Biology subjects

Long, X.

Publications and source records attributed to Long, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Anisogamy drives diverse patterns of sex-role divergence

Male and female animals often differ remarkably in their reproductive behaviours, typified by competing males and caring females. One influential explanation traces sex-role divergence to anisogamy: sex differences in gamete size. This explanation remains controversial, because existing models have not fully resolved how anisogamy leads to secondary sex-role divergence, and exceptions to typical patterns are empirically well-documented. Here, we develop mathematical models linking anisogamy to secondary sex-role evolution, showing that anisogamy drives sex-role divergence along contrasting evolutionary trajectories depending on ecological context. When the sexes differ only in gamete size, male-biased mating competition and offspring care evolve under scramble competition, whereas uncertain paternity shifts the population towards typical patterns. By contrast, anisogamy generally drives typical sex roles under contest competition, although sex-role reversal can emerge as an alternative stable state when care must be apportioned among offspring. Anisogamy can thus explain the striking diversity of sex differences across taxa.

evolutionary biology↗

bioRxiv2026

Myeloid Ecotropic Viral Integration Site 1 Promotes Vascular Smooth Muscle Differentiation through Activation of Myocardin

Myocardin (MYOCD) is the principal trigger-switch for vascular smooth muscle cell (VSMC) growth arrest and the cyto-contractile program of differentiation. While much is known about MYOCD-dependent VSMC differentiation, limited information exists as to its transcriptional regulation. Here, we report moderate mRNA expression of Myeloid Ecotropic viral Integration Site 1 (MEIS1) in both human and mouse VSMCs. MEIS1 mRNA is reduced in parallel with myocardin mRNA and protein under conditions of VSMC de-differentiation. Loss- and gain-of-Meis1 expression studies in cultured human VSMCs and the mouse carotid artery support MEIS1 as an activator of myocardin and VSMC differentiation. CRISPR-mediated knockout of the endogenous Meis1 gene in vitro and elicited lower levels of VSMC contractile markers and an increase in growth rate. Similarly, Femoral artery wire injury, in mice lacking Meis1 showed and increased of neointima formation. Mechanistically, we identified a conserved MEIS1 response element in the proximal promoter of myocardin, that appears to contribute to the promoter activity, suggesting a potential regulatory interaction. These results suggest a previously unrecognized role for the homeodomain protein MEIS1 in the activation of myocardin and the quiescent, VSMC differentiated state.

molecular biology↗

bioRxiv2026

A mycovirus identified from an outbreak fungal species complex reveals a parallel antiviral system

Mycoviruses are prevalent across major fungal lineages, yet none have been reported in the Cryptococcus gattii species complex (CGSC), the causative agent of the largest known fungal outbreak in immunocompetent hosts. Consequently, the occurrence of mycoviruses and the host determinants governing their infection in this important pathogenic clade remain unexplored. Through screening of 386 Cryptococcus isolates, we identified a mycovirus, designated CgTV1, in an environmental isolate of the Cryptococcus gattii species complex (CGSC). CgTV1 is a double-stranded RNA (dsRNA) mycovirus of the genus Totivirus, with a genome encoding a capsid protein and an RNA-dependent RNA polymerase. We showed that CgTV1 establishes a cryptic infection, because neither viral presence nor its clearance significantly alters host transcriptomic profiles, suggesting the existence of mechanisms that maintain virus-host homeostasis. Population genomic analyses reveal that an intact RNAi pathway constitutes a critical genetic barrier, and CgTV1 persistence strictly requires loss of function mutations in both AGO1 and AGO2. By pan-transcriptomics across 43 CGSC strains, we further uncovered an RNase III gene, CAI1, which exhibits high expression in the mycovirus positive isolate. Biochemical analysis indicates that Cai1 directly recognizes and degrades CgTV1 dsRNA, thereby constraining excessive mycoviral proliferation. We further demonstrate that Dicer and Cai1 act in parallel to maintain virus-host homeostasis: their combined ablation results in higher viral loads and more pronounced changes in host gene expression than ablation of either factor alone. Collectively, our findings provide the evidence of the occurrence of a mycovirus in the CGSC and reveal parallel mechanisms that enable cryptic mycoviral infections.

