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Liang S, Qiu X, Cai L, Wei F, Huang J, Liu S. Development of a novel colon adenocarcinoma m6A-related lncRNA pair prognostic model. Transl Cancer Res 2024; 13:3704-3717. [PMID: 39145089 PMCID: PMC11319945 DOI: 10.21037/tcr-23-1883] [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: 10/11/2023] [Accepted: 05/21/2024] [Indexed: 08/16/2024]
Abstract
Background Colon adenocarcinoma (COAD) is among the most prevalent malignancies. Changes to N6-methyladenosine (m6A), the most common RNA modification, can affect how COAD develops. Furthermore, the involvement of long noncoding RNA (lncRNA) in COAD is significant, and it exhibits a close association with m6A modification. Nevertheless, the prognostic significance of lncRNAs that are related to m6A modification in COAD remains unclear. This study aims to establish a m6A-related lncRNA pair signature and reveal its prognostic value in COAD. Methods The current study utilized data from The Cancer Genome Atlas (TCGA) to investigate the predictive significance of m6A-related lncRNA pair signatures in COAD. The identification of m6A-related lncRNAs was conducted through co-expression analysis using the Pearson correlation coefficient. Then, the lncRNA pairs related to prognosis were identified using univariate Cox regression analysis. Receiver operating characteristic (ROC) curves were produced using the least absolute shrinkage and selection operator (LASSO) penalized with Cox analysis to predict overall survival (OS) in order to build a risk score prognostic model. The relationship among the risk scoring model and clinical characteristics, immune-related variables, and medication sensitivity was examined after identifying independent prognostic factors. Results Thirty-five of the 319 lncRNA pairings associated with m6A were linked to a pattern that predicted risk ratings. It was verified that the risk score model was a reliable predictor that stood alone from clinicopathological features. Differences between high- and low-risk groups were found in clinicopathological traits, immune-related variables, and medication sensitivity analysis according to correlation analyses. Conclusions Based on paired differentially expressed m6A-related lncRNAs, the proposed COAD prognostic model demonstrated potential clinical predictive value.
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Affiliation(s)
- Shengmei Liang
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xinze Qiu
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lulu Cai
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Fangyou Wei
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiean Huang
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shiquan Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
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2
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Hu H, Li Z, Xie X, Liao Q, Hu Y, Gong C, Gao N, Yang H, Xiao Y, Chen Y. Insights into the role of RNA m 6A modification in the metabolic process and related diseases. Genes Dis 2024; 11:101011. [PMID: 38560499 PMCID: PMC10978549 DOI: 10.1016/j.gendis.2023.04.038] [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: 01/09/2023] [Accepted: 04/30/2023] [Indexed: 04/04/2024] Open
Abstract
According to the latest consensus, many traditional diseases are considered metabolic diseases, such as cancer, type 2 diabetes, obesity, and cardiovascular disease. Currently, metabolic diseases are increasingly prevalent because of the ever-improving living standards and have become the leading threat to human health. Multiple therapy methods have been applied to treat these diseases, which improves the quality of life of many patients, but the overall effect is still unsatisfactory. Therefore, intensive research on the metabolic process and the pathogenesis of metabolic diseases is imperative. N6-methyladenosine (m6A) is an important modification of eukaryotic RNAs. It is a critical regulator of gene expression that is involved in different cellular functions and physiological processes. Many studies have indicated that m6A modification regulates the development of many metabolic processes and metabolic diseases. In this review, we summarized recent studies on the role of m6A modification in different metabolic processes and metabolic diseases. Additionally, we highlighted the potential m6A-targeted therapy for metabolic diseases, expecting to facilitate m6A-targeted strategies in the treatment of metabolic diseases.
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Affiliation(s)
| | | | | | - Qiushi Liao
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Yiyang Hu
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Chunli Gong
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Nannan Gao
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Huan Yang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Yufeng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Yang Chen
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
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3
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Zhao L, Guo J, Xu S, Duan M, Liu B, Zhao H, Wang Y, Liu H, Yang Z, Yuan H, Jiang X, Jiang X. Abnormal changes in metabolites caused by m 6A methylation modification: The leading factors that induce the formation of immunosuppressive tumor microenvironment and their promising potential for clinical application. J Adv Res 2024:S2090-1232(24)00159-0. [PMID: 38677545 DOI: 10.1016/j.jare.2024.04.016] [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: 02/18/2024] [Revised: 04/14/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) RNA methylation modifications have been widely implicated in the metabolic reprogramming of various cell types within the tumor microenvironment (TME) and are essential for meeting the demands of cellular growth and maintaining tissue homeostasis, enabling cells to adapt to the specific conditions of the TME. An increasing number of research studies have focused on the role of m6A modifications in glucose, amino acid and lipid metabolism, revealing their capacity to induce aberrant changes in metabolite levels. These changes may in turn trigger oncogenic signaling pathways, leading to substantial alterations within the TME. Notably, certain metabolites, including lactate, succinate, fumarate, 2-hydroxyglutarate (2-HG), glutamate, glutamine, methionine, S-adenosylmethionine, fatty acids and cholesterol, exhibit pronounced deviations from normal levels. These deviations not only foster tumorigenesis, proliferation and angiogenesis but also give rise to an immunosuppressive TME, thereby facilitating immune evasion by the tumor. AIM OF REVIEW The primary objective of this review is to comprehensively discuss the regulatory role of m6A modifications in the aforementioned metabolites and their potential impact on the development of an immunosuppressive TME through metabolic alterations. KEY SCIENTIFIC CONCEPTS OF REVIEW This review aims to elaborate on the intricate networks governed by the m6A-metabolite-TME axis and underscores its pivotal role in tumor progression. Furthermore, we delve into the potential implications of the m6A-metabolite-TME axis for the development of novel and targeted therapeutic strategies in cancer research.
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Affiliation(s)
- Liang Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; Department of Colorectal Anal Surgery, Shenyang Coloproctology Hospital, Shenyang 110002, China.
| | - Junchen Guo
- Department of Radiology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Shasha Xu
- Department of Gastroendoscopy, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Meiqi Duan
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Baiming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - He Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Yihan Wang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Haiyang Liu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Zhi Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Hexue Yuan
- Department of Colorectal Anal Surgery, Shenyang Coloproctology Hospital, Shenyang 110002, China.
| | - Xiaodi Jiang
- Department of Infectious Disease, Shengjing Hospital of China Medical University, Shenyang 110020, China.
| | - Xiaofeng Jiang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
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4
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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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5
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Lu Y, Wang S, Chi T, Zhao Y, Guo H, Wang H, Feng L. DNA damage repair-related gene signature for identifying the immune status and predicting the prognosis of hepatocellular carcinoma. Sci Rep 2023; 13:18978. [PMID: 37923899 PMCID: PMC10624694 DOI: 10.1038/s41598-023-45999-z] [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: 07/31/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
The heterogeneity of hepatocellular carcinoma (HCC) poses a challenge for accurate prognosis prediction. DNA damage repair genes (DDRGs) have an impact on a wide range of malignancies. However, the relevance of these genes in HCC prognosis has received little attention. In this study, we aimed to develop a prognostic signature to identify novel therapy options for HCC. We acquired mRNA expression profiles and clinical data for HCC patients from The Cancer Genome Atlas (TCGA) database. A polygenic prognostic model for HCC was constructed using selection operator Cox analysis and least absolute shrinkage. The model was validated using International Cancer Genome Consortium (ICGC) data. Overall survival (OS) between the high-risk and low-risk groups was compared using Kaplan‒Meier analysis. Independent predictors of OS were identified through both univariate and multivariate Cox analyses. To determine immune cell infiltration scores and activity in immune-related pathways, a single-sample gene set enrichment analysis was performed. The protein and mRNA expression levels of the prognostic genes between HCC and normal liver tissues were also examined by immunohistochemistry (IHC), immunofluorescence (IF) and quantitative real-time PCR (qRT-PCR). A novel ten-gene signature (CHD1L, HDAC1, KPNA2, MUTYH, PPP2R5B, NEIL3, POLR2L, RAD54B, RUVBL1 and SPP1) was established for HCC prognosis prediction. Patients in the high-risk group had worse OS than those in the low-risk group. Receiver operating characteristic curve analysis confirmed the predictive ability of this prognostic gene signature. Multivariate Cox analysis showed that the risk score was an independent predictor of OS. Functional analysis revealed a strong association with cell cycle and antigen binding pathways, and the risk score was highly correlated with tumor grade, tumor stage, and types of immune infiltrate. High expression levels of the prognostic genes were significantly correlated with increased sensitivity of cancer cells to antitumor drugs. IHC, IF and qRT-PCR all indicated that the prognostic genes were highly expressed in HCC relative to normal liver tissue, consistent with the results of bioinformatics analysis. Ten DDRGs were utilized to create a new signature for identifying the immunological state of HCC and predicting prognosis. In addition, blocking these genes could represent a promising treatment.
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Affiliation(s)
- Yongpan Lu
- Department of Plastic Surgery, Shandong University of Traditional Chinese Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Jingshi Road, Jinan, 250014, Shandong, China
| | - Sen Wang
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Tingting Chi
- Department of Acupuncture and Rehabilitation, The Affiliated Qingdao Hai Ci Hospital of Qingdao University (West Hospital Area), Qingdao, 266000, Shandong, China
| | - Yuli Zhao
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Huimin Guo
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Jining Medical College, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Haizheng Wang
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Li Feng
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China.
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6
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Zhao SS, Liu J, Wu QC, Zhou XL. Role of histone lactylation interference RNA m 6A modification and immune microenvironment homeostasis in pulmonary arterial hypertension. Front Cell Dev Biol 2023; 11:1268646. [PMID: 37771377 PMCID: PMC10522917 DOI: 10.3389/fcell.2023.1268646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a severe disease resulting from progressive increases in pulmonary vascular resistance and pulmonary vascular remodeling, ultimately leading to right ventricular failure and even death. Hypoxia, inflammation, immune reactions, and epigenetic modifications all play significant contributory roles in the mechanism of PAH. Increasingly, epigenetic changes and their modifying factors involved in reprogramming through regulation of methylation or the immune microenvironment have been identified. Among them, histone lactylation is a new post-translational modification (PTM), which provides a novel visual angle on the functional mechanism of lactate and provides a promising diagnosis and treatment method for PAH. This review detailed introduces the function of lactate as an important molecule in PAH, and the effects of lactylation on N6-methyladenosine (m6A) and immune cells. It provides a new perspective to further explore the development of lactate regulation of pulmonary hypertension through histone lactylation modification.
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Affiliation(s)
- Shuai-shuai Zhao
- Department of Cardiac Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Jinlong Liu
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Qi-cai Wu
- Department of Cardiac Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Xue-liang Zhou
- Department of Cardiac Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, China
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7
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Hu J, Lin H, Wang C, Su Q, Cao B. METTL14‑mediated RNA methylation in digestive system tumors. Int J Mol Med 2023; 52:86. [PMID: 37539726 PMCID: PMC10555478 DOI: 10.3892/ijmm.2023.5289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
N6‑methyladenosine (m6A) RNA methylation is one of the most common post‑transcriptional modification mechanism in eukaryotes. m6A is involved in almost all stages of the mRNA life cycle, specifically regulating its stability, splicing, export and translation. Methyltransferase‑like 14 (METTL14) is a particularly important m6A methylation 'writer' that can recognize RNA substrates. METTL14 has been documented to improve the activity and catalytic efficiency of METTL3. However, as individual proteins they can also regulate different biological processes. Malignancies in the digestive system are some of the most common malignancies found in humans, which are typically associated with poor prognoses with limited clinical solutions. METTL14‑mediated methylation has been implicated in both the potentiation and inhibition of digestive system tumor growth, cell invasion and metastasis, in addition to drug resistance. In the present review, the research progress and regulatory mechanisms of METTL14‑mediated methylation in digestive system malignancies were summarized. In addition, future research directions and the potential for its clinical application were examined.
