Biology subjects

Yuan, H.

Publications and source records attributed to Yuan, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Early-life mucosal T cells direct intestinal stem cell fate via a coordinated developmental program

Although early-life immunity was once considered immature, the human fetal immune system is dynamic and compartmentalized by the second trimester. By 21 weeks of gestation, T lymphocytes become a major immune population in the fetal small intestine (SI), yet their functional roles within this tissue remain largely undefined. To explore their unique contributions to intestinal development, we established an ex vivo co-culture system in which mucosal T cells isolated from fetal, neonatal, or adult SI donors were cultured with tissue-derived 3D SI organoids derived from various ages. Homeostatic early-life (fetal and neonatal) SI T cells uniquely promoted organoid generation, a metric of stem cell renewal, by upregulating cell cycle-associated gene programs. These early-life T cells also directed intestinal stem cell differentiation toward the secretory lineage in both growth and differentiation phase, highlighting that T cells poise stem cells to adopt secretory fates. T cells from infants with necrotizing enterocolitis (NEC) - an inflammatory intestinal disease affecting predominantly preterm infants - failed to activate these same programs, suggesting a pathologic role for T cells in NEC. T cells from the adult SI similarly failed to support organoid growth or differentiation, revealing developmentally specialized, nonimmune functions for early-life T cells in the intestine. Similarly, T cells derived from cord blood did not enhance organoid generation, indicating that this function is not necessarily a generalized feature of early-life T cells but rather is restricted to mucosal T cells. Organoids derived from adults or NEC, however, could re-enter regenerative states when co-cultured with fetal T cells, indicating that fetal T cells can restore stem cell self-renewal across developmentally and disease-imposed states. We further identified that T cell-derived soluble factors alone were insufficient to modulate intestinal stem cell fate, implying the need for physical interactions. Concordant with this finding, we report that T cells heavily localize to the stem cell niche during prenatal development, where they express factors involved in Notch, Wnt, and growth factor signaling to support fetal stem cell function. Collectively, these findings reveal a coordinated developmental program in which fetal SI T cells balance stem cell self-renewal and differentiation, identifying a developmental immune-epithelial axis that can be harnessed to restore intestinal regeneration.

immunology↗

bioRxiv2026

A versatile, positive-going voltage indicator that enables accessible two-photon recordings in vivo

Genetically encoded voltage indicators (GEVIs) enable cell-type-specific optical readout of membrane potential, but two-photon (2P) spike detection has been hampered by low signal-to-noise and ultrafast off-kinetics, restricting use to specialized microscopes. We introduce FORCE1s, a green, positive-going GEVI engineered to make robust 2P voltage imaging broadly accessible. FORCE1s brightens from a dark baseline during depolarization, reports spikes with [~]100% {Delta}F/F in awake mice, and displays repolarization kinetics that are tuned for reliable spike detection at sub-kilohertz frame rates. As a result, FORCE1s supports spike-resolved multi-cell recordings on standard resonant-scanning microscopes, and further scales to larger fields of view and neuron counts on advanced modalities. FORCE1s also enables multiplexed voltage-neurotransmitter imaging and extended recordings in freely moving mice using a compact, affordable MEMS-based 2P miniscope. Together, these advances establish FORCE1s as a community-ready tool that democratizes deep-tissue voltage imaging across platforms and experimental contexts.

neuroscience↗

bioRxiv2026

Linking Genetic Risk to Disease-Relevant Cellular States via Metacell-Informed Modeling with ICePop

