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Wu Y, Li L, Wang L, Zhang S, Zeng Z, Lu J, Wang Z, Zhang Y, Zhang S, Li H, Chen T. m 1A regulator-mediated methylation modification patterns correlated with autophagy to predict the prognosis of hepatocellular carcinoma. BMC Cancer 2024; 24:506. [PMID: 38649860 PMCID: PMC11034060 DOI: 10.1186/s12885-024-12235-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND N1-methyladenosine (m1A), among the most common internal modifications on RNAs, has a crucial role to play in cancer development. The purpose of this study were systematically investigate the modification characteristics of m1A in hepatocellular carcinoma (HCC) to unveil its potential as an anticancer target and to develop a model related to m1A modification characteristics with biological functions. This model could predict the prognosis for patients with HCC. METHODS An integrated analysis of the TCGA-LIHC database was performed to explore the gene signatures and clinical relevance of 10 m1A regulators. Furthermore, the biological pathways regulated by m1A modification patterns were investigated. The risk model was established using the genes that showed differential expression (DEGs) between various m1A modification patterns and autophagy clusters. These in vitro experiments were subsequently designed to validate the role of m1A in HCC cell growth and autophagy. Immunohistochemistry was employed to assess m1A levels and the expression of DEGs from the risk model in HCC tissues and paracancer tissues using tissue microarray. RESULTS The risk model, constructed from five DEGs (CDK5R2, TRIM36, DCAF8L, CYP26B, and PAGE1), exhibited significant prognostic value in predicting survival rates among individuals with HCC. Moreover, HCC tissues showed decreased levels of m1A compared to paracancer tissues. Furthermore, the low m1A level group indicated a poorer clinical outcome for patients with HCC. Additionally, m1A modification may positively influence autophagy regulation, thereby inhibiting HCC cells proliferation under nutrient deficiency conditions. CONCLUSIONS The risk model, comprising m1A regulators correlated with autophagy and constructed from five DEGs, could be instrumental in predicting HCC prognosis. The reduced level of m1A may represent a potential target for anti-HCC strategies.
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Affiliation(s)
- Yingmin Wu
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 561113, Guiyang, China.
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China.
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China.
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 561113, Guiyang, China.
| | - Lian Li
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 561113, Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 561113, Guiyang, China
| | - Long Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 561113, Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 561113, Guiyang, China
| | - Shenjie Zhang
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China
| | - Zhirui Zeng
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 561113, Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 561113, Guiyang, China
| | - Jieyu Lu
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 561113, Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 561113, Guiyang, China
| | - Zhi Wang
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China
| | - Yewei Zhang
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China
| | - Shilong Zhang
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China
| | - Haiyang Li
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China.
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China.
| | - Tengxiang Chen
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 561113, Guiyang, China.
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550004, Guiyang, China.
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China.
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 561113, Guiyang, China.
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Wu T, Liao L, Wu T, Chen S, Yi Q, Xu M. IGF2BP2 promotes glycolysis and hepatocellular carcinoma stemness by stabilizing CDC45 mRNA via m6A modification. Cell Cycle 2023; 22:2245-2263. [PMID: 37985379 PMCID: PMC10730143 DOI: 10.1080/15384101.2023.2283328] [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: 05/25/2023] [Accepted: 10/09/2023] [Indexed: 11/22/2023] Open
Abstract
A growing number of studies have shown the prognostic importance of Cell division cycle protein 45 (CDC45) in hepatocellular carcinoma (HCC). This study aims to investigate the biological function and mechanism of CDC45 in HCC. The differential expression and prognostic significance of CDC45 in HCC and normal tissues were analyzed by bioinformatics. CDC45 was knocked down and the biological effects of CDC45 in HCC in vitro and in vivo were measured. Subsequently, using RNA m6A colorimetry and Methylated RNA Immunoprecipitation (MeRIP), the levels of m6A modification of total RNA and CDC45 were evaluated in cells. RIP was applied to establish that CDC45 and insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) interact. A test using actinomycin D was performed to gauge the stability of the CDC45 mRNA. Furthermore, the regulatory role of IGF2BP2 on CDC45 expression in HCC progression was explored by overexpressing IGF2BP2. High expression of CDC45 was correlated with poor prognosis in HCC patients. Knocking down CDC45 inhibited HCC cell proliferation, migration, invasion, EMT, stemness, and glycolysis, and promoted apoptosis, which was verified through in vitro experiments. Additionally, IGF2BP2 was highly expressed in HCC cells, and it was found to interact with CDC45. Knocking down IGF2BP2 resulted in reduced stability of CDC45 mRNA. Moreover, overexpression of IGF2BP2 promoted HCC cell proliferation, migration, invasion, EMT, stemness, and glycolysis, while inhibiting apoptosis, which was reversed by knocking down CDC45. In general, IGF2BP2 promoted HCC glycolysis and stemness by stabilizing CDC45 mRNA via m6A modification. [Figure: see text].