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Affiliation(s)
- Jiexuan Hu
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Haishan Lin
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Cong Wang
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Qiang Su
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Bangwei Cao
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
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8
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Tűzesi Á, Hallal S, Satgunaseelan L, Buckland ME, Alexander KL. Understanding the Epitranscriptome for Avant-Garde Brain Tumour Diagnostics. Cancers (Basel) 2023; 15:cancers15041232. [PMID: 36831575 PMCID: PMC9954771 DOI: 10.3390/cancers15041232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
RNA modifications are diverse, dynamic, and reversible transcript alterations rapidly gaining attention due to their newly defined RNA regulatory roles in cellular pathways and pathogenic mechanisms. The exciting emerging field of 'epitranscriptomics' is predominantly centred on studying the most abundant mRNA modification, N6-methyladenine (m6A). The m6A mark, similar to many other RNA modifications, is strictly regulated by so-called 'writer', 'reader', and 'eraser' protein species. The abundance of genes coding for the expression of these regulator proteins and m6A levels shows great potential as diagnostic and predictive tools across several cancer fields. This review explores our current understanding of RNA modifications in glioma biology and the potential of epitranscriptomics to develop new diagnostic and predictive classification tools that can stratify these highly complex and heterogeneous brain tumours.
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Affiliation(s)
- Ágota Tűzesi
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Susannah Hallal
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Neurosurgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia
| | - Laveniya Satgunaseelan
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Michael E. Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Kimberley L. Alexander
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Neurosurgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia
- Correspondence:
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9
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Fang F, Wang P, Huang H, Ye M, Liu X, Li Q. m 6A RNA methylation regulator-based signature for prognostic prediction and its potential immunological role in uterine corpus endometrial carcinoma. BMC Cancer 2022; 22:1364. [PMID: 36581816 PMCID: PMC9801604 DOI: 10.1186/s12885-022-10490-x] [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: 07/07/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Uterine corpus endometrial carcinoma (UCEC) is the most common female pelvic malignancy worldwide. N6-methyladenosine (m6A) plays an important role in various cellular responses, especially in cancer progression. However, the correlation between prognostic UCEC and m6A RNA methylation regulators remains unclear. METHODS We used The Cancer Genome Atlas (TCGA) to provide a gene signature that could improve the prognostic evaluation of UCEC patients according to the distinct genetic trait of m6A RNA methylation regulators from a bioinformatics perspective. After comparing UCEC subgroups with different genetic profiles of m6A regulators, we identified 71 differentially expressed genes associated with overall survival (OS) and generated a nine-gene signature through least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Finally, we used in vitro and in vivo tumor cell experiments as well as the immune correlation analysis to verify the function of each gene in the proposed gene signature. RESULTS Time-dependent receiver operating characteristic (ROC) curves revealed that the proposed gene signature could predict the outcome of UCEC patients accurately. We found that CDKN2A mainly acted from the perspective of tumor cells, while COL4A4, PXDN, TIGIT, CHODL, LMO3, KCNJ12, L1CAM, and EPHB1 might play a role in UCEC from an immunological point of view. CONCLUSIONS From an epigenetics perspective, the m6A RNA methylation regulator-based gene signature can predict the prognosis of UCEC patients and immune therapeutic efficacy.
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Affiliation(s)
- Fang Fang
- grid.452929.10000 0004 8513 0241Department of Laboratory Medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China ,grid.452929.10000 0004 8513 0241Anhui Province Clinical Research Center for Critical Respiratory Medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China
| | - Peipei Wang
- grid.443626.10000 0004 1798 4069School of Medical Information, Wannan Medical College, Wuhu, 241001 China ,grid.443626.10000 0004 1798 4069Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, 241001 China
| | - Haoyu Huang
- grid.452929.10000 0004 8513 0241Department of Laboratory Medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China ,grid.452929.10000 0004 8513 0241Anhui Province Clinical Research Center for Critical Respiratory Medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China
| | - Mingquan Ye
- grid.443626.10000 0004 1798 4069School of Medical Information, Wannan Medical College, Wuhu, 241001 China ,grid.443626.10000 0004 1798 4069Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, 241001 China
| | - Xiaocen Liu
- grid.452929.10000 0004 8513 0241Department of Nuclear medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China
| | - Qingqing Li
- grid.443626.10000 0004 1798 4069School of Medical Information, Wannan Medical College, Wuhu, 241001 China ,grid.443626.10000 0004 1798 4069Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, 241001 China
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10
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Kuang Y, Cheng Y, Wang J, Li H, Cao X, Wang Y. KIAA1429
mediates epithelial mesenchymal transition in sorafenib‐resistant hepatocellular carcinoma through
m6A
methylation modification. Cancer Med 2022; 12:7222-7233. [PMID: 36420693 PMCID: PMC10067093 DOI: 10.1002/cam4.5432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a primary liver cancer with high mortality. The long-term use of sorafenib, a targeted drug for hepatocellular carcinoma, will lead to drug resistance, and patients are prone to cancer metastasis, the molecular mechanism of which is still unclear. METHODS In our study, we constructed a sorafenib-resistant hepatocellular carcinoma cell line (HepG2/Sora) and validated the resistance in vivo and in vitro. Transwell assays confirmed the invasion and migration abilities of cells. Colorimetric assays confirmed that the level of m6A methylation modification in cells. RT-qPCR and Western blot assays confirmed that the expression levels of KIAA1429 in HepG2/Sora cells and tissues. The EMT related proteins were detected by Western blot assay. RESULTS Transwell and Western blot assays confirmed that HepG2/Sora cells had higher invasion and migration abilities and showed EMT phenomena. Colorimetric assays confirmed that the level of m6A methylation modification was upregulated in HepG2/Sora cells. Transwell and Western blot assays confirmed that inhibiting m6A methylation in HepG2/Sora cells inhibited their invasion, migration ability and EMT phenomenon. RT-qPCR and Western blot assays confirmed that the expression levels of KIAA1429 in HepG2/Sora cells and tissues was increased. Silencing KIAA1429 in HepG2/Sora cells inhibited their invasion, migration ability and EMT phenomenon. Finally, we found that the medium supernatant of sorafenib-resistant HepG2/Sora cells induced vascular production of EA.hy926 cells, and silencing KIAA1429 inhibited this induction effect. CONCLUSION We suggest that KIAA1429 promotes sorafenib-resistant hepatocellular carcinoma invasion, migration and EMT by mediating m6A methylation. KIAA1429 with its mediated m6A methylation may be a key factor for sorafenib-resistant patients prone to cancer cell metastasis.
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Affiliation(s)
- Ye Kuang
- Yan'An Hospital Medical Laboratory Kunming China
| | - Yun Cheng
- Yan'An Hospital Medical Laboratory Kunming China
| | - Jia Wang
- Yan'An Hospital Medical Laboratory Kunming China
| | - Hongyan Li
- Yan'An Hospital Medical Laboratory Kunming China
| | | | - Yang Wang
- Yan'An Hospital Medical Laboratory Kunming China
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11
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Su Z, Xu L, Dai X, Zhu M, Chen X, Li Y, Li J, Ge R, Cheng B, Wang Y. Prognostic and clinicopathological value of m6A regulators in human cancers: a meta-analysis. Aging (Albany NY) 2022; 14:8818-8838. [DOI: 10.18632/aging.204371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Zhangci Su
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - Leyao Xu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - Xinning Dai
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - Mengyao Zhu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, P.R. China
| | - Xiaodan Chen
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - Yuanyuan Li
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - Jie Li
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - Ruihan Ge
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - Bin Cheng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - Yun Wang
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
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12
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Zhang C, Dai D, Zhang W, Yang W, Guo Y, Wei Q. Role of m6A RNA methylation in the development of hepatitis B virus-associated hepatocellular carcinoma. J Gastroenterol Hepatol 2022; 37:2039-2050. [PMID: 36066844 DOI: 10.1111/jgh.15999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/10/2022] [Accepted: 09/03/2022] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most common liver malignancy that can be developed from hepatitis B and cirrhosis. Many pathophysiological alterations, including hepatitis B virus (HBV) DNA integration, oxidative stress, cytokine release, telomerase homeostasis, mitochondrial damage, epigenetic modification, and tumor microenvironment, are involved in the biological process from hepatitis B to cirrhosis and HCC. N6-methyladenosine (m6A), as an epitranscriptomic modification of RNAs, can regulate the stability, splicing, degradation, transcription, and translation of downstream target RNAs in HBV and liver cancer cells. m6A regulators (writers, erasers, and readers) play an important role in the pathogenesis of HBV-associated HCC by regulating cell proliferation, apoptosis, migration, autophagy, differentiation, inflammation, angiogenesis, and tumor microenvironment. This review summarizes the current progress of m6A methylation in the molecular mechanisms, biological functions, and potential clinical implications of HBV-associated HCC.
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Affiliation(s)
- Cheng Zhang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China.,Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Dongjun Dai
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wangjian Zhang
- School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenjun Yang
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yinglu Guo
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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13
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Hou M. Exploring novel independent prognostic biomarkers for hepatocellular carcinoma based on TCGA and GEO databases. Medicine (Baltimore) 2022; 101:e31376. [PMID: 36316888 PMCID: PMC9622571 DOI: 10.1097/md.0000000000031376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) has become the fifth most common cancer globally, with the second-highest mortality rate and poor survival outcomes. In our research, we aimed to use The Cancer Genome Atlas and gene expression omnibus databases to identify potential genetic biomarkers to predict and improve the survival rate of HCC patients. METHODS In GSE60502, GSE76427, and GSE84402, we performed differential expression analysis to obtain differentially expressed genes (DEGs). In the The Cancer Genome Atlas database, the FPKM expression profile was subjected to weighted gene co-expression analysis to obtain modules closely related to HCC. We received common genes by intersecting the genes in the module with the differential genes. Then, we fused the common genes' expression profiles, survival time, and survival status for univariate, Least Absolute Shrinkage and Selection Operator, and multivariate COX regression analysis to obtain prognostic genes. Predictive genes were performed in K-M survival analysis and combined with clinical data for independent predictive analysis. RESULTS After differential expression analysis, GSE60502 obtained 1107 DEGs, GSE76427 obtained 424 DEGs, and GSE84402 obtained 1668 DEGs. Through weighted gene co-expression analysis analysis, we can see that the blue and brown modules were closely associated with HCC. After single and multivariate COX regression analysis, we found that suppressor of cytokine signaling 2 (SOCS2) and SERPINF2 were independent prognostic genes for HCC. After survival analysis, HCC patients with high expression of SOCS2 and SERPINF2 had a longer survival time. These 2 genes in normal liver tissues were higher than in HCC at the transcriptional level. CONCLUSION SOCS2 and SERPINF2 were new independent prognostic genes of HCC. So, they may provide new treatment methods and measures for diagnosing HCC.
