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Kurata H, Harun-Or-Roshid M, Mehedi Hasan M, Tsukiyama S, Maeda K, Manavalan B. MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models. Methods 2024; 227:37-47. [PMID: 38729455 DOI: 10.1016/j.ymeth.2024.05.004] [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: 09/22/2023] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
RNA modification serves as a pivotal component in numerous biological processes. Among the prevalent modifications, 5-methylcytosine (m5C) significantly influences mRNA export, translation efficiency and cell differentiation and are also associated with human diseases, including Alzheimer's disease, autoimmune disease, cancer, and cardiovascular diseases. Identification of m5C is critically responsible for understanding the RNA modification mechanisms and the epigenetic regulation of associated diseases. However, the large-scale experimental identification of m5C present significant challenges due to labor intensity and time requirements. Several computational tools, using machine learning, have been developed to supplement experimental methods, but identifying these sites lack accuracy and efficiency. In this study, we introduce a new predictor, MLm5C, for precise prediction of m5C sites using sequence data. Briefly, we evaluated eleven RNA sequence-derived features with four basic machine learning algorithms to generate baseline models. From these 44 models, we ranked them based on their performance and subsequently stacked the Top 20 baseline models as the best model, named MLm5C. The MLm5C outperformed the-state-of-the-art predictors. Notably, the optimization of the sequence length surrounding the modification sites significantly improved the prediction performance. MLm5C is an invaluable tool in accelerating the detection of m5C sites within the human genome, thereby facilitating in the characterization of their roles in post-transcriptional regulation.
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Affiliation(s)
- Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Md Harun-Or-Roshid
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Md Mehedi Hasan
- Division of Biotetecnology and Molecular Medicine, Department of Pathobiological Science, School of Veterinary Medicine, Lousiana State University, Baton Rouge, LA 70803, USA
| | - Sho Tsukiyama
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Kazuhiro Maeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Balachandran Manavalan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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2
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Li H, Liu H, Zhu D, Dou C, Gang B, Zhang M, Wan Z. Biological function molecular pathways and druggability of DNMT2/TRDMT1. Pharmacol Res 2024; 205:107222. [PMID: 38782147 DOI: 10.1016/j.phrs.2024.107222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
5-methylcytosine (m5C) is among the most common epigenetic modification in DNA and RNA molecules, and plays an important role in the animal development and disease pathogenesis. Interestingly, unlike other m5C DNA methyltransferases (DNMTs), DNMT2/TRDMT1 has the double-substrate specificity and adopts a DNMT-similar catalytic mechanism to methylate RNA. Moreover, it is widely involved in a variety of physiological regulatory processes, such as the gene expression, precise protein synthesis, immune response, and disease occurrence. Thus, comprehending the epigenetic mechanism and function of DNMT2/TRDMT1 will probably provide new strategies to treat some refractory diseases. Here, we discuss recent studies on the spatiotemporal expression pattern and post-translational modifications of DNMT2/TRDMT1, and summarize the research advances in substrate characteristics, catalytic recognition mechanism, DNMT2/TRDMT1-related genes or proteins, pharmacological application, and inhibitor development. This review will shed light on the pharmacological design by targeting DNMT2/TRDMT1 to treat parasitic, viral and oncologic diseases.
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Affiliation(s)
- Huari Li
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China; College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei Province 430070, PR China.
| | - Huiru Liu
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei Province 430070, PR China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Chengli Dou
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Baocai Gang
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Mengjie Zhang
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Ziyu Wan
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
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3
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Li Y, Jin H, Li Q, Shi L, Mao Y, Zhao L. The role of RNA methylation in tumor immunity and its potential in immunotherapy. Mol Cancer 2024; 23:130. [PMID: 38902779 PMCID: PMC11188252 DOI: 10.1186/s12943-024-02041-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
RNA methylation, a prevalent post-transcriptional modification, has garnered considerable attention in research circles. It exerts regulatory control over diverse biological functions by modulating RNA splicing, translation, transport, and stability. Notably, studies have illuminated the substantial impact of RNA methylation on tumor immunity. The primary types of RNA methylation encompass N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G), and 3-methylcytidine (m3C). Compelling evidence underscores the involvement of RNA methylation in regulating the tumor microenvironment (TME). By affecting RNA translation and stability through the "writers", "erasers" and "readers", RNA methylation exerts influence over the dysregulation of immune cells and immune factors. Consequently, RNA methylation plays a pivotal role in modulating tumor immunity and mediating various biological behaviors, encompassing proliferation, invasion, metastasis, etc. In this review, we discussed the mechanisms and functions of several RNA methylations, providing a comprehensive overview of their biological roles and underlying mechanisms within the tumor microenvironment and among immunocytes. By exploring how these RNA modifications mediate tumor immune evasion, we also examine their potential applications in immunotherapy. This review aims to provide novel insights and strategies for identifying novel targets in RNA methylation and advancing cancer immunotherapy efficacy.
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Affiliation(s)
- Yan Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoer Jin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Qingling Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Liangrong Shi
- Department of Radiology, Xiangya Hospital, 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.
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- 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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4
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Meng H, Miao H, Zhang Y, Chen T, Yuan L, Wan Y, Jiang Y, Zhang L, Cheng W. YBX1 promotes homologous recombination and resistance to platinum-induced stress in ovarian cancer by recognizing m5C modification. Cancer Lett 2024; 597:217064. [PMID: 38880223 DOI: 10.1016/j.canlet.2024.217064] [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: 03/24/2024] [Revised: 05/20/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
Platinum-based chemotherapy causes genetic damage and induces apoptosis in ovarian cancer cells. Enhancing the ability to resist platinum drug-induced DNA damage and apoptotic stress is critical for tumor cells to acquire drug resistance. Here, we found that Y-box binding protein 1 (YBX1) was highly expressed in cisplatin-resistant patient-derived organoids (PDOs) and was a crucial gene for alleviating platinum-induced stress and maintaining drug resistance characteristics in ovarian cancer cells. Mechanistically, YBX1 recognized m5C modifications in CHD3 mRNA and maintained mRNA stability by recruiting PABPC1 protein. This regulatory process enhanced chromatin accessibility and improved the efficiency of homologous recombination (HR) repair, facilitating tumor cells to withstand platinum-induced apoptotic stress. In addition, SU056, an inhibitor of YBX1, exhibited the potential to reverse platinum resistance in subcutaneous and PDO orthotopic xenograft models. In conclusion, YBX1 is critical for ovarian cancer cells to alleviate the platinum-induced stress and may be a potential target for reversing drug-resistant therapies.
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Affiliation(s)
- Huangyang Meng
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China; Maternal and Child Center Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huixian Miao
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China; Maternal and Child Center Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yashuang Zhang
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China; Maternal and Child Center Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tian Chen
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China
| | - Lin Yuan
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China
| | - Yicong Wan
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China
| | - Yi Jiang
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China
| | - Lin Zhang
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China; Maternal and Child Center Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Wenjun Cheng
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China; Branch Of National Clinical Research Center For Gynecology and Obstetrics, China; Maternal and Child Center Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Seigel GM, Onwumere O, Sauane M, Lopez S, Shang E, Habiba H, Redenti S, Grossniklaus HE, Gharbaran R. ALYREF/THOC4 expression and cell growth modulation in retinoblastoma. Pathol Res Pract 2024; 260:155392. [PMID: 38880039 DOI: 10.1016/j.prp.2024.155392] [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: 04/06/2024] [Revised: 05/17/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024]
Abstract
In this study, we tested the hypothesis that ALYREF/THOC4, a poor prognostic factor in different cancer types, has potential as a drug target and prognostic biomarker for retinoblastoma (RB). Immunostaining (IHC), Western blot, and RT-qPCR analyses detected overexpression of ALYREF in the RB cell lines Y79, RB143, WERI-RB1, and RB116. IHC analysis on RB tumor array showed that 11/14 of RB tumors were ALYREF+ to varying degrees, with eight tumors at maximum 3+ intensity. The IHC analysis also detected ALYREF+ cells in normal retina, mainly in the inner nuclear and ganglion cell layer, while some tumor-bearing human eyes were ALYREF+ in the optic nerve suggesting a role in optic invasion/tumor invasion. The expression of ALYREF within the tumor itself, in the optic nerve, as well as in adjacent "normal" retina, suggest that this pattern of expression may lead to ALYREF being a potentially useful prognostic indicator for RB, as it is for other tumors. siRNA knockdown of ALYREF resulted in a 40 % decrease in cell growth in both WERI-RB1 and Y79 cells (p<0.05) and this was associated with decreased expression of mRNAs for the cell proliferation markers Ki67 and PCNA (p<0.005). These results suggest a role for ALYREF in RB cell growth regulation and its potential as both a target and a biomarker for tumor growth inhibition by anti-cancer therapies.
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Affiliation(s)
- Gail M Seigel
- Department of Communicative Disorders and Sciences, University at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA
| | - Onyekwere Onwumere
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA; Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY 10016 USA, USA
| | - Moira Sauane
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA; Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY 10016 USA, USA
| | - Sual Lopez
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA
| | - Enyuan Shang
- Department of Biological Sciences, Bronx Community College/City University of New York, 2155 University Avenue, Bronx, NY 10453, USA
| | - Habiba Habiba
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA
| | - Stephen Redenti
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA; Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY 10016 USA, USA
| | | | - Rajendra Gharbaran
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA; Department of Biological Sciences, Bronx Community College/City University of New York, 2155 University Avenue, Bronx, NY 10453, USA.
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6
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Zhao Z, Zhou Y, Lv P, Zhou T, Liu H, Xie Y, Wu Z, Wang X, Zhao H, Zheng J, Jiang X. NSUN4 mediated RNA 5-methylcytosine promotes the malignant progression of glioma through improving the CDC42 mRNA stabilization. Cancer Lett 2024; 597:217059. [PMID: 38876383 DOI: 10.1016/j.canlet.2024.217059] [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: 03/26/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
5-Methylcytosine (m5C) methylation is a significant post-transcriptional modification that play a crucial role in the development and progression of numerous cancers. Whereas the functions and molecular mechanisms underlying m5C methylation in gliomas remain unclear. This study dedicated to explore changes of m5C levels and the clinical significance of the m5C writer NSUN4 in gliomas. We found that high m5C levels were negatively related to prognosis of patients with glioma. Moreover, gain- and loss-of-function experiments revealed the role of NSUN4 in enhancing m5C modification of mRNA to promote the malignant progression of glioma. Mechanistically speaking, NSUN4-mediated m5C alterations regulated ALYREF binding to CDC42 mRNA, thereby impacting the mRNA stability of CDC42. We also demonstrated that CDC42 promoted glioma proliferation, migration, and invasion by activating the PI3K-AKT pathway. Additionally, rescue experiments proved that CDC42 overexpression weaken the inhibitory effect of NSUN4 knockdown on the malignant progression of gliomas in vitro and in vivo. Our findings elucidated that NSUN4-mediated high m5C levels promote ALYREF binding to CDC42 mRNA and regulate its stability, thereby driving the malignant progression of glioma. This provides theoretical support for targeted the treatment of gliomas.
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Affiliation(s)
- Zhen Zhao
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yujie Zhou
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Peng Lv
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ting Zhou
- Department of Gynaecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hanyuan Liu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Youxi Xie
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhipeng Wu
- Department of Neurosurgery, Weifang People's Hospital, Weifang, China
| | - Xuan Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongyang Zhao
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Jianglin Zheng
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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7
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Chen M, Chen Y, Wang K, Deng X, Chen J. Non‐m 6A RNA modifications in haematological malignancies. Clin Transl Med 2024; 14:e1666. [PMID: 38880983 PMCID: PMC11180698 DOI: 10.1002/ctm2.1666] [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: 11/05/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 06/18/2024] Open
Abstract
Dysregulated RNA modifications, stemming from the aberrant expression and/or malfunction of RNA modification regulators operating through various pathways, play pivotal roles in driving the progression of haematological malignancies. Among RNA modifications, N6-methyladenosine (m6A) RNA modification, the most abundant internal mRNA modification, stands out as the most extensively studied modification. This prominence underscores the crucial role of the layer of epitranscriptomic regulation in controlling haematopoietic cell fate and therefore the development of haematological malignancies. Additionally, other RNA modifications (non-m6A RNA modifications) have gained increasing attention for their essential roles in haematological malignancies. Although the roles of the m6A modification machinery in haematopoietic malignancies have been well reviewed thus far, such reviews are lacking for non-m6A RNA modifications. In this review, we mainly focus on the roles and implications of non-m6A RNA modifications, including N4-acetylcytidine, pseudouridylation, 5-methylcytosine, adenosine to inosine editing, 2'-O-methylation, N1-methyladenosine and N7-methylguanosine in haematopoietic malignancies. We summarise the regulatory enzymes and cellular functions of non-m6A RNA modifications, followed by the discussions of the recent studies on the biological roles and underlying mechanisms of non-m6A RNA modifications in haematological malignancies. We also highlight the potential of therapeutically targeting dysregulated non-m6A modifiers in blood cancer.