genetics↗

bioRxiv2026

Loss of the Coronary Artery Disease Risk Gene Leiomodin1 in Vascular Smooth Muscle Cells Triggers Rapid Onset Coronary Atherosclerosis

BackgroundAtherosclerosis is the primary underlying cause of coronary artery disease (CAD). Leiomodin1 is a vascular smooth muscle cell (VSMC)-restricted CAD risk gene whose role in coronary artery pathophysiology is unknown. Global loss of Leiomodin1 causes lethal neonatal visceral myopathy, requiring unique approaches for study in VSMCs. MethodsSeveral distinct Leiomodin1 mutant mouse models were generated by clustered regularly interspaced short palindromic repeats (CRISPR). Control (Lmod1WT) and VSMC-restricted Lmod1 knockout (Lmod1SMKO) mice were subjected to various atherogenic regimens. Atherosclerosis and LMOD1 expression in mouse and human coronary arteries were assessed by histopathology and confocal immunofluorescence microscopy. Coronary arteries from Lmod1WT and Lmod1SMKO mice were analyzed with assorted stains and antibodies, immunogold lineage tracing, spatial metabolomics/transcriptomics, and single-cell RNA sequencing (scRNA-seq). Mouse aortic SMCs from Lmod1WT and Lmod1SMKO mice were subjected to lipid loading with lentiviruses expressing wild-type Lmod1, a nucleation deficient Leiomodin1 (Lmod1ND), or a short hairpin RNA (shRNA) targeting Thrombospondin (Thbs1). ResultsUnder atherogenic conditions, Lmod1SMKO mice displayed unremarkable vessels in several organs but developed diffuse and occlusive coronary atherosclerosis. No such disease was observed in Lmod1WT mice. Time-course studies documented lipid insudation and VSMC foam cell formation in the coronary arteries of Lmod1SMKO mice as early as six days post-regimen. Immunogold lineage tracing demonstrated 46% of coronary plaque cells being of VSMC origin, with most showing evidence of lipid uptake. An intronic deletion of Lmod1, containing a conserved region where the single nucleotide variant associated with CAD exists, showed attenuated LMOD1 expression; heterozygous Lmod1SMKO mice, with a similar reduction in LMOD1, showed no CAD. Spatial metabolomics uncovered multiple lipid species within coronary atheromata of Lmod1SMKO mice, and spatial/scRNA-seq of similar coronary lesions disclosed altered lipid pathways with a consistent elevation in Thbs1. In vitro mechanistic studies revealed lipid accumulation in Lmod1SMKO VSMCs that was rescued by Lmod1WT, Lmod1ND, and Thbs1 shRNA. VSMC-restricted expression of Lmod1ND in mice resulted in negligible coronary atherosclerosis. ConclusionsUnder proatherogenic conditions, Lmod1SMKO mice present with rapidly manifesting coronary atherosclerosis that appears to be independent of the actin nucleation function of LMOD1. Targeting Thbs1 represents a viable strategy to mitigate VSMC foam cell formation. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIVascular smooth muscle cell (VSMC) loss of Leiomodin1 (Lmod1) causes diffuse and occlusive coronary atherosclerosis in mice, with little or no such disease in other vascular beds. C_LIO_LIA novel immunogold lineage tracing assay shows VSMC migration to the intima as early as six days following an atherogenic regimen, and quantitative studies demonstrate that 46% of coronary plaque cells are of SMC origin. C_LIO_LIThe coronary phenotype appears to be independent of LMOD1s actin nucleation activity, but VSMC lipid uptake is thrombospondin-dependent. C_LI What are the clinical implications?O_LILMOD1 is an annotated smooth muscle cell-restricted risk allele for human coronary artery disease (CAD), offering new insight into the role of smooth muscle cells in atherogenesis. C_LIO_LIThe rapidly manifesting CAD phenotype in Lmod1 knockout mice enables expedited testing of novel therapeutics to mitigate disease progression. C_LIO_LINew insight into LMOD1 pathobiology will help inform further SNV interrogation of the LMOD1 locus for CAD risk in patients. C_LI

pathology↗

bioRxiv2026

A regulatory role of novel long non-coding RNA, BAZ1A-AS1, in vascular smooth muscle cell functions during neointima formation in human saphenous veins

