Biology subjects

Jan, L. Y.

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

12 recordsLinked to original sources

bioRxiv2026

Synaptic activity controls local exposure of an 'eat-me' signal via ANO3-ITPR1 signaling

Neuronal synapses are eliminated during brain development and disease through pruning by glial cells. Individual synapses are marked for engulfment by eat-me signals, which include externalized phosphatidylserine. In apoptotic cells, phosphatidylserine externalization is driven by caspase-dependent activation of Xkr scramblases1 and inactivation of specific flippases2. Localized caspase activation at neuronal synapses can mediate spatially-restricted synaptic phosphatidylserine exposure leading to synapse pruning by glial cells during development and neurodegeneration3-6. It is unknown which caspase-regulated flippases and scramblases promote synaptic phosphatidylserine exposure and whether there are any caspase-independent mechanisms of phosphatidylserine exposure relevant for synapse elimination. To address this question, we here develop a scalable CRISPR screening approach, COMPASS-seq (compartment-anchored sgRNA screen sequencing), to uncover the genetic underpinnings of subcellular phenotypes. COMPASS-seq is compatible with in vitro and in vivo systems and a wide range of subcellular compartments; we here apply it to the neuronal synapse. We discover that inhibition of the caspase-independent, calcium-activated anoctamin ANO3 (TMEM16C) is sufficient to increase synapse numbers in vivo. ANO3 co-localizes with IP3 receptor 1 (ITPR1), a calcium channel in the endoplasmic reticulum, to form a postsynaptic signaling platform that drives spatially restricted phosphatidylserine exposure at synapses. Activation of the ITPR1 calcium channel activity is sufficient to drive synaptic phosphatidylserine exposure via an ANO3-dependent but caspase-independent mechanism. Our results suggest a mechanism for integrating synaptic activity information to control synaptic pruning. The role of ANO3 in regulating synapses could shed light on the mechanisms underlying its numerous associations with both dementia7 and other neurological diseases8,9.

neuroscience↗

bioRxiv2026

Protocol for assessing lysosomal ion channel function in mammalian cells using lysosomal patch-clamp technique

This protocol describes manual whole-endolysosome patch-clamp recordings from pharmacologically or genetically enlarged endolysosomes in cultured mammalian cells. Steps include vesicle enlargement, fabrication and fire-polishing of high-resistance pipettes, mechanical dissection and isolation of enlarged vesicles, giga-seal formation, and configuration to whole-endolysosome modes. For complete details on the use and execution of this protocol, please refer to Wang et al1.

cell biology↗

bioRxiv2026

Calcium-dependent synaptic proteomics reveals EGFR signaling at active synapses

Activity-dependent remodeling of the synaptic proteome is essential for circuit maturation, plasticity, and adaptation. However, these molecular changes are transient and spatially sparse in intact neural circuits, making them difficult to resolve under physiological conditions. To address this challenge, we developed synaptic Cal-ID, a synapse-targeted, calcium-dependent proximity labeling strategy that enables activity-resolved proteomic profiling under native physiological conditions. Using synaptic Cal-ID, we uncover an unexpected mechanism by which synaptic activity locally engages epidermal growth factor receptor (EGFR) signaling. We identify two novel synaptic proteins, Anks1a and Ubash3b, that are rapidly recruited following activity and cooperatively promote postsynaptic enrichment and signaling of EGFR. Disruption of this pathway impairs synaptic maturation, plasticity, and memory. Together, these findings reveal how neuronal activity establishes local signaling competence at active synapses by concentrating the molecular machinery required to engage a broadly acting growth factor pathway.