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Affiliation(s)
- Meiling Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Yuanzhong Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
| | - Kitty Wang
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Xiaolan Deng
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
- Gehr Family Center for Leukemia ResearchCity of Hope Medical Center and Comprehensive Cancer CenterDuarteCaliforniaUSA
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Yang L, Tang L, Min Q, Tian H, Li L, Zhao Y, Wu X, Li M, Du F, Chen Y, Li W, Li X, Chen M, Gu L, Sun Y, Xiao Z, Shen J. Emerging role of RNA modification and long noncoding RNA interaction in cancer. Cancer Gene Ther 2024; 31:816-830. [PMID: 38351139 PMCID: PMC11192634 DOI: 10.1038/s41417-024-00734-2] [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: 07/11/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
RNA modification, especially N6-methyladenosine, 5-methylcytosine, and N7-methylguanosine methylation, participates in the occurrence and progression of cancer through multiple pathways. The function and expression of these epigenetic regulators have gradually become a hot topic in cancer research. Mutation and regulation of noncoding RNA, especially lncRNA, play a major role in cancer. Generally, lncRNAs exert tumor-suppressive or oncogenic functions and its dysregulation can promote tumor occurrence and metastasis. In this review, we summarize N6-methyladenosine, 5-methylcytosine, and N7-methylguanosine modifications in lncRNAs. Furthermore, we discuss the relationship between epigenetic RNA modification and lncRNA interaction and cancer progression in various cancers. Therefore, this review gives a comprehensive understanding of the mechanisms by which RNA modification affects the progression of various cancers by regulating lncRNAs, which may shed new light on cancer research and provide new insights into cancer therapy.
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Affiliation(s)
- Liqiong Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Lu Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Qi Min
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Hua Tian
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Linwei Li
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Wanping Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Xiaobing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Meijuan Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Li Gu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Yuhong Sun
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
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9
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Meng S, Jiangtao B, Haisong W, Mei L, Long Z, Shanfeng L. RNA m 5C methylation: a potential modulator of innate immune pathways in hepatocellular carcinoma. Front Immunol 2024; 15:1362159. [PMID: 38807595 PMCID: PMC11131105 DOI: 10.3389/fimmu.2024.1362159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
RNA 5-methylcytosine (m5C) methylation plays a crucial role in hepatocellular carcinoma (HCC). As reported, aberrant m5C methylation is closely associated with the progression, therapeutic efficacy, and prognosis of HCC. The innate immune system functions as the primary defense mechanism in the body against pathogenic infections and tumors since it can activate innate immune pathways through pattern recognition receptors to exert anti-infection and anti-tumor effects. Recently, m5C methylation has been demonstrated to affect the activation of innate immune pathways including TLR, cGAS-STING, and RIG-I pathways by modulating RNA function, unveiling new mechanisms underlying the regulation of innate immune responses by tumor cells. However, research on m5C methylation and its interplay with innate immune pathways is still in its infancy. Therefore, this review details the biological significance of RNA m5C methylation in HCC and discusses its potential regulatory relationship with TLR, cGAS-STING, and RIG-I pathways, thereby providing fresh insights into the role of RNA methylation in the innate immune mechanisms and treatment of HCC.
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Affiliation(s)
| | | | | | | | | | - Li Shanfeng
- Department of Interventional Vascular Surgery, Affiliated Hospital of Hebei University, Baoding, China
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10
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Ge Y, Weng H, Sun Y, Wu M. Integrated single-cell and spatial transcriptomic analysis reveals YBX1 drives immune regulation in GBM progression. Heliyon 2024; 10:e29451. [PMID: 38628755 PMCID: PMC11019236 DOI: 10.1016/j.heliyon.2024.e29451] [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: 12/12/2023] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The RNA modification 5-methylcytosine (m5C) is widespread across various RNA types, significantly impacting RNA stability and translational efficiency. Accumulating evidence highlights its significant role within the tumorigenesis and progression of multiple malignancies. Nevertheless, the specific process through m5C is implicated in Glioblastoma (GBM) remains unclear. We conducted acomprehensive analysis of m5C expression distribution in single-cell GBM data. Our findings revealed elevated m5C scores in GBM single-cell data compared to the normal group. Additionally, multiple tumors exhibited significantly higher m5C scores than the normal group. Moreover, there was a positive correlation observed between the m5C score and inflammation score. m5C regulatory factor YBX1 exhibited a heightened expression in GBM, correlating closely with metastatic tendencies and an unfavorable prognosis across various cancer types. YBX1 has different biological functions in myeloid cells 1 and myeloid cells 2. YBX1 may act as immunosuppressive regulator by inhibiting the NF-κB pathway and inflammatory response in myeloid cells 1. YBX1 is essential for immune infiltrates, which creates a highly immunosuppressive tumor microenvironment by TNF signaling pathway in myeloid cells 2. YBX1+ neoplastic cells promote cell proliferation by NF-κB pathway. APOE mediates the interaction of YBX1+ myeloid cells and neoplastic cells by NF-κB.
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Affiliation(s)
- Yanshan Ge
- Hunan Provincial Tumor Hospital / the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Huiting Weng
- Department of Clinical Nursing, The Second Xiangya Hospital of Central South University, Changsha, 410008, Hunan, China
| | - Yingnan Sun
- Hunan Provincial Tumor Hospital / the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital / the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, 410008, Hunan, China
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11
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Chen H, Liu H, Zhang C, Xiao N, Li Y, Zhao X, Zhang R, Gu H, Kang Q, Wan J. RNA methylation-related inhibitors: Biological basis and therapeutic potential for cancer therapy. Clin Transl Med 2024; 14:e1644. [PMID: 38572667 PMCID: PMC10993167 DOI: 10.1002/ctm2.1644] [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: 12/30/2023] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/05/2024] Open
Abstract
RNA methylation is widespread in nature. Abnormal expression of proteins associated with RNA methylation is strongly associated with a number of human diseases including cancer. Increasing evidence suggests that targeting RNA methylation holds promise for cancer treatment. This review specifically describes several common RNA modifications, such as the relatively well-studied N6-methyladenosine, as well as 5-methylcytosine and pseudouridine (Ψ). The regulatory factors involved in these modifications and their roles in RNA are also comprehensively discussed. We summarise the diverse regulatory functions of these modifications across different types of RNAs. Furthermore, we elucidate the structural characteristics of these modifications along with the development of specific inhibitors targeting them. Additionally, recent advancements in small molecule inhibitors targeting RNA modifications are presented to underscore their immense potential and clinical significance in enhancing therapeutic efficacy against cancer. KEY POINTS: In this paper, several important types of RNA modifications and their related regulatory factors are systematically summarised. Several regulatory factors related to RNA modification types were associated with cancer progression, and their relationships with cancer cell migration, invasion, drug resistance and immune environment were summarised. In this paper, the inhibitors targeting different regulators that have been proposed in recent studies are summarised in detail, which is of great significance for the development of RNA modification regulators and cancer treatment in the future.
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Affiliation(s)
- Huanxiang Chen
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- School of Life ScienceZhengzhou UniversityZhengzhouChina
| | - Hongyang Liu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Chenxing Zhang
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Nan Xiao
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yang Li
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | | | - Ruike Zhang
- Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Huihui Gu
- Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Qiaozhen Kang
- School of Life ScienceZhengzhou UniversityZhengzhouChina
| | - Junhu Wan
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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12
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Zhang Y, Jia Q, Li F, Luo X, Wang Z, Wang X, Wang Y, Zhang Y, Li M, Bian L. Identification of molecular subtypes and a prognostic signature based on m6A/m5C/m1A-related genes in lung adenocarcinoma. Sci Rep 2024; 14:7543. [PMID: 38555384 PMCID: PMC10981664 DOI: 10.1038/s41598-024-57910-5] [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: 12/27/2023] [Accepted: 03/22/2024] [Indexed: 04/02/2024] Open
Abstract
Lung cancer, specifically the histological subtype lung adenocarcinoma (LUAD), has the highest global occurrence and fatality rate. Extensive research has indicated that RNA alterations encompassing m6A, m5C, and m1A contribute actively to tumorigenesis, drug resistance, and immunotherapy responses in LUAD. Nevertheless, the absence of a dependable predictive model based on m6A/m5C/m1A-associated genes hinders accurately predicting the prognosis of patients diagnosed with LUAD. In this study, we collected patient data from The Cancer Genome Atlas (TCGA) and identified genes related to m6A/m5C/m1A modifications using the GeneCards database. The "ConsensusClusterPlus" R package was used to produce molecular subtypes by utilizing genes relevant to m6A/m5C/m1A identified through differential expression and univariate Cox analyses. An independent prognostic factor was identified by constructing a prognostic signature comprising six genes (SNHG12, PABPC1, IGF2BP1, FOXM1, CBFA2T3, and CASC8). Poor overall survival and elevated expression of human leukocyte antigens and immune checkpoints were correlated with higher risk scores. We examined the associations between the sets of genes regulated by m6A/m5C/m1A and the risk model, as well as the immune cell infiltration, using algorithms such as ESTIMATE, CIBERSORT, TIMER, ssGSEA, and exclusion (TIDE). Moreover, we compared tumor stemness indices (TSIs) by considering the molecular subtypes related to m6A/m5C/m1A and risk signatures. Analyses were performed based on the risk signature, including stratification, somatic mutation analysis, nomogram construction, chemotherapeutic response prediction, and small-molecule drug prediction. In summary, we developed a prognostic signature consisting of six genes that have the potential for prognostication in patients with LUAD and the design of personalized treatments that could provide new versions of personalized management for these patients.
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Affiliation(s)
- Yu Zhang
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Qiuye Jia
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Fangfang Li
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Xuan Luo
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Zhiyuan Wang
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Xiaofang Wang
- Department of Pathology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yanghao Wang
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Yinglin Zhang
- Wenshan People's Hospital, Yunnan, Yunnan Province, China
| | - Muye Li
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China
| | - Li Bian
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming, 650302, Yunnan, China.
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13
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Alhammadi MA, Bajbouj K, Talaat IM, Hamoudi R. The role of RNA-modifying proteins in renal cell carcinoma. Cell Death Dis 2024; 15:227. [PMID: 38503745 PMCID: PMC10951318 DOI: 10.1038/s41419-024-06479-y] [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: 07/06/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 03/21/2024]
Abstract
Gene expression is one of the most critical cellular processes. It is controlled by complex mechanisms at the genomic, epigenomic, transcriptomic, and proteomic levels. Any aberration in these mechanisms can lead to dysregulated gene expression. One recently discovered process that controls gene expression includes chemical modifications of RNA molecules by RNA-modifying proteins, a field known as epitranscriptomics. Epitranscriptomics can regulate mRNA splicing, nuclear export, stabilization, translation, or induce degradation of target RNA molecules. Dysregulation in RNA-modifying proteins has been found to contribute to many pathological conditions, such as cancer, diabetes, obesity, cardiovascular diseases, and neurological diseases, among others. This article reviews the role of epitranscriptomics in the pathogenesis and progression of renal cell carcinoma. It summarizes the molecular function of RNA-modifying proteins in the pathogenesis of renal cell carcinoma.
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Affiliation(s)
- Muna A Alhammadi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
| | - Khuloud Bajbouj
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Basic Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States of America.
| | - Iman M Talaat
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Pathology Department, Faculty of Medicine, Alexandria University, 21131, Alexandria, Egypt.
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
- Division of Surgery and Interventional Science, University College London, London, NW3 2PS, United Kingdom.
- ASPIRE Precision Medicine Research Institute Abu Dhabi, University of Sharjah, Sharjah, United Arab Emirates.
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah, United Arab Emirates.
