As lipidomics approaches its 25th anniversary, we explore how lipid research has matured over the years while highlighting emerging innovations that are expanding our ability to study these diverse, life-critical biomole...As lipidomics approaches its 25th anniversary, we explore how lipid research has matured over the years while highlighting emerging innovations that are expanding our ability to study these diverse, life-critical biomolecules. In particular, we showcase the community-driven, open-access databases, software, and educational resources made freely available through the ELIXIR Core Data Resource LIPID MAPS for the benefit of both established and new researchers.
Phenotypic plasticity, the ability to change diverse traits without altering genomic information, is fundamental for organismal adaptations to changing environments. The mitogen-activated protein kinase (MAPK) pathway pl...Phenotypic plasticity, the ability to change diverse traits without altering genomic information, is fundamental for organismal adaptations to changing environments. The mitogen-activated protein kinase (MAPK) pathway plays a key role in cellular adaptations to changing environments. To analyze the contributions of the MAPK p38 and its interaction partners to phenotypic plasticity in an animal, we established an in vivo proximity labeling proteomics method called ContinuumID. With this method, we built an atlas of PMK-1 physical interactors during development, in specific tissues, and during exposure to osmotic, ultraviolet, or oxidative stressors. We identified multiple stable and dynamic developmental stage-, tissue-, and stress-specific PMK-1 interactors. Phenotypic analyses of animals in which specific interactors were knocked down revealed considerable variability of diverse PMK-1-dependent outputs. These included target gene expression, survival under stress, lysosomal homeostasis during development, and neuronal integrity during aging. PMK-1 interactors exerted positive, negative, and neutral contributions to these outputs within and across functional pathways. Comparing developmental and stress-induced activation of PMK-1 and the regulatory functions of its interactors revealed that PMK-1 integrates the regulation of highly conserved protein synthesis and RNA processing pathways with that of rapidly changing signaling and metabolic adaptations to confer distinct survival advantages or disadvantages during stress.
Neuropathic pain is a debilitating condition that lacks effective treatments. Corticotropin-releasing hormone (CRH) is associated with the central neural circuits involved in stress and pain. Here, we identified a periph...Neuropathic pain is a debilitating condition that lacks effective treatments. Corticotropin-releasing hormone (CRH) is associated with the central neural circuits involved in stress and pain. Here, we identified a peripheral CRH-mediated signaling axis in dorsal root ganglion (DRG) and spinal neurons underlying neuropathic pain. Spared nerve injury (SNI) in male mice increased the abundance of CRH in small- and medium-diameter DRG neurons, specifically in their central terminals in the spinal dorsal horn. DRG-specific knockdown of CRH alleviated neuropathic pain. SNI increased expression by inducing the binding of the transcription factor SMAD1 to the promoter. Silencing SMAD1 in the DRG reduced neuropathic pain symptoms, which was accompanied by a decrease in the amount of CRH in the DRG tissue. Pharmacological antagonism of CRH receptor 2 (CRHR2), but not of CRHR1, attenuated neuropathic pain and suppressed the activation of spinal neurons and glia. Spinal CRHR2 predominantly localized to excitatory neurons and somatostatin-positive interneurons in the superficial dorsal horn. These findings reveal a SMAD1-CRH-CRHR2 axis in DRG-to-spine signaling that promotes neuropathic pain and suggest that CRHR2 antagonists be explored for its management.
For patients with kidney failure, peritoneal dialysis (PD) is an alternative kidney replacement therapy to hemodialysis. Long-term PD efficacy is limited by multicellular pathologies induced by the hyperosmotic PD fluids...For patients with kidney failure, peritoneal dialysis (PD) is an alternative kidney replacement therapy to hemodialysis. Long-term PD efficacy is limited by multicellular pathologies induced by the hyperosmotic PD fluids, including vasculopathy and fibroangiogenic remodeling of the peritoneum, which lack targeted pharmacological interventions. We developed a deep secretome profiling workflow in a coculture system using a human peritoneal mesothelial cell line and primary human lymphatic endothelial cells to characterize the influence of PD fluid on communication between these cell types. This approach uncovered extracellular and intracellular signaling patterns absent in standard monocultures and identified 1910 human proteins that revealed extracellular regulatory processes central to PD-associated peritoneal pathology. Integration of the coculture secretome and cellular proteomes with effluent and plasma proteomes derived from patients with PD revealed cell type-specific signaling networks and groups of proteins correlating with clinical parameters such as ultrafiltration capacity, transport kinetics, and inflammation. Functional validation demonstrated that lithium chloride supplementation partially counteracted fibroangiogenic signaling and affected key PD fluid-induced processes, including PDGFC-driven lymphangiogenesis, syndecan-4 ectodomain shedding by endothelial cells, and a mesothelial switch from NOTCH1 to NOTCH3 synthesis. These findings suggest new potential pharmacological strategies to mitigate peritoneal fibrosis and vasculopathy, offering a framework for future therapeutic innovation in PD and beyond.
