All alpha- and beta-coronaviruses encode nonstructural protein 1 (Nsp1), a major virulence factor that restricts host gene expression. Herein, using Nsp1 from divergent alpha- and beta-coronaviruses (SARS-CoV-2, MERS-CoV, and HCoV-229E), we reveal all tested coronavirus Nsp1 proteins have intrinsic endonuclease activity. Furthermore, this endonuclease function is abolished when a conserved arginine-lysine motif in the N-terminal domain (NTD) is disrupted. For SARS-CoV-2 Nsp1, the eukaryotic Initiation Factor 3g (eIF3g) and the 40S ribosome act as cofactors for enhancing the endonuclease function, but these host factors are not conserved for the endonuclease function of MERS-CoV and HCoV-229E Nsp1. We propose that SARS-CoV-2 Nsp1 uses eIF3g and the 40S ribosome to enhance its affinity for RNA and target host mRNAs. Similar enhancement in endonuclease activity is observed when Nsp1 from SARS-CoV-2, MERS-CoV, and HCoV-229E are cis-tethered to an RNA-binding module. Collectively, our results show that endonuclease activity is intrinsic to Nsp1 across divergent coronavirus genera, and this endonuclease activity is likely targeted towards host mRNAs via a diverse set of host mRNA binding cofactors.
Deciphering the functional roles of G protein-coupled receptors (GPCRs) oligomers requires defining their structural organization, which remains a challenge due to the inherent flexibility of their 7 transmembrane (TM) domains. Here, we focused on determining homodimer interfaces of the chemokine receptor CCR2, a major component of the inflammatory response, for which no antagonist has yet been approved. We generated models of CCR2 homodimers combining homology modeling, a conventional in silico approach, or an AI-based AlphaFold-Multimer predictions, with molecular dynamics simulations. We determined the biological relevance of our predicted models by in cellulo cross-linking experiments, introducing a cysteine in each predicted interface. This in cellulo assay supported the homology modeling predictions, but not those predicted by AlphaFold-Multimer, and demonstrated that CCR2 forms homodimers by at least two different interfaces involving the transmembrane domains TM5 (I5) or TM5 and TM6 (I56). This structural arrangement of the CCR2 homodimer represents a valuable model for further studies on the functional consequences of dimerization and for the rational design of CCR2-selective drugs.
Deoxysphingolipids (dSLs) are atypical sphingolipids that accumulate in several pathological settings, yet their impact on hematologic malignancies is poorly understood. Here, we investigate the pathways and mechanisms of deoxysphinganine (dSA) cytotoxicity in lymphoma cells and its potential as a therapeutic agent. dSA exhibited markedly greater cytotoxicity than canonical sphingoid bases in lymphoma cell lines, yet induced only cytostatic effects in normal human T cells, indicating a therapeutically exploitable window. Inhibition of ceramide synthase blocked the generation of deoxy(dihydro)ceramides, prevented mitochondrial depolarization, caspase activation, ER stress, and DNA damage, establishing CerS-dependent deoxysphingolipids as essential mediators of dSA-induced death. Mechanistically, dSA engaged a mitochondrial apoptotic pathway, with DNA damage occurring downstream of mitochondrial permeabilization and caspase activation, while PERK-driven ER stress occurred in parallel and was dispensable for cytotoxicity. Subtype-specific engagement of ER stress and DNA damage further suggests that dSL signaling is shaped by lineage context. The differential sensitivity between malignant lymphoid cells and normal T cells, together with the central role of CerS-derived deoxy(dihydro)ceramides, highlights deoxysphingolipid metabolism as a druggable vulnerability in lymphoma. These findings support further exploration of dSA-based strategies and targeted modulation of dSL synthesis as a novel therapeutic avenue for non-solid hematologic malignancies.
