Biology subjects

Wan, X.

Publications and source records attributed to Wan, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Scaling genetic discovery through automated post-GWAS interpretation

Genome-wide association studies (GWAS) have made association discovery systematic and cumulative, yet evidence for interpreting associated loci remains selective, heterogeneous and difficult to accumulate across studies. Here we present Post-GWAS Intelligence (PGI), which couples context-dependent post-GWAS analysis to a common representation of analysis-derived evidence. Its multi-agent engine, VariantAgent, executes workflows, records tool-derived results in standardized variant-centred units and generates trait-level interpretations linked to their analytical basis and evidential status. Complementary benchmarks showed that VariantAgent outperformed tested general-purpose and biomedical agents, with its largest advantage when success required both a correct answer and a valid analytical trace. Across 34 published GWAS, VariantAgent achieved a mean per-study recovery of 82.1% for directly comparable findings. The largest gains lay downstream of association mapping, where uniform analysis extended published interpretations and identified regulatory relationships at established risk loci not previously reported in the source studies. Analysis of 1,041 GWAS yielded 530,949 evidence units and corresponding reports, which PGI organized into a cross-trait catalogue. Catalogue interrogation resolved an apparent cross-trait overlap into distinct signals and trait-specific biological hypotheses. This work demonstrates how PGI can extend genetic discovery beyond association mapping by enabling biological evidence to accumulate across studies.

genetics↗

bioRxiv2026

14-3-3 Enables β-Adrenergic Regulation of the Cardiac Sodium Channel at the Intercalated Disc

Background: Beta-Adrenergic stimulation enables the heart to adapt electrical activity to increased physiological demand. Although the cardiac sodium channel Nav1.5 is essential for impulse propagation, the mechanisms underlying its acute beta-adrenergic regulation, particularly within distinct cardiomyocyte membrane domains, remain poorly understood. We investigated whether the phosphorylation-sensitive adaptor protein 14-3-3 mediates this regulation. Methods and Results: Using automated patch-clamp electrophysiology in HEK293 cells and human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we found that isoproterenol rapidly increased sodium current (INa) and promoted channel activation at more hyperpolarized potentials, whereas PKA inhibition reduced INa. Disruption of 14-3-3 function abolished these responses without substantially altering basal sodium current or Nav1.5 surface expression. Macropatch recordings from ventricular myocytes revealed that isoproterenol preferentially enhanced INa at the intercalated disc, an effect prevented by 14-3-3 inhibition. Proximity ligation assays further demonstrated increased Nav1.5/14-3-3 proximity following beta-adrenergic stimulation. Systematic mutagenesis identified S460 in the Nav1.5 DI-DII linker as a critical determinant of acute PKA-dependent regulation. Molecular modeling predicted that S460 phosphorylation stabilizes the Nav1.5/14-3-3 interaction. In CRISPR-engineered S460A iPSC-CMs, acute beta-adrenergic regulation of INa was abolished, whereas the isoproterenol-induced increase in conduction velocity was significantly attenuated. Computational simulations further predicted that enhanced intercalated-disc sodium current supports increased conduction velocity across varying conditions of electrical coupling and pacing rate. Conclusions: Our findings identify 14-3-3 and S460 as critical determinants of spatially selective beta-adrenergic regulation of Nav1.5 at the cardiac intercalated disc. This mechanism provides a molecular link between sympathetic signaling and cardiac sodium current regulation, supporting the concept that localized enhancement of Nav1.5 function contributes to the adaptation of cardiac conduction during increased sympathetic demand.

molecular biology↗

bioRxiv2026

Hierarchical distribution matching enables comprehensive characterization of common and condition-specific cell niches in spatial omics data

Deciphering cell niches in complex tissues is essential for understanding tissue structure and disease. Recent advances in spatial omics have enabled subcellular resolution and accurate cell identity mapping. However, robust delineation of cell niches and disease-associated spatial patterns remains difficult. We introduce Harmonics, a novel computational framework that systematically identifies both common and condition-specific cell niches from spatial omics data through hierarchical distribution matching. Harmonics also includes a suite of downstream modules that facilitate comprehensive niche characterization. We demonstrate its scalability, accuracy and generalizability across datasets spanning diverse species, tissues, diseases, spatial modalities, and technological platforms. For condition-agnostic datasets, Harmonics outperforms baseline methods in both accuracy and robustness, and further demonstrates the capability to resolve niche structures at finer granularity. Across diverse diseases including pulmonary fibrosis, triple-negative breast cancer, and colorectal cancer, Harmonics enables precise identification of condition-specific niches and reveals disease-associated dynamics, subtype-specific spatial patterns, and structured immune architectures. We envision Harmonics as a practical and versatile tool for spatial niche analysis that can be applied across a wide range of biological contexts and seamlessly integrated with existing spatial omics workflows.

