Biology subjects

Sun, Y.

Publications and source records attributed to Sun, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

A generalizable system for antigenic peptide targeting across HLA-I allotypes

T cell receptors (TCRs) and TCR-mimicking antibodies recognize peptide antigens in the context of specific Human Leucocyte Antigen (HLA-I) allotypes, and the extreme polymorphism of the HLA locus limits the breadth of immunotherapy development. Key barriers include divergent molecular surfaces on HLA proteins and differences in the peptide structure. As a result, existing modalities cannot confer therapeutic coverage across patients of divergent genetic backgrounds. Here, we develop an approach which combines a peptide conformational prediction tool, PepPred, with a cross-HLA binding protein engineering system, TRACeR-I1, to outline a generalized framework for developing binders (xTRACeRs) with compatibility across HLA allotypes while maintaining high levels of specificity towards the peptide antigen. We use our system to develop and validate xTRACeRs against clinically relevant, established peptide antigens presented across common alleles within five HLA-A/B/C supertypes2. Cryo-EM structures of xTRACeR-pHLA complexes for an oncofetal antigen from PRAME and a neuroblastoma-specific peptide from PHOX2B reveal effective mechanisms to navigate polymorphic HLA surface residues, and extensive interactions with the peptide. We implemented these two xTRACeRs as Chimeric Antigen Receptor (CAR) T cells and demonstrated their potent killing efficacy and specificity. Overcoming restriction across HLA supertypes lifts a key barrier in HLA-targeted immunotherapy by expanding patient coverage.

synthetic biology↗

bioRxiv2026

An Engineered Halotolerant Chimeric T7 RNA Polymerase for High-Yield, Low-Immunogenicity Synthesis of RNA via Simple Batch Transcription

The rapid advancement of mRNA therapeutics has imposed stringent requirements on both the quality and scalability of in vitro transcription (IVT) products. However, the accumulation of double-stranded RNA (dsRNA) byproducts and 3-terminal heterogeneity during T7 RNA polymerase (T7 RNAP)-mediated transcription can robustly trigger deleterious innate immune responses and compromise translation efficiency. Existing enzyme engineering strategies frequently struggle to reconcile the trade-offs between salt tolerance, volumetric productivity, and product purity. Here, we report a novel engineering strategy for halotolerant T7 RNAP by fusing optimized mutant polymerases with diverse DNA-binding domains (e.g., Sso7d, MC1). This approach orchestrated the development of a series of chimeric T7 RNAP mutants designed to bolster catalytic activity and template selectivity under high-salt conditions while concurrently suppressing RNA-dependent RNA polymerase (RdRP) activity. Our lead chimeric mutants exhibited exceptional salt tolerance and processivity in the presence of up to 270 mM NaCl. Notably, these mutants significantly diminished dsRNA formation to less than 0.001%, while markedly improving transcript integrity and 3 homogeneity, thereby facilitating superior translation efficiency for both linear mRNA and circular RNA (circRNA). Crucially, this heightened salt tolerance does not necessitate a trade-off in RNA yield, affording broader flexibility for downstream process optimization. In an enzymatic circRNA synthesis system, these mutants enabled a non-fed-batch configuration with high initial rNTP concentrations (15 mM each), resulting in a 50% increase in yield and achieving an unprecedented titer of 15 mg/mL. This research provides a robust enzymological solution that harmonizes quality and productivity for the industrial-scale manufacturing of high-concentration, low-immunogenicity RNA.

genomics↗

bioRxiv2026

AAV-NRF2 protects retinal and choroidal vasculature in a GDF15-dependent manner in an oxidative damage model of AMD