Whether the fecal metabolome differs according to intensive low-density lipoprotein cholesterol (LDL-C) target achievement among statin-treated patients is unclear. In this cross-sectional study, 124 statin-treated adults with chronic disease were stratified by fasting LDL-C into a target-achieved group (< 70 mg/dL, n = 52) and a target-not-achieved group (≥ 70 mg/dL, n = 72). Stool samples were profiled by untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry, and multivariable models adjusted for age, sex, chronic kidney disease, and angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use were used to identify metabolites independently associated with target achievement. Statin dose, treatment duration and glucose-lowering therapy were also compared between the groups. Paired 16S rRNA gene sequencing data available for a subset (n = 86) were used for integrative correlation and network analyses. Partial least-squares discriminant analysis showed separation between the two groups. Eight annotated metabolites-glutamine, glutamate, phenylalanine, N-acetyl-L-phenylalanine, L-methionine, N-acetyl-L-methionine, lysine, and N-methyl-D-aspartic acid, predominantly amino acids and their derivatives-were present at lower fecal levels in participants who achieved the LDL-C target. Metabolite set enrichment analysis implicated amino acid and nitrogen metabolism, and multiomics network analysis identified an Anaerotruncus-centered amino acid module with high degree centrality. In conclusion, LDL-C target achievement under statin therapy was associated with a coherent "low fecal amino acid" signature and an Anaerotruncus-linked microbe-metabolite hub. These findings suggest that intestinal nutrient handling and gut microbial amino acid metabolism may contribute to variability in LDL-C response, and they warrant prospective mechanistic evaluation.
Metabolic dysfunction-associated liver disease (MASLD) arises from the accumulation of triglycerides within the liver. MASLD can advance to metabolic dysfunction-associated steatohepatitis (MASH), cirrhosis, and hepatocellular carcinoma. Monoacylglycerol acyltransferase 2 (MOGAT2) is essential for triglyceride synthesis and plays a significant role in regulating lipid metabolism. Here, we demonstrate the ability of a new human MOGAT 2 inhibitor, VB-85387, to inhibit the development of MASLD/MASH and further define its effects on the key metabolic pathways that progress MASH development. MASLD/MASH was induced using a methionine, choline-deficient diet (LMCD) or by streptozotocin treatment combined with high fat diet feeding (STAM-HFD). VB-85387 significantly mitigated the severity of MASLD and reduced signs of MASH in mice subjected to these two distinct diets. VB-85387-treated mice exhibited decreased fibrosis, evidenced by reduced hepatic triglyceride concentrations, hydroxyproline levels, and collagen deposition. NAS scores were consistently lower in VB-85387-treated mice across both models. VB-85387-treated mice showed induced PPARα signaling and reduced SREBP transcription, demonstrating a likely role for VB-85387 in regulating lipogenesis and fatty acid β-oxidation. STAM-HFD treated mice showed lower NF-κBp65 activation, which was associated with lower TNFα expression. IL-1β and IFNβ levels were also both reduced, suggesting VB-85387 can reduce pro-inflammatory pattern recognition receptor signaling. In addition, treatment suppressed IL-4/IL-6-dependent JAK activation. Overall, VB-85387 inhibited MASLD development by reducing liver triglyceride levels, fibrosis, and meta-inflammatory signaling. VB-85387 was as effective or superior to the MOGAT2 inhibitor phase I clinical trial drug BMS-963272 in reducing MASLD and fibrosis. VB-85387 has considerable potential for developing therapeutics targeting MASLD/MASH.
Glioma represents one of the most aggressive tumors in the central nervous system, with clinical management facing significant challenges including high recurrence rates and therapeutic resistance. Ferroptosis, an iron-dependent form of cell death, holds potential for glioma treatment, yet tumor cells frequently develop evasion mechanisms. This study elucidates the molecular mechanisms by which hypoxic microenvironment confers ferroptosis resistance in glioma cells, focusing on the pivotal role of the HIF-1α/SREBP1 signaling axis and its downstream effectors FASN and SCD1. Our experimental results demonstrate that hypoxic conditions significantly upregulate HIF-1α expression and confer resistance to RSL3-induced ferroptosis. Mechanistic studies reveal that HIF-1α promotes SREBP1 activation, which subsequently upregulates FASN and SCD1 expression to suppress lipid peroxidation.Furthermore, the HIF-1α-specific inhibitor PX-478 effectively reverses hypoxia-induced ferroptosis resistance and significantly enhances tumor cell sensitivity to ferroptosis inducers. In vivo experiments confirm the potent antitumor effects of PX-478 combined with RSL3. This study systematically elucidates the role of the HIF-1α-SREBP1-FASN/SCD1 signaling axis in ferroptosis regulation in glioma, providing important theoretical foundations and experimental support for developing HIF-1α-targeted ferroptosis therapies.
