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Biology subjects

Rong, Y.

Publications and source records attributed to Rong, Y..

At least 19 recordsLinked to original sources

Astrocytic μ-δ opioid receptor heterodimers mediate the antidepressant effects of ketamine's metabolite

A deeper understanding of the targets and mechanisms of fast-acting antidepressants, exemplified by ketamine, remains indispensable for better therapeutic strategies and understanding depression. Beyond the canonical neuron-centric NMDAR inhibition hypothesis, brain opioid system and glia-mediated processes are increasingly implicated in ketamines antidepressant efficacy, yet their precise contributions remain poorly understood. Here, we demonstrate that one major metabolite of ketamine, (2R,6R)-hydroxynorketamine (HNK), selectively targets -{delta} opioid receptor heterodimers (-{delta}-ORs) on astrocytes. By promoting the formation and/or stabilization of -{delta}-ORs, HNK engages Gs-coupled signaling, elevates intracellular cAMP, phosphorylates CREB (p-CREB) levels and Ca{superscript 2} dynamics in astrocytes, and consequently restores key astrocytic proteins and functions in depression models. Disrupting -{delta}-OR assembly or Gs signaling abolishes HNK-mediated antidepressant responses both in vitro and in vivo. Collectively, astrocytic opioid receptor heterodimers are critical to antidepressant responses and HNK may serve as a prototype compound for targeting astrocyte dysfunction across a wide range of brain disorders.

neuroscience↗

Axonal swelling as a neuron-specific compartment to sequester and expel misfolded proteins

Neurons are long-lived, highly specialized cells with extended neurites, requiring precise control of misfolded proteins over time and space. Yet, where misfolded proteins are directed and how quality-control pathways adapt during aging are still unresolved. Here, we identify a neuron-specific quality-control compartment that emerges in neurites as aggresome function declines with age, which we call SolAS (Soluble Misfolded Proteins-induced Axonal Swellings). These structures not only sequester misfolded proteins but also facilitate their clearance via microvesicles and exophers. During aging, neurite SolAS and soma aggresomes function hierarchically to maintain proteostasis, with aggresomes acting as the primary sequestration sites in young neurons and SolAS taking over this role as their function declines with age. This transition is driven by a shift from a ubiquitin-dominant to a SUMO-dominant balance. Moreover, solid pathogenic amyloids, such as GA50, can be converted into soluble forms and sequestered into SolAS via SUMO fusion, thereby reducing neurotoxicity. Our findings identify a previously unrecognized neuronal quality-control pathway critical for proteostasis during aging.

neuroscience↗

Single-vessel transcriptome map pathological landscapes and reveal NR2F2-mediated smooth muscle cell phenotype acquisition in capillary malformations

BackgroundCapillary malformation (CM) is a congenital vascular anomaly affecting the skin, mucosa, and brain, yet the understanding of its vascular pathogenesis remains limited. MethodsWe applied spatial whole-transcriptome profiling (GeoMx) and gene set enrichment analysis within CM lesions at single vasculature level. Differentially expressed genes were validated by immunofluorescence staining. Phosphoproteomics was profiled to uncover lesion- wide phosphorylation sites on proteins. Single-cell RNA sequencing was performed on CM- derived induced pluripotent stem cells (iPSCs) to determine differentiation trajectories of lesional vascular lineages. In silico gene perturbation was used to predict candidate genes for modulating vascular pathological progression, followed by functional validation in CM iPSC-derived endothelial cells (ECs) using a Tet-on system. ResultsA spatial transcriptomic atlas was constructed, and pathological landscape of individual CM vasculature was delineated. CM vessels exhibited hallmarks of endothelial-to-mesenchymal transition (EndMT), including disruption of adherens junctions (AJs), vascular identity transitions, and metabolic remodeling. Phosphoproteomics confirmed that differentially phosphorylated proteins were enriched in EndMT- and AJ-related pathways. Aberrant expression of venous transcriptional factor NR2F2 was observed in lesional ECs and correlated with progressive enlargement from capillaries to larger-caliber vessels containing multiple layers of smooth muscle cells (SMCs). In CM iPSCs, differentiation course yielded reduced ECs but increased SMCs. In silico knockout simulation predicted NR2F2 as a crucial regulator of facilitating SMC phenotype in CM. Consistently, enforced NR2F2 expression during iPSC differentiation suppressed endothelial markers while inducing SMC-associated genes. ConclusionsSingle CM vasculature displays pathological hallmarks characterized by EndMT and AJ disruption, leading to progressive vascular remodeling. NR2F2 functions as a central regulatory factor orchestrating the acquisition of the SMC phenotype, thereby representing a potential therapeutic target in CM.