Genome-wide association studies (GWAS) have implicated thousands of loci in complex diseases, but translating these population-level signals into specific cellular contexts remains a central challenge. Integrating GWAS with single-cell transcriptomics data has enabled systematic identification of disease-relevant cell types, yet existing methods face a fundamental tradeoff: approaches like seismic that optimized for statistical power operate at the annotated cell-type level and miss heterogeneous disease signals concentrated in specific cellular states, while single-cell-resolution approaches like scDRS that capture such heterogeneity often lack sufficient power to detect subtle associations. Here we present ICePop (Informative Cell Populations), a framework that resolves this tradeoff by performing disease-cell type association at metacell resolution, thus achieving statistical power comparable to cell-type-level methods while detecting heterogeneous disease signals within cell types. In simulations against seismic and scDRS, ICePop maintains appropriate false positive rates and demonstrates superior power when disease effects are concentrated in cellular subpopulations. Applied to Tabula Muris across 81 traits and 120 cell types, ICePop identifies 1,684 disease-cell type associations, including the preferential vulnerability of differentiated gut epithelial cells in ulcerative colitis and loss of cell identity in immune-stressed lung capillary endothelial cells underlying their association with lung function. Clustering diseases by metacell association profiles reveals groupings that diverge from genetic risk-based clustering, including separation of blood cell count traits from immune diseases despite shared genetic architecture, reflecting differences in cellular rather than genetic etiology. In autism spectrum disorder, ICePop identifies preferential enrichment of genetic risk in specific enteric neuron subtypes, implicating dysfunction of the enteric nervous system in gastrointestinal comorbidities. ICePops resolution of disease-relevant cell states within annotated cell types enables generation of testable, cell-state-specific hypotheses about disease mechanisms and therapeutic targets.

genomics↗

bioRxiv2026

Neurodegeneration risk variants promote lysosomal TMEM106B fibrilaccumulation

Variants in TMEM106B and GRN, which encode lysosomal proteins, interact through unknown mechanisms to increase the risk of age-related cognitive decline and neurodegeneration. Here, we show that these variants converge on a single molecular intermediate: the cleaved intra-lysosomal fibril core of TMEM106B, a precursor to amyloid fibrils that accumulate in the aging brain. A protein-coding TMEM106B risk variant (p.T185) drives fibril core accumulation by impairing its degradation and GRN risk variants amplify this effect. Mice over-expressing the fibril core develop hallmarks of neurodegeneration, and cryo-electron tomography reveals intra-lysosomal fibrils in cultured neurons, mice, and diseased human brain. In GRN-mutation carriers, in whom fibril burden is greatest, fibrils extrude through ruptured lysosomal membranes. These findings identify intra-lysosomal TMEM106B fibrillization as a convergent neurodegeneration mechanism and potential therapeutic target.

cell biology↗

bioRxiv2026

Co-evolution of Oncogenic KRAS Signaling and LILRBhigh Macrophages Drives Pancreatic Cancer Recurrence

Pancreatic ductal adenocarcinoma (PDAC) frequently recurs after surgical resection, indicating that residual disease is sustained by coordinated tumor-microenvironment interactions. To define the biological basis of recurrence, we leverage large-scale clinical data from 2,710 patients, deeply characterized multi-omics profiling (whole-exome, bulk RNA, and single-nucleus sequencing) of 36 matched primary and locally recurrent PDACs, an in-house multiplex spatial imaging cohort of 190 patients, and extensive public datasets. Recurrent tumors were characterized by increased KRAS mutant allele dosage and reinforced KRAS signaling, accompanied by expansion of basal-like malignant cell states. In parallel, we identified an immunosuppressive macrophage population marked by high LILRB expression that spatially co-localized with KRAS-activated tumor cells. Functional studies showed that LILRB4+ macrophages enhanced tumor cell plasticity and progression, whereas inhibition of macrophage LILRB4 suppressed these phenotypes. Notably, a first-in-class human anti-LILRB4 antibody reduced macrophage-driven tumor traits, and dual targeting of KRAS signaling and LILRB4 achieved superior tumor control in macrophage-containing mouse models. These findings reveal a co-evolved tumor-immune niche underlying PDAC recurrence and nominate the KRAS-LILRB4 axis as a therapeutic vulnerability.

cancer biology↗

bioRxiv2026

Metabolic control of mitochondrial plasticity and extracellular vesicle biology drives Cryptococcus neoformans virulence

