Biology subjects

Fan, Y.

Publications and source records attributed to Fan, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

A haplotype-resolved T2T genome assembly of Indigofera pseudotinctoria reveals the genetic basis of flavonoid biosynthesis in Chinese Indigo

Indigofera pseudotinctoria, commonly known as Chinese Indigo, is a multifunctional leguminous shrub widely distributed in East Asia, valued for its medicinal, ecological, and forage importance, and naturally adapted to drought and nutrient-poor soils. However, the absence of genomic resources has hindered insights into the genetic basis of its bioactive metabolites and adaptive traits. Here, we present a haplotype-resolved, telomere-to-telomere (T2T) reference genome of I. pseudotinctoria, which represents the first complete genome within the genus Indigofera. By integrating PacBio HiFi sequencing, Oxford Nanopore ultra-long reads, and Hi-C chromatin conformation sequencing technologies, we successfully constructed two gap-free haplotypes assemblies (647.38 Mb and 657.52 Mb), characterized by high BUSCO completeness and QV scores, and fully captured all telomeric sequences. Comparative analysis between haplotypes revealed extensive synteny but notable structural heterozygosity but notable structural heterozygosity. Approximately 46% of structural variations overlap with genic or regulatory regions, leading to allele-specific expression divergence. Between the two haplotypes, we identified 2,607 and 2,331 haplotype-specific genes, reflecting a complementary functional specialization in defense and repair versus metabolism and growth. Integrative transcriptomic and metabolomic profiling across six tissues reconstructed the flavonoid biosynthetic network and identified MYB, bHLH, NAC, WRKY, and ERF transcription factors regulating five key pharmacologically active flavonoids (Calycosin, Butein, Sulfuretin, Chrysoeriol, and Genistin). These results collectively uncover the haplotype-specific regulatory and structural basis of Indigofera pseudotinctoria and establish a high-quality genomic framework for evolutionary, medicinal, and metabolic engineering studies in leguminous plants, and provide a framework for molecular breeding and bioactive compound discovery in medicinal legumes.

genomics↗

bioRxiv2025

Interconnected axes of phenotypic plasticity drive coordinated cellular behaviour and worse clinical outcomes in breast cancer

Phenotypic plasticity plays a key role in cancer progression and metastasis, enabling cancer cells to adapt and evolve, but precisely how distinct axes governing phenotypic plasticity interact to shape tumour progression and patient outcomes remains unclear. We investigated five major interconnected axes of plasticity in ER-positive (ER+) breast cancer: Metabolic Reprogramming, Epithelial-to-Mesenchymal Plasticity (EMP), Luminal-Basal (Lineage) Switching, Stemness, and Drug-resistance using network dynamics simulations, integrative bulk and single-cell transcriptomic analyses and patient survival analyses. We show that these axes are not independent but drive one another, forming two mutually inhibiting teams of nodes enabling specified cellular behaviour. One team (favouring high glycolysis, stem-like, basal-like, mesenchymal/hybrid and tamoxifen-resistant phenotype) was found to be associated with aggressive progression and worse survival. On the other hand, the opposing team (favouring high oxidative phosphorylation, non-stem-like, luminal-like, epithelial and tamoxifen-sensitive phenotype) correlated with better outcomes. Importantly, altering one axis of plasticity often drove coordinated responses along other axes and vice versa. Our findings establish phenotypic plasticity in cancer as a coordinated, multi-axis dynamical process, thus suggesting novel strategies to disrupt systems-level reprogramming enabling metastasis and therapeutic resistance.

systems biology↗

bioRxiv2025

YAP1 Depletion Enhances TAZ and its Complexation with TEAD4 and AP-1 Heterodimer C-JUN/FOSB to Promote Gastric Cancer Progression and Metastases

