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Chen X, Jiang R, Huang X, Chen L, Hu X, Wei Y. Long Noncoding RNA NKX2-1-AS1 Accelerates Non-Small Cell Lung Cancer Progression through the miR-589-5p/NME1 Axis. Cell Biochem Biophys 2024:10.1007/s12013-024-01472-w. [PMID: 39117986 DOI: 10.1007/s12013-024-01472-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2024] [Indexed: 08/10/2024]
Abstract
Non-small cell lung cancer (NSCLC) is the most common malignancy worldwide, with a high death rate. Long noncoding RNA (LncRNA) NKX2-1 antisense RNA 1 (NKX2-1-AS1) has been reported to be an oncogene in lung tumorigenesis. However, the precise mechanism of NKX2-1-AS1 underlying NSCLC progression is blurry. The intention of our research was to probe the potential mechanism of NKX2-1-AS1 underlying NSCLC. NKX2-1-AS1 expression and relevant downstream gene expression were measured using RT-qPCR. Cell proliferation and apoptosis were determined by MTT assay, EdU assay along with flow cytometry analysis. Cell migratory and invasive abilities were inspected by transwell assay. Western blot and immunofluorescence staining were utilized to assess the levels of epithelial-mesenchymal transition (EMT)-related proteins. RNA pull-down together with luciferase reporter assays were performed to verify the interaction between NKX2-1-AS1 and its downstream RNAs. Xenograft tumor-bearing mouse models were built to analyze tumor growth in vivo. The results suggested that NKX2-1-AS1 was upregulated in NSCLC patient tissues and cell lines. NKX2-1-AS1 deficiency suppressed cell proliferation, migration, invasion and EMT while elevated apoptosis. NKX2-1-AS1 bound to miR-589-5p, and NME/NM23 nucleoside diphosphate kinase 1 (NME1) was targeted by miR-589-5p in NSCLC cells. Additionally, NKX2-1-AS1 accelerated the progression of NSCLC by regulating miR-589-5p/NME1 axis. NKX2-1-AS1 knockdown repressed tumor growth in vivo. In conclusion, NKX2-1-AS1 accelerated the NSCLC progression through interacting with miR-589-5p for NME1 upregulation, which may provide clues for NSCLC targeting therapy.
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Affiliation(s)
- Xiaoying Chen
- Department of Respiratory and Critical Care Medicine, The Second Peoples' Hospital of Lishui, Lishui, China
| | - Ruilai Jiang
- Department of Respiratory and Critical Care Medicine, The Second Peoples' Hospital of Lishui, Lishui, China
| | - Xiaocheng Huang
- Department of Respiratory and Critical Care Medicine, The Second Peoples' Hospital of Lishui, Lishui, China
| | - Ling Chen
- Department of Respiratory and Critical Care Medicine, The Second Peoples' Hospital of Lishui, Lishui, China
| | - Xiaogang Hu
- Department of Respiratory and Critical Care Medicine, The Second Peoples' Hospital of Lishui, Lishui, China
| | - Yanbin Wei
- Department of Respiratory and Critical Care Medicine, The Second Peoples' Hospital of Lishui, Lishui, China.
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Zhao L, Li Q, Zhou T, Liu X, Guo J, Fang Q, Cao X, Geng Q, Yu Y, Zhang S, Deng T, Wang X, Jiao Y, Zhang M, Liu H, Tan H, Xiao C. Role of N6-methyladenosine in tumor neovascularization. Cell Death Dis 2024; 15:563. [PMID: 39098905 PMCID: PMC11298539 DOI: 10.1038/s41419-024-06931-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: 10/18/2023] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024]
Abstract
Tumor neovascularization is essential for the growth, invasion, and metastasis of tumors. Recent studies have highlighted the significant role of N6-methyladenosine (m6A) modification in regulating these processes. This review explores the mechanisms by which m6A influences tumor neovascularization, focusing on its impact on angiogenesis and vasculogenic mimicry (VM). We discuss the roles of m6A writers, erasers, and readers in modulating the stability and translation of angiogenic factors like vascular endothelial growth factor (VEGF), and their involvement in key signaling pathways such as PI3K/AKT, MAPK, and Hippo. Additionally, we outline the role of m6A in vascular-immune crosstalk. Finally, we discuss the current development of m6A inhibitors and their potential applications, along with the contribution of m6A to anti-angiogenic therapy resistance. Highlighting the therapeutic potential of targeting m6A regulators, this review provides novel insights into anti-angiogenic strategies and underscores the need for further research to fully exploit m6A modulation in cancer treatment. By understanding the intricate role of m6A in tumor neovascularization, we can develop more effective therapeutic approaches to inhibit tumor growth and overcome treatment resistance. Targeting m6A offers a novel approach to interfere with the tumor's ability to manipulate its microenvironment, enhancing the efficacy of existing treatments and providing new avenues for combating cancer progression.
