Biology subjects

He, R.

Publications and source records attributed to He, R..

At least 19 recordsLinked to original sources

bioRxiv2026

SPACE-Tag Enables High-Throughput Spatial Chromatin Profiling With CUT&Tag

Spatial epigenomics maps chromatin states within intact tissues, yet current methods remain limited by accessibility and scale. We developed SPACE-Tag, a spatial CUT&Tag framework that converts epigenetic marks-associated DNA into polyadenylated RNA through T7 based linear amplification, enabling direct integration with standard spatial transcriptomic workflows. Applied to the mouse brain, SPACETag resolved activating and repressive chromatin landscapes, recovered region-specific gene regulatory programs across anatomical domains, and showed strong correlation with existing bulk and single cell reference data. We generated an integrated multimodal atlas of the aging mouse brain, profiling five histone modifications and the transcriptome in parallel across the adult lifespan to establish the largest spatial multimodal dataset to date. This analysis uncovered sharp regional divergence with aging in the brain: fiber tracts showed widespread transcriptional downregulation, often without nearby chromatin state transitions, whereas the isocortex showed coordinated chromatin transcriptome changes, including an H3K4me1 peak module that increased with age, was enriched at super-enhancers and linked to upregulation of neuronal plasticity regulators. These findings highlight the power of multimodal and high throughput spatial genomics in uncovering the divergent regulatory logic that governs tissue-specific vulnerability and resilience in the aging brain.

genomics↗

bioRxiv2026

Substrate-induced asymmetry coordinates lipoprotein handover and abaucin trapping in Acinetobacter baumannii LolDF

The homodimeric lipoprotein transporter LolDF supports outer-membrane biogenesis in Acinetobacter baumannii. How homodimeric LolDF generates directional lipoprotein transport, and how the reported two- and four-abaucin states are related, remain unclear. Using defined lipidated AbLolB and AbLolA, we show that substrate binding breaks LolF symmetry: LolFB primarily accommodates the lipid anchor, LolFA positions the adjacent polypeptide, and LolA docks asymmetrically through the LolF hook and an AbLolA-specific loop. C1 reconstruction of the wide abaucin state reveals non-equivalent central ligands, whereas C2 processing of the same particles averages this asymmetry; the two peripheral ligands form a stable inhibitory core, while the central sites are conditionally occupied in the expanded cavity. Abaucin inhibits ATPase activity and LolA-mediated transfer from substrate-associated LolDF, supporting a unified mechanism in which substrate-induced asymmetry organizes productive handover and its conformational plasticity is redirected during inhibition.

molecular biology↗

bioRxiv2026

Brain state locks silent memories in a trained fly connectome

Complete connectomes now exist for insect nervous systems, but whether a fixed wiring diagram can learn, and what its memories consist of, is unknown. Here, we trained a spiking model of the whole male Drosophila central nervous system, 167,106 neurons with fixed wiring, to plan moves and to remember a visual cue. Spikes write the cue into neuronal adaptation, which holds it silently until the next input reads it out. Cells that hold the trace are enriched for transcripts of a calcium-activated potassium channel in fly cell atlases. The learned readout recalls the trace only in the brain state of learning: the same trace evokes a different response at another delay, and a disease-like loss of potassium current rewrites the trace and changes how it is read. Learning in the new state is spared. Memory failure can arise from a change of state rather than a loss of storage.

neuroscience↗

bioRxiv2026

In situ loading of biologics on and tissue redirection of circulating extracellular vesicles with an anchoring nanobody

