Biology subjects

Lee, M.

Publications and source records attributed to Lee, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Kindlin-1 loss disrupts vascular and extracellular matrix organisation to sustain hypoxia in cutaneous squamous cell carcinoma

Kindlin-1, encoded by FERMT1, is an essential integrin co-activator that regulates cell-extracellular matrix (ECM) adhesion, tissue architecture, and microenvironment signalling. Loss-of-function mutations in FERMT1 cause Kindler epidermolysis bullosa, which is strongly associated with aggressive cutaneous squamous cell carcinoma (cSCC). Although Kindlin-1 deficiency promotes hypoxia and invasion, the impacts on ECM-vascular organisation and oxygen homeostasis are not known. Here, using genetic deletion of Kindlin-1 in a murine model of cSCC across 2D cultures, 3D spheroids, and in vivo tumours, combined with collagen and vascular imaging and spatial mixed-effects modelling, we show that Kindlin-1 loss uncouples ECM-vascular regulation, driving hypoxia and tumour progression. Tumours in which Kindlin-1 was deleted displayed a dense but dysfunctional vascular network, with reduced tissue-to-vessel and inter-bifurcation distances, increased vessel alignment, and persistent hypoxia despite increased vascular density. Collagen deposition was reduced and fibres were straighter, indicating a simplified, invasion-permissive matrix. Hypoxia increased Vegfa and Angpt1 expression while reducing Col1a1, and hypoxia-responsive spheroids confirmed greater hypoxia and invasiveness in Kindlin-1-deficient cells. Transcriptomic analysis revealed enrichment of ECM degradation and vascular dysfunction pathways, including upregulation of matrix-remodelling and vascular permeability genes such as Mmp13, Mmp3, and Ptgs2, alongside reduced collagen-associated and vascular homeostasis genes. Spatial modelling further showed disrupted collagen-vascular coupling and an association between hypoxia and reduced vessel diameter, consistent with dysfunctional angiogenesis rather than improved perfusion. These changes arose early and independently of tumour size, establishing impaired integrin activation as a central mechanism linking ECM degradation, vascular dysfunction, and sustained hypoxia in aggressive cSCC.

cancer biology↗

bioRxiv2026

The Impact of Smoking Status on the Genomic Landscape of Lung Squamous Cell Carcinoma

PurposeComprehensive genomic profiling (CGP) has changed the treatment paradigm for non-small cell lung cancer (NSCLC) with the advent of molecularly targeted therapies for actionable genomic alterations (AGA). Despite this, the use of CGP is suboptimal, particularly in squamous cell lung cancer (sqNSCLC), which is more closely associated with smoking exposure and a lack of AGAs. We hypothesized that the prevalence of AGAs is inversely correlated with the chronicity and extent of smoking exposure in patients with sqNSCLC. Experimental DesignWe retrospectively evaluated all patients with liquid biopsy testing via Guardant 360CDX or Guardant360 in the context of any sqNSCLC diagnosis at the City of Hope Comprehensive Cancer Center between 10/2020 and 7/2023. The data was obtained on 2/23/24. Social and clinical histories were evaluated to assess the frequency of AGAs in patients with no or remote smoking history. ResultsOf the 56 patients in the initial evaluation, 24% (n=13) were non-smokers or remote smokers (greater than 20 years from cessation). Of these 13 patients, eight (61.5%) harbored AGA. Of these 8 patients, alterations observed included EGFR exon 19 deletion (50%, n=4), MET exon 14 skipping mutation (25%, n=2), EGFR G719S (13%, n=1), EGFR E114K (13%, n=1). Of those patients harboring AGAs that received NCCN-concordant matched targeted therapy, the objective response rate (ORR) with targeted agents was 50% and the clinical benefit rate (CBR) was 83.3%. ConclusionsThese data support the use of CGP in sqNSCLC particularly in patients with remote or no smoking exposure. Statement of translational relevanceThese data demonstrate high frequency of actionable genomic alterations (AGAs) in patients diagnosed with squamous cell lung cancer (sqNSCLC) with remote or no smoking history. Specifically, enrichment of EGFR and MET gene alterations were observed. These findings support the use of comprehensive molecular profiling in sqNSCLC. Furthermore, treatment outcomes demonstrate frequent objective responses and high clinical benefit rate supporting the use of targeted therapies in sqNSCLC harboring AGAs. This analysis provided rationale for further research of larger datasets investigating therapeutic approaches in sqNSCLC, which may have significant implications for consensus guideline recommendations and routine clinical practice.

