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Cong Z, Zhao H, Zhang S, You T, Xie Y. LAGE3 promotes angiogenesis on hepatocellular carcinoma by stabilizing VEGFA mRNA. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167196. [PMID: 38653358 DOI: 10.1016/j.bbadis.2024.167196] [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: 01/05/2024] [Revised: 03/22/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
RNA modification plays important roles in various physiological and pathological process. LAGE3 is a component of EKC/KEOPS complex, which is probably involved in the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs, but its exact role in HCC is less studied. Our study reveals that LAGE3 exhibits upregulated expression in HCC compared with normal hepatocellular tissue. High expression of LAGE3 promotes hepatocellular cell proliferation and migration. Further investigations suggest that the increased expression of LAGE3 cloud lead to upregulated VEGFA secretion and angiogenesis in HCC. The mechanistic study reveals LAGE3 is required for the VEGFA mRNA stability. This research may open new avenues for diagnosis and targeted therapy in HCC.
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MESH Headings
- Humans
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/metabolism
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Vascular Endothelial Growth Factor A/metabolism
- Vascular Endothelial Growth Factor A/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/pathology
- Cell Proliferation/genetics
- RNA Stability
- Gene Expression Regulation, Neoplastic
- Cell Movement/genetics
- Cell Line, Tumor
- Male
- Female
- Angiogenesis
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Affiliation(s)
- Zhuangzhi Cong
- Department of Hepatobiliary Surgery, Third Affiliated Hospital of Naval Military Medical University, Shanghai, China
| | - Huan Zhao
- Department of General Surgery, Third Affiliated Hospital of Naval Military Medical University, Shanghai, China
| | - Shuyu Zhang
- Department of Hepatobiliary Surgery, Third Affiliated Hospital of Naval Military Medical University, Shanghai, China
| | - Tiangeng You
- Department of Hepatobiliary Surgery, Third Affiliated Hospital of Naval Military Medical University, Shanghai, China.
| | - Yanting Xie
- Department of Hepatobiliary Surgery, Third Affiliated Hospital of Naval Military Medical University, Shanghai, China.
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2
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Yan B, Liao P, Liu S, Lei P. Comprehensive pan-cancer analysis of inflammatory age-clock-related genes as prognostic and immunity markers based on multi-omics data. Sci Rep 2024; 14:10468. [PMID: 38714870 PMCID: PMC11076581 DOI: 10.1038/s41598-024-61381-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory age (iAge) is a vital concept for understanding the intricate interplay between chronic inflammation and aging in the context of cancer. However, the importance of iAge-clock-related genes (iAge-CRGs) across cancers remains unexplored. This study aimed to explore the mechanisms and applications of these genes across diverse cancer types. We analyzed profiling data from over 10,000 individuals, covering 33 cancer types, 750 small molecule drugs, and 24 immune cell types. We focused on DCBLD2's function at the single-cell level and computed an iAge-CRG score using GSVA. This score was correlated with cancer pathways, immune infiltration, and survival. A signature was then derived using univariate Cox and LASSO regression, followed by ROC curve analysis, nomogram construction, decision curve analysis, and immunocytochemistry. Our comprehensive analysis revealed epigenetic, genomic, and immunogenomic alterations in iAge-CRGs, especially DCBLD2, leading to abnormal expression. Aberrant DCBLD2 expression strongly correlated with cancer-associated fibroblast infiltration and prognosis in multiple cancers. Based on GSVA results, we developed a risk model using five iAge-CRGs, which proved to be an independent prognostic index for uveal melanoma (UVM) patients. We also systematically evaluated the correlation between the iAge-related signature risk score and immune cell infiltration. iAge-CRGs, particularly DCBLD2, emerge as potential targets for enhancing immunotherapy outcomes. The strong correlation between abnormal DCBLD2 expression, cancer-associated fibroblast infiltration, and patient survival across various cancers underscores their significance. Our five-gene risk signature offers an independent prognostic tool for UVM patients, highlighting the crucial role of these genes in suppressing the immune response in UVM.Kindly check and confirm whether the corresponding affiliation is correctly identified.I identified the affiliation is correctly.thank you.Per style, a structured abstract is not allowed so we have changed the structured abstract to an unstructured abstract. Please check and confirm.I confirm the abstract is correctly ,thank you.
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Affiliation(s)
- Bo Yan
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Pan Liao
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- The School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Shan Liu
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Ping Lei
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
- The School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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3
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Ma H, Hong Y, Xu Z, Weng Z, Yang Y, Jin D, Chen Z, Yue J, Zhou X, Xu Z, Fei F, Li J, Song W. N 6-methyladenosine (m 6A) modification in hepatocellular carcinoma. Biomed Pharmacother 2024; 173:116365. [PMID: 38452654 DOI: 10.1016/j.biopha.2024.116365] [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: 12/21/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/09/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the deadliest cancers of human, the tumor-related death of which ranks third among the common malignances. N6-methyladenosine (m6A) methylation, the most abundant internal modification of RNA in mammals, participates in the metabolism of mRNA and interrelates with ncRNAs. In this paper, we overviewed the complex function of m6A regulators in HCC, including regulating the tumorigenesis, progression, prognosis, stemness, metabolic reprogramming, autophagy, ferroptosis, drug resistance and tumor immune microenvironment (TIME). Furthermore, we elucidated the interplay between m6A modification and non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). Finally, we summarized the potential of m6A regulators as diagnostic biomarkers. What's more, we reviewed the inhibitors targeting m6A enzymes as promising therapeutic targets of HCC. We aimed to help understand the function of m6A methylation in HCC systematically and comprehensively so that more effective strategies for HCC treatment will be developed.
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Affiliation(s)
- Hehua Ma
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yuxin Hong
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhenzhen Xu
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Zuyi Weng
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yuanxun Yang
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Dandan Jin
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhiyou Chen
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jing Yue
- Department of Gynaecology and Obstetrics, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Xuan Zhou
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Zhi Xu
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Fei Fei
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Juan Li
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
| | - Wei Song
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
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Li X, Zhao X, Yin R, Yuan M, Zhang Y, Li X. TGF-β2-induced alterations of m6A methylation in hTERT RPE-1 cells. Exp Eye Res 2024; 241:109839. [PMID: 38395214 DOI: 10.1016/j.exer.2024.109839] [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: 08/30/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
N6-methyladenosine (m6A) is a major type of RNA modification implicated in various pathophysiological processes. Transforming growth factor β2 (TGF-β2) induces epithelial-mesenchymal transition (EMT) in retinal pigmental epithelial (RPE) cells and promotes the progression of proliferative vitreoretinopathy (PVR). However, the role of m6A methylation in the EMT of human telomerase reverse transcriptase (hTERT) retinal pigmental epithelium (RPE)-1 cells has not been clarified. Here, we extracted RNA from RPE cells subjected to 0 or 20 ng/mL TGF-β2 for 72 h and identified differentially methylated genes (DMGs) by m6A-Seq and differentially expressed genes (DEGs) by RNA-Seq. We selected the genes related to EMT by conjoint m6A-Seq/RNA-Seq analysis and verified them by qRT-PCR. We then confirmed the function of m6A methylation in the EMT of RPE cells by knocking down the methyltransferase METTL3 and the m6A reading protein YTHDF1. Sequencing yielded 5814 DMGs and 1607 DEGs. Conjoint analysis selected 467 genes altered at the m6A and RNA levels that are closely associated with the EMT-related TGF-β, AGE-RAGE, PI3K-Akt, P53, and Wnt signaling pathways. We also identified ten core EMT genes ACTG2, BMP6, CDH2, LOXL2, SNAIL1, SPARC, BMP4, EMP3, FOXM1, and MYC. Their RNA levels were evaluated by qRT-PCR and were consistent with the sequencing results. We observed that METTL3 knockdown enhanced RPE cell migration and significantly upregulated the EMT markers N-cadherin (encoded by CDH2), fibronectin (FN), Snail family transcription repressor (SLUG), and vimentin. However, YTHDF1 knockdown had the opposite effects and decreased both cell migration and the N-cadherin, FN, and SLUG expression levels. The present study clarified TGF-β2-induced m6A- and RNA-level differences in RPE cells, indicated that m6A methylation might regulate EMT marker expression, and showed that m6A could regulate TGF-β2-induced EMT.
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Affiliation(s)
- Xue Li
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China
| | - Xueru Zhao
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China
| | - Ruijie Yin
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China
| | - Min Yuan
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China
| | - Yongya Zhang
- Henan Provincial People's Hospital, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaohua Li
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China.
