Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 181 records · Page 10Linked to original sources

bioRxiv2026

A FZD4/LRP5 agonist restores pericyte coverage and vascular integrity by increasing PDGFB signaling

Pericytes, specialized mural cells of capillaries, fulfill crucial physiological functions including promoting endothelial barrier function and regulating angiogenesis. Pericyte loss or dysfunction represents a central pathological feature in diabetic retinopathy (DR) and is increasingly recognized in neurodegenerative diseases as well as in poor stroke outcomes, underscoring an urgent need for therapies that restore pericyte function or promote their regeneration. Here, we utilized a Frizzled4 (FZD4) and Low-Density Lipoprotein Receptor-Related Protein 5 (LRP5) agonist antibody (F4L5.13) to investigate the functional consequences of mimicking {beta}-catenin-dependent signaling in CNS endothelial cells (ECs), which is physiologically induced by Norrin or WNT7A/B. In platelet-derived growth factor subunit B (Pdgfb) EC-specific knockout (ECKO) mice, a model of severe developmental pericyte deficiency with secondary blood-retina barrier (BRB) defects and hemorrhages, F4L5.13 significantly promoted retinal pericyte/mural cell proliferation and coverage, improved BRB function, reduced hemorrhages, and normalized vascular morphology. F4L5.13 restored Pdgfb mRNA expression levels from non-recombined cells in Pdgfb ECKO retinas. These findings highlight interactions of {beta}-catenin-dependent signaling and PDGFB production, identify a key pharmacodynamic action of F4L5.13 distinct from anti-VEGF therapies, and suggest that FZD4/LRP5 agonists may have uses as a regenerative pharmacology approach that promotes pericyte coverage in the neurovascular unit.

developmental biology↗

bioRxiv2026

Programming Biomolecular Interactions with All-Atom Generative Model

Biomolecular interactions lie at the core of cellular life, spanning diverse molecular modalities from small molecules to nucleic acids and proteins. Nevertheless, design strategies remain separated despite shared physicochemical principles of molecular recognition. Here we present AnewOmni, a unified generative framework trained on more than 5 million biomolecular complexes, that enables transferable molecular design across molecular scales by assembling chemically meaningful building blocks at atomic resolution. We further introduce programmable graph prompts to support user-defined chemical, topological, and geometric steering during generation, exploring hybrid and unconventional chemistries beyond canonical structures. We demonstrate that transferable learning of interaction patterns and physical constraints across molecular modalities is possible, via an atom-to-block latent space capturing both atomic details and structural priors. The framework successfully designed small molecules, peptides, and nanobodies targeting the challenging KRAS G12D switch II pocket, as well as orthosteric peptides and allosteric small-molecule inhibitors for PCSK9 in the absence of known binding site, achieving 23%-75% success with only low-throughput validation, bypassing modality-specific high-throughput screening. AnewOmni is the first to succeed in functional molecular design across all scales, from small chemical entities to large biologics, and represents a stepstone towards general molecular reasoning engines, advocating a generative foundation model for biomolecular interactions to enter regimes where data and human intuition remain limited.

bioengineering↗

bioRxiv2026

STEVE: Single-cell Transcriptomics Expression Visualization and Evaluation

Single-cell RNA sequencing (scRNA-seq) has become a key technology for characterizing cell-type heterogeneity in complex tissues. However, its utility depends on accurate and reproducible cell-type annotation, which remains a major analytical challenge. Although hundreds of computational tools have been developed for automated annotation, there is currently no systematic framework to evaluate annotation robustness in a dataset-specific manner or within the context of complete analytical pipelines. Here, we present STEVE (Single-cell Transcriptomics Expression Visualization and Evaluation), a quantitative framework designed to assess the accuracy, robustness, and reproducibility of cell-type annotation in scRNA-seq studies. STEVE implements three complementary in silico evaluation modules: (i) Subsampling Evaluation to quantify annotation stability under varying reference sizes and data partitions; (ii) Novel Cell Evaluation to assess the ability to detect previously unseen cell types; and (iii) Annotation Benchmarking to compare alternative annotation tools against ground-truth labels. In addition, STEVE includes a Reference Transfer Annotation module that enables cross-dataset cell-type mapping using external reference datasets. All modules are built upon a unified probabilistic framework that provides consistent confidence estimation across evaluation scenarios. We evaluated STEVE across four independent scRNA-seq datasets with experimentally defined or expert-curated cell-type labels. Our results show that annotation robustness is strongly influenced by the annotation method, biological separability, dataset complexity, and batch effects. STEVE provides a practical framework for quantifying annotation uncertainty and improving reproducibility in single-cell transcriptomic analyses. STEVE is freely available at GitHub (https://github.com/XiaoDongLab/STEVE).

