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Zhou R, Yin L, Zhang X, Zhu K. SFRP1 reduces neutrophil infiltration and inhibits the Wnt/β-catenin pathway to alleviate oral submucous fibrosis. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00945-9. [PMID: 39017751 DOI: 10.1007/s11626-024-00945-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
Abstract
Oral submucous fibrosis (OSF) is a precancerous condition characterized by oral mucosal atrophy with fibrosis of the submucosal tissue. OSF has a high prevalence, and treatment requires improvement. Our study aims to investigate the role and mechanism of secreted frizzled-related protein 1 (SFRP1) in OSF. We constructed an arecoline-induced OSF mice model. Through Pearson's correlation analysis, we investigated the association between SFRP1 levels and expressions of proteins related to the Wnt/β-catenin signaling pathway, as well as the correlation between SFRP1 levels and the degree of neutrophil infiltration. Moreover, neutrophil infiltration intensity, tissue fibrosis degree, and levels of β-catenin, Cyclin D1, and c-myc were evaluated after SFRP1 overexpression treatment through immunohistochemical and biochemical assays. A Wnt/β-catenin pathway activator was used to investigate the molecular mechanism of SFRP1 in the arecoline-induced OSF cell model. Compared with the control group, mice in the OSF group exhibited increased collagen deposition and more severe fibrosis in the oral mucosal tissue (OMT). In the OMT of OSF mice, the levels of SFRP1 were decreased. The levels of SFRP1 exhibited a negative correlation with the levels of Wnt/β-catenin proteins and neutrophil infiltration in the OMT. Upon SFRP1 overexpression, there was a reduction in neutrophil infiltration and fibrosis in the OMT, as well as inhibition of Wnt/β-catenin-related proteins. In vitro, the Wnt/β-catenin pathway activator further reversed the effect of SFRP1 overexpression on OSF. SFRP1 attenuates OSF by reducing neutrophil infiltration and inhibiting the Wnt/β-catenin pathway.
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Affiliation(s)
- Rong Zhou
- Department of Stomatology, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Lin Yin
- Department of Stomatology, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Xin Zhang
- Department of Stomatology, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Keke Zhu
- Department of Stomatology, The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China.
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Hayashi Y, Hashimoto M, Takaoka K, Takemoto T, Takakura N, Kidoya H. Tumor endothelial cell-derived Sfrp1 supports the maintenance of cancer stem cells via Wnt signaling. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00899-y. [PMID: 38625488 DOI: 10.1007/s11626-024-00899-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/17/2024]
Abstract
Cancer stem cells (CSCs), which are critical targets for cancer therapy as they are involved in drug resistance to anticancer drugs, and metastasis, are maintained by angiocrine factors produced by particular niches that form within tumor tissue. Secreted frizzled-related protein 1 (Sfrp1) is an extracellular protein that modulates Wnt signaling. However, the cells that produce Sfrp1 in the tumor environment and its function remain unclear. We aimed to elucidate angiocrine factors related to CSC maintenance, focusing on Sfrp1. Although Sfrp1 is a Wnt pathway-related factor, its impact on tumor tissues remains unknown. We investigated the localization of Sfrp1 in tumors and found that it is expressed in some tumor vessels. Analysis of mice lacking Sfrp1 showed that tumor growth was suppressed in Sfrp1-deficient tumor tissues. Flow cytometry analysis indicated that CSCs were maintained in the early tumor growth phase in the Sfrp1 knockout (KO) mouse model of tumor-bearing cancer. However, tumor growth was inhibited in the late tumor growth phase because of the inability to maintain CSCs. Real-time PCR results from tumors of Sfrp1 KO mice showed that the expression of Wnt signaling target genes significantly decreased in the late stage of tumor growth. This suggests that Sfrp1, an angiocrine factor produced by the tumor vascular niche, is involved in Wnt signaling-mediated mechanisms in tumor tissues.
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Affiliation(s)
- Yumiko Hayashi
- Department of Integrative Vascular Biology, Faculty of Medical Science, Fukui University, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Yoshida, Fukui, 910-1193, Japan
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Masakazu Hashimoto
- Laboratory for Embryogenesis, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Katsuyoshi Takaoka
- Laboratory for Embryology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Tatsuya Takemoto
- Laboratory for Embryology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Nobuyuki Takakura
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- World Premier Institute Immunology Frontier Research Center, Integrated Frontier Research for Medical Science Division, Osaka University, Suita, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Hiroyasu Kidoya
- Department of Integrative Vascular Biology, Faculty of Medical Science, Fukui University, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Yoshida, Fukui, 910-1193, Japan.
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
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Demirkiran N, Aydin B, Pehlivan M, Yuce Z, Sercan HO. Study of the effect of sFRP1 protein on molecules involved in the regulation of DNA methylation in CML cell line. Med Oncol 2024; 41:109. [PMID: 38592567 DOI: 10.1007/s12032-024-02336-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
Wnt-signaling pathway plays a crucial role in the pathogenesis and progression of Chronic Myeloid Leukemia (CML). sFRP1 is involved in the suppression of the Wnt-signaling pathway and has been shown to be epigenetically silenced by promoter hypermethylation during CML progression. DNMT3A plays a crucial role in promoter hypermethylation and is responsible for establishing methylation patterns. We aimed to analyze the relationship between sFRP1 expression and DNMT3A, TET1, TET2 and TET3 proteins that are responsible for maintaining cellular methylation patterns; along with miRNAs miR144-3p and miR-767-5p that are known to be associated with these proteins. CML cell lines K562 and K562S which stably expresses sFRP1, were used to compare the changes in miR144-3p and miR-767-5p expression. DNMT3A, TET1, TET2 and TET3 protein levels were analyzed by Western blot. In K562S cells the expression of miR-144-3p and miR-767-5p were decreased along with DNMT3A and TET1 protein levels. On the contrary, TET2 protein was increased. Our results support other reports involving sFRP1 and methylation dynamics; as well as opening new avenues of exploration. Our data supports the conclusion that re-expression of sFRP1 protein alters the expression of factors that play important roles in the overall methylation patterns in the leukemic cell line K562.
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Affiliation(s)
- Nazli Demirkiran
- Department of Medical Biology and Genetics, Dokuz Eylul University Faculty of Medicine, Inciralti, 35340, Izmir, Turkey
| | - Bengusu Aydin
- Department of Medical Biology and Genetics, Dokuz Eylul University Faculty of Medicine, Inciralti, 35340, Izmir, Turkey
| | - Melek Pehlivan
- Department of Medical Laboratory Techniques, Izmir Katip Celebi University, Vocational School of Health Services, Izmir, Turkey
| | - Zeynep Yuce
- Department of Medical Biology and Genetics, Dokuz Eylul University Faculty of Medicine, Inciralti, 35340, Izmir, Turkey
| | - H Ogun Sercan
- Department of Medical Biology and Genetics, Dokuz Eylul University Faculty of Medicine, Inciralti, 35340, Izmir, Turkey.
