1
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Yang L, Ying J, Tao Q, Zhang Q. RNA N 6-methyladenosine modifications in urological cancers: from mechanism to application. Nat Rev Urol 2024; 21:460-476. [PMID: 38347160 DOI: 10.1038/s41585-023-00851-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2023] [Indexed: 08/04/2024]
Abstract
The N6-methyladenosine (m6A) modification is the most common modification of messenger RNAs in eukaryotes and has crucial roles in multiple cancers, including in urological malignancies such as renal cell carcinoma, bladder cancer and prostate cancer. The m6A RNA modification is controlled by three types of regulators, including methyltransferases (writers), demethylases (erasers) and RNA-binding proteins (readers), which are responsible for gene regulation at the post-transcriptional level. This Review summarizes the current evidence indicating that aberrant or dysregulated m6A modification is associated with urological cancer development, progression and prognosis. The complex and context-dependent effects of dysregulated m6A modifications in urological cancers are described, along with the potential for aberrantly expressed m6A regulators to provide valuable diagnostic and prognostic biomarkers as well as new therapeutic targets.
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Affiliation(s)
- Lei Yang
- Department of Urology, Peking University First Hospital, Institute of Urology, National Research Center for Genitourinary Oncology, Peking University, Beijing, China
| | - Jianming Ying
- Department of Pathology, Cancer Institute and Cancer Hospital, Peking Union Medical College (PUMC), Chinese Academy of Medical Sciences, Beijing, China
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital, Institute of Urology, National Research Center for Genitourinary Oncology, Peking University, Beijing, China.
- Department of Urology, Peking University Binhai Hospital, Tianjin, China.
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2
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Sun Y, Jin D, Zhang Z, Ji H, An X, Zhang Y, Yang C, Sun W, Zhang Y, Duan Y, Kang X, Jiang L, Zhao X, Lian F. N6-methyladenosine (m6A) methylation in kidney diseases: Mechanisms and therapeutic potential. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194967. [PMID: 37553065 DOI: 10.1016/j.bbagrm.2023.194967] [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: 03/27/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
The N6-methyladenosine (m6A) modification is regulated by methylases, commonly referred to as "writers," and demethylases, known as "erasers," leading to a dynamic and reversible process. Changes in m6A levels have been implicated in a wide range of cellular processes, including nuclear RNA export, mRNA metabolism, protein translation, and RNA splicing, establishing a strong correlation with various diseases. Both physiologically and pathologically, m6A methylation plays a critical role in the initiation and progression of kidney disease. The methylation of m6A may also facilitate the early diagnosis and treatment of kidney diseases, according to accumulating research. This review aims to provide a comprehensive overview of the potential role and mechanism of m6A methylation in kidney diseases, as well as its potential application in the treatment of such diseases. There will be a thorough examination of m6A methylation mechanisms, paying particular attention to the interplay between m6A writers, m6A erasers, and m6A readers. Furthermore, this paper will elucidate the interplay between various kidney diseases and m6A methylation, summarize the expression patterns of m6A in pathological kidney tissues, and discuss the potential therapeutic benefits of targeting m6A in the context of kidney diseases.
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Affiliation(s)
- Yuting Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - De Jin
- Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Ziwei Zhang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Hangyu Ji
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuedong An
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuehong Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cunqing Yang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenjie Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuqing Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingying Duan
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaomin Kang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Jiang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuefei Zhao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengmei Lian
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
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3
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Ding W, Zhang M, Zhang P, Zhang X, Sun J, Lin B. Identification of anoikis-related subtypes and immune landscape in kidney renal clear cell carcinoma. Sci Rep 2023; 13:18069. [PMID: 37872217 PMCID: PMC10593771 DOI: 10.1038/s41598-023-45069-4] [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: 06/20/2023] [Accepted: 10/15/2023] [Indexed: 10/25/2023] Open
Abstract
Anoikis is a specific form of programmed cell death induced by the loss of cell contact with the extracellular matrix and other cells, and plays an important role in organism development, tissue homeostasis, disease development and tumor metastasis. We comprehensively investigated the expression patterns of anoikis-related genes (ARGs) in kidney renal clear cell carcinoma (KIRC) from public databases. Anoikis-related prognostic signatures were established based on four ARGs expression, in which KIRC patients were assigned different risk scores and divided into two different risk groups. In addition, four ARGs expression was validated by qRT-PCR. A better prognosis was observed in the low-risk group, but with lower immune activity (including immune cells and immune-related functions) in the tumor microenvironment. Combined with the relevant clinical characteristics, a nomogram for clinical application was established. Receiver operating characteristics (ROC) and calibration curves were constructed to demonstrate the predictive power of this risk signature. In addition, higher risk scores were significantly and positively correlated with higher gene expression of tumor mutation load (TMB), immune checkpoints (ICPs) and mismatch repair (MMR)-related proteins in general. The results also suggested that the high-risk group was more sensitive to immunotherapy and certain chemotherapeutic agents. Anoikis-related prognostic signatures may provide a better understanding of the roles of ARGs and offer new perspectives for clinical prognosis and individualized treatment.
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Affiliation(s)
- Wencong Ding
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Min Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Ping Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Xianghong Zhang
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Junwei Sun
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Biying Lin
- The Department of Nephrology and Hemopurification Center, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China.
