Biology subjects

Wu, C.

Publications and source records attributed to Wu, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Tumor-derived stearic acid induces macrophage Egr2 signaling to suppress anti-tumor immunity in breast cancer

BackgroundMacrophages in breast cancer are highly heterogeneous and targeting both tissue-resident and bone marrow-derived macrophages represents a high-potential strategy in breast cancer immunotherapy. MethodsMyeloid-specific Egr2 knockout (KO) mice were used to determine roles of macrophage Egr2 signaling in tumor progression and anti-tumor immune responses. RNA-seq analysis and Flow cytometry were used to examine regulation of Egr2 in tumor-associated macrophages (TAMs) and fatty acid-stimulated macrophages. Tumor cell and macrophage admixture study was used to evaluate effects of fatty acid educated macrophages on anti-tumor responses. ResultsHere we showed that early growth response 2 (Egr2) was highly expressed in mammary tissue macrophages and recruited macrophages upon tumor progression. Depletion of Egr2 in myeloid cells significantly decreased the immunosuppressive function of polarized M2-like macrophages and TAMs. Tumor progression was delayed in myeloid cell Egr2 knockout mice, which was associated with enhanced function of effector CD8+ T cells and NK cells. Mechanistically, we showed that retinol and nicotinamide metabolism in TAMs were impaired after Egr2 depletion. Further, tumor cell-derived stearic acid (SA) was identified as an important fatty acid inducing Egr2 expression. SA stimulation induced macrophage-mediated immunosuppression in an Egr2 dependent manner. Addition of oleic acid (OA) uniquely repressed SA-induced Egr2 expression and immunosuppressive activity in macrophages. ConclusionsOur study thus uncovers a novel SA-Egr2 pathway driving macrophage immunosuppression and novel molecular mechanism of OA mediated anti-tumor effect. WHAT IS ALREADY KNOWN ON THIS TOPICLipid-associated macrophages (LAMs) accumulate lipids and promote immune suppression, tumor growth and metastasis in breast cancers. Fatty acids play a dual, complex role in tumor immunity, acting as both pro-tumorigenic and anti-tumorigenic effects. However, molecular mechanisms underlying fatty acid modulated macrophages and their roles in tumor remain not fully elucidated. WHAT THIS STUDY ADDSWe demonstrate that Egr2 is essential for the immunosuppressive function of IL-4 polarized M2-like macrophages and TAMs. Tumor cell-derived stearic acid (SA) was identified as an important fatty acid inducing Egr2 expression and immunosuppression in macrophages. Adding oleic acid (OA) uniquely repressed SA-induced Egr2 expression and immunosuppression. HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYSA-Egr2 axis is a novel pathway driving macrophage immunosuppression. OA treatment enhances macrophage anti-tumor immunity via inhibiting Egr2 signaling and immunosuppression. The data supports the notion that diets enriched in OA may have potential for prevention and suppression of breast cancer.

immunology↗

bioRxiv2026

Supramolecular hydrogel viscoelasticity regulates in situ tertiary lymphoid neogenesis

Tertiary lymphoid structures (TLSs) are organized three-dimensional immune niches associated with improved antitumor immunity, which has galvanized efforts to induce them artificially using biomaterials. However, these strategies have largely focused on soluble cue delivery, leaving the role of scaffold physical properties poorly understood. Here, we developed injectable, liposome-crosslinked supramolecular hydrogels spanning soft and stiff formulations to determine how scaffold mechanical properties regulate in situ tertiary lymphoid neogenesis. The formulations differed in their viscoelastic properties while maintaining broadly comparable release of ovalbumin and LIGHT. Soft hydrogels underwent distributed cellular infiltration and material replacement, transitioning from an early myeloid-rich response to vascularized, lymphoid-dominant tissues containing B-cell-rich aggregates adjacent to T-cell regions, with B-cell organization peaking at day 14. Single-cell RNA sequencing revealed that transient interferon-associated neutrophil and macrophage states in the early niche preceded the emergence of TLS-associated transcriptional programs across lymphoid and myeloid populations. In contrast, stiff hydrogels resisted infiltration and perpetuated a niche dominated by activated myeloid cells with limited lymphoid organization. Prophylactically implanted soft hydrogels improved early melanoma control relative to stiff hydrogels under checkpoint blockade, and a single soft-hydrogel implantation restrained tumor growth even without checkpoint blockade. Together, these findings establish scaffold mechanics and remodeling as active regulators of engineered immune-tissue organization and provide design principles for directing the development of local TLS-like niches.

