Biology subjects

Wang, S.

Publications and source records attributed to Wang, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Epithelial Self-Organization Patterns the Tadpole Oral Disc

Vertebrate epidermal organs are generally patterned through epithelial-mesenchymal interactions, but whether such interactions are essential for all epidermal organs remains unclear. Here we show that the elaborate oral disc of anuran tadpoles arises by partitioning a continuous oral epithelium into developmentally distinct jaw, tooth-row and papilla modules, in the absence of a mesenchymal organizer. Spatially restricted epithelial programs specify, maintain and differentiate these modules, enabling their semi-independent development. Perturbation of lef1, hoxc13, sox7 and pitx2 selectively disrupts individual modules. The resulting module-specific reductions, expansions and rearrangements mirror oral-disc configurations that have evolves repeatedly across anurans. These findings indicate that differential deployment of shared epithelial programs can generates selectable variation in the tadpole oral disc, allowing transient larval feeding structures to diversify independently of adult ecology and enabling tadpoles to exploit diverse ecological niches. Epidermal self-organization can therefore generate structural complexity, promote functional diversification and enhance evolvability in transient vertebrate organs.

developmental biology↗

bioRxiv2026

Linking H3K36me3 to transcriptional dynamics

Genes are transcribed in bursts as they fluctuate between on and off states, in a process modulated by histone modifications. The mammalian histone methyltransferase SETD2 is solely responsible for depositing H3K36 trimethylation, which recruits histone deacetylases and regulates histone occupancy. Nucleosomes are known to act as a barrier to transcription elongation and have been observed to impact elongation rate. H3K36me3 has been associated with long pausing sites in gene bodies and is implicated in reducing speed of successive RNA polymerase II. However, the role of SETD2 and H3K36me3 in transcriptional dynamics are unknown. Here we show upon SETD2 knockout and H3K36me3 depletion in murine C2C12 myoblast cells that overall gene expression is reduced and splicing fidelity affected, as 5' mutually exclusive exons are favoured over 3' ones. Furthermore, transcriptional burst size is reduced, while bursting frequency increased. A simple mathematical model suggests that the observed changes in transcriptional dynamics can be explained by less stringently controlled polymerase pausing in the gene bodies of H3K36me3 depleted cells.

systems biology↗

bioRxiv2026

ZmPMI3 phosphomannose isomerase kinetics is associated with natural variation of watersoluble carbohydrate content in mature maize stem

Mature maize stems accumulate substantial amounts of water-soluble carbohydrates (WSC) providing an accessible carbon pool for industrial bioconversion. However, the genetic factors controlling WSC reserves under field conditions remain poorly resolved. In this study, we quantified total WSC including glucose, fructose, sucrose contents in the internode below the first ear of a genetically diverse maize panel at physiological maturity and associated trait variation with genome-wide SNP data. The panel displayed extensive variation in stem WSCs content, with values ranging up to 50.4 % of dry weight. Genome-wide association mapping identified 20 quantitative trait loci associated with individual sugars or total WSC content. One fructose associated region contained two adjacent gene annotations predicted to encode fragments of a phosphomannose isomerase. Sequence comparison, cDNA amplification and protein structure prediction supported a unified gene model, here designated as ZmPMI3. Biochemical characterization showed ZmPMI3 catalyzes the reversible conversion between mannose-6-phosphate and fructose-6-phosphate, a central reaction in carbohydrate metabolism. Natural protein haplotypes with distinct kinetic properties were identified correlating with significant differences in stem WSC content. Together, these findings identify ZmPMI3 as a candidate contributor to natural variation in maize stem carbohydrate reserves, potentially through altered hexose-phosphate partitioning.