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H3K27me3 Inactivates SFRP1 to Promote Cell Proliferation via Wnt/β-Catenin Signaling Pathway in Esophageal Squamous Cell Carcinoma. Dig Dis Sci 2023; 68:2463-2473. [PMID: 36933113 DOI: 10.1007/s10620-023-07892-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 02/21/2023] [Indexed: 03/19/2023]
Abstract
BACKGROUND Histone methylations are generally considered to play an important role in multiple cancers by regulating cancer-related genes. AIMS This study aims to investigate the effects of H3K27me3-mediated inactivation of tumor suppressor gene SFRP1 and its function in esophageal squamous cell carcinoma (ESCC). METHODS We performed ChIP-seq on H3K27me3-enriched genomic DNA fragments in ESCC cells to screen out tumor suppressor genes that may be regulated by H3K27me3. ChIP-qPCR and Western blot were employed to explore the regulating mechanisms between H3K27me3 and SFRP1. Expression level of SFRP1 was assessed by quantitative real-time polymerase chain reaction (q-PCR) in 29 pairs of ESCC surgical samples. SFRP1 function in ESCC cells were detected by cell proliferation assay, colony formation assay and wound-healing assay. RESULTS Our results indicated that H3K27me3 was widely distributed in the genome of ESCC cells. Specifically, we found that H3K27me3 deposited on the upstream region of SFRP1 promoter and inactivated SFRP1 expression. Furthermore, we found SFRP1 was significantly down-regulated in ESCC tissues compared with the adjacent non-tumor tissues, and SFRP1 expression was significantly associated with TNM stage and lymph node metastasis. In vitro cell-based assay indicated that over-expression of SFRP1 significantly suppressed cell proliferation and negatively correlated with the expression of β-catenin in the nucleus. CONCLUSIONS Our study revealed a previously unrecognized finding that H3K27me3-mediated SFRP1 inhibit the cell proliferation of ESCC through inactivation of Wnt/β-catenin signaling pathway.
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Dong L, Sun Q, Song F, Song X, Lu C, Li Y, Song X. Identification and verification of eight cancer-associated fibroblasts related genes as a prognostic signature for head and neck squamous cell carcinoma. Heliyon 2023; 9:e14003. [PMID: 36938461 PMCID: PMC10018481 DOI: 10.1016/j.heliyon.2023.e14003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) can exert their immunosuppressive effects by secreting various effectors that are involved in the regulation of tumor-infiltrating immune cells as well as other immune components in the tumor immune microenvironment (TIME), thereby promoting tumorigenesis, progression, metastasis, and drug resistance. Although a large number of studies suggest that CAFs play a key regulatory role in the development of head and neck squamous cell carcinoma (HNSCC), there are limited studies on the relevance of CAFs to the prognosis of HNSCC. In this study, we identified a prognostic signature containing eight CAF-related genes for HNSCC by univariate Cox analysis, lasso regression, stepwise regression, and multivariate Cox analysis. Our validation in primary cultures of CAFs from human HNSCC and four human HNSCC cell lines confirmed that these eight genes are indeed characteristic markers of CAFs. Immune cell infiltration differences analysis between high-risk and low-risk groups according to the eight CAF-related genes signature hinted at CAFs regulatory roles in the TIME, further revealing its potential role on prognosis. The signature of the eight CAF-related genes was validated in different independent validation cohorts and all showed that it was a valid marker for prognosis. The significantly higher overall survival (OS) in the low-risk group compared to the high-risk group was confirmed by Kaplan-Meier (K-M) analysis, suggesting that the signature of CAF-related genes can be used as a non-invasive predictive tool for HNSCC prognosis. The low-risk group had significantly higher levels of tumor-killing immune cell infiltration, as confirmed by CIBERSORT analysis, such as CD8+ T cells, follicular helper T cells, and Dendritic cells (DCs) in the low-risk group. In contrast, the level of infiltration of pro-tumor cells such as M0 macrophages and activated Mast cells (MCs) was lower. It is crucial to delve into the complex mechanisms between CAFs and immune cells to find potential regulatory targets and may provide new evidence for subsequently targeted immunotherapy. These results suggest that the signature of the eight CAF-related genes is a powerful indicator for the assessment of the TIME of HNSCC. It may provide a new and reliable potential indicator for clinicians to predict the prognosis of HNSCC, which may be used to guide treatment and clinical decision-making in HNSCC patients. Meanwhile, CAF-related genes are expected to become tumor biomarkers and effective targets for HNSCC.
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Key Words
- CAFs, Cancer-associated fibroblasts
- CSCs, cancer stem cells
- Cancer-associated fibroblasts
- DCs, Dendritic cells
- EMT, epithelial mesenchymal transition
- GEO, Gene Expression Omnibus
- GEPIA, Gene Expression Profiling Interactive Analysis
- GO, Gene Ontology
- GSEA, Gene Set Enrichment Analysis
- HNSCC, head and neck squamous cell carcinoma
- HR, Hazard Ratio
- Head and neck squamous cell carcinoma
- Immune cell infiltration
- K-M, Kaplan-Meier
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MCs, Mast cells
- NFs, normal fibroblasts
- OS, overall survival
- OSCC, oral squamous cell carcinomas
- Prognostic signature
- ROC, receiver operating characteristic
- TAMs, tumor-associated macrophages
- TCGA, The Cancer Genome Atlas
- TIME, tumor immune microenvironment
- TME, tumor microenvironment
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Affiliation(s)
- Lei Dong
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Qi Sun
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Fei Song
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Xiaoyu Song
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Congxian Lu
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
| | - Yumei Li
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
- Corresponding author. Yumei Li: Department of Otorhinolaryngology Head and Neck Surgery. Yantai Yuhuangding Hospital, No.20, Yuhuangding East Road, Zhifu District, Yantai, Shandong, 264000, China.
| | - Xicheng Song
- Department of Otorhinolaryngology Head and Neck Surgery, Yantai Yuhuangding Hospital, Shandong University, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases
- Corresponding author. Xicheng Song: Department of Otorhinolaryngology Head and Neck Surgery. Yantai Yuhuangding Hospital, No.20, Yuhuangding East Road, Zhifu District, Yantai, Shandong, 264000, China.
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Identification and Validation of Potentially Clinically Relevant CpG Regions within the Class 2 Tumor Suppressor Gene SFRP1 in Pancreatic Cancer. Cancers (Basel) 2023; 15:cancers15030683. [PMID: 36765639 PMCID: PMC9913221 DOI: 10.3390/cancers15030683] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In pancreatic cancer treatment, tumor stage-dependent chemotherapies are used to prolong overall survival. By measuring DNA promoter hypermethylation in the plasma of patients with stage IV pancreatic cancer, it was recently shown that promoter DNA methylation of the tumor suppressor gene SFRP1 has a high value for predicting failure of drug treatment with gemcitabine. In this study, we therefore aimed to identify as precisely as possible the region in the SFRP1 promoter that is frequently hypermethylated in pancreatic cancer tissue. First, we used the TCGA data set to define CpG-rich regions flanking the SFRP1 transcription start site that were significantly more methylated in pancreatic cancer compared to normal pancreatic acinar tissue. A core CpG island was identified that exhibited abundant tumor DNA methylation and anti-correlation of SFRP1 mRNA expression. To validate our in silico results, we performed bisulfide conversion followed by DNA pyrosequencing of 28 matched formalin-fixed, paraffin-embedded (FFPE) pancreatic cancer cases and six pancreatic cancer cell lines. A defined block of seven CpG sites within the core CpG island was identified, which confirmed our in silico results by showing significantly higher SFRP1 methylation in pancreatic cancer specimens than in normal pancreatic tissue. By selecting this core CpG island, we were able to determine a median overall survival benefit for the low SFRP1 methylation group compared to the high SFRP1 methylation group (702 versus 517 days, p = 0.01) in the TCGA pancreatic cancer cohort. We propose a compact pyrosequencing assay that can be used in the future to further investigate the prognostic value of SFRP1 promoter hypermethylation in predicting pancreatic cancer chemoresistance. Therefore, instead of DNA analysis from blood (liquid biopsy), DNA easily extractable from cancer tissue blocks (FFPE material) could be used.
