUSCC cohort, we confirmed the predictive ability of mesenchymal markers and epithelial marker expression in PFS and OS of ccRCC patients. After generating Cox regression models, EMT markers (CDH1, SNAI1, VIM, and TWIST1) were independent prognostic factors of both PFS and OS in ccRCC patients. Our preliminary EMT prediction model can facilitate further screening of EMT biomarkers and cast a better understanding of EMT gene function in ccRCC.
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Affiliation(s)
- Hua Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fei Ren
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jun Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hong-Kai Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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17
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Wu G, Xu Y, Li L, Li J, Ruan N, Dong J, Si Z, Xia Q, Wang Q. Tripartite-motif family genes associated with cancer stem cells affect tumor progression and can assist in the clinical prognosis of kidney renal clear cell carcinoma. Int J Med Sci 2020; 17:2905-2916. [PMID: 33173411 PMCID: PMC7646106 DOI: 10.7150/ijms.51260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/08/2020] [Indexed: 11/17/2022] Open
Abstract
Ubiquitination is presently a hot topic in the field of oncology. The tripartite-motif (TRIM) family of proteins represents one of the largest classes of putative single protein RING-finger E3 ubiquitin ligases, which play an essential role in the ubiquitination of proteins in the body. At the same time, research related to cancer stem cells (CSCs) is increasing in popularity in the field of oncology. CSCs are potentially chemically resistant and can be selectively enriched in patients receiving chemotherapy, ultimately leading to adverse outcomes, such as treatment failure and cancer recurrence. There is a close relationship between multiple TRIM family genes and CSCs. Accumulating evidence suggests that TRIM family proteins are expressed in diverse human cancers and act as regulators of oncoproteins or tumor suppressor proteins. In this study, we used biological information to explore the potential function of TRIM family genes related to CSCs in the development of pan-cancer. Kidney renal clear cell carcinoma (KIRC) is one of the deadliest malignant tumors in the world. Owing to its complex molecular and cellular heterogeneity, the effectiveness of existing KIRC-related risk prediction models is not satisfactory at present. Therefore, we focused on the potential role of these TRIM family genes in KIRC and used seven TRIM family genes to establish a prognostic risk model. This model includes TRIM16, TRIM32, TRIM24, TRIM8, TRIM27, PML, and TRIM11. In conclusion, this study provides further insight into the prognosis of KIRC, which may guide treatment.
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Affiliation(s)
- Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, China
| | - Yingkun Xu
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
| | - Lin Li
- Department of Orthopedics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
| | - Jianyi Li
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
| | - Ningke Ruan
- The Nursing College of Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Jian Dong
- Department of Sports Medicine and Adult Reconstructive Surgery, The Affiliated Drum Tower Hospital of Nanjing University School of Medicine, Nanjing, Jiangsu, 210008, China
| | - Zhuyuan Si
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
| | - Qinghua Xia
- Department of Urology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Qifei Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, China
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18
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Liu D, Zhou G, Shi H, Chen B, Sun X, Zhang X. Downregulation of Transmembrane protein 40 by miR-138-5p Suppresses Cell Proliferation and Mobility in Clear Cell Renal Cell Carcinoma. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2270. [PMID: 32884956 PMCID: PMC7461706 DOI: 10.30498/ijb.2019.85193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Clear cell renal cell carcinoma (ccRCC) represents approximately 70% of RCC,as the most frequent histological subtype of RCC. MiR-138-5p, a tumor-related microRNA (miRNA), has been reported to be implicated in the diverse types of human malignancies, but its role in ccRCCremains unclear. Objective The study was designed to investigate the functional behaviors and regulatory mechanisms of miR-138-5p in ccRCC. Materials and Methods Quantitative real-time PCR and western blotting analyses were performed to determine the expression of miR-138-5p and TMEM40 in ccRCC tissues. Pearson's correlation coefficient was utilized to evaluate the correlation between miR-138-5p and TMEM40 expression. The function of miR-138-5p and TMEM40 in the cell proliferation, migration and invasion of ccRCC cells (786-O and ACHN) was assessed by CCK-8, colony formation, wound healing and transwell assay, respectively. A luciferase reporter assay was performed to confirm the direct binding of miR-138-5p to the target gene TMEM40. Results We found the expression of miR-138-5p was significantly down-regulated, while TMEM40 was remarkably up-regulated in ccRCC tissues. TMEM40 expression was discovered to be inversely correlated with miR-138-5p expression in ccRCC tissues. Functional studies demonstrated that miR-138-5p overexpression or TMEM40 knockdown significantly suppressed ccRCC cell proliferation, migration and invasion in vitro. Notably, we experimentally confirmed that miR-138-5p directly recognizes the 3'-UTR of the TMEM40 transcript and down-regulated its expression in ccRCC cells. Conclusions Taken together, our findings provide the first clues regarding the role of miR-138-5p as a tumor suppressor in ccRCC by directly targeting of TMEM40.
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Affiliation(s)
- Dongcao Liu
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Guang Zhou
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Hongbo Shi
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Bin Chen
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Xiaosong Sun
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Xuejun Zhang
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
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19
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Yang JF, Shi SN, Xu WH, Qiu YH, Zheng JZ, Yu K, Song XY, Li F, Wang Y, Wang R, Qu YY, Zhang HL, Zhou XQ. Screening, identification and validation of CCND1 and PECAM1/CD31 for predicting prognosis in renal cell carcinoma patients. Aging (Albany NY) 2019; 11:12057-12079. [PMID: 31850854 PMCID: PMC6949065 DOI: 10.18632/aging.102540] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/19/2019] [Indexed: 12/14/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common cancers worldwide. Despite intense efforts to elucidate its pathogenesis, the molecular mechanisms and genetic characteristics of this cancer remain unknown. In this study, three expression profile data sets (GSE15641, GSE16441 and GSE66270) were integrated to identify candidate genes that could elucidate functional pathways in ccRCC. Expression data from 63 ccRCC tumors and 54 normal samples were pooled and analyzed. The GSE profiles shared 379 differentially expressed genes (DEGs), including 249 upregulated genes, and 130 downregulated genes. A protein-protein interaction network (PPI) was constructed and analyzed using STRING and Cytoscape. Functional and signaling pathways of the shared DEGs with significant p values were identified. Kaplan-Meier plots of integrated expression scores were used to analyze survival outcomes. These suggested that FN1, ICAM1, CXCR4, TYROBP, EGF, CAV1, CCND1 and PECAM1/CD31 were independent prognostic factors in ccRCC. Finally, to investigate early events in renal cancer, we screened for the hub genes CCND1 and PECAM1/CD31. In summary, integrated bioinformatics analysis identified candidate DEGs and pathways in ccRCC that could improve our understanding of the causes and underlying molecular events of ccRCC. These candidate genes and pathways could be therapeutic targets for ccRCC.
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Affiliation(s)
- Jian-Feng Yang
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Shen-Nan Shi
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yun-Hua Qiu
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Jin-Zhou Zheng
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Kui Yu
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Xiao-Yun Song
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Feng Li
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Yu Wang
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Rui Wang
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Xi-Qiu Zhou
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200126, China
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20
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Xu WH, Shi SN, Wang J, Xu Y, Tian X, Wan FN, Cao DL, Qu YY, Zhang HL, Ye DW. The Role of Serine Peptidase Inhibitor Kazal Type 13 (SPINK13) as a Clinicopathological and Prognostic Biomarker in Patients with Clear Cell Renal Cell Carcinoma. Med Sci Monit 2019; 25:9458-9470. [PMID: 31825950 PMCID: PMC6926094 DOI: 10.12659/msm.917754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background The serine peptidase inhibitor Kazal type 13 (SPINK13) gene has tumor suppressor activity, but its role in renal cell carcinoma (RCC) remains unknown. This study aimed to investigate mRNA expression of SPINK13 in clear cell renal cell carcinoma (CCRCC) in human tissue and to use bioinformatics data to investigate the role of SPINK13 expression as a clinicopathological and prognostic biomarker for patients with CCRCC. Material/Methods Patients with CCRCC (N=533) with available RNA sequence data from The Cancer Genome Atlas (TCGA)-CCRCC database were analyzed with patients who had a tissue diagnosis of CCRCC (N=305) at the Fudan University Shanghai Cancer Center (FUSCC). Differential transcriptional and proteome expression profiles were obtained from the ONCOMINE cancer microarray database, TCGA, and the Human Protein Atlas (HPA) database. Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) measured SPINK13 mRNA expression in 305 samples of CCRCC tissue from the FUSCC. The effects of clinicopathological parameters on progression-free survival (PFS) and overall survival (OS) were analyzed using the Kaplan-Meier and log-rank test. Results Transcriptional and proteome expression of SPINK13 were significantly increased CCRCC tissue samples. Increased SPINK13 mRNA expression was significantly associated with reduced PFS and OS in 838 patients with CCRCC patients from the two independent cohorts, the FUSCC and the TCGA-CCRCC cohorts (p<0.01). Gene set enrichment analysis (GSEA) showed that SPINK13 expression was involved in complement, apical junction, epithelial-mesenchymal transition (EMT), glycolysis, hypoxia, and inflammation signaling pathways. Conclusions Increased expression of SPINK13 was associated with poor prognosis in patients with CCRCC.
