Biology subjects

Song, Y.

Publications and source records attributed to Song, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Personalized Neoantigen Vaccines Synergize with Immune Checkpoint Therapy and CD8-Targeted Cytokines to Control B-Cell Lymphoma

Personalized neoantigen (neoAg) vaccines have shown clinical promise in solid tumors1-8, yet their efficacy and mechanism of action in hematopoietic malignancies remain poorly defined9-11. Herein, we establish an immunocompetent syngeneic A20 B-cell lymphoma platform to test the efficacy of neoAg vaccines used either as mono- or combinatorial therapies with other immunotherapies12-17. Whereas subcutaneous A20 tumors were refractory to single-agent PD-1 or CTLA4 therapy, they were eradicated in a T cell-dependent manner in 90% of syngeneic hosts treated with dual immune checkpoint therapy (dual ICT, i.e., PD-1 + CTLA4). By mapping antigen specificity of dual-ICT-elicited T cells, we identified and validated dominant endogenous A20 MHC-I and MHC-II neoantigens and designed therapeutic synthetic long peptide (SLP) vaccines containing these neoepitopes. This vaccine (A20 neoVAX) promoted robust neoAg-specific CD4{square} and CD8{square} T cell responses in naive syngeneic BALB/c mice and induced tumor rejection in [~]70% of subcutaneous tumor-bearing mice. In addition, nearly all mice rejected their subcutaneous A20 tumors when A20 neoVAX was combined with PD-1. To render the results of this study more physiologic, we developed a systemic A20 lymphoma model and found that dual ICT failed to control tumor progression and A20 neoVAX delayed tumor progression and prolonged animal survival but did not induce tumor rejection. In contrast, A20 neoVAX plus dual ICT achieved durable systemic tumor elimination. Mechanistically, the combination of A20 neoVAX plus dual ICT amplified priming of A20 neoAg-specific T cells, prevented T cell dysfunction, sustained the cytotoxic capacity of tumor-specific CD8+ T cells, and induced Th1-skewing of CD4+ T cells in tumor and peripheral compartments. To increase the clinical relevance of these findings and to minimize potential adverse events in tumor-bearing, therapeutically treated individuals, we substituted CD8-targeted cytokine muteins (CD8-IL2 or CD8-IL21) for CTLA4. These agents represent genetically modified forms of IL-2 or IL-21 that selectively stimulate CD8+ T cells but have significantly reduced capacity to activate chronic inflammation and immunosuppressive functions of other immune cells. Whereas mice bearing systemic A20 lymphoma treated with either nothing, A20 neoVAX, or A20 neoVAX + CD8-IL2 failed to control tumor outgrowth, 66.7% of tumor-bearing mice treated with A20 neoVAX + CD8-IL2 + PD-1 rejected their tumors. In similar experiments in which CD8-IL21 was substituted for CD8-IL2, tumor clearance was also observed in two-thirds of A20-bearing mice but now rejection occurred in the absence of PD1. Together, these data define a framework for optimal personalized neoAg vaccination in B-lymphoma and demonstrate that neoAg vaccines can safely synergize with CD8+ T cell-selective immunotherapies to prevent T-cell dysfunction and generate durable systemic anti-tumor immunity.

immunology↗

bioRxiv2026

Individual-tree phenology reveals climate-dependent responses to urban thermal heterogeneity across U.S. cities

