Biology subjects

Shen, C.

Publications and source records attributed to Shen, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Therapeutic Potential of iPSC-Derived TH+FOXA2+ Neuronal Extracellular Vesicles in Parkinson's Disease Revealed by Organoid and Rodent Models

Background: Parkinson's disease (PD) is characterized by the progressive loss of midbrain dopaminergic (DA) neurons and aberrant alpha-synuclein (alpha-syn) aggregation, yet disease-modifying therapies that simultaneously retard neurodegeneration and foster regeneration remain lacking. Methods: In this study, we isolated extracellular vesicles (TH and FOXA2 double-positive cell-derived EVs) from TH and FOXA2 double-positive differentiated neural cells, a distinct midbrain floor-plate-derived neural cell population that co-expresses the floor-plate transcription factor FOXA2 together with TH and should therefore not be equated with conventional mature midbrain dopaminergic neurons, and systematically evaluated their therapeutic potential across three complementary models: A53T transgenic mice, 6-OHDA-lesioned rats, and 6-OHDA-treated human midbrain organoids. Integrative transcriptomic and single-cell sequencing analyses, together with toxicological evaluations in rodents and non-human primates, were performed to investigate the underlying mechanisms and safety profile. These TH and FOXA2 double-positive cells were generated using a fully suspension-based, matrix-free, and chemically defined differentiation system devoid of N2/B27 supplements and fetal bovine serum (FBS). This approach offers a simple, controllable, low-cost, and scalable platform with high batch-to-batch consistency for EV manufacturing. Throughout this study, the term "TH and FOXA2 double-positive cells" refers to this distinct TH and FOXA2 double-positive cell population and should not be interpreted as conventional terminally differentiated dopaminergic neurons. Results: Intranasal administration of TH and FOXA2 double-positive cell-derived EVs in A53T mice and 6-OHDA-lesioned rats significantly ameliorated motor deficits, increased nigral tyrosine hydroxylase (TH)-positive neuron counts, reduced alpha-syn aggregation, and suppressed gliosis. In human midbrain organoids, TH and FOXA2 double-positive cell-derived EVs preserved DA neuronal morphology and reduced GFAP and alpha-syn expression. Notably, when EVs were administered simultaneously with 6-OHDA modeling rather than after modeling was completed, the protective effect was stronger. Multi-omics analysis revealed that TH and FOXA2 double-positive cell-derived EVs reversed pathological signatures of interferon-responsive microglia and oxidative stress-adapted astrocytes, while restoring WNT- and non-canonical WNT-mediated intercellular communications. Safety evaluations showed no discernible organ toxicity. Conclusions: TH and FOXA2 double-positive cell-derived EVs exert neuroprotective effects across multiple PD models by modulating specific glial subpopulations and reinstating development-associated signaling pathways. Together with a fully suspension-based, matrix-free, and N2/B27-free differentiation process that enables low-cost, scalable, and highly reproducible manufacturing, TH and FOXA2 double-positive cell-derived EVs represent a promising therapeutic candidate for Parkinson's disease.

neuroscience↗

bioRxiv2026

A Tumor-Pituitary-Stromal Axis Promotes Colorectal Cancer Progression

Peripheral tumors can reprogram systemic physiology, yet how they engage central endocrine organs to remodel the local tumor microenvironment is unknown. We found that colorectal cancer (CRC) elevates circulating BMP2, which activates pituitary signaling and enhances endocrine output. Increased pituitary-derived growth hormone acted on growth hormone receptor-expressing cancer-associated fibroblasts (CAFs), inducing a p21-dependent senescence-like state and tumor-promoting secretory program. Disruption of pituitary BMP signaling or fibroblast GHR reduced tumor growth, whereas fibroblast-specific depletion of p21 abrogated GHR-dependent tumor promotion. In patients with CRC, elevated pituitary metabolic activity correlated with stromal p21 expression and tumor burden. Our study reveals a tumor-pituitary-stromal signaling axis through which a peripheral malignancy recruits a central endocrine organ to remotely shape its own microenvironment and promote disease progression.

cancer biology↗

bioRxiv2026

Global transmission architecture of VIM carbapenemases reveals host-specific dissemination strategies