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Affiliation(s)
- Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China (mainland).,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland)
| | - Shen-Nan Shi
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland).,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China (mainland)
| | - Jun Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China (mainland).,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland)
| | - Yue Xu
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China (mainland).,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland)
| | - Fang-Ning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China (mainland).,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland)
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China (mainland).,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland)
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China (mainland).,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland)
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China (mainland).,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland)
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China (mainland).,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China (mainland)
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21
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Prognostic implications of Aquaporin 9 expression in clear cell renal cell carcinoma. J Transl Med 2019; 17:363. [PMID: 31703694 PMCID: PMC6842264 DOI: 10.1186/s12967-019-2113-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/26/2019] [Indexed: 12/27/2022] Open
Abstract
Background Growing evidence has demonstrated immune reactivity as a confirmed important carcinogenesis and therapy efficacy for clear cell renal cell carcinoma (ccRCC). Aquaporin 9 (AQP9) is involved in many immune-related signals; however, its role in ccRCC remains to be elucidated. This study investigated AQP9 expression in tumor tissues and defined the prognostic value in ccRCC patients. Methods A total of 913 ccRCC patients with available RNA-sequence data from the Cancer Genome Atlas (TCGA) database and Fudan University Shanghai Cancer Center (FUSCC) were consecutively recruited in analyses. Differential transcriptional and proteome expression profiles were obtained and validated using multiple datasets. A partial likelihood test from Cox regression analysis was developed to address the influence of independent factors on progression-free survival (PFS) and overall survival (OS). The Kaplan–Meier method and log-rank test were performed to assess survival. Receiver operating characteristic (ROC) curves were used to describe binary classifier value of AQP9 using area under the curve (AUC) score. Functional enrichment analyses and immune infiltration analysis were used to describe significantly involved hallmark pathways of hub genes. Results Significantly elevated transcriptional and proteomic AQP9 expressions were found in ccRCC samples. Increased AQP9 mRNA expression was significantly associated with advanced clinicopathological parameters and correlated with shorter PFS and OS in TCGA and FUSCC cohorts (p < 0.001). ROC curves suggested the significant diagnostic and prognostic ability of AQP9 (PFS, AUC = 0.823; OS, AUC = 0.828). Functional annotations indicated that AQP9 is involved in the most significant hallmarks including complement, coagulation, IL6/JAK–STAT3, inflammatory response and TNF-alpha signaling pathways. Conclusion Our study revealed that elevated AQP9 expression was significantly correlated with aggressive progression, poor survival and immune infiltrations in ccRCC patients, and we validated its prognostic value in a real-world cohort. These data suggest that AQP9 may act as an oncogene and a promising prognostic marker in ccRCC.
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22
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Weiss A, Le Roux-Bourdieu M, Zoetemelk M, Ramzy GM, Rausch M, Harry D, Miljkovic-Licina M, Falamaki K, Wehrle-Haller B, Meraldi P, Nowak-Sliwinska P. Identification of a Synergistic Multi-Drug Combination Active in Cancer Cells via the Prevention of Spindle Pole Clustering. Cancers (Basel) 2019; 11:E1612. [PMID: 31652588 PMCID: PMC6826636 DOI: 10.3390/cancers11101612] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
A major limitation of clinically used cancer drugs is the lack of specificity resulting in toxicity. To address this, we performed a phenotypically-driven screen to identify optimal multidrug combinations acting with high efficacy and selectivity in clear cell renal cell carcinoma (ccRCC). The search was performed using the Therapeutically Guided Multidrug Optimization (TGMO) method in ccRCC cells (786-O) and nonmalignant renal cells and identified a synergistic low-dose four-drug combination (C2) with high efficacy and negligible toxicity. We discovered that C2 inhibits multipolar spindle pole clustering, a survival mechanism employed by cancer cells with spindle abnormalities. This phenotype was also observed in 786-O cells resistant to sunitinib, the first line ccRCC treatment, as well as in melanoma cells with distinct percentages of supernumerary centrosomes. We conclude that C2-treatment shows a high efficacy in cells prone to form multipolar spindles. Our data suggest a highly effective and selective C2 treatment strategy for malignant and drug-resistant cancers.
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Affiliation(s)
- Andrea Weiss
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Morgan Le Roux-Bourdieu
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Marloes Zoetemelk
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - George M Ramzy
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Magdalena Rausch
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Daniela Harry
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Marijana Miljkovic-Licina
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Department of Pathology and Immunology, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Katayoun Falamaki
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Bernard Wehrle-Haller
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Patrick Meraldi
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Department of Cell Physiology and Metabolism, University of Geneva Medical School, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
| | - Patrycja Nowak-Sliwinska
- Institute of Pharmaceutical Sciences of Western Switzerland, Faculty of Sciences, University of Geneva, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
- Translational Research Centre in Oncohaematology, 1 Rue Michel-Servet, CMU, 1211 Geneva 4, Switzerland.
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23
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Xu WH, Xu Y, Wang J, Wan FN, Wang HK, Cao DL, Shi GH, Qu YY, Zhang HL, Ye DW. Prognostic value and immune infiltration of novel signatures in clear cell renal cell carcinoma microenvironment. Aging (Albany NY) 2019; 11:6999-7020. [PMID: 31493764 PMCID: PMC6756904 DOI: 10.18632/aging.102233] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022]
Abstract
Growing evidence has highlighted the immune response as an important feature of carcinogenesis and therapeutic efficacy in clear cell renal cell carcinoma (ccRCC). This study categorized ccRCC cases into high and low score groups based on their immune/stromal scores generated by the ESTIMATE algorithm, and identified an association between these scores and prognosis. Differentially expressed tumor environment (TME)-related genes extracted from common upregulated components in immune and stromal scores were described using functional annotations and protein–protein interaction (PPI) networks. Most PPIs were selected for further prognostic investigation. Many additional previously neglected signatures, including AGPAT9, AQP7, HMGCS2, KLF15, MLXIPL, PPARGC1A, exhibited significant prognostic potential. In addition, multivariate Cox analysis indicated that MIXIPL and PPARGC1A were the most significant prognostic signatures, and were closely related to immune infiltration in TCGA cohort. External prognostic validation of MIXIPL and PPARGC1A was undertaken in 380 ccRCC cases from a real-world cohort. These findings indicate the relevance of monitoring and manipulation of the microenvironment for ccRCC prognosis and precision immunotherapy.
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Affiliation(s)
- Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yue Xu
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Suzhou 215000, P.R. China
| | - Jun Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Fang-Ning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Hong-Kai Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
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24
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Zhu Q, Yu L, Qin Z, Chen L, Hu H, Zheng X, Zeng S. Regulation of OCT2 transcriptional repression by histone acetylation in renal cell carcinoma. Epigenetics 2019; 14:791-803. [PMID: 31088315 PMCID: PMC6615535 DOI: 10.1080/15592294.2019.1615354] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/16/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
Renal cell carcinoma (RCC) is a common malignant tumour affecting the urinary system, and multidrug resistance is one of the major reasons why chemotherapy for this type of cancer often fails. Previous studies have shown that loss of the human organic cation transporter OCT2 is the main factor contributing to oxaliplatin resistance in RCC, and that DNA hypermethylation and histone methylation play important roles in the transcriptional repression of OCT2 in RCC. In this study, we found that histone acetylation also regulates OCT2 repression in RCC and elucidated the underlying mechanisms. In normal renal cells, HDAC7 combines with MYC at the OCT2 promoter, resulting in a decrease in free HDAC7, which in turn increases the levels of H3K18ac and H3K27ac at the OCT2 promotor and activates OCT2 expression. In RCC cells, however, the interaction between HDAC7 and MYC does not occur, which leads a high abundance of HDAC7 and low levels of H3K18ac and H3K27ac at the OCT2 promoter, thereby resulting in the inhibition of OCT2 transcription. We found that combined treatment using the DNA methylation inhibitor decitabine and the histone deacetylase inhibitor vorinostat significantly increased the expression of OCT2 in RCC cell lines, which sensitized these cells to oxaliplatin. We accordingly propose that the combination of anticancer agents and epigenetic drugs can provide a novel chemotherapeutic regimen.