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Affiliation(s)
- Miaomiao Hou
- Microimmune, 3201 Hospital, Hanzhong City, Shaanxi Province, China
- *Correspondence: Miaomiao Hou, Microimmune, 3201 Hospital, Hanzhong City, Shaanxi Province, China (e-mail: )
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14
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Hong J, Cai X. Construction of a Novel Oxidative Stress Response-Related Gene Signature for Predicting the Prognosis and Therapeutic Responses in Hepatocellular Carcinoma. DISEASE MARKERS 2022; 2022:6201987. [PMID: 36133439 PMCID: PMC9484914 DOI: 10.1155/2022/6201987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC) is a highly heterogeneous malignancy with poor outcomes, and the assessment of its prognosis as well as its response to therapy is still challenging. In this study, we aimed to construct an oxidative stress response-related genes-(OSRGs-) based gene signature for predicting prognosis and estimating treatment response in patients with HCC. We integrated the transcriptomic data and clinicopathological information of HCC patients from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. LASSO Cox regression analysis was utilized to establish an integrated multigene signature in the TCGA cohort, and its prediction performance was validated in the ICGC cohort. The CIBERSORT algorithm was employed to evaluate immune cell infiltration. The response rate to immune checkpoint inhibition (ICI) therapy was assessed using a TIDE platform. Drug activity data from the Cancer Genome Project and NCI-60 human cancer cell lines were used to predict sensitivity to chemotherapy. We successfully established a gene signature comprising G6PD, MT3, CBX2, CDKN2B, CCNA2, MAPT, EZH2, and SLC7A11. The risk score of each patient, which was determined by the multigene signature, was identified as an independent prognostic marker. The immune cell infiltration patterns, response rates to ICI therapy, and the estimated sensitivity of 89 chemotherapeutic drugs were associated with risk scores. Individual prognostic genes were also associated with susceptibility to various FDA-approved drugs. Our study indicates that a comprehensive transcriptomic analysis of OSRGs can provide a reliable molecular model to predict prognosis and therapeutic response in patients with HCC.
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Affiliation(s)
- Junjie Hong
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xiujun Cai
- Key Laboratory of Laparoscopic Technique Research of Zhejiang Province, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
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15
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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: 13] [Impact Index Per Article: 6.5] [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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16
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Shi B, Liu WW, Yang K, Jiang GM, Wang H. The role, mechanism, and application of RNA methyltransferase METTL14 in gastrointestinal cancer. Mol Cancer 2022; 21:163. [PMID: 35974338 PMCID: PMC9380308 DOI: 10.1186/s12943-022-01634-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Gastrointestinal cancer is the most common human malignancy characterized by high lethality and poor prognosis. Emerging evidences indicate that N6-methyladenosine (m6A), the most abundant post-transcriptional modification in eukaryotes, exerts important roles in regulating mRNA metabolism including stability, decay, splicing, transport, and translation. As the key component of the m6A methyltransferase complex, methyltransferase-like 14 (METTL14) catalyzes m6A methylation on mRNA or non-coding RNA to regulate gene expression and cell phenotypes. Dysregulation of METTL14 was deemed to be involved in various aspects of gastrointestinal cancer, such as tumorigenesis, progression, chemoresistance, and metastasis. Plenty of findings have opened up new avenues for exploring the therapeutic potential of gastrointestinal cancer targeting METTL14. In this review, we systematically summarize the recent advances regarding the biological functions of METTL14 in gastrointestinal cancer, discuss its potential clinical applications and propose the research forecast.
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Affiliation(s)
- Bin Shi
- Department of Anorectal Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Heifei, China
| | - Wei-Wei Liu
- School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ke Yang
- School of Clinical Medicine, Clinical College of Anhui Medical University, Hefei, China
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, China.
| | - Hao Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. .,Core Unit of National Clinical Research Center for Laboratory Medicine, Heifei, China.
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17
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Comprehensive Analysis of N6-Methyladenosine (m6A) Writers, Erasers, and Readers in Cervical Cancer. Int J Mol Sci 2022; 23:ijms23137165. [PMID: 35806168 PMCID: PMC9266832 DOI: 10.3390/ijms23137165] [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: 05/21/2022] [Revised: 06/17/2022] [Accepted: 06/25/2022] [Indexed: 01/09/2023] Open
Abstract
There is growing scientific evidence for the crucial role of post-transcriptional RNA modifications in carcinogenesis, progression, metastasis, and drug resistance across various cancer entities. N6-methyladenosine (m6A) is the most abundant type of RNA modification. m6A is coordinated by a dynamic interplay of ‘writers’ (METTL3, METTL4, METTL14, WTAP, KIAA1429), ‘erasers’ (FTO, ALKBH5), and ‘readers’ (HNRNPA2B1, HNRNPC, YTHDC1, YTHDC1, YTHDF1-3). In this study, we comprehensively examined protein and mRNA expression levels of m6A writers, readers, and erasers in two cervical cancer (CC) cohorts (UHB CC cohort, N = 118; TCGA CC cohort, N = 307) with regard to clinical outcomes. In the UHB CC cohort, high protein expression levels of METTL14 (p = 0.016), WTAP (p = 0.007), KIAA1439 (p < 0.001), ALKBH5 (p < 0.001), HNRNPC (p = 0.012), YTHDC1 (p < 0.001), and YTHDF3 (p = 0.004) were significantly associated with a shorter overall survival (OS). In the TCGA CC cohort, mRNA expression levels of METTL14 (p = 0.012), WTAP (p = 0.041), KIAA1429 (p = 0.016), and YTHDC1 (p = 0.026) showed prognostic values. However, after correction for multiple testing, statistical significance remained only for m6A protein expression levels (q < 0.1). Our study points towards dysregulated m6A modification in CC. Hence, m6A might serve as a promising prognostic biomarker and therapeutical target in CC.
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18
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Liu J, Zhang W, Wang J, Lv Z, Xia H, Zhang Z, Zhang Y, Wang J. Construction and validation of N6-methyladenosine long non-coding RNAs signature of prognostic value for early biochemical recurrence of prostate cancer. J Cancer Res Clin Oncol 2022; 149:1969-1983. [PMID: 35731271 DOI: 10.1007/s00432-022-04040-y] [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: 04/12/2022] [Accepted: 04/23/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Early biochemical recurrence (eBCR) indicated a high risk for potential recurrence and metastasis in prostate cancer. The N6-methyladenosine (m6A) methylation modification played an important role in prostate cancer progression. This study aimed to develop a m6A lncRNA signature to accurately predict eBCR in prostate cancer. METHODS Pearson correlation analysis was first conducted to explore m6A lncRNAs and univariate Cox regression analysis was further performed to identify m6A lncRNAs of prognostic roles for predicting eBCR in prostate cancer. The m6A lncRNA signature was constructed by least absolute shrinkage and selection operator analysis (LASSO) in training cohort and further validated in test cohort. Furthermore, half maximal inhibitory concentration (IC50) values were utilized to explore potential effective drugs for high-risk group in this study. RESULTS Five hundred and thirty-eighth m6A lncRNAs were searched out through Pearson correlation analysis and 25 out of 538 m6A lncRNAs were identified to pose prediction roles for eBCR in prostate cancers. An m6A lncRNA signature including 5 lncRNAs was successfully built in training cohort. The high-risk group derived from m6A lncRNA signature could efficiently predict eBCR occurrence in both training (p < 0.001) and test cohort (p = 0.002). ROC analysis also confirmed that lncRNA signature in this study posed more accurate prediction roles for eBCR occurrence when compared with PSA, TNM stages and Gleason scores. Drug sensitivity analysis further discovered that various drugs could be potentially utilized to treat high-risk samples in this study. CONCLUSIONS The m6A lncRNA signature in this study could be utilized to efficiently predict eBCR occurrence, various clinical characteristic and immune microenvironment for prostate cancer.
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Affiliation(s)
- Jingchao Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730, China
| | - Wei Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730, China
| | - Jiawen Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730, China
| | - Zhengtong Lv
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730, China
| | - Haoran Xia
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730, China
| | - Zhipeng Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730, China
| | - Yaoguang Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730, China.
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730, China.
| | - Jianye Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 DaHua Road, Dong Dan, Beijing, 100730, China.
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan SANTIAO, Beijing, 100730, China.
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19
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Ralser DJ, Condic M, Klümper N, Ellinger J, Staerk C, Egger EK, Kristiansen G, Mustea A, Thiesler T. Comprehensive immunohistochemical analysis of N6-methyladenosine (m6A) writers, erasers, and readers in endometrial cancer. J Cancer Res Clin Oncol 2022; 149:2417-2424. [PMID: 35731272 PMCID: PMC10129960 DOI: 10.1007/s00432-022-04083-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/20/2022] [Indexed: 10/17/2022]
Abstract
PURPOSE N6-methyladenosine (m6A) is the most frequent type of messenger RNA (mRNA) modification and is implicated in diverse physiological processes. The procedure of m6A RNA modification is regulated by a dynamic interaction of writers (METTL3, METTL4, METTL14, WTAP, KIAA1429), erasers (FTO, ALKBH5), and readers (HNRNPA2B1, HNRNPC, YTHDC1, YTHDC1, YTHDF1-3). In the oncological context, alterations in m6A were identified to be critically involved in tumorigenesis, proliferation, angiogenesis, and drug resistance across diverse cancer entities including endometrial cancer (EC). METHODS In this study, we comprehensively examined the protein expression of m6A writers, readers and erasers by immunohistochemical staining in a cohort of N = 65 EC patients. Protein expression data were analyzed with regard to clinical outcomes. RESULTS We identified enhanced protein expression levels of METTL3, METTL14, FTO, HNRNPA2B1, and HNRNPC, respectively to be of prognostic value and linked to a shortened overall survival in EC. CONCLUSION Overall, our study points toward dysregulated m6A modification in EC and its possibility to serve as a promising prognostic biomarker.
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Affiliation(s)
- Damian J Ralser
- Department of Gynecology and Gynecological Oncology, University Hospital Bonn, Bonn, Germany.
| | - Mateja Condic
- Department of Gynecology and Gynecological Oncology, University Hospital Bonn, Bonn, Germany
| | - Niklas Klümper
- Department of Urology and Pediatric Urology, University Hospital Bonn, Bonn, Germany
| | - Jörg Ellinger
- Department of Urology and Pediatric Urology, University Hospital Bonn, Bonn, Germany
| | - Christian Staerk
- Department of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Eva K Egger
- Department of Gynecology and Gynecological Oncology, University Hospital Bonn, Bonn, Germany
| | | | - Alexander Mustea
- Department of Gynecology and Gynecological Oncology, University Hospital Bonn, Bonn, Germany
| | - Thore Thiesler
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
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20
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Xue MQ, Wang YL, Wang JC, Wang XD, Wang XJ, Zhang YQ. Comprehensive analysis of the PD-L1 and immune infiltrates of N6-methyladenosine related long non-coding RNAs in bladder cancer. Sci Rep 2022; 12:10082. [PMID: 35710698 PMCID: PMC9203575 DOI: 10.1038/s41598-022-14097-x] [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: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
Bladder cancer (BLCA) is one of the most frequent genitourinary cancers, with a high rate of morbidity and mortality. The connection of m6A-related lncRNAs with PD-L1 and tumor immune microenvironment (TIME) in BLCA prognosis was extensively investigated in this study, which could suggest novel therapeutic targets for further investigation. 30 m6A-associated lncRNAs with predictive values from the TCGA data set were identified with co-expression analysis. Cluster2 was correlated with a poor prognosis, upregulated PD-L1 expression, and higher immune ratings. Cluster2 had larger amounts of resting CD4 memory-activated T cells, M2 macrophages, neutrophils, and NK cells infiltration. "CHEMOKINE SIGNALING PATHWAY" was the most significantly enriched signaling pathway according to GSEA, which may play an important role in the different immune cell infiltrates between cluster1/2. The risk model for m6A-related lncRNAs could be employed in a prognostic model to predict BLCA prognosis, regardless of other clinical features. Collectively, m6A-related lncRNAs were linked to PD-L1 and TIME, which would dynamically affect the number of tumor-infiltrating immune cells. m6A-related lncRNAs may be key mediators of PD-L1 expression and immune cells infiltration and may strongly affect the TIME of BLCA.