Colitis imposes epigenetic changes that prime colonic stem cells for tumor growth.Colitis imposes epigenetic changes that prime colonic stem cells for tumor growth.
Kaur K, Alippe Y, Wang C
… +12 more, Semenkovich NP, Hassan MG, Bhagat S, Khanna K, Li Y, Pokhrel N, Peterson T, Scheller EL, Veis DJ, Abu-Amer Y, Faccio R, Mbalaviele G
Activation of the NLRP3 inflammasome can drive bone resorption by osteoclasts in various inflammatory conditions. Here, we identified Tmem178, a protein that restrains Ca fluxes by limiting SOCE activation, as an inhibit...Activation of the NLRP3 inflammasome can drive bone resorption by osteoclasts in various inflammatory conditions. Here, we identified Tmem178, a protein that restrains Ca fluxes by limiting SOCE activation, as an inhibitor of NLRP3 inflammasome activation and the bone-resorbing activity of osteoclasts. We found that NLRP3 abundance gradually decreased during osteoclastogenesis but was restored by treatment with the bacterial product LPS. LPS and the NLRP3 activator nigericin stimulated this inflammasome in macrophages, as expected, but not in osteoclasts or their lineage-committed precursors. This differential NLRP3 activation was due to Tmem178, a protein abundant in osteoclasts that suppressed NLRP3 inflammasome nucleation. Accordingly, NLRP3 inflammasome activation was robust in osteoclasts lacking Tmem178 or in wild-type osteoclasts exposed to high Ca concentrations. In vivo studies demonstrated that inflammasome formation was enhanced under conditions in which osteoclasts efficiently release Ca from bone and that deletion of rescued the osteopenic phenotype characteristic of mice. Thus, our results indicate that Tmem178 potently restricts Ca influx in osteoclasts, thereby suppressing NLRP3 inflammasome activation.
Ca flux is a key trigger of NLRP3 inflammasome activation, but bone-resorbing osteoclasts operate in a Ca-rich environment created during bone resorption. In this issue of , Kaur reveal that osteoclasts prevent inflamma...Ca flux is a key trigger of NLRP3 inflammasome activation, but bone-resorbing osteoclasts operate in a Ca-rich environment created during bone resorption. In this issue of , Kaur reveal that osteoclasts prevent inflammasome activation by limiting Ca influx through the membrane protein Tmem178, thereby protecting bone from excessive resorption driven by inflammatory signaling.
Cardiomyocytes depend on local translation for growth and can undergo directed growth in length or width in response to different stimuli. Protein synthesis is augmented during concentric hypertrophy, which leads to thic...Cardiomyocytes depend on local translation for growth and can undergo directed growth in length or width in response to different stimuli. Protein synthesis is augmented during concentric hypertrophy, which leads to thickening of the heart muscle by increasing cardiomyocyte width. Protein synthesis is controlled at the translation initiation step, when ribosome loading onto transcripts is regulated by the sequential phosphorylation of the eukaryotic initiation factor 4E-binding protein 1 (4EBP1). Here, we identified a mode of 4EBP1 phosphorylation that was associated with concentric hypertrophy in cultured cardiomyocytes and mouse hearts. Whereas canonical phosphorylation of 4EBP1 by mTORC1 regulates global protein synthesis rates, mTORC1- and nuclear ERK-dependent phosphorylation of 4EBP1 was specifically activated during concentric but not eccentric hypertrophy. Nuclear ERK-dependent phosphorylation of 4EBP1 at Ser was necessary and sufficient to relocalize translation initiation sites closer to the nuclei. ERK activation drove redistribution of ribosomes and nascent translation toward the center of the cardiomyocyte without altering global mRNA distribution, leading to spatially enriched deposition of new sarcomeric protein in the cardiomyocyte interior. Together, these findings demonstrate that global protein synthesis can be spatially regulated by the activation of different kinases in distinct subcellular compartments and identify a mechanism that drives concentric hypertrophy.