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4
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Wang Q, Fan X, Sheng Q, Yang M, Zhou P, Lu S, Gao Y, Kong Z, Shen N, Lv Z, Wang R. N6-methyladenosine methylation in kidney injury. Clin Epigenetics 2023; 15:170. [PMID: 37865763 PMCID: PMC10590532 DOI: 10.1186/s13148-023-01586-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023] Open
Abstract
Multiple mechanisms are involved in kidney damage, among which the role of epigenetic modifications in the occurrence and development of kidney diseases is constantly being revealed. However, N6-methyladenosine (M6A), a well-known post-transcriptional modification, has been regarded as the most prevalent epigenetic modifications in higher eukaryotic, which is involved in various biological processes of cells such as maintaining the stability of mRNA. The role of M6A modification in the mechanism of kidney damage has attracted widespread attention. In this review, we mainly summarize the role of M6A modification in the progression of kidney diseases from the following aspects: the regulatory pattern of N6-methyladenosine, the critical roles of N6-methyladenosine in chronic kidney disease, acute kidney injury and renal cell carcinoma, and then reveal its potential significance in the diagnosis and treatment of various kidney diseases. A better understanding of this field will be helpful for future research and clinical treatment of kidney diseases.
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Affiliation(s)
- Qimeng Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Xiaoting Fan
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Qinghao Sheng
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Meilin Yang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Ping Zhou
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Shangwei Lu
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Ying Gao
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Zhijuan Kong
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Ning Shen
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Zhimei Lv
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
| | - Rong Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
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5
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Li N, Zhu Z, Deng Y, Tang R, Hui H, Kang Y, Rana TM. KIAA1429/VIRMA promotes breast cancer progression by m 6 A-dependent cytosolic HAS2 stabilization. EMBO Rep 2023; 24:e55506. [PMID: 37705505 PMCID: PMC10561361 DOI: 10.15252/embr.202255506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/14/2023] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
N6 -methyladenosine (m6 A), the most abundant internal modification in eukaryotic mRNA, plays important roles in many physiological and pathological processes, including the development and progression of cancer. RNA modification by m6 A is regulated by methyltransferases, demethylases, and m6 A-binding proteins that function in large part by regulating mRNA expression and function. Here, we investigate the expression of m6 A regulatory proteins in breast cancer. We find that expression of KIAA1429/VIRMA, a component of the m6 A methyltransferase complex, is upregulated in breast cancer tissue and correlates positively with poor survival. KIAA1429/VIRMA is mislocalized to the cytosol of breast cancer tissues and cell lines, and shRNA-mediated knockdown inhibits breast cancer cell proliferation, migration, and invasion. Mechanistically, KIAA1429/VIRMA is shown to bind to the m6 A-dependent RNA-binding protein insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), leading to recruitment and stabilization of m6 A-modified hyaluronan synthase 2 (HAS2) mRNA. HAS2 mRNA and KIAA1429/VIRMA mRNA levels correlate positively in breast cancer tissues, suggesting that the KIAA1429/VIRMA-IGF2BP3-HAS2 axis promotes breast cancer growth and contributes to poor prognosis.
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Affiliation(s)
- Na Li
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Zhouting Zhu
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Yufei Deng
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Rachel Tang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Hui Hui
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Yuqi Kang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Program in Immunology, Bioinformatics and Systems Biology ProgramInstitute for Genomic MedicineLa JollaCAUSA
- San Diego Center for Precision Immunotherapy, Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
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Gui CP, Wei JH, Zhang C, Tang YM, Shu GN, Wu RP, Luo JH. Single-cell and spatial transcriptomics reveal 5-methylcytosine RNA methylation regulators immunologically reprograms tumor microenvironment characterizations, immunotherapy response and precision treatment of clear cell renal cell carcinoma. Transl Oncol 2023; 35:101726. [PMID: 37379773 DOI: 10.1016/j.tranon.2023.101726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/24/2023] [Accepted: 06/18/2023] [Indexed: 06/30/2023] Open
Abstract
Clear cell Renal Cell Carcinoma (ccRCC) is a highly heterogeneous disease, making it challenging to predict prognosis and therapy efficacy. In this study, we aimed to explore the role of 5-methylcytosine (m5C) RNA modification in ccRCC and its potential as a predictor for therapy response and overall survival (OS). We established a novel 5-methylcytosine RNA modification-related gene index (M5CRMRGI) and studied its effect on the tumor microenvironment (TME) using single-cell sequencing data for in-depth analysis, and verified it using spatial sequencing data. Our results showed that M5CRMRGI is an independent predictor of OS in multiple datasets and exhibited outstanding performance in predicting the OS of ccRCC. Distinct mutation profiles, hallmark pathways, and infiltration of immune cells in TME were observed between high- and low-M5CRMRGI groups. Single-cell/spatial transcriptomics revealed that M5CRMRGI could reprogram the distribution of tumor-infiltrating immune cells. Moreover, significant differences in tumor immunogenicity and tumor immune dysfunction and exclusion (TIDE) were observed between the two risk groups, suggesting a better response to immune checkpoint blockade therapy of the high-risk group. We also predicted six potential drugs binding to the core target of the M5CRMRGI signature via molecular docking. Real-world treatment cohort data proved once again that high-risk patients were appropriate for immune checkpoint blockade therapy, while low-risk patients were appropriate for Everolimus. Our study shows that the m5C modification landscape plays a role in TME distribution. The proposed M5CRMRGI-guided strategy for predicting survival and immunotherapy efficacy, we reported here, might also be applied to more cancers other than ccRCC.