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Affiliation(s)
- Qianying Zhu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhiyuan Qin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lu Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Haihong Hu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoli Zheng
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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25
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Kuloğlu T, Artaş G, Yardim M, Sahin I, Aydin Y, Beyoğlu N, Özercan IH, Yalcin MH, Ugur K, Aydin S. Immunostaining characteristics of irisin in benign and malignant renal cancers. Biotech Histochem 2019; 94:435-441. [PMID: 30896263 DOI: 10.1080/10520295.2019.1586998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We investigated the expression of irisin in renal cancers using immunocytochemistry. Irisin has been reported to exhibit anticancer properties. The study groups consisted of 22 cases each of control renal tissue, oncocytoma, chromophobe renal cell carcinoma (RCC), clear cell RCC (Fuhrman nuclear grades 1, 2, 3 and 4) and papillary RCC. We evaluated 10 slides for each of 176 cases. Slides were immunostained for irisin and histoscores were calculated for the prevalence and strength of immunostaining. Fuhrman nuclear grade 1, 2, 3 clear cell RCC and papillary RCC exhibited no irisin immunoreactivity. Irisin immunoreactivity was observed in some Fuhrman nuclear grade 4 RCCs. We found a significant decrease in irisin staining in chromophobe RCC compared to the control. Immunoreactivity in the oncocytoma tissue was comparable to the control group. Irisin immunoreactivity in chromophobe RCC decreased and no immunoreactivity was observed in Fuhrman nuclear grade 1, 2, 3 clear cell RCC and papillary RCC. Immunistochemical screening of irisin in renal oncocytomas and renal cancers may be useful for differential diagnosis.
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Affiliation(s)
- T Kuloğlu
- Department of Histology and Embryology, School of Medicine, Firat University , Elazig
| | - G Artaş
- Department of Pathology, School of Medicine, Firat University , Elazig , Turkey
| | - M Yardim
- Department of Medical Biochemistry (Firat Hormones Research Group), School of Medicine, Firat University , Elazig , Turkey
| | - I Sahin
- Department of Medical Biochemistry (Firat Hormones Research Group), School of Medicine, Firat University , Elazig , Turkey.,Department of Medical Biology, School of Medicine, Erzincan Binali Yildirim University , Erzincan , Turkey
| | - Y Aydin
- Faculty of Veterinary Medicine, Ankara University , Ankara , Turkey
| | - N Beyoğlu
- School of Medicine, Firat University , Elazig , Turkey
| | - I H Özercan
- Department of Pathology, School of Medicine, Firat University , Elazig , Turkey
| | - M H Yalcin
- Department of Histology and Embryology, Faculty of Veterinary Medicine, Firat University , Elazig , Turkey
| | - K Ugur
- Department of Endocrinology and Metabolism Disease, School of Medicine, Firat University , Elazig , Turkey
| | - S Aydin
- Department of Medical Biochemistry (Firat Hormones Research Group), School of Medicine, Firat University , Elazig , Turkey
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26
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Wang ZR, Wei JH, Zhou JC, Haddad A, Zhao LY, Kapur P, Wu KJ, Wang B, Yu YH, Liao B, He DL, Chen W, Margulis V, Hsieh JT, Luo JH. Validation of DAB2IP methylation and its relative significance in predicting outcome in renal cell carcinoma. Oncotarget 2017; 7:31508-19. [PMID: 27129174 PMCID: PMC5058774 DOI: 10.18632/oncotarget.8971] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/02/2016] [Indexed: 12/21/2022] Open
Abstract
We have recently reported tumor suppressive role of DAB2IP in RCC development. In this study, We identified one CpG methylation biomarker (DAB2IP CpG1) located UTSS of DAB2IP that was associated with poor overall survival in a cohort of 318 ccRCC patients from the Cancer Genome Atlas (TCGA). We further validated the prognostic accuracy of DAB2IP CpG methylation by pyrosequencing quantitative methylation assay in 224 ccRCC patients from multiple Chinese centers (MCHC set), and 239 patients from University of Texas Southwestern Medical Center at Dallas (UTSW set) by using FFPE samples. DAB2IP CpG1 can predict the overall survival of patients in TCGA, MCHC, and UTSW sets independent of patient age, Fuhrman grade and TNM stage (all p<0.05). DAB2IP CpG1 successfully categorized patients into high-risk and low-risk groups with significant differences of clinical outcome in respective clinical subsets, regardless of age, sex, grade, stage, or race (HR: 1.63-7.83; all p<0.05). The detection of DAB2IP CpG1 methylation was minimally affected by ITH in ccRCC. DAB2IP mRNA expression was regulated by DNA methylation in vitro. DAB2IP CpG1 methylation is a practical and repeatable biomarker for ccRCC, which can provide prognostic value that complements the current staging system.
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Affiliation(s)
- Zong-Ren Wang
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jin-Huan Wei
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Jian-Cheng Zhou
- Department of Urology, Shaanxi Provincial People's Hospital, Shaanxi, China
| | - Ahmed Haddad
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Liang-Yun Zhao
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, Yunnan, China
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Kai-Jie Wu
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Bin Wang
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Yan-Hong Yu
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, Yunnan, China
| | - Bing Liao
- Department of Pathology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Da-Lin He
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Wei Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Vitaly Margulis
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jer-Tsong Hsieh
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jun-Hang Luo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
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Yuan L, Chen L, Qian K, Qian G, Wu CL, Wang X, Xiao Y. Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC). GENOMICS DATA 2017; 14:132-140. [PMID: 29159069 PMCID: PMC5683669 DOI: 10.1016/j.gdata.2017.10.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/12/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022]
Abstract
Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC (n = 97). Six hub genes (CCNB2, CDC20, CEP55, KIF20A, TOP2A and UBE2C) were identified in both co-expression and protein-protein interaction (PPI) networks, which were highly correlated with pathologic stage. The significance of expression of the hub genes in ccRCC was ranked top 4 among all cancers and correlated with poor prognosis. Functional analysis revealed that the hub genes were significantly enriched in cell cycle regulation and cell division. Gene set enrichment analysis suggested that the samples with highly expressed hub gene were correlated with cell cycle and p53 signaling pathway. Taken together, six hub genes were identified to be associated with progression and prognosis of ccRCC, and they might lead to poor prognosis by regulating p53 signaling pathway.
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Key Words
- Clear cell renal cell carcinoma (ccRCC)
- Co-expression network analysis
- DAVID, Database for Annotation, Visualization and Integrated Discovery
- DEG, differentially expressed gene
- DEGs, differentially expressed genes
- GS, gene significance
- GSEA, enrichment analysis and gene set enrichment
- HPA, human protein atlas
- Hub genes
- MEs, module eigengenes
- MS, module significance
- PPI, protein-protein interaction
- Prognosis
- Progression
- SAM, significance analysis of microarrays
- STRING, search tool for the retrieval of interacting genes
- TCGA, the cancer genome atlas
- TOM, topological overlap matrix
- WGCNA, weighted gene co-expression network analysis
- ccRCC, clear cell renal cell carcinoma
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Affiliation(s)
- Lushun Yuan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, The Fifth Hospital of Wuhan, Wuhan, China
| | - Guofeng Qian
- Department of Endocrinology, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Corresponding author.
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Correspondence to: Y. Xiao, Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.Department of Biological RepositoriesZhongnan Hospital of Wuhan UniversityWuhanChina
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28
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Wang J, Wang S, Luan Y, Zhang W, Sun C, Cheng G, Li K, Xin Q, Lin Z, Qi T, Kong F. Overexpression of NEDD9 in renal cell carcinoma is associated with tumor migration and invasion. Oncol Lett 2017; 14:8021-8027. [PMID: 29344245 PMCID: PMC5755160 DOI: 10.3892/ol.2017.7231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/07/2017] [Indexed: 12/19/2022] Open
Abstract
Scaffold protein neural precursor cell expressed, developmentally downregulated 9 (NEDD9) is a member of the Crk-associated substrate protein family and is known to be a biomarker in multiple cancer types. It serves a critical function in regulating cell proliferation, migration, invasion and survival. The objective of this study was to evaluate the potential effects of NEDD9 in renal cell carcinoma (RCC). The expression of NEDD9 was analyzed by immunohistochemistry, western blotting and reverse transcription-quantitative polymerase chain reaction. NEDD9 protein and mRNA levels were significantly upregulated in RCC tissues compared with normal tissues (P<0.001). Furthermore, the NEDD9 immunostaining level was significantly associated with primary tumor stage and tumor, node, metastasis stage (P<0.05). High NEDD9 expression resulted in significantly lower survival rates for patients compared with normal NEDD9 expression (P<0.01). In addition, wound healing and transwell assays indicated that NEDD9 depletion by small interfering RNA significantly attenuated the migration and invasion of RCC cells (P<0.001). The present data suggested that NEDD9 may be a novel target for prevention and treatment of RCC metastasis and recurrence.
