151
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Cell-Derived Vesicles for mRNA Delivery. Pharmaceutics 2022; 14:pharmaceutics14122699. [PMID: 36559192 PMCID: PMC9787719 DOI: 10.3390/pharmaceutics14122699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The clinical translation of messenger mRNA (mRNA)-based therapeutics requires safe and effective delivery systems. Although considerable progress has been made on the development of mRNA delivery systems, many challenges, such as the dose-limiting toxicity and specific delivery to extrahepatic tissues, still remain. Cell-derived vesicles, a type of endogenous membranous particle secreted from living cells, can be leveraged to load mRNA during or after their biogenesis. Currently, they have received increasing interest for mRNA delivery due to their natural origin, good biocompatibility, cell-specific tropism, and unique ability to cross physiological barriers. In this review, we provide an overview of recent advances in the naturally occurring mRNA delivery platforms and their biomedical applications. Furthermore, the future perspectives on clinical translation of cell-derived vesicles have been discussed.
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152
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Zhou H, Shi BJ. New roles of DNA-binding and forkhead-associated domains of Fkh1 and Fkh2 in cellular functions. Cell Biochem Funct 2022; 40:888-902. [PMID: 36121195 DOI: 10.1002/cbf.3750] [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: 05/26/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
Two yeast forkhead transcription factors Fkh1 and Fkh2 regulate the transcription of CLB2 cluster genes important for mitosis. Both proteins contain a DNA-binding domain (DBD) and a forkhead-associated domain (FHAD), which are essential for ternary complex formation with transcription factor Mcm1, the transcription of CLB2 cluster genes and the physical interaction with Ndd1 and Clb2. Fkh2 also contains an additional C' domain that contains six consensus Cdk phosphorylation sites, but the function of this domain is dispensable. Here, we found new roles of the DBD, the FHAD, and the C' domain of Fkh1 and Fkh2 in cellular functions. The Fkh2 DBD determines the genetic interaction with NDD1, while both the FHAD and DBD of Fkh1 or Fkh2 determine cell morphology and stability of their own transcripts. Both HFADs, but not DBDs, also mediate physical interaction between Fkh1 and Fkh2. DBD and HFAD of Fkh1 and DBD, but not HFAD, of Fkh2 are also fundamental for nuclear localization. However, the Fkh2-specific C' domain has no role in these aspects except in the stability of some fkh mutant transcripts, which is either increased or decreased in the presence of this domain. These findings reveal that Fkh1 and Fkh2 have multiple cellular functions and function mainly via their DBD and FHAD through a domain-controlled feedback regulation mechanism.
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Affiliation(s)
- Hui Zhou
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
| | - Bu-Jun Shi
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
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153
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Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N 6-methyladenine. Sci Rep 2022; 12:19583. [PMID: 36380112 PMCID: PMC9666514 DOI: 10.1038/s41598-022-23585-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Covalent modifications of standard DNA/RNA nucleobases affect epigenetic regulation of gene expression by modulating interactions between nucleic acids and protein readers. We derive here the absolute binding free energies and analyze the binding modalities between key modified nucleobases 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (m6A) and all non-prolyl/non-glycyl protein side chains using molecular dynamics simulations and umbrella sampling in both water and methanol, the latter mimicking the low dielectric environment at the dehydrated nucleic-acid/protein interfaces. We verify the derived affinities by comparing against a comprehensive set of high-resolution structures of nucleic-protein complexes involving 5mC. Our analysis identifies protein side chains that are highly tuned for detecting cytosine methylation as a function of the environment and can thus serve as microscopic readers of epigenetic marks. Conversely, we show that the relative ordering of sidechain affinities for 5hmC and m6A does not differ significantly from those for their precursor bases, cytosine and adenine, respectively, especially in the low dielectric environment. For those two modified bases, the effect is more nuanced and manifests itself primarily at the level of absolute changes in the binding free energy. Our results contribute towards establishing a quantitative foundation for understanding, predicting and modulating the interactions between modified nucleic acids and proteins at the atomistic level.
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154
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Zhang D, Li Y, Zhong Q, Wang A, Weng J, Gong L, Li G. Ribonucleic Acid Folding Prediction Based on Iterative Multiscale Simulation. J Phys Chem Lett 2022; 13:9957-9966. [PMID: 36260782 DOI: 10.1021/acs.jpclett.2c01342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
RNA folding prediction is a challenge. Currently, many RNA folding models are coarse-grained (CG) with the potential derived from the known RNA structures. However, this potential is not suitable for modified and entirely new RNA. It is also not suitable for the folding simulation of RNA in the real cellular environment, including many kinds of molecular interactions. In contrast, our proposed model has the potential to address these issues, which is a multiscale simulation scheme based on all-atom (AA) force fields. We fit the CG force field using the trajectories generated by the AA force field and then iteratively perform molecular dynamics (MD) simulations of the two scales. The all-atom molecular dynamics (AAMD) simulation is mainly responsible for the correction of RNA structure, and the CGMD simulation is mainly responsible for efficient conformational sampling. On the basis of this scheme, we can successfully fold three RNAs belonging to a hairpin, a pseudoknot, and a four-way junction.
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Affiliation(s)
- Dinglin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
| | - Qinglu Zhong
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
| | - Junben Weng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Lidong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian116029, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
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155
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A Whole New Comprehension about ncRNA-Encoded Peptides/Proteins in Cancers. Cancers (Basel) 2022; 14:cancers14215196. [PMID: 36358616 PMCID: PMC9654040 DOI: 10.3390/cancers14215196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/15/2022] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary The advent of bioinformatics and high-throughput sequencing have disclosed the complexity of ORFs in ncRNAs. Thus, there is a dire need to deep into the real role of ncRNA-encoded proteins/peptides. Considerable progress has been achieved in several fields, ranging from the mechanism translation of ORFs in ncRNAs to various reliable detection means and experimental approaches. Several studies have been stressing functions and mechanisms of ncRNA-encoded peptides/proteins in cancers, which are helpful for us to understand the specific biological regulating procedure. Innovative research on animal models confirms the potential of clinical applications, such as being tumor biomarkers, antitumor drugs and cancer vaccines. In this review, we conclude the latest discoveries of ncRNA-encoded peptides/proteins, we are looking forwards to accelerating the pace of detection and diagnosis development in cancers. Abstract It is generally considered that non-coding RNAs do not encode proteins; however, more recently, studies have shown that lncRNAs and circRNAs have ORFs which are regions that code for peptides/protein. On account of the lack of 5′cap structure, translation of circRNAs is driven by IRESs, m6A modification or through rolling amplification. An increasing body of evidence have revealed different functions and mechanisms of ncRNA-encoded peptides/proteins in cancers, including regulation of signal transduction (Wnt/β-catenin signaling, AKT-related signaling, MAPK signaling and other signaling), cellular metabolism (Glucose metabolism and Lipid metabolism), protein stability, transcriptional regulation, posttranscriptional regulation (regulation of RNA stability, mRNA splicing and translation initiation). In addition, we conclude the existing detection technologies and the potential of clinical applications in cancer therapy.
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156
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Borišek J, Aupič J, Magistrato A. Establishing the catalytic and regulatory mechanism of
RNA
‐based machineries. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jure Borišek
- Theory Department National Institute of Chemistry Ljubljana Slovenia
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157
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Niu R, Wang L, Yang W, Sun L, Tao J, Sun H, Mei S, Wang W, Feng K, Qian D, Bai X. MicroRNA-582-5p targeting Creb1 modulates apoptosis in cardiomyocytes hypoxia/reperfusion-induced injury. Immun Inflamm Dis 2022; 10:e708. [PMID: 36301033 PMCID: PMC9601879 DOI: 10.1002/iid3.708] [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: 05/25/2022] [Revised: 08/10/2022] [Accepted: 08/30/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Myocardial ischemia-reperfusion injury (MIRI) caused by the reperfusion therapy of myocardial ischemic diseases is a kind of major disease that threatens human health and lives severely. There are lacking of effective therapeutic measures for MIRI. MicroRNAs (miRNAs) are abundant in mammalian species and play a critical role in the initiation, promotion, and progression of MIRI. However, the biological role and molecular mechanism of miRNAs in MIRI are not entirely clear. METHODS We used bioinformatics analysis to uncover the significantly different miRNA by analyzing transcriptome sequencing data from myocardial tissue in the mouse MIRI model. Multiple miRNA-related databases, including miRdb, PicTar, and TargetScan were used to forecast the downstream target genes of the differentially expressed miRNA. Then, the experimental models, including male C57BL/6J mice and HL-1 cell line, were used for subsequent experiments including quantitative real-time polymerase chain reaction analysis, western blot analysis, hematoxylin and eosin staining, flow cytometry, luciferase assay, gene interference, and overexpression. RESULTS MiR-582-5p was found to be differentially upregulated from the transcriptome sequencing data. The elevated levels of miR-582-5p were verified in MIRI mice and hypoxia/reperfusion (H/R)-induced HL-1 cells. Functional experiments revealed that miR-582-5p promoted apoptosis of H/R-induced HL-1 cells via downregulating cAMP-response element-binding protein 1 (Creb1). The inhibiting action of miR-582-5p inhibitor on H/R-induced apoptosis was partially reversed after Creb1 interference. CONCLUSIONS Collectively, the research findings reported that upregulation of miR-582-5p promoted H/R-induced cardiomyocyte apoptosis by inhibiting Creb1. The potential diagnostic and therapeutic strategies targeting miR-582-5p and Creb1 could be beneficial for the MIRI treatment.