bioinformatics↗

bioRxiv2026

A Genetic Tool for Specific Tracking of Mature Neutrophils

Tracking mature neutrophils remains challenging due to the lack of reliable cell surface markers. Although CD101 is a promising candidate for mature neutrophils, its stability under pathological conditions is unclear. Using a CD101-tdTomato reporter mouse model, we confirmed that the reporting system does not alter CD101 expression, and tdTomato fluorescence is predominantly expressed in mature neutrophils across peripheral tissues. Further analysis revealed that CD101+ and tdTomato+ neutrophils display identical characteristics of mature neutrophil, including poly-segmented nuclei, cell size, and key functions under homeostasis. By comparing tdTomato fluorescence with CD101 protein levels, we demonstrate that reduced CD101 expression under pathological states was not attributed to shedding or degradation. Our finding enhances CD101 as a robust and reliable marker of neutrophil maturity, providing a foundation for future applications in spatial transcriptomics and lineage tracing studies to dissect neutrophil heterogeneity and function. Highlights of the studyO_LIIn CD101-tdTomato homozygous mice, tdTomato is predominantly expressed in neutrophils and labels nearly 100% of mature neutrophils, aligning with the phenotype of CD101+ mature neutrophils; C_LIO_LIThe CD101-tdTomato reporting system does not interrupt CD101 expression or neutrophil functions; C_LIO_LICD101 remains a stable and reliable cell surface marker for labeling mature neutrophils, even under pathological conditions. C_LI

immunology↗

bioRxiv2026

CEACAM5/6+ Tumor Cells and IL-1β+ Macrophages Drive Resistance to Chemo-immunotherapy in Gastric Cancer

Chemo-immunotherapy is a first-line treatment for advanced gastric cancer, yet response rates remain limited and resistance mechanisms are poorly defined. Here we generate a single-cell atlas of 542,121 cells from 35 patients treated with anti-PD-1 plus chemotherapy, profiling pre- and post-treatment tumors linked to clinical response. Integrating spatial transcriptomics, immunohistochemistry, and bulk RNA sequencing, we identify two temporally distinct resistance programs. Intrinsic resistance in pre-treatment non-responders is marked by enrichment of CEACAM5/6 tumor cells that form immune-excluded spatial niches characterized by macrophage recruitment and CD8 T-cell exhaustion. Acquired resistance in post-treatment non-responders is driven by expansion of IL-1{beta} macrophages, which induces coordinated NF-{kappa}B activation across tumor and stromal compartments, promoting PD-L1 upregulation, epithelial-mesenchymal transition, and chronic inflammation. These findings delineate an evolutionary trajectory of resistance and nominate CEACAM5/6 and IL-1{beta} as predictive biomarkers and therapeutic targets to improve anti-PD-1-based combination strategies.

cancer biology↗

bioRxiv2026

Transcranial direct current stimulation combined cognitive training modulates risk-taking behavior in older adults

Risk-taking behavior is a complex cognitive function that often declines with aging, contributing to impaired decision-making and reduced quality of life. While transcranial direct current stimulation (tDCS) has shown promising effects in modulating cognitive function, its influence on ecologically valid, complex behaviors like risky decision-making in older adults remains poorly understood. We investigated whether a single-session stimulation over the medial orbitofrontal cortex (MOFC) combined with cognitive training could enhance decision-making in healthy older adults. In a randomized, sham-controlled study, bilateral MOFC stimulation (left/anode, right/cathode) was applied during a training task based on the Iowa Gambling Task. Pre- and post-intervention assessments utilized conventional behavioral measures and the Values-Plus-Perseveration computational model, alongside task-related fMRI to examine MOFC network changes. Compared to sham, tDCS significantly enhanced the ability to distinguish advantageous from disadvantageous options. Modeling analysis revealed stimulation-induced changes in multiple latent components, such as learning rate, loss aversion, and perseveration decay. Generalized Psychophysiological Interaction analysis showed that tDCS reconfigured the MOFC network by reducing fronto-frontal hyper-connectivity and enhancing fronto-striatal connectivity. These behavioral improvements were specifically associated with the left MOFC network targeted by anodal stimulation. Our results provide causal evidence that tDCS can mitigate age-related impairments in risk-taking by reconfiguring MOFC-related networks. These findings advance the mechanistic understanding of tDCS in aging and highlight its potential as an intervention to prevent age-related decline in decision making.

