Biology subjects

Zhang, Y.-L.

Publications and source records attributed to Zhang, Y.-L..

12 recordsLinked to original sources

bioRxiv2026

Distal conformational steering by N-terminal pyroglutamylation enables subtype-selective GPCR activation across Aplysia PRXamide and human Neuromedin U signaling

Post-translational modifications (PTMs) diversify neuropeptide function, yet how minimal modifications encode receptor specificity without direct contact remains a fundamental challenge in chemical biology. Pyroglutamylation (pQ), a prevalent N-terminal PTM in bioactive peptides, introduces a rigid cyclic constraint, yet its mechanistic role in receptor signaling is unclear. Here, using two newly identified endogenous Aplysia PRXamide receptors (ApPRXa R1 and ApPRXa-R2) as a model system, we find that the same ligand, MMG2-pDPb (pQPPLPRYamide), produces opposite functional outcomes: pQ suppresses ApPRXa-R1 activation while enhancing ApPRXa-R2 activation. In vitro and in silico analyses demonstrate that the N-terminal pQ/Q remains solvent-exposed and does not directly contact receptor residues. Instead, pQ reshapes the ligand conformational ensemble and redistributes interaction networks across shared receptor contact sites. Strikingly, this molecular logic extends to mammalian Neuromedin U (NmU) receptors, as canine NmU (pQFLFRPRNamide) similarly biases subtype preference of human NmU receptors. Both static and dynamic analyses further reveal that receptor pocket mechanics determine the direction of this modulation: a loose and permissive pocket better accommodates the rigid pQ-constrained ligand, whereas a more compact pocket favors the non-pyroglutamylated ligand. These findings define a "PTM distal steering" mechanism that bridges "lock-key" and "induced-fit" paradigms and establish a general principle by which a minimal, non-contacting modification encodes receptor preference through ligand conformational biasing and pocket-dependent permissiveness, providing a chemical framework for optimizing stable, conformation-biased neuropeptide analogs.

biochemistry↗

bioRxiv2026

Discovery of GluA3 preferring AMPA receptor positive allosteric modulator BRD3290

Schizophrenia is a debilitating neuropsychiatric disease that lacks effective treatments for many symptom domains including negative, cognitive and sleep disturbances. Lack of clear disease etiology has hampered the development of new, effective treatments for the unmet needs of people with schizophrenia. Large scale human genetics have identified rare loss of function mutations that substantially increase risk of developing schizophrenia, including in GRIA3, the gene that encodes the GluA3 receptor subunit of the AMPA receptor (AMPAR). Several drug discovery programs have been aimed at developing AMPAR positive allosteric modulators (PAMs) as a novel treatment for schizophrenia. Despite intense drug discovery efforts, there are no FDA approved AMPAR PAMs. We therefore hypothesized that selectively targeting GluA3, the AMPAR subunit implicated by human genetics, could yield a safer and more effective AMPAR PAM for the potential treatment of schizophrenia. Using a combination of medicinal chemistry, in vitro, and in vivo studies, we discovered BRD3290, a GluA3-preferring AMPAR PAM with reasonable potency in heterologous cells, as well as favorable tolerability and brain exposure. Peripheral administration of BRD3290 engaged an established AMPAR PAM target engagement biomarker but did not improve performance of wildtype mice in the novel object recognition task (NOR), in contrast to the nonselective AMPAR PAM PF-4778574, which improved mouse NOR. These findings suggest that the GluA3 selectivity profile of BRD3290 was insufficient to enhance cognitive function in this mouse NOR paradigm. This work highlights the challenges of AMPAR subtype-selective modulation and provides molecular insights into the ability to develop subtype-selective AMPAR PAMs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/740780v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1577f62org.highwire.dtl.DTLVardef@16c1750org.highwire.dtl.DTLVardef@16eaef3org.highwire.dtl.DTLVardef@19fdb6f_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Hierarchical Assembly of Native Cytoplasmic Lattices Revealed by Cryo-EM