BackgroundNeointimal proliferation (NP) is a major cause of stenosis and occlusion in arteries and veins. Human saphenous veins (HSV), often used for coronary artery bypass grafting, frequently fail in part due to NP. Long non-coding RNAs (lncRNAs) have emerged as critical regulators of vascular smooth muscle cell (VSMC) phenotype, yet lncRNAs governing NP in human veins remain largely uncharacterized. Methods and ResultsUsing an ex vivo model of NP in human SV, we performed bulk RNA sequencing on SV tissues with and without NP. Among differentially expressed lncRNAs, we identified a previously uncharacterized transcript, Bromodomain Adjacent to Zinc Finger A1 antisense 1 (BAZ1A-AS1), and its predicted cis-regulatory partner gene BAZ1A, as markedly upregulated during NP and predominantly enriched in VSMCs. Both transcripts were induced by genotoxic stimuli, with BAZ1A-AS1 showing transient induction preceding sustained BAZ1A upregulation, consistent with a priming role in the DNA damage response. Silencing of either BAZ1A-AS1 or BAZ1A attenuated VSMC proliferation and migration, accompanied by upregulation of contractile markers and suppression of proliferative and inflammatory transcriptional programs. ChIRP-qPCR demonstrated that BAZ1A-AS1 physically interacts with 3' distal exons of BAZ1A at the DNA level while selectively engaging CNN1, CCND1, and IL6 mRNAs, indicating mechanistically distinct chromatin- and RNA-level regulatory functions. Baz1a haploinsufficiency attenuated neointima formation and preserved VSMC contractile identity in a mouse carotid artery ligation model. ConclusionsWe identify BAZ1A-AS1 and BAZ1A as stress-responsive regulators of VSMC phenotype, operating through dual mechanisms of cis-regulatory chromatin interaction and selective mRNA engagement, and demonstrate a novel role for the BAZ1A-AS1/BAZ1A axis in promoting NP.

physiology↗

bioRxiv2025

HINS: HLA-mediated immunogenic neoantigen score for robust prediction of immune checkpoint blockade response

Immune checkpoint blockade (ICB) therapy response prediction provides remarkable genomic and transcriptomic gains and has successfully understood the molecular mechanisms underlying various cancers. However, only a subset of patients with advanced tumors currently benefits from ICB therapies, which at times incur considerable side effects and costs. Developing predictive tools for ICB response has remained a serious challenge because of the complexity of the immune response and the shortage of large cohorts of ICB-treated patients that include both omics and response data. Here, based on a pooled genomic dataset of 919 patients across multiple solid tumors treated with anti-PD-(L)1 or anti-CTLA-4, we constructed human leukocyte antigen class I (HLA-I)-mediated immunogenic neoantigen score (HINS). HINS is a predictor of ICB response using neoantigen quality and HLA evolutionary divergence to integrate the factors associated with immune activation and evasion. It yielded an overall accuracy of AUC=0.853, outperforming existing predictors and capturing more than 75% true responders. Experimental analysis indicated that patients with higher HINS were more likely to undergo survival benefits following ICB therapy. Our results highlighted the transcriptional and genomic correlations between HINS-identified molecule features and ICB response, such as immunoresponsive gene enrich pathways, favorable and unfavorable genomic subgroups, and hotspot somatic events in driver genes. This study presented an interpretable, accurate deep-learning method using meaningful predictive features to predict the response to ICB, providing biological insights into the complexity of the determinants underlying immunotherapy.

bioinformatics↗

bioRxiv2025

HGS+ enlarged vesicular compartment serves as site for coronavirus assembly at later infection stage