Extracellular vesicles (EVs) are promising nanocarriers of therapeutic macromolecules, but ex vivo production, cargo loading and quality control constrains clinical translation. Here we demonstrate that NEV3, an EV-anchoring nanobody identified by phage display, binds EVs from multiple sources through interactions involving fibronectin and loads diverse proteins onto EVs, resulting in enhanced intracellular delivery and biological activities in vitro and in vivo. Conjugating NEV3 to target proteins hijacks circulating EVs, prolonging circulation and altering tissue distribution in vivo. When fused with an GFP nanobody or protein A, NEV3 enabled simultaneous capture and loading of circulating GFP or immunoglobulin G (IgG) antibodies on endogenous EVs with enhanced intracellular delivery in vitro and redistribution to liver in vivo. Intravenous protein A-NEV3 significantly reduced circulating IgG and anti-dsDNA antibodies in systemic lupus erythematosus mice with improved survival and reduced pathologies. Intravenous anti-transferrin receptor-protein A-NEV3 redirected circulating EVs to muscle and alleviated muscle pathologies in dystrophin-deficient mdx mice. Our study demonstrates that NEV3 enables in situ loading of protein therapeutics and tissue-specific delivery of circulating EVs, providing a modular strategy for loading cargo onto and redirecting circulating EVs in vivo.

bioengineering↗

bioRxiv2026

A unique intestinal epithelial cell that expresses canonical lymphoid genes

Enterocytes and intestinal secretory cells harbor innate immunity. However, certain transcriptional programs -even beyond rearranged T- and B-cell receptor genes- are considered the exclusive purview of adaptive immune cells, including abundant and diverse intestinal intra-epithelial lymphocytes (IELs). Here, we identify and characterize columnar intestinal secretory cells that co-express classic epithelial and lymphoid genes, including Ptprc, Cd3e, Cd8a, and Gzma/b but not T- or B-cell receptors. These previously unrecognized epithelium-derived lymphoid-like cells (EDLCs) differ from any known resident cell type, including IELs or tuft cells. Rare in healthy mouse and human intestines, their numbers increase upon IL-25 stimulation or IL-10 receptor deficiency in vivo and upon IL-13 stimulation in vitro. EDLC chromatin is uniquely accessible at thousands of cis-elements, including lymphoid and epithelial loci. These findings reveal a transcriptionally and epigenetically distinct intestinal epithelial derivative that expresses prominent lymphoid character.

cell biology↗

bioRxiv2026

A tumor-cell MHC-II program is associated with checkpoint-blockade outcomes across stages of bladder cancer

Purpose: A minority of patients with bladder cancer derive lasting benefit from immunotherapy, and current biomarkers capture only part of the biology. We evaluated whether tumor-cell MHC class II defines an immune state associated with outcome across disease stages and after PD-1/PD-L1 blockade. Experimental Design: We localized differential MHC-II activity to malignant epithelial cells by single-nucleus and single-cell RNA sequencing and confirmed HLA-DR expression by immunohistochemistry in 122 specimens. Chromatin profiling and IFN-{gamma} stimulation of cell lines and primary tumors supported derivation of an 11-gene tumor-cell program. Associations were tested in 434 patients with non-muscle-invasive disease, 82 receiving neoadjuvant pembrolizumab, and 288 receiving atezolizumab for metastatic disease. Results: Tumor-cell MHC-II was present in approximately one third of bladder cancers, and malignant cells accounted for the differential signal between MHC-II-high and MHC-II-low tumors. The program was inducible by IFN-{gamma} through JAK/STAT signaling. Within luminal non-muscle-invasive disease, MHC-II-low status was associated with progression (HR 3.31, 95% CI 1.37 to 7.99). In PURE-01, the 11-gene program was associated with pathological complete response (52% versus 24%, p = 0.018) and recurrence-free survival (p = 0.0054), retaining an independent association in models including tumor mutational burden and PD-L1. In bladder-primary metastatic disease, program-high status was associated with overall survival in unadjusted analysis (HR 0.62, 95% CI 0.44 to 0.89); the association did not extend to upper tract tumors (interaction p = 0.0018). Conclusions: Tumor-cell MHC-II defines an inducible state associated with outcomes across bladder cancer stages and after checkpoint blockade, supporting prospective evaluation by RNA and immunohistochemistry.

cancer biology↗

bioRxiv2026

stEDGE enables edge-guided multiscale reconstruction of hierarchical spatial domains and transition interfaces in spatial transcriptomics

