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JCI Insight Oct 2023Abnormal macrophage polarization is generally present in autoimmune diseases. Overwhelming M1 macrophage activation promotes the continuous progression of inflammation,...
Abnormal macrophage polarization is generally present in autoimmune diseases. Overwhelming M1 macrophage activation promotes the continuous progression of inflammation, which is one of the reasons for the development of autoimmune diseases. However, the underlying mechanism is still unclear. Here we explore the function of Regulatory factor X1 (RFX1) in macrophage polarization by constructing colitis and lupus-like mouse models. Both in vivo and in vitro experiments confirmed that RFX1 can promote M1 and inhibit M2 macrophage polarization. Furthermore, we found that RFX1 promoted DNA demethylation of macrophage polarization-related genes by increasing APOBEC3A/Apobec3 expression. We identified a potential RFX1 inhibitor, adenosine diphosphate (ADP), providing a potential strategy for treating autoimmune diseases.
Topics: Animals; Mice; Autoimmune Diseases; DNA Demethylation; Inflammation; Macrophage Activation; Macrophages; Regulatory Factor X1
PubMed: 37733446
DOI: 10.1172/jci.insight.165546 -
Angewandte Chemie (International Ed. in... Feb 2024N -methyladenosine (m A) is a prevalent post-transcriptional RNA modification, and the distribution and dynamics of the modification play key epitranscriptomic roles in...
N -methyladenosine (m A) is a prevalent post-transcriptional RNA modification, and the distribution and dynamics of the modification play key epitranscriptomic roles in cell development. At present, the human AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family member ALKBH3 is the only known mRNA m A demethylase, but its catalytic mechanism remains unclear. Here, we present the structures of ALKBH3-oligo crosslinked complexes obtained with the assistance of a synthetic antibody crystallization chaperone. Structural and biochemical results showed that ALKBH3 utilized two β-hairpins (β4-loop-β5 and β'-loop-β'') and the α2 helix to facilitate single-stranded substrate binding. Moreover, a bubble-like region around Asp194 and a key residue inside the active pocket (Thr133) enabled specific recognition and demethylation of m A- and 3-methylcytidine (m C)-modified substrates. Mutation of Thr133 to the corresponding residue in the AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family members FTO or ALKBH5 converted ALKBH3 substrate selectivity from m A to N -methyladenosine (m A), as did Asp194 deletion. Our findings provide a molecular basis for understanding the mechanisms of substrate recognition and m A demethylation by ALKBH3. This study is expected to aid structure-guided design of chemical probes for further functional studies and therapeutic applications.
Topics: Humans; RNA; Alpha-Ketoglutarate-Dependent Dioxygenase FTO; RNA, Messenger; Demethylation; Ferrous Compounds; AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase
PubMed: 38158383
DOI: 10.1002/anie.202313900 -
Clinical Epigenetics Aug 2023Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this...
BACKGROUND
Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this epigenetic mechanism is functional in cancer or is a mere consequence of the carcinogenic process remains to be elucidated.
RESULTS
In this work, we performed an integrative multi-omic approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human CRC samples and a set of 8 colon cancer cell lines. As a proof of concept, we combined recent CRISPR-Cas9 epigenome editing tools (dCas9-TET1, dCas9-TET-IM) with a customized arrayed gRNA library to modulate the DNA methylation status of 56 promoters previously linked with strong epigenetic repression in CRC, and we monitored the potential functional consequences of this DNA methylation loss by means of a high-content cell proliferation screen. Overall, the epigenetic modulation of most of these DNA methylated regions had a mild impact on the reactivation of gene expression and on the viability of cancer cells. Interestingly, we found that epigenetic reactivation of RSPO2 in the tumour context was associated with a significant impairment in cell proliferation in p53 cancer cell lines, and further validation with human samples demonstrated that the epigenetic silencing of RSPO2 is a mid-late event in the adenoma to carcinoma sequence.
CONCLUSIONS
These results highlight the potential role of DNA methylation as a driver mechanism of CRC and paves the way for the identification of novel therapeutic windows based on the epigenetic reactivation of certain tumour suppressor genes.
Topics: Humans; DNA Methylation; DNA Demethylation; Epigenesis, Genetic; Carcinogenesis; Colonic Neoplasms; Mixed Function Oxygenases; Proto-Oncogene Proteins
PubMed: 37612734
DOI: 10.1186/s13148-023-01546-1 -
Experimental & Molecular Medicine Dec 2020Lysine-specific histone demethylase 1 (LSD1) represents the first example of an identified nuclear protein with histone demethylase activity. In particular, it plays a... (Review)
Review
Lysine-specific histone demethylase 1 (LSD1) represents the first example of an identified nuclear protein with histone demethylase activity. In particular, it plays a special role in the epigenetic regulation of gene expression, as it removes methyl groups from mono- and dimethylated lysine 4 and/or lysine 9 on histone H3 (H3K4me1/2 and H3K9me1/2), behaving as a repressor or activator of gene expression, respectively. Moreover, it has been recently found to demethylate monomethylated and dimethylated lysine 20 in histone H4 and to contribute to the balance of several other methylated lysine residues in histone H3 (i.e., H3K27, H3K36, and H3K79). Furthermore, in recent years, a plethora of nonhistone proteins have been detected as targets of LSD1 activity, suggesting that this demethylase is a fundamental player in the regulation of multiple pathways triggered in several cellular processes, including cancer progression. In this review, we analyze the molecular mechanism by which LSD1 displays its dual effect on gene expression (related to the specific lysine target), placing final emphasis on the use of pharmacological inhibitors of its activity in future clinical studies to fight cancer.
