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Xi P, Zhang Z, Liu Y, Nie Y, Gong B, Liu J, Huang H, Liu Z, Sun T, Xie W. Multidimensional comprehensive and integrated analysis of the potential function of TMEM25 in renal clear cell carcinoma with low expression status. Aging (Albany NY) 2024; 16:367-388. [PMID: 38189809 PMCID: PMC10817401 DOI: 10.18632/aging.205372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND Transmembrane 25(TMEM25) stands out as a potential prognostic biomarker and therapeutic target in the realm of cancer, yet its precise mechanism of action within clear cell renal cell carcinoma (ccRCC) remains unclear. MATERIALS AND METHODS Gene expression data and clinically relevant information extracted from The Cancer Genome Atlas (TCGA) and Gene expression omnibus (GEO) databases unveil the expression patterns of TMEM25 within renal clear cell carcinoma, which reveals its prognostic and diagnostic significance. The protein expression data is available via the Human Protein Atlas (HPA) database. Further, qPCR experiments conducted on cells and tissues provide strong evidence of the gene's expression status. Additionally, they explore the correlations between TMEM25 expression and DNA methylation, gene mutations, immune cell infiltration, and drug sensitivity within this specific tumor context. RESULTS At both the RNA and protein levels, TMEM25 displays a noteworthy downregulation in expression, which is consistently linked to an unfavorable prognosis. Receiver Operating Characteristic (ROC) curve analysis, univariate and multivariate Cox regression analyses confirmed the ability of TMEM25 to diagnose and determine prognosis in ccRCC. Its expression related closely with various immune cell types, immune checkpoints, immune inhibitors, and MHC molecules. Within ccRCC tissues, TMEM25 DNA methylation levels are observed to be elevated, and this upregulation is observed across various conditions. TMEM25 mutations also have an impact on the prognosis of ccRCC patients and the results of drug sensitivity analyses are useful for clinical decision-making. CONCLUSIONS TMEM25 in ccRCC could potentially function as a tumor suppressor gene, holding substantial promise as a novel biomarker for diagnosing, treating, and prognosticating ccRCC patients.
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Affiliation(s)
- Ping Xi
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Zhicheng Zhang
- Department of Surgery, Fuzhou First People’s Hospital, Fuzhou 344000, Jiangxi Province, China
| | - Yifu Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yechen Nie
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ji Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Hao Huang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ziwen Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Wenjie Xie
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
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Luo Z, Wang Y, Bi X, Ismtula D, Wang H, Guo C. Cytokine-induced apoptosis inhibitor 1: a comprehensive analysis of potential diagnostic, prognosis, and immune biomarkers in invasive breast cancer. Transl Cancer Res 2023; 12:1765-1786. [PMID: 37588751 PMCID: PMC10425657 DOI: 10.21037/tcr-23-34] [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: 01/07/2023] [Accepted: 06/07/2023] [Indexed: 08/18/2023]
Abstract
Background Cytokine-induced apoptosis inhibitor 1 (CIAPIN1) is strictly associated with the incidence and progress of several malignant tumors, but its effect on invasive breast cancer (IBC) remains unclear. We directed to research the potential diagnostic and prognostic significance of CIAPIN1 in IBC. Methods The Cancer Genome Atlas (TCGA) database and Tumor Immune Estimation Resource (TIMER) database were utilized to examine CIAPIN1 expression level in IBC and its relationship with clinicopathological features. The diagnostic value and prognostic importance of CIAPIN1 in IBC were assessed by Kaplan-Meier analysis, Cox regression analysis, receiver operating characteristic (ROC) curve and nomogram model. The STRING database and enrichment analysis were utilized to discover the interacting proteins, biological roles and possible cellular mechanisms related to CIAPIN1. The methylation status of CIAPIN1 was analyzed using MethSurv database and the University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN). By using Spearman correlation assessment, how the expression of CIAPIN1 was related to TP53, immune checkpoint genes and immune cell infiltration was determined. Results CIAPIN1 mRNA and protein levels were overexpressed in IBC, and significantly correlated with T stage, histological type, age, ER status, PR status and PAM50 (P<0.001). CIAPIN1 overexpression significantly decreased overall survival, distant metastasis free survival (DMFS) and relapse free survival in IBC patients (P<0.001). Similarly, hypermethylation of CIAPIN1 was associated with adverse outcomes in IBC patients. Multivariate Cox analysis identified CIAPIN1 as a potential risk factor for disease specific survival (DSS) and progression free survival (PFS) in individuals with IBC. The outcomes of the ROC curve showed that CIAPIN1 had a better accuracy in predicting ER(-), PR(-) and Asian breast cancer subtypes. Furthermore, there was a substantial correlation between the CIAPIN1 expression level in IBC and immune cell infiltration, TP53, and immune checkpoint genes. Conclusions The high expression of CIAPIN1 in IBC is significantly related to the infiltration status of various tumor immune cells and the poor prognosis of IBC patients. According to this current study, CIAPIN1 is a promising diagnostic and prognostic marker for IBC.