Rapid urbanization is altering the seasonal life cycles, or phenology, of urban trees. Diverse species composition and heterogeneous urban thermal environments can generate pronounced phenological variation within cities, yet such fine-scale seasonality remains poorly understood. This limits the ability to anticipate localized ecosystem services and disservices, including canopy cooling and pollen exposure. Here, we analyzed individual-tree phenology and their response to temperature across 76 cities in the contiguous United States by integrating municipal street-tree inventories, PlanetScope satellite time series, and 1-km near-surface urban air-temperature data. We quantified intra-city and cross-city phenological variation, estimated species-level associations between phenology and fine-scale urban temperature, and tested whether these associations vary with regional climatic context. Intra-city phenological variation rivaled cross-city variation for 33.3% of species in spring and 53.7% in fall. Temperature-phenology associations were widespread: warmer local urban environments were associated with earlier spring onset in 51.5% of cases and delayed fall senescence in 66.5%, with approximately two-thirds of these responses cascading to longer growing seasons. These associations varied with regional climate, generally showing stronger spring advancement and fall delay in cooler and wetter cities, but weaker or reversed responses in hotter or drier cities. Together, these results suggest that urban tree phenology is shaped by interactions among fine-scale urban temperature, species identity, and regional climate. Accounting for this heterogeneity can improve predictions of urban forest function and inform climate-resilient species selection and management. Plain Language SummaryStreet trees within the same city do not all leaf out in spring or lose their leaves in fall at the same time. This seasonal timing, called phenology, affects services such as shade and cooling, as well as disservices such as pollen exposure. We studied individual tree phenology and their temperature response in 76 U.S. cities using street-tree records, satellite observations, and local air-temperature data. We asked how much phenology varies within cities, how it responds to neighborhood-scale temperature differences, and whether these responses depend on regional climate. Variation within a city was often as large as variation among cities, especially in fall. Trees in warmer parts of cities generally leafed out earlier and lost their leaves later, often extending the growing season. However, these responses were stronger in cooler and wetter cities and weaker or sometimes reversed in hotter or drier cities. These findings show that urban tree seasonality depends on local temperature, species identity, and regional climate, which should be considered when selecting and managing trees for future cities. Key PointsO_LISubstantial within-city phenological variation is not captured by city-level averages. C_LIO_LIFine-scale temperature shaped phenology and growing-season length, but responses varied across species, cities, and phases. C_LIO_LITemperature sensitivity depended on regional climate, weakening or reversing in hotter or drier cities. C_LI

ecology↗

bioRxiv2026

Antibody evasion and receptor binding of SARS-CoV-2 variants PQ.16.1.1 and RK.1

The recent global expansion of the SARS-CoV-2 variant NB.1.8.1 has driven the emergence of sublineages PQ.16.1.1 and RK.1, which independently acquired the D420N mutation in their receptor-binding domains and and now dominate the Asia-Pacific region. Evaluations utilizing surface plasmon resonance and pseudovirus assays demonstrate that these sublineages exhibit significantly reduced human ACE2 receptor engagement compared to their parental strain. However, this functional cost is offset by a marked ability to evade humoral immunity, specifically demonstrating profound resistance to Class 1 neutralizing monoclonal antibodies and convalescent plasma from Wuhan-Hu-1-primed individuals. This convergent evolution exemplifies a classical viral trade-off, sacrificing receptor binding efficiency to escape population-level immune pressure. Consequently, these findings suggest these variants will soon spread globally and emphasize the critical need for ongoing surveillance to monitor D420N-carrying lineages.

immunology↗

bioRxiv2026

Promoter architecture decodes response regulator phosphorylation into distinct transcriptional logics in Pseudomonas aeruginosa