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Chen Z, Li Z, Li C, Li B, Wang H, Nong D, Li X, Huang G, Lin J, Li W. Speckle-type POZ protein could play a potential inhibitory role in human renal cell carcinoma. BMC Cancer 2022; 22:1277. [PMID: 36474188 PMCID: PMC9727862 DOI: 10.1186/s12885-022-10340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Speckle-type POZ protein(SPOP), a substrate adaptor of Cul3 ubiquitin ligase, plays crucial roles in solid neoplasms by promoting the ubiquitination and degradation of substrates. Limited studies have shown that SPOP is overexpressed in human renal cell carcinoma (RCC) tissue. However, the exact role of SPOP in RCC remains unclear and needs to be further elucidated. The present study showed that SPOP was expressed at different levels in different RCC cell lines. The purpose of this study was to explore the roles of SPOP in the biological features of RCC cells and the expression levels of SPOP in human tissue microarray (TMA) and kidney tissues. METHODS Here, SPOP was overexpressed by lentiviral vector transfection in ACHN and Caki-1 cells, and SPOP was knocked down in Caki-2 cells with similar transfection methods. The transfection efficiency was evaluated by quantitative PCR and western blotting analyses. The role of SPOP in the proliferation, migration, invasion and apoptosis of cell lines was determined by the MTT, wound-healing, transwell and flow cytometry assays. Moreover, the cells were treated with different drug concentrations in proliferation and apoptosis assays to investigate the effect of sunitinib and IFN-α2b on the proliferation and apoptosis of SPOP-overexpressing cells and SPOP-knockdown RCC cells. Finally, immunohistochemical staining of SPOP was performed in kidney tissues and TMAs, which included RCC tissues and corresponding adjacent normal tissues. RESULTS Overexpression of SPOP inhibited cell proliferation, migration and invasion and increased cell apoptosis. Interestingly, sunitinib and IFN-α2b at several concentrations increased the proliferation inhibitory rate and total apoptosis rate of cells overexpressing SPOP. The findings of the present study showed that the SPOP protein was significantly expressed at low levels in most clear cell RCC (ccRCC) tissues and at relatively high levels in the majority of adjacent normal tissues and kidney tissues. Kaplan-Meier survival analysis showed that there was no statistically significant difference in cumulative survival based on the data of different SPOP expression levels in TMA and patients. CONCLUSIONS In contrast to previous studies, our findings demonstrated that overexpression of SPOP might suppress the progression of RCC cells, which was supported by cell experiments and immunohistochemical staining. SPOP could be a potential tumour inhibitor in RCC.
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Affiliation(s)
- Zhi Chen
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Zuan Li
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Chunlin Li
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Bingcai Li
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Haojian Wang
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Deyong Nong
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Ximing Li
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Guihai Huang
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Junhao Lin
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
| | - Wei Li
- grid.410652.40000 0004 6003 7358Department of Urology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy Of Medical Sciences, Nanning, China
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Serth J, Peters I, Katzendorn O, Dang TN, Moog J, Balli Z, Reese C, Hennenlotter J, Grote A, Lafos M, Tezval H, Kuczyk MA. Identification of a Novel Renal Metastasis Associated CpG-Based DNA Methylation Signature (RMAMS). Int J Mol Sci 2022; 23:ijms231911190. [PMID: 36232491 PMCID: PMC9569431 DOI: 10.3390/ijms231911190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Approximately 21% of patients with renal cell cancer (RCC) present with synchronous metastatic disease at the time of diagnosis, and metachronous metastatic disease occurs in 20–50% of cases within 5 years. Recent advances in adjuvant treatment of aggressive RCC following surgery suggest that biomarker-based prediction of risk for distant metastasis could improve patient selection. Biometrical analysis of TCGA-KIRC data identified candidate loci in the NK6 homeobox 2 gene (NKX6-2) that are hypermethylated in primary metastatic RCC. Analyses of NKX6-2 DNA methylation in three gene regions including a total of 16 CpG sites in 154 tumor-adjacent normal tissue, 189 RCC, and 194 metastatic tissue samples from 95 metastasized RCC patients revealed highly significant tumor-specific, primary metastatic-specific, and metastatic tissue-specific hypermethylation of NKX6-2. Combined CpG site methylation data for NKX6-2 and metastasis-associated genes (INA, NHLH2, and THBS4) demonstrated similarity between metastatic tissues and metastatic primary RCC tissues. The random forest method and evaluation of an unknown test cohort of tissues using receiver operator characteristic curve analysis revealed that metastatic tissues can be differentiated by a median area under the curve of 0.86 (p = 1.7 × 10−8–7.5 × 10−3) in 1000 random runs. Analysis of variable importance demonstrated an above median contribution for decision-making of at least one CpG site in each of the genes, suggesting superior informativity for sites annotated to NHLH2 and NKX6-2. Thus, DNA methylation of NKX6-2 is associated with the metastatic state of RCC tissues and contributes to a four-gene-based statistical predictor of tumoral and metastatic renal tissues.
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Affiliation(s)
- Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
- Correspondence:
| | - Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Olga Katzendorn
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Tu N. Dang
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Joana Moog
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Zarife Balli
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Christel Reese
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Jörg Hennenlotter
- Department of Urology, University of Tübingen, 72076 Tübingen, Germany
| | - Alexander Grote
- Department of Neurosurgery, University Hospital Gießen und Marburg, 35043 Marburg, Germany
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Markus A. Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
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Age-Related DNA Methylation in Normal Kidney Tissue Identifies Epigenetic Cancer Risk Susceptibility Loci in the ANKRD34B and ZIC1 Genes. Int J Mol Sci 2022; 23:ijms23105327. [PMID: 35628134 PMCID: PMC9141100 DOI: 10.3390/ijms23105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
Both age-dependent and age-independent alteration of DNA methylation in human tissues are functionally associated with the development of many malignant and non-malignant human diseases. TCGA-KIRC data were biometrically analyzed to identify new loci with age-dependent DNA methylation that may contribute to tumor risk in normal kidney tissue. ANKRD34B and ZIC1 were evaluated as candidate genes by pyrosequencing of 539 tissues, including 239 normal autopsy, 157 histopathologically tumor-adjacent normal, and 143 paired tumor kidney samples. All candidate CpG loci demonstrated a strong correlation between relative methylation levels and age (R = 0.70−0.88, p < 2 × 10−16) and seven out of 10 loci were capable of predicting chronological age in normal kidney tissues, explaining 84% of the variance (R = 0.92). Moreover, significantly increased age-independent methylation was found for 9 out of 10 CpG loci in tumor-adjacent tissues, compared to normal autopsy tissues (p = 0.001−0.028). Comparing tumor and paired tumor-adjacent tissues revealed two patient clusters showing hypermethylation, one cluster without significant changes in methylation, and a smaller cluster demonstrating hypomethylation in the tumors (p < 1 × 10−10). Taken together, our results show the presence of additional methylation risk factors besides age for renal cancer in normal kidney tissue. Concurrent tumor-specific hypermethylation suggests a subset of these loci are candidates for epigenetic renal cancer susceptibility.
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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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Kubiliute R, Zalimas A, Bakavicius A, Ulys A, Jankevicius F, Jarmalaite S. Clinical Significance of ADAMTS19, BMP7, SIM1, and SFRP1 Promoter Methylation in Renal Clear Cell Carcinoma. Onco Targets Ther 2021; 14:4979-4990. [PMID: 34675538 PMCID: PMC8502107 DOI: 10.2147/ott.s330341] [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: 07/23/2021] [Accepted: 08/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney tumors, accounting for the majority of deaths from genitourinary cancers. The currently used nomograms for predicting patient outcomes are based on clinical-pathological characteristics only; however, a significant number of ccRCC survivors with similar radiological and histological features still demonstrate a different clinical course of the disease. This study aimed at the identification of novel DNA methylation biomarkers for the monitoring of patients with ccRCC. Methods Gene expression profiling by SurePrint G3 Human GE 8×60K Microarrays was performed in 4 ccRCC tissues and adjacent non-cancerous renal tissue (NRT) samples. Four down-regulated genes were selected for further DNA methylation status analysis in 123 ccRCC and 45 NRT samples using methylation-specific PCR (MSP). Results DNA methylation changes of ADAMTS19, BMP7, SIM1, and SFRP1 were cancer-specific with significantly (P<0.050) higher methylation frequency (37%, 20%, 18%, and 42%, respectively) in tumor tissues. The methylated status of at least one gene was significantly related to various clinical-pathological parameters, including tumor size, Fuhrman and WHO/ISUP grades, intravascular invasion, and necrosis. Moreover, the methylated status of multimarker panel ADAMTS19, BMP7 & SFRP1 was predictive for poorer overall survival (HR, 4.11; 95% CI, 1.22–13.86). Conclusion In conclusion, DNA methylation of the three-gene panel consisting of ADAMTS19, BMP7 & SFRP1 supposedly predicts the outcome of patients diagnosed with ccRCC and possibly might be used to enrich the current prognostic tools.
