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1.
Mol Cell ; 84(8): 1611-1625.e3, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38640896

ABSTRACT

We recently reported the distribution of N4-acetylcytidine (ac4C) in HeLa mRNA at base resolution through chemical reduction and the induction of C:T mismatches in sequencing (RedaC:T-seq). Our results contradicted an earlier report from Schwartz and colleagues utilizing a similar method termed ac4C-seq. Here, we revisit both datasets and reaffirm our findings. Through RedaC:T-seq reanalysis, we establish a low basal error rate at unmodified nucleotides that is not skewed to any specific mismatch type and a prominent increase in C:T substitutions as the dominant mismatch type in both treated wild-type replicates, with a high degree of reproducibility across replicates. In contrast, through ac4C-seq reanalysis, we uncover significant data quality issues including insufficient depth, with one wild-type replicate yielding 2.7 million reads, inconsistencies in reduction efficiencies between replicates, and an overall increase in mismatches involving thymine that could obscure ac4C detection. These analyses bolster the detection of ac4C in HeLa mRNA through RedaC:T-seq.


Subject(s)
Cytidine/analogs & derivatives , Nucleotides , Humans , Reproducibility of Results , RNA, Messenger/genetics
2.
Proc Natl Acad Sci U S A ; 121(17): e2320713121, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38621119

ABSTRACT

As the SARS-CoV-2 virus continues to spread and mutate, it remains important to focus not only on preventing spread through vaccination but also on treating infection with direct-acting antivirals (DAA). The approval of Paxlovid, a SARS-CoV-2 main protease (Mpro) DAA, has been significant for treatment of patients. A limitation of this DAA, however, is that the antiviral component, nirmatrelvir, is rapidly metabolized and requires inclusion of a CYP450 3A4 metabolic inhibitor, ritonavir, to boost levels of the active drug. Serious drug-drug interactions can occur with Paxlovid for patients who are also taking other medications metabolized by CYP4503A4, particularly transplant or otherwise immunocompromised patients who are most at risk for SARS-CoV-2 infection and the development of severe symptoms. Developing an alternative antiviral with improved pharmacological properties is critical for treatment of these patients. By using a computational and structure-guided approach, we were able to optimize a 100 to 250 µM screening hit to a potent nanomolar inhibitor and lead compound, Mpro61. In this study, we further evaluate Mpro61 as a lead compound, starting with examination of its mode of binding to SARS-CoV-2 Mpro. In vitro pharmacological profiling established a lack of off-target effects, particularly CYP450 3A4 inhibition, as well as potential for synergy with the currently approved alternate antiviral, molnupiravir. Development and subsequent testing of a capsule formulation for oral dosing of Mpro61 in B6-K18-hACE2 mice demonstrated favorable pharmacological properties, efficacy, and synergy with molnupiravir, and complete recovery from subsequent challenge by SARS-CoV-2, establishing Mpro61 as a promising potential preclinical candidate.


Subject(s)
Antiviral Agents , Cytidine/analogs & derivatives , Hepatitis C, Chronic , Hydroxylamines , Lactams , Leucine , Nitriles , Proline , Ritonavir , Humans , Animals , Mice , Antiviral Agents/pharmacology , Clinical Protocols , Drug Combinations
3.
Proc Natl Acad Sci U S A ; 121(24): e2400378121, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38830096

ABSTRACT

Epitranscriptomic RNA modifications have emerged as important regulators of the fate and function of viral RNAs. One prominent modification, the cytidine methylation 5-methylcytidine (m5C), is found on the RNA of HIV-1, where m5C enhances the translation of HIV-1 RNA. However, whether m5C functionally enhances the RNA of other pathogenic viruses remains elusive. Here, we surveyed a panel of commonly found RNA modifications on the RNA of hepatitis B virus (HBV) and found that HBV RNA is enriched with m5C as well as ten other modifications, at stoichiometries much higher than host messenger RNA (mRNA). Intriguingly, m5C is mostly found on the epsilon hairpin, an RNA element required for viral RNA encapsidation and reverse transcription, with these m5C mainly deposited by the cellular methyltransferase NSUN2. Loss of m5C from HBV RNA due to NSUN2 depletion resulted in a partial decrease in viral core protein (HBc) production, accompanied by a near-complete loss of the reverse transcribed viral DNA. Similarly, mutations introduced to remove the methylated cytidines resulted in a loss of HBc production and reverse transcription. Furthermore, pharmacological disruption of m5C deposition led to a significant decrease in HBV replication. Thus, our data indicate m5C methylations as a critical mediator of the epsilon elements' function in HBV virion production and reverse transcription, suggesting the therapeutic potential of targeting the m5C methyltransfer process on HBV epsilon as an antiviral strategy.


