Biology subjects

Lin, C.-Y.

Publications and source records attributed to Lin, C.-Y..

At least 19 recordsLinked to original sources

bioRxiv2026

BI-TfR1 CapX rapidly transits the blood-brain barrier for efficient, low-dose gene delivery throughout the CNS

Safe, efficient gene delivery throughout the CNS remains a central obstacle to treating genetic diseases of the brain and spinal cord. We describe BI-TfR1 CapX, a human transferrin receptor (TfR1)-binding AAV capsid that, after a low intravenous dose in adult humanized TFRC mice, transduced more than 80% of cortical and spinal neurons and ~60% of cortical astrocytes, with reduced distribution and expression in several peripheral tissues relative to AAV9. Unlike other engineered BBB-crossing capsids, CapX bound the CNS vasculature within minutes and a large fraction of its genomes reached parenchymal nuclei within 24 hours. Delivering a Prnp-targeted epigenetic silencer (Prnp-CHARM), CapX reduced brain Prnp mRNA by over 95% requiring 18-fold fewer vector genomes per brain cell than AAV-PHP.eB for 50% lowering. A CapX delivered dual-vector cytosine base editor installed a protein-truncating PRNP stop codon lowering brain prion protein by 80%. These properties make CapX an attractive vehicle for human CNS gene therapy.

neuroscience↗

bioRxiv2026

Transcription-Coupled Chromatin Reinforcement Maintains the Mature Cardiomyocyte State

Chromatin homeostasis is fundamental to maintaining transcriptional programs that stabilize cell states while permitting plasticity for timely state transitions. However, mechanisms that actively sustain mature cell states after their establishment remain poorly defined despite being essential for lifelong maintenance of specialized cellular functions. Here we demonstrate that the transcription-coupled chromatin regulator RNF20 is crucial for maintaining chromatin accessibility at identity-associated promoters that support mature cardiomyocyte transcriptional programs in adult murine cardiomyocytes. Depletion of RNF20 progressively erodes the transcriptional, structural, and functional integrity of adult cardiomyocytes and activates AP-1-associated stress-responsive enhancer elements without cell-cycle re-entry. Spatial transcriptomics further revealed a subendocardial localization of this stress-responsive state. Together, these findings support a model in which transcription-coupled chromatin reinforcement continuously stabilizes the mature cardiomyocyte attractor state while constraining transitions toward pathological cell states.

genetics↗

bioRxiv2026

Overexpression of miR-424(322)/-503 induces severe dilated cardiomyopathy by regulating the fatty acid oxidation gene expression program

Fatty acid oxidation (FAO) is a major energy source in the adult heart, and disruption of cardiac metabolism is closely associated with heart failure. Here, we investigated the effects of cardiac-specific overexpression of the H19X-encoded miR-424(322)/-503 cluster using an inducible transgenic mouse model. Sustained miR-424(322)/-503 overexpression caused rapid metabolic and functional deterioration, with early impairment of fatty acid oxidation. Short-term induction reduced FAO activity and downregulated genes involved in lipid metabolism, while glycolytic enzyme activity remained largely unchanged. Continued miR-424(322)/-503 expression subsequently led to severe dilated cardiomyopathy characterized by ventricular dilation, wall thinning, fibrosis, reduced contractility, and high mortality. Importantly, disease progression was dependent on the level and duration of miR-424(322)/-503 expression, as intermittent or lower-dose induction delayed cardiac dysfunction and prolonged survival. Withdrawal of miR-424(322)/-503 expression after the onset of dysfunction promoted substantial functional recovery. Together, these findings identify miR-424(322)/-503 as a potent regulator of cardiac metabolic reprogramming that disrupts fatty acid metabolism and drives progressive heart failure.

molecular biology↗

bioRxiv2026

Sex-Specific Remodeling Phenotypes of the Tricuspid Valve Leaflets in an Ovine Model of Functional Tricuspid Regurgitation

