1
|
Jiang X, Zhan L, Tang X. RNA modifications in physiology and pathology: Progressing towards application in clinical settings. Cell Signal 2024; 121:111242. [PMID: 38851412 DOI: 10.1016/j.cellsig.2024.111242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
The potential to modify individual nucleotides through chemical means in order to impact the electrostatic charge, hydrophobic properties, and base pairing of RNA molecules is harnessed in the medical application of stable synthetic RNAs like mRNA vaccines and synthetic small RNA molecules. These modifications are used to either increase or decrease the production of therapeutic proteins. Additionally, naturally occurring biochemical alterations of nucleotides play a role in regulating RNA metabolism and function, thereby modulating essential cellular processes. Research elucidating the mechanisms through which RNA modifications govern fundamental cellular functions in multicellular organisms has enhanced our comprehension of how irregular RNA modification profiles can lead to human diseases. Collectively, these fundamental scientific findings have unveiled the molecular and cellular functions of RNA modifications, offering new opportunities for therapeutic intervention and paving the way for a variety of innovative clinical strategies.
Collapse
Affiliation(s)
- Xue Jiang
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, Jiangsu 223005, China
| | - Lijuan Zhan
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, Jiangsu 223005, China.
| | - Xiaozhu Tang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| |
Collapse
|
2
|
Wang S, Xu L, Wang D, Zhao S, Li K, Ma F, Yao Q, Zhang Y, Wu Z, Shao Y, Song S, Yan W. YTHDF1 promotes the osteolytic bone metastasis of breast cancer via inducing EZH2 and CDH11 translation. Cancer Lett 2024; 597:217047. [PMID: 38871245 DOI: 10.1016/j.canlet.2024.217047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
Bone metastasis is common in breast cancer and more effective therapies are required, however, its molecular mechanism is poorly understood. Additionally, the role of the m6A reader YTHDF1 in bone metastasis of breast cancer has not been reported. Here, we reveal that the increased expression of YTHDF1 is clinically correlated with breast cancer bone metastases. YTHDF1 promotes migration, invasion, and osteoblast adhesion and induces osteoclast differentiation of cancer cells in vitro and vivo. Mechanically, RNA-seq, MeRIP-seq and RIP-seq analysis, and molecular biology experiments demonstrate that YTHDF1 translationally enhances EZH2 and CDH11 expression by reading m6A-enriched sites of their transcripts. Moreover, adeno-associated virus (AAV) was used to deliver shYTHDF1 (shYTHDF1-AAV) in intratibial injection models, eliciting a significant suppressive effect on breast cancer bone metastatic formation and osteolytic destruction. Overall, we uncovered that YTHDF1 promotes osteolytic bone metastases of breast cancer by inducing EZH2 and CDH11 translation.
Collapse
Affiliation(s)
- Shuoer Wang
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Nuclear Medicine, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lun Xu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dongliang Wang
- Department of Nuclear Medicine, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Songjiao Zhao
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kun Li
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fen Ma
- Shanghai Key Laboratory of Compound Chinese Medicines, The MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, China; Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Qianlan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yunkui Zhang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Wu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Shao
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shaoli Song
- Department of Nuclear Medicine, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| |
Collapse
|
3
|
Yang Y, Gao Y, Liu XS, Huang ZM, Zhang Y, Zhang YH, Liu ZY, Chen YX, Pei ZJ. FASTKD1 as a diagnostic and prognostic biomarker for STAD: Insights into m6A modification and immune infiltration. Exp Ther Med 2024; 28:305. [PMID: 38873045 PMCID: PMC11170332 DOI: 10.3892/etm.2024.12594] [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: 12/15/2023] [Accepted: 04/19/2024] [Indexed: 06/15/2024] Open
Abstract
Fas-activated serine/threonine kinase domain 1 (FASTKD1), a known modulator of mitochondrial-mediated cell death and survival processes, has garnered attention for its potential role in various biological contexts. However, its involvement in gastric cancer remains unclear. Thus, the present study aimed to investigate the relationship between FASTKD1 expression and key factors, including clinicopathological characteristics, immune infiltration and m6A modification in stomach adenocarcinoma (STAD). The expression of FASTKD1 was analyzed in STAD and normal adjacent tissues to assess its association with clinicopathological characteristics and survival prognosis. Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used in this study. Additionally, the findings were validated through immunohistochemical staining. Co-expression analysis of FASTKD1 was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) enrichment analysis, Gene Set Enrichment Analysis (GSEA) and LinkedOmics database analysis. An in-depth analysis was conducted using databases, such as Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), GEO and TCGA to explore the potential correlation between FASTKD1 expression and immune infiltration and m6A modification in STAD. The results revealed that FASTKD1 was significantly upregulated across different tumor types, including STAD. Notably, FASTKD1 was able to distinguish between tumor and normal tissue samples with accuracy. Furthermore, the expression levels of FASTKD1 were significantly associated with clinical stage and survival. Through GO/KEGG enrichment analysis and GSEA, it was revealed that the genes co-expressed with FASTKD1 were active in a variety of biological processes. Within the TIMER, GEPIA and TCGA databases, a notable inverse correlation was observed between FASTKD1 expression and the abundance of immune cell subsets. Notably, significant correlations were established between FASTKD1 and m6A modification genes, YTHDF1 and LRPPRC, in both TCGA and GEO datasets. In conclusion, FASTKD1 may serve a significant role in m6A modification and immune infiltration processes, making it a potentially valuable diagnostic and prognostic biomarker in STAD.
Collapse
Affiliation(s)
- Yi Yang
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yan Gao
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan, Hubei 442000, P.R. China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
- Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Xu-Sheng Liu
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Zhong-Min Huang
- Department of Medical Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yu Zhang
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yao-Hua Zhang
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Yu-Xuan Chen
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Shiyan, Hubei 442000, P.R. China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
- Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| |
Collapse
|
4
|
Nian Z, Deng M, Ye L, Tong X, Xu Y, Xu Y, Chen R, Wang Y, Mao F, Xu C, Lu R, Mao Y, Xu H, Shen X, Xue X, Guo G. RNA epigenetic modifications in digestive tract cancers: Friends or foes. Pharmacol Res 2024; 206:107280. [PMID: 38914382 DOI: 10.1016/j.phrs.2024.107280] [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: 04/24/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Digestive tract cancers are among the most common malignancies worldwide and have high incidence and mortality rates. Thus, the discovery of more effective diagnostic and therapeutic targets is urgently required. The development of technologies to accurately detect RNA modification has led to the identification of numerous RNA chemical modifications in humans (epitranscriptomics) that are involved in the occurrence and development of digestive tract cancers. RNA modifications can cooperatively regulate gene expression to facilitate normal physiological functions of the digestive system. However, the dysfunction of relevant RNA-modifying enzymes ("writers," "erasers," and "readers") can lead to the development of digestive tract cancers. Consequently, targeting dysregulated enzyme activity could represent a potent therapeutic strategy for the treatment of digestive tract cancers. In this review, we summarize the most widely studied roles and mechanisms of RNA modifications (m6A, m1A, m5C, m7G, A-to-I editing, pseudouridine [Ψ]) in relation to digestive tract cancers, highlight the crosstalk between RNA modifications, and discuss their roles in the interactions between the digestive system and microbiota during carcinogenesis. The clinical significance of novel therapeutic methods based on RNA-modifying enzymes is also discussed. This review will help guide future research into digestive tract cancers that are resistant to current therapeutics.
Collapse
Affiliation(s)
- Zekai Nian
- Second Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Ming Deng
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yixi Xu
- School of public administration, Hangzhou Normal University, Hangzhou, China
| | - Yiliu Xu
- Research Center of Fluid Machinery Engineering & Technology, Jiangsu University, Zhenjiang, China
| | - Ruoyao Chen
- Second Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Yulin Wang
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Feiyang Mao
- Second Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Chenyv Xu
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ruonan Lu
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Yicheng Mao
- Ophthalmology College, Wenzhou Medical University, Wenzhou, China
| | - Hanlu Xu
- Ophthalmology College, Wenzhou Medical University, Wenzhou, China
| | - Xian Shen
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| |
Collapse
|
5
|
Li T, Cheng C, Liu J. Chemical and Enzyme-Mediated Chemical Reactions for Studying Nucleic Acids and Their Modifications. Chembiochem 2024; 25:e202400220. [PMID: 38742371 DOI: 10.1002/cbic.202400220] [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: 03/19/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
Nucleic acids are genetic information-carrying molecules inside cells. Apart from basic nucleotide building blocks, there exist various naturally occurring chemical modifications on nucleobase and ribose moieties, which greatly increase the encoding complexity of nuclei acids, contribute to the alteration of nucleic acid structures, and play versatile regulation roles in gene expression. To study the functions of certain nucleic acids in various biological contexts, robust tools to specifically label and identify these macromolecules and their modifications, and to illuminate their structures are highly necessary. In this review, we summarize recent technique advances of using chemical and enzyme-mediated chemical reactions to study nucleic acids and their modifications and structures. By highlighting the chemical principles of these techniques, we aim to present a perspective on the advancement of the field as well as to offer insights into developing specific chemical reactions and precise enzyme catalysis utilized for nucleic acids and their modifications.
Collapse
Affiliation(s)
- Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
| | - Chongguang Cheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
- Life Sciences Institute, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, 310009, Zhejiang Province, China
| |
Collapse
|
6
|
Fernandez Rodriguez G, Tarullo M, Fatica A. N 6-methyladenosine (m 6A) RNA modification in chronic myeloid leukemia: unveiling a novel therapeutic target. Cell Mol Life Sci 2024; 81:326. [PMID: 39085650 DOI: 10.1007/s00018-024-05379-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/02/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
N6-methyladenosine (m6A), the most prevalent internal mRNA modification, plays a critical role in physiological processes by regulating gene expression through modulation of mRNA metabolism at multiple stages. In recent years, m6A has garnered significant attention for a deeper understanding of the initiation, progression, and drug resistance of various cancers, including hematological malignancies. Dysregulation of m6A has been implicated in both cancer promotion and suppression. m6A methylation is a complex regulatory process involving methyltransferases (writers), demethylases (erasers), and proteins that recognize specific m6A modifications (readers). This intricate interplay presents challenges for precisely modulating m6A levels, either globally or at specific sites. This review specifically focuses on the role of m6A in chronic myeloid leukemia (CML), a blood cancer characterized by the BCR-ABL1 fusion. We emphasize its impact on leukemia cell survival and drug resistance mechanisms. Notably, inhibitors targeting m6A regulators show promise in preclinical models, suggesting a potential therapeutic avenue for CML. Integrating our understanding of m6A biology with current treatment strategies may lead to more effective therapies, especially for patients with advanced-stage or resistant CML.