Subject(s)
Cytidine , Hepatitis B virus , RNA, Viral , Reverse Transcription , Hepatitis B virus/genetics , Hepatitis B virus/metabolism , Hepatitis B virus/physiology , RNA, Viral/genetics , RNA, Viral/metabolism , Cytidine/analogs & derivatives , Cytidine/metabolism , Cytidine/genetics , Humans , Reverse Transcription/genetics , Methylation , Virus Replication/genetics , Epigenesis, Genetic , Virion/metabolism , Virion/genetics , Transcriptome
4.
RNA ; 30(5): 583-594, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38531654

ABSTRACT

In recent years, concerted efforts to map and understand epitranscriptomic modifications in mRNA have unveiled new complexities in the regulation of gene expression. These studies cumulatively point to diverse functions in mRNA metabolism, spanning pre-mRNA processing, mRNA degradation, and translation. However, this emerging landscape is not without its intricacies and sources of discrepancies. Disparities in detection methodologies, divergent interpretations of functional outcomes, and the complex nature of biological systems across different cell types pose significant challenges. With a focus of N4-acetylcytidine (ac4C), this review endeavors to unravel conflicting narratives by examining the technological, biological, and methodological factors that have contributed to discrepancies and thwarted research progress. Our goal is to mitigate detection inconsistencies and establish a unified model to elucidate the contribution of ac4C to mRNA metabolism and cellular equilibrium.


Subject(s)
Cytidine/analogs & derivatives , RNA Processing, Post-Transcriptional , RNA, Messenger/genetics , RNA/genetics
5.
RNA ; 30(7): 938-953, 2024 Jun 17.
Article in English | MEDLINE | ID: mdl-38697668

ABSTRACT

The functional analysis of epitranscriptomic modifications in RNA is constrained by a lack of methods that accurately capture their locations and levels. We previously demonstrated that the RNA modification N4-acetylcytidine (ac4C) can be mapped at base resolution through sodium borohydride reduction to tetrahydroacetylcytidine (tetrahydro-ac4C), followed by cDNA synthesis to misincorporate adenosine opposite reduced ac4C sites, culminating in C:T mismatches at acetylated cytidines (RedaC:T). However, this process is relatively inefficient, resulting in <20% C:T mismatches at a fully modified ac4C site in 18S rRNA. Considering that ac4C locations in other substrates including mRNA are unlikely to reach full penetrance, this method is not ideal for comprehensive mapping. Here, we introduce "RetraC:T" (reduction to tetrahydro-ac4C and reverse transcription with amino-dATP to induce C:T mismatches) as a method with enhanced ability to detect ac4C in cellular RNA. In brief, RNA is reduced through NaBH4 or the closely related reagent sodium cyanoborohydride (NaCNBH3) followed by cDNA synthesis in the presence of a modified DNA nucleotide, 2-amino-dATP, that preferentially binds to tetrahydro-ac4C. Incorporation of the modified dNTP substantially improved C:T mismatch rates, reaching stoichiometric detection of ac4C in 18S rRNA. Importantly, 2-amino-dATP did not result in truncated cDNA products nor increase mismatches at other locations. Thus, modified dNTPs are introduced as a new addition to the toolbox for detecting ac4C at base resolution.