Spatial transcriptomic technologies enable high-resolution mapping of tissue architecture, yet most computational methods still represent tissues as flat spatial partitions, limiting their ability to resolve spatial domain boundaries, gradual transition regions and nested hierarchies. Here we present stEDGE, an edge-guided and interpretable framework for multiscale reconstruction of spatial domain hierarchies and transition-associated states in spatial transcriptomics. Unlike conventional domain-first approaches, stEDGE first estimates local boundary structure and uses it to guide the reconstruction of fine-grained spatial domains. We further introduce a domain transition index (DTI) to quantify domain-level transition propensity and integrate DTI with inter-domain similarity and boundary strength to organize fine domains into a coherent multilevel hierarchy. A tree-guided gene attribution strategy then distinguishes shared parent-level programs from branch-specific specialization across hierarchical spatial states. Across 15 benchmarked tissue sections spanning diverse tissues, technologies and spatial resolutions, stEDGE reconstructs developmental, inflammatory, tumor and brain architectures beyond conventional domain partitioning. Applied to cell-resolved Xenium profiling of fibrotic human lung, stEDGE further reveals lesion-associated remodeling as a coherent multiscale hierarchy in which remodeling interfaces coexist with a stable macrophage-associated airway/lumen state and spatially organized TLS-like lymphoid niches. Together, stEDGE provides a unified framework for modeling how stable compartments, domain boundaries, remodeling interfaces, localized niches and multiscale gene programs are jointly organized across spatial scales.

bioinformatics↗

bioRxiv2026

Generation and application of human pluripotent stem cells derived peri-nervoids

Autologous nerve grafts remain the gold standard for peripheral nerve repair, but donor scarcity, donor-site morbidity and incomplete functional recovery limit their use. Schwann cells (SCs) drive autograft-mediated regeneration, yet their limited availability and expansion impede SC-based therapies. Here, we generated human pluripotent stem cell-derived SCs, motor neuron-enriched spinal cord organoids and nociceptive sensory neuron-enriched dorsal root ganglion organoids, and assembled them into a nerve-like construct termed the Peri-nervoid. Single-cell RNA sequencing revealed context-dependent SC plasticity: axonal co-culture promoted myelination, whereas axonal transection induced a repair phenotype resembling SC dedifferentiation during Wallerian degeneration. Following transplantation into 7-mm sciatic nerve defects in NSG mice, human SCs survived and remyelinated regenerating host axons, while axon-containing grafts enhanced regeneration relative to SC-only grafts. No abnormal proliferation, systemic toxicity or major-organ histopathology was detected. These findings position the Peri-nervoid as a scalable, developmentally inspired platform for developing engineered grafts for peripheral nerve repair.

bioengineering↗

bioRxiv2026

Coevolution-driven reconstruction of multi-taxa siderophore interaction networks reveals topological diversity of microbial exploitation

Microbial communities are shaped by secreted metabolites that mediate ecological interactions, yet predicting these interactions from genomic sequences remains difficult, because the specific recognition between co-functional metabolites (CFMs), such as siderophores, and their receptor proteins (Rec) cannot be inferred from gene annotation alone. This difficulty arises from three factors: the prevalence of Rec-mediated exploitation, the lack of high-accuracy functional annotations, and the absence of genomic co-localization between functionally paired CFM-Rec in Gram-positive bacteria. Here we present the Coevolution-based Interaction Model (CIM), an automated framework that maps specific CFM-Rec pairings directly from uncurated genomic datasets. Using a dynamic joint optimization strategy that accounts for exploitation asymmetry and avoids combinatorial explosion, CIM identifies functional pairings solely through evolutionary covariation. We validated this approach by reconstructing macroscale iron scavenging networks across nine bacterial taxa. Experiments confirmed that CIM can bridge genomic distances exceeding 3 Mb in the Gram-positive genus Rhodococcus to identify unlinked cognate receptors, and can accurately predict cross-utilization by exploiter strains despite substantial receptor sequence heterogeneity in Burkholderiaceae and Rhizobiaceae. Finally, topological analysis of the reconstructed networks shows that siderophore exploitation acts as a universal topological glue, fusing fragmented microbial populations into highly connected communities, and that the exploitability of siderophore production reverses depending on network modularity. CIM thus offers a scalable, sequence-to-ecology approach for predicting interactions mediated by secondary metabolites in microbial communities.