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5
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Zhang C, Huang Y, Liang M, Wu J, Wang G. Characterization of m6A RNA methylation mediated immune heterogeneity and functional validation in hepatocellular carcinoma. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38409934 DOI: 10.1002/tox.24167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND N6 -methyladenosine (m6 A) mediates RNA modification in various biological processes. It plays a key role in hepatocellular carcinoma (HCC) through regulating methyltransferase. The present study aims to analyze the correlation between the m6 A and the immune status of HCC, and to construct an m6 A-related prognostic signature for HCC. METHODS HCC subtypes with different m6 A modification activities were identified based on the m6 A-related genes. Lasso Cox regression was applied to construct an m6 A-related prognostic model for HCC. Then, the prognostic potential of the constructed signature was evaluated and validated in the external validation dataset. Small interfering RNAs were designed to knockdown FBXO5. CCK-8 assay, Edu staining, wound healing assay, and Transwell cell invasion assay were used to detect cell proliferation, migration, and invasion ability. RESULTS Two m6 A-related HCC subtypes were identified. The m6 A modification active group showed an immune suppressive microenvironment compared to the m6 A modification inactive group. The differentially expressed genes (DEGs) between the HCC subtypes were screened. Enrichment analysis was performed using the DEGs. Subsequently, an m6 A-related prognostic model was established. The prognostic model performed well in both training and validation datasets. Moreover, knockdown of FBXO5, one of the genes in the prognostic model, inhibited the proliferation, migration, and invasion of HepG2 cells. CONCLUSIONS The heterogeneity of m6 A RNA methylation is associated with immune status in HCC. The constructed m6 A-related gene-based signature can predict the prognosis of HCC patients. The genes in the prognostic model also have therapeutic potential for HCC.
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Affiliation(s)
- Chongyou Zhang
- Department of neurobiology, Harbin Medical University, Harbin, China
| | - Yang Huang
- Department of gastroenterology, Heilongjiang red cross sengong general hospital, Harbin, China
| | - Ming Liang
- Department of infectious, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jinrong Wu
- Department of anaesthesiology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guangyou Wang
- Department of neurobiology, Harbin Medical University, Harbin, China
- Ministry of Education Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
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Shi Q, Chu Q, Zeng Y, Yuan X, Wang J, Zhang Y, Xue C, Li L. Non-coding RNA methylation modifications in hepatocellular carcinoma: interactions and potential implications. Cell Commun Signal 2023; 21:359. [PMID: 38111040 PMCID: PMC10726651 DOI: 10.1186/s12964-023-01357-0] [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: 08/30/2023] [Accepted: 10/14/2023] [Indexed: 12/20/2023] Open
Abstract
RNA methylation modification plays a crucial role as an epigenetic regulator in the oncogenesis of hepatocellular carcinoma (HCC). Numerous studies have investigated the molecular mechanisms underlying the methylation of protein-coding RNAs in the progression of HCC. Beyond their impact on mRNA, methylation modifications also influence the biological functions of non-coding RNAs (ncRNAs). Here, we present an advanced and comprehensive overview of the interplay between methylation modifications and ncRNAs in HCC, with a specific focus on their potential implications for the tumor immune microenvironment. Moreover, we summarize promising therapeutic targets for HCC based on methylation-related proteins. In the future, a more profound investigation is warranted to elucidate the effects of ncRNA methylation modifications on HCC pathogenesis and devise valuable intervention strategies. Video Abstract.
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Affiliation(s)
- Qingmiao Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Qingfei Chu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yifan Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xin Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jinzhi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yaqi Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chen Xue
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, China.
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Zhang W, Wu T, Zhang Y, Kang W, Du C, You Q, Chen X, Jiang Z. Targeting m 6A binding protein YTHDFs for cancer therapy. Bioorg Med Chem 2023; 90:117373. [PMID: 37329678 DOI: 10.1016/j.bmc.2023.117373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/28/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023]
Abstract
N6-methyladenosine (m6A) is the most common mRNA modification in mammalians. The function and dynamic regulation of m6A depends on the "writer", "readers" and "erasers". YT521-B homology domain family (YTHDF) is a class of m6A binding proteins, including YTHDF1, YTHDF2 and YTHDF3. In recent years, the modification of m6A and the molecular mechanism of YTHDFs have been further understood. Growing evidence has shown that YTHDFs participate in multifarious bioprocesses, particularly tumorigenesis. In this review, we summarized the structural characteristics of YTHDFs, the regulation of mRNA by YTHDFs, the role of YTHDF proteins in human cancers and inhibition of YTHDFs.
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Affiliation(s)
- Weikun Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Tingting Wu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuejiao Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenjing Kang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Chenyu Du
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xuetao Chen
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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Wang S, Gao S, Ye W, Li Y, Luan J, Lv X. The emerging importance role of m6A modification in liver disease. Biomed Pharmacother 2023; 162:114669. [PMID: 37037093 DOI: 10.1016/j.biopha.2023.114669] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
N6-methyladenosine (m6A) modification, as one of the most common types of inner RNA modification in eukaryotes, plays a multifunctional role in normal and abnormal biological processes. This type of modification is modulated by m6A writer, eraser and reader, which in turn impact various processes of RNA metabolism, such as RNA processing, translation, nuclear export, localization and decay. The current academic view holds that m6A modification exerts a crucial role in the post-transcriptional modulation of gene expression, and is involved in multiple cellular functions, developmental and disease processes. However, the potential molecular mechanism and specific role of m6A modification in the development of liver disease have not been fully elucidated. In our review, we summarized the latest research progress on m6A modification in liver disease, and explored how these novel findings reshape our knowledge of m6A modulation of RNA metabolism. In addition, we also illustrated the effect of m6A on liver development and regeneration to prompt further exploration of the mechanism and role of m6A modification in liver physiology and pathology, providing new insights and references for the search of potential therapeutic targets for liver disease.
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Affiliation(s)
- Sheng Wang
- Department of Pharmacy, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui Province, China; The Key Laboratory of Anti-inflammatory and Immune medicines, Ministry of Education, Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Institute for Liver Disease of Anhui Medical University, Hefei, Anhui Province, China
| | - Songsen Gao
- Department of Orthopedics (Spinal Surgery), The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
| | - Wufei Ye
- Department of Pharmacy, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui Province, China
| | - Yueran Li
- Department of Pharmacy, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui Province, China
| | - Jiajie Luan
- Department of Pharmacy, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui Province, China
| | - Xiongwen Lv
- The Key Laboratory of Anti-inflammatory and Immune medicines, Ministry of Education, Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Institute for Liver Disease of Anhui Medical University, Hefei, Anhui Province, China.
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9
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Lei L, Du LX, He YL, Yuan JP, Wang P, Ye BL, Wang C, Hou Z. Dictionary learning LASSO for feature selection with application to hepatocellular carcinoma grading using contrast enhanced magnetic resonance imaging. Front Oncol 2023; 13:1123493. [PMID: 37091168 PMCID: PMC10118007 DOI: 10.3389/fonc.2023.1123493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/17/2023] [Indexed: 04/09/2023] Open
Abstract
IntroductionThe successful use of machine learning (ML) for medical diagnostic purposes has prompted myriad applications in cancer image analysis. Particularly for hepatocellular carcinoma (HCC) grading, there has been a surge of interest in ML-based selection of the discriminative features from high-dimensional magnetic resonance imaging (MRI) radiomics data. As one of the most commonly used ML-based selection methods, the least absolute shrinkage and selection operator (LASSO) has high discriminative power of the essential feature based on linear representation between input features and output labels. However, most LASSO methods directly explore the original training data rather than effectively exploiting the most informative features of radiomics data for HCC grading. To overcome this limitation, this study marks the first attempt to propose a feature selection method based on LASSO with dictionary learning, where a dictionary is learned from the training features, using the Fisher ratio to maximize the discriminative information in the feature.MethodsThis study proposes a LASSO method with dictionary learning to ensure the accuracy and discrimination of feature selection. Specifically, based on the Fisher ratio score, each radiomic feature is classified into two groups: the high-information and the low-information group. Then, a dictionary is learned through an optimal mapping matrix to enhance the high-information part and suppress the low discriminative information for the task of HCC grading. Finally, we select the most discrimination features according to the LASSO coefficients based on the learned dictionary.Results and discussionThe experimental results based on two classifiers (KNN and SVM) showed that the proposed method yielded accuracy gains, compared favorably with another 5 state-of-the-practice feature selection methods.