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Affiliation(s)
- M Q Xue
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Y L Wang
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Henan Bioengineering Technology Reseach Center, Zhengzhou, 450010, People's Republic of China.
| | - J C Wang
- Henan Bioengineering Technology Reseach Center, Zhengzhou, 450010, People's Republic of China
| | - X D Wang
- Henan General Hospital, Zhengzhou, 450002, People's Republic of China
| | - X J Wang
- Henan General Hospital, Zhengzhou, 450002, People's Republic of China
| | - Y Q Zhang
- Zhengzhou Technical College, Zhengzhou, 450010, People's Republic of China
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21
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Ren SH, Qin YF, Qin H, Wang HD, Li GM, Zhu YL, Sun CL, Shao B, Zhang JY, Hao JP, Wang H. N6-Methyladenine-Related Signature for Immune Microenvironment and Response to Immunotherapy in Hepatocellular Carcinoma. Int J Gen Med 2022; 15:3525-3540. [PMID: 35386863 PMCID: PMC8978579 DOI: 10.2147/ijgm.s351815] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/21/2022] [Indexed: 12/31/2022] Open
Abstract
Background The prognostic value of m6A-related genes in hepatocellular carcinoma (HCC) and its correlation with the immune microenvironment still requires further investigation. Methods Consensus clustering by m6A related genes was used to classify 374 patients with HCC from The Cancer Genome Atlas (TCGA) database. Then we performed the least absolute shrinkage and selection operator (LASSO) to construct the m6A related genes model. The International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) datasets were used to verify and evaluate the model. ESTIMATE, CIBERSORTx, the expression levels of immune checkpoint genes, and TIDE were used to investigate the tumor microenvironment (TME) and the response to immunotherapy. Gene set enrichment analyses (GSEA), tumor-associated macrophages (TAMs), and gene-drug sensitivity were also analyzed. Results By expression value and regression coefficient of five m6A related genes, we constructed the risk score of each patient. The patients with a higher risk score had a considerably poorer prognosis in the primary and validated cohort. For further discussing TME and the response to immunotherapy, we divided the entire set into two groups based on the risk score. Our findings implied that the tumor-infiltrating lymphocytes (TILs) were proportional to the risk scores, which seemed to contradict that patients with higher scores had a poor prognosis. Further, we found that the high-risk group had higher expression of PD-L1, CTLA-4, and PDCD1, indicating immune dysfunction, which may be a fundamental reason for poor prognosis. This was further reinforced by the fact that the low-risk group responded better than the high-risk group to monotherapy and combination therapy. Conclusion The m6A related risk score is a new independent prognostic factor that correlates with immunotherapy response. It can provide a new therapeutic strategy for improving individual immunotherapy in HCC.
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Affiliation(s)
- Shao-Hua Ren
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Ya-Fei Qin
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Hong Qin
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Hong-da Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Guang-Ming Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Yang-Lin Zhu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Cheng-Lu Sun
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Bo Shao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Jing-Yi Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Jing-Peng Hao
- Department of Anorectal Surgery, The Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Hao Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
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Zhao Y, Song Q, Xu F, Zhou Y, Zuo X, Zhang Z. Pyroptosis-Related Risk Signature Exhibits Distinct Prognostic, Immune, and Therapeutic Landscapes in Hepatocellular Carcinoma. Front Genet 2022; 13:823443. [PMID: 35368686 PMCID: PMC8965507 DOI: 10.3389/fgene.2022.823443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/03/2022] [Indexed: 01/26/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a common abdominal cancer. The existing therapeutic approaches often fail to achieve satisfactory results. Pyroptosis, an inflammatory form of programmed cell death, provides new ideas for anticancer treatment. However, the roles of pyroptosis-related (PR) genes (PRGs) in HCC remain elusive. Methods: Differentially expressed genes (DEGs) (n = 22) were screened out using TCGA and GTEx databases. A novel PR risk signature was constructed through Lasso regression analysis. Its prognostic value was evaluated through a series of survival analyses and was tested in ICGC and GSE14520 cohorts. CIBERSORT, ssGSEA, and ESTIMATE methods were employed to determine the effects of the PR risk score on the tumor immune microenvironment (TIM). The TIDE scoring system, IMvigor210 cohort, GSE109211 dataset, and GSDC database were applied to explore the associations of the PR risk score with therapeutic effects. The biofunctions of WNK1 in hepatocellular cancer (HC) cells were confirmed through qPCR, colony formation, and Transwell assays. Results: Overall, 22 of 45 PRGs (48.9%) were abnormally expressed in HCC samples. Then, a PR risk signature consisting of eight PRGs was constructed. A high PR risk score led to an unfavorable prognosis. The PR risk score was identified as an independent prognostic factor of HCC and could increase the decision-making benefit of the traditional TNM model. In addition, we established a nomogram containing the clinical stage and PR risk score to predict the survival rates of HCC patients. The prognostic value of the PR model was successfully validated in ICGC and GSE14520 cohorts. Moreover, high PR risk conferred the decreased infiltration level of CD8+ T cells and weakened the activities of "cytolytic activity" pathways. As for therapeutic correlation, a high PR risk score seemed to imply a poor efficacy of PD-1/L1 inhibitors and sorafenib. Finally, the overexpression of WNK1 could promote the proliferation, migration, and invasion of HC cells. Conclusions: The PR risk score was closely related to the prognosis, antitumor immune process, therapeutic outcomes, and malignant progression of HCC. WNK1, the core regulator of pyroptosis, possesses pro-oncogenic abilities, showing promise as a novel treatment target.
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Affiliation(s)
- Yidi Zhao
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qingya Song
- Xi'an Medical Emergency Center, Xi'an, China
| | - Fangshi Xu
- Department of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Yang Zhou
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoli Zuo
- Department of Orthopedics, Second Affiliated Hospital of Xi'a Jiaotong University, Xi'an, China
| | - Zhengliang Zhang
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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23
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Li W, Gao Y, Jin X, Wang H, Lan T, Wei M, Yan W, Wang G, Li Z, Zhao Z, Jiang X. Comprehensive analysis of N6-methylandenosine regulators and m6A-related RNAs as prognosis factors in colorectal cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:598-610. [PMID: 35070494 PMCID: PMC8753275 DOI: 10.1016/j.omtn.2021.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022]
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and has been a leading cause of cancer-related death worldwide in recent years. N6-methyladenosine (m6A) methylation is the most abundant epigenetic modification of various types of RNAs, and it plays a vital role in promoting cancer development. Here, we obtained SNV and transcriptome data of CRC from The Cancer Genome Atlas (TCGA). We demonstrated that most m6A methylation regulators were aberrantly expressed in individuals with CRC. The abnormal expression of m6A regulators was caused by their different copy number variation (CNV) patterns, and alteration of m6A regulators was significantly correlated with prognosis and tumor stage. By using weighted coexpression network analysis (WGCNA), we identified m6A-related long noncoding RNAs (lncRNAs) and mRNAs; then we used least absolute shrinkage and selection operator (LASSO) Cox regression analysis to construct m6A-related lncRNA and mRNA prognostic signatures in the TCGA dataset. Furthermore, a nomogram with clinicopathological features, lncRNA risk scores, and mRNA risk scores was established, which showed a strong ability to forecast the overall survival of the individuals with CRC in training and testing sets. In conclusion, m6A methylation regulators played a vital role in affecting the prognosis of subjects with CRC, and m6A-related lncRNAs and mRNAs revealed underlying mechanisms in CRC tumorigenesis and progression.
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Affiliation(s)
- Wei Li
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yingchao Gao
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaojing Jin
- Department of Emergency, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Haobo Wang
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Tianhao Lan
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ming Wei
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Weitao Yan
- Department of Breast Surgery, The First People's Hospital of Qinhuangdao, Hebei, China
| | - Guiqi Wang
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhongxin Li
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zengren Zhao
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xia Jiang
- Department of General Surgery, Hebei Key Laboratory of Colorectal Cancer Precision Diagnosis and Treatment, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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24
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Mobet Y, Liu X, Liu T, Yu J, Yi P. Interplay Between m6A RNA Methylation and Regulation of Metabolism in Cancer. Front Cell Dev Biol 2022; 10:813581. [PMID: 35186927 PMCID: PMC8851358 DOI: 10.3389/fcell.2022.813581] [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: 11/12/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Methylation of adenosine in RNA to N6-methyladenosine (m6A) is widespread in eukaryotic cells with his integral RNA regulation. This dynamic process is regulated by methylases (editors/writers), demethylases (remover/erasers), and proteins that recognize methylation (effectors/readers). It is now evident that m6A is involved in the proliferation and metastasis of cancer cells, for instance, altering cancer cell metabolism. Thus, determining how m6A dysregulates metabolic pathways could provide potential targets for cancer therapy or early diagnosis. This review focuses on the link between the m6A modification and the reprogramming of metabolism in cancer. We hypothesize that m6A modification could dysregulate the expression of glucose, lipid, amino acid metabolism, and other metabolites or building blocks of cells by adaptation to the hypoxic tumor microenvironment, an increase in glycolysis, mitochondrial dysfunction, and abnormal expression of metabolic enzymes, metabolic receptors, transcription factors as well as oncogenic signaling pathways in both hematological malignancies and solid tumors. These metabolism abnormalities caused by m6A’s modification may affect the metabolic reprogramming of cancer cells and then increase cell proliferation, tumor initiation, and metastasis. We conclude that focusing on m6A could provide new directions in searching for novel therapeutic and diagnostic targets for the early detection and treatment of many cancers.
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Affiliation(s)
- Youchaou Mobet
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Laboratory of Biochemistry, Faculty of Science, University of Douala, Douala, Cameroon
| | - Xiaoyi Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Tao Liu, ; Jianhua Yu, ; Ping Yi,
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA, United States
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Los Angeles, CA, United States
- Comprehensive Cancer Center, City of Hope, Los Angeles, CA, United States
- *Correspondence: Tao Liu, ; Jianhua Yu, ; Ping Yi,
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Tao Liu, ; Jianhua Yu, ; Ping Yi,
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25
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Guan Q, Lin H, Miao L, Guo H, Chen Y, Zhuo Z, He J. Functions, mechanisms, and therapeutic implications of METTL14 in human cancer. J Hematol Oncol 2022; 15:13. [PMID: 35115038 PMCID: PMC8812173 DOI: 10.1186/s13045-022-01231-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 02/06/2023] Open
Abstract
RNA modification plays a crucial role in many biological functions, and its abnormal regulation is associated with the progression of cancer. Among them, N6-methyladenine (m6A) is the most abundant RNA modification. Methyltransferase-like 14 (METTL14) is the central component of the m6A methylated transferase complex, which is involved in the dynamic reversible process of m6A modification. METTL14 acts as both an oncogene and tumor suppressor gene to regulate the occurrence and development of various cancers. The abnormal m6A level induced by METTL14 is related to tumorigenesis, proliferation, metastasis, and invasion. To date, the molecular mechanism of METTL14 in various malignant tumors has not been fully studied. In this paper, we systematically summarize the latest research progress on METTL14 as a new biomarker for cancer diagnosis and its biological function in human tumors and discuss its potential clinical application. This study aims to provide new ideas for targeted therapy and improved prognoses in cancer.
