Constitutive androstane receptor (CAR) and pregnane X receptor (PXR) are closely related nuclear receptors with overlapping regulatory functions in xenobiotic clearance but distinct roles in endobiotic metabolism. Car activation has been demonstrated to ameliorate hypercholesterolemia by regulating cholesterol metabolism and bile acid elimination, whereas PXR activation is associated with hypercholesterolemia and liver steatosis. Here we show a human CAR agonist/PXR antagonist, MI-883, which effectively regulates genes related to xenobiotic metabolism and cholesterol/bile acid homeostasis by leveraging CAR and PXR interactions in gene regulation. Through comprehensive analyses utilizing lipidomics, bile acid metabolomics, and transcriptomics in humanized PXR-CAR-CYP3A4/3A7 mice fed high-fat and high-cholesterol diets, we demonstrate that MI-883 significantly reduces plasma cholesterol levels and enhances fecal bile acid excretion. This work paves the way for the development of ligands targeting multiple xenobiotic nuclear receptors. Such ligands hold the potential for precise modulation of liver metabolism, offering new therapeutic strategies for metabolic disorders.

• MeSH
• cholesterol * metabolismus   krev   MeSH
• cytochrom P-450 CYP3A metabolismus   genetika   MeSH
• dieta s vysokým obsahem tuků * škodlivé účinky   MeSH
• hypercholesterolemie * farmakoterapie   metabolismus   MeSH
• hypolipidemika farmakologie   terapeutické užití   MeSH
• játra metabolismus   účinky léků   MeSH
• konstitutivní androstanový receptor * MeSH
• lidé MeSH
• metabolismus lipidů účinky léků   MeSH
• modely nemocí na zvířatech MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• pregnanový X receptor * metabolismus   genetika   MeSH
• pyridiny MeSH
• receptory cytoplazmatické a nukleární * metabolismus   agonisté   genetika   MeSH
• regulace genové exprese účinky léků   MeSH
• žlučové kyseliny a soli * metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 1,4-bis(2-(3,5-dichloropyridyloxy))benzene MeSH Prohlížeč
• cholesterol * MeSH
• cytochrom P-450 CYP3A MeSH
• hypolipidemika MeSH
• konstitutivní androstanový receptor * MeSH
• pregnanový X receptor * MeSH
• pyridiny MeSH
• receptory cytoplazmatické a nukleární * MeSH
• žlučové kyseliny a soli * MeSH

The classic plant growth-promoting phytohormone cytokinin has been identified and established as a mediator of pathogen resistance in different plant species. However, the resistance effect of structurally different cytokinins appears to vary and may regulate diverse mechanisms to establish resistance. Hence, we comparatively analysed the impact of six different adenine- and phenylurea-type cytokinins on the well-established pathosystem Nicotiana tabacum-Pseudomonas syringae. The efficiency of resistance effects was evaluated based on impacts on the host plant defence response by scoring infection symptoms and the direct impact on the pathogen by assessment of proliferation in planta. To identify common and cytokinin-specific components involved in resistance effects, transcriptome profiling and targeted metabolomics were conducted in leaves treated with the different cytokinins. We observed clearly different potentials of the tested cytokinins in either suppressing infection symptoms or pathogen proliferation. Gene regulation and metabolite analyses revealed cytokinin-type specific impacts on defence components, such as salicylic acid and related signalling, expression of PR proteins, and regulation of specialised metabolism. Cytokinins also strongly affected plant cell physiological parameters, such as a remarkable decrease in amino acid pools. Hence, this study provides comparative information on the efficiency of diverse cytokinins in mediating resistance in one well-studied pathosystem and insights into the specific regulation of resistance effects mediated by different cytokinin molecules. This is particularly relevant for studies on the function of cytokinins or other phytohormones and compounds interacting with cytokinin activities in the context of pathogen infections and other stress scenarios, considering the diverse cytokinins present in plants.