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14
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Yuan Y, Fan Y, Tang W, Sun H, Sun J, Su H, Fan H. Identification of ALYREF in pan cancer as a novel cancer prognostic biomarker and potential regulatory mechanism in gastric cancer. Sci Rep 2024; 14:6270. [PMID: 38491127 PMCID: PMC10942997 DOI: 10.1038/s41598-024-56895-5] [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: 10/07/2023] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
ALYREF is considered as a specific mRNA m5C-binding protein which recognizes m5C sites in RNA and facilitates the export of RNA from the nucleus to the cytoplasm. Expressed in various tissues and highly involved in the transcriptional regulation, ALYREF has the potential to become a novel diagnostic marker and therapeutic target for cancer patients. However, few studies focused on its function during carcinogenesis and progress. In order to explore the role of ALYREF on tumorigenesis, TCGA and GTEx databases were used to investigate the relationship of ALYREF to pan-cancer. We found that ALYREF was highly expressed in majority of cancer types and that elevated expression level was positively associated with poor prognosis in many cancers. GO and KEGG analysis showed that ALYREF to be essential in regulating the cell cycle and gene mismatch repair in tumor progression. The correlation analysis of tumor heterogeneity indicated that ALYREF could be specially correlated to the tumor stemness in stomach adenocarcinoma (STAD). Furthermore, we investigate the potential function of ALYREF on gastric carcinogenesis. Prognostic analysis of different molecular subtypes of gastric cancer (GC) unfolded that high ALYREF expression leads to poor prognosis in certain subtypes of GC. Finally, enrichment analysis revealed that ALYREF-related genes possess the function of regulating cell cycle and apoptosis that cause further influences in GC tumor progression. For further verification, we knocked down the expression of ALYREF by siRNA in GC cell line AGS. Knockdown of ALYREF distinctly contributed to inhibition of GC cell proliferation. Moreover, it is observed that knocked-down of ALYREF induced AGS cells arrested in G1 phase and increased cell apoptosis. Our findings highlighted the essential function of ALYREF in tumorigenesis and revealed the specific contribution of ALYREF to gastric carcinogenesis through pan-cancer analysis and biological experiments.
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Affiliation(s)
- Yujie Yuan
- The Key Laboratory of Developmental Genes and Human Diseases, Department of Medical Genetics and Developmental Biology, School of Medicine, Ministry of Education, Southeast University, Nanjing, 210009, China
| | - Yiyang Fan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wenqing Tang
- School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Hui Sun
- School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Jinghan Sun
- School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Hongmeng Su
- The Key Laboratory of Developmental Genes and Human Diseases, Department of Medical Genetics and Developmental Biology, School of Medicine, Ministry of Education, Southeast University, Nanjing, 210009, China
| | - Hong Fan
- The Key Laboratory of Developmental Genes and Human Diseases, Department of Medical Genetics and Developmental Biology, School of Medicine, Ministry of Education, Southeast University, Nanjing, 210009, China.
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15
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YE XING, TUO ZHOUTING, CHEN KAI, WU RUICHENG, WANG JIE, YU QINGXIN, YE LUXIA, MIYAMOTO AKIRA, YOO KOOHAN, ZHANG CHI, WEI WURAN, LI DENGXIONG, FENG DECHAO. Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF). Oncol Res 2024; 32:503-515. [PMID: 38361753 PMCID: PMC10865740 DOI: 10.32604/or.2024.045050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/01/2023] [Indexed: 02/17/2024] Open
Abstract
The increasing interest in RNA modifications has significantly advanced epigenomic and epitranscriptomic technologies. This study focuses on the immuno-oncological impact of ALYREF in human cancer through a pan-cancer analysis, enhancing understanding of this gene's role in cancer. We observed differential ALYREF expression between tumor and normal samples, correlating strongly with prognosis in various cancers, particularly kidney renal papillary cell carcinoma (KIRP) and liver hepatocellular carcinoma (LIHC). ALYREF showed a negative correlation with most tumor-infiltrating cells in lung squamous cell carcinoma (LUSC) and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), while positive correlations were noted in LIHC, kidney chromophobe (KICH), mesothelioma (MESO), KIRP, pheochromocytoma and paraganglioma (PARD), and glioma (GBMLGG). Additionally, ALYREF expression was closely associated with tumor heterogeneity, stemness indices, and a high mutation rate in TP53 across these cancers. In conclusion, ALYREF may serve as an oncogenic biomarker in numerous cancers, meriting further research attention.
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Affiliation(s)
- XING YE
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - ZHOUTING TUO
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - KAI CHEN
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - RUICHENG WU
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - JIE WANG
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - QINGXIN YU
- Department of Pathology, Ningbo Diagnostic Pathology Center, Ningbo, 315021, China
| | - LUXIA YE
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - AKIRA MIYAMOTO
- Department of Rehabilitation, West Kyushu University, Kanzaki-shi, 842-8585, Japan
| | - KOO HAN YOO
- Department of Urology, Kyung Hee University, Seoul, 446 701, South Korea
| | - CHI ZHANG
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - WURAN WEI
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - DENGXIONG LI
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - DECHAO FENG
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
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16
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Pan A, Xue Y, Ruan X, Dong W, Wang D, Liu Y, Liu L, Lin Y, E T, Lin H, Xu H, Liu X, Wang P. m5C modification of LINC00324 promotes angiogenesis in glioma through CBX3/VEGFR2 pathway. Int J Biol Macromol 2024; 257:128409. [PMID: 38016610 DOI: 10.1016/j.ijbiomac.2023.128409] [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: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Angiogenesis plays a major role in tumor initiation, progression, and metastasis. This is why finding antiangiogenic targets is essential in the treatment of gliomas. In this study, NSUN2 and LINC00324 were significantly upregulated in conditionally cultured glioblastoma endothelial cells (GECs). Knockdown of NSUN2 or LINC00324 inhibits GECs angiogenesis. NSUN2 increased the stability of LINC00324 by m5C modification and upregulated LINC00324 expression. LINC00324 competes with the 3'UTR of CBX3 mRNA to bind to AUH protein, reducing the degradation of CBX3 mRNA. In addition, CBX3 directly binds to the promoter region of VEGFR2, enhances VEGFR2 transcription, and promotes GECs angiogenesis. These findings demonstrated NSUN2/LINC00324/CBX3 axis plays a crucial role in regulating glioma angiogenesis, which provides new strategies for glioma therapy.
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Affiliation(s)
- Aini Pan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Weiwei Dong
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Di Wang
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yunhui Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Libo Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yang Lin
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Tiange E
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Hongda Lin
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Hailing Xu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xiaobai Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China..
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17
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Zhao Y, Xing C, Peng H. ALYREF (Aly/REF export factor): A potential biomarker for predicting cancer occurrence and therapeutic efficacy. Life Sci 2024; 338:122372. [PMID: 38135116 DOI: 10.1016/j.lfs.2023.122372] [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: 10/04/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
5-Methylcytosine (m5C) methylation is present in almost all types of RNA as an essential epigenetic modification. It is dynamically modulated by its associated enzymes, including m5C methyltransferases (NSUN, DNMT and TRDMT family members), demethylases (TET family and ALKBH1) and binding proteins (YTHDF2, ALYREF and YBX1). Among them, aberrant expression of the RNA-binding protein ALYREF can facilitate a variety of malignant phenotypes such as maintenance of proliferation, malignant heterogeneity, metastasis, and drug resistance to cell death through different regulatory mechanisms, including pre-mRNA processing, mRNA stability, and nuclear-cytoplasmic shuttling. The induction of these cellular processes by ALYREF results in treatment resistance and poor outcomes for patients. However, there are currently few reports of clinical applications or drug trials related to ALYREF. In addition, the looming observations on the role of ALYREF in the mechanisms of carcinogenesis and disease prognosis have triggered considerable interest, but critical evidence is not available. For example, animal experiments and ALYREF small molecule inhibitor trials. In this review, we, therefore, revisit the literature on ALYREF and highlight its importance as a prognostic biomarker for early prevention and as a therapeutic target.
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Affiliation(s)
- Yan Zhao
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Cheng Xing
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Changsha, Hunan 410011, China; Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan 410011, China.
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18
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Wang R, Yang Y, Lu T, Cui Y, Li B, Liu X. Circulating cell-free DNA-based methylation pattern in plasma for early diagnosis of esophagus cancer. PeerJ 2024; 12:e16802. [PMID: 38313016 PMCID: PMC10838104 DOI: 10.7717/peerj.16802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024] Open
Abstract
With the increased awareness of early tumor detection, the importance of detecting and diagnosing esophageal cancer in its early stages has been underscored. Studies have consistently demonstrated the crucial role of methylation levels in circulating cell-free DNA (cfDNA) in identifying and diagnosing early-stage cancer. cfDNA methylation pertains to the methylation state within the genomic scope of cfDNA and is strongly associated with cancer development and progression. Several research teams have delved into the potential application of cfDNA methylation in identifying early-stage esophageal cancer and have achieved promising outcomes. Recent research supports the high sensitivity and specificity of cfDNA methylation in early esophageal cancer diagnosis, providing a more accurate and efficient approach for early detection and improved clinical management. Accordingly, this review aims to present an overview of methylation-based cfDNA research with a focus on the latest developments in the early detection of esophageal cancer. Additionally, this review summarizes advanced analytical technologies for cfDNA methylation that have significantly benefited from recent advancements in separation and detection techniques, such as methylated DNA immunoprecipitation sequencing (MeDIP-seq). Recent findings suggest that biomarkers based on cfDNA methylation may soon find successful applications in the early detection of esophageal cancer. However, large-scale prospective clinical trials are required to identify the potential of these biomarkers.
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Affiliation(s)
- Rui Wang
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Yue Yang
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Tianyu Lu
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Youbin Cui
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Bo Li
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Xin Liu
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
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Ding Y, Bajpai AK, Wu F, Lu W, Xu L, Mao J, Li Q, Pan Q, Lu L, Wang X. 5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia. Aging (Albany NY) 2024; 16:2340-2361. [PMID: 38277218 PMCID: PMC10911375 DOI: 10.18632/aging.205484] [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: 09/22/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024]
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous malignant disease of the blood cell. The current therapies for AML are unsatisfactory and the molecular mechanisms underlying AML are unclear. 5-methylcytosine (m5C) is an important posttranscriptional modification of mRNA, and is involved in the regulation of mRNA stability, translation, and other aspects of RNA metabolism. However, based on our knowledge of published literature, the role of the m5C regulators has not been explored in AML till date. In this study, we clarified the expression and gene variants of m5C regulators in AML and found that most m5C regulators were differentially expressed and correlated with disease prognosis. We also found that the methylation status of certain m5C regulators (e.g., DNMT3A, DNMT3B) affects the survival of AML patients. Two m5C modification subtypes, and high- and low-risk subgroups identified based on the expression of m5C regulators showed significant differences in the prognosis as well as immune cell infiltration. In addition, most of the m5C regulators were found to be correlated with miRNA expression in AML, as well as IC50 values of many drugs. The miRNA and GSVA analysis were used to identify the different miRNAs and KEGG or hallmark pathways between high- and low-risk subgroups. We also built a prognostic model based on m5C regulators, which was validated by two GSE databases. To verify the reliability of our analysis and conclusions, qPCR was used to identify the expressions of m5C regulators between normal and AML. In summary, we comprehensively explored the molecular characteristics of m5C regulators and built a prognostic model in AML. We proposed new mechanistic insights into the role of m5C in multiple databases and clinical data, which may pave novel ways for the development of therapeutic strategies.
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Affiliation(s)
- Yuhong Ding
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Akhilesh K. Bajpai
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Cente, Memphis, TN 38163, USA
| | - Fengxia Wu
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Weihua Lu
- Department of Hematology and Oncology, The Branch Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Lin Xu
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Jiawei Mao
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Qiang Li
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Qi Pan
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Lu Lu
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Cente, Memphis, TN 38163, USA
| | - Xinfeng Wang
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
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20
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Xu R, Wang Y, Kuang Y. Multi-omic analyses of m5C readers reveal their characteristics and immunotherapeutic proficiency. Sci Rep 2024; 14:1651. [PMID: 38238581 PMCID: PMC10796763 DOI: 10.1038/s41598-024-52110-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/13/2024] [Indexed: 01/22/2024] Open
Abstract
5-methylcytosine (m5C) is a post-transcriptional RNA modification identified, m5C readers can specifically identify and bind to m5C. ALYREF and YBX1 as members of m5C readers that have garnered increasing attention in cancer research. However, comprehensive analysis of their molecular functions across pancancer are lacking. Using the TCGA and GTEx databases, we investigated the expression levels and prognostic values of ALYREF and YBX1. Additionally, we assessed the tumor microenvironment, immune checkpoint-related genes, immunomodulators, Tumor Immune Dysfunction and Exclusion (TIDE) score and drug resistance of ALYREF and YBX1. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) analyses were performed to investigate the potential functions associated with m5C readers and coexpressed genes. Aberrant expression of ALYREF and YBX1 was observed and positively associated with prognosis in KIRP, LGG and LIHC. Furthermore, the expression levels of ALYREF and YBX1 were significantly correlated with immune infiltration of the tumor microenvironment and immune-related modulators. Last, our analysis revealed significant correlations between ALYREF, YBX1 and eIFs. Our study provides a substantial understanding of m5C readers and the intricate relationship between ALYREF, YBX1, eIFs, and mRNA dynamics. Through multidimensional analysis of immune infiltration and drug sensitivity/resistance in ALYREF and YBX1, we propose a possibility for combined modality therapy utilizing m5C readers.