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Affiliation(s)
- Lei Lei
- College of Information Science and Engineering, Jiaxing University, Jiaxing, China
- *Correspondence: Lei Lei, ; Ying-Long He,
| | - Li-Xin Du
- Medical Imaging Department, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Ying-Long He
- School of Mechanical Engineering Sciences, University of Surrey, Guildford, United Kingdom
- *Correspondence: Lei Lei, ; Ying-Long He,
| | - Jian-Peng Yuan
- Department of Radiology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Pan Wang
- Medical Imaging Department, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Bao-Lin Ye
- College of Information Science and Engineering, Jiaxing University, Jiaxing, China
| | - Cong Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - ZuJun Hou
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
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10
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Shen Y, Wang X, Ni Z, Xu S, Qiu S, Zheng W, Zhang J. Identification of acetyl-CoA carboxylase alpha as a prognostic and targeted candidate for hepatocellular carcinoma. Clin Transl Oncol 2023:10.1007/s12094-023-03137-1. [PMID: 36976490 DOI: 10.1007/s12094-023-03137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE The de novo lipogenesis has been a longstanding observation in hepatocellular carcinoma (HCC). However, the prognostic value and carcinogenic roles of the enzyme Acetyl-CoA carboxylase alpha (ACACA) in HCC remains unknown. METHODS The proteins with remarkable prognostic significance were screened out from The Cancer Proteome Atlas Portal (TCPA) database. Furthermore, the expression characteristics and prognostic value of ACACA were evaluated in multiple databases and the local HCC cohort. The loss-of-function assays were performed to uncover the potential roles of ACACA in steering malignant behaviors of HCC cells. The underlying mechanisms were conjectured by bioinformatics and validated in HCC cell lines. RESULTS ACACA was identified as a crucial factor of HCC prognosis. Bioinformatics analyses showed that HCC patients with higher expression of ACACA protein or mRNA levels had poor prognosis. Knockdown of ACACA remarkably crippled the proliferation, colony formation, migration, invasion, epithelial-mesenchymal transition (EMT) process of HCC cells and induced the cell cycle arrest. Mechanistically, ACACA might facilitate the malignant phenotypes of HCC through aberrant activation of Wnt/β-catenin signaling pathway. In addition, ACACA expression was associated with the dilute infiltration of immune cells including plasmacytoid DC (pDC) and cytotoxic cells by utilization of relevant database analysis. CONCLUSION ACACA could be a potential biomarker and molecular target for HCC.
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Affiliation(s)
- Yiping Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Xin Wang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Zhiyu Ni
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Shiyu Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Shi Qiu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China.
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Jie Zhang
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
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11
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Chen L, Gao Y, Xu S, Yuan J, Wang M, Li T, Gong J. N6-methyladenosine reader YTHDF family in biological processes: Structures, roles, and mechanisms. Front Immunol 2023; 14:1162607. [PMID: 36999016 PMCID: PMC10043241 DOI: 10.3389/fimmu.2023.1162607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
As the most abundant and conserved internal modification in eukaryote RNAs, N6-methyladenosine (m6A) is involved in a wide range of physiological and pathological processes. The YT521-B homology (YTH) domain-containing family proteins (YTHDFs), including YTHDF1, YTHDF2, and YTHDF3, are a class of cytoplasmic m6A-binding proteins defined by the vertebrate YTH domain, and exert extensive functions in regulating RNA destiny. Distinct expression patterns of the YTHDF family in specific cell types or developmental stages result in prominent differences in multiple biological processes, such as embryonic development, stem cell fate, fat metabolism, neuromodulation, cardiovascular effect, infection, immunity, and tumorigenesis. The YTHDF family mediates tumor proliferation, metastasis, metabolism, drug resistance, and immunity, and possesses the potential of predictive and therapeutic biomarkers. Here, we mainly summary the structures, roles, and mechanisms of the YTHDF family in physiological and pathological processes, especially in multiple cancers, as well as their current limitations and future considerations. This will provide novel angles for deciphering m6A regulation in a biological system.
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Affiliation(s)
- Lin Chen
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Gao
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Simiao Xu
- Division of Endocrinology, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Branch of National Clinical Research Center for Metabolic Disease, Wuhan, China
| | - Jinxiong Yuan
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Wang
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tianyu Li
- Trauma Center/Department of Emergency and Traumatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Gong
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jun Gong,
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12
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Zhu Y, Li J, Yang H, Yang X, Zhang Y, Yu X, Li Y, Chen G, Yang Z. The potential role of m6A reader YTHDF1 as diagnostic biomarker and the signaling pathways in tumorigenesis and metastasis in pan-cancer. Cell Death Dis 2023; 9:34. [PMID: 36707507 PMCID: PMC9883452 DOI: 10.1038/s41420-023-01321-4] [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: 11/26/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/29/2023]
Abstract
m6A is an important RNA methylation in progression of various human cancers. As the m6A reader protein, YTHDF1 is reported to accelerate m6A-modified mRNAs translation in cytoplasm. It is highly expressed in various human cancers and contributes to the progression and metastasis of cancers. YTHDF1 was closely associated with poor prognosis and also used as a molecular marker for clinical diagnosis or therapy in human cancers. It has been reported to promote chemoresistance to Adriamycin, Cisplatin and Olaparib by increasing mRNA stability of its target molecule. Moreover, it contributes to CSC-like characteristic of tumor cells and inducing the antitumor immune microenvironment. Here, we reviewed the clinical diagnostic and prognostic values of YTHDF1, as well as the molecular mechanisms of YTHDF1 in progression and metastasis of human cancers.
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Affiliation(s)
- Yanan Zhu
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Jing Li
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Hang Yang
- grid.415444.40000 0004 1800 0367Department of Rehabilitation Medicine, The Second Affiliated Hospital of Kunming Medical University, 650106 Kunming, Yunnan China
| | - Xinyi Yang
- grid.413458.f0000 0000 9330 9891Guizhou Medical University, 550004 Guiyang, Guizhou China
| | - Ya Zhang
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Xinchao Yu
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Ying Li
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Gangxian Chen
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Zuozhang Yang
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
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13
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Ren W, Yuan Y, Li Y, Mutti L, Peng J, Jiang X. The function and clinical implication of YTHDF1 in the human system development and cancer. Biomark Res 2023; 11:5. [PMID: 36650570 PMCID: PMC9847098 DOI: 10.1186/s40364-023-00452-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/26/2022] [Indexed: 01/19/2023] Open
Abstract
YTHDF1 is a well-characterized m6A reader protein that is essential for protein translation, stem cell self-renewal, and embryonic development. YTHDF1 regulates target gene expression by diverse molecular mechanisms, such as promoting protein translation or modulating the stability of mRNA. The cellular levels of YTHDF1 are precisely regulated by a complicated transcriptional, post-transcriptional, and post-translational network. Very solid evidence supports the pivotal role of YTHDF1 in embryonic development and human cancer progression. In this review, we discuss how YTHDF1 influences both the physiological and pathological biology of the central nervous, reproductive and immune systems. Therefore we focus on some relevant aspects of the regulatory role played by YTHDF1 as gene expression, complex cell networking: stem cell self-renewal, embryonic development, and human cancers progression. We propose that YTHDF1 is a promising future cancer biomarker for detection, progression, and prognosis. Targeting YTHDF1 holds therapeutic potential, as the overexpression of YTHDF1 is associated with tumor resistance to chemotherapy and immunotherapy.
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Affiliation(s)
- Wenjun Ren
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Yixiao Yuan
- grid.452206.70000 0004 1758 417XKey Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongwu Li
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Luciano Mutti
- grid.264727.20000 0001 2248 3398Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USA ,grid.158820.60000 0004 1757 2611Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2 67100 L’Aquila, Italy
| | - Jun Peng
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Xiulin Jiang
- grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
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14
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Tabnak P, Ghasemi Y, Natami M, Khorram R, Ebrahimnezhad M. Role of m 6A modification in dysregulation of Wnt/β-catenin pathway in cancer. Biomed Pharmacother 2023; 157:114023. [PMID: 36403567 DOI: 10.1016/j.biopha.2022.114023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most abundant post-transcriptional regulation of RNAs in eukaryotes. Dysregulation of m6A readers, writers, and erasers can significantly promote tumorigenesis by altering the expression of various genes. Wnt/β-catenin is an evolutionarily conserved signaling pathway that has recently been linked to the pathogenesis of many cancers. Given the significance of this pathway in regulating normal tissue homeostasis and stem cell differentiation, a subtle understanding of the molecular mechanism underlying its dysregulation is required for effective targeting. There is mounting evidence that m6A regulators are highly implicated in the dysregulation of the Wnt/β-catenin signaling pathway. Since m6A regulators can affect Wnt pathway components and dysregulation of either leads to carcinogenesis, this study aims to clarify the relationship between m6A regulators and the Wnt/β-catenin signaling pathway to investigate their combined impact on tumorigenesis.
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Affiliation(s)
- Peyman Tabnak
- Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5165665931, Iran.
| | - Yaser Ghasemi
- Faculty of Pharmacy, Ramsar Campus, Mazandaran University of Medical Sciences, Ramsar, Iran.
| | - Mohammad Natami
- Department of Urology, Shahid Mohammadi Hospital, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Roya Khorram
- Bone and Joint Diseases Research Center, Department of Orthopedic Surgery, Shiraz University of Medical Sciences, Shiraz, Iran.