BACKGROUND:Lipoprotein(a) [Lp(a)] reflects inherited atherothrombotic risk, whereas the C-reactive protein-triglyceride-glucose index (CTI) integrates systemic inflammation, triglyceride-related lipid disturbance, and glucose-related metabolic stress. Their individual and joint association with angiographic coronary lesion burden in acute coronary syndrome (ACS) remain incompletely defined. We examined whether CTI complements Lp(a) in characterizing coronary lesion burden in ACS. MATERIALS AND METHODS:This retrospective, single-center study included 2,836 consecutive patients with ACS who underwent coronary angiography. Coronary lesion burden was assessed using continuous Gensini score, a high Gensini score, and multivessel disease (MVD). Multivariable regression, restricted cubic spline analyses, CTI-stratified analyses, incremental receiver operating characteristic analyses, and internally validated machine-learning analyses with SHAP interpretation were performed. RESULTS:Higher Lp(a) and CTI level were both associated with greater coronary lesion burden. Compared with Lp(a) <75 nmol/L, Lp(a) ≥175 nmol/L was associated with high Gensini score (OR, 1.51 [95% CI, 1.17-1.96]) and MVD (OR, 1.69 [95% CI, 1.27-2.26]). Each 1-SD increase in CTI was associated with high Gensini score (OR, 1.47 [95% CI, 1.35-1.60]) and MVD (OR, 1.18 [95% CI, 1.08-1.28]). Among inflammatory-lipid indices, CTI showed the most consistent associations and provided the largest numerical incremental discrimination beyond Lp(a). The associaton between ver high Lp(a) and coronary lesion burden was more pronounced at higher CTI levels, particular for MVD. Machine-learning analyses further supported the relevance of both CTI and Lp(a). CONCLUSIONS:In patients with ACS, higher Lp(a) and CTI level were associated with greater angiographic coronary lesion burden. CTI may complement Lp(a) by capturing inflammatory-metabolic status, supporting their joint assessment for more refined characterization of lesion-burden risk in ACS.
Lipoprotein metabolism is significantly different between mice and humans thus making it difficult to model disorders of human lipid metabolism in transgenic mice. Systemic lipoprotein metabolism is predominantly governed by hepatocytes, and mice with humanized livers display human-like lipid profiles. Here we report a highly efficient method to knock out genes in human hepatocytes while retaining their ability to repopulate immune deficient rodents. As proof-of-principle Fah deficient, immune compromised mice were repopulated with Apolipoprotein B (APOB) knockout human hepatocytes. Mice humanized with knockout cells recapitulated typical features of human hypobetalipoproteinemia. We conclude that at least some human lipid metabolism disorders can be modeled in liver chimeric mice using human knockout hepatocytes.
Upstream open reading frames (uORFs) in 5’ untranslated regions regulate downstream translation, and many encode functional peptides. Despite their importance, no comprehensive plant uORF database with experimental validation exists. Here we present the Plant uORF-pep Database (https://plantuorf-pep.com), a multi-evidence resource encompassing 16.2M uORF records across 30 plant species. The database integrates four evidence layers: (1) Ribo-seq translation evidence from six species, including uORF-level validation of 5.3K Arabidopsis uORFs; (2) cross-species conservation analysis across 10 plants, identifying 85K genes with conserved uORFs; (3) machine learning-based translation probability prediction for 5M uORFs (Random Forest, 78.9% accuracy); and (4) discovery of 6.6K conserved but unannotated uORF peptides prioritized as experimental candidates. The web interface supports gene search, batch query, and data download. By bridging computational prediction with experimental and evolutionary evidence, Plant uORF-pep fills a critical gap for plant uORF research and functional peptide discovery.