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Affiliation(s)
- Rui Xu
- Department of Development Planning, International Medical Opening-up Pilot Zone (China), Fangchenggang, Guangxi Province, China
| | - Yue Wang
- Department of Endocrinology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China.
| | - Ye Kuang
- Department of Medical Laboratory, Yan'An Hospital of Kunming City, Kunming, Yunnan Province, China.
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21
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Wei H, Xu Y, Lin L, Li Y, Zhu X. A review on the role of RNA methylation in aging-related diseases. Int J Biol Macromol 2024; 254:127769. [PMID: 38287578 DOI: 10.1016/j.ijbiomac.2023.127769] [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: 09/18/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.
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Affiliation(s)
- Hong Wei
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Department of Neurology, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuhao Xu
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuefeng Li
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China.
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.
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22
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Rodrigues P, Bangali H, Ali E, Nauryzbaevish AS, Hjazi A, Fenjan MN, Alawadi A, Alsaalamy A, Alasheqi MQ, Mustafa YF. The mechanistic role of NAT10 in cancer: Unraveling the enigmatic web of oncogenic signaling. Pathol Res Pract 2024; 253:154990. [PMID: 38056132 DOI: 10.1016/j.prp.2023.154990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
N-acetyltransferase 10 (NAT10), a versatile enzyme, has gained considerable attention as a significant player in the complex realm of cancer biology. Its enigmatic role in tumorigenesis extends across a wide array of cellular processes, impacting cell growth, differentiation, survival, and genomic stability. Within the intricate network of oncogenic signaling, NAT10 emerges as a crucial agent in multiple cancer types, such as breast, lung, colorectal, and leukemia. This compelling research addresses the intricate complexity of the mechanistic role of NAT10 in cancer development. By elucidating its active participation in essential physiological processes, we investigate the regulatory role of NAT10 in cell cycle checkpoints, coordination of chromatin remodeling, and detailed modulation of the delicate balance between apoptosis and cell survival. Perturbations in NAT10 expression and function have been linked to oncogenesis, metastasis, and drug resistance in a variety of cancer types. Furthermore, the bewildering interactions between NAT10 and key oncogenic factors, such as p53 and c-Myc, are deciphered, providing profound insights into the molecular underpinnings of cancer pathogenesis. Equally intriguing, the paradoxical role of NAT10 as a potential tumor suppressor or oncogene is influenced by context-dependent factors and the cellular microenvironment. This study explores the fascinating interplay of genetic changes, epigenetic changes, and post-translational modifications that shape the dual character of NAT10, revealing the delicate balance between cancer initiation and suppression. Taken together, this overview delves deeply into the enigmatic role of NAT10 in cancer, elucidating its multifaceted roles and its complex interplay with oncogenic networks.
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Affiliation(s)
- Paul Rodrigues
- Department of Computer Engineering, College of Computer Science, King Khalid University, Al-Faraa, Saudi Arabia.
| | - Harun Bangali
- Department of Computer Engineering, College of Computer Science, King Khalid University, Al-Faraa, Saudi Arabia
| | - Eyhab Ali
- College of Chemistry, Al-Zahraa University for Women, Karbala, Iraq
| | - Abdreshov Serik Nauryzbaevish
- Institute of Genetics and Physiology SC MSHE RK, Laboratory of Physiology Lymphatic System, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Mohammed N Fenjan
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Iraq
| | - Ali Alsaalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul 41001, Iraq
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23
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Liu HT, Rau CS, Liu YW, Hsieh TM, Huang CY, Chien PC, Lin HP, Wu CJ, Chuang PC, Hsieh CH. Deciphering the Divergent Gene Expression Landscapes of m6A/m5C/m1A Methylation Regulators in Hepatocellular Carcinoma Through Single-Cell and Bulk RNA Transcriptomic Analysis. J Hepatocell Carcinoma 2023; 10:2383-2395. [PMID: 38164510 PMCID: PMC10758181 DOI: 10.2147/jhc.s448047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction RNA modifications mediated by the m6A, m1A, and m5C regulatory genes are crucial for the progression of malignancy. This study aimed to explore the expression of regulator genes for m6A/m5C/m1A methylation at the single-cell level and to validate their expression in cancerous and adjacent para-cancerous liver tissues of adult patients with HCC who underwent tumor resection. Methods The bulk sequencing from The Cancer Genome Atlas (TCGA) database and the single-cell RNA sequencing (scRNA-seq) data obtained from the Gene Expression Omnibus (GEO) database were used to identify the dysregulated m6A/m5C/m1A genes for hepatocellular carcinoma (HCC). A real-time polymerase chain reaction (real-time PCR) was used to measure the expression of dysregulated m6A/m5C/m1A genes in collected human HCC tissues and compared with adjacent para-cancerous liver tissues. Immune cell infiltration with these significantly expressed methylation-related genes was evaluated using Timer2.0. Results A discrepancy in m6A/m5C/m1A gene expression was observed between bulk sequencing and scRNA-seq. The clustered heatmap of the scRNA-seq-identified dysregulated m6A/m5C/m1A genes in TCGA cohort revealed heterogeneous expression of these methylation regulators within the cancer, whereas their expression in the adjacent liver tissues was more homogeneous. The real-time PCR validated the significant overexpression of DNMT1, NSUN5, TRMT6, IGF2BP1, and IGFBP3, which were identified using scRNA-seq, and IGFBP2, which was identified using bulk sequencing. These dysregulated methylation genes are mainly correlated with the infiltration of natural killer cells. Discussion This study suggests that cellular diversity inside tumors contributes to the discrepancy in the expression of methylation regulator genes between traditional bulk sequencing and scRNA-seq. This study identified five regulatory genes that will be the focus of further studies regarding the function of m6A/m5C/m1A in HCC.
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Affiliation(s)
- Hang-Tsung Liu
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Cheng-Shyuan Rau
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Yueh-Wei Liu
- Department of General Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Ting-Min Hsieh
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Chun-Ying Huang
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Peng-Chen Chien
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Hui-Ping Lin
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Chia-Jung Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Pei-Chin Chuang
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, 83301, Taiwan
| | - Ching-Hua Hsieh
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
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24
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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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25
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Zheng L, Duan Y, Li M, Wei J, Xue C, Chen S, Wei Q, Tang F, Xiong W, Zhou M, Deng H. Deciphering the vital roles and mechanism of m5C modification on RNA in cancers. Am J Cancer Res 2023; 13:6125-6146. [PMID: 38187052 PMCID: PMC10767349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
5-methylcytosine (m5C modification) plays an essential role in tumors, which affects different types of RNA, the expression of downstream target genes, and downstream pathways, thus participating in the tumor process. However, the effect of m5C modification on RNA in tumors and the exact mechanism have not been systematically reviewed. Therefore, we reviewed the status and sites of m5C modification, as well as the expression pattern and biological functions of m5C regulators in tumors, and further summarized the effects and regulation mechanism of m5C modification on messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA) and other RNA in tumors. Finally, we summed up the interaction network, potential application, and value in clinical diagnosis and treatment of tumors. Taken together, this review benefits revealing the mechanism of m5C modification in tumor progression and provides new strategies for tumor diagnosis and treatment.
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Affiliation(s)
- Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Yumei Duan
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Qingqing Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Faqing Tang
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of The Chinese Ministry of Education, Central South UniversityChangsha, Hunan, China
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha, Hunan, China
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha, Hunan, China
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26
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Shao D, Liu C, Wang Y, Lin J, Cheng X, Han P, Li Z, Jian D, Nie J, Jiang M, Wei Y, Xing J, Guo Z, Wang W, Yi X, Tang H. DNMT1 determines osteosarcoma cell resistance to apoptosis by associatively modulating DNA and mRNA cytosine-5 methylation. FASEB J 2023; 37:e23284. [PMID: 37905981 DOI: 10.1096/fj.202301306r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/17/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023]
Abstract
Cellular apoptosis is a central mechanism leveraged by chemotherapy to treat human cancers. 5-Methylcytosine (m5C) modifications installed on both DNA and mRNA are documented to regulate apoptosis independently. However, the interplay or crosstalk between them in cellular apoptosis has not yet been explored. Here, we reported that promoter methylation by DNMT1 coordinated with mRNA methylation by NSun2 to regulate osteosarcoma cell apoptosis. DNMT1 was induced during osteosarcoma cell apoptosis triggered by chemotherapeutic drugs, whereas NSun2 expression was suppressed. DNMT1 was found to repress NSun2 expression by methylating the NSun2 promoter. Moreover, DNMT1 and NSun2 regulate the anti-apoptotic genes AXL, NOTCH2, and YAP1 through DNA and mRNA methylation, respectively. Upon exposure to cisplatin or doxorubicin, DNMT1 elevation drastically reduced the expression of these anti-apoptotic genes via enhanced promoter methylation coupled with NSun2 ablation-mediated attenuation of mRNA methylation, thus rendering osteosarcoma cells to apoptosis. Collectively, our findings establish crosstalk of importance between DNA and RNA cytosine methylations in determining osteosarcoma resistance to apoptosis during chemotherapy, shedding new light on future treatment of osteosarcoma, and adding additional layers to the control of gene expression at different epigenetic levels.
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Affiliation(s)
- Dongxing Shao
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
| | - Cihang Liu
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
| | - Yingying Wang
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
| | - Jing Lin
- Department of Laboratory Medicine, the Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaolei Cheng
- Department of Anesthesiology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, China
| | - Pei Han
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhen Li
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
| | - Dongdong Jian
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Junwei Nie
- R&D Department, Vazyme Biotech Co., Ltd, Nanjing, China
| | | | - Yuanzhi Wei
- R&D Department, Vazyme Biotech Co., Ltd, Nanjing, China
| | - Junyue Xing
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
- Henan Key Laboratory of Chronic Disease Management, Department of Health Management Center, Henan Provincial People's Hospital, Department of Health Management Center of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhiping Guo
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
- Henan Key Laboratory of Chronic Disease Management, Department of Health Management Center, Henan Provincial People's Hospital, Department of Health Management Center of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Wengong Wang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xia Yi
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hao Tang
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
- Henan Key Laboratory of Chronic Disease Management, Department of Health Management Center, Henan Provincial People's Hospital, Department of Health Management Center of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
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Zhang Y, Chen XN, Zhang H, Wen JK, Gao HT, Shi B, Wang DD, Han ZW, Gu JF, Zhao CM, Xue WY, Zhang YP, Qu CB, Yang Z. CDK13 promotes lipid deposition and prostate cancer progression by stimulating NSUN5-mediated m5C modification of ACC1 mRNA. Cell Death Differ 2023; 30:2462-2476. [PMID: 37845385 PMCID: PMC10733287 DOI: 10.1038/s41418-023-01223-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) regulate cell cycle progression and the transcription of a number of genes, including lipid metabolism-related genes, and aberrant lipid metabolism is involved in prostate carcinogenesis. Previous studies have shown that CDK13 expression is upregulated and fatty acid synthesis is increased in prostate cancer (PCa). However, the molecular mechanisms linking CDK13 upregulation and aberrant lipid metabolism in PCa cells remain largely unknown. Here, we showed that upregulation of CDK13 in PCa cells increases the fatty acyl chains and lipid classes, leading to lipid deposition in the cells, which is positively correlated with the expression of acetyl-CoA carboxylase (ACC1), the first rate-limiting enzyme in fatty acid synthesis. Gain- and loss-of-function studies showed that ACC1 mediates CDK13-induced lipid accumulation and PCa progression by enhancing lipid synthesis. Mechanistically, CDK13 interacts with RNA-methyltransferase NSUN5 to promote its phosphorylation at Ser327. In turn, phosphorylated NSUN5 catalyzes the m5C modification of ACC1 mRNA, and then the m5C-modified ACC1 mRNA binds to ALYREF to enhance its stability and nuclear export, thereby contributing to an increase in ACC1 expression and lipid deposition in PCa cells. Overall, our results disclose a novel function of CDK13 in regulating the ACC1 expression and identify a previously unrecognized CDK13/NSUN5/ACC1 pathway that mediates fatty acid synthesis and lipid accumulation in PCa cells, and targeting this newly identified pathway may be a novel therapeutic option for the treatment of PCa.
