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Genna V, Reyes-Fraile L, Iglesias-Fernandez J, Orozco M. Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design. Curr Opin Struct Biol 2024; 87:102838. [PMID: 38759298 DOI: 10.1016/j.sbi.2024.102838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/10/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
RNA vaccines have made evident to society what was already known by the scientific community: nucleic acids will be the "drugs of the future." By modifying the genome, interfering in transcription or translation, and by introducing new catalysts into the cell or by mimicking antibody effects, nucleic acids can generate therapeutic activities that are not accessible by any other therapeutic agents. There are, however, challenges that need to be solved in the next few years to make nucleic acids usable in a wide range of therapeutic scenarios. This review illustrates how simulation methods can help achieve this goal.
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Affiliation(s)
- Vito Genna
- NBD|Nostrum Biodiscovery, Josep Tarradellas 8-10, Barcelona 08019, Spain. https://twitter.com/_VitoGenna_
| | - Laura Reyes-Fraile
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Sixfold Bioscience Ltd, Translational & Innovation Hub, 84 Wood Ln, London W12 0BZ, United Kingdom
| | | | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain.
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2
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Boyd RD, Kennebeck MM, Miranda AA, Liu Z, Silverman SK. Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination. Nucleic Acids Res 2024:gkae639. [PMID: 39051544 DOI: 10.1093/nar/gkae639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
DNA and RNA nucleobase modifications are biologically relevant and valuable in fundamental biochemical and biophysical investigations of nucleic acids. However, directly introducing site-specific nucleobase modifications into long unprotected oligonucleotides is a substantial challenge. In this study, we used in vitro selection to identify DNAzymes that site-specifically N-alkylate the exocyclic nucleobase amines of particular cytidine, guanosine, and adenosine (C, G and A) nucleotides in DNA substrates, by reductive amination using a 5'-benzaldehyde oligonucleotide as the reaction partner. The new DNAzymes each require one or more of Mg2+, Mn2+, and Zn2+ as metal ion cofactors and have kobs from 0.04 to 0.3 h-1, with rate enhancement as high as ∼104 above the splinted background reaction. Several of the new DNAzymes are catalytically active when an RNA substrate is provided in place of DNA. Similarly, several new DNAzymes function when a small-molecule benzaldehyde compound replaces the 5'-benzaldehyde oligonucleotide. These findings expand the scope of DNAzyme catalysis to include nucleobase N-alkylation by reductive amination. Further development of this new class of DNAzymes is anticipated to facilitate practical covalent modification and labeling of DNA and RNA substrates.
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Affiliation(s)
- Robert D Boyd
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Morgan M Kennebeck
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Aurora A Miranda
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Zehui Liu
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Scott K Silverman
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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3
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Bártová E. Epigenetic and gene therapy in human and veterinary medicine. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae006. [PMID: 38751572 PMCID: PMC11095531 DOI: 10.1093/eep/dvae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/12/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
Gene therapy is a focus of interest in both human and veterinary medicine, especially in recent years due to the potential applications of CRISPR/Cas9 technology. Another relatively new approach is that of epigenetic therapy, which involves an intervention based on epigenetic marks, including DNA methylation, histone post-translational modifications, and post-transcription modifications of distinct RNAs. The epigenome results from enzymatic reactions, which regulate gene expression without altering DNA sequences. In contrast to conventional CRISP/Cas9 techniques, the recently established methodology of epigenetic editing mediated by the CRISPR/dCas9 system is designed to target specific genes without causing DNA breaks. Both natural epigenetic processes and epigenetic editing regulate gene expression and thereby contribute to maintaining the balance between physiological functions and pathophysiological states. From this perspective, knowledge of specific epigenetic marks has immense potential in both human and veterinary medicine. For instance, the use of epigenetic drugs (chemical compounds with therapeutic potential affecting the epigenome) seems to be promising for the treatment of cancer, metabolic, and infectious diseases. Also, there is evidence that an epigenetic diet (nutrition-like factors affecting epigenome) should be considered as part of a healthy lifestyle and could contribute to the prevention of pathophysiological processes. In summary, epigenetic-based approaches in human and veterinary medicine have increasing significance in targeting aberrant gene expression associated with various diseases. In this case, CRISPR/dCas9, epigenetic targeting, and some epigenetic nutrition factors could contribute to reversing an abnormal epigenetic landscape to a healthy physiological state.