cancer biology↗

bioRxiv2026

Substrate-derived peptides for selective covalent inhibition of protein tyrosine kinases

Protein tyrosine kinases are important regulators of cell signaling, and aberrant kinase activity contributes to many human diseases, including cancers. All protein tyrosine kinases share a highly-conserved ATP binding pocket but diverge in their substrate binding sites in order to mediate distinct signaling events. Many potent and efficacious ATP-competitive tyrosine kinase inhibitors have been developed, however it remains challenging to achieve on-target selectivity across different kinases and target specific disease mutants, given the high degree of conservation in the ATP-binding pocket. By contrast, the variable substrate-binding site offers an opportunity for selective inhibition, provided molecules can be targeted to this site. Here, we present a modular strategy to design selective, peptide-based covalent inhibitors of tyrosine kinases with a distinct binding mode from existing ATP-competitive inhibitors. Using Src kinase as a model system, we demonstrate that Src-selective reactivity can be achieved by first designing an optimized substrate peptide and then strategically positioning an electrophile on the peptide to target a non-conserved cysteine on the kinase. We show that substrate-derived covalent peptides can inhibit kinase activity, bind simultaneously with an ATP-competitive inhibitor, and even inhibit the activity of kinases bearing a common drug resistance mutation. We further explore the application of this approach to develop an inhibitor of the cancer-relevant fibroblast growth factor receptor 1 kinase that shows selectivity for an oncogenic mutant over the wild-type enzyme. Our modular strategy to generate selective covalent peptides targeting protein tyrosine kinases provides a promising framework for future chemical probe and drug development efforts.

biochemistry↗

bioRxiv2026

Fast and Ultra-Capable Protein Design: Advancing the Frontier Through Atomistic SE(3)-Equivariance with Genie 3

Despite the breakneck pace of progress in protein design methodology, frontier problems remain challenging, with leading methods struggling to design high-affinity binders, scaffold multiple functional motifs, or stabilize large multi-domain proteins. Recent research efforts have focused on two areas: improving model reasoning when generating active sites or binding interfaces, and improving concordance between the design process and the in silico oracle used to select promising designs. In addressing the first, the field has shifted towards all-atom models that capture sidechain conformations in atomistic detail by eschewing data-efficient SE(3)-equivariance, mirroring the evolution of AlphaFold2 to AlphaFold3. In addressing the second, recent work has focused on replacing generative models employing diffusion or flow-matching with hallucination approaches that directly optimize the oracle in sequence space; this improves success rates but reduces computational efficiency. Here, we close and surpass the generation-hallucination gap by revisiting SE(3)-equivariance using a branched polymer treatment of protein structures. The resulting diffusion model, Genie 3, achieves state-of-the-art performance on binder design, motif scaffolding, and unconditional generation, while being significantly faster than the best existing methods. We use Genie 3 to design a nanomolar binder of Nipah Glycoprotein G, a tetramer with minimal structural or biophysical characterization, as part of the Adaptyv Bio Nipah Competition, achieving a 12.5% success rate. Taken together, our results present a new frontier in protein design capability and a reexamination of the role of SE(3)-equivariance in molecular modeling.

bioinformatics↗

bioRxiv2026

SubCellSpace: Automated characterization of subcellular mRNA localization patterns in spatial transcriptomics

