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1.
Molecules ; 29(9)2024 Apr 27.
Article in English | MEDLINE | ID: mdl-38731514

ABSTRACT

While FXR has shown promise in regulating bile acid synthesis and maintaining glucose and lipid homeostasis, undesired side effects have been observed in clinical trials. To address this issue, the development of intestinally restricted FXR modulators has gained attention as a new avenue for drug design with the potential for safer systematic effects. Our review examines all currently known intestinally restricted FXR ligands and provides insights into the steps taken to enhance intestinal selectivity.


Subject(s)
Receptors, Cytoplasmic and Nuclear , Humans , Receptors, Cytoplasmic and Nuclear/metabolism , Ligands , Animals , Bile Acids and Salts/metabolism , Bile Acids and Salts/chemistry , Intestinal Mucosa/metabolism , Intestinal Mucosa/drug effects , Intestines/drug effects
2.
J Cell Mol Med ; 28(10): e18409, 2024 May.
Article in English | MEDLINE | ID: mdl-38769917

ABSTRACT

Farnesoid X receptor (FXR), a ligand-activated transcription factor, plays an important role in maintaining water homeostasis by up-regulating aquaporin 2 (AQP2) expression in renal medullary collecting ducts; however, its role in the survival of renal medullary interstitial cells (RMICs) under hypertonic conditions remains unclear. We cultured primary mouse RMICs and found that the FXR was expressed constitutively in RMICs, and that its expression was significantly up-regulated at both mRNA and protein levels by hypertonic stress. Using luciferase and ChIP assays, we found a potential binding site of nuclear factor kappa-B (NF-κB) located in the FXR gene promoter which can be bound and activated by NF-κB. Moreover, hypertonic stress-induced cell death in RMICs was significantly attenuated by FXR activation but worsened by FXR inhibition. Furthermore, FXR increased the expression and nuclear translocation of hypertonicity-induced tonicity-responsive enhance-binding protein (TonEBP), the expressions of its downstream target gene sodium myo-inositol transporter (SMIT), and heat shock protein 70 (HSP70). The present study demonstrates that the NF-κB/FXR/TonEBP pathway protects RMICs against hypertonic stress.


Subject(s)
Kidney Medulla , NF-kappa B , Signal Transduction , Animals , NF-kappa B/metabolism , Mice , Kidney Medulla/metabolism , Kidney Medulla/cytology , Osmotic Pressure , Aquaporin 2/metabolism , Aquaporin 2/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Male , Mice, Inbred C57BL , HSP70 Heat-Shock Proteins/metabolism , HSP70 Heat-Shock Proteins/genetics , Promoter Regions, Genetic , Cells, Cultured , Gene Expression Regulation , Symporters/metabolism , Symporters/genetics , Receptors, Cytoplasmic and Nuclear
3.
Curr Rev Clin Exp Pharmacol ; 19(3): 225-233, 2024.
Article in English | MEDLINE | ID: mdl-38708917

ABSTRACT

Farnesoid X receptor (FXR) was identified as an orphan nuclear receptor resembling the steroid receptor in the late '90s. Activation of FXR is a crucial step in many physiological functions of the liver. A vital role of FXR is impacting the amount of bile acids in the hepatocytes, which it performs by reducing bile acid synthesis, stimulating the bile salt export pump, and inhibiting its enterohepatic circulation, thus protecting the hepatocytes against the toxic accumulation of bile acids. Furthermore, FXR mediates bile acid biotransformation in the intestine, liver regeneration, glucose hemostasis, and lipid metabolism. In this review, we first discuss the mechanisms of the disparate pleiotropic actions of FXR agonists. We then delve into the pharmacokinetics of Obeticholic acid (OCA), the first-in-class selective, potent FXR agonist. We additionally discuss the clinical journey of OCA in humans, its current evidence in various human diseases, and its plausible roles in the future.


Subject(s)
Chenodeoxycholic Acid , Chenodeoxycholic Acid/analogs & derivatives , Receptors, Cytoplasmic and Nuclear , Humans , Receptors, Cytoplasmic and Nuclear/agonists , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/drug effects , Chenodeoxycholic Acid/pharmacology , Chenodeoxycholic Acid/therapeutic use , Animals , Bile Acids and Salts/metabolism , Lipid Metabolism/drug effects , Liver/metabolism , Liver/drug effects
4.
J Exp Clin Cancer Res ; 43(1): 148, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38773631

