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Organic Letters Jan 2024We demonstrate the use of the symmetrical diethyl(dimethyl)difluoromethylene bisphosphonate reagent for the synthesis of terminal and unsymmetrical difluoromethylene...
We demonstrate the use of the symmetrical diethyl(dimethyl)difluoromethylene bisphosphonate reagent for the synthesis of terminal and unsymmetrical difluoromethylene bisphosphonates, close analogues of biologically important molecules. The difference in reactivity of the methyl and ethyl groups in the symmetrical diethyl(dimthyl)difluoromethylene bisphosphonate is exploited in a stepwise demethylation-condensation sequence to functionalize either side of the reagent to allow the generation of a series of close bioisosteres of natural pyrophosphate molecules, including ADPr, CDP-glycerol and CDP-ribitol.
Topics: Diphosphonates; Hydrocarbons, Fluorinated
PubMed: 38215221
DOI: 10.1021/acs.orglett.3c04211 -
International Journal of Molecular... Dec 2023Breast Cancer (BC) was the most common female cancer in incidence and mortality worldwide in 2020. Similarly, BC was the top female cancer in the USA in 2022. Risk... (Review)
Review
Breast Cancer (BC) was the most common female cancer in incidence and mortality worldwide in 2020. Similarly, BC was the top female cancer in the USA in 2022. Risk factors include earlier age at menarche, oral contraceptive use, hormone replacement therapy, high body mass index, and mutations in 1/2 genes, among others. BC is classified into Luminal A, Luminal B, HER2-like, and Basal-like subtypes. These BC subtypes present differences in gene expression signatures, which can impact clinical behavior, treatment response, aggressiveness, metastasis, and survival of patients. Therefore, it is necessary to understand the epigenetic molecular mechanism of transcriptional regulation in BC, such as DNA demethylation. Ten-Eleven Translocation (TET) enzymes catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) on DNA, which in turn inhibits or promotes the gene expression. Interestingly, the expression of TET enzymes as well as the levels of the 5hmC epigenetic mark are altered in several types of human cancers, including BC. Several studies have demonstrated that TET enzymes and 5hmC play a key role in the regulation of gene expression in BC, directly (dependent or independent of DNA de-methylation) or indirectly (via interaction with other proteins such as transcription factors). In this review, we describe our recent understanding of the regulatory and physiological function of the TET enzymes, as well as their potential role as biomarkers in BC biology.
Topics: Humans; Female; Breast Neoplasms; BRCA1 Protein; BRCA2 Protein; Carcinogenesis; DNA
PubMed: 38203443
DOI: 10.3390/ijms25010272 -
International Journal of Molecular... Sep 2023Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most... (Review)
Review
Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, , and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the model, is important for future efforts to develop new crop varieties.
Topics: Humans; Arabidopsis; Escherichia coli; DNA Repair; DNA Damage; DNA, Plant
PubMed: 37834194
DOI: 10.3390/ijms241914746 -
Environmental Science & Technology Oct 2023Contaminants of emerging concern (CECs) in the environment undergo various transformations, leading to the formation of transformation products (TPs) with a modified...
Contaminants of emerging concern (CECs) in the environment undergo various transformations, leading to the formation of transformation products (TPs) with a modified ecological risk potential. Although the environmental significance of TPs is increasingly recognized, there has been relatively little research to understand the influences of such transformations on subsequent ecotoxicological safety. In this study, we used four pairs of CECs and their methylated or demethylated derivatives as examples to characterize changes in bioaccumulation and acute toxicity in , as a result of methylation or demethylation. The experimental results were further compared to quantitative structure-activity relationship (QSAR) predictions. The methylated counterpart in each pair generally showed greater acute toxicity in , which was attributed to their increased hydrophobicity. For example, the LC values of methylparaben (34.4 ± 4.3 mg L) and its demethylated product (225.6 ± 17.3 mg L) differed about eightfold in . The methylated derivative generally exhibited greater bioaccumulation than the demethylated counterpart. For instance, the bioaccumulation of methylated acetaminophen was about 33-fold greater than that of acetaminophen. predictions via QSARs aligned well with the experimental results and suggested an increased persistence of the methylated forms. The study findings underline the consequences of simple changes in chemical structures induced by transformations such as methylation and demethylation and highlight the need to consider TPs to achieve a more holistic understanding of the environmental fate and risks of CECs.