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Affiliation(s)
- Raimonda Kubiliute
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,National Cancer Institute, Vilnius, Lithuania
| | - Algirdas Zalimas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,National Cancer Institute, Vilnius, Lithuania
| | - Arnas Bakavicius
- National Cancer Institute, Vilnius, Lithuania.,Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.,Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | - Feliksas Jankevicius
- Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.,Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Sonata Jarmalaite
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,National Cancer Institute, Vilnius, Lithuania
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12
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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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13
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A Genome-Wide Profiling of Glioma Patients with an IDH1 Mutation Using the Catalogue of Somatic Mutations in Cancer Database. Cancers (Basel) 2021; 13:cancers13174299. [PMID: 34503108 PMCID: PMC8428353 DOI: 10.3390/cancers13174299] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Glioma patients that present a somatic mutation in the isocitrate dehydrogenase 1 (IDH1) gene have a significantly better prognosis and overall survival than patients with the wild-type genotype. An IDH1 mutation is hypothesized to occur early during cellular transformation and leads to further genetic instability. A genome-wide profiling of glioma patients in the Catalogue of Somatic Mutations in Cancer (COSMIC) database was performed to classify the genetic differences in IDH1-mutant versus IDH1-wildtype patients. This classification will aid in a better understanding of how this specific mutation influences the genetic make-up of glioma and the resulting prognosis. Key differences in co-mutation and gene expression levels were identified that correlate with an improved prognosis. Abstract Gliomas are differentiated into two major disease subtypes, astrocytoma or oligodendroglioma, which are then characterized as either IDH (isocitrate dehydrogenase)-wild type or IDH-mutant due to the dramatic differences in prognosis and overall survival. Here, we investigated the genetic background of IDH1-mutant gliomas using the Catalogue of Somatic Mutations in Cancer (COSMIC) database. In astrocytoma patients, we found that IDH1 is often co-mutated with TP53, ATRX, AMBRA1, PREX1, and NOTCH1, but not CHEK2, EGFR, PTEN, or the zinc finger transcription factor ZNF429. The majority of the mutations observed in these genes were further confirmed to be either drivers or pathogenic by the Cancer-Related Analysis of Variants Toolkit (CRAVAT). Gene expression analysis showed down-regulation of DRG2 and MSN expression, both of which promote cell proliferation and invasion. There was also significant over-expression of genes such as NDRG3 and KCNB1 in IDH1-mutant astrocytoma patients. We conclude that IDH1-mutant glioma is characterized by significant genetic changes that could contribute to a better prognosis in glioma patients.
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14
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Liang F, Wang R, Du Q, Zhu S. An Epithelial-Mesenchymal Transition Hallmark Gene-Based Risk Score System in Head and Neck Squamous-Cell Carcinoma. Int J Gen Med 2021; 14:4219-4227. [PMID: 34393501 PMCID: PMC8354775 DOI: 10.2147/ijgm.s327632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022] Open
Abstract
Background Epithelial-to-mesenchymal transition (EMT) program plays a critical role in cancer. Thus, we attempted to generate a risk score system according to the expression pattern of different EMT hallmark genes in head and neck squamous-cell carcinoma (HNSC). Methods Differentially expressed EMT hallmark genes were screened to generate a risk score (RS) on TCGA HNSC dataset. The relative prognostic value of the RS compared to clinicopathological characteristics was explored using multivariable Cox analysis. Functional enrichment analysis was performed to reveal the biological characteristics. An external dataset was applied to validate the prognostic value of the RS. Results Nine genes constituted the EMT hallmark gene-based RS, which is significantly associated with poor prognosis and could successfully divide patients with HNSC into high- and low-risk groups. The RS was also an independent prognostic indicator compared to routine clinical factors. Conclusion We proposed and validated a nine-EMT hallmark gene-based risk score system in HNSC.
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Affiliation(s)
- Feifei Liang
- Department of Radiation Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Rensheng Wang
- Department of Radiation Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Qinghua Du
- Department of Radiation Oncology, Second Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Shangyong Zhu
- Department of Ultrasound, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
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15
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Weighted Gene Coexpression Network Analysis to Construct Competitive Endogenous RNA Network in Chromogenic Renal Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5589101. [PMID: 34222474 PMCID: PMC8213485 DOI: 10.1155/2021/5589101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/24/2021] [Indexed: 12/02/2022]
Abstract
Aim This study is aimed at constructing the competing endogenous RNA (ceRNA) network in chromophobe renal cell carcinoma (ChRCC). Methods Clinical and RNA sequence profiles of patients with ChRCC, including messenger RNAs (mRNAs), microRNAs (miRNAs), and long noncoding RNAs (lncRNAs), were obtained from The Cancer Genome Atlas (TCGA) database. “edgeR” and “clusterProfiler” packages were utilized to obtain the expression matrices of differential RNAs (DERNAs) and to conduct gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Weighted gene coexpression network analysis (WGCNA) was performed to screen the highly related RNAs, and miRcode, StarBase, miRTarBase, miRDB, and TargetScan datasets were used to predict the connections between them. Univariate and multivariate Cox proportional hazards regressions were performed in turn to elucidate prognosis-related mRNAs in order to construct the ceRNA regulatory network. Results A total of 1628 DElncRNAs, 104 DEmiRNAs, and 2619 DEmRNAs were identified. WGCNA showed significant correlation in 1534 DElncRNAs, 98 DEmiRNAs, and 2543 DEmRNAs, which were related to ChRCC. Fourteen DEmiRNAs, 113 DElncRNAs, and 43 DEmRNAs were screened. Nine mRNAs (ALPL, ARHGAP29, CADM2, KIT, KLRD1, MYBL1, PSD3, SFRP1, and SLC7A11) significantly contributed to the overall survival (OS) of patients with ChRCC (P < 0.05). Furthermore, two mRNAs (CADM2 and SFRP1) appeared to be independent risk factors for ChRCC. Conclusion The findings revealed the molecular mechanism of ChRCC and potential therapeutic targets for the disease.
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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Katzendorn O, Peters I, Dubrowinskaja N, Tezval H, Tabrizi PF, von Klot CA, Hennenlotter J, Lafos M, Kuczyk MA, Serth J. DNA methylation of tumor associated calcium signal transducer 2 (TACSTD2) loci shows association with clinically aggressive renal cell cancers. BMC Cancer 2021; 21:444. [PMID: 33882870 PMCID: PMC8061065 DOI: 10.1186/s12885-021-08172-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 04/08/2021] [Indexed: 01/02/2023] Open
Abstract
Background DNA methylation is frequently observed in the development and progression of many human tumors as well as renal cell cancer (RCC). Tumor Associated Calcium Signal Transducer 2 (TACSTD2) participates in cell cycle progression through MAPK signalling pathway activation. Moreover, tumor-specific hypermethylation and association with aggressive cancer characteristics has been found for lung adenocarcinoma, hepatocellular carcinoma and cholangiocarcinoma. Whether TACSTD2 is tumor specifically hypermethylated in RCC or shows association of methylation with adverse clinicopathological parameters and survival of patients has not been investigated at yet. Methods Quantitative methylation-specific PCR (qMSP) analysis of a locus in the intron 1 region of TACSTD2 gene was carried out in a cross-sectional study of 127 paired RCC and normal samples. In silico analysis of TACSTD2 methylation in the TCGA Kidney Renal Clear Cell Carcinoma (KIRC) dataset of 280 patients served as validation cohort. Statistical analyses were carried out using the two-sided paired t-test for matched tumor and normal sample comparisons, logistic regression for subgroup comparisons, Cox regression for analysis of recurrence free survival (RFS) and Pearson correlation analysis for correlation of TACSTD2 methylation and TACSTD2 mRNA in KIRC data. Results Higher methylation levels in RCC were significantly associated with advanced disease (p < 0.001), high tumor stage (p = 0.003), tumor differentiation (p = 0.033) and presence of lymph node (p = 0.021) or distant metastases (p = 0.008). TACSTD2 hypermethylation was associated with a shorter RFS of patients and demonstrate statistical independency from clinical parameters as state of metastasis, tumor stage, grade and state of advanced disease. In silico validation using TCGA KIRC data also demonstrated association of TACSTD2 loci with adverse clinicopathology and shortened RFS of patients. In addition, in silico analyses of TCGA KIRC data showed an inverse correlation between DNA methylation levels of TACSTD2 and mRNA expression. Conclusions Our results suggest an association between TACSTD2 methylation and disease progression and clinical course of RCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08172-1.