systems biology↗

bioRxiv2026

Regulation of Chlamydia trachomatis infection in the female genital tract by type I and type II interferons

Following an intravaginal inoculation with Chlamydia trachomatis, mice deficient in type I interferon receptor IFNR1 (IFNR1-/-) significantly increased the yield of live chlamydiae on days 3 & 5 but reduced it to the level of wild-type mice by day 7, while mice deficient in type II interferon receptor IFN{gamma}R1 (IFN{gamma}R1-/-) significantly increased the chlamydial yield by day 5 and the increase persisted throughout the remainder of the infection course. These observations reveal a temporal division of labor between type I & II interferons in regulating C. trachomatis infection in the female genital tract. Interestingly, mice deficient in both IFNR1 & IFN{gamma}R1 exhibited higher mortality and shed more chlamydial organisms than IFN{gamma}R1-/- mice by week 6, suggesting that IFNR1 remains critical for inhibiting C. trachomatis at late stages. An anti-IFNR1 antibody blockade significantly increased chlamydial yields in IFN{gamma}R1-/- mice, suggesting that the anti-chlamydial activities of type I & II interferon systems are both distinct and overlapping throughout the infection course. Furthermore, the anti-chlamydial activity of type I interferon signaling is localized to the lower vagina, while that of type II interferon signaling is localized to the upper vagina. Thus, we have demonstrated that type I & II interferons function complementarily and synergistically in time and space to control C. trachomatis infection, laying the foundation for further elucidating the mechanisms of IFN regulation of chlamydial infection and for developing interventional and preventive strategies against C. trachomatis in the female genital tract. ImportanceLack of information on the precise roles of type I and type II interferons during chlamydial infection has hindered the development of interferon-based strategies to prevent chlamydial infection and pathogenicity. The current study has revealed a temporal division of labor between type I & type II interferons in regulating chlamydial infection in the female genital tract, with type I acting earlier than type II during the innate phase. Nevertheless, type I remains critical for cooperating with type II to suppress chlamydia 6 weeks after infection. Finally, type I interferons seem to mainly target chlamydial infection in the lower vagina, while type II interferons target the infection in the upper vagina. These new findings on the distinct and overlapping roles of type I and type II interferons in regulating chlamydial infection may guide the development of interferon-based precision strategies to reduce chlamydial infection and pathogenicity in the female genital tract.

immunology↗

bioRxiv2026

Kidney medulla macrophages maintain a free flow of urine by sensing force

Blockade by sedimentary particles, such as mineral crystals, is a continuous risk the kidney tubule faces. To prevent that, kidney resident macrophages form transepithelial protrusions and remove intratubular sedimentary particles, a behavior particularly prevailing in the medulla over the cortex. However, the molecular mechanisms underlying this characteristic behavior of medulla macrophages are incompletely understood. In this study, we identified that the medulla had higher mechanical stiffness than the cortex in steady state, which was further elevated when kidney stone formed. Increased tissue rigidity was sensed by medulla macrophages via mechanoreceptor Piezo1, which promoted macrophage protrusion formation and their ability to clean the tubules. Loss of Piezo1 expression in kidney macrophages predisposed mice to intratubular accumulation of mineral crystal in steady state and accelerated kidney stone formation during oxalate intake challenge. Signaling via Piezo1 mobilized molecules involved in cell adhesion and protrusion assembly, including Talin2 and focal adhesion kinase (FAK). Finally, we developed a first-of-its-kind cell-based therapy for the treatment of experimental nephrolithiasis by exploiting macrophage Piezo1 activity, and this strategy shows great promise for future translational research.

physiology↗

bioRxiv2026

Novel Muscle-Tropic AAV Capsids with Dramatically Enhanced Transduction and Safety Profiles in Non-Human Primates