BackgroundDysregulation of the Hippo signaling pathway, characterized by aberrant activation of the transcriptional coactivators YAP1 and TAZ, drives tumour progression, immunosuppression and metastasis. Hippo pathway components are emerging therapeutic targets in several solid tumours, however, the expression profiles of Hippo coactivators YAP1, TAZ and their transcriptional factors TEAD1-4 in gastric cancer peritoneal metastases (GCPMs) and their therapeutic value are unknown. ObjectiveTo determine expression status of YAP1, TAZ and TEAD1-4 in GCPMs; and to evaluate whether dual targeting of YAP1 and TAZ provides superior antitumour activity compared with inhibition of either coactivator alone. DesignExpression of YAP1, TAZ and TEAD1-4 was examined in GCPMs by single-cell RNA sequencing and co-immunofluorescent staining. Functional studies using genetic knockout and antisense oligonucleotide (ASO) inhibition of YAP1 or TAZ were performed to assess antineoplastic effects in vitro and in vivo. Co-immunoprecipitation and luciferase reporter assays were used to characterize YAP1/TAZ interactions with TEADs and AP-1 components (JUN and FOSB) and to quantify transcriptional activity. Antitumour efficacy was validated in patient-derived xenograft (PDX) and KP-Luc2 syngeneic models. ResultsYAP1, TAZ, and TEADs1- 4 were highly coexpressed in GCPMs and correlated with poor survival. YAP1 inhibition alone elicited compensatory upregulation of TAZ, while combined inhibition of both coactivators maximally repressed cell proliferation and invasion in vitro, and tumor growth in vivo. Increased TAZ complexation with TEAD4 and AP-1 (c-JUN and FOSB) heterodimer was observed following YAP1 knockdown or pharmacological ASO inhibition. Dual inhibition of YAP1 and TAZ was required to maximally suppress YAP1/TAZ expression and reduce their nuclear accumulation, transactivation of TEAD, and activation of downstream genes. ConclusionsThese findings show that combined YAP1 and TAZ inhibition holds promise for the treatment of GCPMs, a highly lethal disease with an urgent need for novel treatment options. WHAT IS ALREADY KNOWN ON THIS TOPICO_LIGastric cancer with peritoneal metastasis (GCPM), occurring in > 45% of gastric cancer (GC) patients, is a highly lethal malignancy with limited therapeutic options. C_LIO_LIThe Hippo pathway mediator Yes-associated protein 1 (YAP1) is intimately involved in chemoresistance, cancer stemness properties, and the epithelial-to-mesenchymal transition in gastric and other cancers. C_LIO_LIWhile YAP1 represents a promising therapeutic target, clinical trial of YAP1 antisense oligonucleotides has been disappointing. C_LI WHAT THIS STUDY ADDSO_LIHippo coactivators YAP1, TAZ and their main transcription factors TEAD1-4 are markedly upregulated in GCPMs and associated with poor prognosis. C_LIO_LIAntisense targeting of YAP1 results in compensatory upregulation of its paralog TAZ. C_LIO_LIUpon YAP1 depletion, TAZ forms transcriptional complexes with TEAD4 and the AP-1 heterodimer (JUN and FOSB). C_LIO_LIDual targeting of YAP1 and TAZ, by oligonucleotides, achieves maximal suppression of tumour growth in vitro and in vivo. C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYO_LIThese findings provide a strong mechanistic rationale for co-targeting YAP1 and TAZ as a therapeutic approach in metastatic gastric cancer. C_LIO_LIDual Hippo coactivator inhibition could inform the design of future clinical trials aimed at improving outcomes for patients with GCPMs. C_LI

cancer biology↗

bioRxiv2025

Cell-type-resolved NRXN1 isoforms across human brain tissues and hiPSC organoids

NRXN1 undergoes extensive alternative splicing that generates a highly diverse repertoire of isoforms, diversifying protein-protein interactions, shaping synaptic specialization, and contributing to neuropsychiatric disease when disrupted. However, the splicing landscape of NRXN1 across distinct human brain cell types remains poorly defined. Because NRXN1 expression level is relatively low in adult brains and human induced pluripotent stem cell (hiPSC) derived neurons, single-cell long-read cDNA sequencing often provides insufficient coverage to capture its full isoform diversity, particularly across heterogeneous cell populations. To address this gap, we developed an integrative sequencing strategy that combines single-cell transcriptomics, targeted enrichment of NRXN1 transcripts, and long-read sequencing. This approach reveals a comprehensive catalog of cell-type resolved NRXN1 isoforms across adult and fetal human postmortem brains as well as hiPSC-derived cortical organoids. From the adult prefrontal cortex (PFC) region, our analyses reveal distinct splicing programs across interneuron subtypes, pyramidal neurons, and glial lineages. Comparisons between prenatal and adult brains indicate that NRXN1 isoform profiles are established during early development and remain stable throughout neuronal maturation. In hiPSC organoid models, splicing profiles partially mirror both developmental and mature brain patterns, with a subset of splice sites exhibiting cell type - and stage-specific divergence. In the cerebellum of an autism case and in organoids derived from schizophrenia patients, carrying non-recurrent heterozygous NRXN1 deletions, we identify disrupted isoform expression and mutant NRXN1 isoforms and characterize their distribution across diverse cell types. Using this integrated long-read sequencing framework in patient-derived organoids, we further show that antisense oligonucleotide (ASO) targeting of mutant splice junctions reduces gain-of-function NRXN1 isoforms and reshapes splicing patterns in a cell type-specific manner, providing a platform for evaluating ASO efficiency. Together, these findings help understand the cell type-specific splicing landscape of NRXN1 and establish a framework for decoding cell type-specific isoform diversity and assessing transcript-targeted therapies for genes with low expression levels.