neuroscience↗

bioRxiv2026

Connectome lateralization in autism across the first 14 years: heterogeneity related to developmental stage, hemisphere, and pathophysiology

Hemispheric lateralization is fundamental feature to neurodevelopment, yet its dynamic evolution in autism across childhood and underlying molecular mechanisms remain unknown. Thus, using a large-scale resting-state fMRI dataset (n = 1553, ages 1-14), we investigated developmental heterogeneity in connectome lateralization. At the group level, abnormalities in dynamic connectome lateralization strength (DCLS) progressed from focal patterns in early childhood ([≤] 6 years) to widespread distributions by late childhood ([≤] 14 years), independent of symptom severity. The late-stage patterns were validated using the ABIDE dataset (n=153). Late childhood also showed marked increases in inter-individual heterogeneity. These alterations were significantly associated with clinical phenotypes, transcriptomic profiles, and multiple neurotransmitter systems, with distinct patterns across childhood groups. Our findings reveal a developmentally dynamic trajectory of connectome lateralization in autism and highlight late childhood as a critical window for stage- and individual-specific interventions tailored to substantial individual heterogeneity.

neuroscience↗

bioRxiv2026

Mapping the MIF-2 Chemokine Interactome Reveals MIF-2-CCL20 Complex Formation in Liver Fibrosis

D-dopachrome tautomerase (D-DT/MIF-2) is an inflammatory cytokine, atypical chemokine (ACK) and member of the macrophage migration-inhibitory factor (MIF) family. While interactions among classical chemokines (CKs) are established, ACK-CK interactions remain underexplored. Here, we screened for MIF-2 binding-partners using a protein array encompassing all CKs and selected ACKs, and validated candidate interactors by surface-plasmon resonance. CCL20/MIP-3 was prioritized based on RNA-sequencing suggesting induction during liver fibrosis. MIF-2/CCL20 complex formation was verified by microscale thermophoresis and interaction interfaces mapped using peptide array and in-silico modeling. The deduced binding-site near the MIF-2 tautomerase pocket was consistent with inhibition of its tautomerase activity by CCL20. We found both proteins abundantly expressed in human liver tissue, with a positive correlation. Pull-down confirmed complex formation and proximity ligation assay demonstrated MIF-2/CCL20 complexes in liver in situ, with higher levels in fibrotic tissue. Functionally, MIF-2/CCL20 complexes suppressed MIF-2-driven CD4 T-cell chemotaxis and fibroblast IL-6 secretion, indicating modulation of immune and stromal responses. This study extends the ACK interactome to MIF-2 and suggests ACK/CK complexes modulate chemokine activities in liver fibrosis.

immunology↗

bioRxiv2026

Opposing regulatory logics converge on ABA receptors to govern the trade-off between growth and drought acclimation

Plants dynamically balance growth with stress responses through abscisic acid (ABA). How ABA signaling, but how ABA sensitivity is finely tuned is unclear. Here, we uncover a regulatory network of leucine-rich repeat receptor-like kinases (LRR-RLKs) that directly controls ABA receptors stability. We identify GASSHO1 (GSO1) as a core component that phosphorylates the PYL2 and PYL4 receptors, targeting them for degradation and thus serving as a brake on ABA signaling. Under drought stress, ABA accumulates and suppresses expression of GSO1-activating CIF peptides, releasing this brake to increase PYLs and sensitivity. This mechanism opposes our previously identified CEPR2 pathway, where drought-induced CEP peptides inhibit the kinase to stabilize PYLs. The integration of these two antagonistic modules within an LRR-RLK network enables precise, dynamic control of ABA perception. This work reveals a molecular framework explaining how plants calibrate the critical balance between growth and drought acclimation.