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Affiliation(s)
- Lu Zhao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital, Capital Medical University, Beijing, China
| | - Qinshan Li
- Institute of Precision Medicine of Guizhou Province, Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, 550004, China
- Department of Clinical Biochemistry, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, Guizhou, 550004, China
| | - Tongliang Zhou
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xuan Liu
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Jing Guo
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Qing Fang
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xiaoxue Cao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Qishun Geng
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Yang Yu
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Songjie Zhang
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Tingting Deng
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xing Wang
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Yi Jiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Mengxiao Zhang
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Honglin Liu
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China.
- China-Japan Friendship Hospital, Capital Medical University, Beijing, China.
| | - Haidong Tan
- Department of Hepatobiliary Surgery, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Cheng Xiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China.
- China-Japan Friendship Hospital, Capital Medical University, Beijing, China.
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Zhang H, Tang Y, Zhou Y, Wang Y, Si H, Li L, Tang B. DNAzyme-RCA-based colorimetric and lateral flow dipstick assays for the point-of-care testing of exosomal m5C-miRNA-21. Chem Sci 2024; 15:9345-9352. [PMID: 38903234 PMCID: PMC11186332 DOI: 10.1039/d4sc02648a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 06/22/2024] Open
Abstract
Methylation of microRNAs (miRNAs) is a post-transcriptional modification that affects miRNA activity by altering the specificity of miRNAs to target mRNAs. Abnormal methylation of miRNAs in cancer suggests their potential as a tumor marker. However, the traditional methylated miRNA detection mainly includes mass spectrometry, sequencing and others; complex procedures and reliance on large instruments greatly limit their application in point-of-care testing (POCT). Based on this, we developed DNAzyme-RCA-based gold nanoparticle (AuNP) colorimetric and lateral flow dipstick (LFD) assays to achieve convenient detection of exosomal 5-methylcytosine miRNA-21 (m5C-miRNA-21) for the first time. The two assays achieved specific recognition and linear amplification of m5C-miRNA-21 through the DNAzyme triggered RCA reaction and color output with low background interference through AuNP aggregation induced by base complementary pairing. The lowest concentration of m5C-miRNA-21 visible to the naked eye of the two assays can reach 1 pM and 0.1 pM, respectively. Detection of exosomal m5C-miRNA-21 in clinical blood samples showed that the expression level of m5C-miRNA-21 in colorectal cancer patients was significantly higher than that in healthy individuals. This approach not only demonstrates a new strategy for the detection of colorectal cancer but also provides a reference for the development of novel diagnostic tools for other miRNA methylation-related diseases.