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Affiliation(s)
- Jue Wang
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China.,Key Laboratory for Kidney Regeneration of Shandong Province, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Si Wang
- Department of Neurology, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Yun Luan
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China.,Key Laboratory for Kidney Regeneration of Shandong Province, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Wenhua Zhang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Chao Sun
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Guanghui Cheng
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Kailin Li
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Qian Xin
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Zhaomin Lin
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Tonggang Qi
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Feng Kong
- Central Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China.,Key Laboratory for Kidney Regeneration of Shandong Province, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
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29
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Yang MQ, Li D, Yang W, Zhang Y, Liu J, Tong W. A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer. Comput Struct Biotechnol J 2017; 15:463-470. [PMID: 29158875 PMCID: PMC5683705 DOI: 10.1016/j.csbj.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/16/2017] [Accepted: 09/24/2017] [Indexed: 12/17/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common and most aggressive form of renal cell cancer (RCC). The incidence of RCC has increased steadily in recent years. The pathogenesis of renal cell cancer remains poorly understood. Many of the tumor suppressor genes, oncogenes, and dysregulated pathways in ccRCC need to be revealed for improvement of the overall clinical outlook of the disease. Here, we developed a systems biology approach to prioritize the somatic mutated genes that lead to dysregulation of pathways in ccRCC. The method integrated multi-layer information to infer causative mutations and disease genes. First, we identified differential gene modules in ccRCC by coupling transcriptome and protein-protein interactions. Each of these modules consisted of interacting genes that were involved in similar biological processes and their combined expression alterations were significantly associated with disease type. Then, subsequent gene module-based eQTL analysis revealed somatic mutated genes that had driven the expression alterations of differential gene modules. Our study yielded a list of candidate disease genes, including several known ccRCC causative genes such as BAP1 and PBRM1, as well as novel genes such as NOD2, RRM1, CSRNP1, SLC4A2, TTLL1 and CNTN1. The differential gene modules and their driver genes revealed by our study provided a new perspective for understanding the molecular mechanisms underlying the disease. Moreover, we validated the results in independent ccRCC patient datasets. Our study provided a new method for prioritizing disease genes and pathways.
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Key Words
- AUC, Area Under Curve
- Causative mutation
- DEG, Differentially expressed gene
- DGM, Differential gene module
- Gene module
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- Pathways
- Protein-protein interaction
- RCC, Renal cell cancer
- ROC, Receiver Operating Characteristic
- SVM, Support vector machine
- TCGA, The Cancer Genome Atlas
- ccRCC
- ccRCC, Clear cell renal cell carcinoma
- eQTL
- eQTL, Expression quantitative trait loci
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Affiliation(s)
- Mary Qu Yang
- Joint Bioinformatics Graduate Program, Department of Information Science, George W. Donaghey College of Engineering and Information Technology, University of Arkansas at Little Rock, USA
- University of Arkansas for Medical Sciences, 2801 S. University Ave, Little Rock, AR 72204, USA
| | - Dan Li
- Joint Bioinformatics Graduate Program, Department of Information Science, George W. Donaghey College of Engineering and Information Technology, University of Arkansas at Little Rock, USA
- University of Arkansas for Medical Sciences, 2801 S. University Ave, Little Rock, AR 72204, USA
| | - William Yang
- School of Computer Science, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA
| | - Yifan Zhang
- Joint Bioinformatics Graduate Program, Department of Information Science, George W. Donaghey College of Engineering and Information Technology, University of Arkansas at Little Rock, USA
- University of Arkansas for Medical Sciences, 2801 S. University Ave, Little Rock, AR 72204, USA
| | - Jun Liu
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Weida Tong
- Divisions of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
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30
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Mahalingaiah PKS, Ponnusamy L, Singh KP. Oxidative stress-induced epigenetic changes associated with malignant transformation of human kidney epithelial cells. Oncotarget 2017; 8:11127-11143. [PMID: 27655674 PMCID: PMC5355252 DOI: 10.18632/oncotarget.12091] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/05/2016] [Indexed: 12/17/2022] Open
Abstract
Renal Cell Carcinoma (RCC) in humans is positively influenced by oxidative stress status in kidneys. We recently reported that adaptive response to low level of chronic oxidative stress induces malignant transformation of immortalized human renal tubular epithelial cells. Epigenetic alterations in human RCC are well documented, but its role in oxidative stress-induced malignant transformation of kidney cells is not known. Therefore, the objective of this study was to evaluate the potential role of epigenetic changes in chronic oxidative stress-induced malignant transformation of HK-2, human renal tubular epithelial cells. The results revealed aberrant expression of epigenetic regulatory genes involved in DNA methylation (DNMT1, DNMT3a and MBD4) and histone modifications (HDAC1, HMT1 and HAT1) in HK-2 cells malignantly transformed by chronic oxidative stress. Additionally, both in vitro soft agar assay and in vivo nude mice study showing decreased tumorigenic potential of malignantly transformed HK-2 cells following treatment with DNA de-methylating agent 5-aza 2’ dC further confirmed the crucial role of DNA hypermethyaltion in oxidative stress-induced malignant transformation. Changes observed in global histone H3 acetylation (H3K9, H3K18, H3K27 and H3K14) and decrease in phospho-H2AX (Ser139) also suggest potential role of histone modifications in increased survival and malignant transformation of HK-2 cells by oxidative stress. In summary, the results of this study suggest that epigenetic reprogramming induced by low levels of oxidative stress act as driver for malignant transformation of kidney epithelial cells. Findings of this study are highly relevant in potential clinical application of epigenetic-based therapeutics for treatments of kidney cancers.
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Affiliation(s)
- Prathap Kumar S Mahalingaiah
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, Texas, USA
| | - Logeswari Ponnusamy
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, Texas, USA
| | - Kamaleshwar P Singh
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, Texas, USA
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31
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Gu YF, Cohn S, Christie A, McKenzie T, Wolff N, Do QN, Madhuranthakam AJ, Pedrosa I, Wang T, Dey A, Busslinger M, Xie XJ, Hammer RE, McKay RM, Kapur P, Brugarolas J. Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade. Cancer Discov 2017; 7:900-917. [PMID: 28473526 DOI: 10.1158/2159-8290.cd-17-0292] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/29/2017] [Accepted: 05/02/2017] [Indexed: 12/22/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is characterized by BAP1 and PBRM1 mutations, which are associated with tumors of different grade and prognosis. However, whether BAP1 and PBRM1 loss causes ccRCC and determines tumor grade is unclear. We conditionally targeted Bap1 and Pbrm1 (with Vhl) in the mouse using several Cre drivers. Sglt2 and Villin proximal convoluted tubule drivers failed to cause tumorigenesis, challenging the conventional notion of ccRCC origins. In contrast, targeting with PAX8, a transcription factor frequently overexpressed in ccRCC, led to ccRCC of different grades. Bap1-deficient tumors were of high grade and showed greater mTORC1 activation than Pbrm1-deficient tumors, which exhibited longer latency. Disrupting one allele of the mTORC1 negative regulator, Tsc1, in Pbrm1-deficient kidneys triggered higher grade ccRCC. This study establishes Bap1 and Pbrm1 as lineage-specific drivers of ccRCC and histologic grade, implicates mTORC1 as a tumor grade rheostat, and suggests that ccRCCs arise from Bowman capsule cells.Significance: Determinants of tumor grade and aggressiveness across cancer types are poorly understood. Using ccRCC as a model, we show that Bap1 and Pbrm1 loss drives tumor grade. Furthermore, we show that the conversion from low grade to high grade can be promoted by activation of mTORC1. Cancer Discov; 7(8); 900-17. ©2017 AACR.See related commentary by Leung and Kim, p. 802This article is highlighted in the In This Issue feature, p. 783.
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Affiliation(s)
- Yi-Feng Gu
- Department of Internal Medicine, Hematology-Oncology Division, The University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shannon Cohn
- Department of Internal Medicine, Hematology-Oncology Division, The University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Alana Christie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Tiffani McKenzie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Nicholas Wolff
- Department of Internal Medicine, Hematology-Oncology Division, The University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Quyen N Do
- Department of Radiology and the Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ananth J Madhuranthakam
- Department of Radiology and the Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ivan Pedrosa
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Radiology and the Advanced Imaging Research Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Tao Wang
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas.,Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Anwesha Dey
- Department of Molecular Oncology, Genentech, South San Francisco, California
| | | | - Xian-Jin Xie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Robert E Hammer
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Renée M McKay
- Department of Internal Medicine, Hematology-Oncology Division, The University of Texas Southwestern Medical Center, Dallas, Texas.,Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas. .,Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - James Brugarolas
- Department of Internal Medicine, Hematology-Oncology Division, The University of Texas Southwestern Medical Center, Dallas, Texas. .,Kidney Cancer Program, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
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32
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Zhang Q, Yi X, Yang Z, Han Q, Di X, Chen F, Wang Y, Yi Z, Kuang Y, Zhu Y. Overexpression of G6PD Represents a Potential Prognostic Factor in Clear Cell Renal Cell Carcinoma. J Cancer 2017; 8:665-673. [PMID: 28367246 PMCID: PMC5370510 DOI: 10.7150/jca.16858] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/23/2016] [Indexed: 11/24/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) participates in glucose metabolism and it acts as the rate-limiting enzyme of the pentose phosphate pathway (PPP). Recently, G6PD dysregulation has been found in a variety of human cancers. Through analyzing published data in The Cancer Genome Atlas (TCGA), our pilot study indicated that G6PD mRNA expression was significantly higher in advanced Fuhrman grade in clear cell renal cell carcinoma (ccRCC). These clues promoted us to further evaluate the expression profile of G6PD and its prognostic impact in patients with ccRCC. In this study, G6PD expression levels were analyzed in 149 human ccRCC and normal tissues using immunohistochemistry. The results showed that compared with that in the normal renal samples, G6PD was found highly expressed in 51.0% of ccRCC (p<0.05). High expression of G6PD was significantly correlated to tumor extent, lymph node metastasis, Fuhrman grade, and TNM stage of ccRCC (all p<0.05). Moreover, positive G6PD expression was associated with poorer overall survival in ccRCC (p<0.001). In Cox regression analyses, high expression of G6PD also could be an independent prognostic factor for overall survival in ccRCC (p=0.007). This study suggests that overexpression of G6PD is associated with advanced disease status and therefore may become an important prognosticator for poor outcomes in ccRCC, as well as a potential therapeutic target for developing effective treatment modalities.