neuroscience↗

bioRxiv2025

An extensive forward genetic screen identifies the HWS-AGO1 axis as pivotal for target mimicry-mediated miRNA degradation in Arabidopsis

Target RNAs have emerged as key regulators of miRNA stability, thereby influencing development and physiological processes in both plants and animals. The F-box protein HAWAIIAN SKIRT (HWS) has been characterized as a crucial factor in targeted miRNA degradation in plants (pTMD), a process triggered by a specific type of target RNA called target mimicry. However, the precise mechanism by which HWS functions is still poorly understood. We previously established a genetic reporter system based on Short Tandem Target Mimicry of miR160 (STTM160) triggered miR160 degradation, resulting in pleiotropic developmental defects that are easy to monitor. Here, through an extensive forward genetic screen, we identified fourteen additional hws alleles that near-completely restored STTM160-induced developmental defects, highlighting a central role for HWS in pTMD. Intriguingly, we discovered two adjacent amino acid substitutions (R421K and G422D) in the PAZ domain of AGO1 that significantly suppressed the STTM160 phenotype. Similar to HWS dysfunction, the AGO1 R421K substitution caused a significant retention of target mimicry RNAs in AGO1 immunoprecipitates, suggesting that the R421 residue of AGO1 may cooperate with HWS for the clearance of AGO1-miRNA-target mimicry complexes. Although the R/G mutations only impacted a small set of endogenous miRNA levels, they were sufficient to rescue the developmental defects caused by HWS overexpression (HWS-OE), suggesting that the developmental abnormalities caused by HWS-OE largely depend on the AGO1-miRNA pathway. Taken together, our findings provide a solid genetic evidence for the coordination of HWS and AGO1 in pTMD.

plant biology↗

bioRxiv2025

Integrating host plants and a natural enemy into MaxEnt improves global suitability predictions for Semanotus bifasciatus

BACKGROUNDSemanotus bifasciatus is a major conifer pest that causes severe wood damage. The parasitoid Sclerodermus guani is its important natural enemy. However few studies have jointly considered host plants and enemy effects when predicting pest ranges. We applied the optimized MaxEnt model and, on this basis, constructed two models: the "host-pest" model and the "host-pest-enemy" model, to predict the potential global distribution of S. bifasciatus under future scenarios and to explore the effects of climate change and the introduction of biotic interactions. RESULTSResults showed that the climate-only model projected 2.73 x 10{square} km{superscript 2} of suitable area under the historical climate condition, concentrated in Asia, North America and Europe, with expansion toward higher latitudes. The expansion of host plants further enhanced pest habitat suitability, nearly doubling the predicted range (5.46 x 10{square} km{superscript 2}) and increasing the mean suitability. Moreover, the potential distribution of S. guani overlapped extensively with S. bifasciatus, reducing the total suitable area of S. bifasciatus by up to 2.67 x 10{square} km{superscript 2}, and mean suitability declined by nearly 40%, indicating effective suppression of pest risk. Centroid shifts were consistently northward, though magnitude and fragmentation varied among models. CONCLUSIONIntegrating host availability and enemy suppression improves the realism of distribution forecasts for S. bifasciatus. The study highlights the roles of biotic factors in shaping pest suitability and identifies potential future high-risk regions of infestation. These insights provide a solid scientific foundation for targeted monitoring, and the strategic application of biological control in adaptive forest pest management.

