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Acetylcytidine modification of DDX41 and ZNF746 by N-acetyltransferase 10 contributes to chemoresistance of melanoma

ABSTRACT: Acetylcytidine modification of DDX41 and ZNF746 by N-acetyltransferase 10 contributes to chemoresistance of melanoma

PROVIDER: PRJNA1124148 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29420264.fastq.gz	Fastqsanger.gz
	SRR29420265.fastq.gz	Fastqsanger.gz

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Acetylcytidine modification of DDX41 and ZNF746 by N-acetyltransferase 10 contributes to chemoresistance of melanoma

Project description:We performed RNA-seq to analyse the different expression genes of DTIC-resistant (DR) A375 cells and wild-type control.

2024-09-13 | GSE269940 | GEO

Inherited and somatic defects in DDX41 in myeloid neoplasms

Project description:Most cases of adult myeloid neoplasms are routinely assumed to be sporadic. Here, we describe an adult familial acute myeloid leukemia (AML) syndrome caused by germline mutations in the DEAD/H-Box helicase gene DDX41. DDX41 was also found to be affected by somatic mutations in sporadic cases of myeloid neoplasms as well as in a biallelic fashion in 50% of patients with germline DDX41 mutations. Moreover, corresponding deletions on 5q35.3 present in 6% of cases lead to haploinsufficient DDX41 expression. DDX41 lesions caused altered pre-mRNA splicing and RNA processing. DDX41 is exemplary of other RNA helicase genes also affected by somatic mutations, suggesting that they constitute a family of tumor suppressor genes. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples.

2015-04-01 | E-GEOD-66668 | biostudies-arrayexpress

N4-acetylcytidine of Nop2 mRNA is Required to the Transition of Morula-to-Blastocyst

Project description:N-acetyltransferase 10 (NAT10)-mediated N4-acetylcytidine (ac4C) modification is crucial for mRNA stability and translation efficiency, yet the underlying function in mammalian preimplantation embryos remains unclear.

2023-07-17 | GSE236943 | GEO

NAT10-mediated N4-acetylcytidine of RNA Contributes to Post-transcriptional Regulation of Mouse Oocyte Maturation In Vitro

Project description:N4-acetylcytidine (ac4C), a newly identified epigenetic modification within mRNAs, has been characterized as a crucial regulator of mRNA stability and translation efficiency. And NAT10 is the only known RNA acetyltransferase. In our study, we documented the down-regulated expression of both ac4C and NAT10 during meiotic maturation of mouse oocytes. NAT10 knockdown resulted in ac4C reduction and impaired mouse oocyte maturation in vitro. These results indicated that NAT10-mediated ac4C modification plays a critical regulatory role in oocyte meiotic maturation. We further performed high-throughput sequencing with NAT10-overexpressed HEK293T cells and NAT10-binding transcripts to investigate the genes modulated by NAT10-mediated ac4C modification.

2021-07-11 | GSE179429 | GEO

Histone N-terminal acetyltransferase NAA40 links one-carbon metabolism to chemoresistance

Project description:Histone N-terminal acetyltransferase NAA40 links one-carbon metabolism to chemoresistance

| PRJNA704699 | ENA

Inherited and somatic defects in DDX41 in myeloid neoplasms

2015-04-01 | GSE66668 | GEO

R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instabilityR-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability

Project description:Transcription can pose a threat to genomic stability through the formation of R-loops that obstruct the progression of replication forks. R-loops are three-stranded nucleic acid structures formed by an RNA-DNA hybrid with a displaced non-template DNA strand. We developed RDProx to identify proteins that regulate R-loops in human cells. RDProx relies on the expression of the hybrid-binding domain (HBD) of Ribonuclease H1 (RNaseH1) fused to the ascorbate peroxidase (APEX2), which permits mapping of the R-loop proximal proteome using quantitative mass spectrometry. We associated R-loop regulation with different cellular proteins and identified a role of the tumor suppressor DEAD box protein 41 (DDX41) in opposing R-loop-dependent genomic instability. Depletion of DDX41 resulted in replication stress, double strand breaks and increased inflammatory signaling. Furthermore, DDX41 opposes accumulation of R-loops at gene promoters and its loss leads to upregulated expression of TGFβ and NOTCH signaling genes. Germline loss-of-function mutations in DDX41 lead to predisposition to acute myeloid leukemia (AML) in adulthood. We propose that accumulation of co-transcriptional R-loops, associated gene expression changes and inflammatory response contribute to the development of familial AML with mutated DDX41.

