Biology subjects

Chew, Y. L.

Publications and source records attributed to Chew, Y. L..

7 recordsLinked to original sources

bioRxiv2026

Synaptic proteomics identifies cathepsin B as a regulator of synapse remodelling during learning

Learning requires dynamic changes in synaptic protein composition. Most synaptic proteomic studies capture endpoint snapshots following training, overlooking molecular changes occurring during learning itself. We previously established TurboID proximity proteomics as an approach to capture protein-level changes during learning in the nervous system of Caenorhabditis elegans. Here, we apply this strategy to synapses. Trained synapses exhibited a distinct proteome compared with mock-trained controls, with pathways enriched for neurotransmission, synaptic reorganisation, protein trafficking, and autophagy. Enrichment of autophagy proteins led us to investigate the cathepsin B orthologue CPR-4, a previously uncharacterised candidate for learning identified exclusively in trained synapses. Functional validation identified CPR-4 as a novel regulator of memory: CPR-4 is required for learning, and the absence of CPR-4 results in trained synaptic proteomes that are more like those of mock-trained synapses. Our findings support a model through which CPR-4 promotes synaptic remodelling required for learning through targeted protein clearance.

neuroscience↗

bioRxiv2025

ALS/FTD-associated TDP-43 mutations promote fragility of genes governing excitatory neurotransmission via topoisomerase IIβ impairment

Abnormal TAR DNA/RNA-binding protein 43 (TDP-43) is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), characterized by cytoplasmic mis-localization, aggregation, and pathogenic mutations. Altered excitatory neuronal transmission is an early functional defect in these diseases; however, the underlying mechanisms remain unclear. Neuronal activity can induce DNA double-strand breaks (DSBs), suggesting a potential link between altered excitability and genomic instability. Here, we demonstrate for the first time that TDP-43 is involved in neuronal activity-induced DSBs. Moreover, we show that ALS/FTD-associated TDP-43 mutations (A90V and A315T) disrupt this mechanism, leading to the accumulation of DSBs and altered neuronal activity compared to wild-type TDP-43 protein. Using the BLISS technique, we mapped genome-wide DSBs in primary mouse neurons expressing wild-type or mutant (A90V, A315T) TDP-43 and found enrichment of DSBs within genes regulating excitatory transmission. Mechanistically, the TDP-43 A90V mutation impairs topoisomerase II{beta} function, resulting in enzyme trapping and/or DNA supercoiling that predisposes DNA to breaks. Notably, this impairment is partially rescued by tyrosyl-DNA phosphodiesterase 2 (Tdp2) overexpression. These findings uncover a novel mechanism linking aberrant neuronal activity and DNA damage, bridging two key pathological hallmarks of ALS/FTD associated with TDP-43 dysfunction. It also paves the way for developing novel therapeutic approaches that rely on targeted DSB repair and/or modulating topoisomerase II{beta}-DNA complexes. HighlightsO_LIALS/FTD linked TDP-43 mutants, unlike wild type, induce DSBs in key neuronal genes C_LIO_LITDP-43 driven DSBs impair neuronal transmission, linking two ALS/FTD pathologies C_LIO_LITDP-43 pathology impairs topoisomerase II{beta}, leading to DSB C_LI

neuroscience↗

bioRxiv2025

Dopaminergic Modulation of Short-Term Associative Memory in Caenorhabditis elegans

Forgetting, the inability to retrieve previously encoded memories, is an active process involving neurotransmission, second messenger signalling, and cytoskeletal modifications. Forgetting is thought to be essential to remove irrelevant memories and to increase the capacity to encode new memories. Therefore, identifying key regulators of active forgetting is crucial to advance our understanding of neuroplasticity. In this study, we utilised the compact and tractable Caenorhabditis elegans model to investigate the role of the neurotransmitter dopamine in forgetting. We conducted butanone associative learning assays based on an established protocol and used mutant strains deficient in dopamine synthesis (tyrosine hydroxylase CAT-2 and dopamine transporter DAT-1) and signalling (G protein-coupled receptors DOP-1, DOP-2, and DOP-3) to assess the impact on learning and memory retention. Learning was measured immediately post-training, and memory retention was evaluated every 0.5 hours up to 2 hours. Our results show that animals lacking dopamine display a modest enhancement in learning relative to wild-type, with the learned association persisting for at least 2 hours after training. We also found that D2-like receptors DOP-2 and DOP-3 act together to modulate the forgetting process, with D1-like receptor DOP-1 functioning redundantly. Furthermore, re-expression of CAT-2 tyrosine hydroxylase in ADE and/or CEP neurons was unable to rescue the memory retention phenotype observed in cat-2 mutants, suggesting that dopamine release from all dopaminergic neurons is required to modulate forgetting. These findings highlight the critical role of dopamine in forgetting, consistent with findings in Drosophila, and suggest potential relevance for understanding memory retention during healthy ageing and in conditions with dopamine imbalances such as Parkinsons disease.