Oocytes depend on maternal factors for maturation and early embryogenesis. Cytoplasmic lattices (CPLs) are distinctive fibrillar structures in mammalian oocyte cytoplasm implicated in maternal factor storage and developmental competence, yet their molecular composition and architecture remain elusive. Here, we use cryo-electron microscopy to resolve the high-resolution structure of native mouse oocyte CPLs. We identify 14 intrinsic components of multiple copies that assemble into filaments in which PADI6-mediated self-assembly and two subtypes of subcortical maternal complexes (SCMCs) form the core scaffold. Unexpectedly, we discover that /{beta}-tubulin dimers and two autoinhibited ubiquitination modules (UHRF1-UBE2D3, SKP1-FBXW18) are internal components of CPLs. We also uncover multivalent interactions that organize adjacent CPL filaments into higher-order helical bundles. By integrating CPL structure with biochemical and proteomic data, we propose a hierarchical assembly mechanism of CPLs, from subcomplexes to filaments to supramolecular lattices. Our study offers mechanistic insights into how maternal proteins are spatially organized to ensure successful early embryonic development and provides a structural foundation for understanding female infertility related to CPL-associated gene mutations.

developmental biology↗

bioRxiv2025

GPR34 regulation of disease-associated microglial states and responses to physiological stimuli

Expression of the G protein coupled receptor GPR34 is highly enriched in microglia and has been reported to be downregulated in several brain disease contexts, including Alzheimers disease (AD) and multiple sclerosis (MS). GPR34 function is poorly understood, as is its role in regulation of microglial states. Using RNA-sequencing, we find that microglia from Gpr34 knockout (KO) mouse brains exhibited a transcriptomic shift toward disease-associated microglia (DAM) and inflammatory profiles, partially resembling the microglial phenotype seen in 5xFAD AD model mice. Moreover, when Gpr34 KO mice were crossed with 5xFAD mice, the DAM transcriptional profile of microglia and glial pathology were further enhanced beyond the already robust DAM signature driven by 5xFAD alone. This occurred without affecting amyloid plaque burden. Human stem cell-derived microglia (iMGLs) lacking GPR34 showed reduced calcium (Ca{superscript 2}) and phosphorylated ERK (pERK) signaling in response to stimulation with known GPR34 agonists (lyso-phosphatidylserine (lysoPS) and myelin), as well as transcriptomic changes in immune regulation and cell proliferation related pathways. Interestingly, GPR34 KO iMGLs were selectively impaired in phagocytosis of myelin but not amyloid-{beta} (A{beta}) or E. coli, and showed a diminished transcriptional response elicited by myelin. Together, these findings suggest that GPR34 is important for maintaining microglia in a homeostatic state, promotes phagocytosis of and transcriptional response to myelin, and limits microglial activation in neurodegenerative disease conditions.

neuroscience↗

bioRxiv2025

A neuroendocrine principle: Pancreatic islets actively shape sympathetic innervation

Survival critically depends on maintaining blood glucose levels to provide essential energy, especially during emergencies such as the fight-or-flight response, when timely glucose control via neural integration is vital. However, pancreatic islets constitute only a small fraction of the pancreas and are dispersed throughout the organ, raising the fundamental question of how the nervous system coordinates synchronized control of multiple islets. Using whole-organ clearing and 3D imaging, we mapped pancreatic sympathetic innervation, revealing specialized anatomical integration between sympathetic nerves and islets. Transplanted islets intrinsically attracted sympathetic nerves independent of their native environment. Chronic islet injury disrupted sympathetic innervation and markedly impaired nerve regeneration after denervation. Sympathetic denervation markedly elevated islet-derived Reg2 and Reg3{beta}; administration of these proteins accelerated sympathetic regeneration and improved islet graft function. Our findings identify an islet-sympathetic architecture actively maintained by islets, uncovering an endocrine-driven mechanism for neural regulation, highlighting Reg2 and Reg3{beta} as therapeutic candidates for diabetes management.

neuroscience↗

bioRxiv2025

PANDA: A simple and affordable chamber system for measuring the whole-plant net CO2 flux

The carbon (C) balance of plants is the sum of all source and sink processes. However, due to methodological limitations, most studies focus predominantly on measurements of leaf-level assimilation and respiration, with less attention given to these processes in heterotrophic organs or the whole-plant level. As a result, knowledge of the whole-plant net C balance is scarce, limiting our understanding of the dynamics between C source and sink activities. Therefore, we developed an easily reproducible chamber system for continuous measurements of whole-plant net CO2 fluxes. We present the obtained dynamics of net CO2 fluxes of several C3 and CAM species, including germinating Quercus robur, over several days, as well as the whole-plant net CO2 flux temperature response of Q. robur seedlings, identifying the temperature thresholds at which they shift from a net CO2 sink to source. We show distinct diel patterns of net CO2 fluxes in C3 plants, likely driven by a dynamic diurnal up- and downregulation of sink activities in woody C3 plants. These patterns appear temperature-driven, suggesting a dynamic response of plants sink and source activity to environmental drivers. Our results highlight the importance of whole-plant C balance measurements for understanding plant responses to environmental conditions.