bioengineering↗

bioRxiv2026

A Minimally Invasiveness Hybrid Brain-Computer Interface: A Distributed, Scalable and Evolvable Architecture for Whole Brain Access

Brain-computer interfaces face a fundamental trade-off between the signal fidelity and stimulation precision of noninvasive systems and the surgical burden and scalability of invasive systems. Non-invasive BCIs suffer from low signal quality and poor stimulation accuracy due to the skull barrier and the variability introduced by the scalp and skull. Existing invasive BCIs rely on traumatic surgical procedures or brain-penetrating electrodes, which limits their spatial extensibility, application, and patient acceptance. Here, we introduce a minimally invasive hybrid BCI architecture that uses the skull as a distributed interface layer rather than treating it solely as a barrier. The hybrid BCI comprises four integrated components: (1) the safe and smart micro-hole craniotomy; (2) distributed microelectrodes subcutaneously implanted in micro-holes in the skull with the distal end in contact with the dura; (3) an external bi-directional wearable headset for coupling, recording, stimulation, and channel selection; and (4) an AI-assisted planning and control agent. Animal studies have shown that micro-holes with a diameter of 300-800 m can be safely and conveniently prepared at any predefined locations across the skull without impairing the dura. In vivo experiments on rats demonstrate that the hybrid BCI with skull-implanted microelectrodes evidently increases resting-state spectral power and improves the signal-to-noise ratio of somatosensory and steady-state visual evoked responses compared to the scalp EEG; the computational modelling shows that distributed skull-dura microelectrodes can increase the intracranial electrical field strength and steer focused temporal-interference fields towards predefined deep brain targets. These findings will lay a solid foundation for future endeavors in wireless integration, safety evaluation and clinical benefits of the hybrid BCI. In summary, we propose the hybrid BCI as a distinct minimally invasive BCI paradigm with the great potential as a distributed, scalable, and upgradable neural interface that can expand the clinical application of minimally invasive BCI techniques.

bioengineering↗

bioRxiv2026

LeafRank: A phylodynamic framework for inferring relative fitness from single-cell phylogenies in chromosomally unstable tumors

Tumors contain cancer cells with diverse growth potentials that shape evolutionary trajectories, yet this fitness diversity remains difficult to quantify in cases of whole-genome duplication (WGD) and chromosomal instability. We present LeafRank, a mathematical framework that leverages single-cell DNA-seq phylogenies to infer the relative fitness of individual cells. Using a multi-type branching process model, LeafRank integrates full tree topology, including branch lengths and bifurcation patterns, to estimate marginal fitness probabilities under punctuated evolutionary regimes driven by rare driver events. To account for elevated aberration rates following WGD, we introduce a tree-rescaling strategy that adjusts for lineage-specific genomic instability. Unlike methods focused on predefined subclones, LeafRank ranks all sampled cells, enabling flexible assessment of growth heterogeneity. Simulations demonstrate high accuracy across spatial and non-spatial virtual tumors. Applied to ovarian cancer, LeafRank reveals directional and parallel selection in WGD tumors and identifies recurrent copy number events enriched in high-fitness lineages. WGD lineages do not show immediate growth advantages but acquire fitness through subsequent alterations.

bioinformatics↗

bioRxiv2026

In situ structural basis for the LHCSR3-mediated photoprotection of photosystem II

Energy-dependent quenching (qE) represents a critical mechanism for photosynthetic organisms to mitigate photodamage caused by excessive light. In green algae, LHCSR3 protein plays a central role in qE, activated by thylakoid lumen acidification and associated with photosystem II (PSII) to dissipate excess energy. Despite extensive efforts, the assembly and energy dissipation mechanisms of PSII-LHCSR3 have remained unknown. Here, we present the in situ structures of the PSII supercomplex embedded in the native thylakoid membranes of Chlamydomonas reinhardtii in both quenched (LHCSR3-bound) and unquenched (LHCSR3-free) states at near-atomic resolutions. Our results demonstrate that in high-light-acclimated cells, LHCSR3 binds to PSII peripheral antenna CP26 and associates with an extra LHCII trimer (eLHCII). Structural comparison of LHCSR3 with other light-harvesting complexes reveals possible protonation-induced conformational changes in LHCSR3 and rearrangements of its two pigment clusters, which potentially serve as quenching sites to dissipate excess energy transferred from CP26 and eLHCII. Our findings provide a direct visualization of how photoprotection is spatially organized in vivo and have implications for engineering natural and artificial photosynthetic systems with more dynamic photoprotection.