The localized translation of transcripts is a universal phenomenon across biological domains. Many examples of subcellular RNA localization and their functional importance have been described. However, these examples remain anecdotal, and a more systematic genome and cell-type-wide analysis is needed. Current spatial transcriptomic techniques can characterize hundreds to thousands of transcript species at subcellular resolutions, enabling the large-scale investigation of subcellular mRNA localization. Here we describe SubCellSpace, a computational framework to learn general representations of mRNA localization patterns. By embedding observed single-cell subcellular localization patterns (SLPs) to an interpretable latent space, SubCellSpace can detect and statistically infer the presence of SLPs, uncover colocalizing gene-pairs and characterize cellular heterogeneity for pattern-presentation. We benchmark SubCellSpace in both synthetic and real data, showing it can correctly detect previously described apical/basal polarized genes in the enterocytes of mouse small-intestine, as well as encode the enterocytes orientation. Additionally, we provide a tailored spatial transcriptomics validation dataset for benchmarking SLP identification based on transcripts previously described to be enriched near subcellular structures in HEK293T cells. We propose a practical and computationally-efficient classification workflow that automatically detects localized transcript species and quantifies their degree of patterning, while controlling false positive rates. Finally, we showcase SubCellSpace in both supervised and unsupervised settings, to either classify pre-determined SLPs or to explore spatial patterning without specifying pattern types a priori. Automated AI models such as SubCellSpace and their integration in spatial transcriptomics analysis workflows will help characterize previously undiscovered subcellular RNA localization phenomena, providing novel insights into post-transcriptional regulation mechanisms.

bioinformatics↗

bioRxiv2026

ENPP1 buffers extracellular cGAMP in brown adipose tissue to limit insulin resistance

The ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) has long been linked with metabolic diseases, with the common ENPP1 K173Q (historically K121Q) variant conferring increased risk for type 2 diabetes (T2D). However, the mechanistic basis of this association has remained unclear. Here, we demonstrate that the K173Q variant has decreased cGAMP hydrolysis activity, suggesting that this loss of enzymatic function could contribute to its pathogenesis. Using a cGAMP-hydrolysis-deficient knock-in mouse (Enpp1H362A), we show that selective loss of this activity leads to a primary defect in energy expenditure and exacerbates high-fat diet (HFD)-induced weight gain and insulin resistance. An unbiased in vivo glucose-uptake screen reveals brown adipose tissue (BAT) as a focal site of metabolic impairment, characterized by profound extracellular cGAMP accumulation and a selective failure of insulin-stimulated glucose uptake. Mechanistically, we demonstrate that nutrient excess drives mitochondrial DNA leakage in brown adipocytes, triggering cGAMP production and export. Excess cGAMP directly propagates STING-dependent suppression of glucose uptake and lipogenesis in brown adipocytes. Additionally, when ENPP1-mediated clearance is compromised, extracellular cGAMP acts as a paracrine immunotransmitter that remodels the BAT microenvironment by recruiting and polarizing macrophages toward an M1-like phenotype. Together, our findings nominate the impaired ENPP1-dependent buffering of extracellular cGAMP as one mechanism by which ENPP1 variants influence metabolic homeostasis.

immunology↗

bioRxiv2026

Disrupted glial-mediated synaptic refinement in Fragile X syndrome

Fragile X syndrome (FXS), the most common inherited cause of intellectual disability and autism, results from the loss of the RNA-binding protein fragile X mental retardation protein (FMRP). FMRP is a translational regulator and is highly expressed in glial cells, where its role in neural circuit development remains poorly defined. Here, it was observed that Fmr1 knockout mice exhibit reduced synapse size and accelerated eye-specific segregation. To examine which cell-types participate in this process, a multi-omic framework was applied to FXS model mice at postnatal day 7, a critical window for synaptic remodeling in the retinogeniculate pathway, an established model system utilized to study synaptic pruning. Single-cell transcriptomics revealed coordinated alterations in microglia, astrocytes, and neurons in genes linked to synaptic pruning. Computational modeling further demonstrated enhanced astrocyte-to-microglia signaling, particularly through Ephrin A (EphA)- and semaphorin-mediated pathways, while lipidomic profiling revealed reductions in EphA-associated lipid species required for lipid raft stability and receptor localization. Consistent with these observations, a glial engulfment assay indicated that FXS microglia and astroglia over-engulf synaptic material in the lateral geniculate nucleus, supporting the transcriptomic profile. Together, these findings identify impaired glial-driven synaptic refinement as an early mechanistic feature of FXS pathogenesis, highlighting the genes involved in this process as potential therapeutic targets during circuit development.