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Affiliation(s)
- Hao Zhang
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
| | - Yue Tang
- Department of Emergency Medicine, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University Jinan 250014 P. R. China
| | - Yingshun Zhou
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
| | - Yiguo Wang
- First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital Jinan 250014 P. R. China
| | - Haibin Si
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
| | - Lu Li
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
| | - Bo Tang
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
- Laoshan Laboratory Qingdao 266237 P. R. China
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Qiu Z, Yuan X, Wang X, Liu S. Crosstalk between m6A modification and non-coding RNAs in HCC. Cell Signal 2024; 117:111076. [PMID: 38309550 DOI: 10.1016/j.cellsig.2024.111076] [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: 10/28/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/05/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide, with high morbidity and occurrence. Although various therapeutic approaches have been rapidly developed in recent years, the underlying molecular mechanisms in the pathogenesis of HCC remain enigmatic. The N6-methyladenosine (m6A) RNA modification is believed to regulate RNA metabolism and further gene expression. This process is intricately regulated by multiple regulators, such as methylases and demethylases. Non-coding RNAs (ncRNAs) are involved in the regulation of the epigenetic modification, mRNA transcription and other biological processes, exhibiting crucial roles in tumor occurrence and development. The m6A-ncRNA interaction has been implicated in the malignant phenotypes of HCC and plays an important role in drug resistance. This review summarizes the effect of m6A-ncRNA crosstalk on HCC progression and their clinical implications as prognostic markers and therapeutic targets in this disease.
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Affiliation(s)
- Zitong Qiu
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, PR China
| | - Xingxing Yuan
- Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin, Heilongjiang 150006, PR China
| | - Xinyue Wang
- International Education College, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, PR China
| | - Songjiang Liu
- Department of Oncology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, PR China.
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Bao Q, Zeng Y, Lou Q, Feng X, Jiang S, Lu J, Ruan B. Clinical significance of RNA methylation in hepatocellular carcinoma. Cell Commun Signal 2024; 22:204. [PMID: 38566136 PMCID: PMC10986096 DOI: 10.1186/s12964-024-01595-w] [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: 02/03/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a primary liver malignancy with high mortality rates and poor prognosis. Recent advances in high-throughput sequencing and bioinformatic technologies have greatly enhanced the understanding of the genetic and epigenetic changes in liver cancer. Among these changes, RNA methylation, the most prevalent internal RNA modification, has emerged as a significant contributor of the development and progression of HCC. Growing evidence has reported significantly abnormal levels of RNA methylation and dysregulation of RNA-methylation-related enzymes in HCC tissues and cell lines. These alterations in RNA methylation play a crucial role in the regulation of various genes and signaling pathways involved in HCC, thereby promoting tumor progression. Understanding the pathogenesis of RNA methylation in HCC would help in developing prognostic biomarkers and targeted therapies for HCC. Targeting RNA-methylation-related molecules has shown promising potential in the management of HCC, in terms of developing novel prognostic biomarkers and therapies for HCC. Exploring the clinical application of targeted RNA methylation may provide new insights and approaches for the management of HCC. Further research in this field is warranted to fully understand the functional roles and underlying mechanisms of RNA methylation in HCC. In this review, we described the multifaceted functional roles and potential mechanisms of RNA methylation in HCC. Moreover, the prospects of clinical application of targeted RNA methylation for HCC management are discussed, which may provide the basis for subsequent in-depth research on RNA methylation in HCC.
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Affiliation(s)
- Qiongling Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, National Medical Center for Infectious Diseases, Zhejiang University School of Medicine, No. 79 Qingchun Road, Shangcheng District, Hangzhou, Zhejiang, 310003, China
| | - Yifan Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, National Medical Center for Infectious Diseases, Zhejiang University School of Medicine, No. 79 Qingchun Road, Shangcheng District, Hangzhou, Zhejiang, 310003, China
| | - Qizhuo Lou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, National Medical Center for Infectious Diseases, Zhejiang University School of Medicine, No. 79 Qingchun Road, Shangcheng District, Hangzhou, Zhejiang, 310003, China
| | - Xuewen Feng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, National Medical Center for Infectious Diseases, Zhejiang University School of Medicine, No. 79 Qingchun Road, Shangcheng District, Hangzhou, Zhejiang, 310003, China
| | - Shuwen Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, National Medical Center for Infectious Diseases, Zhejiang University School of Medicine, No. 79 Qingchun Road, Shangcheng District, Hangzhou, Zhejiang, 310003, China
| | - Juan Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, National Medical Center for Infectious Diseases, Zhejiang University School of Medicine, No. 79 Qingchun Road, Shangcheng District, Hangzhou, Zhejiang, 310003, China.
| | - Bing Ruan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, National Medical Center for Infectious Diseases, Zhejiang University School of Medicine, No. 79 Qingchun Road, Shangcheng District, Hangzhou, Zhejiang, 310003, China.