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Affiliation(s)
- Zhiwen Luo
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yiyang Wang
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiaojuan Bi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Dilimulati Ismtula
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Haiyan Wang
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Chenming Guo
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Yu Z, Chen G, Feng Z, Li Y, Yu H, Shi W, Gou X, Zhang C, Peng X. Establishing a prognostic model based on five starvation-related long non-coding RNAs for clear cell renal cell carcinoma. Aging (Albany NY) 2023; 15:6736-6748. [PMID: 37341994 PMCID: PMC10415547 DOI: 10.18632/aging.204816] [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: 03/14/2023] [Accepted: 06/06/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND Starvation-induced tumor microenvironment significantly alters genetic profiles including long non-coding RNAs (lncRNAs), further regulating the malignant biological characteristics (invasion and migration) of clear cell renal cell carcinoma (ccRCC). METHODS Transcriptome RNA-sequencing data of 539 ccRCC tumors and 72 normal tissues were acquired from the TCGA and paired clinical samples of 50 ccRCC patients. In vitro experiments, such as qPCR, migration and invasion assays were applied to reveal the clinical relevance of LINC-PINT, AC108449.2 and AC007637.1. RESULTS 170 lncRNAs were verified as starvation-related lncRNAs (SR-LncRs), of which 25 lncRNAs were associated with overall survival in ccRCC patients. Furthermore, a starvation-related risk score model (SRSM) was built based on the expression levels of LINC-PINT, AC108449.2, AC009120.2, AC008702.2 and AC007637.1. ccRCC patients with high level of LINC-PINT expression were divided into high-risk group and led to higher mortality, but AC108449.2 and AC007637.1 were contrary. Analogously, LINC-PINT was highly expressed in ccRCC cell lines and tumor tissues, especially in patients with advanced stage, T-stage and M-stage, while AC108449.2 and AC007637.1 showed the opposite results. In addition, the increased levels of AC108449.2 and AC007637.1 were significantly correlated with grade. Silencing LINC-PINT reduced the invasion and migration characteristics of ccRCC cells. SiR-AC108449.2 and siR-AC007637.1 enhanced the ability of invasion and migration in ccRCC cells. CONCLUSIONS In this study, we find the clinical significance of LINC-PINT, AC108449.2 and AC007637.1 in predicting the prognosis of ccRCC patients and verify their correlation with various clinical parameters. These findings provide an advisable risk score model for ccRCC clinical decision-making.
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Affiliation(s)
- Zhou Yu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Urology, Suining Central Hospital, Suining, Sichuan, China
| | - Guo Chen
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Chongqing, China
| | - Zhenwei Feng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Chongqing, China
| | - Yang Li
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Chongqing, China
| | - Haitao Yu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Chongqing, China
| | - Wei Shi
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Chongqing, China
| | - Xin Gou
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunlin Zhang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Chongqing, China
| | - Xiang Peng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, Chongqing, China
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Chiu YW, Su YF, Yang CC, Liu CJ, Chen YJ, Cheng HC, Wu CH, Chen PY, Lee YH, Chen YL, Chen YT, Peng CY, Lu MY, Yu CH, Kao SY, Fwu CW, Huang YF. Is OLP potentially malignant? A clue from ZNF582 methylation. Oral Dis 2023; 29:1282-1290. [PMID: 34967949 DOI: 10.1111/odi.14120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Whether oral lichen planus (OLP) was potentially malignant remains controversial. Here, we examined associations of ZNF582 methylation (ZNF582m ) with OLP lesions, dysplastic features and squamous cell carcinoma (OSCC). MATERIALS AND METHODS This is a case-control study. ZNF582m was evaluated in both lesion and adjacent normal sites of 42 dysplasia, 90 OSCC and 43 OLP patients, whereas ZNF582m was evaluated only in one mucosal site of 45 normal controls. High-risk habits affecting ZNF582m such as betel nut chewing and cigarette smoking were also compared in those groups. RESULTS OLP lesions showed significantly lower ZNF582m than those of dysplasia and OSCC. At adjacent normal mucosa, ZNF582m increased from patients of OLP, dysplasia, to OSCC. In addition, ZNF582m at adjacent normal sites in OLP patients was comparable to normal mucosa in control group. Dysplasia/OSCC patients with high-risk habits exhibited significantly higher ZNF582m than those without high-risk habits. However, ZNF582m in OLP patients was not affected by those high-risk habits. CONCLUSIONS OLP is unlikely to be potentially malignant based on ZNF582m levels. ZNF582m may also be a potential biomarker for distinguishing OLP from true dysplastic features and OSCC, and for monitoring the malignant transformation of OLP, potentially malignant disorders with dysplastic features and OSCC.