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Affiliation(s)
- Cheng-Peng Gui
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
| | - Jin-Huan Wei
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Chi Zhang
- Department of Urology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Yi-Ming Tang
- Department of Urology, Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Guan-Nan Shu
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Rong-Pei Wu
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
| | - Jun-Hang Luo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China; Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
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7
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Zhu TY, Hong LL, Ling ZQ. Oncofetal protein IGF2BPs in human cancer: functions, mechanisms and therapeutic potential. Biomark Res 2023; 11:62. [PMID: 37280679 PMCID: PMC10245617 DOI: 10.1186/s40364-023-00499-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent and well-characterized internal chemical modification in eukaryotic RNA, influencing gene expression and phenotypic changes by controlling RNA fate. Insulin-like growth factor-2 mRNA-binding proteins (IGF2BPs) preferentially function as m6A effector proteins, promoting stability and translation of m6A-modified RNAs. IGF2BPs, particularly IGF2BP1 and IGF2BP3, are widely recognized as oncofetal proteins predominantly expressed in cancer rather than normal tissues, playing a critical role in tumor initiation and progression. Consequently, IGF2BPs hold potential for clinical applications and serve as a good choice for targeted treatment strategies. In this review, we discuss the functions and mechanisms of IGF2BPs as m6A readers and explore the therapeutic potential of targeting IGF2BPs in human cancer.
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Affiliation(s)
- Tian-Yu Zhu
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- The Second School of Clinical Medicine, Wenzhou Medical University, No.109 Xueyuan West Road, Wenzhou, 325027 Zhejiang, China
- Jinhua People's Hospital, No.267 Danxi East Road, Jinhua, 321000 Zhejiang, China
| | - Lian-Lian Hong
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Zhi-Qiang Ling
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- The Second School of Clinical Medicine, Wenzhou Medical University, No.109 Xueyuan West Road, Wenzhou, 325027 Zhejiang, China.
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Xiong Z, Han Z, Pan W, Zhu X, Liu C. Correlation between chromatin epigenetic-related lncRNA signature (CELncSig) and prognosis, immune microenvironment, and immunotherapy in non-small cell lung cancer. PLoS One 2023; 18:e0286122. [PMID: 37224123 DOI: 10.1371/journal.pone.0286122] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Chromatin regulators drive cancer epigenetic changes, and lncRNA can play an important role in epigenetic changes as chromatin regulators. We used univariate Cox, LASSO, and multivariate Cox regression analysis to select epigenetic-associated lncRNA signatures. Twenty-five epigenetic-associated lncRNA signatures (CELncSig) were identified to establish the immune prognostic model. According to Kaplan-Meier analysis, the overall survival of the high-risk group was significantly lower than the low-risk group. Receiver operating characteristic (ROC) curves, C-index, survival curve, nomogram, and principal component analysis (PCA) were performed to validate the risk model. In GO/KEGG analysis, differentially expressed lncRNAs were correlated with the PI3K-Akt pathway, suggesting that they were highly associated with the metastasis of LUAD. Interestingly, in the immune escape analysis, the TIDE score was lower, and the possibility of immune dysfunction is also slighter in the high-risk group, which means they still have the potential to receive immunotherapy. And CELncsig is highly correlated with immune pathways T_cell_co-inhibition and Check-point. Also, the IMvigor210 cohort analysis indicated that our risk-scoring model has significant potential clinical application value in lung cancer immunotherapy. And we also screened out ten potential chemotherapy agents using the 'pRRophetic' package.
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Affiliation(s)
- Zhuolong Xiong
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Computational Systems Biology Lab (CSBL), Institute of Bioinformatics, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Zenglei Han
- Department of Pathology, Qingdao Municipal Hospital, Qingdao, China
| | - Weiyi Pan
- Computational Systems Biology Lab (CSBL), Institute of Bioinformatics, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), Institute of Bioinformatics, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou Medical College, Hangzhou, China
| | - Caixin Liu
- Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
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Yang Z, Zhang W, Li L, Hu N, Dong X, Chen Y, Cai W, Yin L, Liu F, Tang D, Dai Y. The novel putative methyltransferase METTL7A as one prognostic biomarker potentially associated with immune infiltration in human renal cancer. Heliyon 2023; 9:e15371. [PMID: 37123902 PMCID: PMC10133759 DOI: 10.1016/j.heliyon.2023.e15371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Among urological cancers, renal cancer has the highest fatality rate. In a previous pan-cancer study of the METTL family, we observed a stronger association between the METTL family members and the risk of renal cancer compared to other cancers. Among these members, METTL7A, a potential methyltransferase, was identified as a protective factor, although its role and mechanism in renal cancer remain unclear. In this study, we utilized public databases to examine the expression of METTL7A in renal cancer tissues and normal tissues and found that METTL7A expression was much lower in renal cancer tissues. We also noticed a link between low METTL7A expression and poor prognosis for patients. According to the results of our functional enrichment analysis, METTL7A may have a role in immunological functions in renal cancer. METTL7A expression was strongly linked with the degrees of immune cell infiltration and expression of numerous immunological components. METTL7A had significantly different effects on the survival times of renal cancer patients with high or low immune infiltration. Our findings suggest that METTL7A may be used as both a prognostic biomarker and an immunological target for kidney cancer. In conclusion, our study sheds light on the importance of METTL7A in renal cancer and emphasizes the potential of targeting METTL7A as a novel therapeutic strategy for kidney cancer.