neuroscience↗

bioRxiv2026

Topographic structure and function of locus coeruleus norepinephrine neurons

Norepinephrine (NE) is released throughout most of the central nervous system by neurons in the locus coeruleus (LC). We found a relationship between the morphologies, gene expression, and activity of LC-NE neurons in mice. Axonal projections of individual neurons were extensive but largely confined to subsets of brain regions. Axonal projections and graded gene expression correlated with locations of cell bodies in LC. In a behavioral task requiring ongoing learning from actions, neurons in dorsal LC projecting to the cerebral cortex were excited when mice made a different choice from the previous one and by reward prediction errors, a signal driving learning. Background activity of neurons in ventral LC was higher when mice ignored stimuli indicating potential reward availability. These observations reveal a topographically organized structure and function of a neurotransmitter system and show that it contains learning signals for flexible behavior.

neuroscience↗

bioRxiv2026

Epigenomics identifies three sources of DNA methylation in Streptococcus mutans UA159

DNA methylation is a widespread but incompletely characterized regulatory feature of bacterial genomes. While restriction-modification systems represent well-studied sources of DNA methylation, the full complement of methyltransferases shaping bacterial epigenomes and their physiological consequences remain poorly understood. Here, we used Oxford Nanopore sequencing to comprehensively map DNA methylation in the model oral pathogen Streptococcus mutans UA159. Genome-wide analysis identified extensive N6-methyladenosine (6mA) modification and revealed three predominant methylation motifs. Using targeted deletion mutants, we demonstrate that methylation at GATC sites is mediated by the conserved DpnII restriction-modification system, while a novel bipartite CGANNNNNNNTCY/RGANNNNNNNTCA motif is methylated by the HsdM component of the type I Hsd restriction-modification system. The remaining 6mA sites corresponded to a CTGNAG/CTNCAG motif, defining the activity of a third methyltransferase. Genetic and epigenomic analyses identified SMU.43 as the enzyme responsible for this modification, which we designate DnmA, a novel orphan adenine methyltransferase with homology to regulatory methyltransferases rather than defense-associated systems. Functional characterization of single and double mutants revealed that distinct methylation systems differentially influence biofilm formation and antagonistic interactions with the commensal, Streptococcus sanguinis. Notably, loss of dnmA reversed biofilm and aggregation defects associated with deletion of dpnII, indicating epistatic interactions between methylation pathways. Together, this study resolves the major sources of DNA methylation in S. mutans UA159, identifies a novel regulatory methyltransferase, and highlights the utility of nanopore sequencing for bacterial epigenome discovery. These findings expand our understanding of bacterial DNA methylation and suggest that epigenomic enzymes may represent targets for modulation of microbial physiology and virulence.

microbiology↗

bioRxiv2026

Orthogonal Transposons for Iterative Genome Engineering of Mammalian Cells.

The contemporary shift toward multispecific antibodies, antibody-drug conjugates (ADCs), and bespoke glycoengineered therapeutics have exposed the limitations of standard genomic engineering tools. This paper presents a novel iterative engineering paradigm utilizing the Leap-In Transposase(R) platform. By leveraging a suite of three mutually orthogonal transposase-transposon systems, we demonstrate the sequential modification of the Chinese Hamster Ovary (CHO) genome to achieve three distinct functional outcomes: (i) First, the creation of a glutamine synthetase (GS)-deficient host (CHO-K1-GS) via targeted knockdown, (ii) Second, the integration of multiple copies of a model therapeutic IgG1 for expression, and (iii) Third, the subsequent knockdown of the fucosylation pathway to modulate the glycan profile of the expressed IgG1. Genetic stability (copy number & sequence) of each integration event was confirmed using Targeted Locus Amplification (TLA) and Next-Generation Sequencing (NGS). Functional stability (expression levels, metabolic phenotype, and glycan phenotypes) was confirmed using standard cell culture and analytical techniques. Crucially, the truly orthogonal nature of the transposase-transposon pairs prevents cross-mobilization and ensures the structural and functional integrity of previously integrated cargo. This study establishes a "What You See Is What You Get" (WYSIWYG) methodology that provides a robust, scalable, and predictable framework for developing next-generation complex biopharmaceutical manufacturing cell lines.

bioengineering↗

bioRxiv2026

Membrane contact site resident PTP1B limits superoxide production by suppressing a Syk-Shc1-Phagocyte Oxidase relay.