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Affiliation(s)
- Tao Wu
- Department of Hepatobiliary Surgery, Yueyang Central Hospital, Yueyang, China
- Department of Urology Surgery, Yueyang Central Hospital, Yueyang, China
| | - Li Liao
- Department of Hepatobiliary Surgery, Yueyang Central Hospital, Yueyang, China
| | - Tao Wu
- Department of Urology Surgery, Yueyang Central Hospital, Yueyang, China
| | - Shuai Chen
- Department of Urology Surgery, Yueyang Central Hospital, Yueyang, China
| | - Qilin Yi
- Department of Hepatobiliary Surgery, Yueyang Central Hospital, Yueyang, China
| | - Min Xu
- Department of Hepatobiliary Surgery, Yueyang Central Hospital, Yueyang, China
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Deng Z, Hou J, Xu H, Lei Z, Li Z, Zhu H, Yu X, Yang Z, Jin X, Sun J. The Prognostic Value of a lncRNA Risk Model Consists of 9 m6A Regulator-Related lncRNAs in Hepatocellular Carcinoma (HCC). Evol Bioinform Online 2023; 19:11769343221142013. [PMID: 36655172 PMCID: PMC9841875 DOI: 10.1177/11769343221142013] [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: 05/05/2022] [Accepted: 11/03/2022] [Indexed: 01/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver. Although the RNA modification N6-methyladenine (m6A) has been reported to be involved in HCC carcinogenesis, early diagnostic markers and promising personalized therapeutic targets are still lacking. In this study, we identified that 19 m6A regulators and 34 co-expressed lncRNAs were significantly upregulated in HCC samples; based on these factors, we established a prognostic signal of HCC associated with 9 lncRNAs and 19 m6A regulators using LASSO Cox regression analysis. Kaplan-Meier survival estimate revealed correlations between the risk scores and patients' OS in the training and validation dataset. The ROC curve demonstrated that the risk score-based curve has satisfactory prediction efficiency for both training and validation datasets. Multivariate Cox's proportional hazard regression analysis indicated that the risk score was an independent risk factor within the training and validation dataset. In addition, the risk score could distinguish HCC patients from normal non-cancerous samples and HCC samples of different pathological grades. Eventually, 232 mRNAs were co-expressed with these 9 lncRNAs according to GSE101685 and GSE112790; these mRNAs were enriched in cell cycle and cell metabolic activities, drug metabolism, liver disease-related pathways, and some important cancer related pathways such as p53, MAPK, Wnt, RAS and so forth. The expression of the 9 lncRNAs was significantly higher in HCC samples than that in the neighboring non-cancerous samples. Altogether, by using the Consensus Clustering, PCA, ESTIMATE algorithm, LASSO regression model, Kaplan-Meier survival assessment, ROC curve analysis, and multivariate Cox's proportional hazard regression model analysis, we established a prognostic marker consisting of 9 m6A regulator-related lncRNAs that markers may have prognostic and diagnostic potential for HCC.
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Affiliation(s)
- Zhen Deng
- Department of Hepatobiliary and Pancreatic Surgery, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Jiaxing Hou
- Department of Hepatobiliary and Pancreatic Surgery, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongbo Xu
- Department of Hepatobiliary and Pancreatic Surgery, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhao Lei
- Department of Hepatobiliary and Pancreatic Surgery, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhiqiang Li
- Department of Hepatobiliary and Pancreatic Surgery, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongwei Zhu
- Department of Hepatobiliary and Pancreatic Surgery, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhi Yang
- Department of Colorectal & Anal Surgery, General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoxin Jin
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jichun Sun
- Department of Hepatobiliary and Pancreatic Surgery, the Third Xiangya Hospital, Central South University, Changsha, China,Jichun Sun, Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha 410013, China.
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4
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Wang Y, Li T, Liu H, Liang Y, Wang G, Fu G, Takatsuki M, Qu H, Jing F, Li J, Jiang M. N6-methyladenosine methylation-related genes YTHDF2, METTL3, and ZC3H13 predict the prognosis of hepatocellular carcinoma patients. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1398. [PMID: 36660669 PMCID: PMC9843341 DOI: 10.21037/atm-22-5964] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is a common primary malignant tumor and cause of cancer-related death in humans. Increasing evidence indicates that an imbalance in N6-methyladenosine (m6A) methylation is strongly linked to the occurrence and development of cancer. We used comprehensive bioinformatics to establish a potential prognostic model of HCC based on m6A methylation-related genes. And case analyses were used to verify the results. Methods The clinical data and gene expressions were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. The prognostic value of m6A methylation-related genes in HCC patients and their relationship with the immune microenvironment were explored by comprehensive bioinformatics analyses. We also collected pathological specimens from 70 patients with HCC from the Department of Pathology, Affiliated Hospital of Qingdao University, and performed immunohistochemical staining on the specimens. We compared tumor specimens from 27 patients positive for METTL3, YTHDF2, and ZC3H13 staining with their adjacent normal tissues and against 27 patient specimens negative for METTL3, YTHDF2, and ZC3H13. The influence of METTL3, YTHDF2, and ZC3H13 on survival was analyzed, and the prognostic model for METTL3, YTHDF2, and ZC3H13 in HCC was verified by clinical data. Results Most m6A methylation-related genes showed significantly different expressions between cancer and normal tissues. Three candidate m6A methylation-related genes (YTHDF2, METTL3, and ZC3H13) were significantly correlated with the overall survival (OS) of HCC patients. A Kaplan-Meier survival analysis indicated a worse prognosis of high-risk patients than that of low-risk patients. Immunological analysis showed that the high-risk group was more likely to have higher follicular helper T cell counts and lower resting memory CD4 T cell counts. The expression of YTHDF2, METTL3, and ZC3H13 was validated by other databases, including the Oncomine database, the Human Protein Atlas (HPA), and the Kaplan-Meier plotter. Conclusions Our prognostic model based on m6A methylation-related genes effectively predicted the prognosis of HCC patients.