Two-component systems convert environmental signals into transcriptional responses, but how one response-regulator phosphorylation state produces different outputs at different promoters remains unclear. Here we show that promoter architecture determines how the ParR response regulator in Pseudomonas aeruginosa interprets phosphorylation. Phenotypic, transcriptomic, biochemical and promoter-engineering analyses showed that phosphorylation of the conserved ParR receiver residue Asp57 lowered DNA-occupancy thresholds across target promoters. Individual promoters, however, converted this shared increase in binding into activation, repression or phosphorylation-dependent sign switching. Chromosomally D57 ParR variants reproduced these behaviours at endogenous loci and altered antibiotic susceptibility, biofilm formation and virulence-associated phenotypes. Mapping and engineering of representative promoters identified a two-tier cis-regulatory code: half-site sequence compatibility determines productive ParR engagement, whereas spacer length determines regulatory sign and magnitude. Spacer swaps were sufficient to reprogram promoter logic between regulatory modes. These findings separate regulator state from promoter decoding and show how bacterial promoter architecture can diversify the outputs of a shared phosphorylation signal. ImportancePseudomonas aeruginosa is an opportunistic pathogen that survives antimicrobial treatment and adapts to diverse host environments by rapidly changing gene expression. How a single sensory pathway generates different, and sometimes opposing, responses across many genes has remained unclear. We show that the regulatory protein ParR does not impose one fixed transcriptional program. Instead, the DNA architecture of each target promoter determines whether the same phosphorylation signal activates, represses, or reverses gene expression. The sequence and spacing of ParR recognition sites form a compact regulatory code, and changing spacer length alone can reprogram promoter behavior. Different ParR states were also associated with changes in antibiotic susceptibility, biofilm formation, and virulence-associated phenotypes. Our findings explain how one bacterial signaling pathway can generate diverse physiological outcomes without additional regulators and provide a framework for understanding regulatory flexibility in Pseudomonas aeruginosa and for engineering genetic circuits with multiple outputs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/740031v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1b6ec28org.highwire.dtl.DTLVardef@4a3f2eorg.highwire.dtl.DTLVardef@79e528org.highwire.dtl.DTLVardef@b3aa77_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Promoter architecture diversifies ParR-dependent transcription in Pseudomonas aeruginosa

Two-component systems convert environmental signals into transcriptional responses, but how one response-regulator phosphorylation state produces different outputs at different promoters remains unclear. Here we show that promoter architecture determines how the ParR response regulator in Pseudomonas aeruginosa interprets phosphorylation. Phenotypic, transcriptomic, biochemical and promoter-engineering analyses showed that phosphorylation of the conserved ParR receiver residue Asp57 lowered DNA-occupancy thresholds across target promoters. Individual promoters, however, converted this shared increase in binding into activation, repression or phosphorylation-dependent sign switching. Chromosomally D57 ParR variants reproduced these behaviours at endogenous loci and altered antibiotic susceptibility, biofilm formation and virulence-associated phenotypes. Mapping and engineering of representative promoters identified a two-tier cis-regulatory code: half-site sequence compatibility determines productive ParR engagement, whereas spacer length determines regulatory sign and magnitude. Spacer swaps were sufficient to reprogram promoter logic between regulatory modes. These findings separate regulator state from promoter decoding and show how bacterial promoter architecture can diversify the outputs of a shared phosphorylation signal. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/738673v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1a0a26forg.highwire.dtl.DTLVardef@10836a8org.highwire.dtl.DTLVardef@3c6cd8org.highwire.dtl.DTLVardef@10dfefb_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsParR coordinates antibiotic resistance, biofilm formation and virulence-linked phenotypes in P. aeruginosa. Promoters convert ParR phosphorylation into activation, repression or sign switching. Half-site compatibility and spacer length form a cis-regulatory code for ParR output.

biochemistry↗

bioRxiv2026

Direct probabilistic quantification of mosaic loss of chromosome Y from sequencing data

Loss of chromosome Y (LOY) is the most common aneuploidy in aging men and is increasingly recognized as a marker of aging and genomic instability. Because LOY occurs in mosaic form, its degree reflects the fraction of cells lacking the Y chromosome. Existing SNP-array- and sequencing-based methods rely largely on single genomic features and indirect transformations to estimate this fraction. We developed BaySeq-Y, a Bayesian method that directly estimates LOY mosaicism from sequencing data using VCF files with read depth (DP) and allelic depth (AD). Within a rigorous Bayesian framework, BaySeq-Y integrates complementary LOY-associated genomic features, including decreased read depth and allelic imbalance, and can additionally leverage haplotype phasing to improve precision. In simulations and fluorescence in situ hybridization validation (FISH), BaySeq-Y provided accurate estimates and outperformed existing methods. Applications to ROSMAP and GTEx supported its biological relevance through transcriptomic validation, demonstrating its utility for quantifying LOY across diverse sequencing datasets.