ecology↗

bioRxiv2025

Human Organoids Reveal PTEN-driven Mesendoderm Specification via Retinoic Acid Signaling Suppression

During early embryogenesis, epiblast cells ingress through the primitive streak (PS) and commit to a mesendoderm (MES) fate, giving rise to both mesodermal and endodermal lineages. Despite advancements in human organoid technology for modeling pre-implantation blastocyst stage, robust systems that accurately recapitulate MES specification and PS formation during the post-implantation stage remain limited. Here, we show that human induced pluripotent stem cells can be used to generate three-dimensional MES organoids that faithfully mimic in vivo human MES specification, particularly from the anterior PS. We demonstrate that MES organoid formation is dependent on PTEN expression and that loss of PTEN severely impairs the formation of mesoderm and definitive endoderm derivatives arising from MES organoids. To elucidate the molecular mechanisms underlying these defects, we conducted an integrative multi-omics analysis, including transcriptome, chromatin accessibility profiling, metabolism, and phosphoproteomics, on wild-type and PTEN-/-MES cells. These analyses revealed that PTEN suppresses retinoic acid (RA) signaling during MES lineage commitment. Furthermore, we identified the RA-degrading enzyme CYP26A1 as a downstream effector of PTEN. Notably, while excessive RA induced by PTEN ablation is detrimental to MES cell generation, physiological levels of RA are necessary. Collectively, our human MES organoids offer a valuable model for dissecting early human development, and our findings identify PTEN as a key regulator of MES fate commitment through inhibition of RA signaling.

developmental biology↗

bioRxiv2025

Transcriptomic Signature and PROTAC Strategy Revealed Histone Lysine Demethylase as a Target of Anticancer Activity of Deferiprone.

Deferiprone (DFP) is an iron chelator approved for treating iron overload in thalassemia patients. Recent observations have suggested that DFP has promising anticancer activities ascribed to several mechanisms including reduction of the intracellular free labile iron and zinc ion pools and inhibition of the activities of other intracellular targets, including ribonucleotide reductase (RNR). We previously reported that DFP inhibits the demethylase activities of several Fe(II)/- ketoglutarate dependent histone lysine demethylases (KDMs) at much lower concentrations at which it inhibits RNR activities and/or reduces the labile intracellular iron and zinc ion pools. In this study, we used RNA sequencing (RNA seq) and PROTACs strategies to validate and quantify the contribution of intracellular KDM inhibition to the antiproliferative activities of DFP. We report herein that DFP elicited gene expression signature that is largely similar to that of JIB-04, an established KDM inhibitor (KDMi), in two breast cancer (BCa) cells (MCF-7 and MDA-MD-231). Importantly, RNA seq revealed that DFP and JIB-04 downregulated the expression of hypoxia-inducible factor 1 (HIF-1), an oncogene whose expression is commonly modulated through histone demethylation mediated by KDMs and degraded by several KDMi. Moreover, DFP-derived PROTACs elicited enhanced cancer cell selective antiproliferative activities and intracellular on-target effects, downregulating several KDMs implicated in the etiology of BCa cells, including a strong degradation of KDMs 2A, 3A and 5B, and a moderate degradation of KDMs 4A-C, 5C, 6B. Collectively, our data supports KDM inhibition as a key mechanism of anticancer activity of DFP and identifies PROTAC is a viable strategy to obtain novel DFP analogs with improved potency and therapeutic index.

cancer biology↗

bioRxiv2025

DHHC21 is a STIM1 protein S-acyltransferase that modulates immune function in vivo

Depletion of calcium from ER stores leads to the activation of calcium channels on the plasma membrane. This process is termed store-operated calcium entry (SOCE). The proteins STIM1 and STIM2 function as ER calcium sensors, and upon store depletion, they undergo a conformational change that allows them to bind to and gate Orai calcium channels on the plasma membrane. We have shown that both Orai1 and STIM1 are dynamically S-acylated after store depletion, which is required for SOCE. These results suggest the requirement of a calcium-activated protein S-acyltransferase such as DHHC21. Here, we show that DHHC21 is essential for SOCE in vitro and in vivo. Using the depilated mouse model that expresses DHHC21 but can no longer be activated by calcium, we show that DHHC21 activation is required for STIM1 S-acylation and subsequent calcium entry. Plasma membrane-localized DHHC21 is dynamically recruited into Orai1/STIM1 puncta upon store depletion, where it physically binds to STIM1. Finally, we show that depilated mice phenocopy many aspects of autoimmune lymphoproliferative syndrome (ALPS), including defective Fas-mediated calcium release, T cell death, neutropenia, and increased serum vitamin B12 levels. These results suggest that dynamic S-acylation has underappreciated and expansive roles in second messenger signaling and immune system function. Targeting DHHC21 may be therapeutically beneficial for ALPS and diseases associated with deregulated activation of STIM1, such as tubular aggregate myopathy and Stormorken syndrome.