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Affiliation(s)
- Rui‐Ze Niu
- Department of Cardiac SurgeryKunming Medical University First Affiliated HospitalKunmingYunnanChina,Department of Animal ZoologyKunming Medical UniversityKunmingYunnanChina
| | - Lu‐Qiao Wang
- Department of CardiologyKunming Medical University First Affiliated HospitalKunmingYunnanChina
| | - Wei Yang
- Department of AnesthesiologyKunming Medical University First Affiliated HospitalKunmingYunnanChina
| | - Li‐Zhong Sun
- Department of Cardiovascular Surgery, Beijing Anzhen Hospital, Beijing Institute of Heart, Lung and Blood Vessel DiseasesCapital Medical UniversityBeijingChina
| | - Jie Tao
- Department of Cardiac SurgeryKunming Medical University First Affiliated HospitalKunmingYunnanChina
| | - Huang Sun
- Department of CardiologyKunming Medical University First Affiliated HospitalKunmingYunnanChina
| | - Song Mei
- Department of Cardiac SurgeryKunming Medical University First Affiliated HospitalKunmingYunnanChina
| | - Wen‐Jie Wang
- Department of Cardiac SurgeryKunming Medical University First Affiliated HospitalKunmingYunnanChina
| | - Ke‐Xiang Feng
- Department of Cardiac SurgeryKunming Medical University First Affiliated HospitalKunmingYunnanChina
| | - Dian‐Lun Qian
- Department of Cardiac SurgeryKunming Medical University First Affiliated HospitalKunmingYunnanChina
| | - Xiang‐Feng Bai
- Department of Cardiac SurgeryKunming Medical University First Affiliated HospitalKunmingYunnanChina
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158
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Jousma J, Han Z, Yan G, Nukala SB, Kwon Y, Thi Le HH, Li Y, Ong SB, Lee WH, Ong SG. Alteration of the N 6-methyladenosine epitranscriptomic profile in synthetic phthalate-treated human induced pluripotent stem cell-derived endothelial cells. Epigenomics 2022; 14:1139-1155. [PMID: 36314267 PMCID: PMC9710528 DOI: 10.2217/epi-2022-0110] [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: 04/03/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Background: This study aimed to characterize the N6-methyladenosine epitranscriptomic profile induced by mono(2-ethylhexyl) phthalate (MEHP) exposure using a human-induced pluripotent stem cell-derived endothelial cell model. Methods: A multiomic approach was employed by performing RNA sequencing in parallel with an N6-methyladenosine-specific microarray to identify mRNAs, lncRNAs, and miRNAs affected by MEHP exposure. Results: An integrative multiomic analysis identified relevant biological features affected by MEHP, while functional assays provided a phenotypic characterization of these effects. Transcripts regulated by the epitranscriptome were validated with quantitative PCR and methylated RNA immunoprecipitation. Conclusion: The authors' profiling of the epitranscriptome expands the scope of toxicological insights into known environmental toxins to under surveyed cellular contexts and emerging domains of regulation and is, therefore, a valuable resource to human health.
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Affiliation(s)
- Jordan Jousma
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Zhenbo Han
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Gege Yan
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Sarath Babu Nukala
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Youjeong Kwon
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Hoai Huong Thi Le
- Department of Basic Medical Sciences, University of Arizona College of Medicine, ABC-1 Building, 425 North 5th Street, Phoenix, AZ 85004, USA
| | - Ya Li
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
| | - Sang-Bing Ong
- Department of Medicine & Therapeutics, Faculty of Medicine, Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- Centre for Cardiovascular Genomics & Medicine (CCGM), Lui Che Woo Institute of Innovative Medicine, CUHK, Hong Kong SAR, China
- Hong Kong Hub of Paediatric Excellence (HK HOPE), Hong Kong Children's Hospital (HKCH), Kowloon Bay, Hong Kong SAR, China
- Kunming Institute of Zoology – The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources & Molecular Research of Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan, China
| | - Won Hee Lee
- Department of Basic Medical Sciences, University of Arizona College of Medicine, ABC-1 Building, 425 North 5th Street, Phoenix, AZ 85004, USA
| | - Sang-Ging Ong
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
- Department of Medicine & Therapeutics, Faculty of Medicine, Chinese University of Hong Kong (CUHK), Hong Kong SAR, China
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL 60612, USA
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159
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Boo SH, Ha H, Kim YK. m 1A and m 6A modifications function cooperatively to facilitate rapid mRNA degradation. Cell Rep 2022; 40:111317. [PMID: 36070699 DOI: 10.1016/j.celrep.2022.111317] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/25/2022] [Accepted: 08/16/2022] [Indexed: 11/03/2022] Open
Abstract
N6-Methyladenosine (m6A), the most abundant internal mRNA modification, affects multiple steps in gene expression. Mechanistically, the binding of YTHDF2 to m6A on mRNAs elicits rapid mRNA degradation by recruiting several RNA degrading enzymes. Here, we show that N1-methyladenosine (m1A), another type of RNA modification, accelerates rapid m6A RNA degradation. We identify HRSP12 as an RNA-binding protein that recognizes m1A. The binding of HRSP12 to m1A promotes efficient interaction of YTHDF2 with m6A, consequently facilitating endoribonucleolytic cleavage via the RNase P/MRP complex. Transcriptome-wide analyses also reveal that mRNAs harboring both m1A and m6A are downregulated in an HRSP12-dependent manner compared with mRNAs harboring m6A only. Accordingly, a subset of endogenous circular RNAs that harbor m6A and associate with YTHDF2 in an HRSP12-dependent manner is also subjected to m1A-facilitated rapid degradation. Together, our observations provide compelling evidence for crosstalk between different RNA modifications.
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Affiliation(s)
- Sung Ho Boo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hongseok Ha
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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160
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Feng Q, Wang D, Xue T, Lin C, Gao Y, Sun L, Jin Y, Liu D. The role of RNA modification in hepatocellular carcinoma. Front Pharmacol 2022; 13:984453. [PMID: 36120301 PMCID: PMC9479111 DOI: 10.3389/fphar.2022.984453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/11/2022] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly mortal type of primary liver cancer. Abnormal epigenetic modifications are present in HCC, and RNA modification is dynamic and reversible and is a key post-transcriptional regulator. With the in-depth study of post-transcriptional modifications, RNA modifications are aberrantly expressed in human cancers. Moreover, the regulators of RNA modifications can be used as potential targets for cancer therapy. In RNA modifications, N6-methyladenosine (m6A), N7-methylguanosine (m7G), and 5-methylcytosine (m5C) and their regulators have important regulatory roles in HCC progression and represent potential novel biomarkers for the confirmation of diagnosis and treatment of HCC. This review focuses on RNA modifications in HCC and the roles and mechanisms of m6A, m7G, m5C, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and pseudouridine (ψ) on its development and maintenance. The potential therapeutic strategies of RNA modifications are elaborated for HCC.
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Affiliation(s)
- Qiang Feng
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Tianyi Xue
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Chao Lin
- School of Grain Science and Technology, Jilin Business and Technology College, Changchun, China
| | - Yongjian Gao
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Liqun Sun
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Dianfeng Liu
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Dianfeng Liu,
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161
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Role of Epitranscriptomic and Epigenetic Modifications during the Lytic and Latent Phases of Herpesvirus Infections. Microorganisms 2022; 10:microorganisms10091754. [PMID: 36144356 PMCID: PMC9503318 DOI: 10.3390/microorganisms10091754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/27/2022] [Accepted: 08/27/2022] [Indexed: 11/24/2022] Open
Abstract
Herpesviruses are double-stranded DNA viruses occurring at a high prevalence in the human population and are responsible for a wide array of clinical manifestations and diseases, from mild to severe. These viruses are classified in three subfamilies (Alpha-, Beta- and Gammaherpesvirinae), with eight members currently known to infect humans. Importantly, all herpesviruses can establish lifelong latent infections with symptomatic or asymptomatic lytic reactivations. Accumulating evidence suggest that chemical modifications of viral RNA and DNA during the lytic and latent phases of the infections caused by these viruses, are likely to play relevant roles in key aspects of the life cycle of these viruses by modulating and regulating their replication, establishment of latency and evasion of the host antiviral response. Here, we review and discuss current evidence regarding epitranscriptomic and epigenetic modifications of herpesviruses and how these can influence their life cycles. While epitranscriptomic modifications such as m6A are the most studied to date and relate to positive effects over the replication of herpesviruses, epigenetic modifications of the viral genome are generally associated with defense mechanisms of the host cells to suppress viral gene transcription. However, herpesviruses can modulate these modifications to their own benefit to persist in the host, undergo latency and sporadically reactivate.
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162
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Cheng H, Li Z. Advances and Perspectives of Pharmaceutical Nanotechnology in mRNA therapy. Pharm Nanotechnol 2022; 10:PNT-EPUB-125850. [PMID: 36028972 DOI: 10.2174/2211738510666220825145124] [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: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/22/2022]
Affiliation(s)
- Hui Cheng
- Nankai University School of Medicine, Tianjin 300071, China
| | - Zongjin Li
- Nankai University School of Medicine, Tianjin 300071, China
- The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, College of Life Sciences, Tianjin 300071, China
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163
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Ling H, Cao CH, Han K, Lv YR, Ma XD, Cao JH, Chen JW, Li S, Lin JL, Fang YJ, Pan ZZ, Xie D, Wang FW. CEP63 upregulates YAP1 to promote colorectal cancer progression through stabilizing RNA binding protein FXR1. Oncogene 2022; 41:4433-4445. [PMID: 35989368 DOI: 10.1038/s41388-022-02439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Abstract
Abnormal regulation of centrosome components can induce chromosome instability and tumorigenesis. Centrosomal protein 63 (CEP63) is a vital member for assembling centrosome. Yet, the involvement of CEP63 in cancer pathogenesis remains unclear. Here we identify CEP63 as an important mediator for RNA-binding proteins (RBPs) to facilitate regulation on their RNA targets in colorectal cancer (CRC). We demonstrate that CEP63 protein is upregulated in a large cohort of colorectal cancer tissues and predicts poor prognosis, and USP36 is identified for stabilizing CEP63 by enhancing its K48-dependent deubiquitination. CEP63 overexpression promotes the proliferation and tumor growth of CRC cells in vitro and in vivo. Furthermore, we find that CEP63 can promote cancer stem-like cell properties by enhancing YAP1 expression through binding with and inhibiting the K63-ubiquitylation degradation of RBP FXR1 in CRC cells. Importantly, we further verify that the KH domain of FXR1 is necessary for the interaction between CEP63 and FXR1. Moreover, microtube motor proteins can form a complex with CEP63 and FXR1 to mediate the regulation of FXR1 on RNA targets. Additionally, we also confirm that CEP63 can bind and regulate multiple RBPs. In conclusion, our findings unveil an unrecognized CEP63/RBPs/RNA axis that CEP63 may perform as an adapter facilitating the formation of RBPs complex to regulate RNA progression and discover the role of CEP63 involved in signal transduction and RNA regulation, providing potential therapeutic target for CRC patients.
