Shining Light on Enigmatic Chloride Channels
Chloride is the only major free anion in animal cells. Transport of chloride and other organic anions across membranes plays an essential role in maintaining volume and ionic homeostasis of cells as well as membrane-bound intracellular organelles. Despite their importance, chloride channels are considerably under-studied compared to ion channels conducting cations (Na+, K+, and Ca2+). Diverse chloride channel activities on cell and organelle membranes have been observed by electrophysiology. However, many of their molecular identities remain unknown. Several factors contribute to this lack of progress. Unlike cation channels, there are no sequence homologies among different chloride channel families, highlighting their independent evolutionary origins. The lack of high-affinity channel ligands (e.g. toxins) hinders direct biochemical purification. Expression cloning, an otherwise powerful technique, is hampered by the endogenous expression of various chloride currents in popular expression systems. To solve these puzzles, we have developed high-throughput cell-based assays for anion flux, and through functional genomics screens, identified two new families of genes (SWELL1/LRRC8A and PAC/TMEM206) encoding the volume-regulated anion channel (VRAC) and proton-activated chloride (PAC) channel, respectively. With these discoveries, we have already begun to reveal their exciting new biology: SWELL1 in neuron-glia interactions (beyond cell volume regulation) and PAC in endosomal physiology. We are uniquely positioned to further probe their physiological function and fundamental mechanisms of volume and pH sensing. We will also systematically identify other unknown chloride channels. The overall goal of our unique research program is to arrive at a comprehensive understanding of the role of under-explored but important chloride channels in cellular physiology, combining biophysical and genetic approaches to link structure to function and to enable new pharmacology targeting them in diseases.
SWELL1 Channel: A Critical Role in the Release of Signaling Molecules and Cell-Cell Communication
Keeping cell volume constant is essential for maintaining cellular function and homeostasis. How the volume of cells is regulated and how their dysregulation contributes to diseases are two fundamental questions in biology and medicine. Chloride is the only major free anion in cells. Its movement across membranes plays a critical role in volume regulation and many other physiological processes. For example, increases in intracellular osmolarity (e.g., accumulation of metabolites in cancer cells) or decreases in extracellular osmolarity induce water influx across the cell membrane via a process known as osmosis. The resulting cell swelling activates a ubiquitously expressed Volume-Regulated Anion Channel (VRAC), which mediates the release of chloride and organic osmolytes out of the cells, thus facilitating water efflux by osmosis and leading to volume decrease and homeostasis. The activity of VRAC had been known since the 1980s, with hundreds of publications. However, despite intense search, its molecular identity remained a mystery. To solve this puzzle, we developed a high-throughput cell-based YFP quenching assay for anion flux. With this technology, we performed a genome-wide RNAi screen with a siRNA library targeting ~20,000 human genes. This led to the discovery of a novel membrane protein SWELL1 (aka LRRC8A, with 17 leucine-rich repeats (LRR) in the intracellular C-terminus), as an essential subunit of VRAC (Cell, 2014). We showed that VRAC is formed by diverse heteromers of SWELL1 and at least one of its four homologs (LRRC8B-8E) (Cell 2016), composition of which may determine substrate selectivity. This breakthrough opened up the field of volume regulation and it created unprecedented opportunities for studying fundamental volume-sensing mechanisms and their physiological relevance.
Cell swelling is a common pathological feature of many diseases. However, how it contributes to pathogenesis is poorly understood. A unique feature of VRAC is its large pore which can conduct chloride as well as small organic anions. We discovered that cell swelling predisposes astrocytes to release excess glutamate into the extracellular space through Swell1-depedent VRAC leading to “excitotoxicity”, a central mechanism for neuronal cell death. Knocking out Swell1 in astrocytes attenuated glutamate-dependent neuronal hyper-excitability and protected mice from brain damage after ischemic stroke (Neuron, 2019). Our study directly links VRAC to excitotoxicity and provides a strong rationale for targeting Swell1 for the treatment of stroke and many other neurological diseases associated with excitotoxicity.
A paradigm shift in neuroscience is the appreciation that glia (astrocytes and microglia) exert powerful influences on neuronal function. The mechanisms underlying glia-neuron interactions, however, remain poorly defined. For example, addictive drugs are known to hijack the mesolimbic dopaminergic system to increase midbrain ventral tegmental area (VTA) dopamine neuron activity and cause excesses dopamine release, thus driving addictive behaviors. This is partly achieved by inhibiting local GABA interneurons in the VTA, which leads to disinhibition of dopamine neurons. Until recently, the role of astrocytes in this VTA neural circuit and in addiction was unknown. Excitingly, we found that Swell1 channel in astrocytes can also mediate non-vesicular release of inhibitory neurotransmitter GABA (Neuron, 2023). Repeated cocaine exposure potentiated tonic GABA release from VTA astrocytes through VRAC and increased tonic inhibition of VTA GABA interneurons, thus downregulating their activities and disinhibiting dopamine neurons. Attenuation of this tonic inhibition by deleting Swell1 specifically in VTA astrocytes reduced cocaine-evoked changes in neuronal activity and in reward behaviors in mice. Thus, this work identifies a novel mechanism for cocaine reward involving astrocytes and Swell1 channel-mediated tonic inhibition.
