Biology subjects

Tang, A.

Publications and source records attributed to Tang, A..

At least 19 recordsLinked to original sources

bioRxiv2026

(2R,6R)-Hydroxynorketamine elicits rapid antidepressant effects by promoting astrocytic μ-δ opioid receptor heterodimerization

Ketamine produces rapid antidepressant effects but is constrained by psychotomimetic properties and abuse potential. The ketamine metabolite (2R,6R)-hydroxynorketamine (HNK) shows antidepressant-like efficacy without N-methyl-D-aspartate receptor (NMDAR) blockade, yet its upstream targets remain unclear. Here we show that HNK potentiates hippocampal excitatory transmission and reverses stress-induced behavioural deficits through opioid receptor signaling. Pharmacological and genetic analyses reveal a requirement for both {micro}- and {delta}-opioid receptors in astrocytes. Chronic stress reduces {micro}-{delta} receptor heterodimers in the hippocampus, and a single dose of HNK restores their abundance. PAINT-MINFLUX nanoscopy quantifies increased {micro}-{delta} heterodimerization, and molecular dynamics simulations indicate selective binding of HNK to the {micro}-receptor protomer via Asp147 and Tyr148. Mutating these residues abolishes HNK-driven heterodimer formation, downstream signaling and rapid antidepressant-like effects in vivo. Astrocytic {micro}-{delta} opioid receptor heterodimers thus represent a targetable mechanism for next-generation rapid-acting antidepressants.

neuroscience↗

bioRxiv2026

Chronic subthreshold intermittent theta burst stimulation promotes structural axon initial segment plasticity in cortical neurons

Repetitive transcranial magnetic stimulation (rTMS) is used widely in neuroscience to study and alter neural plasticity. The cellular mechanisms underlying the effect of rTMS on the brain remain unclear but is primarily thought to act via activity-dependent synaptic plasticity mechanisms. Here we investigated whether chronic repetitive magnetic stimulation in vitro and in vivo can induce another form of activity-dependent neural plasticity, axon initial segment (AIS) plasticity. Cortical neurons isolated from postnatal wild-type mice were stimulated with 6 hours of sham, repetitive magnetic stimulation in the form of intermittent theta-burst stimulation (iTBS), or 15 mM potassium chloride, with changes to AIS location and length measured +0 hours and +24 hours post-stimulation. In addition, adult transgenic mice expressing green fluorescent protein at the AIS received daily sham or iTBS over the primary motor cortices for 7 consecutive days and processed for microscopy 3 hours after the last stimulation. Analysis of neurons stimulated in vitro showed that chronic iTBS caused bidirectional and time-dependent shifts to the AIS position relative to the soma and a delayed shortening of the AIS length at +24 hours. In the adult mice, 7 consecutive days of daily iTBS decreased AIS lengths in layers 2/3 and 5 pyramidal neurons. Our findings provide in vitro and in vivo evidence that rTMS induces neuronal plasticity outside of the synapse, which may contribute to the long-lasting effect of rTMS on the brain with repeated stimulation protocols.

neuroscience↗

bioRxiv2026

Repetitive transcranial magnetic stimulation induces protocol and layer specific transcriptomic plasticity in the human cortex

Repetitive transcranial magnetic stimulation is a popular method of non-invasive brain stimulation used to study the human brain and treat neurological disorders. However, despite over three decades of use, the cellular mechanisms underlying its effects remain unknown which has limited its use. Using spatial transcriptomics on excised human cortical tissue, we characterized and mapped changes to gene expression following stimulation with two common stimulation protocols. We find that repetitive magnetic stimulation alters the expression of genes related to neuronal and glial plasticity mechanisms that were mostly cortical layer, cell type, and protocol dependent. These findings show that repetitive transcranial magnetic stimulation acts on multiple neural plasticity mechanisms simultaneously in the human brain, which to some extent, can be biased by the stimulation frequency used.

neuroscience↗

bioRxiv2026

TernTables: A Statistical Analysis and Table Generation Web Interface for Clinical and Biomedical Research