plant biology↗

bioRxiv2026

High temperature ligation enables in vitro assembly of eukaryotic genes

Our ability to efficiently construct synthetic DNA products is essential to studying and engineering biology. There is an abundance of widely adopted DNA assembly technologies suitable for generating synthetic constructs from diverse DNA inputs, but these techniques suffer from low specificity of connection during assembly, which decreases the accuracy, efficiency, and throughput of construction. Here we propose a broadly applicable paradigm for DNA assembly, High Temperature (HighT) assembly, that lowers misconnection rates by ligating complementary single strand DNA overhangs at reaction temperatures significantly higher than their predicted melting temperatures. By expanding the concept of melting temperature to demarcate smaller association fractions of DNA duplexes, we characterize HighT and demonstrate 40 percentage points increase in accuracy, and 4 orders of magnitude increase in yield of transformants when applying the technique to conventional assembly technologies. HighT is then applied to develop cloning pipelines for the development of efficient assembly-to-integration protocols, the construction of specific low-abundance isoforms of medically relevant proteins from human gDNA and oligos, and the de novo construction of a 10 kb, GC rich genomic region from the functionally extinct Northern White Rhinoceros created entirely in vitro.

molecular biology↗

bioRxiv2026

Structural basis for phosphorylation-induced inactivation of the rice ammonium transporter AMT1;1

Ammonium (NH4+) uptake and transport in plants are mediated by ammonium transporters (AMTs), which are tightly regulated by phosphorylation to prevent excess ammonium influx and toxic accumulation. However, the mechanism of phosphorylation-mediated inactivation is unique and remains unclear. Here, we report cryo-EM structures of the rice (Oryza sativa) ammonium transporter OsAMT1;1 in its wild-type and phosphomimetic variant T452D states. OsAMT1;1 forms a stable homotrimer, with conserved motifs affirming a shared transport mechanism within the AMT/MEP/Rh superfamily. Our structural analysis reveals that T452D phosphomimetic stabilizes an intracellular salt-bridge network and maintains the channel in a closed state, in which the ICL5 loop positions the hydrophobic plug residue Leu360 near the cytoplasmic exit to occlude the channel exit and abolish complementation capacity. Our findings elucidate phosphorylation-induced inactivation mechanism for the plant AMT1 subfamily, providing a structural paradigm for the post-translational regulation of nutrient uptake.

biophysics↗

bioRxiv2026

Filling the Missing Puzzle: Integrating Interaction and Evolutionary Information to Enhance Protein Fitness Prediction in Inverse Folding

Protein inverse folding, which infers compatible amino acid sequences from a given backbone structure, is central to rational protein design. Current methods rely largely on sequence recovery rate as the evaluation metric, emphasizing structural compatibility but seldom addressing function. Yet functional activity depends on the proper network of non-covalent interactions-protein-ligand contacts being a prime example. We argue that function-oriented protein design is governed by three complementary constraints: structural, interaction, and evolutionary, none of which are handled in a unified manner by existing pretrained models. To bridge this gap, we introduce zPolaron, a graph neural network built on protein-ligand complexes for functional protein design. zPolaron represents residues and ligand atoms as a heterogeneous graph and jointly encodes structural, interaction, and evolutionary information by fusing physical-interaction-enhanced graph representations with ESM-2 embeddings. Across multiple fitness prediction benchmarks, zPolaron outperforms all baselines, with gains evident across structural, interaction, and evolutionary dimensions. Wet-lab experiments further confirm its utility in functional enzyme screening and design: the optimized CalA6-D205A-S160G mutant achieves a 17.84-fold improvement in activity, while the CalB-I121M mutant yields a 1.91-fold increase. Together, these results show that integrating interaction and evolutionary information fills the missing puzzle of inverse folding, enhancing protein fitness prediction beyond structural compatibility. zPolaron is available at https://github.com/zelixirSH/zPolaron.

bioinformatics↗

bioRxiv2026

DEPICT enables sample-centric therapeutic prioritization across evolving and spatially heterogeneous tumor states