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Affiliation(s)
- Yu-Wei Chiu
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yee-Fun Su
- iStat Biomedical Co., Ltd, New Taipei City, Taiwan
| | - Cheng-Chieh Yang
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Oral & Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chung-Ji Liu
- Department of Oral and Maxillofacial Surgery, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yi-Ju Chen
- iStat Biomedical Co., Ltd, New Taipei City, Taiwan
| | - Han-Chieh Cheng
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Oral & Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Cheng-Hsien Wu
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Oral & Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Pei-Yin Chen
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Hsien Lee
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yen-Lin Chen
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yi-Tzu Chen
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Yu Peng
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ming-Yi Lu
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chuan-Hang Yu
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Shou-Yen Kao
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Oral & Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | | | - Yu-Feng Huang
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- College of Oral Medicine, Chung Shan Medical University, Taichung, Taiwan
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Yang W, Zhang Z, Li L, Zhang K, Xu Y, Xia M, Zhou J, Gong Y, Chen J, Gong K. ZNF582 overexpression restrains the progression of clear cell renal cell carcinoma by enhancing the binding of TJP2 and ERK2 and inhibiting ERK2 phosphorylation. Cell Death Dis 2023; 14:212. [PMID: 36966163 PMCID: PMC10039855 DOI: 10.1038/s41419-023-05750-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/27/2023]
Abstract
Recent evidences have suggested that Zinc finger protein 582 (ZNF582) plays different important roles in various tumors, but its clinical role, biological function and regulatory mechanism in clear cell renal cell carcinoma (ccRCC) are still vague. Through analyzing GEO and TCGA-KIRC data and validation with local samples, we identified the low expression pattern of ZNF582 in ccRCC. Decreased ZNF582 expression is correlated with higher tumor stage and grade, distant metastasis and poor prognosis. By analyzing the DNA methylation data of ccRCC in TCGA-KIRC and using Massarray DNA methylation and demethylation analysis, we confirmed the hypermethylation status of ZNF582 in ccRCC and its negative regulation on ZNF582 expression. Using cell phenotype experiments and orthotopic kidney tumor growth models, we determined the inhibitory effect of ZNF582 overexpression on ccRCC growth and metastasis in vivo and in vitro. Mechanistically, using TMT (Tandem mass tags) quantitative proteomics test, Co-IP (Co-immunoprecipitation) and Western Blot experiments, we clarified that ZNF582 binds to TJP2 and up-regulates TJP2 protein expression. Increased TJP2 protein combines with ERK2 to promote ERK2 protein expression and suppresses the phosphorylation of ERK2, thereby inhibiting the growth and metastasis of ccRCC. In general, our findings provide the first solid theoretical rationale for targeting ZNF582/TJP2/ERK2 axis to improve ccRCC treatment.
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Affiliation(s)
- Wuping Yang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Zedan Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Lei Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Kenan Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Yawei Xu
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Mancheng Xia
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Jingcheng Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China.
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China.
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China.
| | - Jinchao Chen
- Department of Urologic Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, P.R. China.
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China.
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China.
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China.
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Wang J, Yang C, Cao H, Yang J, Meng W, Yu M, Yu L, Wang B. Hypermethylation-Mediated lncRNA MAGI2-AS3 Downregulation Facilitates Malignant Progression of Laryngeal Squamous Cell Carcinoma via Interacting With SPT6. Cell Transplant 2023; 32:9636897231154574. [PMID: 36852700 PMCID: PMC9986895 DOI: 10.1177/09636897231154574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have an effect on the occurrence and progression of a considerable number of diseases, especially cancer. Existing research has suggested that MAGI2 antisense RNA 3 (MAGI2-AS3) takes on a critical significance in the development of hepatocellular carcinoma and lung cancer. However, the functions of MAGI2-AS3 in laryngeal squamous cell carcinoma (LSCC) remain unclear. In this study, MAGI2-AS3 expression level in LSCC tissue and cell lines was detected, and the effect of MAGI2-AS3 overexpressed on LSCC phenotypes and the possible influence mechanisms were examined. MAGI2-AS3 was downregulated in the tissues of LSCC patients versus non-tumor tissues, and it was correlated with advanced TNM (tumor, node, metastasis) stage and lymph node metastases, as indicated by the results of this study. MAGI2-AS3 inhibited the proliferation, migration, and invasion of LSCC cells in vitro and in vivo. Furthermore, the hypermethylation level of the MAGI2-AS3 promoter region was indicated by bisulfite genomic sequencing and methylation-specific polymerase chain reaction, such that MAGI2-AS3 expression was downregulated. Besides, MAGI2-AS3 promoter hypermethylation was regulated by DNA methyltransferase 1 (DNMT1), and MAGI2-AS3 expression was reversed by 5-Aza-2'-deoxycytidine (5-Aza). Moreover, the result of the RNA pull-down experiment suggested that 38 proteins were enriched in the MAGI2-AS3 group versus the control group in TU177 cells. To be specific, SPT6 (ie, a conserved protein) was enriched by fold change >10. SPT6 knockdown reduced the antitumor effect of MAGI2-AS3 in TU177 and AMC-HN-8 cells. Meanwhile, SPT6 overexpression inhibited the proliferation, metastasis, and invasion of TU177 and AMC-HN-8 cells. As revealed by the above findings, DNMT1-regulated MAGI2-AS3 promoter hypermethylation led to downregulated MAGI2-AS3 expression, such that the presence and progression of LSCC were inhibited in an SPT6 binding-dependent manner.
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Affiliation(s)
- Jiantao Wang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chuan Yang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huan Cao
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jianwang Yang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wenxia Meng
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Miaomiao Yu
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lei Yu
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Baoshan Wang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Gong Q, Guo Z, Sun W, Du X, Jiang Y, Liu F. CX3CL1 promotes cell sensitivity to ferroptosis and is associated with the tumor microenvironment in clear cell renal cell carcinoma. BMC Cancer 2022; 22:1184. [PMCID: PMC9670481 DOI: 10.1186/s12885-022-10302-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
An increasing number of studies have demonstrated that CX3CL1 is involved in the development of tumors and may thus be considered a new potential therapeutic target for them. However, the function of CX3CL1 in clear cell renal cell carcinoma (ccRCC) remains poorly defined.
Methods
The pan-cancer expression pattern and prognostic value of CX3CL1 were evaluated in this study. Moreover, the relationship of CX3CL1 expression with the tumor microenvironment, especially the tumor immune microenvironment, was analyzed. Our analyses employed public repository data. Additionally, we generated stable CX3CL1-overexpressing 786-O cells to determine the role of CX3CL1 in vitro via cell viability and transwell assays. A xenograft tumor model was used to determine the role of CX3CL1 in vivo. The association between CX3CL1 and ferroptosis sensitivity of tumor cells was assessed using Ferrostatin-1.