BackgroundModerate to severe tricuspid regurgitation (TR) affects approximately 1.6 million Americans, yet more than 90% of patients with significant TR remain untreated. Women exhibit higher TR prevalence and more rapid disease progression than men, but the valve-intrinsic mechanisms underlying these sex disparities remain unclear. We hypothesized that sex and circulating testosterone influence tricuspid leaflet remodeling during right-sided pressure overload. MethodsFemale, castrated male (C-Male), and non-castrated male (NC-Male) adult Dorset sheep (n = 45) underwent pulmonary artery banding (PAB) and were followed for 13 {+/-} 1.5 weeks. Tricuspid leaflets were evaluated using morphometry, 3D profilometry, biaxial mechanical testing, histology, and bulk RNA sequencing. Sex-stratified differential gene expression was performed, and pathway enrichment of key biological processes were compared between sexes. ResultsPAB produced a uniform hemodynamic stimulus and equivalent moderate-to-severe TR across sex groups. Despite similar TR burden, leaflet remodeling diverged substantially by sex and castration status. C-Males developed the broadest remodeling phenotype, characterized by diffuse multi-leaflet growth, thickening, increased nuclei count, and low-strain stiffening. Females demonstrated more restricted leaflet and region-specific structural and cellular changes, along with circumferential low-strain stiffening. NC-Males exhibited preferential septal remodeling characterized by growth, thickening, increased nuclei count, and radial high-strain stiffening. Transcriptomic analysis revealed that females upregulated a focused matricellular remodeling program enriched for extracellular space organization (67 DEGs; FDR=0.025), whereas C-Males activated coordinated extracellular matrix and apoptosis-regulatory programs (388 DEGs; FDR=0.009). In contrast, NC-Males exhibited broad transcriptional response (406 DEGs) without significant pathway enrichment. ConclusionsTricuspid leaflet maladaptation during pressure overload is sex-dependent and testosterone-sensitive, involving distinct structural, mechanical, and transcriptional remodeling programs. These findings identify sex and testosterone status as previously under-recognized modulators of tricuspid valve remodeling and may help explain clinical sex disparities in TR progression. NOVELTY AND SIGNIFICANCE What is known?O_LIPulmonary hypertension and right ventricular pressure overload are linked to tricuspid leaflet remodeling through leaflet thickening, enlargement, and altered mechanical properties. C_LIO_LISex and sex-steroid hormones regulate fibrosis and extracellular matrix remodeling in cardiovascular tissues, but their role in tricuspid leaflet remodeling remains poorly understood. C_LI What new information does this article contribute?O_LISex and circulating testosterone status influence the magnitude, spatial distribution, biomechanical behavior, and transcriptional organization of tricuspid leaflet remodeling during pressure overload. C_LIO_LIFemales, castrated males, and non-castrated males develop distinct remodeling programs characterized by focused matricellular remodeling, coordinated extracellular matrix/apoptosis signaling, and diffuse transcriptional activation, respectively. C_LIO_LIThese findings identify sex and hormonal status as biological regulators of tricuspid valve maladaptation during functional tricuspid regurgitation. C_LI SummarySex differences in tricuspid regurgitation progression are recognized clinically, yet the mechanobiological basis underlying these disparities remains poorly understood. Using a controlled ovine model of pressure overload-induced secondary tricuspid regurgitation, we demonstrated that tricuspid leaflet maladaptation is a sex-specific and testosterone-sensitive process spanning structural, mechanical, and transcriptional scales. Under comparable hemodynamic overload, all animals developed significant tricuspid regurgitation, but leaflet remodeling patterns diverged substantially across sexes. Castrated male sheep exhibited the broadest maladaptive phenotype, characterized by diffuse multi-leaflet growth and thickening, increased low-stretch stiffness, and coordinated extracellular matrix and apoptosis-regulatory transcriptional programs. Female sheep developed more spatially restricted remodeling accompanied by a focused matricellular and extracellular matrix secretory response, whereas non-castrated male sheep demonstrated selective leaflet remodeling with broad, but less coordinated, transcriptional activation. Different remodeling patterns emerged in females and castrated males despite comparable testosterone levels, suggesting that testosterone depletion alone does not fully explain these tricuspid valve remodeling phenotypes. These findings establish sex and testosterone status as previously underrecognized biological regulators of tricuspid leaflet maladaptation and support the emerging view that valve leaflets are active, mechanobiologically responsive, participants in functional tricuspid regurgitation progression.

bioengineering↗

bioRxiv2026

The Mechanical and Biological Evolution of Pressure Ulcer Formation and Healing in Mice