Metabolic adaptation to nutrient stress is a key but poorly understood driver of fungal virulence. Here, we show that a dominant East Asian lineage of Cryptococcus neoformans (VNIa-5), which disproportionately infects immunocompetent hosts, has undergone lineage-specific rewiring of glucose-responsive stress pathways. Integrating population genomics, transcriptomics, and experimental infection models, we demonstrate that VNIa-5s clinical dominance is not explained by environmental prevalence. Instead, selective activation of Snf1 signalling links glucose limitation to mitochondrial tubularisation, extracellular vesicle remodelling, and enhanced melanization. Under low-glucose conditions, VNIa-5 exhibits marked mitochondrial plasticity and extracellular vesicle compositional shifts resembling hypervirulent outbreak lineages of Cryptococcus gattii. Following experimental induction of dormancy, VNIa-5 shows significantly increased virulence in vivo compared with the closely related but clinically rare VNIa-31 subclade, with host survival tightly correlated with mitochondrial morphology. These findings identify metabolic stress integration as a central mechanism shaping cryptococcal virulence and disease in immunocompetent human hosts.

microbiology↗

bioRxiv2026

BayesR3AD: Joint analysis of additive and dominance in Bayesian mixture models

BackgroundGenomic prediction in livestock is predominantly based on additive models, even though dominance and other non-additive effects can contribute appreciably to phenotypic variance for fitness and fertility traits. Bayesian mixture models, such as Bayes R, have proven effective for modelling sparse, heterogeneous additive SNP effects, but most implementations do not explicitly accommodate dominance. In this study, we extended BayesR3 to jointly model additive and dominance marker effects within a unified Bayesian mixture framework, denoted BayesR3AD, and used this method to estimate additive and dominance effects for fertility and cow survival (longevity) in Holstein cattle. ResultsUsing real Holstein genotypes (227,942 animals, 74,626 SNPs), we simulated phenotypes with additive and dominance effects. When dominance was present in the simulated data, BayesR3AD improved prediction accuracy of genetic values by +0.1011 (0.6144 vs 0.5133; {approx}19.7% relative) compared with the additive-only BayesR3 model and recovered additive and dominance variance components without bias. Under purely additive simulations, dominance mixture components were effectively empty, confirming that the extended model shrinks unnecessary dominance effects toward zero. In real fertility data, including calving interval (63,378 records) and survival (68,514 records), BayesR3AD estimated small dominance variance ({approx}1-3% of total genetic variance). The model highlighted a very large additive loci at 57.82 Mb on BTA18 for both calving interval and survival. concordant with previous GWAS studies of Holstein fertility. Additionally, a large dominance effect was found at 44.37 Mb on BTA18 for calving interval implicating a heterozygote advantage that increases fertility. ConclusionsBayesR3AD provides a practical extension of BayesR3 that captures both additive and dominance contributions to genomic prediction. The method is robust, reverting effectively to the additive model when dominance is absent, while delivering accurate variance decomposition, and potential gains in prediction accuracy when dominance is present. Application to Holstein fertility traits demonstrates that dominance can be detected and quantified without compromising additive inference, supporting improved prediction of total genetic merit. While validated in cattle, BayesR3AD can be directly applied to other species to better model and predict traits related to fitness.

genetics↗

bioRxiv2026

A role for ETV1 and endothelial cell-derived extracellular vesicle microRNAs in priming fibroblast response to vesicle-bound FGF2

Communication between various cell types following wounding is paramount for proper healing and regeneration of injured tissue. Endothelial cells and fibroblasts are critical cellular players involved in cutaneous wound repair, yet their communication mechanisms are not well understood. It has previously been shown that extracellular vesicles derived from endothelial cells (ECEVs) induce dermal fibroblasts to express a gene signature correlated with FGF2-mediated cancer associated fibroblast (CAF) activation, under the control of transcription factor ETV1. In this report, we utilize loss-of-function studies to define the mechanistic role of ETV1 in conferring this ECEV-induced transcriptomic shift and functional change in fibroblasts. Additionally, we identify highly expressed ECEV microRNAs and examine their potential contribution to the ECEV mechanism through downstream gene modulation. In summary, we describe a plausible mechanism by which both ETV1 and top ECEV microRNAs promote a genotypic and phenotypic shift in dermal fibroblasts that have taken up ECEVs.

