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Wang J, Jin J, Liang Y, Zhang Y, Wu N, Fan M, Zeng F, Deng F. miR-21-5p/PRKCE axis implicated in immune infiltration and poor prognosis of kidney renal clear cell carcinoma. Front Genet 2022; 13:978840. [PMID: 36186442 PMCID: PMC9516396 DOI: 10.3389/fgene.2022.978840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022] Open
Abstract
Kidney renal clear cell carcinoma (KIRC or ccRCC) is the most notorious subtype of renal cell carcinoma for its poor prognosis. Mounting evidence has highlighted the key role of PRKCE in the initiation and development of several types of human cancer, including kidney renal clear cell carcinoma (KIRC). However, the mechanism of PRKCE aberrant expression and the specific clinical correlation of PRKCE expression with immune cell infiltration in KIRC remains elusive. Therefore, we analyzed the relationship between PRKCE and KIRC using many databases, including Oncomine, TCGA, GTEx, TIMER, and GEO. We found that PRKCE decreased in KIRC tumor tissue compared to normal tissue. The Kaplan-Meier Plotter analysis and Univariate and Multivariate Cox analyses were used to evaluate the association between PRKCE and clinicopathological variables and prognosis. Low PRKCE expression was associated with poor survival and histologic grade, T stage, pathologic stage, and M stage. Besides, the C-indexes and calibration plots of the nomogram based on multivariate analysis showed an effective predictive performance for KIRC patients. In addition, PRKCE may be positively correlated with inflammation and negatively correlated with proliferation, metastasis, and invasion as identified by CancerSEA. Moreover, overexpression of PRKCE suppressed ACHN and Caki-1 cell proliferation, migration, and invasion in vitro. Additionally, methylation level data acquired from UALCAN, DiseaseMeth, CCLE, LinkedOmics, and MEXPRESS was used to investigate the relationship between PRKCE expression and PRKCE methylation level. Furthermore, upstream potential miRNA predictions were further performed to explore the mechanism of PRKCE decreased expression in KIRC using multiple online databases available on publicly assessable bioinformatics platforms. High PRKCE methylation levels and hsa-miR-21-5p may contribute to PRKCE low expression in KIRC. Finally, an analysis of immune infiltration indicated that PRKCE was associated with immune cell infiltration. Importantly, PRKCE may affect prognosis partially by regulating immune infiltration in KIRC. In summary, PRKCE may serve as a novel prognostic biomarker reflecting immune infiltration level and a novel therapeutic target in KIRC.
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Affiliation(s)
- Jinxiang Wang
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jie Jin
- Department of Clinical Laboratory, the Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Yanling Liang
- Department of Clinical Laboratory, the Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
- Department of Clinical Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yihe Zhang
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Nisha Wu
- Department of Clinical Laboratory, the Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Mingming Fan
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Fangyin Zeng
- Department of Clinical Laboratory, the Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Fangyin Zeng, ; Fan Deng,
| | - Fan Deng
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Fangyin Zeng, ; Fan Deng,
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Zhao J, Liang J, Yang Y, Sun G, Zhang X, Zhao J, Hu X, Chen J, Zhu S, Ni Y, Zhang Y, Dai J, Wang Z, Wang Z, Zeng Y, Yao J, Chen N, Shen P, Liu Z, Zeng H. Integrated multi-omics analyses reveal that BCAM is associated with epigenetic modification and tumor microenvironment subtypes of clear cell renal cell carcinoma. Clin Epigenetics 2022; 14:99. [PMID: 35941663 PMCID: PMC9361577 DOI: 10.1186/s13148-022-01319-2] [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: 02/21/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is the most common and highly heterogeneous subtype of renal cell carcinoma. Dysregulated basal cell adhesion molecule (BCAM) gene is associated with poor prognosis in various cancers. However, the dysregulated functions and related multi-omics features of BCAM in ccRCC stay unclear. RESULTS BCAM expression was aberrantly downregulated in ccRCC and correlated with adverse pathological parameters and poor prognosis. Low mRNA expression of BCAM was remarkably associated with its CpG methylation levels and BAP1 mutation status. Patients with lower-expressed BCAM concomitant with BAP1 mutation had a worse prognosis. Using RNA-seq data from The cancer genome atlas, we found that compared to the BCAM-high expression subgroup, ccRCC patients in the BCAM-low expression subgroup had significantly higher levels of immune infiltration, higher immune checkpoint expression levels and lower TIDE (tumor immune dysfunction and exclusion) score, indicating potential better response to immunotherapy. Data from the Clinical Proteomic Tumor Analysis Consortium further validated the association between low BCAM expression and CD8 + inflamed phenotype at protein level. Meanwhile, our results suggested that the angiogenesis-related pathways were enriched in the BCAM-high expression subgroup. More importantly, according to the data from the GDSC database, we revealed that the BCAM-high expression subgroup should be more sensitive to anti-angiogenetic therapies, including sorafenib, pazopanib and axitinib. CONCLUSIONS These results suggest that BCAM could serve as a biomarker distinguishing different tumor microenvironment phenotypes, predicting prognosis and helping therapeutic decision-making for patients with ccRCC.
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Affiliation(s)
- Junjie Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Yang Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Guangxi Sun
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Xingming Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Jinge Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Xu Hu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Junru Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Sha Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Yuchao Ni
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Yaowen Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Jindong Dai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Zhipeng Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Zilin Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Yuhao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Jin Yao
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Ni Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Pengfei Shen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China
| | - Zhenhua Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China.
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu City, 610041, Sichuan Province, People's Republic of China.
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Katzendorn O, Peters I, Dubrowinskaja N, Moog JM, Reese C, Tezval H, Faraj Tabrizi P, Hennenlotter J, Lafos M, Kuczyk MA, Serth J. DNA Methylation in INA, NHLH2, and THBS4 Is Associated with Metastatic Disease in Renal Cell Carcinoma. Cancers (Basel) 2021; 14:cancers14010039. [PMID: 35008203 PMCID: PMC8750163 DOI: 10.3390/cancers14010039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
The detection of DNA methylation in primary tumor tissues could be relevant for early stratification of aggressive renal cell carcinomas (RCCs) as a basis for future personalized adjuvant therapy. Methylated TCGA KIRC based candidate CpG loci in INA, NHLH2, and THBS4 that are possibly associated with RCC metastasis were evaluated by pyrosequencing in 154 paired normal adjacent and primary tumor tissues, as well as in 202 metastatic tissues. Statistical analysis was carried out by bivariate logistic regression for group comparisons, log rank survival analysis, and unsupervised and supervised analysis for the classification of tumors. Increased methylation of INA, NHLH2, and THBS4 loci were significantly associated with distant metastasis in primary tumors (p < 0.05), tissue-specific hypermethylation in metastatic (p = 7.88 × 10-8, 5.57 × 10-10, 2.06 × 10-7) and tumor tissues (p = 3.72 × 10-24, 3.17 × 10-13, 1.58 × 10-19), and shortened progression free survival in patients (p = 0.03). Combined use of CpG site-specific methylation permits the discrimination of tissues with metastatic disease and reveals a significant contribution of CpG sites in all genes to the statistical classification model. Thus, metastasis in RCC is significantly associated with methylation alterations in INA, NHLH2, and THBS4 loci, providing independent information for the potential early detection of aggressive renal cancers as a rationale for stratifying patients to adjuvant therapies.
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Affiliation(s)
- Olga Katzendorn
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Natalia Dubrowinskaja
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Joana M. Moog
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Christel Reese
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Pouriya Faraj Tabrizi
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Jörg Hennenlotter
- Department of Urology, Eberhard Karls University of Tuebingen, 72076 Tuebingen, Germany;
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, 30625 Hannover, Germany;
| | - Markus A. Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany; (O.K.); (I.P.); (N.D.); (J.M.M.); (C.R.); (H.T.); (P.F.T.); (M.A.K.)
- Correspondence: ; Tel.: +49-511-532-6673
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Yao ZY, Xing C, Liu YW, Xing XL. Identification of Two Immune Related Genes Correlated With Aberrant Methylations as Prognosis Signatures for Renal Clear Cell Carcinoma. Front Genet 2021; 12:750997. [PMID: 34925447 PMCID: PMC8674690 DOI: 10.3389/fgene.2021.750997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Almost 75% of renal cancers are renal clear cell carcinomas (KIRC). Accumulative evidence indicates that epigenetic dysregulations are closely related to the development of KIRC. Cancer immunotherapy is an effective treatment for cancers. The aim of this study was to identify immune-related differentially expressed genes (IR-DEGs) associated with aberrant methylations and construct a risk assessment model using these IR-DEGs to predict the prognosis of KIRC. Two IR-DEGs (SLC11A1 and TNFSF14) were identified by differential expression, correlation analysis, and Cox regression analysis, and risk assessment models were established. The area under the receiver operating characteristic (ROC) curve (AUC) was 0.6907. In addition, we found that risk scores were significantly associated with 31 immune cells and factors. Our present study not only shows that two IR-DEGs can be used as prognosis signatures for KIRC, but also provides a strategy for the screening of suitable prognosis signatures associated with aberrant methylation in other cancers.
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Affiliation(s)
- Zhi-Yong Yao
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China.,The First Affiliated Hospital of Hunan University of Medicine, Huaihua, China
| | - Chaoqung Xing
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China
| | - Yuan-Wu Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China
| | - Xiao-Liang Xing
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua, China.,The First Affiliated Hospital of Hunan University of Medicine, Huaihua, China
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5
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Tan P, Chen H, Huang Z, Huang M, Du Y, Li T, Chen Z, Liu Y, Fu W. MMP25-AS1/hsa-miR-10a-5p/SERPINE1 axis as a novel prognostic biomarker associated with immune cell infiltration in KIRC. Mol Ther Oncolytics 2021; 22:307-325. [PMID: 34553021 PMCID: PMC8426181 DOI: 10.1016/j.omto.2021.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/25/2021] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play a significant role in multiple human cancers as competing endogenous RNAs (ceRNAs). However, a systematic mRNA-microRNA (miRNA)-lncRNA network linked to kidney renal clear cell carcinoma (KIRC) prognosis has not been described. In this study, we aimed to identify the prognosis-related ceRNA regulatory network and analyzed its relationship with immune cell infiltration to predict KIRC patient survival. The MMP25-AS1/hsa-miR-10a-5p/SERPINE1 ceRNA network related to the prognosis of KIRC was obtained through bioinformatics analysis based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Meanwhile, we constructed a three-gene-based survival predictor model, which could be referential for future clinical research. Methylation analyses suggested that the abnormal upregulation of the SERPINE1 likely resulted from hypomethylation. Furthermore, the immune infiltration analysis showed that the MMP25-AS1/hsa-miR-10a-5p/SERPINE1 axis could affect the changes in the tumor immune microenvironment and the development of KIRC by affecting the expression of chemokines (CCL4, CCL5, CXCL13, and XCL2). Tumor Immune Dysfunction and Exclusion (TIDE) analysis indicated that the high expression of SERPINE1 might be related to tumor immune evasion in KIRC. In summary, the current study constructing the MMP25-AS1/hsa-miR-10a-5p/SERPINE1 ceRNA network might be a novel significant prognostic factor associated with the diagnosis and prognosis of KIRC.