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15
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Verghese M, Wilkinson E, He YY. Recent Advances in RNA m 6A Modification in Solid Tumors and Tumor Immunity. Cancer Treat Res 2023; 190:95-142. [PMID: 38113000 DOI: 10.1007/978-3-031-45654-1_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] [Indexed: 12/21/2023]
Abstract
An analogous field to epigenetics is referred to as epitranscriptomics, which focuses on the study of post-transcriptional chemical modifications in RNA. RNA molecules, including mRNA, tRNA, rRNA, and other non-coding RNA molecules, can be edited with numerous modifications. The most prevalent modification in eukaryotic mRNA is N6-methyladenosine (m6A), which is a reversible modification found in over 7000 human genes. Recent technological advances have accelerated the characterization of these modifications, and they have been shown to play important roles in many biological processes, including pathogenic processes such as cancer. In this chapter, we discuss the role of m6A mRNA modification in cancer with a focus on solid tumor biology and immunity. m6A RNA methylation and its regulatory proteins can play context-dependent roles in solid tumor development and progression by modulating RNA metabolism to drive oncogenic or tumor-suppressive cellular pathways. m6A RNA methylation also plays dynamic roles within both immune cells and tumor cells to mediate the anti-tumor immune response. Finally, an emerging area of research within epitranscriptomics studies the role of m6A RNA methylation in promoting sensitivity or resistance to cancer therapies, including chemotherapy, targeted therapy, and immunotherapy. Overall, our understanding of m6A RNA methylation in solid tumors has advanced significantly, and continued research is needed both to fill gaps in knowledge and to identify potential areas of focus for therapeutic development.
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Affiliation(s)
- Michelle Verghese
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA
- Pritzker School of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Emma Wilkinson
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA
- Committee on Cancer Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA.
- Committee on Cancer Biology, University of Chicago, Chicago, IL, 60637, USA.
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16
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Qu N, Zhang X, Wu X, Zhou X, Deng Z, Ma L, Liu Y, Ge W, Jiang H, Xu L, Jiang H. Clinical implications of m6A‐related regulators YTHDF1 and YTHDF2 in hepatocellular carcinoma. PRECISION MEDICAL SCIENCES 2022. [DOI: 10.1002/prm2.12085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Nanfang Qu
- Department of Gastroenterology Affiliated Hospital of Guilin Medical University Guilin People's Republic of China
| | - Xuemei Zhang
- Department of Pathology Affiliated Hospital of Guilin Medical University Guilin People's Republic of China
| | - Xianbin Wu
- Department of Gastroenterology Nanning Second Peoples Hospital Nanning People's Republic of China
| | - Xia Zhou
- Emergency Department Guizhou Provincial People's Hospital Guizhou People's Republic of China
| | - Zhejun Deng
- Department of Gastroenterology The First Affiliated Hospital of Guangxi Medical University Nanning People's Republic of China
| | - Lei Ma
- Department of Gastroenterology Affiliated Hospital of Guilin Medical University Guilin People's Republic of China
| | - Yanhua Liu
- Department of Gastroenterology Affiliated Hospital of Guilin Medical University Guilin People's Republic of China
| | - Wenhong Ge
- Department of Gastroenterology Affiliated Hospital of Guilin Medical University Guilin People's Republic of China
| | - Huanghuang Jiang
- Department of Gastroenterology Affiliated Hospital of Guilin Medical University Guilin People's Republic of China
| | - Longkuan Xu
- Department of Pathology Affiliated Hospital of Guilin Medical University Guilin People's Republic of China
| | - Haixing Jiang
- Department of Gastroenterology The First Affiliated Hospital of Guangxi Medical University Nanning People's Republic of China
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17
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Feng Q, Wang D, Xue T, Lin C, Gao Y, Sun L, Jin Y, Liu D. The role of RNA modification in hepatocellular carcinoma. Front Pharmacol 2022; 13:984453. [PMID: 36120301 PMCID: PMC9479111 DOI: 10.3389/fphar.2022.984453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/11/2022] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly mortal type of primary liver cancer. Abnormal epigenetic modifications are present in HCC, and RNA modification is dynamic and reversible and is a key post-transcriptional regulator. With the in-depth study of post-transcriptional modifications, RNA modifications are aberrantly expressed in human cancers. Moreover, the regulators of RNA modifications can be used as potential targets for cancer therapy. In RNA modifications, N6-methyladenosine (m6A), N7-methylguanosine (m7G), and 5-methylcytosine (m5C) and their regulators have important regulatory roles in HCC progression and represent potential novel biomarkers for the confirmation of diagnosis and treatment of HCC. This review focuses on RNA modifications in HCC and the roles and mechanisms of m6A, m7G, m5C, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and pseudouridine (ψ) on its development and maintenance. The potential therapeutic strategies of RNA modifications are elaborated for HCC.
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Affiliation(s)
- Qiang Feng
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Tianyi Xue
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Chao Lin
- School of Grain Science and Technology, Jilin Business and Technology College, Changchun, China
| | - Yongjian Gao
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Liqun Sun
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Dianfeng Liu
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Dianfeng Liu,
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18
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Fang Z, Mei W, Qu C, Lu J, Shang L, Cao F, Li F. Role of m6A writers, erasers and readers in cancer. Exp Hematol Oncol 2022; 11:45. [PMID: 35945641 PMCID: PMC9361621 DOI: 10.1186/s40164-022-00298-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/04/2022] [Indexed: 02/06/2023] Open
Abstract
The N(6)-methyladenosine (m6A) modification is the most pervasive modification of human RNAs. In recent years, an increasing number of studies have suggested that m6A likely plays important roles in cancers. Many studies have demonstrated that m6A is involved in the biological functions of cancer cells, such as proliferation, invasion, metastasis, and drug resistance. In addition, m6A is closely related to the prognosis of cancer patients. In this review, we highlight recent advances in understanding the function of m6A in various cancers. We emphasize the importance of m6A to cancer progression and look forward to describe future research directions.
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Affiliation(s)
- Zhen Fang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Wentong Mei
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Chang Qu
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiongdi Lu
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
| | - Feng Cao
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Fei Li
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.
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19
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Maimaiti A, Tuersunniyazi A, Meng X, Pei Y, Ji W, Feng Z, Jiang L, Wang Z, Kasimu M, Wang Y, Shi X. N6-methyladenosine RNA methylation regulator-related alternative splicing gene signature as prognostic predictor and in immune microenvironment characterization of patients with low-grade glioma. Front Genet 2022; 13:872186. [PMID: 35937991 PMCID: PMC9355308 DOI: 10.3389/fgene.2022.872186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background: N6-methyladenosine (m6A) RNA methylation is an important epigenetic modification affecting alternative splicing (AS) patterns of genes to regulate gene expression. AS drives protein diversity and its imbalance may be an important factor in tumorigenesis. However, the clinical significance of m6A RNA methylation regulator-related AS in the tumor microenvironment has not been investigated in low-grade glioma (LGG). Methods: We used 12 m6A methylation modulatory genes (WTAP, FTO, HNRNPC, YTHDF2, YTHDF1, YTHDC2, ALKBH5, YTHDC1, ZC3H13, RBM15, METTL14, and METTL3) from The Cancer Genome Atlas (TCGA) database as well as the TCGA-LGG (n = 502) dataset of AS events and transcriptome data. These data were downloaded and subjected to machine learning, bioinformatics, and statistical analyses, including gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Univariate Cox, the Least Absolute Shrinkage and Selection Operator (LASSO), and multivariable Cox regression were used to develop prognostic characteristics. Prognostic values were validated using Kaplan-Maier survival analysis, proportional risk models, ROC curves, and nomograms. The ESTIMATE package, TIMER database, CIBERSORT method, and ssGSEA algorithm in the R package were utilized to explore the role of the immune microenvironment in LGG. Lastly, an AS-splicing factor (SF) regulatory network was examined in the case of considering the role of SFs in regulating AS events. Results: An aggregate of 3,272 m6A regulator-related AS events in patients with LGG were screened using six machine learning algorithms. We developed eight AS prognostic characteristics based on splice subtypes, which showed an excellent prognostic prediction performance. Furthermore, quantitative prognostic nomograms were developed and showed strong validity in prognostic prediction. In addition, prognostic signatures were substantially associated with tumor immune microenvironment diversity, ICB-related genes, and infiltration status of immune cell subtypes. Specifically, UGP2 has better promise as a prognostic factor for LGG. Finally, splicing regulatory networks revealed the potential functions of SFs. Conclusion: The present research offers a novel perspective on the role of AS in m6A methylation. We reveal that m6A methylation regulator-related AS events can mediate tumor progression through the immune-microenvironment, which could serve as a viable biological marker for clinical stratification of patients with LGG so as to optimize treatment regimens.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | | | - Xianghong Meng
- Department of Neurosurgery, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy Centre, Shenzhen University, Shenzhen, China
| | - Yinan Pei
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Wenyu Ji
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhaohai Feng
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Lei Jiang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zengliang Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Maimaitijiang Kasimu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Xin Shi, ; Yongxin Wang,
| | - Xin Shi
- Department of Neurosurgery, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy Centre, Shenzhen University, Shenzhen, China
- *Correspondence: Xin Shi, ; Yongxin Wang,
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20
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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: 7] [Impact Index Per Article: 3.5] [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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Liu Y, Fu B, Yu Z, Song G, Zeng H, Gong Y, Ding Y, Huang D. Identification of KRBA1 as a Potential Prognostic Biomarker Associated with Immune Infiltration and m6A Modification in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2022; 9:497-516. [PMID: 35669909 PMCID: PMC9166909 DOI: 10.2147/jhc.s363862] [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: 03/15/2022] [Accepted: 05/21/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) is a malignancy with high incidence, but its prognosis is not optimistic. KRBA1 is a member of the KRAB family and participates in the regulation of gene transcription. However, no studies have focused on the role of KRBA1 in HCC. Patients and Methods In this study, we first analyzed the expression of KRBA1 in HCC using TCGA and ICGC databases and validated by Immunohistochemistry in clinical HCC samples. The Wilcoxon rank-sum test was used to determine the relationship between KRBA1 expression and clinicopathological features. Subsequently, we used Kaplan-Meier online website analysis and Cox regression model to predict the prognostic value of KRBA1 in HCC patients. Furthermore, the functions of KRBA1 were identified by enrichment analysis. TIMER and GSCALite were used to investigate the relationship between KRBA1 expression in HCC and immune infiltration and drug targets, respectively. Finally, the relationship between KRBA1 expression and m6A modification in HCC was analyzed using the TCGA and ICGA datasets. Results The results showed that KRBA1 was upregulated in HCC and was associated with many clinicopathological features. High KRBA1 causes poor overall survival and may be an independent risk factor for HCC. KRBA1 tends to be hypermethylated and associated with poor prognosis in HCC compared with normal tissues. Enrichment analysis indicates that KRBA1 is associated with cell cycle and immune processes, and TIMER analysis shows that KRBA1 expression is associated with infiltration levels and immune characteristics of various immune cells. Silenced KRBA1 evidently reduced three chemokine expression in HCC cells. Drug sensitivity analysis showed that KRBA1 was sensitive to 39 drug small molecules. KRBA1 showed a strong positive correlation with five m6A related genes. Conclusion KRBA1 is a prognostic biomarker associated with HCC immunity and m6a modification, serving as an effective target for the diagnosis and treatment of HCC.