bioinformatics↗

bioRxiv2026

CryoMV: Structure-Prior-Guided Modeling and Real-Particle Validation of Continuous Conformational Transitions in Cryo-EM

Continuous protein conformations are essential for understanding fundamental biological processes and supporting drug discovery. Although cryo-EM can resolve individual states at high resolution, recovering continuous heterogeneity from 2D particle images remains challenging. High noise, motion blur, and limited structural priors make it difficult to accurately generate and validate high-resolution continuous conformations using raw particle data. Here, we introduce cryoMV, a framework that integrates structure-prior-guided modeling with real-particle validation for continuous conformational transitions. CryoMV uses reference density maps to establish structural anchors and motion priors, models candidate transition paths between selected conformations, and transfers the learned representation to raw 2D cryo-EM particle images. Each candidate conformation is subsequently evaluated using the estimated particle poses and contrast transfer functions. Supported conformations are reconstructed through raw particle back-projection and assessed using canonical half-maps and Fourier shell correlation. On EMPIAR-10516 and EMPIAR-10345, cryoMV achieves excellent performance in terms of robustness, verifiability, and reconstruction resolution. By incorporating structure-prior modeling and evidence from the raw particles, cryoMV offers an explicit mechanism for assessing whether generated conformations are supported by experimental data and provides a practical approach to reducing model-induced artifacts in continuous cryo-EM heterogeneity analysis.

bioinformatics↗

bioRxiv2026

CryoFlex characterizes structural motion between conformations directly from cryo-EM density maps

Heterogeneous cryo-EM reconstruction methods can resolve multiple conformational states, but understanding their functional implications often requires determining which regions move between states and quantifying their displacement magnitudes. Comparing atomic models can quantify motion, but flexible regions are often incompletely modeled. Direct map comparison is limited by variable map quality and ambiguous correspondence between displaced density features. Here, we present CryoFlex, a method that estimates the direction and magnitude of structural motion directly from reconstructed density maps of selected states. The resulting motion analysis supports functional interpretation and guides downstream structure processing. CryoFlex localized and quantified structural motion across diverse map pairs, including those with incomplete atomic-model coverage or weak local density. Against C; displacements, CryoFlex achieved an endpoint error of about 1 angstrom. In separate benchmarks, it outperformed registration baselines on clean and noisy inputs. Thus, CryoFlex complements heterogeneous reconstruction workflows with direct quantification of structural motion between reconstructed states.

bioinformatics↗

bioRxiv2026

Exploratory profiling of defense system signatures in Klebsiella pneumoniae clonal populations

Bacterial defense systems against bacteriophages are critical for bacterial genome stability and fitness, yet their distribution and epidemiological relevance in Klebsiella pneumoniae remain unexplored. We aimed to characterize defense system signatures across major K. pneumoniae clonal lineages and evaluate their utility as genomic signatures for tracking clonal dissemination. Here, we analyzed 6,346 genomes to characterize population structure, defense system signatures, and their coevolution with resistance determinants and plasmid backbones. PopPUNK clustering resolved 146 lineages that stratified into major clonal lineages (G-ST-KL combinations) with distinct resistance and virulence profiles. DefenseFinder and PADLOC identified 320 distinct defense systems, revealing that each clonal lineage harbors a unique defensotype characterized by systematic module replacement rather than stochastic gene loss. Co-occurrence networks further showed that these systems are organized into lineage-specific functional modules, with contrasting architectures even among lineages sharing the same sequence type. Integration of defense, resistance, and plasmid data uncovered strong lineage-specific associations, whereby broad-host-range plasmid backbones acquired distinct defense-resistance payloads in different clonal backgrounds. Geographic and host-niche analyses demonstrated that defense system distribution reflects clonal lineage expansion rather than independent geographic selection, and analysis of 689 Chinese genomes confirmed vertical inheritance of lineage-specific signatures along transmission chains. Collectively, defense systems in K. pneumoniae are organized into lineage-specific defensotypes shaped by synergistic modules and clonal evolutionary dynamics. Defense system profiling provides an additional layer of epidemiological resolution beyond conventional typing and offers practical utility for genomic surveillance, particularly in resource-limited settings where PCR-based detection of conserved systems could serve as a rapid proxy for identifying high-risk K. pneumoniae clones.