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6
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Xu Q, Ren N, Ren L, Yang Y, Pan J, Shang H. RNA m6A methylation regulators in liver cancer. Cancer Cell Int 2024; 24:1. [PMID: 38166832 PMCID: PMC10763310 DOI: 10.1186/s12935-023-03197-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
Liver cancer is one of the most common cancers in the world and a primary cause of cancer-related death. In recent years, despite the great development of diagnostic methods and targeted therapies for liver cancer, the incidence and mortality of liver cancer are still on the rise. As a universal post-transcriptional modification, N6-methyladenosine (m6A) modification accomplishes a dynamic and reversible m6A modification process, which is executed by three types of regulators, methyltransferases (called writers), demethylases (called erasers) and m6A-binding proteins (called readers). Many studies have shown that m6A RNA methylation has an important impact on RNA metabolism, whereas its regulation exception is bound up with the occurrence of human malignant tumors. Aberrant methylation of m6A RNA and the expression of related regulatory factors may be of the essence in the pathogenesis and progression of liver cancer, yet the precise molecular mechanism remains unclear. In this paper, we review the current research situations of m6A methylation in liver cancer. Among the rest, we detail the mechanism by which methyltransferases, demethylases and m6A binding proteins regulate the occurrence and development of liver cancer by modifying mRNA. As well as the potential effect of m6A regulators in hepatocarcinogenesis and progression. New ideas and approaches will be given to the prevention and treatment of liver cancer through the following relevant research results.
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Affiliation(s)
- Qiaoping Xu
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Westlake University School of Medicine, Hangzhou, 310006, China
| | - Ning Ren
- Fourth Clinical Medical College of Zhejiang, Chinese Medical University, Hangzhou, 310051, Zhejiang, China
| | - Lanqi Ren
- Fourth Clinical Medical College of Zhejiang, Chinese Medical University, Hangzhou, 310051, Zhejiang, China
| | - Yibei Yang
- Fourth Clinical Medical College of Zhejiang, Chinese Medical University, Hangzhou, 310051, Zhejiang, China
| | - Junjie Pan
- Fourth Clinical Medical College of Zhejiang, Chinese Medical University, Hangzhou, 310051, Zhejiang, China
| | - Hongkai Shang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Westlake University School of Medicine, Hangzhou, 310006, China.
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China.
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.
- Department of Gynecology, Hangzhou First People's Hospital, Hangzhou, China.
- Department of Gynecology, Westlake University School of Medicine, Hangzhou, China.
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Jayasree PJ, Dutta S, Karemore P, Khandelia P. Crosstalk Between m6A RNA Methylation and miRNA Biogenesis in Cancer: An Unholy Nexus. Mol Biotechnol 2023:10.1007/s12033-023-00921-w. [PMID: 37831403 DOI: 10.1007/s12033-023-00921-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
N6-methyladenosine (m6A) is one of the most prevalent internal reversible chemical modification of RNAs in eukaryotes, which has attracted widespread attention recently owing to its regulatory roles in a plethora of normal developmental processes and human diseases like cancer. Deposition of the m6A mark on RNAs is mediated by the dynamic interplay between m6A regulatory proteins such as m6A RNA methyltransferases (m6A writers), m6A RNA demethylases (m6A erasers) and m6A RNA binding proteins (m6A readers). m6A regulators are ectopically expressed in various cancer types, often leading to aberrant expression of tumor-suppressor and oncogenic mRNAs either directly or indirectly via regulating the biogenesis of non-coding RNAs like miRNAs. miRNAs are tiny regulators of gene expression, which often impact various hallmarks of cancer and thus influence tumorigenesis. It is becoming increasingly clear that m6A RNA modification impacts biogenesis and function of miRNAs, and recent studies have interestingly, uncovered many miRNAs whose biogenesis and function are regulated by m6A writers, erasers and readers. In this review, we discuss various mechanisms by which m6A RNA methylation regulates miRNA biogenesis, the functional crosstalk between m6A RNA methylation and miRNAs and how it modulates various aspects of tumorigenesis. The potential of m6A RNA methylation regulated miRNAs as biomarkers and novel therapeutic targets to treat various cancers is also addressed.