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Affiliation(s)
- Han Ling
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Chen-Hui Cao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China.,Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Kai Han
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China.,Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yong-Rui Lv
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Xiao-Dan Ma
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Jing-Hua Cao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Jie-Wei Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Si Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Jin-Long Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Yu-Jing Fang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China.,Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zhi-Zhong Pan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China.,Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Dan Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China. .,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Feng-Wei Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China.
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164
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Yun D, Yang Z, Zhang S, Yang H, Liu D, Grützmann R, Pilarsky C, Britzen-Laurent N. An m5C methylation regulator-associated signature predicts prognosis and therapy response in pancreatic cancer. Front Cell Dev Biol 2022; 10:975684. [PMID: 36060802 PMCID: PMC9437259 DOI: 10.3389/fcell.2022.975684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/28/2022] [Indexed: 11/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most aggressive digestive malignancy due to frequent late-stage diagnosis, rapid progression and resistance to therapy. With increasing PDAC incidence worldwide, there is an urgent need for new prognostic biomarkers and therapy targets. Recently, RNA methylation has emerged as a new tumorigenic mechanism in different cancers. 5-methylcytosine (m5C) is one of the most frequent RNA modifications and occurs on a variety of RNA species including mRNA, thereby regulating gene expression. Here we investigated the prognostic role of m5C-regulator-associated transcriptional signature in PDAC. We evaluated m5C-regulator status and expression in 239 PDAC samples from publicly available datasets. We used unsupervised consensus clustering analyses to classify PDACs based on m5C-regulator expression. From the resulting signature of differentially expressed genes (DEGs), we selected prognosis-relevant DEGs to stratify patients and build a scoring signature (m5C-score) through LASSO and multivariate Cox regression analyses. The m5C-score represented a highly significant independent prognostic marker. A high m5C-score correlated with poor prognosis in different PDAC cohorts, and was associated with the squamous/basal subtype as well as activated cancer-related pathways including Ras, MAPK and PI3K pathways. Furthermore, the m5C-score correlated with sensitivity to pathway-specific inhibitors of PARP, EGFR, AKT, HER2 and mTOR. Tumors with high m5C-score were characterized by overall immune exclusion, low CD8+ T-cell infiltration, and higher PD-L1 expression. Overall, the m5C-score represented a robust predictor of prognosis and therapy response in PDAC, which was associated with unfavorable molecular subtypes and immune microenvironment.
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Affiliation(s)
- Duo Yun
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Zhirong Yang
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Shuman Zhang
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hai Yang
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Dongxue Liu
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christian Pilarsky
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nathalie Britzen-Laurent
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- *Correspondence: Nathalie Britzen-Laurent,
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165
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Zhang S, Xiong Y, Wang W, Zhang E, Gu Y, Liu Y, Zeng Z, Tang F, Ouyang Y. Identification of the crosstalk among four types of adenosine-related RNA modification in pan-cancer. Cancer Sci 2022; 113:3633-3636. [PMID: 35965405 PMCID: PMC9530861 DOI: 10.1111/cas.15503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Shichao Zhang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yu Xiong
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Weirong Wang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Erdong Zhang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yan Gu
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Yang Liu
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Zhu Zeng
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Fuzhou Tang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Yan Ouyang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
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166
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Krul SE, Costa GJ, Hoehn SJ, Valverde D, Oliveira LMF, Borin AC, Crespo-Hernández CE. Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-Aza-7-Deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet. Photochem Photobiol 2022; 99:693-705. [PMID: 35938218 DOI: 10.1111/php.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The guanine derivative, 5-aza-7-deazaguanine (5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art Extended Multi-State Complete Active Space Second-Order Perturbation Theory. It is demonstrated that excitation to the lowest energy 1 ππ* state of 5N7C G results in complex dynamics leading to ca. 10 to 30-fold slower relaxation (depending on solvent) compared to guanine. A significant conformational change occurs at the S1 minimum, resulting in a 10-fold greater fluorescence quantum yield compared to guanine. The fluorescence quantum yield and S1 decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S1 minimum and the S1 /S0 conical intersection going from water to propanol. The longer lifetimes might make 5N7C G more photochemical active to adjacent nucleobases than guanine or other nucleobases within DNA.
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Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Gustavo J Costa
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Danillo Valverde
- Unité de Chimie Physique Theorique et Structurale, Namur Institute of Structured Matter, Université de Namur, B-5000, Namur, Belgium
| | - Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Carlos E Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
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167
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Hai Y, Kawachi A, He X, Yoshimi A. Pathogenic Roles of RNA-Binding Proteins in Sarcomas. Cancers (Basel) 2022; 14:cancers14153812. [PMID: 35954475 PMCID: PMC9367343 DOI: 10.3390/cancers14153812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
RNA-binding proteins (RBPs) are proteins that physically and functionally bind to RNA to regulate the RNA metabolism such as alternative splicing, polyadenylation, transport, maintenance of stability, localization, and translation. There is accumulating evidence that dysregulated RBPs play an essential role in the pathogenesis of malignant tumors including a variety of types of sarcomas. On the other hand, prognosis of patients with sarcoma, especially with sarcoma in advanced stages, is very poor, and almost no effective standard treatment has been established for most of types of sarcomas so far, highlighting the urgent need for identifying novel therapeutic targets based on the deep understanding of pathogenesis. Therefore, defining the network of interactions between RBPs and disease-related RNA targets will contribute to a better understanding of sarcomagenesis and identification of a novel therapeutic target for sarcomas.
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Affiliation(s)
- Yu Hai
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Asuka Kawachi
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Xiaodong He
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Akihide Yoshimi
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Correspondence: ; Tel.: +81-3-3542-2511
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168
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Shen Y, Wang S, Wu Y. A Novel m6A-Related LncRNA Signature for Predicting Prognosis, Chemotherapy and Immunotherapy Response in Patients with Lung Adenocarcinoma. Cells 2022; 11:cells11152399. [PMID: 35954243 PMCID: PMC9368324 DOI: 10.3390/cells11152399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023] Open
Abstract
N6-methyladenosine (m6A) and long non-coding RNA (lncRNA) have been associated with cancer prognosis and the effect of immunotherapy. However, the roles of m6A-related lncRNAs in the prognosis and immunotherapy in lung adenocarcinoma (LUAD) patients remain unclear. We evaluated the m6A modification patterns of 695 samples based on m6A regulators, and prognostic m6A-related lncRNAs were identified via a weighted gene co-expression network analysis. Twelve abnormal m6A regulators and nine prognostic lncRNAs were identified. The tumor microenvironment cell-infiltrating characteristics of three m6A-related lncRNA clusters were highly consistent with the three immune phenotypes of tumors, including immune-excluded, immune-inflamed and immune-desert phenotypes. The lncRNA score system was established, and high lncRNA score patients were associated with better overall survival. The lncRNA score was correlated with the expression of the immune checkpoints. Two immunotherapy cohorts supported that the high lncRNA score enhanced the response to anti-PD-1/L1 immunotherapy and was remarkably correlated with the inflamed immune phenotype, showing significant therapeutic advantages and clinical benefits. Furthermore, the patients with high lncRNA scores were more sensitive to erlotinib and axitinib. The lncRNA score was associated with the expression of miRNA and the regulation of post-transcription. We constructed an applied lncRNA score-system to identify eligible LUAD patients for immunotherapy and predict the sensitivity to chemotherapeutic drugs.
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Affiliation(s)
- Yefeng Shen
- Institute for Pathology, University Hospital of Cologne, 50937 Cologne, Germany;
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Shaochun Wang
- Department of Oncology, Shijiazhuang People’s Hospital, Shijiazhuang 050000, China;
| | - Yuanzhou Wu
- Department of Thoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
- Correspondence:
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169
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A review on CRISPR/Cas-based epigenetic regulation in plants. Int J Biol Macromol 2022; 219:1261-1271. [DOI: 10.1016/j.ijbiomac.2022.08.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/13/2022] [Accepted: 08/29/2022] [Indexed: 01/09/2023]
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170
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Gosset-Erard C, Lechner A, Wolff P, Aubriet F, Leize-Wagner E, Chaimbault P, François YN. Optimization of nucleotides dephosphorylation for RNA structural characterization by tandem mass spectrometry hyphenated with separation methods. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1208:123396. [PMID: 35917777 DOI: 10.1016/j.jchromb.2022.123396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 12/12/2022]
Abstract
As part of RNA characterization, the identification of post-transcriptional modifications can be performed using hyphenation of separation methods with mass spectrometry. To identify RNA modifications with those methods, a first total digestion followed by a dephosphorylation step are usually required to reduce RNA to nucleosides. Even though effective digestion and dephosphorylation are essential to avoid further complications in analysis and data interpretation, to our knowledge, no standard protocol is yet referenced in the literature. Therefore, the aim of this work is to optimize the dephosphorylation step using a total extract of transfer RNA (tRNA)1 from B. taurus as a model and to determine and fix two protocols, leading to complete dephosphorylation, based on time and bacterial alkaline phosphatase (BAP)2 consumptions. Capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) was used to estimate the dephosphorylation efficiency of both protocols on many canonical and modified nucleotides. For a timesaving protocol, we established that full dephosphorylation was obtained after a 4-hour incubation at 37 °C with 7.5 U of BAP for 1 µg of tRNA. And for a BAP-saving protocol, we established that full dephosphorylation was obtained 3.0 U of BAP after an overnight incubation at 37 °C. Both protocols are suitable for quantitative analyses as no loss of analytes is expected. Moreover, they can be widely used for all other RNA classes, including messenger RNA or ribosomal RNA.