The precise site of coronavirus assembly remains poorly characterized. In this study, we observed that coronavirus infection induces the host factor hepatocyte growth factor-regulated tyrosine kinase substrate (HGS) to form distinct HGS enlarged vesicular compartments at later infection stage. Confocal and live-cell super-resolution microscopy showed that viral structural proteins colocalize with these HGS enlarged vesicular compartments. Correspondingly, APEX2-based electron microscopy (APEX2-EM) and immuno-EM analyses confirmed the presence of assembled virions within these unique HGS compartments, identifying them as sites of virion assembly. This was further supported by cryogenic correlated light and electron microscopy (cryo-CLEM), which captured ongoing virion formation occurring within HGS enlarged vesicles. Crucially, whole cell volume EM revealed that HGS deficiency abolishes these vesicular compartments and markedly reduces assembled virions. Lastly, we demonstrated that HGS vesicular compartments are rearranged from Golgi and endosome/lysosome by coronavirus infection. Together, these findings establish that coronavirus-induced HGS vesicular compartments function as essential platforms for virion assembly at later infection stage.

microbiology↗

bioRxiv2025

Targeting the host factor HGS-viral membrane protein interaction in coronavirus infection

While current antivirals primarily target viral proteins, host-directed strategies remain underexplored. Here, we performed a genome-wide CRISPRi screening to identify the host protein, Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (HGS), as essential for the pan-coronaviruses infection both in vitro and in vivo. Mechanistically, HGS directly interacts with the viral membrane (M) protein, facilitating its trafficking to the ER-Golgi intermediate compartment (ERGIC) for virion assembly. Conversely, HGS deficiency caused M retention in the ER, blocking assembly. Leveraging this interaction, we designed M-derived peptides and screened over 5,000 FDA-approved drugs, identifying riboflavin tetrabutyrate (RTB). Both the peptides and RTB bind HGS and disrupt its interaction with the M protein, leading to M retention in the ER and subsequent blockade of virion assembly. These agents demonstrated broad anti-pan-coronavirus activity in vitro and in vivo. Collectively, our findings establish HGS as a druggable host target and identify RTB as a promising broad-spectrum antiviral candidate.

microbiology↗

bioRxiv2025

Stem-like Prostate Remodeling in Obesity Mediates Resistance to 5α-Reductase Inhibition Therapy in BPH

Benign prostatic hyperplasia (BPH) is closely associated with obesity and metabolic syndrome. Although 5-reductase inhibitors (5ARIs) are widely used to treat BPH, their effectiveness varies significantly, particularly in obese patients. However, the mechanisms by which obesity affects prostate growth and modulates therapeutic responses remain poorly understood. In mice, highfat diet (HFD) increased prostate weight and induced SRD5A2-independent epithelial remodeling with expansion of proximal urethral luminal epithelial cells. ScRNA-seq of prostate tissues from Srd5a2null and control mice on HFD showed enrichment of proximal stem-like populations, reduced androgen signaling, and activation of WNT and NOTCH pathways via heightened stromal-epithelial crosstalk. Clinically, BMI gain, regardless of 5ARI use, correlated with transition zone growth, stronger activity of stem-cell signatures, reduced SRD5A2, and androgen signaling downregulation. Xenium spatial profiling indicated that BMI gain expands stem-like epithelial populations and a NOTCHenriched periepithelial stromal niche surrounding epithelial compartments, supporting stemness. Patients with substantial BMI gain were less responsive to 5ARI, whereas weight control plus 5ARI therapy synergistically improved outcomes. In conclusion, BMI gain promotes proximal prostate enlargement through an SRD5A2-independent stem-like cell mediated pathway that blunts 5ARI efficacy. Combining pharmacotherapy with weight control yields superior efficacy and supports individualized management of BPH.

pathology↗

bioRxiv2025

GeoGAT-site: A Face-Centered Geometric Graph Attention Network for Protein-Protein Interface Prediction