Subject(s)
Cytidine , DNA, Complementary , Cytidine/analogs & derivatives , Cytidine/chemistry , Cytidine/metabolism , Cytidine/genetics , DNA, Complementary/genetics , RNA/genetics , RNA/chemistry , RNA/metabolism , Humans , Borohydrides/chemistry , Oxidation-Reduction , Reverse Transcription , RNA, Ribosomal, 18S/genetics , RNA, Ribosomal, 18S/metabolism
6.
Brief Bioinform ; 25(3)2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38701415

ABSTRACT

N4-acetylcytidine (ac4C) is a modification found in ribonucleic acid (RNA) related to diseases. Expensive and labor-intensive methods hindered the exploration of ac4C mechanisms and the development of specific anti-ac4C drugs. Therefore, an advanced prediction model for ac4C in RNA is urgently needed. Despite the construction of various prediction models, several limitations exist: (1) insufficient resolution at base level for ac4C sites; (2) lack of information on species other than Homo sapiens; (3) lack of information on RNA other than mRNA; and (4) lack of interpretation for each prediction. In light of these limitations, we have reconstructed the previous benchmark dataset and introduced a new dataset including balanced RNA sequences from multiple species and RNA types, while also providing base-level resolution for ac4C sites. Additionally, we have proposed a novel transformer-based architecture and pipeline for predicting ac4C sites, allowing for highly accurate predictions, visually interpretable results and no restrictions on the length of input RNA sequences. Statistically, our work has improved the accuracy of predicting specific ac4C sites in multiple species from less than 40% to around 85%, achieving a high AUC > 0.9. These results significantly surpass the performance of all existing models.


Subject(s)
Cytidine , Cytidine/analogs & derivatives , RNA , Cytidine/genetics , RNA/genetics , RNA/chemistry , Humans , Computational Biology/methods , Animals , Software , Algorithms
7.
EMBO Rep ; 25(4): 1814-1834, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38413733

ABSTRACT

Stress granules are an integral part of the stress response that are formed from non-translating mRNAs aggregated with proteins. While much is known about stress granules, the factors that drive their mRNA localization are incompletely described. Modification of mRNA can alter the properties of the nucleobases and affect processes such as translation, splicing and localization of individual transcripts. Here, we show that the RNA modification N4-acetylcytidine (ac4C) on mRNA associates with transcripts enriched in stress granules and that stress granule localized transcripts with ac4C are specifically translationally regulated. We also show that ac4C on mRNA can mediate localization of the protein NOP58 to stress granules. Our results suggest that acetylation of mRNA regulates localization of both stress-sensitive transcripts and RNA-binding proteins to stress granules and adds to our understanding of the molecular mechanisms responsible for stress granule formation.


Subject(s)
Cytidine , Cytidine/analogs & derivatives , Stress Granules , RNA, Messenger/genetics , RNA, Messenger/metabolism , Cytidine/genetics , Cytidine/metabolism , RNA-Binding Proteins/metabolism
8.
Plant J ; 119(3): 1418-1432, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38824612

ABSTRACT

DNA-protein crosslinks (DPCs) are highly toxic DNA lesions represented by proteins covalently bound to the DNA. Persisting DPCs interfere with fundamental genetic processes such as DNA replication and transcription. Cytidine analog zebularine (ZEB) has been shown to crosslink DNA METHYLTRANSFERASE1 (MET1). Recently, we uncovered a critical role of the SMC5/6-mediated SUMOylation in the repair of DPCs. In an ongoing genetic screen, we identified two additional candidates, HYPERSENSITIVE TO ZEBULARINE 2 and 3, that were mapped to REGULATOR OF TELOMERE ELONGATION 1 (RTEL1) and polymerase TEBICHI (TEB), respectively. By monitoring the growth of hze2 and hze3 plants in response to zebularine, we show the importance of homologous recombination (HR) factor RTEL1 and microhomology-mediated end-joining (MMEJ) polymerase TEB in the repair of MET1-DPCs. Moreover, genetic interaction and sensitivity assays showed the interdependency of SMC5/6 complex, HR, and MMEJ in the homology-directed repair of MET1-DPCs in Arabidopsis. Altogether, we provide evidence that MET1-DPC repair in plants is more complex than originally expected.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Cytidine , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/genetics , Cytidine/analogs & derivatives , Cytidine/metabolism , Cytidine/pharmacology , Recombinational DNA Repair , DNA Repair , DNA, Plant/genetics , DNA, Plant/metabolism , DNA Damage
9.
J Virol ; 98(1): e0135023, 2024 Jan 23.
Article in English | MEDLINE | ID: mdl-38169284