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Affiliation(s)
- Qiao Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Xiaojia Yi
- Department of pathology, The Second Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Zhe Yang
- Department of pathology, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Qiaoqiao Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Xuesong Di
- Department of organ transplantation, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Fufei Chen
- Department of organ transplantation, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Yanling Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Zihan Yi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
| | - Yingmin Kuang
- Department of organ transplantation, The First Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Yuechun Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Yunnan, China
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33
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Bhagat TD, Zou Y, Huang S, Park J, Palmer MB, Hu C, Li W, Shenoy N, Giricz O, Choudhary G, Yu Y, Ko YA, Izquierdo MC, Park ASD, Vallumsetla N, Laurence R, Lopez R, Suzuki M, Pullman J, Kaner J, Gartrell B, Hakimi AA, Greally JM, Patel B, Benhadji K, Pradhan K, Verma A, Susztak K. Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer. J Biol Chem 2017; 292:837-846. [PMID: 27909050 PMCID: PMC5247657 DOI: 10.1074/jbc.m116.745208] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 11/22/2016] [Indexed: 01/15/2023] Open
Abstract
Clear cell renal cell carcinoma (CCRCC) is an incurable malignancy in advanced stages and needs newer therapeutic targets. Transcriptomic analysis of CCRCCs and matched microdissected renal tubular controls revealed overexpression of NOTCH ligands and receptors in tumor tissues. Examination of the TCGA RNA-seq data set also revealed widespread activation of NOTCH pathway in a large cohort of CCRCC samples. Samples with NOTCH pathway activation were also clinically distinct and were associated with better overall survival. Parallel DNA methylation and copy number analysis demonstrated that both genetic and epigenetic alterations led to NOTCH pathway activation in CCRCC. NOTCH ligand JAGGED1 was overexpressed and associated with loss of CpG methylation of H3K4me1-associated enhancer regions. JAGGED2 was also overexpressed and associated with gene amplification in distinct CCRCC samples. Transgenic expression of intracellular NOTCH1 in mice with tubule-specific deletion of VHL led to dysplastic hyperproliferation of tubular epithelial cells, confirming the procarcinogenic role of NOTCH in vivo Alteration of cell cycle pathways was seen in murine renal tubular cells with NOTCH overexpression, and molecular similarity to human tumors was observed, demonstrating that human CCRCC recapitulates features and gene expression changes observed in mice with transgenic overexpression of the Notch intracellular domain. Treatment with the γ-secretase inhibitor LY3039478 led to inhibition of CCRCC cells in vitro and in vivo In summary, these data reveal the mechanistic basis of NOTCH pathway activation in CCRCC and demonstrate this pathway to a potential therapeutic target.
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Affiliation(s)
- Tushar D Bhagat
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Yiyu Zou
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Shizheng Huang
- the Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104
| | - Jihwan Park
- the Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104
| | - Matthew B Palmer
- the Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104
| | - Caroline Hu
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Weijuan Li
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Niraj Shenoy
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Orsolya Giricz
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Gaurav Choudhary
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Yiting Yu
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Yi-An Ko
- the Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104
| | - María C Izquierdo
- the Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104
| | - Ae Seo Deok Park
- the Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104
| | | | - Remi Laurence
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Robert Lopez
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Masako Suzuki
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - James Pullman
- the Department of Pathology, Montefiore Medical Center, Bronx, New York 10467
| | - Justin Kaner
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | | | - A Ari Hakimi
- the Sloan Kettering Cancer Center, New York, New York 10065, and
| | - John M Greally
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | | | | | - Kith Pradhan
- From the Albert Einstein College of Medicine, Bronx, New York 10461
| | - Amit Verma
- From the Albert Einstein College of Medicine, Bronx, New York 10461,
| | - Katalin Susztak
- the Renal Electrolyte and Hypertension Division, Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104,
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34
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Tezval H, Dubrowinskaja N, Peters I, Reese C, Serth K, Atschekzei F, Hennenlotter J, Stenzl A, Kuczyk MA, Serth J. Tumor Specific Epigenetic Silencing of Corticotropin Releasing Hormone -Binding Protein in Renal Cell Carcinoma: Association of Hypermethylation and Metastasis. PLoS One 2016; 11:e0163873. [PMID: 27695045 PMCID: PMC5047469 DOI: 10.1371/journal.pone.0163873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/15/2016] [Indexed: 02/03/2023] Open
Abstract
The relevance of Corticotropin Releasing Hormone (CRH)-system in human malignancies is a question of growing interest. Here we investigated hypermethylation and epigenetic silencing of the CRH-Binding Protein (CRHBP) gene in clear cell renal cell cancer (ccRCC). Relative methylation of the CRHBP CpG island (CGI) was determined in 17 tumor cell lines as well as 86 ccRCC samples and 66 paired normal tissues using pyrosequencing and quantitative methylation specific PCR of bisulfite converted DNA. Results were statistically compared with relative mRNA expression levels of CRHBP and clinicopathological parameters of patients. Re-expression of CRHBP following 5-aza-2´-deoxycytidine treatment was investigated by quantitative mRNA expression analysis. Real-time impedance analysis was applied for analysis of invasiveness of renal tumor cells following si-RNA knockdown of CRHBP expression or ectopic expression of CRHBP. We found the CRHBP CGI to be frequently methylated in tumor cell lines of renal, prostatic, and bladder cancer. Comparison of methylation in normal and paired renal cancer tissue specimens revealed hypermethylation of the CRHBP CGI in tumors (p<1*10−12). DNA methylation and decreased mRNA expression were correlated (R = 0.83, p<1*10−12). Tumor cell lines showed 5-aza-2´-deoxycytidine dependent reduction of methylation and re-expression of CRHBP was associated with altered cellular invasiveness of renal cancer cells in real-time impedance invasion assays. Hypermethylation and inverse relationship with mRNA expression were validated in silico using the TCGA network data. We describe for the first time tumor specific epigenetic silencing of CRHBP and statistical association with aggressive tumors thus suggesting the CRH system to contribute to the development of kidney cancer.
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Affiliation(s)
- Hossein Tezval
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Natalia Dubrowinskaja
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Inga Peters
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Christel Reese
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Katrin Serth
- Department of Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Faranaz Atschekzei
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Jörg Hennenlotter
- Department of Urology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Arnulf Stenzl
- Department of Urology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Markus A. Kuczyk
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urological Oncology, Hannover Medical School, Hannover, Germany
- * E-mail:
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Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine. BMC Cancer 2016; 16:485. [PMID: 27422173 PMCID: PMC4947293 DOI: 10.1186/s12885-016-2539-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/08/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Patients with clear cell renal cell carcinoma (ccRCC) have few therapeutic options, as ccRCC is unresponsive to chemotherapy and is highly resistant to radiation. Recently targeted therapies have extended progression-free survival, but responses are variable and no significant overall survival benefit has been achieved. Commercial ccRCC cell lines are often used as model systems to develop novel therapeutic approaches, but these do not accurately recapitulate primary ccRCC tumors at the genomic and transcriptional levels. Furthermore, ccRCC exhibits significant intertumor genetic heterogeneity, and the limited cell lines available fail to represent this aspect of ccRCC. Our objective was to generate accurate preclinical in vitro models of ccRCC using tumor tissues from ccRCC patients. METHODS ccRCC primary single cell suspensions were cultured in fetal bovine serum (FBS)-containing media or defined serum-free media. Established cultures were characterized by genomic verification of mutations present in the primary tumors, expression of renal epithelial markers, and transcriptional profiling. RESULTS The apparent efficiency of primary cell culture establishment was high in both culture conditions, but genotyping revealed that the majority of cultures contained normal, not cancer cells. ccRCC characteristically shows biallelic loss of the von Hippel Lindau (VHL) gene, leading to accumulation of hypoxia-inducible factor (HIF) and expression of HIF target genes. Purification of cells based on expression of carbonic anhydrase IX (CA9), a cell surface HIF target, followed by culture in FBS enabled establishment of ccRCC cell cultures with an efficiency of >80 %. Culture in serum-free conditions selected for growth of normal renal proximal tubule epithelial cells. Transcriptional profiling of ccRCC and matched normal cell cultures identified up- and down-regulated networks in ccRCC and comparison to The Cancer Genome Atlas confirmed the clinical validity of our cell cultures. CONCLUSIONS The ability to establish primary cultures of ccRCC cells and matched normal kidney epithelial cells from almost every patient provides a resource for future development of novel therapies and personalized medicine for ccRCC patients.