pathology↗

Accurate Protein-Protein Interactions Modeling through Physics-informed Geometric Invariant Learning

AlphaFold has set a new standard for predicting protein structures from primary sequences; however, it faces challenges with protein complexes across species, engineered proteins, and antigen-antibody, where co-evolutionary signals may be sparse or missing. Herein, we present ProTact, a SE(3)-invariant geometric graph neural network that integrates physics-informed geometric complementarity and trigonometric constraints as robust inductive biases to enhance protein-protein contact predictions. ProTact is applicable to both experimental and predicted monomer structures and utilizes a modulated key point matching algorithm to approximate accurate docking poses. Experimental evaluations demonstrate that ProTact consistently outperforms state-of-the-art sequence-based and structure-based methods on benchmark datasets, achieving notable relative improvements of 31.63% in Precision@10 for CASP 13 and 14 targets, and 31.94% for DIPS-Plus datasets. Moreover, when combined with AlphaFold3 as re-scoring functions, ProTact surpasses its default confidence scores, offering over 30.48% improvements in the low-MSA contexts. We anticipate that the proposed framework will advance our understanding of protein interactions, functions, and design.

bioinformatics↗

Partially differentiated enterocytes in ileal and distal-colonic human F508del-CF-enteroids 1 secrete fluid in response to forskolin and linaclotide.

Constipation causes significant morbidity in Cystic Fibrosis (CF) patients. Using CF patient (F508del) derived ex vivo ileal and distal colonic/rectal enteroids as a model and the Forskolin Induced Swelling Assay (FIS), we compared CFTR mediated fluid secretion in human enterocytes across the crypt-villus axis. CFTR expression and FIS decreased as enterocytes differentiated from crypt to become partially differentiated and then mature villus cells. While there was no FIS response in undifferentiated (crypt enterocytes) F508del-CF enteroids, partially differentiated F508del-CF enteroids had a swelling response to forskolin (cAMP) and linaclotide (cGMP) which was [~]48%, and [~]67% of the response in healthy enteroids, respectively and was prevented by a CFTR inhibitor. Also, linaclotide and a general PDE inhibitor independently enhanced combined CFTR-modulator-induced FIS response from partially differentiated F508del-CF enteroids. These findings demonstrate that partially differentiated ileal and distal colonic F508del-CFTR enteroids can be stimulated to secrete fluid by cAMP and cGMP.

physiology↗

Silicon-rhodamine-enabled Identification (SeeID) for Near-Infrared Light Controlled Proximity Labeling In Vitro and In Vivo

Advancement in fluorescence imaging techniques enables the study of protein dynamics and localization with unprecedented spatiotemporal resolution. However, current imaging tools are unable to elucidate dynamic protein interactomes underlying imaging observations. In contrast, proteomics tools such as proximity labeling enable the analysis of protein interactomes at a single time point but lack information about protein dynamics. We herein developed Silicon-rhodamine-enabled Identification (SeeID) for near-infrared light controlled proximity labeling that could bridge the gap between imaging and proximity labeling. SeeID was benchmarked through characterization of various organelle-specific proteomes and the KRAS protein interactome. The fluorogenic nature of SiR allows for intracellular proximity labeling with high subcellular specificity. Leveraging SiR as both a fluorophore and a photocatalyst, we developed a protocol that allows the study of dynamic protein interactomes of Parkin during mitophagy. We discovered the association of the proteasome complex with Parkin at early time points, indicating the involvement of the ubiquitin-proteasome system for protein degradation in the early phase of mitophagy. In addition, by virtue of the deep tissue penetration of near-infrared light, we achieved spatiotemporally controlled proximity labeling in vivo across the mouse brain cortex with a labeling depth of [~]2 mm using an off-the-shelf 660 nm LED light set-up.