cell biology↗

bioRxiv2026

Unleashed condensation by recurrent mutations of an epigenetic regulator promotes cancer

The pathological mechanisms and significance for the prevalent hotspot mutations in disordered protein regions are poorly understood. ASXL1 is an obligate co-factor for BAP1 in H2AK119 deubiquitination. ASXL1 mutations are very frequent in myeloid malignancies, and are mostly C-terminal truncating mutations concentrated in a specific disordered region of ASXL1. ASXL1 truncations are gain-of-function mutations that promote myeloid malignancies, but the underlying mechanisms remain poorly understood. Here we show that the frequently truncated mutants of ASXL1 possess an intrinsic property of forming phase-separated biomolecular condensates, and this property is normally suppressed by the frequently deleted regions. A disease-mutant of the endogenous ASXL1 in leukemia cells forms dynamic nuclear co-condensates with other endogenous factors important for gene activation. The ASXL1 disease-mutants can greatly enhance H2A deubiquitination activity of BAP1 in cells and in vitro reconstituted system, enhance myeloid leukemia cell growth, and promote leukemogenesis in a mouse transplant model by turning on myeloid leukemogenic transcriptional programs. However, substitution of residues important for condensation disrupted or impaired all these abilities, suggesting that the condensation property is crucially important for the ASXL1 mutants in promoting cancer. Moreover, we discover that the conserved negative charges in the highly disordered and frequently deleted region on ASXL1 suppress the condensation of the wild type ASXL1. Charge-neutralizing mutations in this region restores condensation of the full-length ASXL1, and are sufficient to turn ASXL1 into a leukemogenic protein. Biochemical, biophysical, and simulation analyses suggest the intramolecular interactions normally mask the N-terminal region in engaging intermolecular interactions required for phase separation, and disease truncations escape from the regulatory interactions and unleash the phase separation property to form nuclear hubs to promote expression of tumorigenic gene programs. Finally, by showing a striking correlation of the mutation frequencies with the condensation properties and leukemogenesis activity for a series of human patient mutations, we suggest that dysregulation of condensation is a central mechanism for ASXL1 mutations in promoting myeloid malignancies. This suggests that dysregulation of condensation may be a key mechanism for some of the prevalent hotspot disease mutations in the disordered proteomes.

biochemistry↗

bioRxiv2026

TREM2 agonist antibody rebuilds the resident synovial macrophage lining barrier in rheumatoid arthritis

Rheumatoid arthritis (RA) can be viewed as a disease of barrier failure, in which CX3CR1+/TREM2+ synovial tissue-resident macrophages that form the lining barrier over cartilage and bone become fragmented and disorganized. However, how to therapeutically rebuild this barrier--and how macrophage states transition during repair--remain unclear. We engineered TR-Ab19, a mouse-selective agonistic antibody against TREM2, as a precision tool to initiate and interrogate barrier repair in vivo. TR-Ab19 engages TREM2-linked downstream signaling and redirects synovial macrophages from Clec4d+ inflammatory/proliferative programs toward TREM2+CX3CR1+Aqp1+ barrier-like states, thereby rebuilding the lining barrier. Across collagen-induced arthritis (CIA) and serum-transfer arthritis (STA) models, TR-Ab19 reduces synovitis, preserves cartilage and bone microarchitecture, limits osteoclastogenesis, and attenuates systemic cytokines and B-cell abnormalities. Single-cell RNA-seq with trajectory and cell-cell communication analyses reveal a TREM2-dependent shift toward a barrier-dominant macrophage ecosystem. Together, these findings establish antibody-mediated reprogramming of resident synovial macrophages as a barrier-centered strategy for RA and provide a framework for instructing macrophage niches in chronic inflammation.