2021-11-25 | PXD024517 | Pride

Comparative expression study regarding leukemia samples with DDX41 mutation

Project description:Genetic expression profiling (GEP) has previously proven useful in B-ALL for identifying signatures of oncogenes, with the recognition of novel subgroups, as well as with outcome. Therefore, we adopted GEP of bonemarrow samples of B-ALL with t(9;22) to uncover the contribution of DDX41 to leukemogenesis. The germline mutations of DDX41, also known as DEAD box RNA helicase 41, have been found in about 1.5% of myeloid neoplasms (MNs). Development of MDS/AML is relatively common in germline DDX41 mutations. However, a variety of hematological malignancies (HMs) have been reported. We report a novel case of bi-alleleic DDX41 mutations in B-cell lymphoblastic leukemia (B-ALL), with unusual location of DDX41 mutations. The gene expression profile (GEP) of Ph+ B-ALL with bi-alleleic DDX41 mutations showed heterogeneously transitional GEP and altered gene expression levels of genes involved in the process essential for red blood cells and myeloid cell differentiation were noted. We report that DDX41 mutations are unusual but can be an underlying event in Ph+B-ALL and screening DDX41 mutations can be also informative for patients awaiting for haploidentical stem cell transplantation and choosing the therapy.

2022-02-07 | GSE196107 | GEO

DDX41 inhibits cancer cell proliferation and regulates immune response expression

Project description:DDX41, a member of the DEXDc family of helicases and an innate immune protein, senses cytosolic DNA and bacterial secondary messengers and initiates signaling via the adaptor STING to induce type 1 interferon (IFN) response in dendritic cells. However, DDX41 function in tumor progression is poorly understood. Here we found that the DDX41 inhibited proliferation and promoted apoptosis, reported the whole transcriptome profiling in HeLa cells. RNA-seq analyses revealed that the overexpression of DDX41 resulted in 959 genes being differentially expressed (504 up-regulated and 455 down-regulated) compared to the control in HeLa cells. Interestingly, functional clustering pathway enrichment analysis of transcription identified antigen processing and presentation pathways were significantly activated in DDX41 overexpression samples, but alternative splicing enriched in the epidermal growth factor receptor signaling pathway and fibroblast growth factor receptor signaling pathway. The five antigen processing and processing genes, which could regulate cross-presentation of antigens and protective antitumor immune responses, were significantly upregulated, suggesting DDX41 is the key player in tumor immunity. In conclusion, our RNA-seq data identified molecules and pathways involved in the mechanisms of DDX41 that adds to the understanding of critical DDX41 tumorigenesis functions.

2021-02-10 | GSE122986 | GEO

Histone N-terminal acetyltransferase NAA40 links one-carbon metabolism to chemoresistance

Project description:Epigenetic regulation and metabolism are highly interconnected, but it remains unclear if this interplay is harnessed by cancer cells to evade chemotherapy. Here, using transcriptomic and metabolomic analysis in colorectal cancer cells, we demonstrate that N-alpha-acetyltransferase 40 (NAA40), which catalyzes N-terminal acetylation of histones H4 and H2A, controls the expression of key one-carbon metabolic enzymes and the abundance of corresponding metabolites. Specifically, we show that NAA40 deficiency induces the methionine cycle thereby increasing global histone methylation and attenuates transcription of the metabolic gene thymidylate synthase (TYMS) whose product is targeted by 5-fluorouracil (5-FU). Accordingly, we show that NAA40 activates TYMS by preventing deposition of H2A/H4S1ph at the nuclear periphery and confers resistance against the antimetabolite 5-FU in vitro and in xenografts. Consistently, in primary tumours NAA40 expression associates with TYMS levels and poorer 5-FU response. Overall these findings define a novel role for NAA40 in controlling cellular metabolism and chemoresistance.

2021-11-15 | GSE167474 | GEO

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