Biology subjects

Wen, Y.

Publications and source records attributed to Wen, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Quantal PCR: A Calibrator-Free Method for Determining the Unit for Nucleic Acid Quantification

Quantitative polymerase chain reaction (qPCR) is limited in measuring absolute nucleic acid copy numbers due to the inherent variability of calibrators. Here, we introduce the Quantal PCR (quPCR), a novel method that eliminates the need for calibrators by defining an intrinsic quantal unit derived from the thermodynamic and kinetic properties of the replication system. This approach first determines amplification efficiency at high template concentrations, which is then used as the replication probability to construct quantification cycle (Cq) distribution profiles. These profiles are compared with those from limiting dilution PCR to derive the Cq value for the minimal quantal-replication unit ("quCq"), enabling calculation of the sample copy number. Validation using a dual-target DNA template showed near-identical copy numbers using two distinct target-specific replication systems. Thus, quPCR represents a new method for absolute nucleic acid quantification at the single-molecule level, offering a calibrator-free alternative for absolute quantification.

biochemistry↗

bioRxiv2025

Theta-Band Temporal Interference Stimulation of the Dorsal Anterior Cingulate Cortex Enhances Prediction Error Processing in Individuals With Food Addiction

BackgroundPrediction error (PE) signals encode discrepancies between expected and actual outcomes and are linked to medial frontal theta dynamics in the dorsal anterior cingulate cortex (dACC). However, causal evidence that dACC theta mechanisms contribute to PE gain in humans remains limited. Transcranial temporal interference stimulation (tTIS) enables non-invasive modulation of deep cortical targets and provides a strategy to probe dACC theta circuitry. ObjectiveTo determine whether theta-band tTIS targeting the dACC modulates the neural gain of prediction error encoding during reward processing. MethodsThirty-four participants with elevated food addiction-related symptoms were randomized in a single-blind, sham-controlled pre-post design to active theta-band tTIS or sham stimulation. Under satiety, participants completed a food incentive delay task while EEG was recorded before and after stimulation. Feedback-related negativity (FRN) was analyzed at mean and single-trial levels using mixed-effects models with behavioral and Rescorla-Wagner model-derived prediction errors. Stimulus-preceding negativity (SPN) indexed anticipatory processing. ResultsTheta-band tTIS selectively modulated feedback-stage prediction error encoding. It altered the trial-level FRN-prediction error slope, with pre-to-post changes differing between groups for both behavioral ({beta} = 1.74, p = .049) and model-derived prediction errors ({beta} = 1.77, p = .048). At the mean ERP level, FRN became more negative after active stimulation (t16 = 2.75, p = .014), whereas SPN was unaffected. ConclusionTheta-band tTIS targeting the dACC modulates neural sensitivity to prediction errors during reward feedback, providing causal evidence that medial frontal theta dynamics regulate the neural gain of prediction error encoding.

neuroscience↗

bioRxiv2025

Eosinophil-derived COX-2 protects against experimental colitis through the PGE2-IL-22 axis

Inflammatory bowel disease (IBD) is driven by a breakdown in immune regulation and epithelial barrier function, yet the contribution of eosinophils to this process has remained poorly defined and controversial. While eosinophils infiltrate the intestinal mucosa during both flares and remission, their role in shaping disease outcomes is unclear. Our RNA-seq analyses of colonic eosinophils isolated from dextran sulfate sodium (DSS)-treated mice revealed a significant upregulation of cyclooxygenase (Cox)-2 (gene name, Ptgs2). Eosinophil-specific deletion of Cox-2 (Ptgs2fl/fleoCre+/-) reduced IL-22 production and exacerbated DSS- and trinitrobenzene sulfonic acid (TNBS)-induced colitis, characterized by greater weight loss, higher disease activity, colon shortening, and epithelial injury. Administration of recombinant IL-22 reversed these phenotypes. Mechanistically, eosinophil-derived COX-2 enhanced IL-22 production by type 3 Innate lymphoid cells (ILC3s) through prostaglandin E2 (PGE2) signaling. Consistently, Ptgs2fl/fleoCre+/-mice exhibited reduced colonic PGE2 levels, while PGE2 analog treatment restored IL-22 production and mucosal protection. Our findings identify eosinophil-derived COX-2 and PGE2 as a critical regulator of IL-22 production during colitis, uncovering a previously unrecognized eosinophil-ILC3 crosstalk that safeguards the intestinal barrier and represents a promising therapeutic target in IBD. Significance StatementThe role of eosinophils in inflammatory bowel disease (IBD) has remained unresolved. We identify eosinophil-derived COX-2 as the main source of prostaglandin E2 (PGE2) in colitis, which drives IL-22 production by ILC3s to maintain epithelial protection. This discovery defines a protective eosinophil/PGE2/IL-22 circuit and reveals a therapeutic target to strengthen barrier defense in IBD.

