Biology subjects

Ji, H.

Publications and source records attributed to Ji, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Genome-engineered C. elegans strains with sex-transformed neurons and gut

The sexual identity of specific tissues can be altered through cell-autonomous manipulation of the sex determination pathway in the nematode Caenorhabditis elegans. Previously described sexually mosaic strains carried multicopy transgenic arrays that are potentially subject to transgene silencing or misexpression artefacts. We used here the CRISPR/Cas9 system to engineer strains in which coding sequences for either a masculinizing agent (FEM-3) or a feminizing agent (intracellular domain of TRA-2) are inserted with a trans-splicing system at the 3 end of endogenous genetic loci that are known to be expressed in either a neuron-specific (rab-3) or gut-specific (elt-2) manner. We validate the tissue-specific sex-transformations induced by these genomic manipulations through expression analysis of known sex-specific genes and through assaying behavioral readouts. These strains may serve the worm community as standard reference tools to study the consequences of tissue-specific sex transformations.

neuroscience↗

bioRxiv2026

Programmable antigen-presenting scaffolds expand rare tumor-antigen-specific T cells from peripheral blood

Adoptive cellular therapies can be effective against solid tumors but rely on the identification and expansion of rare tumor-reactive T cells (TRTs). Here, we utilize antigen-presenting cell-mimetic scaffolds (APC-ms), a modular biomaterial platform that presents defined peptide-HLA and co-stimulatory ligands on a fluid lipid bilayer to selectively recover rare antigen-specific T cells from peripheral blood. Independent variation of peptide-HLA, co-stimulatory ligands, and cytokine support defined a formulation that enriched MART-1-specific T cells to above 2% of CD8+ T cells in 35 of 50 HLA-A*02:01+ healthy donors from low or undetectable baseline frequencies. Compared with mo-DCs, APC-ms achieved greater fold expansion of MART-1-specific T cells with increased functional avidity and preservation of an early differentiation phenotype, and generated a higher number of MART-1-specific clonotypes. In five of eight patients with treatment-naive melanoma, APC-ms could enrich MART-1-specific T cells to a median of 13.7% of CD8+ cells (range 0.30 - 57.2%) Moreover, APC-ms could expand T cells specific for an HLA-A*24:01-restricted personal neoantigen that were previously undetectable in peripheral blood of a patient with melanoma. These findings establish APC-ms as a tunable platform for the recovery of rare TRTs from peripheral blood, supporting its further development for therapeutic TCR discovery and personalized adoptive cell therapy.

immunology↗

bioRxiv2026

Glycosaminoglycan presentation-dependent regulation of glial responses by Orion during Drosophila neuronal pruning

Neuronal pruning refines neural circuits by eliminating unnecessary connections to ensure proper nervous system function. In Drosophila mushroom body gamma-neuron remodeling, the chemokine-like protein Orion is required for astrocyte infiltration and phagocytosis. This study investigated whether glial responses depend on how Orion is presented. We found that Orion interacts with glycosaminoglycans (GAG) associated to proteoglycans, which are essential for proper axon pruning. Tethering Orion to the gamma-neuron plasma membrane, mimicking glycosaminoglycan binding, was sufficient to induce astrocyte infiltration into axon bundles. However, membrane-bound Orion alone could not efficiently support phagocytosis, which additionally requires a soluble and mobile Orion pool. We also identified exosomes carrying GAG-bound Orion as potential mediators of neuronal remodeling. These findings provide the first evidence that glial infiltration can be uncoupled from phagocytosis, demonstrating that the mode of Orion presentation regulates distinct glial mechanisms during neuronal remodeling.