Oxidative stress is proposed to be a driver of age-related diseases. Age-related macular degeneration is one such disease, where the retinal pigment epithelium (RPE) is affected early in the disease. Vasculature damage also occurs, sometimes preceding RPE damage. To model some aspects of dry AMD, we used the NaIO3 mouse model of oxidative damage. Disruption of the deep retinal vascular plexus, disorganization and death of capillaries within the choriocapillaris, and marked electroretinographic decline were observed. AAV overexpressing the transcription factor, NRF2, which induces anti-oxidation enzymes and represses inflammation, was tested for protection of damage. The BEST1 promoter limited expression to the RPE. The RPE, photoreceptors, and vascular architecture in both retinal and choroidal compartments were protected. Conditioned medium from RPE-choroid explants, infected by AAV8/BEST1-NRF2, was sufficient to transfer partial protection in vivo, indicating that NRF2 induces a protective secreted factor(s). Analysis of RNA-seq data identified growth differentiation factor 15 (GDF15) as a candidate downstream mediator. Injection of recombinant GDF15 reproduced key protective phenotypes in vivo, whereas Gdf15-deficiency attenuated NRF2-mediated rescue. Pharmacologic inhibition of TGF-{beta} receptor signaling diminished NRF2 associated protection, supporting involvement of this signaling pathway. In a laser-induced choroidal neovascularization model, intravitreal GDF15 injection reduced fluorescein leakage and lesion size. These findings support a model in which NRF2 activation in the RPE induces expression of GDF15, which is capable of protecting the RPE, photoreceptors, and the retinal and choroidal vasculature. NRF2 and GDF15 have therapeutic potential for ocular diseases, as well as for other diseases with vascular pathology.

cell biology↗

bioRxiv2026

Co-expression of IBDV VP2 and H9N2 HA by recombinant HVT induces high protection against both pathogens in chickens

Infectious bursal disease virus (IBDV) and H9N2 avian influenza virus (AIV) are significant global threats to poultry health and production. While IBDV induces severe immunosuppression, undermining host defense and vaccine efficacy, H9N2 AIV is characterized by widespread prevalence, persistent shedding, and substantial economic losses. Conventional inactivated vaccines often fail to elicit robust cellular immunity and necessitate multiple booster doses, underscoring the urgent requirement for advanced multivalent vaccination platforms. To address this, we developed a recombinant herpesvirus of turkey (rHVT BAC-VP2-HA) using a bacterial artificial chromosome (BAC) vector system, engineered to co-express the major protective antigen VP2 of IBDV and the hemagglutinin (HA) of H9N2 AIV. Genetic stability and in vitro characterization confirmed that the recombinant exhibited replication kinetics and plaque morphology comparable to parental HVT, with stable antigen expression. In SPF chickens, rHVT BAC-VP2-HA induced strong humoral immune responses against both target antigens, comparable to those elicited by a commercial inactivated vaccine. Crucially, the recombinant virus significantly enhanced cellular immunity, evidenced by markedly elevated CD3+CD8+ T cell responses. Upon challenge, the recombinant conferred high clinical protection (86%) against virulent IBDV, significantly ameliorating bursal pathology and reducing viral loads. Notably, it provided complete (100%) protection against H9N2 AIV, effectively abolishing viral shedding and suppressing viral replication in respiratory tissues. These results demonstrate that rHVT BAC-VP2-HA is a safe and efficacious candidate capable of eliciting humoral and cellular immune responses, offering a promising strategy for the integrated control of major poultry diseases. ImportanceInfectious bursal disease virus (IBDV) and H9N2 avian influenza virus (AIV) are major pathogens that frequently co-circulate in poultry, where IBDV-induced immunosuppression compromises the efficacy of vaccination against other infectious diseases. Conventional inactivated vaccines primarily induce humoral immunity and are often insufficient to prevent viral shedding or provide broad protection against multiple pathogens. In this study, we developed a recombinant herpesvirus of turkeys (HVT) vaccine co-expressing the IBDV VP2 and H9N2 HA antigens and demonstrated that it induces both robust antibody responses and enhanced CD8+ T cell immunity. Notably, this vaccine not only provided effective protection against IBDV but also completely prevented viral shedding following H9N2 challenge. These findings highlight the advantage of HVT-vectored multivalent vaccines in eliciting balanced immune responses and controlling virus transmission, providing important insights for the development of next-generation vaccines against immunosuppressive and respiratory viral co-infections in poultry.