Protein-protein interactions (PPIs) underpin the intricate machinery of cellular life, orchestrating processes from signal transduction to metabolic regulation, yet their precise interface prediction remains a cornerstone challenge in structural biology, demanding scalable computational paradigms that balance accuracy and efficiency. Herein, we present GeoGAT-site, a pioneering geometric graph attention network that leverages face-centered surface fingerprints extracted from three-dimensional protein architectures to forecast interaction sites. Diverging from conventional vertex-centric approaches, our face-centered methodology achieves a 3.64-fold acceleration in patch generation, mitigating computational bottlenecks while preserving granular surface descriptors. At its core, GeoGAT-site incorporates a bespoke attention mechanism that adaptively modulates inter-facial distances and normal vector orientations, synergistically integrating spatial geometries with physicochemical attributes for nuanced interface delineation. Harnessing a meticulously curated dataset of 150 million face-centered fingerprints from over 20,000 structurally diverse proteins, the model attains robust generalization across heterogeneous interaction motifs. Empirical validation on an independent cohort of 167 protein complexes yields a ROC AUC of 0.89, surpassing established benchmarks including MaSIF-site (0.845), SPPIDER (0.65), and PSIVER (0.63). By furnishing high-fidelity interface annotations, GeoGAT-site augments downstream structural modeling paradigms through targeted constraints, thereby providing a versatile scaffold for unraveling PPI dynamics with profound implications for therapeutic discovery, protein redesign, and molecular epistemology.

bioinformatics↗

bioRxiv2025

Stromal SRD5A2 promotes prostate growth through WNT5A-LEF1-IGF1 signaling in benign prostatic hyperplasia

Steroid 5-reductase type 2 (SRD5A2) is a key enzyme in androgen metabolism and a pharmacologic target in benign prostatic hyperplasia (BPH). While SRD5A2 is known to mediate stromal-epithelial interactions that influence prostate growth, the relationship between baseline SRD5A2 expression and prostate volume remains unclear. In this study, we analyzed SRD5A2 expression in human prostate tissues from the Medical Therapy of Prostatic Symptoms (MTOPS) trial and institutional biorepository cohorts. Quantitative assessments were performed and correlations were evaluated between expression level of SRD5A2, WNT5A, prostate volume, and tissue signaling profiles. SRD5A2 expression was significantly associated with total prostate and transition zone volume in both human cohorts. Stromal-specific WNT5A expression showed a strong positive correlation with SRD5A2, while neither serum nor tissue dihydrotestosterone levels correlated with SRD5A2 expression. In Srd5a2-null mice, Wnt5a expression in the prostate stroma was dependent on Srd5a2 and showed region-specific regulation. Mechanistically, SRD5A2 overexpression in human prostate stromal cells upregulated WNT5A and Lymphoid Enhancer-Binding Factor 1 (LEF1), activated insulin-like growth factor 1 (IGF1) signaling, increased proliferation, and reduced apoptosis. Conditioned media from these cells enhanced epithelial proliferation through paracrine IGF1 activity, independent of epithelial WNT signaling. This study provides the first evidence that SRD5A2 promotes prostate growth through a stromal WNT5A-LEF1-IGF1 paracrine signaling axis, functioning independently of androgen levels. These findings suggest a novel therapeutic mechanism relevant for BPH patients with resistance to conventional 5-reductase inhibitor therapy.

pathology↗

bioRxiv2025

THLANet: A Deep Learning Framework for Predicting TCR-pHLA Binding in Immunotherapy Applications