immunology↗

bioRxiv2025

A matrix-mimicking bioadhesive epicardium for tunable modulation of biomechanics in the acutely infarcted heart

Mitigating adverse tissue remodeling after a heart attack or myocardial infarction (MI) is critical to prevent the development of heart failure. Among various post-MI treatment strategies, mechanical reinforcement of the infarcted region with epicardial patches has promise due to its consistent improvement of chronic cardiac function and its drug- or biologic-free nature. However, despite the variety of patch materials studied to date, the lack of a programmable platform that predictably modifies early-stage cardiac biomechanics to different degrees has prevented further optimization of this strategy. Here, we introduce the matrix-mimicking bioadhesive epicardium (MMBE), a platform that can be rationally designed to achieve a wide range of anisotropic mechanical properties to offer quantifiable mechanical reinforcement of the heart upon application. The platform synergistically combines fully programmable direct-ink-writing of extracellular matrix-inspired crimped fibers and a bioadhesive for sutureless integration to the epicardium. The MMBE platform achieves an array of matrix-mimicking mechanical properties and acute modulation of cardiac biomechanics using numerical analysis, in silico studies and experimental characterizations. Furthermore, the feasibility of the MMBE platform in an in vivo rat model of MI is demonstrated. The MMBE platform can be used to systematically identify patch design parameters that alter post-MI remodeling without introducing confounding biological variables.

bioengineering↗

bioRxiv2025

Degeneration and Impaired Resilience of Skull Bone and Hematopoietic Bone Marrow

Bone marrow health is central to transplantations, blood formation, and cancer progression. However, the bone marrow niche deteriorates with age, impairing haematopoietic stem cell function. Contrary to a recent report1 suggesting skull marrow resists ageing, our multi-laboratory investigation reveals the opposite: the skull marrow is among the vulnerable sites of age-related decline. Ageing skull niches consistently show loss of mesenchymal and osteoprogenitors, suppression of angiogenic and lymphatic programs, adipocyte accumulation, vascular senescence, DNA replication stress, mitochondrial dysfunction, cellular senescence, and heightened inflammation. Proteomic profiling further highlights this vulnerability, demonstrating that vertebral niches--unlike the skull--are relatively spared from these ageing hallmarks. Together, these convergent datasets overturn the notion of skull-specific resilience and instead establish the skull marrow as a fragile, degenerating environment. These findings redefine marrow ageing and highlight the skull as a critical, clinically relevant target for sustaining blood and immune health and reducing vulnerability to haematological disease.

cell biology↗

bioRxiv2025

Regulatory network and spatial modeling reveal cooperative mechanisms of resistance and immune escape in ER+ breast cancer

Despite significant progress, the treatment of estrogen receptorpositive (ER+) breast cancer remains clinically challenging due to reversible drug resistance and immune evasion. Drug resistance often arises as cells undergo a dynamic epithelial-to-mesenchymal transition (EMT), while elevated PD-L1 levels contribute to immune escape. While these phenotypic features can variably co-occur, the impact of co-occurrence on the availability of synergistic treatment strategies remains unknown. To investigate their interplay, we constructed an ER-EMT-PD-L1 gene regulatory network and simulated these networks as coupled ordinary differential equations with biologically informed parameters, to generate steady-state expression profiles. Our study revealed that the relevant overarching network generated antagonistic epithelial and mesenchymal modules, capable of producing monostable, bistable, and tristable dynamics. We further examined the link between phenotypes and immune evasion by quantifying average PD-L1 expression, and found that epithelial-sensitive states consistently exhibited low PD-L1. In contrast, hybrid- and mesenchymal-resistant states were associated with high PD-L1, highlighting a strong coupling between EMT, resistance, and immune evasion. Extending on these network-level insights, we further used a spatially explicit agent-based model seeded with GRN-derived phenotypes to probe tumor behavior under therapeutic pressure. Simulations revealed that tumor escape required co-occurrence of therapy resistance, motility, and immune suppression, with plasticity and multistability further promoting adaptive persistence. Lastly, we identified combination therapies predicted to constrain malignant diversification and enhanced immune accessibility. Taken together, our modeling work links regulatory dynamics with tumor-level adaptation and underscores potential strategies to therapeutically reprogram cell states toward sensitivity.