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Affiliation(s)
- Clarisse Gosset-Erard
- Université de Lorraine, LCP-A2MC, F-57000 Metz, France; Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
| | - Antony Lechner
- Architecture et Réactivité de l'ARN (ARN) UPR 9002, CNRS, Université de Strasbourg, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade FRC 1589, CNRS, Strasbourg, France.
| | - Philippe Wolff
- Architecture et Réactivité de l'ARN (ARN) UPR 9002, CNRS, Université de Strasbourg, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade FRC 1589, CNRS, Strasbourg, France.
| | | | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
| | | | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
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171
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Mersinoglu B, Cristinelli S, Ciuffi A. The Impact of Epitranscriptomics on Antiviral Innate Immunity. Viruses 2022; 14:v14081666. [PMID: 36016289 PMCID: PMC9412694 DOI: 10.3390/v14081666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
Epitranscriptomics, i.e., chemical modifications of RNA molecules, has proven to be a new layer of modulation and regulation of protein expression, asking for the revisiting of some aspects of cellular biology. At the virological level, epitranscriptomics can thus directly impact the viral life cycle itself, acting on viral or cellular proteins promoting replication, or impacting the innate antiviral response of the host cell, the latter being the focus of the present review.
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172
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Zhao C, Xu G, Zhang X, Ye Y, Cai W, Shao Q. RNA m6A modification orchestrates the rhythm of immune cell development from hematopoietic stem cells to T and B cells. Front Immunol 2022; 13:839291. [PMID: 35935968 PMCID: PMC9354743 DOI: 10.3389/fimmu.2022.839291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 06/28/2022] [Indexed: 11/15/2022] Open
Abstract
RNA, one of the major building blocks of the cell, participates in many essential life processes. RNA stability is well-established to be closely related to various RNA modifications. To date, hundreds of different RNA modifications have been identified. N6-methyladenosine (m6A) is one of the most important RNA modifications in mammalian cells. An increasing body of evidence from recently published studies suggests that m6A modification is a novel immune system regulator of the generation and differentiation of hematopoietic stem cells (HSCs) and immune cells. In this review, we introduce the process and relevant regulatory mechanisms of m6A modification; summarize recent findings of m6A in controlling HSC generation and self-renewal, and the development and differentiation of T and B lymphocytes from HSCs; and discuss the potential mechanisms involved.
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Affiliation(s)
- Chuanxiang Zhao
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Guoying Xu
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Xiaoxian Zhang
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Yunfeng Ye
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Weili Cai
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
| | - Qixiang Shao
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an, China
- Reproductive Sciences Institute, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
- *Correspondence: Qixiang Shao,
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173
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Yang X, Patil S, Joshi S, Jamla M, Kumar V. Exploring epitranscriptomics for crop improvement and environmental stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:56-71. [PMID: 35567875 DOI: 10.1016/j.plaphy.2022.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m5C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.
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Affiliation(s)
- Xiangbo Yang
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, PR China.
| | - Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
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174
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Chen L, Wang WJ, Liu Q, Wu YK, Wu YW, Jiang Y, Liao XQ, Huang F, Li Y, Shen L, Yu C, Zhang SY, Yan LY, Qiao J, Sha QQ, Fan HY. NAT10-mediated N4-acetylcytidine modification is required for meiosis entry and progression in male germ cells. Nucleic Acids Res 2022; 50:10896-10913. [PMID: 35801907 PMCID: PMC9638909 DOI: 10.1093/nar/gkac594] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/15/2022] [Accepted: 06/25/2022] [Indexed: 12/03/2022] Open
Abstract
Post-transcriptional RNA modifications critically regulate various biological processes. N4-acetylcytidine (ac4C) is an epi-transcriptome, which is highly conserved in all species. However, the in vivo physiological functions and regulatory mechanisms of ac4C remain poorly understood, particularly in mammals. In this study, we demonstrate that the only known ac4C writer, N-acetyltransferase 10 (NAT10), plays an essential role in male reproduction. We identified the occurrence of ac4C in the mRNAs of mouse tissues and showed that ac4C undergoes dynamic changes during spermatogenesis. Germ cell-specific ablation of Nat10 severely inhibits meiotic entry and leads to defects in homologous chromosome synapsis, meiotic recombination and repair of DNA double-strand breaks during meiosis. Transcriptomic profiling revealed dysregulation of functional genes in meiotic prophase I after Nat10 deletion. These findings highlight the crucial physiological functions of ac4C modifications in male spermatogenesis and expand our understanding of its role in the regulation of specific physiological processes in vivo.
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Affiliation(s)
| | | | | | | | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yu Jiang
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiu-Quan Liao
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Fei Huang
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yang Li
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Chao Yu
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
- College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Song-Ying Zhang
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Li-Ying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing 100191, China
| | - Jie Qiao
- Correspondence may also be addressed to Jie Qiao. Tel: +86 571 88981751;
| | - Qian-Qian Sha
- Correspondence may also be addressed to Qian-Qian Sha. Tel: +86 20 89169199;
| | - Heng-Yu Fan
- To whom correspondence should be addressed. Tel: +86 571 88981370;
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175
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Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. Microbiol Mol Biol Rev 2022; 86:e0005721. [PMID: 35862724 PMCID: PMC9491204 DOI: 10.1128/mmbr.00057-21] [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] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in “long COVID” patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.
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176
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Koide EM, Abbott EA, Helbing CC. Uncovering early thyroid hormone signalling events through temperature-mediated activation of molecular memory in the cultured bullfrog tadpole tail fin. Gen Comp Endocrinol 2022; 323-324:114047. [PMID: 35472316 DOI: 10.1016/j.ygcen.2022.114047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/10/2022] [Accepted: 04/21/2022] [Indexed: 11/04/2022]
Abstract
Thyroid hormone (TH) is a critical signalling molecule for all vertebrate organisms, playing a crucial role in postembryonic development. The best-studied mechanism of TH response is through modulating gene expression, however TH's involvement in coordinating the early steps in the TH signal transduction pathway is still poorly understood. The American bullfrog, Rana [Lithobates] catesbeiana, is a useful model to study these early responses as tadpole post-embryonic development in the form of metamorphosis of the tadpole into a frog can be experimentally induced by TH exposure. The rate of TH-induced metamorphosis can be modulated by temperature where sufficiently cold temperatures (5 °C) completely halt precocious metamorphosis. Interestingly, when premetamorphic tadpoles exposed to exogenous THs at 5 °C are shifted to permissive temperatures (24 °C), their metamorphic rate exceeds that of TH-exposed tadpoles at the permissive temperature. This suggests that a molecular memory of TH exposure is retained at 5 °C even after THs are cleared at this low temperature. However, the molecular memory machinery is poorly understood. Herein we use RNA-seq analysis to identify potential components of the molecular memory in cultured tail fin that allows for the recapitulation of the molecular memory phenomenon. Eighty-one gene transcripts were TH-responsive at 5 °C compared to matched controls indicating that the molecular memory is more complex than previously thought. Many of these transcripts encode transcription factors including thyroid hormone-induced B/Zip, thibz, and a novel krüppel-like factor family member, klfX. Actinomycin D and cycloheximide treatment had no effect on their TH induction suggesting that a change in transcription or translation is not required. Rather a change in RNA stability may be a possible mechanism contributing to the molecular memory. The ability to manipulate temperature and TH response in cultured organs provide an exciting opportunity to further elucidate the early TH signalling mechanisms during postembryonic development.
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Affiliation(s)
- E M Koide
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - E A Abbott
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - C C Helbing
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada.
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177
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Kocheril PA, Moore SC, Lenz KD, Mukundan H, Lilley LM. Progress Toward a Multiomic Understanding of Traumatic Brain Injury: A Review. Biomark Insights 2022; 17:11772719221105145. [PMID: 35719705 PMCID: PMC9201320 DOI: 10.1177/11772719221105145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Traumatic brain injury (TBI) is not a single disease state but describes an array
of conditions associated with insult or injury to the brain. While some
individuals with TBI recover within a few days or months, others present with
persistent symptoms that can cause disability, neuropsychological trauma, and
even death. Understanding, diagnosing, and treating TBI is extremely complex for
many reasons, including the variable biomechanics of head impact, differences in
severity and location of injury, and individual patient characteristics. Because
of these confounding factors, the development of reliable diagnostics and
targeted treatments for brain injury remains elusive. We argue that the
development of effective diagnostic and therapeutic strategies for TBI requires
a deep understanding of human neurophysiology at the molecular level and that
the framework of multiomics may provide some effective solutions for the
diagnosis and treatment of this challenging condition. To this end, we present
here a comprehensive review of TBI biomarker candidates from across the
multiomic disciplines and compare them with known signatures associated with
other neuropsychological conditions, including Alzheimer’s disease and
Parkinson’s disease. We believe that this integrated view will facilitate a
deeper understanding of the pathophysiology of TBI and its potential links to
other neurological diseases.