plant biology↗

bioRxiv2026

CryoGO enables high-resolution structural profiling of endogenous cellular macromolecules

Resolving macromolecular structures within their native cellular environment is essential for connecting molecular architecture to physiological function, yet the field lacks accessible, high-throughput methods for generating suitable specimens from cells. Here, we introduce cryoGO (on-Grid Opening cryo-electron microscopy), a simple, rapid, and scalable strategy that mechanically opens cells directly on EM grids to produce cell-derived specimens for high-resolution single-particle cryo-EM. This approach enables near-atomic structure determination of diverse endogenous macromolecular assemblies spanning a broad molecular-weight range. We show that cryoGO captures the rich ribosomal conformational and compositional landscape while preserving physiological state distributions and aspects of spatial heterogeneity originating from cells. Furthermore, this rapid workflow enables time-resolved structural profiling, capturing both long-term cellular adaptation and acute remodeling on timescales of seconds. Compatible with standard cryo-EM infrastructure and diverse biological samples, while requiring only small numbers of cells, cryoGO lowers the technical barrier to high-resolution native structural biology.

biophysics↗

bioRxiv2026

Boosting carbon fixation and microbial dynamics in the coastal sediment ecosystem through large-scale cultivation of Gracilariopsis lemaneiformis

Microorganisms are the key drivers of carbon cycling in coastal marine sediment ecosystems, significantly influencing carbon storage and release during Gracilariopsis lemaneiformis cultivation. This study employed 16S rRNA sequencing, a high-throughput qPCR chip, and carbon isotope labeling to assess the impact of G. lemaneiformis cultivation on carbon cycling processes in coastal sediments. A comparative analysis was conducted between cultivated zones (GZ) of G. lemaneiformis and adjacent control zones (CZ). The results indicated that macroalgae cultivation significantly modified sediment-seawater exchange dynamics and accelerated carbon cycling within coastal marine sediment ecosystems. Furthermore, G. lemaneiformis cultivation increased the abundance of genes linked to polysaccharide degradation and carbon fixation pathways, thereby enhancing carbon cycling efficiency. The ecosystem multifunctional index, calculated based on carbon fixation gene abundance, was significantly higher in GZ compared to CZ. Incubation experiments using 13C-NaHCO3 demonstrated that cultivation markedly elevated the carbon fixation rate of sediment, emphasizing a higher potential for carbon sequestration in sedimentary environments cultivated with macroalgae. Additionally, cultivation significantly altered sediment microbial communities, simplifying their structural complexity. Key microbial taxa identified via k-core species analysis--including Subgroup10 of Desulfobacterota and MBNT15, correlated strongly with carbon fixation rates, indicating their pivotal roles in sediment carbon cycling processes. This study provides critical insights into how large-scale macroalgae cultivation influences coastal carbon dynamics and informs strategies for optimizing carbon management in aquaculture ecosystems. ImportanceGracilariopsis lemaneiformis cultivation is a widely promoted eco-aquaculture model along Southeast Chinas coast. This study finds it can drastically boost carbon sequestration efficiency in coastal sediments. Through field comparison and isotope tracing, we confirm that key carbon-fixing microbes in farmed sediments show significantly higher activity, with far stronger carbon storage potential than non-farmed zones. This research delivers direct scientific evidence for scaling up macroalgae farming to unlock new blue carbon gains, and offers a practical new solution for optimizing carbon management in aquaculture ecosystems.