microbiology↗

bioRxiv2026

Bridging LLM Reasoning and Chemical Knowledge via an Evolutionary Multi-Agent Framework for Molecular Synthesis

MotivationMolecular design faces the dual challenge of navigating a vast chemical space while ensuring experimental synthesizability. Traditional models are constrained by small datasets, restricting their scalability and broader chemical context. In contrast, Large Language Models (LLMs) encapsulate extensive synthesis protocols derived from vast scientific literature, yet they struggle to leverage this potential due to severe hallucinations and a superficial grasp of rigorous chemical logic. ResultsWe propose EvoSyn, an evolutionary multi-agent framework that synergizes LLM reasoning with domain experts for preference-aware molecular synthesis. EvoSyn orchestrates a dual-process evolutionary paradigm: a co-evolving process that collaboratively aligns linguistic capabilities with multi-objective constraints, and a self-evolving process formulated as a Markov Game. Through evolution and reinforcement learning, agents actively learn from mistakes, utilizing domain feedback to penalize invalid proposals and ground generation in feasible reaction pathways. Extensive evaluations on comprehensive benchmarks demonstrate that EvoSyn significantly outperforms state-of-the-art baselines. These results highlight that by integrating LLM-guided self-evolution with rigorous domain validation to mitigate hallucinations, EvoSyn effectively yields molecules that are both bioactive and synthetically actionable. Availability and implementationImplementation code is available as supplementary material. Contactyangyd25@mail.sysu.edu.cn Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2026

Salvianolic acids are natural senolytics and increase lifespan in old age

Cellular senescence plays a critical role in chronological aging and is implicated in the onset and progression of multiple age-related disorders. Targeting senescent cells represents a promising strategy to reduce disease burden and improve healthspan. Here we report the senotherapeutic properties of salvianolic acid (SA) family members, specifically A (SAA), B (SAB) and E (SAE). From a natural medicinal agent library, we identified selective cytotoxicity of these SA compounds against senescent cells across diverse senescence types and cell lineages. Mechanistically, SAA, SAB and SAE enhance ROS production and target glutathione S-transferase Pi1 (GSTP1), a redox homeostasis modulator, inducing both apoptosis and ferroptosis in senescent cells. Incorporation of SAs into chemotherapeutic regimens enhanced anticancer efficacy and prolonged post-treatment survival. Intermittent SA administration improved physical function and increased healthspan and lifespan in aged mice. Collectively, our study establishes SAs as an emerging class of natural senolytics (phenolic acids) with the capacity to delay aging and alleviate age-related pathologies in advanced life.

cell biology↗

bioRxiv2026

Foxp4+ Mandibular Skeletal Stem Cells Orchestrate Bone/Tooth Development and Regeneration

The identity of stem/progenitor cells that drive mandible/tooth development and regeneration remains poorly understood. Here, we show that cranial neural crest-derived Foxp4+ mesenchymal cells condense to form Meckels cartilage, and simultaneously promote mandible development and tooth germ formation. In postnatal mandibles, Foxp4+ cells localize in the endosteum, periosteum and dental pulp, which undergo osteogenesis and odontogenesis under steady state, as well as chondrogenesis during fracture repair. Importantly, transplantation of embryonic or adult Foxp4+CD200+CD105- mandibular skeletal stem cells (mdSSCs) generate ectopic bone and tooth. In contrast, genetic ablation of Foxp4+ cells severely impairs mandible/tooth development and delays fracture healing. Mechanistically, we find that primary cilia critically regulate mdSSC maintenance and differentiation into bone and tooth. FOXP4+PDPN+CADM1+ mdSSCs also exist in adult human mandible, which generate ectopic bone and intact tooth upon transplantation into immunodeficient mice. Taken together, we identify Foxp4+ mdSSCs with potential therapeutic applications in regenerating mandibular bone and tooth.