Research on virus nucleic acid-protein interactions is important to understand infection and guide antiviral drug design. In previous studies we showed that the human rhinovirus (RV) genomic RNA is organized as a dodecahedral cage formed by 30 RNA duplex elements anchored to capsid concavities. We showed also that capsid-RNA duplex interactions include conserved tryptophans, neutral polar residues, and many positively charged residues that promote virion assembly and restrain RNA release by stabilizing the negatively charged RNA duplex structure. The present study expands our understanding of the capsid-RNA duplex interface in RV by addressing the structural and functional roles of conserved patches of negatively charged capsid residues interposed between each RNA duplex and its binding site at the capsid inner surface. The initial hypothesis was that electrostatic repulsion between anionic residues and RNA phosphates would lead to functional effects opposite to those previously found for cationic residues that can electrostatically attract RNA phosphates. In fact, those anionic residues do not oppose, but act together with cationic residues at the RNA duplex binding sites to promote virion assembly and restrain RNA release. Cryogenic electron microscopy analysis showed that negatively charged residues at the capsid-RNA duplex interfaces have a different structural role than positively charged residues, even though they all play similar functional roles. A tentative model is discussed to explain the functional effects of the complex distribution of negative and positive electrostatic potential found at capsid-RNA duplex interfaces in RV.
ATP-dependent chromatin remodelers of the CHD family regulate genome organisation and transcription, yet their dynamic behaviour in native chromatin remains unclear. Here, we performed in vivo single-molecule tracking of the CHD remodeler Hrp3 in live Schizosaccharomyces pombe cells to quantify its chromatin interaction dynamics. By generating domain-deletion mutants (Δchromo, ATPaseK406A (ATPase-dead), Δcoupling region, DNA binding domains (ΔSANT, ΔSLIDE), and ΔDUF), we systematically dissected the contribution of each domain to DNA binding in vivo. While some observations align with previous in vitro studies, key differences highlight the critical influence of the cellular chromatin environment on remodeler function. We find that Hrp3 exhibits specific binding only with constitutive heterochromatin, but not with euchromatin or facultative heterochromatin. We tested the effect of altered histone acetylation and methylation on the chromatin binding dynamics of Hrp3. Our data demonstrated the chromatin context-dependent binding of Hrp3: reduced acetylation allows binding of Hrp3 with euchromatin, increased acetylation reduces binding of Hrp3 with heterochromatin, and reduced methylation increases the binding of Hrp3 with heterochromatin. Interestingly, we found specific binding of Hrp3 with mitotic chromosomes, suggesting its role in maintaining heterochromatin silencing during mitosis and probably contributing to epigenetic memory. Collectively, our results demonstrate that Hrp3 chromatin binding is highly sensitive to epigenetic modifications and chromatin compaction and cannot be fully predicted from in vitro studies alone. Given the conservation of CHD remodelers and their links to human diseases, this study provides important insights into how epigenetic therapies, such as HDAC inhibitors, may modulate chromatin remodeler dynamics and influence gene expression.
Parkinson's disease (PD) is characterized by progressive dopaminergic neurodegeneration associated with oxidative stress, mitochondrial dysfunction, endoplasmic reticulum (ER) stress, and impaired proteostasis. In this study, we investigated the role of Up-Regulated Gene 7 (URG7), an ER-resident protein, in regulating cellular stress responses in SH-SY5Y neuroblastoma cells exposed to 6-hydroxydopamine (6-OHDA), a widely used in vitro model of PD. URG7 overexpression significantly enhanced activation of the adaptive unfolded protein response (UPR), particularly the PERK/eIF2α/ATF4 pathway, while limiting ER stress-induced damage. Moreover, URG7 promoted protein quality control mechanisms by stimulating both the ubiquitin-proteasome system and autophagy, as demonstrated by increased ubiquitination, proteasome activity, and upregulation of Beclin-1 and LC3-II. URG7 also prevented intracellular calcium overload and reduced the expression of proteins involved in the SOCE pathway, thereby preserving calcium homeostasis under oxidative stress conditions. In addition, URG7 attenuated G1 cell cycle arrest and reduced the expression of pro-apoptotic markers, including p53, p21, Bax, and cleaved PARP, while promoting pro-survival signaling pathways such as AKT and ERK1/2. Collectively, these findings identify URG7 as an important regulator of adaptive stress responses and suggest its possible involvement in neuroprotective mechanisms associated with neurodegenerative disorders characterized by oxidative stress.