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Affiliation(s)
- Philip A Kocheril
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Shepard C Moore
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kiersten D Lenz
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Laura M Lilley
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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178
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Rodriguez W, Muller M. Shiftless, a Critical Piece of the Innate Immune Response to Viral Infection. Viruses 2022; 14:v14061338. [PMID: 35746809 PMCID: PMC9230503 DOI: 10.3390/v14061338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/08/2022] [Accepted: 06/16/2022] [Indexed: 12/14/2022] Open
Abstract
Since its initial characterization in 2016, the interferon stimulated gene Shiftless (SHFL) has proven to be a critical piece of the innate immune response to viral infection. SHFL expression stringently restricts the replication of multiple DNA, RNA, and retroviruses with an extraordinary diversity of mechanisms that differ from one virus to the next. These inhibitory strategies include the negative regulation of viral RNA stability, translation, and even the manipulation of RNA granule formation during viral infection. Even more surprisingly, SHFL is the first human protein found to directly inhibit the activity of the -1 programmed ribosomal frameshift, a translation recoding strategy utilized across nearly all domains of life and several human viruses. Recent literature has shown that SHFL expression also significantly impacts viral pathogenesis in mouse models, highlighting its in vivo efficacy. To help reconcile the many mechanisms by which SHFL restricts viral replication, we provide here a comprehensive review of this complex ISG, its influence over viral RNA fate, and the implications of its functions on the virus-host arms race for control of the cell.
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179
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He T, Guo H, Xia L, Shen X, Huang Y, Wu X, Jiang X, Xu Y, Tan Y, Zhang Y, Tan D. Alterations of RNA Modification in Mouse Germ Cell-2 Spermatids Under Hypoxic Stress. Front Mol Biosci 2022; 9:871737. [PMID: 35775084 PMCID: PMC9237606 DOI: 10.3389/fmolb.2022.871737] [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: 02/08/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Hypoxia is a known stress factor in mammals and has been shown to potentially impair male fertility, which manifests as spermatogenic dysfunction and decreased semen quality. Studies have shown that RNA modifications, the novel post-transcriptional regulators, are involved in spermatogenesis, and hypoxia-induced alterations in RNA modification in testes and sperm cells may be associated with impaired spermatogenesis in mice. However, the molecular mechanisms via which RNA modifications influence spermatogenesis under hypoxic stress conditions are unclear. In this study, we generated a mouse Germ Cell-2 spermatid (GC-2spd) hypoxia model by culturing cells in a 1% O2 incubator for 48 h or treating them with CoCl2 for 24 h. The hypoxia treatment significantly inhibited proliferation and induced apoptosis in GC-2spd cells. The RNA modification signatures of total RNAs (2 types) and differentially sized RNA fragments (7 types of approximately 80 nt-sized tRNAs; 9 types of 17–50 nt-sized sncRNAs) were altered, and tRNA stability was partially affected. Moreover, the expression profiles of sncRNAs, such as microRNAs, tsRNAs, rsRNAs, and ysRNAs, were significantly regulated, and this might be related to the alterations in RNA modification and subsequent transcriptomic changes. We comprehensively analyzed alterations in RNA modification signatures in total RNAs, tRNAs (approximately 80 nt), and small RNAs (17–50 nt) as well as the expression profiles of sncRNAs and transcriptomes in hypoxia-treated GC-2spd cells; our data suggested that RNA modifications may be involved in cellular responses under hypoxic stress conditions and could provide a basis for a better understanding of the molecular mechanisms underlying male infertility.
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Affiliation(s)
- Tong He
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Huanping Guo
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Lin Xia
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xipeng Shen
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yun Huang
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Xiao Wu
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xuelin Jiang
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yinying Xu
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yi Tan
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Yunfang Zhang
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- *Correspondence: Yunfang Zhang, ; Dongmei Tan,
| | - Dongmei Tan
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
- *Correspondence: Yunfang Zhang, ; Dongmei Tan,
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180
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Alagia A, Gullerova M. The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine. Front Cell Dev Biol 2022; 10:915685. [PMID: 35721489 PMCID: PMC9204050 DOI: 10.3389/fcell.2022.915685] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our understanding of cellular programming and responses to environmental cues. One of the key modifications, m5C, has been identified as a contributor to regulation of the DNA damage response (DDR). However, the various mechanisms of dynamic m5C deposition and removal, and the role m5C plays within the cell, remains to be fully understood.
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Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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181
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RNA modifications can affect RNase H1-mediated PS-ASO activity. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:814-828. [PMID: 35664704 PMCID: PMC9136273 DOI: 10.1016/j.omtn.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/07/2022] [Indexed: 11/21/2022]
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182
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Morreel K, t’Kindt R, Debyser G, Jonckheere S, Sandra P. Diving into the Structural Details of In Vitro Transcribed mRNA Using Liquid Chromatography–Mass Spectrometry-Based Oligonucleotide Profiling. LCGC EUROPE 2022. [DOI: 10.56530/lcgc.eu.jk3969w4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The production process of in vitro transcribed messenger RNA (IVT-mRNA)-based vaccines has matured in recent years, partly due to the fight against infectious diseases such as COVID-19. One key to success has been the use of modified, next to canonical, nucleotides and the efficient addition of a Cap-structure and poly A tail to the 5’ and 3’ end, respectively, of this massive biomolecule. These important features affect mRNA stability and impact translation efficiency, consequently boosting the optimization and implementation of liquid chromatography–mass spectrometry (LC–MS)-based oligonucleotide profiling methods for their characterization. This article will provide an overview of these LC–MS methods at a fundamental and application level. It will be shown how LC–MS is implemented in mRNA-based vaccine analysis to determine the capping efficiency and the poly A tail length, and how it allows, via RNA mapping, (i) to determine the mRNA sequence, (ii) to screen the fidelity of the manufactured modifications, and (iii) to identify and quantify unwanted modifications resulting from manufacturing or storage, and sequence variants resulting from mutation or transcription errors.
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183
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Shekibi M, Heng S, Nie G. MicroRNAs in the Regulation of Endometrial Receptivity for Embryo Implantation. Int J Mol Sci 2022; 23:ijms23116210. [PMID: 35682889 PMCID: PMC9181585 DOI: 10.3390/ijms23116210] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/13/2022] [Accepted: 05/28/2022] [Indexed: 12/13/2022] Open
Abstract
Development of endometrial receptivity is crucial for successful embryo implantation and pregnancy initiation. Understanding the molecular regulation underpinning endometrial transformation to a receptive state is key to improving implantation rates in fertility treatments such as IVF. With microRNAs (miRNAs) increasingly recognized as important gene regulators, recent studies have investigated the role of miRNAs in the endometrium. Studies on miRNAs in endometrial disorders such as endometriosis and endometrial cancer have been reviewed previously. In this minireview, we aim to provide an up-to-date knowledge of miRNAs in the regulation of endometrial receptivity. Since endometrial remodelling differs considerably between species, we firstly summarised the key events of the endometrial cycle in humans and mice and then reviewed the miRNAs identified so far in these two species with likely functional significance in receptivity establishment. To date, 29 miRNAs have been reported in humans and 15 miRNAs in mice within various compartments of the endometrium that may potentially modulate receptivity; miRNAs regulating the Wnt signalling and those from the let-7, miR-23, miR-30, miR-200 and miR-183 families are found in both species. Future studies are warranted to investigate miRNAs as biomarkers and/or therapeutic targets to detect/improve endometrial receptivity in human fertility treatment.
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184
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Zhu Y, Wu W, Chen S, Zhang Z, Zhang G, Li J, Jiang M. Mettl3 downregulation in germinal vesicle oocytes inhibits mRNA decay and the 1st polar body extrusion during maturation. Biol Reprod 2022; 107:765-778. [PMID: 35639638 DOI: 10.1093/biolre/ioac112] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/18/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022] Open
Abstract
In oocytes, mRNA decay is essential for maturation and subsequent events, such as maternal-zygotic transition, zygotic genomic activation, and embryo development. Reversible N6-methyladenosine RNA methylation directly regulates transcription, pre-mRNA splicing, mRNA export, mRNA stability, and translation. Here, we identified that downregulation of N6-methyladenosine modification by microinjecting a methyltransferase-like 3 (Mettl3)-specific small interfering RNA into mouse germinal vesicle oocytes led to defects in meiotic spindles and the 1st polar body extrusion during maturation in vitro. By further quantitative real-time polymerase chain reaction and Poly(A)-tail assay analysis, we found that N6-methyladenosine methylation mainly acts by reducing deadenylation of mRNAs mediated by the Carbon catabolite repression 4 (CCR4)- negative on TATA less-(NOT) system, thereby causing mRNA accumulation in oocytes. Meanwhile, transcriptome analysis of germinal vesicle oocytes revealed the downregulation of transcripts of several genes encoding ribosomal subunits proteins in the Mettl3 small interfering RNA treated group, suggesting that N6-methyladenosine modification might affect translation. Together, our results indicate that RNA methylation accelerates mRNA decay, confirming the critical role of RNA clearance in oocyte maturation.
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Affiliation(s)
- Yan Zhu
- Medical Experiment Center, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Wenjiao Wu
- Medical Experiment Center, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Shaoqing Chen
- Center for Reproductive Medicine, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Zhen Zhang
- Medical Experiment Center, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Guangli Zhang
- Center for Reproductive Medicine, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Jie Li
- Medical Experiment Center, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Manxi Jiang
- Center for Reproductive Medicine, Guangdong Second Provincial General Hospital, Guangdong, PR China
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185
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Boo SH, Ha H, Lee Y, Shin MK, Lee S, Kim YK. UPF1 promotes rapid degradation of m 6A-containing RNAs. Cell Rep 2022; 39:110861. [PMID: 35613594 DOI: 10.1016/j.celrep.2022.110861] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/03/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotic mRNAs and affects RNA processing and metabolism. When YTHDF2, an m6A-recognizing protein, binds to m6A, it facilitates the destabilization of m6A-containing RNAs (m6A RNAs). Here, we demonstrate that upstream frameshift 1 (UPF1), a key factor for nonsense-mediated mRNA decay, interacts with YTHDF2, thereby triggering rapid degradation of m6A RNAs. The UPF1-mediated m6A RNA degradation depends on a specific interaction between UPF1 and N-terminal residues 101-168 of YTHDF2, UPF1 ATPase/helicase activities, and UPF1 interaction with proline-rich nuclear receptor coactivator 2 (PNRC2), a decapping-promoting factor preferentially involved in nonsense-mediated mRNA decay. Furthermore, transcriptome-wide analyses show that YTHDF2-bound mRNAs that are not substrates for HRSP12-RNase P/MRP-mediated endoribonucleolytic cleavage are destabilized with a higher dependency on UPF1. Collectively, our data indicate dynamic and multilayered regulation of the stability of m6A RNAs and highlight the multifaceted role of UPF1 in mRNA decay.