neuroscience↗

bioRxiv2026

WTR: A Toolkit for Functional Anterograde Transsynaptic Circuit Mapping

The brain coordinates animal physiology and behavior via neuronal circuits. To understand and simulate brain functions, it is essential to delineate the synaptic connectivity between neurons. Transsynaptic tracers serve as powerful tools for such purposes. In response to the demand for anterograde tracers for circuit mapping and functional interrogation, we developed WTR, a fusion protein of mammalian codon-optimized WGA, TEV-protease cleavage sequence, and Recombinase. WTR expressed via AAV vectors in cell-type-specific starter neurons reaches their postsynaptic neurons and releases Cre/Flpo upon exposure to TEV-protease expressed in downstream neurons. Accompanied by Cre/Flpo-dependent expression of EGFP, GCaMP7s, or ChR2, the toolkit enables labeling, recording, or manipulation of downstream neurons. We utilized WTR to characterize downstream neurons of either glutamatergic or GABAergic neurons in the preoptic area of anterior hypothalamus for their differential actions in thermoregulation or stress responses, respectively. These results establish WTR as a versatile platform for functional anterograde circuit mapping.

neuroscience↗

bioRxiv2025

Atypical developmental remodeling of dopamine neurons involves AKT-GSK3β signaling and glia-mediated axon degeneration

Neuronal remodeling is essential for sculpting neural circuits, and its disruption has been implicated in neurodevelopmental and neuropsychiatric disorders. Yet the molecular and cellular diversity of remodeling across neuron types remains incompletely understood. Here, we uncover a distinct remodeling mode in a subtype of Drosophila dopamine neurons (DANs) critical for learning, memory, sleep, and locomotion. Unlike the stereotypical pruning-then-regrowth paradigm, these DANs undergo a transient axon overgrowth followed by selective pruning during metamorphosis. Remarkably, DAN axon pruning proceeds independently of canonical ecdysone signaling and instead involves neuron-intrinsic AKT-GSK3{beta} signaling and extrinsic glial activity. Disruption of AKT-GSK3{beta} signaling alters microtubule stability and impairs glial recruitment and clearance of axonal debris. Notably, the role of AKT-GSK3{beta} is cell-type specific, underscoring mechanistic diversity in remodeling programs. These findings reveal an unexpected overgrowth-then-pruning developmental trajectory, establishing DANs as a powerful model to uncover the mechanisms underlying neuronal remodeling, circuit maturation, and neurodegeneration.

neuroscience↗

bioRxiv2025

A cell-based scrambling assay reveals phospholipid headgroup preference of TMEM16F on the plasma membrane

The asymmetric resting distribution of the three major phospholipid classes on the mammalian plasma membrane, with phosphatidylserine and phosphatidylethanolamine mostly on the inner leaflet, and phosphatidylcholine mostly on the outer leaflet, is maintained by ATP-dependent flippases and floppases that exhibit headgroup selectivity. Upon signaling cues, this asymmetry can be dissipated by various phospholipid scramblases, allowing cells to respond to stimuli and adapt to different physiological contexts. The prevailing view in the field is that phospholipid scramblases on the plasma membrane act without headgroup preference. Here we report contrary experimental evidence based on a phospholipid scrambling assay that quantifies the fluorescence polarization of nitrobenzoxadiazole-labeled phospholipids for kinetic monitoring of phospholipid scrambling on the plasma membrane of living cells. Our experiments reveal that the plasma membrane-residing calcium-activated phospholipid scramblase TMEM16F preferentially acts on phosphatidylserine and phosphatidylcholine over phosphatidylethanolamine. Significance StatementPhospholipid scramblases on the mammalian plasma membrane are thought to act promiscuously without preference for headgroup. Thoroughly addressing this question, however, requires the development of new methodologies. We devised a cell-based phospholipid scrambling assay that utilizes the fluorescence polarization of nitrobenzoxadiazole (NBD)-labeled phospholipids, allowing the monitoring of their scrambling in a native environment. We discovered that the plasma membrane-residing calcium-activated phospholipid scramblase TMEM16F preferentially acts on phosphatidylserine and phosphatidylcholine over phosphatidylethanolamine. Major Classification: Biological Sciences; Minor Classification: Cell biology, Biophysics and Computational Biology