molecular biology↗

A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxyacids

Medium- and branched-chain diols and amino alcohols are important industrial solvents, polymer building blocks, cosmetics and pharmaceutical ingredients, yet biosynthetically challenging to produce. Here, we present a novel approach utilising a modular polyketide synthase (PKS) platform for the efficient production of these compounds. This platform takes advantage of a versatile loading module from the rimocidin PKS and NADPH-dependent terminal thioreductases (TRs), previously untapped in engineered PKSs. Reduction of the terminal aldehyde with specific alcohol dehydrogenases enables production of diols, oxidation enables production of hydroxy acids, and transamination with specific transaminases enables production of various amino alcohols. Furthermore, replacement of the malonyl-coenzyme A (CoA)-specific acyltransferase (AT) in the extension module with methyl- or ethylmalonyl- CoA-specific ATs enables production of branched-chain diols and amino alcohols. In total, we demonstrated production of nine 1,3-diols (including the difficult-to-produce insect repellent and cosmetic ingredient 2-ethyl-1,3-hexanediol), six amino alcohols, and two carboxylic acids using our PKS platform in Streptomyces albus. Finally, tuning production of the PKS acyl-CoA substrates enabled production of high titers of specific diols and amino alcohols (1 g/L diol titer in shake flasks), demonstrating high tunability and efficiency of the platform.

bioengineering↗

Mettl5 coordinates protein production and degradation of PERIOD to regulate sleep in Drosophila

Sleep plays a critical role in animal physiology, primarily governed by the brain, and its disruption is prevalent in various brain disorders. Mettl5 is associated with intellectual disability (ID), which often includes sleep disturbances. However, the mechanism underlying these sleep disruptions in ID remains poorly understood. In this study, we investigated the sleep phenotypes resulting from Drosophila Mettl5 mutations. Rescue experiments revealed that Mettl5 functions predominantly within neurons and glia marked by Mettl5-Gal4 to regulate sleep. Previous work established that Mettl5 forms a complex with Trmt112 to influence rRNA methylation. Notably, a mutation in Trmt112 mutation recapitulated these sleep disturbances, implicating translational regulation by the Mettl5/Trmt112 complex. Subsequent RNA-seq and Ribo-seq analyses of Mettl51bp mutants uncovered downstream effects, including altered expression of proteasome components and clock genes. Rescue experiments confirmed that the net increase in PERIOD protein underlies the sleep phenotype. This study illuminates the interplay between ribosome function, clock genes, and the proteasome in sleep regulation, highlighting the integrated roles of protein synthesis and degradation. These findings could potentially provide an example for in vivo study of rRNA methylation function, expand our understanding of protein homeostasis in sleep and offer insights into the sleep phenotypes associated with ID.

genetics↗

The longitudinal behavioral effects of acute exposure to galactic cosmic radiation in female C57BL/6J mice: implications for deep space missions, female crews, and potential antioxidant countermeasures

Galactic cosmic radiation (GCR) is an unavoidable risk to astronauts that may affect mission success. Male rodents exposed to 33-beam-GCR (33-GCR) show short-term cognitive deficits but reports on female rodents and long-term assessment is lacking. Here we asked: What are the longitudinal behavioral effects of 33-GCR on female mice? Also, can an antioxidant/anti-inflammatory compound mitigate the impact of 33-GCR? Mature (6-month-old) C57BL/6J female mice received the antioxidant CDDO-EA (400 {micro}g/g of food) or a control diet (vehicle, Veh) for 5 days and either Sham-irradiation (IRR) or whole-body 33-GCR (0.75Gy) on the 4th day. Three-months post-IRR, mice underwent two touchscreen-platform tests: 1) location discrimination reversal (which tests behavior pattern separation and cognitive flexibility, two abilities reliant on the dentate gyrus) and 2) stimulus-response learning/extinction. Mice then underwent arena-based behavior tests (e.g. open field, 3-chamber social interaction). At the experiment end (14.25-month post-IRR), neurogenesis was assessed (doublecortin-immunoreactive [DCX+] dentate gyrus neurons). Female mice exposed to Veh/Sham vs. Veh/33-GCR had similar pattern separation (% correct to 1st reversal). There were two effects of diet: CDDO-EA/Sham and CDDO-EA/33-GCR mice had better pattern separation vs. their respective control groups (Veh/Sham, Veh/33-GCR), and CDDO-EA/33-GCR mice had better cognitive flexibility (reversal number) vs. Veh/33-GCR mice. Notably, one radiation effect/CDDO-EA countereffect also emerged: Veh/33-GCR mice had worse stimulus-response learning (days to completion) vs. all other groups, including CDDO-EA/33-GCR mice. In general, all mice show normal anxiety-like behavior, exploration, and habituation to novel environments. There was also a change in neurogenesis: Veh/33-GCR mice had fewer DCX+ dentate gyrus immature neurons vs. Veh/Sham mice. Our study implies space radiation is a risk to a female crews longitudinal mission-relevant cognitive processes and CDDO-EA is a potential dietary countermeasure for space-radiation CNS risks.