bioengineering↗

bioRxiv2026

3D Cell-Matrix Mechanical Interaction Models for Cancer Invasion and Drug Evaluation

Cancer cells breach the extracellular matrix (ECM) using both protease-driven degradation and force-driven physical remodeling, yet most anti-metastatic drug screens still rely on biochemical assays that overlook cell-matrix mechanical reciprocity. Here, we present a fully synthetic 3D invasion platform based on cellular force-responsive polyisocyanide (PIC) hydrogels that isolates biophysical invasion mechanisms. Cell-generated forces align and densify the PIC fibrous network, reproducing hallmark matrix remodeling seen in the tumor microenvironment. A constitutive model, parameterized by the critical stress for strain stiffening effect, links matrix nonlinear elasticity to pericellular stiffening, long-range mechanotransmission, and intercellular coupling. Using this system, we show that breast cancer cells invade by pulling and pushing the network even when matrix metalloproteinases are inhibited, revealing a physical bypass of protease blockade. Accordingly, broad-spectrum metalloproteinase inhibitors that suppress invasion in Matrigel fail to inhibit invasion here, exposing a limitation of current drug-evaluation pipelines. In co-culture, cancer-associated fibroblasts markedly accelerate invasion by generating aligned fiber tracks through higher contractility, implicating CAF-driven mechanical remodeling as a key route for breaching barriers during metastasis. The platform is thermoresponsive, compatible with standard Transwell formats, enables direct imaging of fiber architecture and invasion fronts, and decouples biophysical from biochemical cues for mechanism-aware, animal-free assessment of anti-metastatic therapies.

cancer biology↗

bioRxiv2026

Light-entrained chromatin priming poises rapid metamorphosis in a marine sponge

The most widespread animal life cycle includes a planktonic larval stage that is environmentally induced to settle and rapidly metamorphose into a benthic juvenile. Although this transition is critical for survival, how planetary cues such as light interact with local ecological signals to prepare the genome for such rapid reprogramming remains poorly understood. Here, using the sponge Amphimedon queenslandica, we integrate time-resolved transcriptomic and chromatin accessibility profiling across larval competence, settlement, and the first hours of metamorphosis. We show that diminishing light at sunset is associated with extensive chromatin remodelling in swimming larvae prior to settlement, despite relatively modest changes in gene expression. Upon environmental induction by a coralline alga, metamorphosis is accompanied by the rapid and transient activation of a large suite of deeply conserved transcription factors, including AP-1/bZIP family members, whose binding motifs are enriched in newly accessible regulatory regions near differentially expressed genes. Larvae prevented from experiencing sunset by constant light fail to settle and instead adopt an alternative transcriptional and chromatin state characterised by widespread loss of accessibility and repression of competence-associated transcription factors, including the circadian regulator CLOCK and other bHLH-PAS factors. These observations support a model in which light-entrained transcriptional activity establishes an anticipatory, permissive chromatin landscape that enables immediate and coordinated transcriptional reprogramming upon environmental induction. We propose that such chromatin priming may represent a broadly deployed regulatory strategy underlying the speed and robustness of metamorphosis in biphasic animal life cycles.

developmental biology↗

bioRxiv2026

Radiosynthesis and Evaluation of Novel Cholesterol 24-Hydroxylase Positron Emission Tomography Tracers