cell biology↗

bioRxiv2026

Metabolic dehalogenation of halomethanes by mercury methylators

Mercury (Hg) methylators play key roles in the global Hg cycle. Nonetheless, the Hg methylators are widely present in Hg-absent environments and the Hg methylation is a cometabolic process without cell growth, which leave the origin and evolution of the Hg methylation as a mystery. Here, we reported the CCl4/trihalomethane-to-dihalomethane dehalogenation by model Hg methylators in a metabolic way. Heterologously-expressed HgcAB catalyzed both the CCl4 dechlorination and Hg methylation. Halomethanes were shown to sustain the Hg-methylation community without adding external carbon source, electron donor and acceptor. Metadata analyses suggested the halomethane dehalogenation potential of Hg methylators at the global scale. These results, together with much higher global flux and kinetic Vmax of the metabolic halomethanes dehalogenation relative to the co-metabolic Hg methylation, suggested halomethanes as the potential HgcAB substrates for the evolution of Hg methylation.

microbiology↗

bioRxiv2026

Pathogen-induced formation of a nascent organelle derived from mitochondria

Intracellular pathogens extensively remodel host cells to create environments that support their survival and replication. How pathogens manipulate host organelle biology to promote infection remains a central question in microbial pathogenesis. Here we show that the human parasite Toxoplasma gondii induces the biogenesis of acidified compartments derived from host mitochondria that promote parasite growth. Following infection, host mitochondria shed large structures positive for outer mitochondrial membrane (OMM), termed SPOTs. SPOTs matured into multivesicular compartments that engulfed cytosolic protein and functional lysosomes. The acquisition of host lysosomes by SPOTs required host ESCRT machinery and the parasite effector TgGRA7, and drove the acidification of the SPOT lumen. Disrupting SPOT acidification impaired parasite proliferation, implicating SPOT maturation in parasite fitness. These findings show that an intracellular pathogen co-opts host machinery to drive the formation of a nascent organelle derived from mitochondria, and raise the possibility that mitochondria can be reprogrammed to generate new organelles with specialized functions. One-Sentence SummaryAn intracellular pathogen hijacks host mitochondrial membranes and ESCRT machinery to generate an acidified organelle that supports parasite replication.

microbiology↗

bioRxiv2026

SpaFlow depicts the dynamics of ligand-receptor interaction in spatial transcriptomics data

Spatial transcriptomics (ST) enables the study of cell-cell communication in native tissue context, but current methods for the ligand-receptor interaction (LRI) inference generally rely on static, distance-based assumptions. Here we present SpaFlow, a reaction-diffusion framework that models ligand diffusion, binding, dissociation, production and degradation to infer spatially resolved LRI activity and hotspots from ST data. Across paired 10x Visium and CosMx metastatic renal cell carcinoma datasets, SpaFlow outperformed existing methods in recovering spatially coherent LRIs, with inferred LRI activity showing stronger association with downstream signaling. In hepatocellular carcinoma after neoadjuvant immunotherapy, SpaFlow identified CXCL12-CXCR4 hotspots enriched at immune-rich tumor boundaries in responders. In aging mouse heart, SpaFlow resolved niche-specific pro-fibrotic and senescence-associated signaling, highlighting Postn-Itgav/Itgb5 as an additional pro-fibrotic axis and Angptl2-Pirb as a candidate mediator of inter-niche senescence-related communication. In human idiopathic pulmonary fibrosis lung, SpaFlow localized CXCL12-CXCR4 signaling between adventitial fibroblasts and CD4 T cells, CD8 T cells, and B cells in the fibrotic surrounding regions. Together, SpaFlow provides a physically informed framework for quantifying spatially constrained cell-cell communication and mechanistically interpreting signaling patterns in complex tissues.

bioinformatics↗

bioRxiv2026

Application of a High-Biomimetic Tumor Organoid-CAF Co-Culture Model for the Efficacy Evaluation of CAR-T Drugs