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Affiliation(s)
- Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 612 00, the Czech Republic
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4
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Kennebeck MM, Kaminsky CK, Massa MA, Das PK, Boyd RD, Bishka M, Tricarico JT, Silverman SK. DNAzyme-Catalyzed Site-Specific N-Acylation of DNA Oligonucleotide Nucleobases. Angew Chem Int Ed Engl 2024; 63:e202317565. [PMID: 38157448 PMCID: PMC10873475 DOI: 10.1002/anie.202317565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
We used in vitro selection to identify DNAzymes that acylate the exocyclic nucleobase amines of cytidine, guanosine, and adenosine in DNA oligonucleotides. The acyl donor was the 2,3,5,6-tetrafluorophenyl ester (TFPE) of a 5'-carboxyl oligonucleotide. Yields are as high as >95 % in 6 h. Several of the N-acylation DNAzymes are catalytically active with RNA rather than DNA oligonucleotide substrates, and eight of nine DNAzymes for modifying C are site-specific (>95 %) for one particular substrate nucleotide. These findings expand the catalytic ability of DNA to include site-specific N-acylation of oligonucleotide nucleobases. Future efforts will investigate the DNA and RNA substrate sequence generality of DNAzymes for oligonucleotide nucleobase N-acylation, toward a universal approach for site-specific oligonucleotide modification.
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Affiliation(s)
- Morgan M Kennebeck
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Caroline K Kaminsky
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Maria A Massa
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Prakriti K Das
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Robert D Boyd
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Michelle Bishka
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - J Tomas Tricarico
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Scott K Silverman
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
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5
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Thalalla Gamage S, Howpay Manage SA, Chu TT, Meier JL. Cytidine Acetylation Across the Tree of Life. Acc Chem Res 2024; 57:338-348. [PMID: 38226431 DOI: 10.1021/acs.accounts.3c00673] [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] [Indexed: 01/17/2024]
Abstract
Acetylation plays a critical role in regulating eukaryotic transcription via the modification of histones. Beyond this well-documented function, a less explored biological frontier is the potential for acetylation to modify and regulate the function of RNA molecules themselves. N4-Acetylcytdine (ac4C) is a minor RNA nucleobase conserved across all three domains of life (archaea, bacteria, and eukarya), a conservation that suggests a fundamental role in biological processes. Unlike many RNA modifications that are controlled by large enzyme families, almost all organisms catalyze ac4C using a homologue of human Nat10, an essential disease-associated acetyltransferase enzyme.A critical step in defining the fundamental functions of RNA modifications has been the development of methods for their sensitive and specific detection. This Account describes recent progress enabling the use of chemical sequencing reactions to map and quantify ac4C with single-nucleotide resolution in RNA. To orient readers, we first provide historical background of the discovery of ac4C and the enzymes that catalyze its formation. Next, we describe mechanistic experiments that led to the development of first- and second-generation sequencing reactions able to determine ac4C's position in a polynucleotide by exploiting the nucleobase's selective susceptibility to reduction by hydride donors. A notable feature of this chemistry, which may serve as a prototype for nucleotide resolution RNA modification sequencing reactions more broadly, is its ability to drive a penetrant and detectable gain of signal specifically at ac4C sites. Emphasizing practical applications, we present how this optimized chemistry can be integrated into experimental workflows capable of sensitive, transcriptome-wide analysis. Such readouts can be applied to quantitatively define the ac4C landscape across the tree of life. For example, in human cell lines and yeast, this method has uncovered that ac4C is highly selective, predominantly occupying dominant sites within rRNA (rRNA) and tRNA (tRNA). By contrast, when we extend these analyses to thermophilic archaea they identify the potential for much more prevalent patterns of cytidine acetylation, leading to the discovery of a role for this modification in adaptation to environmental stress. Nucleotide resolution analyses of ac4C have also allowed for the determination of structure-activity relationships required for short nucleolar RNA (snoRNA)-catalyzed ac4C deposition and the discovery of organisms with unexpectedly divergent tRNA and rRNA acetylation signatures. Finally, we share how these studies have shaped our approach to evaluating novel ac4C sites reported in the literature and highlight unanswered questions and new directions that set the stage for future research in the field.
