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Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer II

ABSTRACT: The m⁶A reader proteins YTHDF1–3 are key post-transcriptional regulators of m⁶A-modified transcripts in mammalian cells, and have emerged as critical contributors to the pathogenesis of triple-negative breast cancer (TNBC). Given their role in promoting tumorigenic phenotypes, YTHDF1–3 represent promising therapeutic targets. In this study, we identified ellagic acid (EA), a natural small molecule, as a pan-inhibitor of YTHDF proteins. To investigate the translational consequences of YTHDF inhibition, we performed ribosome profiling (Ribo-seq) to assess the global impact of EA on mRNA translation in TNBC cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE303590 | GEO | 2026/03/24

REPOSITORIES: GEO

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Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer I

Project description:The m⁶A reader proteins YTHDF1–3 are key post-transcriptional regulators of methylated transcripts and have been implicated in the progression of triple-negative breast cancer (TNBC). Owing to their roles in sustaining malignant phenotypes, YTHDF1–3 are attractive targets for therapeutic intervention. Here, we identify ellagic acid (EA), a naturally occurring polyphenol, as a pan-inhibitor of YTHDF proteins. To investigate the effect of YTHDF inhibition on mRNA stability, we performed RNA lifetime sequencing (RNA lifetime-seq) to profile transcriptome-wide RNA decay dynamics in EA-treated TNBC cells.

2026-03-24 | GSE303589 | GEO

RNA-seq analysis CARM1 inhibitor Ellagic acid effect on MDA-MB-231 cells

Project description:Ellagic acid is a kind of polyphenol lactone, which is widely found in various fruits and nuts. It’s the natural inhibitor of CARM1. Ellagic acid was reported to inhibit breast cancer growth and metastasis. But the mechanism of Ellagic acid has not been investivaged clearly in triple-negative breast cancer (TNBC). Our results indicate that direct inhibition of CDK4 by Ellagic acid limits breast cancer proliferation and metastasis. Our research has determined the molecular basis of Ellagic acid effect in TNBC, which may provide new ideas and drugs for cancer therapy.

2024-04-07 | GSE171618 | GEO

Dynamic O-GlcNAcylation of YTHDF proteins controls translation of m6A-modified mRNA

Project description:N6-methyladenosine (m6A) is the most abundant internal mRNA nucleotide modification in mammals, regulating critical aspects of cell physiology and differentiation. The YTHDF proteins are the primary readers of m6A modifications and exert physiological functions of m6A in the cytosol. Elucidating the regulatory mechanisms of YTHDF proteins is critical to understanding m6A biology. Here, we report a mechanism that protein post-translational modifications control the biological functions of the YTHDF proteins. We find that YTHDF1 and YTHDF3, but not YTHDF2, carry high levels of nutrient-sensing O-GlcNAc modifications. O-GlcNAc modification attenuates the translation promoting function of YTHDF1 and YTHDF3 by blocking their interactions with proteins associated with mRNA translation. We further demonstrate that O-GlcNAc modifications on YTHDF1 and YTHDF2 regulate the assembly, stability, and disassembly of stress granule, facilitating rapid exchange of m6A-modified mRNAs in stress granules for recovery from stress. Therefore, our results discover an important regulatory pathway of YTHDF functions, adding an additional layer of complexity to the post-transcriptional regulation function of mRNA m6A.

2023-08-31 | GSE216570 | GEO

Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer II

Project description:Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer II

| PRJNA1295890 | ENA

Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer I

Project description:Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer I

| PRJNA1295893 | ENA

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [Polysome]

Project description:N6-methyladenosine (m6A) plays critical roles in gene expression control by recruiting the cytoplasmic reader proteins YTHDF1,2 and 3. Recently, the function of YTHDF proteins and whether they bind to shared or distinct sets of methylated mRNAs in cells has been the subject of debate. Here, we developed TRIBE-STAMP, an approach for single-molecule detection of the target RNAs of two RNA binding proteins simultaneously in cells. Applying TRIBE-STAMP to the YTHDF proteins revealed that most target mRNAs are shared among the three YTHDF proteins. Surprisingly, we also found that individual mRNA molecules can be bound by more than one YTHDF protein throughout their lifetime. Furthermore, we show that YTHDF proteins bind sequentially to target methylated mRNAs, with YTHDF1 binding before YTHDF2 or YTHDF3. Our data reveal shared molecular interactions among the YTHDF proteins and support a model in which YTHDF1 and YTHDF3 are unlikely to promote rapid mRNA decay.

2022-10-28 | GSE201538 | GEO

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [TRIBE_STAMP]

2022-10-28 | GSE200712 | GEO

Single-molecule analysis of RNA:protein interactions reveals sequential binding of different YTHDF proteins to the same mRNA molecules [RIP-Seq]

2022-10-28 | GSE201540 | GEO

Transcriptome Analysis of Signaling Pathways Targeted by Ellagic Acid in Hepatocellular Carcinoma Cells

Project description:Ellagic acid (EA) possesses prominent inhibitory activities against various cancers, including hepatocellular carcinoma (HCC). Recent study showing EA’s activities in suppressing HCC cell proliferation and tumor formation, we further demonstrate that EA reduces cell viability, and induces DNA damage and cell cycle arrest at G1 phase. Employing RNA-Seq, we identified 5765 differentially expressed genes (DEGs) encoding proteins with over 2.0-fold change in EA-treated HepG2 cells. Following Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, the DEGs caused by EA treatment showed significant enrichment in pathways regulating DNA replication and cell cycle progression. Consistently, integrative analyses of this RNA-seq dataset with a TCGA-LIHC dataset derived from HCC patients confirmed these two pathways as EA’s primary targets. Furthermore, we identified p21 as a primary target gene of EA using the interaction network analysis of the DEGs regulating these pathways. Consistent with the results of our bioinformatic analyses, p21 knockdown desensitized four different liver cancer cell lines to EA treatment. Collectively, our study demonstrated that EA primarily targeted the G1/S phase checkpoint and DNA synthesis to inhibit HCC cell proliferation.

2021-04-02 | GSE171311 | GEO

Ellagic Acid Enhances Longevity and Healthspan in Caenorhabditis elegans via Insulin/IGF-1 Signaling Pathway

Project description:The role of ellagic acid (EA), a natural antioxidant, in regulating anti-aging and its underlying mechanisms remains unclear. In this study, we investigated the anti-aging effects and molecular mechanisms of EA in Caenorhabditis elegans (C. elegans). Our results demonstrate that EA extends the lifespan of C. elegans, enhances motility, reduces lipofuscin accumulation, and improves overall healthspan. Additionally, EA reduces reactive oxygen species (ROS) accumulation in C. elegans under conditions of heat and oxidative stress. The insulin/IGF-1 signaling (IIS) pathway, a key regulator of longevity and stress resistance in C. elegans, was found to mediate EA's effects. EA treatment did not extend the lifespan of mutants defective in daf-2, daf-16, hsf-1, hlh-30, and skn-1, confirming that EA’s lifespan-extending effect operates through the IIS pathway. Furthermore, EA treatment increased the expression of stress response genes downstream of the IIS pathway. Based on RNA sequencing data, we further explored the molecular mechanisms and potential regulatory roles of EA in anti-aging.

2025-05-10 | GSE295741 | GEO

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