Carbapenemase-producing Gram-negative bacteria carrying Verona integron-encoded metallo-{beta}-lactamase (VIM) pose a persistent global threat, yet the mechanisms driving their worldwide dissemination remain poorly resolved. We analysed 5,617 blaVIM-positive genomes collected from 73 countries or regions across six continents between 1999 and 2025 to reconstruct the global epidemiology and transmission architecture of VIM carbapenemases. Forty VIM variants were identified across 16 bacterial genera, revealing marked host preferences and temporal shifts. VIM-2 dominated global circulation, whereas VIM-1 and VIM-4 remained prominent among Enterobacterales. Strikingly, VIM spread followed distinct host-specific evolutionary strategies. In Pseudomonas aeruginosa, dissemination was largely clone-driven, with high-risk lineages ST111 and ST235 supporting long-term persistence through lineage expansion and stable inheritance. By contrast, Enterobacterales were dominated by horizontal transmission through broad-host-range IncHI2A, IncA, and IncC plasmids, although only a limited subset of plasmid-VIM combinations achieved intercontinental spread. Among 2,828 loci with sufficient flanking sequence, 96.2% were embedded within integrative genetic elements, frequently nested with insertion sequences and phage-related elements, revealing a multilayered mobile-element network underlying VIM persistence. Structural analyses showed a highly conserved metallo-{beta}-lactamase scaffold but recurrent diversification near substrate-interacting residues, particularly positions 224 and 228. Shared genetic clusters between human-associated and environmental isolates further suggested cross-niche circulation. Together, these findings establish a hierarchical, host-dependent framework for global VIM dissemination, integrating clonal expansion, plasmid transfer, and nested mobile genetic elements. ImportanceBy analysing 5,617 blaVIM-positive genomes worldwide, this study reveals a host-dependent transmission architecture of VIM carbapenemases. In P. aeruginosa, VIM dissemination is mainly driven by expansion of successful high-risk clones, particularly ST111 and ST235, whereas in Enterobacterales it is primarily mediated by broad-host-range plasmids enabling cross-species transfer. Global VIM spread is not driven by a single dominant pathway but by a limited number of successful clone-plasmid-mobile element combinations, while most genetic backgrounds remain regionally restricted. These findings define a hierarchical transmission model of VIM evolution and provide insights for genomic surveillance and targeted control of metallo-{beta}-lactamase-mediated antimicrobial resistance.

microbiology↗

bioRxiv2026

A high-throughput method to computationally develop candidate adverse outcome pathways in humans: a proof of concept with insecticides and Parkinson Disease

Adverse outcome pathways (AOPs) describe stressor non-specific sequences of events between a first molecular trigger (molecular initiating event, MIE), causally linked key events (KEs), and an adverse outcome (AO). AOPs are intended to aid in chemical toxicity testing as a new approach methodology. However, commonly used AOP development methods depend on manual curation, which is labor intensive. As a result, there are still relatively few AOPs and a huge number of toxicity mechanisms and possible adverse outcomes remain undescribed. Therefore, systematic and high-throughput approaches to predict new AOPs are needed. Here, we developed and implemented a data integration-based framework to generate new candidate AOPs using insecticides and Parkinson Disease as a proof of concept. We integrated and statistically linked disconnected databases (e.g., Comparative Toxicogenomics Database, Human Protein Atlas, and Gene Ontology) to form MIE - KE (cell level) - KE (tissue level) - AO candidate AOPs. Through this systematic process, we generated 562,117 candidate AOPs, which we then scored using a weight of evidence (WoE) approach and prioritized 12,756 AOPs with a WoE >0.5. Through random sampling of 100 prioritized AOPs, we found 70% had external literature supporting their biological plausibility, and only 15% represented identifiably implausible associations. The prioritized AOPs describe varied mechanisms of toxicity related to e.g., MAPK, PTEN, and FGFR signaling pathways, with "increases phosphorylation of MAPK1" as the most frequent MIE. Our AOP generating approach yields consistently structured AOPs and can complement existing and emerging development methods to expand AOP coverage across different stressors and outcomes.

pharmacology and toxicology↗

bioRxiv2026

Mapping immune cellular landscapes and vaccine responses across a spectrum of health and immunodeficiency.