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Affiliation(s)
- Yun Wang
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China;,Department of Radiotherapy, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China;,Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Tianjun Li
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Haiping Liu
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, China
| | - Yu Liang
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, China
| | - Guanqun Wang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Guangming Fu
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Mitsuhisa Takatsuki
- Department of Digestive and General Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Haijun Qu
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fanbo Jing
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jing Li
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Man Jiang
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China;,Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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5
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Liu ZC, Li LH, Li DY, Gao ZQ, Chen D, Song B, Jiang BH, Dang XW. KIAA1429 regulates alternative splicing events of cancer-related genes in hepatocellular carcinoma. Front Oncol 2022; 12:1060574. [PMID: 36505780 PMCID: PMC9732450 DOI: 10.3389/fonc.2022.1060574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Hepatocellular carcinoma (HCC) remains one of the most fatal malignancies with high morbidity and mortality rates in the world, whose molecular pathogenesis is incompletely understood. As an RNA-binding protein participating in the processing and modification of RNA, KIAA1429 has been proved to be implicated in the pathogenesis of multiple cancers. However, how KIAA1429 functions in alternative splicing is not fully reported. In the current study, multi-omics sequencing data were used to analyze and decipher the molecular functions and the underlying mechanisms of KIAA1429 in HCC samples. RNA sequencing data (RNA-seq) analysis demonstrated that in HCCLM3 cells, alternative splicing (AS) profiles were mediated by KIAA1429. Regulated AS genes (RASGs) by KIAA1429 were enriched in cell cycle and apoptosis-associated pathways. Furthermore, by integrating the RNA immunoprecipitation and sequencing data (RIP-seq) of KIAA1429, we found that KIAA1429-bound transcripts were highly overlapping with RASGs, indicating that KIAA1429 could globally regulate the alternative splicing perhaps by binding to their transcripts in HCCLM3 cells. The overlapping RASGs were also clustered in cell cycle and apoptosis-associated pathways. In particular, we validated the regulated AS events of three genes using clinical specimens from HCC patients, including the exon 6 of BPTF gene and a marker gene of HCC. In summary, our results shed light on the regulatory functions of KIAA1429 in the splicing process of pre-mRNA and provide theoretical basis for the targeted therapy of HCC.
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Affiliation(s)
- Zhao-chen Liu
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lu-Hao Li
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ding-Yang Li
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhi-Qiang Gao
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co. Ltd, Zhengzhou, China
| | - Bin Song
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co. Ltd, Zhengzhou, China
| | - Bing-Hua Jiang
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiao-wei Dang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Xiao-wei Dang,
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Ma W, Wu T. RNA m6A modification in liver biology and its implication in hepatic diseases and carcinogenesis. Am J Physiol Cell Physiol 2022; 323:C1190-C1205. [PMID: 36036444 PMCID: PMC9576175 DOI: 10.1152/ajpcell.00214.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotic RNAs. This modification is regulated by three different factors (writers, erasers, and readers) and affects multiple aspects of RNA metabolism, including RNA splicing, nuclear export, translation, stability and decay. The m6A-mediated modification plays important roles in posttranscriptional regulation of gene expression and mediates a variety of cellular and biological processes. Accordingly, deregulation in m6A modification is closely related to the occurrence and development of human diseases. The liver is the largest digestive and metabolic organ in human and recent studies have shown that m6A modification is importantly implicated in liver cellular and physiological functions and in the pathogenesis of hepatic diseases and cancers. In the current review, we summarize the functions of m6A in RNA metabolism and its roles in liver cell biology and discuss its implication in hepatic diseases and carcinogenesis.
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Affiliation(s)
- Wenbo Ma
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
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N6-Methyladenosine RNA-Binding Protein YTHDF1 in Gastrointestinal Cancers: Function, Molecular Mechanism and Clinical Implication. Cancers (Basel) 2022; 14:cancers14143489. [PMID: 35884552 PMCID: PMC9320224 DOI: 10.3390/cancers14143489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic mRNA and plays a crucial role in the occurrence and development of diseases. YTHDF1 is the most powerful and abundant m6A-encoded RNA reader. In this review, we summarize the evidence of the involvement of YTHDF1 in gastrointestinal cancers, its molecular mechanisms of action, and therapeutic implications. Abstract N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic cell mRNA, and this modification plays a key role in regulating mRNA translation, splicing, and stability. Emerging evidence implicates aberrant m6A as a crucial player in the occurrence and development of diseases, especially GI cancers. Among m6A regulators, YTHDF1 is the most abundant m6A reader that functionally connects m6A-modified mRNA to its eventual fate, mostly notably protein translation. Here, we summarized the function, molecular mechanisms, and clinical implications of YTHDF1 in GI cancers. YTHDF1 is largely upregulated in multiple GI cancer and its high expression predicts poor patient survival. In vitro and in vivo experimental evidence largely supports the role of YTDHF1 in promoting cancer initiation, progression, and metastasis, which suggests the oncogenic function of YTHDF1 in GI cancers. Besides, YTHDF1 overexpression is associated with changes in the tumor microenvironment that are favorable to tumorigenesis. Mechanistically, YTHDF1 regulates the expression of target genes by promoting translation, thereby participating in cancer-related signaling pathways. Targeting YTHDF1 holds therapeutic potential, as the overexpression of YTHDF1 is associated with tumor resistance to chemotherapy and immunotherapy. In summary, YTHDF1-mediated regulation of m6A modified mRNA is an actionable target and a prognostic factor for GI cancers.
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Zhu W, Xu Z, Huang M, Wang X, Ren X, Cai Y, Peng B, Liang Q, Chen X, Yan Y. Downregulated ADARB1 Facilitates Cell Proliferation, Invasion and has Effect on the Immune Regulation in Ovarian Cancer. Front Bioeng Biotechnol 2022; 9:792911. [PMID: 35004651 PMCID: PMC8733684 DOI: 10.3389/fbioe.2021.792911] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/08/2021] [Indexed: 02/05/2023] Open
Abstract
Ovarian cancer (OC) is typically diagnosed at an advanced stage and poses a significant challenge to treatment and recovery. Rencently, Adenosine deaminase RNA-specific B1 (ADARB1), an adenosine-to-inosine (A-to-I) RNA-editing enzyme, has been found to play an essential role in the development of cancer. However, the specific function of ADARB1 in ovarian cancer is still not fully understood. Here, we investigated the effects of ADARB1 on OC biology. By conducting bioinformatics analyses of several public databases, we found significantly decreased ADARB1 expression in OC cells and tissues. Moreover, RT-PCR and western blot showed lower ADARB1 expression in OVCAR3, HO8910pm and A2780 OC cells compared to human normal ovarian epithelial cell IOSE. Cell proliferation assay and clone formation assay showed that overexpression of ADARB1 (ADARB1-OE) inhibited the proliferation of tumor cells. Wound healing and transwell assay indicated that ADARB1-OE could suppress OC cell invasion and metastasis. Kaplan-Meier methods revealed that the patients with low level of ADARB1 displayed poor prognosis. TISIDB databases were further used to analyze the roles of ADARB1 in tumor-immune system interactions in OC patients. Furthermore, ADARB1-OE down-regulated the expression of phosphorylated AKT. Combination of ADARB1-OE and AKT inhibitor MK2206 exerted stronger cell growth inhibition. Thus, our investigation demonstrated that low levels of ADARB1 might be a potential target in the tumorigenesis and prognostic evaluation of OC patients.