immunology↗

bioRxiv2025

Decoding Neoantigen-encoding Tumor-Specific Transcripts Unveils a Shared Target Reservoir for Immunotherapy in Hepatocellular Carcinoma

Background and AimsPrimary liver cancer, predominantly hepatocellular carcinoma (HCC), has limited therapeutic options. While mutation-derived neoantigen vaccine holds promise, its success is hindered by low antigen availability. This study explores transcriptome-derived neoantigens (neoantigen-encoding tumor-specific transcripts, neoTSTs) in HCC, characterizing their features, generation mechanisms, and therapeutic potential. Approach and ResultsWe analyzed RNA-seq data from 1,013 liver cancer patients and constructed a multi-layered reference dataset. Using a customized pipeline, we identified an average of 60 neoTSTs per patient, significantly surpassing mutation-derived neoantigens (neoMuts). NeoTSTs exhibited higher population frequencies, with 73.1% providing multiple epitopes, and were validated through mass spectrometry and HLA transgenic mouse models. Mechanistically, neoTSTs were generated via retained introns, transposable element activation, HNF4A-regulated alternative promoters, and de novo transmembrane domain (TMD) generation. Single-cell analysis revealed neoTSTs cover >75% of tumor cells and identified antigen-presenting cancer-associated fibroblasts (apCAFs) that enriched in immunotherapy responders and amplified CD4 T-cell responses via MHC-II presentation. In murine HCC models, neoTST vaccination outperformed neoMuts, inducing dual MHC-I/II activation and significant tumor growth inhibition. ConclusionsNeoTSTs represent a superior neoantigen source in HCC, compensating for the limitations of mutation-derived targets. Their abundance, sharedness, and dual MHC pathway activation highlight their potential for personalized immunotherapy, particularly in low-TMB tumors. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/692877v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1bedfedorg.highwire.dtl.DTLVardef@5f6c95org.highwire.dtl.DTLVardef@d1deb5org.highwire.dtl.DTLVardef@743e85_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

The Age-Dependent Resident Myonuclear Multi-Omic Response to a Skeletal Muscle Hypertrophic Stimulus

A detailed analysis of how muscle fiber nuclei (myonuclei) respond to a hypertrophic stimulus would provide a critical step toward understanding compromised skeletal muscle plasticity with age. We used recombination-independent doxycycline-inducible myonucleus-specific fluorescent labelling, tissue RNA-sequencing, myonuclear DNA methylation analysis, multi-omic integration, and single myonucleus RNA-sequencing to define the molecular characteristics of adult (6-8 month) and aged (24 month) murine skeletal muscle after acute mechanical overload (MOV). In adult and aged MOV muscles, we found that: 1) similarities in the transcriptional response to loading - specifically in metabolism genes - were partly explained by a post-transcriptional microRNA-mediated mechanism, which we corroborated using an inducible muscle fiber-specific miR-1 knockout model, 2) differences in age-dependent transcriptional responses were linked to the magnitude and location of differential DNA methylation in resident myonuclei, specifically around hypertrophy-associated genes such as Myc, Runx1, Mybph, Ankrd1, collagen genes, and minichromosome maintenance genes, 3) adult and aged resident myonuclear transcriptomes had differing enrichment for innervation-related transcripts as well as unique transcriptional profiles in an Atf3+ "sarcomere assembly" population after MOV, and 4) cellular deconvolution analysis supports a role for neuromuscular junction regulation in age-specific hypertrophic adaptation. These data are a roadmap for uncovering molecular targets to enhance aged muscle adaptability.