Clinical research dissemination is frequently hindered by administrative friction and methodological inconsistency. To address these barriers, we developed TernTables, a freely available, open-source web application (https://www.tern-tables.com/) and R package (https://cran.r-project.org/package=TernTables) that streamlines the transition from raw data to formatted results for descriptive and univariate clinical reporting. The system integrates a client-side screening protocol for protected health information (PHI) with a rule-based decision tree that selects and executes appropriate frequency-based, parametric, or non-parametric statistical tests based on data distribution and class. TernTables generates publication-ready summary tables in Microsoft Word format, complemented by dynamically generated methods text and the underlying R code to ensure complete transparency and reproducibility. Validation using a landmark clinical trial dataset demonstrated concordance with established biostatistical approaches for descriptive and univariate analyses. TernTables is designed to supplement, not replace, formal statistical consultation by standardizing routine descriptive and univariate workflows, allowing biostatistical expertise to be focused on complex analyses and study design. By lowering technical and financial barriers, the platform democratizes access to rigorous statistical workflows while maintaining methodological excellence and reducing "researcher degrees of freedom."

bioinformatics↗

bioRxiv2026

Programmable artificial RNA condensates in mammalian cells

Artificial biomolecular condensates have emerged as powerful tools to control cellular behaviors. Here we introduce a method to build artificial condensates within living mammalian cells through the design of modular RNA motifs formed by a single, short strand of RNA. These condensates emerge spontaneously, creating RNA-rich compartments that remain separated from their surrounding environment. The RNA sequences include stem-loop domains that fold as the RNA is transcribed, and then condense in the nucleus and cytoplasm through loop-loop interactions. These sequences can be optimized and diversified, enabling the generation of distinct, non-mixing condensate populations and the programmable control of their subcellular localization. The RNA motifs can also be modified to recruit small molecules, proteins, and RNA molecules in a sequence-specific manner to the RNA-rich phase. By introducing additional RNAs that link two distinct types of condensates, we can create droplets with multiple subcompartments, whose organization can be controlled by tuning the stoichiometry of different RNA sequences. These artificial condensates provide a versatile platform for studying and manipulating molecular functions inside living cells.

synthetic biology↗

bioRxiv2026

Scaling perturbations: beyond genome-scale CRISPR screens

CRISPR screens have become essential tools for systematically probing gene function from basic biology to drug discovery, yet important frontiers remain beyond genome scale. Probing regulatory elements, interpreting genetic variants, and mapping genetic interactions all challenge the sensitivity and scalability of existing approaches. Here we introduce two synergistic technologies to address these limitations. PORTAL (Perturbation Output via Reporter Transcriptional Activity in Lineages) shifts pooled genetics toward quantitative RNA phenotypes, encoding perturbation effects in expressed transcripts to enable single-molecule measurements with lineage or single-cell resolution. CAP cloning (Covalently closed Assembly Products) bypasses bacterial transformation to enable construction of ultrahigh-complexity lentiviral libraries. Combining these advances, we construct a genetic interaction map spanning 665,856 pairwise perturbations across 46 million clonal lineages--the largest exhaustive map in human cells and the first at this scale using a non-fitness phenotype. More broadly, this work charts a path toward comprehensive genetic interaction mapping in human cells.

systems biology↗

bioRxiv2025

Differential expression analysis in single cell and spatial RNASeq without model assumptions

Gene up(down)regulation findings in single cell and spatial RNASeq can be inconsistent despite remarkable progress in technology. False findings in high-quality samples raise concerns about assumptions behind widely accepted data analysis approaches. We therefore propose a weighted averaging approach for data analysis without assuming anything besides randomness of technical noise. This approach is closely related to prior work on statistics of cluster-randomized experiments. We show that weighing transcript counts based on measured noise variances and utilizing weighted rather than standard unweighted tests reduces both false positive and false negative findings. Our approach eliminates the need for parametrizing data distributions and/or rescaling transcript counts, which may cause artifacts by distorting and biasing the data. The resulting analysis is less complex and produces more consistent differential gene expression estimates.

genomics↗

bioRxiv2025

Convection-enhanced delivery of dexamethasone in glioma suppresses myeloid inflammation while avoiding systemic toxicities

Dexamethasone is widely used to control cerebral edema and inflammation in glioblastoma, but its benefits are limited by systemic toxicities and adverse prognostic associations. We evaluated local administration of dexamethasone via convection-enhanced delivery (CED) to maximize intratumoral anti-inflammatory effects by increasing local corticosteroid exposure while minimizing systemic exposure. In two glioma mouse models, continuous intraparenchymal infusion of dexamethasone was well tolerated with no adverse effects. Pharmacokinetic analyses supported preferential intratumoral distribution and reduced systemic exposure with CED compared with systemic dosing. Single-nucleus RNA sequencing (snRNA-seq) and immunohistochemistry showed attenuation of glioma-associated inflammation with downregulation of reactive microglial/macrophage programs and reduced tumor-infiltrating myeloid cells with a morphology consistent with a less activated state. Experiments in human induced pluripotent stem cell (iPSC)-derived microglia confirmed that dexamethasone directly suppresses inflammatory gene expression, indicating a conserved mechanism across species. This inflammatory suppression was recapitulated in both immortalized microglial (HMC3) and macrophage (THP1) cell lines. These findings suggest that localized dexamethasone delivered by CED reprograms the glioma immune microenvironment and achieves control of inflammation without the systemic adverse effects associated with standard systemic dexamethasone therapy. This clinically translatable strategy may improve symptom management and provide a platform for integrating local immunomodulation with future glioblastoma therapies.