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Affiliation(s)
- Peng Tan
- Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Hao Chen
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou 646000, China
| | - Zhiwei Huang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou 646000, China
| | - Meizhou Huang
- Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Yichao Du
- Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Tongxi Li
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou 646000, China
| | - Zhongyao Chen
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou 646000, China
| | - Yu Liu
- General Surgery, Xichang People’s Hospital, Xichang 615000, China
| | - Wenguang Fu
- Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, Luzhou 646000, China
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6
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You Y, Ren Y, Liu J, Qu J. Promising Epigenetic Biomarkers Associated With Cancer-Associated-Fibroblasts for Progression of Kidney Renal Clear Cell Carcinoma. Front Genet 2021; 12:736156. [PMID: 34630525 PMCID: PMC8495159 DOI: 10.3389/fgene.2021.736156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/08/2021] [Indexed: 12/24/2022] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is the most common malignant kidney tumor as its characterization of highly metastatic potential. Patients with KIRC are associated with poor clinical outcomes with limited treatment options. Up to date, the underlying molecular mechanisms of KIRC pathogenesis and progression are still poorly understood. Instead, particular features of Cancer-Associated Fibroblasts (CAFs) are highly associated with adverse outcomes of patients with KIRC, while the precise regulatory mechanisms at the epigenetic level of KIRC in governing CAFs remain poorly defined. Therefore, explore the correlations between epigenetic regulation and CAFs infiltration may help us better understand the molecular mechanisms behind KIRC progression, which may improve clinical outcomes and patients quality of life. In the present study, we identified a set of clinically relevant CAFs-related methylation-driven genes, NAT8, TINAG, and SLC17A1 in KIRC. Our comprehensive in silico analysis revealed that the expression levels of NAT8, TINAG, and SLC17A1 are highly associated with outcomes of patients with KIRC. Meanwhile, their methylation levels are highly correlates with the severity of KIRC. We suggest that the biomarkers might contribute to CAFs infiltration in KIRC. Taken together, our study provides a set of promising biomarkers which could predict the progression and prognosis of KIRC. Our findings could have potential prognosis and therapeutic significance in the progression of KIRC.
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Affiliation(s)
- Yongke You
- Department of Nephrology, Shenzhen University General Hospital, Shenzhen, China
| | - Yeping Ren
- Department of Nephrology, Shenzhen University General Hospital, Shenzhen, China
| | - Jikui Liu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jianhua Qu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, China
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Epigenetic Biomarkers of Renal Cell Carcinoma for Liquid Biopsy Tests. Int J Mol Sci 2021; 22:ijms22168846. [PMID: 34445557 PMCID: PMC8396354 DOI: 10.3390/ijms22168846] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
Renal cell carcinomas (RCC) account for 2–3% of the global cancer burden and are characterized by the highest mortality rate among all genitourinary cancers. However, excluding conventional imagining approaches, there are no reliable diagnostic and prognostic tools available for clinical use at present. Liquid biopsies, such as urine, serum, and plasma, contain a significant amount of tumor-derived nucleic acids, which may serve as non-invasive biomarkers that are particularly useful for early cancer detection, follow-up, and personalization of treatment. Changes in epigenetic phenomena, such as DNA methylation level, expression of microRNAs (miRNAs), and long noncoding RNAs (lncRNAs), are observed early during cancer development and are easily detectable in biofluids when morphological changes are still undetermined by conventional diagnostic tools. Here, we reviewed recent advances made in the development of liquid biopsy-derived DNA methylation-, miRNAs- and lncRNAs-based biomarkers for RCC, with an emphasis on the performance characteristics. In the last two decades, a mass of circulating epigenetic biomarkers of RCC were suggested, however, most of the studies done thus far analyzed biomarkers selected from the literature, used relatively miniature, local, and heterogeneous cohorts, and suffered from a lack of sufficient validations. In summary, for improved translation into the clinical setting, there is considerable demand for the validation of the existing pool of RCC biomarkers and the discovery of novel ones with better performance and clinical utility.
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Marques-Magalhães Â, Graça I, Miranda-Gonçalves V, Henrique R, Lopez M, Arimondo PB, Jerónimo C. Anti-neoplastic and demethylating activity of a newly synthetized flavanone-derived compound in Renal Cell Carcinoma cell lines. Biomed Pharmacother 2021; 141:111681. [PMID: 34139552 DOI: 10.1016/j.biopha.2021.111681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Renal Cell Carcinoma (RCC) is on the top 10 of the most incident cancers worldwide, being a third of patients diagnosed with advanced disease, for which no curative therapies are currently available. Thus, new effective therapeutic strategies are urgently needed. Herein, we tested the antineoplastic effect of newly synthesized 3-nitroflavanones (MLo1302) on RCC cell lines. 786-O, Caki2, and ACHN cell lines were cultured and treated with newly synthesized 3-nitroflavanones. IC50 values were calculated based on the effect on cell viability assessed by MTT assay, after 72 h of exposure. MLo1302 displayed antineoplastic properties in RCC cell lines through marked reduction of cell viability, increased apoptosis and DNA damage, and morphometric alterations indicating a less aggressive phenotype. MLo1302 induced a significant reduction of global DNA methylation and DNMT mRNA levels, increasing global DNA hydroxymethylation and TET expression. Moreover, MLo1302 decreased DNMT3A activity in RCC cell lines, demethylated and re-expressed hypermethylated genes in CAM-generated tumors. A marked in vivo decrease in tumor growth and angiogenesis was also disclosed. MLo1302 disclosed antineoplastic and demethylating activity in RCC cell lines, constituting a potential therapeutic agent for RCC patients.
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Affiliation(s)
- Ângela Marques-Magalhães
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Inês Graça
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal
| | - Vera Miranda-Gonçalves
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal
| | - Marie Lopez
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Université de Montpellier, ENSCM UMR 5247, Montpellier 34296, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR3523, Paris 75724, France
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto 4200-072, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal.
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9
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Miao Y, Cao F, Li P, Liu P. DNA methylation of Hugl-2 is a prognostic biomarker in kidney renal clear cell carcinoma. Clin Exp Pharmacol Physiol 2021; 48:44-53. [PMID: 32754907 PMCID: PMC7821335 DOI: 10.1111/1440-1681.13390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 01/13/2023]
Abstract
It has been reported that loss of Hugl-2 contributes to tumour formation and progression in vitro and in vivo. However, whether Hugl-2 levels decrease during kidney renal clear cell carcinoma (KIRC) and the mechanism involved remain unknown. This study aimed to investigate whether DNA methylation of Hugl-2 reduces its expression, leading to the progression and poor prognosis of KIRC. Hugl-2 methylation and mRNA expression and KIRC clinicopathological data were extracted from The Cancer Genome Atlas (TCGA), and relationships among these factors were analyzed using UALCAN, MethHC, Wanderer and LinkedOmics web tools. We found that Hugl-2 mRNA and protein levels were reduced in KIRC tissues. Moreover, Hugl-2 mRNA levels were related to tumour grade and overall survival, and Hugl-2 methylation was increased in KIRC. According to the results of methylation-specific PCR, KIRC cells had higher Hugl-2 DNA methylation levels than HKC cells. Moreover, Hugl-2 DNA methylation correlated negatively with Hugl-2 mRNA and was also related to the pathology and T stage of KIRC patients. KIRC patients with high Hugl-2 DNA methylation also had shorter overall survival. Additionally, methylation of cg08827674, a Hugl-2 probe, was related to pathologic stage, T stage, neoplasm histologic grade, serum calcium level without laterality, M stage, N stage, and ethnicity. Furthermore, treatment with the DNA methylation inhibitor decitabine resulted in upregulation of Hugl-2 mRNA and protein levels in KIRC cell lines. These results indicate that Hugl-2 DNA methylation may be both a prognostic marker and a therapeutic target in KIRC.
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Affiliation(s)
- Yi Miao
- Center for Translational MedicineThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
- Key Laboratory for Tumor Precision Medicine of Shaanxi ProvinceThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
| | - Fang Cao
- Center for Translational MedicineThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
- Key Laboratory for Tumor Precision Medicine of Shaanxi ProvinceThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
| | - Pingping Li
- Center for Translational MedicineThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
- Key Laboratory for Tumor Precision Medicine of Shaanxi ProvinceThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
| | - Peijun Liu
- Center for Translational MedicineThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
- Key Laboratory for Tumor Precision Medicine of Shaanxi ProvinceThe First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
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10
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Andersson-Evelönn E, Vidman L, Källberg D, Landfors M, Liu X, Ljungberg B, Hultdin M, Rydén P, Degerman S. Combining epigenetic and clinicopathological variables improves specificity in prognostic prediction in clear cell renal cell carcinoma. J Transl Med 2020; 18:435. [PMID: 33187526 PMCID: PMC7666468 DOI: 10.1186/s12967-020-02608-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 11/05/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Metastasized clear cell renal cell carcinoma (ccRCC) is associated with a poor prognosis. Almost one-third of patients with non-metastatic tumors at diagnosis will later progress with metastatic disease. These patients need to be identified already at diagnosis, to undertake closer follow up and/or adjuvant treatment. Today, clinicopathological variables are used to risk classify patients, but molecular biomarkers are needed to improve risk classification to identify the high-risk patients which will benefit most from modern adjuvant therapies. Interestingly, DNA methylation profiling has emerged as a promising prognostic biomarker in ccRCC. This study aimed to derive a model for prediction of tumor progression after nephrectomy in non-metastatic ccRCC by combining DNA methylation profiling with clinicopathological variables. METHODS A novel cluster analysis approach (Directed Cluster Analysis) was used to identify molecular biomarkers from genome-wide methylation array data. These novel DNA methylation biomarkers, together with previously identified CpG-site biomarkers and clinicopathological variables, were used to derive predictive classifiers for tumor progression. RESULTS The "triple classifier" which included both novel and previously identified DNA methylation biomarkers together with clinicopathological variables predicted tumor progression more accurately than the currently used Mayo scoring system, by increasing the specificity from 50% in Mayo to 64% in our triple classifier at 85% fixed sensitivity. The cumulative incidence of progress (pCIP5yr) was 7.5% in low-risk vs 44.7% in high-risk in M0 patients classified by the triple classifier at diagnosis. CONCLUSIONS The triple classifier panel that combines clinicopathological variables with genome-wide methylation data has the potential to improve specificity in prognosis prediction for patients with non-metastatic ccRCC.
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Affiliation(s)
| | - Linda Vidman
- Department of Mathematics and Mathematical Statistics, Umeå University, 901 87, Umeå, Sweden
| | - David Källberg
- Department of Mathematics and Mathematical Statistics, Umeå University, 901 87, Umeå, Sweden.,Department of Statistics, USBE, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, 901 87, Umeå, Sweden
| | - Xijia Liu
- Department of Mathematics and Mathematical Statistics, Umeå University, 901 87, Umeå, Sweden
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, 901 87, Umeå, Sweden
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, 901 87, Umeå, Sweden.