Topics: Alternative Splicing; Animals; Biomarkers, Tumor; Demethylation; Epigenesis, Genetic; Gene Expression Regulation; Histone Demethylases; Histones; Humans; Lysine; Molecular Targeted Therapy; Protein Binding; Protein Processing, Post-Translational; Protein Stability; Receptors, Cytoplasmic and Nuclear; Structure-Activity Relationship
PubMed: 33318631
DOI: 10.1038/s12276-020-00542-2 -
Mutation Research. Reviews in Mutation... 2021APE2 is a rising vital player in the maintenance of genome and epigenome integrity. In the past several years, a series of studies have shown the critical roles and... (Review)
Review
APE2 is a rising vital player in the maintenance of genome and epigenome integrity. In the past several years, a series of studies have shown the critical roles and functions of APE2. We seek to provide the first comprehensive review on several aspects of APE2 in genome and epigenome integrity. We first summarize the distinct functional domains or motifs within APE2 including EEP (endonuclease/exonuclease/phosphatase) domain, PIP box and Zf-GRF motifs from eight species (i.e., Homo sapiens, Mus musculus, Xenopus laevis, Ciona intestinalis, Arabidopsis thaliana, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Trypanosoma cruzi). Then we analyze various APE2 nuclease activities and associated DNA substrates, including AP endonuclease, 3'-phosphodiesterase, 3'-phosphatase, and 3'-5' exonuclease activities. We also examine several APE2 interaction proteins, including PCNA, Chk1, APE1, Myh1, and homologous recombination (HR) factors such as Rad51, Rad52, BRCA1, BRCA2, and BARD1. Furthermore, we provide insights into the roles of APE2 in various DNA repair pathways (base excision repair, single-strand break repair, and double-strand break repair), DNA damage response (DDR) pathways (ATR-Chk1 and p53-dependent), immunoglobulin class switch recombination and somatic hypermutation, as well as active DNA demethylation. Lastly, we summarize critical functions of APE2 in growth, development, and diseases. In this review, we provide the first comprehensive perspective which dissects all aspects of the multiple-function protein APE2 in genome and epigenome integrity.
Topics: Animals; Arabidopsis Proteins; DNA Damage; DNA Demethylation; DNA Repair; Endonucleases; Epigenome; Humans; Immunity; Rad51 Recombinase; Saccharomyces cerevisiae
PubMed: 34083046
DOI: 10.1016/j.mrrev.2020.108347 -
Water Research May 2022Mercury (Hg) and its compounds are a kind of worldwide concerned persistent toxic pollutants. As the major primary producer in the ocean, microalgae are expected to play...
Mercury (Hg) and its compounds are a kind of worldwide concerned persistent toxic pollutants. As the major primary producer in the ocean, microalgae are expected to play an important role in the cycling and accumulation of Hg in marine ecosystems by either uptake Hg species from seawater or involving in the transformations of Hg species. However, there is still lack of clear knowledge on whether microalgae can induce the methylation and demethylation of Hg in aquatic environments. In this study, Hg isotope dilution and isotope addition techniques were utilized to determine the methylation and demethylation potential of Hg at concentrations comparable to that in natural environments by 15 common marine microalgae (8 species of Diatoms, 4 species of Dinoflagellates, 2 species of Chlorophyta and 1 species of Chrysophyte). Methylation of inorganic Hg was found to be negligible in the culture of all tested marine microalgae, while 6 species could significantly induce the demethylation of methylmercury (MeHg). The rates of microalgae mediated MeHg demethylation were at the same order of magnitude as that of photodemethylation, indicating that marine microalgae may play an important role in the degradation of MeHg in marine environments. Further studies suggest that the demethylation of MeHg by the microalgae may be mainly caused by their extracellular secretions (via photo-induce demethylation) and associated bacteria, rather than the direct demethylation of MeHg by microalgae cells. In addition, it was found that thiol groups may be the major component in microalgal extracellular secretions that lead to the photo-demethylation of MeHg.
Topics: Demethylation; Ecosystem; Mercury; Methylation; Microalgae
PubMed: 35290869
DOI: 10.1016/j.watres.2022.118266 -
Environmental Science & Technology Jan 2024Many contaminants of emerging concern (CECs) have reactive functional groups and may readily undergo biotransformations, such as methylation and demethylation. These...