Beyond neurotransmitters in the brain, the importance of Swell1 channels in glia-neuron interactions is further highlighted by our finding of its role in ATP release (Science Advances, 2023). Following peripheral nerve injury, extracellular ATP-mediated purinergic signaling is crucial for spinal cord microglia activation and neuropathic pain. We found that VRAC in microglia can be activated during inflammation, leading to ATP release. Microglia-specific Swell1 conditional knockout (cKO) mice had reduced peripheral nerve injury-induced increase in extracellular ATP in the spinal cord, and decreased spinal microgliosis, dorsal horn neuronal hyperactivity, and neuropathic pain-like behaviors. These findings identify Swell1 channel in microglia as a key spinal cord determinant of neuropathic pain.
The importance of Swell1 channel in diverse diseases motivates us to develop novel therapies targeting it. Repurposing existing drugs provides the quickest possible transition from bench to bedside. Using the high-throughput assay described above, we screened an FDA-approved drug library, and excitingly, discovered Dicumarol as a potent Swell1 channel blocker (Science Advances, 2023). Originally isolated from molding sweet-clover hay, Dicumarol is the prototype of the hydroxycoumarin anticoagulant drugs that deplete vitamin K in the blood. As a proof-of-principle, we showed that intrathecal delivery of Dicumarol alleviated nerve injury-induced mechanical allodynia in mice. Thus, Dicumarol and its many derivatives are potential therapeutic agents for neuropathic pain and other diseases with abnormal VRAC activity.
Discovery of Proton-Activated Chloride (PAC) channel and its surprising role in organelle physiology
Acidic pH is crucial for the function of intracellular organelles in the secretory and endocytic pathways. Acidosis is also one of the pathological hallmarks of many diseases. However, the molecular mechanisms of the cellular response to acid are not fully understood. Acid activates a chloride channel activity in many cell types. Prior to our work, its molecular identity and its biophysical properties were unknown. To search for genes encoding this channel, we established an acid-induced YFP quenching assay and performed an unbiased RNAi screen with an arrayed siRNA library targeting 2,725 human proteins predicted to have ≥2 TMs (a characteristic shared by all known ion channels). Remarkably, a single gene TMEM206 (PAC) stood out, with 3 siRNAs markedly reducing the quenching response (Science, 2019). We established PAC as a pore-forming subunit of the proton-activated chloride channel. We found that PAC plays an important role in acid-induced cell death and ischemic brain damage in mice by mediating chloride influx and inducing cell swelling (Science, 2019). Thus, it represents a novel drug target for ischemic stroke and other diseases associated with tissue acidosis.
With no obvious sequence homology to other membrane proteins, PAC represents a completely new type of ion channel. Collaborating with Wei Lü’s lab, we determined cryo-EM structures at both neutral and acidic pHs (Nature, 2020). Combining structural analysis with electrophysiology and molecular dynamics simulations, we made rapid progress and identified unique molecular mechanisms underlying anion selectivity, pH-sensing and gating (PNAS, 2022), desensitization (eLife, 2022), and unconventional regulation by an important signaling lipid PIP2 (eLife, 2023).
Vesicular acidification is generated by the vacuolar H+ ATPase, which pumps protons into the lumen. Acidification requires chloride as the principal counter-ion to shunt the luminal positive potential generated by proton pumping. Over the last two decades, the CLC family exchangers (CLC3-7) were thought to be the only mediators of endosomal chloride movement, mediating influx through their 2Cl− (in)/1H+ (out) exchange activity. We challenged this dogma by serendipitously discovering that PAC, although initially known as a cell-surface channel, is a bona fide endosomal chloride channel (Cell Reports, 2021). It traffics from the plasma membrane to early and recycling endosomes via the classical YxxL trafficking motif, and its activity can be recorded by whole-endolysosomal patch-clamp recording. We revealed that endosomal PAC channels function as low pH sensors and prevent hyper-acidification by releasing chloride from the lumen. This presents a new model for how chloride is regulated to control acidification of endosomes. Endosomal acidification is central to receptor and ligand sorting, trafficking, recycling, and degradation. Given PAC’s wide expression, we expect a broad role for this new channel in many physiological processes involving receptor endocytosis.