ABSTRACT

BACKGROUND: Primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) are distinct hematological malignancies of B-cell origin that share many biological, molecular, and clinical characteristics. In particular, the JAK/STAT signaling pathway is a driver of tumor development due to multiple recurrent mutations, particularly in STAT6. Furthermore, the XPO1 gene that encodes exportin 1 (XPO1) shows a frequent point mutation (E571K) resulting in an altered export of hundreds of cargo proteins, which may impact the success of future therapies in PMBL and cHL. Therefore, targeted therapies have been envisioned for these signaling pathways and mutations. METHODS: To identify novel molecular targets that could overcome the treatment resistance that occurs in PMBL and cHL patients, we have explored the efficacy of a first-in-class HSP110 inhibitor (iHSP110-33) alone and in combination with selinexor, a XPO1 specific inhibitor, both in vitro and in vivo. RESULTS: We show that iHSP110-33 decreased the survival of several PMBL and cHL cell lines and the size of tumor xenografts. We demonstrate that HSP110 is a cargo of XPO1wt as well as of XPO1E571K. Using immunoprecipitation, proximity ligation, thermophoresis and kinase assays, we showed that HSP110 directly interacts with STAT6 and favors its phosphorylation. The combination of iHSP110-33 and selinexor induces a synergistic reduction of STAT6 phosphorylation and of lymphoma cell growth in vitro and in vivo. In biopsies from PMBL patients, we show a correlation between HSP110 and STAT6 phosphorylation levels. CONCLUSIONS: These findings suggest that HSP110 could be proposed as a novel target in PMBL and cHL therapy.


Subject(s)
Exportin 1 Protein , Hodgkin Disease , Karyopherins , Receptors, Cytoplasmic and Nuclear , Humans , Karyopherins/antagonists & inhibitors , Karyopherins/metabolism , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors , Animals , Mice , Hodgkin Disease/drug therapy , Hodgkin Disease/pathology , Hodgkin Disease/metabolism , Hodgkin Disease/genetics , Lymphoma, B-Cell/drug therapy , Lymphoma, B-Cell/metabolism , Lymphoma, B-Cell/pathology , Lymphoma, B-Cell/genetics , HSP110 Heat-Shock Proteins/metabolism , HSP110 Heat-Shock Proteins/genetics , Cell Line, Tumor , Mediastinal Neoplasms/drug therapy , Mediastinal Neoplasms/metabolism , Mediastinal Neoplasms/pathology , Mediastinal Neoplasms/genetics , Xenograft Model Antitumor Assays , Triazoles/pharmacology , Triazoles/therapeutic use , Hydrazines/pharmacology , Hydrazines/therapeutic use , Female , STAT6 Transcription Factor/metabolism , Molecular Targeted Therapy
5.
Biochim Biophys Acta Mol Basis Dis ; 1870(5): 167221, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38718845

ABSTRACT

BACKGROUND: Short bowel syndrome (SBS) features nutrients malabsorption and impaired intestinal barrier. Patients with SBS are prone to sepsis, intestinal flora dysbiosis and intestinal failure associated liver disease. Protecting intestinal barrier and preventing complications are potential strategies for SBS treatment. This study aims to investigate the effects of farnesoid X receptor (FXR) agonist, obeticholic acid (OCA), have on intestinal barrier and ecological environment in SBS. METHODS AND RESULTS: Through testing the small intestine and serum samples of patients with SBS, impaired intestinal barrier was verified, as evidenced by reduced expressions of intestinal tight junction proteins (TJPs), increased levels of apoptosis and epithelial cell damage. The intestinal expressions of FXR and related downstream molecules were decreased in SBS patients. Then, global FXR activator OCA was used to further dissect the potential role of the FXR in a rat model of SBS. Low expressions of FXR-related molecules were observed on the small intestine of SBS rats, along with increased proinflammatory factors and damaged barrier function. Furthermore, SBS rats possessed significantly decreased body weight and elevated death rate. Supplementation with OCA mitigated the damaged intestinal barrier and increased proinflammatory factors in SBS rats, accompanied by activated FXR-related molecules. Using 16S rDNA sequencing, the regulatory role of OCA on gut microbiota in SBS rats was witnessed. LPS stimulation to Caco-2 cells induced apoptosis and overexpression of proinflammatory factors in vitro. OCA incubation of LPS-pretreated Caco-2 cells activated FXR-related molecules, increased the expressions of TJPs, ameliorated apoptosis and inhibited overexpression of proinflammatory factors. CONCLUSIONS: OCA supplementation could effectively ameliorate the intestinal barrier disruption and inhibit overexpression of proinflammatory factors in a rat model of SBS and LPS-pretreated Caco-2 cells. As a selective activator of FXR, OCA might realize its protective function through FXR activation.


Subject(s)
Chenodeoxycholic Acid , Disease Models, Animal , Intestinal Mucosa , Receptors, Cytoplasmic and Nuclear , Short Bowel Syndrome , Animals , Chenodeoxycholic Acid/analogs & derivatives , Chenodeoxycholic Acid/pharmacology , Short Bowel Syndrome/metabolism , Short Bowel Syndrome/drug therapy , Short Bowel Syndrome/pathology , Rats , Humans , Male , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/agonists , Intestinal Mucosa/metabolism , Intestinal Mucosa/drug effects , Intestinal Mucosa/pathology , Gastrointestinal Microbiome/drug effects , Female , Rats, Sprague-Dawley , Apoptosis/drug effects , Middle Aged , Intestine, Small/metabolism , Intestine, Small/drug effects , Intestine, Small/pathology , Adult , Tight Junction Proteins/metabolism
6.
Elife ; 122024 May 15.
Article in English | MEDLINE | ID: mdl-38747706