cell biology↗

bioRxiv2025

Engineering Linear Cap-independent mRNA Vaccines with Intrinsic Adjuvanticity for Potent Cancer Immunotherapy

mRNA cancer vaccines have shown promising efficacy in early-phase clinical trials, but existing platforms struggle to boost antitumor efficacy without added cost or complexity. Here, we present a streamlined linear cap-independent RNA (LciRNA) cancer vaccine platform that achieves stable expression in vivo without 5 capping or ribonucleotide modification, and innately stimulates immune responses to enhance antitumor immunity. By fusing a UPA protective sequence, composed of a viral exoribonuclease-resistant RNA (xrRNA) and a poly(A) binding protein (PABP) motif, with an optimized Enterovirus A internal ribosome entry site, LciRNA resists 5 exonuclease decay and drives superior in vivo expression. Mechanistically, UPA sequence not only impedes exonuclease-mediated decay but also recruits RNA-binding proteins to stabilize LciRNA. Moreover, LciRNA robustly activates dendritic cell pattern-recognition receptor pathways, promotes dendritic cell maturation, and upregulates proinflammatory signals. In murine melanoma and HPV-associated tumor models, it elicits strong systemic and intra-tumoral T cell responses and superior tumor control, demonstrating how immune stimulation-translation synergy underpins its efficacy. This work establishes a next-generation cost-effective mRNA cancer vaccine platform with simplified production and enhanced efficacy, highlighting immuno-translation coupling as a paradigm for future mRNA cancer vaccines.

bioengineering↗

bioRxiv2025

Axially swept dithered light-sheet microscope to reveal cardiac morphology

Understanding cardiac microstructure and vascular networks in their entirety is critical for assessing cardiovascular development, disease progression, and therapeutic interventions. Light-sheet microscopy combined with tissue clearing enables high-resolution volumetric imaging of intact organs but faces limitations in trabeculated myocardium due to trade-offs among light-sheet thickness, effective range, and frame rate. We exploit temporal dynamics that govern illumination-detection interplay to maintain uniform resolution across specimens. Building on this, we implemented high-speed dithered light-sheet (DiLS) illumination, extending the confocal region by over 40% and enhancing the space-bandwidth product while preserving optical sectioning. Integration of DiLS with a sweeping approach establishes the axially swept dithered light-sheet (AS-DiLS), which enhances imaging throughput while preserving axial resolution and enables uniform illumination up to 12.5-millimeter range. AS-DiLS delivers near-isotropic resolution (~2.5 m) for investigating intricate ventricular trabeculae, vasculature, and extracellular matrix, providing a scalable platform for comprehensive cardiovascular morphology and topology assessment from embryos to adults. TeaserVolumetric imaging reveals microstructure and vascular networks in their entirety with near-isotropic resolution.

bioengineering↗

bioRxiv2025

Telomere 3'-overhang attrition and persistent telomeric DNA damage response in failing human hearts