Cholesterol 24-hydroxylase (CH24H or CYP46A1) is a pivotal enzyme in brain cholesterol metabolism and has emerged as a therapeutic and imaging target in neurodegenerative disorders. Although [18F]Cholestify ([18F]CHL-2205) has shown promise as a positron emission tomography (PET) tracer for imaging of CYP46A1, the impact of cyclopropyl moiety conformation on binding and imaging performance remains unexplored. Here, we report the rational design and preliminary evaluation of novel CYP46A1 PET tracers, in which the left-side cyclopropyl group was modified into bridged, spirocyclic, and fused bicyclic architectures to probe steric and conformational effects. All compounds 9-11 exhibited high CYP46A1 affinity (IC50 = 0.19-0.28 nM). Radiosynthesis of [18F]9-11 was achieved via copper-mediated [18F]fluorination, providing practical non-decay-corrected radiochemical yields of 10-34% with excellent radiochemical purity (>98%). In vitro autoradiography in rat brain sections demonstrated specific and regionally selective binding, comparable to that observed for [18F]CHL-2205. These cyclopropyl-derived scaffolds establish a scaffold-driven strategy for PET tracer development, providing a robust framework for further structure-activity relationship studies and the rational optimization of CYP46A1 PET tracers.

pharmacology and toxicology↗

bioRxiv2025

DNA replication errors drive genome-wide small inverted triplication dynamics

Structural variants (SVs) have a profound impact on phenotype and diversity and are associated with human diseases. To explore the origination of SVs, we have analyzed 1,340 cancer genomes with annotation of 4,608 novel small inverted triplication (SIT) events and found that FEN1 is strongly associated with SIT incidence. Then, we performed long-read sequencing and developed PacBioR to annotate SITs in yeast FEN1 mutant cells. We found that SIT structures mimic classic inverted triplications but with a smaller DUP/IN/DUP structure of 184/160/184 bp on average, with a spacer sequence of 30 bp and breakpoint junction of 6 bp. We further showed that breakpoints of SITs preferentially occurred at nucleosome midpoints, aligned with Okazaki fragment termini, and those harbored in plasmids were precisely eliminated via DNA polymerase slippage over SIT-derived hairpin structures. This study provides mechanistic insight into SIT origination and offers practical tools for future studies on genome rearrangements.

genetics↗

bioRxiv2025

AI Identifies Broadly Neutralizing Antibodies from an IGHV1-69 Public Antibody Class Exerting Continued Selection Over SARS-CoV-2

R1-32-like public antibodies, characterized by shared IGHV1-69/IGLV1-40 usage, are elicited in more than 50% of individuals with COVID-19 and have been implicated in driving recurrent mutations at L452SARS2 and F490SARS2 within their convergent epitope in the SARS-CoV-2 spike receptor-binding domain. These mutations effectively mediate escape from non-affinity-matured R1-32-like antibodies with germline-like sequences. Here, we characterize four affinity-matured R1-32-like antibodies, C092, C807, BD56-104, and BD56-597, that tolerate L452SARS2 and F490SARS2 mutations. We show that this tolerance arises from residues introduced by somatic hypermutation at convergent positions across multiple CDR loops and surrounding regions, thereby creating additional contacts that reinforce epitope binding. An unusual N354SARS2 glycosylation site, which emerged in BA.2.86 and became fixed in its descendants, is linked to escape from affinity-matured R1-32-like antibodies, implying ongoing selection by this public antibody class. Using an AI model trained on integrated structural, neutralization, and binding data, we further identified ZL525, an ultrapotent R1-32-like antibody with pan-SARS-CoV-2 variant activity, including against the highly evasive KP.3 variant carrying the N354SARS2 glycosylation, and broad sarbecovirus cross-reactivity extending to SARS-CoV-1. Together, these findings show how affinity maturation enables public antibodies to adapt to viral antigenic drift, reveal their role in shaping SARS-CoV-2 antigenic evolution, and demonstrate the potential of AI-empowered strategies for discovering broadly neutralizing antibodies.