ABSTRACT

Quiescence (G0) maintenance and exit are crucial for tissue homeostasis and regeneration in mammals. Here, we show that methyl-CpG binding protein 2 (Mecp2) expression is cell cycle-dependent and negatively regulates quiescence exit in cultured cells and in an injury-induced liver regeneration mouse model. Specifically, acute reduction of Mecp2 is required for efficient quiescence exit as deletion of Mecp2 accelerates, while overexpression of Mecp2 delays quiescence exit, and forced expression of Mecp2 after Mecp2 conditional knockout rescues cell cycle reentry. The E3 ligase Nedd4 mediates the ubiquitination and degradation of Mecp2, and thus facilitates quiescence exit. A genome-wide study uncovered the dual role of Mecp2 in preventing quiescence exit by transcriptionally activating metabolic genes while repressing proliferation-associated genes. Particularly disruption of two nuclear receptors, Rara or Nr1h3, accelerates quiescence exit, mimicking the Mecp2 depletion phenotype. Our studies unravel a previously unrecognized role for Mecp2 as an essential regulator of quiescence exit and tissue regeneration.


Subject(s)
Methyl-CpG-Binding Protein 2 , Animals , Methyl-CpG-Binding Protein 2/metabolism , Methyl-CpG-Binding Protein 2/genetics , Mice , Mice, Knockout , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/genetics , Cell Cycle , Liver Regeneration/genetics , Gene Expression Regulation
7.
Cell Mol Life Sci ; 81(1): 202, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38691171

ABSTRACT

Glial cells constitute nearly half of the mammalian nervous system's cellular composition. The glia in C. elegans perform majority of tasks comparable to those conducted by their mammalian equivalents. The cephalic sheath (CEPsh) glia, which are known to be the counterparts of mammalian astrocytes, are enriched with two nuclear hormone receptors (NHRs)-NHR-210 and NHR-231. This unique enrichment makes the CEPsh glia and these NHRs intriguing subjects of study concerning neuronal health. We endeavored to assess the role of these NHRs in neurodegenerative diseases and related functional processes, using transgenic C. elegans expressing human alpha-synuclein. We employed RNAi-mediated silencing, followed by behavioural, functional, and metabolic profiling in relation to suppression of NHR-210 and 231. Our findings revealed that depleting nhr-210 changes dopamine-associated behaviour and mitochondrial function in human alpha synuclein-expressing strains NL5901 and UA44, through a putative target, pgp-9, a transmembrane transporter. Considering the alteration in mitochondrial function and the involvement of a transmembrane transporter, we performed metabolomics study via HR-MAS NMR spectroscopy. Remarkably, substantial modifications in ATP, betaine, lactate, and glycine levels were seen upon the absence of nhr-210. We also detected considerable changes in metabolic pathways such as phenylalanine, tyrosine, and tryptophan biosynthesis metabolism; glycine, serine, and threonine metabolism; as well as glyoxalate and dicarboxylate metabolism. In conclusion, the deficiency of the nuclear hormone receptor nhr-210 in alpha-synuclein expressing strain of C. elegans, results in altered mitochondrial function, coupled with alterations in vital metabolite levels. These findings underline the functional and physiological importance of nhr-210 enrichment in CEPsh glia.


Subject(s)
Caenorhabditis elegans , Disease Models, Animal , Mitochondria , Neuroglia , Parkinson Disease , alpha-Synuclein , Animals , Caenorhabditis elegans/metabolism , Caenorhabditis elegans/genetics , Mitochondria/metabolism , Neuroglia/metabolism , Parkinson Disease/metabolism , Parkinson Disease/pathology , Parkinson Disease/genetics , Humans , alpha-Synuclein/metabolism , alpha-Synuclein/genetics , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans Proteins/genetics , Animals, Genetically Modified , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/genetics , Dopamine/metabolism , Metabolomics , RNA Interference
8.
PLoS One ; 19(4): e0301447, 2024.
Article in English | MEDLINE | ID: mdl-38557762

ABSTRACT

Rexinoids are agonists of nuclear rexinoid X receptors (RXR) that heterodimerize with other nuclear receptors to regulate gene transcription. A number of selective RXR agonists have been developed for clinical use but their application has been hampered by the unwanted side effects associated with the use of rexinoids and a limited understanding of their mechanisms of action across different cell types. Our previous studies showed that treatment of organotypic human epidermis with the low toxicity UAB30 and UAB110 rexinoids resulted in increased steady-state levels of all-trans-retinoic acid (ATRA), the obligatory ligand of the RXR-RAR heterodimers. Here, we investigated the molecular mechanism underlying the increase in ATRA levels using a dominant negative RXRα that lacks the activation function 2 (AF-2) domain. The results demonstrated that overexpression of dnRXRα in human organotypic epidermis markedly reduced signaling by resident ATRA, suggesting the existence of endogenous RXR ligand, diminished the biological effects of UAB30 and UAB110 on epidermis morphology and gene expression, and nearly abolished the rexinoid-induced increase in ATRA levels. Global transcriptome analysis of dnRXRα-rafts in comparison to empty vector-transduced rafts showed that over 95% of the differentially expressed genes in rexinoid-treated rafts constitute direct or indirect ATRA-regulated genes. Thus, the biological effects of UAB30 and UAB110 are mediated through the AF-2 domain of RXRα with minimal side effects in human epidermis. As ATRA levels are known to be reduced in certain epithelial pathologies, treatment with UAB30 and UAB110 may represent a promising therapy for normalizing the endogenous ATRA concentration and signaling in epithelial tissues.