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Affiliation(s)
- Zhiqian Yang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Wei Zhang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
- Guangdong Fapon Biopharma Inc, Innovative Markers Department, Dongguan 523808, China
| | - Lintai Li
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
- Guangdong Fapon Biopharma Inc, Innovative Markers Department, Dongguan 523808, China
| | - Nan Hu
- Key Renal Laboratory of Shenzhen, Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Xiangnan Dong
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Yumei Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Wanxia Cai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Lianghong Yin
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Fanna Liu
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
- Corresponding author.
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
- Corresponding author.
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
- Key Renal Laboratory of Shenzhen, Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen 518020, China
- Corresponding author. Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China.
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10
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Li Z, Zheng C, Huang L, Yin X, Wang Z, Liu C, Li B. The landscape of m6A regulators in esophageal cancer: molecular characteristics, immuno-oncology features, and clinical relevance. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1347. [PMID: 36660671 PMCID: PMC9843396 DOI: 10.21037/atm-22-5895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022]
Abstract
Background Squamous cell carcinoma (SCC) and adenocarcinoma (AC) are the two main pathological types of esophageal cancer (EC), which differ in molecular features, genetic variation, and treatment sensitivity. However, as a key process in tumorigenesis and development, the role of N6-methyladenosine (m6A) regulators in esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) is not fully understood. Methods This study systematically compared the role of m6A regulators of ESCC and EAC in terms of molecular characteristics, immuno-oncology characteristics, and clinical relevance, and validated our findings in a long-term follow-up patient cohort. Results There were many differences in m6A regulators between ESCC and EAC in terms of expression patterns, genetic variation, association with tumor pathways, immune signatures, and immunotherapy sensitivity. Furthermore, VIRMA was identified as a factor with opposite functional and prognostic effects in ESCC and EAC. ESCC patients with high VIRMA expression and EAC patients with low VIRMA expression had a better prognosis. Single-center data showed that low expression of FTO may be associated with superior immunotherapy efficacy in ESCC patients. Conclusions The results herein provide novel ideas for understanding the tumor characteristics, occurrence, and development of ESCC and EAC, and suggest new targets for the treatment and intervention of EC.
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Affiliation(s)
- Zhe Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Chunyan Zheng
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Liquan Huang
- Department of Anesthesiology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaoyang Yin
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zhongtang Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Chengxin Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Baosheng Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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11
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Li J, Li Q, Yuan Y, Xie Y, Zhang Y, Zhang R. High CENPA expression in papillary renal cell carcinoma tissues is associated with poor prognosis. BMC Urol 2022; 22:157. [PMID: 36163007 PMCID: PMC9511783 DOI: 10.1186/s12894-022-01106-4] [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: 03/10/2022] [Accepted: 09/19/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE This work focused on investigating the relation of centromeric protein A (CENPA) gene expression with prognosis of papillary renal cell carcinoma (PRCC). METHODS We obtained data from PRCC cases in TCGA. Thereafter, CENPA levels between the paired PRCC and matched non-carcinoma samples were analyzed by Wilcoxon rank-sum test, while the relations of clinicopathological characteristics with CENPA level were examined by logistic regression and Wilcoxon rank-sum test. The prognostic value of CENPA was assessed by plotting the receiver operating feature curve (ROC) and calculating the value of area under curve (AUC). In addition, relations between clinicopathological characteristics and PRCC survival were analyzed through Kaplan-Meier (KM) and Cox regression analyses. After dividing the total number of patients into the trial cohort and the validation cohort in a ratio of 7:3, we constructed a nomogram in trial cohort according to multivariate Cox regression results for predicting how CENPA affected patient survival and used the calibration curve to verify its accuracy in both cohorts. We also determined CENPA levels within cancer and matched non-carcinoma samples through immunohistochemistry (IHC). Finally, we utilized functional enrichment for identifying key pathways related to differentially expressed genes (DEGs) between PRCC cases with CENPA up-regulation and down-regulation. RESULTS CENPA expression enhanced in PRCC tissues compared with healthy counterparts (P < 0.001). CENPA up-regulation was related to pathological TNM stage and clinical stage (P < 0.05). Meanwhile, the ROC curves indicated that CENPA had a remarkable diagnostic capacity for PRCC, and the expression of CENPA can significantly improve the predictive accuracy of pathological TNM stage and clinical stage for PRCC. As revealed by KM curves, PRCC cases with CENPA up-regulation were associated with poor survival compared with those with CENPA down-regulation (Risk ratio, RR = 3.07, 95% CI: 1.58-5.97, P = 0.001). In the meantime, univariate as well as multivariate analysis showed an independent association of CENPA with overall survival (OS, P < 0.05) and the nomogram demonstrated superior predictive ability in both cohorts. IHC analysis indicated that PRCC cases showed an increased CENPA positive rate compared with controls. As revealed by functional annotations, CENPA was enriched into pathways associated with neuroactive ligand receptor interactions, cytokine receptor interactions, extracellular matrix regulators, extracellular matrix glycoproteins and nuclear matrisome. CONCLUSION CENPA expression increases within PRCC samples, which predicts dismal PRCC survival. CENPA may become a molecular prognostic marker and therapeutic target for PRCC patients.