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, 901 87, Umeå, Sweden. .,Department of Clinical Microbiology, Umeå University, Umeå, Sweden.
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11
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12
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Reustle A, Di Marco M, Meyerhoff C, Nelde A, Walz JS, Winter S, Kandabarau S, Büttner F, Haag M, Backert L, Kowalewski DJ, Rausch S, Hennenlotter J, Stühler V, Scharpf M, Fend F, Stenzl A, Rammensee HG, Bedke J, Stevanović S, Schwab M, Schaeffeler E. Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy. Genome Med 2020; 12:32. [PMID: 32228647 PMCID: PMC7106651 DOI: 10.1186/s13073-020-00731-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy. Methods We analyzed HLA-presented peptides by MS-based ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues, and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate targets with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from The Cancer Genome Atlas (TCGA KIRC, n = 452). DNA methylation (TCGA KIRC, n = 273), somatic mutations (TCGA KIRC, n = 392), and gene ontology (GO) and correlations with tumor metabolites (cohort 1, n = 30) and immune-oncological markers (cohort 1, n = 37) were analyzed to characterize regulatory and functional involvements. CD8+ T cell priming assays were used to identify immunogenic peptides. The candidate gene EGLN3 was functionally investigated in cell culture. Results A total of 34,226 HLA class I- and 19,325 class II-presented peptides were identified in ccRCC tissue, of which 443 class I and 203 class II peptides were ccRCC-specific and presented in ≥ 3 tumors. One hundred eighty-five of the 499 corresponding source genes were involved in pathways activated by ccRCC tumors. After validation in the independent cohort from TCGA, 113 final candidate genes remained. Candidates were involved in extracellular matrix organization, hypoxic signaling, immune processes, and others. Nine of the 12 peptides assessed by immunogenicity analysis were able to activate naïve CD8+ T cells, including peptides derived from EGLN3. Functional analysis of EGLN3 revealed possible tumor-promoting functions. Conclusions Integration of HLA ligandomics, transcriptomics, genetic, and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is recommended to expand the treatment landscape of ccRCC.
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Affiliation(s)
- Anna Reustle
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Carolin Meyerhoff
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Siahei Kandabarau
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Florian Büttner
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Daniel J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Steffen Rausch
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Viktoria Stühler
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Marcus Scharpf
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Jens Bedke
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany. .,University of Tuebingen, Tuebingen, Germany. .,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany. .,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany. .,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany.
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
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13
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Peters I, Merseburger AS, Tezval H, Lafos M, Tabrizi PF, Mazdak M, Wolters M, Kuczyk MA, Serth J, von Klot CA. The Prognostic Value of DNA Methylation Markers in Renal Cell Cancer: A Systematic Review. KIDNEY CANCER 2020. [DOI: 10.3233/kca-190069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | | | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Pouriya Faraj Tabrizi
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mehrdad Mazdak
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mathias Wolters
- 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
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
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14
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Singh NP, Vinod PK. Integrative analysis of DNA methylation and gene expression in papillary renal cell carcinoma. Mol Genet Genomics 2020; 295:807-824. [PMID: 32185457 DOI: 10.1007/s00438-020-01664-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Patterns of DNA methylation are significantly altered in cancers. Interpreting the functional consequences of DNA methylation requires the integration of multiple forms of data. The recent advancement in the next-generation sequencing can help to decode this relationship and in biomarker discovery. In this study, we investigated the methylation patterns of papillary renal cell carcinoma (PRCC) and its relationship with the gene expression using The Cancer Genome Atlas (TCGA) multi-omics data. We found that the promoter and body of tumor suppressor genes, microRNAs and gene clusters and families, including cadherins, protocadherins, claudins and collagens, are hypermethylated in PRCC. Hypomethylated genes in PRCC are associated with the immune function. The gene expression of several novel candidate genes, including interleukin receptor IL17RE and immune checkpoint genes HHLA2, SIRPA and HAVCR2, shows a significant correlation with DNA methylation. We also developed machine learning models using features extracted from single and multi-omics data to distinguish early and late stages of PRCC. A comparative study of different feature selection algorithms, predictive models, data integration techniques and representations of methylation data was performed. Integration of both gene expression and DNA methylation features improved the performance of models in distinguishing tumor stages. In summary, our study identifies PRCC driver genes and proposes predictive models based on both DNA methylation and gene expression. These results on PRCC will aid in targeted experiments and provide a strategy to improve the classification accuracy of tumor stages.
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Affiliation(s)
- Noor Pratap Singh
- Center for Computational Natural Sciences and Bioinformatics, IIIT Hyderabad, Hyderabad, 500032, India
| | - P K Vinod
- Center for Computational Natural Sciences and Bioinformatics, IIIT Hyderabad, Hyderabad, 500032, India.
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15
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Zhang W, Han Y, Li W, Cao L, Yan L, Qin C, Gao R. Clinical data analysis reveals the role of OGR1 (GPR68) in head and neck squamous cancer. Animal Model Exp Med 2020; 3:55-61. [PMID: 32318660 PMCID: PMC7167242 DOI: 10.1002/ame2.12105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/13/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Head and neck squamous cancer (HNSC) frequently occurs in the clinic. Revealing the role of the genes that correlate with cancer cell outgrowth will contribute to potential treatment target identification and tumor inhibition. METHODS The gene expression profiles and gene ontology of the proton-sensing G-protein-coupled receptor OGR1 were analyzed using the TCGA (The Cancer Genome Atlas) database. The effects of sex, age, race, and degree of malignancy on HNSC were investigated, and the survival times of HNSC patients with high or low/medium expression levels of OGR1 were compared. Methylation of the OGR1 promoter CpG sites was also investigated and OGR1-related genes were analyzed using gene set enrichment analysis. RESULTS OGR1 is overexpressed in HNSC patients. However, compared with the low/median expression group, the high OGR1 expression group did not have different survival rates. The OGR1 expression level differed across sex, age, race, and degree of malignancy, while the methylation of the OGR1 promoter CpG sites was maintained at a similar level. Gene set enrichment analysis revealed that OGR1 was positively correlated with head and neck cancer, cisplatin resistance, hypoxia, angiogenesis, cell migration, and TGF-β. CONCLUSION The expression of OGR1 correlated with HNSC progression and survival and thus can serve as a potential treatment target and prognostic marker.
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Affiliation(s)
- Wenlong Zhang
- Key Laboratory of Human Disease Comparative Medicine (National Health and Family Planning Commission)The Institute of Laboratory Animal ScienceChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingP.R. China
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijingP.R. China
| | - Yong Han
- Department of PathologyZhejiang Provincial People’s HospitalHangzhouZhejiangP.R. China
- People’s Hospital of Hangzhou Medical CollegeHangzhouZhejiangP.R. China
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang ProvinceHangzhouZhejiangP.R. China
| | - Weisha Li
- Key Laboratory of Human Disease Comparative Medicine (National Health and Family Planning Commission)The Institute of Laboratory Animal ScienceChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingP.R. China
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijingP.R. China
| | - Lin Cao
- Key Laboratory of Human Disease Comparative Medicine (National Health and Family Planning Commission)The Institute of Laboratory Animal ScienceChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingP.R. China
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijingP.R. China
| | - Libo Yan
- Key Laboratory of Human Disease Comparative Medicine (National Health and Family Planning Commission)The Institute of Laboratory Animal ScienceChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingP.R. China
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijingP.R. China
| | - Chuan Qin
- Key Laboratory of Human Disease Comparative Medicine (National Health and Family Planning Commission)The Institute of Laboratory Animal ScienceChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingP.R. China
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijingP.R. China
| | - Ran Gao
- Key Laboratory of Human Disease Comparative Medicine (National Health and Family Planning Commission)The Institute of Laboratory Animal ScienceChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingP.R. China
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijingP.R. China
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16
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Tan Y, Li B, Peng F, Gong G, Li N. Integrative Analysis of Sirtuins and Their Prognostic Significance in Clear Cell Renal Cell Carcinoma. Front Oncol 2020; 10:218. [PMID: 32158696 PMCID: PMC7052292 DOI: 10.3389/fonc.2020.00218] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/07/2020] [Indexed: 11/26/2022] Open
Abstract
Sirtuins, class III histone deacetylases, are involved in multiple biological processes in cancer initiation and progression. However, the diverse expression patterns and prognostic values of sirtuins in cancers have yet to be elucidated. In this study, we first evaluated the expression and prognostic values of sirtuins in multiple cancer cohorts using publicly available TCGA pan-cancer datasets. Pan-cancer survival analysis indicated that 6 out of 7 sirtuin family members were significant associated with prognosis of clear cell renal cell carcinoma (KIRC) patients. SIRT1, SIRT3, SIRT4, and SIRT5 were associated with favorable prognosis of KIRC patients, while SIRT6 and SIRT7 were associated with unfavorable prognosis. The expression levels of SIRT4 and SIRT5 in KIRC tissues were lower than that in normal tissues, while SIRT6 and SIRT7 were higher in KIRC tissues. The expression levels of SIRT1, SIRT3, SIRT5, SIRT6, and SIRT7 were significantly correlated with tumor stage and histological grade. DNA methylation may contribute to the dysregulation of sirtuins. Finally, GSEA was conducted to predict the potential functions of sirtuins in KIRC. Our results may provide novel insights for the development of sirtuins-based cancer therapy in KIRC.
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Affiliation(s)
- Ying Tan
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China
| | - Bijuan Li
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China
| | - Fang Peng
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China
| | - Guanghui Gong
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Ning Li
- Department of Blood Transfusion, Xiangya Hospital, Central South University, Changsha, China
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17
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Li P, Liu J, Li J, Liu P. DNA methylation of CRB3 is a prognostic biomarker in clear cell renal cell carcinoma. Mol Biol Rep 2019; 46:4377-4383. [PMID: 31147860 DOI: 10.1007/s11033-019-04892-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/17/2019] [Indexed: 02/06/2023]
Abstract
Our previous study revealed that CRB3 protein expression was reduced in clear cell renal cell carcinoma (ccRCC) and was associated with TNM stage, pathological grade, and poor prognosis of ccRCC. This study aimed to investigate if DNA methylation of CRB3 decreases its expression, subsequently leading to the progression and poor prognosis of ccRCC. Data for DNA methylation of CRB3, CRB3 mRNA expression, and ccRCC clinicopathological parameters were extracted from the cancer genome atlas (TCGA) database. The relationships among DNA methylation of CRB3, CRB3 mRNA expression, and ccRCC clinicopathological parameters were analyzed using UALCAN, MethHC, LinkedOmics, and Wanderer. We found that CRB3 mRNA levels were lower in ccRCC compared to normal tissues. Methylation of CRB3 increased in ccRCC, with all probes showing differences between ccRCC and normal tissues. Furthermore, CRB3 DNA methylation negatively correlated with CRB3 mRNA expression. CRB3 DNA methylation was also related to pathologic stage, T stage, N stage, and M stage of ccRCC. Overall survival was shorter in ccRCC patients with high CRB3 DNA methylation compared to ccRCC patients with low CRB3 DNA methylation. Methylation of cg24798010, a CRB3 probe, was related to laterality, pathologic stage, T stage, M stage, neoplasm-histologic-grade without N stage, and race. Furthermore, treatment with the DNA methylation inhibitor Decitabine resulted in the upregulation of CRB3 mRNA in ccRCC cell lines. These results indicate that DNA methylation of CRB3 may be both a prognostic marker and therapeutic target for ccRCC.