The tumor microenvironment (TME) is a complex ecosystem composed of tumor cells, cancer-associated fibroblasts (CAFs), immune suppressive cells, and the extracellular matrix (ECM), playing a crucial role in tumor development and CAR-T cell therapy efficacy. CAR-T therapy has shown promise in hematological malignancies but faces challenges in solid tumors due to the TMEs ability to suppress CAR-T cell infiltration, proliferation, and cytotoxicity. Traditional drug evaluation models, such as 2D cell cultures and animal models, have significant limitations due to oversimplification of the in vivo environment or physiological differences between species. Organoid models offer a more biomimetic approach but often fail to fully recapitulate the TMEs complexity and heterogeneity. Our research developed a tumor organoid and CAF co-culture model using the IBAC co-culture chip, demonstrating that CAFs significantly impact CAR-T cell therapy efficacy by forming physical (e.g., fibronectin) and chemical (e.g., IL-10) barriers that prevent CAR-T cell infiltration and cytotoxicity. This model provides a high-biomimetic platform for investigating the TMEs effects on CAR-T therapy and highlights the importance of incorporating a comprehensive stromal component into in vitro models to enhance their predictive power for cancer treatment.

cell biology↗

bioRxiv2026

Application of Engineered NK-92 Cell Extracellular Vesicles in the Treatment of Systemic Lupus Erythematosus

IntroductionSystemic Lupus Erythematosus (SLE) is a chronic autoimmune disease characterized by loss of immune tolerance, autoantibody production, and multi-organ damage. Current therapies, including glucocorticoids and CAR-T/CAR-NK cell therapies, are limited by adverse effects, high cost, and safety concerns. ObjectivesTo develop engineered NK-92 cell-derived extracellular vesicles displaying CD19 single-chain variable fragment (V-CD19-Exo) and evaluate their therapeutic efficacy in an MRL/lpr mouse model of SLE. MethodsThe CD19scFv-LAMP-2B fusion construct was stably expressed in NK-92 cells via lentiviral transduction. Extracellular vesicles were isolated by differential centrifugation and characterized by NTA, TEM, and Western Blot. In vivo efficacy was assessed in MRL/lpr mice through B cell depletion analysis, renal function monitoring, cytokine profiling, autoantibody detection, and survival observation. ResultsV-CD19-Exo significantly reduced splenic CD19{square}CD20{square} B cells from 10.53% to 1.51% (p < 0.0001). Treatment attenuated proteinuria, ameliorated lupus nephritis pathology, reversed splenomegaly, and downregulated serum IgE, IL-17A, IFN-{gamma}, anti-dsDNA, and ANA levels. Notably, V-CD19-Exo improved survival to approximately 80% compared to 25% in untreated controls. ConclusionEngineered NK-92 cell-derived extracellular vesicles represent a novel, safe, and effective cell-free therapeutic strategy for SLE, offering advantages over conventional cell therapies including lower immunogenicity, scalable production, and no requirement for lymphodepletion.

synthetic biology↗

bioRxiv2026

FABP4 Couples Lipid Metabolism to PD-L1 Stabilization in Immunosuppressive Macrophages

Metabolic dysregulation in obesity reshapes immune function, but how lipid signals drive immune suppression remains unclear. Here, we identify a FABP4-PD-L1 axis that links lipid metabolism to immune checkpoint regulation in monocytes and macrophages. Single-cell transcriptomics revealed a distinct FABP4high immunosuppressive macrophage subset enriched under high-fat diet (HFD) conditions, characterized by impaired antigen presentation and elevated PD-L1 expression. Mechanistically, palmitic acid (PA) induces FABP4 and promotes PD-L1 palmitoylation, leading to its stabilization on the cell surface independent of transcriptional regulation. FABP4 is essential for this process, which enables PD-L1 surface stabilization, immunosuppression and mammary tumor progression. In humans, a conserved CD14intCD16 monocyte population exhibits elevated FABP4-PD-L1 signaling and correlates with obesity and invasive breast cancer. These findings establish PD-L1 as a metabolically regulated protein and reveal a mechanism by which lipid excess drives immune evasion, suggesting that targeting FABP4 may enhance responses to immune checkpoint blockade. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/717546v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1fe3f2corg.highwire.dtl.DTLVardef@e587a7org.highwire.dtl.DTLVardef@12d0f75org.highwire.dtl.DTLVardef@151f916_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIFABP4 defines a lipid-responsive, immunosuppressive monocyte/macrophage subset C_LIO_LIFABP4 links lipid sensing to PD-L1 expression in macrophages C_LIO_LIFABP4 enables palmitic acid-dependent PD-L1 palmitoylation and stabilization C_LIO_LIFABP4-PD-L1 signaling correlates with obesity and invasive breast cancer in humans C_LI

immunology↗

bioRxiv2026

Survey of Climate-structured Mycobiomes in Staple Maize: Implications for Endemic Keshan and Kashin-Beck Diseases