BackgroundTelomere homeostasis is critical for normal cellular and organ function, and its dysregulation is implicated in aging and chronic diseases. Although telomere length (TL) is critical for normal telomere function, its functional status can also be altered by many other factors. The organization and protective status of telomere in failing human heart (FHH) remains incompletely understood. MethodsUsing left ventricular tissues from patients with idiopathic dilated cardiomyopathy (IDC), ischemic heart disease (IHD), and non-failing heart (NFH), we performed a comprehensive analysis that included measurements of overall TL and 3 overhang length in left ventricles and cardiomyocytes (CM), assessment of telomere-binding protein associations, and transcriptomic profiling through RNA sequencing. ResultsAlthough TL varied among individuals, reduced median TL was observed only in IDC, while both IDC and IHD showed an increased frequency of very short telomeres, falling below the 5th percentile, in CMs. Strikingly, significant telomere 3-overhang attrition was detected in both disease groups and strongly correlated with elevated H2AX phosphorylated on serine 139 ({gamma}H2AX) in heart tissues, indicating DNA damage. This was accompanied by persistent activation of ataxia telangiectasia mutated (ATM) protein-mediated DNA damage responses and the formation of telomere dysfunction-induced foci (TIFs) in CMs from FHH. Concomitantly, the association of telomeres with the single-stranded telomere-binding protein, Protection of Telomeres 1 (POT1), and the double-stranded telomere-interacting protein, telomere repeat-binding factor 2 (TERF2), was markedly reduced, accompanied by an increase in association of {gamma}H2AX and ssDNA binding protein, RPA with telomeres in IDC and IHD relative to NFH, signifying telomere de-protection. ConclusionsCM telomere dysfunction, characterized by 3 overhang attrition and de-protection, is a common feature in FHH, leading to persistent DNA damage response in telomeres. Better understanding of telomere biology throughout the progression of different heart diseases to heart failure will provide more effective prevention and treatment strategies. GRAPHICAL ABSTRACTHuman telomeres safeguard chromosome ends through a higher-order telomere-loop (t-loop) structure and the shelterin complex, preventing their recognition as DNA double-strand breaks (DSBs). In the failing human heart (FHH) with idiopathic dilated cardiomyopathy (IDC) and ischemic heart disease (IHD), cardiomyocyte telomeres lose protection due to disruption of the shelterin complex, driven by oxidative DNA damage from reactive oxygen species (ROS) targeting G-rich telomeric sequences. This leads to t-loop unfolding, DDR cascade activation, 3 overhang excision, and persistent DNA damage responses with Telomere Dysfunction-Induced Foci (TIFs) formation at the telomeric regions of cardiomyocytes in FHH. The ATM-mediated DDR, along with engagement of both classical non-homologous end joining (cNHEJ) and homologous recombination (HDR) repair pathways, is integral to FHH progression. This study underscores the significance of telomere 3 overhang attrition in the pathogenesis of FHH with IDC and IHD. Unlike changes in overall telomere length, 3 overhang shortening directly correlates with increased DNA damage in human myocardial tissue. Preventing telomere 3 overhang attrition and oxidative damage offers a promising avenue for attenuating heart disease progression toward heart failure. In particular, selective ATM inhibition, as opposed to ATR inhibition, presents a potential therapeutic strategy for patients with IDC and IHD. Future efforts to pinpoint deficiencies in cNHEJ and HDR pathways in failing human hearts may reveal novel targets for heart failure prevention and treatment, providing new strategies in the management of this patient population. CMs, cardiomyocytes; DDR, DNA double-strand break repair; FHH, failing human heart; ROS, reactive oxygen species; t-loop, telomere-loop. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/669993v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1d21937org.highwire.dtl.DTLVardef@757f54org.highwire.dtl.DTLVardef@1fa7472org.highwire.dtl.DTLVardef@1f2e961_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Pediatric CHOP Chemotherapy Acutely Disrupts Satellite-Cell Dynamics and Blunts Muscle Mass in a Sex-Specific Manner

Pediatric cancer survival now exceeds 85 percent owing, in part, advances and use of combination chemotherapy treatments such as CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone). Despite its efficacy, CHOP may cause deleterious off-target effects during critical pediatric development periods such as impairments of skeletal muscle. We evaluated the acute effects of a CHOP administered to C57Bl/6J mice from postnatal day 28 to 48. CHOP slowed body-weight gain and has smaller gastrocnemius fiber cross-sectional area by approximately 25 percent in both sexes. mRNA sequencing detected 214 differentially expressed genes in males and 217 in females relative to controls, yet only 29 transcripts overlapped. Males exhibited downregulation of myogenic regulators, indicating impaired progenitor maintenance, whereas females showed an upregulation of extracellular-matrix and translational machinery genes plus cell-cycle regulators. Using immunohistochemistry to assess satellite cell abundance, there were 60% fewer satellite cells in males and a 40% fewer in females, which supported our transcriptional findings. These results demonstrate that pediatric CHOP acutely disrupts muscle stem-cell dynamics via sex-specific molecular programs and identify satellite-cell depletion as a potential target for preserving muscle health in pediatric cancer survivors.

physiology↗

bioRxiv2025

An Adipose mTORC1 Effector Links Nutrient-induced Ribosomal Protein Translation to Lifespan in Drosophila

Mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability to orchestrate metabolic processes critical for physiological homeostasis and organismal ageing1. While mTORC1 preferentially regulates the translation of 5'-terminal oligopyrimidine (TOP) motif-containing mRNAs that predominantly encode ribosomal proteins (RPs) via the translational repressor 4E-BP 2, this mTORC1 function is resistant to rapamycin inhibition 3. TOP mRNAs are exceptionally abundant, thus imposing a major translational burden on cells; yet how their translation is physiologically tuned and linked to longevity remain unexplored. Here we identify Lsp2, originally known as a storage protein 4, as an adipose effector of mTORC1 that modulates lifespan in Drosophila. Lsp2 is induced by essential amino acids (EAAs) via mTORC1. Genetic ablation of Lsp2 to blunt organismal response to protein diets drives robust lifespan extension without compromising key life-history traits such as reproduction. Translatomic profiling reveals that loss of Lsp2 selectively reduces global TOP mRNA translation in a 4E-BP-dependent manner, thereby extending lifespan via a mechanism distinct from rapamycin inhibition that fails to reduce 4E-BP phosphorylation in vivo. Finally, Lsp2 adipokine promotes 4E-BP phosphorylation and acts systemically across tissues to shape the lifespan responses to dietary protein. Collectively, our findings establish Lsp2 as a novel translational regulator of TOP genes that mechanistically couples physiological ribosomal protein synthesis with organismal longevity.