neuroscience↗

Thyroid Hormone Suppresses Medulloblastoma Progression Through Promoting Terminal Differentiation of Tumor Cells

Hypothyroidism is commonly detected in patients with medulloblastoma (MB). A possible link between thyroid hormone (TH) signaling and MB pathogenicity has not been reported. Here, we find that TH plays a critical role in promoting tumor cell differentiation. Reduction in TH levels frees the TH receptor, TR1, to bind to EZH2 and repress expression of NeuroD1, a transcription factor that drives tumor cell differentiation. Increased TH reverses EZH2-mediated repression of NeuroD1 by abrogating the binding of EZH2 and TR1, thereby stimulating tumor cell differentiation and reducing MB growth. Importantly, TH-induced differentiation of tumor cells is not restricted by the molecular subgroup of MB. These findings establish an unprecedented association between TH signaling and MB pathogenicity, providing solid evidence for TH as a promising modality for MB treatment.

cancer biology↗

Fast and accurate modeling and design of antibody-antigen complex using tFold

Accurate prediction of antibody-antigen complex structures holds significant potential for advancing biomedical research and the design of therapeutic antibodies. Currently, structure prediction for protein monomers has achieved considerable success, and promising progress has been made in extending this achievement to the prediction of protein complexes. However, despite these advancements, fast and accurate prediction of antibody-antigen complex structures remains a challenging and unresolved issue. Existing end-to-end prediction methods, which rely on homology and templates, exhibit sub-optimal accuracy due to the absence of co-evolutionary constraints. Meanwhile, conventional docking-based methods face difficulties in identifying the contact interface between the antigen and antibody and require known structures of individual components as inputs. In this study, we present a fully end-to-end approach for three-dimensional (3D) atomic-level structure predictions of antibodies and antibody-antigen complexes, referred to as tFold-Ab and tFold-Ag, respectively. tFold leverages a large protein language model to extract both intra-chain and inter-chain residue-residue contact information, as well as evolutionary relationships, avoiding the time-consuming multiple sequence alignment (MSA) search. Combined with specially designed modules such as the AI-driven flexible docking module, it achieves superior performance and significantly enhanced speed in predicting both antibody (1.6% RMSD reduction in the CDR-H3 region, thousand times faster) and antibody-antigen complex structures (37% increase in DockQ score, over 10 times faster), compared to AlphaFold-Multimer. Given the performance and speed advantages, we further extend the capability of tFold for structure-based virtual screening of binding antibodies, as well as de novo co-design of both structure and sequence for therapeutic antibodies. The experiment results demonstrate the potential of tFold as a high-throughput tool to enhance processes involved in these tasks. To facilitate public access, we release code and offer a web service for antibody and antigen-antibody complex structure prediction, which is available at https://drug.ai.tencent.com/en.

bioinformatics↗

ZC3H11A mutations cause high myopia by triggering PI3K-AKT and NF-κB mediated inflammatory reactions in humans and mice