Keshan disease (KD) and Kashin-Beck disease (KBD) are geographically restricted disorders in rural China with overlapping environmental and dietary risk factors. Selenium deficiency alone cannot explain their regional heterogeneity. Maize, a dietary staple in endemic areas, represents a key exposure pathway for climate-sensitive foodborne fungi and their metabolites. We profiled maize-associated fungal communities from seven villages across KD-, KBD-, KD-KBD co-endemic, and non-endemic regions using ITS sequencing and integrative bioinformatics. Fungal diversity, composition, trophic structure, and predicted biosynthetic gene cluster potential differed markedly among regions. KD-endemic areas were enriched in saprotrophic taxa such as Penicillium and Aspergillus, KBD-endemic regions favored cold- and humidity-adapted fungi, and KD-KBD co-endemic areas exhibited the highest predicted mycotoxin potential. Fungal patterns were strongly associated with regional temperature and humidity. These findings support a climate-sensitive, foodborne exposome framework, suggesting that variation in maize-associated fungi may contribute to endemic disease risk and highlighting the need for fungal surveillance in public health strategies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/716289v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@2cf23borg.highwire.dtl.DTLVardef@d31e5aorg.highwire.dtl.DTLVardef@6dbcadorg.highwire.dtl.DTLVardef@7e0734_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2026

Generating and navigating single cell dynamics via a geodesic bridge between nonlinear transcriptional and linear latent manifolds

Time-series single-cell RNA sequencing (scRNA-seq) captures cellular processes as sparse and unpaired snapshots, limiting our ability not only to reconstruct continuous cell state transitions, but also to navigate between states in a controlled and interpretable manner. Here we present GeoBridge, a framework modeling cellular dynamics as geodesic trajectories on the transcriptional manifold based on isometric geodesic theory. By learning the geodesic bridge mapping, the method theoretically and computationally transforms time-varying nonlinear transcriptional geodesics (original nonlinear manifold) into constant-velocity straight-line geodesics (latent linear manifold). In the learned geodesic space, continuous interpolation becomes biologically meaningful, enabling reconstruction of unobserved intermediate states and efficient navigation between distinct cellular phenotypes at a single-cell resolution. By mapping interpolated trajectories back to the original gene expression space, GeoBridge recovers smooth transcriptional programs that are robust to noise and snapshot sparsity. Leveraging the derived geodesic potentials, GeoBridge further infers pseudo-temporal trajectories with superior fidelity compared to mainstream approaches from single-snapshot scRNA-seq data without temporal annotation, and directly identifies genes that drive progression along transition paths. We demonstrate the utility of GeoBridge across diverse systems, where GeoBridge resolves EMT-MET progression in cancer stem cells and identifies stage-specific modules as well as the branching cell-fate dynamics in human pluripotent stem cells with higher reconstruction accuracy than state-of-art methods. More importantly, GeoBridge supports single-cell fate navigation in multi-target hematopoietic lineages, allowing neutrophil-biased cells to be virtually guided toward mast-cell fates along biologically plausible paths. Together, GeoBridge establishes a principled method that transforms sparse single-cell measurements into a continuous, controllable landscape for the reconstruction, navigation and manipulation of cellular state transitions.