bioinformatics↗

bioRxiv2026

Characterizing dynamic tissue architectures by identifying cell-type-specific spatiotemporal gene programs with stGP

Cellular gene programs unfold over biological time within spatially organized tissues. The same cell type can activate distinct programs in different spatial domains or multicellular niches. Spatiotemporal transcriptomics enables in situ measurement of these processes; however, the interplay between temporal progression and spatial organization complicates the identification of whether a gene program is influenced by temporal changes, spatial structure, or both. To overcome this challenge, we present spatiotemporal Gene Programs (stGP), a statistical framework for identifying interpretable cell-type-specific gene programs across multi-sample spatiotemporal transcriptomic studies. stGP preserves the molecular identity of each program through shared gene loadings, and decomposes individual cell activity into a temporal component that captures gene program responses over biological time, and a spatial component that characterizes variations within tissue sections. We quantify their relative contributions by estimating their variance components. Through comprehensive simulations and analyses of three spatiotemporal transcriptomic datasets across different tissues and technologies, stGP reveals spatiotemporal gene programs that distinguish preserved tissue architecture from dynamic remodeling. Our framework delineates age-associated cellular responses and uncovers localized program deployment within anatomical regions, aging hotspots, and multicellular niches. Our results establish stGP as an effective and robust framework for dissecting dynamic tissue architecture, providing insights into how cell-type-specific gene programs are coordinated across biological time and spatial microenvironments.

bioinformatics↗

bioRxiv2026

Targeting folate-dependent purine synthesis sensitizes melanoma cells to immune attack through suppressing glycolysis

Cytotoxic T lymphocytes (CTLs) play a central role in antitumor immunity; however, metabolic reprogramming within the tumor microenvironment often compromises their effector function, making metabolic targeting crucial for the improvement of T cell function. Folate-dependent purine synthesis, a core pathway sustaining the nucleotide pool, is highly activated in tumors, yet its role in regulating tumor immune sensitivity remains unclear. Here, by establishing a co-culture system of melanoma cells and human T Cell Receptor (TCR)-engineered T cells, we systematically evaluated the effects of folate-dependent purine synthesis inhibitors on tumor cell response to CD8+ T cell cytotoxicity. We found that inhibition of key enzymes such as methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) and glycinamide ribonucleotide transformylase (GART) markedly enhanced tumor cell sensitivity to T cell killing, an effect also observed with exogenous nucleoside supplementation. Mechanistically, inhibition of folate-dependent purine synthesis suppresses glycolysis by downregulating critical glycolytic enzymes, thereby reducing lactate production. Reduction in lactate further weakens lactylation and stability of the immune checkpoint protein PD-L1. In parallel, impaired purine synthesis disrupts uridine metabolism, blocks ribose salvage, and distally influences glycolysis. Collectively, our study identified the folate-dependent purine synthesis - glycolysis axis as key regulator of tumor immune response and highlights metabolic targeting as a promising strategy to improve cancer immunotherapy.

cancer biology↗

bioRxiv2026

Somatic-to-germline transmission of horizontally acquired extrachromosomal circular DNA in Brassica graft chimeras

Whether somatically acquired traits can contribute to heritable variation has remained an open question in plant biology for over a century. Here, using graft-induced periclinal chimeras between Brassica juncea and Brassica oleracea, we identified extrachromosomal circular DNA (eccDNA) as mobile genetic elements capable of crossing histological boundaries and entering the germline. We demonstrated that grafting could promote the horizontal transfer of eccDNA between somatic cell layers, enabling its stable maintenance in recipient tissues and permitting transmission through sexual reproduction across multiple generations. We found that transmitted eccDNA is non-randomly distributed across the genome, preferentially originating from gene-dense regions, and enriched for features associated with molecular persistence, such as inverted repeats, hairpin-forming sequences, and autonomously replicating sequence (ARS) consensus motifs. These genetic regions conferred replication competence, as evidenced by autonomous propagation in an ARS-less heterologous yeast system. Sexual progeny carrying graft-acquired eccDNA exhibited reproducible and lineage-dependent alterations in leaf morphology and drought tolerance, accompanied by coordinated transcriptional reprogramming. Notably, a subset of inherited eccDNA remained transcriptionally active in progeny, producing transcripts absent from self-grafted controls. Our findings establish eccDNA as heritable extrachromosomal elements that link graft-mediated somatic genetic transfer with stable germline transmission, thereby expanding the molecular scope of heritable variation in plants and providing a conceptual framework for graft-based trait transmission.

plant biology↗

bioRxiv2026

Temporal-deviation-driven community detection uncovers early-warning signals for critical transitions in complex diseases

Early detection of critical transitions in complex diseases is crucial for timely clinical intervention. However, as patients often provide only a single snapshot, identifying sample-specific early-warning signals (EWS) from a dynamical evolution perspective remains challenging, coupled with high-dimensional noise amplification. Here, we present TD-COM, a framework for detecting personalized EWS of critical transitions via single-sample community detection. By constructing a temporal perturbation map STDN, TD-COM captures latent dynamical perturbations inferred from static individual profiles. Synergizing these temporaldeviation signals with static topological features, TD-COM implements a multilevel node filtering strategy during community detection, effectively suppressing single-sample noise. Validated on hour-scale, multi-year, and multi-decade transcriptomic data, TD-COM robustly detects critical states preceding clinical deterioration and uncovers their underlying molecular mechanisms. Comparative experiments demonstrate that TD-COM outperforms existing methods in accuracy and topological robustness. Thus, TD-COM provides a generalizable framework for personalized early warning of complex diseases, particularly when longitudinal sampling is infeasible.

bioinformatics↗

bioRxiv2026

Whole-organism spatial transcriptomics at single-cell resolution in C. elegans

Spatial transcriptomics has advanced our understanding of tissue organization by mapping gene expression in its native context yet applying these techniques to whole organisms remains a significant challenge. Caenorhabditis elegans is well-suited to whole organism-level analysis because its compact size, transparency, reproducible anatomy, and genetic tractability make it possible to link molecular and cellular changes to circuit function and behavior within the same animal. However, current transcriptomic approaches in C. elegans are often limited by spatial resolution or multiplexing capacity, making it challenging to profile multiple gene expression patterns across intact worms while preserving spatial context. Here, we present a single-molecule fluorescence in situ hybridization workflow that enables multiplex imaging with single-cell resolution across the entire worm. This approach allows sequential imaging of one gene per fluorescent channel using two channels across 20 hybridization rounds, enabling the profiling of up to 40 genes while preserving spatial context. We further provide a curated marker-gene panel for reproducible neuron identification, which, together with probabilistic assignment of transcripts to segmented nuclei, enables quantitative measurements of gene expression levels. We used this method to identify up to 86 neuronal classes and reveal sex- and neuron-specific expression patterns at single-cell resolution. Together, these results establish a scalable framework for the spatial analysis of gene expression and cell identity in intact C. elegans.

neuroscience↗

bioRxiv2026

Histone H2BK120 ubiquitination modulates PRC1 activity and H2AK119ub deposition on nucleosomes

Polycomb group and Trithorax group complexes antagonistically regulate developmental gene expression, yet the mechanisms coordinating their interplay remain poorly understood. Here, we uncover a synergistic histone crosstalk in which H2BK120ub (histone H2B ubiquitination at lysine 120), a Trithorax-associated active mark, enhances Polycomb repressive complex 1 (PRC1) activity by directly binding specific PCGF subunits of PRC1 on the nucleosome surface, as shown in cryo-electron microscopy (cryo-EM) analysis. Beyond regulating enzymatic activity, H2BK120ub also modulates the competitive binding between the catalytic RNF2-BMI1 module and the RYBP subunit of noncanonical PRC1.4 complexes to nucleosomes, potentially restricting H2AK119ub (histone H2A ubiquitination at lysine 119) spreading to neighboring nucleosomes. In mouse embryonic stem cells, H2BK120ub directs the deposition of H2AK119ub within the gene bodies of a subset of developmental genes, which exhibit more rapid activation compared to canonical H3K4me3/H3K27me3 bivalent genes. These findings reveal a previously unrecognized mechanism that links active and repressive histone modifications, providing new insights into the intricate chromatin regulation of gene expression during development.