physiology↗

bioRxiv2025

miR-486-3p ameliorates aging-related impaired angiogenesis in adult moyamoya disease by targeting Forkhead Box O4

ObjectiveInvestigate miR-486-3ps role in alleviating age-related angiogenic decline in Moyamoya disease (MMD) by regulating senescent endothelial cells. MethodsClinical analysis of 151 MMD patients correlated age with postoperative angiogenesis (DSA grading). Senescent HUVECs (SA-{beta}-gal>80%) exhibited elevated SASP factors (IL-6/IL-8/MCP-1). Functional assays (EdU/Transwell/Matrigel) and bioinformatics identified miR-486-3p targets, validated via luciferase/Western blot. ResultsPatients [≥]35 years had 3.67-fold higher risk of poor angiogenesis (OR=3.67). Senescent HUVECs showed 10-16-fold higher SASP secretion (p<0.01). miR-486-3p overexpression increased proliferation (EdU+25%), migration (1.7-fold), and tube formation (+40% branches) in senescent cells (p<0.01) and enhanced angiogenesis in vivo (p<0.001). miR-486-3p directly targeted FOXO4, reducing its luciferase activity (-35%) and protein levels (-37%) (p<0.01), suppressing SASP. ConclusionmiR-486-3p enhances post-revascularization angiogenesis in MMD by inhibiting FOXO4-mediated SASP, offering a therapeutic target and predictive biomarker.

molecular biology↗

bioRxiv2025

Poor sleep impairs immune responses and influenza vaccine protection

Disrrupted sleep, a common occurrence among shift workers, older adults, and individuals with sleep disorders, is increasingly recognized as a potential factor interfering with vaccine efficacy. Using a mouse model, we show that two weeks of chronic sleep fragmentation (CSF) before and during influenza vaccination significantly impair humoral immunity and reduce protection against lethal viral challenge. CSF-exposed mice exhibited lower neutralizing antibody titers, diminished IgG subclass responses, and reduced survival after viral challenge, despite preserved antibody binding avidity. Single-cell RNA sequencing and immune receptor profiling revealed altered B cell maturation, abnormal germinal center activation, and plasma cell stress, characterized by activation of unfolded protein response and oxidative stress pathways. CSF also reprogrammed B-cell signaling and disrupted coordination with T-cells. Together, this study showed that CSF compromises vaccine-induced immune responses by affecting multistage of B-cell differentiation, underscoring the importance of considering sleep health in vaccination strategies for vulnerable populations. One Sentence SummaryPoor sleep weakens both the magnitude and quality of immune responses, compromising the protective efficacy of influenza vaccination.

immunology↗

bioRxiv2025

Surface-immobilized fibronectin conformation drives synovial fluid adsorption and film formation

The articular cartilage extracellular matrix (ECM) is a complex network of biomolecules that includes fibronectin (FN). FN acts as an extracellular glue, controlling the assembly of other macromolecular constituents to the ECM. However, how FN participates in the binding and retention of synovial fluid components, the natural lubricant of articulated joints, to form a wear-protecting and lubricating film has not been established. This study reports on the role of FN and its molecular conformation in mediating macromolecular assembly of synovial fluid ad-layers. FN films as precursor films on functionalized surfaces, a model of FNs articular cartilage surface, adsorbed and retained different amounts of synovial fluid (SF) depending on FN conformation. FN conformational changes were induced by depositing FN from bulk solution at pH 7 (extended state) or at pH 4 (unfolded state) on self-assembled monolayers on gold-coated quartz crystals, followed by adsorption of diluted SF (25%) onto FN precursor films. Mass density, thin film compliance, surface morphologies, and the secondary and tertiary structures of adsorbed FN films reveal pH-induced differences. FN films deposited at pH 4 were thicker, more rigid, showed a more homogeneous morphology, and had altered -helix and {beta}-sheet content, compared to FN films deposited at pH 7. FN precursor films deposited at pH 7 adsorbed and retained more synovial fluid than those at pH 4, revealing the importance of FN conformation at the articular cartilage surface to bind and maintain a thin layer of synovial fluid constituents. This knowledge will enable a better understanding of the molecular interactions and synergies between the articular cartilage ECM components and SF. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/650860v2_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@871413org.highwire.dtl.DTLVardef@3712a5org.highwire.dtl.DTLVardef@1a92b78org.highwire.dtl.DTLVardef@164e79f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Disturbing immune homeostasis by neutrophil loss of Uba1 induces VEXAS-like autoinflammatory disease in mice

ObjectiveVEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome is an identified haemato-rheumatoid disease caused by somatic UBA1 mutations in hematopoietic stem cells. We report Uba1 loss in various mouse hematopoietic cell types leads to diverse effects, with approximately 70% Uba1 depletion in neutrophils inducing non-lethal VEXAS-like symptoms. MethodsUsing nine different Cre/flox-mediated conditional-knockout (CKO) models, we interrogated the phenotypes caused by hematopoietic loss of Uba1. Neutrophil-specific depletion of Uba1 were validated and VEXAS-like phenotypes were examined. ResultsUba1 loss in HSCs induces extensive hematopoietic cell death while in B or T cells, or megakaryocytes induces corresponsive cell death but these mutants appear normal. Uba1 loss in monocytes and neutrophils failed to induce cell death and the mutants are viable. Among the models, only Uba1 loss in neutrophils manifests autoinflammatory symptoms including increased counts and percentage of neutrophils, increased proinflammatory cytokines, vacuoles in myeloid cells and dermatitis. Residual Uba1 is about 30% in the mutant neutrophils, which manifest disturbed cellular hemostasis. Genetic loss of Morrbid partially mitigated the VEXAS-like symptoms. ConclusionOur study reveals diverse effects of Uba1 loss in hematopoietic cells and establishes a VEXAS-like murine model, facilitating understanding and potential treatments for this syndrome prevalent in aged men. HIGHLIGHTSO_ST_ABSWHAT IS ALREADY KNOWN ON THIS TOPICC_ST_ABSVEXAS syndrome is a recently identified hematological and immunological disease prevalent in adult man but rarely in adult woman. Somatic mutations in the E1-enzyme encoding gene UBA1 in hematopoietic stem cells is the driver on the top of the genetic etiology of the disease. However, the major pathogenic cell type(s) for VEXAS syndrome has not been experimentally examined and mouse models recapitulating the disease are lacking. WHAT THIS STUDY ADDSO_LIUsing nine different conditional-knockout (CKO) murine models, we interrogated the pleiotropic phenotypes caused by loss of the ubiquitin activation enzyme Uba1 in different hematopoietic cell types; C_LIO_LIOur results demonstrated that among the nine tested CKO mutants, only neutrophil loss of Uba1 results in VEXAS-like autoinflammatory disease; C_LIO_LIThe VEXAS-like symptoms in the S100a8Cre-CKO mutant mice include: increased counts of white blood cells and neutrophils, increased percentage of neutrophils, increased serum level of proinflammatory cytokines (IL-1{beta}, IL-6 and TNF), observation of vacuoles, increased survival, and increased phagocytosis in mutant neutrophils; C_LIO_LIPharmacological treatments with IL-1 inflammatory pathway inhibitors Anakinra or Canakinumab or genetic loss of the myeloid pro-survival regulator Morrbid partially mitigated the VEXAS-like symptoms in the S100a8Cre-CKO mutants; C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYThe study reports a technical strategy of developing the murine models for VEXAS syndrome. In addition, the study dissects cellular and molecular mechanisms, especially the cell-type-dependent tolerance and pathogenicity of loss of function of Uba1, for the occurrence of the autoinflammation diseases in mice. The study provides translational implications in etiology and potential treatment choices for the newly-identified haemato-rheumatoid syndrome in clinical management.

immunology↗

bioRxiv2025

Transcriptomic splicing analysis reveals a gene-independent form of TE reactivation in tumors representing unrecognized source of oncogenes and neoantigens