cell biology↗

bioRxiv2023

SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling

To facilitate our understanding of the often rapid and nuanced dynamics of extracellularly exposed proteomes during signaling events, it is important to devise robust workflows affording fast time resolution without biases and confounding factors. Here, we present Surface-exposed protein Labeling using PeroxidaSe, H2O2, and Tyramide-derivative (SLAPSHOT), to label extracellularly exposed proteins in a rapid, sensitive, and specific manner, while preserving cellular integrity. This experimentally simple and flexible method utilizes recombinant soluble APEX2 peroxidase that is applied to cells, thus circumventing biological perturbations, tedious engineering of tools and cells, and labeling biases. APEX2 neither requires metal cations for activity nor contains disulfide bonds, conferring versatility for a wide spectrum of experimental setups. We applied SLAPSHOT followed by quantitative mass spectrometry-based proteomics analysis to examine the immediate and extensive cell surface expansion and ensuing restorative membrane shedding upon the activation of Scott syndrome-linked TMEM16F, a ubiquitously expressed calcium-dependent phospholipid scramblase and ion channel. Time-course data ranging from one to thirty minutes of calcium stimulation using wild-type and TMEM16F deficient cells revealed intricate co-regulation of known protein families, including those in the integrin and ICAM families. Crucially, we identified proteins that are known to reside in intracellular organelles, including ER, as occupants of the freshly deposited membrane, and mitovesicles as an abundant component and contributor to the extracellularly exposed proteome. Our study not only provides the first accounts of the immediate consequences of calcium signaling on the extracellularly exposed proteome, but also presents a blueprint for the application of SLAPSHOT as a general approach for monitoring extracellularly exposed protein dynamics. HighlightsAn enzyme-driven method to tag extracellularly exposed proteins in an unbiased manner with a superior combination of temporal resolution, spatial specificity, and sensitivity A general approach applicable to primary and scarce cells without involving cellular engineering Short time scale proteome dynamics of Jurkat cells with and without TMEM16F revealed by SLAPSHOT coupled with quantitative mass spectrometry provide insights into phospholipid scrambling-mediated plasma membrane remodeling

biochemistry↗

bioRxiv2021

Steroid hormone signaling activates thermal nociception during Drosophila peripheral nervous system development

Sensory neurons enable animals to detect environmental changes and avoid harm. An intriguing open question concerns how the various attributes of sensory neurons arise in development. Drosophila melanogaster larvae undergo a behavioral transition by robustly activating a thermal nociceptive escape behavior during the second half of larval development (3rd instar). The Class 4 dendritic arborization (C4da) neurons are multimodal sensors which tile the body wall of Drosophila larvae and detect nociceptive temperature, light, and mechanical force. In contrast to the increase in nociceptive behavior in the 3rd instar, we find that ultraviolet light-induced Ca2+ activity in C4da neurons decreases during same period of larval development. Loss of ecdysone receptor has previously been shown to reduce nociception in 3rd instar larvae. We find that ligand dependent activation of ecdysone signaling is sufficient to promote nociceptive responses in 2nd instar larvae and suppress expression of subdued (encoding a TMEM16 channel). Reduction of subdued expression in 2nd instar C4da neurons not only increases thermal nociception but also decreases the response to ultraviolet light. Thus, steroid hormone signaling suppresses subdued expression to facilitate the sensory switch of C4da neurons. This regulation of a developmental sensory switch through steroid hormone regulation of channel expression raises the possibility that ion channel homeostasis is a key target for tuning the development of sensory modalities.

neuroscience↗

bioRxiv2021

Loss of the GARP but not EARP protein complex drives Golgi sterol overload during dendrite remodeling