Accurate treatment selection remains a major challenge in precision oncology because tumors with similar genomic alterations can respond differently to therapy. Most drug-response models evaluate individual drugs or drug-sample pairs, whereas clinical decision-making requires therapies to be prioritized within each tumor context. Here we present DEPICT (Drug Efficacy Prediction via Integrated ConText), a sample-centric deep learning framework that reframes drug-response prediction as the relative prioritization of therapies within an individual tumor context. DEPICT integrates transcriptomic and mutational features with prior alteration-therapy relationship and was trained on 231,880 cell line-drug pairs comprising 941 cancer cell lines and 289 compounds. Without retraining, DEPICT retained predictive performance in independently profiled cell lines, experimentally induced drug-resistant states and matched primary lung tumors and patient-derived organoids. Representations learned exclusively from bulk pharmacogenomic data further captured progressive drug-response states at single-cell resolution and outperformed existing single-cell drug-response inference methods. Applied to spatial transcriptomic data, DEPICT resolved clone-associated therapeutic heterogeneity within individual lung tumors, and predicted regional differences were recapitulated in matched multiregional organoid drug-response assays. These findings establish sample-centric therapeutic prioritization as a transferable strategy for modeling dynamic and spatially heterogeneous drug vulnerabilities across biological scales.

bioinformatics↗

bioRxiv2026

Path Integration Promotes Flexible Navigational Decision Making

Flexible decision making depends on internal representations that capture the latent structure of a task, allowing prior knowledge to be applied in novel circumstances. Spatial navigation provides a useful model for studying flexible choice behavior, because spatial location is itself a latent variable that must be inferred rather than directly perceived. Here, we trained rats on a navigation task that required them to reach the same goal via two distinct paths from different starting locations, and then return to one of the two starting locations before beginning the next trial. Some rats were trained to rely on distal visual landmarks, allowing task states to be identified from current sensory information, whereas others were trained to rely on path integration, requiring task states to be inferred from self-motion information accumulated over the preceding trajectory. Rats trained to rely on path integration acquired the task similarly to rats trained to rely on distal visual landmarks. However, reliance on path integration enhanced rats' ability to generalize their learning to novel situations, including finding the goal from an untrained starting location and adapting to a relocated goal that reversed learned choice sequences. These findings suggest that reliance on path integration promotes the acquisition and use of mental representations that capture the latent spatial structure of navigational tasks, thereby favoring flexible navigational decisions over rigid retrieval of reinforced responses. More broadly, our findings demonstrate how information available during training can shape representations learned from experience and thereby constrain the flexibility of decision making during inference.

neuroscience↗

bioRxiv2026

Activation pathway of the human voltage-gated proton channel

Many protein functions are coupled to proton transfer, yet the underlying mechanisms remain extremely difficult to resolve by experiment or conventional molecular dynamics (MD) simulations. The human voltage-gated proton channel HV1 (hHV1) plays key roles in human physiology, but how voltage and pH together drive its activation remains unresolved. Experimental structures of hHV1 are limited to the X-ray structure of a mouse chimera and NMR models of a truncated hHV1, both representing an intermediate resting state. Here we determine the activation pathway of hHV1, together with structural models of its resting and activated states, using an approach that integrates all-atom continuous constant-pH MD (CpHMD), weighted-ensemble (WE) path sampling, and AlphaFold modeling. Starting from an AlphaFold model selected for consistency with resting-state experimental data, over 100 s of simulations reveal a mechanism in which transmembrane voltage, assisted by proton titration, drives an outward displacement of the transmembrane segment S4 accompanied by a one-click reorganization of countercharge pairings. These events are enabled by a delicately balanced electrostatic landscape and pH-modulated breathing motions in the resting state that prime the channel for protonation-state switches upon voltage sensing, a principle that may underlie other proton-coupled voltage-gating processes. The simulations also uncover lipid-binding sites at which POPG selectively stabilizes the S4-up conformation, whereas POPE can stabilize either state. These predictions are validated against extensive electrophysiology, mutagenesis data, and new smFRET experiments, which support the one-click S4 displacement and the lipid effects. WE-CpHMD, implemented in the AMBER package, is applicable to other proton-coupled processes that remain elusive.

biophysics↗

bioRxiv2026

YGEP: An Integrated Web Platform for Genomic Evaluation and Intelligent Breeding in Yak