Adaptive immunity is a targeted immune response that enables the body to identify and eliminate foreign pathogens, playing a critical role in the anti-tumor immune response. Tumor cell expression of antigens forms the foundation for inducing this adaptive response. However, the human leukocyte antigens (HLA)-restricted recognition of antigens by T-cell receptors (TCR) limits their ability to detect all neoantigens, with only a small subset capable of activating T-cells. Accurately predicting neoantigen binding to TCR is, therefore, crucial for assessing their immunogenic potential in clinical settings. We present THLANet, a deep learning model designed to predict the binding specificity of TCR to neoantigens presented by class I HLAs. THLANet employs evolutionary scale modeling-2 (ESM-2), replacing the traditional embedding methods to enhance sequence feature representation. Using scTCR-seq data, we obtained the TCR immune repertoire and constructed a TCR-pHLA binding database to validate THLANets clinical potential. The models performance was further evaluated using clinical cancer data across various cancer types. Additionally, by analyzing divided complementarity-determining region (CDR3) sequences and simulating alanine scanning of antigen sequences, we unveiled the 3D binding conformations of TCRs and antigens. Predicting TCR-neoantigen pairing remains a significant challenge in immunology, THLANet provides accurate predictions using only the TCR sequence (CDR3{beta}), antigen sequence, and class I HLA, offering novel insights into TCR-antigen interactions. Author summaryT-cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes is fundamental to immune responses. However, predicting their binding poses a significant challenge due to the intricate dynamics of their interactions. We developed THLANet, a novel deep learning model, to address this challenge by integrating the ESM-2 and Transformer-Encoder modules. This approach enhances sequence feature encoding, improving the models generalization capability and enabling accurate predictions of TCR-pHLA binding in clinical datasets. Using data processed from open-source databases, THLANet outperformed existing methods, such as PanPep and pMTnet, in precision-recall metrics across multiple epitopes. Additionally, THLANet demonstrates superior capability in identifying critical binding sites within 3D structures, providing structural insights into TCR-pHLA interactions. THLANet offers a robust framework for advancing immunotherapy research, with potential applications in the development of personalized medicine.

bioinformatics↗

bioRxiv2025

Mate choice against gene drives leads to evolutionary rescue

Artificial gene drives offer a promising approach for controlling populations of agricultural pests, invasive species and disease vectors, such as malaria-carrying mosquitoes. Gene-drive alleles induce a transmission bias, meaning there is a greater than 50% probability that they will be inherited by offspring, facilitating their rapid propagation through populations. When these alleles induce high fitness costs, their spread can lead to the eradication of target populations. While gene drives hold great potential, there are various barriers that can hinder their effectiveness. One such barrier, precopulatory mate choice, has been suggested to impact the spread of gene drives, yet it remains underexplored. Here, we use individual-based simulations to investigate the spread of gene drives while allowing female mating preferences to evolve. In our model, gene-drive alleles exhibit transmission bias but also incur survival costs. Crucially, females are assumed to be able to distinguish between drive carriers and wild-type males based on drive-associated phenotypic differences. Consequently, females can evolve to prefer wild- type or drive-carrying males as mates. Our simulations show that under certain parameter settings, mating preferences against drive carriers can evolve during the spread of a gene drive. This can result in the eradication of the drive alleles and the evolutionary rescue of the population. The impact of mate choice was most pronounced when the gene drive spread relatively slowly, as this allowed more time for preferences against drives to evolve. In addition, evolutionary rescue occurred less frequently for recessive drives than for dominant ones. Our results demonstrate that mate choice can indeed impair the effectives of gene drive as a mechanism of population control and should therefore be seen as a potential risk. We further consider the implications for scientists developing gene drives as a population control technology. Lay summaryMost genes exist in multiple versions called alleles, with each having a 50% chance of being passed on by parents during sexual reproduction. However, some alleles, known as gene drives, manipulate inheritance to spread more widely across populations, even if they reduce the fitness of individuals carrying them. Gene drives occur naturally but can also be engineered in the laboratory. Recent technological advancements have led scientists to explore gene drives as a promising tool for controlling pests, invasive species, and disease vectors like malaria-carrying mosquitoes. However, before releasing any gene drives into the wild, it is crucial to assess their feasibility and potential risks. Here, we used computer simulations to explore how artificial gene drives spread when mate choice is allowed to evolve, assuming females can differentiate between males carrying gene drives and those without them. While gene drives have a transmission advantage, they also reduce the survival of carriers. Our results show that evolution can act rapidly after a gene drive is released. Females evolve to discriminate against drive-carrying males, which can sometimes result in the eradication of the gene drive. When gene drives have high survival costs, this evolutionary response can prevent population extinction, potentially undermining the drives purpose. The impact of mate choice is greatest when gene drives spread slowly, giving more time for evolution to act. These findings highlight the importance of considering mate choice dynamics when developing gene drives for population control.