• MeSH
• cytokininy * metabolismus   MeSH
• listy rostlin mikrobiologie   metabolismus   genetika   MeSH
• nemoci rostlin * mikrobiologie   imunologie   genetika   MeSH
• odolnost vůči nemocem * genetika   MeSH
• Pseudomonas syringae * fyziologie   patogenita   MeSH
• regulace genové exprese u rostlin účinky léků   MeSH
• regulátory růstu rostlin metabolismus   MeSH
• tabák * mikrobiologie   genetika   imunologie   účinky léků   metabolismus   MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• cytokininy * MeSH
• regulátory růstu rostlin MeSH

Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease. Therefore, understanding the molecular regulatory mechanisms underlying the pathogenesis of DKD is imperative. In this study, we aimed to explore the molecular mechanisms of tubule region endothelial dysfunction in early DKD. Early-stage DKD model was established in 16-week-old female db/db mice for 16 weeks. Body weight, glucose level, and urine albumin-to-creatinine ratio (UACR) were measured. Hematoxylin and eosin (H&E) and periodic acid-Schiff (PAS) staining were performed to evaluate pathological lesions. RNA sequencing data of the kidneys and integrated publicly available single-cell and spatial transcriptome datasets were used to investigate the mechanism of endothelial dysfunction. There was a significant increase in body weight (p = 0.001), glucose levels (p=0.0008), and UACR (p=0.006) in db/db mice compared with db/m mice. H&E and PAS staining showed that vacuolar lesions and protein casts of tubules were the major histopathological changes observed in early-stage DKD mice. The apoptotic pathway in endothelial cells was notably activated in DKD, and Thbs1 was identified as the central gene involved in this apoptotic process. Deconvolution of the cell composition in the RNA sequencing data showed a decrease in the proportion of endothelial cells in the DKD mice. Further analysis of the activity and regulatory network of transcription factors showed that Creb1 was activated in both mouse and human early-stage DKD, suggesting that Creb1 activation may be involved in early kidney injury. The endothelial cell apoptotic pathway is activated in DKD, and the proportion of endothelial cells was reduced in the DKD mice, which is significantly associated with Thbs1. Keywords: Diabetic kidney disease, Endothelial dysfunction, RNA sequencing,Thbs1, Creb1.

• MeSH
• apoptóza MeSH
• diabetické nefropatie * patologie   metabolismus   patofyziologie   genetika   MeSH
• endoteliální buňky metabolismus   patologie   MeSH
• ledvinové kanálky patologie   metabolismus   MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• progrese nemoci * MeSH
• protein vázající element responzivní pro cyklický AMP metabolismus   genetika   MeSH
• thrombospondin 1 metabolismus   genetika   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• protein vázající element responzivní pro cyklický AMP MeSH
• thrombospondin 1 MeSH

Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5' end adapter ligation, to comprehensively interrogate the human transcriptome at single-molecule and -nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5' end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key component of RNA metabolism upon cellular stress that is dependent on stress granule formation.

• Klíčová slova
• RNA decay, cell biology, cell line, genetics, genomics, human, mouse, stress response,
• MeSH
• adaptorové proteiny signální transdukční metabolismus   genetika   MeSH
• DNA-helikasy metabolismus   genetika   MeSH
• exoribonukleasy * metabolismus   genetika   MeSH
• fyziologický stres * genetika   MeSH
• lidé MeSH
• proteiny asociované s mikrotubuly MeSH
• proteiny vázající poly-ADP-ribosu * metabolismus   genetika   MeSH
• proteiny vázající RNA MeSH
• ribozomy metabolismus   MeSH
• RNA-helikasy metabolismus   genetika   MeSH
• RRM proteiny * metabolismus   genetika   MeSH
• sekvenční analýza RNA * MeSH
• stabilita RNA * genetika   MeSH
• stresová tělíska metabolismus   genetika   MeSH
• transkriptom MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adaptorové proteiny signální transdukční MeSH
• DNA-helikasy MeSH
• exoribonukleasy * MeSH
• G3BP1 protein, human MeSH Prohlížeč
• G3BP2 protein, human MeSH Prohlížeč
• proteiny asociované s mikrotubuly MeSH
• proteiny vázající poly-ADP-ribosu * MeSH
• proteiny vázající RNA MeSH
• RNA-helikasy MeSH
• RRM proteiny * MeSH
• XRN1 protein, human MeSH Prohlížeč