Acetylcholine from lymphocytes regulates B cell antibody production within germinal centers.Acetylcholine from lymphocytes regulates B cell antibody production within germinal centers.
The high glucose levels characteristic of diabetes can lead to increases in glucose metabolism through the process of glycolysis, resulting in greater production of lactate and in a monosaccharide-based posttranslational...The high glucose levels characteristic of diabetes can lead to increases in glucose metabolism through the process of glycolysis, resulting in greater production of lactate and in a monosaccharide-based posttranslational modification called O-GlcNAcylation. Here, we identified O-GlcNAcylation and lactate production as the molecular mechanisms underlying high glucose-induced cognitive impairment, a prevalent complication of diabetes. A prospective observational study revealed that elevated plasma concentrations of lactate were an independent risk factor for predicting mild cognitive impairment in patients with diabetes. High-glucose treatment of mouse hippocampal neurons increased the O-GlcNAcylation of the transcription factor Creb3, which stabilized the protein by preventing its ubiquitination. The increase in Creb3 subsequently up-regulated the expression of the downstream target gene , which encodes the enzyme lactate dehydrogenase. As a result, lactate production was increased during glycolysis, triggering neuronal apoptosis and cognitive dysfunction in mouse models of type 1 and 2 diabetes. Expression of a Creb3 mutant that could not be O-GlcNAcylated at Ser or competitive blockade of the O-GlcNAcylation of Ser in Creb3 with a short peptide alleviated these effects. This study elucidates a mechanistic link between high glucose-induced Creb3 O-GlcNAcylation and Ldha-mediated lactate production, offering a potential therapeutic strategy for managing diabetes-related cognitive dysfunction.
Vargas JNS, Brown AL, Sun K
… +14 more, Hagemann C, Geary B, Villarroel-Campos D, Bryce-Smith S, Zanovello M, Lombardo M, Majewski S, Tosolini A, Secrier M, Keuss MJ, Serio A, Sleigh JN, Fratta P, Schiavo G
The cell-intrinsic capacity of neurons to regenerate axons requires widespread coordination of the transcriptome, activation of multiple kinases, and reorganization of the cytoskeleton. Axonal repair is also influenced b...The cell-intrinsic capacity of neurons to regenerate axons requires widespread coordination of the transcriptome, activation of multiple kinases, and reorganization of the cytoskeleton. Axonal repair is also influenced by extrinsic activating factors, such as neurotrophins. Here, we found that the neurotrophin BDNF amplifies multiple neuron-intrinsic programs to foster axonal regeneration in human iPSC-derived lower motor neurons (i LMNs). Metabolic RNA sequencing (SLAM-seq) and phosphoproteomic profiling of i LMNs revealed that BDNF temporally regulated the expression and RNA stability of functionally distinct transcriptional programs that included regeneration-associated gene sets, further enhancing their expression. BDNF also regulated the phosphorylation of multiple proteins involved in cytoskeletal dynamics. In compartmentalized cultures of neurons, in which microfluidic chambers isolate somata from their axons, BDNF-induced regeneration depended on axon-specific activation of the ERK-RSK-S6K kinase pathway. The findings show that extrinsic BDNF signaling coordinates intrinsic axon-regeneration programs and highlight the role of spatially regulated kinase activation in this process.
Wnt-β-catenin signaling begins when Wnt ligands engage the receptors Frizzled (Fzd) and LRP5 or LRP6 (LRP5/6), leading to the recruitment and phosphorylation of the intracellular protein Dishevelled (Dvl), which is neces...Wnt-β-catenin signaling begins when Wnt ligands engage the receptors Frizzled (Fzd) and LRP5 or LRP6 (LRP5/6), leading to the recruitment and phosphorylation of the intracellular protein Dishevelled (Dvl), which is necessary for stabilization of the transcriptional coactivator β-catenin. Understanding the mechanisms by which ligand binding to Fzd activates Wnt-β-catenin signaling is crucial for rational ligand design to selectively modulate Wnt responses in the context of diseases and tissue regeneration. Here, we determined that ligand-induced Fzd clustering was the initiating event for the recruitment and phosphorylation of the downstream signaling mediator Dvl. Using synthetic, bivalent antibodies and single-molecule microscopy, we found that Wnts and bivalent Fzd-binding antibodies, but not monovalent antibodies, clustered Fzd at the plasma membrane in cells, activating Dvl independently of LRP5/6. However, β-catenin-mediated signaling required LRP5/6 recruitment as an additional step to enable inhibition of the kinase GSK3α or GSK3β and stabilization of β-catenin. This two-step mechanism may separate Fzd activation from β-catenin pathway output, underlying a mechanism by which Wnts encode signaling specificity and may inform the design of selective Wnt pathway modulators.