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Affiliation(s)
- Wei Zhu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Meiyuan Huang
- Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College, Central South University, Zhuzhou, China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Ren
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
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9
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Liu M, Zhao Z, Cai Y, Bi P, Liang Q, Yan Y, Xu Z. YTH domain family: potential prognostic targets and immune-associated biomarkers in hepatocellular carcinoma. Aging (Albany NY) 2021; 13:24205-24218. [PMID: 34747720 PMCID: PMC8610120 DOI: 10.18632/aging.203674] [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: 07/19/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common high malignancy with insidious onset, invasive fast-growing, high recurrence rate and fatality. YTH domain family plays essential roles in development of HCC. However, the biological function of YTH domain family in HCC have not been clarified. Here, through evaluating the expression profiles of YTH domain family, we found that upregulated YTHDF1 might be more significant and valuable in development and progression of HCC. There was a strong correlation between YTHDC1, YTHDF1 and YTHDF2 and pathological stage of HCC patients. Kaplan-Meier plotter revealed that HCC patients with high level of YTHDF1 and YTHDF2 were highly related to a shorter overall survival time, and low level of YTHDF1 (p = 0.0017) has an important association with a longer progression-free survival time. Genetic alterations using cBioPortal revealed that the alteration rates of YTHDF3 were the highest. We also found that the functions of YTH domain family were linked to several cancer-associated pathways, including peptidyl-serine modification, peptidyl-tyrosine modification and negative regulation of cellular component movement. TIMER database indicated that the YTH domain family had a strong relationship with the infiltration of six types of immune cells (macrophages, neutrophils, CD8+ T-cells, B-cells, CD4+ T-cells and dendritic cells). Next, Ualcan databases revealed that the global methylation levels of YTHDC1 was higher in HCC patients, while YTHDF2 was lower in HCC patients. In conclusion, our findings will enhance the understanding of YTH domain family in HCC pathology, and provide novel insights into YTH-targeted therapy for HCC patients.
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Affiliation(s)
- Miaomiao Liu
- Department of Nuclear Medicine (PET-CT Central), Xiangya Hospital, Central South University, Changsha, China
| | - Zijin Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Bi
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
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10
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Yan Y, Peng J, Liang Q, Ren X, Cai Y, Peng B, Chen X, Wang X, Yi Q, Xu Z. Dynamic m6A-ncRNAs association and their impact on cancer pathogenesis, immune regulation and therapeutic response. Genes Dis 2021; 10:135-150. [PMID: 37013031 PMCID: PMC10066278 DOI: 10.1016/j.gendis.2021.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023] Open
Abstract
Several types of modifications have been proven to participate in the metabolism and processing of different RNA types, including non-coding RNAs (ncRNAs). N-6-methyladenosine (m6A) is a dynamic and reversible RNA modification that is closely involved in the ncRNA homeostasis, and serves as a crucial regulator for multiple cancer-associated signaling pathways. The ncRNAs usually regulate the epigenetic modification, mRNA transcription and other biological processes, displaying enormous roles in human cancers. In this review, we summarized the significant implications of m6A-ncRNA interaction in various types of cancers. In particular, the interplay between m6A and ncRNAs in cancer pathogenesis and therapeutic resistance are being widely recognized. We also discussed the relevance of m6A-ncRNA interaction in immune regulation, followed by the interference on cancer immunotherapeutic procedures. In addition, we briefly highlighted the computation tools that could identify the accurate features of m6A methylome among ncRNAs. In summary, this review would pave the way for a better understanding of the biological functions of m6A-ncRNA crosstalk in cancer research and treatment.
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11
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Li Q, Ren CC, Chen YN, Yang L, Zhang F, Wang BJ, Zhu YH, Li FY, Yang J, Zhang ZA. A Risk Score Model Incorporating Three m6A RNA Methylation Regulators and a Related Network of miRNAs-m6A Regulators-m6A Target Genes to Predict the Prognosis of Patients With Ovarian Cancer. Front Cell Dev Biol 2021; 9:703969. [PMID: 34631700 PMCID: PMC8495156 DOI: 10.3389/fcell.2021.703969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 02/01/2023] Open
Abstract
Ovarian cancer (OC) is the leading cause of cancer-related death among all gynecological tumors. N6-methyladenosine (m6A)-related regulators play essential roles in various tumors, including OC. However, the expression of m6A RNA methylation regulators and the related regulatory network in OC and their correlations with prognosis remain largely unknown. In the current study, we obtained the genome datasets of OC from GDC and GTEx database and analyzed the mRNA levels of 21 key m6A regulators in OC and normal human ovarian tissues. The expression levels of 7 m6A regulators were lower in both the OC tissues and the high-stage group. Notably, the 5-year survival rate of patients with OC presenting low VIRMA expression or high HNRNPA2B1 expression was higher than that of the controls. Next, a risk score model based on the three selected m6A regulators (VIRMA, IGF2BP1, and HNRNPA2B1) was built by performing a LASSO regression analysis, and the moderate accuracy of the risk score model to predict the prognosis of patients with OC was examined by performing ROC curve, nomogram, and univariate and multivariate Cox regression analyses. In addition, a regulatory network of miRNAs-m6A regulators-m6A target genes, including 2 miRNAs, 3 m6A regulators, and 47 mRNAs, was constructed, and one of the pathways, namely, miR-196b-5p-IGF2BP1-PTEN, was initially validated based on bioinformatic analysis and assay verification. These results demonstrated that the risk score model composed of three m6A RNA methylation regulators and the related network of miRNAs-m6A regulators-m6A target genes is valuable for predicting the prognosis of patients with OC, and these molecules may serve as potential biomarkers or therapeutic targets in the future.