Immune responses to infection and vaccination exhibit diversity between individuals that can be shaped by differences in their immune cell landscapes and the signalling, transcriptional, and genetic mechanisms that coordinate immune cell function. Specific antibody deficiency (SAD) and common variable immunodeficiency (CVID) are common forms of predominantly antibody deficiencies that result in poor responses to vaccination. While molecular and cellular causes of the immune dysfunction and poor vaccination responses for individuals with CVID have been reported, immune cell or molecular defects have not yet been identified in SAD. Here, we have used single-cell multi-omics to define the cellular landscapes, transcriptional states, adaptive immune repertoires and protein expression of patients with SAD and CVID before and after polysaccharide vaccination. We discovered that while SAD and CVID exhibit overlapping immune defects, including accumulation of exhausted NK memory cells and dysregulated expression of genes that mediate lipopolysaccharide sensing and clearance by monocytes, individuals with SAD have a unique expansion of cytotoxic CD4+ T cells that correlates with reduced regulatory T cells. In response to vaccination, we observed rapid changes in gene expression associated with lipopolysaccharide responses by monocytes and NF-kB pathway activation in B cells, and an apparent expansion of a CD95+ class-switched memory B cell population that does not occur in patients with lower antigen-specific responses. Together, our findings reveal cellular and molecular factors that underpin variability in vaccine responses and define SAD in a broader spectrum of immune dysfunction.

immunology↗

bioRxiv2026

Heterogeneity-driven adaptive scale graph learning for subcellular spatial transcriptomics

MotivationSpatial transcriptomics enables gene expression profiling within intact tissue sections, providing an important basis for analyzing tissue organization, cellular heterogeneity, and microenvironmental interactions. However, existing spatial structure identification methods often integrate spatial information using fixed neighborhoods or predefined smoothing scales, which limits their ability to adapt to region-specific structural heterogeneity. In homogeneous regions, broader spatial smoothing can help preserve continuous tissue structures, whereas in regions with complex boundaries or mixed cell populations, excessive smoothing may obscure local expression differences and fine-scale structural changes. Therefore, it is necessary to develop an adaptive graph learning framework that can adjust the range of spatial information integration according to tissue structural heterogeneity. ResultsIn this study, we propose HAST, a heterogeneity-driven adaptive-scale graph learning framework for spatial transcriptomics. HAST adaptively determines graph filtering scales according to spatial structural heterogeneity, enabling flexible information aggregation across different tissue regions. It further decomposes gene expression signals into low-frequency structural components and high-frequency residual components, thereby jointly modeling global spatial continuity and local expression variations. Experiments on high-resolution spatial transcriptomics datasets show that HAST improves spatial structure identification and cross-section generalization. Tumor-enriched cluster identification and neighborhood enrichment analysis further demonstrate its ability to characterize tumor-associated spatial regions and microenvironmental organization.

bioinformatics↗

bioRxiv2026

Sequence-Defined Digital Bottlebrush Polymers for Programmable Oligonucleotide Delivery

Oligonucleotide therapeutics hold transformative potential, yet their clinical translation is hindered by delivery barriers, including rapid renal/hepatic clearance and poor organ specificity. Bottlebrush polymers conjugates have emerged as a promising vector to address these limitations, but conventional architectures with uniform backbones can only achieve an unmodifiable, rigid biodistribution profile. Here, we report a library of sequence-defined "digital" bottlebrush polymers, precisely engineered with controlled placements of chemical motifs that modify physiochemical properties - including lipids, cholesterol, and cationic groups - along a polyphosphodiester backbone. Systematic evaluation of the digital bottlebrush polymer library reveals distinct structure-property relationships and enables organ-biased systemic delivery to several traditionally difficult-to-reach tissues, including muscle and skin. In a mouse model of rheumatoid arthritis, a single dose of a spleen-homing polymer-conjugated antisense oligonucleotide targeting TNF- achieves potent knockdown and drives full functional recovery. These findings establish a versatile design framework for tailoring bottlebrush polymers to specific therapeutic applications.

bioengineering↗

bioRxiv2026

Functionalized nanoparticle transforms cold to hot adenoid cystic carcinoma of salivary gland tumour microenvironment in vitro

Adenoid cystic carcinoma (ACC) of salivary gland is a "immune-cold" tumour. Annexin A3 (ANXA3) is an apoptotic protein found to be participating in immune cell infiltration in tumour microenvironment (TME) of various cancer cases. Significant low expressions of ANXA3 protein found in adenoid cystic carcinoma. We hypothesized overexpressing ANXA3 transforms ACC "cold" TME to "hot". We cultured UM-HACC-2A and UFH2 spheroids on extracellular matrix and co cultured them with peripheral blood mononuclear cells. We functionalized FDA (The Food and Drug Administration) approved Poly(lactic-co-glycolic acid) PLGA nanoparticles with anti-cMyb antibody and ANXA3 recombinant protein using streptavidin-biotin conjugation. Upon overexpressing ANXA3 in ACC spheroids in immune coculture model using functionalized nanoparticles, significant increase of tumour infiltrating lymphocytes and decrease in the size of the ACC spheroids observed. Apoptotic profiler assay further confirmed significant upregulation of apoptotic proteins, some of them participate in immune infiltration. Overall, this project exhibits promising results showing potential approach to convert ACC into an immune "hot" tumour.