PubMed: 37769124
DOI: 10.1021/acs.est.3c03242 -
Nature Communications Dec 2023Clonal hematopoiesis (CH) is defined as a single hematopoietic stem/progenitor cell (HSPC) gaining selective advantage over a broader range of HSPCs. When linked to...
Clonal hematopoiesis (CH) is defined as a single hematopoietic stem/progenitor cell (HSPC) gaining selective advantage over a broader range of HSPCs. When linked to somatic mutations in myeloid malignancy-associated genes, such as TET2-mediated clonal hematopoiesis of indeterminate potential or CHIP, it represents increased risk for hematological malignancies and cardiovascular disease. IL1β is elevated in patients with CHIP, however, its effect is not well understood. Here we show that IL1β promotes expansion of pro-inflammatory monocytes/macrophages, coinciding with a failure in the demethylation of lymphoid and erythroid lineage associated enhancers and transcription factor binding sites, in a mouse model of CHIP with hematopoietic-cell-specific deletion of Tet2. DNA-methylation is significantly lost in wild type HSPCs upon IL1β administration, which is resisted by Tet2-deficient HSPCs, and thus IL1β enhances the self-renewing ability of Tet2-deficient HSPCs by upregulating genes associated with self-renewal and by resisting demethylation of transcription factor binding sites related to terminal differentiation. Using aged mouse models and human progenitors, we demonstrate that targeting IL1 signaling could represent an early intervention strategy in preleukemic disorders. In summary, our results show that Tet2 is an important mediator of an IL1β-promoted epigenetic program to maintain the fine balance between self-renewal and lineage differentiation during hematopoiesis.
Topics: Mice; Animals; Humans; Clonal Hematopoiesis; DNA-Binding Proteins; Hematopoiesis; Hematopoietic Stem Cells; Epigenesis, Genetic; Transcription Factors; Dioxygenases
PubMed: 38062031
DOI: 10.1038/s41467-023-43697-y -
British Journal of Cancer Jun 2024Tregs trafficking is controlled by CXCR4. In Renal Cell Carcinoma (RCC), the effect of the new CXCR4 antagonist, R54, was explored in peripheral blood (PB)-Tregs...
BACKGROUND
Tregs trafficking is controlled by CXCR4. In Renal Cell Carcinoma (RCC), the effect of the new CXCR4 antagonist, R54, was explored in peripheral blood (PB)-Tregs isolated from primary RCC patients.
METHODS
PB-Tregs were isolated from 77 RCC patients and 38 healthy donors (HDs). CFSE-T effector-Tregs suppression assay, IL-35, IFN-γ, IL-10, TGF-β1 secretion, and Tregs frequency were evaluated. Tregs were characterised for CTLA-4, PD-1, CD40L, PTEN, CD25, TGF-β1, FOXP3, DNMT1 transcriptional profile. PTEN-pAKT signalling was evaluated in the presence of R54 and/or triciribine (TCB), an AKT inhibitor. Methylation of TSDR (Treg-Specific-Demethylated-Region) was conducted.
RESULTS
R54 impaired PB-RCC-Tregs function, reduced Tregs frequency, the release of IL-35, IL-10, and TGF-β1, while increased IFN-γ Teff-secretion. The CXCR4 ligand, CXCL12, recruited Tregs in RCC while R54 significantly reduced it. IL-2/PMA activates Tregs reducing Tregs while R54 increases it. The AKT inhibitor, TCB, prevented the increase in Tregs R54-mediated. Moreover, R54 significantly reduced FOXP3-TSDR demethylation with DNMT1 and FOXP3 downregulation.
CONCLUSION
R54 impairs Tregs function in primary RCC patients targeting PTEN/PI3K/AKT pathway, reducing TSDR demethylation and FOXP3 and DNMT1 expression. Thus, CXCR4 targeting is a strategy to inhibit Tregs activity in the RCC tumour microenvironment.