Subject(s)
Furylfuramide , Tretinoin , Humans , Retinoid X Receptors/genetics , Retinoid X Receptors/agonists , Retinoid X Receptors/metabolism , Ligands , Tretinoin/pharmacology , Tretinoin/metabolism , Epidermis/metabolism , Receptors, Cytoplasmic and Nuclear
9.
FEBS J ; 291(10): 2091-2093, 2024 May.
Article in English | MEDLINE | ID: mdl-38646863

ABSTRACT

Cellular immortalization is a complex process that requires multiple genetic alterations to overcome restricting barriers, including senescence. Not surprisingly, many of these alterations are associated with cancer; two tumor suppressor pathways, the cellular tumor antigen p53 and p16-Retinoblastoma (RB) pathways, are the best-characterized examples, but their mutations alone are known to be insufficient to drive full immortalization. En et al. identified a role for the lamin B receptor (LBR) in promoting cellular proliferation and immortalization in p53- and RB-deficient cells by maintaining their genome integrity and suppressing senescence. Thus, modulation of LBR could be exploited to treat cancer and potentially also to promote cell rejuvenation.


Subject(s)
Cellular Senescence , Genomic Instability , Lamin B Receptor , Tumor Suppressor Protein p53 , Cellular Senescence/genetics , Humans , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , Receptors, Cytoplasmic and Nuclear/genetics , Receptors, Cytoplasmic and Nuclear/metabolism , Animals , Retinoblastoma Protein/genetics , Retinoblastoma Protein/metabolism , Neoplasms/genetics , Neoplasms/pathology , Neoplasms/metabolism , Cell Proliferation/genetics , Cell Transformation, Neoplastic/genetics , Cell Transformation, Neoplastic/metabolism , Cell Transformation, Neoplastic/pathology
10.
J Virol ; 98(5): e0029924, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38557225

ABSTRACT

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) Ac93 is highly conserved in all sequenced baculovirus genomes, and it plays important roles in both the nuclear egress of nucleocapsids and the formation of intranuclear microvesicles. In this study, we characterized a cellular CRM1-dependent nuclear export signal (NES) of AcMNPV Ac93. Bioinformatic analysis revealed that AcMNPV Ac93 may contain an NES at amino acids 115-125. Green fluorescent protein (GFP) fused to the NES (GFP:NES) of AcMNPV Ac93 is localized to the cytoplasm of transfected cells. Multiple point mutation analysis demonstrated that NES is important for the nuclear export of GFP:NES. Bimolecular fluorescence complementation experiments and co-immunoprecipitation assays confirmed that Ac93 interacts with Spodoptera frugiperda CRM1 (SfCRM1). However, AcMNPV Ac34 inhibits cellular CRM1-dependent nuclear export of GFP:NES. To determine whether the NES in AcMNPV Ac93 is important for the formation of intranuclear microvesicles, an ac93-null AcMNPV bacmid was constructed; the wild-type and NES-mutated Ac93 were reinserted into the ac93-null AcMNPV bacmid. Immunofluorescence analysis showed that Ac93 and SfCRM1 were predominantly colocalized at intranuclear microvesicles in infected cells, while the construct containing point mutations at residues 123 and 125 of Ac93 resulted in a defect in budded virus production and the abolishment of intranuclear microvesicles. Together, these data demonstrate that Ac93 contains a functional NES, which is required for the production of progeny viruses and the formation of intranuclear microvesicles.IMPORTANCEAutographa californica multiple nucleopolyhedrovirus (AcMNPV) Ac93 is important for the formation of intranuclear microvesicles. However, how the baculovirus manipulates Ac93 for the formation of intranuclear microvesicles is unclear. In this study, we identified a nuclear export signal (NES) at amino acids 115-125 of AcMNPV Ac93. Our results showed that the NES is required for the interaction between Ac93 and Spodoptera frugiperda CRM1 (SfCRM1). However, AcMNPV Ac34 inhibits the nuclear export of green fluorescent protein fused to the NES. Our analysis revealed that Ac93 and SfCRM1 were predominantly colocalized at intranuclear microvesicles in AcMNPV-infected cells. Together, our results indicate that Ac93 participates in the formation of intranuclear microvesicles via the Ac93 NES-mediated CRM1 pathway.


Subject(s)
Active Transport, Cell Nucleus , Cell Nucleus , Exportin 1 Protein , Karyopherins , Nuclear Export Signals , Nucleopolyhedroviruses , Receptors, Cytoplasmic and Nuclear , Spodoptera , Nucleopolyhedroviruses/metabolism , Nucleopolyhedroviruses/physiology , Nucleopolyhedroviruses/genetics , Karyopherins/metabolism , Animals , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/genetics , Sf9 Cells , Spodoptera/virology , Cell Nucleus/metabolism , Cell Nucleus/virology , Green Fluorescent Proteins/metabolism , Green Fluorescent Proteins/genetics , Viral Proteins/metabolism , Viral Proteins/genetics
11.
J Ethnopharmacol ; 330: 118209, 2024 Aug 10.
Article in English | MEDLINE | ID: mdl-38663779