Phagocytosis is a specialized endocytic process used by macrophages and dendritic cells to engulf particles, which requires coordinated signaling cascades, cytoskeletal remodeling, and assembly of antimicrobial machinery to eliminate pathogens. During Fc {gamma} receptor (Fc{gamma}R)-mediated phagocytosis, dynamic actin depolymerization at the base of the phagocytic cup creates permissive conditions for endoplasmic reticulum-plasma membrane (ER-PM) membrane contact sites (MCS) to form. We demonstrate that the ER-resident protein tyrosine phosphatase PTP1B localizes to newly formed or expanded ER-PM MCS during phagocytosis and dephosphorylates Syk. Using TIRF microscopy with MCS residents, including MAPPER, STIM1, and E-Syts, we show that actin clearance allows ER proteins to approach the plasma membrane. PTP1B colocalizes with Fc{gamma}Rs in actin-cleared zones and physically interacts with Syk, a critical mediator of phagocytic signaling. Loss of PTP1B led to sustained Syk hyperphosphorylation without affecting phagocytosis. However, the PTP1B-deficient cells showed a {asymp}3-fold increase in NADPH oxidase 2 (NOX2)-mediated superoxide production. Using unbiased proteomics, we identified the adapter protein Shc1 as a critical intermediate linking Syk phosphorylation to NOX2 activation. Shc1 phosphorylation during phagocytosis is dependent on Src family kinases and Syk, while genetic ablation of SHC1 reduced superoxide production by {asymp}40%. Proximity ligation assays reveal enhanced Shc1-p47phox interactions in PTP1B-deficient cells during phagocytosis. These findings establish an SFK-Syk-Shc1-NOX2 signaling axis that PTP1B negatively regulates at MCS between the ER and the forming phagosome, providing new mechanistic insights into antimicrobial responses during phagocytosis.

cell biology↗

bioRxiv2026

Heightened Distraction under Competition in Obsessive-Compulsive Disorder

The present study examine the extent to which attentional resources are allocated toward distracting affective and disorder-relevant pictures under task-relevant competition in participants with obsessive-compulsive disorder (OCD; N = 33) and controls (N = 31). Competition between cues was examined using a foreground task where participants detected coherent motion in a flickering random dot kinematogram (RDK) overlaid on pictures ranging in emotional content (pleasant, neutral, unpleasant, and OCD-evoking pictures). Steady-state visual evoked potentials (ssVEPs) were measured in response to the flickering RDK and served as an index of visuocortical engagement with task-relevant cues. Data were also fitted to the distraction under competition model (DUC), a computational framework of attention selection. Group differences emerged with stronger visuocortical distraction (attenuated task engagement) in the OCD group, driven largely by the unpleasant pictures, followed by the OCD-evoking and pleasant pictures. Furthermore, the DUC model fit well in both groups and supported the results of the univariate analysis, demonstrating the magnitude of the visuocortical distraction observed in response to the unpleasant pictures, and the presence of substantial distraction in response to the OCD-evoking pictures in the OCD group. The present findings provide visuocortical evidence of heightened distraction in response to unpleasant and OCD-evoking pictures under task-relevant competition in OCD.