cancer biology↗

bioRxiv2026

Three distinct profiles of visual category preference within the anterior temporal lobe

The primate visual hierarchy culminates in the anterior temporal lobe (ATL), yet the functional organization of this region remains poorly understood due to magnetic susceptibility artifacts that degrade fMRI signal quality. Here, we leverage a large-scale fMRI dataset from the Human Connectome Project (N = 830, male and female) to characterize visual category preferences within the ATL using a region-of-interest-based approach providing sensitivity in signal-compromised areas. Within the temporal pole (TP) and perirhinal cortex (PR), we identified three distinct profiles of visual category response, each replicated in an independent sample. TP showed a preference for objects over scenes, with a right-hemisphere bias toward animate objects (faces and bodies) over inanimate objects (tools). PR contained two functionally distinct subregions: one preferring faces over other categories, and one responding broadly to objects -- particularly tools and bodies--over scenes. Analysis of spatial location revealed that, unlike the well-characterized topographic organization of category-sensitive regions in posterior occipitotemporal cortex, face- and object-preferring subregions of PR did not show a consistent spatial relationship, suggesting a patchy or "salt-and-pepper" organization. Resting-state functional connectivity analyses demonstrated that ATL subregions have dissociable connectivity profiles: TP showed preferential connectivity with transmodal default mode network regions, while PR subregions were more strongly coupled with occipitotemporal cortex, with each showing preferential connectivity with regions sharing similar category preferences. Together, these findings demonstrate that category sensitivity--a hallmark of the ventral visual stream--extends to the apex of the cortical visual hierarchy. Significance statementUnderstanding the functional organization of the visual system is a central goal of cognitive and systems neuroscience. The anterior temporal lobe (ATL) sits at the top of the brains visual processing hierarchy and is critical for recognizing objects and people, but its internal organization has remained poorly characterized due to technical limitations in brain imaging. Our findings resolve a key gap by demonstrating that the same organizational principle governing the well-studied posterior visual system--the segregation of responses by object category--extends all the way to the apex of the visual hierarchy. This lays essential groundwork for future research understanding interactions between visual and memory systems, and how high-level visual processing breaks down in neurological conditions affecting the ATL.

neuroscience↗

bioRxiv2026

Platelets promote acute liver injury via extracellular vesicles-mediated Aldolase A

Platelets have emerged as active regulators of acute liver injury (ALI), yet the molecular mechanisms underlying their pathogenic functions remain poorly defined. Here, we demonstrate that platelets contribute to liver injury, in part, by metabolically reprogramming Kupffer cells (KCs). We show that platelets are actively recruited to the injured liver and communicate with KCs through extracellular vesicles (EVs), which deliver the glycolytic enzyme aldolase A (ALDOA) into recipient cells. This EV mediated transfer promotes glycolytic reprogramming in KCs, contributing to their proinflammatory activation and amplification of hepatic injury. Genetic ablation of Aldoa in platelets attenuated liver injury, demonstrating a pathogenic role for platelet derived ALDOA in vivo. Pharmacological inhibition of ALDOA with Aldometanib markedly attenuated liver injury. Circulating ALDOA levels were elevated in patients with ALI and correlated with disease severity. These findings uncover a platelet macrophage metabolic axis that drives ALI and nominate ALDOA as a therapeutic target and biomarker.

pathology↗

bioRxiv2026

Rapid optogenetic manipulation of autophagy reveals that the nuclear pore complex is a robust autophagy substrate