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Affiliation(s)
- Olga Katzendorn
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany.
| | - Natalia Dubrowinskaja
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Pouriya Faraj Tabrizi
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Christoph A von Klot
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Jörg Hennenlotter
- Department of Urology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Markus A Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625, Hannover, Germany
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Liu P, Tian W. Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis. PeerJ 2020; 8:e9654. [PMID: 32832275 PMCID: PMC7409785 DOI: 10.7717/peerj.9654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 12/30/2022] Open
Abstract
Background Tumorigenesis is highly heterogeneous, and using clinicopathological signatures only is not enough to effectively distinguish clear cell renal cell carcinoma (ccRCC) and improve risk stratification of patients. DNA methylation (DNAm) with the stability and reversibility often occurs in the early stage of tumorigenesis. Disorders of transcription and metabolism are also an important molecular mechanisms of tumorigenesis. Therefore, it is necessary to identify effective biomarkers involved in tumorigenesis through multi-omics analysis, and these biomarkers also provide new potential therapeutic targets. Method The discovery stage involved 160 pairs of ccRCC and matched normal tissues for investigation of DNAm and biomarkers as well as 318 cases of ccRCC including clinical signatures. Correlation analysis of epigenetic, transcriptomic and metabolomic data revealed the connection and discordance among multi-omics and the deregulated functional modules. Diagnostic or prognostic biomarkers were obtained by the correlation analysis, the Least Absolute Shrinkage and Selection Operator (LASSO) and the LASSO-Cox methods. Two classifiers were established based on random forest (RF) and LASSO-Cox algorithms in training datasets. Seven independent datasets were used to evaluate robustness and universality. The molecular biological function of biomarkers were investigated using DAVID and GeneMANIA. Results Based on multi-omics analysis, the epigenetic measurements uniquely identified DNAm dysregulation of cellular mechanisms resulting in transcriptomic alterations, including cell proliferation, immune response and inflammation. Combination of the gene co-expression network and metabolic network identified 134 CpG sites (CpGs) as potential biomarkers. Based on the LASSO and RF algorithms, five CpGs were obtained to build a diagnostic classifierwith better classification performance (AUC > 99%). A eight-CpG-based prognostic classifier was obtained to improve risk stratification (hazard ratio (HR) > 4; log-rank test, p-value < 0.01). Based on independent datasets and seven additional cancers, the diagnostic and prognostic classifiers also had better robustness and stability. The molecular biological function of genes with abnormal methylation were significantly associated with glycolysis/gluconeogenesis and signal transduction. Conclusion The present study provides a comprehensive analysis of ccRCC using multi-omics data. These findings indicated that multi-omics analysis could identify some novel epigenetic factors, which were the most important causes of advanced cancer and poor clinical prognosis. Diagnostic and prognostic biomarkers were identified, which provided a promising avenue to develop effective therapies for ccRCC.
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Affiliation(s)
- Pengfei Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China.,Children's Hospital of Fudan University, Shanghai, China
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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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Downregulation of SFRP1 is a protumorigenic event in hepatoblastoma and correlates with beta-catenin mutations. J Cancer Res Clin Oncol 2020; 146:1153-1167. [PMID: 32189106 PMCID: PMC7142044 DOI: 10.1007/s00432-020-03182-1] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/11/2020] [Indexed: 12/20/2022]
Abstract
Background Hepatoblastoma (HB) and pediatric hepatocellular carcinoma (HCC) are the most common malignant liver tumors in childhood. Both tumor types exhibit genetic and epigenetic alterations in the WNT/β-catenin signaling pathway, which is a key regulator of liver progenitor cells in embryonic development. The tumors demonstrate a high rate of β-catenin mutations and gene expression changes of several WNT antagonists. However, the role of the WNT inhibitory factor secreted frizzled-related protein 1 (SFRP1) has not been addressed in pediatric liver cancer so far. Results In our study, we investigated the gene expression level, DNA methylation status and functional relevance of SFRP1 in HB cell lines and in pediatric liver tumor patient samples. SFRP1 was downregulated due to DNA promoter methylation in all tested HB cell lines. Overexpression of SFRP1 in HB cell lines diminished tumor cell proliferation, colony formation and migration potential. In addition, the SFRP1-expressing HB cell lines showed reduced WNT/β-catenin signaling pathway activity and decreased expression of WNT target genes. To evaluate the utility of SFRP1 as a biomarker in pediatric liver cancer, we determined the gene expression level and DNA methylation status of SFRP1 in 45 pediatric liver tumor patient samples. The correlation analysis of different clinical parameters and tumor characteristics revealed a significant correlation of reduced SFRP1 expression with the presence of mutant β-catenin. The methylation status of SFRP1 was furthermore associated to a pediatric liver tumor type with HCC-like characteristics, TERT mutations and an older age at diagnosis. Conclusion Altogether, our data demonstrate that the epigenetic suppression of the WNT/β-catenin antagonist SFRP1 has an important impact on the malignant behavior of HB cells. Although SFRP1 methylation is a common event in HCC-like pediatric liver tumors, its potential as a prognostic or diagnostic biomarker needs to be further investigated. Electronic supplementary material The online version of this article (10.1007/s00432-020-03182-1) contains supplementary material, which is available to authorized users.
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Serth J, Peters I, Dubrowinskaja N, Reese C, Albrecht K, Klintschar M, Lafos M, Grote A, Becker A, Hennenlotter J, Stenzl A, Tezval H, Kuczyk MA. Age-, tumor-, and metastatic tissue-associated DNA hypermethylation of a T-box brain 1 locus in human kidney tissue. Clin Epigenetics 2020; 12:33. [PMID: 32070431 PMCID: PMC7029553 DOI: 10.1186/s13148-020-0823-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/03/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND While a considerable number of tumor-specific hypermethylated loci have been identified in renal cell cancer (RCC), DNA methylation of loci showing successive increases in normal, tumoral, and metastatic tissues could point to genes with high relevance both for the process of tumor development and progression. Here, we report that DNA methylation of a locus in a genomic region corresponding to the 3'UTR of the transcription factor T-box brain 1 (TBR1) mRNA accumulates in normal renal tissues with age and possibly increased body mass index. Moreover, a further tissue-specific increase of methylation was observed for tumor and metastatic tissue samples. RESULTS Biometric analyses of the TCGA KIRC methylation data revealed candidate loci for age-dependent and tumor-specific DNA methylation within the last exon and in a genomic region corresponding to the 3'UTR TBR1 mRNA. To evaluate whether methylation of TBR1 shows association with RCC carcinogenesis, we measured 15 tumor cell lines and 907 renal tissue samples including 355 normal tissues, 175 tissue pairs of normal tumor adjacent and corresponding tumor tissue as well 202 metastatic tissues samples of lung, bone, and brain metastases by the use of pyrosequencing. Statistical evaluation demonstrated age-dependent methylation in normal tissue (R = 0.72, p < 2 × 10-16), association with adiposity (P = 0.019) and tumor-specific hypermethylation (P = 6.1 × 10-19) for RCC tissues. Comparison of tumor and metastatic tissues revealed higher methylation in renal cancer metastases (P = 2.65 × 10-6). CONCLUSIONS Our analyses provide statistical evidence of association between methylation of TBR1 and RCC development and disease progression.