plant biology↗

bioRxiv2025

Abnormal Lipid Metabolism and Altered Neuronal Support by Astrocytes Lacking Akap11, a Risk Gene for Schizophrenia and Bipolar Disorder

A-Kinase Anchoring Protein 11 (AKAP11) is a shared genetic risk factor for schizophrenia and bipolar disorder, yet its role in the brain remains poorly understood. Through multi-omic analysis of Akap11 mutant mouse brains and cultured astrocytes, we identified significant transcriptomic, proteomic, and metabolomic alterations. Key findings include the upregulation of cholesterol and fatty acid metabolic pathways, accumulation of lipid species such as cholesteryl esters, triacylglycerols, ceramides, and glycerophospholipids, and elevated levels of 3,5-cyclic AMP and protein kinase A (PKA) signaling. These metabolic perturbations manifested as increased lipid droplet accumulation in Akap11 mutant astrocytes, highlighting AKAP11s critical role in regulating intracellular lipid homeostasis. Mechanistically, AKAP11 functions as an autophagy receptor mediating PKA degradation and interacts with endoplasmic reticulum-resident proteins VAP-A and VAP-B through its FFAT motif, providing possible molecular insight into AKAP11s regulation of lipid metabolism. Co-culture experiments with mouse astrocytes and human induced pluripotent stem cell-derived neurons demonstrated that loss of Akap11 in astrocytes, relative to wild-type, increases excitatory neurotransmission and neuronal activity. Collectively, these findings link AKAP11-mediated lipid and synaptic dysregulation to psychiatric disease risk and highlight the potential role of astrocytes in these disorders.

cell biology↗

bioRxiv2024

Intra-hypothalamic circuit orchestrates β-endorphin release following coital ejaculation in male mice

Survey-based evidence suggests that men experience a distinct post-ejaculation affective state1,2, marked by intense pleasure sometimes compared to the euphoric rush from intravenous injection of opioid drugs such as heroin3. However, the intrinsic neural circuit mechanisms underlying the ejaculation-triggered affective state remain unclear. Here, we discovered that Calbindin1-expressing (Calb1+) neurons in the preoptic area (POA) of the hypothalamus, an evolutionarily conserved regulatory region for male mating behavior4, are specifically activated during ejaculation in male mice. Inhibiting POA Calb1+ neurons prolongs mating and delays ejaculation. Importantly, POA Calb1+ neurons transmit the ejaculation signal and activate proopiomelanocortin-expressing (Pomc+) neurons in the arcuate nucleus of the hypothalamus, which show robust and sustained activity lasting for tens of seconds, specifically upon ejaculation. This activity is accompanied by elevated levels of {beta}-endorphins5, opioid peptides secreted by Pomc+ neurons, post-ejaculation in male mice. Optogenetic activation of Pomc+ neurons increases {beta}-endorphins levels and conditioned placed preference, similar to ejaculation. Conversely, intracerebroventricular (i.c.v.) infusion of drugs blocking Pomc neuropeptides signaling eliminates ejaculation-conditioned place preference. Collectively, these results elucidate an intra-hypothalamic circuit from POA Calb1+ neurons to arcuate Pomc+ neurons that coordinate {beta}-endorphin release with ejaculation, shedding light on the neurobiological basis of the post-ejaculation affective state.

neuroscience↗

bioRxiv2023

Pre-trained Inspired MocFormer: Efficient and Predictive Models of Drug-target Interactions

Drug-target interactions (DTIs) is essential for advancing pharmaceuticals. Traditional drug-target interaction studies rely on labor-intensive laboratory techniques. Still, recent advancements in computing power have elevated the importance of deep learning methods, offering faster, more precise, and cost-effective screening and prediction. Nonetheless, general deep learning methods often yield low-confidence results due to the complex nature of drugs and proteins, bias, limited labeled data, and feature extraction challenges. To address these challenges, a novel two-stage pre-trained framework is proposed for DTIs prediction. In the first stage, pre-trained molecule and protein models develop a comprehensive feature representation, enhancing the frameworks ability to handle drug and protein diversity. This also reduces bias, improving prediction accuracy. In the second stage, a transformer with bilinear pooling and a fully connected layer (FCN) enables predictions based on feature vectors. Comprehensive experiments were conducted using DrugBank dataset and Epigenetic-regulators dataset to evaluate the frameworks effectiveness. The results demonstrate that the proposed framework outperforms the state-of-the-art methods regarding accuracy, area under the ROC curve (AUC), recall, and the area under the precision-recall curve (AUPRC). The code will be available after being accepted: https://github.com/rickwang28574/MocFormer

bioinformatics↗

bioRxiv2022

A hippocampal-hypothalamic circuit essential for anxiety-related behavioral avoidance