Background: The yak (Bos grunniens) is an essential livestock species in high-altitude alpine ecosystems, serving key roles in meat, milk, and wool production as well as ecological maintenance. However, traditional yak breeding systems face several limitations, including fragmented herd data management, inefficient phenotypic collection, missing pedigree records, and high technical barriers to applying genomic technologies. These factors constrain the widespread application of modern genetic evaluation methods in yak breeding programs. Description: We developed the Yak Genomic Evaluation Platform (YGEP, https://yakbreeding.swun.edu.cn/en/), an integrated digital system for yak genetic selection and herd management. YGEP integrates three core analytical modules: pedigree reconstruction, genotype imputation and genomic breeding value estimation. Benchmarking on 706 yaks showed that GBLUP achieved a prediction accuracy of r = 0.96 for cannon bone circumference (CCB), and KBeagle reached 84.0% imputation accuracy with the combined reference panel. Conclusion: YGEP bridges the gap between advanced genomic analytics and practical yak breeding. By integrating pedigree reconstruction, genotype imputation, and GEBV estimation into a user-friendly cloud platform, YGEP effectively eliminates technical and data bottlenecks. Overall, it provides an accessible, scalable, and standardized solution to advance digital herd management and precision genetic improvement in alpine livestock.

bioinformatics↗

bioRxiv2026

Lactate epigenetically shapes tumor cell states in H3K27M diffuse midline gliomas

H3K27M diffuse midline gliomas (DMGs) are lethal and lack treatment options. These tumors exhibit tumor heterogeneity with aggressive oligodendrocyte precursor (OPC)- and mesenchymal (MES)-like cell states. Because all tumor cells bear H3K27M, tumor heterogeneity has been attributed to microenvironmental cues that remain obscure. H3K27M DMGs exhibit increased glycolysis and the Warburg effect to produce lactate. Lactate can directly modify histone lysines including H3K27Lac, and we hypothesized that lactate epigenetically regulates tumor cell states in H3K27M DMGs. We undertook a comprehensive and integrated analysis of H3K27M DMG cell lines, animal models, tumor tissues, and magnetic resonance spectroscopy in patients to decipher the epigenetic roles of lactate. Here, we report that H3K27M cells uniquely exhibit elevation of the activating mark H3K27Lac. We observed significant heterogeneity in lactate levels within tumors, and the addition of exogenous lactate resulted in marked increases in H3K27Lac and the expression of critical OPC- and MES- like gene signature genes, which correlates with poorer patient outcomes. Our therapeutic approach leverages the inhibition of CBP/p300, which deposits both H3K27Lac and H3K27ac. Targeting CBP/p300 effectively reduces both H3K27Lac and H3K27ac levels, suppresses key OPC- and MES-like signatures, and shows efficacy in preclinical models. Collectively, our findings identify lactate as a key player in the epigenetic regulation of tumor cell state heterogeneity and suggest that targeting this pathway offers promise for addressing the heterogeneous complexities of H3K27M DMGs.

molecular biology↗

bioRxiv2026

A long-term organotypic slice culture model of patient high-grade glioma preserving tumor heterogeneity and architecture, and specificity of CAR T cell targeting