microbiology↗

bioRxiv2026

Field–Flow–Front mapping of breast cancer evolutionary dynamics in situ

Tumour progression reflects not only which clones arise but where, when and in what context they expand--dimensions genotype-centred reconstructions leave unresolved. Here we reconstruct breast cancer evolution in situ across 34 Visium HD, 16 Xenium, 32 MIBI-TOF and 10 CODEX samples, serial-section 3D reconstruction, single-cell and bulk transcriptomes, and genome-wide CRISPR dependency profiles. We partition tumours into 296 cancer microzones--stroma-bounded units within which expansion is reconstructed--and define in each a Cancer Progression Metric(CPM) coupling a transcriptomic clock to expansion geometry. Projected onto tissue, CPM yields a Field-Flow-Front model rendering progression as a continuous physical process and resolving subclonal architecture into spatially coherent domains rather than predefined branches. Unexpectedly, the most advanced fronts were not the most proliferative but low-dependency, slow-cycling populations with directional expansion, driven by an extracellular matrix programme whose evolutionary force exceeded inflammation by nearly an order of magnitude yet whose genes were the least cell-autonomous. Under chemotherapy it persisted while its clonal carriers reshuffled, marking a transferable, stroma-coupled front process--not a fixed clone--as the unit of advance. Distilled into an evolutionary advantage load, this front process predicted recurrence and survival across independent cohorts and improved on conventional staging, establishing a tissue-embedded paradigm for mapping tumour evolutionary dynamics, from local fronts to patient outcome.

Cancer Biology↗

bioRxiv2026

A global analysis of climate-driven reversal risks in forests

The integrity of forest-based climate solutions and carbon credits requires persistent carbon storage, but climate change is increasing the risk of natural disturbances that release carbon back into the atmosphere. Using global satellite data, disturbance modeling, and machine learning, we provide the first spatially explicit and scenario-based maps of long-term probability of carbon loss in global forests under different disturbance severities and climate scenarios. We find that North American conifer forests, tropical rainforests, and Asian (sub)tropical dry forests face the greatest risks, and that Eurasian temperate forests, African (sub)tropical dry forests face the lowest. Globally, the likelihood of reversals over 100 years is 31%-42% across all scenarios. Our work helps to maximize the benefits of forest-based climate solutions by informing more strategic project placement and more robust reversal-risk compensation mechanisms, such as buffer pools, and highlights critical additional science to better understand and manage risks of these essential climate solutions. Plain Language SummaryForests can help slow and lessen climate impacts. However, in places this benefit is becoming less reliable as climate change increases natural disturbances such as wildfires, drought, storms, and insect outbreaks, which can release stored carbon back into the atmosphere. In this study, we created the first scenario-based global maps of risks and found that the risk of carbon loss is widespread and highly variable across regions, with especially high vulnerability in North American conifer forests, tropical rainforests, and Asian tropical and subtropical dry forests. Our study highlights the importance of considering disturbance risks when siting forest projects for climate mitigation, and developing protocols for carbon markets, such as in voluntary programs and under the UNFCCC Paris Agreement. Key PointsO_LIA demographic model framework estimates the reversal risk from natural disturbances over 100 years in global forests C_LIO_LISpatially explicit maps under different severity scenarios show variation in the integrated 100-year risk of carbon reversal C_LIO_LISpatially explicit maps estimate the required buffer pool needed to compensate for disturbance-driven reversals in global forests C_LI

ecology↗

bioRxiv2026

Low-Energy Polishing Facilitates Breaking the Resolution Barrier of In Situ Cryo-EM

In situ structural analysis allows direct visualization of protein structures in their native cellular environments, but near-atomic resolution in cellular lamellae has been significantly limited to exceptionally large complexes such as ribosomes. A key factor underlying this limitation is the degradation of data quality of thin lamellae caused by substantial subsurface damage from cryo-focused ion beam (cryo-FIB). Here, we developed a cryogenic low-energy polishing in FIB approach, which reliably produces thin lamellae with low damage across different cell types. This advance, combined with in situ single particles analysis, has pushed down the molecular weight lower limit for in situ reconstruction at near-atomic resolution to [~]400 kDa. We demonstrate this by resolving photosynthetic complexes (3.4 [A] and 3.3 [A]), metabolic enzymes (3.3 [A]), chloroplast ribosome (4.0 [A]) and respiratory chain complexes (3.7 [A]) from Chlamydomonas reinhardtii. Furthermore, the efficient workflow enables rapid structural feedback upon changes in cellular states, offering a practical way to perform multi-condition in situ structural analysis.

