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Zhuang L, Shi G, Sun Y. RNF135 promotes cell proliferation and autophagy in lung adenocarcinoma by promoting the phosphorylation of ULK1. Allergol Immunopathol (Madr) 2024; 52:3-9. [PMID: 38459884 DOI: 10.15586/aei.v52i2.1048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 12/26/2023] [Indexed: 03/11/2024]
Abstract
OBJECTIVE To detect the expression of RING finger protein 135 (RNF135) in lung adenocarcinoma tissues and explore its role in the progression of lung adenocarcinoma. METHODS Bioinformation analysis, quantitative polymerase chain reaction, and immunoblotting technique discovered the expression of RNF135 in lung adenocarcinoma tissues. Cell counting kit-8 and colony formation, immunostaining, and immunoblot assays examined the effects of RNF135 on cell growth and autophagy. Co-immunoprecipitation (Co-IP), immunostaining, and immuoblotting were conducted to confirm the mechanism. RESULTS RNF135 was highly expressed in lung adenocarcinoma. In addition, RNF135 promoted lung adenocarcinoma cell growth. Further, data confirmed that RNF135 promoted autophagy in lung adenocarcinoma cells. Mechanically, RNF135 directly interacted with Unc-51-like autophagy activating kinase 1 (ULK1) to promote its phosphorylation level. CONCLUSION RNF135 promoted cell growth and autophagy in lung adenocarcinoma by promoting the phosphorylation of ULK1.
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Affiliation(s)
- Lichun Zhuang
- Department of Pathology, Jiangyin Fifth People's Hospital, Jiangyin, Jiangsu Province, China
| | - Guanhui Shi
- Department of Pathology, Hongze Hospital, Huaian, Jiangsu Province, China
| | - Yuejun Sun
- Department of Pathology, Affiliated Jiangyin Hospital of Nantong University, Jiangyin, Jiangsu Province, China;
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2
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Kim SC, Kim DW, Cho EJ, Lee JY, Kim J, Kwon C, Kim-Ha J, Hong SK, Choi Y, Yi NJ, Lee KW, Suh KS, Kim W, Kim W, Kim H, Kim YJ, Yoon JH, Yu SJ, Kim YJ. A circulating cell-free DNA methylation signature for the detection of hepatocellular carcinoma. Mol Cancer 2023; 22:164. [PMID: 37803338 PMCID: PMC10557228 DOI: 10.1186/s12943-023-01872-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023] Open
Abstract
To address the shortcomings of current hepatocellular carcinoma (HCC) surveillance tests, we set out to find HCC-specific methylation markers and develop a highly sensitive polymerase chain reaction (PCR)-based method to detect them in circulating cell-free DNA (cfDNA). The analysis of large methylome data revealed that Ring Finger Protein 135 (RNF135) and Lactate Dehydrogenase B (LDHB) are universally applicable HCC methylation markers with no discernible methylation level detected in any other tissue types. These markers were used to develop Methylation Sensitive High-Resolution Analysis (MS-HRM), and their diagnostic accuracy was tested using cfDNA from healthy, at-risk, and HCC patients. The combined MS-HRM RNF135 and LDHB analysis detected 57% of HCC, outperforming the alpha-fetoprotein (AFP) test's sensitivity of 45% at comparable specificity. Furthermore, when used with the AFP test, the methylation assay can detect 70% of HCC. Our findings suggest that the cfDNA methylation assay could be used for HCC liquid biopsy.
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Affiliation(s)
- Si-Cho Kim
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Republic of Korea
- R&D center, LepiDyne Inc, Seoul, Republic of Korea
| | - Da-Won Kim
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Republic of Korea
- R&D center, LepiDyne Inc, Seoul, Republic of Korea
| | - Eun Ju Cho
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jin-Young Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jiwon Kim
- Department of Integrative Bioscience & Biotechnology, College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Chaesun Kwon
- Department of Integrative Bioscience & Biotechnology, College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience & Biotechnology, College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Suk Kyun Hong
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - YoungRok Choi
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nam-Joon Yi
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kwang-Woong Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Suk Suh
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Won Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul, Republic of Korea
| | - Woojin Kim
- Department of Bio-AI convergence, Chungnam National University, Daejeon, Republic of Korea
| | - Hyunsoo Kim
- Department of Bio-AI convergence, Chungnam National University, Daejeon, Republic of Korea
- Department of Convergent Bioscience and Informatics, Chungnam National University, Daejeon, Republic of Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Young-Joon Kim
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Republic of Korea.
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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Zhang Y, Zhang J, Zhang W, Wang M, Wang S, Xu Y, Zhao L, Li X, Li G. Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:573-588. [PMID: 36702236 PMCID: PMC10787015 DOI: 10.1016/j.gpb.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/30/2022] [Accepted: 01/17/2023] [Indexed: 01/25/2023]
Abstract
Studies on the lung cancer genome are indispensable for developing a cure for lung cancer. Whole-genome resequencing, genome-wide association studies, and transcriptome sequencing have greatly improved our understanding of the cancer genome. However, dysregulation of long-range chromatin interactions in lung cancer remains poorly described. To better understand the three-dimensional (3D) genomic interaction features of the lung cancer genome, we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase II (RNAPII), CCCTC-binding factor (CTCF), enhancer of zeste homolog 2 (EZH2), and histone 3 lysine 27 trimethylation (H3K27me3) using long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes, either through loops or domains, and their distributions along the genome were distinct from and complementary to those associated with RNAPII. Cancer-related genes were highly enriched with chromatin interactions, and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes, such as additional repressive interactions on FOXO4 and promoter-promoter interactions between NF1 and RNF135. Knockout of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes, suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes. These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.