ABSTRACT Background: High grade glioma (HGG), encompassing IDH-wildtype glioblastoma (CNS WHO grade 4), diffuse midline glioma (CNS WHO grade 4), oligodendroglioma (IDH-mutant and 1p/19q-codeleted) CNS WHO grade 3, together with IDH-mutant astrocytoma of CNS grade 3 and grade 4, represents the most lethal group of adult diffuse gliomas. Despite significant efforts, obtaining improvements in patient survival has been limited, in part, by difficulties in comprehensive ex vivo modeling of the complexities of HGG. Although organotypic slice cultures and other platforms have shown promise, existing models often fail to capture the intrinsic cellular heterogeneity, microenvironment, and architecture of HGG, restricting investigations into their fundamental biology as well as design of novel therapeutics. Methods: We developed a patient-derived HGG organotypic slice culture (GOSC) platform demonstrating long-term preservation of intrinsic tumor characteristics. Vibratome-sectioned slices were cultured in defined medium under conditions approximating those in situ: reduced oxygen (4%), low glucose (2.5 mM), and no added growth factors. The characteristics of GOSCs after 28 days in culture, including expression of immunotherapy targets, were compared to parental tumors using histological staining, immunofluorescence, multiplexed PhenoCycler (CODEX) imaging, bulk RNA-seq expression profiling, and CAR T cell killing assays. Results: GOSCs preserved the histopathology, cell heterogeneity, tumor microenvironment, and tissue architecture of their parental tumors throughout at least 28 days in culture. Importantly, GOSCs retained parental patterns of immunotherapy target expression, and CAR T cells co-cultured with GOSCs demonstrated target-specific killing consistent with parental tumors. Conclusions: This ex vivo GOSC platform offers long-term preservation of the cellular and structural properties of parental HGG tumors, thereby providing a robust tool for extended preclinical studies, and facilitating development and evaluation of advanced tumor-targeting strategies.

cancer biology↗

bioRxiv2026

A Novel ACLY Inhibitor Induces Transcriptional and Metabolic Reprogramming to Overcome Tyrosine kinase inhibitor Resistance in Lymphoma

Background: Metabolic plasticity contributes to therapeutic resistance in T-cell lymphoma, but the metabolic dependencies underlying tyrosine kinase inhibitor (TKI) resistance remain poorly understood. ATP citrate lyase (ACLY), which converts citrate to cytosolic acetyl-CoA, links glucose metabolism to lipogenesis and acetylation-dependent regulation. We hypothesized that ACLY represents an actionable metabolic vulnerability in lymphoma. Methods: Structure-guided drug discovery and biochemical screening were used to identify the novel ACLY inhibitor VCB1. VCB1 was evaluated against recombinant human ACLY and in TKI-sensitive and TKI-resistant lymphoma models. Antitumor activity was assessed by proliferation, cell-cycle analysis, apoptosis, and immunoblotting, followed by integrated transcriptomic, metabolomic, and lipidomic profiling. Results: Our xenograft study showed that ACLY dependence in ALK+ALCL. We discovered novel ACLY inhibitor VCB1 directly inhibited recombinant ACLY with uM potency (IC, 0.9 uM) and strongly suppressed lymphoma cell growth. In ALK inhibitor-sensitive SUPM2, VCB1 showed an IC of 0.299 uM and retained potency in lorlatinib-resistant SUPM2-LR1000 cells (1.62 uM), whereas BMS-303141 was substantially less active (17.46 and 22.07 uM). VCB1 similarly inhibited BTK inhibitor sensitive and resistant mantle cell lymphoma cell growth (IC, 0.28 and 0.278 uM), compared with BMS-303141 (30.5 and 37.01 uM). Multi-omics profiling revealed suppression of de novo lipogenesis, including ACACA, FASN, and PPARGC1B, together with extensive remodeling of triglyceride, phospholipid, cardiolipin, ceramide, and acylcarnitine species and increased expression of fatty-acid oxidation genes. VCB1 activated the integrated stress response (ISR), inducing ATF4, PPP1R15A, DDIT3, DDIT4 and SESN2, while disrupting purine and pyrimidine metabolism and reducing nucleotide biosynthetic genes, including CAD, DHODH, UCK2, and ATIC. VCB1 further activated an ACLY/ISR/CHAC1 axis associated with reduced GCLC/GCLM expression, glutathione depletion, and a decreased GSH/GSSG ratio, indicating impaired redox homeostasis. TKI-resistant cells exhibited distinct lipid-metabolic remodeling consistent with metabolic plasticity. VCB1 also altered immune-regulatory programs involving PDCD1, TIGIT, CD247, CD226, NFATC2, and inflammatory cytokines. Functionally, VCB1 induced cell cycle arrest and apoptosis. Conclusions: ACLY represents an integrated metabolic and signaling vulnerability in lymphoma. VCB1 suppresses lymphoma growth across TKI-sensitive and resistant models by disrupting lipid and nucleotide metabolism, metabolic adaptation and ISR and redox homeostasis supporting ACLY inhibition as a therapeutic strategy for TKI-resistant lymphoma.