Collapse
MESH Headings
- Humans
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Drug Resistance, Neoplasm/genetics
- Animals
- Methyltransferases/metabolism
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Methylation
Collapse
Affiliation(s)
| | - Marco Tarullo
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy.
| |
Collapse
|
7
|
Zhang L, Mao Z, Yin K, Wang S. Review of METTL3 in colorectal cancer: From mechanisms to the therapeutic potential. Int J Biol Macromol 2024; 277:134212. [PMID: 39069066 DOI: 10.1016/j.ijbiomac.2024.134212] [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: 03/31/2024] [Revised: 07/10/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
N6-methyladenosine (m6A), the most abundant modification in mRNAs, affects the fate of the modified RNAs at the post-transcriptional level and participants in various biological and pathological processes. Increasing evidence shows that m6A modification plays a role in the progression of many malignancies, including colorectal cancer (CRC). As the only catalytic subunit in methyltransferase complex, methyltransferase-like 3 (METTL3) is essential to the performance of m6A modification. It has been found that METTL3 is associated with the prognosis of CRC and significantly influences various aspects of CRC, such as cell proliferation, invasion, migration, metastasis, metabolism, tumor microcirculation, tumor microenvironment, and drug resistance. The relationship between METTL3 and gut-microbiota is also involved into the progression of CRC. Furthermore, METTL3 might be a viable target for CRC treatment to prolong survival. In this review, we comprehensively summarize the function of METTL3 in CRC and the underlying molecular mechanisms. We aim to deepen understanding and offer new ideas for diagnostic biomarkers and therapeutic targets for colorectal cancer.
Collapse
Affiliation(s)
- Lexuan Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory for Laboratory Medicine, Jiangsu University School of Medicine, Zhenjiang, China
| | - Zhenwei Mao
- Department of Laboratory Medicine, Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.
| | - Kai Yin
- Department of General Surgery, Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shengjun Wang
- Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory for Laboratory Medicine, Jiangsu University School of Medicine, Zhenjiang, China.
| |
Collapse
|
8
|
Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJC. Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs. Nat Struct Mol Biol 2024:10.1038/s41594-024-01357-9. [PMID: 39054354 DOI: 10.1038/s41594-024-01357-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 06/17/2024] [Indexed: 07/27/2024]
Abstract
Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.
Collapse
Affiliation(s)
- Gangshun Yi
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Calleva Centre for Evolution and Human Science, Magdalen College, Oxford, UK
| | - Mingda Ye
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Loic Carrique
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Afaf El-Sagheer
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
- Institute for Life Sciences, University of Southampton Highfield Campus, Southampton, UK
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Chris J Norbury
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Peijun Zhang
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Robert J C Gilbert
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Calleva Centre for Evolution and Human Science, Magdalen College, Oxford, UK.
| |
Collapse
|
9
|
Tang Z, Zhang N, Chen S, Fang J, Tang X, Lou Y, Jiang Y, Ma Y, Chen X, Chen Z, Zhan S, Ding X, Ding W, Ma Z. Bipyridine Derivatives as NOP2/Sun RNA Methyltransferase 3 Inhibitors for the Treatment of Colorectal Cancer. J Med Chem 2024. [PMID: 39054645 DOI: 10.1021/acs.jmedchem.4c01323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Based on the structure of caerulomycin A, 90 novel bipyridine derivatives were designed and synthesized. Among these, compound B19 exerted strong antitumor effects in vivo and in vitro. Importantly, NOP2/Sun RNA methyltransferase 3 (NSUN3) protein was identified as the target specific binding to B19, which inhibits oxidative phosphorylation of mitochondrial energy metabolism and enhances glycolytic activity by binding to NSUN3. Knockdown of NSUN3 inhibited both proliferation and migration of colorectal cancer (CRC) cells by activating AMPK-related signaling and inhibiting downstream STAT3 signaling to exert antiproliferative and pro-apoptotic effects. Our findings support the use of NSUN3 inhibitors as promising therapeutic strategies against CRC.
Collapse
Affiliation(s)
- Zhen Tang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Ningjing Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Shuang Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Jiebin Fang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Xinyi Tang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Yijie Lou
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, the First Affiliated Hospital of Zhejiang Chinese Medicine, First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yongjun Jiang
- College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316021, China
| | - Yijun Ma
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Xiaoming Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Zhe Chen
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, the First Affiliated Hospital of Zhejiang Chinese Medicine, First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Shuai Zhan
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Xia Ding
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Wanjing Ding
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Zhongjun Ma
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| |
Collapse
|
10
|
Cai Z, Jiang Z, Li S, Mo S, Wang S, Liang M, Tan X, Zhong W, Zhang L, Deng J, Zhong C, Lu J. RNA modification Regulators' Co-Expression Score (RMRCoeS) predicts biochemical recurrence and therapy response in prostate cancer: A multi-omics and experimental validation study. Int Immunopharmacol 2024; 139:112723. [PMID: 39053228 DOI: 10.1016/j.intimp.2024.112723] [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: 05/07/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Owing to the heterogeneity of prostate cancer (PCa), the clinical indicators traditionally fall short of meeting the requirements for personalized medicine. The realm of RNA modification has emerged as an increasingly relevant domain, shedding light on its pivotal role in tumor heterogeneity. However, the specific contributions of RNA modification regulators within the context of PCa remain largely unexplored. METHODS In this study, we undertook a literature review to summarize the common 8 types of RNA modifications (ac4c, AI, APA, m1A, m5c, m6A, m7G, Ψ) encompassing a total of 84 regulators. Moreover, we integrated multi-center cohorts with Ridge regression to develop the Regulators' Co-Expression Score (RMRCoeS). Then we assessed the role of RMRCoeS in several clinical aspects such as biochemical recurrence (BCR), responses to chemotherapy, androgen receptor signaling inhibitor (ARSI) therapy and immunotherapy in PCa. Finally, we validated the cancer-promoting performance of five hub genes through immunohistochemistry and in vitro assays. RESULTS Within the mutation landscape of RNA modification regulators, we observed a relatively low overall mutation rate. Remarkably, RMRCoeS, comprising 81 RNA modification regulators, exhibited a notable capability for accurately predicting the prognosis and therapeutic responses in PCa patients subjected to BCR, chemotherapy, ARSI therapy, and immunotherapy. A high RMRCoeS was indicative of a poor prognosis and unfavorable therapy responses. Functional enrichment analysis unveiled that RMRCoeS may exert its influence on PCa progression through various metabolic pathways. Furthermore, a higher RMRCoeS showed a positive correlation with elevated CNV mutations. Lastly, we validated the oncogene effects of CPSF4, WBSCR22, RPUSD3, TRMT61A, and NSUN5-five hub regulators-within the context of PCa. CONCLUSION The function of different RNA modifications is interconnected. Comprising eight distinct RNA modifications' regulators, RMRCoeS exhibits multifaceted roles in various aspects of PCa, including disease progression, prognosis, and responses to multiple therapies. Furthermore, we provide the initial validation of the oncogene effect associated with WBSCR22, RPUSD3, TRMT61A and NSUN5 in PCa. Our findings offer novel insights into the significance of RNA modifications in PCa personalized medicine.
Collapse
Affiliation(s)
- Zhouda Cai
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China
| | - Zhaojun Jiang
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China; The Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China
| | - Songbo Li
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Urology, The Second People's Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi 541002, China
| | - Shanshan Mo
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China
| | - Shuo Wang
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, China
| | - Min Liang
- Department of Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China; The Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China
| | - Xiao Tan
- Department of Urology, School of Clinical Medicine, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Weide Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa 999078, Macau
| | - Le Zhang
- Institute for Integrative Genome Biology, University of California, Riverside 92507, CA, USA
| | - Junhong Deng
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
| | - Chuanfan Zhong
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
| | - Jianming Lu
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
| |
Collapse
|
11
|
Sun M, Ren J, Qu X. In situ bioorthogonal-modulation of m 6A RNA methylation in macrophages for efficient eradication of intracellular bacteria. Chem Sci 2024; 15:11657-11666. [PMID: 39055012 PMCID: PMC11268468 DOI: 10.1039/d4sc03629h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
N6-Methyladenosine (m6A) methylation plays a critical role in controlling the RNA fate. Emerging evidence has demonstrated that aberrant m6A methylation in immune cells such as macrophages could alter cell homeostasis and function, which can be a promising target for disease treatment. Despite tremendous progress in regulating the level of m6A methylation, the current methods suffer from the time-consuming operation and annoying off-target effect, which hampers the in situ manipulation of m6A methylation. Here, a bioorthogonal in situ modulation strategy of m6A methylation was proposed. Well-designed covalent organic framework (COF) dots (CIDM) could deprotect the agonist prodrug of m6A methyltransferase, resulting in a considerable hypermethylation of m6A modification. Simultaneously, the bioorthogonal catalyst CIDM showed oxidase (OXD)-mimic activity that further promoted the level of m6A methylation. Ultimately, the potential therapeutic effect of bioorthogonal controllable regulation of m6A methylation was demonstrated through intracellular bacteria eradication. The remarkable antimicrobial outcomes indicate that upregulating m6A methylation in macrophages could reprogram them into the M1 phenotype with high bactericidal activity. We believe that our bioorthogonal chemistry-controlled epigenetics regulatory strategy will provide a unique insight into the development of controllable m6A methylation.
Collapse
Affiliation(s)
- Mengyu Sun
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
- University of Science and Technology of China Hefei Anhui 230029 China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
- University of Science and Technology of China Hefei Anhui 230029 China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
- University of Science and Technology of China Hefei Anhui 230029 China
| |
Collapse
|
12
|
Malka-Tunitsky N, Sas-Chen A. Role of RNA modifications in cancer metastasis. Curr Opin Genet Dev 2024; 87:102232. [PMID: 39047587 DOI: 10.1016/j.gde.2024.102232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/26/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
The epitranscriptome encompasses over 170 post-transcriptional modifications found in various RNA species. RNA modifications play pivotal roles in regulating gene expression by shaping RNA structure and function, implicating the epitranscriptome in diverse biological processes, including pathology progression. This review focuses on research elucidating the roles of the epitranscriptome in cancer metastasis. Metastasis, a primary cause of solid tumor patient mortality, involves a multistep process whereby tumor cells migrate from a primary tumor to distant secondary organs. We discuss RNA modifications found on rRNA, tRNA, and mRNA, highlighting their roles in different stages of metastasis. Understanding mechanisms by which modifications regulate molecular and cellular processes during metastasis is crucial for leveraging epitranscriptomic signatures in cancer diagnosis and treatment.
Collapse
Affiliation(s)
- Nofar Malka-Tunitsky
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6195001 Tel Aviv, Israel. https://twitter.com/@Nofar_MalkaTun
| | - Aldema Sas-Chen
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 6195001 Tel Aviv, Israel.
| |
Collapse
|
13
|
Li F, Li W. Readers of RNA Modification in Cancer and Their Anticancer Inhibitors. Biomolecules 2024; 14:881. [PMID: 39062595 PMCID: PMC11275166 DOI: 10.3390/biom14070881] [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: 06/18/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer treatment has always been a challenge for humanity. The inadequacies of current technologies underscore the limitations of our efforts against this disease. Nevertheless, the advent of targeted therapy has introduced a promising avenue, furnishing us with more efficacious tools. Consequently, researchers have turned their attention toward epigenetics, offering a novel perspective in this realm. The investigation of epigenetics has brought RNA readers to the forefront, as they play pivotal roles in recognizing and regulating RNA functions. Recently, the development of inhibitors targeting these RNA readers has emerged as a focal point in research and holds promise for further strides in targeted therapy. In this review, we comprehensively summarize various types of inhibitors targeting RNA readers, including non-coding RNA (ncRNA) inhibitors, small-molecule inhibitors, and other potential inhibitors. We systematically elucidate their mechanisms in suppressing cancer progression by inhibiting readers, aiming to present inhibitors of readers at the current stage and provide more insights into the development of anticancer drugs.