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Affiliation(s)
- Qian Guan
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Huiran Lin
- Faculty of Medicine, Macau University of Science and Technology, Macau, 999078, China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Huiqin Guo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Yongping Chen
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, 510623, Guangdong, China.
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, 510623, Guangdong, China.
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26
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Advances in the functional roles of N6-methyladenosine modification in cancer progression: mechanisms and clinical implications. Mol Biol Rep 2022; 49:4929-4941. [PMID: 35025029 DOI: 10.1007/s11033-022-07126-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
Abstract
N6-methyladenosine (m6A), the methylation targeting the N6 position of adenosine, is the most common internal modification of mRNA in eukaryotes. Considering the roles of m6A in regulating gene expression, the investigation of m6A roles in the biological processes including cell renewal, differentiation, apoptosis, and invasion of cancer cells has become a hot research topic. There are three kinds of protein involved in m6A regulation. The methyltransferases and demethylases cooperatively regulate the m6A levels, while the m6A reading proteins recognize the m6A sites and mediate multiple m6A-dependent biological functions including mRNA splicing, transfer, translation, and degradation. At present, a large number of studies have found that the changes of m6A levels in tumor cells play a very important role in the occurrence and development of tumors, as well as metastasis and invasion of tumor cells. This review summarizes the different roles of m6A modification in the occurrence and development of various cancers, and discusses the possibility of choosing the m6A related proteins as potential therapeutic targets.
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27
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Zhu XL, Li Q, Shen J, Shan L, Zuo ED, Cheng X. Use of 6 m6A-relevant lncRNA genes as prognostic markers of primary liver hepatocellular carcinoma based on TCGA database. Transl Cancer Res 2021; 10:5337-5351. [PMID: 35116381 PMCID: PMC8797289 DOI: 10.21037/tcr-21-2440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is diagnosed at the middle and advanced stages, negating radical treatment. Identifying specific and effective prognostic HCC biomarkers is important and can facilitate the discovery of potential therapeutic targets. N6-methyladenosine (m6A) and long non-coding RNAs (lncRNAs) are associated with the development of multiple tumors. The role of m6A-relevant lncRNAs in the initiation and progression of HCC is unclear. The aim of the present study was to investigate the expression of m6A-relevant lncRNAs in HCC and to identify new prognostic markers of the disease. METHODS Gene expression and clinical data were retrieved from The Cancer Genome Atlas database. m6A-relevant lncRNAs were identified by co-expression analysis and were screened by univariate Cox regression analysis. Different HCC patient clusters were established via consensus clustering. Gene set enrichment analysis (GSEA) was used to determine the cluster enrichment pathways. A risk score model was constructed, and Kaplan-Meier analysis of the overall survival (OS) between cluster 1 (high risk) and cluster 2 (low risk) was performed. Relationships between the clusters, risk scores, and clinicopathological characteristics were clarified. RESULTS Of the 1,852 m6A-relevant lncRNAs identified, 68 had prognostic relevance. The pathological grade, American Joint Committee on Cancer stage, and T stage of cluster 1 were significantly more advanced than those of cluster 2. Based on GSEA, mitotic spindle, G2M_CHECKPOINT, glycolysis, the phosphoinositide 3-kinase (PI3K) protein kinase B (AKT) mammalian target of rapamycin (mTOR) pathway, and DNA repair were more enriched in cluster 1. Six key m6A-relevant lncRNAs were selected to build a risk score model predicting the prognosis of HCC. The OS of patients in the high-risk group was shorter than that of patients in the low-risk group. Risk score was an independent prognostic factor of HCC patients. CONCLUSIONS The findings indicated that m6A-relevant lncRNAs may be important in the progression of HCC. The risk score model based on the 6 key m6A-relevant lncRNAs can accurately predict the prognosis of patients with HCC.
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Affiliation(s)
- Xiao-Li Zhu
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
| | - Qing Li
- Department of Gastroenterology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
| | - Jie Shen
- Department of Administrative Office, Jiangsu University Affiliated Kunshan Hospital (The First People’s Hospital of Kunshan), Kunshan, China
| | - Li Shan
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
| | - Er-Dong Zuo
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
| | - Xu Cheng
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
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28
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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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29
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Zhou W, Wang X, Chang J, Cheng C, Miao C. The molecular structure and biological functions of RNA methylation, with special emphasis on the roles of RNA methylation in autoimmune diseases. Crit Rev Clin Lab Sci 2021; 59:203-218. [PMID: 34775884 DOI: 10.1080/10408363.2021.2002256] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic vasculitis are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is complex. RNA methylation is known to play a key role in disease progression as it regulates almost all aspects of RNA processing, including RNA nuclear export, translation, splicing, and noncoding RNA processing. This review summarizes the mechanisms, molecular structures of RNA methylations and their roles in biological functions. Similar to the roles of RNA methylation in cancers, RNA methylation in RA and SLE involves "writers" that deposit methyl groups to form N6-methyladenosine (m6A) and 5-methylcytosine (m5C), "erasers" that remove these modifications, and "readers" that further affect mRNA splicing, export, translation, and degradation. Recent advances in detection methods have identified N1-methyladenosine (m1A), N6,2-O-dimethyladenosine (m6Am), and 7-methylguanosine (m7G) RNA modifications, and their roles in RA and SLE need to be further studied. The relationship between RNA methylation and other autoimmune diseases has not been reported, and the roles and mechanisms of RNA modifications in these diseases need to be explored in the future.
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Affiliation(s)
- Wanwan Zhou
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiao Wang
- Department of Clinical Nursing, School of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jun Chang
- Department of Orthopaedics, Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Institute of Prevention and Treatment of Rheumatoid Arthritis, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Department of Pharmacy, School of Life and Health Sciences, Anhui University of Science and Technology, Fengyang, Anhui Province, China
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30
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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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Zhou W, Wang C, Chang J, Huang Y, Xue Q, Miao C, Wu P. RNA Methylations in Cardiovascular Diseases, Molecular Structure, Biological Functions and Regulatory Roles in Cardiovascular Diseases. Front Pharmacol 2021; 12:722728. [PMID: 34489709 PMCID: PMC8417252 DOI: 10.3389/fphar.2021.722728] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 01/05/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality in the world. Despite considerable progress in the diagnosis, treatment and prognosis of CVDs, new diagnostic biomarkers and new therapeutic measures are urgently needed to reduce the mortality of CVDs and improve the therapeutic effect. RNA methylations regulate almost all aspects of RNA processing, such as RNA nuclear export, translation, splicing and non-coding RNA processing. In view of the importance of RNA methylations in the pathogenesis of diseases, this work reviews the molecular structures, biological functions of five kinds of RNA methylations (m6A, m5C, m1a, m6am and m7G) and their effects on CVDs, including pulmonary hypertension, hypertension, vascular calcification, cardiac hypertrophy, heart failure. In CVDs, m6A “writers” catalyze the installation of m6A on RNAs, while “erasers” remove these modifications. Finally, the “readers” of m6A further influence the mRNA splicing, nuclear export, translation and degradation. M5C, m1A, m6Am and m7G are new types of RNA methylations, their roles in CVDs need to be further explored. RNA methylations have become a new research hotspot and the roles in CVDs is gradually emerging, the review of the molecular characteristics, biological functions and effects of RNA methylation on CVDs will contribute to the elucidation of the pathological mechanisms of CVDs and the discovery of new diagnostic markers and therapeutic targets of CVDs.
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Affiliation(s)
- Wanwan Zhou
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Changhui Wang
- Department of Cardiology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Jun Chang
- Department of Orthopaedics, The Fourth Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Yurong Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Qiuyun Xue
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China.,Anhui Provincial Key Laboratory of Applied Basis and Development of Modern Internal Medicine of Traditional Chinese Medicine, The First Affiliated Hospital, Anhui University of Chinese Medicine, Hefei, China
| | - Peng Wu
- Department of Anatomy, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
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Qin S, Mao Y, Chen X, Xiao J, Qin Y, Zhao L. The functional roles, cross-talk and clinical implications of m6A modification and circRNA in hepatocellular carcinoma. Int J Biol Sci 2021; 17:3059-3079. [PMID: 34421350 PMCID: PMC8375232 DOI: 10.7150/ijbs.62767] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. HCC has high rates of death and recurrence, as well as very low survival rates. N6-methyladenosine (m6A) is the most abundant modification in eukaryotic RNAs, and circRNAs are a class of circular noncoding RNAs that are generated by back-splicing and they modulate multiple functions in a variety of cellular processes. Although the carcinogenesis of HCC is complex, emerging evidence has indicated that m6A modification and circRNA play vital roles in HCC development and progression. However, the underlying mechanisms governing HCC, their cross-talk, and clinical implications have not been fully elucidated. Therefore, in this paper, we elucidated the biological functions and molecular mechanisms of m6A modification in the carcinogenesis of HCC by illustrating three different regulatory factors ("writer", "eraser", and "reader") of the m6A modification process. Additionally, we dissected the functional roles of circRNAs in various malignant behaviors of HCC, thereby contributing to HCC initiation, progression and relapse. Furthermore, we demonstrated the cross-talk and interplay between m6A modification and circRNA by revealing the effects of the collaboration of circRNA and m6A modification on HCC progression. Finally, we proposed the clinical potential and implications of m6A modifiers and circRNAs as diagnostic biomarkers and therapeutic targets for HCC diagnosis, treatment and prognosis evaluation.
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Affiliation(s)
- Sha Qin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China; and Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xue Chen
- Early Clinical Trial Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Juxiong Xiao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Qin
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China; and Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Kosvyra A, Ntzioni E, Chouvarda I. Network analysis with biological data of cancer patients: A scoping review. J Biomed Inform 2021; 120:103873. [PMID: 34298154 DOI: 10.1016/j.jbi.2021.103873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/30/2021] [Accepted: 07/18/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND & OBJECTIVE Network Analysis (NA) is a mathematical method that allows exploring relations between units and representing them as a graph. Although NA was initially related to social sciences, the past two decades was introduced in Bioinformatics. The recent growth of the networks' use in biological data analysis reveals the need to further investigate this area. In this work, we attempt to identify the use of NA with biological data, and specifically: (a) what types of data are used and whether they are integrated or not, (b) what is the purpose of this analysis, predictive or descriptive, and (c) the outcome of such analyses, specifically in cancer diseases. METHODS & MATERIALS The literature review was conducted on two databases, PubMed & IEEE, and was restricted to journal articles of the last decade (January 2010 - December 2019). At a first level, all articles were screened by title and abstract, and at a second level the screening was conducted by reading the full text article, following the predefined inclusion & exclusion criteria leading to 131 articles of interest. A table was created with the information of interest and was used for the classification of the articles. The articles were initially classified to analysis studies and studies that propose a new algorithm or methodology. Each one of these categories was further screened by the following clustering criteria: (a) data used, (b) study purpose, (c) study outcome. Specifically for the studies proposing a new algorithm, the novelty presented in each one was detected. RESULTS & Conclusions: In the past five years researchers are focusing on creating new algorithms and methodologies to enhance this field. The articles' classification revealed that only 25% of the analyses are integrating multi-omics data, although 50% of the new algorithms developed follow this integrative direction. Moreover, only 20% of the analyses and 10% of the newly developed methodologies have a predictive purpose. Regarding the result of the works reviewed, 75% of the studies focus on identifying, prognostic or not, gene signatures. Concluding, this review revealed the need for deploying predictive and multi-omics integrative algorithms and methodologies that can be used to enhance cancer diagnosis, prognosis and treatment.