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Dan-shen Yin (DSY), a traditional prescription, has been demonstrated to be effective in decreasing hyperlipidemia and preventing atherosclerosis (AS), but its mechanism remains unknown. We hypothesized that DSY activates farnesoid X receptor (FXR) to promote bile acid metabolism and excretion, thereby alleviating AS. AIM OF THE STUDY: This study was designed to explore whether DSY reduces liver lipid accumulation and prevents AS by activating FXR and increasing cholesterol metabolism and bile acid excretion. MATERIALS AND METHODS: The comprehensive chemical characterization of DSY was analyzed by UHPLC-MS/MS. The AS models of ApoE-/- mice and SD rats was established by high-fat diet and high-fat diet combined with intraperitoneal injection of vitamin D3, respectively. The aortic plaque and pathological changes were used to evaluate AS. Lipid levels, H&E staining and oil red O staining were used to evaluate liver lipid accumulation. The cholesterol metabolism and bile acid excretion were evaluated by enzyme-linked immunosorbent assay, UPLC-QQQ/MS. In vitro, the lipid and FXR/bile salt export pump (BSEP) levels were evaluated by oil red O staining, real-time quantitative polymerase chain reaction (RT-qPCR) and western blotting. RESULTS: A total of 36 ingredients in DSY were identified by UPLC-MS/MS analysis. In vivo, high-dose DSY significantly inhibited aortic intimal thickening, improved arrangement disorder, tortuosity, and rupture of elastic fibers, decreased lipid levels, and reduced the number of fat vacuoles and lipid droplets in liver tissue in SD rats and ApoE-/- mice. Further studies found that high-dose DSY significantly reduced liver lipid and total bile acids levels, increased liver ursodeoxycholic acid (UDCA) and other non-conjugated bile acids levels, increased fecal total cholesterol (TC) levels, and augmented FXR, BSEP, cholesterol 7-alpha hydroxylase (CYP7A1), ATP binding cassette subfamily G5/G8 (ABCG5/8) expression levels, while decreasing ASBT expression levels. In vitro studies showed that DSY significantly reduced TC and TG levels, as well as lipid droplets, while also increasing the expression of ABCG5/8, FXR, and BSEP in both HepG2 and Nr1h4 knockdown HepG2 cells. CONCLUSION: This study demonstrated that DSY promotes bile acid metabolism and excretion to prevent AS by activating FXR. For the prevent of AS and drug discovery provided experimental basis.


Subject(s)
Atherosclerosis , Bile Acids and Salts , Drugs, Chinese Herbal , Rats, Sprague-Dawley , Receptors, Cytoplasmic and Nuclear , Signal Transduction , Animals , Bile Acids and Salts/metabolism , Receptors, Cytoplasmic and Nuclear/metabolism , Male , Drugs, Chinese Herbal/pharmacology , Signal Transduction/drug effects , Atherosclerosis/prevention & control , Atherosclerosis/metabolism , Atherosclerosis/drug therapy , ATP Binding Cassette Transporter, Subfamily B, Member 11/metabolism , Mice , Diet, High-Fat/adverse effects , Mice, Inbred C57BL , Liver/drug effects , Liver/metabolism , Liver/pathology , Lipid Metabolism/drug effects , Mice, Knockout, ApoE , Rats , Humans
12.
Biochim Biophys Acta Gene Regul Mech ; 1867(2): 195025, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38614450

ABSTRACT

Nuclear receptors (NRs) regulate gene expression in critical physiological processes, with their functionality finely tuned by ligand-induced conformational changes. While NRs may sometimes undergo significant conformational motions in response to ligand-binding, these effects are more commonly subtle and challenging to study by traditional structural or biophysical methods. Molecular dynamics (MD) simulations are a powerful tool to bridge the gap between static protein-ligand structures and dynamical changes that govern NR function. Here, we summarize a handful of recent studies that apply MD simulations to study NRs. We present diverse methodologies for analyzing simulation data with a detailed examination of the information each method can yield. By delving into the strengths, limitations and unique contributions of these tools, this review provides guidance for extracting meaningful data from MD simulations to advance the goal of understanding the intricate mechanisms by which ligands orchestrate a range of functional outcomes in NRs.


Subject(s)
Molecular Dynamics Simulation , Receptors, Cytoplasmic and Nuclear , Ligands , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/chemistry , Humans , Protein Binding , Protein Conformation
13.
Mol Nutr Food Res ; 68(9): e2400147, 2024 May.
Article in English | MEDLINE | ID: mdl-38643378

ABSTRACT

SCOPE: Bile acids play a crucial role in lipid absorption and the regulation of lipid, glucose, and energy homeostasis. Coenzyme Q10 (CoQ10), a lipophilic antioxidant, has been recognized for its positive effects on obesity and related glycolipid metabolic disorders. However, the relationship between CoQ10 and bile acids has not yet been evaluated. METHODS AND RESULTS: This study assesses the impact of CoQ10 treatment on bile acid metabolism in mice on a high-fat diet using Ultra-Performance Liquid Chromatography-tandem Mass Spectrometry. CoQ10 reverses the reduction in serum and colonic total bile acid levels and alters the bile acid profile in mice that are caused by a high-fat diet. Seventeen potential targets of CoQ10 in bile acid metabolism are identified by network pharmacology, with six being central to the mechanism. Molecular docking shows a high binding affinity of CoQ10 to five of these key targets. Further analyses indicate that farnesoid X (FXR) receptor and Takeda G-protein coupled receptor 5 (TGR5) may be crucial targets for CoQ10 to regulate bile acid metabolism and exert beneficial effects. CONCLUSION: This study sheds light on the impact of CoQ10 in bile acids metabolism and offers a new perspective on the application of CoQ10 in metabolic health.