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Affiliation(s)
- Pingping Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jie Liu
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Juan Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Peijun Liu
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China. .,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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18
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Evelönn EA, Landfors M, Haider Z, Köhn L, Ljungberg B, Roos G, Degerman S. DNA methylation associates with survival in non-metastatic clear cell renal cell carcinoma. BMC Cancer 2019; 19:65. [PMID: 30642274 PMCID: PMC6332661 DOI: 10.1186/s12885-019-5291-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/07/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is the most common subtype among renal cancer and is associated with poor prognosis if metastasized. Up to one third of patients with local disease at diagnosis will develop metastasis after nephrectomy, and there is a need for new molecular markers to identify patients with high risk of tumor progression. In the present study, we performed genome-wide promoter DNA methylation analysis at diagnosis to identify DNA methylation profiles associated with risk for progress. METHOD Diagnostic tissue samples from 115 ccRCC patients were analysed by Illumina HumanMethylation450K arrays and methylation status of 155,931 promoter associated CpGs were related to genetic aberrations, gene expression and clinicopathological parameters. RESULTS The ccRCC samples separated into two clusters (cluster A/B) based on genome-wide promoter methylation status. The samples in these clusters differed in tumor diameter (p < 0.001), TNM stage (p < 0.001), morphological grade (p < 0.001), and patients outcome (5 year cancer specific survival (pCSS5yr) p < 0.001 and cumulative incidence of progress (pCIP5yr) p < 0.001. An integrated genomic and epigenomic analysis in the ccRCCs, revealed significant correlations between the total number of genetic aberrations and total number of hypermethylated CpGs (R = 0.435, p < 0.001), and predicted mitotic age (R = 0.407, p < 0.001). We identified a promoter methylation classifier (PMC) panel consisting of 172 differently methylated CpGs accompanying progress of disease. Classifying non-metastatic patients using the PMC panel showed that PMC high tumors had a worse prognosis compared with the PMC low tumors (pCIP5yr 38% vs. 8%, p = 0.001), which was confirmed in non-metastatic ccRCCs in the publically available TCGA-KIRC dataset (pCIP5yr 39% vs. 16%, p < 0.001). CONCLUSION DNA methylation analysis at diagnosis in ccRCC has the potential to improve outcome-prediction in non-metastatic patients at diagnosis.
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Affiliation(s)
- Emma Andersson Evelönn
- Department of Medical Biosciences, Umeå University, NUS, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Umeå University, NUS, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Zahra Haider
- Department of Medical Biosciences, Umeå University, NUS, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Linda Köhn
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and andrology, Umeå University, Umeå, Sweden
| | - Göran Roos
- Department of Medical Biosciences, Umeå University, NUS, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Umeå University, NUS, Blg 6M, 2nd floor, SE-90185 Umeå, Sweden
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19
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20
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Marques-Magalhães Â, Graça I, Henrique R, Jerónimo C. Targeting DNA Methyltranferases in Urological Tumors. Front Pharmacol 2018; 9:366. [PMID: 29706891 PMCID: PMC5909196 DOI: 10.3389/fphar.2018.00366] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/28/2018] [Indexed: 12/14/2022] Open
Abstract
Urological cancers are a heterogeneous group of malignancies accounting for a considerable proportion of cancer-related morbidity and mortality worldwide. Aberrant epigenetic traits, especially altered DNA methylation patterns constitute a hallmark of these tumors. Nonetheless, these alterations are reversible, and several efforts have been carried out to design and test several epigenetic compounds that might reprogram tumor cell phenotype back to a normal state. Indeed, several DNMT inhibitors are currently under evaluation for therapeutic efficacy in clinical trials. This review highlights the critical role of DNA methylation in urological cancers and summarizes the available data on pre-clinical assays and clinical trials with DNMT inhibitors in bladder, kidney, prostate, and testicular germ cell cancers.
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Affiliation(s)
- Ângela Marques-Magalhães
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Inês Graça
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
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21
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Modhukur V, Iljasenko T, Metsalu T, Lokk K, Laisk-Podar T, Vilo J. MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data. Epigenomics 2018; 10:277-288. [DOI: 10.2217/epi-2017-0118] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: To develop a web tool for survival analysis based on CpG methylation patterns. Materials & methods: We utilized methylome data from ‘The Cancer Genome Atlas’ and used the Cox proportional-hazards model to develop an interactive web interface for survival analysis. Results: MethSurv enables survival analysis for a CpG located in or around the proximity of a query gene. For further mining, cluster analysis for a query gene to associate methylation patterns with clinical characteristics and browsing of top biomarkers for each cancer type are provided. MethSurv includes 7358 methylomes from 25 different human cancers. Conclusion: The MethSurv tool is a valuable platform for the researchers without programming skills to perform the initial assessment of methylation-based cancer biomarkers.
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Affiliation(s)
| | - Tatjana Iljasenko
- Institute of Computer Science, University of Tartu, 50409 Tartu, Estonia
| | - Tauno Metsalu
- Institute of Computer Science, University of Tartu, 50409 Tartu, Estonia
| | - Kaie Lokk
- United Laboratories of Tartu University Hospital, Tartu University Hospital, 50406 Tartu, Estonia
| | - Triin Laisk-Podar
- Competence Centre on Health Technologies, 50410 Tartu, Estonia
- Women's Clinic, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, 50409 Tartu, Estonia
- Health Data Analytics, Software Technologies & Applications Competence Center STACC, Ülikooli 2, 51003 Tartu, Estonia
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22
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Chopra S, Liu J, Alemozaffar M, Nichols PW, Aron M, Weisenberger DJ, Collings CK, Syan S, Hu B, Desai M, Aron M, Duddalwar V, Gill I, Liang G, Siegmund KD. Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers. Oncotarget 2018; 8:5439-5448. [PMID: 27690297 PMCID: PMC5354921 DOI: 10.18632/oncotarget.12276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/20/2016] [Indexed: 01/17/2023] Open
Abstract
Purpose The clinical management of small renal masses (SRMs) is challenging since the current methods for distinguishing between benign masses and malignant renal cell carcinomas (RCCs) are frequently inaccurate or inconclusive. In addition, renal cancer subtypes also have different treatments and outcomes. High false negative rates increase the risk of cancer progression and indeterminate diagnoses result in unnecessary and potentially morbid surgical procedures. Experimental Design We built a predictive classification model for kidney tumors using 697 DNA methylation profiles from six different subgroups: clear cell, papillary and chromophobe RCC, benign angiomylolipomas, oncocytomas, and normal kidney tissues. Furthermore, the DNA methylation-dependent classifier has been validated in 272 ex vivo needle biopsy samples from 100 renal masses (71% SRMs). Results In general, the results were highly reproducible (89%, n=70) in predicting identical malignant subtypes from biopsies. Overall, 98% of adjacent-normals (n=102) were correctly classified as normal, while 92% of tumors (n=71) were correctly classified malignant and 86% of benign (n=29) were correctly classified benign by this classification model. Conclusions Overall, this study provides molecular-based support for using routine needle biopsies to determine tumor classification of SRMs and support the clinical decision-making.
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Affiliation(s)
- Sameer Chopra
- Department of Urology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jie Liu
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mehrdad Alemozaffar
- Department of Urology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peter W Nichols
- Department of Pathology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Manju Aron
- Department of Pathology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Clayton K Collings
- Department of Urology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sumeet Syan
- Department of Urology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brian Hu
- Department of Urology, Loma Linda University, Loma Linda, CA, USA
| | - Mihir Desai
- Department of Urology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Monish Aron
- Department of Urology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Vinay Duddalwar
- Department of Radiology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Inderbir Gill
- Department of Urology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kimberly D Siegmund
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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23
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Wang L, Cui Y, Sheng J, Yang Y, Kuang G, Fan Y, Jin J, Zhang Q. Epigenetic inactivation of HOXA11, a novel functional tumor suppressor for renal cell carcinoma, is associated with RCC TNM classification. Oncotarget 2017; 8:21861-21870. [PMID: 28423531 PMCID: PMC5400629 DOI: 10.18632/oncotarget.15668] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/16/2017] [Indexed: 11/25/2022] Open
Abstract
Epigenetic inactivation of HOXA11, a putative tumor suppressor, is frequently observed in a number of solid tumors, but has not been described in RCC (renal cell carcinoma). In this study, we investigated the expression, epigenetic changes and the function of HOXA11 in human renal cell carcinoma (RCC). HOXA11 was silenced or down-regulated in RCC cell lines and tissues. Methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS) revealed that the HOXA11 promoter was hypermethylated in 5/6 RCC cell lines. Demethylation treatment resulted in demethylation of the promoter and increased HOXA11 expression in these cell lines. HOXA11 methylation was also detected in 68/95 (70.5%) primary RCC tumors, but only rare adjacent non-malignant renal tissues (13%, 3/23) showed hypermethylation of promoter. We also found that the methylation of HOXA11 was associated with higher TNM classification of RCC (p<0.05). Ectopic expression of HOXA11 led to significant inhibition of proliferation, colony formation, migration and invasion abilities and induced RCC cells apoptosis. Moreover, HOXA11 was found to inhibit Wnt signaling. Thus, our study demonstrated that HOXA11 function as a tumor suppressor in RCC, while it is frequently silenced by promoter methylation in RCC.
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Affiliation(s)
- Lu Wang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China.,Department of Urology, National Urological Cancer Center, Peking University First Hospital, Beijing 100034, China
| | - Yun Cui
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Jindong Sheng
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Yang Yang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Guanyu Kuang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Yu Fan
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China.,Department of Urology, National Research Center for Genitourinary Oncology, Peking University First Hospital, Beijing 100034, China
| | - Jie Jin
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
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24
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Epigenome Aberrations: Emerging Driving Factors of the Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2017; 18:ijms18081774. [PMID: 28812986 PMCID: PMC5578163 DOI: 10.3390/ijms18081774] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/29/2017] [Accepted: 08/12/2017] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC. Although VHL mutations are considered as drivers of ccRCC, they are not sufficient to cause the disease. Recent genome-wide sequencing studies of ccRCC have revealed that mutations of genes coding for epigenome modifiers and chromatin remodelers, including PBRM1, SETD2 and BAP1, are the most common somatic genetic abnormalities after VHL mutations in these tumors. Moreover, recent research has shed light on the extent of abnormal epigenome alterations in ccRCC tumors, including aberrant DNA methylation patterns, abnormal histone modifications and deregulated expression of non-coding RNAs. In this review, we discuss the epigenetic modifiers that are commonly mutated in ccRCC, and our growing knowledge of the cellular processes that are impacted by them. Furthermore, we explore new avenues for developing therapeutic approaches based on our knowledge of epigenome aberrations of ccRCC.