neuroscience↗

bioRxiv2026

Dual plasmepsin IX and X inhibitors are refractory to development of resistance

Artemisinin-based combination therapies (ACTs) remain the cornerstone of malaria treatment, but emerging resistance threatens their efficacy. The potential for the development of drug resistance against plasmepsin X (PMX)-selective inhibitors and dual plasmepsin IX/X (PMIX/X) inhibitors was investigated in Plasmodium falciparum. A series of PMX-selective (WM4, WM76, WM92) and PMIX/X dual inhibitors (WM382, WM09, WM42) were characterised for potency against parasite growth and enzyme inhibition. In vitro selection experiments showed that all compounds had a high barrier to resistance, although parasites with reduced sensitivity to PMX-selective inhibitors could still be selected. Resistance mechanisms involved pmx gene amplification and point mutations (D245N, S315P, S359P, I363L) that alter inhibitor binding. Recombinant expression and Michaelis-Menten kinetics demonstrated that these mutations impair drug binding whilst preserving PMX catalytic function. Reverse genetics confirmed that introducing these mutations into the pmx gene resulted in decreased potency of the inhibitors. In this study, resistance to the PMIX/X dual inhibitors evaluated here could not be selected, despite prolonged selection pressure. Antimalarial Resistome Barcoding (AReBar) assays confirmed the absence of pre-existing resistance to either inhibitor class. Critically, PMIX/X dual inhibitors maintained efficacy against parasites with decreased sensitivity to PMX-selective compounds. These findings demonstrate that dual PMIX/X inhibitors present a substantially higher barrier to resistance than PMX-selective inhibitors, informing antimalarial drug development strategies and highlighting dual-target inhibition as a promising approach to mitigate resistance risks.

microbiology↗

bioRxiv2026

MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies

Single-cell mapping methods convert raw, heterogeneous single-cell datasets into interpretable and comparable representations of biological identity. As reference cell-type taxonomies mature, mapping new datasets to shared references has become a central strategy for enabling cross-study integration, reproducible annotation, and cumulative biological knowledge. Here we present MapMyCells, an open-source framework designed to align diverse single-cell omics datasets to hierarchical reference taxonomies with minimal preprocessing. MapMyCells provides out-of-the-box support for an expanding set of high-quality brain cell-type references generated by the Allen Institute for Brain Science, the BRAIN Initiative, and the Seattle Alzheimers Disease Brain Cell Atlas, including whole-brain mouse and human atlases, aging and Alzheimers disease cohorts, and a cross-species consensus taxonomy initially focused on the basal ganglia. MapMyCells enables efficient mapping of hundreds of thousands of cells on standard workstations without specialized hardware, providing a deterministic, scalable, and modality-agnostic approach that is robust across species and molecular assays. The framework produces interpretable confidence metrics and quantitative summaries of mapping performance, allowing users to evaluate assignment precision and accuracy. We demonstrate the mapping of unlabeled transcriptomic, epigenomic, and spatial datasets to reference taxonomies and describe a general workflow for preparing arbitrary hierarchical taxonomies for reference-based mapping. As the ecosystem of single-cell reference atlases expands, MapMyCells offers a practical and reproducible solution for community-scale cell-type annotation and cross-dataset integration, supporting the development of unified and extensible brain cell atlases.

bioinformatics↗

bioRxiv2026

Ribosome Molecular Aging Shapes Translation Dynamics

Cellular homeostasis relies on continual renewal of cellular components, yet some complexes like ribosomes persist for long periods, raising the question of whether extended molecular age impacts functional fidelity. Here, we introduce a spatiotemporal mapping strategy to resolve biomolecular life stages, and show that intracellular ribosome aging alters translational dynamics at specific transcripts. Molecularly aged ribosomes exhibit impaired elongation at basic amino acid-rich sequences, leading to increased pausing, premature termination, and ribosome collisions. By profiling ribosomal RNA modifications, we find that molecular aging increases the collision propensity of specific ribosome subpopulations. Consistent with our findings, enrichment of aged ribosomes in cells amplifies molecular age-dependent translation defects. In vivo labeling of ribosomes in aged C. elegans demonstrates that molecularly aged ribosomes shape translational dynamics during organismal aging. These findings identify ribosome molecular age as a determinant of translational dynamics, and link molecular aging of a core gene-expression complex to organismal aging. HIGHLIGHTSO_LIA pulse-chase labeling strategy enables mapping subcellular demographics of macromolecular complexes in space and time. C_LIO_LIMolecular aging of ribosomes drives differential mRNA translation and shapes elongation dynamics. C_LIO_LIThe collision propensity of specific ribosome subpopulations increases with molecular age. C_LIO_LIOlder ribosomes shape translation dynamics during organismal aging. C_LI

cell biology↗

bioRxiv2026

Mesoscale molecular architecture of the human striatum across cell types and lifespan