neuroscience↗

bioRxiv2026

SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen

Decoding which antigens activate a given T cell receptor (TCR) is a central challenge in immunology. We present SEEKER, a functional genome-scale library-on-library screening platform built on three elements: a Jurkat-derived T-APC cell (TAPCell) that combinatorially expresses one TCR and one peptide-MHC drawn from separate libraries together with an NFAT activation reporter; encapsulation of single TAPCells in a thermos-reversible hydrogel for isolated clonal expansion, so recognition is read out as intraclonal activation; and dual-asymmetric PCR that links TCR- and pMHC-encoding sequences into a heritable unit, enabling progressive hit enrichment over screening rounds. SEEKER interrogates ~10^8 TCR-pMHC combinations per run without prior knowledge. Screening joint-infiltrating CD8+ T cells from HLA-B*27+ ankylosing spondylitis patients against proteome-wide libraries validated 53 TCR-peptide pairs, uncovered extensive cross-recognition of self and common viral epitopes, and revealed highly polyreactive T cells recognizing up to 80 autoantigens, implicating virus-triggered poly-autoreactivity in multi-organ autoimmune diseases.

immunology↗

bioRxiv2026

Decoding natural scenes from patterned optogenetic responses in mouse visual cortex

A central challenge in developing visual cortical prostheses is to determine how visual stimuli should be transformed into effective patterns of cortical stimulation. Although advances in stimulation technologies, including optogenetics, provide increasingly precise control over cortical activity, it remains unclear whether artificially evoked activity can reproduce the information content of naturally evoked visual representations. Here we establish a quantitative framework for evaluating visual encoding strategies by decoding cortical responses evoked by natural vision and patterned optogenetic stimulation. We developed a novel dual-modal paradigm in awake mice to bridge the gap between endogenous photostimulation and artificial network driving. By co-expressing the high-performance calcium indicator GCaMP6s and the red-shifted, ultra-sensitive opsin rsChRmine-oScarlet in the primary visual cortex (V1), we successfully translated dynamic natural movie frames into patterned, spatiotemporal optogenetic stimulation. Quantitative comparisons of macro-scale dynamics demonstrated that this patterned optogenetic injection evokes cortical states highly comparable and representationally aligned with those driven by actual visual photostimulation. To systematically evaluate the fidelity of these responses, we developed STAR, a deep learning model featuring spatial and temporal attention mechanisms, and successfully reconstructed the frames of natural movies from V1 signals under both experimental modalities. Collectively, our results demonstrate that complex sensory information can be both naturally encoded and synthetically injected into V1 circuits with high decoding fidelity. This work provides an empirical and computational proof-of-concept for intelligent, closed-loop biomimetic encoders, establishing a robust framework for next-generation cortical visual neuroprostheses and bidirectional brain-machine interfaces.

neuroscience↗

bioRxiv2026

Cross-species spatial profiling links progranulin to an immune suppressive niche in brain metastasis

Immune checkpoint inhibitors (ICI) have revolutionized the treatment of brain metastasis (BM), demonstrating intracranial response rates and durability not previously seen with other therapies. However, approximately 50% of patients do not respond to ICI, and the brain-specific interactions that shape anti-tumor immunity remain poorly understood. We profiled five syngeneic BM models using spatial transcriptomics, identifying myeloid-rich niches enriched for interferon-responsive and disease-associated microglia (DAM)-like programs. Ligand-receptor colocalization analyses identified progranulin (PGRN) as a candidate mediator of these niches. Host- or tumor-cell Grn loss reduced BM burden, and Grn-deficient macrophages exhibited altered metabolic programs and tumor-cell engulfment in vitro. Across independent human BM datasets, GRN expression was associated with conserved lysosomal and DAM-like myeloid programs, and GRN-high myeloid regions colocalized with immunosuppressive signatures and dysfunctional CD8+ T cell states. These cross-species findings identify PGRN as a candidate mediator of the BM immune niche and support further investigation of its therapeutic relevance.

cancer biology↗

bioRxiv2026

Enhancing Mycobacterial Clearance via Heterologous BCG Prime Boost Strategy Using Recombinant Mycobacterium smegmatis