Brain metastases arise from the spread of cancer cells from tumors residing outside the brain. Immunotherapy and molecularly targeted therapeutics have improved outcomes for some patients with brain metastases, but many...Brain metastases arise from the spread of cancer cells from tumors residing outside the brain. Immunotherapy and molecularly targeted therapeutics have improved outcomes for some patients with brain metastases, but many patients are still faced with a dismal prognosis. The inability to effectively treat these tumors and improve patient survival highlights the dire need for improved therapeutic strategies that ultimately depend on developing a greater understanding of the molecular underpinnings and inner wiring of these tumors. In this Review, we discuss current and emerging insights into the genetics and cellular signaling pathways that contribute to the spread of tumors to the brain. We also discuss potential therapeutic targets in the metabolic vulnerabilities of cells that metastasize to the brain and in the interactions between metastases and the microenvironment.
Pirenzepine (PZ) and muscarinic toxin 7 (MT7) are muscarinic acetylcholine type 1 receptor (MR) antagonists that promote neuritogenesis in primary adult rodent dorsal root ganglion (DRG) sensory neurons, in part through...Pirenzepine (PZ) and muscarinic toxin 7 (MT7) are muscarinic acetylcholine type 1 receptor (MR) antagonists that promote neuritogenesis in primary adult rodent dorsal root ganglion (DRG) sensory neurons, in part through β-arrestin-dependent activation of ERK1/2. Here, we found that PZ and MT7 exhibited β-arrestin-biased agonism at MR. PZ and MT7 recruited β-arrestin 2 to MR and increased ERK phosphorylation in both HEK293 cells and DRG neurons in a concentration-dependent manner. Moreover, ERK activation by MT7 occurred only in MR-positive DRG neurons and did not require G protein signaling or receptor internalization. PZ stimulated MR phosphorylation at multiple serine and threonine residues. Mutation of Ser and Thr in MR suppressed PZ- and MT7-dependent activation of β-arrestins and PZ-dependent β-arrestin binding and ERK activation. The β-arrestin-biased activities of PZ and MT7 required the activity of casein kinase 2 (CK2) but not that of Gα or GPCR kinases (GRKs). Pharmacological or siRNA-based inhibition of CK2 blocked PZ-dependent β-arrestin recruitment, ERK activation, and neurite outgrowth in DRG neurons. These results implicate a GRK- and G protein-independent mechanism for the β-arrestin-biased agonism and antimuscarinic effects of PZ and MT7.
Chronic stress and impaired signaling by the neurotrophic factor BDNF are associated with depression. The heterotrimeric G protein subunits Gα and Gα (Gα) are critical mediators of BDNF signaling in a mouse model of chro...Chronic stress and impaired signaling by the neurotrophic factor BDNF are associated with depression. The heterotrimeric G protein subunits Gα and Gα (Gα) are critical mediators of BDNF signaling in a mouse model of chronic mild stress-induced depression. Here, we found that chronic mild stress impairs the SUMOylation of Gα and, consequently, their formation of signaling complexes with the BDNF receptor TrkB. Impaired SUMOylation of the G protein subunits was the result of a decrease in RAB5-interacting factor (RAB5IF) and a consequent decrease in the translational efficiency of mRNA. RAB5IF silencing or knockout in cultured murine hippocampal neurons impaired BDNF-induced signaling and mitochondrial function that compromised dendritic branching and synaptic density. Neuronal knockdown or conditional knockout of RAB5IF in the mouse hippocampus recapitulated these cellular deficits and induced depressive-like behaviors. Conversely, neuronal overexpression of RAB5IF in the hippocampus mitigated the depressive phenotype. SUMOylation of Gα at Lys was required for BDNF-induced formation of TrkB-SUMO2-Gα complexes and activation of downstream Akt-mTOR signaling. Neuronal knockdown of SUMO2 or hippocampal overexpression of a Gα mutant that could not be SUMOylated impaired BDNF signaling and induced depressive-like behaviors in mice. The findings reveal that the RAB5IF-SUMO2-Gα signaling axis is crucial for TrkB signaling and preventing depressive behaviors.