molecular biology↗

bioRxiv2026

Macrophage Iron Metabolism in Allografts and Tumors

Macrophages are present at high frequencies in transplanted organs and solid tumors. These infiltrating macrophages are highly tuned by tissue niche signals. However, the underlying mechanisms that orchestrate the activation of distinct macrophage populations remain unclear. Here, using heart transplantation and tumor implantation models, we found that macrophages in cardiac allografts exhibited higher intracellular iron (Fe2+) level and higher expression of the iron transporter SLC11A1 than those in the solid tumors. In mice, the myeloid-specific deletion of Slc11a1 alleviated the proinflammatory state of macrophages and cardiac allografts rejection. Together, our findings identify SLC11A1 as a new player in immune response regulation, implicating SLC11A1 as a therapeutic target for both allograft and tumor rejection. This preprint reports initial findings; additional experiments are ongoing and will be included in a future full manuscript.

immunology↗

bioRxiv2026

A human gut-BBB-brain microphysiological model for studying neurodegenerative diseases

The gut-brain axis has emerged as a crucial factor in neurodegeneration, with growing evidence linking gut dysbiosis and metabolic dysfunction to Alzheimers disease (AD) progression. Unfortunately, the lack of human-relevant in vitro models limits our ability to effectively explore the mechanism of this axis. To address this gap, we have developed a human induced pluripotent stem cell (iPSC)-derived gut-blood-brain barrier (BBB)-brain microphysiological system that enables systematic investigation of gut-brain interaction in the context of AD under controlled conditions. Our findings reveal that the interaction between gut and brain organoids can promote the maturation of brain organoids, making them more similar to their physiological characteristics in vivo. Additionally, co-culture gut and brain organoids better recapitulates the pathological features of AD. We also discovered that gut organoids of AD can trigger neurodegenerative disease manifestations in healthy brain organoids. In summary, our microphysiological system provides a novel and versatile in vitro platform for studying the interaction between the gut and brain in neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Synthetic analogue of adrenocorticotropic hormone, ACTH(4-7)PGP delays neurological manifestations in diseases of mucopolysaccharidosis III spectrum by reducing neuroinflammation and rescuing neurotransmission, synaptogenesis, and axonal demyelination

Mucopolysaccharidosis III (MPS III or Sanfilippo disease) is a spectrum of 4 genetic disorders (MPS IIIA-D), caused by defects in the genes SGSH, NAGLU, HGSNAT and GNS encoding enzymes involved in degradation of heparan sulfate (HS). HS accumulates in brain tissues and causes neuronal dysfunction and neurodegeneration leading to neuropsychiatric problems, developmental delays, childhood dementia, blindness and death during the second decade of life. Previously, we demonstrated that pathophysiological mechanisms, underlying MPS IIIC in mouse models, involves functional pathological changes, affecting synaptogenesis and synaptic transmission and leading to learning and memory deficits. These results suggested that a treatment for MPS III could be developed by using compounds inducing synaptogenesis. In the current study, we tested the efficacy of a synthetic peptide ACTH(4-7)PGP, an analog of adrenocorticotropic hormone fragment, previously used as a neuroprotective and anti-inflammatory medication for treatment of acute neurological conditions, including stroke. We show that intranasal administration of ACTH(4-7)PGP restores defective synaptic transmission in CA1 pyramidal neurons of MPS IIIA and MPS IIIC mouse models and rescues the decrease in synaptic proteins in cultured MPS IIIC mouse hippocampal neurons and iPSC-derived neurons of human MPS IIIA, MPS IIIB and MPS IIIC patients. Furthermore, daily intranasal administration of ACTH(4-7)PGP to MPS IIIC and MPS IIIA mice reduces hyperactivity and rescues defects in working and spatial memory, delays progression of CNS pathology including neuroinflammation and axonal demyelination, and increases the lifespan. Together with the absence of any adverse reactions to ACTH(4-7)PGP in the MPS III and WT mice, our results justify testing the drugs efficacy in clinical settings.

genetics↗

bioRxiv2026

Gut Microbiota Dysbiosis-Mediated Gut NLRP3 Inflammasome Activation Exacerbates Corticospinal Tract Injury After Intracerebral Hemorrhage