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Affiliation(s)
- P J Jayasree
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Hyderabad, Telangana, 500078, India
| | - Shalmoli Dutta
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Hyderabad, Telangana, 500078, India
| | - Pragati Karemore
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Hyderabad, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Hyderabad, Telangana, 500078, India.
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Yao Y, Lv J, Wang G, Hong X. Multi-omics analysis and validation of the tumor microenvironment of hepatocellular carcinoma under RNA modification patterns. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:18318-18344. [PMID: 38052560 DOI: 10.3934/mbe.2023814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
BACKGROUND Multiple types of RNA modifications are associated with the prognosis of hepatocellular carcinoma (HCC) patients. However, the overall mediating effect of RNA modifications on the tumor microenvironment (TME) and the prognosis of patients with HCC is unclear. METHODS Thoroughly analyze the TME, biological processes, immune infiltration and patient prognosis based on RNA modification patterns and gene patterns. Construct a prognostic model (RNA modification score, RNAM-S) to predict the overall survival (OS) in HCC patients. Analyze the immune status, cancer stem cell (CSC), mutations and drug sensitivity of HCC patients in both the high and low RNAM-S groups. Verify the expression levels of the four characteristic genes of the prognostic RNAM-S using in vitro cell experiments. RESULTS Two modification patterns and two gene patterns were identified in this study. Both the high-expression modification pattern and the gene pattern exhibited worse OS. A prognostic RNAM-S model was constructed based on four featured genes (KIF20A, NR1I2, NR2F1 and PLOD2). Cellular experiments suggested significant dysregulation of the expression levels of these four genes. In addition, validation of the RNAM-S model using each data set showed good predictive performance of the model. The two groups of HCC patients (high and low RNAM-S groups) exhibited significant differences in immune status, CSC, mutation and drug sensitivity. CONCLUSION The findings of the study demonstrate the clinical value of RNA modifications, which provide new insights into the individualized treatment for patients with HCC.
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Affiliation(s)
- Yuanqian Yao
- Guangxi University of Chinese medicine, NanNing 530000, China
| | - Jianlin Lv
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530000, China
| | - Guangyao Wang
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530000, China
| | - Xiaohua Hong
- Guangxi University of Chinese medicine, NanNing 530000, China
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9
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Qi YN, Liu Z, Hong LL, Li P, Ling ZQ. Methyltransferase-like proteins in cancer biology and potential therapeutic targeting. J Hematol Oncol 2023; 16:89. [PMID: 37533128 PMCID: PMC10394802 DOI: 10.1186/s13045-023-01477-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/10/2023] [Indexed: 08/04/2023] Open
Abstract
RNA modification has recently become a significant process of gene regulation, and the methyltransferase-like (METTL) family of proteins plays a critical role in RNA modification, methylating various types of RNAs, including mRNA, tRNA, microRNA, rRNA, and mitochondrial RNAs. METTL proteins consist of a unique seven-beta-strand domain, which binds to the methyl donor SAM to catalyze methyl transfer. The most typical family member METTL3/METTL14 forms a methyltransferase complex involved in N6-methyladenosine (m6A) modification of RNA, regulating tumor proliferation, metastasis and invasion, immunotherapy resistance, and metabolic reprogramming of tumor cells. METTL1, METTL4, METTL5, and METTL16 have also been recently identified to have some regulatory ability in tumorigenesis, and the rest of the METTL family members rely on their methyltransferase activity for methylation of different nucleotides, proteins, and small molecules, which regulate translation and affect processes such as cell differentiation and development. Herein, we summarize the literature on METTLs in the last three years to elucidate their roles in human cancers and provide a theoretical basis for their future use as potential therapeutic targets.