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Affiliation(s)
- A Kosvyra
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - E Ntzioni
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Chouvarda
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Zhang P, Liu G, Lu L. N6-Methylandenosine-Related lncRNA Signature Is a Novel Biomarkers of Prognosis and Immune Response in Colon Adenocarcinoma Patients. Front Cell Dev Biol 2021; 9:703629. [PMID: 34336856 PMCID: PMC8321625 DOI: 10.3389/fcell.2021.703629] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is the most common type of colon cancer. To date, however, the prognostic values of m6A RNA methylation-related long non-coding RNAs (lncRNAs) in COAD are largely unknown. Materials and Methods The m6A-related lncRNAs were identified from The Cancer Genome Atlas (TCGA) data set. Univariate and multivariate Cox regression analyses were performed to explore the prognostic m6A-related lncRNAs. Consistent clustering analysis was performed to classify the COAD patients into different subgroups based on the expression of m6A-related lncRNAs. The potential biological functions as well as differences in the stemness index and tumor immune microenvironment between different subgroups were analyzed. The prognostic m6A-related lncRNAs were used to establish an m6A-related lncRNA risk model to predict prognosis and survival status. Results We identified 31 m6A-associated lncRNAs with prognostic values from the TCGA data set. Based on the expression of prognostic m6A-associated lncRNAs, TCGA-COAD patients were classified into three clusters using consistent clustering analysis. There was a low correlation of tumor stemness between the three clusters but a significant correlation with the tumor immune microenvironment as well as the tumor mutational load. Thirty-one prognostic-related m6A-associated lncRNAs were used to construct a risk model, which was further determined by survival analysis, receiver operating characteristic (ROC) curve, and univariate and multifactor Cox analysis. The m6A-related risk model demonstrates good performance in predicting prognosis and survival status. The model-based high-risk group exhibited poorer overall survival (OS) compared with the low-risk group. Conclusion In this study, we construct a risk model that consists of 31 m6A-related lncRNAs with independent prognostic values in COAD. Our study shows the critical roles of these 31 m6A-related lncRNAs in the tumor immune microenvironment, indicating the prospect of informing prognostic stratification and the development of immunotherapeutic strategies for COAD patients.
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Affiliation(s)
- Peiling Zhang
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Guolong Liu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lin Lu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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Huang J, Shao Y, Gu W. Function and clinical significance of N6-methyladenosine in digestive system tumours. Exp Hematol Oncol 2021; 10:40. [PMID: 34246319 PMCID: PMC8272376 DOI: 10.1186/s40164-021-00234-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/03/2021] [Indexed: 12/21/2022] Open
Abstract
RNA modification, like DNA methylation, histone modification, non-coding RNA modification and chromatin rearrangement, plays an important role in tumours. N6-methyladenosine (m6A) is the most abundant RNA modification in cells, and it regulates RNA transcription, processing, splicing, degradation, and translation. m6A-associated proteins have been used as new biomarkers and therapeutic targets for tumour prediction and monitoring. There are three main types of proteins involved in m6A methylation: methyltransferases (METTL3, METTL14, WTAP, RBM15, ZC3H13 and KIAA1429), demethylases (FTO, ALKBH5 and ALKBH3) and RNA-binding proteins (YTHDF1-3, YTHDC1-2, IGF2BPs and HNRNPs). This article reviews the origins, characteristics and functions of m6A and its relationship with digestive system tumours based on recent research. The expression of m6A regulators can be used as an evaluation indicator of tumour growth and progression and as a prognostic indicator. In-depth research on m6A methylation in digestive system tumours may provide new directions for clinical prediction and further treatment.
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Affiliation(s)
- Junchao Huang
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
| | - Yingjie Shao
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
| | - Wendong Gu
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
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Lin Y, Yao Y, Wang Y, Wang L, Cui H. PD-L1 and Immune Infiltration of m 6A RNA Methylation Regulators and Its miRNA Regulators in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5516100. [PMID: 34055974 PMCID: PMC8147529 DOI: 10.1155/2021/5516100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/01/2021] [Indexed: 01/27/2023]
Abstract
BACKGROUND The aim of this study was to systematically evaluate the relationship between the expression of m6A RNA methylation regulators and prognosis in HCC. METHODS We compared the expression of m6A methylation modulators and PD-L1 between HCC and normal in TCGA database. HCC samples were divided into two subtypes by consensus clustering of data from m6A RNA methylation regulators. The differences in PD-L1, immune infiltration, and prognosis between the two subtypes were further compared. The LASSO regression was used to build a risk score for m6A modulators. In addition, we identified miRNAs that regulate m6A regulators. RESULTS We found that fourteen m6A regulatory genes were significantly differentially expressed between HCC and normal. HCC samples were divided into two clusters. Of these, there are higher PD-L1 expression and poorer overall survival (OS) in cluster 1. There was a significant difference in immune cell infiltration between cluster 1 and cluster 2. Through the LASSO model, we obtained 12 m6A methylation regulators to construct a prognostic risk score. Compared with patients with a high-risk score, patients with a low-risk score had upregulated PD-L1 expression and worse prognosis. There was a significant correlation between risk score and tumor-infiltrating immune cells. Finally, we found that miR-142 may be the important regulator for m6A RNA methylation in HCC. CONCLUSION Our results suggest that m6A RNA methylation modulators may affect the prognosis through PD-L1 and immune cell infiltration in HCC patients. In addition, the two clusters may be beneficial for prognostic stratification and improving immunotherapeutic efficacy.
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Affiliation(s)
- Yingxue Lin
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Yinhui Yao
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Ying Wang
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Lingdi Wang
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Haipeng Cui
- Department of Pathophysiology, Chengde Medical University, Anyuan Road, Shuangqiao District, Chengde, Hebei, China
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Lin Z, Xu Q, Miao D, Yu F. An Inflammatory Response-Related Gene Signature Can Impact the Immune Status and Predict the Prognosis of Hepatocellular Carcinoma. Front Oncol 2021; 11:644416. [PMID: 33828988 PMCID: PMC8019928 DOI: 10.3389/fonc.2021.644416] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, which makes the prognostic prediction challenging. As part of the active cross-talk between the tumor and the host, inflammatory response in the tumor or its microenvironment could affect prognosis. However, the prognostic value of inflammatory response-related genes in HCC remains to be further elucidated. Methods In this study, the mRNA expression profiles and corresponding clinical data of HCC patients were downloaded from the public database. The least absolute shrinkage and selection operator Cox analysis was utilized to construct a multigene prognostic signature in the TCGA cohort. HCC patients from the ICGC cohort were used for validation. Kaplan Meier analysis was used to compare the overall survival (OS) between high- and low-risk groups. Univariate and multivariate Cox analyses were applied to determine the independent predictors for OS. Single-sample gene set enrichment analysis was utilized to calculate the immune cell infiltration score and immune related pathway activity. Gene set enrichment analysis was implemented to conduct GO terms and KEGG pathways. The qRT-PCR and immunohistochemistry were utilized to perform the mRNA and protein expression of prognostic genes between HCC tissues and normal liver tissues respectively. Results An inflammatory response-related gene signature model was constructed by LASSO Cox regression analysis. Compared with the low-risk group, patients in the high-risk group showed significantly reduced OS. Receiver operating characteristic curve analysis confirmed the predictive capacity of the prognostic gene signature. Multivariate Cox analysis revealed that the risk score was an independent predictor for OS. Functional analysis indicated that immune status was definitely different between two risk groups, and cancer-related pathways were enriched in high-risk group. The risk score was significantly correlated with tumor grade, tumor stage and immune infiltrate types. The expression levels of prognostic genes were significantly correlated with sensitivity of cancer cells to anti-tumor drugs. Furthermore, the expression of prognostic genes showed significant difference between HCC tissues and adjacent non-tumorous tissues in the separate sample cohort. Conclusion A novel signature constructed with eight inflammatory response-related genes can be used for prognostic prediction and impact the immune status in HCC. Moreover, inhibition of these genes may be a therapeutic alternative.
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Affiliation(s)
- Zhuo Lin
- Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Accurate Diagnosis and Treatment of Chronic Liver Diseases, Key Laboratory of Zhejiang Province, Wenzhou, China
| | - Qian Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan Miao
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fujun Yu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Li Q, Ni Y, Zhang L, Jiang R, Xu J, Yang H, Hu Y, Qiu J, Pu L, Tang J, Wang X. HIF-1α-induced expression of m6A reader YTHDF1 drives hypoxia-induced autophagy and malignancy of hepatocellular carcinoma by promoting ATG2A and ATG14 translation. Signal Transduct Target Ther 2021; 6:76. [PMID: 33619246 PMCID: PMC7900110 DOI: 10.1038/s41392-020-00453-8] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/15/2020] [Accepted: 12/08/2020] [Indexed: 12/29/2022] Open
Abstract
N6-methyladenosine (m6A), and its reader protein YTHDF1, play a pivotal role in human tumorigenesis by affecting nearly every stage of RNA metabolism. Autophagy activation is one of the ways by which cancer cells survive hypoxia. However, the possible involvement of m6A modification of mRNA in hypoxia-induced autophagy was unexplored in human hepatocellular carcinoma (HCC). In this study, specific variations in YTHDF1 expression were detected in YTHDF1-overexpressing, -knockout, and -knockdown HCC cells, HCC organoids, and HCC patient-derived xenograft (PDX) murine models. YTHDF1 expression and hypoxia-induced autophagy were significantly correlated in vitro; significant overexpression of YTHDF1 in HCC tissues was associated with poor prognosis. Multivariate cox regression analysis identified YTHDF1 expression as an independent prognostic factor in patients with HCC. Multiple HCC models confirmed that YTHDF1 deficiency inhibited HCC autophagy, growth, and metastasis. Luciferase reporter assays and chromatin immunoprecipitation demonstrated that HIF-1α regulated YTHDF1 transcription by directly binding to its promoter region under hypoxia. The results of methylated RNA immunoprecipitation sequencing, proteomics, and polysome profiling indicated that YTHDF1 contributed to the translation of autophagy-related genes ATG2A and ATG14 by binding to m6A-modified ATG2A and ATG14 mRNA, thus facilitating autophagy and autophagy-related malignancy of HCC. Taken together, HIF-1α-induced YTHDF1 expression was associated with hypoxia-induced autophagy and autophagy-related HCC progression via promoting translation of autophagy-related genes ATG2A and ATG14 in a m6A-dependent manner. Our findings suggest that YTHDF1 is a potential prognostic biomarker and therapeutic target for patients with HCC.