bioinformatics↗

bioRxiv2026

TDP-43 subtypes shape transcriptomic signatures in Alzheimer's disease

TAR DNA-binding protein 43 (TDP-43) pathology frequently co-occurs with Tau neurofibrillary tangles (NFTs) and amyloid {beta} plaques in Alzheimers disease (AD), driving significant clinical heterogeneity. Whether TDP-43 engages autonomous molecular programs or instead amplifies Tau-driven neurodegeneration remains difficult to resolve, largely because these pathologies often co-occur. To separate these overlapping signatures, we generated regionally resolved transcriptomic profiles from cognitively normal controls (Controls), neuropathologically defined cohorts of AD, AD with limbic-predominant age-related TDP-43 encephalopathy (AD/LATE), and frontotemporal lobar degeneration (FTLD-TDP), categorizing them by their distinct TDP-43 subtypes (types and {beta} for AD/LATE; types A and B for FTLD-TDP). By integrating transcriptomic profiles with quantitative measures of phosphorylated TDP-43 (pTDP-43) and Tau (pTau), we separated pathology-associated signals within mixed disease contexts. We found that TDP-43 is linked to distinct transcriptomic programs in AD/LATE that are largely uncoupled from Tau burden and diverge from those observed in FTLD-TDP. These signatures showed regional specificity, with transcriptomic remodeling occurring in the amygdala across both diseases, whereas frontal cortex alterations were largely restricted to FTLD-TDP. Furthermore, by stratifying cases by TDP-43 morphological subtype, we unmasked specific biological trajectories, from immune activation to unique cellular vulnerabilities, that are not apparent in unstratified cohorts. Together, our findings provide a framework for decoupling mixed proteinopathies and demonstrate that TDP-43 shapes autonomous, subtype-dependent transcriptional landscapes in AD.

neuroscience↗

bioRxiv2026

Visual gamma stimulation causes prolonged enhancement of low-frequency blood flow oscillations across cortical regions in mice

IntroductionGamma entrainment using sensory stimuli (GENUS) uses 40Hz-pulsed sensory stimuli to entrain neural activity in the gamma band (30-150Hz). However, the effect of GENUS on low-frequency vascular oscillations has not been fully explored. ObjectivesThe objective of this study is to elucidate the effect of GENUS on vasomotion in healthy mice and potential confounds for future application in disease studies. MethodsHead-fixed, awake C57Bl/6 mice (n=18; 9M 9F) aged between 18 to 60 weeks were subjected to white light of either 40Hz visual flicker (GENUS), or constant stimulus (control). Blood flow was imaged using laser speckle contrast imaging (LSCI) before, during, immediately after 1 hour of stimulus, and 30min after the stimulus termination. ResultsA linear mixed-effects model showed that GENUS enhanced the magnitude of 0.2-0.4Hz blood flow oscillations by 38% during stimulation and by 30% at 30 minutes after stimulation compared to control when controlled for age, sex, and other factors. The effect on vasomotion was distributed across many cortical regions not limited to visual areas and lasted beyond 24 hours post-stimulus. ConclusionThese results support the exploration of GENUS for increasing vasomotion in therapeutic contexts. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/729102v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@1deee2eorg.highwire.dtl.DTLVardef@e71833org.highwire.dtl.DTLVardef@1e5c4f0org.highwire.dtl.DTLVardef@1e4832e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Growth-resolved genome-scale metabolic modeling of Priestia megaterium SR7 validated by chemostat and 13-C flux analysis

Priestia megaterium SR7 is a promising candidate chassis for bioprocess engineering, but its development is limited by the availability of condition-grounded, mechanistic models that can translate experimental measurements into predictive design hypotheses. Here, we present PMSR7, a genome-scale metabolic model for SR7, and evaluate it under a growth-resolved chemostat framework spanning a dilution-rate series. Stable steady states were established across the growth regime, with the highest dilution rate (D = 1.1538 h-{superscript 1}) excluded from growth interpretation due to biomass collapse. Extracellular carbon fluxes were quantified by NMR and reported as mean {+/-} SD, providing an experimental basis for model comparison. PMSR7 was benchmarked using MEMOTE against representative reference reconstructions, supporting structural consistency suitable for constraint-based analyses. Under growth-resolved simulations, ATP demand scaled linearly with growth rate, enabling inference of maintenance-energy behavior across the regime. Growth-dependent feasibility and magnitude of overflow secretion were evaluated for acetate, lactate, and formate using feasible-space analyses, highlighting both agreement and regime-sensitive limitations. Finally, growth-resolved leucine and valine production was assessed in both raw and fold-change space, with experimental means compared against median-based summaries of sampled model distributions to account for feasible-space skew. Together, these results establish PMSR7 as a reproducible, quality-benchmarked platform for SR7 chassis development and provide a framework for iterative experimental integration in non-model organisms, where the dominant challenge is achieving congruence between measured physiology and model-feasible behavior.