Collapse
Affiliation(s)
| | - Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China;
| |
Collapse
|
14
|
Han X, Zhu Y, Ke J, Zhai Y, Huang M, Zhang X, He H, Zhang X, Zhao X, Guo K, Li X, Han Z, Zhang Y. Progression of m 6A in the tumor microenvironment: hypoxia, immune and metabolic reprogramming. Cell Death Discov 2024; 10:331. [PMID: 39033180 PMCID: PMC11271487 DOI: 10.1038/s41420-024-02092-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Recently, N6-methyladenosine (m6A) has aroused widespread discussion in the scientific community as a mode of RNA modification. m6A comprises writers, erasers, and readers, which regulates RNA production, nuclear export, and translation and is very important for human health. A large number of studies have found that the regulation of m6A is closely related to the occurrence and invasion of tumors, while the homeostasis and function of the tumor microenvironment (TME) determine the occurrence and development of tumors to some extent. TME is composed of a variety of immune cells (T cells, B cells, etc.) and nonimmune cells (tumor-associated mesenchymal stem cells (TA-MSCs), cancer-associated fibroblasts (CAFs), etc.). Current studies suggest that m6A is involved in regulating the function of various cells in the TME, thereby affecting tumor progression. In this manuscript, we present the composition of m6A and TME, the relationship between m6A methylation and characteristic changes in TME, the role of m6A methylation in TME, and potential therapeutic strategies to provide new perspectives for better treatment of tumors in clinical work.
Collapse
Affiliation(s)
- Xuan Han
- First Clinical College of Changzhi Medical College, Changzhi, China
| | - Yu Zhu
- Linfen Central Hospital, Linfen, China
| | - Juan Ke
- Linfen Central Hospital, Linfen, China
| | | | - Min Huang
- Linfen Central Hospital, Linfen, China
| | - Xin Zhang
- Linfen Central Hospital, Linfen, China
| | | | | | | | | | | | - Zhongyu Han
- School of Medicine and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | | |
Collapse
|
15
|
Cristalli C, Scotlandi K. Targeting DNA Methylation Machinery in Pediatric Solid Tumors. Cells 2024; 13:1209. [PMID: 39056791 PMCID: PMC11275080 DOI: 10.3390/cells13141209] [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: 05/20/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic regulatory mechanism that plays a critical role in a variety of cellular processes, including the regulation of cell fate during development, maintenance of cell identity, and genome stability. DNA methylation is tightly regulated by enzymatic reactions and its deregulation plays an important role in the development of cancer. Specific DNA methylation alterations have been found in pediatric solid tumors, providing new insights into the development of these tumors. In addition, DNA methylation profiles have greatly contributed to tune the diagnosis of pediatric solid tumors and to define subgroups of patients with different risks of progression, leading to the reduction in unwanted toxicity and the improvement of treatment efficacy. This review highlights the dysregulated DNA methylome in pediatric solid tumors and how this information provides promising targets for epigenetic therapies, particularly inhibitors of DNMT enzymes (DNMTis). Opportunities and limitations are considered, including the ability of DNMTis to induce viral mimicry and immune signaling by tumors. Besides intrinsic action against cancer cells, DNMTis have the potential to sensitize immune-cold tumors to immunotherapies and may represent a remarkable option to improve the treatment of challenging pediatric solid tumors.
Collapse
Affiliation(s)
- Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| |
Collapse
|
16
|
Rehwinkel J, Mehdipour P. ADAR1: from basic mechanisms to inhibitors. Trends Cell Biol 2024:S0962-8924(24)00120-X. [PMID: 39030076 DOI: 10.1016/j.tcb.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/21/2024]
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) converts adenosine to inosine in double-stranded RNA (dsRNA) molecules, a process known as A-to-I editing. ADAR1 deficiency in humans and mice results in profound inflammatory diseases characterised by the spontaneous induction of innate immunity. In cells lacking ADAR1, unedited RNAs activate RNA sensors. These include melanoma differentiation-associated gene 5 (MDA5) that induces the expression of cytokines, particularly type I interferons (IFNs), protein kinase R (PKR), oligoadenylate synthase (OAS), and Z-DNA/RNA binding protein 1 (ZBP1). Immunogenic RNAs 'defused' by ADAR1 may include transcripts from repetitive elements and other long duplex RNAs. Here, we review these recent fundamental discoveries and discuss implications for human diseases. Some tumours depend on ADAR1 to escape immune surveillance, opening the possibility of unleashing anticancer therapies with ADAR1 inhibitors.
Collapse
Affiliation(s)
- Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Parinaz Mehdipour
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK.
| |
Collapse
|
17
|
Yuan W, Zhang R, Lyu H, Xiao S, Guo D, Zhang Q, Ali DW, Michalak M, Chen XZ, Zhou C, Tang J. Dysregulation of tRNA methylation in cancer: Mechanisms and targeting therapeutic strategies. Cell Death Discov 2024; 10:327. [PMID: 39019857 PMCID: PMC11254935 DOI: 10.1038/s41420-024-02097-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
tRNA is the RNA type that undergoes the most modifications among known RNA, and in recent years, tRNA methylation has emerged as a crucial process in regulating gene translation. Dysregulation of tRNA abundance occurs in cancer cells, along with increased expression and activity of tRNA methyltransferases to raise the level of tRNA modification and stability. This leads to hijacking of translation and synthesis of multiple proteins associated with tumor proliferation, metastasis, invasion, autophagy, chemotherapy resistance, and metabolic reprogramming. In this review, we provide an overview of current research on tRNA methylation in cancer to clarify its involvement in human malignancies and establish a theoretical framework for future therapeutic interventions targeting tRNA methylation processes.
Collapse
Affiliation(s)
- Wenbin Yuan
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Rui Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Shuai Xiao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Dong Guo
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Qi Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
| |
Collapse
|
18
|
Li S, Pei XY, Liu XY, Wang SL, Xu W, Wang JJ, Feng Z, Ding H, Zhang YF, Zhang R. Sensitive fluorescence detection of miRNA-124 in cardiomyocytes under oxidative stress using a nucleic acid probe. Heliyon 2024; 10:e33588. [PMID: 39040278 PMCID: PMC11260977 DOI: 10.1016/j.heliyon.2024.e33588] [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: 08/01/2023] [Revised: 05/26/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs of 18-25 bases. miRNAs are also important new biomarkers that can be used for disease diagnosis in the future. Studies have shown that miR-124 levels are significantly elevated during acute myocardial infarction (AMI) and play a key role in the cardiovascular system. A variety of methods have been established to detect myocardial infarction-related miRNAs. However, most require complex miRNA extraction and isolation, and these methods are virtually undetectable when RNA levels are low in the sample. It may lead to biased results. Thus, it is necessary to develop a technique that can detect miRNA without extracting it, which means that intracellular detection is of great significance. Here, we improved the traditional silicon spheres and obtained a biosensor that could effectively capture and detect specific noncoding nucleic acids through the layer-by-layer assembly method. The sensor is protected by hyaluronic acid so it can successfully escape the lysosome into the cell and achieve detection. With the help of a full-featured microplate reader, we determined that the detection limit of the biosensor could reach 1 fM, meeting the needs of intracellular detection. At the same time, we prepared an oxidative stress cardiomyocyte infarction model and successfully captured the overexpressed miR-124 in the infarcted cells to achieve in situ detection. This study could provide a new potential tool to develop miRNAs for sensitive diagnosis in AMI, and the proposed strategy implies its potential for biomedical research.
Collapse
Affiliation(s)
- Shuo Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Xiang-Yu Pei
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Xin-Yi Liu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Shu-Liang Wang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Wen Xu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Jing-Jing Wang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Zhen Feng
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Han Ding
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Rui Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
| |
Collapse
|
19
|
Zhou Z, Fan B, Qiu Q, Cheng H, Wang L, Wu Y, Xie J, Ni C, Li N. Pan-cancer analysis and experimental validation reveal FAM72D as a potential novel biomarker and therapeutic target in lung adenocarcinoma. Gene 2024; 928:148764. [PMID: 39013484 DOI: 10.1016/j.gene.2024.148764] [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: 03/25/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Cancers, particularly lung adenocarcinoma (LUAD), represent a major global health concern. However, the role of FAM72D in various cancers, including LUAD, remains poorly understood. METHODS We utilized databases such as The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx) and online tools to investigate the correlation between FAM72D expression and its prognostic, diagnostic, and mutational significance, as well as its impact on immune cell infiltration across multiple cancers. Additionally, we developed LUAD cell lines overexpressing FAM72D to confirm its oncogenic role. RESULTS FAM72D expression was elevated in cancerous tissues compared to noncancerous tissues, with diagnostic and prognostic implications in many cancers, including LUAD. Moreover, associations were identified between FAM72D expression and diverse immune subtypes, alongside factors such as microsatellite instability, neoantigens, and tumour mutational burden across pan-cancers. Additionally, FAM72D was associated with immune infiltration and various immune checkpoint-related genes in LUAD. In vitro experiments demonstrated that FAM72D promoted cell proliferation, colony formation, and migration, while inhibiting apoptosis in LUAD cells. CONCLUSIONS Our study establishes associations between FAM72D expression and diagnosis, prognosis, and tumour immunity across multiple cancers, as well as its oncogenic effects in LUAD. FAM72D shows promise as a biomarker and therapeutic target in LUAD.
Collapse
Affiliation(s)
- Zonglang Zhou
- Department of Respiratory and Critical Care Medicine, Center for Respiratory Medicine, The Fourth Affiliated Hospital, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Bingfu Fan
- Graduate School of Bengbu Medical College, Bengbu, Anhui, China
| | - Qinming Qiu
- Department of Psychiatry, Huzhou Third Municipal Hospital, Huzhou, China
| | - Hongrong Cheng
- Department of Neurology, The Fourth Affiliated Hospital, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Li Wang
- The Fourth Affiliated Hospital, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Yibo Wu
- Department of Orthopedics, Xixi Hospital of Hangzhou, Hangzhou, China
| | - Jun Xie
- Department of Nephrology, Center for Regeneration and Aging Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
| | - Cheng Ni
- Department of Cardiology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Ning Li
- Department of Respiratory and Critical Care Medicine, Center for Respiratory Medicine, The Fourth Affiliated Hospital, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
| |
Collapse
|
20
|
Chen Y, Liu M, Lu M, Luo L, Han Z, Liu X. Exploring the impact of m 6A modification on immune diseases: mechanisms and therapeutic implication. Front Immunol 2024; 15:1387582. [PMID: 39072324 PMCID: PMC11272477 DOI: 10.3389/fimmu.2024.1387582] [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: 02/18/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
N6-methyladenosine (m6A) is a chemical modification of RNA and has become a widely discussed topic among scientific researchers in recent years. It is distributed in various organisms, including eukaryotes and bacteria. It has been found that m6A is composed of writers, erasers and readers and is involved in biological functions such as splicing, transport and translation of RNA. The balance of the human immune microenvironment is important for human health abnormalities. Increasing studies have found that m6A affects the development of immune diseases such as inflammatory enteritis and systemic lupus erythematosus (SLE) by participating in the homeostatic regulation of the immune microenvironment in vivo. In this manuscript, we introduce the composition, biological function, regulation of m6A in the immune microenvironment and its progression in various immune diseases, providing new targets and directions for the treatment of immune diseases in clinical practice.