biophysics↗

bioRxiv2026

GalaxyVS: Exploring 100-Billion Compounds in Seconds

We present GalaxyVS, a hardware-software co-designed virtual screening framework built to explore the 100-billion commercially accessible chemical space in seconds, deployed at the National Supercomputing Center in Tianjin. Built upon the dense vector retrieval paradigm of DrugCLIP, GalaxyVS bypasses the structural dependencies and computational overhead of classical docking to enable rapid screening against experimentally determined as well as geometrically feasible pockets on AlphaFold-predicted structures. To scale this paradigm to the 100-billion level, the system must overcome the significant computational burden of offline representation encoding, critical memory and I/O bottlenecks during online retrieval, and the risks of diversity collapse and precision loss within final screening results. Utilizing the heterogeneous supercomputing infrastructure, GalaxyVS accelerates the offline encoding through deep operator adaptations and resolves online retrieval bottlenecks via disk-native vector indexing coupled with in-memory staging to ensure both broad accessibility and high throughput. Concurrently, a two-stage refinement protocol effectively mitigates diversity collapse and ensures high-fidelity affinity ranking. Consequently, GalaxyVS achieves a daily scoring throughput of 1.5 x 1016 target-ligand pairs, representing a six-orders-of-magnitude leap over previous supercomputing records. Driven by this throughput, we screened nearly 100,000 protein structures across six species against the 100-billion compound library in just 16 hours. The resulting comprehensive cross-species interaction landscape, GalaxyDB, will be openly released at https://galaxyvs.drugclip.com.

bioinformatics↗

bioRxiv2026

Magnetically guided macrophage immunobots coordinate iron-metabolic cascades and immunogenic ferroptosis for tumor immunotherapy

Adoptive cell therapy (ACT) remains challenging in solid tumors, where poor tumor infiltration, metabolic heterogeneity, and an immunosuppressive tumor microenvironment (TME) constrain therapeutic efficacy. Here, we developed a magnetically actuated macrophage-based immune microrobot (immunobot) for active solid tumor immunotherapy. Immunobots were constructed by loading bone marrow-derived macrophages (BMDMs) with lipopolysaccharide-modified Janus L1-FePt magnetic microrollers (LMRs), enabling hard-magnetic actuation. Optimized LMR loading supported robust propulsion, retention under flow, and enhanced barrier penetration. LMRs further promoted M1-like polarization through LPS-driven inflammatory activation and FePt-derived labile iron-amplified oxidative stress, with altered iron homeostasis, increased reactive oxygen species (ROS), and enhanced NF-{kappa}B signaling. Immunobots also induced ferroptosis-associated immunogenic cell death in tumor cells. In vivo, magnetically guided immunobots suppressed tumor growth, reprogrammed tumor-associated macrophages (TAMs), promoted dendritic cell maturation, and enhanced CD8 T cell activation. This work establishes a microrobotic immunotherapy platform for active magnetic transport, iron-metabolic regulation, and immune remodeling in solid tumors.

bioengineering↗

bioRxiv2026

Protonated Structure of EmrE Reveals C-terminal Tail Gating Mechanism

The multidrug efflux pump EmrE is one of the smallest known active transporters and has become a model system for studying multidrug recognition and transport. While recent high-resolution structures have illuminated its dynamic substrate binding pocket, the conformations of its interhelical loops and C-terminal tail, regions critical for controlling proton coupling and gating, remain poorly characterized. Here, we report the high-resolution structure of protonated S64V EmrE determined using solution and solid-state NMR data. This new structural model shows the C-terminal tail occluding the open face of the transport pore, providing a structural basis for how EmrE minimizes proton leak in the absence of substrate. These findings support growing evidence that relatively simple model transporters must leverage an occluded state during alternating access to avoid physiologically unfavorable proton leak.

biophysics↗

bioRxiv2026

Melanin regulates mitochondrial dynamics, metabolism and inflammatory signaling to protect the retina