cancer biology↗

bioRxiv2025

Generating functional and multistate proteins with a multimodal diffusion transformer

Generating proteins with the full diversity and complexity of functions found in nature is a grand challenge in protein design. Here, we present ProDiT, a multimodal diffusion model that unifies sequence and structure modeling paradigms to enable the design of functional proteins at scale. Trained on sequences, 3D structures, and annotations for 214M proteins across the evolutionary landscape, ProDiT generates diverse, novel proteins that preserve known active and binding site motifs and can be successfully conditioned on a wide range of molecular functions, spanning 465 Gene Ontology terms. We introduce a diffusion sampling protocol to design proteins with multiple functional states, and demonstrate this protocol by scaffolding enzymatic active sites from carbonic anhydrase and lysozyme to be allosterically deactivated by a calcium effector. Our results showcase ProDiTs unique capacity to satisfy design specifications inaccessible to existing generative models, thereby expanding the protein design toolkit.

bioinformatics↗

bioRxiv2025

The long non-coding RNA Dreg1 is required for optimal ILC2 development

Gata3 is an essential transcription factor for the development of several distinct immune cell lineages such as T cells, natural killer (NK) cells and innate lymphoid cells (ILC). As such, the levels and timing of Gata3 expression are critical for directing lineage fate decisions. The Gata3 locus has a complex and dynamic distal regulatory enhancer landscape. Recently we identified a non-coding RNA, Dreg1, located immediately upstream of the classic +280kb T/NK cell enhancer (Tce1). To test its function, we excised the Dreg1 locus in mice and observed a selective reduction of group 2 ILCs (ILC2) across multiple tissues, but mature T, NK and other ILC lineages remained unchanged. In bone marrow, common innate lymphoid cell progenitors (ILCP) increased while ILC2 progenitors (ILC2P) decreased, with a modest reduction of Gata3 in upstream progenitors consistent with an early developmental bottleneck. Chromatin profiling showed the Dreg1 locus is accessible in early lymphoid progenitors and became decorated with H3K27ac in ILCP in a Tcf1-dependent manner. Furthermore, Tcf1-deficient cells did not express Dreg1 and showed alterations in the epigenetic landscape of the Dreg1 locus. Finally, we discovered that potential homologues of Dreg1 harboured in a syntenic enhancer of GATA3 are also highly expressed in human ILC2. Taken together we conclude that Dreg1 is a Tcf1-dependent non-coding RNA critical for fine tuning the high level of Gata3 required for the optimal development of the ILC2 lineage.

immunology↗

bioRxiv2025

Normal aging impacts the extent and diversity of neural plasticity induced in the mouse brain with repetitive transcranial magnetic stimulation

Repetitive transcranial magnetic stimulation (rTMS) is an attractive tool to promote healthy brain ageing in older adults and treat age-related neurological conditions. Despite its popularity, the neurological processes and plasticity mechanisms altered by rTMS in the aged brain, and where these changes occur in the brain are unknown. Furthermore, it is not known why different rTMS protocols induce different changes in the aged brain, or why rTMS is less effective in older adults compared to younger adults. Using spatial transcriptomics, we uncovered that rTMS primarily acts on genes related to synaptic plasticity in both cortical and subcortical circuits in aged mice, but the specific changes were dependent on the brain region and even down to individual cortical layers in the motor and somatosensory cortices. Comparing our results from aged mice to young adult mice revealed that rTMS acts on a larger variety of neural plasticity mechanisms in the young adult brain, and that rTMS was less effective at altering gene expression related to neural plasticity in the aged brain, but this varied between brain regions and the protocol of rTMS applied. These findings provide a comprehensive map of the mechanisms altered by rTMS across the aged brain and highlight the need to consider the effect of ageing when optimising rTMS protocols for older populations.

neuroscience↗

bioRxiv2025

Diet-induced phospholipid remodeling dictates ferroptosis sensitivity and tumorigenesis in the pancreas