Transposable elements (TEs) are reactivated in tumors and serve as significant contributors to tumor transcriptomic complexity and heterogeneity. However, their repetitive nature and diverse transcriptional forms have hindered efforts to characterize TE-derived transcripts independent of host gene contexts. Here, using our self-developed splicing-junction analysis tool ASJA, we systematically interrogated TE transcription across 32 cancer types, identifying transcripts autonomously initiated from and exclusively spliced among TEs with high TE content, termed TEtrans. Our analysis revealed 5,361 TEtrans exhibiting pan-cancer prevalence, tumor-specific expression and features of mature transcripts, including canonical splicing, 5 caps and polyA tails. Mostly unannotated and enriched in intergenic regions, TEtrans are predominantly derived from primate-specific classes with conserved splice pattern. TEtrans burden demonstrates heterogeneous associations with prognosis and immune activity across cancers, while their expression can be epigenetically dual-regulated by stemness- and inflammation-associated transcription factors. Functional studies uncovered that TEtrans could act as oncogenes, exemplified by tsTE1, a HERVH-derived transcript that promotes colorectal cancer proliferation by enhancing TOP1-mediated DNA supercoil relaxation. Remarkably, [~]7.2% of TEtrans are identified to encode tumor neoantigens, including viral proteins and unannotated peptides, which are shared among patients and validated by proteogenomic analysis. These TEtrans-derived neoantigens are immunogenic both in vitro and in vivo, and exceed neoepitopes from genomic alterations in abundance per tumor, particularly in cancers with low mutational burden. Collectively, as a gene-independent form of TE-derived transcripts, TEtrans represents a unique source of oncogenes and tumor neoantigens, expanding the functional repertoire of TEs in cancer biology and offering new avenues for therapeutic targeting. HighlightsO_LITEtrans are tumor-specific transcripts with conserved splicing patterns, predominantly derived from primate TEs in intergenic regions. C_LIO_LITEtrans expression is epigenetically activated and dually regulated by stemness/inflammation transcription factors. C_LIO_LITEtrans function as oncogenes, exemplified by tsTE1 enhancing TOP1-mediated DNA relaxation. C_LIO_LITEtrans encode tumor neoantigens that elicit CD8+ T cell responses, providing targets for immunotherapy, especially in low-mutation tumors. C_LI Abstract figure O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/640928v1_ufig1.gif" ALT="Figure 1"> View larger version (78K): org.highwire.dtl.DTLVardef@1d2d4cforg.highwire.dtl.DTLVardef@918f14org.highwire.dtl.DTLVardef@489465org.highwire.dtl.DTLVardef@1069d17_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Spatiotemporal dynamics of Hemerocallis citrina habitat suitability in China under climate change scenarios

ObjectiveHemerocailis citrina, a perennial herb belonging to the Hemerocailis genus in the Apophaceae family, has been utilized as both food and medicine for thousands of years. Additionally, it is considered a traditional dominant cash crop in China. Therefore, analyzing the spatio-temporal distribution characteristics of climate sustability of H. citrina in current and future climatic conditions is crucial for its stable industry development in China. MethodENMTools was used to screen the data of 287 distribution points of H. citrina. 37 environmental variables affecting the distribution of H. citrina were selected, the MaxEnt model and Geographic Information System (ArcGIS) were used to simulate the potential distribution patterns of H. citrina in 5 periods (current, future 2040 s, 2060 s, 2080 s, and 2100 s), and the dominant climate factors affecting the distribution of H. citrina were analyzed through contribution rate, displacement importance value, and jackknife test. Results(1) The average AUC value of 10 cross-validated fits under the ROC curve for the training dataset was 0.933, and the average AUC value of 10 cross-validated fits for the test dataset was 0.901, this indicates that the simulation stability and reliability are highest when incorporating all three types of environmental variables. (2) The main environmental factors identified affecting their distribution include the lowest temperature of the coldest month, average temperature of the coldest quarter, slope, elevation, and carbonate or lime content, as determined by the contribution rate of cutting method, displacement contribution rate, and single factor response curve. (3) The model prediction showed that H. citrina was widely distributed in 34 provincial regions of China under the current climate conditions, with a suitable area of 646.81 km2. (4) Under the future emission scenarios, the suitable habitat for H. citrina is projected to shrink and not shift to higher latitudes, indicating a negative impact of climate warming on its distribution, which will reduce the suitable habitat and narrow the ecological niche. Temperature and precipitation have been identified as important factors affecting the distribution of H. citrina. Although H. citrinas suitable habitat is expected to decrease to varying degrees in the future, the distribution area is relatively stable and there will still be a broad natural habitat in the future. ConclusionThe species distribution model was used to predict the future temporal and spatial distribution of climate-suitable areas for H. citrina in China. Based on the models simulation results, it is recommended that north and southeast China become the main planting areas for H. citrina in the future, with Sichuan and other regions as key development areas. Additionally, other regions should prioritize developing suitable cash crops based on local conditions.

