Biology subjects

Lee, C.

Publications and source records attributed to Lee, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecule-resolved inference reveals the spatial organization of transcriptional programs

Transcriptional programs encode cellular identity and physiological activity, linking gene regulation to cellular phenotypes. Although spatial transcriptomics measures individual RNA molecules across intact tissues, most analyses aggregate them into cells or pixels, obscuring molecular level functional dynamics. We introduce FICTURE2, a statistical model that infers the transcriptional program from which each individual molecule is generated, using gene identity and spatial context alone without segmentation or binning. FICTURE2 learns programs with distinct spatial distributions, ranging from millimeter-scale continuous transition to micron-scale subcellular localization, the coexisting patterns of which then reveal both cellular identity and physiological activity with unified interpretations. FICTURE2 supports both unsupervised and reference-guided inference and is orders of magnitude more efficient than alternative approaches, enabling systematic analysis of large-scale spatial datasets as we demonstrate in data across diverse tissue types profiled by various spatial technologies.

genomics↗

bioRxiv2026

Acute social defeat induces cannabinoid type 1 receptor-dependent synaptic depression in the anterior ventral subiculum to anterior hypothalamic nucleus pathway to drive social avoidance in male mice

BACKGROUND: Social avoidance is a protective response that limits exposure to harmful social stimuli. Although avoidance is a characteristic stress phenotype, its circuit-level regulation remains unclear. The ventral subiculum (vSUB), a major hippocampal output, projects to the anterior hypothalamic nucleus (AHN), a key region for stress responses. METHODS: Male mice underwent acute social defeat stress (ASDS) or subthreshold social defeat stress. We combined social interaction, open field, and elevated plus maze testing with optogenetic-assisted slice recording, pharmacology, pathway-specific chemogenetics and optogenetics, retrograde and anterograde transsynaptic tracing, and in situ hybridization. RESULTS: ASDS induced presynaptic depression at anterior vSUB (avSUB) [->] AHN synapses through a glucocorticoid- and cannabinoid type 1 receptor (CB1R)-dependent mechanism, while posterior vSUB (pvSUB) [->] AHN synapses were unaffected. Infusing a CB1R antagonist into the AHN before ASDS attenuated both the synaptic depression and the social avoidance. Chemogenetic activation of the avSUB [->] AHN pathway during ASDS attenuated social avoidance, whereas its inhibition induced avoidance under subthreshold stress. Optogenetic activation of the avSUB [->] AHN pathway produced an immediate increase in social approach. Anterograde tracing revealed that anterior and posterior vSUB neurons project to largely separate AHN populations. The pvSUB [->] AHN pathway modulates anxiety-like behavior without altering social approach. CONCLUSIONS: These findings reveal specialized roles for vSUB subregions in social and emotional responses, and identify presynaptic gating of the avSUB [->] AHN synapse as a control point for stress-induced social withdrawal.

neuroscience↗

bioRxiv2026

ATP1A3 E815K Disrupts Sodium Homeostasis and Excitability in Human Alternating Hemiplegia of Childhood Neurons

Alternating hemiplegia of childhood (AHC) is a rare neurodevelopmental disorder primarily caused by heterozygous de novo mutations in the ATP1A3 gene, which encodes the neuron-specific catalytic 3 subunit of the P-type Na/K-ATPase. Among these, the E815K variant is the second most frequent ATP1A3 mutation in AHC and is associated with the most severe clinical phenotypes, characterized by frequent epileptic and dystonic episodes and profound developmental impairment, making it a key target for mechanistic study. Although E815K was shown to disrupt pump function in heterologous systems and animal models, its impact on human neurons remain poorly understood. To investigate its disease-relevant pathophysiology, we generated induced pluripotent stem cells (iPSCs) from an AHC patient carrying the E815K mutation and differentiated them into mature neurons. Patient-derived neurons displayed normal differentiation and synaptogenesis, with preserved evoked synaptic transmission. However, 3-specific Na/K pump currents were nearly abolished, whereas 1 activity remained intact. This selective dysfunction was associated with a depolarized resting membrane potential, reduced input resistance, and diminished intrinsic excitability. Patient neurons generated fewer action potentials in response to depolarizing current steps, displayed altered firing patterns, and showed significantly decreased voltage-gated sodium current densities, while potassium conductance remained unaffected. Taken together, these results indicate that the ATP1A3 E815K mutation disrupts intracellular sodium homeostasis and consequently modifies the excitability of human neurons. Overall, these findings provide mechanistic insight into the molecular pathophysiology underlying this AHC variant and thereby establish a patient-derived neuronal model which serves as a platform for future drug screening approaches and therapeutic investigation.