Results
Our findings indicated the involvement of CX3CL1 in the occurrence and development of ccRCC by acting as a tumor suppressor. We also found that ccRCC patients with high CX3CL1 expression showed better clinical outcomes than those with low CX3CL1 expression. The findings of our epigenetic study suggested that the expression of CX3CL1 in ccRCC is correlated with its DNA methylation level. Furthermore, the CX3CL1 expression level was closely related to the infiltration level of CD8+ T cells into the tumor microenvironment (TME). CX3CL1 showed different predictive values in different immunotherapy cohorts. Finally, CX3CL1 overexpression inhibited tumor cell proliferation and metastasis and promoted tumor ferroptosis sensitivity in ccRCC.
Conclusions
This study revealed the role of CX3CL1 as a tumor suppressor in ccRCC. Our findings indicated that CX3CL1 plays a crucial role in regulating the ccRCC TME and is a potential predictor of immunotherapy outcomes in ccRCC. We also found that CX3CL1 can promote ferroptosis sensitivity in ccRCC cells.
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Construction and Characterization of n6-Methyladenosine-Related lncRNA Prognostic Signature and Immune Cell Infiltration in Kidney Renal Clear Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:7495183. [PMID: 36213821 PMCID: PMC9536954 DOI: 10.1155/2022/7495183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022]
Abstract
Background. Kidney renal clear cell carcinoma (KIRC) lacks effective prognostic biomarkers and the role and mechanism of N6-methyladenosine (m6A) modification of long noncoding RNAs (lncRNAs) in KIRC remain unclear. Methods. We extracted standard mRNA-sequencing and clinical data from the TCGA database. The prognostic risk model was obtained by Lasso regression and Cox regression. We randomly divided the samples into training and test sets, each taking half of the cases. Based on Lasso regression and Cox regression for training set, the prognostic risk signature was constructed; risk scores were calculated with the R package “glmnet.” Based on the median value of the prognostic risk score, risk scores were calculated for each patient and we divided all KIRC samples into high-risk and low-risk groups. Then, high- and low-risk subtypes were established and their prognosis, clinical features, and immune infiltration microenvironment were evaluated in test set and the entire sampled data set. The reliability of the prognostic model was confirmed by receiver operating characteristic curve analysis. Results. We found 28 prognostic m6A-related lncRNAs and established a m6A-related lncRNAs prognostic signature.
The signature showed a better predictive ability than other clinical indicators, including tumor node metastasis classification (TNM), histological, and pathological stages. In the high-risk group, M0 macrophages, CD8+ T cells, and regulatory T cells had significantly higher scores. Contrarily, in the low-risk group, activated dendritic cells, M1 macrophages, mast resting cells, and monocytes had significantly higher scores. In the high-risk group, LSECtin was overexpressed. In the low-risk group, PD-L1 was overexpressed. Moreover, high-risk patients may benefit more from AZ628. Conclusions. In conclusion, prognosis prediction of patients with KIRC and new insights for immunotherapy are provided by the m6A-related lncRNA prognostic signature.
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Khorkova O, Stahl J, Joji A, Volmar CH, Zeier Z, Wahlestedt C. Natural antisense transcripts as drug targets. Front Mol Biosci 2022; 9:978375. [PMID: 36250017 PMCID: PMC9563854 DOI: 10.3389/fmolb.2022.978375] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
The recent discovery of vast non-coding RNA-based regulatory networks that can be easily modulated by nucleic acid-based drugs has opened numerous new therapeutic possibilities. Long non-coding RNA, and natural antisense transcripts (NATs) in particular, play a significant role in networks that involve a wide variety of disease-relevant biological mechanisms such as transcription, splicing, translation, mRNA degradation and others. Currently, significant efforts are dedicated to harnessing these newly emerging NAT-mediated biological mechanisms for therapeutic purposes. This review will highlight the recent clinical and pre-clinical developments in this field and survey the advances in nucleic acid-based drug technologies that make these developments possible.
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Affiliation(s)
- Olga Khorkova
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Jack Stahl
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Aswathy Joji
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
- Department of Chemistry, University of Miami, Miami, FL, United States
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Zane Zeier
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
- Department of Chemistry, University of Miami, Miami, FL, United States
- *Correspondence: Claes Wahlestedt,
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10
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Di Mauro S, Scamporrino A, Filippello A, Di Marco M, Di Martino MT, Scionti F, Di Pino A, Scicali R, Malaguarnera R, Purrello F, Piro S. Mitochondrial RNAs as Potential Biomarkers of Functional Impairment in Diabetic Kidney Disease. Int J Mol Sci 2022; 23:ijms23158198. [PMID: 35897772 PMCID: PMC9331991 DOI: 10.3390/ijms23158198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
Type 2 diabetes and renal damage are strictly linked. The progressive increase in T2D incidence has stimulated the interest in novel biomarkers to improve the diagnostic performance of the commonly utilized markers such as albuminuria and eGFR. Through microarray method, we analyzed the entire transcriptome expressed in 12 serum samples of diabetic patients, six without DKD and six with DKD; the downregulation of the most dysregulated transcripts was validated in a wider cohort of 69 patients by qPCRs. We identified a total of 33 downregulated transcripts. The downregulation of four mitochondrial messenger RNAs (MT-ATP6, MT-ATP8, MT-COX3, MT-ND1) and other two transcripts (seysnoy, skerdo) was validated in patients with eGFR stage G3 versus G2 and G1. The four messenger RNAs correlated with creatinine and eGFR stages, while seysnoy and skerdo were associated with white blood cell values. All transcripts correlated also with Blood Urea Nitrogen. The four mitochondrial messenger RNAs had a high diagnostic performance in G3 versus G2 discrimination, with AUC values above 0.8. The most performant transcript was MT-ATP6, with an AUC of 0.846; sensitivity = 90%, specificity = 76%, p-value = 7.8 × 10−5. This study led to the identification of a specific molecular signature of DKD, proposing the dosage of RNAs, especially mitochondrial RNAs, as noninvasive biomarkers of diabetes complication.