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Affiliation(s)
- Yan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mohan Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangqi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Yao Xu
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China.
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Sarmah D, Meredith WO, Weber IK, Price MR, Birtwistle MR. Predicting anti-cancer drug combination responses with a temporal cell state network model. PLoS Comput Biol 2023; 19:e1011082. [PMID: 37126527 PMCID: PMC10174488 DOI: 10.1371/journal.pcbi.1011082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 05/11/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Cancer chemotherapy combines multiple drugs, but predicting the effects of drug combinations on cancer cell proliferation remains challenging, even for simple in vitro systems. We hypothesized that by combining knowledge of single drug dose responses and cell state transition network dynamics, we could predict how a population of cancer cells will respond to drug combinations. We tested this hypothesis here using three targeted inhibitors of different cell cycle states in two different cell lines in vitro. We formulated a Markov model to capture temporal cell state transitions between different cell cycle phases, with single drug data constraining how drug doses affect transition rates. This model was able to predict the landscape of all three different pairwise drug combinations across all dose ranges for both cell lines with no additional data. While further application to different cell lines, more drugs, additional cell state networks, and more complex co-culture or in vivo systems remain, this work demonstrates how currently available or attainable information could be sufficient for prediction of drug combination response for single cell lines in vitro.
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Affiliation(s)
- Deepraj Sarmah
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
| | - Wesley O. Meredith
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
| | - Ian K. Weber
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
- The University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Madison R. Price
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
- College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Marc R. Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
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5
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Saeliw T, Kanlayaprasit S, Thongkorn S, Songsritaya K, Sanannam B, Sae-Lee C, Jindatip D, Hu VW, Sarachana T. Epigenetic Gene-Regulatory Loci in Alu Elements Associated with Autism Susceptibility in the Prefrontal Cortex of ASD. Int J Mol Sci 2023; 24:ijms24087518. [PMID: 37108679 PMCID: PMC10139202 DOI: 10.3390/ijms24087518] [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: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Alu elements are transposable elements that can influence gene regulation through several mechanisms; nevertheless, it remains unclear whether dysregulation of Alu elements contributes to the neuropathology of autism spectrum disorder (ASD). In this study, we characterized transposable element expression profiles and their sequence characteristics in the prefrontal cortex tissues of ASD and unaffected individuals using RNA-sequencing data. Our results showed that most of the differentially expressed transposable elements belong to the Alu family, with 659 loci of Alu elements corresponding to 456 differentially expressed genes in the prefrontal cortex of ASD individuals. We predicted cis- and trans-regulation of Alu elements to host/distant genes by conducting correlation analyses. The expression level of Alu elements correlated significantly with 133 host genes (cis-regulation, adjusted p < 0.05) associated with ASD as well as the cell survival and cell death of neuronal cells. Transcription factor binding sites in the promoter regions of differentially expressed Alu elements are conserved and associated with autism candidate genes, including RORA. COBRA analyses of postmortem brain tissues showed significant hypomethylation in global methylation analyses of Alu elements in ASD subphenotypes as well as DNA methylation of Alu elements located near the RNF-135 gene (p < 0.05). In addition, we found that neuronal cell density, which was significantly increased (p = 0.042), correlated with the expression of genes associated with Alu elements in the prefrontal cortex of ASD. Finally, we determined a relationship between these findings and the ASD severity (i.e., ADI-R scores) of individuals with ASD. Our findings provide a better understanding of the impact of Alu elements on gene regulation and molecular neuropathology in the brain tissues of ASD individuals, which deserves further investigation.
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Affiliation(s)
- Thanit Saeliw
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Songphon Kanlayaprasit
- Systems Neuroscience of Autism and Psychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Surangrat Thongkorn
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kwanjira Songsritaya
- The M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Bumpenporn Sanannam
- Division of Anatomy, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani 12120, Thailand
| | - Chanachai Sae-Lee
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Depicha Jindatip
- Systems Neuroscience of Autism and Psychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA
| | - Tewarit Sarachana
- Systems Neuroscience of Autism and Psychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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6
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Yao Y, Gong G, Guo Z, Zhang D. A pan-cancer analysis of ring finger protein 135 and its relationship to triple-negative breast cancer proliferation and metastasis. Aging (Albany NY) 2022; 14:9758-9772. [PMID: 36495591 PMCID: PMC9792201 DOI: 10.18632/aging.204429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Ring finger protein 135 (RNF135) is an E3 ubiquitin ligase with RING finger domains that plays a crucial role in the development of several forms of cancer. Neither the expression profile of RNF135 nor its importance in the diagnosis of pan-cancer have been elucidated as of yet. With the aid of The Cancer Genome Atlas and Gene Expression Omnibus, we have fully mapped the expression profiles, prognostic relevance, genetic modification, immune cell infiltration, and tumor heterogeneity of RNF135 in 33 malignant tumors. RNF135 was expressed inconsistently in various cancers, and variations in RNF135 expression predicted survival outcomes for cancer patients. There was a strong correlation between the levels of the RNF135 genetic mutation and some tumor progression. In addition, a strong correlation was seen between RNF135 expression and immune cell infiltration, tumor mutation burden, microsatellite instability, and immunoregulators. In contrast, the correlation between RNF135 expression and triple-negative breast cancer was investigated in this study. RNF135 may boost the proliferation, migration, and invasion of TNBC cells, according to cell experiments. RNF135 might be utilized as a biomarker to anticipate how a tumor will behave and may have a significant role in how TNBC cells grow and migrate, according to the findings of this study.