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Affiliation(s)
- Yue Liu
- Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China.,Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Bidong Fu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Gelin Song
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Yongqi Ding
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Da Huang
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
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22
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Cheng Z, Gong L, Cai Q. LncRNA00978 contributes to growth and metastasis of hepatocellular carcinoma cells via mediating microRNA-125b-5p/SOX12 pathway. Bioengineered 2022; 13:11228-11239. [PMID: 35485164 PMCID: PMC9208515 DOI: 10.1080/21655979.2022.2063648] [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] [Indexed: 11/17/2022] Open
Abstract
As a malignant tumor, HCC (hepatocellular carcinoma) is featured by a high recurrence rate with a poor prognosis. Increasing evidence supports an important role of lincRNAs in HCC. Here, the purpose of the study was to explore the function of LINC00978 (long non-coding RNA00978) in HCC and the underlying mechanisms. LINC00978 expression and its association with the progression of HCC were analyzed using HCC TCGA datasets. LINC00978 expression in tissues was measured using real-time PCR. Then, we knocked down LINC00978 in HCC cells to explore its effect on cellular invasion, proliferation, and migration. Finally, we investigated the potential molecular mechanism of LINC00978 by dual Luciferase reporter assay, FISH (fluorescence in situ hybridization) and RIP (RNA immunoprecipitation). LINC00978 expression was remarkably increased in HCC. A high level of LINC00978 was associated with poor prognosis of HCC. Additionally, LINC00978 silencing could repress the growth and metastasis of HCC cells. Mechanistically, it was revealed that LINC00978 could sponge microRNA-125b-5p and identified SOX12 (SRY-Box Transcription Factor 12) as a direct target gene of microRNA-125b-5p. More importantly, the suppressed effect of LINC00978 silencing on the metastasis and growth of HCC cells could be rescued by miR-125b-5p inhibition and overexpressed SOX12. LINC00978/microRNA-125b-5p/SOX12 axis promoted liver cancer migration, invasion, and proliferation, which could be used as a possible therapeutic target for the treatment of hepatocellular carcinoma.
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Affiliation(s)
- Zhiqing Cheng
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Putian University, Putian, Fujian, China
| | - Limei Gong
- Department of General Medicine, Affiliated Hospital of Putian University, Putian, Fujian, China
| | - Qinghe Cai
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Putian University, Putian, Fujian, China
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23
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Chen Z, Hu Y, Jin L, Yang F, Ding H, Zhang L, Li L, Pan T. The Emerging Role of N6-Methyladenosine RNA Methylation as Regulators in Cancer Therapy and Drug Resistance. Front Pharmacol 2022; 13:873030. [PMID: 35462896 PMCID: PMC9022635 DOI: 10.3389/fphar.2022.873030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/14/2022] [Indexed: 12/18/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation has been considered the most prevalent, abundant, and conserved internal transcriptional modification throughout the eukaryotic mRNAs. Typically, m6A RNA methylation is catalyzed by the RNA methyltransferases (writers), is removed by its demethylases (erasers), and interacts with m6A-binding proteins (readers). Accumulating evidence shows that abnormal changes in the m6A levels of these regulators are increasingly associated with human tumorigenesis and drug resistance. However, the molecular mechanisms underlying m6A RNA methylation in tumor occurrence and development have not been comprehensively clarified. We reviewed the recent findings on biological regulation of m6A RNA methylation and summarized its potential therapeutic strategies in various human cancers.
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Affiliation(s)
- Zhaolin Chen
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Hospital, Hefei, China
| | - Ying Hu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Le Jin
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Hospital, Hefei, China
| | - Fan Yang
- Department of Clinical Medical, The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Haiwen Ding
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Hospital, Hefei, China
| | - Lei Zhang
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Hospital, Hefei, China
| | - Lili Li
- Department of Hematopathology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tingting Pan
- Department of General Surgery, Diagnosis and Therapy Center of Thyroid and Breast, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Hospital, Hefei, China
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24
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Wu S, He G, Liu S, Cao Y, Geng C, Pan H. Identification and validation of the N6-methyladenosine RNA methylation regulator ZC3H13 as a novel prognostic marker and potential target for hepatocellular carcinoma. Int J Med Sci 2022; 19:618-630. [PMID: 35582419 PMCID: PMC9108408 DOI: 10.7150/ijms.69645] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 11/22/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation has been implicated in various malignancies. This study aimed to identify prognostic signature based on m6A methylation regulators for hepatocellular carcinoma (HCC) and provide candidate targets for HCC treatment. In this study, the expression levels, prognostic values, correlation with tumor grades and genetic variations of m6A-related genes in HCC were evaluated using bioinformatics analyses. Interestingly, the results show that methyltransferase zinc finger CCCH-type containing 13 (ZC3H13) was expressed at a significantly low level in HCC. Survival outcome analysis suggested that significant correlations existed between ZC3H13 downregulation and poor overall survival (OS) and poor recurrence-free survival (RFS) in HCC patients. Therefore, ZC3H13 was chosen for further experimental validation. The expression of ZC3H13 in HCC cell lines was investigated by western blotting. Knockdown of ZC3H13 significantly enhanced the migration and invasion of HCC cells, as demonstrated by wound healing and transwell assays. Moreover, upregulating ZC3H13 repressed the growth of xenograft tumors in vivo. Functional and pathway enrichment analyses indicated that ZC3H13 might be involved in transcriptional dysregulation or the JAK-STAT signaling pathway in cancer. Additionally, ZC3H13 expression was significantly correlated with lymphocytes and immunomodulators. Therefore, ZC3H13 is a promising candidate as a novel biomarker and therapeutic target for HCC.
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Affiliation(s)
- Shuang Wu
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, People's Republic of China
- Department of Medicine, Qingdao University, Qingdao, Shandong 266071, People's Republic of China
| | - Guifang He
- Medical Animal Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, People's Republic of China
| | - Shihai Liu
- Medical Animal Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, People's Republic of China
| | - Yongxian Cao
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, People's Republic of China
| | - Chao Geng
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, People's Republic of China
| | - Huazheng Pan
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, People's Republic of China
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25
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Zhao X, Li X, Li X. Multiple roles of m6A methylation in epithelial–mesenchymal transition. Mol Biol Rep 2022; 49:8895-8906. [DOI: 10.1007/s11033-022-07368-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/11/2022] [Indexed: 01/17/2023]
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26
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Tang F, Chen L, Gao H, Xiao D, Li X. m6A: An Emerging Role in Programmed Cell Death. Front Cell Dev Biol 2022; 10:817112. [PMID: 35141221 PMCID: PMC8819724 DOI: 10.3389/fcell.2022.817112] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/10/2022] [Indexed: 12/20/2022] Open
Abstract
Programmed cell death is an active extinction process, including autophagy, ferroptosis, pyroptosis, apoptosis, and necroptosis. m6A is a reversible RNA modification which undergoes methylation under the action of methylases (writers), and is demethylated under the action of demethylases (erasers). The RNA base site at which m6A is modified is recognized by specialized enzymes (readers) which regulate downstream RNA translation, decay, and stability. m6A affects many aspects of mRNA metabolism, and also plays an important role in promoting the maturation of miRNA, the translation and degradation of circRNA, and the stability of lncRNA. The regulatory factors including writers, erasers and readers promote or inhibit programmed cell death via up-regulating or down-regulating downstream targets in a m6A-dependent manner to participate in the process of disease. In this review, we summarize the functions of m6A with particular reference to its role in programmed cell death.
