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YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [RIP-Seq]

ABSTRACT: YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [RIP-Seq]

PROVIDER: PRJNA850412 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19736833_1.fastq.gz	Fastqsanger.gz
	SRR19736833_2.fastq.gz	Fastqsanger.gz
	SRR19736834_1.fastq.gz	Fastqsanger.gz
	SRR19736834_2.fastq.gz	Fastqsanger.gz
	SRR19736835_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [RIP-Seq]

Project description:RNA N6-methyladenosine (m6A) modification is implicated in cancer progression. However, the impact of m6A on the antitumor effects of radiotherapy and the related mechanisms are unknown. Here we show that ionizing radiation (IR) induces immunosuppressive myeloid-derived suppressor cell (MDSC) expansion and YTHDF2 expression in both murine models and humans. Following IR, loss of Ythdf2 in myeloid cells augments antitumor immunity and overcomes tumor radioresistance by altering MDSC differentiation and inhibiting MDSC infiltration and suppressive function. The remodeling of the landscape of MDSC populations by local IR is reversed by Ythdf2 deficiency. IR-induced YTHDF2 expression relies on NF-κB signaling; YTHDF2 in turn leads to NF-κB activation by directly binding and degrading transcripts encoding negative regulators of NF-κB signaling, resulting in an IR-YTHDF2-NF-κB circuit. Pharmacological inhibition of YTHDF2 overcomes MDSC-induced immunosuppression and improves combined IR and/or anti-PD-L1 treatment. Thus, YTHDF2 is a promising target to improve radiotherapy (RT) and RT/immunotherapy combinations.

2023-04-28 | GSE206379 | GEO

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells

Project description:YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells

| PRJNA850417 | ENA

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [MeRIP-Seq]

2023-04-28 | GSE206384 | GEO

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [CITE-Seq]

2023-04-28 | GSE206381 | GEO

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [scRNA-Seq]

2023-04-28 | GSE206378 | GEO

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [scRNA-Seq]

Project description:YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [scRNA-Seq]

| PRJNA850413 | ENA

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [MeRIP-Seq]

Project description:YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [MeRIP-Seq]

| PRJNA850421 | ENA

YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [CITE-Seq]

Project description:YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [CITE-Seq]

| PRJNA850409 | ENA

Anti YTHDF2 RIP-seq to identify YTHDF2 target mRNAs in P0 mouse retinas

Project description:To identify the target mRNAs of the m6A reader protein YTHDF2, we carired out anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P0 wild type mouse retinas was pulled down by rabbit polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. To determine which gene is enriched, we computed the FPKM from RIP elute to input and any fold change greater than 2 was considered enriched. Finally, Biological replicates of anti-YTHDF2 RIP-Seq identified 1639 transcripts. This study provides a gene list which shows mRNA binding with YTHDF2 in mouse retina.

2022-03-15 | GSE145390 | GEO

Anti-YTHDF2 RIP-Seq to identify YTHDF2 target mRNAs in hippocampus

Project description:To identify the target mRNAs of the m6A reader protein YTHDF2 in mouse hippocampus, we carired out anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P40 wild type mouse hippocampus was pulled down by rabbit polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina Novaseq 6000. The filtered reads were aligned to the mouse reference genome (GRCm38) using BWA mem (v 0.7.12).Then the MACS2 (version 2.1.0) peak calling software was used to identify regions of IP enrichment over background, followed by the motif detected by Homer (Heinz et al., 2010). Peak related genes are then confirmed by PeakAnnotator. Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified. Finally, Biological replicates of anti-YTHDF2 RIP-Seq identified 408 mRNAs transcripts. This study provides gene lists which shows mRNA binding with YTHDF2 in mouse hippocampus.

2023-01-19 | GSE171791 | GEO

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