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Affiliation(s)
- Sung Ho Boo
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hongseok Ha
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yujin Lee
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Min-Kyung Shin
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sena Lee
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea; Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea.
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186
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Hasan MM, Tsukiyama S, Cho JY, Kurata H, Alam MA, Liu X, Manavalan B, Deng HW. Deepm5C: A deep learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy. Mol Ther 2022; 30:2856-2867. [PMID: 35526094 PMCID: PMC9372321 DOI: 10.1016/j.ymthe.2022.05.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022] Open
Abstract
As one of the most prevalent post-transcriptional epigenetic modifications, N5-methylcytosine (m5C), plays an essential role in various cellular processes and disease pathogenesis. Therefore, it is important accurately identify m5C modifications in order to gain a deeper understanding of cellular processes and other possible functional mechanisms. Although a few computational methods have been proposed, their respective models have been developed using small training datasets. Hence, their practical application is quite limited in genome-wide detection. To overcome the existing limitations, we propose Deepm5C, a bioinformatics method to identify RNA m5C sites in the throughout human genome. To develop Deepm5C, we constructed a novel benchmarking dataset and investigated a mixture of three conventional feature encoding algorithms and a feature derived from word embedding approaches. Afterwards, four variants of deep learning classifiers and four commonly used conventional classifiers were employed and trained with the four encodings, ultimately obtaining 32 baseline models. A stacking strategy is effectively utilized by integrating the predicted output of the optimal baseline models and trained with a 1-D convolutional neural network. As a result, the Deepm5C predictor achieved excellent performance during cross-validation with a Matthews correlation coefficient and accuracy of 0.697 and 0.855, respectively. The corresponding metrics during the independent test were 0.691 and 0.852, respectively. Overall, Deepm5C achieved a more accurate and stable performance than the baseline models and significantly outperformed the existing predictors, demonstrating the effectiveness of our proposed hybrid framework. Furthermore, Deepm5C is expected to assist community-wide efforts in identifying putative m5Cs and formulate the novel testable biological hypothesis.
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Affiliation(s)
- Md Mehedi Hasan
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112 USA.
| | - Sho Tsukiyama
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Jae Youl Cho
- Molecular Immunology Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Md Ashad Alam
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112 USA
| | - Xiaowen Liu
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112 USA
| | - Balachandran Manavalan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea.
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112 USA.
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187
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Regulation of CLB6 expression by the cytoplasmic deadenylase Ccr4 through its coding and 3’ UTR regions. PLoS One 2022; 17:e0268283. [PMID: 35522675 PMCID: PMC9075657 DOI: 10.1371/journal.pone.0268283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/26/2022] [Indexed: 01/14/2023] Open
Abstract
RNA stability control contributes to the proper expression of gene products. Messenger RNAs (mRNAs) in eukaryotic cells possess a 5’ cap structure and the 3’ poly(A) tail which are important for mRNA stability and efficient translation. The Ccr4-Not complex is a major cytoplasmic deadenylase and functions in mRNA degradation. The CLB1-6 genes in Saccharomyces cerevisiae encode B-type cyclins which are involved in the cell cycle progression together with the cyclin-dependent kinase Cdc28. The CLB genes consist of CLB1/2, CLB3/4, and CLB5/6 whose gene products accumulate at the G2-M, S-G2, and late G1 phase, respectively. These Clb protein levels are thought to be mainly regulated by the transcriptional control and the protein stability control. Here we investigated regulation of CLB1-6 expression by Ccr4. Our results show that all CLB1-6 mRNA levels were significantly increased in the ccr4Δ mutant compared to those in wild-type cells. Clb1, Clb4, and Clb6 protein levels were slightly increased in the ccr4Δ mutant, but the Clb2, Clb3, and Clb5 protein levels were similar to those in wild-type cells. Since both CLB6 mRNA and Clb6 protein levels were most significantly increased in the ccr4Δ mutant, we further analyzed the cis-elements for the Ccr4-mediated regulation within CLB6 mRNA. We found that there were destabilizing sequences in both coding sequence and 3’ untranslated region (3’ UTR). The destabilizing sequences in the coding region were found to be both within and outside the sequences corresponding the cyclin domain. The CLB6 3’ UTR was sufficient for mRNA destabilization and decrease of the reporter GFP gene and this destabilization involved Ccr4. Our results suggest that CLB6 expression is regulated by Ccr4 through the coding sequence and 3’ UTR of CLB6 mRNA.
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188
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Bornewasser L, Domnick C, Kath-Schorr S. Stronger together for in-cell translation: natural and unnatural base modified mRNA. Chem Sci 2022; 13:4753-4761. [PMID: 35655897 PMCID: PMC9067582 DOI: 10.1039/d2sc00670g] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/01/2022] [Indexed: 12/18/2022] Open
Abstract
The preparation of highly modified mRNAs and visualization of their cellular distribution are challenging. We report in-cell application of in vitro transcribed mRNA containing natural base modifications and site-specifically introduced artificial nucleotides. Click chemistry on mRNA allows visualization in cells with excellent signal intensities. While non-specific introduction of reporter groups often leads to loss in mRNA functionality, we combined the benefits from site-specificity in the 3′-UTR incorporated unnatural nucleotides with the improved translation efficiency of the natural base modifications Ψ and 5mC. A series of experiments is described to observe, quantify and verify mRNA functionality. This approach represents a new way to visualize mRNA delivery into cells and monitor its spread on a cellular level and translation efficiency. We observed increased protein expression from this twofold chemically modified, artificial mRNA counterbalancing a reduced transfection rate. This synergetic effect can be exploited as a powerful tool for future research on mRNA therapeutics. Introducing unnatural base modifications site-specifically into the 3′-UTR of an mRNA bearing natural base modifications allows efficient visualization in cells by click chemistry. An enhanced protein expression in cells is observed from this twofold modified mRNA.![]()
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Affiliation(s)
- Lisa Bornewasser
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Christof Domnick
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Stephanie Kath-Schorr
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
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189
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Zhao C, Xie W, Zhu H, Zhao M, Liu W, Wu Z, Wang L, Zhu B, Li S, Zhou Y, Jiang X, Xu Q, Ren C. LncRNAs and their RBPs: How to influence the fate of stem cells? Stem Cell Res Ther 2022; 13:175. [PMID: 35505438 PMCID: PMC9066789 DOI: 10.1186/s13287-022-02851-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
Stem cells are distinctive cells that have self-renewal potential and unique ability to differentiate into multiple functional cells. Stem cell is a frontier field of life science research and has always been a hot spot in biomedical research. Recent studies have shown that long non-coding RNAs (lncRNAs) have irreplaceable roles in stem cell self-renewal and differentiation. LncRNAs play crucial roles in stem cells through a variety of regulatory mechanisms, including the recruitment of RNA-binding proteins (RBPs) to affect the stability of their mRNAs or the expression of downstream genes. RBPs interact with different RNAs to regulate gene expression at transcriptional and post-transcriptional levels and play important roles in determining the fate of stem cells. In this review, the functions of lncRNAs and their RBPs in self-renewal and differentiation of stem cell are summarized. We focus on the four regulatory mechanisms by which lncRNAs and their RBPs are involved in epigenetic regulation, signaling pathway regulation, splicing, mRNA stability and subcellular localization and further discuss other noncoding RNAs (ncRNAs) and their RBPs in the fate of stem cells. This work provides a more comprehensive understanding of the roles of lncRNAs in determining the fate of stem cells, and a further understanding of their regulatory mechanisms will provide a theoretical basis for the development of clinical regenerative medicine.
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Affiliation(s)
- Cong Zhao
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Wen Xie
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Hecheng Zhu
- Changsha Kexin Cancer Hospital, Changsha, 410205, China
| | - Ming Zhao
- Changsha Kexin Cancer Hospital, Changsha, 410205, China
| | - Weidong Liu
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Zhaoping Wu
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Lei Wang
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Bin Zhu
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Shasha Li
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Yao Zhou
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Xingjun Jiang
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China. .,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Qiang Xu
- Department of Orthopedics, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, 412007, China. .,School of Materials Science and Engineering, Central South University, Changsha, 410083, China.
| | - Caiping Ren
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China. .,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China.
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190
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Gray JS, Wani SA, Campbell MJ. Epigenomic alterations in cancer: mechanisms and therapeutic potential. Clin Sci (Lond) 2022; 136:473-492. [PMID: 35383835 DOI: 10.1042/cs20210449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022]
Abstract
The human cell requires ways to specify its transcriptome without altering the essential sequence of DNA; this is achieved through mechanisms which govern the epigenetic state of DNA and epitranscriptomic state of RNA. These alterations can be found as modified histone proteins, cytosine DNA methylation, non-coding RNAs, and mRNA modifications, such as N6-methyladenosine (m6A). The different aspects of epigenomic and epitranscriptomic modifications require protein complexes to write, read, and erase these chemical alterations. Reflecting these important roles, many of these reader/writer/eraser proteins are either frequently mutated or differentially expressed in cancer. The disruption of epigenetic regulation in the cell can both contribute to cancer initiation and progression, and increase the likelihood of developing resistance to chemotherapies. Development of therapeutics to target proteins involved in epigenomic/epitranscriptomic modifications has been intensive, but further refinement is necessary to achieve ideal treatment outcomes without too many off-target effects for cancer patients. Therefore, further integration of clinical outcomes combined with large-scale genomic analyses is imperative for furthering understanding of epigenomic mechanisms in cancer.