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Affiliation(s)
- Stefania Di Mauro
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Alessandra Scamporrino
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Agnese Filippello
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Maurizio Di Marco
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy;
| | - Francesca Scionti
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy;
| | - Antonino Di Pino
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Roberto Scicali
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | | | - Francesco Purrello
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
- Correspondence: ; Tel.: +39-095-759-8401
| | - Salvatore Piro
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
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11
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Wang J, Katsaros D, Biglia N, Fu Y, Benedetto C, Loo L, Wang Z, Yu H. LncRNA ZNF582-AS1 Expression and Methylation in Breast Cancer and Its Biological and Clinical Implications. Cancers (Basel) 2022; 14:2788. [PMID: 35681777 PMCID: PMC9179509 DOI: 10.3390/cancers14112788] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Long non-coding RNAs (lncRNAs) play an important role in cellular activities and functions, but our understanding of their involvement in cancer is limited. Methods: TCGA data on RNA expression and DNA methylation were analyzed for lncRNAs' association with breast cancer survival, using the Cox proportional hazard regression model. Fresh tumor samples and clinical information from 361 breast cancer patients in our study were used to confirm the TCGA finding on ZNF582-AS1. A RT-qPCR method was developed to measure ZNF582-AS1 expression. Survival associations with ZNF582-AS1 were verified with a meta-analysis. In silico predictions of molecular targets and cellular functions of ZNF582-AS1 were performed based on its molecular signatures and nucleotide sequences. Results:ZNF582-AS1 expression was lower in breast tumors than adjacent normal tissues. Low ZNF582-AS1 was associated with high-grade or ER-negative tumors. Patients with high ZNF582-AS1 had a lower risk of relapse and death. These survival associations were confirmed in a meta-analysis and remained significant after adjustment for tumor grade, disease stage, patient age, and hormone receptor status. Correlation analysis indicated the possible suppression of ZNF582-AS1 expression by promoter methylation. Bioinformatics interrogation of molecular signatures suggested that ZNF582-AS1 could suppress tumor cell proliferation via downregulating the HER2-mediated signaling pathway. Analysis of online data also suggested that HIF-1-related transcription factors could suppress ZNF582-AS1 expression, and the lncRNA might bind to hsa-miR-940, a known oncogenic miRNA in breast cancer. Conclusions: ZNF582-AS1 may play a role in suppressing breast cancer progression. Elucidating the lncRNA's function and regulation may improve our understanding of the disease.
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Affiliation(s)
- Junlong Wang
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Dionyssios Katsaros
- Department of Surgical Sciences, Gynecology, AOU Città della Salute, University of Torino School of Medicine, 10124 Turin, Italy; (D.K.); (C.B.)
| | - Nicoletta Biglia
- Department of Surgical Sciences, Division of Obstetrics and Gynecology, University of Torino School of Medicine, Mauriziano Hospital, 10124 Turin, Italy;
| | - Yuanyuan Fu
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Chiara Benedetto
- Department of Surgical Sciences, Gynecology, AOU Città della Salute, University of Torino School of Medicine, 10124 Turin, Italy; (D.K.); (C.B.)
| | - Lenora Loo
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
| | - Zhanwei Wang
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
| | - Herbert Yu
- University of Hawaii Cancer Center, Honolulu, HI 96813, USA; (J.W.); (Y.F.); (L.L.); (Z.W.)
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12
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Zeng X, Chen K, Li L, Tian J, Ruan W, Hu Z, Peng D, Chen Z. Epigenetic activation of RBM15 promotes clear cell renal cell carcinoma growth, metastasis and macrophage infiltration by regulating the m6A modification of CXCL11. Free Radic Biol Med 2022; 184:135-147. [PMID: 35381326 DOI: 10.1016/j.freeradbiomed.2022.03.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/09/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common kidney malignancy that is characterized by poor prognosis. RNA-binding motif protein 15 (RBM15) has been identified as an oncogene in multiple tumors. Nevertheless, the function and mechanism of RBM15 in ccRCC are not clear. In this study, RBM15 was found to be upregulated in ccRCC cells and tissues. RBM15 enhanced the proliferation, clone formation, migration, invasion and epithelial-interstitial transition of ccRCC cells. Enhanced RBM15 was caused by the abundant histone 3 acetylation modification of the RBM15 promoter induced by EP300/CBP. RBM15 enhanced the stability of CXCL11 mRNA in an m6A-dependent manner. Moreover, RBM15 was found to promote macrophage infiltration and M2 polarization by promoting the secretion of CXCL11 in ccRCC cells in vitro and in vivo. Our findings highlight the function of RBM15 in ccRCC and reveal a novel identified EP300/CBP-RBM15-CXCL11 signaling axis, which promotes ccRCC progression and provides new insight into ccRCC therapy.