Many contaminants of emerging concern (CECs) have reactive functional groups and may readily undergo biotransformations, such as methylation and demethylation. These transformations have been reported to occur during human metabolism and wastewater treatment, leading to the propagation of CECs. When treated wastewater and biosolids are used in agriculture, CECs and their transformation products (TPs) are introduced into soil-plant systems. However, little is known about whether transformation cycles, such as methylation and demethylation, take place in higher plants and hence affect the fate of CECs in terrestrial ecosystems. In this study, we explored the interconversion between four common CECs (acetaminophen, diazepam, methylparaben, and naproxen) and their methylated or demethylated TPs in cells and whole wheat seedlings. The methylation-demethylation cycle occurred in both plant models with demethylation generally taking place at a greater degree than methylation. The transformation rate of demethylation or methylation was dependent on the bond strength of R-CH, with demethylation of methylparaben or methylation of acetaminophen being more pronounced. Although not explored in this study, these interconversions may exert influences on the behavior and biological activity of CECs, particularly in terrestrial ecosystems. The study findings demonstrated the prevalence of transformation cycles between CECs and their methylated or demethylated TPs in higher plants, contributing to a more complete understanding of risks of CECs in the human-wastewater-soil-plant continuum.
Topics: Humans; Wastewater; Water Pollutants, Chemical; Acetaminophen; Ecosystem; Soil; Methylation; Demethylation; Environmental Monitoring; Parabens
PubMed: 38240245
DOI: 10.1021/acs.est.3c03171 -
Journal of Agricultural and Food... Mar 20225-Demethylated polymethoxyflavones (5-OH PMFs) are the most unique monodemethylated PMFs with relatively low polarities and are proved to possess better anticancer and...
5-Demethylated polymethoxyflavones (5-OH PMFs) are the most unique monodemethylated PMFs with relatively low polarities and are proved to possess better anticancer and anti-inflammatory effects than their respective permethoxylated ones. However, their detailed metabolic fates have not been fully studied. 5-Demethylsinensetin (5-OH Sin), being one of the 5-demethylated citrus PMFs, was used in the present research to investigate its biotransformation in pharmacokinetics and excretion in rats. The results showed that 5-OH Sin was mostly accumulated in the large intestine, indicating its poor absorption in the small intestine. In addition, 5,3'-didemethylsinensetin and 5,4'-didemethylsinensetin were identified as two dominated metabolites of 5-OH Sin, and the C-3' position of 5-OH Sin was more facile to be demethylated in systemic circulation. Moreover, other than demethylation reactions, the methylation transformation of 5-OH Sin and its metabolites were also observed and quantified, suggesting that the bidirectional biotransformation between 5-OH Sin and its parent compound, Sin, occurred under conditions.
Topics: Animals; Biotransformation; Citrus; Demethylation; Flavones; Methylation; Rats
PubMed: 35230106
DOI: 10.1021/acs.jafc.1c07509 -
Science (New York, N.Y.) Dec 2022Active DNA demethylation maintains enhancer activity in nonproliferating cells but can damage DNA.
Active DNA demethylation maintains enhancer activity in nonproliferating cells but can damage DNA.
Topics: DNA Demethylation; Macrophages; Neurons; Enhancer Elements, Genetic; Humans; DNA Breaks, Single-Stranded
PubMed: 36454845
DOI: 10.1126/science.adf3171 -
Neuroendocrinology 2022Neurons expressing estrogen receptor (ER) ɑ in the arcuate (ARC) and ventromedial (VMH) nuclei of the hypothalamus sex-specifically control energy homeostasis, sexual...
INTRODUCTION
Neurons expressing estrogen receptor (ER) ɑ in the arcuate (ARC) and ventromedial (VMH) nuclei of the hypothalamus sex-specifically control energy homeostasis, sexual behavior, and bone density. Females have more ERɑ neurons in the VMH and ARC than males, and the sex difference in the VMH is eliminated by neonatal treatment with testosterone or a DNA methylation inhibitor.
OBJECTIVE
Here, we tested the roles of testosterone and DNA methylation/demethylation in development of ERɑ in the ARC.
METHODS
ERɑ was examined at birth and weaning in mice that received vehicle or testosterone subcutaneously, and vehicle or DNA methyltransferase inhibitor intracerebroventricularly, as neonates. To examine effects of DNA demethylation on the ERɑ cell number in the ARC, mice were treated neonatally with small interfering RNAs against ten-eleven translocase enzymes. The methylation status of the ERɑ gene (Esr1) was determined in the ARC and VMH using pyrosequencing of bisulfite-converted DNA.
RESULTS
A sex difference in ERɑ in the ARC, favoring females, developed between birth and weaning and was due to programming effects of testosterone. Neonatal inhibition of DNA methylation decreased ERɑ in the ARC of females, and an inhibition of
de methylation increased ERɑ in the ARC of males. The promoter region of Esr1 exhibited a small sex difference in percent of total methylation in the ARC (females > males) that was opposite to that in the VMH (males > females).CONCLUSION
DNA methylation and demethylation regulate ERɑ cell number in the ARC, and methylation correlates with activation of Esr1 in this region.
Topics: Animals; Arcuate Nucleus of Hypothalamus; DNA Methylation; Demethylation; Estrogen Receptor alpha; Female; Male; Mice; Sex Characteristics; Testosterone
PubMed: 34547753
DOI: 10.1159/000519671