Autophagy, a conserved recycling process, manages intracellular quality control to mitigate stress. To determine the rapid effects of autophagy perturbation, we developed the first optogenetic tool to rapidly inhibit autophagy, termed ASAP. Our approach leverages light-induced proteolytic cleavage to selectively inhibit autophagy within 5 minutes of light exposure, providing a precise and dynamic approach to study autophagy regulation. Proteomic profiling with ASAP revealed the most tightly regulated autophagy substrates along with novel, previously unidentified substrates, including nuclear pore complex (NPC) proteins. Interestingly, autophagy regulates quality control of cytoplasmic complexes of nucleoporins via specific LC3-interacting regions (LIRs), sparing nuclear pore complex proteins embedded in the nuclear envelope. Upon rapid autophagy inhibition, incomplete nucleoporin complexes accumulate and instead of undergoing autophagic degradation, cytoplasmic nucleoporin complexes aggregate in processing bodies (P bodies). Using ASAP, we demonstrate rapid and specific inhibition of autophagy, revealing that nuclear pore complex proteins are tightly regulated autophagy substrates.

cell biology↗

bioRxiv2026

Targeting matrix metalloproteinase-14 disrupts DNA repair and reduces viability in adrenocortical carcinoma

BackgroundAdrenocortical carcinoma (ACC) is a rare and aggressive endocrine cancer with limited treatment options and poor prognosis. Identifying novel therapeutic targets requires understanding the molecular drivers of ACC progression and establishing translational models for preclinical validation. ResultsMatrix metalloproteinase-14 (MMP-14) is the most highly expressed MMP in ACC, and high MMP-14 expression is associated with worse overall and disease-free survival. We demonstrate that MMP-14 is essential for ACC cell survival and serves an unexpected role in maintaining genome stability. Genetic silencing or pharmacologic inhibition of MMP-14 significantly reduced viability in both NCI-H295R cells and patient-derived tumor organoids (PTOs). MMP-14 knockdown induced CHK1 activation and S-phase checkpoint arrest. Mechanistically, MMP-14 translocates to the nucleus and binds to chromatin following DNA damage induced by ionizing radiation or cisplatin. Loss of MMP-14 resulted in accumulation of DNA double-strand breaks, as evidenced by increased {gamma}H2AX foci, and impaired non-homologous end joining (NHEJ)-mediated repair. ConclusionsThese findings reveal a novel nuclear function for MMP-14 in DNA repair and identify MMP-14 as a promising therapeutic target in ACC. Targeting MMP-14 may sensitize ACC tumors to DNA-damaging chemotherapy by impairing the repair of therapy-induced lesions.

cancer biology↗

bioRxiv2026

Cryo-EM reveals the structural basis of subtype-specific, noncompetitive inhibition of the human P2X3 receptor

P2X receptors are ATP-gated cation channels, and the P2X3 subtype plays crucial roles in peripheral sensory neurons, including in chronic pain and chronic cough. Accordingly, P2X3 has attracted substantial interest as a therapeutic target. Gefapixant, a negative allosteric modulator (NAM) of P2X3, has been approved in some countries for the treatment of chronic cough; however, its limited selectivity for P2X3 homomers over P2X2/P2X3 heteromers is associated with taste disturbance as a prominent adverse effect. These limitations have motivated the development of next-generation NAMs with improved subtype selectivity, but their subtype-specific allosteric inhibition mechanisms are unclear. Here, we report the cryo-EM structure of the human P2X3 receptor in complex with ATP and the P2X3-selective next-generation NAM sivopixant, an investigational drug. Sivopixant binds to an allosteric site at the portal of the central pocket in the extracellular domain, and structure-based mutational analysis by electrophysiology identifies key residues required for sivopixant-dependent inhibition of human P2X3. Comparisons with P2X structures from other subtypes, together with gain-of-function mutants, define a structural basis for subtype-selective allosteric inhibition of the P2X3 receptor. Furthermore, structural comparisons with apo and ATP-bound open states of P2X3 receptors, together with molecular dynamics simulations, revealed that sivopixant expands the upper body domain to suppress the lower-body movements required for channel activation, thereby preventing channel opening even in the presence of ATP.

biophysics↗

bioRxiv2025

CRISPR screening reveals genetic regulators associated with the evolution of eye degeneration