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Li HL, Han L, Chen HR, Meng F, Liu QH, Pan ZQ, Bai J, Zheng JN. PinX1 serves as a potential prognostic indicator for clear cell renal cell carcinoma and inhibits its invasion and metastasis by suppressing MMP-2 via NF-κB-dependent transcription. Oncotarget 2016; 6:21406-20. [PMID: 26033551 PMCID: PMC4673274 DOI: 10.18632/oncotarget.4011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/14/2015] [Indexed: 12/19/2022] Open
Abstract
PIN2/TRF1-interacting telomerase inhibitor 1 (PinX1) is a novel cloned gene which has been identified as a major haploinsufficient tumor suppressor essential for maintaining telomerase activity, the length of telomerase and chromosome stability. This study explored the clinical significance and biological function of PinX1 in human clear cell renal cell carcinoma (ccRCC). The clinical relevance of PinX1 in ccRCC was evaluated using tissue microarray and immunohistochemical staining in two independent human ccRCC cohorts. Our data demonstrated that PinX1 expression was dramatically decreased in ccRCC tissues compared with normal renal tissues and paired adjacent non-tumor tissues. Low PinX1 expression was significantly correlated with depth of invasion, lymph node metastasis and advanced TNM stage in patients, as well as with worse overall and disease-specific survival. Cox regression analysis revealed that PinX1 expression was an independent prognostic factor for ccRCC patients. Moreover, PinX1 inhibited the migration and invasion of ccRCC by suppressing MMP-2 expression and activity via NF-κB-dependent transcription in vitro. In vivo studies confirmed that PinX1 negatively regulated ccRCC metastasis and the expression of MMP-2 and NF-κB-p65. These findings indicate that PinX1 suppresses ccRCC metastasis and may serve as a ccRCC candidate clinical prognostic marker and a potential therapeutic target.
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Affiliation(s)
- Hai-Long Li
- The First Clinical Medical College, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical College, Xuzhou, Jiangsu, China.,Department of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical College, Xuzhou, Jiangsu, China
| | - Li Han
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical College, Xuzhou, Jiangsu, China
| | - Hai-Rong Chen
- Department of Occupational Medicine and Environmental Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fei Meng
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical College, Xuzhou, Jiangsu, China
| | - Qing-Hua Liu
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical College, Xuzhou, Jiangsu, China
| | - Zhen-Qiang Pan
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical College, Xuzhou, Jiangsu, China.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jin Bai
- Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical College, Xuzhou, Jiangsu, China.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun-Nian Zheng
- The First Clinical Medical College, Nanjing Medical University, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory of Biological Cancer Therapy, Xuzhou Medical College, Xuzhou, Jiangsu, China.,Department of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical College, Xuzhou, Jiangsu, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical College, Xuzhou, Jiangsu, China
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Xing T, He H. Epigenomics of clear cell renal cell carcinoma: mechanisms and potential use in molecular pathology. Chin J Cancer Res 2016; 28:80-91. [PMID: 27041930 DOI: 10.3978/j.issn.1000-9604.2016.02.09] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one frequent form of urologic malignancy with numerous genetic and epigenetic alterations. This review summarizes the recent major findings of epigenetic alterations including DNA methylation, histone modifications, microRNAs and recently identified long noncoding RNAs in the development and progression of ccRCC. These epigenetic profilings can provide a promising means of prognostication and early diagnosis for patients with ccRCCs. With the developed high-throughput technologies nowadays, the epigenetic analyses will have possible clinical applications in the molecular pathology of ccRCC.
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Affiliation(s)
- Tianying Xing
- 1 Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, 2 Department of Urology, Peking University Third Hospital, Beijing 100191, China
| | - Huiying He
- 1 Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, 2 Department of Urology, Peking University Third Hospital, Beijing 100191, China
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38
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MicroRNAs in clear cell renal cell carcinoma: biological functions and applications. J Kidney Cancer VHL 2015; 2:140-152. [PMID: 28326269 PMCID: PMC5345517 DOI: 10.15586/jkcvhl.2015.40] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/18/2015] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRs) are small noncoding RNAs that govern many biological processes. They frequently acquire a gain or a loss of function in cancer and hence play a causative role in the development and progression of neoplasms. They could be used as biomarkers to improve our knowledge on diagnosis, prognosis and drug resistance, and to attempt therapeutic approaches in several types of cancer including clear cell renal cell carcinoma (ccRCC). ccRCC is the most predominant subtype of RCC that accounts for about 90% of all renal cancers. Since ccRCC is generally asymptomatic until very late, it is difficult to diagnose early. Moreover, in the absence of preventive treatments for metastatic ccRCC after surgical resection of the primary cancer, predictive prognostic biomarkers are needed in order to achieve appropriate therapies. Herein the role of miRs in the biology of ccRCC and the potential applications of these molecules are discussed. Moreover, future applications in the diagnostic and prognostic field, as well as their impact on drug response and therapeutic targets are also explored. Their use in clinical practice as molecular biomarkers alone, or in combination with other biological markers could accelerate progress, help design personalized therapies, limit side effects, and improve quality of life of ccRCC patients.
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39
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The epigenetic landscape of clear-cell renal cell carcinoma. J Kidney Cancer VHL 2015; 2:90-104. [PMID: 28326264 PMCID: PMC5345536 DOI: 10.15586/jkcvhl.2015.33] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 05/26/2015] [Indexed: 01/29/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of all kidney tumors. During the last few years, epigenetics has emerged as an important mechanism in ccRCC pathogenesis. Recent reports, involving large-scale methylation and sequencing analyses, have identified genes frequently inactivated by promoter methylation and recurrent mutations in genes encoding chromatin regulatory proteins. Interestingly, three of detected genes (PBRM1, SETD2 and BAP1) are located on chromosome 3p, near the VHL gene, inactivated in over 80% ccRCC cases. This suggests that 3p alterations are an essential part of ccRCC pathogenesis. Moreover, most of the proteins encoded by these genes cooperate in histone H3 modifications. The aim of this review is to summarize the latest discoveries shedding light on deregulation of chromatin machinery in ccRCC. Newly described ccRCC-specific epigenetic alterations could potentially serve as novel diagnostic and prognostic biomarkers and become an object of novel therapeutic strategies.
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40
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Genetic polymorphism in extracellular regulators of Wnt signaling pathway. BIOMED RESEARCH INTERNATIONAL 2015; 2015:847529. [PMID: 25945348 PMCID: PMC4402192 DOI: 10.1155/2015/847529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/05/2015] [Indexed: 11/18/2022]
Abstract
The Wnt signaling pathway is mediated by a family of secreted glycoproteins through canonical and noncanonical mechanism. The signaling pathways are regulated by various modulators, which are classified into two classes on the basis of their interaction with either Wnt or its receptors. Secreted frizzled-related proteins (sFRPs) are the member of class that binds to Wnt protein and antagonizes Wnt signaling pathway. The other class consists of Dickkopf (DKK) proteins family that binds to Wnt receptor complex. The present review discusses the disease related association of various polymorphisms in Wnt signaling modulators. Furthermore, this review also highlights that some of the sFRPs and DKKs are unable to act as an antagonist for Wnt signaling pathway and thus their function needs to be explored more extensively.
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Gramicidin A: A New Mission for an Old Antibiotic. J Kidney Cancer VHL 2015; 2:15-24. [PMID: 28326255 PMCID: PMC5345515 DOI: 10.15586/jkcvhl.2015.21] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 01/15/2015] [Indexed: 01/01/2023] Open
Abstract
Gramicidin A (GA) is a channel-forming ionophore that renders biological membranes permeable to specific cations which disrupts cellular ionic homeostasis. It is a well-known antibiotic, however it’s potential as a therapeutic agent for cancer has not been widely evaluated. In two recently published studies, we showed that GA treatment is toxic to cell lines and tumor xenografts derived from renal cell carcinoma (RCC), a devastating disease that is highly resistant to conventional therapy. GA was found to possess the qualities of both a cytotoxic drug and a targeted angiogenesis inhibitor, and this combination significantly compromised RCC growth in vitro and in vivo. In this review, we summarize our recent research on GA, discuss the possible mechanisms whereby it exerts its anti-tumor effects, and share our perspectives on the future opportunities and challenges to the use of GA as a new anticancer agent.