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Affiliation(s)
- Yiqun Yao
- Department of Breast and Thyroid Surgery, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, China
| | - Guanyu Gong
- Department of Oncology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, China
| | - Zijian Guo
- Department of Breast and Thyroid Surgery, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, China
| | - Dianlong Zhang
- Department of Breast and Thyroid Surgery, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, China
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7
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Bioinformatics analysis identified RGS4 as a potential tumor promoter in glioma. Pathol Res Pract 2022; 240:154225. [DOI: 10.1016/j.prp.2022.154225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/31/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022]
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8
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Lin K, Shen SH, Lu F, Zheng P, Wu S, Liao J, Jiang X, Zeng G, Wei D. CRISPR screening of E3 ubiquitin ligases reveals Ring Finger Protein 185 as a novel tumor suppressor in glioblastoma repressed by promoter hypermethylation and miR-587. J Transl Med 2022; 20:96. [PMID: 35183197 PMCID: PMC8858481 DOI: 10.1186/s12967-022-03284-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/30/2022] [Indexed: 11/10/2022] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive malignant primary brain tumor. E3 ligases play important functions in glioma pathogenesis. CRISPR system offers a powerful platform for genome manipulation, while the screen of E3 ligases in GBM still remains to be explored. Here, we first constructed an E3 ligase small guide RNA (sgRNAs) library for glioma cells growth screening. After four passages, 299 significantly enriched or lost genes (SELGs) were compared with the initial state. Then the clinical significance of SELGs were validated and analyzed with TCGA glioblastoma and CGGA datasets. As RNF185 showed lost signal, decreased expression and favorable prognostic significance, we chose RNF185 for functional analysis. In vitro overexpressed cellular phenotype showed that RNF185 was a tumor suppressor in two glioma cell lines. Finally, the molecular mechanism of decreased RNF185 expression was investigated and increased miR-587 expression and DNA hypermethylation was evaluated. This study would provide a link between the molecular basis and glioblastoma pathogenesis, and a novel perspective for glioblastoma treatment.
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9
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Wang X, Chen M, Liang X, Bai Y, Zeng J, Xu X, Li H, Wang J, Fan K, Zhao G. RNF135 Promoter Methylation Is Associated With Immune Infiltration and Prognosis in Hepatocellular Carcinoma. Front Oncol 2022; 11:752511. [PMID: 35145901 PMCID: PMC8821516 DOI: 10.3389/fonc.2021.752511] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/16/2021] [Indexed: 12/02/2022] Open
Abstract
RING finger protein 135 has an important role in the occurrence of many cancers; however its regulation and function of RNF135 in hepatocellular carcinoma remains unknown. The promoter methylation status and mRNA expression of RNF135 was evaluated by methylation-specific PCR, semi-quantitative RT-PCR, and real-time quantitative PCR in HCC tissues and cell lines, and further analyzed from The Cancer Genome Atlas database. Wound healing assay, transwell migration, cell viability, and colony formation assay were performed to investigate the function of RNF135. GSEA analysis, TIMER database, and ESTIMATE algorithm were used to decipher the associated pathway and immune infiltration. The survival analysis was applied to assess the prognostic value of RNF135. RNF135 expression was downregulated in HCC tissues and 5 of 8 HCC cell lines, and was negatively correlated with its promoter hypermethylation. Demethylating regent decitabine restored RNF135 expression on the cellular level. Knockdown of RNF135 expression enhanced the migration of HCC cells, while RNF135 overexpression and decitabine treatment repressed cell migration. Bioinformatics analysis and immunohistochemistry revealed a positive relationship between RNF135 expression and six immune cell infiltrates (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells). Survival analysis disclosed that RNF135 hypermethylation is independently associated with poor clinical outcomes in HCC. Decreased RNF135 expression driven by promoter hypermethylation frequently occurred in HCC and associated with prognosis of HCC. RNF135 functions as a tumor suppressor and is involved in tumor immune microenvironment in HCC.
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Affiliation(s)
- Xiao Wang
- Inner Mongolia Key Laboratory of Endoscopic Digestive Diseases, Endoscopy Center, Inner Mongolia People’s Hospital, Hohhot, China
| | - Mengke Chen
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiong Liang
- Inner Mongolia Key Laboratory of Endoscopic Digestive Diseases, Endoscopy Center, Inner Mongolia People’s Hospital, Hohhot, China
| | - Yu Bai
- Inner Mongolia Key Laboratory of Endoscopic Digestive Diseases, Endoscopy Center, Inner Mongolia People’s Hospital, Hohhot, China
| | - Judeng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xiaoyi Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Hao Li
- Inner Mongolia Key Laboratory of Endoscopic Digestive Diseases, Endoscopy Center, Inner Mongolia People’s Hospital, Hohhot, China
| | - Jing Wang
- Department of Clinical Medicine, The First Bethune Hospital of Jilin University, Changchun, China
| | - Keyu Fan
- Anesthesiology, Dalian Medical University, Dalian, China
| | - Guijun Zhao
- Inner Mongolia Key Laboratory of Endoscopic Digestive Diseases, Endoscopy Center, Inner Mongolia People’s Hospital, Hohhot, China
- *Correspondence: Guijun Zhao,
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Zhu K, Bai H, Mu M, Xue Y, Duan Z. Knockdown of RNF6 inhibits HeLa cervical cancer cell growth via suppression of MAPK/ERK signaling. FEBS Open Bio 2021; 11:2041-2049. [PMID: 34081837 PMCID: PMC8255836 DOI: 10.1002/2211-5463.13216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
Ring finger protein 6 (RNF6) is implicated in various human malignancies, but its function in cervical cancer (CC) is incompletely understood. Here, we explored the biological significance of RNF6 in HeLa CC cells and the underlying regulatory mechanisms. The expression of RNF6 was observed to be high in both primary tissues and CC cells. RNF6 promoted HeLa CC cell growth. Knockdown of RNF6 in CC cells resulted in suppression of proliferation and promotion of apoptosis. Moreover, elevation of RNF6 had an adverse effect on the prognosis of CC. Subsequent analyses showed that these effects may be mediated via activation of ERK signaling. These findings provide evidence that the knockdown of RNF6 suppresses the MAPK/ERK pathway to regulate the growth of CC cells, which suggests that RNF6 may have potential as a target for diagnosis and treatment for CC.