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Affiliation(s)
- Supuni Thalalla Gamage
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Shereen A Howpay Manage
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - T Thu Chu
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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Mei Z, Shen Z, Pu J, Liu Q, Liu G, He X, Wang Y, Yue J, Ge S, Li T, Yuan Y, Yang L. NAT10 mediated ac4C acetylation driven m 6A modification via involvement of YTHDC1-LDHA/PFKM regulates glycolysis and promotes osteosarcoma. Cell Commun Signal 2024; 22:51. [PMID: 38233839 PMCID: PMC10795323 DOI: 10.1186/s12964-023-01321-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: 05/15/2023] [Accepted: 09/14/2023] [Indexed: 01/19/2024] Open
Abstract
The dynamic changes of RNA N6-methyladenosine (m6A) during cancer progression participate in various cellular processes. However, less is known about a possible direct connection between upstream regulator and m6A modification, and therefore affects oncogenic progression. Here, we have identified that a key enzyme in N4-acetylcytidine (ac4C) acetylation NAT10 is highly expressed in human osteosarcoma tissues, and its knockdown enhanced m6A contents and significantly suppressed osteosarcoma cell growth, migration and invasion. Further results revealed that NAT10 silence inhibits mRNA stability and translation of m6A reader protein YTHDC1, and displayed an increase in glucose uptake, a decrease in lactate production and pyruvate content. YTHDC1 recognizes differential m6A sites on key enzymes of glycolysis phosphofructokinase (PFKM) and lactate dehydrogenase A (LDHA) mRNAs, which suppress glycolysis pathway by increasing mRNA stability of them in an m6A methylation-dependent manner. YTHDC1 partially abrogated the inhibitory effect caused by NAT10 knockdown in tumor models in vivo, lentiviral overexpression of YTHDC1 partially restored the reduced stability of YTHDC1 caused by lentiviral depleting NAT10 at the cellular level. Altogether, we found ac4C driven RNA m6A modification can positively regulate the glycolysis of cancer cells and reveals a previously unrecognized signaling axis of NAT10/ac4C-YTHDC1/m6A-LDHA/PFKM in osteosarcoma. Video Abstract.
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Affiliation(s)
- Zhongting Mei
- Department of Pharmacology, (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Zhihua Shen
- Department of Clinical Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Pharmacy, (The University Key Laboratory of Drug Research, Heilongjiang Province), The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaying Pu
- Department of Clinical Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Pharmacy, (The University Key Laboratory of Drug Research, Heilongjiang Province), The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qian Liu
- Department of Pharmacology, (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Guoxin Liu
- Department of Pharmacology, (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Xuting He
- Department of Clinical Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Pharmacy, (The University Key Laboratory of Drug Research, Heilongjiang Province), The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yang Wang
- Department of Clinical Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Pharmacy, (The University Key Laboratory of Drug Research, Heilongjiang Province), The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jinrui Yue
- Department of Clinical Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Pharmacy, (The University Key Laboratory of Drug Research, Heilongjiang Province), The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shiyu Ge
- Department of Pharmacology, (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Tao Li
- Department of Pharmacology, (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Ye Yuan
- Department of Clinical Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China.
- National Key Laboratory of Frigid Cardiovascular Disease, Harbin, China.