High-fat diet (HFD) intake has been linked to an increased risk of pancreatic ductal adenocarcinoma (PDAC), a lethal and therapy-resistant cancer. However, whether and how specific dietary fats drive cancer development remains unresolved. Leveraging an oncogenic Kras-driven mouse model that closely mimics human PDAC progression, we screened a dozen isocaloric HFDs differing solely in fat source and representing the diversity of human fat consumption. Unexpectedly, diets rich in oleic acid - a monounsaturated fatty acid (MUFA) typically associated with good health - markedly enhanced tumorigenesis. Conversely, diets high in polyunsaturated fatty acids (PUFAs) suppressed tumor progression. Relative dietary fatty acid saturation levels (PUFA/MUFA) governed pancreatic membrane phospholipid composition, lipid peroxidation, and ferroptosis sensitivity in mice, concordant with circulating PUFA/MUFA levels being linked to altered PDAC risk in humans. These findings directly implicate dietary unsaturated fatty acids in controlling ferroptosis susceptibility and tumorigenesis, supporting potential "precision nutrition" strategies for PDAC prevention.

cancer biology↗

bioRxiv2025

Repeated application of bifocal transcranial alternating current stimulation (tACS) improves network connectivity and driving performance: a double-blind sham control study

Mounting evidence suggests that transcranial alternating current stimulation (tACS) can enhance response inhibition, a cognitive process crucial for sustained effort and decision-making. However, most prior studies have focused on within-session effects, with limited investigation into the effects of repeated applications, which are crucial for clinical applications. We examined the effects of repeated bifocal tACS targeting the right inferior frontal gyrus (rIFG) and pre-supplementary motor area (preSMA), regions implicated in response inhibition, on inhibitory control. We also explored changes to functional connectivity and whether this stimulation improved simulated driving performance. Thirty young adults (18-35 years) were assigned to either a sham or tACS group (20 Hz, 20 minutes), undergoing five stimulation sessions over two weeks. Resting-state electroencephalography (EEG) was used to assess functional connectivity between the preSMA and rIFG during the first and fifth bifocal tACS sessions and at a 7-day follow-up. Response inhibition was measured using a stop-signal task (SST) administered throughout the sessions. Participants completed two simulated driving tasks (braking, general driving) before the first and after the final tACS intervention. Results revealed a significant improvement in functional connectivity in the tACS group across sessions, although no changes were observed in response inhibition and the braking task. Notably, general driving performance improved, with participants demonstrating closer adherence to the speed limit and greater spare attentional capacity. These findings highlight the potential of repeated bifocal tACS to enhance functional connectivity and related cognitive and motor processes, suggesting promising clinical applications for addressing issues related to cortical connectivity.

neuroscience↗

bioRxiv2025

Old World alphaviruses use distinct mechanisms to infect brain microvascular endothelial cells for neuroinvasion

Several alphaviruses bypass the blood-brain barrier (BBB), causing debilitating or fatal encephalitis. Sindbis virus (SINV) has been extensively studied in vivo to understand alphavirus neuropathogenesis; yet the molecular details of neuroinvasion at the BBB remain poorly understood. We investigated alphavirus-BBB interactions by pairing a physiologically relevant, human pluripotent stem cell derived model of brain microvascular endothelial cells (BMECs) with SINV strains of opposite neuroinvasiveness. Our system demonstrates that SINV neuroinvasion correlates with robust infection of the BBB. Specifically, SINV genetic determinants of neuroinvasion enhance viral entry into BMECs. We also identify solute carrier family 2 member 3 (SLC2A3, also named GLUT3) as a potential BMEC-specific entry factor exploited for neuroinvasion. Strikingly, efficient BBB infection is a conserved phenotype that correlates with the neuroinvasive capacity of several Old World alphaviruses, including chikungunya virus. Here, we reveal BBB infection as a shared pathway for alphavirus neuroinvasion that can be targeted for preventing alphavirus-induced encephalitis.

microbiology↗

bioRxiv2024

Data-driven discovery of cell-type-directed network-correcting combination therapy for Alzheimer's disease