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25
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Joosten SC, Deckers IA, Aarts MJ, Hoeben A, van Roermund JG, Smits KM, Melotte V, van Engeland M, Tjan-Heijnen VC. Prognostic DNA methylation markers for renal cell carcinoma: a systematic review. Epigenomics 2017; 9:1243-1257. [PMID: 28803494 DOI: 10.2217/epi-2017-0040] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM Despite numerous published prognostic methylation markers for renal cell carcinoma (RCC), none of these have yet changed patient management. Our aim is to systematically review and evaluate the literature on prognostic DNA methylation markers for RCC. MATERIALS & METHODS We conducted an exhaustive search of PubMed, EMBASE and MEDLINE up to April 2017 and identified 49 publications. Studies were reviewed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, assessed for their reporting quality using the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) criteria, and were graded to determine the level of evidence (LOE) for each biomarker. RESULTS We identified promoter methylation of BNC1, SCUBE3, GATA5, SFRP1, GREM1, RASSF1A, PCDH8, LAD1 and NEFH as promising prognostic markers. Extensive methodological heterogeneity across the included studies was observed, which hampers comparability and reproducibility of results, providing a possible explanation why these biomarkers do not reach the clinic. CONCLUSION Potential prognostic methylation markers for RCC have been identified, but they require further validation in prospective studies to determine their true clinical value.
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Affiliation(s)
- Sophie C Joosten
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Ivette Ag Deckers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Maureen J Aarts
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Ann Hoeben
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Joep G van Roermund
- Department of Urology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M Smits
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands.,Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Vivianne C Tjan-Heijnen
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
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26
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Zhang G, Xu Z, Wang N. Network of microRNA, transcription factors, target genes and host genes in human mesothelioma. Exp Ther Med 2017; 13:3039-3046. [PMID: 28587377 DOI: 10.3892/etm.2017.4296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/16/2016] [Indexed: 12/15/2022] Open
Abstract
Significant progress has been made into the elucidation of the etiology of mesothelioma at the level of the genes and miRNA. Nevertheless, researchers in this field remain unable to systematically construct a network that demonstrates the specific relationships between genes, miRNA and transcription factors (TFs). TFs are key regulatory elements that control gene expression. In the present study, according to the transcriptional regulatory rule, three regulatory networks were constructed using experimentally validated elements to explore the pathogenesis of mesothelioma. We focused on the regulatory relationship between the miRNA and its host gene, the miRNA and its target gene, and the miRNA and TFs. Expressed, related and global networks were constructed, and the similarities and differences between them were analyzed. Notably, the differentially expressed network used in the present study, which was based on experimentally validated data, contained numerous incorrect expression signal pathways for the pathogenesis of mesothelioma. In theory, if these errors are corrected, this cancer may be prevented or cured. Subsequent analysis of the differentially expressed nodes and pathways may help to explain the pathogenesis of mesothelioma. Notably, some of these exhibited a self-adaption relationship, which was detected by listing the upstream and downstream elements in a table with differentially expressed genes and miRNA. The findings of the present study demonstrated detailed transcriptional regulation, which may serve as a reference to aid further elucidation of the pathogenesis of mesothelioma.
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Affiliation(s)
- Guanhua Zhang
- Department of Software Engineering, Jilin University, Changchun, Jilin 130012, P.R. China.,Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Zhiwen Xu
- Department of Software Engineering, Jilin University, Changchun, Jilin 130012, P.R. China.,Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin 130012, P.R. China.,Department of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Ning Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin 130012, P.R. China.,Department of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, P.R. China
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27
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Abstract
The majority of kidney cancers are associated with mutations in the von Hippel-Lindau gene and a small proportion are associated with infrequent mutations in other well characterized tumour-suppressor genes. In the past 15 years, efforts to uncover other key genes involved in renal cancer have identified many genes that are dysregulated or silenced via epigenetic mechanisms, mainly through methylation of promoter CpG islands or dysregulation of specific microRNAs. In addition, the advent of next-generation sequencing has led to the identification of several novel genes that are mutated in renal cancer, such as PBRM1, BAP1 and SETD2, which are all involved in histone modification and nucleosome and chromatin remodelling. In this Review, we discuss how altered DNA methylation, microRNA dysregulation and mutations in histone-modifying enzymes disrupt cellular pathways in renal cancers.
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Affiliation(s)
- Mark R Morris
- Brain Tumour Research Centre, Wolverhampton School of Sciences, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Farida Latif
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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28
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Xin J, Xu R, Lin S, Xin M, Cai W, Zhou J, Fu C, Zhen G, Lai J, Li Y, Zhang P. Clinical potential of TCF21 methylation in the diagnosis of renal cell carcinoma. Oncol Lett 2016; 12:1265-1270. [PMID: 27446425 PMCID: PMC4950740 DOI: 10.3892/ol.2016.4748] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/24/2016] [Indexed: 01/06/2023] Open
Abstract
The aim of the present study was to investigate the clinical potential of transcription factor (TCF) 21 methylation in the diagnosis of renal cell carcinoma (RCC). TCF21 methylation levels were quantified in renal tissues (55 cases of RCC tissue and 22 cases of normal tissue) and urine samples (33 cases of urine samples with RCC and 15 cases of normal urine samples) using pyrosequencing. Spearman's rank correlation coefficient was used to investigate the correlation between TCF21 methylation levels and clinical parameters (gender, age, smoking history, Fuhrman grade and clinical stage). The receiver operating characteristic (ROC) curve was utilized to evaluate the accuracy of predictive diagnosis of RCC. TCF21 methylation levels were significantly increased in RCC samples compared with normal renal tissues and urine samples. The Spearman's correlation analysis revealed that the TCF21 methylation level was positively associated with age (P=0.002), smoking (P=0.017) and Fuhrman grade (P=0.045) in RCC tissues and was positively associated with tumor size (P<0.001), Fuhrman grade (P=0.017) and clinical stage (P=0.017) in urine samples. ROC curves revealed that the cut-off value, sensitivity and specificity were 23.61, 89.00 and 61.90%, respectively in tissue samples, and 26.84, 79 and 100%, respectively in urine samples. Furthermore, there were significant differences in the area under the curve between the tissue and urine samples (P=0.004). The results of the present study indicate that TCF21 may be used as a biomarker for diagnosing RCC, and TCF21 methylation levels in urine samples may be a useful means of diagnosing RCC.
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Affiliation(s)
- Jun Xin
- Department of Urology, The First Hospital of Quanzhou Affiliated Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Rong Xu
- Department of Pharmacy, Quanzhou Medical College, Quanzhou, Fujian 362011, P.R. China
| | - Shaokun Lin
- Department of Urology, The First Hospital of Quanzhou Affiliated Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Minghua Xin
- Department of Urology, The First Hospital of Quanzhou Affiliated Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Wenjie Cai
- Department of Urology, The First Hospital of Quanzhou Affiliated Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Jin Zhou
- Department of Urology, The First Hospital of Quanzhou Affiliated Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Changde Fu
- Department of Urology, The First Hospital of Quanzhou Affiliated Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Guangfu Zhen
- Department of Urology, General Hospital of the People's Liberation Army, Beijing 100853, P.R. China
| | - Jinjin Lai
- Department of Urology, The First Hospital of Quanzhou Affiliated Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Yue Li
- Xiamen Xinchuang Bio-Technology Co. Ltd, Xiamen, Fujian 361021, P.R. China
| | - Pengfeng Zhang
- Xiamen Xinchuang Bio-Technology Co. Ltd, Xiamen, Fujian 361021, P.R. China
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29
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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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30
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Specific genomic aberrations predict survival, but low mutation rate in cancer hot spots, in clear cell renal cell carcinoma. Appl Immunohistochem Mol Morphol 2016; 23:334-42. [PMID: 24992170 PMCID: PMC4431677 DOI: 10.1097/pai.0000000000000087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Supplemental Digital Content is available in the text. Detailed genetic profiling of clear cell renal cell carcinoma (ccRCC) has revealed genomic regions commonly affected by structural changes and a general genetic heterogeneity. VHL and PBRM1, both located at chromosome 3p, are 2 major genes mutated at high frequency but apart from these aberrations, the mutational landscape in ccRCC is largely undefined. Potential prognostic information given by the genomic changes appears to depend on the particular cohort studied. We analyzed a Swedish ccRCC cohort of 74 patients and found common changes (loss or gain occurring in >20% of the tumors) in 12 chromosomal regions (1p, 3p, 3q, 5q, 6q, 7p, 7q 8p, 9p, 9q, 10q, and 14q). A poor outcome was associated with gain of 7q and losses on 9p, 9q, and 14q. These aberrations were more frequent in metastasized tumors, suggesting alterations of genes important for tumor progression. Sequencing of 48 genes implicated in cancer revealed that only VHL, TP53, and PTEN were mutated at a noticeable frequency (51%, 9%, and 9%, respectively). Shorter relative telomere length (RTL) has been associated with loss of specific chromosomal regions in ccRCC tumors, but we could not verify this finding. However, a significantly lower tumor/nontumor (T/N) RTL ratio was detected for tumors with losses in 4q or 9p. In conclusion, poor outcome in ccRCC was associated with gain of 7q and loss on 9p, 9q, and 14q, whereas the mutation rate overall was low in a screen of cancer-associated genes.
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31
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Evelönn EA, Degerman S, Köhn L, Landfors M, Ljungberg B, Roos G. DNA methylation status defines clinicopathological parameters including survival for patients with clear cell renal cell carcinoma (ccRCC). Tumour Biol 2016; 37:10219-28. [PMID: 26831665 DOI: 10.1007/s13277-016-4893-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/19/2016] [Indexed: 12/20/2022] Open
Abstract
Epigenetic alterations in the methylome have been associated with tumor development and progression in renal cell carcinoma (RCC). In this study, 45 tumor samples, 12 tumor-free kidney cortex tissues, and 24 peripheral blood samples from patients with clear cell RCC (ccRCC) were analyzed by genome-wide promoter-directed methylation arrays and related to clinicopathological parameters. Unsupervised hierarchical clustering separated the tumors into two distinct methylation groups (clusters A and B), where cluster B had higher average methylation and increased number of hypermethylated CpG sites (CpGs). Furthermore, tumors in cluster B had, compared with cluster A, a larger tumor diameter (p = 0.033), a higher morphologic grade (p < 0.001), a higher tumor-node-metastasis (TNM) stage (p < 0.001), and a worse prognosis (p = 0.005). Higher TNM stage was correlated to an increase in average methylation level (p = 0.003) and number of hypermethylated CpGs (p = 0.003), whereas a number of hypomethylated CpGs were mainly unchanged. However, the predicted age of the tumors based on methylation profile did not correlate with TNM stage, morphological grade, or methylation cluster. Differently methylated (DM) genes (n = 840) in ccRCC samples compared with tumor-free kidney cortex samples were predominantly hypermethylated and a high proportion were identified as polycomb target genes. The DM genes were overrepresented by transcription factors, ligands, and receptors, indicating functional alterations of significance for ccRCC progression. To conclude, increased number of hypermethylated genes was associated with increased TNM stage of the tumors. DNA methylation classification of ccRCC tumor samples at diagnosis can serve as a clinically applicable prognostic marker in ccRCC.