- Department of Pharmacy, (The University Key Laboratory of Drug Research, Heilongjiang Province), The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Lei Yang
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
- Key Laboratory of Hepatosplenic Surgery of Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
- NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
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Jia J, Cao X, Wei Z. DLC-ac4C: A Prediction Model for N4-acetylcytidine Sites in Human mRNA Based on DenseNet and Bidirectional LSTM Methods. Curr Genomics 2023; 24:171-186. [PMID: 38178985 PMCID: PMC10761336 DOI: 10.2174/0113892029270191231013111911] [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: 07/03/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction N4 acetylcytidine (ac4C) is a highly conserved nucleoside modification that is essential for the regulation of immune functions in organisms. Currently, the identification of ac4C is primarily achieved using biological methods, which can be time-consuming and labor-intensive. In contrast, accurate identification of ac4C by computational methods has become a more effective method for classification and prediction. Aim To the best of our knowledge, although there are several computational methods for ac4C locus prediction, the performance of the models they constructed is poor, and the network structure they used is relatively simple and suffers from the disadvantage of network degradation. This study aims to improve these limitations by proposing a predictive model based on integrated deep learning to better help identify ac4C sites. Methods In this study, we propose a new integrated deep learning prediction framework, DLC-ac4C. First, we encode RNA sequences based on three feature encoding schemes, namely C2 encoding, nucleotide chemical property (NCP) encoding, and nucleotide density (ND) encoding. Second, one-dimensional convolutional layers and densely connected convolutional networks (DenseNet) are used to learn local features, and bi-directional long short-term memory networks (Bi-LSTM) are used to learn global features. Third, a channel attention mechanism is introduced to determine the importance of sequence characteristics. Finally, a homomorphic integration strategy is used to limit the generalization error of the model, which further improves the performance of the model. Results The DLC-ac4C model performed well in terms of sensitivity (Sn), specificity (Sp), accuracy (Acc), Mathews correlation coefficient (MCC), and area under the curve (AUC) for the independent test data with 86.23%, 79.71%, 82.97%, 66.08%, and 90.42%, respectively, which was significantly better than the prediction accuracy of the existing methods. Conclusion Our model not only combines DenseNet and Bi-LSTM, but also uses the channel attention mechanism to better capture hidden information features from a sequence perspective, and can identify ac4C sites more effectively.
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Affiliation(s)
- Jianhua Jia
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China
| | - Xiaojing Cao
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China
| | - Zhangying Wei
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China
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Wang J, Shi L, Tang Q, Zhu X, Wu M, Liu W, Li B, Jin Y. Self-assembly of DNA-gold nanoaggregate for visual detection of thymidine kinase 1 (TK1) mRNA via lateral flow assay. Mikrochim Acta 2023; 190:454. [PMID: 37910317 DOI: 10.1007/s00604-023-06036-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Nucleic acid lateral flow assay (NALFA) with gold nanoparticles (AuNPs) as colorimetric probes have been extensively adopted for point-of-care testing (POCT). However, the sensitivity of NALFA still needs to be improved. Herein, DNA-gold nanoaggregate (DNA-AuNA) was assembled as a signal amplification probe of NALFA for sensitive detection of tumor marker TK1 mRNA. Four functional oligonucleotides with complementary pairs were assembled to form DNA-AuNA that coupled more AuNPs to improve sensitivity. Thus, the limit of detection (LOD) was 0.36 pM, which is lower than that of conventional AuNPs-based NALFA. Moreover, the bioassay showed good reproducibility, stability, and specificity for detecting TK1 mRNA. The detection of TK1 mRNA in human serum was also satisfactory. Therefore, DNA-AuNA-based NALFA provides a sensitive method for portable detection of TK1 mRNA.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Anal Chem for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Lu Shi
- Key Laboratory of Anal Chem for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Qiaorong Tang
- Key Laboratory of Anal Chem for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Xinyu Zhu
- Key Laboratory of Anal Chem for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Mengmeng Wu
- Key Laboratory of Anal Chem for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Wei Liu
- Key Laboratory of Anal Chem for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Baoxin Li
- Key Laboratory of Anal Chem for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Yan Jin
- Key Laboratory of Anal Chem for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China.