Adeno-associated virus (AAV) gene therapy holds immense promise for treating muscular dystrophies, yet its efficacy and safety are constrained by the suboptimal tissue tropism of natural serotypes. Here, we employed the REACH platform, which combines rational design and directed evolution, to engineer muscle targeting vectors. Systemic administration in non-human primates (NHPs) revealed that lead candidate M1 mediates a >10-fold increase in skeletal muscle transduction compared to the AAV9 and 2-3 fold higher than MyoAAV, while concurrently achieving a remarkable 183-fold reduction in liver distribution. Furthermore, M1 exhibited significant de-targeting from key off-target tissues, including dorsal root ganglia (11 fold), lung (27 fold), spleen (2 fold), and kidney (2 fold). These findings demonstrate that the REACH platform can generate AAV capsids with simultaneously enhanced muscle tropism and favorable safety profiles, addressing a critical bottleneck in muscle-directed gene therapy.

bioengineering↗

bioRxiv2026

Causally validated phase-amplitude coupling enables high-fidelity motor decoding for next-generation brain-computer interfaces

Modern Brain-Computer Interfaces (BCIs) face a fundamental performance plateau due to their reliance on broad spectral power reduction (Event-Related Desynchronization, ERD) as the primary decoding feature. ERD acts as a coarse metabolic proxy for cortical activation, discarding the high-frequency temporal syntax necessary for high-dimensional motor control. Here, we demonstrate that Phase-Amplitude Coupling (PAC)--specifically, the phase-locking of high-gamma (70-150 Hz) firing to residual Beta oscillations--provides a high-fidelity temporal feature for decoding motor intent. Using high-density electrocorticography (HD-ECoG) during motor imagery, we show that incorporating Beta-PAC into machine-learning classifiers (LDA/SVM) significantly outperforms traditional power-based features. To definitively validate the causal robustness of this feature against mathematically-derived artifacts, we leveraged a rare in vivo human structural lesion model. In a patient with focal tumor infiltration of the motor tract, the metabolic gate (ERD) was preserved, yet structural uncoupling completely abolished Beta-PAC, collapsing network topology and reducing single-trial decoding accuracy to chance levels. Our findings causally validate Beta-PAC as a robust, independent control signal, establishing a physiological foundation for next-generation, phase-dependent neuroprostheses.

neuroscience↗

bioRxiv2026

Identification of AAV Capsids with Enhanced Intravitreal Transduction and Favorable Safety Profile in Non-Human Primates

We report the discovery of novel adeno-associated virus (AAV) capsid variants engineered for superior intravitreal (IVT) gene delivery to the primate retina. Utilizing the REACH platform, we constructed a diverse AAV variant library and employed a multi-stage screening strategy involving in vitro selection on human retinal pigment cells followed by direct in vivo screening in non-human primates (NHPs). Following IVT administration in NHPS of a barcoded variant pool, next-generation sequencing analysis of retinal tissues identified lead candidates (e.g., E52, E54, and E57) that achieved transduction levels in the neural retina and RPE 5-10 fold higher than the benchmark R100. Concurrently, these high-potency variants exhibited an exceptional ocular confinement profile, with minimal to undetectable vector genome distribution in systemic organs. This combination of markedly enhanced retinal transduction and stringent local tropism establishes these engineered capsids as promising next-generation vectors for the treatment of inherited and acquired retinal diseases via a minimally invasive IVT route.

bioengineering↗

bioRxiv2026

A global metagenomic atlas uncovers ubiquitous biosynthetic potential linked to adaptation in extreme environments

Extreme environments impose severe physicochemical stresses that drive microorganisms to evolve specialized survival strategies. Microbial secondary metabolites determined by biosynthetic gene clusters (BGCs) are recognized as important mediators of microbial adaptation to environmental stress. However, their ecological roles, particularly habitat-dependent preferences across different environments, remain poorly understood. Although extreme environments provide opportunities to mine microbiomes for unique adaptations, such research is hampered by a lack of systematic overview of its genomic diversity, BGC diversity, and the relationships between them. Here, we constructed a standardized extremophilic genomic catalogue (SEGC) from 1,462 metagenomic samples spanning seven representative extreme habitats. The catalogue comprised 54,661 metagenome-assembled genomes representing 21,805 species, 66.1% of which were previously uncharacterized. With this catalogue, we identified 162,855 BGCs distributed across 81.5% of MAGs. Gene cluster family analysis showed the strong habitat dependence largely explained by species-level habitat specificity. Terpene biosynthetic pathways illustrated habitat-linked adaptive strategies, with hopan-22-ol biosynthesis enriched in acid mine, deep sea and hydrothermal plume environments, while retinal-based phototrophy predominated in cryosphere and saline-alkaline habitats. Metatranscriptomic analyses supported in situ activity of these pathways. In conclusion, we presented a global atlas of biosynthetic potential across extreme-environment microbiota and revealed habitat-dependent patterns of secondary metabolism linked to microbial survival.