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Affiliation(s)
- Junwu Li
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Qinke Li
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Yang Yuan
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Yiteng Xie
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Yuanfeng Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China.
| | - Ronggui Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China.
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12
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Multifaceted Roles of the N6-Methyladenosine RNA Methyltransferase METTL3 in Cancer and Immune Microenvironment. Biomolecules 2022; 12:biom12081042. [PMID: 36008936 PMCID: PMC9406229 DOI: 10.3390/biom12081042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 12/24/2022] Open
Abstract
As the most abundant internal mRNA modification in eukaryotic cells, N6-methyladenosine (m6A) has emerged as an important regulator of gene expression and has a profound impact on cancer initiation and progression. mRNA m6A modification is regulated by m6A methyltransferases, demethylases and reader proteins to fine tune gene expression at the post-transcriptional level. The most well-studied m6A methyltransferase, METTL3, plays critical roles in regulating gene expression and affecting the outcome of various cancers. In this review, we discuss the multifaceted roles of METTL3 in regulating specific molecular signaling pathways in different types of cancers and the recent progress on how METTL3 impacts the tumor immune microenvironment. Finally, we discuss future directions and the potential for therapeutic targeting of METTL3 in cancer treatment.
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13
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Wu X, Deng Z, Liao X, Ruan X, Qu N, Pang L, Shi X, Qin S, Jiang H. Establishment of Prognostic Signatures of N6-Methyladenosine-Related lncRNAs and Their Potential Functions in Hepatocellular Carcinoma Patients. Front Oncol 2022; 12:865917. [PMID: 35734590 PMCID: PMC9207396 DOI: 10.3389/fonc.2022.865917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/06/2022] [Indexed: 12/23/2022] Open
Abstract
N6-methyladenosine (m6a)-related mRNAs and lncRNAs have been explored for their functions in several cancers. The present study aimed to identify potential signatures of m6a-related lncRNAs in hepatocellular carcinoma (HCC). We downloaded the expression and clinical data from The Cancer Genome Atlas (TCGA) database. The interacted mRNAs and lncRNAs, prognosis-related lncRNAs, potential metabolic pathways of lncRNAs, immune infiltration of various cells, and CD274 (PD-L1) -related lncRNAs were analyzed. Then, in vitro experiments explored the role of AC012073.1 (LOC105377626) in HCC cell lines. We found that candidate 14 lncRNA signatures play functions in HCC maybe by affecting immune infiltration, cell cycle, Notch signaling pathway, etc. LncRNA AC012073.1 (LOC105377626) functions as oncogenic roles in affecting HCC prognosis.
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Affiliation(s)
- Xianbin Wu
- Department of Gastroenterology, The First Afliated Hospital of Guangxi Medical University, Nanning, China.,Department of Gastroenterology, The Third Affifiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhejun Deng
- Department of Gastroenterology, The First Afliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaomin Liao
- Department of Gastroenterology, The First Afliated Hospital of Guangxi Medical University, Nanning, China
| | - Xianxian Ruan
- Department of Gastroenterology, The First Afliated Hospital of Guangxi Medical University, Nanning, China
| | - Nanfang Qu
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Lixing Pang
- Department of Gastroenterology, The Third Affifiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaoyan Shi
- Department of Gastroenterology, The First Afliated Hospital of Guangxi Medical University, Nanning, China
| | - Shanyu Qin
- Department of Gastroenterology, The First Afliated Hospital of Guangxi Medical University, Nanning, China
| | - Haixing Jiang
- Department of Gastroenterology, The First Afliated Hospital of Guangxi Medical University, Nanning, China
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14
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Li J, Wei S, Zhang Y, Lu S, Zhang X, Wang Q, Yan J, Yang S, Chen L, Liu Y, Huang Z. Comprehensive Analyses of Mutation-Derived Long-Chain Noncoding RNA Signatures of Genome Instability in Kidney Renal Papillary Cell Carcinoma. Front Genet 2022; 13:874673. [PMID: 35547247 PMCID: PMC9082950 DOI: 10.3389/fgene.2022.874673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The role of long-chain noncoding RNA (lncRNA) in genomic instability has been demonstrated to be increasingly importance. Therefore, in this study, lncRNAs associated with genomic instability were identified and kidney renal papillary cell carcinoma (KIRP)-associated predictive features were analysed to classify high-risk patients and improve individualised treatment. Methods: The training (n = 142) and test (n = 144) sets were created using raw RNA-seq and patient’s clinical data of KIRP obtained from The Cancer Genome Atlas (TCGA).There are 27 long-chain noncoding RNAs (lncRNAs) that are connected with genomic instability, these lncRNAs were identified using the ‘limma’ R package based on the numbers of somatic mutations and lncRNA expression profiles acquired from KIRP TCGA cohort. Furthermore, Cox regression analysis was carried out to develop a genome instability-derived lncRNA-based gene signature (GILncSig), whose prognostic value was confirmed in the test cohort as well as across the entire KIRP TCGA dataset. Results: A GILncSig derived from three lncRNAs (BOLA3-AS1, AC004870, and LINC00839), which were related with poor KIRP survival, was identified, which was split up into high- and low-risk groups. Additionally, the GILncSig was found to be an independent prognostic predictive index in KIRP using univariate and multivariate Cox analysis. Furthermore, the prognostic significance and characteristics of GilncSig were confirmed in the training test and TCGA sets. GilncSig also showed better predictive performance than other prognostic lncRNA features. Conclusion: The function of lncRNAs in genomic instability and the genetic diversity of KIRP were elucidated in this work. Moreover, three lncRNAs were screened for prediction of the outcome of KIRP survival and novel insights into identifying cancer biomarkers related to genomic instability were discussed.