The human striatum is a central hub for a diverse array of motor, cognitive, and affective behaviors, yet it lacks obvious cytoarchitectural boundaries that define functional territories. Here, we uncover a robust and molecularly defined mesoscale architecture in the human striatum. Using Slide-tags, a scalable single-nucleus spatial transcriptomics technology, we profiled 1.1 million cells across the full span of the anterior striatum of 19 postmortem donors, spatially mapping all striatal populations. Our data uncover a natural subdivision of the striatum into six zones, each defined by molecularly distinct populations of medium spiny neurons, and featuring spatially coordinated neuron-astrocyte signaling. Relative to MSNs in ventral zones, MSNs in dorsal zones exhibit higher expression of genes for synaptic remodeling and plasticity via ephrin and TGF-beta, while the ventral zone is defined by greater expression of semaphorin, protein chaperone, and hedgehog signaling pathways. By imputing zonal identities onto a larger single-nucleus RNA-seq cohort of 131 donors, we find that the dorsal zones exhibit greater age-related transcriptional changes, and that overall, the gene-expression differences that define spatial zonation patterns are attenuated with advancing age. This atlas provides a mesoscale molecular definition of human striatal anatomy, linking cell type identity to functional specialization and aging susceptibility.

neuroscience↗

bioRxiv2026

Unconstrained dosing agar (UDA) Reduces Stress in Mouse Oral Administration

BackgroundOral gavage is the standard method for delivering drugs and other substances orally in rodent studies, but it can cause significant stress and risk injury. To improve animal welfare and reduce confounding stress effects, this study aimed to replace oral gavage by developing and testing a new voluntary ingestion method that is easy to adopt, minimizes stress in mice, and is suitable for a wide range of compounds. ResultsWe developed a soft agar formulation with an appealing scent and taste that mice readily consumed without fasting or restraint. We called this method "unconstrained dosing agar" (UDA). Analysis of fecal corticosterone levels demonstrated that the method is associated with low stress in the animals. After training, mice quickly consumed the agar units. Body weight gain was unaffected by the treatment. ConclusionsThis study introduces a simple, low-stress method for administering substances orally in mice. By encouraging voluntary consumption and removing the need for fasting or restraint, this method provides a practical alternative to oral gavage and could improve animal welfare and experimental consistency.

animal behavior and cognition↗

bioRxiv2026

Retrotransposons Promote Clonal Hematopoiesis Through Aging-Related Stromal Inflammation

Clonal hematopoiesis (CH) is an age-related phenomenon driven by the expansion of mutant hematopoietic stem cell (HSC) clones, most commonly harboring mutations in DNMT3A. While inflammation is known to promote CH, the upstream triggers of this inflammatory state remain unclear. We show that aging selectively upregulates retrotransposons in the non-hematopoietic cell compartment of the murine bone marrow, particularly in mesenchymal stromal cells. Using in vivo competitive transplant models, we demonstrate that retrotransposon-induced inflammation cell-extrinsically promotes Dnmt3a-mutant HSC expansion. This competitive advantage arises from mutant HSC resistance to inflammation-driven cell cycle perturbations. Mechanistically, we show that retrotransposon activation induces type I interferon signaling via viral mimicry, such that stromal knockdown of either Irf3 or Sting abrogates the competitive advantage of Dnmt3a-mutant HSCs. Our findings establish stromal-selective retrotransposon reactivation as a previously unrecognized, non-cell-autonomous source of inflammation that contributes to age-associated CH. Key PointsO_LIRetrotransposons remodel the aging niche through viral mimicry pathways to promote Dnmt3a-mutant clonal hematopoiesis. C_LIO_LIRetrotransposon-mediated inflammation impairs wild-type HSC fitness, while Dnmt3a-mutant HSCs resist inflammatory changes. C_LI

cancer biology↗