bioengineering↗

bioRxiv2025

Predictive in vitro profiling of LNP-induced innate immune response using an iPSC-derived monocyte model

Lipid nanoparticles (LNPs) are a powerful drug delivery platform advancing vaccines and gene therapies. While their efficacy and safety has been found to be closely linked to innate immune activation, current in vitro models are unable to predict immune responses reliably. Conventional models, such as PBMCs, are limited by donor variability and inconsistent sensitivity. To address this, we developed a cytokine profiling platform using induced pluripotent stem cell (iPSC)-derived monocytes (iMonocytes), a physiologically relevant innate immune cell type that plays a key role in immune surveillance and inflammation. iPSCs provide a renewable, uniform monocyte source for consistent, high-sensitivity LNP screening. When tested with LNPs of graded immunostimulatory potency, iMonocytes showed improved reproducibility and strong correlation with in vivo cytokine responses. This platform enables evaluation of cargo- and dose-dependent effects, providing a robust and scalable tool for preclinical assessment and rational design of LNP therapeutics.

bioengineering↗

bioRxiv2025

VesiclePy: A Machine Learning Vesicle Analysis Toolbox for Volume Electron Microscopy

Vesicles are critical components of neurons that package neurotransmitters and neuropeptides for their release, in order to communicate with other neurons and cells. However, due to their small size, the reconstruction of the full vesicle endowment across an entire neuronal morphology remains challenging. To achieve this, we have used, as a tool to identify and visualize vesicles, Volume Electron Microscopy (vEM), a method that has the nanoscale resolution to detect individual vesicle boundaries, content, and 3D locations. However, the large volume of vEM datasets poses a challenge in the segmentation, classification, and spatial analysis of tens of thousands of vesicles and their target cell in 3D. Here we report the development of VesiclePy, an integrated pipeline for automated segmentation, classification, proofreading, and spatial analysis of vesicles, relative to neuron masks in large-volume electron microscopy data. Our package integrates the efficiency of deep learning and the accuracy of human proofreading and provides a streamlined package in chunked processing and accurate indexing, localization, and visualization of single vesicle resolution in large vEM data. We demonstrate the viability of VesiclePy using high-pressure frozen serial EM data of Hydra vulgaris and quantify the performance of the package using ground truth manual annotations. We show that VesiclePy can process a multiterabyte serial EM dataset, efficiently annotate 53,851 vesicles from 20 complete neurons, and classify vesicles into 5 types. Each vesicle has a unique ID and 3D location for further spatial analysis in relation to neuron or non-neuronal targets nearby. Finally, by combining vesicle data and morphological information of each neuron, we can quantitatively cluster neurons into subtypes. VesiclePy is available at https://github.com/PytorchConnectomics/VesiclePy under an MIT license.

neuroscience↗

bioRxiv2025

JointMap identified SERPINA3+ chondrocytes as a therapeutic target for osteoarthritis

BackgroundOsteoarthritis (OA) is a prevalent degenerative joint disease that affects nearly half of the population aged over 65. Recent single-cell transcriptional studies have identified heterogeneous OA-specific chondrocyte subtypes, yet a unified subtype-classification remains incomplete. MethodsIn this study, we integrated a total of 545,946 cells to develop JointMap, an interspecies atlas. The chondrocyte subtypes were analyzed using machine learning algorithms were validated via human samples, animal models, and in vitro cell culture. We performed KAS-seq and analyzed the spatial characters for JointMap. ResultsBased on clinical diagnosis and cross-omic indexes, we identified a novel OA-elevated chondrocyte subtype, SERPINA3+ chondrocytes. Notably, we uncovered their upregulated chondrogenesis function and intercellular communication patterns as potential therapeutic targets. ConclusionsIn summary, JointMap provides a unified framework for the systematic annotation of chondral tissues across species and helps in the identification of druggable networks for articular diseases.