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Affiliation(s)
- Yong Zhang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
| | - Xiao-Nan Chen
- Department of Urology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, 110004, P R China
| | - Hong Zhang
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Jin-Kun Wen
- Department of Biochemistry and Molecular Biology, Ministry of Education of China, Hebei Medical University, No. 361 Zhongshan E Rd, Shijiazhuang, 050017, China
| | - Hai-Tao Gao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Bei Shi
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Dan-Dan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Zhen-Wei Han
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Jun-Fei Gu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chen-Ming Zhao
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Wen-Yong Xue
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Yan-Ping Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Chang-Bao Qu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
| | - Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
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Liu T, Wang Y, Li Z, Sun L, Yang K, Chen J, Han X, Qi L, Zhou X, Wang P. Establishment of a new molecular subtyping and prognostic signature with m6A/m5C/m1A/m7G regulatory genes for hepatocellular carcinoma. Heliyon 2023; 9:e21285. [PMID: 38027812 PMCID: PMC10660009 DOI: 10.1016/j.heliyon.2023.e21285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/19/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background RNA modification, including m6A, m5C, m1A, and m7G, participated in tumor progress. Therefore, the purpose of the present study was to explore the role of m6A/m5C/m1A/m7G regulatory genes in the prognosis and tumor microenvironment (TME) for hepatocellular carcinoma (HCC). Methods 71 m6A/m5C/m1A/m7G regulatory genes expression for HCC was detected, differentially expressed genes were screened, and molecular forms were classified by unsupervised consensus clustering. Cox regression and the Least Absolute Shrinkage and Selection Operator (LASSO) analysis were applied to establish a prognostic signature. Time-dependent receiver operating characteristic (ROC) curves were evaluated for clinical effectiveness and accuracy of the prognostic hazard model. In cluster subtypes and risk models, the differences in prognosis, immune cell infiltration, immune checkpoint, immunotherapy, and drug sensitivity between different subtypes were evaluated. Results HCC patients were classified into two clusters (cluster 1 and cluster 2) according to the expression of 71 m6A/m5C/m1A/m7G regulatory genes. Cluster 1 had a poor prognosis and different immune cell infiltration. Cluster 1 had higher immune checkpoint expression and TIDE score than cluster 2. Subsequently, we construct a five-gene prognostic model of m6A/m5C/m1A/m7G regulatory genes (YTHDF2, YTHDF1,YBX1, TRMT61A, TRMT10C). The Kaplan-Meier and ROC curve analysis showed that the prognostic signature exhibited good predictability. The risk score was considered an independent poor prognostic index. The high-risk group had higher immune checkpoint expression and higher TIDE scores. 5-Fluorouracil, docetaxel, doxorubicin, etoposide, gemcitabine, paclitaxel, sorafenib, and vinblastine were more suitable for high-risk patients. ECM receptor interaction, cell cycle, and Leishmania infection were enriched in the high-risk group. Conclusion The clustering subgroups and prognostic model of m6A/m5C/m1A/m7G regulatory genes were linked with bad prognosis and TME for HCC, and had the potential to be a novel tool to evaluate the outcomes of HCC patients.
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Affiliation(s)
- Ting Liu
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People's Republic of China
| | - Yang Wang
- Department of General Surgical Department, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People’s Republic of China
| | - Zhizhao Li
- Department of Cardiovasology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, China
| | - Lei Sun
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People's Republic of China
| | - Kun Yang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People's Republic of China
| | - Jiamin Chen
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People's Republic of China
| | - Xiaoyi Han
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People's Republic of China
| | - Liming Qi
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People's Republic of China
| | - Xingang Zhou
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People's Republic of China
| | - Peng Wang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing 100015, People's Republic of China
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Yang S, Luo Y, Zhou D, Xiang J, Xi X. RNA 5-Methylcytosine regulators are associated with cell adhesion and predict prognosis of endometrial cancer. Transl Cancer Res 2023; 12:2556-2571. [PMID: 37969377 PMCID: PMC10643971 DOI: 10.21037/tcr-23-742] [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: 04/28/2023] [Accepted: 09/21/2023] [Indexed: 11/17/2023]
Abstract
Background RNA methylation is a significant form of post-transcriptional modification that has been implicated in various diseases, including cancers. One prominent type of RNA methylation is 5-Methylcytosine (m5C), which primarily regulates RNA stability, transcription, and translation. However, the role of m5C-related gene regulation in cell adhesion within uterine corpus endometrial carcinoma (UCEC) remains unexplored. Therefore, the objective of this study was to investigate the association between RNA m5C methylation and UCEC and develop a prognostic predictive model to forecast survival outcomes in UCEC patients. Methods The RNA datasets were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The dataset was used to explore the interaction relationships of m5C regulators in UCEC. Unsupervised clustering analysis identified clusters with distinct m5C modification patterns. Different clusters underwent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment level analysis to investigate the effects of pathways related to m5C methylation, which were further validated through in vitro cellular experiments. A prognostic predictive model was developed using the least absolute shrinkage and selection operator (LASSO) and multivariate regression analysis. Results Two clusters with distinct m5C modification patterns were identified using unsupervised cluster analysis. Furthermore, the prognosis of cluster 2 was found to be worse. Enrichment analysis showed alterations in cell adhesion-related pathways in both clusters, as well as differences between the clusters. Through this analysis, we identified 25 genes with significant prognostic value. Finally, a prognostic predictive model comprising NSUN2 and YBX1 was constructed. Conclusions In conclusion, diverse m5C modification patterns display distinct cell adhesion properties in UCEC, which are correlated with prognosis and offer significant potential as prognostic markers for UCEC assessment. We developed a prognostic predictive model to accurately predict the prognosis of UCEC.
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Affiliation(s)
- Shimin Yang
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifan Luo
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongmei Zhou
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiangdong Xiang
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaowei Xi
- Department of Gynecology and Obstetrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhang Z, Zhang Y, Cai Y, Li D, He J, Feng Z, Xu Q. NAT10 regulates the LPS-induced inflammatory response via the NOX2-ROS-NF-κB pathway in macrophages. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119521. [PMID: 37307924 DOI: 10.1016/j.bbamcr.2023.119521] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/08/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023]
Abstract
Periodontitis is a chronic osteolytic inflammatory disease resulting from complex dynamic interactions among bacterial pathogens and the host immune response. Macrophages play a vital role in the pathogenesis of periodontitis by triggering periodontal inflammation and inducing periodontium destruction. N-Acetyltransferase 10 (NAT10) is an acetyltransferase that has been shown to catalyse N4-acetylcytidine (ac4C) mRNA modification and is related to cellular pathophysiological processes, including the inflammatory immune response. Nevertheless, whether NAT10 regulates the inflammatory response of macrophages in periodontitis remains unclear. In this study, the expression of NAT10 in macrophages was found to decrease during LPS-induced inflammation. NAT10 knockdown significantly reduced the generation of inflammatory factors, while NAT10 overexpression had the opposite effect. RNA sequencing revealed that the differentially expressed genes were enriched in the NF-κB signalling pathway and oxidative stress. Both the NF-κB inhibitor Bay11-7082 and the ROS scavenger N-acetyl-L-cysteine (NAC) could reverse the upregulation of inflammatory factors. NAC inhibited the phosphorylation of NF-κB, but Bay11-7082 had no effect on the production of ROS in NAT10-overexpressing cells, suggesting that NAT10 activated the LPS-induced NF-κB signalling pathway by regulating ROS generation. Furthermore, the expression and stability of Nox2 was promoted after NAT10 overexpression, indicating that Nox2 may be a potential target of NAT10. In vivo, the NAT10 inhibitor Remodelin reduced macrophage infiltration and bone resorption in ligature-induced periodontitis mice. In summary, these results showed that NAT10 accelerated LPS-induced inflammation via the NOX2-ROS-NF-κB pathway in macrophages and that its inhibitor Remodelin might be of potential therapeutic significance in periodontitis treatment.
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Affiliation(s)
- Zhanqi Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yiwen Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yongjie Cai
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Di Li
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Jinlin He
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Zhihui Feng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Qiong Xu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
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Zhang M, Zuo Y, Guo J, Yang L, Wang Y, Tan M, Guo X. A novel signature for predicting prognosis and immune landscape in cutaneous melanoma based on anoikis-related long non-coding RNAs. Sci Rep 2023; 13:16332. [PMID: 37770477 PMCID: PMC10539372 DOI: 10.1038/s41598-023-39837-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/31/2023] [Indexed: 09/30/2023] Open
Abstract
Anoikis is a unique form of apoptosis associated with vascularization and distant metastasis in cancer. Eliminating anoikis resistance in tumor cells could be a promising target for improving the prognosis of terminal cancer patients. However, current studies have not elaborated on the prognosis effect of anoikis-related long non-coding RNAs (lncRNAs) in cutaneous melanoma. Pre-processed data, including RNA sequences and clinical information, were retrieved from TCGA and GTEx databases. After a series of statistical analyses, anoikis-related lncRNAs with prognostic significance were identified, and a unique risk signature was constructed. Risk scores were further analyzed in relation to the tumor microenvironment, tumor immune dysfunction and exclusion, immune checkpoint genes, and RNA methylation genes. The indicators were also used to predict the potentially sensitive anti-cancer drugs. An anoikis-related lncRNAs risk signature consisting of LINC01711, POLH-AS1, MIR205HG, and LINC02416 was successfully established in cutaneous melanoma. Overall survival and progression-free survival of patients were strongly linked with the risk score, independently of other clinical factors. The low-risk group exhibited a more beneficial immunological profile, was less affected by RNA methylation, and was more sensitive to the majority of anti-cancer drugs, all of which indicated a better prognostic outcome. The 4 hub lncRNAs may be fundamental to studying the mechanism of anoikis in cutaneous melanoma and provide personalized therapy for salvaging drug resistance.
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Affiliation(s)
- Miao Zhang
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yuzhi Zuo
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Guo
- Vascular Surgery Department, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Lushan Yang
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yizhi Wang
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Meiyun Tan
- Department of Orthopaedics, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
| | - Xing Guo
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
- Center of Ambulatory Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
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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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Ma Y, Sun Y, Zhao X, Li J, Fu X, Gong T, Zhang X. Identification of m 5C-related lncRNAs signature to predict prognosis and therapeutic responses in esophageal squamous cell carcinoma patients. Sci Rep 2023; 13:14499. [PMID: 37666951 PMCID: PMC10477299 DOI: 10.1038/s41598-023-41495-6] [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: 09/28/2022] [Accepted: 08/28/2023] [Indexed: 09/06/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) has a dismal prognosis because of atypical early symptoms and heterogeneous therapeutic responses. 5-methylcytosine (m5C) modification plays an important role in the onset and development of many tumors and is widespread in long non-coding RNA (lncRNA) transcripts. However, the functions of m5C and lncRNAs in ESCC have not been completely elucidated. Herein, this study aimed to explore the role of m5C-related lncRNAs in ESCC. The RNA-seq transcriptome profiles and clinical information were downloaded from the TCGA-ESCC database. Pearson analysis was used to identify m5C-related lncRNAs. Then we established the m5C-related lncRNAs prognostic signature (m5C-LPS) using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analysis. Then, the prognostic value of m5C-LPS was evaluated internally and externally using the TCGA-ESCC and GSE53622 databases through multiple methods. We also detected the expression of these lncRNAs in ESCC cell lines and patient tissues. Fluorescence in situ hybridization (FISH) was used to detect the prognostic value of specific lncRNA. In addition, clinical parameters, immune status, genomic variants, oncogenic pathways, enrichment pathways, and therapeutic response features associated with m5C-LPS were explored using bioinformatics methods. We constructed and validated a prognostic signature based on 9 m5C-related lncRNAs (AC002091.2, AC009275.1, CAHM, LINC02057.1, AC0006329.1, AC037459.3, AC064807.1, ATP2B1-AS1, and UBAC2-AS1). The quantitative real-time polymerase chain reaction (qRT-PCR) revealed that most lncRNAs were upregulated in ESCC cell lines and patient tissues. And AC002091.2 was validated to have significant prognostic value in ESCC patients. A composite nomogram was generated to facilitate clinical practice by integrating this signature with the N stage. Besides, patients in the low-risk group were characterized by good clinical outcomes, favorable immune status, and low oncogenic alteration. Function enrichment analysis indicated that the risk score was associated with mRNA splicing, ncRNA processing, and DNA damage repair response. At the same time, we found significant differences in the responses to chemoradiotherapy between the two groups, proving the value of m5C-LPS in treatment decision-making in ESCC. This study established a novel prognostic signature based on 9 m5C-related lncRNAs, which is a promising biomarker for predicting clinical outcomes and therapeutic response in ESCC.