Collapse
Affiliation(s)
- Yutong Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Min Liu
- Department of Traditional Chinese Medicine, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, Zhejiang, China
| | - Miao Lu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Linling Luo
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhongyu Han
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xide Liu
- Department of Traditional Chinese Medicine, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, Zhejiang, China
| |
Collapse
|
21
|
Wu P, Zhang Q, Zhong P, Chai L, Luo Q, Jia C. Development of a prognostic risk model of uveal melanoma based on N7-methylguanosine-related regulators. Hereditas 2024; 161:22. [PMID: 38987843 PMCID: PMC11234703 DOI: 10.1186/s41065-024-00324-0] [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: 12/19/2022] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Uveal melanoma (UVM) stands as the predominant type of primary intraocular malignancy among adults. The clinical significance of N7-methylguanosine (m7G), a prevalent RNA modifications, in UVM remains unclear. METHODS Primary information from 80 UVM patients were analyzed as the training set, incorporating clinical information, mutation annotations and mRNA expression obtained from The Cancer Genome Atlas (TCGA) website. The validation set was carried out using Gene Expression Omnibus (GEO) database GSE22138 and GSE84976. Kaplan-Meier and Cox regression of univariate analyses were subjected to identify m7G-related regulators as prognostic genes. RESULT A prognostic risk model comprising EIF4E2, NUDT16, SNUPN and WDR4 was established through Cox regression of LASSO. Evaluation of the model's predictability for UVM patients' prognosis by Receiver Operating Characteristic (ROC) curves in the training set, demonstrated excellent performance Area Under the Curve (AUC) > 0.75. The high-risk prognosis within the TCGA cohort exhibit a notable worse outcome. Additionally, an independent correlation between the risk score and overall survival (OS) among UVM patients were identified. External validation of this model was carried out using the validation sets (GSE22138 and GSE84976). Immune-related analysis revealed that patients with high score of m7G-related risk model exhibited elevated level of immune infiltration and immune checkpoint gene expression. CONCLUSION We have developed a risk prediction model based on four m7G-related regulators, facilitating effective estimate UVM patients' survival by clinicians. Our findings shed novel light on essential role of m7G-related regulators in UVM and suggest potential novel targets for the diagnosis, prognosis and therapy of UVM.
Collapse
Affiliation(s)
- Pingfan Wu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Qian Zhang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Peng Zhong
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Li Chai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Qiong Luo
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Chengyou Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China.
| |
Collapse
|
22
|
Lu L, Zhang X, Zhou Y, Shi Z, Xie X, Zhang X, Gao L, Fu A, Liu C, He B, Xiong X, Yin Y, Wang Q, Yi C, Li X. Base-resolution m 5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach. Mol Cell 2024:S1097-2765(24)00528-8. [PMID: 39002544 DOI: 10.1016/j.molcel.2024.06.021] [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: 12/04/2023] [Revised: 06/03/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
5-methylcytosine (m5C) is a prevalent RNA modification crucial for gene expression regulation. However, accurate and sensitive m5C sites identification remains challenging due to severe RNA degradation and reduced sequence complexity during bisulfite sequencing (BS-seq). Here, we report m5C-TAC-seq, a bisulfite-free approach combining TET-assisted m5C-to-f5C oxidation with selective chemical labeling, therefore enabling direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites. With m5C-TAC-seq, we comprehensively profiled the m5C methylomes in human and mouse cells, identifying a substantially larger number of confident m5C sites. Through perturbing potential m5C methyltransferases, we deciphered the responsible enzymes for most m5C sites, including the characterization of NSUN5's involvement in mRNA m5C deposition. Additionally, we characterized m5C dynamics during mESC differentiation. Notably, the mild reaction conditions and preservation of nucleotide composition in m5C-TAC-seq allow m5C detection in chromatin-associated RNAs. The accurate and robust m5C-TAC-seq will advance research into m5C methylation functional investigation.
Collapse
Affiliation(s)
- Liang Lu
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaoting Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuenan Zhou
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zuokun Shi
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiwen Xie
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xinyue Zhang
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Liaoliao Gao
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Anbo Fu
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Cong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Bo He
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xushen Xiong
- The Second Affiliated Hospital and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Xiaoyu Li
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
| |
Collapse
|
23
|
Bernal YA, Durán E, Solar I, Sagredo EA, Armisén R. ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer. Int J Mol Sci 2024; 25:7424. [PMID: 39000531 PMCID: PMC11242177 DOI: 10.3390/ijms25137424] [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: 05/04/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Epitranscriptomics is a field that delves into post-transcriptional changes. Among these modifications, the conversion of adenosine to inosine, traduced as guanosine (A>I(G)), is one of the known RNA-editing mechanisms, catalyzed by ADARs. This type of RNA editing is the most common type of editing in mammals and contributes to biological diversity. Disruption in the A>I(G) RNA-editing balance has been linked to diseases, including several types of cancer. Drug resistance in patients with cancer represents a significant public health concern, contributing to increased mortality rates resulting from therapy non-responsiveness and disease progression, representing the greatest challenge for researchers in this field. The A>I(G) RNA editing is involved in several mechanisms over the immunotherapy and genotoxic drug response and drug resistance. This review investigates the relationship between ADAR1 and specific A>I(G) RNA-edited sites, focusing particularly on breast cancer, and the impact of these sites on DNA damage repair and the immune response over anti-cancer therapy. We address the underlying mechanisms, bioinformatics, and in vitro strategies for the identification and validation of A>I(G) RNA-edited sites. We gathered databases related to A>I(G) RNA editing and cancer and discussed the potential clinical and research implications of understanding A>I(G) RNA-editing patterns. Understanding the intricate role of ADAR1-mediated A>I(G) RNA editing in breast cancer holds significant promise for the development of personalized treatment approaches tailored to individual patients' A>I(G) RNA-editing profiles.
Collapse
Affiliation(s)
- Yanara A Bernal
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo Durán
- Subdepartamento de Genómica y Genética Molecular, Sección Genética Humana, Instituto de Salud Pública de Chile, Avenida Marathon 1000, Ñuñoa, Santiago 7780050, Chile
| | - Isidora Solar
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Eduardo A Sagredo
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-171 77 Stockholm, Sweden
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| |
Collapse
|
24
|
Jin W, Yao Y, Fu Y, Lei X, Fu W, Lu Q, Tong X, Xu Q, Su W, Hu X. WTAP/IGF2BP3-mediated GBE1 expression accelerates the proliferation and enhances stemness in pancreatic cancer cells via upregulating c-Myc. Cell Mol Biol Lett 2024; 29:97. [PMID: 38961325 PMCID: PMC11223412 DOI: 10.1186/s11658-024-00611-8] [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: 12/20/2023] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is one of the most malignant cancers with highly aggressiveness and poor prognosis. N6-methyladenosine (m6A) have been indicated to be involved in PC development. Glucan Branching Enzyme 1 (GBE1) is mainly involved in cell glycogen metabolism. However, the function of GBE1 and Whether GBE1 occurs m6A modification in PC progression remains to be illustrated. METHODS The clinical prognosis of GBE1 was analyzed through online platform. The expression of GBE1 was obtained from online platform and then verified in normal and PC cell lines. Lentivirus was used to generated GBE1 stable-overexpression or knockdown PC cells. Cell Counting Kit (CCK-8), colony formation assay, sphere formation assay and flow cytometry assay were conducted to analyze cell proliferation and stemness ability in vitro. Subcutaneous and orthotopic mouse models were used to verify the function of GBE1 in vivo. RNA immunoprecipitation (RIP) assay, RNA stability experiment and western blots were conducted to explore the molecular regulation of GBE1 in PC. RESULTS GBE1 was significantly upregulated in PC and associated with poor prognosis of PC patients. Functionally, GBE1 overexpression facilitated PC cell proliferation and stemness-like properties, while knockdown of GBE1 attenuated the malignancy of PC cells. Importantly, we found the m6A modification of GBE1 RNA, and WTAP and IGF2BP3 was revealed as the m6A regulators to increase GBE1 mRNA stability and expression. Furthermore, c-Myc was discovered as a downstream gene of GBE1 and functional rescue experiments showed that overexpression of c-Myc could rescue GBE1 knockdown-induced PC cell growth inhibition. CONCLUSIONS Our study uncovered the oncogenic role of GBE1/c-Myc axis in PC progression and revealed WTAP/IGF2BP3-mediated m6A modification of GBE1, which highlight the potential application of GBE1 in the targeted therapy of PC.
Collapse
Affiliation(s)
- Weiwei Jin
- Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yanru Yao
- Hangzhou Medical College, Hangzhou, China
| | - Yuhan Fu
- Hangzhou Medical College, Hangzhou, China
| | | | - Wen Fu
- The Medical College of Qingdao University, Qingdao, China
| | - Qiliang Lu
- The Medical College of Qingdao University, Qingdao, China
| | - Xiangmin Tong
- Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Qiuran Xu
- Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
| | - Wei Su
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.
| | - Xiaoge Hu
- Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
| |
Collapse
|
25
|
Deng Y, Zhou J, Li HB. The physiological and pathological roles of RNA modifications in T cells. Cell Chem Biol 2024:S2451-9456(24)00222-8. [PMID: 38986618 DOI: 10.1016/j.chembiol.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/20/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
RNA molecules undergo dynamic chemical modifications in response to various external or cellular stimuli. Some of those modifications have been demonstrated to post-transcriptionally modulate the RNA transcription, localization, stability, translation, and degradation, ultimately tuning the fate decisions and function of mammalian cells, particularly T cells. As a crucial part of adaptive immunity, T cells play fundamental roles in defending against infections and tumor cells. Recent findings have illuminated the importance of RNA modifications in modulating T cell survival, proliferation, differentiation, and functional activities. Therefore, understanding the epi-transcriptomic control of T cell biology enables a potential avenue for manipulating T cell immunity. This review aims to elucidate the physiological and pathological roles of internal RNA modifications in T cell development, differentiation, and functionality drawn from current literature, with the goal of inspiring new insights for future investigations and providing novel prospects for T cell-based immunotherapy.