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Affiliation(s)
- Kang Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Xi'an Jiaotong University, China
| | - He Bai
- Department of General Surgery Department, The First Affiliated Hospital of Xi'an Medical University, China
| | - Mingzhu Mu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Xi'an Jiaotong University, China
| | - Yuanyuan Xue
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Xi'an Jiaotong University, China
| | - Zhao Duan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Xi'an Jiaotong University, China
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11
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Identification of key genes in benign prostatic hyperplasia using bioinformatics analysis. World J Urol 2021; 39:3509-3516. [PMID: 33564912 DOI: 10.1007/s00345-021-03625-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/30/2021] [Indexed: 01/17/2023] Open
Abstract
PURPOSE This study aimed to identify differentially expressed genes (DEGs) and pathways in benign prostatic hyperplasia (BPH) by comprehensive bioinformatics analysis. METHODS Data of the gene expression microarray (GSE6099) were downloaded from GEO database. DEGs were obtained by GEO2R. Functional and enrichment analyses of selected genes were performed using DAVID database. Protein-protein interaction network was constructed through STRING. Anterior gradient 2 (ARG2) and lumican (LUM) staining in paraffin-embedded specimens from BPH and normal prostate (NP) were detected by immunohistochemistry (IHC). Differences between groups were analyzed by the Student's t test. RESULTS A total of 24 epithelial DEGs and 39 stromal DEGs were determined. The GO analysis results showed that epithelial DEGs between BPH and NP were enriched in biological processes of glucose metabolic process, glucose homeostasis and negative regulation of Rho protein signal transduction. For DEGs in stroma, enriched biological processes included response to ischemia, antigen processing and presentation, cartilage development, T cell costimulation and energy reserve metabolic process. ARG2, as one of the epithelial DEGs, was mainly located in epithelial cells of prostate. In addition, LUM is primarily expressed in the stroma. We further confirmed that compared with NP, the BPH have the lower ARG2 protein level (p = 0.029) and higher LUM protein level (p = 0.003) using IHC. CONCLUSIONS Our study indicated that there are possible differentially expressed genes in epithelial and stromal cells, such as ARG2 and LUM, which may provide a novel insight for the pathogenesis of BPH.
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12
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Scholz N, Kurian KM, Siebzehnrubl FA, Licchesi JDF. Targeting the Ubiquitin System in Glioblastoma. Front Oncol 2020; 10:574011. [PMID: 33324551 PMCID: PMC7724090 DOI: 10.3389/fonc.2020.574011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma is the most common primary brain tumor in adults with poor overall outcome and 5-year survival of less than 5%. Treatment has not changed much in the last decade or so, with surgical resection and radio/chemotherapy being the main options. Glioblastoma is highly heterogeneous and frequently becomes treatment-resistant due to the ability of glioblastoma cells to adopt stem cell states facilitating tumor recurrence. Therefore, there is an urgent need for novel therapeutic strategies. The ubiquitin system, in particular E3 ubiquitin ligases and deubiquitinating enzymes, have emerged as a promising source of novel drug targets. In addition to conventional small molecule drug discovery approaches aimed at modulating enzyme activity, several new and exciting strategies are also being explored. Among these, PROteolysis TArgeting Chimeras (PROTACs) aim to harness the endogenous protein turnover machinery to direct therapeutically relevant targets, including previously considered "undruggable" ones, for proteasomal degradation. PROTAC and other strategies targeting the ubiquitin proteasome system offer new therapeutic avenues which will expand the drug development toolboxes for glioblastoma. This review will provide a comprehensive overview of E3 ubiquitin ligases and deubiquitinating enzymes in the context of glioblastoma and their involvement in core signaling pathways including EGFR, TGF-β, p53 and stemness-related pathways. Finally, we offer new insights into how these ubiquitin-dependent mechanisms could be exploited therapeutically for glioblastoma.