neuroscience↗

bioRxiv2026

Disentangling the Crabtree and Warburg effects across syngeneic non-tumor and tumor cells.

Oxidative phosphorylation (OxPhos) and substrate-level phosphorylation (SLP) are the primary biochemical mechanisms for ATP generation in mammalian cells. Increased dependency on SLP can arise from either transient (e.g., Crabtree effect) or chronic (e.g., Warburg effect) suppression of OxPhos. We evaluated the steady-state bioenergetics of quiescent and proliferating mouse cells matched in genetic background and cell biology, including primary thioglycollate-elicited peritoneal macrophages, malignant VM-M3 glioma with macrophage characteristics, and malignant CT-2A astrocytoma. Data are presented showing: 1) OxPhos insufficiency was the primary bioenergetic hallmark of proliferating malignant cells. 2) Dysregulated proliferation was associated with lower metabolic flexibility under nutrient stress than was growth arrest or regulated proliferation. 3) The Crabtree effect was present in macrophages and involved a glucose- and time-dependent suppression of OxPhos coupled to ATP production through SLP and resistance to mitochondrial inhibitors; lowering glucose concentration or substituting glucose with respiratory fuels increased OxPhos and restored sensitivity to mitochondrial inhibitors. 4) The Warburg effect in tumor cells involved a persistent SLP dependency and resistance to mitochondrial inhibitors under equivalent glucose-replete conditions. 5) OxPhos could sustain the regulated proliferation of non-tumor cells in the absence of a Warburg effect. Collectively, our findings emphasize that comparisons between normal and cancer cell metabolism require long-term experimental endpoints that ensure steady-state ATP sufficiency.

cancer biology↗

bioRxiv2026

Predicted structure of the complete CPLANE complex reveals novel interactors and mechanisms of Jbts17 during ciliogenesis

Cilia are highly conserved organelles that use hundreds of unique proteins to drive extracellular motility and serve as signaling hubs for eukaryotic cells. The Ciliogenesis and Planar Polarity Effector (CPLANE) protein complex controls basal body docking during early ciliogenesis and recruits the intraflagellar transport (IFT) proteins to the base of growing cilia. Leveraging recent advantages in deep learning neural networks and high-performance computing, we predict the structure of JBTS17, the largest CPLANE subunit, and the tertiary structure of the complete CPLANE complex, revealing direct contacts between JBTS17 and three other CPLANE members. We then used this model for an in silico protein-protein interaction screen that identified several novel JBTS17 interactors. Experiments in Xenopus confirmed a functional link in vivo between Jbts17 and the Spinocerebellar ataxia-associated protein TTBK2. The data provide new insights into mechanisms of CPLANE function during ciliogenesis and demonstrate the power of modeling protein complexes for the discovery of physical and functional protein interactions in cell homeostasis and disease.