Collapse
Affiliation(s)
- Yu Deng
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Zhou
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Geriatrics, Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Chongqing International Institute for Immunology, Chongqing 401320, China.
| |
Collapse
|
26
|
Luo Y, Tian W, Kang D, Wu L, Tang H, Wang S, Zhang C, Xie Y, Zhang Y, Xie J, Deng X, Zou H, Wu H, Lin H, Wei W. RNA modification gene WDR4 facilitates tumor progression and immunotherapy resistance in breast cancer. J Adv Res 2024:S2090-1232(24)00266-2. [PMID: 38960276 DOI: 10.1016/j.jare.2024.06.029] [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: 12/04/2023] [Revised: 06/30/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024] Open
Abstract
INTRODUCTION Growing interest toward RNA modification in cancer has inspired the exploration of gene sets related to multiple RNA modifications. However, a comprehensive elucidation of the clinical value of various RNA modifications in breast cancer is still lacking. OBJECTIVES This study aimed to provide a strategy based on RNA modification-related genes for predicting therapy response and survival outcomes in breast cancer patients. METHODS Genes related to thirteen RNA modification patterns were integrated for establishing a nine-gene-containing signature-RMscore. Alterations of tumor immune microenvironment and therapy response featured by different RMscore levels were assessed by bulk transcriptome, single-cell transcriptome and genomics analyses. The biological function of key RMscore-related molecules was investigated by cellular experiments in vitro and in vivo, using flow cytometry, immunohistochemistry and immunofluorescence staining. RESULTS This study has raised an effective therapy strategy for breast cancer patients after a well-rounded investigation of RNA modification-related genes. With a great performance of predicting patient prognosis, high levels of the RMscore proposed in this study represented suppressive immune microenvironment and therapy resistance, including adjuvant chemotherapy and PD-L1 blockade treatment. As the key contributor of the RMscore, inhibition of WDR4 impaired breast cancer progression significantly in vitro and in vivo, as well as participated in regulating cell cycle and mTORC1 signaling pathway via m7G modification. CONCLUSION Briefly, this study has developed promising and effective tactics to achieve the prediction of survival probabilities and treatment response in breast cancer patients.
Collapse
Affiliation(s)
- Yongzhou Luo
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Wenwen Tian
- Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, No.78, Hengzhigang Road, Guangzhou 510095, China
| | - Da Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Linyu Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Sifen Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Chao Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Yi Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Yue Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hao Zou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hao Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China.
| | - Huan Lin
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Weidong Wei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China.
| |
Collapse
|
27
|
Hu C, Song S, Zhao S, Xue Z, Zhu X. METTL14 contributes to the progression of nasopharyngeal carcinoma through regulating the stability of AOC1 mRNA. Hereditas 2024; 161:20. [PMID: 38956710 PMCID: PMC11221105 DOI: 10.1186/s41065-024-00317-z] [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: 01/28/2024] [Accepted: 04/19/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a malignant epithelial tumor of the nasopharyngeal mucosa with a high incidence rate all over the world. Methyltransferase-like 14 (METTL14) is a major RNA N6-adenosine methyltransferase implicated in tumor progression by regulating RNA function. This study is designed to explore the biological function and mechanism of METTL14 in NPC. METHODS METTL14 and Amine oxidase copper containing 1 (AOC1) expression were detected by real-time quantitative polymerase chain reaction (RT-qPCR). The protein levels of METTL14, AOC1, Cyclin D1, B-cell lymphoma-2 (Bcl-2), and N-cadherin were measured using western blot. Cell proliferation, cycle progression, apoptosis, migration, and invasion were assessed using 5-ethynyl-2'-deoxyuridine (EdU), Colony formation, flow cytometry, wound scratch, and transwell assays. The interaction between METTL14 and AOC1 was verified using RNA immunoprecipitation (RIP), methylated RNA immunoprecipitation (MeRIP), and dual-luciferase reporter assays. The biological role of METTL14 on NPC tumor growth was examined by the xenograft tumor model in vivo. RESULTS METTL14 and AOC1 were highly expressed in NPC tissues and cells. Moreover, METTL14 knockdown might block NPC cell proliferation, migration, invasion, and induce cell apoptosis in vitro. In mechanism, METTL14 might enhance the stability of AOC1 mRNA via m6A methylation. METTL14 silencing might repress NPC tumor growth in vivo. CONCLUSION METTL14 might boosted the development of NPC cells partly by regulating the stability of AOC1 mRNA, which provided a promising therapeutic target for NPC treatment.
Collapse
Affiliation(s)
- Changan Hu
- Department of ENT & HN Surgery, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, No. 86 Songwen Road, Lishui District, Nanjing, China
| | - Shengguan Song
- Department of ENT & HN Surgery, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, No. 86 Songwen Road, Lishui District, Nanjing, China
| | - Shanglong Zhao
- Department of ENT & HN Surgery, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, No. 86 Songwen Road, Lishui District, Nanjing, China
| | - Zhen Xue
- Department of ENT & HN Surgery, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, No. 86 Songwen Road, Lishui District, Nanjing, China
| | - Xiwen Zhu
- Department of ENT & HN Surgery, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, No. 86 Songwen Road, Lishui District, Nanjing, China.
| |
Collapse
|
28
|
Zeng X, Lu Y, Zeng T, Liu W, Huang W, Yu T, Tang X, Huang P, Li B, Wei H. RNA demethylase FTO participates in malignant progression of gastric cancer by regulating SP1-AURKB-ATM pathway. Commun Biol 2024; 7:800. [PMID: 38956367 PMCID: PMC11220007 DOI: 10.1038/s42003-024-06477-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: 10/05/2023] [Accepted: 06/20/2024] [Indexed: 07/04/2024] Open
Abstract
Gastric cancer (GC) is the 5th most prevalent cancer and the 4th primary cancer-associated mortality globally. As the first identified m6A demethylase for removing RNA methylation modification, fat mass and obesity-associated protein (FTO) plays instrumental roles in cancer development. Therefore, we study the biological functions and oncogenic mechanisms of FTO in GC tumorigenesis and progression. In our study, FTO expression is obviously upregulated in GC tissues and cells. The upregulation of FTO is associated with advanced nerve invasion, tumor size, and LNM, as well as the poor prognosis in GC patients, and promoted GC cell viability, colony formation, migration and invasion. Mechanistically, FTO targeted specificity protein 1 and Aurora Kinase B, resulting in the phosphorylation of ataxia telangiectasia mutated and P38 and dephosphorylation of P53. In conclusion, the m6A demethylase FTO promotes GC tumorigenesis and progression by regulating the SP1-AURKB-ATM pathway, which may highlight the potential of FTO as a diagnostic biomarker for GC patients' therapy response and prognosis.
Collapse
Affiliation(s)
- Xueliang Zeng
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
- Department of Pharmacy, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Yao Lu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Taohui Zeng
- Department of Pharmacy, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Wenyu Liu
- Department of Pharmacy, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Weicai Huang
- Department of Pharmacy, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Tingting Yu
- Department of Pharmacy, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Xuerui Tang
- Department of Pharmacy, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Panpan Huang
- Department of Pharmacy, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Bei Li
- Department of Pharmacy, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, 341000, China.
| | - Hulai Wei
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
| |
Collapse
|
29
|
George JW, Cancino RA, Griffin Miller JL, Qiu F, Lin Q, Rowley MJ, Chennathukuzhi VM, Davis JS. Characterization of m6A Modifiers and RNA Modifications in Uterine Fibroids. Endocrinology 2024; 165:bqae074. [PMID: 38946397 PMCID: PMC11222979 DOI: 10.1210/endocr/bqae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 06/07/2024] [Accepted: 06/20/2024] [Indexed: 07/02/2024]
Abstract
Uterine leiomyoma or fibroids are prevalent noncancerous tumors of the uterine muscle layer, yet their origin and development remain poorly understood. We analyzed RNA expression profiles of 15 epigenetic mediators in uterine fibroids compared to myometrium using publicly available RNA sequencing (RNA-seq) data. To validate our findings, we performed RT-qPCR on a separate cohort of uterine fibroids targeting these modifiers confirming our RNA-seq data. We then examined protein profiles of key N6-methyladenosine (m6A) modifiers in fibroids and their matched myometrium, showing no significant differences in concordance with our RNA expression profiles. To determine RNA modification abundance, mRNA and small RNA from fibroids and matched myometrium were analyzed by ultra-high performance liquid chromatography-mass spectrometry identifying prevalent m6A and 11 other known modifiers. However, no aberrant expression in fibroids was detected. We then mined a previously published dataset and identified differential expression of m6A modifiers that were specific to fibroid genetic subtype. Our analysis also identified m6A consensus motifs on genes previously identified to be dysregulated in uterine fibroids. Overall, using state-of-the-art mass spectrometry, RNA expression, and protein profiles, we characterized and identified differentially expressed m6A modifiers in relation to driver mutations. Despite the use of several different approaches, we identified limited differential expression of RNA modifiers and associated modifications in uterine fibroids. However, considering the highly heterogenous genomic and cellular nature of fibroids, and the possible contribution of single molecule m6A modifications to fibroid pathology, there is a need for greater in-depth characterization of m6A marks and modifiers in a larger and diverse patient cohort.
Collapse
Affiliation(s)
- Jitu W George
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Veterans Affairs Nebraska Western Iowa Health Care System, Omaha, NE 68105, USA
| | - Rosa A Cancino
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jennifer L Griffin Miller
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Fang Qiu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Qishan Lin
- RNA Epitranscriptomics and Proteomics Resource, Department of Chemistry, University at Albany, Albany, NY 12222, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Varghese M Chennathukuzhi
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - John S Davis
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Veterans Affairs Nebraska Western Iowa Health Care System, Omaha, NE 68105, USA
| |
Collapse
|
30
|
Huang XY, Shen JY, Huang K, Wang L, Sethi G, Ma Z. Cuproptosis in cancers: Function and implications from bench to bedside. Biomed Pharmacother 2024; 176:116874. [PMID: 38850661 DOI: 10.1016/j.biopha.2024.116874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/15/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Copper, an indispensable micronutrient, is implicated in numerous vital biological processes and is essential for all physiological activities. Recently, the discovery of a novel type of copper-dependent cell death, known as cuproptosis, has shed light on its role in cancer development. Extensive research is currently underway to unravel the mechanisms underlying cuproptosis and its correlation with various cancer types. In this review, we summarize the findings regarding the roles and mechanisms of cuproptosis in various cancer types, including colorectal cancer, lung cancer, gastric cancer, breast cancer, liver cancer and cutaneous melanoma. Furthermore, the effects of copper-related agents such as copper chelators and copper ionophores on cell proliferation, apoptosis, angiogenesis, tumor immunity, and chemotherapy resistance have been explored in cancer preclinical and clinical trials. These insights provide promising avenues for the development of prospective anticancer drugs aimed at inducing cuproptosis.