Anxiety over perceived threats triggers avoidance behavior, but the underlying neural circuit mechanism remains poorly understood. Taking hints from the deep connection between anxiety and predator defense, we examined the role of the anterior hypothalamic nucleus (AHN), a critical node in the predator defense network, in anxiety-related behaviors. By recording Ca2+ transients in behaving mice, we found that activity of AHN GABAergic (AHNVgat+) neurons showed individually stable increases when animals approached unfamiliar objects in an open field (OF) or explored the open arm of an elevated plus-maze (EPM). Moreover, AHNVgat+ neuron activity foreshadowed behavioral retreats and correlated with object and open-arm avoidance. Crucially, exploration-triggered optogenetic inhibition of AHNVgat+ neurons dramatically reduced avoidance behaviors. Furthermore, retrograde viral tracing identified the ventral subiculum (vSub) of the hippocampal formation as a significant input to AHNVgat+ neurons in driving avoidance behaviors. Thus, the activity of the hippocampal-hypothalamic pathway promotes idiosyncratic anxiety-related behavioral avoidance.

neuroscience↗

bioRxiv2020

A single-cell transcriptome atlas during Cashmere goat hair follicle morphogenesis

Cashmere, also known as soft gold, is produced from the secondary hair follicles in Cashmere goats and its therefore of significance to investigate the molecular profiles during Cashmere goat hair follicle development. However, our current understanding of the machinery underlying Cashmere goat hair follicle remains largely unexplored and researches regarding hair follicle development mainly used the mouse as a research model. To provides comprehensively understanding on the cellular heterogeneity and cell lineage cell fate decisions, we performed single-cell RNA sequencing on 19,705 single cells from induction (embryonic day 60), organogenesis (embryonic day 90) and cytodifferentiation (embryonic day 120) stages of fetus Cashmere goat dorsal skin. Unsupervised clustering analysis identified 16 cell clusters and their corresponding cell types were also unprecedentedly characterized. Based on the lineage inference, we revealed detailed molecular landscape along the dermal and epidermal cell lineage developmental pathways. Notably, by cross-species comparasion of single cell data with murine model, we revelaed conserved programs during dermal condensate fate commitment and the heterochrony development of hair follicle development between mouse and Cashmere goat were also discussed here. Our work here delineate unparalleled molecular profiles of different cell populations during Cashmere goat hair follicle morphogenesis and provide a valuable resource for identifying biomarkers during Cashmere goat hair follicle development.

developmental biology↗

bioRxiv2020

Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China

Emerging and re-emerging infectious diseases, such as SARS, MERS, Zika and highly pathogenic influenza present a major threat to public health1-3. Despite intense research effort, how, when and where novel diseases appear are still the source of considerable uncertainly. A severe respiratory disease was recently reported in the city of Wuhan, Hubei province, China. At the time of writing, at least 62 suspected cases have been reported since the first patient was hospitalized on December 12nd 2019. Epidemiological investigation by the local Center for Disease Control and Prevention (CDC) suggested that the outbreak was associated with a sea food market in Wuhan. We studied seven patients who were workers at the market, and collected bronchoalveolar lavage fluid (BALF) from one patient who exhibited a severe respiratory syndrome including fever, dizziness and cough, and who was admitted to Wuhan Central Hospital on December 26th 2019. Next generation metagenomic RNA sequencing4 identified a novel RNA virus from the family Coronaviridae designed WH-Human-1 coronavirus (WHCV). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that WHCV was most closely related (89.1% nucleotide similarity similarity) to a group of Severe Acute Respiratory Syndrome (SARS)-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) previously sampled from bats in China and that have a history of genomic recombination. This outbreak highlights the ongoing capacity of viral spill-over from animals to cause severe disease in humans.

pathology↗