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Affiliation(s)
- Qian Li
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
| | - Chen-Chen Ren
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
| | - Yan-Nan Chen
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
| | - Li Yang
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
| | - Feng Zhang
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
| | - Bao-Jin Wang
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan International Joint Laboratory of Ovarian Malignant Tumor, Zhengzhou, China
| | - Yuan-Hang Zhu
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
| | - Fei-Yan Li
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
| | - Jun Yang
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
| | - Zhen-An Zhang
- Department of Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Province Women and Children's Hospital, Zhengzhou, China
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12
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Yan Y, Liang Q, Xu Z, Yi Q. Integrative bioinformatics and experimental analysis revealed down-regulated CDC42EP3 as a novel prognostic target for ovarian cancer and its roles in immune infiltration. PeerJ 2021; 9:e12171. [PMID: 34616622 PMCID: PMC8449529 DOI: 10.7717/peerj.12171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/26/2021] [Indexed: 02/05/2023] Open
Abstract
Ovarian cancer is a significant clinical challenge as no effective treatments are available to enhance patient survival. Recently, N6-methyladenosine (m6A) RNA modification has been demonstrated to play a pivotal role in tumorigenesis and progression. However, the roles of m6A target genes in ovarian cancer haven’t been clearly illustrated. In this study, we presented a comprehensive bioinformatics and in vitro analysis to evaluate the roles of m6A target genes. Cell division cycle 42 effector protein 3 (CDC42EP3), one probable m6A target gene, was identified to be down-regulated in ovarian cancer tissues and cells. Meanwhile, quantitative PCR (qPCR) and western blot were used to confirm the down-regulated CDC42EP3 in ovarian cancer cells A2780 and TOV112D. The biological function of CDC42EP3 in ovarian cancer was further validated with several algorithms, such as PrognoScan, K-M plotter, LinkedOmics and TISIDB. These findings indicated that lower expression of CDC42EP3 was correlated with poor prognosis in patients with ovarian cancer. In addition, CDC42EP3 expression was significantly associated with a diverse range of tumor-infiltrating immune cells, including natural killer cells (NK), T central memory cells (Tcm), T gamma delta cells (Tgd), etc. Taken together, this study uncovered the potential roles of m6A target gene CDC42EP3 in the regulation of immune microenvironment in the ovarian cancer, and identified CDC42EP3 as a novel prognostic target.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiaoli Yi
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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13
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Dolicka D, Foti M, Sobolewski C. The Emerging Role of Stress Granules in Hepatocellular Carcinoma. Int J Mol Sci 2021; 22:ijms22179428. [PMID: 34502337 PMCID: PMC8430939 DOI: 10.3390/ijms22179428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are small membrane-free cytosolic liquid-phase ordered entities in which mRNAs are protected and translationally silenced during cellular adaptation to harmful conditions (e.g., hypoxia, oxidative stress). This function is achieved by structural and functional SG components such as scaffold proteins and RNA-binding proteins controlling the fate of mRNAs. Increasing evidence indicates that the capacity of cells to assemble/disassemble functional SGs may significantly impact the onset and the development of metabolic and inflammatory diseases, as well as cancers. In the liver, the abnormal expression of SG components and formation of SG occur with chronic liver diseases, hepatocellular carcinoma (HCC), and selective hepatic resistance to anti-cancer drugs. Although, the role of SG in these diseases is still debated, the modulation of SG assembly/disassembly or targeting the expression/activity of specific SG components may represent appealing strategies to treat hepatic disorders and potentially cancer. In this review, we discuss our current knowledge about pathophysiological functions of SGs in HCC as well as available molecular tools and drugs capable of modulating SG formation and functions for therapeutic purposes.
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14
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Wu H, Xu H, Jia D, Li T, Xia L. METTL3-induced UCK2 m 6A hypermethylation promotes melanoma cancer cell metastasis via the WNT/β-catenin pathway. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1155. [PMID: 34430596 PMCID: PMC8350655 DOI: 10.21037/atm-21-2906] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 01/12/2023]
Abstract
Background Melanoma is a highly aggressive, malignant skin tumor with a statistically high mortality rate. N6-methyladenosine (m6A) modification is involved in a variety of biological processes, including tumorigenesis. m6A modifications regulate the fate and functions of RNA, such as mRNA stability, nuclear processing, transport, localization, translation, primary microRNA (miRNA) processing, and RNA-protein interactions. Several members (including METTL3, METTL14, FTO, ALKBH5, and YTHDF2) are actively involved in a variety of human cancers. However, the basic mechanism of the involvement of uridine cytidine kinase 2 (UCK2) in melanoma metastasis has not been studied. UCK2 is upregulated in a variety of malignancies. However, the complex molecular mechanisms and therapeutic effects of UCK2 in melanoma remain unclear. Methods The expression of UCK2 was evaluated by qRT-PCR. The effects of UCK2 on the biological characteristics of PC cells were investigated on the basis of loss-of-function analyses. Immunoprecipitation-qPCR (MeRIP-qPCR) was performed to identify the m6A targeted effect of UCK2 in melanoma cancer. Results Based on the bioinformatics analysis in this study, up-regulation of UCK2 could be essential in melanoma cancer, and associated with poor survival. Furthermore, the m6A modification regulated by METTL3 led to UCK2 increased messenger RNA (mRNA) stability in melanoma cancer. Functional and mechanistic experiments indicated that UCK2 enhanced the metastasis of melanoma cancer cells through the WNT/β-catenin pathway. Conclusion In this study, we found that m6A-METTL3 axis induced abnormal UCK2 expression plays a role in melanoma metastasis by enhancing the Wnt/β-catenin pathway, which may provide new clues for melanoma metastasis. It also provides a potential target for the prevention and treatment of melanoma.