Bacille Calmette-Guerin (BCG) remains the only licensed tuberculosis (TB) vaccine, yet its protective efficacy against adult pulmonary TB is limited. To overcome this, we evaluated a novel recombinant Mycobacterium smegmatis (rMs) booster vaccine expressing Ag85B and ESAT-6 via the pMyong2 vector, combined with oat-derived {beta}-glucan adjuvant, to enhance BCG-primed immunity. BALB/c mice were primed with BCG and boosted twice with homologous BCG or varying doses of rMs with or without {beta}-glucan. Five weeks post-booster, mice were challenged intraperitoneally with M. tuberculosis H37Ra. Systemic bacterial clearance in liver tissue, cell-mediated immunity IFN-{gamma}, IL-17a, and antibody responses IgG, IgG2c, IgA were evaluated 3 weeks post-challenge. All rMs booster groups (rMs, high-dose rMs H, low-dose with {beta}-glucan, rMs {beta}) achieved complete systemic clearance of H37Ra with no detectable CFUs (colony forming unit), significantly outperforming mock-vaccinated and repeated BCG groups (**p < 0.01). Repeated BCG revaccination showed higher bacterial loads than single BCG (***p < 0.001), confirming no booster effect. Low-dose rMs with {beta}-glucan maintained 100% survival and total bacterial elimination despite a 50% dose reduction. Immune markers did not strictly correlate with clearance. Homologous BCG revaccination provides no additive protection, whereas pMyong2-based rMs confers robust systemic bacterial clearance. Adjuvanting with {beta}-glucan enables dose reduction while preserving maximum efficacy, establishing rMs as a promising heterologous TB booster candidate.

immunology↗

bioRxiv2026

Integrin-identity shapes and mechanotemporally encodes the fibroblast transcriptome

Fibroblast transcriptomic states reflect physiological and pathological tissue contexts, yet the upstream determinants that stabilize these states remain poorly defined. Integrins mediate extracellular matrix (ECM) adhesion and biochemical signaling, but whether they encode mechanical constraints into stable transcriptomic programs is unclear. Using engineered mouse fibroblasts, bulk and single-cell transcriptomics, and controlled micromechanical confinement, we show that integrins can shape the transcriptomic landscape. The bulk transcriptome of fibroblasts expressing V- and {beta}1-class indicates a shared mechanosensitive baseline, except when these integrin classes are expressed individually. We also found integrin-specific gene clusters, including {beta}1-class integrin-dependent enrichment of Areg, Epha7, Lhpp and Igf2r, which regulate development, regeneration and disease, and altered YAP1 targeted gene expression. At single-cell resolution under confinement, {beta}1-class integrins sustain a progenitor-associated program, whereas their loss or V-class enrichment promotes a constitutively activated state linked to injury repair and wound healing. Mechanical confinement and confinement duration further reshapes these states in an integrin-identity-dependent manner. Our findings establish integrin-identity as a determinant of how fibroblasts transduce mechanotemporal inputs from the cell surface to the nucleus.

Cell Biology↗

bioRxiv2026

Regulatory architecture controlling terminal differentiation of an interoceptive paraneuron in C. elegans

Interoceptive paraneurons are neuron-like cells located within internal epithelial cell surfaces that sense internal stimuli to evoke specific behavioral or physiological responses. The elucidation of terminal differentiation programs of paraneurons is expected to provide insights into how epithelial cells acquire neuron-like feature during development and possibly also over evolutionary time. We define here transcriptional programs that control the terminal differentiation of an interoceptive paraneuron class in the nematode C. elegans, called uv1. The uv1 cells sense mechanosensory inputs in the uterus and signal via the HSN neurons to modulate egg-laying behavior. We show that like in canonical neurons, the neuron-like secretory features of uv1 are controlled by a combination of CUT homeobox genes, while the combinatorial terminal gene battery that defines the unique functional features of uv1 is jointly controlled by a combination of at least three transcription factors, a LIM homeodomain (LIN-11), a SoxD (EGL-13) and a Pax family (EGL-38) protein. These factors act in a terminal selector-type manner to jointly co-regulate the many distinct uv1-paraneuron specific molecular features, such as sensory receptors, neuromodulatory receptors and neuropeptides, as well as uv1s tyraminergic identity. Our findings demonstrate notable similarities in the dichotomous architecture of gene regulatory programs of neurons and paraneurons.

developmental biology↗

bioRxiv2026

Quantifying Cross-Modal Association Confidence for Single-Cell RNA-ATAC Integration