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Affiliation(s)
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, SE-90185, Umeå, Sweden
| | - Linda Köhn
- Department of Medical Biosciences, Pathology, Umeå University, SE-90185, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, SE-90185, Umeå, Sweden
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Göran Roos
- Department of Medical Biosciences, Pathology, Umeå University, SE-90185, Umeå, Sweden.
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Becket E, Chopra S, Duymich CE, Lin JJ, You JS, Pandiyan K, Nichols PW, Siegmund KD, Charlet J, Weisenberger DJ, Jones PA, Liang G. Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma. Cancer Res 2016; 76:1954-64. [PMID: 26759245 DOI: 10.1158/0008-5472.can-15-2622] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/28/2015] [Indexed: 12/15/2022]
Abstract
Alterations in chromatin accessibility independent of DNA methylation can affect cancer-related gene expression, but are often overlooked in conventional epigenomic profiling approaches. In this study, we describe a cost-effective and computationally simple assay called AcceSssIble to simultaneously interrogate DNA methylation and chromatin accessibility alterations in primary human clear cell renal cell carcinomas (ccRCC). Our study revealed significant perturbations to the ccRCC epigenome and identified gene expression changes that were specifically attributed to the chromatin accessibility status whether or not DNA methylation was involved. Compared with commonly mutated genes in ccRCC, such as the von Hippel-Lindau (VHL) tumor suppressor, the genes identified by AcceSssIble comprised distinct pathways and more frequently underwent epigenetic changes, suggesting that genetic and epigenetic alterations could be independent events in ccRCC. Specifically, we found unique DNA methylation-independent promoter accessibility alterations in pathways mimicking VHL deficiency. Overall, this study provides a novel approach for identifying new epigenetic-based therapeutic targets, previously undetectable by DNA methylation studies alone, that may complement current genetic-based treatment strategies. Cancer Res; 76(7); 1954-64. ©2016 AACR.
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Affiliation(s)
- Elinne Becket
- Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Sameer Chopra
- Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Christopher E Duymich
- Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Justin J Lin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Jueng Soo You
- Department of Biochemistry, School of Medicine Konkuk University, Seoul, Korea
| | - Kurinji Pandiyan
- Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Peter W Nichols
- Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Kimberly D Siegmund
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Jessica Charlet
- Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Peter A Jones
- Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California. Van Andel Research Institute, Grand Rapids, Michigan
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
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Fernandes DS, Lopes JM. Pathology, therapy and prognosis of papillary renal carcinoma. Future Oncol 2015; 11:121-32. [PMID: 25572787 DOI: 10.2217/fon.14.133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Papillary renal cell carcinoma (pRCC) accounts for approximately 10% of renal parenchymal tumors. There are two pRCC subtypes reported in several studies, but at present, there is limited molecular evidence to validate this pRCC subtyping in the daily routine. The utility of subtyping pRCC is based on reports describing that pRCC subtype is an independent predictor of outcome, with type 1 tumors showing significantly better survival than type 2 tumors. In this article, we summarize the relevant knowledge on pRCC regarding tumor features: clinical presentation, histopathology, electron microscopy, immunohistochemistry, cytogenetics, genetic/molecular and prognosis. We present an overview of the currently available pRCC treatment options and some of the new promising agents.
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Osman WM, Youssef NS. Combined use of COX-1 and VEGF immunohistochemistry refines the histopathologic prognosis of renal cell carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:8165-8177. [PMID: 26339385 PMCID: PMC4555713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/22/2015] [Indexed: 06/05/2023]
Abstract
The course of RCC is asymptomatic, resulting in 25-30% of patients presenting with metastatic disease at time of diagnosis. The development of novel agents targeting angiogenesis and signal transduction pathways has improved patient outcomes. Role of cyclooxygenase in cancer development has been the subject of close scrutiny. COX-1 has been recognized to be involved in regulation of angiogenesis. To date, no immunohistochemical studies have been performed to assess the possible association between COX-1 and VEGF in RCC. This study is designed to evaluate the relationship between these two proteins in RCC. Also, the relationship between their combined immunohistochemical expression and different clinicopathological prognostic parameters in RCC is investigated. Immunohistochemical expression of COX-1 and VEGF was evaluated retrospectively on 64 cases of primary RCC including: 45 clear cell carcinoma, 12 papillary carcinoma and 7 of chromophope carcinoma. High COX-1 expression was detected in 62.5% of RCCs with a significant association with tumor grade (P=0.028), and highly significant relationship with tumor size and stage (P=0.001). There was a highly significant relationship between the VEGF score and tumor size (P=0.001), and stage (P=0.006). There was a positive correlation between COX-1 and VEGF expression score (P=0.001). Combined expression of both markers predicts high stage tumors (stage III/IV). Immunohistochemical expression of COX-1 and VEGF is associated with poor prognostic parameters in RCC. Their combined expression has a beneficial role in prediction of high stage tumors (III/IV).
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Affiliation(s)
- Wesam M Osman
- Department of Pathology, Faculty of Medicine, Ain Shams University Cairo, Egypt
| | - Nermeen S Youssef
- Department of Pathology, Faculty of Medicine, Ain Shams University Cairo, Egypt
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Arai E, Gotoh M, Tian Y, Sakamoto H, Ono M, Matsuda A, Takahashi Y, Miyata S, Totsuka H, Chiku S, Komiyama M, Fujimoto H, Matsumoto K, Yamada T, Yoshida T, Kanai Y. Alterations of the spindle checkpoint pathway in clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas. Int J Cancer 2015; 137:2589-606. [PMID: 26061684 PMCID: PMC4755138 DOI: 10.1002/ijc.29630] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 04/15/2015] [Accepted: 05/20/2015] [Indexed: 01/08/2023]
Abstract
CpG-island methylator phenotype (CIMP)-positive clear cell renal cell carcinomas (RCCs) are characterized by accumulation of DNA hypermethylation of CpG islands, clinicopathological aggressiveness and poor patient outcome. The aim of this study was to clarify the molecular pathways participating in CIMP-positive renal carcinogenesis. Genome (whole-exome and copy number), transcriptome and proteome (two-dimensional image converted analysis of liquid chromatography-mass spectrometry) analyses were performed using tissue specimens of 87 CIMP-negative and 14 CIMP-positive clear cell RCCs and corresponding specimens of non-cancerous renal cortex. Genes encoding microtubule-associated proteins, such as DNAH2, DNAH5, DNAH10, RP1 and HAUS8, showed a 10% or higher incidence of genetic aberrations (non-synonymous single-nucleotide mutations and insertions/deletions) in CIMP-positive RCCs, whereas CIMP-negative RCCs lacked distinct genetic characteristics. MetaCore pathway analysis of CIMP-positive RCCs revealed that alterations of mRNA or protein expression were significantly accumulated in six pathways, all participating in the spindle checkpoint, including the "The metaphase checkpoint (p = 1.427 × 10(-6))," "Role of Anaphase Promoting Complex in cell cycle regulation (p = 7.444 × 10(-6))" and "Spindle assembly and chromosome separation (p = 9.260 × 10(-6))" pathways. Quantitative RT-PCR analysis revealed that mRNA expression levels for genes included in such pathways, i.e., AURKA, AURKB, BIRC5, BUB1, CDC20, NEK2 and SPC25, were significantly higher in CIMP-positive than in CIMP-negative RCCs. All CIMP-positive RCCs showed overexpression of Aurora kinases, AURKA and AURKB, and this overexpression was mainly attributable to increased copy number. These data suggest that abnormalities of the spindle checkpoint pathway participate in CIMP-positive renal carcinogenesis, and that AURKA and AURKB may be potential therapeutic targets in more aggressive CIMP-positive RCCs.
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Affiliation(s)
- Eri Arai
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahiro Gotoh
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Ying Tian
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Masaya Ono
- Division of Chemotherapy and Clinical Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Akio Matsuda
- Department of Allergy and Immunology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoriko Takahashi
- Bioscience Department, Business Development Division, Mitsui Knowledge Industry Co. Ltd, Tokyo, Japan
| | - Sayaka Miyata
- Bioscience Department, Business Development Division, Mitsui Knowledge Industry Co. Ltd, Tokyo, Japan
| | - Hirohiko Totsuka
- Bioinformatics Group, Research and Development Center, Solution Division 4, Hitachi Government and Public Corporation System Engineering Ltd, Tokyo, Japan
| | - Suenori Chiku
- Science Solutions Division, Mizuho Information and Research Institute, Inc, Tokyo, Japan
| | - Motokiyo Komiyama
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Kenji Matsumoto
- Department of Allergy and Immunology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tesshi Yamada
- Division of Chemotherapy and Clinical Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yae Kanai
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
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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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Hypermethylation of the 16q23.1 tumor suppressor gene ADAMTS18 in clear cell renal cell carcinoma. Int J Mol Sci 2015; 16:1051-65. [PMID: 25569086 PMCID: PMC4307290 DOI: 10.3390/ijms16011051] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/23/2014] [Indexed: 01/11/2023] Open
Abstract
To identify tumor suppressor genes (TSGs) silenced by hypermethylation and discover new epigenetic biomarkers for early cancer detection. ADAMTS18, located at 16q23.1, has been reported to be a critical TSG in multiple primary tumors; however, this has not yet been verified in clear cell renal cell carcinoma (ccRCC). We explored epigenetic alterations in this gene in ccRCC and analyzed possible clinicopathological associations. We examined ADAMTS18 gene expression and methylation by semi-quantitative reverse transcription PCR (RT-PCR) and methylation-specific polymerase chain reaction (MSP) in 5 ccRCC-derived cell lines before and after treatment with 5-aza-2'-deoxycytidine (5-AzaC). MSP was further performed for 101 ccRCC primary tumors and 20 adjacent normal tissues. Some cell lines and specimens were examined by subsequent bisulfite genomic sequencing (BGS) and real-time PCR. Further, we analyzed the relationship between the ADAMTS18 gene methylation and clinicopathological features, including short-term disease-free survival (DFS), in patients with ccRCC. ADAMTS18 down-regulation and hypermethylation were detected in the ccRCC-derived cell lines using RT-PCR and MSP. Treatment with 5-AzaC reversed the hypermethylation of the ADAMTS18 gene and restored its expression. Hypermethylation was further detected in 44 of 101 (43.6%) primary tumors and 3 of 20 (15.0%) adjacent normal tissues. However, a significant difference between both groups was observed (p = 0.02). BGS analysis and real-time PCR were subsequently performed to confirm the results of RT-PCR and MSP. Furthermore, the methylation status of ADAMTS18 was not significantly associated with gender, age, location, tumor diameter, pathological stage, nuclear grade or short-term DFS in patients with ccRCC (p > 0.05). The ADAMTS18 gene is often down-regulated by hypermethylation in ccRCC-derived cell lines and primary tumors, indicating its critical role as a TSG in ccRCC. We conclude that ADAMTS18 gene hypermethylation may be involved in the tumorigenesis of ccRCC and may serve as a novel biomarker for this disease.