ABSTRACT

Epitranscriptomic RNA modifications can regulate the stability of mRNA and affect cellular and viral RNA functions. The N4-acetylcytidine (ac4C) modification in the RNA viral genome was recently found to promote viral replication; however, the mechanism by which RNA acetylation in the host mRNA regulates viral replication remains unclear. To help elucidate this mechanism, the roles of N-acetyltransferase 10 (NAT10) and ac4C during the infection and replication processes of the alphavirus, Sindbis virus (SINV), were investigated. Cellular NAT10 was upregulated, and ac4C modifications were promoted after alphavirus infection, while the loss of NAT10 or inhibition of its N-acetyltransferase activity reduced alphavirus replication. The NAT10 enhanced alphavirus replication as it helped to maintain the stability of lymphocyte antigen six family member E mRNA, which is a multifunctional interferon-stimulated gene that promotes alphavirus replication. The ac4C modification was thus found to have a non-conventional role in the virus life cycle through regulating host mRNA stability instead of viral mRNA, and its inhibition could be a potential target in the development of new alphavirus antivirals.IMPORTANCEThe role of N4-acetylcytidine (ac4C) modification in host mRNA and virus replication is not yet fully understood. In this study, the role of ac4C in the regulation of Sindbis virus (SINV), a prototype alphavirus infection, was investigated. SINV infection results in increased levels of N-acetyltransferase 10 (NAT10) and increases the ac4C modification level of cellular RNA. The NAT10 was found to positively regulate SINV infection in an N-acetyltransferase activity-dependent manner. Mechanistically, the NAT10 modifies lymphocyte antigen six family member E (LY6E) mRNA-the ac4C modification site within the 3'-untranslated region (UTR) of LY6E mRNA, which is essential for its translation and stability. The findings of this study demonstrate that NAT10 regulated mRNA stability and translation efficiency not only through the 5'-UTR or coding sequence but also via the 3'-UTR region. The ac4C modification of host mRNA stability instead of viral mRNA impacting the viral life cycle was thus identified, indicating that the inhibition of ac4C could be a potential target when developing alphavirus antivirals.


Subject(s)
Alphavirus Infections , Antigens, Surface , GPI-Linked Proteins , N-Terminal Acetyltransferases , Sindbis Virus , Virus Replication , Humans , Alphavirus Infections/genetics , Antigens, Surface/genetics , Cytidine/analogs & derivatives , GPI-Linked Proteins/genetics , RNA, Messenger/genetics , Sindbis Virus/physiology , Cell Line , N-Terminal Acetyltransferases/genetics , RNA Stability
10.
Ann Intern Med ; 177(1): JC7, 2024 01.
Article in English | MEDLINE | ID: mdl-38163374

ABSTRACT

SOURCE CITATION: Sommer I, Ledinger D, Thaler K, et al. Outpatient treatment of confirmed COVID-19: a living, rapid evidence review for the American College of Physicians (version 2). Ann Intern Med. 2023;176:1377-1385. 37722115.


Subject(s)
COVID-19 , Cytidine , Hydroxylamines , Lactams , Leucine , Nitriles , Outpatients , Proline , Humans , Antiviral Agents/therapeutic use , COVID-19 Drug Treatment , Cytidine/analogs & derivatives , Ritonavir/therapeutic use , SARS-CoV-2
11.
Clin Infect Dis ; 78(6): 1531-1535, 2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38170452

ABSTRACT

Within a multistate clinical cohort, SARS-CoV-2 antiviral prescribing patterns were evaluated from April 2022-June 2023 among nonhospitalized patients with SARS-CoV-2 with risk factors for severe COVID-19. Among 3247 adults, only 31.9% were prescribed an antiviral agent (87.6% nirmatrelvir/ritonavir, 11.9% molnupiravir, 0.5% remdesivir), highlighting the need to identify and address treatment barriers.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , SARS-CoV-2 , Humans , Antiviral Agents/therapeutic use , Male , Middle Aged , Female , Adult , Aged , Risk Factors , Ritonavir/therapeutic use , COVID-19/epidemiology , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/therapeutic use , Alanine/therapeutic use , Alanine/analogs & derivatives , Practice Patterns, Physicians'/statistics & numerical data , Cytidine/analogs & derivatives , Hydroxylamines
12.
Anal Chem ; 96(18): 6870-6874, 2024 05 07.
Article in English | MEDLINE | ID: mdl-38648202