cell biology↗

bioRxiv2026

Creation of a High-Resolution, Continually Evolvable Lineage Tracer

Cellular diversity is required for the proper function of many tissues, including the retina, with its ~130 cell types.1-3 Previous lineage studies suggested that retinal progenitor cells (RPCs) generate cell diversity through biased cell divisions.4-9 However, the extent to which each progenitor cell contributes to diversity, and the overarching rules governing the lineages of the collection of progenitor cells, are unknown. While classic lineage tracing approaches including retroviral labeling4,6,10, dye injection11,12, and time-lapse microscopy13,14 were used to make the foundational insights regarding retinal lineages, they cannot be used to interrogate multigenerational lineages at scale. Here we describe the creation of an evolvable lineage tracing tool, "SCRIBBLE" for Sequential Combinatorial Recorder for Iterative Barcode-Based Lineage Evolution. SCRIBBLE uses prime editor to iteratively edit a barcode sequence while preserving the order of genesis of clonally related progeny. Through a series of rationally designed high-throughput screens and design optimizations, we identified novel sequences that support a high level of barcode editing and information content. Evaluation of SCRIBBLE in embryonic mouse retina recapitulated known lineages in retinal development, demonstrating that SCRIBBLE is capable of high-resolution lineage tracing in a complex tissue.

developmental biology↗

bioRxiv2026

Convergent evolution of extreme snout elongation in deep-sea fishes reveals constrained trajectories

Phenotypic extremes are scattered across the Tree of Life, suggesting that evolutionary constraints often limit their emergence. Yet striking departures from standard body plans, such as elongate snouts, have evolved convergently across deep time. We investigate extreme morphologies in two distantly related deep-sea fish clades: spikefishes (pufferfish relatives) and snipefishes (seahorse relatives). Using spikefishes as a study system, including all 24 living and fossil species, we integrated genome-wide phylogenomic data with a fossil and extant morphological character matrix, skull shape and dentition analyses from 64 CT scans, phenotypic and divergence matrices from >200 X-rays, functional manipulations of freshly collected and cleared-and-stained specimens, and formal convergence test across 300 percomorph species. We show that snout elongation evolved independently twice within spikefishes, reaching intermediate and extreme conditions along one predictable, ordered trajectory of additive skeletal rearrangements. Snout bones form a highly integrated, semi-autonomous module that channels evolutionary change along intrinsic lines of least resistance, coinciding with accelerated cranial evolution and expanded morphospaces in a clade with enhanced cranial mobility. Snipefishes converge on the same body plan through largely non-homologous elements and distinct linkage mechanics, except for near-identical vomer convergence. Extreme morphologies can emerge when phenotypic integration aligns with functional innovation, guiding evolution along repeatable trajectories.

evolutionary biology↗

bioRxiv2026

Parents' neural dynamics in response to their children's speech

The development of speech in human children is a protracted process that depends on social experience. From early life, young children produce vocalizations in the presence of others, which affords unique opportunities for feedback about how to communicate successfully. However, for feedback to happen, young childrens speech needs to effect change in the brains of their caregivers. Using dual-brain functional near-infrared spectroscopy (fNIRS) to measure real-time communication between caregivers and their 2- to 3-year-old children (n = 56), we found that children's vocalizations selectively modulated caregivers' brain activity. Parents' brains showed a rapid response to children's production of speech that was communicatively advanced (multiword utterances) vs. less advanced (babble). The findings imply that if part of learning to talk is figuring out how to get your communication partner to listen, then early conversations likely present continuous opportunities for feedback that guide children toward advances in spoken language.

neuroscience↗

bioRxiv2026

Maintenance of quantitative genetic variation in regions of restricted recombination via associative overdominance

Mutation-selection balance is the most plausible general mechanism for the maintenance of additive genetic variance (VA) for quantitative traits in natural populations. It is well established that the genetic variants affecting traits (QTLs) are widely distributed across species' genomes. At the same time, unconditionally deleterious mutations are also expected to be common, with those with the largest fitness effects tending to be strongly recessive. Many genomes possess regions of restricted recombination that could result in tight linkage between largely recessive deleterious alleles, conditions which can lead to elevated heterozygosity via associative overdominance (AOD). Here we show that weakly selected QTLs linked to genomic regions exhibiting AOD can elevate VA above what is expected in the absence of unconditionally deleterious mutations. Selection on traits when VA is maintained by AOD, however, may expose recessive deleterious alleles as homozygotes, reducing fitness. Thus, while AOD may contribute to the maintenance of VA, variation maintained in this way may not be readily accessible by natural or artificial selection.