neuroscience↗

bioRxiv2024

Identifying regulators of associative learning using a protein-labelling approach in C. elegans

The ability to learn and form memories is critical for animals to make choices that promote their survival. The biological processes underlying learning and memory are mediated by a variety of genes in the nervous system, acting at specific times during memory encoding, consolidation, and retrieval. Many studies have utilised candidate gene approaches or random mutagenesis screens in model animals to explore the key molecular drivers for learning and memory. We propose a complementary approach to identify this network of learning regulators: the proximity-labelling tool TurboID, which promiscuously biotinylates neighbouring proteins, to snapshot the proteomic profile of neurons during learning. To do this, we expressed the TurboID enzyme in the entire nervous system of C. elegans and exposed animals to biotin only during the training step of an appetitive gustatory learning paradigm. Our approach revealed hundreds of proteins specific to trained worms, including components of molecular pathways previously implicated in memory in multiple species such as insulin signalling, G protein-coupled receptor signalling, and MAP kinase signalling. Most (87-95%) of the proteins identified are neuronal, with relatively high representation for neuron classes involved in locomotion and learning. We validated several novel regulators of learning, including cholinergic receptors (ACC-1, ACC-3, LGC-46) and putative arginine kinase F46H5.3. These previously uncharacterised learning regulators all showed a clear impact on appetitive gustatory learning, with F46H5.3 showing an additional effect on aversive gustatory memory. Overall, we show that proximity labelling can be used in the brain of a small animal as a feasible and effective method to advance our knowledge on the biology of learning.

neuroscience↗

bioRxiv2021

Neuropeptide signalling shapes feeding and reproductive behaviours in male C. elegans

Sexual dimorphism occurs where different sexes of the same species display differences in characteristics not limited to reproduction. For the nematode Caenorhabditis elegans, in which the complete neuroanatomy has been solved for both hermaphrodites and males, sexually dimorphic features have been observed both in terms of the number of neurons and in synaptic connectivity. In addition, male behaviours, such as food-leaving to prioritise searching for mates, have been attributed to neuropeptides released from sex-shared or sex-specific neurons. In this study, we show that the lury-1 neuropeptide gene shows a sexually dimorphic expression pattern; being expressed in pharyngeal neurons in both sexes but displaying additional expression in tail neurons only in the male. We also show that lury-1 mutant animals show sex differences in feeding behaviours, with pharyngeal pumping elevated in hermaphrodites but reduced in males. LURY-1 also modulates male mating efficiency, influencing motor events during contact with a hermaphrodite. Our findings indicate sex-specific roles of this peptide in feeding and reproduction in C. elegans, providing further insight into neuromodulatory control of sexually dimorphic behaviours.

neuroscience↗

bioRxiv2021

Exploiting flow cytometry for the unbiased quantification of protein inclusions in Caenorhabditis elegans

The aggregation of proteins into inclusions or plaques is a prominent hallmark of a diverse range of pathologies including neurodegenerative diseases. The quantification of such inclusions in Caenorhabditis elegans models of aggregation is usually achieved by fluorescence microscopy or other techniques involving biochemical fractionation of worm lysates. Here, we describe a simple and rapid flow cytometry-based approach that allows fluorescently-tagged inclusions to be enumerated in whole worm lysate in a quantitative and unbiased fashion. We demonstrate that this technique is applicable to multiple C. elegans models of aggregation and importantly, can be used to monitor the dynamics of inclusion formation in response to heat shock and during aging. This includes the characterisation of physicochemical properties of inclusions, such as their size, which may reveal how aggregate formation is distinct in different tissues or at different stages of pathology or aging. This new method can be used as a powerful technique for the medium- to high-throughput quantification of inclusions in future studies of genetic or chemical modulators of aggregation in C. elegans.

molecular biology↗

bioRxiv2019

Automated analysis of sleep in adult C. elegans with closed-loop assessment of state-dependent neural activity

Sleep, a state of quiescence associated with growth and restorative processes, is conserved across species. Invertebrates including the nematode Caenorhabditis elegans exhibit sleep-like states during development and periods of satiety and stress. Here we describe two methods to study behavior and associated neural activity during sleep and awake states in adult C. elegans. A large microfluidic device facilitates population-wide assessment of long-term sleep behavior over 12 h, including effects of fluid flow, oxygen, feeding, odors, and genetic perturbations. Smaller devices allow simultaneous recording of sleep behavior and neuronal activity, and a closed-loop sleep detection system delivers chemical stimuli to individual animals to assess sleep-dependent changes to neural responses. Sleep increased the arousal threshold to aversive chemical stimulation, yet sensory neuron (ASH) and first-layer interneuron (AIB) responses were unchanged. This localizes adult sleep-dependent neuromodulation within interneurons presynaptic to the AVA premotor interneurons, rather than afferent sensory circuits.

neuroscience↗