High myopia (HM) is a severe form of refractive error that results in irreversible visual impairment and even blindness. However, the genetic and pathological mechanisms underlying this condition are not yet fully understood. From a cohort of 1015 patients with high myopia in adolescents, likely pathogenic missense mutations were identified in the ZC3H11A gene in four patients by whole exome sequencing. This gene is a zinc finger and stress-induced protein that plays a significant role in regulating nuclear mRNA export. To better understand the function and molecular pathogenesis of myopia in relation to gene mutations, a Zc3h11a knock-out (KO) mouse model was created. The heterozygous KO (Het-KO) mice exhibited significant shifts in refraction towards myopia. Myopia-related factors, including TGF-{beta}1, MMP-2 and IL-6 were found to be upregulated in the retina or sclera, and electroretinography and immunofluorescence staining results showed dysfunction and reduced number of bipolar cells in the retina. Transmission electron microscopy findings suggesting ultrastructural abnormalities of the retina and sclera. Retinal transcriptome sequencing showed that 769 genes were differentially expressed, and Zc3h11a was found to have a negative impact on the PI3K-AKT and NF-{kappa}B signaling pathways by quantitative PCR and western blotting. In summary, this study characterized a new candidate pathogenic gene associated with high myopia, and indicated that the ZC3H11A protein may serve as a stress-induced nuclear response trigger, and its abnormality causes disturbances in a series of inflammatory and myopic factors. These findings offer potential therapeutic intervention targets for controlling the development of HM.

genetics↗

Air-Liquid-Interface Reorganizes Membrane Lipid and Enhance Recruitment of Slc26a3 to Lipid-Rich Domains in Human Colon

Background and AimsCholesterol-rich membrane domains, also called lipid rafts (LR), are specialized membrane domains that provide a platform for intracellular signal transduction. Membrane proteins often cluster in LR that further aggregate into larger platform-like structures that are enriched in ceramide and are called ceramide-rich platforms (CRPs). The role of CRPs in the regulation of intestinal epithelial functions remains unknown. Down Regulated in Adenoma (DRA) is an intestinal Cl-/HCO3- antiporter which is enriched in LR. However, little is known regarding the mechanisms involved in the regulation of DRA activity. MethodsAir liquid interface (ALI) was created by removing apical media for a specified number of days from 12-14 days post confluency Caco-2/BBe cells or confluent colonoid monolayer grown as submerged cultures. Confocal imaging was used to examine the dimensions of membrane microdomains that contain DRA. ResultsDRA expression and activity were enhanced by culturing Caco-2/BBe cells and human colonoids using an ALI culture method. ALI causes an increase in acid sphingomyelinase (ASMase) activity, an enzyme responsible for enhancing ceramide content in the plasma membrane. ALI cultures expressed a larger number of DRA-containing platforms with dimensions >2 m compared to cells grown as submerged cultures. ASMase inhibitor, desipramine disrupted CRPs and reduced the ALI-induced increase in DRA expression in the apical membrane. Exposing normal human colonoid monolayers to ALI increased the ASMase activity and enhanced differentiation of colonoids along with enhancing basal and forskolin-stimulated DRA activity. ConclusionsALI increases DRA activity and expression by increasing ASMase activity and platform formation in Caco-2/BBe cells and by enhancing the differentiation of normal human colonoids. SynopsisAir-liquid interface (ALI) enhances total and brush border DRA expression and activity in Caco-2/BBe cells and human colonoids by causing differentiation of enterocytes and acid sphingomyelinase-dependent enhanced retention of DRA in ceramide-rich platform-like structures at the plasma membrane.

cell biology↗

A Versatile Deep Graph Contrastive Learning Framework for Single-cell Proteomics Embedding

The advance of single-cell proteomics sequencing technology sheds light on the research in revealing the protein-protein interactions, the post-translational modifications, and the proteoform dynamics of proteins in a cell. However, the uncertainty estimation for peptide quantification, data missingness, severe batch effects and high noise hinder the analysis of single-cell proteomic data. It is a significant challenge to solve this set of tangled problems together, where existing methods tailored for single-cell transcriptome do not address. Here, we proposed a novel versatile framework scPROTEIN, composed of peptide uncertainty estimation based on a multi-task heteroscedastic regression model and cell embedding learning based on graph contrastive learning designed for single-cell proteomic data analysis. scPROTEIN estimated the uncertainty of peptide quantification, denoised the protein data, removed batch effects and encoded single-cell proteomic-specific embeddings in a unified framework. We demonstrate that our method is efficient for cell clustering, batch correction, cell-type annotation and clinical analysis. Furthermore, our method can be easily plugged into single-cell resolved spatial proteomic data, laying the foundation for encoding spatial proteomic data for tumor microenvironment analysis.

bioinformatics↗

An endolysosome membrane transformation process for engulfment of autophagosomes independently of ESCRT