molecular biology↗

bioRxiv2026

Rapid and Quantitative Phage Susceptibility Test by Ramanome

Antimicrobial resistance poses an escalating global threat, renewing interest in bacteriophage therapy as a precision alternative to antibiotics. However, clinical translation remains hindered by the lack of rapid and quantitative phage susceptibility testing (PST) platforms capable of evaluating host range, infection potency, and effective multiplicity of infection (MOI). Here we present RPST, a ramanome-based phenotypic platform that captures infection-induced remodeling of bacterial macromolecular composition to unify these diagnostic requirements within a single workflow. RPST integrates four Raman biomarkers into a Composite Infection Index (CII), enabling rapid and lysis-independent discrimination between susceptible and resistant bacterial populations within [~]1 hour, with 96.0% categorical concordance (24/25) to plaque assays. As a continuous population-level metric, CII quantifies the proportion of infected cells, allowing quantitative ranking of phage potency against shared hosts. By resolving CII trajectories across the MOI and time, RPST further determines the minimal effective MOI, which is the lowest phage-to-bacterium ratio sustaining self-propagating infection, thereby defining the lower boundary for therapeutic feasibility. Together, these capabilities transform PST from static compatibility assays into a dynamic and quantitative framework that bridges in vitro infectivity assessment and infection dynamics relevant to phage therapy. Impact StatementBased on the rapid emergence of antimicrobial resistance, this study introduces RPST, a novel ramanome-based phage susceptibility testing platform. RPST detects phage-induced biochemical remodeling in bacteria within [~]1 hour, achieving 96.0% concordance with gold-standard plaque assays. By integrating four Raman biomarkers into a Composite Infection Index, it not only distinguishes susceptible from resistant strains but also quantifies phage potency and determines the minimal effective multiplicity of infection required for self-sustaining infection. This transformative approach moves beyond binary diagnostics to offer a dynamic, quantitative framework for precision phage therapy, significantly accelerating therapeutic decision-making and enhancing our ability to combat resistant infections.

microbiology↗

bioRxiv2025

CryoDDM: CryoEM denoising diffusion model for heterogeneous conformational reconstruction

Heterogeneous protein reconstruction can reveal the relationship between protein dynamics and function, which represents one of the foremost challenges in cryogenic electron microscopy (cryo-EM) single-particle analysis (SPA). However, high-intensity noise results in inaccurate parameter estimation during classification and reconstruction, making it difficult to capture the subtle motions of proteins. Here, we present the Cryo-EM denoising diffusion model (CryoDDM), which denoises images while preserving high-frequency structural information, benefiting conformational heterogeneity classification and reconstruction. The image denoised by CryoDDM can be used to improve downstream analysis, enhance reconstruction resolution, discover new protein conformations, and map out conformational variations. Validated against tree diverse experimental datasets, spanning a proteasome, a membrane protein and a spike protein, our results consistently demonstrate the accuracy and superiority of CryoDDM. By guiding reconstruction with denoised images, CryoDDM enables high-resolution reconstruction of heterogeneous conformations, paving the way to illuminate fundamental questions in structural biology. The CryoDDM project are published at https://github.com/BIT-FuweiLi/CryoDDM.

bioinformatics↗

bioRxiv2025

Psoralen Enhances Direct Cardiac Reprogramming via PPARα Activation and Promotion of Mitochondrial Fission

BACKGROUNDCell-based therapy is a promising strategy for heart repair and regeneration. However, its clinical application has been hampered by the low efficiency of cell direct reprogramming and the immature state of the inducing cells. Developing novel strategies to enhance direct reprogramming efficiency and yield mature functional cardiomyocytes remains a critical challenge. METHODSWe evaluated the effect of Psr on cardiac reprogramming using RepSox and Forskolin (RF) as the baseline cocktail. Reprogramming efficiency, cardiomyocyte marker expression, and calcium handling were assessed by RT-qPCR, immunofluorescence. Ultrastructural features were examined by transmission electron microscopy. Metabolic profiles were analyzed using Seahorse assays. Transcriptomic changes were explored by RNA sequencing, followed by pathway and protein-protein interaction analyses. A myocardial infarction (MI) mouse model was used for in vivo validation. RESULTSSupplementation with Psr (10 M) markedly enhanced the induction of induced cardiomyocytes (iCMs), leading to earlier appearance of beating clusters (day 1 vs. day 6-8), improved sarcomere organization, robust calcium transients, and higher energy metabolism. Transcriptomic profiling identified activation of the PPAR signaling pathway, with PPAR, RXRG, and UCP1 as central regulators. Mechanistically, Psr promoted mitochondrial fission, thereby facilitating metabolic remodeling essential for cardiomyocyte maturation. In vivo, RF+Psr treatment significantly improved cardiac function and reduced fibrosis after MI compared to RF alone. CONCLUSIONPsr enhances direct cardiac reprogramming by activating PPAR signaling and promoting mitochondrial fission. These findings provide a novel mechanistic framework and suggest psoralen as a promising natural enhancer for cardiac regeneration strategies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/681288v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@13a5d27org.highwire.dtl.DTLVardef@b9cce5org.highwire.dtl.DTLVardef@3afef8org.highwire.dtl.DTLVardef@1398972_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Cyclohexyl acetate functions like a volatile sex pheromone mimic in Caenorhabditis nematodes