Collapse
Affiliation(s)
- Xin-Yi Huang
- School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China
| | - Jia-Yang Shen
- School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China
| | - Ke Huang
- School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China
| | - Lingzhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, 117599 Singapore; Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore; NUS Centre for Cancer Research (N2CR), National University of Singapore, 117599 Singapore.
| | - Zhaowu Ma
- School of Basic Medicine, Health Science Center, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China.
| |
Collapse
|
31
|
Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
Collapse
Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
| |
Collapse
|
32
|
Liang Y, Yin W, Cai Z, Luo H, Liu Q, Zhong C, Chen J, Lin Z, Huang Y, Liang Z, Deng J, Zhong W, Cai C, Lu J. N6-methyladenosine modified lncRNAs signature for stratification of biochemical recurrence in prostate cancer. Hum Genet 2024; 143:857-874. [PMID: 37758909 DOI: 10.1007/s00439-023-02603-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]
Abstract
Nonmutational epigenetic reprogramming is a crucial mechanism contributing to the pronounced heterogeneity of prostate cancer (PCa). Among these mechanisms, N6-methyladenosine (m6A)-modified long non-coding RNAs (lncRNAs) have emerged as key players. However, the precise roles of m6A-modified lncRNAs in PCa remain to be elucidated. In this study, methylated RNA immunoprecipitation sequencing (MeRIP-seq) was conducted on primary and metastatic PCa samples, leading to the identification of 21 lncRNAs exhibiting differential methylation and expression patterns. We further established a PCa prognostic signature, named m6A-modified lncRNA score (mLs), based on 9 differential methylated lncRNAs in 4 multicenter cohorts. The high mLs score cohort exhibited a tendency for earlier biochemical recurrence (BCR) compared to the low mLs score cohort. Remarkably, the predictive performance of the mLs score surpassed that of five previously reported lncRNA-based signatures. Functional enrichment analysis underscored a negative correlation between the mLs score and lipid metabolism. Additionally, through MeRIP-qPCR, we pinpointed a hub gene, MIR210HG, which was validated through in vitro and in vivo experiments. These findings collectively illuminate the landscape of m6A-methylated lncRNAs in PCa tissue via MeRIP-seq and harness this information to prognosticate PCa outcomes using the mLs score. Furthermore, our study validates, both experimentally and mechanistically, the facilitative role of MIR210HG in driving PCa progression.
Collapse
Affiliation(s)
- Yingke Liang
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China
| | - Wenjun Yin
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, Guangdong, China
| | - Zhouda Cai
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China
| | - Hongwei Luo
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China
| | - Qinwei Liu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology, Guangzhou, 510230, Guangdong, China
| | - Chuanfan Zhong
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Jiahong Chen
- Department of Urology, Huizhou Municipal Central Hospital, Huizhou, 516001, Guangdong, China
| | - Zhuoyuan Lin
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510282, Guangdong, China
| | - Yaqiang Huang
- Department of Urology, Zhongshan City People's Hospital, Zhongshan, 528403, Guangdong, China
| | - Zhenguo Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China
| | - Junhong Deng
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China
| | - Weide Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Chao Cai
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou Institute of Urology, Guangzhou, 510230, Guangdong, China.
| | - Jianming Lu
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China.
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, Guangdong, China.
| |
Collapse
|
33
|
Wu Q, Tavazoie SF. Translational control by VARS in melanoma. Nat Cell Biol 2024; 26:1023-1024. [PMID: 38849540 DOI: 10.1038/s41556-024-01430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
|
34
|
Chen X, Zhang MY, Ji XL, Li R, Wang QX, Qu YQ. A novel nomogram model for lung adenocarcinoma subtypes based on RNA-modification regulatory genes. Heliyon 2024; 10:e33106. [PMID: 39022104 PMCID: PMC11252981 DOI: 10.1016/j.heliyon.2024.e33106] [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: 08/04/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024] Open
Abstract
Background In non-small cell lung cancer (NSCLC), lung adenocarcinoma (LUAD) is the most common subtype. RNA modification has become the frontier and hotspot of current tumor research. Results In this study, 109 genes that regulate RNA modifications were identified according to The Cancer Genome Atlas (TCGA). A differential gene expression analysis identified 46 differentially expressed RNA modification regulatory genes (DERRGs). LUAD samples were stratified into two distinct clusters based on the expression of these DERRGs. A significant correlation was observed between these clusters and patient survival rates, as well as clinical features. Furthermore, a four-DERRG signature (EIF3B, HNRNPC, IGF2BP1, and METTL3) developed using LASSO regression. According to the calculated risk scores from this signature, LUAD patients were categorized into high-risk and low-risk groups. Patients in the low-risk group exhibited a more favorable prognosis. A prognostic nomogram was crafted, integrating the four-DERRGs signature with clinical parameters. The nomogram was revealed that OS, age, clinical stage, immune cell infiltration, and immune checkpoint molecule expression were significantly linked to the OS of LUAD. GSEA analysis found that the DERRGs were primarily regulated immune pathways. Conclusions This study developed four DERRGs signatures and formulated a nomogram model for precise prognosis estimation in LUAD patients. The study's insights are instrumental for advancing diagnosis, prognosis, and therapeutic strategies for LUAD.
Collapse
Affiliation(s)
- Xiao Chen
- Department of Pulmonary and Critical Care Medicine, Tai'an City Central Hospital, Tai'an, China
| | - Meng-Yu Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Jinan Traditional Chinese Medicine Hospital, Jinan, China
| | - Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Qing-Xiang Wang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| |
Collapse
|
35
|
Li C, Chen K, Fang Q, Shi S, Nan J, He J, Yin Y, Li X, Li J, Hou L, Hu X, Kellis M, Han X, Xiong X. Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases. CELL GENOMICS 2024:100605. [PMID: 38981476 DOI: 10.1016/j.xgen.2024.100605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/17/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Crosstalk between N6-methyladenosine (m6A) and epigenomes is crucial for gene regulation, but its regulatory directionality and disease significance remain unclear. Here, we utilize quantitative trait loci (QTLs) as genetic instruments to delineate directional maps of crosstalk between m6A and two epigenomic traits, DNA methylation (DNAme) and H3K27ac. We identify 47 m6A-to-H3K27ac and 4,733 m6A-to-DNAme and, in the reverse direction, 106 H3K27ac-to-m6A and 61,775 DNAme-to-m6A regulatory loci, with differential genomic location preference observed for different regulatory directions. Integrating these maps with complex diseases, we prioritize 20 genome-wide association study (GWAS) loci for neuroticism, depression, and narcolepsy in brain; 1,767 variants for asthma and expiratory flow traits in lung; and 249 for coronary artery disease, blood pressure, and pulse rate in muscle. This study establishes disease regulatory paths, such as rs3768410-DNAme-m6A-asthma and rs56104944-m6A-DNAme-hypertension, uncovering locus-specific crosstalk between m6A and epigenomic layers and offering insights into regulatory circuits underlying human diseases.
Collapse
Affiliation(s)
- Chengyu Li
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Kexuan Chen
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Qianchen Fang
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Shaohui Shi
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Jiuhong Nan
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Jialin He
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Yafei Yin
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaoyu Li
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingyun Li
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Lei Hou
- Department of Medicine, Biomedical Genetics Section, Boston University, Boston, MA 02118, USA
| | - Xinyang Hu
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China; The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xikun Han
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Xushen Xiong
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China; State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China.
| |
Collapse
|
36
|
Wu Z, Zhou R, Li B, Cao M, Wang W, Li X. Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets. Cell Prolif 2024:e13692. [PMID: 38943267 DOI: 10.1111/cpr.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024] Open
Abstract
High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.
Collapse
Affiliation(s)
- Zhijing Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruixin Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baizao Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingyu Cao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenlong Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Cancer in Hunan Province, Changsha, Hunan, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| |
Collapse
|
37
|
Garbo S, D'Andrea D, Colantoni A, Fiorentino F, Mai A, Ramos A, Tartaglia GG, Tancredi A, Tripodi M, Battistelli C. m6A modification inhibits miRNAs' intracellular function, favoring their extracellular export for intercellular communication. Cell Rep 2024; 43:114369. [PMID: 38878288 DOI: 10.1016/j.celrep.2024.114369] [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: 10/13/2023] [Revised: 04/19/2024] [Accepted: 05/31/2024] [Indexed: 07/02/2024] Open
Abstract
Epitranscriptomics represents a further layer of gene expression regulation. Specifically, N6-methyladenosine (m6A) regulates RNA maturation, stability, degradation, and translation. Regarding microRNAs (miRNAs), while it has been reported that m6A impacts their biogenesis, the functional effects on mature miRNAs remain unclear. Here, we show that m6A modification on specific miRNAs weakens their coupling to AGO2, impairs their function on target mRNAs, determines their delivery into extracellular vesicles (EVs), and provides functional information to receiving cells. Mechanistically, the intracellular functional impairment is caused by m6A-mediated inhibition of AGO2/miRNA interaction, the EV loading is favored by m6A-mediated recognition by the RNA-binding protein (RBP) hnRNPA2B1, and the EV-miRNA function in the receiving cell requires their FTO-mediated demethylation. Consequently, cells express specific miRNAs that do not impact endogenous transcripts but provide regulatory information for cell-to-cell communication. This highlights that a further level of complexity should be considered when relating cellular dynamics to specific miRNAs.
Collapse
Affiliation(s)
- Sabrina Garbo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy
| | - Daniel D'Andrea
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
| | - Alessio Colantoni
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Fiorentino
- Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies Sapienza University of Rome, Ple. Aldo Moro 5, 00185 Rome, Italy
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6XA, UK
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Andrea Tancredi
- Dipartimento Metodi e Modelli per l'Economia, il Territorio e la Finanza MEMOTEF, Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Tripodi
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
| | - Cecilia Battistelli
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
| |
Collapse
|
38
|
Lv X, Zhang R, Li S, Jin X. tRNA Modifications and Dysregulation: Implications for Brain Diseases. Brain Sci 2024; 14:633. [PMID: 39061374 PMCID: PMC11274612 DOI: 10.3390/brainsci14070633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 07/28/2024] Open
Abstract
Transfer RNAs (tRNAs) are well-known for their essential function in protein synthesis. Recent research has revealed a diverse range of chemical modifications that tRNAs undergo, which are crucial for various cellular processes. These modifications are necessary for the precise and efficient translation of proteins and also play important roles in gene expression regulation and cellular stress response. This review examines the role of tRNA modifications and dysregulation in the pathophysiology of various brain diseases, including epilepsy, stroke, neurodevelopmental disorders, brain tumors, Alzheimer's disease, and Parkinson's disease. Through a comprehensive analysis of existing research, our study aims to elucidate the intricate relationship between tRNA dysregulation and brain diseases. This underscores the critical need for ongoing exploration in this field and provides valuable insights that could facilitate the development of innovative diagnostic tools and therapeutic approaches, ultimately improving outcomes for individuals grappling with complex neurological conditions.
Collapse
Affiliation(s)
- Xinxin Lv
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
| | - Ruorui Zhang
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Shanshan Li
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
| | - Xin Jin
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
| |
Collapse
|
39
|
Xu H, Zheng Y, Wu J, Zhang R, Zhao Q, Chen S, Peng W, Cai D, Gao Y, Chen X, Li D, Yuan S, Li G, Nan A. circSORBS1 inhibits lung cancer progression by sponging miR-6779-5p and directly binding RUFY3 mRNA. J Transl Med 2024; 22:590. [PMID: 38915053 PMCID: PMC11197270 DOI: 10.1186/s12967-024-05423-0] [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: 05/07/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024] Open
Abstract
Lung cancer is the primary cause of cancer-related death worldwide, and its global incidence and mortality rates remain high. The differential expression of circular RNAs (circRNAs) can affect the development of cancer, but the mechanisms by which circRNAs regulate lung cancer progression remain unclear. In this study, we identified circSORBS1, a circRNA that has not been previously described in lung cancer and is significantly underexpressed in lung cancer tissues, blood and cell lines, and the low expression of circSORBS1 correlated with tumour grade and prognosis. In vitro and in vivo functional experiments revealed that circSORBS1 overexpression inhibited cell proliferation and migration while enhancing apoptosis. Mechanistically, circSORBS1 acts as a sponge for miR-6779-5p, indirectly inhibiting RUFY3 mRNA degradation. Simultaneously, it binds to RUFY3 mRNA to enhance its stability. This dual regulatory mechanism leads to an increase in RUFY3 protein levels, which ultimately activates the YWHAE/BAD/BCL2 apoptotic signalling pathway and suppresses lung cancer progression. Our findings not only increase the knowledge about the regulatory pattern of circRNA expression but also provide new insights into the mechanisms by which circRNAs regulate lung cancer development.