Membrane trafficking is essential for sculpting neuronal morphology. The GARP and EARP complexes are conserved tethers that regulate vesicle trafficking in the secretory and endolysosomal pathways, respectively. Both complexes contain the Vps51, Vps52, and Vps53 proteins, and a complex-specific protein: Vps54 in GARP and Vps50 in EARP. In Drosophila, we find that both complexes are required for dendrite morphogenesis during developmental remodeling of multidendritic class IV da (c4da) neurons. Having found that sterol accumulates at the trans-Golgi network (TGN) in Vps54KO/KO neurons, we investigated genes that regulate sterols and related lipids at the TGN. Overexpression of oxysterol binding protein (Osbp) or knockdown of the PI4K four wheel drive (fwd) exacerbates the Vps54KO/KO phenotype, whereas eliminating one allele of Osbp rescues it, suggesting that excess sterol accumulation at the TGN is, in part, responsible for inhibiting dendrite regrowth. These findings distinguish the GARP and EARP complexes in neurodevelopment and implicate vesicle trafficking and lipid transfer pathways in dendrite morphogenesis.

cell biology↗

bioRxiv2019

Single Cell RNAseq Reveals A Critical Role of Chloride Channels in Airway Development

The conducting airway forms a protective mucosal barrier and is the primary target of airway disorders. To better understand how airway developmental programs are established to support air breathing and barrier functions, we constructed a single-cell atlas of the human and mouse developing trachea. In this study, we uncover hitherto unrecognized heterogeneity of cell states with distinct differentiation programs and immune features of the developing airway. In addition, we find ubiquitous expression of CFTR and ANO1/TMEM16A chloride channels in the embryonic airway epithelium. We show that genetic inactivation of TMEM16A leads to airway defects commonly seen in cystic fibrosis patients with deficient CFTR, alters the differentiation trajectory of airway basal progenitors, and results in mucus cell hyperplasia and aberrant epithelial antimicrobial expression. Together, our study illuminates conserved developmental features of the mammalian airway and implicates chloride homeostasis as a key player in regulating mucosal barrier formation and function relevant to early onset airway diseases.

developmental biology↗

bioRxiv2019

Dynamic Change of Electrostatic Field in TMEM16F Permeation Pathway Shifts Its Ion Selectivity

TMEM16F is activated by elevated intracellular Ca2+, and functions both as a small-conductance ion channel permeable to Ca2+ and as a phospholipid scramblase. It is important to hold this positive feedback in check to prevent prolonged Ca2+-overloading in cells. We hypothesize that TMEM16F shifts its ion selectivity so that it is more permeable to Cl- than cations at high intracellular Ca2+ concentration. We tested this hypothesis with the Q559K mutant that shows no current rundown in excised patch with prolonged Ca2+ elevation. Recorded in NaCl-based solution, the channel shifted its ion selectivity from Na+-selective to Cl--selective when intracellular Ca2+ was increased. The ion selectivity switch did not correlate with changes of channel open state. Rather, it was indicative of an alteration of electrostatic field in the permeation pathway. Shifting ion-selectivity synergistically by intracellular divalent ions and membrane potential could work as a built-in mechanism that allows TMEM16F to brake the positive feedback.

biophysics↗

bioRxiv2016

Sexually satiated male Drosophila melanogaster uses gustatory-to-neuropeptide integrative circuits to reduce time investment for mating

Males rely on a time investment strategy to maximize reproductive success. Here we report a novel behavioral plasticity whereby male fruit flies exhibit a shortened mating duration when sexually satiated, which we named Shorter-Mating-Duration (SMD). SMD requires the sexually dimorphic Gr5a-positive neurons for detecting female body pheromones. The memory circuitry within the ellipsoid body (EB) and mushroom body (MB) brain regions is crucial for SMD, which depends on the circadian clock genes Clock and cycle, but not timeless or period. SMD also relies on signaling via the neuropeptide sNPF, but not PDF or NPF. Sexual experience modifies the neuronal activity of a subset of sNPF-positive neurons involved in neuropeptide signaling, which modulates SMD. Thus, our study delineates the molecular and cellular basis for SMD - a plastic social behavior that serves as a model system to study how the brain switches the internal states between sexual drive and satiety.

neuroscience↗