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Affiliation(s)
- Jian Li
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Shimei Wei
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yan Zhang
- Department of Pediatrics, Shanxi Children's Hospital, Taiyuan, China
| | - Shuangshuang Lu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xiaoxu Zhang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qiong Wang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jiawei Yan
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Sanju Yang
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Liying Chen
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Yunguang Liu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhijing Huang
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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15
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Wu J, Wei Y, Miao C, Wang S, Wang X, Wang Z. Essential m 6A Methylation Regulator HNRNPC Serves as a Targetable Biomarker for Papillary Renal Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:9411692. [PMID: 35502201 PMCID: PMC9056237 DOI: 10.1155/2022/9411692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022]
Abstract
m6A RNA modification is a common abundant posttranscriptional modification of mRNAs occurring in cancer growth and progression. Accumulated evidence has proved that HNRNPC, which acts as a m6A reader, plays an essential role in the promotion of cancer occurrence and development; nevertheless, the role of HNRNPC in papillary renal cell carcinoma remained to be discovered. In this study, we comprehensively identified HNRNPC as a hub gene involved in m6A modification in pRCC. Then, the expression level, survival outcomes, PPI network, function enrichment, immune cell infiltration, and single-cell analysis were performed. Finally, we found that HNRNPC significantly promoted renal cell carcinoma proliferation and migration in vitro. In conclusion, our work proved that HNRNPC may act as a momentous m6A regulator, as well as a potential targetable biomarker for pRCC.
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Affiliation(s)
- Jiajin Wu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital, No. 300 Guangzhou Road, Nanjing 210029, China
| | - Yuang Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital, No. 300 Guangzhou Road, Nanjing 210029, China
| | - Chenkui Miao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital, No. 300 Guangzhou Road, Nanjing 210029, China
| | - Songbo Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital, No. 300 Guangzhou Road, Nanjing 210029, China
| | - Xiaoyi Wang
- Core Facility Center, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital, No. 300 Guangzhou Road, Nanjing 210029, China
- Jiangsu Clinical Medical Research Institution, Nanjing 210029, China
| | - Zengjun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital, No. 300 Guangzhou Road, Nanjing 210029, China
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16
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Mo L, Meng L, Huang Z, Yi L, Yang N, Li G. An analysis of the role of HnRNP C dysregulation in cancers. Biomark Res 2022; 10:19. [PMID: 35395937 PMCID: PMC8994388 DOI: 10.1186/s40364-022-00366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/20/2022] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins C (HnRNP C) is part of the hnRNP family of RNA-binding proteins. The relationship between hnRNP C and cancers has been extensively studied, and dysregulation of hnRNP C has been found in many cancers. According to existing public data, hnRNP C could promote the maturation of new heterogeneous nuclear RNAs (hnRNA s, also referred to as pre-mRNAs) into mRNAs and could stabilize mRNAs, controlling their translation. This paper reviews the regulation and dysregulation of hnRNP C in cancers. It interacts with some cancer genes and other biological molecules, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and double-stranded RNAs (dsRNAs). Even directly binds to them. The effects of hnRNP C on biological processes such as alternative cleavage and polyadenylation (APA) and N6-methyladenosine (m6A) modification differ among cancers. Its main function is regulating stability and level of translation of cancer genes, and the hnRNP C is regarded as a candidate biomarker and might be valuable for prognosis evaluation.