Pressure ulcers arise from sustained mechanical loading that impairs perfusion and damages skin tissues, yet the coupled mechanical and biological mechanisms of their formation and healing remain poorly characterized. We addressed this gap using a mouse model in which dorsal skin underwent 72 hours of magnet-induced ischemia followed by reperfusion, with tissue collected at 0, 3, 6, and 9 days and compared with baseline controls. From each mouse, we obtained paired samples from pressure ulcer and remote control (non-loaded) sites, mapped thickness by tissue profilometry, and performed equibiaxial testing with full-field digital image correlation and inverse finite element analysis to estimate regional material parameters. In parallel, we quantified CD31+ vasculature, F4/80+ macrophages, collagen content, and key cytokines. Pressure ulcer sites were compressed and thinner at Day 0, developed ulcers by Day 3, and continued to remodel through Day 9. Mechanical tests revealed heterogeneous strain fields with elevated deformation along ulcer borders, while remote control tissue deformed more homogeneously. These mechanical changes evolved alongside dynamic vessel and macrophage repopulation, increased collagen content at early time points, and cytokine upregulation within pressure ulcer tissue. Collectively, our data define the spatiotemporal co-evolution of tissue geometry, mechanics, collagen remodeling, and inflammation in pressure ulcers and provide a quantitative foundation for predictive mechanobiological models.

bioengineering↗

bioRxiv2026

The Tricuspid Valve Maladapts in a Pulmonary Hypertension Rat Model

Tricuspid valve regurgitation is a frequent valve lesion and, if severe, an independent predictor of mortality. In most patients, the valve itself has historically been considered intact. Yet, we have previously shown that the valve may not be an innocent bystander. In multiple sheep models, we have shown that the tricuspid valve thickens and stiffens. This remodeling may contribute to valve disease. Our goal is to extend our investigation of tricuspid valve remodeling to a rodent model, potentially opening scientific opportunity and enabling scaling our studies. To this end, we used pulmonary artery banding (PAB) in male rats to induce pressure overload and right ventricular remodeling. After excising the tricuspid valve, we quantified anterior leaflet morphology, mapped anterior leaflet thickness using optical coherence tomography, and evaluated anterior leaflet belly mechanics using a custom bulge testing system. Compared with SHAM controls, PAB increased anterior leaflet area. Moreover, anterior leaflets in PAB animals exhibited region-specific thickening, with the largest increases near the annulus. Finally, anterior leaflets in PAB animals were significantly less compliant. However, leaflet stiffening stemmed from aforementioned thickening, i.e., structural stiffening, not constitutive stiffening. Our findings demonstrate that we can reliably quantify leaflet area, thickness, and stiffness in the minuscule tricuspid valves of rats. We also show that tricuspid valve remodeling is not ovine-specific, but also affects the tricuspid valves of rats. Together, our findings support our hypothesis that tricuspid valves are not innocent bystanders in regurgitation, and that rats may serve as a scalable model system for future investigations. NEW & NOTEWORTHYUsing a rat pulmonary artery banding model of pulmonary hypertension, we show that chronic right ventricular pressure overload induces leaflet enlargement and region-specific thickness remodeling of the tricuspid valve. Although structural mechanical metrics change under pressure loading, normalization by thickness reveals that geometric remodeling rather than intrinsic material stiffening predominates. These findings highlight leaflet structural (mal)adaptation as a potential contributor to functional tricuspid regurgitation and underscore the importance of considering leaflet geometry in therapeutic strategies.

physiology↗

bioRxiv2026

Nanopore event detection in a simple and adaptive way

Nanopore read-out, that is the current signals measured across nanometer-sized openings in dielectric membranes or through natural protein channels, enables the detection, identification and sequencing of individual molecules. The detection can take place by analyzing the events of single biomolecules interacting with the pore. The accuracy in the detection of these single events is key for identification of physicochemical properties of analyte molecules. To this end, we further develop a very simple, fast, almost parameter-free, and adaptable cluster-based event detection (CBED) algorithm that clusters the nanopore signals prior to detecting nanopore events. The algorithm is validated against two other event detection schemes with respect to simplicity and efficiency. For this, nanopore data from four different experiments stemming from different laboratories that vary in the nanopore type, size, and analyte are considered. The comparison is made on the basis of the number of events detected, their quality, and the most important features extracted from nanopore events. Our results underline the higher efficiency and less noise of the CBED detected events for biological nanopore data and the need for an on-the-fly adaptivity of the baseline current for a class of solid-state nanopore data.