Collapse
Affiliation(s)
- Haotian Xu
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Yue Zheng
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Jiaxi Wu
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Ruirui Zhang
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Qingyun Zhao
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Sixian Chen
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Wenyi Peng
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Dunyu Cai
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Yihong Gao
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Xingcai Chen
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Deqing Li
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Shengyi Yuan
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Gang Li
- School of Public Health, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China.
| | - Aruo Nan
- School of Public Health, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China.
| |
Collapse
|
40
|
Li KJ, Hong Y, Yu YZ, Xie Z, Lv DJ, Wang C, Xie T, Chen H, Chen ZS, Zeng J, Zhao SC. NAT10 Promotes Prostate Cancer Growth and Metastasis by Acetylating mRNAs of HMGA1 and KRT8. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2310131. [PMID: 38922788 DOI: 10.1002/advs.202310131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/22/2024] [Indexed: 06/28/2024]
Abstract
N4-acetylcytidine (ac4C) is essential for the development and migration of tumor cells. According to earlier research, N-acetyltransferase 10 (NAT10) can increase messenger RNAs (mRNAs) stability by catalyzing the synthesis of ac4C. However, little is known about NAT10 expression and its role in the acetylation modifications in prostate cancer (PCa). Thus, the biological function of NAT10 in PCa is investigated in this study. Compared to paraneoplastic tissues, the expression of NAT10 is significantly higher in PCa. The NAT10 expression is strongly correlated with the pathological grade, clinical stage, Gleason score, T-stage, and N-stage of PCa. NAT10 has the ability to advance the cell cycle and the epithelial-mesenchymal transition (EMT), both of which raise the malignancy of tumor cells. Mechanistically, NAT10 enhance the stability of high mobility group AT-hook 1 (HMGA1) by acetylating its mRNA, thereby promoting cell cycle progression to improve cell proliferation. In addition, NAT10 improve the stability of Keratin 8 (KRT8) by acetylating its mRNA, which promotes the progression of EMT to improve cell migration. This findings provide a potential prognostic or therapeutic target for PCa.
Collapse
Affiliation(s)
- Kang-Jing Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Urology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yaying Hong
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yu-Zhong Yu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zhiyue Xie
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Dao-Jun Lv
- Department of Urology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Chong Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Tao Xie
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Hong Chen
- Luoyang Key Laboratory of Organic Functional Molecules, College of Food and Drug, Luoyang Normal University, Luoyang, Henan, 471934, P. R. China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Jianwen Zeng
- Department of Urology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Urology, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, 510900, China
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510500, China
| |
Collapse
|
41
|
Chen XH, Guo KX, Li J, Xu SH, Zhu H, Yan GR. Regulations of m 6A and other RNA modifications and their roles in cancer. Front Med 2024:10.1007/s11684-024-1064-8. [PMID: 38907157 DOI: 10.1007/s11684-024-1064-8] [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: 08/04/2023] [Accepted: 01/17/2024] [Indexed: 06/23/2024]
Abstract
RNA modification is an essential component of the epitranscriptome, regulating RNA metabolism and cellular functions. Several types of RNA modifications have been identified to date; they include N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), N4-acetylcytidine (ac4C), etc. RNA modifications, mediated by regulators including writers, erasers, and readers, are associated with carcinogenesis, tumor microenvironment, metabolic reprogramming, immunosuppression, immunotherapy, chemotherapy, etc. A novel perspective indicates that regulatory subunits and post-translational modifications (PTMs) are involved in the regulation of writer, eraser, and reader functions in mediating RNA modifications, tumorigenesis, and anticancer therapy. In this review, we summarize the advances made in the knowledge of different RNA modifications (especially m6A) and focus on RNA modification regulators with functions modulated by a series of factors in cancer, including regulatory subunits (proteins, noncoding RNA or peptides encoded by long noncoding RNA) and PTMs (acetylation, SUMOylation, lactylation, phosphorylation, etc.). We also delineate the relationship between RNA modification regulator functions and carcinogenesis or cancer progression. Additionally, inhibitors that target RNA modification regulators for anticancer therapy and their synergistic effect combined with immunotherapy or chemotherapy are discussed.
Collapse
Affiliation(s)
- Xin-Hui Chen
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Kun-Xiong Guo
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Jing Li
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Shu-Hui Xu
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Huifang Zhu
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Guang-Rong Yan
- Biomedicine Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Disease, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, State Key Laboratory of Respiratory Disease, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| |
Collapse
|
42
|
Nie F, Jiang J, Ning J. Exploration of the prognostic value of methylation regulators related to m5C in papillary thyroid carcinoma. Medicine (Baltimore) 2024; 103:e38623. [PMID: 38905403 PMCID: PMC11191899 DOI: 10.1097/md.0000000000038623] [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: 02/01/2023] [Accepted: 05/28/2024] [Indexed: 06/23/2024] Open
Abstract
The incidence of papillary thyroid carcinoma (PTC) has increased significantly in recent years, and for patients with metastatic and recurrent PTC, the options for treatment currently available are insufficient. To date, the exact molecular mechanism underlying PTC is still not fully understood. 5-Methylcytosine (m5C) RNA methylation is associated with the prognosis of a variety of tumors. However, the molecular mechanisms and biomarkers associated with m5C in the diagnosis, treatment, and prognosis of this disease have not been fully elucidated. Ten m5C regulators with significantly different expression levels were included in this study. Immune infiltration analysis revealed significant negative correlations between most of these regulators and regulatory T cells. TRDMT1, NSUN5, and NSUN6 had high weights and strong correlations in the protein-protein interaction network. Using gene ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis, 1489 differentially expressed genes were screened from The Cancer Genome Atlas messenger RNA matrix, indicating that these differentially expressed genes were significantly enriched in various pathways and functions related to cancers. Four m5C regulators, NSUN2, NSUN4, NSUN6, and DNMT3B, were screened as prognostic markers by least absolute shrinkage and selection operator regression analysis, and NSUN2 and NSUN6 were identified as risk factors for poor prognosis. We found that the prognostic prediction model constructed using the m5C regulators NSUN2, NSUN4, NSUN6, and DNMT3B showed good prognostic prediction ability and diagnostic ability. This model was applied to predict the survival probability of patients with PTC, the prediction ability of 5-year survival was the best. The multi-factor prognostic prediction model combined with the tumor node metastasis stage and risk score grouping showed better prognostic predictive power.
Collapse
Affiliation(s)
- Furong Nie
- Department of Endocrinology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, Guangdong, China
| | - Jiacheng Jiang
- Department of Hepatology, The First Hospital of Hunan University of Chinese Medicine, Changsha 410007, Hunan, China
| | - Jie Ning
- Department of Endocrinology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, Guangdong, China
| |
Collapse
|
43
|
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.
Collapse
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.
| |
Collapse
|
44
|
Zálešák F, Nai F, Herok M, Bochenkova E, Bedi RK, Li Y, Errani F, Caflisch A. Structure-Based Design of a Potent and Selective YTHDC1 Ligand. J Med Chem 2024; 67:9516-9535. [PMID: 38787793 PMCID: PMC11181329 DOI: 10.1021/acs.jmedchem.4c00599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
N6-Adenosine methylation (m6A) is a prevalent post-transcriptional modification of mRNA, with YTHDC1 being the reader protein responsible for recognizing this modification in the cell nucleus. Here, we present a protein structure-based medicinal chemistry campaign that resulted in the YTHDC1 inhibitor 40, which shows an equilibrium dissociation constant (Kd) of 49 nM. The crystal structure of the complex (1.6 Å resolution) validated the design. Compound 40 is selective against the cytoplasmic m6A-RNA readers YTHDF1-3 and YTHDC2 and shows antiproliferative activity against the acute myeloid leukemia (AML) cell lines THP-1, MOLM-13, and NOMO-1. For the series of compounds that culminated into ligand 40, the good correlation between the affinity in the biochemical assay and antiproliferative activity in the THP-1 cell line provides evidence of YTHDC1 target engagement in the cell. The binding to YTHDC1 in the cell is further supported by the cellular thermal shift assay. Thus, ligand 40 is a tool compound for studying the role of YTHDC1 in AML.
Collapse
Affiliation(s)
- František Zálešák
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Francesco Nai
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Marcin Herok
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Elena Bochenkova
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Rajiv K. Bedi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Francesco Errani
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| |
Collapse
|
45
|
Lehmann U. Epigenetic Therapies in Triple-Negative Breast Cancer: Concepts, Visions, and Challenges. Cancers (Basel) 2024; 16:2164. [PMID: 38927870 PMCID: PMC11202282 DOI: 10.3390/cancers16122164] [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: 03/27/2024] [Revised: 05/17/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Breast cancer, the most frequent malignancy in women worldwide, is a molecularly and clinically very heterogeneous disease. Triple-negative breast cancer is defined by the absence of hormone receptor and growth factor receptor ERBB2/HER2 expression. It is characterized by a more aggressive course of disease and a shortage of effective therapeutic approaches. Hallmarks of cancer cells are not only genetic alterations, but also epigenetic aberrations. The most studied and best understood alterations are methylation of the DNA base cytosine and the covalent modification of histone proteins. The reversibility of these covalent modifications make them attractive targets for therapeutic intervention, as documented in numerous ongoing clinical trials. Epidrugs, targeting DNA methylation and histone modifications, might offer attractive new options in treating triple-negative breast cancer. Currently, the most promising options are combination therapies in which the epidrug increases the efficiency of immuncheckpoint inhibitors. This review focusses exclusively on DNA methylation and histone modifications. In reviewing the knowledge about epigenetic therapies in breast cancer, and especially triple-negative breast cancer, the focus is on explaining concepts and raising awareness of what is not yet known and what has to be clarified in the future.