Albino individuals are clinically recognized to exhibit heightened susceptibility to light-induced retinal injury, yet the cellular and metabolic mechanisms underlying this vulnerability remain poorly defined. Here, we investigated whether retinal pigment epithelium (RPE) pigmentation governs mitochondrial structure, metabolism, and inflammatory responses that ultimately determine retinal resilience to blue light stress. Using pigmented (C57BL/6J) and albino (Balb/c) mice, we demonstrate that albino animals exhibit markedly increased retinal phototoxicity following blue light exposure, manifested by fundus lesions, outer nuclear layer (ONL) disruption, and structural degeneration evident by OCT. Primary RPE cultures derived from albino mice exhibited profound difference in mitochondrial morphology, characterized by increased mitochondrial number, reduced size, and enhanced fragmentation, accompanied by elevated mitochondrial DNA copy number. These structural changes correlated with transcriptional skewing toward mitochondrial fission (increased Drp1) and suppression of mitochondrial fusion (Mfn1, Mfn2, OPA1). Functionally, albino and depigmented RPE displayed impaired oxidative phosphorylation, reduced ATP production, and diminished reliance on mitochondrial pyruvate carrier (MPC)-dependent metabolism. In parallel, albino RPE demonstrated cell-cycle accumulation at G2/M and heightened basal and blue light-induced secretion of pro-inflammatory cytokines, particularly IFN-{beta}1, IL-6, and TNF-. Importantly, exogenous melanin supplementation partially restored mitochondrial fusion gene expression, pyruvate-dependent respiration, and inflammatory restraint. Together, these findings identify melanin as a critical regulator of RPE mitochondrial architecture, metabolic substrate utilization, and inflammatory signaling, providing a mechanistic framework to explain enhanced photo-vulnerability in the albino retina. These insights establish pigmentation-dependent mitochondrial metabolism as a determinant of retinal resilience and suggest mitochondrial bioenergetics as a therapeutic target.

cell biology↗

bioRxiv2026

The Cappuccino interactome reveals an intracellular role for Semaphorin-2a in Drosophila oogenesis

The spatiotemporal regulation of an actin mesh during Drosophila oogenesis is essential for proper localization of cell polarity determinants that establish the future patterning of the embryo. Here, we reveal an unexpected role for Semaphorin-2a (Sema2a) in actin mesh regulation and oogenesis. Sema2a classically functions as a secreted guidance cue that binds its cognate Plexin-B (PlexB) receptor to establish neural circuits. In contrast, we find that Sema2a is expressed inside the germarium, germline, and follicle cells of the developing ovary. Sema2a mutants possess small ovaries that fail to develop past mid-oogenesis. We demonstrate that Sema2a interacts with Cappuccino (Capu), a key actin nucleator crucial for building the actin mesh in Drosophila oocytes. Sema2a inhibits the actin assembly activity of Capu in vitro. Furthermore, genetic interaction between Sema2a and Capu influences mesh density and disrupts oskar mRNA localization. PlexB mutants, however, exhibit wild-type size ovaries with oskar mRNA localization distinct from Sema2a mutants, confirming the non-canonical role of Sema2a in oogenesis. SummaryThis study reveals a novel interaction between the actin nucleator Cappuccino and the typically secreted neural guidance factor Semaphorin-2a. It is shown that Semaphorin-2a inhibits the actin polymerization activity of Cappuccino in vitro and play an intracellular role in oogenesis.

cell biology↗

bioRxiv2026

Integrated analysis of leukemic mutations and transcriptomes at the single-cell level

Single-cell RNA-sequencing-based characterization of cells that belong to the neoplastic clone is a major challenge in hematologic neoplasms, where malignant and normal cells coexist. Confident molecular profiling requires simultaneous analysis of gene expression and genetic mutations in individual cells, an ability that is not supported by the standard 10X Genomics workflow. Here, we systematically evaluated the potential and limitations of repurposing amplified cDNA generated during the 10X Genomics 3' workflow for post-hoc genotyping of individual cells. We first established a mixed leukemic cell line system comprising one cell line with KIT point mutations and another with the BCR::ABL1 fusion gene. Targeted long-read PacBio sequencing enabled post-hoc assignment of mutation data to transcriptionally profiled cells, but recovery differed between targets. Consistent with ambient RNA in microfluidics-based single-cell workflows, mutation-associated transcripts were detected in cells not expected to carry the corresponding mutations, illustrating how transcript recovery complicates cell-level genotype assignment. Target-specific thresholds mitigated this source of misclassification. In primary chronic myeloid leukemia samples, the post-hoc approach detected BCR::ABL1-positive cells at diagnosis, but not during imatinib treatment. Together, we present a framework for adding mutation status to cells already profiled using the 10X Genomics workflow and highlight broader considerations for transcript-based single-cell genotyping.