systems biology↗

bioRxiv2026

Intron 13 retention expands the ADAR1 isoform repertoire to rewire PKR signaling and promote tumorigenesis

For decades, the biology of ADAR1 has been framed around two major isoforms: the nuclear-enriched p110 and the predominantly cytoplasmic p150. Here, we reveal an unexpected repertoire expansion of ADAR1 isoforms that is driven by intron retention. Specifically, intron 13 (I13) can be retained in ADAR1 transcripts, conferred by an evolutionarily conserved weaker 5SS. In addition, we found that the I13 retention (I13R) is negatively autoregulated by ADAR1 through antagonizing the binding of hnRNPA1 to I13 in an editing-independent manner. Despite being sensitive to nonsense-mediated decay, I13R generates two previously uncharacterized truncated isoforms - p90 and p130, that both lack the C-terminal portion of the deaminase domain. Intriguingly, ADAR1p90 - a derivative of the canonical nuclear-enriched p110 isoform - is predominantly cytoplasmic, that effectively represses PKR and eIF2 activation through the sequestration of immunogenic double-stranded RNA (dsRNA) substrates. Furthermore, in a colorectal cancer (CRC) cohort, p90 levels are increased in most tumors relative to matched normal tissues that positively correlates with hnRNPA1 expression. Functionally, xenografts expressing ADAR1p90 grow significantly faster and larger than those expressing ADAR1p110, indicating enhanced tumorigenic potential. These findings revise the canonical view of ADAR1 isoforms, demonstrating that intron retention can generate alternative isoforms with augmented functions that tumors readily exploit. One Sentence SummaryThe conserved retention of I13 in ADAR1 transcripts gives rise to previously uncharacterized C-terminal truncated cytoplasmic ADAR1 isoforms, p90 and p130, which, although devoid of catalytic activity, sequester immunogenic dsRNA substrates, thereby preventing PKR binding and downstream activation of eIF2.

cell biology↗

bioRxiv2026

Flytrap-Inspired Mesh-Trap Bioelectronics for Full Spherical Electrophysiological Interrogation of 3D Tissues

Three-dimensional (3D) in vitro tissue models are emerging as powerful platforms for studying development, disease, and therapeutic responses, where close monitoring of electrophysiological activity is essential. However, existing probing methods remain limited in accessibility or spatiotemporal resolution for comprehensive electrophysiological mapping of suspended 3D tissues that closely mimic the native environments. Here we introduce a Venus flytrap-inspired bioelectronic mesh system that enables the full spherical enclosure of 3D tissues in a suspended configuration. The system consists of two hemispherical meshes that envelop the tissue, constructed from highly flexible, stretchable, cell-scale ribbons interconnected into a tissue-compliant network with integrated recording electrode arrays. This architecture enables intimate, conformal tissue integration and supports stable electrophysiological recordings over 300 days. The high-resolution recordings allow precise tracking of local dynamics and correlated global signaling, enabling comprehensive assessment of tissue development as well as detailed evaluation of drug responses for disease modeling. Beyond single tissues, the mesh architecture is extended to fully enclose assembloids composed of multiple tissues, enabling characterization of cross-tissue signaling relevant to advanced heterogenous tissue modeling. Furthermore, the system is translated into array-based platforms, demonstrated by a 4x4 array integrating 1024 electrodes, for high-throughput tissue sampling and cross-study analysis. The developed bioelectronic system and integration method provide a broadly applicable platform to advance electrophysiological studies across diverse tissues and organoids.