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Affiliation(s)
- Nico Scholz
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Kathreena M. Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, United Kingdom
| | - Florian A. Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
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13
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β-Elemene Inhibits the Proliferation and Migration of Human Glioblastoma Cell Lines via Suppressing Ring Finger Protein 135. Balkan J Med Genet 2020; 23:43-49. [PMID: 32953408 PMCID: PMC7474225 DOI: 10.2478/bjmg-2020-0002] [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] [Indexed: 12/29/2022] Open
Abstract
β-Elemene is commonly used as an anti-cancer agent in different types of cancers and its effects on glioblastoma have been studied through different pathways. However, its effect through ring finger protein 135 (RNF135, OMIM 611358) (RNF135), which is upregulated in glioblastomas, has not yet been explored. The current study is focused on the effects of β-elemene on human glioblastoma cell lines U251, U118, A172 and U87 through RNF13 5. A cell counting kit-8 assay and wound healing assay have been utilized to test the proliferation and migration of the cells. Western blot and quantitative real-time-polymerase chain reaction (qRT-PCR) were used to evaluate the level of expression of RNF135. A model of nude mice was used to explore progression of the tumor in vivo. It was observed that increasing treatment time or dose of β-elemene remarkably decreased viability of the cells. The cells that were treated with β-elemene had a much lower speed of moving toward the gap in comparison to untreated cell lines. β-Elemene-treated cells showed a much lower level of expression of RNF135 mRNA than control groups (p <0.05) and the levels of RNF135 protein were lower in the cells treated with β-elemene than in control groups (p <0.05). Moreover, tumor progression in subcutaneous xenograft nude mice was delayed with the injection of β-elemene. Altogether, our findings suggest that β-elemene inhibits proliferation, migration and tumorigenicity of human glioblastoma cells through suppressing RNF135.
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14
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Park CS, De T, Xu Y, Zhong Y, Smithberger E, Alarcon C, Gamazon ER, Perera MA. Hepatocyte gene expression and DNA methylation as ancestry-dependent mechanisms in African Americans. NPJ Genom Med 2019; 4:29. [PMID: 31798965 PMCID: PMC6877651 DOI: 10.1038/s41525-019-0102-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022] Open
Abstract
African Americans (AAs) are an admixed population with widely varying proportion of West African ancestry (WAA). Here we report the correlation of WAA to gene expression and DNA methylation in AA-derived hepatocytes, a cell type important in disease and drug response. We perform mediation analysis to test whether methylation is a mediator of the effect of ancestry on expression. GTEx samples and a second cohort are used as validation. One hundred and thirty-one genes are associated with WAA (FDR < 0.10), 28 of which replicate and represent 220 GWAS phenotypes. Among PharmGKB pharmacogenes, VDR, PTGIS, ALDH1A1, CYP2C19, and P2RY1 nominally associate with WAA (p < 0.05). We find 1037 WAA-associated, differentially methylated regions (FDR < 0.05), with hypomethylated genes enriched in drug-response pathways. In conclusion, WAA contributes to variability in hepatocyte expression and DNA methylation with identified genes previously implicated for diseases disproportionately affecting AAs, including cardiovascular (PTGIS, PLAT) and renal (APOL1) disease, and drug response (CYP2C19).
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Affiliation(s)
- C. S. Park
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - T. De
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Y. Xu
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
- Center for Translational Data Science, University of Chicago, Chicago, IL USA
| | - Y. Zhong
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - E. Smithberger
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - C. Alarcon
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - E. R. Gamazon
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Vanderbilt University School of Medicine, Nashville, TN USA
- Data Science Institute, Vanderbilt University, Nashville, TN USA
- Clare Hall, University of Cambridge, Cambridge, UK
| | - M. A. Perera
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
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15
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Zhang D, Wei H, Xue H, Guo S, Wu B, Kuang Z. Backbone 1H, 13C, and 15N resonance assignments of the PRY-SPRY domain of RNF135. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:299-304. [PMID: 31065957 DOI: 10.1007/s12104-019-09895-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
RING finger protein 135 (RNF135, also named Riplet or REUL) exerts multiple biological functions and its C-terminal PRY-SPRY/B30.2 domain is indispensable for most of these functions. RNF135 interacts with RIG-I (retinoic acid-inducible gene-I) via the PRY-SPRY domain and ubiquitinates RIG-I to promote innate anti-viral signaling, while mutations in the RNF135 gene can cause the Macrocephaly, macrosomia, facial dysmorphism (MMFD) syndrome, and RNF135 reportedly regulates the proliferation of glioblastoma cells as well as tongue cancer cells. Nevertheless, structure of full-length RNF135 or its PRY-SPRY domain has not been determined, and structural basis for molecular interactions involving RNF135 is largely unknown. Here we report the backbone 1H, 13C, and 15N chemical shift assignments of the PRY-SPRY domain of RNF135 and the secondary structure elements predicted based on chemical shifts, as well as the perturbations caused by the R286H mutation that is associated with MMFD syndrome. We found that the mutation did not alter the gross structure of the PRY-SPRY domain, so it may have impaired RNF135 function by affecting protein-protein interactions mediated by the domain.
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Affiliation(s)
- Danting Zhang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Huan Wei
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Shujun Guo
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Zhihe Kuang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China.
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16
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Zhang Y, Sui R, Chen Y, Liang H, Shi J, Piao H. Downregulation of miR-485-3p promotes glioblastoma cell proliferation and migration via targeting RNF135. Exp Ther Med 2019; 18:475-482. [PMID: 31258684 PMCID: PMC6566029 DOI: 10.3892/etm.2019.7600] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 04/11/2019] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that serve pivotal roles in human diseases. Several miRNAs, such as miR-485-3p, have been identified as potential biomarkers for predicting overall survival of patients with glioblastoma (GBM). However, the underlying mechanism of miRNAs in promoting GBM progression remains unknown. In the present study, decreased miR-485-3p expression was detected in tumor tissues from patients with GBM. Using western blot analysis, reverse transcription-quantitative PCR and dual luciferase reporter assay, ring finger protein 135 (RNF135) was confirmed as a target gene of miR-485-3p in GBM cells. Through silencing of RNF135, miR-485-3p inactivated the mitogen-activated protein kinase/ERK1/2 pathway in GBM cells. Moreover, functional assays demonstrated that miR-485-3p inhibited GBM cell proliferation and migration whilst overexpression of RNF135 reversed this effect. Additionally, a negative correlation between miR-485-3p and RNF135 mRNA expression was observed in tissues from patients with glioblastoma. In conclusion, the present results demonstrated that miR-485-3p functioned as a tumor suppressor which suggested that miR-485-3p might have a role in GBM progression.