evolutionary biology↗

bioRxiv2025

Quantifying feedback among traits in coevolutionary models

Phenotypic traits rarely evolve in isolation. Instead, multiple traits typically interact, resulting in complex coevolutionary dynamics. Such dynamics can be predicted using mathematical frameworks such as adaptive dynamics and quantitative genetics. Selection gradients play a crucial role in these frameworks, describing the direction and strength of selection and predicting evolutionary trajectories and potential endpoints. Current theory focuses mainly on analysing how traits change in response to selection. However, selection gradients also change over time as traits evolve. For a complete understanding of coevolutionary dynamics, it is consequently essential to examine how trait changes feed back to influence the selection environment. Here, we develop a general framework for investigating coevolutionary feedback between traits and selection gradients. Rather than relying on verbal interpretation of causal relationships, our approach explicitly quantifies the various pathways by which traits and selection gradients influence one another. Our framework can be applied both to adaptive-dynamic models and to quantitative-genetic models under the weak selection limit. We illustrate our approach with three examples that showcase its potential to deepen our understanding of established models.

evolutionary biology↗

bioRxiv2025

The Single Cell Landscape of the Human Vein After Arteriovenous Fistula Creation and Implications for Maturation Failure

The biological mechanisms underlying arteriovenous fistula (AVF) maturation in hemodialysis patients remain poorly understood despite decades of research. To address this gap, we investigated the cellular changes in the venous wall after fistula creation in histological biopsies of longitudinal veins and AVF samples (N=23 patients). Using single-cell RNA sequencing of 70,281 cells from pre-access veins, mature, and failed AVFs (N=20 patients), we created a complementary transcriptomic atlas of the human vein before and after anastomosis. Postoperatively, the fistula exhibited increased intimal hyperplasia and cell number but reduced cell density, indicating that extracellular matrix (ECM) deposition was more prominent than cell accumulation. Analysis of 14,475 cells from fistulas obtained within one week of creation revealed that inflammation drives early adaptation across all vascular cell types. This includes the pro-inflammatory activation of endothelial cells (ECs) and production of a hyaluronic acid-rich neointima by fibroblasts. By 13 {+/-} 6 weeks, transcriptomic profiles continue to reflect active healing of the vasculature by ECM-producing myofibroblasts and fibroblasts that were found localized throughout the vascular wall, including the intima, using immunofluorescence and in-situ hybridization. Postoperative ECs maintained significant hemostatic adaptations and upregulation of inflammatory molecules (ACKR3, ICAM1, IL1R1, COL8A1) supporting their role as gatekeepers of immune cell infiltration. Comparative analyses of failed versus mature AVFs revealed persistent inflammatory signaling among macrophages, ECs, myofibroblasts, and fibroblasts in association with AVF failure. These findings uncover previously unrecognized cellular and molecular patterns in human veins following AVF creation, providing novel insights and potential therapeutic targets to improve AVF outcomes. TRANSLATIONAL STATEMENTArteriovenous fistulas (AVF) are a special type of blood vessels that provides access to a patients bloodstream during hemodialysis treatments. The AVF is surgically created by connecting an artery and a vein, after which the vein heals and enlarges in a process called "maturation". We do not fully understand how maturation occurs. This prevents us from designing therapies that ensure proper enlargement of the AVF, which fails in up to 40% of patients. This study investigates how a vein transforms into an AVF in 43 patients with end-stage kidney disease undergoing surgery for AVF creation. We analyze the modifications of structural components of the vein and of diverse populations of cells that direct healing and maturation. Our findings suggest that, contrary to current beliefs, the best therapies to improve AVF maturation should target the accumulation of non-cellular components in the vein and the inflammatory factors that trigger such accumulation.

molecular biology↗

bioRxiv2025

Light induces Phytochrome B SUMOylation to recruit the immune regulator NPR1 in nuclear condensates to control immunity in plants