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Affiliation(s)
- Xing Zeng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Le Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jihua Tian
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Weiqiang Ruan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Dan Peng
- Department of Nuclear Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhi Chen
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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13
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Chen W, Tang D, Lin J, Huang X, Lin S, Shen G, Dai Y. Exosomal circSHKBP1 participates in non-small cell lung cancer progression through PKM2-mediated glycolysis. Mol Ther Oncolytics 2022; 24:470-485. [PMID: 35229026 PMCID: PMC8844869 DOI: 10.1016/j.omto.2022.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/24/2022] [Indexed: 11/04/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) has a high morbidity and mortality, and it is imperative to explore the latent pathogenesis mechanism of NSCLC progression to find potential prognostic biomarkers and therapeutic targets. The present study aimed to explore the biological function of circSHKBP1 in NSCLC. circSHKBP1 was found to be upregulated in NSCLC tissues and cell lines and was enriched in exosomes derived from NSCLC cells. Exosomal circSHKBP1 enhanced the proliferation, migration, invasion, and stemness of NSCLC cells. miRNA-1294 was identified as a target for circSHKBP1, and circSHKBP1 upregulated PKM2 expression by sponging miR-1294. Exosomal circSHKBP1 regulated glycolysis through PKM2 in a HIF-1α-dependent manner in NSCLC cells and promoted M2 polarization and macrophage recruitment. Moreover, exosomal circSHKBP1 promoted NSCLC cell growth, metastasis, and M2 infiltration in vivo. Thus, exosomal circSHKBP1 participated in the progression of NSCLC via the miR-1294/PKM2 axis. circSHKBP1 may be potential biomarker for the diagnosis and treatment of NSCLC.
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14
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OUP accepted manuscript. Toxicol Sci 2022; 187:311-324. [DOI: 10.1093/toxsci/kfac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Zhang S, Qin J, Zhao Y, Wang J, Tian Z. Identification of molecular patterns and diagnostic biomarkers in juvenile idiopathic arthritis based on the gene expression of m 6A regulators. Front Pediatr 2022; 10:930119. [PMID: 36160781 PMCID: PMC9497457 DOI: 10.3389/fped.2022.930119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Abstract
The role of N 6-methyladenosine modification in immunity is increasingly being appreciated. However, the landscape of m6A regulators in juvenile idiopathic arthritis (JIA) is poorly understood. Thus, this study explored the impact of m6A modification and related lncRNAs in JIA immune microenvironment. Fourteen m6A regulators and eight lncRNAs were identified as potential diagnostic biomarkers for JIA. Two diagnostic models for JIA were also constructed. The putative molecular regulatory mechanism of FTO-mediated m6A modification in JIA was hypothesized. Three distinct m6A patterns mediated by 26 m6A regulators and three diverse lncRNA clusters mediated by 405 lncRNAs were thoroughly investigated. They exhibited dramatically diverse immune microenvironments and expression of HLA genes. The identification of two separate subtypes of enthesitis-related arthritis implies that our work may aid in the establishment of a more precise categorization system for JIA. m6A modification-related genes were obtained, and their underlying biological functions were explored. The m6Ascore system developed for individual JIA patients may be utilized to evaluate the immunological state or molecular pattern, thereby offering therapy recommendations. In short, through the investigation of the m6A regulators in JIA, the current work may contribute to our knowledge of the pathophysiology of JIA.
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Affiliation(s)
- Shibo Zhang
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Qin
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuechao Zhao
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jian Wang
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhiliang Tian
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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16
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Zhu R, Li X, Cai Z, Liang S, Yuan Y, Xu Y, Lai D, Zhao H, Yang W, Bian J, Liu L, Xu G. Risk Scores Based on Six Survival-Related RNAs in a Competing Endogenous Network Composed of Differentially Expressed RNAs Between Clear Cell Renal Cell Carcinoma Patients Carrying Wild-Type or Mutant Von Hippel-Lindau Serve Well to Predict Malignancy and Prognosis. Front Oncol 2021; 11:726671. [PMID: 34760693 PMCID: PMC8573174 DOI: 10.3389/fonc.2021.726671] [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: 06/17/2021] [Accepted: 10/01/2021] [Indexed: 12/24/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) carrying wild-type Von Hippel–Lindau (VHL) tumor suppressor are more invasive and of high morbidity. Concurrently, competing endogenous RNA (ceRNA) network has been suggested to play an important role in ccRCC malignancy. In order to understand why the patients carrying wild-type VHL gene have high degrees of invasion and morbidity, we applied bioinformatics approaches to identify 861 differentially expressed RNAs (DE-RNAs) between patients carrying wild-type and patients carrying mutant VHL from The Cancer Genome Atlas (TCGA) database, established a ceRNA network including 122 RNAs, and elected six survival-related DE-RNAs including Linc00942, Linc00858, RP13_392I16.1, hsa-miR-182-5p, hsa-miR-183-5p, and PAX3. Examining clinical samples from our hospital revealed that patients carrying wild-type VHL had significantly higher levels of all six RNAs than those carrying mutant VHL. Patients carrying wild-type VHL had significantly higher risk scores, which were calculated based on expression levels of all six RNAs, than those carrying mutant VHL. Patients with higher risk scores had significantly shorter survival times than those with lower risk scores. Therefore, the risk scores serve well to predict malignancy and prognosis.