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Affiliation(s)
- Fajuan Tang
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lin Chen
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hu Gao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Dongqiong Xiao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Dongqiong Xiao, ; Xihong Li,
| | - Xihong Li
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Dongqiong Xiao, ; Xihong Li,
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27
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Cai Y, Jia Y. Circular RNA SOX5 promotes the proliferation and inhibits the apoptosis of the hepatocellular carcinoma cells by targeting miR-502-5p/synoviolin 1 axis. Bioengineered 2022; 13:3362-3370. [PMID: 35048790 PMCID: PMC8973662 DOI: 10.1080/21655979.2022.2029110] [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] [Indexed: 12/31/2022] Open
Abstract
We aimed to explore the role of circ-SOX5 in the pathogenesis of hepatocellular carcinoma (HCC). The circRNAs in HCC were screened using the GEO database. RT-qPCR was used to detect mRNA expression. Targeting relationships were confirmed by dual luciferase reporter assay and RNA pull-down assay. CCK-8 and EDU staining were used to measure cell viability and proliferation, respectively. Cell apoptosis was determined using flow cytometry. Protein expression was determined by Western blotting. Circ-SOX5 expression was increased in HCC tissues. Inhibition of circ-SOX5 expression reduced the viability, proliferation, and colony formation, and increased the apoptosis of HCC cells. However, miR-502-5p inhibition or overexpression of synoviolin 1 (SYVN1) can reverse the effects of circ-SOX5 knockdown on proliferation and apoptosis. This study demonstrated that the circ-SOX5/miR-502-5p/SYVN1 axis promotes the development of HCC by regulating cell apoptosis. Therefore, circ-SOX5 may be a potential biomarker of HCC.
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Affiliation(s)
- Yu Cai
- Department of General Surgery, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, China
| | - Yuanyuan Jia
- Department of Faculty Development and Teaching Evaluation Office, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, China
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28
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Shi X, Zhang J, Jiang Y, Zhang C, Luo X, Wu J, Li J. Comprehensive Analyses of the Expression, Genetic Alteration, Prognosis Significance, and Interaction Networks of m 6A Regulators Across Human Cancers. Front Genet 2022; 12:771853. [PMID: 35003212 PMCID: PMC8733627 DOI: 10.3389/fgene.2021.771853] [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: 09/07/2021] [Accepted: 11/23/2021] [Indexed: 02/03/2023] Open
Abstract
Accumulating lines of evidence indicate that the deregulation of m6A is involved in various cancer types. The m6A RNA methylation is modulated by m6A methyltransferases, demethylases, and reader proteins. Although the aberrant expression of m6A RNA methylation contributes to the development and progression of multiple cancer types, the roles of m6A regulators across numerous types of cancers remain largely unknown. Here, we comprehensively investigated the expression, genetic alteration, and prognosis significance of 20 commonly studied m6A regulators across diverse cancer types using TCGA datasets via bioinformatic analyses. The results revealed that the m6A regulators exhibited widespread dysregulation, genetic alteration, and the modulation of oncogenic pathways across TCGA cancer types. In addition, most of the m6A regulators were closely relevant with significant prognosis in many cancer types. Furthermore, we also constructed the protein–protein interacting network of the 20 m6A regulators, and a more complex interacting regulatory network including m6A regulators and their corresponding interacting factors. Besides, the networks between m6A regulators and their upstream regulators such as miRNAs or transcriptional factors were further constructed in this study. Finally, the possible chemicals targeting each m6A regulator were obtained by bioinformatics analysis and the m6A regulators–potential drugs network was further constructed. Taken together, the comprehensive analyses of m6A regulators might provide novel insights into the m6A regulators’ roles across cancer types and shed light on their potential molecular mechanisms as well as help develop new therapy approaches for cancers.
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Affiliation(s)
- Xiujuan Shi
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Jieping Zhang
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Yuxiong Jiang
- School of Medicine, Tongji University, Shanghai, China
| | - Chen Zhang
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaoli Luo
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China
| | - Jiawen Wu
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China
| | - Jue Li
- Clinical Research Center for Mental Disorders, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China.,Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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29
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Chen Z, Zhong X, Xia M, Zhong J. The roles and mechanisms of the m6A reader protein YTHDF1 in tumor biology and human diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1270-1279. [PMID: 34853726 PMCID: PMC8609105 DOI: 10.1016/j.omtn.2021.10.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
YTHDF1 is the most versatile and powerful reader protein of N6-methyladenosine (m6A)-modified RNA, and it can recognize both G(m6A)C and A(m6A)C RNAs as ligands without sequence selectivity. YTHDF1 regulates target gene expression by different mechanisms, such as promoting translation or regulating the stability of mRNA. Numerous studies have shown that YTHDF1 plays an important role in tumor biology and nontumor lesions by mediating the protein translation of important genes or by affecting the expression of key factors involved in many important cell signaling pathways. Therefore, in this review we focus on some of the roles of YTHDF1 in tumor biology and diseases.
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Affiliation(s)
- Zuyao Chen
- Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,The First Affiliated Hospital, Institute Center of Clinical Medicine, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,Department of Otorhinolaryngology, The First Affiliated Hospital, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Xiaolin Zhong
- Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,The First Affiliated Hospital, Institute Center of Clinical Medicine, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Min Xia
- Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,The First Affiliated Hospital, Institute Center of Clinical Medicine, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Jing Zhong
- Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,The First Affiliated Hospital, Institute Center of Clinical Medicine, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
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30
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Chen J, Zhang Q, Liu T, Tang H. Roles of M6A Regulators in Hepatocellular Carcinoma: Promotion or Suppression. Curr Gene Ther 2021; 22:40-50. [PMID: 34825870 DOI: 10.2174/1566523221666211126105940] [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: 04/27/2021] [Revised: 06/15/2021] [Accepted: 10/14/2021] [Indexed: 11/22/2022]
Abstract
Hepatocellular carcinoma (HCC) is the sixth globally diagnosed cancer with a poor prognosis. Although the pathological factors of hepatocellular carcinoma are well elucidated, the underlying molecular mechanisms remain unclear. N6-methyladenosine (m6A) is an adenosine methylation occurring at the N6 site, which is the most prevalent modification of eukaryotic mRNA. Recent studies have shown that m6A can regulate gene expression, thus modulating the processes of cell self-renewal, differentiation, and apoptosis. The methyls in m6A are installed by methyltransferases ("writers"), removed by demethylases ("erasers") and recognized by m6A-binding proteins ("readers"). In this review, we discuss the roles of above regulators in the progression and prognosis of HCC, and summarize the clinical association between m6A modification and hepatocellular carcinoma, so as to provide more valuable information for clinical treatment.
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Affiliation(s)
- Jiamao Chen
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Qian Zhang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Ting Liu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Hua Tang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
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31
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Wu G, Yang Y, Zhu Y, Li Y, Zhai Z, An L, Liu M, Zheng Y, Wang Y, Zhou Y, Guo Q. Comprehensive Analysis to Identify the Epithelial-Mesenchymal Transition-Related Immune Signatures as a Prognostic and Therapeutic Biomarkers in Hepatocellular Carcinoma. Front Surg 2021; 8:742443. [PMID: 34722623 PMCID: PMC8554059 DOI: 10.3389/fsurg.2021.742443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/13/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a highly heterogeneous disease with the high rates of the morbidity and mortality due to the lack of the effective prognostic model for prediction. Aim: To construct a risk model composed of the epithelial–mesenchymal transition (EMT)-related immune genes for the assessment of the prognosis, immune infiltration status, and chemosensitivity. Methods: We obtained the transcriptome and clinical data of the HCC samples from The Cancer Genome Atlas (TCGA) and The International Cancer Genome Consortium (ICGC) databases. The Pearson correlation analysis was applied to identify the differentially expressed EMT-related immune genes (DE-EMTri-genes). Subsequently, the univariate Cox regression was introduced to screen out the prognostic gene sets and a risk model was constructed based on the least absolute shrinkage and selection operator-penalized Cox regression. Additionally, the receiver operating characteristic (ROC) curves were plotted to compare the prognostic value of the newly established model compared with the previous model. Furthermore, the correlation between the risk model and survival probability, immune characteristic, and efficacy of the chemotherapeutics were analyzed by the bioinformatics methods. Results: Six DE-EMTri-genes were ultimately selected to construct the prognostic model. The area under the curve (AUC) values for 1-, 2-, and 3- year were 0.773, 0.721, and 0.673, respectively. Stratified survival analysis suggested that the prognosis of the low-score group was superior to the high-score group. Moreover, the univariate and multivariate analysis indicated that risk score [hazard ratio (HR) 5.071, 95% CI 3.050, 8.432; HR 4.396, 95% CI 2.624, 7.366; p < 0.001] and stage (HR 2.500, 95% CI 1.721, 3.632; HR 2.111, 95% CI 1.443, 3.089; p < 0.001) served as an independent predictive factors in HCC. In addition, the macrophages, natural killer (NK) cells, and regulatory T (Treg) cells were significantly enriched in the high-risk group. Finally, the patients with the high-risk score might be more sensitive to cisplatin, doxorubicin, etoposide, gemcitabine, and mitomycin C. Conclusion: We established a reliable EMTri-genes-based prognostic signature, which may hold promise for the clinical prediction.