ABSTRACT

Accurate detection of endogenous miRNA modifications, such as N6-methyladenosine (m6A), 7-methylguanosine (m7G), and 5-methylcytidine (m5C), poses significant challenges, resulting in considerable uncertainty regarding their presence in mature miRNAs. In this study, we demonstrate for the first time that liquid chromatography coupled with a tandem mass spectrometry (LC-MS/MS) nucleoside analysis method is a practical tool for quantitatively analyzing human miRNA modifications. The newly designed liquid-solid two-step hybridization (LSTH) strategy enhances specificity for miRNA purification, while LC-MS/MS offers robust capability in recognizing modifications and sufficient sensitivity with detection limits ranging from attomoles to low femtomoles. Therefore, it provides a more reliable approach compared to existing techniques for revealing modifications in endogenous miRNAs. With this approach, we characterized m6A, m7G, and m5C modifications in miR-21-5p, Let-7a/e-5p, and miR-10a-5p isolated from cultured cells and observed unexpectedly low abundance (<1% at each site) of these modifications.


Subject(s)
Adenosine , Cytidine , Guanosine , MicroRNAs , Humans , Adenosine/analogs & derivatives , Adenosine/analysis , Cytidine/analogs & derivatives , Guanosine/analogs & derivatives , Guanosine/analysis , Liquid Chromatography-Mass Spectrometry , MicroRNAs/analysis , Nucleic Acid Hybridization , Tandem Mass Spectrometry
13.
J Med Virol ; 96(5): e29642, 2024 May.
Article in English | MEDLINE | ID: mdl-38708812

ABSTRACT

Molnupiravir, an oral direct-acting antiviral effective in vitro against SARS-CoV-2, has been largely employed during the COVID-19 pandemic, since December 2021. After marketing and widespread usage, a progressive increase in SARS-CoV-2 lineages characterized by a higher transition/transversion ratio, a characteristic signature of molnupiravir action, appeared in the Global Initiative on Sharing All Influenza Data (GISAID) and International Nucleotide Sequence Database Collaboration (INSDC) databases. Here, we assessed the drug effects by SARS-CoV-2 whole-genome sequencing on 38 molnupiravir-treated persistently positive COVID-19 outpatients tested before and after treatment. Seventeen tixagevimab/cilgavimab-treated outpatients served as controls. Mutational analyses confirmed that SARS-CoV-2 exhibits an increased transition/transversion ratio seven days after initiation of molnupiravir. Moreover we observed an increased G->A ratio compared to controls, which was not related to apolipoprotein B mRNAediting enzyme, catalytic polypeptide-like (APOBEC) activity. In addition, we demonstrated for the first time an increased diversity and complexity of the viral quasispecies.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , Cytidine/analogs & derivatives , Genome, Viral , Hydroxylamines , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , SARS-CoV-2/drug effects , Antiviral Agents/therapeutic use , Antiviral Agents/pharmacology , Hydroxylamines/pharmacology , Hydroxylamines/therapeutic use , Male , Female , Case-Control Studies , Middle Aged , Cytidine/therapeutic use , Cytidine/pharmacology , Aged , Adult , Whole Genome Sequencing , Genetic Variation , Uridine/pharmacology , COVID-19/virology , Mutation
14.
Insect Mol Biol ; 33(5): 516-533, 2024 Oct.
Article in English | MEDLINE | ID: mdl-38864655