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Affiliation(s)
- Ye Zhang
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Rui Sui
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Yi Chen
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Haiyang Liang
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Ji Shi
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Haozhe Piao
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
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17
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Lai Y, Liang M, Hu L, Zeng Z, Lin H, Yi G, Li M, Liu Z. RNF135 is a positive regulator of IFN expression and involved in RIG-I signaling pathway by targeting RIG-I. FISH & SHELLFISH IMMUNOLOGY 2019; 86:474-479. [PMID: 30508673 DOI: 10.1016/j.fsi.2018.11.070] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/21/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
RIG-I-like receptors (RLRs) play a key role in antiviral and inflammatory responses. Increasing evidence indicates that ubiquitination is crucial for regulation of RIG-I signaling pathway. Several ubiquitin ligases were reported to be involved in RIG-I-mediated signal transduction. In the present study, we demonstrated zebrafish RING finger protein 135 (zbRNF135) was a critical player in the regulation of RIG-I signaling pathway. zbRNF135 mRNA was widely expressed in different tissues of zebrafish. The expression of zbRNF135 was up-regulated post poly(I:C) treatment in vivo and in vitro. Furthermore, the expression profiles of RIG-I signaling pathway related genes (LGP2, MDA5, RIG-I, MAVS, TRAF3, IRF3 and IRF7), together with its downstream molecules (IFN1, ISG15, Mx and PKR), were up-regulated by overexpression of zbRNF135 in ZF4 cells. Luciferase and ubiquitination assays revealed that overexpression of zbRNF135 facilitated zebrafish RIG-I (zbRIG-I)-mediated IFN1 promoter activation by mediating K63-linked ubiquitination of zbRIG-I. The co-immunoprecipitation assay showed that zbRNF135 specifically interacted with zbRIG-I. Our study indicated that zbRNF135 participated in innate immune response through modulating RIG-I signaling pathway.
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Affiliation(s)
- Yuxiong Lai
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - Min Liang
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - La Hu
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - Zicheng Zeng
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - Hai Lin
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - Gao Yi
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - Ming Li
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - Zhaoyu Liu
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
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18
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Wu H, Li X, Feng M, Yao L, Deng Z, Zao G, Zhou Y, Chen S, Du Z. Downregulation of RNF138 inhibits cellular proliferation, migration, invasion and EMT in glioma cells via suppression of the Erk signaling pathway. Oncol Rep 2018; 40:3285-3296. [PMID: 30272353 PMCID: PMC6196598 DOI: 10.3892/or.2018.6744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/21/2018] [Indexed: 12/19/2022] Open
Abstract
Glioma is the most common adult malignant primary brain tumor; however, the effect of chemotherapy is often limited by drug‑resistance and poor prognosis is common. Ring finger protein 138 (RNF138) belongs to the E3 ligase family, and has significantly higher expression level in glioma tissue than in noncancerous brain tissues. Epithelial-mesenchymal-transition (EMT) has a critical role in cancer invasion and metastasis, ultimately leading to increased cell motility and resistance to genotoxic agents. Extracellular‑signal regulated kinase (Erk) pathways promote the growth of glioma cells and enhance tumor invasion, with a role in the progression of EMT. However, the association between RNF138 and human glioma progression remains poorly understood. Relatively little is known about the association between RNF138, Erk, and EMT in glioma progression. In the current study, experiments were performed to explore the potential roles and mechanisms of RNF138 in glioblastoma in vitro and in vivo. Glioma cell line proliferation, migration and invasion were inhibited by knockdown of RNF138 in vitro. By lowering the RNF138 expression, cleaved caspase3 and E‑cadherin were upregulated, while phospho‑Erk1/2, vimentin, MMP2, HIF‑1α and VEGF were downregulated in U87 and U251 cells in vitro. In vivo findings revealed that the growth of U87 cell‑transplanted tumors in nude mice was inhibited in tumors with RNF138 knockdown. These findings suggested that downregulation of RNF138 inhibited glioma cell proliferation, migration, and invasion, and reversed EMT, potentially via Erk signaling pathway. Therefore, RNF138 may be a potential therapeutic target against glioma.
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Affiliation(s)
- Haibin Wu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Xuetao Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Ming Feng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Lin Yao
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Zhitong Deng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Guozheng Zao
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Youxin Zhou
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Sansong Chen
- Department of Neurosurgery, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Ziwei Du
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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19
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Fiscon G, Conte F, Licursi V, Nasi S, Paci P. Computational identification of specific genes for glioblastoma stem-like cells identity. Sci Rep 2018; 8:7769. [PMID: 29773872 PMCID: PMC5958093 DOI: 10.1038/s41598-018-26081-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/25/2018] [Indexed: 12/15/2022] Open
Abstract
Glioblastoma, the most malignant brain cancer, contains self-renewing, stem-like cells that sustain tumor growth and therapeutic resistance. Identifying genes promoting stem-like cell differentiation might unveil targets for novel treatments. To detect them, here we apply SWIM - a software able to unveil genes (named switch genes) involved in drastic changes of cell phenotype - to public datasets of gene expression profiles from human glioblastoma cells. By analyzing matched pairs of stem-like and differentiated glioblastoma cells, SWIM identified 336 switch genes, potentially involved in the transition from stem-like to differentiated state. A subset of them was significantly related to focal adhesion and extracellular matrix and strongly down-regulated in stem-like cells, suggesting that they may promote differentiation and restrain tumor growth. Their expression in differentiated cells strongly correlated with the down-regulation of transcription factors like OLIG2, POU3F2, SALL2, SOX2, capable of reprogramming differentiated glioblastoma cells into stem-like cells. These findings were corroborated by the analysis of expression profiles from glioblastoma stem-like cell lines, the corresponding primary tumors, and conventional glioma cell lines. Switch genes represent a distinguishing feature of stem-like cells and we are persuaded that they may reveal novel potential therapeutic targets worthy of further investigation.