cancer biology↗

bioRxiv2026

Genetic exchange drives relatedness of large linear and circular extrachromosomal elements of archaea

Archaeal extra-chromosomal elements (ECEs) play key roles in archaeal host biology and evolution, yet little is known about their diversity and interactions with each other. Here, we report 42 complete 66 - 165 kbp genomes: 23 "Klingons", 8 "Romulans" and "Romulan-like elements", and 11 "Ferengi", three new families of archaeal ECEs from diverse terrestrial environments. Methylation patterns, phylogenetics and gene sharing analyses suggest that Klingons and Romulans associate with Candidatus Methanoperedens and Ferengi are likely hosted by Candidatus Bathyarchaeaota. Like known archaeal viruses and plasmids, these ECEs both have circular genomes and replicate bi-directionally, unlike the linear Borg and mini-Borg ECEs that also replicate in Methanoperedens. The new ECE genomes all encode genes for methylation, glycosylation, protein degradation, and novel TnpB-like enzymes, which may interact with novel CRISPR-like arrays. All genomes also encode proteins with strong structural similarity to archaeal viral capsid proteins, and some are predicted to multimerize into pentameric or hexameric subunit capsid-like arrays and thus may encapsulate themselves. The three new ECE families share gene content with each other and with Borgs and mini-Borgs, often concentrated in specific genomic regions. Discordance among single gene and genomic phylogenies suggests that apparent relatedness of the five distinct ECE types stems from extensive horizontal gene transfer, rather than evolution from a common ancestor. The three new families of ECEs broaden our understanding of the diversity of archaeal ECEs and highlight the role of horizontal gene transfer in modulating the archaeal and archaeal ECE gene pools.

genomics↗

bioRxiv2026

Auditing Protein-Protein Interaction Signals with Sparse Autoencoder Fingerprints

Protein language models have become a dominant foundation for sequence-based protein-protein interaction (PPI) prediction, but their generalization remains limited under stringent evaluation, and benchmark accuracy alone cannot reveal whether a PPI predictor learns partner-specific biological signals or exploits contextual shortcuts. Here we introduce AuditPPI, an interpretable framework that transforms sparse-autoencoder (SAE) features from a frozen protein language model into order-invariant pair fingerprints, recasting PPI prediction as an auditable tabular-learning problem. AuditPPI achieves competitive predictive performance across diverse PPI benchmarks while enabling multiscale auditing of the information supporting its predictions. Protein-level audits show that partner-independent participation signals remain substantial in conventional benchmarks, including protein-disjoint benchmark, but are largely insufficient for pair-level discrimination in topology- and degree-controlled benchmark. Pair-level analyses further show that removing protein identity overlap does not eliminate contextual structure: protein-disjoint benchmarking retains strong subcellular co-localization signals and benchmark-dependent feature matching captured by SAE co-activation and absolute-difference. Structural analyses, however, provide little evidence that these predictive signals are specifically grounded in PPI interfaces: feature enrichment at interfaces for protein-disjoint benchmark was no longer detectable after controlling for surface exposure, and contact-specific enrichment was observed for only a small fraction of testable SAE feature pairs. AuditPPI therefore separates predictive success from mechanistic fidelity and provides a practical framework for evaluating whether sequence-based PPI predictors capture partner-specific biological signals instead of contextual shortcuts.

bioinformatics↗

bioRxiv2026

A synaptic wiring diagram underlying modality-specific ascending pathways of the superficial spinal dorsal horn

