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Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [ChIP-seq]

ABSTRACT: Fatty acid homeostasis is critical for normal cellular physiology and leads to severe diseases when deregulated. Here we report Nucleoside-Diphosphate Kinase 1 and 2 (NME1/2) as major cellular co-enzyme A (CoA) and acetyl-CoA binding proteins and negative regulators of de novo lipogenesis (DNL). Structural studies demonstrate that Nme1 recognizes CoA through its nucleotide moiety, which competes for binding with ADP/ATP. By using a Nme2 ko mouse model, we observe that NME2 is required for the gene transcriptional response to a high fat diet (HFD) in liver cells, leading to a repression of lipogenesis and the activation of a protective gene response. Nme2 ko mice submitted to a HFD challenge are unable to repress key lipogenic genes, resulting in an excessive triglyceride synthesis and liver steatosis. Mechanistically, the NME2-dependent down-regulation of DNL in response to HFD changes the balance for the use of acetyl-CoA between the competing paths of acetylation and DNL, thereby increasing TSS-targeted histone acetylation and gene activation. A structure-guided generation of a NME1 mutant, with intact NDK activity, but unable to bind CoA, directly demonstrates the functional impact of acetyl-CoA/CoA binding by NME1/2 in repressing DNL. Taken together, these findings highlight a yet unknow protective liver response to HFD, regulated by multi-ligand binding proteins which act as direct sensors for the cellular levels of NDP/NTP and CoA/acetyl-CoA.

ORGANISM(S): Mus musculus

PROVIDER: GSE198687 | GEO | 2023/08/01

REPOSITORIES: GEO

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Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [RNA-seq]

Project description:Fatty acid homeostasis is critical for normal cellular physiology and leads to severe diseases when deregulated. Here we report Nucleoside-Diphosphate Kinase 1 and 2 (NME1/2) as major cellular co-enzyme A (CoA) and acetyl-CoA binding proteins and negative regulators of de novo lipogenesis (DNL). Structural studies demonstrate that Nme1 recognizes CoA through its nucleotide moiety, which competes for binding with ADP/ATP. By using a Nme2 ko mouse model, we observe that NME2 is required for the gene transcriptional response to a high fat diet (HFD) in liver cells, leading to a repression of lipogenesis and the activation of a protective gene response. Nme2 ko mice submitted to a HFD challenge are unable to repress key lipogenic genes, resulting in an excessive triglyceride synthesis and liver steatosis. Mechanistically, the NME2-dependent down-regulation of DNL in response to HFD changes the balance for the use of acetyl-CoA between the competing paths of acetylation and DNL, thereby increasing TSS-targeted histone acetylation and gene activation. A structure-guided generation of a NME1 mutant, with intact NDK activity, but unable to bind CoA, directly demonstrates the functional impact of acetyl-CoA/CoA binding by NME1/2 in repressing DNL. Taken together, these findings highlight a yet unknow protective liver response to HFD, regulated by multi-ligand binding proteins which act as direct sensors for the cellular levels of NDP/NTP and CoA/acetyl-CoA.

2023-08-01 | GSE198686 | GEO

Expression data from livers of high fat fed rats treated with ACC inhibitor PF-04923503

Project description:Fundamental alterations in lipid metabolism including increased rates of de novo lipogenesis (DNL), reduced fatty acid oxidation (FAOX) and ectopic lipid accumulation in skeletal muscle and liver are characteristic of type 2 diabetes mellitus (T2DM) and have been hypothesized to directly contribute to the molecular pathogenesis of the disease. Acetyl-CoA carboxylase (ACC) catalyzes the formation of malonyl-CoA, the rate limiting substrate for DML and key regulator of FAOX. ACC inhibitors have the potential to pharmacologically rebalance these metabolic alterations. In the present study, PF-04923503, a potent dual ACC1/ACC2 inhibitor with properties optimized for in vivo studies, suppressed levels of malonyl-CoA in primary hepatocytes, rat skeletal muscle ex vivo, as well as rat liver and skeletal muscle in vivo. This impact on malonyl-CoA was directly correlated (r2>0.9) with reduced hepatic DNL and inversely correlated with incresed rates of FAOX (r2>0.9). The pharmacological eccfect of PF-04923503 persisted with chronic treatment. High-fat fed rats treated with PF-04923503 for six weeks showed dose-dependent reductions in skeletal muscle and liver lipid accumulation. These changes correlated directly with markers for improved insulin sensitization. However, liver gene expression indicates that pharmacological inhibition results in compensation by up-regualtion of genes involved with DNL. These results suggest that pharmacological inhibition of ACC may have utility to help rebalance metabolic abnormalities in T2DM and improve insulin sensitivity. Differential gene expression was assessed by Affymetrix microarray experiments for 15 liver samples across 3 pharmacological treatment groups (vehicle control 0.5% methylcellulose had 5 samples, PF-04923503 10mpk had 5 samples, PF-04923503 30mpk had 5 samples)

2011-06-30 | E-GEOD-28058 | biostudies-arrayexpress

A bacteria-derived tetramerized protein ameliorates nonalcoholic steatohepatitis (NASH) in mice via binding and relocating acetyl-coA carboxylase

Project description:Increased de novo lipogenesis (DNL) is a major feature of nonalcoholic steatohepatitis (NASH). None of the drug targeting the catalytic activity of acetyl-CoA carboxylase (ACC), the rate-limiting enzyme in the DNL process, has been approved by FDA. Whether cytosolic ACC1 can be regulated spatially is unknown. Herein, we found that streptavidin, which is a bacterium derived tetrameric protein, forms cytosolic condensates and efficiently induce a spatial re-localization of ACC1 in liver cells, concomitant with inhibited lipid accumulation. Both SA tetrameric structure and multivalent protein interaction are required for condensates formation. Interestingly, the condensates are further characterized as gel-like membraneless organelle (SAGMO) and significantly restrict the cytosolic dispersion of ACC1 and fatty acid synthase (FASN). Notably, AAV mediated delivery of SA partially blocks mice liver DNL and ameliorate NASH without eliciting hypertriglyceridemia. In summary, our study demonstrates that insulating lipogenesis-related proteins by SAGMO might be effective for NASH treatment.