Nematodes communicate via diverse sex pheromones, including long-range volatile signals, short-range chemical cues, and contact-dependent molecules. While the ascaroside family of small molecules that mediate short-range attraction is well characterized, the identities and roles of volatile sex pheromones (VSPs) that act over longer ranges remain unknown. Using GC-MS analysis of crude VSP extracts, we identified cyclohexyl acetate (CA) as a candidate mimic, sharing retention time and mass spectral features with natural VSPs. Behavioral assays demonstrated that CA acts as a concentration-dependent, male-specific attractant in Caenorhabditis. Pre-exposure to VSPs induced cross-adaptation to CA, suggesting shared sensory processing. Surprisingly, genetic and calcium imaging analyses revealed that CA perception is mediated primarily by AWCon (str-2-expressing) neurons and involves VSPs chemoreceptor srd-1-independent pathways, which are distinct from the neural pathways involved in natural VSPs perception. These findings establish that CA is not a major component of VSPs but a structural and functional mimic of nematode VSPs, operating through a parallel sensory circuit. Although the endogenous source of CA remains unknown, its structural and behavioral mimicry provides new insights into the complexity of chemosensory signaling and the potential for interspecies chemical eavesdropping in nematode ecology.

biochemistry↗

bioRxiv2025

A male-derived volatile sex pheromone in nematodes identified through its mimicry by a predator

Recent studies demonstrated that the predacious fungi Arthrobotrys oligospora emits a mixture of volatile chemical cues that function to attract nematode prey. The strong attraction elicited by one of the mixture components, methyl 3-methyl-2-butenoate (MMB), was highly female- and hermaphrodite-specific within several Caenorhabditis species, including C. remanei and C. elegans, suggesting that MMB might function as a mimic of an endogenous, male-produced, volatile sex pheromone (VSP) within these species. Here, we report evidence that MMB is produced by C. remanei males at levels that are attractive to C. remanei females and C. elegans hermaphrodites. Notably, MMB production was not detected for C. elegans males; a finding which correlates with behavioral assays for which worm-conditioned media (WCM) prepared from C. remanei, but not from C. elegans adult males is strongly attractive to both C. remanei females and C. elegans hermaphrodites. Our findings establish MMB as the first chemically identified VSP in nematodes and show that A. oligospora exploits a dual strategy of chemical deception--mimicry and eavesdropping--to enhance prey capture.

animal behavior and cognition↗

bioRxiv2025

NicheScope: Identifying Multicellular Niches and Niche-Regulated Cell States in Spatial Transcriptomics

The functional state of a cell is intrinsically linked to its local microenvironment, or cell niche, a complex milieu formed by multiple interacting cell types. Deciphering how these multicellular niches regulate cell states is fundamental to understanding tissue biology and disease mechanisms, yet remains challenging with current computational approaches. Here, we present NicheScope, a computational framework for transcriptome-wide identification and characterization of Multicellular Niches (MCNs) and their corresponding Niche-Regulated Cell States (NRCSs) from spatial transcriptomics data. NicheScope operates on the principle that a cells transcriptional state is associated with its local multicellular composition. It employs a robust statistical approach to jointly model neighborhood composition and transcriptome-wide gene expression, enabling the simultaneous discovery of MCNs, defined by specific combinations of neighboring cell types, and their associated NRCSs, characterized by distinct gene programs. We demonstrate NicheScopes power and versatility across diverse tissues and platforms, including lymph node, lung adenocarcinoma, and head and neck cancer. NicheScope reproducibly dissected established tissue structures in lymph nodes across tissue regions and platforms, uncovered clinically relevant tumor cell-associated MCNs in lung adenocarcinoma, and revealed shared and condition-specific MCNs in primary and metastatic tumors. Our results establish NicheScope as a powerful, robust, scalable, and interpretable framework for dissecting the spatial and functional organization of complex tissues, providing new insights into multicellular coordination in health and disease.

bioinformatics↗