bioinformatics↗

bioRxiv2025

SpatialZoomer: multi-scale feature analysis of spatial transcriptomics

Single-cell resolution spatial transcriptomics (ST) provides a great opportunity to explore the complex cellular contents in different tissues. In this study, we introduce SpatialZoomer, a spectral graph-based method that applies a set of low-pass filters to efficiently extract spatial molecular features from ST data at multiple resolutions or scales, including the single cell scale, the niche scale with dozens of closely interacting cells, and the domain scale with spatially-organized cell contents. The corresponding "critical" scales can be automatically identified by partitioning a cross-scale similarity map. Results show that SpatialZoomer can identify disease-progression signals at specific scales in Alzheimers Disease, and spatial context dependent cell subtypes in tumor microenvironment. The extracted multi-scale features also uncovered spatially heterogeneous niches in cancer. SpatialZoomer also takes advantage of high computational efficiency and low hardware requirements.

bioinformatics↗

bioRxiv2025

Metabolic Immunosuppression Mediated by Proliferative CD168+TAMs in Colon Cancer

The role of non-monocyte-derived, in situ proliferating tumor associated macrophages (TAMs) in tumor progression has been underappreciated. Proliferative TAM subsets likely represent critical mediators in establishing the immunosuppressive microenvironment, given the susceptibility of TAMs to be hijacked by malignant cells for pro-tumorigenic functions. However, the regulatory networks governing their self-renewal circuitry and lineage bifurcation remained undefined. Combining single cell RNA sequencing of human and murine colon tumors, we identified CD168+ TAMs, a hyperproliferative subpopulation with FOXM1-dependent maintenance of replicative competence. Spatial multi-omics and functional validation revealed that this subset exhibited peritumoral localization and underwent immunosuppressive polarization through cholesterol-coordinated CX3CL1-CX3CR1 signaling. Colon cancer-specific lipid metabolic rewiring elevates glycerophospholipid and cholesterol flux, with PLA2G7-mediated glycerophospholipid catabolism promoting CX3CR1 expression in TAMs. Thus, the CX3CR1 signaling-driven immunosuppressive effect of CD168+ TAM is an integrated response to tumor-specific metabolic features. Targeting the CD168+ TAMs may enable therapeutic strategies for metabolic-immune reshaping in colon cancers.

cancer biology↗

bioRxiv2025

A simple liquid 3D cell culture paradigm models oxidative mitochondrial metabolism of epithelial breast cancer cells with relevance for lung metastases.

Three-dimensional (3D) cell culture systems have emerged as powerful tools for modeling tumor biology in ex vivo settings. However, the diverse array of available 3D culture methods presents challenges in selecting the most appropriate model for specific research questions. This study provides a comparative analysis of breast cancer cells (SUM149, IBC-3, and MDA-MB-468) in the mammosphere culture (SphC) model or an "emboli" culture (EmC) model, which enrich for cancer stem cells and epithelial features, respectively. The EmC model, designed originally for inflammatory breast cancer, is characterized by media viscosity and mechanical rocking of the culture vessel. Notably, cells in EmC showed a distinct and durable reduction in cell proliferation ex vivo while demonstrating increased capacity to establish experimental lung metastases in vivo. Ultrastructural quantitative analysis of electron microscopy images suggested that cells in EmC acquire nuclear and mitochondrial features that resemble those of tumor tissue. Proteomics, single-cell transcriptomics, and metabolic flux analyses showed that cells in EmC and SphC favor mitochondrial oxidative metabolism (OXPHOS) and glycolysis, respectively. EmC rendered cells hypersensitive to OXPHOS inhibition, but more resistant to oxidative stress. Several genes associated with lung metastasis, including ID1, were specifically enriched in EmC. Given the emerging role of OXPHOS in cancer cell survival during dissemination and as established metastases, we propose that the EmC paradigm is a suitable ex vivo model to study signaling pathways relevant for tumor tissue and to assess drug sensitivities and resistance mechanisms of metastatic breast cancer cells ex vivo. SIGNIFICANCEThis study provides an in-depth characterization of a resource-efficient yet powerful 3D culture paradigm to improve the physiological relevance of ex vivo approaches. Applicable to epithelial cancers, this model offers a platform to accelerate the discovery of physiologically relevant signaling pathways and specific cancer cell vulnerabilities.

cancer biology↗