While multimodal sequencing technologies are rapidly advancing, most single-cell and spatial datasets still measure only a single modality. Integrative computational methods for separately profiled single-cell RNA-seq (scRNA-seq) and ATAC-seq (scATAC-seq) data typically rely on the assumption that gene expression correlates with the chromatin accessibility of nearby regulatory regions. However, the strength and reliability of these correlations vary substantially across genes, and incorporating low-confidence associations can compromise integration accuracy. Here, we introduce the CLIC (Cross-modality Link Confidence) score, a quantitative measure of the empirical concordance between gene expression and nearby chromatin accessibility, derived from diverse single-cell multiome datasets from the ENCODE project. CLIC scores provide prior confidence estimates for gene-peak associations across modalities. Building on this, we propose a hybrid feature selection strategy that intersects highly variable genes with high-CLIC genes, generating feature sets that better align with the assumptions of cross-modal integration methods. Across diverse publicly available single-cell and spatial datasets, and multiple state-of-the-art integration frameworks, our approach consistently improves the integration of gene expression and chromatin accessibility data, enhancing both robustness and biological interpretability. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/723400v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@13208b8org.highwire.dtl.DTLVardef@1da7808org.highwire.dtl.DTLVardef@1fe5c53org.highwire.dtl.DTLVardef@5f4e2a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Reciprocal repulsions enforce heterotypic dendrite segregation in an olfactory circuit

How dendrites of different neurons segregate into discrete spatial domains during neural circuit assembly is poorly understood. Here, using the Drosophila olfactory system, we found that heterophilic interactions between two cell-surface proteins Teneurin-m (Ten-m) and Capricious (Caps) drive dendrite segregation. Ten-m and Caps are expressed in largely inverse patterns across projection neuron (PN) types when PNs are establishing their dendritic territories. Loss of Ten-m in Ten-m+ PNs causes their dendrites to invade Caps+ territories, whereas loss of Caps in Caps+ PNs causes dendrite invasion into Ten-m+ territories. Structure-guided mutations that abolish Ten- m-Caps binding disrupt dendrite segregation, whereas the same mutation on Ten-m preserves its homophilic attraction in a synaptic partner matching assay. These results support a model in which mutual repulsions between two inversely expressed cell-surface proteins drive dendrite segregation into discrete glomerular territories.

neuroscience↗

bioRxiv2026

Identification of a neural circuit that enables safe, long-term torpor in mice

Torpor, a state of regulated hypothermia and hypometabolism, is a critical survival strategy in certain mammals. Previous studies established the primacy of neuron control in initiating acute torpor. However, whether neuromodulation can safely sustain torpor over the long term, and the specific governing pathways, remain unanswered challenges limiting its translational potential. Here we identify a distinct preoptic neuronal population expressing General control nonderepressible 2 ( G neurons) in mice that is essential and sufficient for torpor induction. Strikingly, sustained and selective activation of G neurons induces a stable, weeks-long torpid state (G neuron-driven long-term torpor, GLT), from which animals arouse without obvious behavioral deficits or tissue pathology. In contrast, long-term torpor driven by pan-neuronal activation of the same brain region (PLT) causes multiple post-recovery damages, underscoring the unique safety profile of selective pathway of G neurons. In a mouse cancer model, GLT directly suppressed tumor proliferation and markedly sensitized tumors to chemotherapy, achieving profound therapeutic outcomes. Together, we delineate a distinct neuronal population safely enabling prolonged torpor. This establishes a specific paradigm for inducing a stable and sustained hypometabolic state, providing a transformative platform for fundamental physiological research and pioneering clinical strategies against chronic pathologies such as cancer.

neuroscience↗

bioRxiv2026

AI-Guided Structure-Aware Modeling and Thermal Proteomics Reveal Direct Demethylzeylasteral-ACLY Interaction