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Affiliation(s)
- Yuan Ma
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Yuchen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xu Zhao
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Jing Li
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xing Fu
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Tuotuo Gong
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China.
| | - Xiaozhi Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China.
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Hu S, Yang M, Xiao K, Yang Z, Cai L, Xie Y, Wang L, Wei R. Loss of NSUN6 inhibits osteosarcoma progression by downregulating EEF1A2 expression and activation of Akt/mTOR signaling pathway via m 5C methylation. Exp Ther Med 2023; 26:457. [PMID: 37614424 PMCID: PMC10443047 DOI: 10.3892/etm.2023.12156] [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: 12/05/2022] [Accepted: 06/29/2023] [Indexed: 08/25/2023] Open
Abstract
As an important 5-methylcytidine (m5C) methyltransferase, NOP2/Sun RNA methyltransferase family member 6 (NSUN6) has been reported to play an important role in the progression of several diseases. However, the role of NSUN6 in the progression of osteosarcoma (OS) remains unclear. This study aimed to identify the role of NSUN6 in the progression of OS and clarify the potential molecular mechanism. The present study discovered that NSUN6 was upregulated in OS and a higher NSUN6 expression was a strong indicator for poorer prognosis of patients with OS. In addition, the loss of NSUN6 led to reduced proliferation, migration and invasion of OS cells. Through bioinformatics analysis, RNA immunoprecipitation (RIP) and methylated RIP assays, eukaryotic elongation factor 1 α-2 (EEF1A2) was identified and validated as a potential target of NSUN6 in OS. Mechanistically, the expression of EEF1A2 was significantly suppressed following NSUN6 knockdown due to reduced EEF1A2 mRNA stability in an m5C-dependent manner. Meanwhile, NSUN6 deficiency inhibited m5C-dependent activation of Akt/mTOR signaling pathway. In addition, genetic overexpression of EEF1A2 or pharmacological activation of the Akt signaling pathway counteracted the suppressive effects of NSUN6 deficiency on the proliferation, invasion and migration of OS cells. The current findings suggested that NSUN6 may serve as a potential therapeutic target for OS treatment.
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Affiliation(s)
- Sang Hu
- Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Min Yang
- Department of Orthopedics, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Kangwen Xiao
- Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Zhiqiang Yang
- Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Lin Cai
- Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yuanlong Xie
- Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Linlong Wang
- Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Renxiong Wei
- Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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Yang Q, Wang M, Xu J, Yu D, Li Y, Chen Y, Zhang X, Zhang J, Gu J, Zhang X. LINC02159 promotes non-small cell lung cancer progression via ALYREF/YAP1 signaling. Mol Cancer 2023; 22:122. [PMID: 37537569 PMCID: PMC10401734 DOI: 10.1186/s12943-023-01814-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/25/2023] [Indexed: 08/05/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Long non-coding RNAs (lncRNAs) have emerged as key regulators of cancer development and progression, and as promising biomarkers for the diagnosis and prognosis of cancer. In this study, we identified a new lncRNA (LINC02159) that was upregulated in the tumor tissues and serum of non-small cell lung cancer (NSCLC) patients. We demonstrated that knockdown of LINC02159 inhibited NSCLC cell proliferation, migration, and invasion, but induced cell apoptosis and cell cycle arrest in vitro and retarded tumor growth in vivo, while overexpression of LINC02159 led to the opposite effect. We discovered that LINC02159 was highly correlated with cancer growth and metastasis-related pathways by using transcriptomic analysis and that YAP1 was a potential target gene of LINC02159. Mechanistically, LINC02159 bound to the Aly/REF export factor (ALYREF) to enhance the stability of YAP1 messenger RNA (mRNA) via m5C modification, which led to the overexpression of YAP1 and the activation of the Hippo and β-catenin signaling pathways in NSCLC cells. Rescue experiments showed that LINC01259 promoted NSCLC progression in a YAP1- and ALYREF-dependent manner. In conclusion, LINC02159 plays an oncogenic role in NSCLC progression by regulating ALYREF/YAP1 signaling, and it has the potential to be utilized as a diagnostic marker and therapeutic target for NSCLC.
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Affiliation(s)
- Qiurong Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Maoye Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jing Xu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Dan Yu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Yixin Li
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Yanke Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaoxin Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jiahui Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jianmei Gu
- Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, 226300, China.
| | - Xu Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
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Wang X, Kong X, Feng X, Jiang DS. Effects of DNA, RNA, and Protein Methylation on the Regulation of Ferroptosis. Int J Biol Sci 2023; 19:3558-3575. [PMID: 37497000 PMCID: PMC10367552 DOI: 10.7150/ijbs.85454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Ferroptosis is a form of programmed cell death characterized by elevated intracellular ferrous ion levels and increased lipid peroxidation. Since its discovery and characterization in 2012, considerable progress has been made in understanding the regulatory mechanisms and pathophysiological functions of ferroptosis. Recent findings suggest that numerous organ injuries (e.g., ischemia/reperfusion injury) and degenerative pathologies (e.g., aortic dissection and neurodegenerative disease) are driven by ferroptosis. Conversely, insufficient ferroptosis has been linked to tumorigenesis. Furthermore, a recent study revealed the effect of ferroptosis on hematopoietic stem cells under physiological conditions. The regulatory mechanisms of ferroptosis identified to date include mainly iron metabolism, such as iron transport and ferritinophagy, and redox systems, such as glutathione peroxidase 4 (GPX4)-glutathione (GSH), ferroptosis-suppressor-protein 1 (FSP1)-CoQ10, FSP1-vitamin K (VK), dihydroorotate dehydrogenase (DHODH)-CoQ, and GTP cyclohydrolase 1 (GCH1)-tetrahydrobiopterin (BH4). Recently, an increasing number of studies have demonstrated the important regulatory role played by epigenetic mechanisms, especially DNA, RNA, and protein methylation, in ferroptosis. In this review, we provide a critical analysis of the molecular mechanisms and regulatory networks of ferroptosis identified to date, with a focus on the regulatory role of DNA, RNA, and protein methylation. Furthermore, we discuss some debated findings and unanswered questions that should be the foci of future research in this field.
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Affiliation(s)
- Xiancan Wang
- Department of Cardiovascular Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Xianghai Kong
- Department of Intervention & Vascular Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and echnology, Wuhan, 430014, Hubei, China
| | - Xin Feng
- Division of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ding-Sheng Jiang
- Division of Cardiovascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China
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Zhang H, Zhai X, Liu Y, Xia Z, Xia T, Du G, Zhou H, Franziska Strohmer D, Bazhin AV, Li Z, Wang X, Jin B, Guo D. NOP2-mediated m5C Modification of c-Myc in an EIF3A-Dependent Manner to Reprogram Glucose Metabolism and Promote Hepatocellular Carcinoma Progression. RESEARCH (WASHINGTON, D.C.) 2023; 6:0184. [PMID: 37398932 PMCID: PMC10313139 DOI: 10.34133/research.0184] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023]
Abstract
Mitochondrial dysfunction and glycolysis activation are improtant hallmarks of hepatocellular carcinoma (HCC). NOP2 is an S-adenosyl-L-methionine-dependent methyltransferase that regulates the cell cycle and proliferation activities. In this study, found that NOP2 contributes to HCC progression by promoting aerobic glycolysis. Our results revealed that NOP2 was highly expressed in HCC and that it was associated with unfavorable prognosis. NOP2 knockout in combination with sorafenib enhanced sorafenib sensitivity, which, in turn, led to marked tumor growth inhibition. Mechanistically, we identified that NOP2 regulates the c-Myc expression in an m5C-modification manner to promote glycolysis. Moreover, our results revealed that m5C methylation induced c-Myc mRNA degradation in an eukaryotic translation initiation factor 3 subunit A (EIF3A)-dependent manner. In addition, NOP2 was found to increase the expression of the glycolytic genes LDHA, TPI1, PKM2, and ENO1. Furthermore, MYC associated zinc finger protein (MAZ) was identified as the major transcription factor that directly controlled the expression of NOP2 in HCC. Notably, in a patient-derived tumor xenograft (PDX) model, adenovirus-mediated knockout of NOP2 maximized the antitumor effect and prolonged the survival of PDX-bearing mice. Our cumulative findings revealed the novel signaling pathway MAZ/NOP2/c-Myc in HCC and uncovered the important roles of NOP2 and m5C modifications in metabolic reprogramming. Therefore, targeting the MAZ/NOP2/c-Myc signaling pathway is suggested to be a potential therapeutic strategy for the treatment of HCC.
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Affiliation(s)
- Hao Zhang
- Department of Hepatobiliary and Pancreatic Surgery,
Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Hepatobiliary Surgery,
The Second Hospital of Shandong University, Jinan, China
- Organ Transplant Department,
Qilu Hospital of Shandong University, Jinan, China
| | - Xiangyu Zhai
- Department of Hepatobiliary Surgery,
The Second Hospital of Shandong University, Jinan, China
- Organ Transplant Department,
Qilu Hospital of Shandong University, Jinan, China
| | - Yanfeng Liu
- Department of Hepatobiliary Surgery,
Qilu Hospital of Shandong University, Jinan, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery,
Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tong Xia
- Organ Transplant Department,
Qilu Hospital of Shandong University, Jinan, China
| | - Gang Du
- Organ Transplant Department,
Qilu Hospital of Shandong University, Jinan, China
| | - Huaxin Zhou
- Department of Hepatobiliary Surgery,
The Second Hospital of Shandong University, Jinan, China
| | - Dorothee Franziska Strohmer
- Department of General, Visceral, and Transplant Surgery,
Ludwig-Maximilians-University Munich, Munich, Germany
| | - Alexandr V. Bazhin
- Department of General, Visceral, and Transplant Surgery,
Ludwig-Maximilians-University Munich, Munich, Germany
| | - Ziqiang Li
- Department of Hepatobiliary and Pancreatic Surgery,
Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xianqiang Wang
- Department of Pediatrics Surgery,
The Seventh Medical Center of PLA General Hospital, National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Bin Jin
- Department of Hepatobiliary Surgery,
The Second Hospital of Shandong University, Jinan, China
- Organ Transplant Department,
Qilu Hospital of Shandong University, Jinan, China
| | - Deliang Guo
- Department of Hepatobiliary and Pancreatic Surgery,
Zhongnan Hospital of Wuhan University, Wuhan, China
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Gai S, He L, He M, Zhong X, Jiang C, Qin Y, Jiang M. Anticancer Activity and Mode of Action of Cu(II), Zn(II), and Mn(II) Complexes with 5-Chloro-2- N-(2-quinolylmethylene)aminophenol. Molecules 2023; 28:4876. [PMID: 37375431 DOI: 10.3390/molecules28124876] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Developing a new generation of anticancer metal-based drugs that can both kill tumor cells and inhibit cell migration is a promising strategy. Herein, we synthesized three Cu(II), Zn(II), and Mn(II) complexes derived from 5-chloro-2-N-(2-quinolylmethylene)aminophenol (C1-C3). Among these complexes, the Cu(II) complex (C1) showed significantly greater cytotoxicity toward lung cancer cell lines than cisplatin. C1 inhibited A549 cell metastasis and suppressed the growth of the A549 tumor in vivo. In addition, we confirmed the anticancer mechanism of C1 by triggering multiple mechanisms, including inducing mitochondrial apoptosis, acting on DNA, blocking cell cycle arrest, inducing cell senescence, and inducing DNA damage.