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Affiliation(s)
- Ya-Nan Qi
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, P.R. China
| | - Zhu Liu
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, P.R. China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, P.R. China
| | - Lian-Lian Hong
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, P.R. China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, P.R. China
| | - Pei Li
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, P.R. China.
| | - Zhi-Qiang Ling
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, P.R. China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, P.R. China.
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10
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Xiong Q, Zhang Y. Small RNA modifications: regulatory molecules and potential applications. J Hematol Oncol 2023; 16:64. [PMID: 37349851 PMCID: PMC10286502 DOI: 10.1186/s13045-023-01466-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
Small RNAs (also referred to as small noncoding RNAs, sncRNA) are defined as polymeric ribonucleic acid molecules that are less than 200 nucleotides in length and serve a variety of essential functions within cells. Small RNA species include microRNA (miRNA), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), tRNA-derived small RNA (tsRNA), etc. Current evidence suggest that small RNAs can also have diverse modifications to their nucleotide composition that affect their stability as well as their capacity for nuclear export, and these modifications are relevant to their capacity to drive molecular signaling processes relevant to biogenesis, cell proliferation and differentiation. In this review, we highlight the molecular characteristics and cellular functions of small RNA and their modifications, as well as current techniques for their reliable detection. We also discuss how small RNA modifications may be relevant to the clinical applications for the diagnosis and treatment of human health conditions such as cancer.
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Affiliation(s)
- Qunli Xiong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
- Abdominal Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
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Ma W, Wu T. RNA m6A modification in liver biology and its implication in hepatic diseases and carcinogenesis. Am J Physiol Cell Physiol 2022; 323:C1190-C1205. [PMID: 36036444 PMCID: PMC9576175 DOI: 10.1152/ajpcell.00214.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotic RNAs. This modification is regulated by three different factors (writers, erasers, and readers) and affects multiple aspects of RNA metabolism, including RNA splicing, nuclear export, translation, stability and decay. The m6A-mediated modification plays important roles in posttranscriptional regulation of gene expression and mediates a variety of cellular and biological processes. Accordingly, deregulation in m6A modification is closely related to the occurrence and development of human diseases. The liver is the largest digestive and metabolic organ in human and recent studies have shown that m6A modification is importantly implicated in liver cellular and physiological functions and in the pathogenesis of hepatic diseases and cancers. In the current review, we summarize the functions of m6A in RNA metabolism and its roles in liver cell biology and discuss its implication in hepatic diseases and carcinogenesis.
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Affiliation(s)
- Wenbo Ma
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
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Wen X, Wang J, Wang Q, Liu P, Zhao H. Interaction between N6-methyladenosine and autophagy in the regulation of bone and tissue degeneration. Front Bioeng Biotechnol 2022; 10:978283. [PMID: 36072293 PMCID: PMC9443517 DOI: 10.3389/fbioe.2022.978283] [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: 06/25/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
Bone and tissue degeneration are the most common skeletal disorders that seriously affect people’s quality of life. N6-methyladenosine (m6A) is one of the most common RNA modifications in eukaryotic cells, affecting the alternative splicing, translation, stability and degradation of mRNA. Interestingly, increasing number of evidences have indicated that m6A modification could modulate the expression of autophagy-related (ATG) genes and promote autophagy in the cells. Autophagy is an important process regulating intracellular turnover and is evolutionarily conserved in eukaryotes. Abnormal autophagy results in a variety of diseases, including cardiomyopathy, degenerative disorders, and inflammation. Thus, the interaction between m6A modification and autophagy plays a prominent role in the onset and progression of bone and tissue degeneration. In this review, we summarize the current knowledge related to the effect of m6A modification on autophagy, and introduce the role of the crosstalk between m6A modification and autophagy in bone and tissue degeneration. An in-depth knowledge of the above crosstalk may help to improve our understanding of their effects on bone and tissue degeneration and provide novel insights for the future therapeutics.
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