bioengineering↗

bioRxiv2026

Architectural Confinement and Seasonal Forcing Shape Cross-Domain Pathogen Assemblages in Complex Built Environments

Airborne microbial pathogens in built environments (BEs) may pose potential health threats, yet the ecological mechanisms governing their assembly and persistence across interconnected architectural spaces are less studied. Here, we conducted a year-long, multi-spatial investigation across a university campus complex, sampling the exhaust outlets of three indoor environments and the adjacent outdoor inlets. By integrating the 16S rRNA gene and ITS sequencing from 437 paired bacterial-fungal samples, we characterized the spatiotemporal dynamics of airborne opportunistic pathogen-containing genera. Our study showed that spatial filtering emerged as the dominant determinant of pathogen community structure, with confined elevator environments serving as reservoirs of pathogens with limited but continuous microbial influx from surrounding spaces. Superimposed on this spatial baseline, bacterial and fungal pathogens displayed distinct seasonal dynamics. Opportunistic fungal pathogens such as Fusarium peaked during autumn and winter, possibly driven by enhanced aerosol persistence and dispersal under cooler, drier conditions. In contrast, bacterial pathogens exhibited greater temporal resilience, with key taxa such as Listeria transcribed actively during winter, predisposing them to increased relative abundance during spring. Cross-domain ecological networks further revealed the dynamic interactions among pathogens, centered on the skeletal structure mediated by the keystone fungal pathogen Aspergillus, suggesting that coordinated microbial interactions reinforced pathogen persistence across seasons. Together, our findings support a unified ecological framework in which pathogen dynamics within BEs arise from the coupled effects of spatial filtering, climatic modulation, and biotic interactions. These results provide a foundation for transitioning from static environmental control toward predictive pathogen management in BEs. ImportanceBEs are the primary settings of human microbial exposure, yet the ecological principles governing the persistence of airborne pathogens across interconnected indoor spaces remain poorly resolved. Most previous indoor studies have focused on isolated environments or single microbial groups, limiting our understanding of how pathogens are maintained and redistributed within complex architectural systems. By integrating bacterial and fungal community dynamics across spatial environments over four seasons, this year-long study demonstrates that the ecology of airborne pathogens is not static, but is instead dictated by a complex interplay of spatial, climatic, and biological forces. Our findings identify enclosed, high-transit elevator spaces as critical hotspots for pathogen accumulation and highlight the role of seasonal ecological reorganization in driving airborne health risks. More broadly, this work establishes a systems-level ecological framework for understanding airborne pathogen dynamics in BEs and provides a conceptual basis for developing more adaptive strategies for indoor microbial risk management.

microbiology↗

bioRxiv2026

Primary productivity declines when species composition and climate are mismatched

Climate change drives shifts in species composition, but turnover in many communities lags behind the current pace of change. Anticipating the impact of the resulting community-climate disequilibria on ecosystem functioning is critical. Present-day communities may already be out of equilibrium with climate, providing an opportunity to estimate the effects of disequilibrium before they become more widespread. We analyzed plant community composition and function data from [~]60,000 rangeland monitoring sites across the western US to measure how community-climate disequilibrium contributes to spatial and temporal variation in net primary productivity (NPP) - a key ecosystem function. We found that communities were already substantially out of equilibrium with climate and accounting for this disequilibrium helped explain patterns of NPP. Communities farthest from equilibrium were less productive than those that were closely matched with climate. Our findings suggest that future increases in community-climate disequilibrium may further impair ecosystem functioning.

ecology↗

bioRxiv2026

Combined Checkpoint Inhibition Amplifies Post-Infarction Injury via T Cell-Mediated Macrophage Activation