Subject(s)
Bile Acids and Salts , Diet, High-Fat , Dietary Supplements , Mice, Inbred C57BL , Molecular Docking Simulation , Network Pharmacology , Receptors, Cytoplasmic and Nuclear , Ubiquinone , Ubiquinone/analogs & derivatives , Ubiquinone/pharmacology , Bile Acids and Salts/metabolism , Animals , Receptors, Cytoplasmic and Nuclear/metabolism , Male , Receptors, G-Protein-Coupled/metabolism , Mice
14.
Nat Genet ; 56(5): 953-969, 2024 May.
Article in English | MEDLINE | ID: mdl-38627598

ABSTRACT

The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This knowledge gap is caused by the difficulty involved with studying multiple cell types in different states and locations, particularly when these are transient. We have combined Stereo-seq (spatiotemporal enhanced resolution omics-sequencing) with single-cell transcriptomic profiling of 473,290 cells to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. Our integrative study dissects in detail the molecular gradients controlling liver cell function, systematically defining how gene networks are dynamically modulated through intercellular communication to promote regeneration. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as a rheostat linking inflammation to Wnt/ß-catenin signaling for facilitating hepatocyte proliferation. Our data and analytical pipelines lay the foundation for future high-definition tissue-scale atlases of organ physiology and malfunction.


Subject(s)
Homeostasis , Liver Regeneration , Liver , Wnt Signaling Pathway , Animals , Liver Regeneration/genetics , Mice , Liver/metabolism , Wnt Signaling Pathway/genetics , Hepatocytes/metabolism , Hepatocytes/cytology , Cell Proliferation/genetics , Single-Cell Analysis , Gene Regulatory Networks , Gene Expression Profiling/methods , Transcriptome , Mice, Inbred C57BL , Receptors, Cytoplasmic and Nuclear/genetics , Receptors, Cytoplasmic and Nuclear/metabolism , Male
15.
Elife ; 122024 Apr 23.
Article in English | MEDLINE | ID: mdl-38652113

ABSTRACT

Lymphoid restricted membrane protein (LRMP) is a specific regulator of the hyperpolarization-activated cyclic nucleotide-sensitive isoform 4 (HCN4) channel. LRMP prevents cAMP-dependent potentiation of HCN4, but the interaction domains, mechanisms of action, and basis for isoform-specificity remain unknown. Here, we identify the domains of LRMP essential for this regulation, show that LRMP acts by disrupting the intramolecular signal transduction between cyclic nucleotide binding and gating, and demonstrate that multiple unique regions in HCN4 are required for LRMP isoform-specificity. Using patch clamp electrophysiology and Förster resonance energy transfer (FRET), we identified the initial 227 residues of LRMP and the N-terminus of HCN4 as necessary for LRMP to associate with HCN4. We found that the HCN4 N-terminus and HCN4-specific residues in the C-linker are necessary for regulation of HCN4 by LRMP. Finally, we demonstrated that LRMP-regulation can be conferred to HCN2 by addition of the HCN4 N-terminus along with mutation of five residues in the S5 region and C-linker to the cognate HCN4 residues. Taken together, these results suggest that LRMP inhibits HCN4 through an isoform-specific interaction involving the N-terminals of both proteins that prevents the transduction of cAMP binding into a change in channel gating, most likely via an HCN4-specific orientation of the N-terminus, C-linker, and S4-S5 linker.


Subject(s)
Cyclic AMP , Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels , Membrane Proteins , Muscle Proteins , Receptors, Cytoplasmic and Nuclear , Signal Transduction , Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels/metabolism , Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels/genetics , Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels/chemistry , Cyclic AMP/metabolism , Humans , Membrane Proteins/metabolism , Membrane Proteins/genetics , Animals , Protein Binding , HEK293 Cells , Potassium Channels/metabolism , Potassium Channels/genetics , Potassium Channels/chemistry , Patch-Clamp Techniques , Fluorescence Resonance Energy Transfer , Protein Isoforms/metabolism , Protein Isoforms/genetics
16.
Int J Mol Sci ; 25(8)2024 Apr 09.
Article in English | MEDLINE | ID: mdl-38673728

