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.

Activation of the NLRP3 inflammasome can drive bone resorption by osteoclasts in various inflammatory conditions. Here, we identified Tmem178, a protein that restrains Ca2+ 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 Ca2+ concentrations. In vivo studies demonstrated that inflammasome formation was enhanced under conditions in which osteoclasts efficiently release Ca2+ from bone and that deletion of Nlrp3 rescued the osteopenic phenotype characteristic of Tmem178-/- mice. Thus, our results indicate that Tmem178 potently restricts Ca2+ influx in osteoclasts, thereby suppressing NLRP3 inflammasome activation.

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 (i3 LMNs). Metabolic RNA sequencing (SLAM-seq) and phosphoproteomic profiling of i3 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.

β-Arrestins are multifunctional, intracellular proteins that regulate the desensitization, internalization, and signaling of more than 800G 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.

Polyunsaturated fatty acids in a Western diet activate RXRα to promote Crohn's disease pathogenesis.

Wnt ligands stimulate β-catenin-dependent (canonical) or β-catenin-independent (noncanonical) signaling, depending on which co-receptors are recruited to the Wnt receptor FZD. Both pathways are initiated by receptor oligomerization into signalosomes and involve a largely overlapping set of downstream effectors. To resolve the assembly of Wnt signalosomes with high spatiotemporal resolution for extended times, we developed single-molecule tracking and localization microscopy based on labeling with reversibly binding nanobodies (rbTALM). We engineered nanobody-tag pairs with finely tuned binding affinities to ensure single-molecule tracking with high fidelity while also permitting continuous exchange of photobleached labels. Multicolor rbTALM imaging enabled simultaneous tracking and super-resolution imaging of three different tagged Wnt co-receptors in the same cell for more than 1 hour at video rate. Time-lapse correlation analyses uncovered cooperative association of canonical (LRP6) and noncanonical (ROR2) Wnt co-receptors with FZD8 into a common, hybrid Wnt signalosome. These findings demonstrate the potential for rbTALM imaging for exploring nanoscale dynamics across millisecond to hour timescales and for deciphering the molecular dynamics that underlie signaling complex formation.

Metabolic control of chromatin and gene expression is emerging as a key mechanism influencing critical neuronal functions. Here, we found that the intermediary metabolite acetate enhanced long-term memory in female mice, which was associated with epigenetic and transcriptional remodeling in the dorsal hippocampus. Acetate-enhanced memory was driven by increased acetylation of the histone variant H2A.Z and increased expression of genes implicated in learning in the female dorsal hippocampus. The effect of acetate on dorsal hippocampal histone modifications and gene expression differed markedly between the sexes during critical windows of memory consolidation and recall, and home cage exposure to acetate without the learning and recall tasks did not recapitulate these effects. These findings elucidate the ways in which acetate exposure enhances memory.

Most adhesion G protein-coupled receptors (AGPCRs) are activated by the intramolecular binding of a tethered agonist, which is exposed by shear force-induced dissociation of the N- and C-terminal fragments of AGPCRs. The decrypted tethered agonist binds to its orthosteric site in the C-terminal fragment to stabilize the active state of the AGPCR. Corticosteroids have been proposed to be orthosteric agonists for GPR97/ADGRG3. Here, we showed that GPR97/ADGRG3 is activated by the canonical tethered agonist mechanism. In cell-based luciferase reporter assays and receptor/G protein reconstitution assays, GPR97/ADGRG3 was stimulated by agonist peptidomimetics and by 3-acetoxydihydrodeoxygeduin (3-α-DOG), a partial agonist of the ADGRG subfamily, but not by corticosteroids. We showed that GPR97 was a promiscuous AGPCR that coupled to G13, Gs, and Gi but not to Gq. GPR97 is abundant in neutrophils, which undergo cell shape changes and polarization and migrate upon activation. GPR97 activation by tethered agonist peptidomimetics or 3-α-DOG robustly stimulated cAMP production, polarization, and chemotaxis in human and mouse neutrophils. These effects in mouse neutrophils required GPR97 and were not mimicked by the corticosteroid beclomethasone in either cell type. Together, our results demonstrate that GPR97/ADGRG3 uses a tethered agonist mechanism to activate G protein signaling and induce neutrophil polarization and migration.

Hydroxycarboxylic acid receptor 1 (HCAR1) is a class A G protein-coupled receptor (GPCR) that is activated by the endogenous metabolite l-lactate and that plays an important role in various metabolic and inflammatory disorders. HCAR1 uses distinct ligand recognition and self-activation mechanisms to mediate specific pathophysiological functions through Gαi/o and β-arrestin signaling pathways. To support effective drug development targeting HCAR1, we investigated ligand recognition and activation mechanisms through cryo-electron microscopy (cryo-EM) structures of the HCAR1-Gαi1 complex in the apo state or with l-lactate or with the synthetic agonist CHBA. Compared with other HCARs, HCAR1 has a more compact binding pocket, which is stabilized by three unique disulfide bonds. l-lactate exhibited a flexible binding mode and relatively weak intermolecular interactions, thus requiring millimolar concentrations for receptor activation. In contrast, the binding of CHBA was more stable because of its chlorinated benzene ring, thus resulting in improved agonist potency. Structural comparisons with HCAR2 identified critical residues that restrict the size of the binding pocket of HCAR1 and influence ligand selectivity. Self-activation of HCAR1 is driven by conformational rearrangements within extracellular loop 2, with Phe168ECL2 playing a pivotal role as the key agonist. Together, these results clarify the mechanisms underlying HCAR1 activation, self-activation, and ligand selectivity, providing a structural framework for the design of high-affinity, selective agonists and inverse agonists with minimized off-target effects.

A bacterial virulence factor subverts host cell apoptosis by acting as a protein recombinase.