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Affiliation(s)
- Hao Wu
- Department of Bone and Soft-Tissue Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Haochao Xu
- Department of Bone and Soft-Tissue Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Dongdong Jia
- Department of Bone and Soft-Tissue Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Tao Li
- Department of Bone and Soft-Tissue Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Liming Xia
- Department of Bone and Soft-Tissue Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
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15
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Qin S, Mao Y, Chen X, Xiao J, Qin Y, Zhao L. The functional roles, cross-talk and clinical implications of m6A modification and circRNA in hepatocellular carcinoma. Int J Biol Sci 2021; 17:3059-3079. [PMID: 34421350 PMCID: PMC8375232 DOI: 10.7150/ijbs.62767] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. HCC has high rates of death and recurrence, as well as very low survival rates. N6-methyladenosine (m6A) is the most abundant modification in eukaryotic RNAs, and circRNAs are a class of circular noncoding RNAs that are generated by back-splicing and they modulate multiple functions in a variety of cellular processes. Although the carcinogenesis of HCC is complex, emerging evidence has indicated that m6A modification and circRNA play vital roles in HCC development and progression. However, the underlying mechanisms governing HCC, their cross-talk, and clinical implications have not been fully elucidated. Therefore, in this paper, we elucidated the biological functions and molecular mechanisms of m6A modification in the carcinogenesis of HCC by illustrating three different regulatory factors ("writer", "eraser", and "reader") of the m6A modification process. Additionally, we dissected the functional roles of circRNAs in various malignant behaviors of HCC, thereby contributing to HCC initiation, progression and relapse. Furthermore, we demonstrated the cross-talk and interplay between m6A modification and circRNA by revealing the effects of the collaboration of circRNA and m6A modification on HCC progression. Finally, we proposed the clinical potential and implications of m6A modifiers and circRNAs as diagnostic biomarkers and therapeutic targets for HCC diagnosis, treatment and prognosis evaluation.
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Affiliation(s)
- Sha Qin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China; and Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xue Chen
- Early Clinical Trial Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Juxiong Xiao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Qin
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China; and Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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16
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Huang J, Shao Y, Gu W. Function and clinical significance of N6-methyladenosine in digestive system tumours. Exp Hematol Oncol 2021; 10:40. [PMID: 34246319 PMCID: PMC8272376 DOI: 10.1186/s40164-021-00234-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/03/2021] [Indexed: 12/21/2022] Open
Abstract
RNA modification, like DNA methylation, histone modification, non-coding RNA modification and chromatin rearrangement, plays an important role in tumours. N6-methyladenosine (m6A) is the most abundant RNA modification in cells, and it regulates RNA transcription, processing, splicing, degradation, and translation. m6A-associated proteins have been used as new biomarkers and therapeutic targets for tumour prediction and monitoring. There are three main types of proteins involved in m6A methylation: methyltransferases (METTL3, METTL14, WTAP, RBM15, ZC3H13 and KIAA1429), demethylases (FTO, ALKBH5 and ALKBH3) and RNA-binding proteins (YTHDF1-3, YTHDC1-2, IGF2BPs and HNRNPs). This article reviews the origins, characteristics and functions of m6A and its relationship with digestive system tumours based on recent research. The expression of m6A regulators can be used as an evaluation indicator of tumour growth and progression and as a prognostic indicator. In-depth research on m6A methylation in digestive system tumours may provide new directions for clinical prediction and further treatment.
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Affiliation(s)
- Junchao Huang
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
| | - Yingjie Shao
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
| | - Wendong Gu
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
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17
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Luo X, Cao M, Gao F, He X. YTHDF1 promotes hepatocellular carcinoma progression via activating PI3K/AKT/mTOR signaling pathway and inducing epithelial-mesenchymal transition. Exp Hematol Oncol 2021; 10:35. [PMID: 34088349 PMCID: PMC8176587 DOI: 10.1186/s40164-021-00227-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) modification, as the most abundant RNA modification, widely participates in the physiological process and is involved in multiple disease progression, especially cancer. YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) is a pivotal m6A "reader" protein, which has been reported in multiple cancers. However, the role and molecular mechanism of YTHDF1 in HCC are still not fully elucidated. METHODS Based on various bioinformatics databases, q-RT PCR, western blot, and a tissue microarray containing 90 HCC samples, we examined the expression of YTHDF1 in HCC. Then, we applied the loss-of-function experiments to explore the role of YTHDF1 in HCC by in vitro and in vivo assays. Finally, we performed the gene set enrichment analysis (GSEA) to predict the potential signaling pathway of YTHDF1 involved in HCC and further verified this prediction. RESULTS YTHDF1 was overexpressed in HCC and associated with HCC grade. Depletion of YTHDF1 markedly impaired the proliferation, migration, invasion, and cell cycle process of HCC cells. Mechanistically, YTHDF1 promoted the growth of HCC cells via activating the PI3K/AKT/mTOR signaling pathway. Moreover, we also demonstrated that the epithelial-mesenchymal transition (EMT) mediated the promoting effect of YTHDF1 on the migration and invasion of HCC cells. CONCLUSIONS YTHDF1 contributes to the progression of HCC by activating PI3K/AKT/mTOR signaling pathway and inducing EMT.