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Affiliation(s)
- Guozhi Wu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Yuan Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Yu Zhu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Hematology, the First Hospital of Lanzhou University, Lanzhou, China
| | - Yemao Li
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Zipeng Zhai
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Lina An
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Min Liu
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
| | - Qinghong Guo
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Gastroenterology, Lanzhou University, Lanzhou, China
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Liu J, Huang L, Zhu Y, He Y, Zhang W, Lei T, Xuan J, Xiao B, Li L, Zhou Q, Sun Z. Exploring the Expression and Prognostic Value of the TCP1 Ring Complex in Hepatocellular Carcinoma and Overexpressing Its Subunit 5 Promotes HCC Tumorigenesis. Front Oncol 2021; 11:739660. [PMID: 34676169 PMCID: PMC8525800 DOI: 10.3389/fonc.2021.739660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/08/2021] [Indexed: 01/20/2023] Open
Abstract
T-complex protein-1 ring complex (TRiC), also known as Chaperonin Containing T-complex protein-1 (CCT), is a multisubunit chaperonin required for the folding of nascent proteins. Mounting evidence suggests that TRiC also contributes to the development and progression of tumors, but there are limited studies on pathogenic functions in hepatocellular carcinoma (HCC). We comprehensively evaluated the expression pattern and biological functions of TRiC subunits using The Cancer Genome Atlas and The Human Protein Atlas. Expression levels of TRiC subunits TCP1, CCT2/3/4/5/6A/7/8 were significantly upregulated in HCC tissues at both transcript and protein levels, which predicted shorter overall survival (OS). Moreover, high mutation rates were found in several CCT subunits, and patients with altered CCT genes exhibited poorer clinical outcomes. Functional enrichment analysis showed that co-regulated genes were preferentially involved in 'protein folding' and 'microtubule-based process', while genes co-expressed with CCT subunits were primarily involved in 'ribosome' and 'spliceosome'. Knockout of CCT5 in a HCC cell line reduced while overexpression enhanced proliferation rate, cycle transition, migration, and invasion. In conclusion, these findings suggest that subunits of the TRiC may be potential biomarkers for the diagnosis of HCC and play an important role in the occurrence and development of HCC.
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Affiliation(s)
- Jiahui Liu
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Ling Huang
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Yi Zhu
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Yongyin He
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Weiyun Zhang
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Ting Lei
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Junfeng Xuan
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
| | - Bin Xiao
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Linhai Li
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Quan Zhou
- Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China.,Laboratory of Basic Medical Science, General Hospital of Southern Theater Command of PLA, Guangzhou, China
| | - Zhaohui Sun
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, General Hospital of Southern Theater Command of People's Liberation Army (PLA), Guangzhou, China
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33
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Si T, Huang Z, Jiang Y, Walker-Jacobs A, Gill S, Hegarty R, Hamza M, Khorsandi SE, Jassem W, Heaton N, Ma Y. Expression Levels of Three Key Genes CCNB1, CDC20, and CENPF in HCC Are Associated With Antitumor Immunity. Front Oncol 2021; 11:738841. [PMID: 34660300 PMCID: PMC8515852 DOI: 10.3389/fonc.2021.738841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is the most common primary liver cancer with a low 5-year survival rate. The heterogeneity of HCC makes monotherapy unlikely. The development of diagnostic programs and new treatments targeting common genetic events in the carcinogenic process are providing further insights into the management of HCC. The aim of this study was firstly to validate key genes that are involved in promoting HCC development and as biomarkers for early diagnosis and, secondly, to define their links with antitumor immunity including inhibitory checkpoints. Methods Multiple databases including Gene Expression Omnibus (GEO), Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier Plotter, UALCAN, and Oncomine were used for target gene screening and establishment of a co-expression network. Clinical data and RNAseq of 367 HCC patients were downloaded from the Cancer Genome Atlas (TCGA) database. The diagnostic and prognostic value of screened genes were tested by receiver operating characteristic (ROC) curve and correlation analysis. The links with the key genes in HCC and antitumor immunity were defined using both blood and liver tissue collected prospectively from HCC patients in our center. Results Upregulation of CCNB1, CDC20, and CENPF was commonly observed in HCC and are involved in the p53 signal pathway. The hepatic mRNA expression levels of these three genes were strongly associated with patients' prognosis and expressed high value of area under the ROC curve (AUC). Further analysis revealed that these three genes were positively correlated with the gene expression levels of IFN-γ, TNF-α, and IL-17 in peripheral blood. In addition, the expression of CENPF showed positive correlation with the percentage of CD8pos T cells and negative correlation with the percentage of CD4pos T cells in the peripheral blood. In the HCC microenvironment, the transcript levels of these three genes and inhibitory checkpoint molecules including PD-1, CTLA-4, and TIM-3 were positively correlated. Conclusion The upregulation of CCNB1, CDC20, and CENPF genes was a common event in hepatocarcinogenesis. Expression levels of CCNB1, CDC20, and CENPF showed potential for early diagnosis and prediction of prognosis in HCC patients. There is a close association between three genes and Th1/Th17 cytokines as well as the count of CD4pos and CD8pos T cells. The positive correlation between the three genes and inhibitory checkpoint genes, PD-1, CTLA-4, and TIM-3, indicates that these genes are linked with weakened antitumor immunity in HCC. Our findings may provide further insights into developing novel therapies for HCC.
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Affiliation(s)
- Tengfei Si
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Zhenlin Huang
- The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanhang Jiang
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Abigail Walker-Jacobs
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Shaqira Gill
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Robert Hegarty
- Pediatric Liver, GI and Nutrition Centre, King's College Hospital, London, United Kingdom
| | - Mohammad Hamza
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Shirin Elizabeth Khorsandi
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom.,Transplant Service, King's College Hospital, London, United Kingdom.,The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, United Kingdom
| | - Wayel Jassem
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom.,Transplant Service, King's College Hospital, London, United Kingdom
| | - Nigel Heaton
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom.,Transplant Service, King's College Hospital, London, United Kingdom
| | - Yun Ma
- Institute of Liver Studies, King's College Hospital, Department of Inflammation Biology, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
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Liu L, Liu B, Yu J, Zhang D, Shi J, Liang P. Development of a Toll-Like Receptor-Based Gene Signature That Can Predict Prognosis, Tumor Microenvironment, and Chemotherapy Response for Hepatocellular Carcinoma. Front Mol Biosci 2021; 8:729789. [PMID: 34621787 PMCID: PMC8490642 DOI: 10.3389/fmolb.2021.729789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/16/2021] [Indexed: 11/19/2022] Open
Abstract
Objective: Emerging evidence highlights the implications of the toll-like receptor (TLR) signaling pathway in the pathogenesis and therapeutic regimens of hepatocellular carcinoma (HCC). Herein, a prognostic TLR-based gene signature was conducted for HCC. Methods: HCC-specific TLRs were screened in the TCGA cohort. A LASSO model was constructed based on prognosis-related HCC-specific TLRs. The predictive efficacy, sensitivity, and independency of this signature was then evaluated and externally verified in the ICGC, GSE14520, and GSE76427 cohorts. The associations between this signature and tumor microenvironment (stromal/immune score, immune checkpoint expression, and immune cell infiltrations) and chemotherapy response were assessed in HCC specimens. The expression of TLRs in this signature was verified in HCC and normal liver tissues by Western blot. Following si-MAP2K2 transfection, colony formation and apoptosis of Huh7 and HepG2 cells were examined. Results: Herein, we identified 60 HCC-specific TLRs. A TLR-based gene signature (MAP2K2, IRAK1, RAC1, TRAF3, MAP3K7, and SPP1) was conducted for HCC prognosis. High-risk patients exhibited undesirable outcomes. ROC curves confirmed the well prediction performance of this signature. Multivariate Cox regression analysis demonstrated that the signature was an independent prognostic indicator. Also, high-risk HCC was characterized by an increased immune score, immune checkpoint expression, and immune cell infiltration. Meanwhile, high-risk patients displayed higher sensitivity to gemcitabine and cisplatin. The dysregulation of TLRs in the signature was confirmed in HCC. MAP2K2 knockdown weakened colony formation and elevated apoptosis of Huh7 and HepG2 cells. Conclusion: Collectively, this TLR-based gene signature might assist clinicians to select personalized therapy programs for HCC patients.