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Liu Y, Wang X, Liu Y, Yang J, Mao W, Feng C, Wu X, Chen X, Chen L, Dong P. N4-acetylcytidine-dependent GLMP mRNA stabilization by NAT10 promotes head and neck squamous cell carcinoma metastasis and remodels tumor microenvironment through MAPK/ERK signaling pathway. Cell Death Dis 2023; 14:712. [PMID: 37914704 PMCID: PMC10620198 DOI: 10.1038/s41419-023-06245-6] [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: 04/25/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
N4-acetylcytidine (ac4C) is a post-transcriptional RNA modification that regulates in various important biological processes. However, its role in human cancer, especially lymph node metastasis, remains largely unknown. Here, we demonstrated N-Acetyltransferase 10 (NAT10), as the only known "writer" of ac4C mRNA modification, was highly expressed in head and neck squamous cell carcinoma (HNSCC) patients with lymph node metastasis. High NAT10 levels in the lymph nodes of patients with HNSCC patients are a predictor of poor overall survival. Moreover, we found that high expression of NAT10 was positively upregulated by Nuclear Respiratory Factor 1 (NRF1) transcription factor. Gain- and loss-of-function experiments displayed that NAT10 promoted cell metastasis in mice. Mechanistically, NAT10 induced ac4C modification of Glycosylated Lysosomal Membrane Protein (GLMP) and stabilized its mRNA, which triggered the activation of the MAPK/ERK signaling pathway. Finally, the NAT10-specific inhibitor, remodelin, could inhibit HNSCC tumorigenesis in a 4-Nitroquinoline 1-oxide (4NQO)-induced murine tumor model and remodel the tumor microenvironment, including angiogenesis, CD8+ T cells and Treg recruitment. These results demonstrate that NAT10 promotes lymph node metastasis in HNSCC via ac4C-dependent stabilization of the GLMP transcript, providing a potential epitranscriptomic-targeted therapeutic strategy for HNSCC.
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Affiliation(s)
- Yuanyuan Liu
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xing Wang
- Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330046, China
- Centre for Medical Research and Translation, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, China
| | - Yuying Liu
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Jianqiang Yang
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, School of Medicine, Atlanta, GA, 30322, USA
| | - Wei Mao
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Chen Feng
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xiaoliang Wu
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, 510086, China
| | - Xinwei Chen
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| | - Lixiao Chen
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| | - Pin Dong
- Department of Otolaryngology: Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
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10
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Wang C, Hou X, Guan Q, Zhou H, Zhou L, Liu L, Liu J, Li F, Li W, Liu H. RNA modification in cardiovascular disease: implications for therapeutic interventions. Signal Transduct Target Ther 2023; 8:412. [PMID: 37884527 PMCID: PMC10603151 DOI: 10.1038/s41392-023-01638-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/15/2023] [Accepted: 09/03/2023] [Indexed: 10/28/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death in the world, with a high incidence and a youth-oriented tendency. RNA modification is ubiquitous and indispensable in cell, maintaining cell homeostasis and function by dynamically regulating gene expression. Accumulating evidence has revealed the role of aberrant gene expression in CVD caused by dysregulated RNA modification. In this review, we focus on nine common RNA modifications: N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, adenosine-to-inosine (A-to-I) RNA editing, and modifications of U34 on tRNA wobble. We summarize the key regulators of RNA modification and their effects on gene expression, such as RNA splicing, maturation, transport, stability, and translation. Then, based on the classification of CVD, the mechanisms by which the disease occurs and progresses through RNA modifications are discussed. Potential therapeutic strategies, such as gene therapy, are reviewed based on these mechanisms. Herein, some of the CVD (such as stroke and peripheral vascular disease) are not included due to the limited availability of literature. Finally, the prospective applications and challenges of RNA modification in CVD are discussed for the purpose of facilitating clinical translation. Moreover, we look forward to more studies exploring the mechanisms and roles of RNA modification in CVD in the future, as there are substantial uncultivated areas to be explored.