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Affiliation(s)
- Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
- SysBio Centre of Systems Biology, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
- SysBio Centre of Systems Biology, Rome, Italy
| | - Valerio Licursi
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Sergio Nasi
- Department of Biology and Biotecnology - Charles Darwin, "Sapienza" University of Rome, Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
- SysBio Centre of Systems Biology, Rome, Italy.
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20
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Okamoto M, Kouwaki T, Fukushima Y, Oshiumi H. Regulation of RIG-I Activation by K63-Linked Polyubiquitination. Front Immunol 2018; 8:1942. [PMID: 29354136 PMCID: PMC5760545 DOI: 10.3389/fimmu.2017.01942] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/18/2017] [Indexed: 12/19/2022] Open
Abstract
RIG-I is a pattern recognition receptor and recognizes cytoplasmic viral double-stranded RNA (dsRNA). Influenza A virus, hepatitis C virus, and several other pathogenic viruses are mainly recognized by RIG-I, resulting in the activation of the innate immune responses. The protein comprises N-terminal two caspase activation and recruitment domains (2CARDs), an RNA helicase domain, and the C-terminal domain (CTD). The CTD recognizes 5′-triphosphate viral dsRNA. After recognition of viral dsRNA, the protein harbors K63-linked polyubiquitination essential for RIG-I activation. First, it was reported that TRIM25 ubiquitin ligase delivered K63-linked polyubiquitin moiety to the 2CARDs. The polyubiquitin chain stabilizes a structure called the 2CARD tetramer, in which four 2CARDs assemble and make a core that promotes the aggregation of the mitochondrial antiviral-signaling (MAVS) protein on mitochondria. MAVS aggregation then triggers the signal to induce the innate immune responses. However, subsequent studies have reported that Riplet, MEX3C, and TRIM4 ubiquitin ligases are also involved in K63-linked polyubiquitination and the activation of RIG-I. MEX3C and TRIM4 mediate polyubiquitination of the 2CARDs. By contrast, Riplet ubiquitinates the CTD. The physiological significance of each ubiquitin ligases has been shown by knockout and knockdown studies, but there appears to be contradictory to evidence reported in the literature. In this review, we summarize recent findings related to K63-linked polyubiquitination and propose a model that could reconcile current contradictory theories. We also discuss the physiological significance of the ubiquitin ligases in the immune system against viral infection.
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Affiliation(s)
- Masaaki Okamoto
- Faculty of Life Sciences, Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takahisa Kouwaki
- Faculty of Life Sciences, Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshimi Fukushima
- Faculty of Life Sciences, Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Oshiumi
- Faculty of Life Sciences, Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,PRESTO, Japan Science and Technology Agency, Kumamoto, Japan
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21
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Nagy Á, Garzuly F, Padányi G, Szűcs I, Feldmann Á, Murnyák B, Hortobágyi T, Kálmán B. Molecular Subgroups of Glioblastoma- an Assessment by Immunohistochemical Markers. Pathol Oncol Res 2017; 25:21-31. [PMID: 28948518 DOI: 10.1007/s12253-017-0311-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022]
Abstract
Comprehensive molecular characterization of and novel therapeutic approaches to glioblastoma have been explored as a result of advancements in biotechnologies. In this study, we aimed to bring basic research discoveries closer to clinical practice and ultimately incorporate molecular classification into the routine histopathological evaluation of grade IV gliomas. Integrated results of genome-wide sequencing, transcriptomic and epigenomic analyses by The Cancer Genome Atlas Network defined the classic, proneural, neural and mesenchymal subtypes of this tumor. In a retrospective cohort, we analyzed selected subgroup-defining molecular markers in formalin-fixed paraffin-embedded surgical specimens by immunohistochemistry. Quantitative and qualitative scores of marker expression were tested in hierarchical cluster analyses to evaluate segregations of the molecular subgroups, which then were correlated with clinical parameters including patients' age, gender and overall survival. Our study has confirmed the separation of molecular glioblastoma subgroups with clear trends regarding clinical correlations. Future analyses in a larger, prospective cohort using similar methods are expected to facilitate the development of a molecular diagnostic panel that may complement routine histological work up and support prognostication as well as treatment decisions in glioblastoma.
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Affiliation(s)
- Ádám Nagy
- Faculty of Health Sciences, School of Graduate Studies, University of Pécs, Pécs, Hungary
| | - Ferenc Garzuly
- Markusovszky University Teaching Hospital, University of Pecs, 5. Markusovszky Street, Szombathely, 9700, Hungary
| | - Gergely Padányi
- Markusovszky University Teaching Hospital, University of Pecs, 5. Markusovszky Street, Szombathely, 9700, Hungary
| | | | - Ádám Feldmann
- Faculty of Medicine, Institute of Behavioral Sciences, University of Pécs, Pécs, Hungary
| | - Balázs Murnyák
- Department of Pathology, Division of Neuropathology, University of Debrecen, Debrecen, Hungary
| | - Tibor Hortobágyi
- Department of Pathology, Division of Neuropathology, University of Debrecen, Debrecen, Hungary
| | - Bernadette Kálmán
- Faculty of Health Sciences, School of Graduate Studies, University of Pécs, Pécs, Hungary. .,Markusovszky University Teaching Hospital, University of Pecs, 5. Markusovszky Street, Szombathely, 9700, Hungary.