Target deconvolution of bioactive natural products (NPs) is frequently hampered by the inability of traditional thermal shift assays to distinguish direct ligand binding from indirect proteomic stabilization. Here, we developed an integrated target discovery framework combining MAPS-iTSA thermal proteomics with a structure-aware graph neural network (HoloGNN). This strategy identified ATP-citrate lyase (ACLY) as a high-confidence target of Demethylzeylasteral, a bioactive triterpenoid from Tripterygium wilfordii. Crucially, orthogonal biochemical assays, including surface plasmon resonance and limited proteolysis, validated its direct binding (KD = 9.86 M) and profound enzymatic inhibition (IC50 = 3.84 M). To establish the relevance of this interaction in the context of the source herb, thermal profiling of Tripterygium wilfordii extract together with ACLY-based affinity-ultrafiltration mass spectrometry supported ACLY engagement and identified Demethylzeylasteral as an ACLY-binding constituent. Given the established role of ACLY-mediated lipid metabolic reprogramming in psoriasis, we further evaluated the pharmacological significance of this interaction. Demethylzeylasteral suppressed keratinocyte proliferation, alleviated imiquimod-induced psoriasiform dermatitis, and reduced inflammatory cytokine expression in vivo. Single-cell RNA sequencing further revealed reversal of ACLY-SREBP-associated lipogenic reprogramming in keratinocytes. Collectively, these findings establish ACLY as a functionally relevant target of DEM and provide a robust AI-chemoproteomic paradigm for mechanism-guided NP drug discovery.

biochemistry↗

bioRxiv2026

Fixative eXchange (FX)-seq: Scalable Single-nucleus RNA Sequencing Analysis of PFA-fixed or FFPE Tissue

Single-nucleus RNA sequencing (snRNA-seq) of clinical formalin-fixed, paraffin-embedded (FFPE) samples has long been a challenge due to low reverse transcription (RT) yields. Here, we present Fixative-eXchange (FX)-seq, a highly scalable snRNA-seq method for heavily paraformaldehyde (PFA)-fixed and/or FFPE samples. We employ an organocatalyst to facilitate the removal of PFA crosslinks to increase RT yield and additional regiospecific Pt(II)-based crosslinking of RNA molecules to prevent leakage. FX-seq reveals cellular heterogeneity across multiple fixed samples by analyzing 321,710 nuclei, including PFA-fixed tissue, FFPE blocks, thin FFPE and hematoxylin and eosin (H&E)-stained sections from mouse brain and human cancer specimens such as gastrointestinal stromal tumor and colorectal cancer. FX-seq enables integrated analysis with pathologist annotation to label tumor and non-tumor regions of H&E-stained sections. FX-seq can also be applied to PFA-perfusion-based animal studies, large human cohort studies, and personalized drug treatment through precision medicine.

genomics↗

bioRxiv2026

Process optimization and antidepression multi-target mechanisms of Total Flavonoids from Hemerocallis citrina Baroni: An integrated approach combining DES-UAE, network pharmacology, and experimental validation

ObjectiveThis study aimed to establish a green and efficient ultrasonic-assisted deep eutectic solvent (DES) extraction method for total flavonoids from Hemerocallis citrina Baroni (TFHC) and to elucidate its multi-target antidepressant mechanism using an integrated strategy of network pharmacology, molecular docking, and in vitro validation. MethodsAn ultrasonic-assisted DES extraction using choline chloride-ethylene glycol was optimized via response surface methodology. The TFHC extract was profiled by UPLC-ESI-MS/MS. A network pharmacology approach was employed to predict core targets and pathways of TFHC constituents against depression, with key interactions validated by molecular docking. The neuroprotective effects of TFHC were evaluated in vitro using a corticosterone (CORT)-induced injury model in PC-12 cells, assessing cell viability (MTT assay) and levels of 5-HT, BDNF, TNF-, and CORT (ELISA). ResultsThe optimized DES extraction yielded 16.63 {+/-} 0.13 mg/g of TFHC. UPLC-ESI-MS/MS identified fourteen flavonoids, with quercetin, kaempferol, and rutin being most abundant. Network pharmacology revealed six core targets (AKT1, TNF, IL6, IL1{beta}, TP53, PTGS2) and implicated pathways including PI3K-AKT and TNF. Molecular docking confirmed strong binding affinities ([≤] -4.25 kcal/mol) between major flavonoids and core targets. In vitro, TFHC significantly alleviated CORT-induced cytotoxicity, restored 5-HT and BDNF levels, and suppressed TNF- and CORT elevation, with effects comparable or superior to fluoxetine. ConclusionsTFHC exerts antidepressant-like effects through a multi-target mechanism involving neuroinflammation suppression, neurotrophic support, and HPA axis modulation. The green DES extraction combined with mechanistic insights positions TFHC as a promising candidate for phytotherapeutic antidepressant development.