The spinal cord dorsal horn transforms tactile, thermal, pruritic, and nociceptive signals from peripheral somatosensory neurons into outputs to the brain, but how dorsal horn circuits organize diverse inputs into modality-selective ascending pathways is poorly understood. Using dSC1, a large-scale electron microscopy dataset of the mouse dorsal horn, we mapped the circuitry connecting primary sensory afferents to projection neurons of the anterolateral tract (ALT), a principal pathway conveying somatosensory information to the brain. We find that afferents encoding distinct modalities are routed onto connectivity-defined populations of ALT projection neurons. Nociceptors and cold thermoreceptors directly innervate distinct lamina I ALT projection neuron populations specialized for conveying noxious and cooling signals, respectively, whereas tactile and pruritic signals instead pass through a recurrent, multilayered network involving interneurons called vertical cells before reaching a separate ALT projection population. This distinction, direct versus polysynaptic wiring, underlies marked differences in sensory convergence and establishes segregated ascending channels for conveying signals encoding the principal somatosensory modalities. Together, our findings define an architectural logic by which the dorsal horn integrates and routes tactile, thermal, pruritic, and nociceptive information into distinct ALT output pathways to the brain.

neuroscience↗

bioRxiv2026

Sequence-specific and programmable catalytic degradation of extracellular microRNAs by membrane-anchored DNA nanomachines

Extracellular microRNAs (miRNAs) contribute to metastasis through communication between tumour cells and their microenvironment, yet their sustained, sequence-selective depletion remains challenging. Here we report Programmable RNA-Intercepting Molecular Eraser (PRIME), a membrane-anchored DNA nanomachine that organizes miRNA recognition and catalytic degradation at the cell surface. A double-tetrahedral DNA scaffold positions a programmable recognition hairpin beside RNase H. Target binding generates an RNA/DNA hybrid for RNase H-mediated cleavage, and product release resets the hairpin for subsequent degradation cycles. Membrane-anchored PRIME depleted matched extracellular miRNAs by 70.6-89.4% across lung, breast and cervical cancer cell models. Multi-target PRIME (M-PRIME) inhibited migration by 71.3-96.0% in Transwell assays across these models. To evaluate its therapeutic potential, we established an orthotopic lung-tumour model and an early-intervention breast-cancer lung-colonization model in mice. Aptamer-directed M-PRIME combined with gemcitabine reduced pulmonary tumour burden by 74.5% in established lung tumours and 93.2% in the lung-colonization model. These effects were consistent with PRIME-mediated extracellular miRNA degradation, with circulating target miRNA levels reduced by 77.5-98.7% relative to gemcitabine alone. Together, these findings establish a programmable material strategy for sustained extracellular RNA depletion and support its potential to enhance chemotherapy in preclinical tumour models.

biochemistry↗

bioRxiv2026

Early dynamics of a neutrophil interferon program drive immunotherapy resistance and limit durable anti-tumor immunity

Despite the remarkable success of immune checkpoint blockade (ICB), durable clinical benefit remains limited to a subset of patients, highlighting the need for predictive biomarkers and new therapeutic targets. Here, we investigated the early immune dynamics associated with anti-PD1 responsiveness using longitudinal single-cell transcriptomics, spatial transcriptomics, and neutrophil-specific genetic perturbations in preclinical models of triple-negative breast cancer. We identified a conserved neutrophil interferon-stimulated gene (ISG) program that emerges before overt tumor divergence and predicts resistance to anti-PD1 therapy. Successful treatment was associated with an early reduction of IFN-responsive neutrophils in both blood and tumor tissues, whereas persistent neutrophil IFN signaling correlated with therapeutic resistance. Mechanistically, genetic disruption of either type I or type II interferon signaling in neutrophils enhanced anti-PD1 efficacy and promoted durable anti-tumor immune memory. Spatial analyses further revealed an inverse association between IFN-responsive neutrophils and tertiary lymphoid structure-enriched regions during effective therapy. Together, these findings identify IFN-responsive neutrophils as early determinants of immunotherapy outcome and establish dynamic neutrophil interferon programs as candidate blood-based biomarkers and therapeutic targets for cancer immunotherapy.

cancer biology↗