Lily Yeh Jan

Electrophysiology

University of California, San Francisco

About

Lily Yeh Jan works in Electrophysiology affiliated with University of California, San Francisco.

Lily Yeh Jan is a Professor of Physiology and Biophysics at the University of California, San Francisco School of Medicine. She serves as an Investigator at the Howard Hughes Medical Institute. Her research focuses on ion channels with applications to neuronal and cardiac electrophysiology.

Research focus

Cardiac ion channel regulationMechanisms of heart rate control via GIRK channelsATP-sensitive potassium channels in cardiac functionCalcium-activated chloride channels in cardiovascular physiologyIon channel contributions to cardiac arrhythmias

Impact

600 pubs · 81,386 cites · h-index 171

Training

PhD in Biophysics and Physics
California Institute of Technology
1974
MSc in Physics
California Institute of Technology
1970
BSc in Physics
National Taiwan University
1968

Affiliations

Work Experience

Professor of Physiology and Biophysics

University of California, San Francisco · 1979 - Present

Investigator

Howard Hughes Medical Institute · 1984 - Present

Postdoctoral Research Fellow

Harvard Medical School · 1977 - 1979

Postdoctoral Research Fellow

California Institute of Technology · 1974 - 1977

Publications

Shroff et al.Original Research

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 scramblases 1 and inactivation of specific flippases 2 . Localized caspase activation at neuronal synapses can mediate spatially-restricted synaptic phosphatidylserine exposure leading to synapse pruning by glial cells during development and neurodegeneration 3–6 . 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 dementia 7 and other neurological diseases 8,9 .

Wang et al.Original Research

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

Summary 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 al 1 .

Yong et al.Original Research

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.

Science AdvancesWang et al.Original Research

Nonlinear stiffness of NompC gating spring and its implication in mechanotransduction

Findings reveal nonlinear stiffness in mechanosensitive channels, suggesting enhanced sensitivity to mechanical stimuli.

Chen et al.Original Research

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.

Biophysical JournalWong et al.Original Research

BPS2026 – Tension-mediated feedback between the cortex and phospholipid scramblases underlies plasma membrane blebbing

Live-cell imaging reveals positive feedback loop between cortex detachment and phosphatidylserine exposure during apoptosis and immune evasion.

Biophysical JournalHilten et al.Original Research

BPS2026 – A molecular perspective on TMEM16F-mediated lipid scrambling in complex membranes

Molecular dynamics reveals TMEM16F's role in lipid scrambling and blood clotting through phosphatidylserine exposure.

NeuronWang et al.Original Research

CLN3 mediates chloride efflux from lysosomes

Neurodegenerative diseases, which pose significant challenges for effective treatment, often involve risk variants of lysosomal gene products that disrupt lysosomal function, leading to the accumulation of indigestible materials and damage to brain cells. The lysosome is a degradative organelle and a signaling hub that senses nutrient availability. How lysosomal dysfunction contributes to neurodegenerative diseases is an important open question. In this study, we identified CLN3 (ceroid lipofuscinosis, neuronal 3), an endolysosomal protein that is linked to Batten disease, as an evolutionarily conserved protein that facilitates lysosomal chloride efflux. Additionally, we report that a natural compound with anti-inflammatory properties-the curcumin analog C1, which is a TFEB (transcription factor EB) activator-could enhance CLN3 activity and improve lysosomal function. These findings provide new insight into the role of CLN3 in lysosomal ion homeostasis and raise the possibility that modulation of the TFEB-CLN3 signaling axis may hold therapeutic potential for lysosomal storage disorders.

Proceedings of the National Academy of SciencesTeo et al.Original Research

A cell-based scrambling assay reveals the 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 (FP) of nitrobenzoxadiazole (NBD)-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.

NeuronGuo et al.Original Research

Identification of the peptide Vulnusin, a wound signal that mediates mechanical-injury-induced nociception in Drosophila

Animals can acutely sense a puncture or cut in their skin through nociceptors. However, the molecular identity of such "wound signals" and their receptors on nociceptors remains unknown. In Drosophila larvae, class IV dendritic arborization neurons are multimodal nociceptors that detect harsh touch, heat, and UV light to initiate nociceptive behavior. Here, we identify Vulnusin (from vulnus, a Latin word for wound), an endogenous peptide likely serving as a wound signal. Vulnusin, derived from the larval epidermis, activates PPK1/PPK26 ion channels expressed endogenously on nociceptors and heterologously in Drosophila S2 cells. Moreover, Vulnusin acts together with PPK1/PPK26 to trigger puncture-induced rolling behavior, a response to mechanical injury. These findings establish Vulnusin as a ligand that activates larval nociceptors and mediates mechanical-injury-induced nociception.