evolutionary biology↗

bioRxiv2026

Global tree encoding of atlas-scale single-cell genomics

The rapid expansion of single-cell genomic datasets has led to the compilation of biological resources comprising hundreds of millions of cells across tissues, developmental stages, and disease states. This has underscored the need for scalable and interpretable data representations that preserve the complex relationships and multi-scale organization of cellular states, while remaining computationally tractable at atlas scale. Existing approaches based on discrete abstractions have enabled cell annotation, clustering, and trajectory inference, but are often optimized for local inference tasks and may obscure continuous cellular relationships and multi-resolution structure within complex transcriptional and other genomic landscapes. Moreover, increasing dataset sizes often require information-reduction strategies such as random downsampling, limiting the resolution of rare cell populations and heterogeneous cellular states. Here, we present MILK, a scalable computational framework that organizes high-dimensional single-cell populations into unified tree representations. Across large-scale transcriptomic atlases, MILK enables representative subsampling with preserved information, supporting the tractable application of existing algorithms for tasks including deep generative model training and foundation model benchmarking. Additionally, MILK enables holistic, multi-resolution analyses that capture global developmental trajectories, characterize disease-associated cellular perturbations across tissues, and facilitate comparison of transcriptional programs across species within a coherent hierarchical framework. Together, these results establish the hierarchical organization of biological data as a scalable and unifying representation of cellular identity, enabling integrative analysis of single-cell genomic data across diverse contexts.

genomics↗

bioRxiv2026

Post-transcriptional glucocorticoid receptor signalling synchronises circadian rhythms

Keeping cellular circadian clocks synchronised is critical for cellular and physiological health. Glucocorticoid (GC) hormones are the most potent systemic timing signal for cellular clocks, acting via the glucocorticoid receptor (GR), a transcription factor conventionally thought to synchronise cells by translocating into the nucleus and activating the transcription of clock genes. Our findings overturn this model: acute changes in GR translocation and nascent transcription are both dispensable for GC-resetting of the circadian clock. Instead, physiological GC pulses act post-transcriptionally to rapidly increase Period1 mRNA through enhanced RNA processing, not synthesis. This elevates PER1 protein production which, alone, is sufficient to reset the clock. Yet each pulse resets only a subset of cells, explaining why, in vivo, repeated daily hormonal cues are required for full re-entrainment after jet lag or shift work. We propose a new model for hormonal signalling to the circadian clock and identify RNA processing kinetics as a general regulatory lever for nuclear receptor signalling.

molecular biology↗

bioRxiv2026

PIANO: Probabilistic Inference Autoencoder Networks for multi-Omics enables robust generative modeling of gene expression and scales single-cell integration to 100 million cells

Single-cell RNA technologies enable the routine acquisition of transcriptomic atlases. However, these molecular profiles are influenced by overlapping sources of variation. Since these covariates confound comparisons, data integration is the first step in most analyses. Three challenges remain: correcting strong batch effects, scaling to millions of cells, and modeling how covariates influence gene expression. To address these challenges, we developed PIANO: Probabilistic Inference Autoencoder Networks for multi-Omics, a deep learning framework whose central feature is a generative model of gene expression data. Additionally, PIANO achieves robust integrations and trains 10x faster than previous methods. PIANO accurately integrates single-cell data across species and across single-cell and spatial transcriptomics modalities. As practical applications, PIANO models spatially-resolved gene expression during Alzheimer's disease progression in human brains and integrates over 100 million cancer cells to model drug perturbations. In summary, PIANO's integration and generative modeling capabilities will empower novel insights for countless future studies.

bioinformatics↗

bioRxiv2026

Synaptic engram underlies memory

Memory encoding cells, or engram cells, are sparsely distributed across the brain. Recent findings have shown that memory formation coincides with the strengthening of interregional synaptic connectivity between engram ensembles. However, whether this learning-induced synaptic reorganization causally supports memory, independently or in concert with heterosynaptic and intrinsic plasticity, remains elusive. Here we developed optically implemented spike-timing-dependent plasticity (oSTDP), which induces synaptic depression selectively at target synapses by controlling the relative timing of pre- and postsynaptic activity. In vivo application of oSTDP to the synapses between entorhinal cortex (EC) and dentate gyrus (DG) engram cells caused a significant synaptic depression and the resultant memory impairment. Our results demonstrate that plasticity of functional connectivity between memory-encoding ensembles causally underlies memory.