cancer biology↗

bioRxiv2026

Dissecting inter-focal heterogeneity and convergent immunosuppressive ecosystems in multifocal hepatocellular carcinoma through single-cell and spatial multi-omics

Background Multifocal hepatocellular carcinoma (HCC) comprises spatially separated tumor foci with distinct evolutionary trajectories, posing a major therapeutic challenge. Whether divergent lesions retain shared immune-evasion mechanisms beyond lesion-specific heterogeneity and offer cross-focal therapeutic opportunities remains unknown. Objective To resolve malignant and microenvironmental heterogeneity across tumor foci and identify conserved immunosuppressive programs underlying multifocal HCC progression. Design Matched tumour foci and peritumoural tissues from patients with multifocal HCC underwent integrated single-cell and spatial multi-omics profiling, including scFAST-seq (n=15), scATAC-seq (n=12), and Stereo-seq (n=14). In-house RNA-seq (n=13), public scRNA-seq (HRA001748) and RNA-seq datasets (TCGA-LIHC, OEP000321) were used for validation. Multiplex immunohistochemistry (n=96) and functional assays validated key findings. Results Multifocal HCC exhibited extensive inter-focal heterogeneity in malignant genomic, transcriptional, epigenetic, and evolutionary states, accompanied by diverse immune and stromal landscapes. Despite this divergence, spatially separated tumor foci converged on shared malignant states marked by elevated TMED2 expression and conserved immunosuppressive ecosystems characterized by regulatory T-cell (Treg) and SPP1+/SPRED1+ macrophage enrichment, impaired cytotoxic CD8+ T-cell immunity, and recurrent stromal-vascular remodeling. Mechanistically, malignant hepatocytes engaged SPP1+/SPRED1+ macrophages through C3/C5 complement signaling across divergent tumor foci, while macrophages and Tregs contributed to CD8+ T-cell dysfunction through CD274-PDCD1, CD80/CD86-CTLA4/CD28, and MHC-I-CD8 interactions. A tumor-intrinsic TMED2-ADAR1-dependent A-to-I RNA editing program promoted C3/C5 complement expression and secretion, linking malignant heterogeneity to conserved tumor-immune signaling. Conclusions Despite divergent malignant evolution, multifocal HCC converges on shared immunosuppressive ecosystems. The TMED2-ADAR1-C3/C5 complement axis represents a conserved tumor-immune vulnerability that may enable therapeutic strategies targeting common immune-evasion mechanisms across heterogeneous tumor foci.

cancer biology↗

bioRxiv2026

The cytoplasmic lattice in mammalian eggs sequesters ubiquitination machinery and tubulin in reserve

The cytoplasmic lattice (CPL) in mammalian eggs is essential for early embryonic development, but its molecular components, structural organization, and functional capacity have remained elusive. Here, using cryo-electron microscopy, we show that the CPL filament in mouse eggs contains repeating units with a periodicity of [~]37 nm, and determine its high-resolution, native structure and complete subunit composition. The CPL architecture organizes maternal-effect proteins, ubiquitination machinery, and tubulin into a highly structured reservoir. Maternal-effect proteins form the scaffold of the CPL to sequester a UBE2D-UHRF1 E2-E3 ubiquitination module and three distinct FBXW E3 ubiquitin ligases, notably all in activity-excluded states. The CPL further contains an {beta}-tubulin heterodimer in a GTP-bound state with a calcium ion coordinated to -tubulin, suggesting microtubule assembly-competent tubulin held in reserve. The CPL structure is capped at each end by a terminal unit that lacks a PADI6 dimer, a scaffold component, thereby preventing further oligomerization. Interactions between maternal-effect proteins in adjacent CPL units promote the assembly of a three-dimensional lattice in the egg cytoplasm. Taken together, our work defines how CPL assembly and architecture prime mammalian eggs for ubiquitin-mediated protein degradation and cytoskeletal remodeling during the egg-to-embryo transition.

biophysics↗