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Affiliation(s)
- Qing Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China.,School of Medicine, Southeast University, Nanjing, China
| | - Yong Ni
- Department of Hepatopancreatobiliary Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Liren Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Runqiu Jiang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China.,Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Jing Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Hong Yang
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yuanchang Hu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Jiannan Qiu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China
| | - Liyong Pu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China.
| | - Jinhai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.
| | - Xuehao Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences; NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province, China. .,School of Medicine, Southeast University, Nanjing, China.
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Wang W, Zhang C, Yu Q, Zheng X, Yin C, Yan X, Liu G, Song Z. Development of a novel lipid metabolism-based risk score model in hepatocellular carcinoma patients. BMC Gastroenterol 2021; 21:68. [PMID: 33579192 PMCID: PMC7881464 DOI: 10.1186/s12876-021-01638-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/08/2023] Open
Abstract
Background Liver cancer is one of the most common malignancies worldwide. HCC (hepatocellular carcinoma) is the predominant pathological type of liver cancer, accounting for approximately 75–85 % of all liver cancers. Lipid metabolic reprogramming has emerged as an important feature of HCC. However, the influence of lipid metabolism-related gene expression in HCC patient prognosis remains unknown. In this study, we performed a comprehensive analysis of HCC gene expression data from TCGA (The Cancer Genome Atlas) to acquire further insight into the role of lipid metabolism-related genes in HCC patient prognosis. Methods We analyzed the mRNA expression profiles of 424 HCC patients from the TCGA database. GSEA(Gene Set Enrichment Analysis) was performed to identify lipid metabolism-related gene sets associated with HCC. We performed univariate Cox regression and LASSO(least absolute shrinkage and selection operator) regression analyses to identify genes with prognostic value and develop a prognostic model, which was tested in a validation cohort. We performed Kaplan-Meier survival and ROC (receiver operating characteristic) analyses to evaluate the performance of the model. Results We identified three lipid metabolism-related genes (ME1, MED10, MED22) with prognostic value in HCC and used them to calculate a risk score for each HCC patient. High-risk HCC patients exhibited a significantly lower survival rate than low-risk patients. Multivariate Cox regression analysis revealed that the 3-gene signature was an independent prognostic factor in HCC. Furthermore, the signature provided a highly accurate prediction of HCC patient prognosis. Conclusions We identified three lipid-metabolism-related genes that are upregulated in HCC tissues and established a 3-gene signature-based risk model that can accurately predict HCC patient prognosis. Our findings support the strong links between lipid metabolism and HCC and may facilitate the development of new metabolism-targeted treatment approaches for HCC.
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Affiliation(s)
- Wenjie Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Chen Zhang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Qihong Yu
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China.,Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
| | - Xichuan Zheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Chuanzheng Yin
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Xueke Yan
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Gang Liu
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zifang Song
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China.
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Li Y, Qi D, Zhu B, Ye X. Analysis of m6A RNA Methylation-Related Genes in Liver Hepatocellular Carcinoma and Their Correlation with Survival. Int J Mol Sci 2021; 22:ijms22031474. [PMID: 33540684 PMCID: PMC7867233 DOI: 10.3390/ijms22031474] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) modification on RNA plays an important role in tumorigenesis and metastasis, which could change gene expression and even function at multiple levels such as RNA splicing, stability, translocation, and translation. In this study, we aim to conduct a comprehensive analysis on m6A RNA methylation-related genes, including m6A RNA methylation regulators and m6A RNA methylation-modified genes, in liver hepatocellular carcinoma, and their relationship with survival and clinical features. Data, which consist of the expression of widely reported m6A RNA methylation-related genes in liver hepatocellular carcinoma from The Cancer Genome Atlas (TCGA), were analyzed by one-way ANOVA, Univariate Cox regression, a protein–protein interaction network, gene enrichment analysis, feature screening, a risk prognostic model, correlation analysis, and consensus clustering analysis. In total, 405 of the m6A RNA methylation-related genes were found based on one-way ANOVA. Among them, DNA topoisomerase 2-alpha (TOP2A), exodeoxyribonuclease 1 (EXO1), ser-ine/threonine-protein kinase Nek2 (NEK2), baculoviral IAP repeat-containing protein 5 (BIRC5), hyaluronan mediated motility receptor (HMMR), structural maintenance of chromosomes protein 4 (SMC4), bloom syndrome protein (BLM), ca-sein kinase I isoform epsilon (CSNK1E), cytoskeleton-associated protein 5 (CKAP5), and inner centromere protein (INCENP), which were m6A RNA methylation-modified genes, were recognized as the hub genes based on the protein–protein interaction analysis. The risk prognostic model showed that gender, AJCC stage, grade, T, and N were significantly different between the subgroup with the high and low risk groups. The AUC, the evaluation parameter of the prediction model which was built by RandomForest, was 0.7. Furthermore, two subgroups were divided by consensus clustering analysis, in which stage, grade, and T differed. We identified the important genes expressed significantly among two clusters, including uridine-cytidine kinase 2 (UCK2), filensin (BFSP1), tubulin-specific chaperone D (TBCD), histone-lysine N-methyltransferase PRDM16 (PRDM16), phosphorylase b ki-nase regulatory subunit alpha (PHKA2), serine/threonine-protein kinase BRSK2 (BRSK2), Arf-GAP with coiled-coil (ACAP3), general transcription factor 3C polypep-tide 2 (GTF3C2), and guanine nucleotide exchange factor MSS4 (RABIF). In our study, the m6A RNA methylation-related genes in liver hepatocellular carcinoma were analyzed systematically, including the expression, interaction, function, and prognostic values, which provided an important theoretical basis for m6A RNA methylation in liver cancer. The nine important m6A-related genes could be prognostic markers in the survival time of patients.
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Affiliation(s)
- Yong Li
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Dandan Qi
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Baoli Zhu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China;
- Correspondence: ; Tel.: +86-010-6480-7513
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Li M, Zha X, Wang S. The role of N6-methyladenosine mRNA in the tumor microenvironment. Biochim Biophys Acta Rev Cancer 2021; 1875:188522. [PMID: 33545295 DOI: 10.1016/j.bbcan.2021.188522] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/25/2022]
Abstract
In recent years, the most widely distributed eukaryotic messenger RNA (mRNA) modification, N6-methyladenosine (m6A), has received a large amount of interest, in part due to the development and advances of high-throughput RNA sequencing. The effects of m6A mRNA on tumor progression have been the most widely studied, and large amounts of conflicting data have been reported due to differences in tumor contexts, cell types or cell states. The majority of these studies were related to the significance of m6A mRNA on tumor cells, including on proliferation, stemness, invasion capability, etc. However, it has been noted that tumorigenesis and tumor progression cannot occur without support from the tumor microenvironment (TME), which contains multiple types of stromal cells, such as infiltrating immune cells (IICs), vascular cells, mesenchymal stem cells (MSCs), cancer-associated fibroblasts (CAFs), and various environmental factors. Here, we summarized the contributions of abnormal m6A mRNA in stromal cells within the TME and described the effects of m6A mRNA on TME remodeling.
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Affiliation(s)
- Min Li
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xuan Zha
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shengjun Wang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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42
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Li L, Ye T, Zhang Q, Li X, Ma L, Yan J. The expression and clinical significance of TPM4 in hepatocellular carcinoma. Int J Med Sci 2021; 18:169-175. [PMID: 33390785 PMCID: PMC7738955 DOI: 10.7150/ijms.49906] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/07/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is known as the fifth most common cancer in the world for its poor prognosis. New diagnostic markers and treatments are urgent to discover. To evaluate the protein expression of Tropomyosin4 (TPM4) and investigate its prognostic value in HCC, we collected 110 patients with different degrees of HCC and 10 patients with normal hepatic tissues and performed immunohistochemistry. Western bot was used to evaluate the expression of TPM4 in three HCC cell lines (HepG2, Huh7, SMMC-7721) and normal liver cell line LO2, as well as 7 HCC tissues and 7 normal hepatic tissues. The results of TPM4 staining revealed that TPM4 expression in HCC was higher than that in normal hepatic tissues, which was positive in 51.8% (n=57) and negative in 48.2% (n=53) while in normal hepatic tissues positive staining was in 10% (n=1) and negative staining was in 90% (n=9) (P=0.011). And the expression of TPM4 was related to pT status, grade and stage (P<0.001, P=0.015 and P<0.001, respectively). Western blot results indicated that TPM4 was high expressed in HCC cell line and HCC tissues. In conclusion, we believe that TPM4 can be applied as a diagnostic and prognostic marker to assist the management of HCC.
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Affiliation(s)
- Linjing Li
- Department of Clinical Laboratory Center, The Second Hospital of Lanzhou University, Lanzhou 730000, P.R. China
| | - Tao Ye
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China, 510515
| | - Qingyan Zhang
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China, 510080
| | - Xin Li
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China, 510515
| | - Li Ma
- Department of Clinical Laboratory Center, The Second Hospital of Lanzhou University, Lanzhou 730000, P.R. China
| | - Jing Yan
- Department of Clinical Laboratory Center, The Second Hospital of Lanzhou University, Lanzhou 730000, P.R. China
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Pan XY, Huang C, Li J. The emerging roles of m 6A modification in liver carcinogenesis. Int J Biol Sci 2021; 17:271-284. [PMID: 33390849 PMCID: PMC7757034 DOI: 10.7150/ijbs.50003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
The 'epitranscriptome', a collective term for chemical modifications that influence the structure, metabolism, and functions of RNA, has recently emerged as vitally important for the regulation of gene expression. N6-methyladenosine (m6A), the most prevalent mammalian mRNA internal modification, has been demonstrated to have a pivotal role in almost all vital bioprocesses, such as stem cell self-renewal and differentiation, heat shock or DNA damage response, tissue development, and maternal-to-zygotic transition. Hepatocellular carcinoma (HCC) is prevalent worldwide with high morbidity and mortality because of late diagnosis at an advanced stage and lack of effective treatment strategies. Epigenetic modifications including DNA methylation and histone modification have been demonstrated to be crucial for liver carcinogenesis. However, the role and underlying molecular mechanism of m6A in liver carcinogenesis are mostly unknown. In this review, we summarize recent advances in the m6A region and how these new findings remodel our understanding of m6A regulation of gene expression. We also describe the influence of m6A modification on liver carcinoma and lipid metabolism to instigate further investigations of the role of m6A in liver biological diseases and its potential application in the development of therapeutic strategies.
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Affiliation(s)
- Xue-Yin Pan
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education.,Institute for Liver Diseases of Anhui Medical University
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education.,Institute for Liver Diseases of Anhui Medical University
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education.,Institute for Liver Diseases of Anhui Medical University
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Gu C, Shi X, Dai C, Shen F, Rocco G, Chen J, Huang Z, Chen C, He C, Huang T, Chen C. RNA m 6A Modification in Cancers: Molecular Mechanisms and Potential Clinical Applications. Innovation (N Y) 2020; 1:100066. [PMID: 34557726 PMCID: PMC8454620 DOI: 10.1016/j.xinn.2020.100066] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
N6-Methyladenosine (m6A) RNA modification brings a new dawn for RNA modification researches in recent years. This posttranscriptional RNA modification is dynamic and reversible, and is regulated by methylases ("writers"), demethylases ("erasers"), and proteins that preferentially recognize m6A modifications ("readers"). The change of RNA m6A modification regulates RNA metabolism in eucaryon, including translation, splicing, exporting, decay, and processing. Thereby the dysregulation of m6A may lead to tumorigenesis and progression. Given the tumorigenic role of abnormal m6A expression, m6A regulators may function as potential clinical therapeutic targets for cancers. In this review, we emphasize on the underlying mechanisms of m6A modifications in tumorigenesis and further introduce the potential m6A regulators-associated therapeutic targets for tumor therapy.