Fibrosis contributes to tissue repair, but excessive fibrosis disrupts organ function. Alagille syndrome (ALGS, caused by mutations in JAGGED1) results in liver disease and characteristic fibrosis. Here, we show that Jag1Ndr/Ndr mice, a model for ALGS, recapitulate ALGS-like fibrosis. Single-cell RNA-seq and multi-color flow cytometry of the liver revealed immature hepatocytes and paradoxically low intrahepatic T cell infiltration despite cholestasis in Jag1Ndr/Ndr mice. Thymic and splenic regulatory T cells (Tregs) were enriched and Jag1Ndr/Ndr lymphocyte immune and fibrotic capacity was tested with adoptive transfer into Rag1-/- mice, challenged with dextran sulfate sodium (DSS) or bile duct ligation (BDL). Transplanted Jag1Ndr/Ndr lymphocytes were less inflammatory with fewer activated T cells than Jag1+/+ lymphocytes in response to DSS. Cholestasis induced by BDL in Rag1-/- mice with Jag1Ndr/Ndr lymphocytes resulted in periportal Treg accumulation and three-fold less periportal fibrosis than in Rag1-/- mice with Jag1+/+ lymphocytes. Finally, the Jag1Ndr/Ndr hepatocyte expression profile and Treg overrepresentation were corroborated in patients' liver samples. Jag1-dependent hepatic and immune defects thus interact to determine the fibrotic process in ALGS.

• Klíčová slova
• Alagille syndrome, Fibrosis, Jagged1, Notch, Treg,
• MeSH
• Alagillův syndrom patologie   genetika   MeSH
• buněčná diferenciace * MeSH
• hepatocyty * metabolismus   patologie   MeSH
• jaterní cirhóza * patologie   genetika   MeSH
• lidé MeSH
• modely nemocí na zvířatech MeSH
• myši inbrední C57BL MeSH
• myši knockoutované MeSH
• myši MeSH
• protein jagged-1 * metabolismus   genetika   MeSH
• regulační T-lymfocyty imunologie   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• JAG1 protein, human MeSH Prohlížeč
• Jag1 protein, mouse MeSH Prohlížeč
• protein jagged-1 * MeSH

BACKGROUND: Embryos are regeneration and wound healing masters. They rapidly close wounds and scarlessly remodel and regenerate injured tissue. Regeneration has been extensively studied in many animal models using new tools such as single-cell analysis. However, until now, they have been based primarily on experiments assessing from 1 day post injury. RESULTS: In this paper, we reveal that critical steps initiating regeneration occur within hours after injury. We discovered the regeneration initiating cells (RICs) using single-cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells, and their expression signature suggests they are important for modifying the surrounding extracellular matrix thus regulating development. The absence or deregulation of RICs leads to excessive extracellular matrix deposition and defective regeneration. CONCLUSION: RICs represent a newly discovered transient cell state involved in the initiation of the regeneration process.

• Klíčová slova
• Xenopus laevis, RICs, ROCs, Regeneration,
• MeSH
• analýza jednotlivých buněk MeSH
• extracelulární matrix metabolismus   MeSH
• hojení ran MeSH
• ocas * MeSH
• regenerace * MeSH
• transkriptom MeSH
• Xenopus laevis * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disease characterized by the accumulation of fat in the liver in the absence of excessive alcohol consumption or a secondary cause of hepatic steatosis. The prevalence of NAFLD is increasing worldwide and its management has become a public health concern. Animal models are traditionally used to elucidate disease mechanisms and identify potential drug targets; however, their translational aspects in human diseases have not been fully established. This study aimed to clarify the utility of animal models for translational research by assessing their relevance to human diseases using gene expression analysis. Weighted gene co-expression network analysis of liver tissues from Western diet (WD)-induced NAFLD mice was performed to identify the modules associated with disease progression. Moreover, the similarity of the gene co-expression network across species was evaluated using module preservation analysis. Nineteen disease-associated modules were identified. The brown module was positively associated with disease severity, and functional analyses indicated that it may be involved in inflammatory responses in immune cells. Moreover, the gene co-expression network of the brown module was highly preserved in human NAFLD liver gene expression datasets. These results indicate that WD-induced NAFLD mice have similar gene co-expression networks (especially genes associated with inflammatory responses) to humans and are thought to be a useful experimental tool for preclinical research on NAFLD. Keywords: Nonalcoholic fatty liver disease (NAFLD), Weighted gene co-expression network analysis (WGCNA), Western diet (WD).