High-altitude polycythemia (HAPC) remains prevalent among Tibetans despite genetic adaptations, including EPAS1/HIF2A. Excessive erythrocytosis elevates blood viscosity and increases cardiopulmonary risk, yet erythrocyte metabolic and membrane-lipid mechanisms of HAPC and of therapeutic erythrocytapheresis (TE) remain incompletely defined. We conducted integrated metabolomic and lipidomic profiling of washed erythrocytes from HAPC patients and non-HAPC (NHAPC), and from HAPC patients after TE. Relative to NHAPC, HAPC showed coordinated erythrocyte remodeling spanning amino acid and purine metabolism together with membrane phospholipid and lipid structure (unsaturation and chain length) changes. The disease contrast was multiomic, whereas the acute post-TE contrast was lipid dominant, consistent with apheresis acting primarily through erythrocyte removal. K-means stratification revealed clinically meaningful TE response heterogeneity, but erythrocyte omics did not define stable responder subtypes. These findings point to erythrocyte membrane lipids as a persistent molecular feature of HAPC and of the acute TE response.
Clinically, acute kidney injury (AKI) is one of the most frequent complications of Naja atra (N. atra) envenomation, primarily attributed to snake venom phospholipase A2 (SVPLA2). Although the SVPLA2 inhibitor varespladib shows great therapeutic promise, the underlying mechanisms remain incompletely understood. Herein, we integrated multi-omics and molecular biology approaches to investigate the critical role of SVPLA2 in N. atra venom-induced AKI, as evidenced by pharmacological inhibition with varespladib. Proteomic profiling identified HRAS and CCND1 as key mediators of SVPLA2-induced nephrotoxicity. Mechanistically, SVPLA2 disrupts lipid raft integrity, impairing HRAS palmitoylation-dependent plasma membrane localization and GTPase activity. This defect suppresses phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling, causing apoptosis and cell cycle arrest in renal tubular epithelial cells, enforced activation of PI3K-AKT signaling effectively rescued cells from injury. Beyond direct cytotoxicity, SVPLA2 profoundly remodels the renal immune microenvironment. SVPLA2 enhances glycolysis by upregulating hexokinase 2 (HK2) while suppressing fatty acid oxidation through downregulation of carnitine palmitoyltransferase IA, thereby metabolically driving M1 polarization. This metabolic shift impairs macrophage efferocytosis and sustains inflammatory injury. HK2 knockdown reverses these effects in macrophages. Taken together, this study reveals a dual epithelial-immune mechanism by which SVPLA2 activity critically contributes to N. atra venom-induced AKI, as evidenced by pharmacological inhibition with varespladib. These findings highlight PI3K-AKT signaling and HK2 as potential therapeutic targets for N. atra-triggered AKI. Supplementary key words.
Pancreatic lipase is the major enzyme responsible for breaking down dietary triglycerides in the intestines. A previous report suggested that intestinal angiopoietin-like 4 (ANGPTL4) might serve as an endogenous inhibitor of pancreatic lipase and thus regulate fat absorption. As ANGPTL4 expression is reportedly induced by high-fat-diet feeding, we hypothesized that induction of ANGPTL4 by a high-fat diet would lead to an increased inhibition of pancreatic lipase, less breakdown of dietary triglycerides, and ultimately a reduced rate of postprandial triglyceride absorption. To test this hypothesis, we generated intestinal epithelial cell-specific ANGPTL4 knockout mice, fed them diets with varying levels of fat, and measured postprandial triglyceride absorption and intestinal triglyceride lipase activity. As we hypothesized, we found that chronic high-fat feeding reduced the rate of postprandial triglyceride absorption in mice. However, this regulation of postprandial triglyceride absorption appeared to be largely independent of ANGPTL4, as similar decreases were observed in both wild-type and intestinal epithelial cell-specific ANGPTL4 knockout mice. We conclude that there is mechanism by which chronic high-fat feeding reduces the rate of secretion of dietary triglycerides into the circulation, but that this mechanism does not require intestinal ANGPTL4.