Endolysosome, usually regarded as the cellular recycling bin, digests materials from multiple origins. The materials from different origins are delivered to endolysosome through the vesicle fusion, kiss-and-run mechanisms, CMA or microautophagy. However, it remains unknown whether endolysosome can receive cargo via other ways. Here, we reported another endolysosomal process for receiving materials. In this, endolysosome receives materials by extending two arms which embraces autophagosomes and engulfs the autophagosomes ultimately, but not via the conventional fusion of autophagosomes with endolysosomes. We named this process as LEA (lysosome eats autophagosome) and the endolysosome arms as LF (endolysosome filopodia) provisionally. The endolysosomes with engulfed autophagosomes (LEA endolysosomes) get more autophagosomes via the fusion with other LEA endolysosomes. The engulfed autophagosomes are labelled by F-actin on their membranes and have ER protein Sec61{beta} and peroxisome protein Pex14 inside their lumens, but mitochondria are excluded outside endolysosome. Our discovery of LEA and LF reveal an unidentified endolysosome transformation process which is responsible for receiving cargoes.

cell biology↗

JiangShi: a widely distributed Mucin-like protein essential for Drosophila development

Epithelia exposed to elements of the environment are protected by a mucus barrier in mammals. This barrier also serves to lubricate during organ movements and to mediate substance exchanges between the environmental milieu and internal organs. A major component of the mucus barrier is a class of glycosylated proteins called Mucin. Mucin and mucin-related proteins are widely present in the animal kingdom. Mucin mis-regulation has been reported in many diseases such as cancers and ones involving the digestive and respiratory tracts. Although the biophysical properties of isolated Mucins have been extensively studied, in vivo models remain scarce for the study of their functions and regulations. Here we characterize the Mucin-like JiangShi (JS) protein and its mutations in the fruit fly Drosophila. JS is an extracellular glycoprotein with domain features reminiscent of mammalian non-membranous Mucins, and one of the most widely distributed Mucin-like proteins studied in Drosophila. Both loss and over-production of JS lead to terminal defects in adult structures and organismal death. Although the physiological function of JS remains poorly defined, we present a genetically tractable model system for the in vivo studies of Mucin-like molecules.

developmental biology↗

Kinetic principles underlying pioneer function of GAGA transcription factor in live cells

How pioneer factors interface with chromatin to promote accessibility for transcription control is poorly understood in vivo. Here, we directly visualize chromatin association by the prototypical GAGA pioneer factor (GAF) in live Drosophila hemocytes. Single-particle tracking reveals that the majority of GAF is chromatin-bound, with a stable-binding fraction showing nucleosome-like confinement residing on chromatin for over 2 minutes, far longer than the dynamic range of most transcription factors. These kinetic properties require the full complement of GAFs DNA-binding, multimerization and intrinsically disordered domains, and are autonomous from recruited chromatin remodelers NURF and PBAP, whose activities primarily benefit GAFs neighbors such as HSF. Evaluation of GAF kinetics together with its endogenous abundance indicates that despite on-off dynamics, GAF constitutively and fully occupies chromatin targets, thereby providing a temporal mechanism that sustains open chromatin for transcriptional responses to homeostatic, environmental, and developmental signals.

molecular biology↗

Extrasynaptic NMDA receptors bidirectionally modulate intrinsic excitability of inhibitory neurons

The NMDA subtype glutamate receptors (NMDARs) play important roles in both physiological and pathological processes in the brain. Comparing to their critical roles in synaptic modifications and excitotoxicity in the excitatory neurons, much less is understood about the functional contributions of NMDARs to the inhibitory/GABAergic neurons. By using selective NMDAR inhibitors and potentiators, we here show that NMDARs bi-directionally modulate the intrinsic excitability (defined as spontaneous/evoked spiking activity and EPSP-spike coupling) in the inhibitory/GABAergic neurons. This modulation depends on GluN2C/2D-but not GluN2A/2B-containing NMDARs. We further show that NMDAR modulator EU1794-4 mostly enhances extrasynaptic NMDAR activity, and by using it we demonstrate a significant contribution of extrasynaptic NMDARs to the modulation of intrinsic excitability in the inhibitory neurons. Altogether, this bidirectional modulation of intrinsic excitability reveals a previously less appreciated importance of NMDARs in the second-to-second functioning of inhibitory/GABAergic neurons.

neuroscience↗