ABSTRACT

Many species are threatened by climate change and must rapidly respond to survive in changing environments. Epigenetic modifications, such as DNA methylation, can facilitate plastic responses by regulating gene expression in response to environmental cues. Understanding epigenetic responses is therefore essential for predicting species' ability to rapidly adapt in the context of global environmental change. Here, we investigated the functional significance of different methylation-associated cellular processes on temperature-dependent life history in seed beetles, Callosobruchus maculatus Fabricius 1775 (Coleoptera: Bruchidae). We assessed changes under thermal stress in (1) DNA methyltransferase (Dnmt1 and Dnmt2) expression levels, (2) genome-wide methylation and (3) reproductive performance, with (2) and (3) following treatment with 3-aminobenzamide (3AB) and zebularine (Zeb) over two generations. These drugs are well-documented to alter DNA methylation across the tree of life. We found that Dnmt1 and Dnmt2 were expressed throughout the body in males and females, but were highly expressed in females compared with males and exhibited temperature dependence. However, whole-genome methylation did not significantly vary with temperature, and only marginally or inconclusively with drug treatment. Both 3AB and Zeb led to profound temperature-dependent shifts in female reproductive life history trade-off allocation, often increasing fitness compared with control beetles. Mismatch between magnitude of treatment effects on DNA methylation versus life history effects suggest potential of 3AB and Zeb to alter reproductive trade-offs via changes in DNA repair and recycling processes, rather than or in addition to (subtle) changes in DNA methylation. Together, our results suggest that epigenetic mechanisms relating to Dnmt expression, DNA repair and recycling pathways, and possibly DNA methylation, are strongly implicated in modulating insect life history trade-offs in response to temperature change.


Subject(s)
Coleoptera , DNA Methylation , Epigenesis, Genetic , Reproduction , Animals , Coleoptera/genetics , Coleoptera/physiology , Female , Reproduction/genetics , Temperature , Male , Cytidine/analogs & derivatives , Cytidine/pharmacology , Climate Change
15.
Anal Biochem ; 689: 115495, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38431142

ABSTRACT

RNA modification, N4-acetylcytidine (ac4C), is enzymatically catalyzed by N-acetyltransferase 10 (NAT10) and plays an essential role across tRNA, rRNA, and mRNA. It influences various cellular functions, including mRNA stability and rRNA biosynthesis. Wet-lab detection of ac4C modification sites is highly resource-intensive and costly. Therefore, various machine learning and deep learning techniques have been employed for computational detection of ac4C modification sites. The known ac4C modification sites are limited for training an accurate and stable prediction model. This study introduces GANSamples-ac4C, a novel framework that synergizes transfer learning and generative adversarial network (GAN) to generate synthetic RNA sequences to train a better ac4C modification site prediction model. Comparative analysis reveals that GANSamples-ac4C outperforms existing state-of-the-art methods in identifying ac4C sites. Moreover, our result underscores the potential of synthetic data in mitigating the issue of data scarcity for biological sequence prediction tasks. Another major advantage of GANSamples-ac4C is its interpretable decision logic. Multi-faceted interpretability analyses detect key regions in the ac4C sequences influencing the discriminating decision between positive and negative samples, a pronounced enrichment of G in this region, and ac4C-associated motifs. These findings may offer novel insights for ac4C research. The GANSamples-ac4C framework and its source code are publicly accessible at http://www.healthinformaticslab.org/supp/.


Subject(s)
Cytidine/analogs & derivatives , Machine Learning , RNA , RNA Stability
16.
Cell Commun Signal ; 22(1): 51, 2024 01 17.
Article in English | MEDLINE | ID: mdl-38233839

ABSTRACT

The dynamic changes of RNA N6-methyladenosine (m6A) during cancer progression participate in various cellular processes. However, less is known about a possible direct connection between upstream regulator and m6A modification, and therefore affects oncogenic progression. Here, we have identified that a key enzyme in N4-acetylcytidine (ac4C) acetylation NAT10 is highly expressed in human osteosarcoma tissues, and its knockdown enhanced m6A contents and significantly suppressed osteosarcoma cell growth, migration and invasion. Further results revealed that NAT10 silence inhibits mRNA stability and translation of m6A reader protein YTHDC1, and displayed an increase in glucose uptake, a decrease in lactate production and pyruvate content. YTHDC1 recognizes differential m6A sites on key enzymes of glycolysis phosphofructokinase (PFKM) and lactate dehydrogenase A (LDHA) mRNAs, which suppress glycolysis pathway by increasing mRNA stability of them in an m6A methylation-dependent manner. YTHDC1 partially abrogated the inhibitory effect caused by NAT10 knockdown in tumor models in vivo, lentiviral overexpression of YTHDC1 partially restored the reduced stability of YTHDC1 caused by lentiviral depleting NAT10 at the cellular level. Altogether, we found ac4C driven RNA m6A modification can positively regulate the glycolysis of cancer cells and reveals a previously unrecognized signaling axis of NAT10/ac4C-YTHDC1/m6A-LDHA/PFKM in osteosarcoma. Video Abstract.