Zhang et al.Original Research

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

This research uncovers distinct remodeling in dopamine neurons, revealing roles of AKT-GSK3β signaling and glia in circuit maturation.

Nature Structural & Molecular BiologyJan et al.Review

Wide-ranging cellular functions of ion channels and lipid scramblases in the structurally related TMC, TMEM16 and TMEM63 families

Calcium (Ca2+)-activated ion channels and lipid scramblases in the transmembrane protein 16 (TMEM16) family are structurally related to mechanosensitive ion channels in the TMEM63 and transmembrane channel-like (TMC) families. Members of this structurally related superfamily share similarities in gating transitions and serve a wide range of physiological functions, which is evident from their disease associations. The TMEM16, TMEM63 and TMC families include members with important functions in the cell membrane and/or intracellular organelles such as the endoplasmic reticulum, membrane contact sites, endosomes and lysosomes. Moreover, some members of the TMEM16 family and the TMC family perform dual functions of ion channel and lipid scramblase, leading to intriguing physiological implications. In addition to their physiological functions such as mediating phosphatidylserine exposure and facilitation of extracellular vesicle generation and cell fusion, scramblases are involved in the entry and replication of enveloped viruses. Comparisons of structurally diverse scramblases may uncover features in the lipid-scrambling mechanisms that are likely shared by scramblases. In this Review, the authors discuss the physiological and biophysical functions of structurally related TMC, TMEM16 and TMEM63 families, with an aim to elucidate the mechanisms that control ion channel gating and mechanisms for scrambling lipids in the lipid membranes.

Molecular PharmacologyJanOriginal Research

Voltage sensors

Widely distributed in all kingdoms of life, voltage sensors in the membrane serve important functions via their movements driven by changes of voltage across the membrane (membrane potential). A voltage sensor domain contains four transmembrane segments (S1-S4). The S1-S3 helices form a hydrophobic constriction site (HCS, also known as the gating charge transfer center) that spans roughly one third of the membrane thickness. Flanked by aqueous vestibules connected to extracellular solution above the HCS or cytoplasmic solution below the HCS, the HCS forms a gating pore for the S4 segment bearing multiple basic residues. Membrane potential changes cause S4 to move through the HCS in a 3 10 helical conformation. This S4 translocation generates gating current as the positively charged S4 basic residues traverse the membrane electric field, transferring these gating charges from one aqueous vestibule to the other. For voltage-gated ion channels with their voltage sensor domains connected to pore domains, the HCS in the voltage sensor domain allows S4 but not ions to go through, while the channel pore formed by the pore domains mediates ion permeation. Voltage sensor mutations could result in ω currents that are conducted through the gating pore of mutant voltage-gated ion channels. These ω currents may cause pathological consequences in patients with periodic paralysis. Besides voltage-gated ion channels, the sperm-specific Na + /H + exchanger and voltage-sensing phosphatases contain voltage sensors for membrane potential regulation. Notably, voltage-gated proton channels that are important for pH homeostasis are formed solely by the voltage sensor domain, which mediates proton permeation.

Communications BiologyTuomivaara et al.Original Research

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

To facilitate our understanding of proteome dynamics during signaling events, robust workflows affording fast time resolution without confounding factors are essential. We present Surface-exposed protein Labeling using PeroxidaSe, H

Proceedings of the National Academy of SciencesZubia et al.Original Research

TMEM16F exacerbates tau pathology and mediates phosphatidylserine exposure in phospho-tau-burdened neurons

TMEM16F is a calcium-activated phospholipid scramblase and nonselective ion channel, which allows the movement of lipids bidirectionally across the plasma membrane. While the functions of TMEM16F have been extensively characterized in multiple cell types, the role of TMEM16F in the central nervous system remains largely unknown. Here, we sought to study how TMEM16F in the brain may be involved in neurodegeneration. Using a mouse model that expresses the pathological P301S human tau (PS19 mouse), we found reduced tauopathy and microgliosis in 6- to 7-mo-old PS19 mice lacking TMEM16F. Furthermore, this reduction of pathology can be recapitulated in the PS19 mice with TMEM16F removed from neurons, while removal of TMEM16F from microglia of PS19 mice did not significantly impact tauopathy at this time point. Moreover, TMEM16F mediated aberrant phosphatidylserine exposure in neurons with phospho-tau burden. These studies raise the prospect of targeting TMEM16F in neurons as a potential treatment of neurodegeneration.