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22
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Chu SK, Yang HC. Interethnic DNA methylation difference and its implications in pharmacoepigenetics. Epigenomics 2017; 9:1437-1454. [PMID: 28882057 DOI: 10.2217/epi-2017-0046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
AIM This is the first systematic study to examine the population differentiation effect of DNA methylation on the treatment response and drug absorption, distribution, metabolism and excretion in multiple tissue types and cancer types. MATERIALS & METHODS We analyzed the whole methylome and transcriptome data of primary tumor tissues of four cancer types (breast, colon, head & neck and uterine corpus) and lymphoblastoid cell lines for African and European ancestry populations. RESULTS Ethnicity-associated CpG sites exhibited similar methylation patterns in the two studied populations, but the patterns differed between tumor tissues and lymphoblastoid cell lines. Ethnicity-associated CpG sites may have triggered gene expression, influenced drug absorption, distribution, metabolism and excretion, and showed tumor-specific patterns of methylation and gene regulation. CONCLUSION Ethnicity should be carefully accounted for in future pharmacoepigenetics research.
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Affiliation(s)
- Shih-Kai Chu
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan
| | - Hsin-Chou Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan.,Department of Statistics, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Statistics, National Tsing Hua University, Hsinchu 300, Taiwan.,Instutite of Public Health, National Yang-Ming University, Taipei 112, Taiwan.,School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
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Emerging genotype-phenotype relationships in patients with large NF1 deletions. Hum Genet 2017; 136:349-376. [PMID: 28213670 PMCID: PMC5370280 DOI: 10.1007/s00439-017-1766-y] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/08/2017] [Indexed: 02/07/2023]
Abstract
The most frequent recurring mutations in neurofibromatosis type 1
(NF1) are large deletions encompassing the NF1
gene and its flanking regions (NF1
microdeletions). The majority of these deletions encompass 1.4-Mb and are associated
with the loss of 14 protein-coding genes and four microRNA genes. Patients with
germline type-1 NF1 microdeletions frequently
exhibit dysmorphic facial features, overgrowth/tall-for-age stature, significant
delay in cognitive development, large hands and feet, hyperflexibility of joints and
muscular hypotonia. Such patients also display significantly more cardiovascular
anomalies as compared with patients without large deletions and often exhibit
increased numbers of subcutaneous, plexiform and spinal neurofibromas as compared
with the general NF1 population. Further, an extremely high burden of internal
neurofibromas, characterised by >3000 ml tumour volume, is encountered
significantly, more frequently, in non-mosaic NF1
microdeletion patients than in NF1 patients lacking such deletions. NF1 microdeletion patients also have an increased risk of
malignant peripheral nerve sheath tumours (MPNSTs); their lifetime MPNST risk is
16–26%, rather higher than that of NF1 patients with intragenic NF1 mutations (8–13%). NF1 microdeletion patients, therefore, represent a high-risk group for
the development of MPNSTs, tumours which are very aggressive and difficult to treat.
Co-deletion of the SUZ12 gene in addition to
NF1 further increases the MPNST risk in
NF1 microdeletion patients. Here, we summarise
current knowledge about genotype–phenotype relationships in NF1 microdeletion patients and discuss the potential role of the genes
located within the NF1 microdeletion interval
whose haploinsufficiency may contribute to the more severe clinical
phenotype.
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Knockdown of NUPR1 inhibits the proliferation of glioblastoma cells via ERK1/2, p38 MAPK and caspase-3. J Neurooncol 2016; 132:15-26. [PMID: 28000106 DOI: 10.1007/s11060-016-2337-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 11/12/2016] [Indexed: 12/15/2022]
Abstract
Nuclear protein-1 (NUPR1), located on chromosome 16p11.2, is a stress response factor that plays an important role in the growth and migration of human malignant tumor cells. However, the role of NUPR1 in glioblastoma remains poorly understood. The expression level of NUPR1 was detected by quantitative real-time PCR and immunohistochemistry (IHC). Wound healing, MTT, cell counting and BrdU assays were used to analyze the migration and proliferation of glioblastoma cells after down-regulating NUPR1 expression using a lentiviral vector. FACS analysis and a signaling antibody array kit were used to detect the mechanism by which NUPR1 modulates cell cycle and apoptosis activities in glioblastoma cells. We confirmed that NUPR1 was up-regulated in glioblastoma tissues compared to NB tissues. Down-regulation of NUPR1 suppressed cell migration and proliferation, arrested the cell cycle in the G0/G1 phase and promoted apoptosis in U251 and U87 cells in vitro. Furthermore, the expression levels of phosphorylated ERK1/2, p38 MAPK and cleaved caspase-3 were decreased upon silencing NUPR1 expression in U251 and U87 cells. In summary, NUPR1 plays an important role in the growth and migration of human glioblastoma cells. Knockdown of NUPR1 suppressed glioblastoma cell growth by arresting the cell cycle and inducing cell apoptosis via decreases in the expression of ERK1/2, p38 MAPK and caspase-3.
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