ABSTRACT

BTB and CNC homology 1 (BACH1) represses the expression of genes involved in the metabolism of iron, heme and reactive oxygen species. While BACH1 is rapidly degraded when it is bound to heme, it remains unclear how BACH1 degradation is regulated under other conditions. We found that FBXO22, a ubiquitin ligase previously reported to promote BACH1 degradation, polyubiquitinated BACH1 only in the presence of heme in a highly purified reconstitution assay. In parallel to this regulatory mechanism, TANK binding kinase 1 (TBK1), a protein kinase that activates innate immune response and regulates iron metabolism via ferritinophagy, was found to promote BACH1 degradation when overexpressed in 293T cells. While TBK1 phosphorylated BACH1 at multiple serine and threonine residues, BACH1 degradation was observed with not only the wild-type TBK1 but also catalytically impaired TBK1. The BACH1 degradation in response to catalytically impaired TBK1 was not dependent on FBXO22 but involved both autophagy-lysosome and ubiquitin-proteasome pathways judging from its suppression by using inhibitors of lysosome and proteasome. Chemical inhibition of TBK1 in hepatoma Hepa1 cells showed that TBK1 was not required for the heme-induced BACH1 degradation. Its inhibition in Namalwa B lymphoma cells increased endogenous BACH1 protein. These results suggest that TBK1 promotes BACH1 degradation in parallel to the FBXO22- and heme-dependent pathway, placing BACH1 as a downstream effector of TBK1 in iron metabolism or innate immune response.


Subject(s)
Basic-Leucine Zipper Transcription Factors , F-Box Proteins , Heme , Protein Serine-Threonine Kinases , Proteolysis , Receptors, Cytoplasmic and Nuclear , Humans , Heme/metabolism , Basic-Leucine Zipper Transcription Factors/metabolism , Basic-Leucine Zipper Transcription Factors/genetics , Phosphorylation , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/genetics , F-Box Proteins/metabolism , F-Box Proteins/genetics , HEK293 Cells , Ubiquitination , Cell Line, Tumor , Lysosomes/metabolism , Autophagy , Proteasome Endopeptidase Complex/metabolism
17.
Commun Biol ; 7(1): 371, 2024 Apr 04.
Article in English | MEDLINE | ID: mdl-38575811

ABSTRACT

Cardiac function requires appropriate proteins in each chamber. Atria requires slow myosin to act as reservoirs, while ventricles demand fast myosin for swift pumping. Myosins are thus under chamber-biased cis-regulation, with myosin gene expression imbalances leading to congenital heart dysfunction. To identify regulatory inputs leading to cardiac chamber-biased expression, we computationally and molecularly dissected the quail Slow Myosin Heavy Chain III (SMyHC III) promoter that drives preferential expression to the atria. We show that SMyHC III gene states are orchestrated by a complex Nuclear Receptor Element (cNRE) of 32 base pairs. Using transgenesis in zebrafish and mice, we demonstrate that preferential atrial expression is achieved by a combinatorial regulatory input composed of atrial activation motifs and ventricular repression motifs. Using comparative genomics, we show that the cNRE might have emerged from an endogenous viral element through infection of an ancestral host germline, revealing an evolutionary pathway to cardiac chamber-specific expression.


Subject(s)
Heart Atria , Zebrafish , Mice , Animals , Zebrafish/genetics , Heart Atria/metabolism , Heart Ventricles , Myosins/metabolism , Receptors, Cytoplasmic and Nuclear/metabolism
18.
Commun Biol ; 7(1): 426, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38589567

ABSTRACT

Wilms tumor (WT) is the most common renal malignancy of childhood. Despite improvements in the overall survival, relapse occurs in ~15% of patients with favorable histology WT (FHWT). Half of these patients will succumb to their disease. Identifying novel targeted therapies remains challenging in part due to the lack of faithful preclinical in vitro models. Here we establish twelve patient-derived WT cell lines and demonstrate that these models faithfully recapitulate WT biology using genomic and transcriptomic techniques. We then perform loss-of-function screens to identify the nuclear export gene, XPO1, as a vulnerability. We find that the FDA approved XPO1 inhibitor, KPT-330, suppresses TRIP13 expression, which is required for survival. We further identify synergy between KPT-330 and doxorubicin, a chemotherapy used in high-risk FHWT. Taken together, we identify XPO1 inhibition with KPT-330 as a potential therapeutic option to treat FHWTs and in combination with doxorubicin, leads to durable remissions in vivo.


Subject(s)
Hydrazines , Kidney Neoplasms , Triazoles , Wilms Tumor , Humans , Exportin 1 Protein , Active Transport, Cell Nucleus , Karyopherins/genetics , Karyopherins/metabolism , Receptors, Cytoplasmic and Nuclear/genetics , Receptors, Cytoplasmic and Nuclear/metabolism , Cell Line, Tumor , Apoptosis , Neoplasm Recurrence, Local , Doxorubicin/pharmacology , Wilms Tumor/drug therapy , Wilms Tumor/genetics , Kidney Neoplasms/drug therapy , Kidney Neoplasms/genetics , ATPases Associated with Diverse Cellular Activities/metabolism , Cell Cycle Proteins/metabolism
19.
PLoS One ; 19(4): e0300809, 2024.
Article in English | MEDLINE | ID: mdl-38662778