bioinformatics↗

bioRxiv2026

Hierarchical Assembly of Native Cytoplasmic Lattices Revealed by Cryo-EM

Oocytes depend on maternal factors for maturation and early embryogenesis. Cytoplasmic lattices (CPLs) are distinctive fibrillar structures in mammalian oocyte cytoplasm implicated in maternal factor storage and developmental competence, yet their molecular composition and architecture remain elusive. Here, we use cryo-electron microscopy to resolve the high-resolution structure of native mouse oocyte CPLs. We identify 14 intrinsic components of multiple copies that assemble into filaments in which PADI6-mediated self-assembly and two subtypes of subcortical maternal complexes (SCMCs) form the core scaffold. Unexpectedly, we discover that /{beta}-tubulin dimers and two autoinhibited ubiquitination modules (UHRF1-UBE2D3, SKP1-FBXW18) are internal components of CPLs. We also uncover multivalent interactions that organize adjacent CPL filaments into higher-order helical bundles. By integrating CPL structure with biochemical and proteomic data, we propose a hierarchical assembly mechanism of CPLs, from subcomplexes to filaments to supramolecular lattices. Our study offers mechanistic insights into how maternal proteins are spatially organized to ensure successful early embryonic development and provides a structural foundation for understanding female infertility related to CPL-associated gene mutations.

developmental biology↗

bioRxiv2026

SnakeHichipTF reveals transcription factor logic underlying enhancer-promoter wiring in the human brain

Enhancer-promoter interactions are a central feature of gene regulation, yet the regulatory logic that governs their selective formation in complex tissues remains poorly understood. To address this gap, we developed SnakeHichipTF, a reproducible and scalable framework that integrates multi-engine HiChIP analysis with AI-based footprinting to decode the transcription factor (TF) logic underlying enhancer-promoter wiring. Applying SnakeHichipTF to HiChIP datasets from the human Middle Frontal Gyrus (MFG) and Substantia Nigra (SN), we identified distinct region-biased enhancer interactions associated with differential gene expression. MFG-biased interactions were enriched for cognitive and psychiatric associated GWAS traits, whereas SN-biased interactions preferentially intersected lipid and metabolic trait architectures. Integration of TF footprinting revealed that these region-biased interaction networks are governed by distinct TF programs: MFG-biased interactions preferentially recruited TFs linked to neuronal signaling and transcriptional activation, whereas SN-biased interactions were associated with metabolic and stress-responsive regulators. Interestingly, MFG-biased regulatory interactions were significantly enriched for Human Accelerated Regions (HARs), and HAR-associated genes showed elevated expression in humans relative to non-human primates, indicating that cortical enhancer wiring is embedded within evolutionarily modified regulatory elements. Together, by linking 3D chromatin architecture, TF logic, genetic risk, and evolutionary regulatory elements, SnakeHichipTF provides a general framework for dissecting the mechanistic basis of spatial gene regulation.

genomics↗

bioRxiv2026

SPTBN2 promotes an immunosuppressive tumor microenvironment and cross-resistance to anti-cancer therapies

Immunosuppressive tumor microenvironment (TME) inactivates CD8+ cytotoxic lymphocytes (CTLs). Here, we identify SPTBN2 spectrin as a key immunosuppressive regulator induced in CTLs in response to nutritional deficit. In human pancreatic and colorectal cancers, SPTBN2 expression negatively correlated with CTL infiltration and patients survival. In TME of mouse pancreatic and colorectal adenocarcinomas, SPTBN2 inactivated intratumoral CTLs, stimulated tumor growth and conferred cross-resistance to anti-cancer therapies. SPTBN2 knockout protected CAR T-cells from trogocytosis and increased their memory state. SPTBN2 maintained levels of cell surface proteins such as BTLA that undermine CAR T-cell cytotoxicity and promote exhaustion. Re-expression of BTLA largely reversed phenotypes in SPTBN2-deficient CAR T-cells. In manufactured CAR T cells, SPTBN2 was associated with their clinical failure in pediatric patients with leukemia. Accordingly, ablation of SPTBN2 in CAR T-cells increased their cytotoxicity, in vivo persistence and therapeutic effects indicating that SPTBN2 can be targeted to increase the efficacy of anti-cancer therapies.

cancer biology↗