Topics: Humans; T-Lymphocytes, Regulatory; PTEN Phosphohydrolase; Receptors, CXCR4; Kidney Neoplasms; Carcinoma, Renal Cell; Female; Male; Middle Aged; Aged; Adult; Signal Transduction; Forkhead Transcription Factors
PubMed: 38704478
DOI: 10.1038/s41416-024-02702-x -
Scientific Reports Mar 2024As the most prevalent epitranscriptomic modification, N-methyladenosine (mA) shows important roles in a variety of diseases through regulating the processing, stability...
METTL3 and METTL14-mediated N-methyladenosine modification of SREBF2-AS1 facilitates hepatocellular carcinoma progression and sorafenib resistance through DNA demethylation of SREBF2.
As the most prevalent epitranscriptomic modification, N-methyladenosine (mA) shows important roles in a variety of diseases through regulating the processing, stability and translation of target RNAs. However, the potential contributions of mA to RNA functions are unclear. Here, we identified a functional and prognosis-related mA-modified RNA SREBF2-AS1 in hepatocellular carcinoma (HCC). The expression of SREBF2-AS1 and SREBF2 in HCC tissues and cells was measured by RT-qPCR. mA modification level of SREBF2-AS1 was measured by methylated RNA immunoprecipitation assay. The roles of SREBF2-AS1 in HCC progression and sorafenib resistance were investigated by proliferation, apoptosis, migration, and cell viability assays. The regulatory mechanisms of SREBF2-AS1 on SREBF2 were investigated by Chromatin isolation by RNA purification, RNA immunoprecipitation, CUT&RUN, and bisulfite DNA sequencing assays. Our findings showed that the expression of SREBF2-AS1 was increased in HCC tissues and cells, and positively correlated with poor survival of HCC patients. mA modification level of SREBF2-AS1 was also increased in HCC and positively correlated with poor prognosis of HCC patients. METTL3 and METTL14-induced mA modification upregulated SREBF2-AS1 expression through increasing SREBF2-AS1 transcript stability. Functional assays showed that only mA-modified, but not non-modified SREBF2-AS1 promoted HCC progression and sorafenib resistance. Mechanistic investigations revealed that mA-modified SREBF2-AS1 bound and recruited mA reader FXR1 and DNA 5-methylcytosine dioxygenase TET1 to SREBF2 promoter, leading to DNA demethylation at SREBF2 promoter and the upregulation of SREBF2 transcription. Functional rescue assays showed that SREBF2 was the critical mediator of the oncogenic roles of SREBF2-AS1 in HCC. Together, this study showed that mA-modified SREBF2-AS1 exerted oncogenic roles in HCC through inducing DNA demethylation and transcriptional activation of SREBF2, and suggested mA-modified SREBF2-AS1 as a prognostic biomarker and therapeutic target for HCC.
Topics: Humans; Carcinoma, Hepatocellular; Sorafenib; Liver Neoplasms; DNA Demethylation; Cell Line, Tumor; MicroRNAs; RNA-Binding Proteins; Mixed Function Oxygenases; Proto-Oncogene Proteins; Methyltransferases; Adenosine; Sterol Regulatory Element Binding Protein 2
PubMed: 38486042
DOI: 10.1038/s41598-024-55932-7 -
Cancer Cell International Nov 2023The m6a demethyltransferase ALKBH5 dynamically modulates gene expression and intracellular metabolic molecules by modifying RNA m6a in cancer cells. However, ALKBH5's...
The m6a demethyltransferase ALKBH5 dynamically modulates gene expression and intracellular metabolic molecules by modifying RNA m6a in cancer cells. However, ALKBH5's function in gastric cancer (GC) has remained controversial. This study demonstrates that ALKBH5 is highly expressed in GC. Silencing ALKBH5 hampers proliferation, and metastatic potential, and induces cell death in GC cells. Through a comprehensive analysis of the transcriptome and m6A sequencing, alterations in certain ALKBH5 target genes, including CHAC1, were identified. ALKBH5's demethylation effect regulates CHAC1 RNA stability, leading to reduced CHAC1 expression. Moreover, CHAC1 modulates intracellular ROS levels, influencing the chemotherapy sensitivity of gastric cancer. In summary, our study unveils the pivotal role of the ALKBH5-CHAC1-ROS axis and highlights the significance of m6A methylation in gastric cancer.