It has long been observed that light perception by phytochromes control plant immunity, however, the underpinning molecular mechanism is less well understood. We demonstrate that light mediated SUMO conjugation to Phytochrome B (PhyB) is critical for increasing cellular salicylic-acid (SA) levels to orchestrate systemic acquired resistance (SAR) upon avirulent bacterial infection. SUMOylation is critical for PhyB nuclear condensate formation during light activated immunity. Light induced PhyB SUMOylation recruits NPR1, through its SUMO interacting motif to nuclear condensates to elevate SA levels for immune responses. In the dark during SAR, elevated SA levels substitute for light to maintain PhyB SUMOylation and immune-related photobody formation by stimulating the degradation of PhyB targeting deSUMOylase, OTS1. SUMOylated PhyB-NPR1 immune photobodies associate with TGA transcription factor associated chromatin to trigger immune gene expression. We unravel a mechanism where SUMOylation can enable light to recruit NPR1 to PhyB nuclear condensates to form immune photobodies to regulate plant immunity. HighlightsO_LILight-dependent immunity in plants relies on the SUMO mediated interaction between the photoreceptor PhyB and the Salicylic Acid (SA) receptor NPR1. C_LIO_LILight induced PhyB SUMOylation recruits NPR1 to nuclear condensates which we identify as immune photobodies that elevate SA levels for immune responses. C_LIO_LIIn darkness, SA can replace light in enabling PhyB-NPR1 immune photobody formation by regulating SUMOylation revealing a SA mediated mechanism for controlling PhyB liquid-liquid phase separation. C_LIO_LISUMO-modified PhyB-NPR1 immune photobodies regulate transcriptional activity of immune associated chromatin to shape defence responses in plants. C_LI

plant biology↗

bioRxiv2025

Primate-specific microRNA-1202 regulates dopaminergic neurogenesis by targeting APC2 and modulates WNT/β-catenin signaling pathway in midbrain organoid

MicroRNAs (miRNAs) are generally evolutionarily conserved, but a small number of them are found exclusively in primates. MiR-1202 is a primate-specific miRNA that was previously revealed as being involved in major depression disorder (MDD). Moreover, the genomic locus where miR-1202 locates (6q25.3) is strongly associated with recurrent early-onset MDD and neurodevelopmental disorder. We hypothesize that miR-1202 plays a unique role in the brain in fine-tuning the transcriptional network that governs neurogenesis. Here, we reported that microdeletion of miR-1202 resulted in retarded organoid growth but enhanced dopaminergic (DA) neuron differentiation in midbrain organoids. Integrated analysis of miRNA-interacting targets and transcriptional changes in miR-1202 knockout cells revealed that APC2, a negative regulator of canonical WNT/{beta}-catenin pathway, was a downstream target of miR-1202. Knockdown of APC2 resulted in attenuated DA neurogenesis, in contrast to the enhanced DA neurogenesis in miR-1202 knockout cells. Treatments of the brain organoids with antidepressants increased miR-1202 expression and simultaneously inhibited APC2 expression. Consistently, APC2 expression was found to increase in MDD patients. Our results suggest that miR-1202 regulates dopamine neurogenesis by inhibiting the APC2/WNT signaling pathway, which plays a distinct role in the midbrain-hindbrain regional patterning during the early development of the central nervous system.

cell biology↗

bioRxiv2024

TDP-43 mutations-induced defects in miRNA biogenesis and cytotoxicity by differentially obstructing Dicer activity in Drosophila and in vitro

Mutations in the DNA/RNA-binding protein 43 (TDP-43) can cause amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). As an RNA-binding protein, TDP-43 plays a diverse physiological role in RNA processing and is potentially involved in the pathological progression caused by disease mutations. However, the precise mechanisms linking RNA dysregulation and TDP-43 mutations, which propel disease progression, are not yet fully understood. Here, we demonstrate that TDP-43 and its Drosophila homolog, TBPH, whose mutations crucially perturb Dicer presentation, result in dysregulated miRNA profiles. Genetically modulating the expression or pharmacologically activating Dicer implies unique interactions of TDP-43 A315T and M337V with the Dicer protein, suggesting a specific mechanism of C-terminal disease mutations contributes to the pathological process. Unlike TDP-43 A315T, the M337V mutation causes the assembly of aggregates and reorganizes but functionally preserves the Dicer activity in miRNA processing. Mutations in TDP-43 disrupt miRNA biogenesis by hindering its interaction with Dicer, leading to cytotoxicity and providing mechanistic insight into the pathogenic mutations associated with ALS-FTD.

molecular biology↗