2023-10-25 | GSE245797 | GEO

Nucleoside-Diphosphate Kinase 1 and 2 (Nme1/2) are major cellular co-enzyme A/acetyl-CoA binding factors

Project description:Co-enzyme A is the essential cellular carrier of the acetyl group, largely used in fatty acid synthesis and lysine post-translational modifications of proteins. Following the analysis of the cellular CoA-binding proteome, we identified Nme1/2 as major abundant cytoplasmic CoA-binding proteins. We report a novel mechanism that controls fatty acids synthesis involving ATP-dependent acetyl-CoA binding by Nucleoside Diphosphate Kinases 1 and 2 (Nme1/2).

2023-08-01 | PXD029159 | Pride

Expression data from livers of high fat fed rats treated with ACC inhibitor PF-04923503

2011-06-30 | GSE28058 | GEO

Extracellular Vesicle-Mediated Metastasis Suppressors NME1 and NME2 Modify Lipid Metabolism in Fibroblasts

Project description:Our aim was to understand how vesicular NME1 and NME2 released by breast cancer cells influence the tumour microenvironment. As a model, we used human invasive breast carcinoma cells overexpressing NME1 or NME2, and first analysed in detail the presence of both isoforms in EV subtypes by capillaryWestern immunoassay (WES) and immunoelectron microscopy. Data obtained by both methods showed that NME1 was present in medium-sized EVs or microvesicles, whereas NME2 was abundant in both microvesicles and small-sized EVs or exosomes. Next, human skin-derived fibroblasts were treated with NME1 or NME2 containing EVs, and subsequently mRNA expression changes in fibroblasts were examined. RNAseq results showed that the expression of fatty acid and cholesterol metabolism-related genes was decreased significantly in response to NME1 or NME2 containing EV treatment. We found that FASN (fatty acid synthase) and ACSS2 (acyl-coenzyme A synthetase short-chain family member 2), related to fatty acid synthesis and oxidation, were underexpressed in NME1/2-EV-treated fibroblasts. Our data show an emerging link between NME-containing EVs and regulation of tumour metabolism.

2022-08-21 | GSE211556 | GEO

Analysis of Wild Type and hepatocyte-specific CD36 knockout (CD36LKO) mice liver Transcriptomes under high fat diet (HFD)

Project description:We generated hepatocyte-specific CD36 knockout (CD36LKO) mice to study in vivo effects of CD36 on de novo lipogenesis (DNL) under high fat diet (HFD). Lipid deposition and DNL were analyzed in primary hepatocytes isolated from CD36LKO mice or HepG2 cells with CD36 overexpression. RNA-sequence, co-immunoprecipitation and proximity ligation assay were carried out to determine its role in regulating DNL. Results: Hepatic CD36 expression was upregulated in NAFLD mice and patients, and CD36LKO mice exhibited attenuated HFD-induced hepatic steatosis and insulin resistance. We identified hepatocyte CD36 as a key regulator for DNL in the liver. Sterol regulatory element-binding protein 1 (SREBP1) and its downstream lipogenic enzymes such as FASN, ACCα and ACLY were significantly downregulated in the liver of HFD-fed CD36LKO mice, whereas overexpression CD36 stimulated insulin-mediated DNL and lipid droplet formation in vitro. Mechanistically, CD36 was activated by insulin and formed a complex with insulin induced gene-2 (INSIG2), that disrupts the interaction between SREBP cleavage-activating protein (SCAP) and INSIG2, thereby leading to the translocation of SREBP1 from ER to Golgi for processing. Furthermore, treatment with 25-hydroxycholesterol or betulin, molecules shown to enhance SCAP/INSIG interaction, reversed the effects of CD36 on SREBP1 cleavage.

2022-01-03 | GSE191059 | GEO

BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-seq Fat)

Project description:Glucose and fat metabolism are tightly interconnected where endogenous de novo lipogenesis (DNL) serves to convert carbohydrates directly into lipids. Here, we explored the role of the long isoform Brd4 as a key transcriptional co-activator in lipogenesis. As a member of the Bromo-extraterminal (BET) protein family, Brd4 is characterized by two tandem bromodomains that bind acetylated lysine on both histone and non-histone proteins in chromatin. We found that treatment with MS417, a small molecule inhibitor of Brd4 binding to acetylated lysine, suppresses 3T3-L1 adipocyte differentiation. MS417-treated obese (ob/ob) mice displayed resistance to weight gain and loss of fat from steatotic livers. Comprehensive RNA-seq and ChIP-seq analyses delineate a Brd4-driven gene network required for glycolysis-lipogenesis flux that is shared between glycolytic liver and 3T3-L1 adipocytes, but absent in the non-glycolytic white abdominal fat. Our data further reveal that Brd4 functions to provide specific metabolic resources, such as acetyl-CoA and nicotinamide adenine dinucleotide (NAD) cofactors, in cell types utilizing DNL. Collectively, these findings provide a novel view of the critical role Brd4 plays in orchestrating transcription of a network of genes directing metabolic pathways governing carbohydrate fueled lipid metabolism fundamental for controlling glucose homeostasis and body weight.

2018-03-31 | GSE59161 | GEO

BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-seq Liver)

2018-03-31 | GSE59160 | GEO

BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-Seq 3T3-L1)

2018-03-31 | GSE59159 | GEO