bioinformatics↗

bioRxiv2024

Sirt5 preserves cardiac function in ischemia-reperfusion injury by inhibiting ANT2 lactylation

Myocardial ischemia-reperfusion (IR) injury is the most common type of heart disease. IR-disrupted mitochondrial homeostasis affects heart energy metabolism and function, but the mechanism remains poorly understood. Here we report a cardioprotective role of the mitochondrial protein Sirt5 in a mouse model of cardiac IR injury. The down-regulation of Sirt5 in IR-injured heart is associated with an increased protein lactylation and impaired mitochondrial function. Overexpression of Sirt5 alleviates, whereas conditional knockout of Sirt5 aggravates, mitochondrial damage and cardiac injury. Mechanistically, Sirt5 interacts with the inner mitochondrial membrane protein adenine nucleotide translocase 2 (ANT2), inhibiting its lysine lactylation to promote its association with the outer mitochondrial membrane protein voltage-dependent anion-selective channel 1 (VDAC1). Lactylation-resistant ANT2 efficiently complexes with VDAC1 and improves cardiac function after injury. Therefore, we uncover a Sirt5-regulated interaction of ANT2 and VDAC1 in maintaining mitochondrial homeostasis, highlighting the potential of targeting ANT2 lactylation as a therapeutic strategy in the treatment of cardiac injury. TeaserSirt5 promotes the interaction of mitochondrial proteins to protect mitochondrial homeostasis and improve heart function in ischemia-reperfusion injury.

pathology↗

bioRxiv2024

Identification of distinct subtypes of post-stroke and neurotypical gait behaviors using neural network analysis of kinematic time series data

BackgroundHeterogeneous types of gait impairment are common post-stroke. Studies used supervised and unsupervised machine learning on discrete biomechanical features to summarize the gait cycle and identify common patterns of gait behaviors. However, discrete features cannot account for temporal variations that occur during gait. Here, we propose a novel machine-learning pipeline to identify subgroups of gait behaviors post-stroke using kinematic time series data. MethodsWe analyzed ankle and knee kinematic data during treadmill walking data in 39 individuals post- stroke and 28 neurotypical controls. The data were first input into a supervised dual-stage Convolutional Neural Network-Temporal Convolutional Network, trained to extract temporal and spatial gait features. Then, we used these features to find clusters of different gait behaviors using unsupervised time series k-means. We repeated the clustering process using 10,000 bootstrap training data samples and a Gaussian Mixture Model to identify stable clusters representative of our dataset. Finally, we assessed the kinematic differences between the identified clusters using 1D statistical parametric mapping ANOVA. We then compared gait spatiotemporal and clinical characteristics between clusters using one-way ANOVA. ResultsWe obtained five clusters: two clusters of neurotypical individuals (C1 and C2) and three clusters of individuals post-stroke (S1, S2, S3). C1 had kinematics that resembled the normative gait pattern. Individuals in C2 had a shorter stride time than C1. Individuals in S1 had mild impairment and walked with increased bilateral knee flexion during the loading response. Individuals in S2 had moderate impairment, were the slowest among the clusters, took shorter steps, had increased knee flexion during stance bilaterally and reduced paretic knee flexion during swing. Individuals in S3 had mild impairment, asymmetric swing time, had increased ankle abduction during the gait cycle and reduced dorsiflexion bilaterally during loading response and stance. Every individual was assigned to a cluster with a cluster membership likelihood above 93%. ConclusionsOur results indicate that joint kinematics in individuals post-stroke are distinct from controls, even in those individuals with mild impairment. The three subgroups post-stroke showed distinct kinematic impairments during specific phases in the gait cycle, providing additional information to clinicians for gait retraining interventions.

bioengineering↗