Biology subjects

Vandewyer, E.

Publications and source records attributed to Vandewyer, E..

6 recordsLinked to original sources

bioRxiv2025

DeorphaNN: Virtual screening of GPCR peptide agonists using AlphaFold-predicted active state complexes and deep learning embeddings

Peptide-activated G protein-coupled receptors (GPCRs) regulate critical physiological processes such as metabolism, neural signalling, and endocrine function through their interaction with neuropeptides and peptide hormones. Despite their importance, identifying endogenous peptide agonists for GPCRs remains challenging, particularly for orphan receptors without known ligands. Recent advances in deep learning-based protein structure prediction, exemplified by AlphaFold (AF), have shown application beyond structural modelling, including protein-protein interaction prediction. Given that GPCR-peptide agonist interactions represent a specialized form of protein-protein interaction, we leveraged a dataset of experimentally validated agonist and non-agonist GPCR-peptide interactions from Caenorhabditis elegans to evaluate AF-Multimers ability to distinguish agonist-bound complexes. When modelling GPCR-peptide complexes, AF-Multimer confidence metrics partially discriminate agonist from non-agonist interactions, with improved discrimination achieved by utilizing AF-Multistate-derived active-state templates. We further investigated whether embeddings from the hidden layer of AF-Multimers neural network could distinguish agonist from non-agonist complexes. Feature performance analysis reveals that AF- Multimers pair representations outperform single representations, with distinct subregions of the pair representation providing complementary predictive signals. Building on these insights, we developed DeorphaNN, a graph neural network integrating active-state GPCR-peptide structural predictions, interatomic interactions, and deep learning embeddings to prioritize GPCR-peptide agonist interactions. DeorphaNN generalizes across datasets derived from different species, including annelids and humans, and successfully uncovered peptide agonists for two orphan GPCRs. DeorphaNN offers a novel computational resource to accelerate deorphanization by prioritizing GPCR-peptide agonist candidates for AI-guided experimental validation.

bioinformatics↗

bioRxiv2023

An ancient thyrostimulin-like neuroendocrine pathway regulates growth in Caenorhabditis elegans

In vertebrates, thyrostimulin is a highly conserved glycoprotein hormone that, besides thyroid stimulating hormone (TSH), is a potent ligand of the TSH receptor. Thyrostimulin is considered the most ancestral glycoprotein hormone and orthologs of its subunits, GPA2 and GPB5, are widely conserved across vertebrate and invertebrate animals. Unlike TSH, however, the functions of the thyrostimulin neuroendocrine system remain largely unexplored. Here, we identify a functional thyrostimulin-like signaling system in Caenorhabditis elegans. We show that orthologs of GPA2 and GPB5, together with thyrotropin-releasing hormone (TRH) related neuropeptides, constitute a neuroendocrine pathway that promotes growth in C. elegans. GPA2/GPB5 signaling is required for normal body size and acts through activation of the glycoprotein hormone receptor ortholog FSHR-1. C. elegans GPA2 and GPB5 increase cAMP signaling by FSHR-1 in vitro. Both subunits are expressed in enteric neurons and promote growth by signaling to their receptor in glial cells and the intestine. Impaired GPA2/GPB5 signaling causes bloating of the intestinal lumen. In addition, mutants lacking thyrostimulin-like signaling are defective in defecation behavior. Our study suggests that the thyrostimulin GPA2/GPB5 pathway is an ancient enteric neuroendocrine system that regulates intestinal function in ecdysozoans, and may ancestrally have been involved in the control of organismal growth.

neuroscience↗

bioRxiv2022

System-wide mapping of neuropeptide-GPCR interactions in C. elegans

Neuropeptides are ancient, widespread signaling molecules that underpin almost all brain functions. They constitute a broad ligand-receptor network, mainly by binding to G protein-coupled receptors (GPCRs). However, the organization of the peptidergic network and roles of many neuropeptides remain elusive, as our insight into neuropeptide-receptor interactions is limited and many peptide GPCRs in animal models and humans are still orphan receptors. Here we report a genome-wide neuropeptide-GPCR interaction map in C. elegans. By reverse pharmacology screening of over 55,384 possible interactions, we identify 461 cognate peptide-GPCR couples that uncover a broad signaling network with specific and complex combinatorial interactions encoded across and within single peptidergic genes. These interactions provide insights into neuropeptide functions and evolution. Combining our dataset with phylogenetic analysis supports peptide-receptor co-evolution and conservation of at least 14 bilaterian peptidergic systems in C. elegans. This resource lays a foundation for system-wide analysis of the peptidergic network. HighlightsO_LISystem-wide reverse pharmacology deorphanizes 68 C. elegans peptide GPCRs C_LIO_LIDiscovery of 461 peptide-GPCR pairs and additional ligands for characterized GPCRs C_LIO_LINeuropeptides show specific and complex combinatorial receptor interactions C_LIO_LIPeptide-GPCR pairs support long-range conservation and expansion of peptide systems C_LI

neuroscience↗

bioRxiv2020

Distinct Neuropeptide-Receptor Modules Regulate a Sex-Specific Behavioral Response to a Pheromone