neuroscience↗

bioRxiv2026

Structural Mechanisms of DNAJC13 Dimeric Assembly and InsP6 binding in Recycling Endosome Regulation

The balance of plasma membrane protein degradation and recycling during endocytosis is regulated, in part, by the large J-domain-containing protein DNAJC13/RME-8 and WASH complexes, which function together with Retromer to support cargo trafficking into recycling endosomes. Despite extensive cellular and biochemical studies, the structural basis and proteomic landscape of DNAJC13 function remain elusive. Here, we find that DNAJC13 forms an unexpected antiparallel homodimeric architecture involving distinctive symmetrical interactions between composite IWN1 and -solenoid ARM2 domains in each protomer. Additionally, two PH-like domains of unknown function (PHL2 and PHL3), adjacent to the PI(3)P-binding PHL1 domain, form an unanticipated composite, positively charged pocket occupied by InsP6, as visualized structurally and verified by mass spectrometry. Proteomic profiling of DNAJC13-associated endosomes revealed enrichment of recycling endosomal components and WASH complexes. Mutations disrupting the dimer interface disable recruitment of WASH complexes to endosomes and result in elongated endosomal tubulation. Disruption of InsP6 binding impairs DNAJC13 binding to PI(3)P-containing vesicles in vitro and Transferrin-positive endosomes in cells. We further demonstrate that DNAJC13 dimerization and InsP6 binding promote melanin production during melanosome maturation, a process known to require recycling endosomes. This work provides a structural and mechanistic framework for understanding DNAJC13 function in recycling endosome control.

cell biology↗

bioRxiv2026

Inherited proliferation states organize plant transcriptomes

A central question in plant biology is whether natural transcriptome variation primarily reflects environmental adaptation or intrinsic genetic programs. Using transcriptomes from 665 natural Arabidopsis thaliana accessions, we show that inherited population structure, not environmental gradients, is the primary organizer of global transcriptome architecture. Genomic population structure uniquely explains 30.0% of transcriptome-wide variation, while environmental variables account for only 2.5%. This architecture is dominated by a single co-expression program (proliferation Module Eigengene: prolifME), enriched for cell cycle regulation and ribosome biogenesis, regulated by a bipartite transcription factor architecture, and genetically encoded at discrete loci with broad trans-regulatory effects. This proliferation program is associated with reduced plant size, biomass, growth rate and water-use efficiency, and these relationships persist under common-garden conditions. Gene contributions to this proliferation program are non-randomly conserved in rice and maize across 150-200 million years of divergence. These findings identify an intrinsic transcriptional proliferation program as a primary state of plant population transcriptomes, conserved across plant species.

plant biology↗

bioRxiv2026

The anatomical compartment defines distinct immune remodeling within human visceral adipose tissue during aging

Age-associated inflammation varies across tissues, but whether distinct visceral adipose tissue (VAT) depots undergo inflammatory remodeling in a depot-specific manner remains unclear. Here we profiled human peri-organ VAT, comparing kidney-associated fat (KF, from kidney transplantation donors) and gallbladder-associated fat (GBF, from asymptomatic cholecystectomy patients with incidental polyps), using single-cell RNA sequencing, flow cytometry, intracellular protein profiling and in situ analysis. GBF showed broad tissue-residency and granzyme K-associated remodeling across conventional, regulatory and innate-like lymphocyte compartments, whereas KF showed stronger B cell remodeling, greater myeloid representation and more compartmentalized changes within resident effector-like CD8+ T cell states. We further identified age-associated CD20+ T cells with features consistent with local B-T cell interaction and an antigen-experienced, granzyme K-associated inflammatory memory phenotype. In situ analysis revealed age-associated myeloid accumulation and crown-like structure remodeling, accompanied by distinct myeloid inflammatory programs in KF and GBF. Finally, depot-specific immune signatures associated with clinical indices of adjacent kidney and liver function. These findings indicate that age-associated distinct immune programs within peri-organ VAT depots track with local tissue context and the state of the adjacent organ.