Collapse
Affiliation(s)
- Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
| |
Collapse
|
46
|
Zhang X, An K, Ge X, Sun Y, Wei J, Ren W, Wang H, Wang Y, Du Y, He L, Li O, Zhou S, Shi Y, Ren T, Yang YG, Kan Q, Tian X. NSUN2/YBX1 promotes the progression of breast cancer by enhancing HGH1 mRNA stability through m 5C methylation. Breast Cancer Res 2024; 26:94. [PMID: 38844963 PMCID: PMC11155144 DOI: 10.1186/s13058-024-01847-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND RNA m5C methylation has been extensively implicated in the occurrence and development of tumors. As the main methyltransferase, NSUN2 plays a crucial regulatory role across diverse tumor types. However, the precise impact of NSUN2-mediated m5C modification on breast cancer (BC) remains unclear. Our study aims to elucidate the molecular mechanism underlying how NSUN2 regulates the target gene HGH1 (also known as FAM203) through m5C modification, thereby promoting BC progression. Additionally, this study targets at preliminarily clarifying the biological roles of NSUN2 and HGH1 in BC. METHODS Tumor and adjacent tissues from 5 BC patients were collected, and the m5C modification target HGH1 in BC was screened through RNA sequencing (RNA-seq) and single-base resolution m5C methylation sequencing (RNA-BisSeq). Methylation RNA immunoprecipitation-qPCR (MeRIP-qPCR) and RNA-binding protein immunoprecipitation-qPCR (RIP-qPCR) confirmed that the methylation molecules NSUN2 and YBX1 specifically recognized and bound to HGH1 through m5C modification. In addition, proteomics, co-immunoprecipitation (co-IP), and Ribosome sequencing (Ribo-Seq) were used to explore the biological role of HGH1 in BC. RESULTS As the main m5C methylation molecule, NSUN2 is abnormally overexpressed in BC and increases the overall level of RNA m5C. Knocking down NSUN2 can inhibit BC progression in vitro or in vivo. Combined RNA-seq and RNA-BisSeq analysis identified HGH1 as a potential target of abnormal m5C modifications. We clarified the mechanism by which NSUN2 regulates HGH1 expression through m5C modification, a process that involves interactions with the YBX1 protein, which collectively impacts mRNA stability and protein synthesis. Furthermore, this study is the first to reveal the binding interaction between HGH1 and the translation elongation factor EEF2, providing a comprehensive understanding of its ability to regulate transcript translation efficiency and protein synthesis in BC cells. CONCLUSIONS This study preliminarily clarifies the regulatory role of the NSUN2-YBX1-m5C-HGH1 axis from post-transcriptional modification to protein translation, revealing the key role of abnormal RNA m5C modification in BC and suggesting that HGH1 may be a new epigenetic biomarker and potential therapeutic target for BC.
Collapse
Affiliation(s)
- Xuran Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ke An
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xin Ge
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yuanyuan Sun
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jingyao Wei
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Weihong Ren
- Department of Laboratory Medicine, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Han Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yueqin Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yue Du
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Lulu He
- Biobank of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ouwen Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shaoxuan Zhou
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yong Shi
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Tong Ren
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yun-Gui Yang
- China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Quancheng Kan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China.
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, China.
| |
Collapse
|
47
|
Ma J, Lang B, Wang L, Zhou Y, Fu C, Tian C, Xue L. Pan-Cancer Analysis and Experimental Validation of CEND1 as a Prognostic and Immune Infiltration-Associated Biomarker for Gliomas. Mol Biotechnol 2024:10.1007/s12033-024-01197-4. [PMID: 38836983 DOI: 10.1007/s12033-024-01197-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
Cell cycle exit and neuronal differentiation 1 (CEND1), highly expressed in the brain, is a specific transmembrane protein which plays a tumor suppressor role. This study is performed to investigate the role of CEND1 in various cancers through pan-cancer analysis, and further investigate its functions in gliomas by cell experiments. The expression and subcellular localization of CEND1 in different cancer types were analyzed utilizing the data from the GEPIA, UCSC, UALCAN and HPA databases. Relationships of CEND1 expression with prognosis, immunomodulation-related genes, immune checkpoint genes, microsatellite instability (MSI), tumor mutation burden (TMB) and RNA modifications were analyzed based on the TCGA database. The ESTIMATE algorithm was utilized to evaluate tumors' StromalScore, Immune Score, and ESTIMATES Score. The cBioPortal database was employed to analyze the categories and frequencies of CEND1 gene alterations. Biological functions and co-expression patterns of CEND1 in gliomas were explored using the LinkedOmics database, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. The interactions between CEND1 and drugs were explored employing the Comparative Toxicogenomics Database and molecular docking technology. Cell experiments were conducted to analyze triptonide's effects on glioma cells through CCK-8, flow cytometry and qRT-PCR. CEND1 was lowly expressed in gliomas, and high CEND1 expression was correlated to better overall survival of glioma patients (HR = 0.65, P = 0.02). Deep deletion was the main type of hereditary change of CEND1 mutation. CEND1 expression was markedly associated with immune infiltration, TMB, MSI, and RNA modification in various tumors (r > 0.3, P < 0.05). CEND1 co-expressed genes in gliomas were markedly correlated with immune responses and cell cycle (FDR < 0.05). Triptonide could bind well to CEND1 (-5.0 kcal/mol), and triptonide could facilitate CEND1 expression in glioma cells and cell apoptosis, and block the cell cycle progression (P < 0.05). CEND1 serves as a potential biomarker for pan-cancer. Particularly in gliomas, CEND1 is a key regulator of cell apoptosis and cell cycle, and a potential target for glioma treatment.
Collapse
Affiliation(s)
- Jinyang Ma
- Department of Neurology, The First College of Clinical Medical Sciences, China Three Gorges University & Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
| | - Bojuan Lang
- Department of Pathology, The First College of Clinical Medical Sciences, China Three Gorges University & Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
| | - Lei Wang
- Department of Neurology, The First College of Clinical Medical Sciences, China Three Gorges University & Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China.
| | - Youdong Zhou
- Department of Neurology, The First College of Clinical Medical Sciences, China Three Gorges University & Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
| | - Changtao Fu
- Department of Neurology, The First College of Clinical Medical Sciences, China Three Gorges University & Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
| | - Chunlei Tian
- Department of Neurology, The First College of Clinical Medical Sciences, China Three Gorges University & Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
| | - Lixin Xue
- Department of Neurosurgery, Zhijiang Branch of Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
| |
Collapse
|
48
|
Turgambayeva A, Duisekova S, Tashenova G, Tulebayeva A, Kapanova G, Akhenbekova A, Farooqi AA. Role of TRP channels in carcinogenesis and metastasis: Pathophysiology and regulation by non-coding RNAs. Noncoding RNA Res 2024; 9:359-366. [PMID: 38511066 PMCID: PMC10950581 DOI: 10.1016/j.ncrna.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 03/22/2024] Open
Abstract
In 2021, David Julius and Ardem Patapoutian received Nobel Prize in Physiology or Medicine for their ground-breaking discoveries in the functional characterization of receptors for temperature and touch. Transient receptor potential (TRP) channels have captivated tremendous appreciation as promising drug targets over the past few years because of central involvement in different cancers. Based on the insights gleaned from decades of high-quality research, basic and clinical scientists have unveiled how Transient receptor potential channels regulated cancer onset and progression. Pioneering studies have sparked renewed interest and researchers have started to scratch the surface of mechanistic role of these channels in wide variety of cancers. In this review we have attempted to provide a summary of most recent updates and advancements made in the biology of these channels in context of cancers. We have partitioned this review into different subsections on the basis of emerging evidence about characteristically distinct role of TRPV (TRPV1, TRPV5), TRPM (TRPM3, TRPM7) and TRPC in cancers. Regulation of TRP channels by non-coding RNAs is also a very exciting area of research which will be helpful in developing a sharper understanding of the multi-step aspects of cancers.
Collapse
Affiliation(s)
- Assiya Turgambayeva
- Department Public Health and Management, NJSC, Astana Medical University, Astana, Kazakhstan
| | - Samal Duisekova
- Department Public Health and Management, NJSC, Astana Medical University, Astana, Kazakhstan
| | - Gulnara Tashenova
- Asfendiyarov Kazakh National Medical University, Almaty 050000, Kazakhstan
| | - Aigul Tulebayeva
- Asfendiyarov Kazakh National Medical University, Almaty 050000, Kazakhstan
| | - Gulnara Kapanova
- Al-Farabi Kazakh National University, 71 Al-Farabi Ave, Almaty 050040, Kazakhstan
- Scientific Center of Anti-Infectious Drugs, 75 Al-Farabi Ave, Almaty 050040, Kazakhstan
| | - Aida Akhenbekova
- Asfendiyarov Kazakh National Medical University, Almaty 050000, Kazakhstan
| | | |
Collapse
|
49
|
Hashem M, Mohandesi Khosroshahi E, Aliahmady M, Ghanei M, Soofi Rezaie Y, alsadat Jafari Y, rezaei F, Khodaparast eskadehi R, Kia Kojoori K, jamshidian F, Nabavi N, Rashidi M, Hasani Sadi F, Taheriazam A, Entezari M. Non-coding RNA transcripts, incredible modulators of cisplatin chemo-resistance in bladder cancer through operating a broad spectrum of cellular processes and signaling mechanism. Noncoding RNA Res 2024; 9:560-582. [PMID: 38515791 PMCID: PMC10955558 DOI: 10.1016/j.ncrna.2024.01.009] [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: 11/09/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 03/23/2024] Open
Abstract
Bladder cancer (BC) is a highly frequent neoplasm in correlation with significant rate of morbidity, mortality, and cost. The onset of BC is predominantly triggered by environmental and/or occupational exposures to carcinogens, such as tobacco. There are two distinct pathways by which BC can be developed, including non-muscle-invasive papillary tumors (NMIBC) and non-papillary (or solid) muscle-invasive tumors (MIBC). The Cancer Genome Atlas project has further recognized key genetic drivers of MIBC along with its subtypes with particular properties and therapeutic responses; nonetheless, NMIBC is the predominant BC presentation among the suffering individuals. Radical cystoprostatectomy, radiotherapy, and chemotherapy have been verified to be the common therapeutic interventions in metastatic tumors, among which chemotherapeutics are more conventionally utilized. Although multiple chemo drugs have been broadly administered for BC treatment, cisplatin is reportedly the most effective chemo drug against the corresponding malignancy. Notwithstanding, tumor recurrence is usually occurred following the consumption of cisplatin regimens, particularly due to the progression of chemo-resistant trait. In this framework, non-coding RNAs (ncRNAs), as abundant RNA transcripts arise from the human genome, are introduced to serve as crucial contributors to tumor expansion and cisplatin chemo-resistance in bladder neoplasm. In the current review, we first investigated the best-known ncRNAs, i.e. microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), correlated with cisplatin chemo-resistance in BC cells and tissues. We noticed that these ncRNAs could mediate the BC-related cisplatin-resistant phenotype through diverse cellular processes and signaling mechanisms, reviewed here. Eventually, diagnostic and prognostic potential of ncRNAs, as well as their therapeutic capabilities were highlighted in regard to BC management.
Collapse
Affiliation(s)
- Mehrdad Hashem
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Elaheh Mohandesi Khosroshahi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Melika Aliahmady
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Morvarid Ghanei
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Yasamin Soofi Rezaie
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Yasamin alsadat Jafari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh rezaei
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Ramtin Khodaparast eskadehi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Kimia Kia Kojoori
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - faranak jamshidian
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, V6H3Z6, Vancouver, BC, Canada
| | - Mohsen Rashidi
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Farzaneh Hasani Sadi
- General Practitioner, Kerman University of Medical Sciences, Kerman, 7616913555, Iran
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| |
Collapse
|
50
|
Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024; 56:1235-1249. [PMID: 38871819 PMCID: PMC11263585 DOI: 10.1038/s12276-024-01239-6] [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: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.
Collapse
Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Eunjeong Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
| |
Collapse
|