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Lin YL, Wang YL, Fu XL, Ma JG. Aberrant methylation of PCDH8 is a potential prognostic biomarker for patients with clear cell renal cell carcinoma. Med Sci Monit 2014; 20:2380-5. [PMID: 25416427 PMCID: PMC4251547 DOI: 10.12659/msm.892433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/02/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND PCDH8 is a tumor suppressor that regulates cell adhesin, proliferation, and migration. It is often inactivated by aberrant promoter methylation in several human cancers, including clear cell renal cell carcinoma (CCRCC). The clinical significance of PCDH8 methylation in CCRCC remains unclear. The aim of this study was to investigate the relationship between PCDH8 methylation and clinicopathological characteristics as well as outcome of patients with CCRCC. MATERIAL/METHODS The methylation status of PCDH8 in 153 CCRCC tissues and 97 paired adjacent normal renal tissues were examined using methylation-specific PCR (MSP). Then the relationships between PCDH8 methylation and clinicopathological features as well as progression-free survival of CCRCC patients were evaluated. RESULTS PCDH8 methylation was significantly more frequent in CCRCC tissues compared with normal renal tissues. Moreover, PCDH8 methylation was significantly correlated with advanced clinical stage (P=0.0141), higher grade (P=0.0190), and lymph node metastasis (P=0.0098). In addition, multivariate analysis showed that PCDH8 methylation was independently associated with poor progression-free survival (P=0.0316). CONCLUSIONS PCDH8 methylation is a frequent event in CCRCC and is correlated with unfavorable clinicopathological features. Moreover, PCDH8 methylation may be a useful biomarker to predict the progression of CCRCC.
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Affiliation(s)
- Ying-Li Lin
- Department of Urology, Affiliated Xuzhou Hospital of Jiangsu University (Xuzhou Cancer Hospital), Xuzhou, Jiangsu, China
| | - Yan-Ling Wang
- Department of Anesthesiology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xing-Li Fu
- Health Sciences Center, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jian-Guo Ma
- Department of Urology, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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Bap1 is essential for kidney function and cooperates with Vhl in renal tumorigenesis. Proc Natl Acad Sci U S A 2014; 111:16538-43. [PMID: 25359211 DOI: 10.1073/pnas.1414789111] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Why different species are predisposed to different tumor spectra is not well understood. In particular, whether the physical location of tumor suppressor genes relative to one another influences tumor predisposition is unknown. Renal cancer presents a unique opportunity to explore this question. Renal cell carcinoma (RCC) of clear-cell type (ccRCC), the most common type, begins with an intragenic mutation in the von Hippel-Lindau (VHL) gene and loss of 3p (where VHL is located). Chromosome 3p harbors several additional tumor suppressor genes, including BRCA1-associated protein-1 (BAP1). In the mouse, Vhl is on a different chromosome than Bap1. Thus, whereas loss of 3p in humans simultaneously deletes one copy of BAP1, loss of heterozygosity in the corresponding Vhl region in the mouse would not affect Bap1. To test the role of BAP1 in ccRCC development, we generated mice deficient for either Vhl or Vhl together with one allele of Bap1 in nephron progenitor cells. Six2-Cre;Vhl(F/F);Bap1(F/+) mice developed ccRCC, but Six2-Cre;Vhl(F/F) mice did not. Kidneys from Six2-Cre;Vhl(F/F);Bap1(F/+) mice resembled kidneys from humans with VHL syndrome, containing multiple lesions spanning from benign cysts to cystic and solid RCC. Although the tumors were small, they showed nuclear atypia and exhibited features of human ccRCC. These results provide an explanation for why VHL heterozygous humans, but not mice, develop ccRCC. They also explain why a mouse model of ccRCC has been lacking. More broadly, our data suggest that differences in tumor predisposition across species may be explained, at least in part, by differences in the location of two-hit tumor suppressor genes across the genome.
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44
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Gao Y, Zhao H, Lu Y, Li H, Yan G. MicroRNAs as potential diagnostic biomarkers in renal cell carcinoma. Tumour Biol 2014; 35:11041-50. [PMID: 25095976 DOI: 10.1007/s13277-014-2381-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 07/23/2014] [Indexed: 12/18/2022] Open
Abstract
Emerging evidence has suggested that microRNAs (miRNAs) may be promising novel biomarkers for the diagnosis of renal cell carcinoma (RCC). However, the results of current studies are still conflicting. Hence, we undertake the current meta-analysis to comprehensively assess the diagnostic potential of miRNAs in RCC. The bivariate meta-analysis model was employed to summarize the sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). Summary receiver operating characteristic (SROC) curve and area under the curve (AUC) were used to evaluate the diagnostic accuracy. Subgroup analyses and meta-regression were used to explore the between-study heterogeneity. Deeks' funnel plot asymmetry test was used to test the potential of publication bias. All analyses were performed using STATA software (version 12.0). The pooled sensitivity and specificity of miRNAs for the diagnosis of RCC were 0.85 (95% confidence interval (CI), 0.77-0.90) and 0.84 (95% CI, 0.70-0.92). The value of AUC was 0.91 (95% CI, 0.88-0.93), suggesting that the diagnostic accuracy of miRNAs achieved a relatively high level. Furthermore, subgroup analyses showed that tissue-based miRNA assay is recommended to improve the diagnostic accuracy. In conclusion, the high degree of diagnostic accuracy suggests that miRNA in RCC patients may serve as next-generation biomarkers for detection of the disease. However, large-scale investigations and additional improvements are urgently needed to confirm our results and verify the feasibility of routine clinical utilization.
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Affiliation(s)
- Yongqing Gao
- Department of Clinical Laboratory, Tieling Central Hospital, Tieling, 112000, China
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45
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Sampson VB, David JM, Puig I, Patil PU, de Herreros AG, Thomas GV, Rajasekaran AK. Wilms' tumor protein induces an epithelial-mesenchymal hybrid differentiation state in clear cell renal cell carcinoma. PLoS One 2014; 9:e102041. [PMID: 25025131 PMCID: PMC4099076 DOI: 10.1371/journal.pone.0102041] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 06/13/2014] [Indexed: 12/19/2022] Open
Abstract
The Wilms' tumor transcription factor (WT1) was originally classified as a tumor suppressor, but it is now known to also be associated with cancer progression and poor prognosis in several malignancies. WT1 plays an essential role in orchestrating a developmental process known as mesenchymal-to-epithelial transition (MET) during kidney development, but also induces the reverse process, epithelial-to-mesenchymal transition (EMT) during heart development. WT1 is not expressed in the adult kidney, but shows elevated expression in clear cell renal cell carcinoma (ccRCC). However, the role of WT1 in this disease has not been characterized. In this study, we demonstrate that WT1 is upregulated in ccRCC cells that are deficient in the expression of the von Hippel-Lindau tumor suppressor protein (VHL). We found that WT1 transcriptionally activated Snail, a master transcriptional repressor that is known to induce EMT. Although Snail represses E-cadherin and induces mesenchymal characteristics, we found partial maintenance of E-cadherin and associated epithelial characteristics in kidney cells and ccRCC cells that express WT1, since WT1 upregulates E-cadherin expression and competes with Snail repression. These findings support a novel paradigm in which WT1 induces an epithelial-mesenchymal hybrid transition (EMHT), characterized by Snail up-regulation with E-cadherin maintenance, a tumor cell differentiation state in which cancer cells keep both EMT and MET characteristics which may promote tumor cell plasticity and tumor progression.
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Affiliation(s)
- Valerie B. Sampson
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
| | - Justin M. David
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Isabel Puig
- IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain
| | - Pratima U. Patil
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | | | - George V. Thomas
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon, United States of America
| | - Ayyappan K. Rajasekaran
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- * E-mail:
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46
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Hu CY, Mohtat D, Yu Y, Ko YA, Shenoy N, Bhattacharya S, Izquierdo MC, Park ASD, Giricz O, Vallumsetla N, Gundabolu K, Ware K, Bhagat TD, Suzuki M, Pullman J, Liu XS, Greally JM, Susztak K, Verma A. Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival. Clin Cancer Res 2014; 20:4349-60. [PMID: 24916699 DOI: 10.1158/1078-0432.ccr-14-0494] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE Even though recent studies have shown that genetic changes at enhancers can influence carcinogenesis, most methylomic studies have focused on changes at promoters. We used renal cell carcinoma (RCC), an incurable malignancy associated with mutations in epigenetic regulators, as a model to study genome-wide patterns of DNA methylation at a high resolution. EXPERIMENTAL DESIGN Analysis of cytosine methylation status of 1.3 million CpGs was determined by the HELP assay in RCC and healthy microdissected renal tubular controls. RESULTS We observed that the RCC samples were characterized by widespread hypermethylation that preferentially affected gene bodies. Aberrant methylation was particularly enriched in kidney-specific enhancer regions associated with H3K4Me1 marks. Various important underexpressed genes, such as SMAD6, were associated with aberrantly methylated, intronic enhancers, and these changes were validated in an independent cohort. MOTIF analysis of aberrantly hypermethylated regions revealed enrichment for binding sites of AP2a, AHR, HAIRY, ARNT, and HIF1 transcription factors, reflecting contributions of dysregulated hypoxia signaling pathways in RCC. The functional importance of this aberrant hypermethylation was demonstrated by selective sensitivity of RCC cells to low levels of decitabine. Most importantly, methylation of enhancers was predictive of adverse prognosis in 405 cases of RCC in multivariate analysis. In addition, parallel copy-number analysis from MspI representations demonstrated novel copy-number variations that were validated in an independent cohort of patients. CONCLUSIONS Our study is the first high-resolution methylome analysis of RCC, demonstrates that many kidney-specific enhancers are targeted by aberrant hypermethylation, and reveals the prognostic importance of these epigenetic changes in an independent cohort.