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Affiliation(s)
- Rui Zhu
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiezhao Li
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiduan Cai
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Siyang Liang
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yaoji Yuan
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuyu Xu
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dehui Lai
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haibo Zhao
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Weiqing Yang
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Bian
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Leyuan Liu
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guibin Xu
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Construction of a Novel Immune-Related lncRNA Pair Signature with Prognostic Significance for Kidney Clear Cell Renal Cell Carcinoma. DISEASE MARKERS 2021; 2021:8800358. [PMID: 34512816 PMCID: PMC8429034 DOI: 10.1155/2021/8800358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Background Renal cell carcinoma (RCC) is one of the most common aggressive malignant tumors in the urinary system, among which the clear cell renal cell carcinoma (ccRCC) is the most common subtype. The immune-related long noncoding ribonucleic acids (irlncRNAs) which are abundant in immune cells and immune microenvironment (IME) have potential significance in evaluating the prognosis and effects of immunotherapy. The signature based on irlncRNA pairs and independent of the exact expression level seems to have a latent predictive significance for the prognosis of patients with malignant tumors but has not been applied in ccRCC yet. Method In this article, we retrieved The Cancer Genome Atlas (TCGA) database for the transcriptome profiling data of the ccRCC and performed coexpression analysis between known immune-related genes (ir-genes) and lncRNAs to find differently expressed irlncRNA (DEirlncRNA). Then, we adopted a single-factor test and a modified LASSO regression analysis to screen out ideal DEirlncRNAs and constructed a Cox proportional hazard model. We have sifted 28 DEirlncRNA pairs, 12 of which were included in this model. Next, we compared the area under the curve (AUC), found the cutoff point by using the Akaike information criterion (AIC) value, and distinguished the patients with ccRCC into a high-risk group and a low-risk group using this value. Finally, we tested this model by investigating the relationship between risk score and survival, clinical pathological characteristics, cells in tumor immune microenvironment, chemotherapy, and targeted checkpoint biomarkers. Results A novel immune-related lncRNA pair signature consisting of 12 DEirlncRNA pairs was successfully constructed and tightly associated with overall survival, clinical pathological characteristics, cells in tumor immune microenvironment, and reactiveness to immunotherapy and chemotherapy in patients with ccRCC. Besides, the efficacy of this signature was verified in some commonly used clinicopathological subgroups and could serve as an independent prognostic factor in patients with ccRCC. Conclusions This signature was proven to have a potential predictive significance for the prognosis of patients with ccRCC and the efficacy of immunotherapy.
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Kurmann L, Okoniewski M, Dubey RK. Estradiol Inhibits Human Brain Vascular Pericyte Migration Activity: A Functional and Transcriptomic Analysis. Cells 2021; 10:cells10092314. [PMID: 34571963 PMCID: PMC8472363 DOI: 10.3390/cells10092314] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/24/2021] [Accepted: 09/01/2021] [Indexed: 12/24/2022] Open
Abstract
Stroke is the third leading cause of mortality in women and it kills twice as many women as breast cancer. A key role in the pathophysiology of stroke plays the disruption of the blood–brain barrier (BBB) within the neurovascular unit. While estrogen induces vascular protective actions, its influence on stroke remains unclear. Moreover, experiments assessing its impact on endothelial cells to induce barrier integrity are non-conclusive. Since pericytes play an active role in regulating BBB integrity and function, we hypothesize that estradiol may influence BBB by regulating their activity. In this study using human brain vascular pericytes (HBVPs) we investigated the impact of estradiol on key pericyte functions known to influence BBB integrity. HBVPs expressed estrogen receptors (ER-α, ER-β and GPER) and treatment with estradiol (10 nM) inhibited basal cell migration but not proliferation. Since pericyte migration is a hallmark for BBB disruption following injury, infection and inflammation, we investigated the effects of estradiol on TNFα-induced PC migration. Importantly, estradiol prevented TNFα-induced pericyte migration and this effect was mimicked by PPT (ER-α agonist) and DPN (ER-β agonist), but not by G1 (GPR30 agonist). The modulatory effects of estradiol were abrogated by MPP and PHTPP, selective ER-α and ER-β antagonists, respectively, confirming the role of ER-α and ER-β in mediating the anti-migratory actions of estrogen. To delineate the intracellular mechanisms mediating the inhibitory actions of estradiol on PC migration, we investigated the role of AKT and MAPK activation. While estradiol consistently reduced the TNFα-induced MAPK and Akt phosphorylation, only the inhibition of MAPK, but not Akt, significantly abrogated the migratory actions of TNFα. In transendothelial electrical resistance measurements, estradiol induced barrier function (TEER) in human brain microvascular endothelial cells co-cultured with pericytes, but not in HBMECs cultured alone. Importantly, transcriptomics analysis of genes modulated by estradiol in pericytes showed downregulation of genes known to increase cell migration and upregulation of genes known to inhibit cell migration. Taken together, our findings provide the first evidence that estradiol modulates pericyte activity and thereby improves endothelial integrity.