bioinformatics↗

bioRxiv2026

Combating citrus greening disease by simultaneously targeting the pathogen and callose-mediated phloem occlusion

Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), disrupts sugar transport in citrus due to bacterial proliferation and excessive callose deposition that blocks sieve elements. Unblocking phloem may reduce symptoms, but it is unclear whether targeting CLas or suppressing callose deposition is more critical, as both contribute to phloem dysfunction. This study evaluated whether an integrated strategy targeting both CLas and callose-mediated phloem blockage could more effectively restore phloem transport, carbohydrate allocation, and productivity in HLB-affected citrus. Two complementary field experiments assessed the effects of an antibiotic, a callose inhibitor, and their combination on phloem recovery and source-sink dynamics. The first experiment focused on treatment-induced changes in carbon transport between source and sink shortly after delivery via stem infiltration, capturing immediate physiological responses. The second experiment assessed cumulative carbon allocation to determine sustained effects on assimilate transport and fruit development. Callose inhibitor treatment increased sugar transport but this immediate response did not yield lasting benefits. Antibiotic treatment enhanced carbon import into developing fruits, but these effects were not consistently supported by other physiological indicators. In contrast, the combined treatment reduced callose deposition, improved phloem conductivity and carbon allocation during high sink demand, decreased fruit abscission, and increased the total carbon accumulated in the fruits after physiological fruit drop. Collectively, these results demonstrate that impaired source-sink balance in HLB-affected citrus results from the combination of both pathogen load and host callose accumulation, supporting an integrated strategy that combines pathogen suppression with modulation of host phloem function to improve orchard productivity.

plant biology↗

bioRxiv2025

A 3D Amphioxus Brain Atlas Illuminates the Blueprint of the Ancestral Chordate Brain

Comparative studies on highly complex vertebrate brains have provided insights into the evolutionary history of morphological diversity. However, a long-standing question in vertebrate brain evolution is how the fundamental blueprint emerged. To probe the cellular and molecular origins of brain architecture in the chordate lineage, we performed single-nucleus RNA-seq combined with spatial transcriptomics and generated a three-dimensional cell atlas of the basal chordate amphioxus central nervous system (CNS). This atlas reveals a tripartite organization along the anterior-posterior axis of the adult amphioxus brain, with a rostral retinal/hypothalamic region followed by a di-mesencephalon and caudally, the hindbrain and spinal cord. Notably, we show that the amphioxus brain contains cell clusters resembling the zona limitans intrathalamica and midbrain-hindbrain boundary, both of which demarcate the major brain compartments. Furthermore, expression profiling and gene ontology enrichment analyses support that the cell clusters located in the rostral part of the amphioxus forebrain correspond to vertebrate retinal primordium and hypothalamic cells. However, the absence of key telencephalic marker expression in the amphioxus anterior forebrain suggests that the telencephalon likely represents a vertebrate innovation. Together, our findings establish a spatial transcriptomic framework for the amphioxus CNS and provide a critical link for understanding the evolution of the complex vertebrate brain.

evolutionary biology↗

bioRxiv2025

The genome of the early diverged amphioxus, Asymmetron lucayanum, illuminates the evolution of genome architecture and gene repertoires in cephalochordates

Cephalochordates (amphioxus or lancelet) are considered as living proxies for ancestral chordates due to their key phylogenetic position and slow evolutionary rate. The genomes of living amphioxus thus can help to reveal the genetic basis shaping the evolutionary transition from invertebrates to vertebrates. To gain a comprehensive understanding of the genome architecture in amphioxus, here we generate a chromosome-anchored genome assembly for Asymmetron lucaynum, representing the earliest diverging cephalochordate genus. Our results show that Asymmetron has an enlarged genome compared to those of the other four cephalochordate genomes decoded so far (all in the genus Branchiostoma), causing by pervasive expansions of inter-genic transposable elements (TEs). Nevertheless, both macrosynteny and microsynteny remain highly conserved between Asymmetron and Branchiostoma, enabling reconstruction of the ancestral genomic architecture of the Cephalochordate lineage for tracing genome evolutionary process during Deuterostome and Chordate diversification. By coupling developmental transcriptomic analyses, we further show that purifying selection and constraints on co-transcriptional regulation may have contributed to the maintenance of the conserved microsynteny blocks among cephalochordate species. We also examine the evolutionary history of Hox cluster in cephalochordates and vertebrates, and identify species-specific inversions and TE invasions at this important locus in both Asymmetron and Branchiostoma. Finally, we survey key gene families involved in both innate and adaptive immunity (e.g., TLR, NLR, MHC, and RAG) and uncover their plausible ancestry and evolutionary dynamics in chordates. Taken together, our findings illuminate the genome and gene evolution of cephalochordates and provide valuable resources for understanding the early evolution of chordates and the origin of vertebrates.