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Affiliation(s)
- Jürgen Serth
- Klinik für Urologie und urologische Onkologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, D-30625, Hannover, Germany.
| | - Inga Peters
- Klinik für Urologie und urologische Onkologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, D-30625, Hannover, Germany
| | - Natalia Dubrowinskaja
- Klinik für Urologie und urologische Onkologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, D-30625, Hannover, Germany
| | - Christel Reese
- Klinik für Urologie und urologische Onkologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, D-30625, Hannover, Germany
| | - Knut Albrecht
- Brandenburgisches Landesinstitut für Rechtsmedizin, Lindstedter Chaussee 6, D-14469, Potsdam, Germany
| | - Michael Klintschar
- Institut für Rechtsmedizin, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, D-30625, Hannover, Germany
| | - Marcel Lafos
- Institut für Pathologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, D-30625, Hannover, Germany
| | - Alexander Grote
- Evangelisches Klinikum Bethel, Klinik für Neurochirurgie, Burgsteig 13, D-33617, Bielefeld, Germany
| | - Albert Becker
- Institut für Neuropathologie, Universitätsklinikum Bonn, Sigmund Freud Str. 25, D-53105, Bonn, Germany
| | - Jörg Hennenlotter
- Universitätsklinikum Tübingen, Klinik für Urologie, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | - Arnulf Stenzl
- Universitätsklinikum Tübingen, Klinik für Urologie, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | - Hossein Tezval
- Klinik für Urologie und urologische Onkologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, D-30625, Hannover, Germany
| | - Markus A Kuczyk
- Klinik für Urologie und urologische Onkologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, D-30625, Hannover, Germany
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Baharudin R, Tieng FYF, Lee LH, Ab Mutalib NS. Epigenetics of SFRP1: The Dual Roles in Human Cancers. Cancers (Basel) 2020; 12:E445. [PMID: 32074995 PMCID: PMC7072595 DOI: 10.3390/cancers12020445] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/01/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Secreted frizzled-related protein 1 (SFRP1) is a gene that belongs to the secreted glycoprotein SFRP family. SFRP1 has been classified as a tumor suppressor gene due to the loss of expression in various human cancers, which is mainly attributed by epigenetic inactivation via DNA methylation or transcriptional silencing by microRNAs. Epigenetic silencing of SFRP1 may cause dysregulation of cell proliferation, migration, and invasion, which lead to cancer cells formation, disease progression, poor prognosis, and treatment resistance. Hence, restoration of SFRP1 expression via demethylating drugs or over-expression experiments opens the possibility for new cancer therapy approach. While the role of SFRP1 as a tumor suppressor gene is well-established, some studies also reported the possible oncogenic properties of SFRP1 in cancers. In this review, we discussed in great detail the dual roles of SFRP1 in cancers-as tumor suppressor and tumor promoter. The epigenetic regulation of SFRP1 expression will also be underscored with additional emphasis on the potentials of SFRP1 in modulating responses toward chemotherapeutic and epigenetic-modifying drugs, which may encourage the development of novel drugs for cancer treatment. We also present findings from clinical trials and patents involving SFRP1 to illustrate its clinical utility, extensiveness of each research area, and progression toward commercialization. Lastly, this review provides directions for future research to advance SFRP1 as a promising cancer biomarker.
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Affiliation(s)
- Rashidah Baharudin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia; (R.B.); (F.Y.F.T.)
| | - Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia; (R.B.); (F.Y.F.T.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia
| | - Nurul Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia; (R.B.); (F.Y.F.T.)
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Mo S, Su Z, Heng B, Chen W, Shi L, Du X, Lai C. SFRP1 Promoter Methylation and Renal Carcinoma Risk: A Systematic Review and Meta-Analysis. J NIPPON MED SCH 2018; 85:78-86. [PMID: 29731501 DOI: 10.1272/jnms.2018_85-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIM Epigenetic inactivation of tumor suppressor genes is an important molecular mechanism in the formation and development of human tumors. The purpose of our study was to evaluate the correlation between the methylation level of the secreted frizzled-related protein 1 (SFRP1) gene and the risk of renal cell carcinoma (RCC). METHODS The relevant literature was searched in detail in several electronic databases. The methodological heterogeneity was analyzed by meta-regression and subgroup analyses. The odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were calculated to summarize the dichotomous outcomes of our meta-analysis. RESULTS The ten included articles contained 535 RCC samples and 475 normal controls. The results demonstrated that the methylation level of the SFRP1 promoter region was significantly correlated with an increased incidence of RCC (OR=13.72; 95% CI: 6.01-31.28; P=0.000). Furthermore, the eligible studies that had sufficient clinical data about the RCC cases were included in the analysis, and the results indicated that the frequency of SFRP1 promoter methylation was associated with a higher histological grade (P=0.000), tumor stage (P=0.033), tumor size (≥5 cm; P=0.029), and distant metastasis (P=0.047). CONCLUSION Our results indicate that the methylation level of the SFRP1 promoter region is increased in patients with RCC compared to normal controls and might be involved in the occurrence and development of RCC. Additional well-designed studies are needed to further verify our conclusions.
