Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of FAD subtypes in mouse HCC models

ABSTRACT: In this study, we identified and validated a molecular classification of hepatocellular carcinoma (HCC) based on 42 fatty acid degradation (FAD) genes in clinical samples. We further searched PubMed for the RNA sequencing datasets of mouse models to identify the FAD subtypes in mouse HCC models. A total of 90 samples were collected from five publicly available datasets including 11 mouse HCC models. In addition, the transcriptome sequencing data of 8 samples from our two mouse models (NRAS.MYC.ND and AKT1.MYC.KD) were also included. This dataset aims to explore the transcriptomic characteristics of these two models.

ORGANISM(S): Mus musculus

PROVIDER: GSE202070 | GEO | 2023/05/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of FAD subtypes in mouse HCC models

Project description:Identification of FAD subtypes in mouse HCC models

| PRJNA834137 | ENA

The landscape of immune cells in the mouse HCC model with F1 and F3 subtype

Project description:In this study, we identified and validated a molecular classification of hepatocellular carcinoma (HCC) patients based on 42 fatty acid degradation (FAD) genes. The F1 subtype was characterized by the lowest expression of FAD genes, whereas F3 subtype had the highest expression levels, and F2 had the intermediate expression levels of FAD genes. We characterized the immune microenvironment in HCC patients from different FAD subtypes. To further explore the immune landscape of HCC, we generated the Nras-driven HCC model (belonging to the F1 subtype) and the Akt1-driven HCC model (belonging to the F3 subtype) by hydrodynamic tail vein injection (HTVi) of oncogenes together with the sleeping beauty transposase. The tumor tissues were resected from the liver 14 weeks after the hydrodynamic delivery of the plasmids, isolated for single cells, and prepared for scRNA-seq.

2023-05-01 | GSE202071 | GEO

Hepatitis C virus RNA is 5’ flavin adenine dinucleotide (FAD) capped

Project description:RNA viruses have developed elaborate strategies for 5’ capping and protection of their genomes. However, so far no 5’ RNA cap has been identified for Hepatitis C virus (HCV), which cause chronic infection, liver cirrhosis and cancer in humans4. Here, we demonstrate that the cellular metabolite flavin adenine dinucleotide (FAD) is used as noncanonical initiating nucleotide by the viral RNA-dependent RNA polymerase resulting in a 5’ FAD cap on the HCV RNA. FAD capping is completely conserved for the HCV replication intermediate negative RNA strand and partially for the positive RNA strand. The prototype strain J6/JFH1 RNA is FAD capped when isolated from the liver and serum of a human liver chimeric mouse model and in vitro the FAD capping frequency is ~75 %, which is the highest metabolite RNA capping frequency observed. Furthermore, we show that 5’ FAD capping protects RNA from cell-intrinsic innate immune recognition but has limited effect on HCV RNA stability. These results establish capping with cellular metabolites, such as FAD, as a novel viral RNA capping and immune evasion strategy, which potentially could be used by many viruses for protection of their intermediate RNA strands and thereby affect viral treatment outcomes and persistency.

2022-07-31 | GSE180956 | GEO

Neuronal expression of Alzheimer's disease-associated FAD mouse genotype at 3/6/12 months

Project description:Neuronal expression of Alzheimer's disease-associated FAD mouse genotype at 3/6/12 months.

2019-12-04 | GSE140286 | GEO

Transcriptome analysis using Arabidopsis leaves after exogenous FAD treatment

Project description:Riboflavin (RF) and its cofactors (FMN and FAD) are essential molecules for vital metabolic processes in all organisms. Thus, the flavin metabolism must be tightly regulated in the cells. We previously demonstrated that the intracellular levels of flavins were tightly maintained by the enzymes involved in their synthesis and degradation, inducing a plastidic FAD hydrolase (AtNUDX23), in Arabidopsis. However, information of regulatory factors involved in the flavin homeostasis and transporters in each organelle are mostly limited. Terefore, we tried to identify novel factors involved in the flavin metabolism, such as transcription factors and transporters by a transcriptome analysis after exogenous FAD treatment.

2021-03-18 | GSE169061 | GEO

Pseudomonas sp. ZH-FAD

Project description:Pseudomonas sp. ZH-FAD Genome sequencing and assembly

| PRJNA417872 | ENA

Bacillus amyloliquefaciens strain:Fad 108

Project description:Bacillus amyloliquefaciens strain:Fad 108 Genome sequencing

| PRJNA1066400 | ENA

The interactome of flavin adenine dinucleotide (FAD) with RNA-binding proteins

Project description:We explored the interactome of flavin adenine dinucleotide (FAD) and the matrix of UV-immobilised FAD bound more than 3,000 proteins from SW-620 lysate. GO enrichment analysis showed that about 600 RNA-binding proteins were bound to FAD beads and, surprisingly, more than 40 proteins showed clear dose-dependent binding competition with nanomolar affinities indicating that their direct or indirect interaction with free FAD is both specific and strong. Among the few known consensus sequences for RNA-binding proteins, we selected the PUF motif 5'-UGUANAUA-3' to investigate whether FAD is binding the Pumilio homologs PUM1 and PUM2 in their RNA-binding pocket, as both these proteins showed dose-response behaviour in the FAD versus FAD-beads. Immobilisation of an oligomer containing the consensus sequence on NHS-activated Sepharose beads yielded PUM-beads that did enrich the Pumilio homologs. Oligomer vs FAD-beads and FAD vs PUM-beads together with the FAD vs FAD-beads dose-response competition indicated that the binding of FAD does not seem to influence the binding of the RNA. It is therefore most likely that FAD binding is allosteric for PUMs.

2022-10-06 | PXD036953 | Pride

Cancer cell genetics shaping of the tumor microenvironmentreveals myeloid cell-centric exploitable vulnerabilities in hepatocellular carcinoma [WES 2]

Project description:Hepatocellular carcinoma (HCC) is a highly heterogenous disease associated with an equally dynamic tumor microenvironment (TME). We generated somatic HCC mouse models bearing clinically-relevant oncogenic driver combinations that faithfully recapitulated different human HCC subclasses. Using WES data, we explored the tumor mutation frequencies between models and compared them with human datasets.

2024-02-22 | GSE234897 | GEO

Cancer cell genetics shaping of the tumor microenvironment reveals myeloid cell-centric exploitable vulnerabilities in hepatocellular carcinoma [WES]

2024-04-27 | GSE216716 | GEO