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Affiliation(s)
- Lisa Kurmann
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland;
| | | | - Raghvendra K. Dubey
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland;
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Correspondence:
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Wang Y, Yan K, Wang L, Bi J. Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology. BMC Cancer 2021; 21:727. [PMID: 34167490 PMCID: PMC8229419 DOI: 10.1186/s12885-021-08356-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/29/2021] [Indexed: 12/04/2022] Open
Abstract
Background There is evidence that long non-coding RNA (lncRNA) is related to genetic stability. However, the complex biological functions of these lncRNAs are unclear. Method TCGA - KIRC lncRNAs expression matrix and somatic mutation information data were obtained from TCGA database. “GSVA” package was applied to evaluate the genomic related pathway in each samples. GO and KEGG analysis were performed to show the biological function of lncRNAs-mRNAs. “Survival” package was applied to determine the prognostic significance of lncRNAs. Multivariate Cox proportional hazard regression analysis was applied to conduct lncRNA prognosis model. Results In the present study, we applied computational biology to identify genome-related long noncoding RNA and identified 26 novel genomic instability-associated lncRNAs in clear cell renal cell carcinoma. We identified a genome instability-derived six lncRNA-based gene signature that significantly divided clear renal cell samples into high- and low-risk groups. We validated it in test cohorts. To further elucidate the role of the six lncRNAs in the model’s genome stability, we performed a gene set variation analysis (GSVA) on the matrix. We performed Pearson correlation analysis between the GSVA scores of genomic stability-related pathways and lncRNA. It was determined that LINC00460 and LINC01234 could be used as critical factors in this study. They may influence the genome stability of clear cell carcinoma by participating in mediating critical targets in the base excision repair pathway, the DNA replication pathway, homologous recombination, mismatch repair pathway, and the P53 signaling pathway. Conclusion subsections These data suggest that LINC00460 and LINC01234 are crucial for the stability of the clear cell renal cell carcinoma genome. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08356-9.
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Affiliation(s)
- Yutao Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Kexin Yan
- Department of Dermatology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Linhui Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianbin Bi
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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Yang W, Zhang K, Li L, Xu Y, Ma K, Xie H, Zhou J, Cai L, Gong Y, Gong K. Correction to: Downregulation of lncRNA ZNF582-AS1 due to DNA hypermethylation promotes clear cell renal cell carcinoma growth and metastasis by regulating the N(6)-methyladenosine modification of MT-RNR1. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:167. [PMID: 33985546 PMCID: PMC8117296 DOI: 10.1186/s13046-021-01969-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wuping Yang
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China.,National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Kenan Zhang
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China.,National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Lei Li
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China.,National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Yawei Xu
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China.,National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Kaifang Ma
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China.,National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Haibiao Xie
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China.,National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Jingcheng Zhou
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China.,National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Lin Cai
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China.,National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China. .,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China. .,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China. .,National Urological Cancer Center, Beijing, 100034, People's Republic of China.
| | - Kan Gong
- Department of Urology, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China. .,Hereditary Kidney Cancer Research Center, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China. .,Institute of Urology, Peking University, Beijing, 100034, People's Republic of China. .,National Urological Cancer Center, Beijing, 100034, People's Republic of China.
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Cheng T, Shuang W, Ye D, Zhang W, Yang Z, Fang W, Xu H, Gu M, Xu W, Guan C. SNHG16 promotes cell proliferation and inhibits cell apoptosis via regulation of the miR-1303-p/STARD9 axis in clear cell renal cell carcinoma. Cell Signal 2021; 84:110013. [PMID: 33901578 DOI: 10.1016/j.cellsig.2021.110013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common subtype of renal cell carcinoma (RCC) and causes many deaths. Numerous medical studies have suggested that long noncoding RNAs (lncRNAs) exert their biological functions on ccRCC. Herein, functions of lncRNA SNHG16 in ccRCC cells and the mechanism mediated by SNHG16 were investigated. The expression levels of SNHG16 and its downstream genes in ccRCC cells and RCC tissues were examined utilizing reverse transcription quantitative polymerase chain reaction analyses. Cell counting kit-8 and 5-Ethynyl-2'-deoxyuridine assays were performed to evaluate the proliferation of ccRCC cells, and flow cytometry analyses were employed to determine the apoptosis of ccRCC cells. Western blot analysis was applied to examine protein levels associated with cell proliferation and apoptosis. The combination between SNHG16 and miRNA as well as miRNA and its target gene were explored by luciferase reporter, RNA pull down, and RNA immunoprecipitation assays. The significant upregulation of SNHG16 was observed in RCC tissues and ccRCC cells. SNHG16 downregulation inhibited the proliferation and promoted the apoptosis of ccRCC cells. In addition, SNHG16 served as a competing endogenous RNA for miR-1301-3p, and STARD9 was a target gene of miR-1301-3p in ccRCC cells. SNHG16 upregulated STARD9 expression by binding with miR-1301-3p in ccRCC cells. Rescue assays validated that SNHG16 promoted ccRCC cell promotion and induced ccRCC cell apoptosis by upregulating STARD9 expression. In conclusions, SNHG16 promotes ccRCC cell proliferation and suppresses ccRCC cell apoptosis via interaction with miR-1301-3p to upregulate STARD9 expression in ccRCC cells.
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Affiliation(s)
- Tao Cheng
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Weibing Shuang
- Department of Urology, The First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Dawen Ye
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Wenzhi Zhang
- Innoscience Research Sdn Bhd, Subang Jaya, Malaysia
| | - Zhao Yang
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenge Fang
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Haibin Xu
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Mingli Gu
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Weiqiang Xu
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Chao Guan
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China..
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