Subject(s)
Cytidine/analogs & derivatives , Osteosarcoma , Phosphofructokinases , Humans , Lactate Dehydrogenase 5/metabolism , Phosphofructokinases/metabolism , Acetylation , RNA/metabolism , Glycolysis/genetics , Osteosarcoma/pathology , Phosphofructokinase-1, Muscle Type/metabolism , RNA Splicing Factors/metabolism , Nerve Tissue Proteins/metabolism , N-Terminal Acetyltransferases/metabolism
17.
Physiol Plant ; 176(3): e14403, 2024.
Article in English | MEDLINE | ID: mdl-38923551

ABSTRACT

Renewable energy resources such as biomass are crucial for a sustainable global society. Trees are a major source of lignocellulosic biomass, which can vary in response to different environmental factors owing to epigenetic regulation, such as DNA C-methylation. To investigate the effects of DNA methylation on plant development and wood formation, and its impacts on gene expression, with a focus on secondary cell wall (SCW)-associated genes, Salix purpurea plantlets were cloned from buds derived from a single hybrid tree for both treatment and control conditions. For the treatment condition, buds were exposed to 50 µM zebularine in vitro and a combined strategy of whole-genome bisulfite sequencing (WGBS) and RNA-seq was employed to examine the methylome and transcriptome profiles of different tissues collected at various time points under both conditions. Transcriptomic and methylome data revealed that most of the promoter and gene body demethylation had no marked effects on the expression profiles of genes. Nevertheless, gene expression tended to decrease with the increased methylation levels of genes with highly methylated promoters. Results indicated that demethylation is less evident in centromeric regions and sex chromosomes. Promoters of secondary cell wall-associated genes, such as 4-coumarate-CoA ligase-like and Rac-like GTP-binding protein RHO, were differentially methylated in the secondary xylem samples collected from two-month potted treated plants compared to control samples. Our results provide novel insights into DNA methylation and gene expression landscapes and a basis for investigating the epigenetic regulation of wood formation in S. purpurea as a model plant for bioenergy species.


Subject(s)
Cytidine , DNA Methylation , Gene Expression Regulation, Plant , Salix , Transcriptome , DNA Methylation/drug effects , DNA Methylation/genetics , Cytidine/analogs & derivatives , Cytidine/pharmacology , Cytidine/genetics , Transcriptome/genetics , Transcriptome/drug effects , Salix/genetics , Salix/drug effects , Gene Expression Regulation, Plant/drug effects , Genome, Plant/genetics , Cell Wall/metabolism , Cell Wall/drug effects , Cell Wall/genetics , Epigenesis, Genetic/drug effects
18.
Org Biomol Chem ; 22(4): 735-740, 2024 01 24.
Article in English | MEDLINE | ID: mdl-38168802

ABSTRACT

Molnupiravir, the prodrug for ß-D-N4-hydroxycytidine (NHC), is marketed by Merck as Lagevrio™ against mild-moderate COVID-19, under FDA emergency use authorization. It is the first oral drug against the disease. This work describes two synthetic approaches to NHC and molnupiravir by amide activation in uridine with a peptide-coupling agent and with a 4-chloropyrimidinone nucleoside intermediate.