pharmacology and toxicology↗

bioRxiv2026

Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds

Extracellular matrix (ECM) scaffolds induce type 2 immunity to promote repair. Here, we show that immune cells recruited to ECM-treated murine muscle injuries and clinical soft tissue defects express immune checkpoints. Specifically, TH2 cells and regulatory T cells (Tregs) increase LAG3 expression, while macrophages express PDL2. TCR analysis and a triple-reporter strain for interleukin (IL)-13 and Treg fate-mapping suggest that Tregs in ECM-treated wounds transition into TH2-like exTregs that express LAG3. Immune checkpoint inhibition (ICI) significantly stimulated type 2 immunity in ECM-treated wounds, including increased TH2 cells, Treg transition to TH2-like exTregs, and pro-regenerative macrophages. Moreover, ICI enhanced muscle repair and reduced fibrosis in ECM-treated wounds. Collectively, these findings show Treg/TH2 plasticity in wound healing and introduce a novel ICI application to enhance immune-mediated regeneration.

bioengineering↗

bioRxiv2026

AMPBAN: A Deep Learning Framework Integrating Protein Sequence and Structural Features for Antimicrobial Peptide Prediction

The escalating crisis of antimicrobial resistance poses a devastating and immediate threat to human life. Antimicrobial peptides (AMPs) are a promising antibiotic substitute to combat antimicrobial resistance. Compared with the traditional wet-lab screening approaches, computational models have largely improved the efficiency of predicting antimicrobial peptide. However, most computational models overlook or underutilize the evolution and structural information of peptides, which is crucial for understanding the peptide functions. Here, we proposed a sophisticated deep learning model to predict AMPs, Antimicrobial Peptide Bilinear Attention Network (AMPBAN), which incorporates peptide evolution features from ESM3 protein language model, structure features from ESMFold predicted with equivariant graph neural network (EGNN), and the joint information from sequence and structure learned via Bilinear Attention Network. AMPBAN consistently demonstrated superior accuracy and generalization compared to nine state-of-the-art AMP prediction models across multiple independent benchmarks. Furthermore, an ablation study confirms that our multimodal fusion strategy significantly refines the integration of sequence and structural signals, yielding superior predictive balance over single-modality models. This framework provides a robust tool for the accelerated discovery of novel AMPs and the advancement of next-generation antimicrobial drug development. The datasets, source code and models are available at https://github.com/baiwenhuim/ampban.

bioinformatics↗

bioRxiv2025

Structural semantic evolutionary distance (SSED) unifies the selection of cancer driver genes across macroevolution and tumorigenesis.

The non-random, site-specific enrichment of somatic mutations in cancer driver genes (CDGs) suggests their emergence is governed by underlying evolutionary constraints. However, quantitative methods to define these constraints and their underlying principles remain underexplored. To address this, we introduce the Structural Semantic Evolutionary Distance (SSED), a metric leveraging the pretrained ESM-3 protein language model to quantify evolutionary divergence within a unified structural semantic space. Our analysis demonstrates that CDGs are subject to persistent structural semantic constraints across species, tolerating a significantly narrower range of structural semantic changes during evolution compared to non-CDGs. Crucially, clinically observed oncogenic mutations follow this same principle, favoring minimal structural perturbation as shaped by long-term gene evolution. Such mutations maintain core protein function while conferring a capacity for immune evasion, thereby driving clonal expansion. Guided by this "evolutionary constraint" framework, we successfully predicted and experimentally validated a previously uncharacterized oncogenic mutation, KRAS R135L, in bronchial epithelial cells. Furthermore, clinical cohort analysis demonstrated that SSED acts as an independent predictor of response to immune checkpoint blockade, offering information orthogonal to tumor mutational burden (TMB). This study unifies the evolutionary principles governing CDGs across macroevolutionary and microevolutionary (tumorigenesis) timescales, elucidates the balance between structural adaptability, functional conservation, and immune pressure, and identifies a novel predictive biomarker for cancer immunotherapy.

genetics↗