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Affiliation(s)
- Lixia Liu
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China.,Department of Ultrasound, Affiliated Hospital of Hebei University, Baoding, China
| | - Bin Liu
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jie Yu
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Dongyun Zhang
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Jianhong Shi
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Ping Liang
- Department of Interventional Ultrasound, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
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35
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Qu N, Bo X, Li B, Ma L, Wang F, Zheng Q, Xiao X, Huang F, Shi Y, Zhang X. Role of N6-Methyladenosine (m 6A) Methylation Regulators in Hepatocellular Carcinoma. Front Oncol 2021; 11:755206. [PMID: 34692544 PMCID: PMC8529104 DOI: 10.3389/fonc.2021.755206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/22/2021] [Indexed: 12/21/2022] Open
Abstract
Liver cancer is the fifth most common malignant tumor in terms of incidence and the third leading cause of cancer-related mortality globally. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Although great progress has been made in surgical techniques, hepatic artery chemoembolization, molecular targeting and immunotherapy, the prognosis of liver cancer patients remains very poor. N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic cells and regulates various stages of the RNA life cycle. Many studies have reported that the abnormal expression of m6A-related regulators in HCC represent diagnostic and prognostic markers and potential therapeutic targets. In this review, firstly, we introduce the latest research on m6A-related regulators in detail. Next, we summarize the mechanism of each regulator in the pathogenesis and progression of HCC. Finally, we summarize the potential diagnostic, prognostic and therapeutic value of the regulators currently reported in HCC.
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Affiliation(s)
- Nanfang Qu
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xiaotong Bo
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Bin Li
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Lei Ma
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Feng Wang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qinghua Zheng
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xuhua Xiao
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Fengmei Huang
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yuanyuan Shi
- Department of Oncology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xuemei Zhang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, China
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36
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Wu XR, Chen Z, Liu Y, Chen ZZ, Tang F, Chen ZZ, Li JJ, Liao JL, Cao K, Chen X, Zhou J. Prognostic signature and immune efficacy of m 1 A-, m 5 C- and m 6 A-related regulators in cutaneous melanoma. J Cell Mol Med 2021; 25:8405-8418. [PMID: 34288419 PMCID: PMC8419166 DOI: 10.1111/jcmm.16800] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/18/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
Cutaneous melanoma (CM) is an aggressive cancer; given that initial and specific signs are lacking, diagnosis is often late and the prognosis is poor. RNA modification has been widely studied in tumour progression. Nevertheless, little progress has been made in the signature of N1 -methyladenosine (m1 A), 5-methylcytosine (m5 C), N6 -methyladenosine (m6 A)-related regulators and the tumour microenvironment (TME) cell infiltration in CM. Our study identified the characteristics of m1 A-, m5 C- and m6 A-related regulators based on 468 CM samples from the public database. Using univariate, multivariate and LASSO Cox regression analysis, a risk model of regulators was established and validated by a nomogram on independent prognostic factors. The gene set variation analysis (GSVA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) clarified the involved functional pathways. A combined single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT approach revealed TME of regulator-related prognostic signature. The nine-gene signature stratified the patients into distinct risk subgroups for personalized prognostic assessment. Additionally, functional enrichment, immune infiltration and immunotherapy response analysis indicated that the high-risk group was correlated with T-cell suppression, while the low-risk group was more sensitive to immunotherapy. The findings presented here contribute to our understanding of the TME molecular heterogeneity in CM. Nine m1 A-, m5 C- and m6 A-related regulators may also be promising biomarkers for future research.
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Affiliation(s)
- Xian rui Wu
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zheng Chen
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yang Liu
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zi zi Chen
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Fengjie Tang
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zhi zhao Chen
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jing jing Li
- Department of Plastic Surgery of Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jun lin Liao
- Departments of Medical CosmetologyThe First Affiliated HospitalUniversity of South ChinaHengyangHunanChina
| | - Ke Cao
- Department of Oncology of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xiang Chen
- Department of DermatologyThe Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jianda Zhou
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
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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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Feng ZY, Wang T, Su X, Guo S. Identification of the m 6A RNA Methylation Regulators WTAP as a Novel Prognostic Biomarker and Genomic Alterations in Cutaneous Melanoma. Front Mol Biosci 2021; 8:665222. [PMID: 34291082 PMCID: PMC8287526 DOI: 10.3389/fmolb.2021.665222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/22/2021] [Indexed: 02/03/2023] Open
Abstract
Background: The purpose of our research was to establish a gene signature and determine the prognostic value of m6A methylation regulators in cutaneous melanoma and WTAP as a protective gene in cutaneous melanoma prognosis, we also evaluated gene mutations in cutaneous melanoma. Methods: We downloaded the RNA-seq transcriptome data and the clinical information for cutaneous melanoma patients from the GTEx and TCGA databases. Consensus clustering analysis was applied to divide the samples into two groups. Then the least absolute shrinkage and selection operator (LASSO) analyses were conducted to construct a risk signature, and we use external and internal datasets to verify its predictive value. We further searched the cBioPortal tools to detect genomic alterations and WTAP mutations. Finally, WTAP was further identified as a prognostic factor, and the related mechanisms mediated by WTAP were predicted by gene set enrichment analysis (GSEA). Experimental validations and have been further carried out. Results: Notably, m6A RNA methylation regulators play significant roles in tumorigenesis and development. In total, we selected three subtypes of cutaneous melanoma according to consensus clustering of the m6A RNA methylation regulators, and the stage of cutaneous melanoma was proven to be related to the subtypes. The Cox regression and LASSO analyses built a risk signature including ELF3, ZC3H13 and WTAP. The prognostic value of the risk signature in internal and external datasets have been proven then. The whole-genome and selected gene WTAP mutations were further explored. WTAP as a single prognostic factor was also explored and found to serve as an independent protective prognostic factor. Conclusions: Our study constructed a stable risk signature composed of m6A RNA methylation regulators in cutaneous melanoma. Moreover, WTAP was identified as a valuable prognostic factor and potential molecular target for cutaneous melanoma treatment.
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Affiliation(s)
- Zi-Yi Feng
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ting Wang
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xin Su
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Shu Guo
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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Garbo S, Zwergel C, Battistelli C. m6A RNA methylation and beyond - The epigenetic machinery and potential treatment options. Drug Discov Today 2021; 26:2559-2574. [PMID: 34126238 DOI: 10.1016/j.drudis.2021.06.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/02/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022]
Abstract
m6A is emerging as one of the most important RNA modifications because of its involvement in pathological and physiological events. Here, we provide an overview of this epitranscriptomic modification, beginning with a description of the molecular players involved and continuing with a focus on the role of m6A in the maintenance of stemness, induction of the epithelial to mesenchymal transition (EMT), and tumor progression. Finally, we discuss the state of the art regarding the design and validation of inhibitors of m6A writers or erasers to provide a background for future investigations and for the development of specific therapeutics.
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Affiliation(s)
- Sabrina Garbo
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Department of Excellence 2018-2022, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo 15, 00146 Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Department of Excellence 2018-2022, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Cecilia Battistelli
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Department of Excellence 2018-2022, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
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40
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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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Chi F, Cao Y, Chen Y. Analysis and Validation of circRNA-miRNA Network in Regulating m 6A RNA Methylation Modulators Reveals CircMAP2K4/miR-139-5p/YTHDF1 Axis Involving the Proliferation of Hepatocellular Carcinoma. Front Oncol 2021; 11:560506. [PMID: 33708621 PMCID: PMC7940687 DOI: 10.3389/fonc.2021.560506] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/07/2021] [Indexed: 12/18/2022] Open
Abstract
The m6A RNA methylation modulators play a crucial role in regulating hepatocellular carcinoma (HCC) progression. The circular RNA (circRNA) regulatory network in regulating m6A RNA methylation modulators in HCC remains largely unknown. In this study, 5 prognostic m6A RNA methylation modulators in HCC were identified from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) projects. The differentially expressed microRNAs (DEmiRNAs) and circRNAs (DEcircRNAs) between paired tumor and normal tissues were screened out from TCGA and or Gene Expression Omnibus (GEO) database to construct the circRNA-miRNA- m6A RNA methylation modulator regulatory network, which included three m6A RNA methylation modulators (HNRNPC, YTHDF1, and YTHDF2), 11 DEmiRNAs, and eight DEcircRNAs. Among the network, hsa-miR-139-5p expression was negatively correlated with YTHDF1. Hsa-miR-139-5p low or YTHDF1 high expression was correlated with high pathological grade, advanced stage and poor survival of HCC. Additionally, cell cycle, base excision repair, and homologous recombination were enriched in YTHDF1 high expression group by GSEA. A hub circRNA regulatory network was constructed based on hsa-miR-139-5p/YTHDF1 axis. Furthermore, hsa_circ_0007456(circMAP2K4) was validated to promote HCC cell proliferation by binding with hsa-miR-139-5p to promote YTHDF1 expression. Taken together, we identified certain circRNA regulatory network related to m6A RNA methylation modulators and provided clues for mechanism study and therapeutic targets for HCC.
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Affiliation(s)
- Fanwu Chi
- Cardiovascular Surgery Department, The People's Hospital of Gaozhou, Gaozhou, China
| | - Yong Cao
- Cardiovascular Surgery Department, The People's Hospital of Gaozhou, Gaozhou, China
| | - Yuhan Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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