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Affiliation(s)
- Shijie Mo
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Zexuan Su
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Baoli Heng
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Weijun Chen
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Liping Shi
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Xinghua Du
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Caiyong Lai
- Department of Urology, The First Affiliated Hospital, Jinan University
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25
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Zhu QN, Renaud H, Guo Y. Bioinformatics-based identification of miR-542-5p as a predictive biomarker in breast cancer therapy. Hereditas 2018; 155:17. [PMID: 29371858 PMCID: PMC5769523 DOI: 10.1186/s41065-018-0055-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/04/2018] [Indexed: 01/04/2023] Open
Abstract
Background Tamoxifen is the first-line hormone therapy for estrogen receptor alpha positive (ERα+) breast cancer. However, about 40% of patients with ERα + breast cancer who receive tamoxifen therapy eventually develop resistance resulting in a poor prognosis. The aim of this study was to mine available data sets in the Gene Expression Omnibus (GEO) database, including in vitro (cell lines) and in vivo (tissue samples), and to identify all miRNAs associated with tamoxifen resistance (TamR) in breast cancer. Secondly, this study aimed to predict the key gene regulatory networks of newly found TamR-related miRNAs and evaluate the potential role of the miRNAs and targets as potential prognosis biomarkers for breast cancer patients. Result Microarray data sets from two different studies were used from the GEO database: 1. GSE66607: miRNA of MCF-7 TamR cells; 2. GSE37405: TamR tissues. Differentially expressed microRNAs (miRNAs) were identified in both data sets and 5 differentially expressed miRNAs were found to overlap between the two data sets. Profiles of GSE37405 and data from the Kaplan-Meier Plotter Database (KMPD) along with Gene Expression Profiling Interactive Analysis (GEPIA) were used to reveal the relationship between these 5 miRNAs and overall survival. The results showed that has-miR-542-5p was the only miRNA associated with overall survival of ERα + breast cancer patients who received adjuvant tamoxifen. Targets of has-miR-542-5p were predicted by miRanda and TargetScan, and the mRNA expression of the three 3 target gene, Tyrosine 3-Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Beta (YWHAB), Lymphocyte Antigen 9 (LY9), and Secreted Frizzled Related Protein 1 (SFRP1) were associated with overall survival in 2 different databases. Copy-number alterations (CNAs) of SFRP1 confer survival disadvantage to breast cancer patients and alter the mRNA expression of SFRP1 in cBioPortal database. Conclusion This study indicates that miRNA has-miR-542-5p is associated with TamR and can predict prognosis of breast cancer patients. Furthermore, has-miR-542-5p may be acting through a mechanism involving the target genes YWHAB, LY9, and SFRP1. Overall, has-miR-542-5p is a predictive biomarker and potential target for therapy of breast cancer patients. Electronic supplementary material The online version of this article (10.1186/s41065-018-0055-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiong-Ni Zhu
- 1Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008 People's Republic of China.,2Institute of Clinical Pharmacology, Central South University, Changsha, 410078 People's Republic of China.,3Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078 People's Republic of China
| | - Helen Renaud
- 4University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Ying Guo
- 1Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008 People's Republic of China.,2Institute of Clinical Pharmacology, Central South University, Changsha, 410078 People's Republic of China.,3Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078 People's Republic of China
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26
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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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27
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Mendoza-Pérez J, Gu J, Herrera LA, Tannir NM, Zhang S, Matin S, Karam JA, Wood CG, Wu X. Prognostic significance of promoter CpG island methylation of obesity-related genes in patients with nonmetastatic renal cell carcinoma. Cancer 2017; 123:3617-3627. [PMID: 28543182 DOI: 10.1002/cncr.30707] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/22/2017] [Accepted: 03/13/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND Greater than 40% of renal cell carcinoma (RCC) cases in the United States are attributed to excessive body weight. Moreover, obesity also may be linked to RCC prognosis. However, the molecular mechanisms underlying these associations are unclear. In the current study, the authors evaluated the role of promoter methylation in obesity-related genes in RCC tumorigenesis and disease recurrence. METHODS Paired tumors (TU) and normal adjacent (N-Adj) tissues from 240 newly diagnosed and previously untreated white patients with RCC were examined. For the discovery phase, 63 RCC pairs were analyzed. An additional 177 RCC pairs were evaluated for validation. Pyrosequencing was used to determine CpG methylation in 20 candidate obesity-related genes. An independent data set from The Cancer Genome Atlas also was analyzed for functional validation. The association between methylation and disease recurrence was analyzed using multivariate Cox proportional hazards models and Kaplan-Meier survival analysis. RESULTS Methylation in neuropeptide Y (NPY), leptin (LEP), and leptin receptor (LEPR) was significantly higher in TU compared with N-Adj tissues (P<.0001) in both the discovery and validation groups. High methylation in LEPR was associated with an increased risk of disease recurrence (hazard ratio, 3.15; 95% confidence interval, 1.23-8.07 [P = .02]). Patients with high methylation in LEPR had a shorter recurrence-free survival compared with patients in the low-methylation group (log-rank P = 2.25 × 10-3 ). In addition, high LEPR methylation in TU was associated with more advanced features (P≤.05). Consistent with the findings of the current study, lower LEPR expression in TU compared with N-Adj tissues (P = 1.00 × 10-3 ) was found in data from The Cancer Genome Atlas. CONCLUSIONS Somatic alterations of promoter methylation in the NPY, LEP, and LEPR genes are involved in RCC tumorigenesis. Furthermore, LEPR methylation appears to be associated with RCC recurrence. Future research to elucidate the biology underlying this association is warranted. Cancer 2017;123:3617-27. © 2017 American Cancer Society.
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Affiliation(s)
- Julia Mendoza-Pérez
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Cancer Biomedical Research Unit, National Cancer Institute, Institute of Biomedical Research, National Autonomous University of Mexico, Mexico City, Mexico
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luis A Herrera
- Cancer Biomedical Research Unit, National Cancer Institute, Institute of Biomedical Research, National Autonomous University of Mexico, Mexico City, Mexico
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shanyu Zhang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Surena Matin
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher G Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Verma M. The Role of Epigenomics in the Study of Cancer Biomarkers and in the Development of Diagnostic Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 867:59-80. [PMID: 26530360 DOI: 10.1007/978-94-017-7215-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetics plays a key role in cancer development. Genetics alone cannot explain sporadic cancer and cancer development in individuals with no family history or a weak family history of cancer. Epigenetics provides a mechanism to explain the development of cancer in such situations. Alterations in epigenetic profiling may provide important insights into the etiology and natural history of cancer. Because several epigenetic changes occur before histopathological changes, they can serve as biomarkers for cancer diagnosis and risk assessment. Many cancers may remain asymptomatic until relatively late stages; in managing the disease, efforts should be focused on early detection, accurate prediction of disease progression, and frequent monitoring. This chapter describes epigenetic biomarkers as they are expressed during cancer development and their potential use in cancer diagnosis and prognosis. Based on epigenomic information, biomarkers have been identified that may serve as diagnostic tools; some such biomarkers also may be useful in identifying individuals who will respond to therapy and survive longer. The importance of analytical and clinical validation of biomarkers is discussed, along with challenges and opportunities in this field.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute (NCI), National Institutes of Health (NIH), Suite# 4E102. 9609 Medical Center Drive, MSC 9763, Bethesda, MD, 20892-9726, USA.
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Joosten SC, Hamming L, Soetekouw PM, Aarts MJ, Veeck J, van Engeland M, Tjan-Heijnen VC. Resistance to sunitinib in renal cell carcinoma: From molecular mechanisms to predictive markers and future perspectives. Biochim Biophys Acta Rev Cancer 2014; 1855:1-16. [PMID: 25446042 DOI: 10.1016/j.bbcan.2014.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/29/2014] [Accepted: 11/05/2014] [Indexed: 12/15/2022]
Abstract
The introduction of agents that inhibit tumor angiogenesis by targeting vascular endothelial growth factor (VEGF) signaling has made a significant impact on the survival of patients with metastasized renal cell carcinoma (RCC). Sunitinib, a tyrosine kinase inhibitor of the VEGF receptor, has become the mainstay of treatment for these patients. Although treatment with sunitinib substantially improved patient outcome, the initial success is overshadowed by the occurrence of resistance. The mechanisms of resistance are poorly understood. Insight into the molecular mechanisms of resistance will help to better understand the biology of RCC and can ultimately aid the development of more effective therapies for patients with this infaust disease. In this review we comprehensively discuss molecular mechanisms of resistance to sunitinib and the involved biological processes, summarize potential biomarkers that predict response and resistance to treatment with sunitinib, and elaborate on future perspectives in the treatment of metastasized RCC.
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Affiliation(s)
- S 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.
| | - L Hamming
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - P M Soetekouw
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - M 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.
| | - J Veeck
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands; Institute of Pathology, RWTH Aachen University Hospital, Pauwelsstr. 30, 52074 Aachen, Germany.
| | - M van Engeland
- Dept. of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - V 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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Peters I, Gebauer K, Dubrowinskaja N, Atschekzei F, Kramer MW, Hennenlotter J, Tezval H, Abbas M, Scherer R, Merseburger AS, Stenzl A, Kuczyk MA, Serth J. GATA5 CpG island hypermethylation is an independent predictor for poor clinical outcome in renal cell carcinoma. Oncol Rep 2014; 31:1523-30. [PMID: 24549248 PMCID: PMC3975988 DOI: 10.3892/or.2014.3030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 12/02/2013] [Indexed: 12/25/2022] Open
Abstract
Transcriptional inactivation and CpG island (CGI) methylation of GATA transcription factor family members GATA3 and GATA5 have been reported for a few types of human cancer. Whether high-density CGI methylation of GATA3 or GATA5 is associated with the clinical course of patients with renal cell cancer (RCC) has not been clarified. Quantitative methylation-specific PCR assays were carried out to analyze 25 tumor cell lines including 6 RCC lines and 119 RCC and 87 adjacent normal tissues for the presence of densely methylated sequences. Methylation values were statistically compared with clinicopathological and recurrence-free survival (RFS) data for patients. Comparison of GATA3 and GATA5 methylation in different tumor cell lines revealed a marker-specific methylation characteristic with high and frequent signals for both methylation marks in RCC lines. GATA3 and GATA5 CGI relative methylation levels were found to be strongly associated with the state of metastasis (P=0.003 and P<0.001, respectively) and advanced disease (P=0.024 and P<0.001, respectively). Moreover, an independent decrease in RFS in Cox proportional hazard analysis was found for tumors exhibiting high GATA5 methylation (P<0.001, hazard ratio, 19.3; 95% confidence interval, 4.58–81.6). Epigenetic alterations in GATA family members may be associated with aggressive tumor phenotypes in RCC, and in the case of GATA5, may serve as a new independent molecular marker for aggressiveness and disease progression.