BackgroundThis study aimed to investigate whether combined PD-1/CTLA-4 immune checkpoint inhibition predisposes the heart to a hyperinflammatory state, thereby exacerbating cardiac injury following acute myocardial infarction (MI), a critical unresolved question in cardio-oncology. MethodsMyocardial infarction was induced in Pd1-/-Ctla4+/- mice, a genetic model mimicking combined checkpoint inhibition. Key mechanistic insights were gained through in vivodepletion of CD8+ T cells (using anti-CD8a antibody) and pharmacological inhibition of the JAK-STAT1 pathway (using Tofacitinib). Cardiac function, structural injury, and immune responses were comprehensively assessed via echocardiography, flow cytometry, immunofluorescence, and molecular analyses. ResultsCompared to wild-type controls, Pd1-/-Ctla4+/- mice exhibited significantly increased post-MI mortality, worse cardiac function, and larger infarct size. Mechanistically, the aggravated injury was driven by an amplified infiltration of activated, IFN-{gamma}-producing CD8+ T cells, which activated the JAK-STAT1 pathway in macrophages, polarizing them towards a pro-inflammatory state. Depleting CD8+ T cells or inhibiting the JAK-STAT1 pathway effectively attenuated macrophage-driven inflammation and improved all aspects of post-MI injury. ConclusionsCombined PD-1/CTLA-4 blockade exacerbates post-infarction cardiac injury by promoting CD8+ T cell-mediated activation of macrophages via the JAK-STAT1 axis. This work elucidates MI as a context-dependent immune-related adverse event in ICI therapy and identifies CD8+ T cells and the JAK-STAT1 pathway as promising therapeutic targets for cardioprotection in these patients. RESEARCH PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study identifies acute myocardial infarction (MI) as a potential, context-dependent immune-related adverse event in the setting of combined PD-1/CTLA-4 checkpoint inhibition, shifting the paradigm beyond the classic focus on myocarditis. C_LIO_LIIt elucidates a novel pathogenic axis where combined checkpoint deficiency exacerbates post-MI injury specifically through CD8+ T cell-derived IFN-{gamma}, which activates macrophages via the JAK-STAT1 pathway. C_LI What Question Should Be Addressed Next?O_LIFuture studies should employ anti-PD-1/CTLA-4 monoclonal antibodies in wild-type or humanized mouse models to validate findings and better recapitulate the pharmacokinetics of clinical ICI therapy, strengthening translational relevance. C_LIO_LIThe long-term consequences of this primed inflammatory state on chronic cardiac remodeling, heart failure development, and the potential interplay with atherosclerosis warrant further investigation. C_LI

immunology↗

bioRxiv2026

Long-Lasting Electrohydrodynamically Printed Transparent Soft Microelectrode for Implantable Biointerfaces

Reliable and scalable soft implantable neural interface fabrication remains a key challenge for chronic bioelectronic applications. Here, we present a transparent soft microelectrode fabricated with electrohydrodynamic (EHD) printing, utilizing the fluorinated polymer poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) and poly (3, 4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT: PSS) to form seamless, selectively patterned multilayer structures with low impedance and long-term stability. Controlled in situ curing during printing yields dense, void-free substrate and encapsulation layers, suppressing interfacial defects and ionic pathways, while maintaining high optical transparency (>60%) with PEDOT:PSS. The printed microelectrodes exhibit low impedance, high charge storage and injection capacities, and stable electrochemical behavior under biomimetic conditions. In addition, the devices demonstrate robust mechanical and electromechanical stability under cyclic deformation in both dry and wet environments, as well as under prolonged electrical stimulation. Accelerated aging studies project multi-year operational lifetimes, and in vitro/in vivo biocompatibility assessments confirm excellent tissue integration. These results establish EHD-printed fluorinated polymer-based microelectrodes as a scalable and durable platform for chronic implantable biointerfaces. ToC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/726391v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@f4f717org.highwire.dtl.DTLVardef@8a34a1org.highwire.dtl.DTLVardef@185540dorg.highwire.dtl.DTLVardef@51462a_HPS_FORMAT_FIGEXP M_FIG C_FIG This report presents an electrohydrodynamically printed transparent soft microelectrode for chronic purposes. Electrohydrodynamic printing promotes seamless multilayer structures with selective deposition and long-term mechanical stability. The devices show low impedance, high charge capacity, and robust electrochemical/electromechanical properties. Accelerated aging projects [~]7.2 year lifetimes, and XPS/SEM-EDS confirm strong ion barrier properties and biocompatibility for chronic implantation.