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Affiliation(s)
- Jaimie S Gray
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Sajad A Wani
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Moray J Campbell
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43210, U.S.A
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191
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Shoaib Y, Usman B, Kang H, Jung KH. Epitranscriptomics: An Additional Regulatory Layer in Plants' Development and Stress Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:1033. [PMID: 35448761 PMCID: PMC9027318 DOI: 10.3390/plants11081033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Epitranscriptomics has added a new layer of regulatory machinery to eukaryotes, and the advancement of sequencing technology has revealed more than 170 post-transcriptional modifications in various types of RNAs, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Among these, N6-methyladenosine (m6A) and N5-methylcytidine (m5C) are the most prevalent internal mRNA modifications. These regulate various aspects of RNA metabolism, mainly mRNA degradation and translation. Recent advances have shown that regulation of RNA fate mediated by these epitranscriptomic marks has pervasive effects on a plant's development and responses to various biotic and abiotic stresses. Recently, it was demonstrated that the removal of human-FTO-mediated m6A from transcripts in transgenic rice and potatoes caused a dramatic increase in their yield, and that the m6A reader protein mediates stress responses in wheat and apple, indicating that regulation of m6A levels could be an efficient strategy for crop improvement. However, changing the overall m6A levels might have unpredictable effects; therefore, the identification of precise m6A levels at a single-base resolution is essential. In this review, we emphasize the roles of epitranscriptomic modifications in modulating molecular, physiological, and stress responses in plants, and provide an outlook on epitranscriptome engineering as a promising tool to ensure food security by editing specific m6A and m5C sites through robust genome-editing technology.
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Affiliation(s)
- Yasira Shoaib
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Babar Usman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
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192
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Liu C, Li L, Yang B, Zhao Y, Dong X, Zhu L, Ren X, Huang B, Yue J, Jin L, Zhang H, Wang L. Transcriptome-wide N6-methyladenine methylation in granulosa cells of women with decreased ovarian reserve. BMC Genomics 2022; 23:240. [PMID: 35346019 PMCID: PMC8961905 DOI: 10.1186/s12864-022-08462-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 03/09/2022] [Indexed: 02/07/2023] Open
Abstract
Abstract
Background
The emerging epitranscriptome plays an essential role in female fertility. As the most prevalent internal mRNA modification, N6-methyladenine (m6A) methylation regulate mRNA fate and translational efficiency. However, whether m6A methylation was involved in the aging-related ovarian reserve decline has not been investigated. Herein, we performed m6A transcriptome-wide profiling in the ovarian granulosa cells of younger women (younger group) and older women (older group).
Results
m6A methylation distribution was highly conserved and enriched in the CDS and 3’UTR region. Besides, an increased number of m6A methylated genes were identified in the older group. Bioinformatics analysis indicated that m6A methylated genes were enriched in the FoxO signaling pathway, adherens junction, and regulation of actin cytoskeleton. A total of 435 genes were differently expressed in the older group, moreover, 58 of them were modified by m6A. Several specific genes, including BUB1B, PHC2, TOP2A, DDR2, KLF13, and RYR2 which were differently expressed and modified by m6A, were validated using qRT-PCR and might be involved in the decreased ovarian functions in the aging ovary.
Conclusions
Hence, our finding revealed the transcriptional significance of m6A modifications and provide potential therapeutic targets to promote fertility reservation for aging women.
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193
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RNA-binding proteins and cancer metastasis. Semin Cancer Biol 2022; 86:748-768. [PMID: 35339667 DOI: 10.1016/j.semcancer.2022.03.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins (RBPs) can regulate gene expression through post-transcriptionally influencing all manner of RNA biology, including alternative splicing (AS), polyadenylation, stability, and translation of mRNAs, as well as microRNAs (miRNAs) and circular RNAs (circRNAs) processing. There is accumulating evidence reinforcing the perception that dysregulation or dysfunction of RBPs can lead to various human diseases, including cancers. RBPs influence diverse cancer-associated cellular phenotypes, such as proliferation, apoptosis, senescence, migration, invasion, and angiogenesis, contributing to the initiation and development of tumors, as well as clinical prognosis. Metastasis is the leading cause of cancer-related recurrence and death. Therefore, it is necessary to elucidate the molecular mechanisms behind tumor metastasis. In fact, a growing body of published research has proved that RBPs play pivotal roles in cancer metastasis. In this review, we will summarize the recent advances for helping us understand the role of RBPs in tumor metastasis, and discuss dysfunctions and dysregulations of RBPs affecting metastasis-associated processes including epithelial-mesenchymal transition (EMT), migration, and invasion of cancer cells. Furthermore, we will discuss emerging RBP-based strategy for the treatment of cancer metastasis.
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194
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D’Esposito RJ, Myers CA, Chen AA, Vangaveti S. Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches. Genes (Basel) 2022; 13:genes13030540. [PMID: 35328093 PMCID: PMC8949676 DOI: 10.3390/genes13030540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration.
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Affiliation(s)
- Rebecca J. D’Esposito
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
| | - Christopher A. Myers
- Department of Physics, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Alan A. Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (R.J.D.); (A.A.C.)
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
- Correspondence:
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195
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Liu H, Li D, Sun L, Qin H, Fan A, Meng L, Graves-Deal R, Glass SE, Franklin JL, Liu Q, Wang J, Yeatman TJ, Guo H, Zong H, Jin S, Chen Z, Deng T, Fang Y, Li C, Karijolich J, Patton JG, Wang X, Nie Y, Fan D, Coffey RJ, Zhao X, Lu Y. Interaction of lncRNA MIR100HG with hnRNPA2B1 facilitates m 6A-dependent stabilization of TCF7L2 mRNA and colorectal cancer progression. Mol Cancer 2022; 21:74. [PMID: 35279145 PMCID: PMC8917698 DOI: 10.1186/s12943-022-01555-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Epithelial-to-mesenchymal transition (EMT) is a process linked to metastasis and drug resistance with non-coding RNAs (ncRNAs) playing pivotal roles. We previously showed that miR-100 and miR-125b, embedded within the third intron of the ncRNA host gene MIR100HG, confer resistance to cetuximab, an anti-epidermal growth factor receptor (EGFR) monoclonal antibody, in colorectal cancer (CRC). However, whether the MIR100HG transcript itself has a role in cetuximab resistance or EMT is unknown. METHODS The correlation between MIR100HG and EMT was analyzed by curating public CRC data repositories. The biological roles of MIR100HG in EMT, metastasis and cetuximab resistance in CRC were determined both in vitro and in vivo. The expression patterns of MIR100HG, hnRNPA2B1 and TCF7L2 in CRC specimens from patients who progressed on cetuximab and patients with metastatic disease were analyzed by RNAscope and immunohistochemical staining. RESULTS The expression of MIR100HG was strongly correlated with EMT markers and acted as a positive regulator of EMT. MIR100HG sustained cetuximab resistance and facilitated invasion and metastasis in CRC cells both in vitro and in vivo. hnRNPA2B1 was identified as a binding partner of MIR100HG. Mechanistically, MIR100HG maintained mRNA stability of TCF7L2, a major transcriptional coactivator of the Wnt/β-catenin signaling, by interacting with hnRNPA2B1. hnRNPA2B1 recognized the N6-methyladenosine (m6A) site of TCF7L2 mRNA in the presence of MIR100HG. TCF7L2, in turn, activated MIR100HG transcription, forming a feed forward regulatory loop. The MIR100HG/hnRNPA2B1/TCF7L2 axis was augmented in specimens from CRC patients who either developed local or distant metastasis or had disease progression that was associated with cetuximab resistance. CONCLUSIONS MIR100HG and hnRNPA2B1 interact to control the transcriptional activity of Wnt signaling in CRC via regulation of TCF7L2 mRNA stability. Our findings identified MIR100HG as a potent EMT inducer in CRC that may contribute to cetuximab resistance and metastasis by activation of a MIR100HG/hnRNPA2B1/TCF7L2 feedback loop.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Danxiu Li
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Lina Sun
- The Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China
| | - Ahui Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Lingnan Meng
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Ramona Graves-Deal
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Sarah E Glass
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Jeffrey L Franklin
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Qi Liu
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jing Wang
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Timothy J Yeatman
- Departments of Surgery and Molecular Medicine, TGH Cancer Institute and University of South Florida, Tampa, FL, 33620, USA
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, 210042, Jiangsu, China
| | - Hong Zong
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shuilin Jin
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhiyu Chen
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Ting Deng
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Ying Fang
- The Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China
| | - Cunxi Li
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, 100191, China
| | - John Karijolich
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Xin Wang
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
| | - Robert J Coffey
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA.
| | - Xiaodi Zhao
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
| | - Yuanyuan Lu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
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Mabrouk MT, Huang W, Martinez‐Sobrido L, Lovell JF. Advanced Materials for SARS-CoV-2 Vaccines. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107781. [PMID: 34894000 PMCID: PMC8957524 DOI: 10.1002/adma.202107781] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/28/2021] [Indexed: 05/09/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), has killed untold millions worldwide and has hurtled vaccines into the spotlight as a go-to approach to mitigate it. Advances in virology, genomics, structural biology, and vaccine technologies have enabled a rapid and unprecedented rollout of COVID-19 vaccines, although much of the developing world remains unvaccinated. Several new vaccine platforms have been developed or deployed against SARS-CoV-2, with most targeting the large viral Spike immunogen. Those that safely induce strong and durable antibody responses at low dosages are advantageous, as well are those that can be rapidly produced at a large scale. Virtually all COVID-19 vaccines and adjuvants possess nanoscale or microscale dimensions and represent diverse and unique biomaterials. Viral vector vaccine platforms, lipid nanoparticle mRNA vaccines and multimeric display technologies for subunit vaccines have received much attention. Nanoscale vaccine adjuvants have also been used in combination with other vaccines. To deal with the ongoing pandemic, and to be ready for potential future ones, advanced vaccine technologies will continue to be developed in the near future. Herein, the recent use of advanced materials used for developing COVID-19 vaccines is summarized.