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Affiliation(s)
- Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Kai Gebauer
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Natalia Dubrowinskaja
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Faranaz Atschekzei
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Mario W Kramer
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Joerg Hennenlotter
- Department of Urology, Eberhard-Karls University, D-72076 Tuebingen, Germany
| | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Mahmoud Abbas
- Department of Pathology, Hannover Medical School, D-30625 Hannover, Germany
| | - Ralph Scherer
- Department of Biometry, Hannover Medical School, D-30625 Hannover, Germany
| | - Axel S Merseburger
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Arnulf Stenzl
- Department of Urology, Eberhard-Karls University, D-72076 Tuebingen, Germany
| | - Markus A Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Juergen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, D-30625 Hannover, Germany
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Dubrowinskaja N, Gebauer K, Peters I, Hennenlotter J, Abbas M, Scherer R, Tezval H, Merseburger AS, Stenzl A, Grünwald V, Kuczyk MA, Serth J. Neurofilament Heavy polypeptide CpG island methylation associates with prognosis of renal cell carcinoma and prediction of antivascular endothelial growth factor therapy response. Cancer Med 2014; 3:300-9. [PMID: 24464810 PMCID: PMC3987080 DOI: 10.1002/cam4.181] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/29/2013] [Accepted: 11/19/2013] [Indexed: 12/26/2022] Open
Abstract
Neurofilament Heavy polypeptid (NEFH) belongs to the group of type IV intermediate filament proteins. DNA methylation of the NEFH promoter and loss of expression have previously been shown to activate the AKT/β-catenin pathway in tumor cells. When identifying hypermethylation of the NEFH CpG island (CGI) in renal cell cancer (RCC) we asked whether methylation could provide clinical or prognostic information for RCC and/or predict therapy response in patients with metastatic RCC (mRCC) undergoing antiangiogenic therapy. Relative methylation of the NEFH CGI was analyzed in 132 RCC samples and 83 paired normal tissues using quantitative methylation-specific PCR. Results were statistically compared with tumor histology, clinicopathological parameters, progression-free survival (PFS) as well as with overall survival (OS) in a subset of 18 mRCC patients following antiangiogenic therapy regimens. The NEFH CGI methylation demonstrated a tumor-specific increase (P < 0.001), association with advanced disease (P < 0.001), and distant metastasis (P = 0.005). Higher relative methylation was also significantly associated with a poor PFS (HR = 8.6, P < 0.001) independent from the covariates age, gender, diameter of tumors, state of advanced disease, and local and distant metastasis. Median OS following targeted therapy was 29.8 months for patients with low methylation versus 9.8 months for the group with high methylation (P = 0.028). We identified NEFH methylation as a candidate epigenetic marker for prognosis of RCC patients as well as prediction of anti-vascular endothelial growth factor-based therapy response.
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Dees C, Schlottmann I, Funke R, Distler A, Palumbo-Zerr K, Zerr P, Lin NY, Beyer C, Distler O, Schett G, Distler JHW. The Wnt antagonists DKK1 and SFRP1 are downregulated by promoter hypermethylation in systemic sclerosis. Ann Rheum Dis 2013; 73:1232-9. [DOI: 10.1136/annrheumdis-2012-203194] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Lu D, Dong D, Zhou Y, Lu M, Pang XW, Li Y, Tian XJ, Zhang Y, Zhang J. The tumor-suppressive function of UNC5D and its repressed expression in renal cell carcinoma. Clin Cancer Res 2013; 19:2883-92. [PMID: 23589179 DOI: 10.1158/1078-0432.ccr-12-2978] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE As a newly added member of the UNC5H receptors, the function of UNC5D/H4 in tumorigenesis remains poorly defined. The aim of this study was to examine the expression of UNC5D in primary renal cell carcinomas (RCC), analyze the mechanisms responsible for its downregulation in RCC, and assess its functional relevance to tumor growth and migration. EXPERIMENTAL DESIGN Forty-four paired primary RCCs and corresponding adjacent noncancerous tissues were collected. The mRNA and protein expression level of UNC5D was assessed by reverse transcriptase-PCR, real-time PCR, or immunohistochemistry. Epigenetic alterations in UNC5D promoter and LOH in the UNC5D locus were also analyzed. Ectopic expression of UNC5D in renal cancer cells with silenced expression of UNC5D was used for analysis of the biologic functions of UNC5D. RESULTS UNC5D expression was attenuated in multiple carcinoma cell lines including renal cancer cells. Similar reduction was also observed in primary RCC tissues as compared with paired adjacent noncancerous tissues. Methylation-specific PCR showed hypermethylation in UNC5D promoter in a significant proportion (18 of 44) of tumor tissue (40.9%). LOH of UNC5D was observed in 13 of 44 patients with RCCs (29.5%). Restoration of UNC5D expression in renal cancer cells significantly inhibited cell proliferation, anchorage-dependent and -independent growth, as well as migration and invasion, whereas knockdown of UNC5D promoted cell growth. Furthermore, ectopic expression of UNC5D induced G2-M cell-cycle arrest. CONCLUSIONS UNC5D is a functional tumor suppressor that is frequently downregulated in RCCs due to promoter hypermethylation and LOH.
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Affiliation(s)
- Dan Lu
- Department of Immunology, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Health Science Center, Beijing, China
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Gebauer K, Peters I, Dubrowinskaja N, Hennenlotter J, Abbas M, Scherer R, Tezval H, Merseburger AS, Stenzl A, Kuczyk MA, Serth J. Hsa-mir-124-3 CpG island methylation is associated with advanced tumours and disease recurrence of patients with clear cell renal cell carcinoma. Br J Cancer 2013; 108:131-8. [PMID: 23321515 PMCID: PMC3553529 DOI: 10.1038/bjc.2012.537] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background: Whether methylation of the microRNA (mir)-124-3 CpG island is of relevance for the clinical course of a solid cancer and whether it shows association with clinicopathology or survival of patients with renal cell cancer (RCC) is not known as yet. Methods: In a cross-sectional study, relative methylation of mir-124-3 was measured in 111 RCC samples and 77 paired normal appearing tissues using quantitative methyl-specific PCR. Results were statistically compared with tumour histology, clinicopathological parameters and disease recurrence. Results: We found tumour-specific hypermethylation of mir-124-3 in samples of RCCs with clear cell histology (ccRCC) compared with paired normal appearing tissues (P<0.0001). Methylation was significantly increased in tumours with state of advanced disease (P<0.0001). Higher relative methylation was associated with worse recurrence-free survival in both univariate (hazard ratio=9.37; P=0.0005) as well as bivariate Cox regression analyses considering age, sex, diameter of tumours and state of advanced disease, metastasis and lymph node metastases as covariates (hazard ratios=5.9–18.2; P-values of 0.0003–0.008). Conclusion: We identified mir-124-3 CpG islands (CGI) methylation as a relevant epigenetic mark for ccRCC thus underlining the need for functional studies of potentially affected signalling pathways in kidney tumour models. Methylation of mir-124-3 is suggested as an independent prognosticator for ccRCC.
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Affiliation(s)
- K Gebauer
- Department of Urology, Hannover Medical School, OE6247, Carl-Neuberg-Str.1, 30625 Hannover, Germany
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