PubMed: 38007439
DOI: 10.1186/s12935-023-03129-9 -
The Journal of Biological Chemistry Feb 2024Increased expression of angiotensin II AT receptor (encoded by Agtr1a) and Na-K-Cl cotransporter-1 (NKCC1, encoded by Slc12a2) in the hypothalamic paraventricular...
Increased expression of angiotensin II AT receptor (encoded by Agtr1a) and Na-K-Cl cotransporter-1 (NKCC1, encoded by Slc12a2) in the hypothalamic paraventricular nucleus (PVN) contributes to hypertension development. However, little is known about their transcriptional control in the PVN in hypertension. DNA methylation is a critical epigenetic mechanism that regulates gene expression. Here, we determined whether transcriptional activation of Agtr1a and Slc12a2 results from altered DNA methylation in spontaneously hypertensive rats (SHR). Methylated DNA immunoprecipitation and bisulfite sequencing-PCR showed that CpG methylation at Agtr1a and Slc12a2 promoters in the PVN was progressively diminished in SHR compared with normotensive Wistar-Kyoto rats (WKY). Chromatin immunoprecipitation-quantitative PCR revealed that enrichment of DNA methyltransferases (DNMT1 and DNMT3A) and methyl-CpG binding protein 2, a DNA methylation reader protein, at Agtr1a and Slc12a2 promoters in the PVN was profoundly reduced in SHR compared with WKY. By contrast, the abundance of ten-eleven translocation enzymes (TET1-3) at Agtr1a and Slc12a2 promoters in the PVN was much greater in SHR than in WKY. Furthermore, microinjecting of RG108, a selective DNMT inhibitor, into the PVN of WKY increased arterial blood pressure and correspondingly potentiated Agtr1a and Slc12a2 mRNA levels in the PVN. Conversely, microinjection of C35, a specific TET inhibitor, into the PVN of SHR markedly reduced arterial blood pressure, accompanied by a decrease in Agtr1a and Slc12a2 mRNA levels in the PVN. Collectively, our findings suggest that DNA hypomethylation resulting from the DNMT/TET switch at gene promoters in the PVN promotes transcription of Agtr1a and Slc12a2 and hypertension development.
Topics: Animals; Rats; Blood Pressure; DNA; DNA Demethylation; Hypertension; Hypothalamus; Paraventricular Hypothalamic Nucleus; Rats, Inbred SHR; Rats, Inbred WKY; Receptor, Angiotensin, Type 1; RNA, Messenger; Sympathetic Nervous System; Solute Carrier Family 12, Member 2
PubMed: 38160798
DOI: 10.1016/j.jbc.2023.105597 -
Science Advances Dec 2023Transposons are mobile and ubiquitous DNA molecules that can cause vast genomic alterations. In plants, it is well documented that transposon mobilization is strongly...
Transposons are mobile and ubiquitous DNA molecules that can cause vast genomic alterations. In plants, it is well documented that transposon mobilization is strongly repressed by DNA methylation; however, its regulation at the posttranscriptional level remains relatively uninvestigated. Here, we suggest that transposon RNA is marked by mA RNA methylation and can be localized in stress granules (SGs). Intriguingly, SG-localized AtALKBH9B selectively demethylates a heat-activated retroelement, , and thereby releases it from spatial confinement, allowing for its mobilization. In addition, we show evidence that mA RNA methylation contributes to transpositional suppression by inhibiting virus-like particle assembly and extrachromosomal DNA production. In summary, this study unveils a previously unknown role for mA in the suppression of transposon mobility and provides insight into how transposons counteract the mA-mediated repression mechanism by hitchhiking the RNA demethylase of the host.
Topics: Arabidopsis; Retroelements; RNA; Hot Temperature; DNA Methylation; Terminal Repeat Sequences; Gene Expression Regulation, Plant
PubMed: 38019921
DOI: 10.1126/sciadv.adf3292