Determining the genetic factors contributing to trait evolution is critical for understanding how and why traits evolve; however, establishing which genes underlie the evolution of complex traits remains challenging. The freshwater fish Astyanax mexicanus, a species that includes blind, cave-dwelling and eyed, surface-dwelling fish, is a powerful model for evolutionary genetics. While genetic mapping studies in this species previously identified genomic regions associated with cave-derived traits, few causative genes and genetic changes have been identified. Here, we develop methods to identify and rapidly functionally assess candidate genes in A. mexicanus, focusing on a defining trait of cave animals, eye loss. Candidate genes were identified based on whether they fell within an eye-related quantitative trait locus, were differentially expressed between surface and cave eyes, and showed evidence of positive selection in cavefish. Single-nucleus RNA-sequencing revealed that these candidate genes were expressed in multiple cell types during development, including those in different tissues of the eye. CRISPR-Cas9-based mutagenesis demonstrated that disruption of nine of these candidate genes in surface fish resulted in altered eye size. Perturbation of one of these genes, fibulin-7 (fbln7), revealed changes in eye size across multiple stages of eye development. Together, this work identified multiple genes associated with the evolution of eye degeneration in A. mexicanus. Further, this study represents a roadmap for rapid identification and functional assessment of candidate genes implicated in the evolution of traits in cavefish that can be applied to other evolutionary genetic models.

genetics↗

bioRxiv2025

Exploring the potential value of aloe active components in inhibiting non-small cell lung cancer through network pharmacology

Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality worldwide, and its management is challenged by profound molecular heterogeneity and inevitable resistance to targeted therapies. Natural products offer a valuable reservoir for anticancer drug discovery, yet the therapeutic potential of Aloe vera--a medicinal plant rich in structurally diverse bioactive compounds--remains insufficiently characterised in the context of NSCLC. Here, we employed an integrated strategy combining network pharmacology, protein-protein interaction analysis, Gene Ontology and KEGG enrichment, molecular docking, and 100-ns molecular dynamics simulations to comprehensively elucidate the multi-target and multi-pathway regulatory mechanisms of Aloe vera active constituents against NSCLC. We identified 369 aloe-derived targets and 5519 NSCLC-related genes, with 268 overlapping targets enriched in pathways involving EGFR signalling, PI3K/AKT/mTOR activation, p53 regulation, inflammation, apoptosis, and drug-resistance networks. Core hub genes included TP53, EGFR, AKT1, and STAT3. Molecular docking demonstrated strong spontaneous binding between key aloe compounds (such as aloe-emodin, aloeresin C, quercetin and sitosterols) and wild-type EGFR, mutant EGFR T790M/C797S, AKT1, and p53. Molecular dynamics simulations confirmed stable ligand-protein interactions, favourable hydrogen-bonding networks, and energetically favourable binding free energies. Collectively, our findings reveal a systematic, multi-level regulatory landscape through which Aloe vera may exert anti-NSCLC effects and highlight several candidate molecules with potential to enhance therapeutic efficacy or overcome EGFR-TKI resistance. This study provides a solid theoretical framework for subsequent experimental validation and the development of novel aloe-derived anticancer agents with low toxicity.

bioinformatics↗

bioRxiv2025

A Porcine Model of Intervertebral Disc Injury Recapitulates Human Discogenic Pain via Notochordal Cell Loss and Pain-inducing Nucleus Pulposus Cell Emergence

Lower back pain (LBP) is one of the most common causes of disability, with up to 40% of LBP cases attributed to intervertebral disc (IVD) degeneration. While small animal models are widely used to study IVD and LBP, the small size of their IVDs limits translational and biological relevance. Large animal models more accurately emulate human disease; however, methods of measuring LBP are not well established. Pigs were also considered unfit for LBP research, due to notochordal cells (NCs) persistence through life, unlike humans. We developed a comprehensive porcine model with quantitative measure of discogenic pain via biobehavioral testing (BBT), MRI, and multi-omics tissue analysis of IVD and DRGs. MRI demonstrated the progression of IVD degeneration beginning at 4 weeks post-injury. BBTs showed the development of significant pain responses by week 4 post-injury, supported by transcriptomics of injury matched DRGs. Single cell transcriptomics, trajectory and cell-cell communication analyses suggest that, with injury, NCs are differentiating to nucleus pulposus cells (NPCs). Furthermore, NPCs showed upregulation of cellular stress, neural outgrowth, and inflammation pathway, consistent with pain-inducing distress signals found in human samples. This study establishes novel MRI and BBT-based methods for quantifying LBP in pigs and supports its translational relevance to human discogenic LBP. The identification of LBP-associated clusters mirrors our previous finding in humans. Moreover, the shift of NC to NPC phenotype further supports that the porcine model is relevant to human pathology, as the injury induced accelerated aging and loss of NCs with IVD degeneration and discogenic pain.