ABSTRACT

The nuclear farnesoid X receptor (FXR), a master regulator of bile acid and metabolic homeostasis, is a key target for treatment of nonalcoholic steatohepatitis (NASH). This study compared efficacy of FXR agonists obeticholic acid (OCA) and INT-787 by liver histopathology, plasma biomarkers of liver damage, and hepatic gene expression profiles in the Amylin liver NASH (AMLN) diet-induced and biopsy-confirmed Lepob/ob mouse model of NASH. Lepob/ob mice were fed the AMLN diet for 12 weeks before liver biopsy and subsequent treatment with vehicle, OCA, or INT-787 for 8 weeks. Hepatic steatosis, inflammation, and fibrosis (liver lipids, galectin-3, and collagen 1a1 [Col1a1], respectively), as well as plasma alanine transaminase (ALT) and aspartate transaminase (AST) levels, were assessed. Hepatic gene expression was assessed in Lepob/ob mice that were fed the AMLN diet for 14 weeks then treated with vehicle, OCA, or INT-787 for 2 weeks. INT-787, which is equipotent to OCA but more hydrophilic, significantly reduced liver lipids, galectin-3, and Col1a1 compared with vehicle, and to a greater extent than OCA. INT-787 significantly reduced plasma ALT and AST levels, whereas OCA did not. INT-787 modulated a substantially greater number of genes associated with FXR signaling, lipid metabolism, and stellate cell activation relative to OCA in hepatic tissue. These findings demonstrate greater efficacy of INT-787 treatment compared with OCA in improving liver histopathology, decreasing liver enzyme levels, and enhancing gene regulation, suggesting superior clinical potential of INT-787 for the treatment of NASH and other chronic liver diseases.


Subject(s)
Chenodeoxycholic Acid , Chenodeoxycholic Acid/analogs & derivatives , Disease Models, Animal , Liver , Non-alcoholic Fatty Liver Disease , Receptors, Cytoplasmic and Nuclear , Animals , Non-alcoholic Fatty Liver Disease/drug therapy , Non-alcoholic Fatty Liver Disease/metabolism , Non-alcoholic Fatty Liver Disease/pathology , Non-alcoholic Fatty Liver Disease/genetics , Chenodeoxycholic Acid/pharmacology , Chenodeoxycholic Acid/therapeutic use , Receptors, Cytoplasmic and Nuclear/agonists , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/genetics , Mice , Liver/metabolism , Liver/drug effects , Liver/pathology , Male , Galectin 3/metabolism , Galectin 3/genetics
20.
Mol Metab ; 83: 101932, 2024 May.
Article in English | MEDLINE | ID: mdl-38589002

ABSTRACT

BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common complication of obesity and, in severe cases, progresses to metabolic dysfunction-associated steatohepatitis (MASH). Small heterodimer partner (SHP) is an orphan member of the nuclear receptor superfamily and regulates metabolism and inflammation in the liver via a variety of pathways. In this study, we investigate the molecular foundation of MASH progression in mice with hepatic SHP deletion and explore possible therapeutic means to reduce MASH. METHODS: Hepatic SHP knockout mice (SHPΔhep) and their wild-type littermates (SHPfl/fl) of both sexes were fed a fructose diet for 14 weeks and subjected to an oral glucose tolerance test. Then, plasma lipids were determined, and liver lipid metabolism and inflammation pathways were analyzed with immunoblotting, RNAseq, and qPCR assays. To explore possible therapeutic intersections of SHP and inflammatory pathways, SHPΔhep mice were reconstituted with bone marrow lacking interferon γ (IFNγ-/-) to suppress inflammation. RESULTS: Hepatic deletion of SHP in mice fed a fructose diet decreased liver fat and increased proteins for fatty acid oxidation and liver lipid uptake, including UCP1, CPT1α, ACDAM, and SRBI. Despite lower liver fat, hepatic SHP deletion increased liver inflammatory F4/80+ cells and mRNA levels of inflammatory cytokines (IL-12, IL-6, Ccl2, and IFNγ) in both sexes and elevated endoplasmic reticulum stress markers of Cox2 and CHOP in female mice. Liver bulk RNAseq data showed upregulation of genes whose protein products regulate lipid transport, fatty acid oxidation, and inflammation in SHPΔhep mice. The increased inflammation and fibrosis in SHPΔhep mice were corrected with bone marrow-derived IFNγ-/- myeloid cell transplantation. CONCLUSION: Hepatic deletion of SHP improves fatty liver but worsens hepatic inflammation possibly by driving excess fatty acid oxidation, which is corrected by deletion of IFNγ specifically in myeloid cells. This suggests that hepatic SHP limits fatty acid oxidation during fructose diet feeding but, in doing so, prevents pro-MASH pathways. The IFNγ-mediated inflammation in myeloid cells appears to be a potential therapeutic target to suppress MASH.


Subject(s)
Interferon-gamma , Liver , Mice, Knockout , Myeloid Cells , Receptors, Cytoplasmic and Nuclear , Animals , Female , Male , Mice , Fatty Liver/metabolism , Fatty Liver/genetics , Inflammation/metabolism , Interferon-gamma/metabolism , Lipid Metabolism , Liver/metabolism , Liver/pathology , Liver Cirrhosis/metabolism , Liver Cirrhosis/genetics , Mice, Inbred C57BL , Myeloid Cells/metabolism , Receptors, Cytoplasmic and Nuclear/metabolism , Receptors, Cytoplasmic and Nuclear/genetics
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