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Affiliation(s)
- Moustafa T. Mabrouk
- Department of Biomedical EngineeringUniversity at BuffaloState University of New YorkBuffaloNY14260USA
| | - Wei‐Chiao Huang
- Department of Biomedical EngineeringUniversity at BuffaloState University of New YorkBuffaloNY14260USA
| | - Luis Martinez‐Sobrido
- Division of Disease Intervention and PreventionTexas Biomedical Research InstituteSan AntonioTX78227USA
| | - Jonathan F. Lovell
- Department of Biomedical EngineeringUniversity at BuffaloState University of New YorkBuffaloNY14260USA
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197
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Aguilar G, Pagano N, Manuelidis L. Reduced Expression of Prion Protein With Increased Interferon-β Fail to Limit Creutzfeldt-Jakob Disease Agent Replication in Differentiating Neuronal Cells. Front Physiol 2022; 13:837662. [PMID: 35250638 PMCID: PMC8895124 DOI: 10.3389/fphys.2022.837662] [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: 12/16/2021] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Immortalized uninfected septal (SEP) neurons proliferate but after physiological mitotic arrest they express differentiated neuronal characteristics including enhanced cell-to-cell membrane contacts and ≥ 8 fold increases in host prion protein (PrP). We compared proliferating uninfected and Creutzfeldt-Jakob Disease (CJD) agent infected cells with their arrested counterparts over 33 days by quantitative mRNA and protein blot analyses. Surprisingly, uninfected arrested cells increased interferon-β (IFN-β) mRNA by 2.5–8 fold; IFN-β mRNA elevations were not previously associated with neuronal differentiation. SEP cells with high CJD infectivity titers produced a much larger 40–68-fold increase in IFN-β mRNA, a classic host anti-viral response that is virucidal for RNA but not DNA viruses. High titers of CJD agent also induced dramatic decreases in host PrP, a protein needed for productive agent replication. Uninfected arrested cells produced large sustained 20–30-fold increases in PrP mRNA and protein, whereas CJD arrested cells showed only transient small 5-fold increases in PrP. A > 10-fold increase in infectivity, but not PrP misfolding, induced host PrP reductions that can limit CJD agent replication. In contrast to neuronal lineage cells, functionally distinct migratory microglia with high titers of CJD agent do not induce an IFN-β mRNA response. Because they have 1/50th of PrP of an average brain cell, microglia would be unable to produce the many new infectious particles needed to induce a large IFN-β response by host cells. Instead, microglia and related cells can be persistent reservoirs of infection and spread. Phase separations of agent-associated molecules in neurons, microglia and other cell types can yield new insights into the molecular structure, persistent, and evasive behavior of CJD-type agents.
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198
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Deymier S, Louvat C, Fiorini F, Cimarelli A. ISG20: an enigmatic antiviral RNase targeting multiple viruses. FEBS Open Bio 2022; 12:1096-1111. [PMID: 35174977 PMCID: PMC9157404 DOI: 10.1002/2211-5463.13382] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/31/2022] [Accepted: 02/15/2022] [Indexed: 11/25/2022] Open
Abstract
Interferon‐stimulated gene 20 kDa protein (ISG20) is a relatively understudied antiviral protein capable of inhibiting a broad spectrum of viruses. ISG20 exhibits strong RNase properties, and it belongs to the large family of DEDD exonucleases, present in both prokaryotes and eukaryotes. ISG20 was initially characterized as having strong RNase activity in vitro, suggesting that its inhibitory effects are mediated via direct degradation of viral RNAs. This mechanism of action has since been further elucidated and additional antiviral activities of ISG20 highlighted, including direct degradation of deaminated viral DNA and translational inhibition of viral RNA and nonself RNAs. This review focuses on the current understanding of the main molecular mechanisms of viral inhibition by ISG20 and discusses the latest developments on the features that govern specificity or resistance to its action.
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Affiliation(s)
- Séverine Deymier
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon Inserm, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieur de Lyon, U1111, Lyon, France
| | | | | | - Andrea Cimarelli
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon Inserm, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieur de Lyon, U1111, Lyon, France
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Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes. BIOLOGY 2022; 11:biology11020214. [PMID: 35205080 PMCID: PMC8868631 DOI: 10.3390/biology11020214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
Simple Summary The m6A is the most abundant and well-studied modification of mRNA, and plays an important role in transcription and translation. It is known to be evolutionarily conserved machinery present in the last eukaryotic common ancestor (LECA). The writers and erasers responsible for adding or removing m6A belong to specific protein families, respectively, suggesting that these members are evolutionarily related. However, only some of these mRNA m6A modification-associated proteins have been studied from an evolutionary perspective, while there has been no comprehensive and systematic analysis of the distributions and evolutionary history of N6mA-associated proteins in the three kingdoms of life. In this study, we identified orthologues of all the reported N6mA-associated proteins in 88 organisms from three kingdoms of life and comprehensively reconstructed the evolutionary history of the RNA N6mA modification machinery. The results demonstrate that RNA N6mA-MTases are derived from at least two different types of prokaryotic DNA MTases (class α and β MTases). As the m6A reader, YTH proteins may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from the N-terminals of an R-M system endonuclease. In addition, the origin of eukaryotic ALKBH family proteins is inferred to be driven by at least two occasions of independent HTG from the bacterial ALKB family. Abstract Methylation at the N6-position of adenosine (N6mA) on mRNA (m6A) is one of the most widespread, highly selective and dynamically regulated RNA modifications and plays an important role in transcription and translation. In the present study, a comprehensive analysis of phylogenetic relationships, conserved domain sequence characteristics and protein structure comparisons were employed to explore the distribution of RNA N6mA modification (m6A, m6,6A, m6Am, m6, 6Am and m6t6A)-associated proteins (writers, readers and erasers) in three kingdoms of life and reveal the evolutionary history of these modifications. These findings further confirmed that the restriction-modification (R-M) system is the origin of DNA and RNA N6mA modifications. Among them, the existing mRNA m6A modification system derived from the last eukaryotic common ancestor (LECA) is the evolutionary product of elements from the last universal common ancestor (LUCA) or driven by horizontal gene transfer (HGT) from bacterial elements. The subsequent massive gene gains and losses contribute to the development of unique and diverse functions in distinct species. Particularly, RNA methyltransferases (MTases) as the writer responsible for adding N6mA marks on mRNA and ncRNAs may have evolved from class α and β prokaryotic “orphan” MTases originating from the R-M system. The reader, YTH proteins that specifically recognize the m6A deposit, may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from N-terminals of an R-M system endonuclease. The eraser, which emerged from the ALKB family (ALKBH5 and FTO) in eukaryotes, may be driven by independent HTG from bacterial ALKB proteins. The evolutionary history of RNA N6mA modifications was inferred in the present study, which will deepen our understanding of these modifications in different species.
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Hindle A, Bose C, Lee J, Palade PT, Peterson CJ, Reddy PH, Awasthi S, Singh SP. Rlip Depletion Alters Oncogene Transcription at Multiple Distinct Regulatory Levels. Cancers (Basel) 2022; 14:cancers14030527. [PMID: 35158795 PMCID: PMC8833773 DOI: 10.3390/cancers14030527] [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: 11/30/2021] [Revised: 01/07/2022] [Accepted: 01/15/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Rlip76 is a multifunctional membrane protein that facilitates cancer growth, and its depletion kills cancer cells. We recently found that Rlip depletion also results in broad changes to oncogene and tumor suppressor transcription. The present studies were designed to decipher the unknown downstream signaling pathways and transcriptional regulatory mechanisms driving the effect. Building on prior findings that Rlip depletion induces broad methylomic changes, we found using bioluminescence reporter assays that depletion of Rlip also exerts transcriptional control over several cancer genes through methylation-independent changes in transcription factor-mediated activation of their promoter regions and through additional as yet unidentified mechanisms. These findings have important implications for Rlip-targeted cancer therapy. Abstract Rlip76 (Rlip) is a multifunctional membrane protein that facilitates the high metabolic rates of cancer cells through the efflux of toxic metabolites and other functions. Rlip inhibition or depletion results in broad-spectrum anti-cancer effects in vitro and in vivo. Rlip depletion effectively suppresses malignancy and causes global reversion of characteristic CpG island methylomic and transcriptomic aberrations in the p53-null mouse model of spontaneous carcinogenesis through incompletely defined signaling and transcriptomic mechanisms. The methylome and transcriptome are normally regulated by the concerted actions of several mechanisms that include chromatin remodeling, promoter methylation, transcription factor interactions, and miRNAs. The present studies investigated the interaction of Rlip depletion or inhibition with the promoter methylation and transcription of selected cancer-related genes identified as being affected by Rlip depletion in our previous studies. We constructed novel promoter CpG island/luciferase reporter plasmids that respond only to CpG methylation and transcription factors. We found that Rlip depletion regulated expression by a transcription factor-based mechanism that functioned independently of promoter CpG methylation, lipid peroxidation, and p53 status.
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Affiliation(s)
- Ashly Hindle
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
| | - Chhanda Bose
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
| | - Jihyun Lee
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
- Division of Hematology & Oncology, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Philip T. Palade
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Christopher J. Peterson
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Speech, Language and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Sanjay Awasthi
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
- Division of Hematology & Oncology, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- UMC Cancer Center, UMC Health System, Lubbock, TX 79415, USA
- Correspondence: (S.A.); (S.P.S.); Tel.: +1-806-743-3543 (S.A.); +1-806-743-1540 (S.P.S.)
| | - Sharda P. Singh
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
- Division of Hematology & Oncology, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: (S.A.); (S.P.S.); Tel.: +1-806-743-3543 (S.A.); +1-806-743-1540 (S.P.S.)
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