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Affiliation(s)
- Xiangyuan Luo
- Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Mengdie Cao
- Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fan Gao
- Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xingxing He
- Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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18
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Zhang X, Zhong L, Zou Z, Liang G, Tang Z, Li K, Tan S, Huang Y, Zhu X. Clinical and Prognostic Pan-Cancer Analysis of N6-Methyladenosine Regulators in Two Types of Hematological Malignancies: A Retrospective Study Based on TCGA and GTEx Databases. Front Oncol 2021; 11:623170. [PMID: 33816257 PMCID: PMC8015800 DOI: 10.3389/fonc.2021.623170] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/29/2021] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is one of the most active modification factors of mRNA, which is closely related to cell proliferation, differentiation, and tumor development. Here, we explored the relationship between the pathogenesis of hematological malignancies and the clinicopathologic parameters. The datasets of hematological malignancies and controls were obtained from the TCGA [AML (n = 200), DLBCL (n = 48)] and GTEx [whole blood (n = 337), blood vascular artery (n = 606)]. We analyzed the m6A factor expression differences in normal tissue and tumor tissue and their correlations, clustered the express obvious clinical tumor subtypes, determined the tumor risk score, established Cox regression model, performed univariate and multivariate analysis on all datasets. We found that the AML patients with high expression of IGF2BP3, ALKBH5, and IGF2BP2 had poor survival, while the DLBCL patients with high expression of METTL14 had poor survival. In addition, "Total" datasets analysis revealed that IGF2BP1, ALKBH5, IGF2BP2, RBM15, METTL3, and ZNF217 were potential oncogenes for hematologic system tumors. Collectively, the expressions of some m6A regulators are closely related to the occurrence and development of hematologic system tumors, and the intervention of specific regulatory factors may lead to a breakthrough in the treatment in the future.
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Affiliation(s)
- Xiangsheng Zhang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Guangdong Medical University, Zhanjiang, China
| | - Liye Zhong
- Department of Hematology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhilin Zou
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Guangdong Medical University, Zhanjiang, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
| | - Guosheng Liang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Guangdong Medical University, Zhanjiang, China
| | - Zhenye Tang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Guangdong Medical University, Zhanjiang, China
| | - Kai Li
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Guangdong Medical University, Zhanjiang, China
| | - Shuzhen Tan
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Guangdong Medical University, Zhanjiang, China
| | - Yongmei Huang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Guangdong Medical University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- The Key Lab of Zhanjiang for R&D Marine Microbial Resources in the Beibu Gulf Rim, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Guangdong Medical University, Zhanjiang, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- The Key Lab of Zhanjiang for R&D Marine Microbial Resources in the Beibu Gulf Rim, Guangdong Medical University, Zhanjiang, China
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19
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Qi LW, Jia JH, Jiang CH, Hu JM. Contributions and Prognostic Values of N6-Methyladenosine RNA Methylation Regulators in Hepatocellular Carcinoma. Front Genet 2021; 11:614566. [PMID: 33519919 PMCID: PMC7844396 DOI: 10.3389/fgene.2020.614566] [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: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
Introduction The methylation at position N6 of adenine is called N6-methyladenosine (m6A). This transcriptional RNA modification exerts a very active and important role in RNA metabolism and in other biological processes. However, the activities of m6A associated with malignant liver hepatocellular carcinoma (LIHC) are unknown and are worthy of study. Materials and Methods Using the data of University of California, Santa Cruz (UCSC), the expression of M6A methylation regulators in pan-cancer was evaluated as a screening approach to identify the association of M6A gene expression and 18 cancer types, with a specific focus on LIHC. LIHC datasets of The Cancer Genome Atlas (TCGA) were used to explore the expression of M6A methylation regulators and their clinical significance. Gene Ontology (GO) analysis and Gene Set Enrichment Analysis (GSEA) were used to explore the underlying mechanism based on the evaluation of aberrant expression of m6A methylation regulators. Results The expression alterations of m6A-related genes varied across cancer types. In LIHC, we found that in univariate Cox regression analysis, up-regulated m6A modification regulators were associated with worse prognosis, except for ZC3H13. Kaplan-Meier survival curve analysis indicated that higher expression of methyltransferase-like protein 3 (METTL3) and YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) genes related to the worse survival rate defined by disease-related survival (DSS), overall survival (OS), progression-free interval (PFI), and disease-free interval (DFI). Up-regulated m6A methylation regulator group (cluster2) obtained by consensus clustering was associated with poor prognosis. A six-gene prognostic signature established using the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm performed better in the early (I + II; T1 + T2) stages than in the late (III + IV; T3 + T4) stages of LIHC. Using the gene signature, we constructed a risk score and found that it was an independent predictive factor for prognosis. Using GSEA, we identified processes involved in DNA damage repair and several biological processes associated with malignant tumors that were closely related to the high-risk group. Conclusion In summary, our study identified several genes associated with m6A in LIHC, especially METTL3 and YTHDF1, and confirmed that a risk signature comprised of m6A-related genes was able to forecast prognosis.
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Affiliation(s)
- Li-Wen Qi
- Department of Clinical Oncology, Liaoning Cancer Hospital, Graduate School of Dalian Medical University, Dalian, China
| | - Jian-Hui Jia
- Department of Gastrointestinal Tumor, Liaoning Cancer Hospital, Cancer Hospital of China Medical University, Shenyang, China
| | - Chen-Hao Jiang
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China
| | - Jian-Ming Hu
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China
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20
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Pan XY, Huang C, Li J. The emerging roles of m 6A modification in liver carcinogenesis. Int J Biol Sci 2021; 17:271-284. [PMID: 33390849 PMCID: PMC7757034 DOI: 10.7150/ijbs.50003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
The 'epitranscriptome', a collective term for chemical modifications that influence the structure, metabolism, and functions of RNA, has recently emerged as vitally important for the regulation of gene expression. N6-methyladenosine (m6A), the most prevalent mammalian mRNA internal modification, has been demonstrated to have a pivotal role in almost all vital bioprocesses, such as stem cell self-renewal and differentiation, heat shock or DNA damage response, tissue development, and maternal-to-zygotic transition. Hepatocellular carcinoma (HCC) is prevalent worldwide with high morbidity and mortality because of late diagnosis at an advanced stage and lack of effective treatment strategies. Epigenetic modifications including DNA methylation and histone modification have been demonstrated to be crucial for liver carcinogenesis. However, the role and underlying molecular mechanism of m6A in liver carcinogenesis are mostly unknown. In this review, we summarize recent advances in the m6A region and how these new findings remodel our understanding of m6A regulation of gene expression. We also describe the influence of m6A modification on liver carcinoma and lipid metabolism to instigate further investigations of the role of m6A in liver biological diseases and its potential application in the development of therapeutic strategies.