Intracerebral hemorrhage (ICH) causes severe neurological deficits, largely attributable to corticospinal tract (CST) injury. However, the underlying mechanism remains unclear, which hinders the development of effective treatment methods. Here, we found that CST injury is not only associated with the activation of NLRP3 inflammasome in the surrounding area of the hematoma as expected, and dysfunction of the blood-brain barrier, but also related to the severe imbalance of the gut microbiota, the activation of NLRP3 inflammasome in the gut and the impairment of gut barrier function after ICH. We therefore systematically investigated how the gut NLRP3 inflammasome and gut dysbiosis exacerbate CST injury after ICH. Knockdown of colon NLRP3 significantly attenuated CST injury and downregulated inflammasome signaling in both the peripheral circulation and the peri-hematomal brain. Consistently, antibiotic-mediated gut microbiota depletion suppressed NLRP3 activation in the gut and brain, improved neurological function, and reduced CST damage. Crucially, fecal microbiota transplantation (FMT) from ICH donors established that the exacerbation of CST injury is dependent on gut dysbiosis. While FMT induced severe pathology in control mice, this effect was improved in gut NLRP3 knockdown recipients, demonstrating that gut NLRP3 is essential for mediating the harmful effects of microbiota dysbiosis. Our findings described a causal gut-brain axis in ICH, wherein microbiota dysbiosis activates the gut NLRP3 inflammasome to exacerbate CST injury, thereby identifying the gut NLRP3 inflammasome as a promising therapeutic target.

neuroscience↗

bioRxiv2026

Single-cell transcriptomics reveals transcriptional diversity of sea cucumber perivisceral fluid coelomocytes

Echinoderms possess a complex immune system, primarily relying on coelomocytes - immune cells circulating in coelomic fluids. Over the last few decades, various coelomocytes have been described based on morphological features, with holothuroids exhibiting the highest diversity of cell morphotypes among the different echinoderm classes. However, while the overall immune function of these cells is broadly accepted, their respective functions remain unclear, and molecular data specific to the different cell types are still limited in the literature. In this study, we address this gap in functional information and molecular data by using single-cell RNA sequencing (scRNA-seq) on coelomocytes from the perivisceral fluid of Holothuria forskali. We identified 10 distinct clusters, each assumed to correspond to a distinct transcriptional coelomocyte population. Among these, cluster 0 occupies a central position relative to the others, suggesting it may represent "progenitor cells", whereas cluster 6 is markedly divergent from all other clusters. Functional enrichment analyses revealed that some clusters ensure key immune functions, including pathogen recognition, phagocytosis, complement activation and redox balance regulation. In addition, examination of the processed samples under a microscope confirms the presence of a small proportion of recently discovered carotenocytes (7.0%) in the perivisceral fluid, a cell type rich in carotenoids. By using transcriptomics data previously obtained for this cell type by bulk RNA sequencing (bRNA-seq), it was possible to confidently identify cluster 6 as carotenocytes and provide further insights into their gene expression. While further analyses are needed to link other clusters to the different morphotypes previously described in the literature, this pioneer study presents preliminary data on the functional diversity of holothuroid coelomocytes, which could be of broad interest for a better understanding of holothuroid immunity as well as for the study of immune cell lineage evolution across deuterostomes.

evolutionary biology↗

bioRxiv2026

Oxidation-Driven mtDNA B-Z Transition Activates ZBP1 to Mediate Acetaminophen Hepatotoxicity

Acetaminophen (APAP) overdose induces mitochondrial damage in hepatocytes, leading to secondary toxicity that resists to N-acetylcysteine (NAC) treatment and culminates in hepatocyte death and acute liver failure (ALF)1. The underlying mechanisms remain poorly understood, often necessitating liver transplantation2. Here, we identify oxidative modification-driven B-to-Z transitions in mtDNA as the central pathological driver of APAP-induced ALF. Upon APAP exposure, oxidized mtDNA fragments leak into the cytosol, activating ZBP1 signaling via its Z domain. Genetic inhibition of ZBP1 mitigates liver damage and improves survival. Using synthetic 12-bp dGdC duplexes, we demonstrate that 8-oxoG substitution, even under physiological salt concentrations, is sufficient to induce Z-DNA formation, enabling specific ZBP1 binding through its Z domain. The 8-oxoG repair enzyme OGG13, activated by TH107854, removes 8-oxoG modifications and reverses Z-DNA to B-DNA conformation. In mice with lethal APAP toxicity, delayed NAC treatment results in 50% mortality. In contrast, TH10785 monotherapy increases survival to 90%, while its combination with NAC achieves 100% survival. These results define the oxidized mt Z-DNA-ZBP1 axis as a critical driver of APAP hepatotoxicity, providing fundamental insights into DNA conformational dynamics and therapeutic opportunities in drug-induced liver failure.