genomics↗

bioRxiv2025

Deconstructing the common anteroposterior organisation of adult bilaterian guts

A through-gut is one of the major features of bilaterians. Comparative work among bilaterians has identified common molecular mechanisms during early gut patterning, but the primordial gut later often undergoes different degrees of reorganization in each lineage to form a fully differentiated adult gut with specializations along its anteroposterior (AP) axis. Yet, how the conserved embryonic gut AP pattern relates to the adult guts in diverse bilaterians after metamorphosis is still poorly understood. To unravel the molecular subdivisions of adult guts, we investigated the gut through transcriptomic analyses of five phylogenetically informative species, an annelid, a sea urchin, a hemichordate, a cephalochordate, and a vertebrate. We identified bipartite transcriptional programs defining the AP functional subdivisions. Patterning systems composed of Hox, Parahox, and, surprisingly, other transcription factors (TFs) known to be involved in gut formation in sea urchin larvae are maintained in these adult tissues. Using unbiased analyses, we identified five conserved TF modules corresponding to the AP compartments of the guts that are elaborated or shifted in different species. Our study inferred conserved and modified adult AP patterning modules along bilaterian guts enabling the reconstruction of ancestral bilaterian features with profound implications for the evolution of the bilaterian body plan.

developmental biology↗

bioRxiv2025

Evaporation and Focus Degradation Mitigation in In-Incubator Live Cell Imaging for Capacitance Lab-on-CMOS Microsystem Calibration

Lab-on-CMOS is an instrumentation technology that combines miniaturized bioanalytical hardware with complementary metal-oxide semiconductor (CMOS) electronics to provide integrated biosensing in a compact format. This paper focuses on a class of lab-on-CMOS systems that utilize capacitance sensing as a means to monitor cell cultures and track cell proliferation, as well as other cell life-cycle events. In this paradigm, changes in interfacial capacitance result from the activity of adherent cells at a bioelectronic interface. These changes are mapped to cell proliferation or life-cycle events using a ground-truth measurement such as live cell imaging from real-time microscopy. This paper identifies instrumentation challenges that arise from conducting these ground-truth measurements in a calibrated cell culture environment, i.e., when the lab-on-CMOS system is deployed inside a CO2 cell culture incubator. We show that autofocusing the microscopy column and provisioning the lab-on-CMOS with an immersion lid are two approaches that significantly improve the quality of live cell imaging ground-truth measurements over long periods.

bioengineering↗

bioRxiv2025

Association of GADD45A and favorable outcome in hormone positive breast cancer

BackgroundHormone receptor-positive (HR(+)) breast cancer is the most prevalent subtype in breast cancer, and although treatment options are rapidly increasing, still poses as an unmet need in advanced cases. Growth arrest and DNA damage-inducible alpha (GADD45A) is a gene with known relationship with the cell cycle and DNA damage pathways. Conflicting roles in breast cancer biology have been reported for GADD45A. In our study, we investigate the clinical and molecular association of GADD45A in HR(+) breast cancer, evaluating its prognostic potential and relationship with estrogen signaling. MethodsGADD45A expression was assessed in 100 breast cancer tissue samples from a tissue microarray and correlated with clinicopathologic parameters. Public genomic datasets were analyzed to validate associations between GADD45A expression and clinical outcomes in HR(+)HER2(-) breast cancer. Gene set enrichment analysis (GSEA) was used to investigate pathway correlations. ResultsGADD45A protein levels were highest in HR(+)HER2(-) tumors and positively correlated with estrogen receptor (ER) levels, consistent with a luminal phenotype. No significant association was observed between GADD45A levels and progression-free survival in CDK4/6 inhibitor-treated patients, suggesting limited predictive utility in this context. However, higher GADD45A expression was significantly associated with improved overall and relapse-free survival in HR(+)HER2(-) breast cancer in the METABRIC cohort, but not in HER2(+) or triple- negative subtypes. GSEA revealed a positive association between GADD45A expression and the estrogen late response signature, suggesting a functional link with hormone signaling. ConclusionGADD45A expression is enriched in luminal-type HR(+) breast cancer and correlates with favorable clinical outcomes. While not predictive of CDK4/6 inhibitor response, GADD45A may serve as a surrogate marker of estrogen signaling and improved prognosis. These findings support further investigation into GADD45A as a biomarker for stratification and potentially as a therapeutic target in HR(+) breast cancer.