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Affiliation(s)
- Cong Wang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xuyang Hou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qing Guan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Huiling Zhou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Li Zhou
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, The Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lijun Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jijia Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Feng Li
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wei Li
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Haidan Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
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11
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Holbrook EM, Zambrano CA, Wright CTO, Dubé EM, Stewart JR, Sanders WJ, Frank MG, MacDonald AS, Reber SO, Lowry CA. Mycobacterium vaccae NCTC 11659, a Soil-Derived Bacterium with Stress Resilience Properties, Modulates the Proinflammatory Effects of LPS in Macrophages. Int J Mol Sci 2023; 24:ijms24065176. [PMID: 36982250 PMCID: PMC10049321 DOI: 10.3390/ijms24065176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/10/2023] Open
Abstract
Inflammatory conditions, including allergic asthma and conditions in which chronic low-grade inflammation is a risk factor, such as stress-related psychiatric disorders, are prevalent and are a significant cause of disability worldwide. Novel approaches for the prevention and treatment of these disorders are needed. One approach is the use of immunoregulatory microorganisms, such as Mycobacterium vaccae NCTC 11659, which have anti-inflammatory, immunoregulatory, and stress-resilience properties. However, little is known about how M. vaccae NCTC 11659 affects specific immune cell targets, including monocytes, which can traffic to peripheral organs and the central nervous system and differentiate into monocyte-derived macrophages that, in turn, can drive inflammation and neuroinflammation. In this study, we investigated the effects of M. vaccae NCTC 11659 and subsequent lipopolysaccharide (LPS) challenge on gene expression in human monocyte-derived macrophages. THP-1 monocytes were differentiated into macrophages, exposed to M. vaccae NCTC 11659 (0, 10, 30, 100, 300 µg/mL), then, 24 h later, challenged with LPS (0, 0.5, 2.5, 250 ng/mL), and assessed for gene expression 24 h following challenge with LPS. Exposure to M. vaccae NCTC 11659 prior to challenge with higher concentrations of LPS (250 ng/mL) polarized human monocyte-derived macrophages with decreased IL12A, IL12B, and IL23A expression relative to IL10 and TGFB1 mRNA expression. These data identify human monocyte-derived macrophages as a direct target of M. vaccae NCTC 11659 and support the development of M. vaccae NCTC 11659 as a potential intervention to prevent stress-induced inflammation and neuroinflammation implicated in the etiology and pathophysiology of inflammatory conditions and stress-related psychiatric disorders.
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Affiliation(s)
- Evan M. Holbrook
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Cristian A. Zambrano
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Caelan T. O. Wright
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Elizabeth M. Dubé
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Jessica R. Stewart
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO 80309, USA
| | - William J. Sanders
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Matthew G. Frank
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Andrew S. MacDonald
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9NT, UK
| | - Stefan O. Reber
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christopher A. Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO 80309, USA
- Center for Neuroscience and Center for Microbial Exploration, University of Colorado, Boulder, CO 80309, USA
- Department of Physical Medicine and Rehabilitation and Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), The Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO 80045, USA
- Senior Fellow, inVIVO Planetary Health, of the Worldwide Universities Network (WUN), West New York, NJ 07093, USA
- Correspondence: ; Tel.: +1-303-492-6029; Fax: +1-303-492-0811
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12
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Arango D, Sturgill D, Yang R, Kanai T, Bauer P, Roy J, Wang Z, Hosogane M, Schiffers S, Oberdoerffer S. Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Mol Cell 2022; 82:2797-2814.e11. [PMID: 35679869 PMCID: PMC9361928 DOI: 10.1016/j.molcel.2022.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 12/14/2022]
Abstract
mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. Although cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5' UTRs impacts protein synthesis at the level of initiation. 5' UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed that ac4C in the -1 position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner.
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Affiliation(s)
- Daniel Arango
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Renbin Yang
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Tapan Kanai
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Paulina Bauer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jyoti Roy
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ziqiu Wang
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Masaki Hosogane
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sarah Schiffers
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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13
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Bartee D, Nance KD, Meier JL. Site-Specific Synthesis of N4-Acetylcytidine in RNA Reveals Physiological Duplex Stabilization. J Am Chem Soc 2022; 144:3487-3496. [PMID: 35172571 DOI: 10.1021/jacs.1c11985] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
N4-Acetylcytidine (ac4C) is a post-transcriptional modification of RNA that is conserved across all domains of life. All characterized sites of ac4C in eukaryotic RNA occur in the central nucleotide of a 5'-CCG-3' consensus sequence. However, the thermodynamic consequences of cytidine acetylation in this context have never been assessed due to its challenging synthesis. Here, we report the synthesis and biophysical characterization of ac4C in its endogenous eukaryotic sequence context. First, we develop a synthetic route to homogeneous RNAs containing electrophilic acetyl groups. Next, we use thermal denaturation to interrogate the biochemical effects of ac4C on duplex stability and mismatch discrimination in a native sequence found in human rRNA. Finally, we demonstrate the ability of this chemistry to incorporate ac4C into the complex modification landscape of human tRNA and use duplex melting to highlight an enforcing role for ac4C in this unique sequence context. By enabling ex vivo biophysical analyses of nucleic acid acetylation in its physiological sequence context, these studies establish a chemical foundation for understanding the function of a universally conserved nucleobase in biology and disease.
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Affiliation(s)
- David Bartee
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kellie D Nance
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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