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Affiliation(s)
- Chang Gu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chenyang Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiafei Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Zhengyu Huang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chunji Chen
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Medical Scientist Training Program/Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
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Xu S, Tang L, Dai G, Luo C, Liu Z. Expression of m6A Regulators Correlated With Immune Microenvironment Predicts Therapeutic Efficacy and Prognosis in Gliomas. Front Cell Dev Biol 2020; 8:594112. [PMID: 33240891 PMCID: PMC7683617 DOI: 10.3389/fcell.2020.594112] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
Background N6-methyladenosine (m6A) RNA methylation and tumor immune microenvironment played crucial roles in cancer development. However, their association in gliomas remains to be fully elucidated. Methods A total of 2144 glioma patients from CGGA, TCGA, and Rembrandt databases were extracted in our study, in which 325 were set as the training cohort and 1819 were defined as the validation cohort. Survival differences evaluated by Kaplan-Meier analysis between groups. Patients were clustered into subgroups by consensus clustering. ESTIMATE algorithm was applied to calculate immune and stroma scores. The infiltration of immune cells was characterized by TIMER algorithm. The risk signature was constructed by multivariate Cox regression analysis. Results Nineteen m6A regulators were highly expressed in glioma tissues. The expression of m6A regulators was associated with prognoses, grade, isocitrate dehydrogenase (IDH) status, and 1p19q status of gliomas. Two subgroups were identified by consensus clustering, in which cluster 1 was associated with favorable prognosis, high stroma and immune scores, and high immune infiltration. When the patients were divided into high risk and low risk groups based on their risk scores, we found that patients in the high risk group had poor prognoses. Besides, patients in the high risk group had a higher stroma and immune scores, and higher abundance of immune infiltration. These results were further verified in the validation cohort, which contained three independent datasets. Moreover, patients in the low risk group enjoyed better prognoses without chemoradiotherapy or single chemotherapy. Conclusion Our study revealed that m6A regulators could predict the prognosis and therapeutic efficacy, and were also associated with the immune microenvironment in gliomas.
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Affiliation(s)
- Shengchao Xu
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, China
| | - Lu Tang
- Department of Thoracic Surgery, Xiangya Hospital of Central South University, Changsha, China
| | - Gan Dai
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Chengke Luo
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, China
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Wan Q, Jin L, Wang Z. Comprehensive analysis of cancer hallmarks in cutaneous melanoma and identification of a novel unfolded protein response as a prognostic signature. Aging (Albany NY) 2020; 12:20684-20701. [PMID: 33136551 PMCID: PMC7655195 DOI: 10.18632/aging.103974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/08/2020] [Indexed: 06/11/2023]
Abstract
Molecular pathways regulating the initiation and development of melanoma are potential therapeutic targets for this aggressive skin cancer. Therefore, transcriptome profiles of cutaneous melanoma were obtained from a public database and used to systematically evaluate cancer hallmark pathways enriched in melanoma. Finally, the unfolded protein response pathway was screened out, and the unfolded protein response-related genes were used to develop a robust biomarker that can predict the prognosis of melanoma, especially for younger, metastatic and high Clark level patients. This biomarker was further validated in two other independent datasets. In addition, melanoma patients were divided into high- and low-risk subgroups by applying a risk score system. The high-risk group exhibited higher immune infiltration and higher expression of N6-methyladenosine RNA methylation regulators, and had significantly shorter survival times than the low-risk subgroup. Gene Set Enrichment Analysis revealed that, among the enriched genes, gene sets involved in immune response and the extracellular matrix receptor interaction were significantly activated in the high-risk group. Our findings thus provide a new clinical application for prognostic prediction as well as potential targets for treatment of melanoma.
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Affiliation(s)
- Qi Wan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510064, China
| | - Lin Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510064, China
| | - Zhichong Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510064, China
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Liu W, Zhong C, Lv D, Tang M, Xie F. N6-Methyladenosine RNA Methylation Regulators Have Clinical Prognostic Values in Hepatocellular Carcinoma. Front Genet 2020; 11:863. [PMID: 32903675 PMCID: PMC7438782 DOI: 10.3389/fgene.2020.00863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/15/2020] [Indexed: 01/17/2023] Open
Abstract
Although it is widely accepted that N6-methyladenosine (m6A) RNA methylation plays critical roles in tumorigenesis and progression, the values of m6A modification are less known in hepatocellular carcinoma. The major purpose of our current studies is to investigate the role of m6A regulators in hepatocellular carcinoma and whether it can affect the prognosis of hepatocellular carcinoma. Here we demonstrate that most of the m6A regulators are highly expressed in hepatocellular carcinoma. Furthermore, we cluster hepatocellular carcinoma into two subgroups (cluster 1/2) by applying consensus clustering to m6A regulators. Compared with the cluster 1 subgroup, the cluster 2 subgroup was significantly associated with a higher pathological grade and survival. Based on these findings, we reveal a risk signature by using three m6A regulators, which are not only an independent prognostic marker but also a predictor of the clinicopathological features in hepatocellular carcinoma. In conclusion, m6A regulators are crucial participants in the malignant progression of hepatocellular carcinoma and are potential targets for prognosis.
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Affiliation(s)
- Wei Liu
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Cuiqing Zhong
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Deguan Lv
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Mengjie Tang
- Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Feng Xie
- Department of Pharmacy, The Nanshan District Maternity and Child Healthcare Hospital of Shenzhen, Shenzhen, China
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Shi Y, Zheng C, Jin Y, Bao B, Wang D, Hou K, Feng J, Tang S, Qu X, Liu Y, Che X, Teng Y. Reduced Expression of METTL3 Promotes Metastasis of Triple-Negative Breast Cancer by m6A Methylation-Mediated COL3A1 Up-Regulation. Front Oncol 2020; 10:1126. [PMID: 32766145 PMCID: PMC7381173 DOI: 10.3389/fonc.2020.01126] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
The abnormal m6A modification caused by m6A modulators is a common feature of various tumors; however, little is known about which m6A modulator plays the most important role in triple-negative breast cancer (TNBC). In this study, when analyzing the influence of m6A modulators (METTL3, METTL14, WTAP, FTO, and ALKBH5) on the prognosis of breast cancer, especially in TNBC using several on-line databases, methyltransferase-like 3 (METTL3) was found to have low expression in breast cancer, and was closely associated with short-distance-metastasis-free survival in TNBC. Further investigation showed that knockdown of METTL3 could enhance the ability of migration, invasion, and adhesion by decreasing m6A level in TNBC cell lines. Collagen type III alpha 1 chain (COL3A1) was identified and verified as a target gene of METTL3. METTL3 could down-regulate the expression of COL3A1 by increasing its m6A methylation, ultimately inhibiting the metastasis of TNBC cells. Finally, with immunohistochemistry staining in breast cancer tissues, it was proved that METTL3 expression was negatively correlated with COL3A1 in TNBC, but not in non-TNBC. This study demonstrated the potential mechanism of m6A modification in metastasis and provided potential targets for treatment in TNBC.
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Affiliation(s)
- Yu Shi
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Chunlei Zheng
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Yue Jin
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Bowen Bao
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Duo Wang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Kezuo Hou
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Jing Feng
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Shiying Tang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Xiujuan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Xiaofang Che
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Yuee Teng
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
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Lu J, Qian J, Yin S, Zhou L, Zheng S, Zhang W. Mechanisms of RNA N 6-Methyladenosine in Hepatocellular Carcinoma: From the Perspectives of Etiology. Front Oncol 2020; 10:1105. [PMID: 32733807 PMCID: PMC7358598 DOI: 10.3389/fonc.2020.01105] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
N6-Methyladenosine (m6A) is the most common RNA internal modification in eukaryotic cells. Its regulatory effects at the post-transcriptional level on both messenger RNAs (mRNAs) and noncoding RNAs have been widely studied; these include alternative splicing, stability, translation efficiency, nucleus export, and degradation. m6A modification is implicated in a series of physiological and pathological activities, such as embryonic stem cell differentiation, immunoregulation, adipogenesis, and cancer development. Recently, the significance of m6A methylation has been identified in both viral hepatitis and non-alcohol fatty liver disease (NAFLD), which are major risk factors in the development of hepatocellular carcinoma (HCC). Given the high incidence and mortality rate of HCC worldwide, it is of great importance to elucidate the mechanisms underlying HCC initiation and progression. m6A as an emerging research focus has great potential to facilitate the understanding of HCC, particularly from an etiological perspective. Thus, in this review, we summarize recent progress in understanding m6A modification related to viral hepatitis, NAFLD, and HCC, including their mechanisms and clinical applications.
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Affiliation(s)
- Jiahua Lu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Junjie Qian
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Shengyong Yin
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Wu Zhang
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China.,Institution of Organ Transplantation, Zhejiang University, Hangzhou, China
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Sun L, Liu WK, Du XW, Liu XL, Li G, Yao Y, Han T, Li WY, Gu J. Large-scale transcriptome analysis identified RNA methylation regulators as novel prognostic signatures for lung adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:751. [PMID: 32647676 PMCID: PMC7333141 DOI: 10.21037/atm-20-3744] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background The abnormal expression of genes is an essential factor affecting the prognosis of cancer. RNA modification is a way of regulating post-transcriptional levels, including m6A, m5C, m1A RNA methylation. Studies have found that RNA methylation regulates tumorigenesis development and stem cell regeneration. However, there are few studies on lung adenocarcinoma. This study aims to explore the clinical value of RNA methylation for lung adenocarcinoma. Methods We summarized thirty-one RNA methylation regulators. The training set was obtained from The Cancer Genome Atlas (TCGA) database, and the test set was obtained from the Gene Expression Omnibus (GEO) database. The Wilcoxon test was used to analyze the expression of RNA methylation regulators. We constructed tumor subgroup models and risk models based on the expression of those regulators. Principal component analysis (PCA) and the receiver operating characteristic (ROC) confirmed the accuracy of the models. Real-time polymerase chain reaction (PCR) validates the results in vitro. Results Most RNA methylation regulators had distinct expressions in tumor tissues and adjacent tissues (P<0.05). All the models showed high predictive performance (AUC: 0.65-0.82), and the five-year survival of patients in each group was statistically different (P<0.05). The patients in the high-risk group were more likely to have a higher stage, more lymph node metastases, and distant metastases, showing a poor clinical outcome. Patients with high expression of NOP2 or HNRNP were more likely to have a poorly differentiated in vitro experiment. Conclusions With our study, we found that the expressions of most RNA methylation regulators were significantly different in cancer and para-cancerous tissues. Different molecular phenotypes constructed by RNA methylation regulators can be independent risk factors for the prognosis of lung adenocarcinoma. Our study demonstrates the critical role of RNA methylation in lung adenocarcinoma, and it is expected to supply a reference for the prognostic stratification and treatment strategy development of lung adenocarcinoma.
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Affiliation(s)
- Lei Sun
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wen-Ke Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiao-Wei Du
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China.,Jinzhou Medical University, Jinzhou, China
| | - Xiang-Li Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Gao Li
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Yao Yao
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Tao Han
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Wen-Ya Li
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jia Gu
- Department of Otolaryngology, The First Affiliated Hospital of China Medical University, Shenyang, China
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