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Affiliation(s)
- Shuangshuang Gai
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, School of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin 546199, China
| | - Liqin He
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, School of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin 546199, China
| | - Mingxian He
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, School of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin 546199, China
| | - Xuwei Zhong
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, School of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin 546199, China
| | - Caiyun Jiang
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, School of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin 546199, China
| | - Yiming Qin
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, School of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin 546199, China
| | - Ming Jiang
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, School of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin 546199, China
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Wang R, Cheng X, Chi D, Liu S, Li Q, Chen B, Xi M. M 1A and m 7G modification-related genes are potential biomarkers for survival prognosis and for deciphering the tumor immune microenvironment in esophageal squamous cell carcinoma. Discov Oncol 2023; 14:99. [PMID: 37314494 DOI: 10.1007/s12672-023-00710-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is the most common esophageal malignancy, and RNA methylation has been reported to be involved in the tumorigenesis of ESCC. However, no study has explored methylation modifications in m1A and m7G as prognostic markers for survival prediction in ESCC. METHODS Public gene-expression data and clinical annotation of 254 patients obtained from The Cancer Genome Atlas and the Gene Expression Omnibus databases were analyzed to identify potential consensus clusters of m1A and m7G modification-related genes. The RNA-seq of 20 patients in Sun Yat-Sen University Cancer Center was used as the validation set. Following screening for relevant differentially expressed genes (DEGs) and enrichment pathways were elucidated. DEGs were used to construct risk models using the randomForest algorithm, and the prognostic role of the models was assessed by applying Kaplan-Meier analysis. Extent of immune cell infiltration, drug resistance, and response to cancer treatment among different clusters and risk groups were also evaluated. RESULTS Consensus clustering analysis based on m1A and m7G modification patterns revealed three potential clusters. In total, 212 RNA methylation-related DEGs were identified. The methylation-associated signature consisting of 6 genes was then constructed to calculate methylation-related score (MRScore) and patients were dived into MRScore-high and MRScore-low groups. This signature has satisfied prognostic value for survival of ESCC (AUC = 0.66, 0.67, 0.64 for 2-, 3-, 4- year OS), and has satisfied performance in the validation SYSUCC cohort (AUC = 0.66 for 2- and 3-year OS). Significant correlation between m1A and m7G modification-related genes and immune cell infiltration, and drug resistance was also observed. CONCLUSIONS Transcriptomic prognostic signatures based on m1A and m7G modification-related genes are closely associated with immune cell infiltration in ESCC patients and have important correlations with the therapeutic sensitivity of multiple chemotherapeutic agents.
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Affiliation(s)
- Ruixi Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Esophageal Cancer Institute, Guangzhou, China
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, No. 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Xingyuan Cheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Esophageal Cancer Institute, Guangzhou, China
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, No. 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Dongmei Chi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Esophageal Cancer Institute, Guangzhou, China
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, No. 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Shiliang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Esophageal Cancer Institute, Guangzhou, China
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, No. 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Qiaoqiao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Esophageal Cancer Institute, Guangzhou, China
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, No. 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Baoqing Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Esophageal Cancer Institute, Guangzhou, China.
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, No. 651 Dongfeng East Road, Guangzhou, 510060, China.
| | - Mian Xi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Esophageal Cancer Institute, Guangzhou, China.
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, No. 651 Dongfeng East Road, Guangzhou, 510060, China.
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40
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Chen ZB, He M, Li JYS, Shyy JYJ, Chien S. Epitranscriptional Regulation: From the Perspectives of Cardiovascular Bioengineering. Annu Rev Biomed Eng 2023; 25:157-184. [PMID: 36913673 DOI: 10.1146/annurev-bioeng-081922-021233] [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] [Indexed: 03/11/2023]
Abstract
The central dogma of gene expression involves DNA transcription to RNA and RNA translation into protein. As key intermediaries and modifiers, RNAs undergo various forms of modifications such as methylation, pseudouridylation, deamination, and hydroxylation. These modifications, termed epitranscriptional regulations, lead to functional changes in RNAs. Recent studies have demonstrated crucial roles for RNA modifications in gene translation, DNA damage response, and cell fate regulation. Epitranscriptional modifications play an essential role in development, mechanosensing, atherogenesis, and regeneration in the cardiovascular (CV) system, and their elucidation is critically important to understanding the molecular mechanisms underlying CV physiology and pathophysiology. This review aims at providing biomedical engineers with an overview of the epitranscriptome landscape, related key concepts, recent findings in epitranscriptional regulations, and tools for epitranscriptome analysis. The potential applications of this important field in biomedical engineering research are discussed.
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Affiliation(s)
- Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Ming He
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Julie Yi-Shuan Li
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA;
| | - John Y-J Shyy
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Shu Chien
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA;
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Kapinova A, Mazurakova A, Halasova E, Dankova Z, Büsselberg D, Costigliola V, Golubnitschaja O, Kubatka P. Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine. EPMA J 2023; 14:249-273. [PMID: 37275549 PMCID: PMC10236066 DOI: 10.1007/s13167-023-00323-7] [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: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.
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Affiliation(s)
- Andrea Kapinova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Alena Mazurakova
- Department of Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Erika Halasova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dietrich Büsselberg
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, 24144 Doha, Qatar
| | | | - Olga Golubnitschaja
- Predictive, Preventive, and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
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Li L, Li M, Zheng J, Li Z, Chen X. Knocking down NSUN5 inhibits the development of clear cell renal cell carcinoma by inhibiting the p53 pathway. Aging (Albany NY) 2023; 15:204761. [PMID: 37263638 DOI: 10.18632/aging.204761] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common solid renal tumor. NSUN5, a gene encoding cytosine-5 RNA methyltransferase, has rarely been reported associated with cancer. A bioinformatics analysis revealed that NSUN5 was overexpressed in ccRCC. Gene Ontology and gene set variation analyses showed that NSUN5 was associated with tumor immunity in ccRCC. The effect of immunosuppressive treatment was superior in the low-risk group compared to the high-risk group, and higher stromal score in the high-risk group relative to the low-risk group. A drug sensitivity analysis revealed that the high-risk group was more sensitive to 5-fluorouracil, mitomycin C, methotrexate, and 17-AAG, whereas the low-risk group was more sensitive to crizotinib, sorafenib, foretinib, and ivozanib. NSUN5 knockout decreased ccRCC cell proliferation. The migration speed and number of invasive cells further decreased. The percentage of apoptotic cells increased. In NSUN5-knockout cells, the levels of BAX, caspase-8, caspase-9, and p53 increased significantly, whereas those of Bcl2, CCND1, CCND3, and MMP9 decreased significantly. NSUN5 is highly expressed in ccRCC and inhibits cancer cell invasion, proliferation, and migration while promoting apoptosis by activating the p53 signaling pathway. This study provides insights into the mechanisms of action of NSUN5 in urological tumors and may contribute to improving ccRCC treatment options.
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Affiliation(s)
- Lei Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110000, Liaoning, People’s Republic of China
| | - Mingyang Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110000, Liaoning, People’s Republic of China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110000, Liaoning, People’s Republic of China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110000, Liaoning, People’s Republic of China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang 110000, Liaoning, People’s Republic of China
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Gu X, Ma X, Chen C, Guan J, Wang J, Wu S, Zhu H. Vital roles of m 5C RNA modification in cancer and immune cell biology. Front Immunol 2023; 14:1207371. [PMID: 37325635 PMCID: PMC10264696 DOI: 10.3389/fimmu.2023.1207371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
RNA modification plays an important role in epigenetics at the posttranscriptional level, and 5-methylcytosine (m5C) has attracted increasing attention in recent years due to the improvement in RNA m5C site detection methods. By influencing transcription, transportation and translation, m5C modification of mRNA, tRNA, rRNA, lncRNA and other RNAs has been proven to affect gene expression and metabolism and is associated with a wide range of diseases, including malignant cancers. RNA m5C modifications also substantially impact the tumor microenvironment (TME) by targeting different groups of immune cells, including B cells, T cells, macrophages, granulocytes, NK cells, dendritic cells and mast cells. Alterations in immune cell expression, infiltration and activation are highly linked to tumor malignancy and patient prognosis. This review provides a novel and holistic examination of m5C-mediated cancer development by examining the exact mechanisms underlying the oncogenicity of m5C RNA modification and summarizing the biological effects of m5C RNA modification on tumor cells as well as immune cells. Understanding methylation-related tumorigenesis can provide useful insights for the diagnosis as well as the treatment of cancer.
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Affiliation(s)
- Xinyu Gu
- 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, China
| | - Xiao Ma
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chao Chen
- 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, China
| | - Jun Guan
- 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, China
| | - Jing 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, China
| | - Shanshan Wu
- 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, China
| | - Haihong Zhu
- 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, China
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Liu T, Sun L, Li ZZ, Yang K, Chen JM, Han XY, Qi LM, Zhou XG, Wang P. The m6A/m5C/m1A regulator genes signature reveals the prognosis and is related with immune microenvironment for hepatocellular carcinoma. BMC Gastroenterol 2023; 23:147. [PMID: 37170222 PMCID: PMC10173529 DOI: 10.1186/s12876-023-02776-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/20/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND RNA methylation is a crucial in many biological functions, and its aberrant regulation is associated with cancer progression. N6-Methyladenosine (m6A), 5-Methylcytosine (m5C), N1-methyladenosine (m1A) are common modifications of RNA methylation. However, the effect of methylation of m6A/m5C/m1A in hepatocellular carcinoma (HCC) remains unclear. METHOD The transcriptome datasets, clinic information, and mutational data of 48 m6A/m5C/m1A regulator genes were acquired from the TCGA database, and the prognostic hazard model was established by univariate and Least absolute shrinkage and selection operator (Lasso) regression. The multivariate regression was performed to determine whether the risk score was an independent prognostic indicator. Kaplan-Meier survival analysis and ROC curve analysis were used to evaluate the predictive ability of the risk model. Decision curve analysis(DCA)analysis was conducted to estimate the clinical utility of the risk model. We further analyzed the association between risk score and functional enrichment, tumor immune microenvironment, and somatic mutation. RESULT The four-gene (YTHDF1, YBX1, TRMT10C, TRMT61A) risk signature was constructed. The high-risk group had shorter overall survival (OS) than the low-risk group. Univariate and multivariate regression analysis indicated that risk score was an independent prognostic indicator. Risk scores in male group, T3 + T4 group and Stage III + IV group were higher in female group, T1 + T2 group and stage I + II group. The AUC values for 1-, 2-, and 3-year OS in the TCGA dataset were 0.764, 0.693, and 0.689, respectively. DCA analysis showed that the risk score had a higher clinical net benefit in 1- and 2-year OS than other clinical features.The risk score was positively related to some immune cell infiltration and most immune checkpoints. CONCLUSION We developed a novel m6A/m5C/m1A regulator genes' prognostic model, which could be applied as a latent prognostic tool for HCC and might guide the choice of immunotherapies.
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Affiliation(s)
- Ting Liu
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Lei Sun
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Zhi-Zhao Li
- Department of Cardiovascular, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Kun Yang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Jia-Min Chen
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Xiao-Yi Han
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Li-Ming Qi
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Xin-Gang Zhou
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China.
| | - Peng Wang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China.
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Liu K, Xu P, Lv J, Ge H, Yan Z, Huang S, Li B, Xu H, Yang L, Xu Z, Zhang D. Peritoneal high-fat environment promotes peritoneal metastasis of gastric cancer cells through activation of NSUN2-mediated ORAI2 m5C modification. Oncogene 2023:10.1038/s41388-023-02707-5. [PMID: 37130916 DOI: 10.1038/s41388-023-02707-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023]
Abstract
Peritoneal metastasis (PM) is an important metastatic modality of gastric cancer (GC).It is associated with poor prognosis. The underlying molecular mechanism of PM remains elusive. 5-Methylcytosine (m5C), a posttranscriptional RNA modification, involves in the progression of many tumors. However, its role in GC peritoneal metastasis remains unclear. In our study, transcriptome results suggested that NSUN2 expression was significantly upregulated in PM. And patients with high NSUN2 expression of PM predicted a worse prognosis. Mechanistically, NSUN2 regulates ORAI2 mRNA stability by m5C modification, thereby promoting ORAI2 expression and further promoting peritoneal metastasis and colonization of GC. YBX1 acts as a "reader" by binding to the ORAI2 m5C modification site. Following the uptake of fatty acids from omental adipocytes by GC cells, the transcription factor E2F1 was upregulated, which further promoted the expression of NSUN2 through cis-element. Briefly, these results revealed that peritoneal adipocytes provide fatty acid for GC cells, thus contributing to the elevation of E2F1 and NSUN2 through AMPK pathway, and upregulated NSUN2 activates the key gene ORAI2 through m5C modification, thereby promoting peritoneal metastasis and colonization of gastric cancer.