Dioecious species are a hallmark of the animal kingdom, with opposing sexes responding differently to identical sensory cues. Here, we study the response of C. elegans to the small-molecule pheromone, ascr#8, which elicits opposing behavioral valences in each sex. We identify a novel neuropeptide-neuropeptide receptor (NP/NPR) module that is active in males, but not in hermaphrodites. Using a novel paradigm of neuropeptide rescue that we established, we leverage bacterial expression of individual peptides to rescue the sex-specific response to ascr#8. Concurrent biochemical studies confirmed individual FLP-3 peptides differentially activate two divergent receptors, NPR-10 and FRPR-16. Interestingly, the two of the peptides that rescued behavior in our feeding paradigm are related through a conserved threonine, suggesting that a specific NP/NPR combination sets a male state, driving the correct behavioral valence of the ascr#8 response. Receptor expression within pre-motor neurons reveals novel coordination of male-specific and core locomotory circuitries.

neuroscience↗

bioRxiv2020

Extrasynaptic volume transmission: A novel route for neuropeptide signaling in nematodes

Neural circuit synaptic connectivities (the connectome) provide the anatomical foundation for our understanding of nematode nervous system function. However, other non-synaptic routes of communication are known in invertebrates including extrasynaptic volume transmission (EVT), which enables short- and/or long-range communication in the absence of synaptic connections. Although EVT has been highlighted as a facet of Caenorhabditis elegans neurosignaling, no experimental evidence identifies body cavity fluid (pseudocoelomic fluid; PCF) as a vehicle for either neuropeptide or biogenic amine transmission. In the parasitic nematode Ascaris suum FMRFamide-like peptides encoded on flp-18 potently stimulate female reproductive organs but are only expressed in cells that are anatomically distant from the reproductive organ, with no known synaptic connections to this tissue. Here we report a new non-synaptic mode of signaling in nematodes mediated by neuropeptides within the PCF. Our data show that: (i) A. suum PCF (As-PCF) contains a catalogue of neuropeptides including FMRFamide-like peptides and neuropeptide-like proteins; (ii) the A. suum FMRFamide-like peptide As-FLP-18A dominates the As-PCF peptidome; (iii) As-PCF potently modulates nematode reproductive muscle function ex vivo, mirroring the effects of synthetic FLP-18 peptides; (iv) As-PCF activates the C. elegans FLP-18 receptors NPR-4 and -5; (v) As-PCF alters C. elegans behavior and, (vi) FLP-18 and FLP-18 receptors display pan-phylum distribution in nematodes. Here we provide the first direct experimental evidence that supports an extrasynaptic volume route for neuropeptide transmission in nematodes. These data demonstrate non-synaptic signaling within the nematode functional connectome and are pertinent to receptor deorphanisation approaches underpinning drug discovery programs for nematode pathogens.

neuroscience↗

bioRxiv2019

Neuromedin U signaling regulates memory retrieval of learned salt avoidance in a C. elegans gustatory circuit

Learning and memory are regulated by neuromodulatory pathways, but the contribution and temporal requirement of most neuromodulators in a learning circuit are unknown. Here we identify the evolutionarily conserved neuromedin U (NMU) neuropeptide family as a regulator of memory retrieval in C. elegans gustatory aversive learning. The NMU homolog CAPA-1 and its receptor NMUR-1 are required for the expression of learned salt avoidance. Aversive learning depends on the release of CAPA-1 neuropeptides from sensory ASG neurons that respond to salt stimuli in an experience-dependent manner. Optogenetic silencing of CAPA-1 neurons blocks the immediate retrieval, but not the acquisition, of learned salt avoidance. CAPA-1 subsequently signals through NMUR-1 in AFD sensory neurons to modulate two navigational strategies for salt chemotaxis. Aversive conditioning thus recruits NMU signaling to eventually modulate locomotor programs for expressing learned avoidance behavior. Because NMU signaling is conserved across bilaterian animals, our findings incite further research into its function in other memory and decision-making circuits.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC=\"FIGDIR/small/683888v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (58K):\norg.highwire.dtl.DTLVardef@10bf862org.highwire.dtl.DTLVardef@dfeb7eorg.highwire.dtl.DTLVardef@dda0b8org.highwire.dtl.DTLVardef@62bc95_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