Subject(s)
COVID-19 , Cytidine/analogs & derivatives , Prodrugs , Humans , Hydroxylamines , Antiviral Agents
19.
BMC Infect Dis ; 24(1): 670, 2024 Jul 04.
Article in English | MEDLINE | ID: mdl-38965495

ABSTRACT

BACKGROUND: The clinical benefit of coronavirus disease 2019 (COVID-19) treatments against new circulating variants remains unclear. We sought to describe characteristics and clinical outcomes of highest risk patients with COVID-19 receiving early COVID-19 treatments in Scotland. METHODS: Retrospective cohort study of non-hospitalized patients diagnosed with COVID-19 from December 1, 2021-October 25, 2022, using Scottish administrative health data. We included adult patients who met ≥ 1 of the National Health Service highest risk criteria for early COVID-19 treatment and received outpatient treatment with sotrovimab, nirmatrelvir/ritonavir or molnupiravir, or no early COVID-19 treatment. Index date was defined as the earliest of COVID-19 diagnosis or early COVID-19 treatment. Baseline characteristics and acute clinical outcomes in the 28 days following index were reported. Values of ≤ 5 were suppressed. RESULTS: In total, 2548 patients were included (492: sotrovimab, 276: nirmatrelvir/ritonavir, 71: molnupiravir, and 1709: eligible highest risk untreated). Patients aged ≥ 75 years accounted for 6.9% (n = 34/492), 21.0% (n = 58/276), 16.9% (n = 12/71) and 13.2% (n = 225/1709) of the cohorts, respectively. Advanced renal disease was reported in 6.7% (n = 33/492) of sotrovimab-treated and 4.7% (n = 81/1709) of untreated patients, and ≤ 5 nirmatrelvir/ritonavir-treated and molnupiravir-treated patients. All-cause hospitalizations were experienced by 5.3% (n = 25/476) of sotrovimab-treated patients, 6.9% (n = 12/175) of nirmatrelvir/ritonavir-treated patients, ≤ 5 (suppressed number) molnupiravir-treated patients and 13.3% (n = 216/1622) of untreated patients. There were no deaths in the treated cohorts; mortality was 4.3% (n = 70/1622) among untreated patients. CONCLUSIONS: Sotrovimab was often used by patients who were aged < 75 years. Among patients receiving early COVID-19 treatment, proportions of 28-day all-cause hospitalization and death were low.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , COVID-19 , Disease Progression , SARS-CoV-2 , Humans , Antiviral Agents/therapeutic use , Retrospective Studies , Male , Female , Middle Aged , Aged , SARS-CoV-2/drug effects , COVID-19/mortality , Adult , Treatment Outcome , Scotland/epidemiology , Antibodies, Monoclonal, Humanized/therapeutic use , Ritonavir/therapeutic use , Aged, 80 and over , Cytidine/analogs & derivatives , Hydroxylamines
20.
Bioorg Chem ; 147: 107379, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38643567

ABSTRACT

Coronaviruses are a group of enveloped viruses with non-segmented, single-stranded, and positive-sense RNA genomes. It belongs to the 'Coronaviridae family', responsible for various diseases, including the common cold, SARS, and MERS. The COVID-19 pandemic, which began in March 2020, has affected 209 countries, infected over a million people, and claimed over 50,000 lives. Significant efforts have been made by repurposing several approved drugs including antiviral, to combat the COVID-19 pandemic. Molnupiravir is found to be the first orally acting efficacious drug to treat COVID-19 cases. It was approved for medical use in the UK in November 2021 and other countries, including USFDA, which granted approval an emergency use authorization (EUA) for treating adults with mild to moderate COVID-19 patients. Considering the importance of molnupiravir, the present review deals with its various synthetic strategies, pharmacokinetics, bio-efficacy, toxicity, and safety profiles. The comprehensive information along with critical analysis will be very handy for a wide range of audience including medicinal chemists in the arena of antiviral drug discovery especially anti-viral drugs against any variant of COVID-19.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , COVID-19 , Cytidine , Hydroxylamines , SARS-CoV-2 , Humans , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , Antiviral Agents/chemical synthesis , Hydroxylamines/therapeutic use , Hydroxylamines/chemistry , Hydroxylamines/pharmacology , COVID-19/virology , SARS-CoV-2/drug effects , Cytidine/analogs & derivatives , Cytidine/therapeutic use , Cytidine/pharmacology , Cytidine/chemistry , Cytidine/chemical synthesis , Uridine/pharmacology , Uridine/analogs & derivatives , Uridine/chemical synthesis , Uridine/chemistry , Uridine/therapeutic use , Pandemics , Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Pneumonia, Viral/drug therapy
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