Alzheimers disease (AD) is a multifactorial neurodegenerative disorder characterized by heterogeneous molecular changes across diverse cell types, posing significant challenges for treatment development. To address this, we introduced a cell-type-specific, multi-target drug discovery strategy grounded in human data and real-world evidence. This approach integrates single-cell transcriptomics, drug perturbation databases, and clinical records. Using this framework, letrozole and irinotecan were identified as a potential combination therapy, each targeting AD-related gene expression changes in neurons and glial cells, respectively. In an AD mouse model, this combination therapy significantly improved memory function and reduced AD-related pathologies compared to vehicle and single-drug treatments. Single-nuclei transcriptomic analysis confirmed that the therapy reversed disease-associated gene networks in a cell-type-specific manner. These results highlight the promise of cell-type-directed combination therapies in addressing multifactorial diseases like AD and lay the groundwork for precision medicine tailored to patient-specific transcriptomic and clinical profiles. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/627436v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1e67fd5org.highwire.dtl.DTLVardef@1d2b779org.highwire.dtl.DTLVardef@10b6efforg.highwire.dtl.DTLVardef@1a44394_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Human-mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome

Murine models of Alzheimers disease (AD) are crucial for elucidating disease mechanisms but have limitations in fully representing AD molecular complexities. We comprehensively profiled age-dependent brain proteome and phosphoproteome (n > 10,000 for both) across multiple mouse models of amyloidosis. We identified shared pathways by integrating with human metadata, and prioritized novel components by multi-omics analysis. Collectively, two commonly used models (5xFAD and APP-KI) replicate 30% of the human protein alterations; additional genetic incorporation of tau and splicing pathologies increases this similarity to 42%. We dissected the proteome-transcriptome inconsistency in AD and 5xFAD mouse brains, revealing that inconsistent proteins are enriched within amyloid plaque microenvironment (amyloidome). Determining the 5xFAD proteome turnover demonstrates that amyloid formation delays the degradation of amyloidome components, including A{beta}-binding proteins and autophagy/lysosomal proteins. Our proteomic strategy defines shared AD pathways, identify potential new targets, and underscores that protein turnover contributes to proteome-transcriptome discrepancies during AD progression.

biochemistry↗

bioRxiv2024

Fluorescent pH-sensitive nanosensors enable precise low-volume monitoring in high-throughput bioprocess manufacturing

Abstract / SummaryBiopharmaceutical manufacturing requires precise pH control during production to ensure product quality and process performance. However, achieving this precision in low-volume, high-throughput automated settings present significant challenges with existing technology, often leading to inefficiencies and inaccuracies. This study introduces fluorescent nanosensors as a novel solution for accurate pH monitoring in micro-scale environments. Employing ratiometric fluorescence measurement, these nanosensors use analyte responsive and reference fluorophores in inert polyacrylamide matrices to perform dynamic measurements over pH 3.5 - 7.5. Nanosensors (35.26 {+/-} 3.66 nm diameter) were synthesised with a neutral or positive surface charge (-5.08 {+/-} 4.05 mV and +12.87 {+/-} 1.25 mV, respectively). An automated workflow, using sacrificial and at line sample analysis, was developed by integrating the nanosensors with a TECAN automated liquid handling platform and a fluorescence spectrophotometer. The method was verified using in-process samples obtained from a monoclonal antibody purification, to highlight the compatibility of the nanosensors to different buffer systems in a typical biopharmaceutical manufacturing process. We show that pH-sensitive nanosensors can effectively monitor pH through the various stages of purification, demonstrating high accuracy (pH {+/-} 0.23-0.40) even in sample volumes as low as 12.5 L. The application of nanosensors represents a significant advancement in high-throughput scale-down bioprocess development by enabling precise, automated pH adjustment. This study improves the understanding of biopharmaceutical manufacturing, through the application of fluorescent nanosensors, paving-the-way for optimisations in low-volume and high-throughput product production. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/612862v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1fe2ef1org.highwire.dtl.DTLVardef@bbf524org.highwire.dtl.DTLVardef@1db0edcorg.highwire.dtl.DTLVardef@aca81c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states

Cell atlas projects have nominated recurrent transcriptional states as drivers of biological processes and disease, but their origins, regulation, and properties remain unclear. To enable complementary functional studies, we developed a scalable approach for recapitulating cell states in vitro using CRISPR activation (CRISPRa) Perturb-seq. Aided by a novel multiplexing method, we activated 1,836 transcription factors in two cell types. Measuring 21,958 perturbations showed that CRISPRa activated targets within physiological ranges, that epigenetic features predicted activatable genes, and that the protospacer seed region drove an off-target effect. Perturbations recapitulated in vivo fibroblast states, including universal and inflammatory states, and identified KLF4 and KLF5 as key regulators of the universal state. Inducing the universal state suppressed disease-associated states, highlighting its therapeutic potential. Our findings cement CRISPRa as a tool for perturbing differentiated cells and indicate that in vivo states can be elicited via perturbation, enabling studies of clinically relevant states ex vivo.

systems biology↗