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Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells [RNA-Seq]

ABSTRACT: Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells [RNA-Seq]

PROVIDER: PRJNA788781 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17259263_1.fastq.gz	Fastqsanger.gz
	SRR17259263_2.fastq.gz	Fastqsanger.gz
	SRR17259264_1.fastq.gz	Fastqsanger.gz
	SRR17259264_2.fastq.gz	Fastqsanger.gz
	SRR17259265_1.fastq.gz	Fastqsanger.gz

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Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells

Project description:Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells

| PRJNA788776 | ENA

Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells [Bisulfite-Seq]

Project description:Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells [Bisulfite-Seq]

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Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells [RNA-Seq]

Project description:Acute myeloid leukemia (AML) is a fatal hematological malignancy for most patients, and DNA methyltransferase 3A (DNMT3A) mutations occur in about 30-35% of AML patients. We show graphdiyne oxide (GDYO), a member of two-dimensional carbon nanomaterials3, demonstrates an anti-leukemia effect in vitro and in vivo against AML cells with DNMT3A mutation specifically. Here, we used RNA-seq to depict transcriptome of AML cells with or without GDYO treatment.

2022-08-23 | GSE190871 | GEO

Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells [Bisulfite-Seq]

Project description:Acute myeloid leukemia (AML) is a fatal hematological malignancy for most patients, and DNA methyltransferase 3A (DNMT3A) mutations occur in about 30-35% of AML patients. We show graphdiyne oxide (GDYO), a member of two-dimensional carbon nanomaterials3, demonstrates an anti-leukemia effect in vitro and in vivo against AML cells with DNMT3A mutation specifically. Here, we used reduced representation bisulfite sequencing (RRBS) to depict DNA methylome of AML cells with or without GDYO treatment.

2022-08-23 | GSE190873 | GEO

Graphdiyne oxide nanosheets display anti-leukemia efficacy specifically against DNMT3A-mutant AML cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-08-23 | GSE190874 | GEO

Graphdiyne oxide nanosheets display selective anti-leukemia efficacy against DNMT3A-mutant AML cells.

Project description:DNA methyltransferase 3 A (DNMT3A) is the most frequently mutated gene in acute myeloid leukemia (AML). Although chemotherapy agents have improved outcomes for DNMT3A-mutant AML patients, there is still no targeted therapy highlighting the need for further study of how DNMT3A mutations affect AML phenotype. Here, we demonstrate that cell adhesion-related genes are predominantly enriched in DNMT3A-mutant AML cells and identify that graphdiyne oxide (GDYO) display an anti-leukemia effect specifically against these mutated cells. Mechanistically, GDYO directly interacts with integrin β2 (ITGB2) and c-type mannose receptor (MRC2), which facilitate the attachment and cellular uptake of GDYO. Furthermore, GDYO binds to actin and prevents actin polymerization, thus disrupting the actin cytoskeleton and eventually leading to cell apoptosis. Finally, we validate the in vivo safety and therapeutic potential of GDYO against DNMT3A-mutant AML cells. Collectively, these findings demonstrate that GDYO is an efficient and specific drug candidate against DNMT3A-mutant AML.

| S-EPMC9512932 | biostudies-literature

The N-terminal region of DNMT3A combines multiple chromatin reading motifs to guide recruitment

Project description:DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns. However, the mechanisms underlying DNMT3A recruitment to and function within different chromatin environments remain unclear. Using a combination of biochemical and structural approaches we find that DNMT3A interacts using multiple interfaces with chromatin; directly binding generic nucleosome features as well as site-specific post-translational histone modifications. The N-terminal region, unique to the DNMT3A1 isoform, is essential for these interactions and stabilises H3K36me2-nucleosome recruitment. Intriguingly, in the same region critical for nucleosome binding we also map a ubiquitylation-dependent recruitment motif (UDR). The UDR binds specifically to ubiquitylated H2AK119, explaining the previously observed recruitment to Polycomb-occupied heterochromatin. A cryo-EM structure of DNMT3A1-DNMT3L with a modified nucleosome reveals that the UDR interacts with the nucleosome surface including the acidic patch. Previously unexplained disease-associated mutations are present in the UDR and ablate nucleosome interactions. This leads to an increased understanding of how DNMT3A1 recruitment occurs in the genome and highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome.

2024-10-16 | PXD056554 | Pride

Sarcoma Cell-specific Radiation Sensitization by Titanate Scrolled Nanosheets: Insights from Physicochemical Analysis and Transcriptomic Profiling

Project description:The objective of this in vitro study was to explore the potential of Titanate Scrolled Nanosheets (TNs) in improving the radiation sensitivity of sarcoma cell lines. Enhancing the response of cancer cells to radiation therapy is crucial, and one promising approach involves utilizing metal oxide nanoparticles. We focused on investigating the impact of exposing two human sarcoma cell lines to TNs and ionizing radiation (IR). Our research was prompted by previous in vitro toxicity assessments, revealing a correlation between TNs' toxicity and alterations in intracellular calcium homeostasis. TNs were synthesized via a hydrothermal process using titanium dioxide powder in alkaline solution. Our study quantified the intracellular content of TNs and analyzed their impact on radiation-induced responses. This assessment encompassed PIXE analysis, cell proliferation and transcriptomic analysis. We observed that sarcoma cells internalized TNs, causing alterations in intracellular calcium homeostasis. Irradiation was also found to influence intracellular calcium levels. Transcriptomic analysis revealed marked disparities in the gene expression patterns between the two sarcoma cell lines, suggesting a potential cell-line-dependent nano-sensitization to IR. These results significantly advance our comprehension of the interplay between TNs, IR, and cancer cells, promising potential enhancement of the radiation therapy efficacy.

2024-02-14 | GSE248011 | GEO

The interaction between DNMT3A with H3Kc36me2 modified nucleosomes

Project description:DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns, essential for the dynamic organization of vertebrate genomes. However, the mechanisms underlying DNMT3A1's recruitment and function within different chromatin environments remain unclear. We find that DNMT3A interacts with modified nucleosomes through multivalent interactions, involving both direct binding to chromatin features and site-specific post-translational histone modifications.

2024-12-07 | PXD046529 | Pride

Mouse lung tumor tissue: Dnmt3a KO vs. Dnmt3a WT

Project description:Transcriptional profiling of mouse lung tumors comparing Dnmt3a KO/K-ras G12D mutant with Dnmt3a WT/K-ras G12D mutant. The goal is to search for the difference of mRNA abundance between Dnmt3a KO and WT tumors. Two-condition experiment, KO vs. WT tissure. Biological replicates: 12.

2011-10-25 | E-GEOD-32415 | biostudies-arrayexpress

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