cell biology↗

bioRxiv2026

Heterogeneous and specific localization of mRNAs at dendritic spine and its dependence on microtubule entry and kinesin motor

Local mRNA translation near neuronal synapses is crucial for structural plasticity during brain development and memory formation. Whereas mRNAs are transported from soma to dendrites as individual ribonucleoprotein (RNP) granules, how do they subsequently localize at synapses is unclear. In particular, whether different dendritic mRNAs might display differential synaptic localization and interact with specific postsynaptic proteins remains unexplored. Here we found that two well-known dendritic mRNAs, Actb and Camk2a, are targeted to different subdomains of dendritic spines and delivered to different spine populations after synaptic stimulation. Surprisingly, the induced mRNA localization to dendritic spines is associated with microtubule (MT) entry and specifically requires the MT-associated motor KIF5A. Proximity-labelling proteomics further identifies distinct postsynaptic proteins enriched by Actb and Camk2a, from which we uncover the cytoskeletal protein Septin7 to be co-localized with the two mRNAs at different subdomains of dendritic spines. Our study reveals an unexpectedly specific mRNA localization mechanism at synapses and demonstrates proximity-labelling as a useful approach to map their synaptic partners.

neuroscience↗

bioRxiv2026

Allele-specific splicing modulates protein isoforms and Alzheimer's risk

Despite growing catalogs of genetic variation linked to human traits and diseases, the functional impact of most genetic variants remains poorly understood. Alternative splicing, particularly in the human brain, represents a key layer of post-transcriptional regulation that may mediate genetic effects on gene expression and protein diversity. In this study, we systematically map allele-specific alternative splicing (ASAS) events in postmortem brain tissues from the Mount Sinai Brain Bank cohort, identifying hundreds of genetically regulated splicing events across four brain regions. Using a concordance-based method, we nominate over 500 putative functional SNPs associated with ASAS, many of which overlap splicing QTLs (sQTLs), RNA-binding protein binding sites, and GWAS loci for Alzheimers disease (AD), brain traits, and immune phenotypes. ASAS events are enriched in genes involved in mitochondrial function and frequently occur in 5' untranslated regions (5' UTRs), where they are associated with protein quantitative trait loci (pQTLs), alternative start codons, and isoform-specific domain changes - highlighting an underappreciated mechanism through which noncoding variants can influence translation and proteome complexity. Importantly, we also identify a subset of ASAS events exhibiting disease-specific splicing patterns in AD brains, including functional SNPs with opposing splicing effects between AD and control groups in genes implicated in mitochondrial function and neuronal signaling. Together, our results provide a brain-specific, splicing-resolved map of regulatory variation and uncover novel mechanisms linking genetic variation to transcript and protein-level changes in AD. This work highlights the importance of allele-specific splicing analysis for interpreting noncoding variation in complex human disorders.

genomics↗

bioRxiv2026

SMECT: a framework for benchmarking post-GWAS methods for spatial mapping of cells associated with human complex traits

Spatially resolving the cellular basis of complex human traits is essential for elucidating disease mechanisms, yet the comparative performance of computational methods for this task has not been systematically evaluated. Here, we present SMECT (Spatial Mapping Evaluation of Complex Traits), the first comprehensive framework for systematically evaluating methods that integrate genetic data with spatial transcriptomics. SMECT combines a biologically realistic simulation engine, a curated resource of 21 diverse real-world datasets, and a multi-faceted assessment toolkit. Using this framework, we benchmarked three state-of-the-art methods--DESE, S-LDSC, and scDRS--across 19 complex traits. Our analysis reveals a fundamental trade-off between detection sensitivity and biological specificity. We demonstrate that while S-LDSC identifies extensive spatial signals, it suffers from inflated non-specific significant associations. Conversely, scDRS is highly specific but conservative, performing well only in tissues with strong biological signals while missing subtle associations in sparser datasets. DESE overcomes these limitations, consistently achieving high power and robust specificity across both simulated and real-world scenarios. SMECT provides critical guidelines for method selection and serves as a foundational resource for developing robust spatial analyses of human complex traits. The framework is publicly available at https://github.com/pmglab/smect.

bioinformatics↗