Polyunsaturated fatty acids in a Western diet activate RXRα to promote Crohn's disease pathogenesis.Polyunsaturated fatty acids in a Western diet activate RXRα to promote Crohn's disease pathogenesis.
β-Arrestins are multifunctional, intracellular proteins that regulate the desensitization, internalization, and signaling of more than 800 G protein-coupled receptors (GPCRs) and interact with a diverse array of intracel...β-Arrestins are multifunctional, intracellular proteins that regulate the desensitization, internalization, and signaling of more than 800 G protein-coupled receptors (GPCRs) and interact with a diverse array of intracellular partners. Beyond the plasma membrane, GPCRs can initiate distinct signaling cascades from various subcellular locations, a phenomenon known as "location bias." Here, we investigated how β-arrestins directed location-biased signaling of the angiotensin II type 1 receptor (AT1R) using bioluminescence resonance energy transfer (BRET) conformational biosensors and extracellular signal-regulated kinase (ERK) activity reporters. We found that, in response to the endogenous agonist angiotensin II and the β-arrestin-biased agonist TRV023, β-arrestin 1 and β-arrestin 2 adopted distinct conformations across different subcellular locations, which were associated with different ERK activation profiles. We also uncovered a population of receptor-free, activated β-arrestins in the plasma membrane that exhibited insensitivity to different agonists and promoted ERK activation at the plasma membrane independently of G proteins. These findings deepen our understanding of GPCR signaling complexity and highlight the nuanced roles of β-arrestins beyond traditional G protein pathways.
Cl homeostasis is pivotal during neurodevelopment and in multiple processes in mature neurons, and its disruption is implicated in several neurodevelopmental disorders. Here, we investigated the role of Cl in regulating...Cl homeostasis is pivotal during neurodevelopment and in multiple processes in mature neurons, and its disruption is implicated in several neurodevelopmental disorders. Here, we investigated the role of Cl in regulating DDX3X, an ATP-dependent RNA helicase that is associated with a neurodevelopmental disorder and is involved in stress granule assembly through biomolecular condensation. Cl directly interacted with the DDX3X helicase core in the RNA binding region. This interaction impaired both ATPase and RNA helicase activities at physiologically relevant concentrations in a manner similar to inorganic phosphate and disrupted its condensation propensity in vitro. In neuroblastoma cells, Cl efflux induced the formation of large, persistent DDX3X-containing stress granules. Furthermore, the R326H mutation, which is linked to a severe neurodevelopmental disorder, altered the chemical environment of the Cl-binding site and impaired Cl-sensitive functions. Together, our findings demonstrate that Cl binding regulates DDX3X functions and provide insights into the molecular pathophysiology of a neurodevelopmental disorder-linked mutation in DDX3X.
Plants precisely regulate defense responses to balance energy allocation between growth and immunity. Here, we showed in that the homeodomain-leucine zipper protein 1 (HAT1) functions as a redox-controlled mediator that...Plants precisely regulate defense responses to balance energy allocation between growth and immunity. Here, we showed in that the homeodomain-leucine zipper protein 1 (HAT1) functions as a redox-controlled mediator that restricts defense responses by competing with the master immune regulator NPR1 for interaction with the transcription factor TGA3. Under normal conditions, oxidative modification of HAT1 at Cys, Cys, Cys, and Cys enhanced its binding affinity for TGA3, effectively competing with NPR1 for binding to TGA3 and sequestering TGA3 from target genes to maintain immune suppression. During immune activation in response to a bacterial pathogen, the phytohormone salicylic acid facilitated the reduction of HAT1 by the thioredoxins TRXh3 and TRXh5, thereby destabilizing the HAT1-TGA3 interaction. Salicylic acid also promoted the formation of NPR1-TGA3 complexes that activated defense gene expression. This redox switch mechanism enabled plants to dynamically regulate TGA3 transcriptional activity through reversible redox modification of HAT1. Our findings elucidate how HAT1 serves as a molecular brake to prevent immune overactivation while permitting dynamic response modulation.