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Affiliation(s)
- Xue-Yin Pan
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education.,Institute for Liver Diseases of Anhui Medical University
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education.,Institute for Liver Diseases of Anhui Medical University
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education.,Institute for Liver Diseases of Anhui Medical University
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21
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Xu S, Tang L, Dai G, Luo C, Liu Z. Expression of m6A Regulators Correlated With Immune Microenvironment Predicts Therapeutic Efficacy and Prognosis in Gliomas. Front Cell Dev Biol 2020; 8:594112. [PMID: 33240891 PMCID: PMC7683617 DOI: 10.3389/fcell.2020.594112] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
Background N6-methyladenosine (m6A) RNA methylation and tumor immune microenvironment played crucial roles in cancer development. However, their association in gliomas remains to be fully elucidated. Methods A total of 2144 glioma patients from CGGA, TCGA, and Rembrandt databases were extracted in our study, in which 325 were set as the training cohort and 1819 were defined as the validation cohort. Survival differences evaluated by Kaplan-Meier analysis between groups. Patients were clustered into subgroups by consensus clustering. ESTIMATE algorithm was applied to calculate immune and stroma scores. The infiltration of immune cells was characterized by TIMER algorithm. The risk signature was constructed by multivariate Cox regression analysis. Results Nineteen m6A regulators were highly expressed in glioma tissues. The expression of m6A regulators was associated with prognoses, grade, isocitrate dehydrogenase (IDH) status, and 1p19q status of gliomas. Two subgroups were identified by consensus clustering, in which cluster 1 was associated with favorable prognosis, high stroma and immune scores, and high immune infiltration. When the patients were divided into high risk and low risk groups based on their risk scores, we found that patients in the high risk group had poor prognoses. Besides, patients in the high risk group had a higher stroma and immune scores, and higher abundance of immune infiltration. These results were further verified in the validation cohort, which contained three independent datasets. Moreover, patients in the low risk group enjoyed better prognoses without chemoradiotherapy or single chemotherapy. Conclusion Our study revealed that m6A regulators could predict the prognosis and therapeutic efficacy, and were also associated with the immune microenvironment in gliomas.
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Affiliation(s)
- Shengchao Xu
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, China
| | - Lu Tang
- Department of Thoracic Surgery, Xiangya Hospital of Central South University, Changsha, China
| | - Gan Dai
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Chengke Luo
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, China
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22
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Zhang X, Zhang J, Gao F, Fan S, Dai L, Zhang J. KPNA2-Associated Immune Analyses Highlight the Dysregulation and Prognostic Effects of GRB2, NRAS, and Their RNA-Binding Proteins in Hepatocellular Carcinoma. Front Genet 2020; 11:593273. [PMID: 33193737 PMCID: PMC7649362 DOI: 10.3389/fgene.2020.593273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Karyopherin α2 (KPNA2) was reported to be overexpressed and have unfavorable prognostic effects in many malignancies including hepatocellular carcinoma (HCC). Although its contributions to inflammatory response were reported in many studies, its specific associations with immune infiltrations and immune pathways during cancer progression were unclear. Here, we aimed to identify new markers for HCC diagnosis and prognosis through KPNA2-associated immune analyses. RNA-seq expression data of HCC datasets were downloaded from The Cancer Genome Atlas and International Cancer Genome Consortium. The gene expressions were counts per million normalized. The infiltrations of 24 kinds of immune cells in the samples were evaluated with ImmuCellAI (Immune Cell Abundance Identifier). The Spearman correlations of the immune infiltrations with KPNA2 expression were investigated, and the specific positive correlation of B-cell infiltration with KPNA2 expression in HCC tumors was identified. Fifteen genes in KEGG (Kyoto Encyclopedia of Genes and Genomes) B-cell receptor signaling pathway presented significant correlations with KPNA2 expression in HCC. Among them, GRB2 and NRAS were indicated to be independent unfavorable prognostic factors for HCC overall survival. Clinical Proteomic Tumor Analysis Consortium HCC dataset was investigated to validate the results at protein level. The upregulation and unfavorable prognostic effects of KPNA2 and GRB2 were confirmed, whereas, unlike its mRNA form, NRAS protein was presented to be downregulated and have favorable prognostic effects. Through receiver operating characteristic curve analysis, the diagnostic potential of the three proteins was shown. The RNA-binding proteins (RBPs) of KPNA2, NRAS, and GRB2, downloaded via The Encyclopedia of RNA Interactomes, were investigated for their clinical significance in HCC at protein level. An eight-RBP signature with independent prognostic value and dysregulations in HCC was identified. All the RBPs were significantly correlated with MKI67 expression and at least one of KPNA2, GRB2, and NRAS at protein level in HCC, indicating their roles in HCC progression and the regulation of the three proteins. We concluded that KPNA2, GRB2, NRAS, and their RBPs might have coordinating roles in HCC immunoregulation and progression. They might be new markers for HCC diagnosis and prognosis predication and new targets for HCC immunotherapy.
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Affiliation(s)
- Xiuzhi Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, China
| | - Jialing Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, China
| | - Fenglan Gao
- Department of Pathology, Henan Medical College, Zhengzhou, China
| | - Shasha Fan
- Oncology Department, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, China.,Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, Hunan Normal University, Changsha, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jinzhong Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, China
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