microbiology↗

bioRxiv2026

Novel Engineered AAV Variants Demonstrate Superior Blood-Brain Barrier Penetration and Safety in Non-Human Primates

Systemic delivery of adeno-associated virus (AAV) for gene therapy of central nervous system (CNS) disorders is limited by inefficient blood-brain barrier (BBB) penetration and dose-limiting toxicity in peripheral organs, notably the liver and dorsal root ganglia (DRG)1-5. Here, we report the development of novel AAV variants via a proprietary capsid engineering platform (REACH). In non-human primates (NHPs), intravenous administration of lead variants resulted in transgene expression levels in the brain that were 600-2000 fold higher than AAV9 at the RNA level, concomitant with a 10-50 fold reduction in liver tropism and minimal off-target exposure in the heart and DRG. These engineered capsids achieve unprecedented, pan-CNS transduction with a markedly improved safety profile, representing a transformative platform for treating a broad spectrum of neurological diseases.

neuroscience↗

bioRxiv2026

LRP6-Guided Engineering of AAV9 Variants with Enhanced Blood-Brain Barrier Penetration and Reduced Liver Tropism in Non-Human Primates

The blood-brain barrier (BBB) severely restricts the delivery of systemically administered adeno-associated virus (AAV) vectors for central nervous system (CNS) gene therapy. To overcome this limitation, we engineered a library of AAV9 capsid variants through rational design focused on the low-density lipoprotein receptor-related protein 6 (LRP6), a conserved mediator of transcytosis. A multi-tiered screening strategy, encompassing human BBB endothelial cells followed by neuronal and glial target cells in vitro, identified three lead variants (QL9-21, QL9-22, and QL9-25) with markedly enhanced transduction potential. In mice, these variants achieved a 5-28 fold increase in brain-wide gene delivery compared to AAV9, without elevating hepatic tropism. Crucially, evaluation in non-human primates (NHPs) revealed that the lead variant, QL9-21, mediated a striking 3-40 fold enhancement in viral genome delivery across all examined brain regions versus AAV9, while concurrently reducing liver accumulation by 2.6 fold. Our study establishes an LRP6-guided engineering platform that yields novel AAV9 vectors capable of efficient, species-conserved BBB penetration coupled with a favorable safety profile, representing a significant advance toward clinically translatable CNS gene therapies.

neuroscience↗

bioRxiv2026

TCR signal strength determines Treg instability and discrimination of self versus non-self antigens

Regulatory T cells (Tregs) expressing autoreactive T-cell receptors (TCRs) maintain immune self-tolerance, yet their fate upon antigen encounter remains unclear. Although selected in the thymus for high-affinity self-recognition, the cross-reactive nature of the TCR repertoire allows some Tregs to also recognize foreign antigens with high affinity. Here, we identify cross-reactive destabilization, a process in which high-affinity recognition of foreign antigens erodes Treg stability and redirects lineage fate. Using a thymic-derived Treg (tTreg) TCR capable of recognizing both self and foreign antigens distinct from the self-ligand that mediated its thymic selection, we show that stimulation with high-affinity non-self agonists induces Foxp3 loss and conversion into effector-like ex-Tregs, whereas self-antigen stimulation preserves lineage stability. Treg instability also increases with age and correlates with activation, suggesting that cumulative foreign-antigen exposure drives this process. These findings reveal a signal-strength-dependent model in which strong TCR engagement induces cross-reactive destabilization to balance immune responsiveness and self-tolerance. One Sentence SummaryForeign antigen-driven destabilization of Treg cells balances immunity and tolerance

immunology↗