developmental biology↗

bioRxiv2025

IRCAS: a novel end-to-end approach to identify, rectify and classify comprehensive alternative splicing events in a transcriptome without genome reference

Alternative splicing (AS) is a fundamental post-transcriptional mechanism that amplifies proteomic diversity and enables adaptive responses across eukaryotes. Current AS detection methods rely heavily on reference genomes, limiting their applicability to non-model organisms. Existing reference-free approaches suffer from inaccurate splice site prediction and treat detection and classification as separate processes, resulting in cascading errors. We present IRCAS, an integrated end-to-end framework for reference-free AS analysis, comprising three modules: identification, rectification, and classification. IRCAS employs colored de Bruijn graphs for AS detection, an attention-based CNN for splice site rectification, and a hybrid Graph Neural Network combining GAT and Transformer layers for classification. Evaluation across four species demonstrates substantial improvements: splice site accuracy increased to 92-96% versus 50-55% for existing methods, and end-to-end accuracy reached 83.4% compared to 41.2% for the previous best method. IRCAS establishes a new benchmark for reference-free AS detection in non-model organisms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/689457v1_fig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1162531org.highwire.dtl.DTLVardef@e3c2e2org.highwire.dtl.DTLVardef@10f9032org.highwire.dtl.DTLVardef@c3cb5e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 1.C_FLOATNO Workflow for construction and application of IRCAS. IRCAS is composed of three parts: identification, rectification, classification. (A) Workflow for reference-free AS identification from a raw transcriptomic data. First, according to the input transcripts, we apply BLAST all versus all alignment for preliminary screen. Then we adopt the MkcDBGAS Graph construction strategy. A cDBG was constructed from two sequences using a specified k-mer size. Based on bubble topologies, bubbles were classified into 5 types: SNV-induced, four AS-induced, MX-induced, AL-induced, AF-induced. (B)Workflow for AS position offset rectification and reconstruction of cDBG. Input transcript pairs are converted into a single sequence that includes two virtual nucleotides denoting the splicing start and end sites. SUPPA, a reference-based method, is utilized to determine the true splicing sites. The sequence is encoded into an nx6 vector using one-hot encoding. The offset between the true and predicted splicing sites is calculated and encoded as the ground truth. An attention-based convolutional neural network (CNN) rectification model is trained on these data to predict the offset, enabling the reconstruction of the cDBG with corrected splicing positions. (C) Workflow for 4 types AS classification. For each cDBG, node features, edge features, and global features are extracted. These features are integrated into distinct layers of a graph attention network (GAT)-Transformer hybrid model. This architecture enables high-precision classification of four types of AS events. (D)Workflow for end-to-end application of IRCAS. Transcriptomic data from any species lacking a reference genome is processed by IRCAS, enabling the classification of seven AS types with high accuracy. C_FIG

bioinformatics↗

bioRxiv2025

Inhibition of CGRP receptor ameliorates AD pathology by reprogramming lipid metabolism through HDAC11/LXRβ/ABCA1 signaling

The Calcitonin gene-related peptide (CGRP) receptor has gained attention in Alzheimers Disease (AD) research due to its involvement in regulating neuroinflammation. However, its role and mechanism in AD pathology remain unclear. Here, we demonstrate that CALCRL, a core component of the CGRP receptor, is upregulated in the hippocampus of AD dementia patients and 5xFAD mice. Knockout of the CGRP receptor ligand Calca or pharmacological blockade using Rimegepant (Rim), reduces soluble A{beta}1-42 oligomer-induced neuronal death and glial inflammation. Rim treatment also rescues neurobehavioral impairments, neurodegeneration, and lipid metabolism dysfunction in 5xFAD mice. Mechanistically, these effects are mediated through HDAC11 inhibition, which enhances LXR{beta} acetylation and ABCA1 expression, promoting the reprogramming of neuronal lipid metabolism. Importantly, this CALCRL/HDAC11/LXR{beta}/ABCA1 axis is conserved across both humans and mice. Our findings uncover a novel mechanism underlying AD pathogenesis and highlight the therapeutic potential of targeting CGRP signaling in AD. HIGHLIGHTSInhibition of CGRP receptor ameliorates disease pathology in models of AD HDAC11 mediates CGRP receptor function in AD HDAC11 is a pivotal regulator in lipid metabolism by LXR{beta}/ABCA1 signaling The HDAC11/LXR{beta}/ABCA1 axis is conserved in AD humans and mice

neuroscience↗