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Tian Y, Arai E, Gotoh M, Komiyama M, Fujimoto H, Kanai Y. Prognostication of patients with clear cell renal cell carcinomas based on quantification of DNA methylation levels of CpG island methylator phenotype marker genes. BMC Cancer 2014; 14:772. [PMID: 25332168 PMCID: PMC4216836 DOI: 10.1186/1471-2407-14-772] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/08/2014] [Indexed: 12/23/2022] Open
Abstract
Background The CpG island methylator phenotype (CIMP) of clear cell renal cell carcinomas (ccRCCs) is characterized by accumulation of DNA methylation at CpG islands and poorer patient outcome. The aim of this study was to establish criteria for prognostication of patients with ccRCCs using the ccRCC-specific CIMP marker genes. Methods DNA methylation levels at 299 CpG sites in the 14 CIMP marker genes were evaluated quantitatively in tissue specimens of 88 CIMP-negative and 14 CIMP-positive ccRCCs in a learning cohort using the MassARRAY system. An additional 100 ccRCCs were also analyzed as a validation cohort. Results Receiver operating characteristic curve analysis showed that area under the curve values for the 23 CpG units including the 32 CpG sites in the 7 CIMP-marker genes, i.e. FAM150A, ZNF540, ZNF671, ZNF154, PRAC, TRH and SLC13A5, for discrimination of CIMP-positive from CIMP-negative ccRCCs were larger than 0.95. Criteria combining the 23 CpG units discriminated CIMP-positive from CIMP-negative ccRCCs with 100% sensitivity and specificity in the learning cohort. Cancer-free and overall survival rates of patients with CIMP-positive ccRCCs diagnosed using the criteria combining the 23 CpG units in a validation cohort were significantly lower than those of patients with CIMP-negative ccRCCs (P = 1.41 × 10−5 and 2.43 × 10−13, respectively). Patients with CIMP-positive ccRCCs in the validation cohort had a higher likelihood of disease-related death (hazard ratio, 75.8; 95% confidence interval, 7.81 to 735; P = 1.89 × 10−4) than those with CIMP-negative ccRCCs. Conclusions The established criteria are able to reproducibly diagnose CIMP-positive ccRCCs and may be useful for personalized medicine for patients with ccRCCs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2407-14-772) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Eri Arai
- Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
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Khaliq S, Ajaz S, Firasat S, Shahid S, Hasan AS, Sultan G, Mohsin R, Hashmi A, Mubarak M, Naqvi SAA, Rizvi SAUH, Mehdi SQ, Abid A. Unique molecular alteration patterns in von Hippel-Lindau (VHL) gene in a cohort of sporadic renal cell carcinoma patients from Pakistan. Mutat Res 2014; 763-764:45-52. [PMID: 24727139 DOI: 10.1016/j.mrfmmm.2014.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/05/2014] [Accepted: 03/26/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Shagufta Khaliq
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan; Department of Human Genetics, University of Health Sciences (UHS), Lahore, Pakistan
| | - Sadia Ajaz
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Sadaf Firasat
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Saba Shahid
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Asad Shahzad Hasan
- Department of Oncology, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Gauhar Sultan
- Department of Oncology, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Rehan Mohsin
- Department of Oncology, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Altaf Hashmi
- Department of Oncology, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Muhammed Mubarak
- Department of Histopathology, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Syed Ali Anwar Naqvi
- Department of Urology, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | | | - Syed Qasim Mehdi
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Aiysha Abid
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan.
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Alkamal I, Ikromov O, Tölle A, Fuller TF, Magheli A, Miller K, Krause H, Kempkensteffen C. An epigenetic screen unmasks metallothioneins as putative contributors to renal cell carcinogenesis. Urol Int 2014; 94:99-110. [PMID: 24662736 DOI: 10.1159/000357282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/13/2013] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Functional epigenetic studies aimed to re-express transcriptionally silenced genes in renal cell carcinoma (RCC) may facilitate the ongoing search for appropriate markers supporting clinical decision-making. METHODS The RCC cell line A-498 was treated with the DNA methyltransferase inhibitor zebularine under low-cytotoxicity conditions. RNA chip analyses revealed several upregulated transcripts that were further validated by qPCR on 49 matched pairs of human kidney tissues to identify suitable marker candidates. RESULTS Members of the metallothionein (MT) group were remarkably downregulated in tumor tissues. MT1G and MT1H expression was decreased in 98% of cases, whereas MT2A expression was downregulated in 73% of all cases. Comparison of 308 reactivated transcripts upregulated more than 1.5-fold to published data revealed a high number of shared candidates, which supports the consistency of this experimental approach. CONCLUSION MTs were found to be transcriptionally inactivated in human RCC. Our observations support the hypothesis of a possible involvement of these metalloproteins in renal cell carcinogenesis. Additional functional studies of these genes may provide clues for understanding renal cancers as essentially metabolic diseases.
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Affiliation(s)
- Imad Alkamal
- Klinik für Urologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
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41
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Ćirović S, Vještica J, Mueller CA, Tatić S, Vasiljević J, Milenković S, Mueller GA, Marković-Lipkovski J. NCAM and FGFR1 coexpression and colocalization in renal tumors. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:1402-1414. [PMID: 24817936 PMCID: PMC4014220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 02/05/2014] [Indexed: 06/03/2023]
Abstract
Neural cell adhesion molecule (NCAM) and fibroblast growth factor receptor (FGFR) have a role in epithelial-mesenchymal transformation during tumor genesis. Interplay between both molecules activates FGFR signaling and it could be responsible for tumor development. Renal epithelial tumors were analyzed for FGFR1 and NCAM coexpression by immunohistochemistry and for colocalization of these molecules on the particular tumor cells by triple immunofluorescence. Detection of NCAM isoforms in renal tumors was evaluated by RT-PCR. Applying immunohistochemistry we revealed that the majority of analyzed renal neoplasms, including renal cell carcinoma (RCC) and oncocytoma coexpressed NCAM and FGFR1. Triple immunofluorescent technique confirmed that both markers are commonly colocalized on the same tumor cells. Interestingly, it seemed that different position of NCAM and FGFR1 expression on renal tumor cells is related to renal tumor type or grade: exclusively membranous FGFR1/NCAM expression occurred in low grade clear cell RCC (cRCC); cytoplasmatic and membranous expression was present in high grade cRCC and other RCC types; oncocytoma showed only cytoplasmatic staining of both markers. NCAM-140 and NCAM-120 were detected in almost all analyzed renal neoplasms. Expression of both molecules on different cell compartments in various kidney tumors indicated that NCAM/FGFR1 interaction could play distinct roles in renal tumor genesis.
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MESH Headings
- Adenoma/metabolism
- Adenoma/pathology
- Adenoma, Oxyphilic/metabolism
- Adenoma, Oxyphilic/pathology
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Immunohistochemistry
- Kidney/metabolism
- Kidney/pathology
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Male
- Middle Aged
- Neural Cell Adhesion Molecules/genetics
- Neural Cell Adhesion Molecules/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
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Affiliation(s)
- Sanja Ćirović
- Institute of Pathology, Faculty of Medicine, University of BelgradeSerbia
| | - Jelena Vještica
- Institute of Pathology, Faculty of Medicine, University of BelgradeSerbia
| | - Claudia A Mueller
- Department of Nephrology and Rheumatology, Georg-August-UniversityGöttingen, Germany
| | - Svetislav Tatić
- Institute of Pathology, Faculty of Medicine, University of BelgradeSerbia
| | - Jovan Vasiljević
- Institute of Pathology, Faculty of Medicine, University of BelgradeSerbia
| | | | - Gerhard A Mueller
- Department of Nephrology and Rheumatology, Georg-August-UniversityGöttingen, Germany
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42
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Histone deacetylase inhibitors and epigenetic modifications as a novel strategy in renal cell carcinoma. Cancer J 2014; 19:333-40. [PMID: 23867515 DOI: 10.1097/ppo.0b013e3182a09e07] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent investigations of renal cell carcinoma (RCC) have revealed several epigenetic modifications, as well as alterations in the genes and enzymes that regulate these changes. Preclinical models have revealed that histone gene modifiers and epigenetic alterations may play a critical role in RCC tumorigenesis. Specific changes in DNA methylation and mutations of histone modifiers have been identified and may be associated with an aggressive phenotype. In addition, the potential of reversing the effects of these enzymes and hence reversing the cellular epigenetic landscape to a "normal phenotype" have led to an increasing interest in developing targeted chromatin remodeling agents. However, the translation of the understanding of these changes to the clinic for the treatment of RCC has posed significant challenges, partly due to tumor heterogeneity. This review describes the aberrant histone and DNA alterations recently reported in RCC and highlights the potential targeted chromatin remodeling therapies in the management of this disease.
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43
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Selvakumar P, Owens TA, David JM, Petrelli NJ, Christensen BC, Lakshmikuttyamma A, Rajasekaran AK. Epigenetic silencing of Na,K-ATPase β 1 subunit gene ATP1B1 by methylation in clear cell renal cell carcinoma. Epigenetics 2014; 9:579-86. [PMID: 24452105 DOI: 10.4161/epi.27795] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The Na,K-ATPase or sodium pump carries out the coupled extrusion of Na(+) and uptake of K(+) across the plasma membranes of cells of most higher eukaryotes. We have shown earlier that Na,K-ATPase-β 1 (NaK-β) protein levels are highly reduced in poorly differentiated kidney carcinoma cells in culture and in patients' tumor samples. The mechanism(s) regulating the expression of NaK-β in tumor tissues has yet to be explored. We hypothesized that DNA methylation plays a role in silencing the NaK-β gene (ATP1B1) expression in kidney cancers. In this study, to the best of our knowledge we provide the first evidence that ATP1B1 is epigenetically silenced by promoter methylation in both renal cell carcinoma (RCC) patients' tissues and cell lines. We also show that knockdown of the von Hippel-Lindau (VHL) tumor suppressor gene in RCC cell lines results in enhanced ATP1B1 promoter AT hypermethylation, which is accompanied by reduced expression of NaK-β. Furthermore, treatment with 5-Aza-2'-deoxycytidine rescued the expression of ATP1B1 mRNA as well as NaK-β protein in these cells. These data demonstrate that promoter hypermethylation is associated with reduced NaK-β expression, which might contribute to RCC initiation and/or disease progression.