bioengineering↗

bioRxiv2026

Purinergic signaling promotes gliomagenesis through nuclear calcium transients

Intracellular Ca2+ transients drive key developmental and physiological processes, yet their role in oncogenesis remains incompletely understood. In glioblastoma (GBM), an aggressive brain malignancy, tumor cellular networks exhibit self-sustaining Ca2+ transients that promote tumor growth through unclear mechanisms. Using patient-derived GBM models, we show that these transients depend primarily on intracellular Ca2+ stores and extend to the nucleus to drive tumorigenesis. A neuromodulator screen identified extracellular purines ATP and ADP as potent inducers of both nuclear and cytosolic Ca2+ transients via activation of metabotropic purinergic P2RY1 receptors, whose knockdown attenuates tumorigenicity in vitro and in vivo. Mechanistically, Ca2+ transients promote tumorigenesis via the nuclear Ca2+/calmodulin-dependent kinase CAMK4, which regulates transcriptional and epigenetic programs, as well as ribosomal DNA transcription. From the therapeutic perspective, pharmacologic P2RY1 inhibition suppresses tumor growth in vitro and in vivo. Collectively, these findings reveal a pharmacologically targetable oncogenic mechanism in GBM and possibly other malignancies.

cancer biology↗

bioRxiv2026

Selective Elimination of TP53 Mutant Cells by Transcript-Activated Chromatin Shredding

Genetic mutations that drive cancer often occur in tumor suppressor proteins, including the p53 transcription factor which is altered in [~]40-50% of cases1,2. However, current therapies fail to target most such mutations because the mutant proteins typically lack defined drug-binding pockets, and restoring the endogenous function has proven challenging. Here, we programmed CRISPR-Cas12a2, an RNA-guided nuclease with trans-nucleolytic cleavage activities3,4, to selectively kill cancer cells by targeting cancer-specific transcripts. This approach eliminates cells by inducing trans chromatin cleavage, triggering DNA damage and cell death. Unlike existing methods, RNA-guided Cas12a2 senses cellular RNA signatures to shred chromatin, enabling precise targeting of undruggable mutations. Transcript-activated chromatin shredding provides an innovative paradigm to develop precision disease treatments for undruggable targets.

cell biology↗

bioRxiv2026

Nuclear Speckles Regulate Splicing During Muscle Stem Cell Activation and Aging

Skeletal muscle contains a population of adult stem cells called satellite cells or muscle stem cells (MuSCs) that are responsible for regeneration after injury. MuSCs utilize gene expression programs to maintain quiescence and differentiate after injury and a key regulator of gene expression is splicing, which uniquely changes when transcripts interact with nuclear speckles (NS). NS are membrane-less biomolecular condensates that phase separate proteins, RNAs and chromatin, but how these organelles regulate molecular processes in MuSCs remains unknown. Herein, we build a comprehensive and systems-level understanding of NS influence on alternative splicing, transcriptional regulation and stem cell function before and after injury and in aging. We establish that NS increased in size and number in MuSCs following injury and influence MuSC activation dynamics. We generated a catalog of isoform-resolved splicing events and linked how RNA interactions with NS amplify splicing completion during the injury response. In old age, MuSCs lose NS, yet shifted towards longer, more completely spliced isoforms enriched for RNA binding protein motifs and multivalency. Our studies unveil evidence that RNA interactions with NS shape stem cell state and regenerative responses but are attenuated in old age. HIGHLIGHTSO_LI3D super-resolution imaging of nuclear speckles in muscle stem cells before and after muscle injury shows intricate relationship with activation C_LIO_LIIsoform-resolved profiling of muscle stem cells shows increases in gene expression and splicing during injury response C_LIO_LIMapping RNA interactions with nuclear speckles shows RNAs undergo strongest splicing when proximal to nuclear speckles C_LIO_LIOld aged muscle stem cells lose nuclear speckles and display aberrant splicing, with longer transcripts, more exons, and increased RNA binding protein motifs C_LI

genomics↗