Mammals rely on the integrated stress response (ISR) to maintain essential amino acid (EAA) homeostasis. The kinase GCN2 is a key ISR sensor that is rapidly activated by uncharged tRNAs during EAA deprivation, leading to eIF2α phosphorylation and selective translation of ATF4. ATF4 subsequently orchestrates a transcriptional program regulating amino acid metabolism, redox balance, and autophagy. In this study, we investigated the role of GCN2 in the early hepatic transcriptional response to dietary sulfur amino acids (SAA; methionine and cysteine) deprivation. Using ATF4-luciferase reporter mice, we demonstrate that short-term SAA deprivation rapidly activates the eIF2α-ATF4 pathway within 3 h, with activation primarily localized to the liver. Complementary in vivo and ex vivo approaches revealed that genetic deletion or pharmacological inhibition of GCN2 abolishes early eIF2α phosphorylation and induction of ATF4 target gene, while PERK is dispensable for this response. Furthermore, GCN2 controls the induction of multiple adaptive transcriptional programs involved in amino acid transport, aminoacyl-tRNA synthesis, autophagy, serine biosynthesis, one-carbon metabolism and glutathione degradation highlighting a coordinated adaptive response to acute SAA deprivation. These findings establish GCN2 as a major sensor mediating the early hepatic response to SAA deprivation, and define a transcriptional program essential for maintaining amino acid homeostasis. In contrast, Fgf21 induction occurs independently of GCN2, indicating the existence of parallel adaptive mechanisms. Collectively, this work provides new insight into the early dynamics and molecular specificity of ISR activation in response to acute dietary SAA deprivation.
The formylglycine-generating enzyme (FGE) post-translationally modifies the active site of all human sulfatases. Mutations in the SUMF1 gene encoding FGE may lead to catalytically inactive FGE or destabilize the protein. The resulting lack of sulfatase modification causes the rare disease multiple sulfatase deficiency (MSD). Previously, FGE required elastase treatment for crystallization and the structures lacked copper, although FGE is a copper-dependent enzyme. Here, we show that highly active human FGE purified from insect cells natively contains one copper ion and we report six new crystal structures revealing previously unobserved features. Several structures contain the catalytic copper ion coordinated almost linearly by the two catalytic cysteines. A structure of the MSD-causing E130D variant shows distortions in coordination of a structural Ca2+ explaining its lower stability. As part of exploratory ligand-soaking experiments, a structure of FGE soaked with N-acetyl cysteine methyl ester shows the binding of a small molecule to a site other than the active site highlighting a potential binding site to be explored in the development of pharmacological chaperones for FGE. Crystallization of FGE without elastase treatment resulted in a structure in which the previously missing loop is well defined in the electron density and partly covers the active site, indicating that it needs to adopt a different conformation for substrate binding. This assumption is supported by a second structure in which the loop faces away from the active site and leaves the substrate binding groove open and by the occasional occurrence of crystals in which the loop becomes disordered.
Sequence reversal has been shown to significantly alter the folding and function of ordered proteins. Compared to ordered proteins, the conformations of intrinsically disordered proteins (IDPs) are more dynamic and expanded. Whether the equilibrium properties and functions of IDPs are more tolerant of sequence reversal remains unclear. In this work, we used the microtubule-associated protein Tau as a prototype IDP and investigated the effects of sequence reversal on its equilibrium conformation, phase transitions, and function. We found that the sequence-reversed protein behaved like an IDP, with the similar level of conformational expansion, dynamics, and secondary structure content as its parent protein. Our analysis revealed that the dynamic non-specific electrostatic interactions were not markedly perturbed upon sequence reversal, enabling the sequence-reversed protein to undergo liquid-liquid phase separation as its parent does. On the contrary, our results showed that sequence reversal disrupted residue-specific interactions. Thus, the sequence-reversed protein could not aggregate into amyloid fibrils or assist in microtubule assembly. Taken together, our findings indicate that sequence reversal could have distinct effects on the conformational dynamics, phase transitions, and function of IDPs.