immunology↗

bioRxiv2025

AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies

Elucidating the mechanisms by which broadly neutralizing antibodies (bnAbs) develop to confer durable immunity in humans is pivotal for the rational design of next-generation vaccines and therapeutics. VH3-53/3-66-encoded public antibodies are widely elicited in the population after the COVID-19 pandemic. Here, we isolated 15 VH3-53/3-66-encoded bnAbs from elite neutralizers who experienced sequential SARS-CoV-2 Omicron breakthrough infections. These bnAbs exhibit exceptional potency and breadth against circulating variants and, as members of a long-lived public antibody lineage, likely contribute to durable humoral protection. Genetic analysis of VH3-53/3-66-encoded bnAbs reveals a convergent somatic hypermutation pattern at seven positions in and around the CDR loops that emerges with repeated viral exposures and distinguishes them from non-bnAbs. Grafting these combined mutations onto clinically escaped antibodies broadens their breadth and restores neutralization activity. Structural analysis shows that these convergent mutations cooperatively remodel CDRs to bind and tolerate virus receptor-binding domain mutations. Using an AI-based antibody language model trained on data linking somatic hypermutations to binding affinity and neutralization, the model is able to identify mutational patterns predictive of breadth, enabling the discovery of a rare bnAb with protective activity against the latest variants from early-pandemic antibody repertoires. This demonstrates the feasibility of establishing an AI-empowered pipeline to identify mutation-tolerant bnAbs from early-pandemic antibody repertoires to fight fast-evolving newly introduced viruses.

immunology↗

bioRxiv2025

Living Neurosheets: Engineering readily deployable neural architectures

Inspired by the ability of brain structures to support cognitive processing, the need for reliable queryable neural models, and emerging biohybrid applications, we present Living Neurosheets: practical, malleable, modular, and scalable systems for realizing living neural architectures, bio-inspired or beyond evolutionary precedent. By innervating porous sheets, paper-like substrates are endowed with neural function while retaining exceptional versatility. Pre-programmed porosity anchors deposited neurons for reliable spatial control. Cutting, folding, and stacking allow intuitive design, modular composition, and batch fabrication (by the hundreds) of complex neural motifs that preserve geometry and function for months. Reversible integration with tissue-matched optoelectronics enables both sample reuse across hardware and hardware multiplexing across samples, for high-throughput, multimodal investigations. We illustrate these aspects across tissue topologies, gyri-inspired manifolds, and laminar cortical mimics, attaining control over entrainment, synchronization, propagation, suppression, and augmentation dynamics--key features of in vivo neural activity. Finally, via cross-instrument portability, we fuse spatial transcriptomics and electrophysiology, linking gene programs to emergent dynamics.

neuroscience↗

bioRxiv2025

An inherent T cell-activating mRNA delivery platform for in vivo CAR T generation

The clinical success of CAR T cell therapy has underscored the need for scalable, non-invasive strategies for in vivo T cell engineering. Although mRNA delivery offers a promising alternative, current lipid-based vectors lack intrinsic T cell tropism and often rely on antibody conjugation, complicating manufacturing and raising safety concerns. Here we present an inherent T cell-activating polymer-lipid nanoparticle (ERTLNPs) that enable ligand-free, efficient mRNA transfection and activation of T cells in vivo. ERTLNPs, composed of p-toluenesulfonyl arginine (RT)-functionalized polyethylenimine (denoted as PEI-RT) and helper lipids, preferentially accumulate in the spleen following systemic administration. Without exogenous stimulation, ERTLNPs intrinsically activate T cells, triggering robust mRNA expression and proliferation. Mechanistically, ERTLNPs engage the PI3K/AKT/mTOR signaling axis to reprogram T cell metabolism, promoting expansion while restraining exhaustion. Systemic delivery of mRNA encoding fibroblast activation protein chimeric antigen receptor (mFAP CAR) via ERTLNPs leads to in situ generation of functional CAR T cells, which efficiently eliminate pathological fibroblasts in models of cancer and fibrosis, with minimal off-target effects. This ligand-free, metabolically reprogramming mRNA delivery platform provides a clinically translatable approach for in vivo CAR T cell generation and broadens the landscape of non-viral immunotherapeutic engineering.

bioengineering↗