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Affiliation(s)
- Kanghui Liu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Peng Xu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jialun Lv
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Han Ge
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zhengyuan Yan
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
- Department of Surgery, Nanjing Lishui People's Hospital, Nanjing, 211200, China
| | - Shansong Huang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Bowen Li
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Hao Xu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Li Yang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zekuan Xu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Diancai Zhang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.
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Zuo S, Li L, Wen X, Gu X, Zhuang A, Li R, Ye F, Ge S, Fan X, Fan J, Chai P, Lu L. NSUN2-mediated m 5 C RNA methylation dictates retinoblastoma progression through promoting PFAS mRNA stability and expression. Clin Transl Med 2023; 13:e1273. [PMID: 37228185 DOI: 10.1002/ctm2.1273] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The precise temporal and spatial regulation of N5 -methylcytosine (m5 C) RNA modification plays essential roles in RNA metabolism, and is necessary for the maintenance of epigenome homeostasis. Howbeit, the mechanism underlying the m5 C modification in carcinogenesis remains to be fully addressed. METHODS Global and mRNA m5 C levels were determined by mRNA isolation and anti-m5 C dot blot in both retinoblastoma (RB) cells and clinical samples. Orthotopic intraocular xenografts were established to examine the oncogenic behaviours of RB. Genome-wide multiomics analyses were performed to identify the functional target of NSUN2, including proteomic analysis, transcriptome screening and m5 C-methylated RNA immunoprecipitation sequencing (m5 C-meRIP-seq). Organoid-based single-cell analysis and gene-correlation analysis were performed to verify the NSUN2/ALYREF/m5 C-PFAS oncogenic cascade. RESULTS Herein, we report that NSUN2-mediated m5 C RNA methylation fuels purine biosynthesis during the oncogenic progression of RB. First, we discovered that global and mRNA m5 C levels were significantly enriched in RBs compared to normal retinas. In addition, tumour-specific NSUN2 expression was noted in RB samples and cell lines. Therapeutically, targeted correction of NSUN2 exhibited efficient therapeutic efficacy in RB both in vitro and in vivo. Through multiomics analyses, we subsequently identified phosphoribosylformylglycinamidine synthase (PFAS), a vital enzyme in purine biosynthesis, as a downstream candidate target of NSUN2. The reintroduction of PFAS largely reversed the inhibitory phenotypes in NSUN2-deficient RB cells, indicating that PFAS was a functional downstream target of NSUN2. Mechanistically, we found that the m5 C reader protein ALYREF was responsible for the recognition of the m5 C modification of PFAS, increasing its expression by enhancing its RNA stability. CONCLUSIONS Conclusively, we initially demonstrated that NSUN2 is necessary for oncogenic gene activation in RB, expanding the current understanding of dynamic m5 C function during tumour progression. As the NSUN2/ALYREF/m5 C-PFAS oncogenic cascade is an important RB trigger, our study suggests that a targeted m5 C reprogramming therapeutic strategy may be a novel and efficient anti-tumour therapy approach.
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Affiliation(s)
- Sipeng Zuo
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Lin Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Xuyang Wen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Rui Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Fuxiang Ye
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Jiayan Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Linna Lu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
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NSUN2 promotes osteosarcoma progression by enhancing the stability of FABP5 mRNA via m 5C methylation. Cell Death Dis 2023; 14:125. [PMID: 36792587 PMCID: PMC9932088 DOI: 10.1038/s41419-023-05646-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
5-methylcytosine (m5C) modification, which is mainly induced by the RNA methyltransferase NSUN2 (NOP2/Sun domain family, member 2), is an important chemical posttranscriptional modification in mRNA and has been proven to play important roles in the progression of many cancers. However, the functions and underlying molecular mechanisms of NSUN2-mediated m5C in osteosarcoma (OS) remain unclear. In this study, we found NSUN2 was highly expressed in OS tissues and cells. We also discovered that higher expression of NSUN2 predicted poorer prognosis of OS patients. Our study showed that NSUN2 could promote the progression of OS cells. Moreover, we employed RNA sequencing, RNA immunoprecipitation (RIP), and methylated RIP to screen and validate the candidate targets of NSUN2 and identified FABP5 as the target. We observed that NSUN2 stabilized FABP5 mRNA by inducing m5C modification and further promoted fatty acid metabolism in OS cells. Moreover, both knocking down the expression of FABP5 and adding fatty acid oxidation inhibitor could counterbalance the promoting effect of NSUN2 on the progression of OS. Our study confirms that NSUN2 can up-regulate the expression of FABP5 by improving the stability of FABP5 mRNA via m5C, so as to promote fatty acid metabolism in OS cells, and finally plays the role in promoting the progression of OS. Our findings suggest that NSUN2 is a promising prognostic marker for OS patients and may serve as a potential therapeutic target for OS treatment. A schematic illustration was proposed to summarize our findings.
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Wang X, Guo Z, Yan F. RNA Epigenetics in Chronic Lung Diseases. Genes (Basel) 2022; 13:genes13122381. [PMID: 36553648 PMCID: PMC9777603 DOI: 10.3390/genes13122381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic lung diseases are highly prevalent worldwide and cause significant mortality. Lung cancer is the end stage of many chronic lung diseases. RNA epigenetics can dynamically modulate gene expression and decide cell fate. Recently, studies have confirmed that RNA epigenetics plays a crucial role in the developing of chronic lung diseases. Further exploration of the underlying mechanisms of RNA epigenetics in chronic lung diseases, including lung cancer, may lead to a better understanding of the diseases and promote the development of new biomarkers and therapeutic strategies. This article reviews basic information on RNA modifications, including N6 methylation of adenosine (m6A), N1 methylation of adenosine (m1A), N7-methylguanosine (m7G), 5-methylcytosine (m5C), 2'O-methylation (2'-O-Me or Nm), pseudouridine (5-ribosyl uracil or Ψ), and adenosine to inosine RNA editing (A-to-I editing). We then show how they relate to different types of lung disease. This paper hopes to summarize the mechanisms of RNA modification in chronic lung disease and finds a new way to develop early diagnosis and treatment of chronic lung disease.
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Affiliation(s)
- Xiaorui Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Zhihou Guo
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Furong Yan
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
- Correspondence:
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Jin C, Wang T, Zhang D, Yang P, Zhang C, Peng W, Jin K, Wang L, Zhou J, Peng C, Tan Y, Ji J, Chen Z, Sun Q, Yang S, Tang J, Feng Y, Sun Y. Acetyltransferase NAT10 regulates the Wnt/β-catenin signaling pathway to promote colorectal cancer progression via ac 4C acetylation of KIF23 mRNA. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:345. [PMID: 36522719 PMCID: PMC9753290 DOI: 10.1186/s13046-022-02551-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/26/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND N4-acetylcytidine (ac4C) as a significant RNA modification has been reported to maintain the stability of mRNA and to regulate the translation process. However, the roles of both ac4C and its 'writer' protein N-acetyltransferase 10 (NAT10) played in the disease especially colorectal cancer (CRC) are unclear. At this point, we discover the underlying mechanism of NAT10 modulating the progression of CRC via mRNA ac4C modification. METHODS The clinical significance of NAT10 was explored based on the TCGA and GEO data sets and the 80 CRC patients cohort of our hospital. qRT-PCR, dot blot, WB, and IHC were performed to detect the level of NAT10 and ac4C modification in CRC tissues and matched adjacent tissues. CCK-8, colony formation, transwell assay, mouse xenograft, and other in vivo and in vitro experiments were conducted to probe the biological functions of NAT10. The potential mechanisms of NAT10 in CRC were clarified by RNA-seq, RIP-seq, acRIP-seq, luciferase reporter assays, etc. RESULTS: The levels of NAT10 and ac4C modification were significantly upregulated. Also, the high expression of NAT10 had important clinical values like poor prognosis, lymph node metastasis, distant metastasis, etc. Furthermore, the in vitro experiments showed that NAT10 could inhibit apoptosis and enhance the proliferation, migration, and invasion of CRC cells and also arrest them in the G2/M phase. The in vivo experiments discovered that NAT10 could promote tumor growth and liver/lung metastasis. In terms of mechanism, NAT10 could mediate the stability of KIF23 mRNA by binding to its mRNA 3'UTR region and up-regulating its mRNA ac4c modification. And then the protein level of KIF23 was elevated to activate the Wnt/β-catenin pathway and more β-catenin was transported into the nucleus which led to the CRC progression. Besides, the inhibitor of NAT10, remodelin, was applied in vitro and vivo which showed an inhibitory effect on the CRC cells. CONCLUSIONS NAT10 promotes the CRC progression through the NAT10/KIF23/GSK-3β/β-catenin axis and its expression is mediated by GSK-3β which forms a feedback loop. Our findings provide a potential prognosis or therapeutic target for CRC and remodelin deserves more attention.
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Affiliation(s)
- Chi Jin
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Tuo Wang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Dongsheng Zhang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Peng Yang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Chuan Zhang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Wen Peng
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Kangpeng Jin
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Lu Wang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Jiahui Zhou
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Chaofan Peng
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yuqian Tan
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Jiangzhou Ji
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Zhihao Chen
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Qingyang Sun
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Sheng Yang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Junwei Tang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yifei Feng
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
| | - Yueming Sun
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China
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Chen B, Xi Y, Zhao J, Hong Y, Tian S, Zhai X, Chen Q, Ren X, Fan L, Xie X, Jiang C. m5C regulator-mediated modification patterns and tumor microenvironment infiltration characterization in colorectal cancer: One step closer to precision medicine. Front Immunol 2022; 13:1049435. [PMID: 36532062 PMCID: PMC9751490 DOI: 10.3389/fimmu.2022.1049435] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/09/2022] [Indexed: 12/04/2022] Open
Abstract
Background The RNA modification 5-methylcytosine (m5C) is one of the most prevalent post-transcriptional modifications, with increasing evidence demonstrating its extensive involvement in the tumorigenesis and progression of various cancers. Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related deaths worldwide. However, the role of m5C modulators in shaping tumor microenvironment (TME) heterogeneity and regulating immune cell infiltration in CRC requires further clarification. Results The transcriptomic sequencing data of 18 m5C regulators and clinical data of patients with CRC were obtained from The Cancer Genome Atlas (TCGA) and systematically evaluated. We found that 16 m5C regulators were differentially expressed between CRC and normal tissues. Unsupervised cluster analysis was then performed and revealed two distinct m5C modification patterns that yielded different clinical prognoses and biological functions in CRC. We demonstrated that the m5C score constructed from eight m5C-related genes showed excellent prognostic performance, with a subsequent independent analysis confirming its predictive ability in the CRC cohort. Then we developed a nomogram containing five clinical risk factors and the m5C risk score and found that the m5C score exhibited high prognostic prediction accuracy and favorable clinical applicability. Moreover, the CRC patients with low m5C score were characterized by "hot" TME exhibiting increased immune cell infiltration and higher immune checkpoint expression. These characteristics were highlighted as potential identifiers of suitable candidates for anticancer immunotherapy. Although the high m5C score represented the non-inflammatory phenotype, the CRC patients in this group exhibited high level of sensitivity to molecular-targeted therapy. Conclusion Our comprehensive analysis indicated that the novel m5C clusters and scoring system accurately reflected the distinct prognostic signature, clinicopathological characteristics, immunological phenotypes, and stratifying therapeutic opportunities of CRC. Our findings, therefore, offer valuable insights into factors that may be targeted in the development of precision medicine-based therapeutic strategies for CRC.
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Affiliation(s)
- Baoxiang Chen
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Yiqing Xi
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianhong Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China,Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Yuntian Hong
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Shunhua Tian
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Xiang Zhai
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China
| | - Quanjiao Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, CAS Center for Influenza Research and Early Warning, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xianghai Ren
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Lifang Fan
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Xiaoyu Xie
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
| | - Congqing Jiang
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China,Clinical Center of Intestinal and Colorectal Diseases of Hubei Province (Zhongnan Hospital of Wuhan University), Wuhan, China,Hubei Key Laboratory of Intestinal and Colorectal Diseases (Zhongnan Hospital of Wuhan University), Wuhan, China,*Correspondence: Congqing Jiang, ; Xiaoyu Xie, ; Lifang Fan, ; Xianghai Ren,
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