• MeSH
• játra metabolismus   patologie   MeSH
• lidé MeSH
• modely nemocí na zvířatech * MeSH
• myši inbrední C57BL * MeSH
• myši MeSH
• nealkoholová steatóza jater * genetika   metabolismus   etiologie   patologie   MeSH
• stanovení celkové genové exprese metody   MeSH
• transkriptom * MeSH
• západní dieta * škodlivé účinky   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5' end adaptor ligation, to comprehensively interrogate the human transcriptome at single-molecule and nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5' end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key determinant of RNA metabolism upon cellular stress and dependent on stress-granule formation.

• Publikační typ
• časopisecké články MeSH
• preprinty MeSH

Disuccinimidyl dibutyric urea (DSBU) is a mass spectrometry (MS)-cleavable cross-linker that has multiple applications in structural biology, ranging from isolated protein complexes to comprehensive system-wide interactomics. DSBU facilitates a rapid and reliable identification of cross-links through the dissociation of its urea group in the gas phase. In this study, we further advance the structural capabilities of DSBU by remodeling the urea group into an imide, thus introducing a novel class of cross-linkers. This modification preserves the MS cleavability of the amide bond, granted by the two acyl groups of the imide function. The central nitrogen atom enables the introduction of affinity purification tags. Here, we introduce disuccinimidyl disuccinic imide (DSSI) as a prototype of this class of cross-linkers. It features a phosphonate handle for immobilized metal ion affinity chromatography enrichment. We detail DSSI synthesis and describe its behavior in solution and in the gas phase while cross-linking isolated proteins and human cell lysates. DSSI and DSBU cross-links are compared at the same enrichment depth to bridge these two cross-linker classes. We validate DSSI cross-links by mapping them in high-resolution structures of large protein assemblies. The cross-links observed yield insights into the morphology of intrinsically disordered proteins and their complexes. The DSSI linker might spearhead a novel class of MS-cleavable and enrichable cross-linkers.

• Publikační typ
• časopisecké články MeSH

Crohn's disease (CD) is marked by recurring intestinal inflammation and tissue injury, often resulting in fibrostenosis and bowel obstruction, necessitating surgical intervention with high recurrence rates. To elucidate the mechanisms underlying fibrostenosis in CD, we analyzed the transcriptome of cells isolated from the transmural ileum of patients with CD, including a trio of lesions from each patient: non-affected, inflamed, and stenotic ileum samples, and compared them with samples from patients without CD. Our computational analysis revealed that profibrotic signals from a subset of monocyte-derived cells expressing CD150 induced a disease-specific fibroblast population, resulting in chronic inflammation and tissue fibrosis. The transcription factor TWIST1 was identified as a key modulator of fibroblast activation and extracellular matrix (ECM) deposition. Genetic and pharmacological inhibition of TWIST1 prevents fibroblast activation, reducing ECM production and collagen deposition. Our findings suggest that the myeloid-stromal axis may offer a promising therapeutic target to prevent fibrostenosis in CD.

• Klíčová slova
• Fibrosis, Gastroenterology, Inflammation, Inflammatory bowel disease, Monocytes,
• MeSH
• Crohnova nemoc * metabolismus   patologie   imunologie   MeSH
• dospělí MeSH
• endopeptidasy metabolismus   genetika   MeSH
• extracelulární matrix metabolismus   patologie   MeSH
• fibroblasty * metabolismus   patologie   MeSH
• fibróza * MeSH
• ileum patologie   metabolismus   imunologie   MeSH
• jaderné proteiny metabolismus   genetika   MeSH
• lidé MeSH
• mezibuněčná komunikace MeSH
• monocyty * metabolismus   patologie   imunologie   MeSH
• myši MeSH
• receptory buněčného povrchu metabolismus   genetika   MeSH
• transkripční faktor Twist * metabolismus   genetika   MeSH
• zvířata MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mužské pohlaví MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• endopeptidasy MeSH
• jaderné proteiny MeSH
• receptory buněčného povrchu MeSH
• transkripční faktor Twist * MeSH
• TWIST1 protein, human MeSH Prohlížeč