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Affiliation(s)
- Ponniah Selvakumar
- Nemours Center for Childhood Cancer Research; Alfred I. duPont Hospital for Children; Wilmington, DE USA
| | - Tori A Owens
- Nemours Center for Childhood Cancer Research; Alfred I. duPont Hospital for Children; Wilmington, DE USA
| | - Justin M David
- Nemours Center for Childhood Cancer Research; Alfred I. duPont Hospital for Children; Wilmington, DE USA; Department of Biological Sciences; University of Delaware; Newark, DE USA
| | | | - Brock C Christensen
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; The Geisel School of Medicine at Dartmouth; Hanover, NH USA; Department of Pharmacology and Toxicology; The Geisel School of Medicine at Dartmouth; Hanover, NH USA
| | - Ashakumary Lakshmikuttyamma
- Department of Pharmaceutical Sciences; School of Pharmacy; Thomas Jefferson University; Philadelphia, PA USA
| | - Ayyappan K Rajasekaran
- Nemours Center for Childhood Cancer Research; Alfred I. duPont Hospital for Children; Wilmington, DE USA
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44
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Ricketts CJ, Hill VK, Linehan WM. Tumor-specific hypermethylation of epigenetic biomarkers, including SFRP1, predicts for poorer survival in patients from the TCGA Kidney Renal Clear Cell Carcinoma (KIRC) project. PLoS One 2014; 9:e85621. [PMID: 24454902 PMCID: PMC3893219 DOI: 10.1371/journal.pone.0085621] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/05/2013] [Indexed: 01/08/2023] Open
Abstract
The recent publication of the TCGA Kidney Renal Clear Cell Carcinoma (KIRC) project has provided an immense wealth and breadth of data providing an invaluable tool for confirmation and expansion upon previous observations in a large data set containing multiple data types including DNA methylation, somatic mutation, and clinical information. In clear cell renal cell carcinoma (CCRCC) many genes have been demonstrated to be epigenetically inactivated by promoter hypermethylated and in a small number of cases to be associated with clinical outcome. This study created two cohorts based on the Illumina BeadChip array used to confirm the frequency of tumor-specific hypermethylation of these published hypermethylated genes, assess the impact of somatic mutation or chromosomal loss and provide the most comprehensive assessment to date of the association of this hypermethylation with patient survival. Hypermethylation of the Fibrillin 2 (FBN2) gene was the most consistent epigenetic biomarker for CCRCC across both cohorts in 40.2% or 52.5% of tumors respectively. Hypermethylation of the secreted frizzled-related protein 1 (SFRP1) gene and the basonuclin 1 (BNC1) gene were both statistically associated with poorer survival in both cohorts (SFRP1 - p = <0.0001 or 0.0010 and BNC1 - p = <0.0001 or 0.0380) and represented better independent markers of survival than tumor stage, grade or dimension in one cohort and tumor stage or dimension in the other cohort. Loss of the SFRP1 protein can potentially activate the WNT pathway and this analysis highlighted hypermethylation of several other WNT pathway regulating genes and demonstrated a poorer survival outcome for patients with somatic mutation of these genes. The success of demethylating drugs in hematological malignances and the current trials in solid tumors suggest that the identification of clinically relevant hypermethylated genes combined with therapeutic advances may improve the effectiveness and usefulness of such drugs in clear cell renal cell carcinoma.
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Affiliation(s)
- Christopher J. Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Victoria K. Hill
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - W. Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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45
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Yang OC, Maxwell PH, Pollard PJ. Renal cell carcinoma: translational aspects of metabolism and therapeutic consequences. Kidney Int 2013; 84:667-81. [DOI: 10.1038/ki.2013.245] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 02/08/2023]
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46
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Ricketts CJ, Morris MR, Gentle D, Shuib S, Brown M, Clarke N, Wei W, Nathan P, Latif F, Maher ER. Methylation profiling and evaluation of demethylating therapy in renal cell carcinoma. Clin Epigenetics 2013; 5:16. [PMID: 24034811 PMCID: PMC3848591 DOI: 10.1186/1868-7083-5-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/21/2013] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Despite therapeutic advances in targeted therapy, metastatic renal cell carcinoma (RCC) remains incurable for the vast majority of patients. Key molecular events in the pathogenesis of RCC include inactivation of the VHL tumour suppressor gene (TSG), inactivation of chromosome 3p TSGs implicated in chromatin modification and remodelling and de novo tumour-specific promoter methylation of renal TSGs. In the light of these observations it can be proposed that, as in some haematological malignancies, demethylating agents such as azacitidine might be beneficial for the treatment of advanced RCC. RESULTS Here we report that the treatment of RCC cell lines with azacitidine suppressed cell proliferation in all 15 lines tested. A marked response to azacitidine therapy (>50% reduction in colony formation assay) was detected in the three cell lines with VHL promoter methylation but some RCC cell lines without VHL TSG methylation also demonstrated a similar response suggesting that multiple methylated TSGs might determine the response to demethylating therapies. To identify novel candidate methylated TSGs implicated in RCC we undertook a combined analysis of copy number and CpG methylation array data. Candidate novel epigenetically inactivated TSGs were further prioritised by expression analysis of RCC cell lines pre and post-azacitidine therapy and comparative expression analysis of tumour/normal pairs. Thus, with subsequent investigation two candidate genes were found to be methylated in more than 25% of our series and in the TCGA methylation dataset for 199 RCC samples: RGS7 (25.6% and 35.2% of tumours respectively) and NEFM in (25.6% and 30.2%). In addition three candidate genes were methylated in >10% of both datasets (TMEM74 (15.4% and 14.6%), GCM2 (41.0% and 14.6%) and AEBP1 (30.8% and 13.1%)). Methylation of GCM2 (P = 0.0324), NEFM (P = 0.0024) and RGS7 (P = 0.0067) was associated with prognosis. CONCLUSIONS These findings provide preclinical evidence that treatment with demethylating agents such as azacitidine might be useful for the treatment of advanced RCC and further insights into the role of epigenetic changes in the pathogenesis of RCC.
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Affiliation(s)
- Christopher J Ricketts
- Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark R Morris
- Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- School of Applied Sciences University of Wolverhampton, Wolverhampton WV1 1SV, UK
| | - Dean Gentle
- Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Salwati Shuib
- Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Pathology, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - Michael Brown
- Institute for Cancer Sciences, Cancer Research UK Paterson Institute for Cancer Research, Manchester Academic Health Science Centre, University of Manchester, Manchester M20 4BX, UK
| | - Noel Clarke
- Institute for Cancer Sciences, Cancer Research UK Paterson Institute for Cancer Research, Manchester Academic Health Science Centre, University of Manchester, Manchester M20 4BX, UK
- The Christie Hospital, Wilmslow Road, Manchester M20 4BX, UK
| | - Wenbin Wei
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Paul Nathan
- Mount Vernon Cancer Centre - Medical Oncology, Rickmansworth Road, Northwood, Middlesex HA6 2RN, UK
| | - Farida Latif
- Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Eamonn R Maher
- Centre for Rare Diseases and Personalised Medicine, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- West Midlands Region Genetics Service, Birmingham Women’s Hospital, Edgbaston, Birmingham B15 2TG, UK
- Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK
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Genomics and epigenomics of clear cell renal cell carcinoma: recent developments and potential applications. Cancer Lett 2013; 341:111-26. [PMID: 23933176 DOI: 10.1016/j.canlet.2013.08.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/12/2013] [Accepted: 08/02/2013] [Indexed: 12/21/2022]
Abstract
Majority of clear cell renal cell carcinomas (ccRCCs) are diagnosed in the advanced metastatic stage resulting in dramatic decrease of patient survival. Thereby, early detection and monitoring of the disease may improve prognosis and treatment results. Recent technological advances enable the identification of genetic events associated with ccRCC and reveal significant molecular heterogeneity of ccRCC tumors. This review summarizes recent findings in ccRCC genomics and epigenomics derived from chromosomal aberrations, DNA sequencing and methylation, mRNA, miRNA expression profiling experiments. We provide a molecular insight into ccRCC pathology and recapitulate possible clinical applications of genomic alterations as predictive and prognostic biomarkers.
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48
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Carter JA, Górecki DC, Mein CA, Ljungberg B, Hafizi S. CpG dinucleotide-specific hypermethylation of the TNS3 gene promoter in human renal cell carcinoma. Epigenetics 2013; 8:739-47. [PMID: 23803643 DOI: 10.4161/epi.25075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Tensin3 is a cytoskeletal regulatory protein that inhibits cell motility. Downregulation of the gene encoding Tensin3 (TNS3) in human renal cell carcinoma (RCC) may contribute to cancer cell metastatic behavior. We speculated that epigenetic mechanisms, e.g., gene promoter hypermethylation, might account for TNS3 downregulation. In this study, we identified and validated a TNS3 gene promoter containing a CpG island, and quantified the methylation level within this region in RCC. Using a luciferase reporter assay we demonstrated a functional minimal promoter activity for a 500-bp sequence within the TNS3 CpG island. Pyrosequencing enabled quantitative determination of DNA methylation of each CpG dinucleotide (a total of 43) in the TNS3 gene promoter. Across the entire analyzed CpG stretch, RCC DNA showed a higher methylation level than both non-tumor kidney DNA and normal control DNA. Out of all the CpGs analyzed, two CpG dinucleotides, specifically position 2 and 8, showed the most pronounced increases in methylation levels in tumor samples. Furthermore, CpG-specific higher methylation levels were correlated with lower TNS3 gene expression levels in RCC samples. In addition, pharmacological demethylation treatment of cultured kidney cells caused a 3-fold upregulation of Tensin3 expression. In conclusion, these results reveal a differential methylation pattern in the TNS3 promoter occurring in human RCC, suggesting an epigenetic mechanism for aberrant Tensin downregulation in human kidney cancer.
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Affiliation(s)
- Jessica A Carter
- Institute of Biomedical and Biomolecular Science (IBBS), School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
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Slater AA, Alokail M, Gentle D, Yao M, Kovacs G, Maher ER, Latif F. DNA methylation profiling distinguishes histological subtypes of renal cell carcinoma. Epigenetics 2013; 8:252-67. [PMID: 23428843 DOI: 10.4161/epi.23817] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Renal cell carcinoma (RCC) accounts for around 3% of cancers in the UK, and both incidence and mortality are increasing with the aging population. RCC can be divided into several subtypes: conventional RCC (the most common, comprising 75% of all cases), papillary RCC (15%) and chromophobe RCC (5%). Renal oncocytoma is a benign tumor and accounts for 5% of RCC. Cancer and epigenetics are closely associated, with DNA hypermethylation being widely accepted as a feature of many cancers. In this study the DNA methylation profiles of chromophobe RCC and renal oncocytomas were investigated by utilizing the Infinium HumanMethylation450 BeadChips. Cancer-specific hypermethylation was identified in 9.4% and 5.2% of loci in chromophobe RCC and renal oncocytoma samples, respectively, while the majority of the genome was hypomethylated. Thirty (hypermethylated) and 41 (hypomethylated) genes were identified as differentially methylated between chromophobe RCC and renal oncocytomas (p < 0.05). Pathway analysis identified some of the differentially hypermethylated genes to be involved in Wnt (EN2), MAPK (CACNG7) and TGFβ (AMH) signaling, Hippo pathway (NPHP4), and cell death and apoptosis (SPG20, NKX6-2, PAX3 and BAG2). In addition, we analyzed ccRCC and papillary RCC data available from The Cancer Genome Atlas portal to identify differentially methylated loci in chromophobe RCC and renal oncocytoma in relation to the other histological subtypes, providing insight into the pathology of RCC subtypes and classification of renal tumors.
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Affiliation(s)
- Amy A Slater
- Centre for Rare Diseases and Personalised Medicine, Department of Medical & Molecular Genetics, School of Clinical and Experimental Medicine, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
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50
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Genomics and epigenomics of renal cell carcinoma. Semin Cancer Biol 2013; 23:10-7. [DOI: 10.1016/j.semcancer.2012.06.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 06/05/2012] [Indexed: 12/12/2022]
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