Wang et al.Original Research

Nonlinear compliance of NompC gating spring and its implication in mechanotransduction

Cytoskeleton-tethered mechanosensitive channels (MSCs) utilize compliant proteins or protein domains called gating springs to convert mechanical stimuli into electric signals, enabling sound and touch sensation and proprioception. The mechanical properties of these gating springs, however, remain elusive. Here, we explored the mechanical properties of the homotetrameric NompC complex containing long ankyrin-repeat domains (ARDs). We developed a toehold-mediated strand displacement approach to tether single membrane proteins, allowing us to exert force on them and precisely measure their absolute extension using optical tweezers. Our findings revealed that each ARD has a low stiffness of ~0.7 pN/nm and begins to unfold stepwise at ~7 pN, leading to nonlinear compliance. Our calculations indicate that this nonlinear compliance may help regulate NompC's sensitivity, dynamic range, and kinetics to detect mechanical stimuli. Overall, our research highlights the importance of a compliant and unfolding-refolding gating spring in facilitating a graded response of MSC ion transduction across a wide spectrum of mechanical stimuli.

NeurologyLi et al.Original Research

ANO6 Regulates Lipid Droplets in Astrocyte via Fatty Acid Uptake and Is Involved in Inflammation (P4-9.006)

By comparing lipid droplet storage between control and Ano6 mutant mice, we want to test if ANO6 is involved in lipid metabolism, and then elucidate the pathway underlying the lipid droplet regulation process, to identify the physiological and pathological involvement of ANO6 in inflammation and neurodegeneration.

Nature Cell BiologyLi et al.Original Research

Drosophila TMEM63 and mouse TMEM63A are lysosomal mechanosensory ion channels

Cells sense physical forces and convert them into electrical or chemical signals, a process known as mechanotransduction. Whereas extensive studies focus on mechanotransduction at the plasma membrane, little is known about whether and how intracellular organelles sense mechanical force and the physiological functions of organellar mechanosensing. Here we identify the Drosophila TMEM63 ( Dm TMEM63) ion channel as an intrinsic mechanosensor of the lysosome, a major degradative organelle. Endogenous Dm TMEM63 proteins localize to lysosomes, mediate lysosomal mechanosensitivity and modulate lysosomal morphology and function. Tmem63 mutant flies exhibit impaired lysosomal degradation, synaptic loss, progressive motor deficits and early death, with some of these mutant phenotypes recapitulating symptoms of TMEM63-associated human diseases. Importantly, mouse TMEM63A mediates lysosomal mechanosensitivity in Neuro-2a cells, indicative of functional conservation in mammals. Our findings reveal Dm TMEM63 channel function in lysosomes and its physiological roles in vivo and provide a molecular basis to explore the mechanosensitive process in subcellular organelles.

Nature CommunicationsFeng et al.preclinical

Identified a lipid scrambling pathway along a groove containing the binding pocket for niclosamide and 1PBC, with mutational analysis supporting separate pathways for ion permeation and lipid scrambling.

May enable selective TMEM16F modulation; extends mechanistic insight but leaves open clinical translation.

BrainPinard et al.Original Research

Rare variants in ANO1 , encoding a calcium-activated chloride channel, predispose to moyamoya disease

Moyamoya disease, a cerebrovascular disease leading to strokes in children and young adults, is characterized by progressive occlusion of the distal internal carotid arteries and the formation of collateral vessels. Altered genes play a prominent role in the aetiology of moyamoya disease, but a causative gene is not identified in the majority of cases. Exome sequencing data from 151 individuals from 84 unsolved families were analysed to identify further genes for moyamoya disease, then candidate genes assessed in additional cases (150 probands). Two families had the same rare variant in ANO1, which encodes a calcium-activated chloride channel, anoctamin-1. Haplotype analyses found the families were related, and ANO1 p.Met658Val segregated with moyamoya disease in the family with an LOD score of 3.3. Six additional ANO1 rare variants were identified in moyamoya disease families. The ANO1 rare variants were assessed using patch-clamp recordings, and the majority of variants, including ANO1 p.Met658Val, displayed increased sensitivity to intracellular Ca2+. Patients harbouring these gain-of-function ANO1 variants had classic features of moyamoya disease, but also had aneurysm, stenosis and/or occlusion in the posterior circulation. Our studies support that ANO1 gain-of-function pathogenic variants predispose to moyamoya disease and are associated with unique involvement of the posterior circulation.

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