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Affiliation(s)
- Caroline Y Hu
- Albert Einstein College of Medicine, Bronx, New York
| | - Davoud Mohtat
- Albert Einstein College of Medicine, Bronx, New York
| | - Yiting Yu
- Albert Einstein College of Medicine, Bronx, New York
| | - Yi-An Ko
- Renal Electrolyte and Hypertension Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Niraj Shenoy
- Albert Einstein College of Medicine, Bronx, New York
| | | | - Maria C Izquierdo
- Renal Electrolyte and Hypertension Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ae Seo Deok Park
- Renal Electrolyte and Hypertension Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | | | | | - Kristin Ware
- Department of Pathology, Montefiore Medical Center, New York, New York
| | | | - Masako Suzuki
- Albert Einstein College of Medicine, Bronx, New York
| | - James Pullman
- Department of Pathology, Montefiore Medical Center, New York, New York
| | - X Shirley Liu
- Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts
| | | | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Amit Verma
- Albert Einstein College of Medicine, Bronx, New York.
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Abstract
Renal cell carcinoma of clear-cell type (ccRCC) is an enigmatic tumor type, characterized by frequent inactivation of the VHL gene (infrequently mutated in other tumor types), responsiveness to angiogenesis inhibitors, and resistance to both chemotherapy and conventional radiation therapy. ccRCC tumors exhibit substantial mutation heterogeneity. Recent studies using massively parallel sequencing technologies have implicated several novel driver genes. In VHL wild-type tumors, mutations were discovered in TCEB1, which encodes Elongin C, a protein that binds to VHL and is required for its function. Several additional tumor suppressor genes have been identified near the VHL gene, within a region that is frequently deleted in ccRCC on chromosome 3p: SETD2, BAP1, and PBRM1. Mutations in BAP1 and PBRM1 are largely mutually exclusive and are associated with different tumor biology and patient outcomes. In addition, the mTORC1 pathway is deregulated by mutations in MTOR, TSC1, PIK3CA, and PTEN in approximately 20% of ccRCCs. Mutations in TSC1, and possibly other genes, may predict for sensitivity to mTORC1 inhibitors. These discoveries provide insight into ccRCC development and set the foundation for the first molecular genetic classification of the disease, paving the way for subtype-specific therapies.
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Affiliation(s)
- James Brugarolas
- From the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX.
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48
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Peters I, Dubrowinskaja N, Abbas M, Seidel C, Kogosov M, Scherer R, Gebauer K, Merseburger AS, Kuczyk MA, Grünwald V, Serth J. DNA methylation biomarkers predict progression-free and overall survival of metastatic renal cell cancer (mRCC) treated with antiangiogenic therapies. PLoS One 2014; 9:e91440. [PMID: 24633192 PMCID: PMC3954691 DOI: 10.1371/journal.pone.0091440] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 02/11/2014] [Indexed: 11/26/2022] Open
Abstract
VEGF-targeted therapy increases both the progression-free (PFS) and overall survival (OS) of patients with metastasized renal cell cancer (mRCC). Identification of molecular phenotypes of RCC could improve risk-stratification and the prediction of the clinical disease course. We investigated whether gene-specific DNA hypermethylation can predict PFS and OS among patients undergoing anti-VEGF-based therapy. Primary tumor tissues from 18 patients receiving targeted therapy were examined retrospectively using quantitative methylation-specific PCR analysis of CST6, LAD1, hsa-miR-124-3, and hsa-miR-9-1 CpG islands. PFS and OS were analyzed for first-line and sequential antiangiogenic therapies using the log rank statistics. Sensitivity and specificity were determined for predicting first-line therapy failure. Hypermethylation of CST6 and LAD1 was associated with both a shortened PFS (log rank p = 0.009 and p = 0.004) and OS (p = 0.011 and p = 0.043). The median PFS observed for the high and low methylation groups of CST6 and LAD1 was 2.0 vs.11.4 months. LAD1 methylation had a specificity of 1.0 (95% CI 0.65-1.0) and a sensitivity of 0.73 (95% CI 0.43-0.90) for the prediction of first-line therapy. CST6 and LAD1 methylation are candidate epigenetic biomarkers showing unprecedented association with PFS and OS as well as specificity for the prediction of the response to therapy. DNA methylation markers should be considered for the prospective evaluation of larger patient cohorts in future studies.
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Affiliation(s)
- Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Natalia Dubrowinskaja
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mahmoud Abbas
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Christoph Seidel
- Department of Oncology/Hematology/Bone MarrowTransplantation/Pneumology, University Medical Center Eppendorf, Hamburg, Germany
| | - Michael Kogosov
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Ralph Scherer
- Department of Biometry, Hannover Medical School, Hannover, Germany
| | - Kai Gebauer
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Axel S. Merseburger
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Markus A. Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Viktor Grünwald
- Clinic for Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Germany
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
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Dubrowinskaja N, Gebauer K, Peters I, Hennenlotter J, Abbas M, Scherer R, Tezval H, Merseburger AS, Stenzl A, Grünwald V, Kuczyk MA, Serth J. Neurofilament Heavy polypeptide CpG island methylation associates with prognosis of renal cell carcinoma and prediction of antivascular endothelial growth factor therapy response. Cancer Med 2014; 3:300-9. [PMID: 24464810 PMCID: PMC3987080 DOI: 10.1002/cam4.181] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/29/2013] [Accepted: 11/19/2013] [Indexed: 12/26/2022] Open
Abstract
Neurofilament Heavy polypeptid (NEFH) belongs to the group of type IV intermediate filament proteins. DNA methylation of the NEFH promoter and loss of expression have previously been shown to activate the AKT/β-catenin pathway in tumor cells. When identifying hypermethylation of the NEFH CpG island (CGI) in renal cell cancer (RCC) we asked whether methylation could provide clinical or prognostic information for RCC and/or predict therapy response in patients with metastatic RCC (mRCC) undergoing antiangiogenic therapy. Relative methylation of the NEFH CGI was analyzed in 132 RCC samples and 83 paired normal tissues using quantitative methylation-specific PCR. Results were statistically compared with tumor histology, clinicopathological parameters, progression-free survival (PFS) as well as with overall survival (OS) in a subset of 18 mRCC patients following antiangiogenic therapy regimens. The NEFH CGI methylation demonstrated a tumor-specific increase (P < 0.001), association with advanced disease (P < 0.001), and distant metastasis (P = 0.005). Higher relative methylation was also significantly associated with a poor PFS (HR = 8.6, P < 0.001) independent from the covariates age, gender, diameter of tumors, state of advanced disease, and local and distant metastasis. Median OS following targeted therapy was 29.8 months for patients with low methylation versus 9.8 months for the group with high methylation (P = 0.028). We identified NEFH methylation as a candidate epigenetic marker for prognosis of RCC patients as well as prediction of anti-vascular endothelial growth factor-based therapy response.
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Ma WJ, Zhou Y, Lu D, Dong D, Tian XJ, Wen JX, Zhang J. Reduced expression of Slit2 in renal cell carcinoma. Med Oncol 2013; 31:768. [PMID: 24287947 DOI: 10.1007/s12032-013-0768-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 11/05/2013] [Indexed: 12/22/2022]
Abstract
Slit2, initially identified as an important axon guidance molecule in the nervous system, was suggested to be involved in multiple cellular processes. Recently, Slit2 was reported to function as a potential tumor suppressor in diverse tumors. In this study, we systematically analyzed the expression level of Slit2 in renal cell carcinoma. Compared to paired adjacent non-malignant tissues, both Slit2 mRNA and protein expression were significantly down-regulated in renal cell carcinoma (RCC). Methylation-specific PCR showed that Slit2 promoter was methylated in two renal carcinoma cell lines. Pharmacologic demethylation dramatically induced Slit2 expression in cancer cell lines with weak expression of Slit2. Besides, bisulfite genomic sequencing confirmed that dense methylation existed in Slit2 promoter. Furthermore, in paired RCC samples, Slit2 methylation was observed in 8 out of 38 patients (21.1 %), which was well correlated with the down-regulation of Slit2 in RCC. Therefore, Slit2 may also be a potential tumor suppressor in RCC, which is down-regulated in RCC partially due to promoter methylation.
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Affiliation(s)
- Wei-Jie Ma
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China
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