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Affiliation(s)
- Liyi Mo
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lijuan Meng
- Department of Ultrasonography, Second Affiliated Hospital, University of South China, Hengyang, 421001, Hunan, China
| | - Zhicheng Huang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lan Yi
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Nanyang Yang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Guoqing Li
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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17
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Chen R, Ouyang P, Su L, Xu X, Lian P, Li Y, Gao Q, Zhang Y, Nie S, Luo F, Xu R, Zhang X, Li X, Cao Y, Gao P, Kang J, Wu J, Li L. Nanoparticles targeting at methylases with high correlation to N6-methyladenosine-related lncRNA signatures as potential therapy of kidney clear cell carcinoma. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.03.074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Li H, Jiang H, Huang Z, Chen Z, Chen N. Prognostic Value of an m 5C RNA Methylation Regulator-Related Signature for Clear Cell Renal Cell Carcinoma. Cancer Manag Res 2021; 13:6673-6687. [PMID: 34471382 PMCID: PMC8404088 DOI: 10.2147/cmar.s323072] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/02/2021] [Indexed: 12/27/2022] Open
Abstract
Purpose Clear cell renal cell carcinoma (ccRCC) is highly heterogeneous and is one of the most lethal types of cancer within the urinary system. Aberrant expression of 5-methylcytosine (m5C) RNA methylation regulators has been shown to result in occurrence and progression of tumors. However, the role of these regulators in ccRCC remains unclear. Materials and Methods We extracted RNA sequencing expression data with corresponding clinical information of patients with ccRCC from The Cancer Genome Atlas (TCGA) database. We then compared the expression profiles of m5C RNA methylation regulators between normal and ccRCC tissues, and determined different subtypes through consensus clustering analysis. In addition, we constructed a prognostic signature and evaluated it using a range of bioinformatics approaches. The expression of signature-related genes was subsequently verified in the clinical samples using qRT-PCR. Results We identified 12 differentially expressed m5C RNA methylation regulators between cancer and normal control samples. Two clusters of patients with ccRCC and diverse clinicopathological characteristics and prognoses were then determined through consensus clustering analysis. Functional annotations revealed that m5C RNA regulators were significantly correlated with the ccRCC progression. Moreover, we constructed a four-gene risk score signature (comprised of NOP2, NSUN4, NSUN6, and TET2) and divided the patients with ccRCC into high- and low-risk groups based on the median risk score. The risk score was associated with clinicopathological features and was an independent prognostic indicator of ccRCC. Our stratified analysis results suggest that the signature has high prognostic value. Based on qRT-PCR results, the NOP2 and NSUN4 mRNA expressions were higher and those of NSUN6 and TET2 were lower in ccRCC tissues than in normal tissues. Conclusion Our results demonstrate that m5C RNA methylation regulators may affect ccRCC progression and could be exploited for diagnostic and prognostic purposes.
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Affiliation(s)
- Hanrong Li
- Department of Extracorporeal Shock Wave Lithotripsy, Meizhou People's Hospital (Huangtang Hospital), Meizhou, Guangdong, People's Republic of China
| | - Huiming Jiang
- Department of Urology, Meizhou People's Hospital (Huangtang Hospital), Meizhou, Guangdong, People's Republic of China
| | - Zhicheng Huang
- Department of Urology, Meizhou People's Hospital (Huangtang Hospital), Meizhou, Guangdong, People's Republic of China
| | - Zhilin Chen
- Department of Urology, Meizhou People's Hospital (Huangtang Hospital), Meizhou, Guangdong, People's Republic of China
| | - Nanhui Chen
- Department of Urology, Meizhou People's Hospital (Huangtang Hospital), Meizhou, Guangdong, People's Republic of China
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19
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Yu J, Mao W, Sun S, Hu Q, Wang C, Xu Z, Liu R, Chen S, Xu B, Chen M. Identification of an m6A-Related lncRNA Signature for Predicting the Prognosis in Patients With Kidney Renal Clear Cell Carcinoma. Front Oncol 2021; 11:663263. [PMID: 34123820 PMCID: PMC8187870 DOI: 10.3389/fonc.2021.663263] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
Purpose This study aimed to construct an m6A-related long non-coding RNAs (lncRNAs) signature to accurately predict the prognosis of kidney clear cell carcinoma (KIRC) patients using data obtained from The Cancer Genome Atlas (TCGA) database. Methods The KIRC patient data were downloaded from TCGA database and m6A-related genes were obtained from published articles. Pearson correlation analysis was implemented to identify m6A-related lncRNAs. Univariate, Lasso, and multivariate Cox regression analyses were used to identifying prognostic risk-associated lncRNAs. Five lncRNAs were identified and used to construct a prognostic signature in training set. Kaplan-Meier curves and receiver operating characteristic (ROC) curves were applied to evaluate reliability and sensitivity of the signature in testing set and overall set, respectively. A prognostic nomogram was established to predict the probable 1-, 3-, and 5-year overall survival of KIRC patients quantitatively. GSEA was performed to explore the potential biological processes and cellular pathways. Besides, the lncRNA/miRNA/mRNA ceRNA network and PPI network were constructed based on weighted gene co-expression network analysis (WGCNA). Functional Enrichment Analysis was used to identify the biological functions of m6A-related lncRNAs. Results We constructed and verified an m6A-related lncRNAs prognostic signature of KIRC patients in TCGA database. We confirmed that the survival rates of KIRC patients with high-risk subgroup were significantly poorer than those with low-risk subgroup in the training set and testing set. ROC curves indicated that the prognostic signature had a reliable predictive capability in the training set (AUC = 0.802) and testing set (AUC = 0.725), respectively. Also, we established a prognostic nomogram with a high C-index and accomplished good prediction accuracy. The lncRNA/miRNA/mRNA ceRNA network and PPI network, as well as functional enrichment analysis provided us with new ways to search for potential biological functions. Conclusions We constructed an m6A-related lncRNAs prognostic signature which could accurately predict the prognosis of KIRC patients.