immunology↗

bioRxiv2026

Multimodal characterization of variation in neuronal types in the mouse basal ganglia

AbstractThe basal ganglia (BG) are a set of topographically organized, interconnected structures that are pivotal for regulating volitional movement and other aspects of cognitive, motivational, and affective behavior. Recently generated taxonomies of transcriptomically-defined cell types (T-types) have revealed both fine-grained distinctions in gene expression between neurons in these structures as well as continuous transcriptomic variation across similar T-types1-9, which are both related to location within a structure. However, it remains unclear to what extent these and other cellular properties co-vary with each other. Therefore, we performed Patch-seq experiments10,11 on over 900 neurons in mouse brain slices from BG to provide an integrated view of the co-variation between gene expression, location, physiology, and morphology measured from the same neurons. Medium spiny neurons (MSNs) from both the direct and indirect pathways across the dorsal and ventral striatum follow a gene expression gradient that varies in a dorsolateral to ventromedial direction; we find that this gradient also corresponds with systematic differences in action potential kinetics and dendritic arborization. Our analysis also characterizes additional multimodal dimensions of MSN variation, such as those between direct and indirect pathway neurons and between matrix and striosome neurons. Furthermore, through comparison with Patch-seq data from macaque, we demonstrate that the relationship between the transcriptomic/spatial gradient and electrophysiological and morphological properties is conserved across these two species. We also find that properties of striatal interneurons, such as action potential kinetics, vary across the striatum in a manner consistent with the MSN gradient. Outside the striatum, our multimodal Patch-seq dataset from the globus pallidus, subthalamic nucleus, and substantia nigra enabled us to characterize transcriptomically-defined types and link them to prior descriptions of cell types in these structures. Finally, we examined to what extent the MSN transcriptomic/spatial gradient persisted across different stages of the BG circuit by comparing Patch-seq neurons to reconstructed whole-neuron morphologies and the topography of their interareal projections, finding that the gradient is better preserved in GPe and GPi compared to SNr. Our study links transcriptomic variation across T-types in mouse BG to spatial localization and phenotypic differences at the level of individual cells, improving our understanding of cell type architecture in topographically organized circuits of the brain.

neuroscience↗

bioRxiv2026

MOTS-c Coordinates Inter-Organellar Proteostasis for Adaptation to Chronic Metabolic Stress

Mitochondrial communication coordinates adaptive responses across organelles to sustain cellular homeostasis, a network that declines with age and contributes to loss of proteostasis. Here, we identify MOTS-c, an exercise-induced mitochondrial-derived peptide (MDP) encoded within the 12S rRNA locus, as an inter-organellar arm of the mitochondrial stress response (MSR) that links mitochondrial signaling to endoplasmic reticulum (ER) proteostasis and enables adaptation to chronic stress. Using progressive stress media (PSM), a model of gradual and multifactorial metabolic stress, we show that MOTS-c enables adaptation through a biphasic program: acutely, a reversible, ATF4-independent suppression of protein synthesis; and chronically, an ATF6-biased ER unfolded protein response (UPRER) with tempered ATF4 engagement and coordinated metabolic remodeling. Whereas mitochondrial unfolded protein response (UPRmt) pathways have been extensively characterized in acute, genetic, and sustained models of mitochondrial perturbation, this work reveals how mitochondrial communication actively engages ER proteostasis during progressive and persistent metabolic stress. By expanding proteostatic capacity while tempering terminal stress signaling, MOTS-c enables cells to withstand chronic stress. Together, these findings define a MOTS-c-dependent arm of the MSR that integrates mitochondrial communication with ER proteostasis to promote chronic metabolic stress adaptation.

Cell Biology↗