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Affiliation(s)
- JunJie Yu
- Medical College, Southeast University, Nanjing, China
| | - WeiPu Mao
- Medical College, Southeast University, Nanjing, China
| | - Si Sun
- Medical College, Southeast University, Nanjing, China
| | - Qiang Hu
- Medical College, Southeast University, Nanjing, China
| | - Can Wang
- Medical College, Southeast University, Nanjing, China
| | - ZhiPeng Xu
- Medical College, Southeast University, Nanjing, China
| | - RuiJi Liu
- Medical College, Southeast University, Nanjing, China
| | - SaiSai Chen
- Medical College, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Department of Urology, Affiliated Lishui People's Hospital of Southeast University, Nanjing, China
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20
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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21
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Zhu W, Wang JZ, Wei JF, Lu C. Role of m6A methyltransferase component VIRMA in multiple human cancers (Review). Cancer Cell Int 2021; 21:172. [PMID: 33731118 PMCID: PMC7968318 DOI: 10.1186/s12935-021-01868-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022] Open
Abstract
N6-Methyladenosine (m6A) modification is one of the most widely distributed RNA modifications in eukaryotes. It participates in various RNA functions and plays vital roles in tissue development, stem cell formation and differentiation, heat shock response control, and circadian clock controlling, particularly during tumor development. The reversible regulation of m6A modification is affected by the so-called ‘reader’, ‘writer’ and ‘eraser’. As a required component and the largest methyltransferase, vir-like m6A methyltransferase associated (VIRMA) can promote the progression of cancer and is associated with poor survival in multiple types of cancer. The present review investigated the role of VIRMA in various types of cancer. In an m6A-dependent or -independent manner, VIRMA can play an oncogenic role by regulating cancer cell proliferation, migration and invasion, metastasis, apoptosis resistance and tumor growth in different pathways by targeting stem factors, CCAT1/2, ID2, GATA3, CDK1, c-Jun, etc. VIRMA can also predict better prognosis in kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP) and papillary thyroid carcinoma by TCGA analysis. The obvious oncogenic roles of VIRMA observed in different types of cancer and the mechanisms of VIRMA promoting cancers provided the basis for potential therapeutic targeting for cancer treatments.
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Affiliation(s)
- Wei Zhu
- Precision Medicine Center, First Affiliated Hospital of Gannan Medical University, 128 Jinling Road, Ganzhou, 341000, China.,Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Jing-Zi Wang
- Department of Urology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Ji-Fu Wei
- Precision Medicine Center, First Affiliated Hospital of Gannan Medical University, 128 Jinling Road, Ganzhou, 341000, China. .,Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China.
| | - Chen Lu
- Precision Medicine Center, First Affiliated Hospital of Gannan Medical University, 128 Jinling Road, Ganzhou, 341000, China.
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22
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Yu J, Mao W, Xu B, Chen M. Construction and validation of an autophagy-related long noncoding RNA signature for prognosis prediction in kidney renal clear cell carcinoma patients. Cancer Med 2021; 10:2359-2369. [PMID: 33650306 PMCID: PMC7982638 DOI: 10.1002/cam4.3820] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/30/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose The purpose of this study was to identify autophagy‐associated long noncoding RNAs (ARlncRNAs) using the kidney renal clear cell carcinoma (KIRC) patient data from The Cancer Genome Atlas (TCGA) database and to construct a prognostic risk‐related ARlncRNAs signature to accurately predict the prognosis of KIRC patients. Methods The KIRC patient data were originated from TCGA database and were classified into a training set and testing set. Seven prognostic risk‐related ARlncRNAs, identified using univariate, lasso, and multivariate Cox regression analysis, were used to construct prognostic risk‐related signatures. Kaplan–Meier curves and receiver operating characteristic (ROC) curves as well as independent prognostic factor analysis and correlation analysis with clinical characteristics were utilized to evaluate and verify the specificity and sensitivity of the signature in training set and testing set, respectively. Two nomograms were established to predict the probable 1‐, 3‐, and 5‐year survival of the KIRC patients. In addition, the lncRNA‐mRNA co‐expression network was constructed and Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify biological functions of ARlncRNAs. Results We constructed and verified a prognostic risk‐related ARlncRNAs signature in training set and testing set, respectively. We found the survival time of KIRC patients with low‐risk scores was significantly better than those with high‐risk scores in training set and testing set. ROC curves suggested that the area under the ROC (AUC) value for prognostic risk score signature was 0.81 in training set and 0.705 in testing set. And AUC values corresponding to 1‐, 3‐, and 5 years of OS were 0.809, 0.753, and 0.794 in training set and 0.698, 0.682, and 0.754 in testing set, respectively. We established the two nomograms that confirmed high C‐index and accomplished good prediction accuracy. Conclusions We constructed a prognostic risk‐related ARlncRNAs signature that could accurately predict the prognosis of KIRC patients.
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Affiliation(s)
- JunJie Yu
- Department of medical college, Southeast University, Nanjing, China
| | - WeiPu Mao
- Department of medical college, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Southeast University Zhongda hospital, Nanjing, China
| | - Ming Chen
- Department of Urology, Southeast University Zhongda hospital, Nanjing, China
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