cancer biology↗

bioRxiv2025

Evolutionary dynamics of FoxQ2 transcription factors across metazoans: A tale of three ancient paralogs

FoxQ2 is a highly conserved class of Forkhead-box transcription factors expressed on the anterior side of the body in cnidarians and bilaterians. Despite this conserved expression pattern, recent phylogenetic analyses have revealed a complex and rapid evolution of this class, with several taxon-specific duplications and losses. Until recently, FoxQ2 was thought to be lost in most vertebrate lineages, and its presence and localization in different vertebrate groups remains unclear. To reconcile these conflicting reports of conservation and divergence, here we present a comprehensive analysis of the phylogenetic relationships and expression patterns of FoxQ2 genes across metazoans. By combining phylogenetics and synteny analyses of FoxQ2 sequences from 21 animal phyla, we uncover the presence of three ancient FoxQ2 paralogs in bilaterians, which we name FoxQ2a, FoxQ2b and FoxQ2c. All three FoxQ2 paralogs are present in the chordate lineage and two are conserved in vertebrates, indicating a richer repertoire of vertebrate Fox genes than previously estimated. To investigate the expression of FoxQ2 genes across bilaterians, we mined expression data from existing single cell transcriptomic datasets of mollusk, acoel, amphioxus and zebrafish development, and expanded it using fluorescent in situ hybridization in amphioxus, lamprey, skate, zebrafish and chicken. Our analysis demonstrates the conserved anterior expression of FoxQ2a and FoxQ2b paralogs while also revealing a novel domain of FoxQ2c expression within the chordate endoderm, including in amphioxus, lamprey and skate. Finally, we devise a method to predict conserved transcription factor binding sites across the three extant amphioxus genera with specificity to developmental stage and cell-type identity. This suggests conserved regulatory interactions for the expression of FoxQ2a across deuterostomes. Overall, this work clarifies the complex evolutionary history of FoxQ2 genes and identifies a newly discovered endodermally-expressed Fox gene, FoxQ2c. We further propose that the early duplication of FoxQ2a and FoxQ2b, along with their redundant functions, provided the ideal background for subfunctionalization, contributing to the fast evolutionary rate of FoxQ2 sequences observed in bilaterians.

evolutionary biology↗

bioRxiv2025

Identification of QTL for reproductive success under heat stress conditions through a tomato MAGIC population

Heat stress threatens tomato productivity by reducing pollen viability, fruit set, and consequently, overall yield. While heat-tolerant traits are predominantly found in wild tomatoes, the introgression of heat tolerance into elite cultivars remains challenging due to linkage drag. To address this issue, the World Vegetable Center developed a Multi-parent Advanced Generation Inter-Cross (MAGIC) population, derived from crosses between four heat-tolerant and disease-resistant cultivars. Phenotypic evaluations revealed that fruit number accounted for approximately 57% of reproductive output, making it a critical selection index for heat tolerance. A total of 16,350 SNPs were developed for the MAGIC population, and genome-wide association studies (GWAS) identified 50 QTLs linked to the evaluated traits. Notably, three QTLs on chromosomes 1, 3 and 11 emerged as hubs influencing multiple reproductive traits, underscoring their critical role in heat tolerance. SL4.0CH11_47205149 associated with fruit number was converted into a Kompetitive Allele-Specific PCR (KASP) marker and validated for its significant association with yield. The identification of key QTLs and the prioritization of fruit number as a primary determinant of reproductive success offer valuable insights for targeted breeding strategies. HighlightNumber of fruits is crucial for selecting heat-tolerant tomatoes in open fields. A marker linked to high fruit production helps develop high-yielding tomatoes better suited to withstand climate change.

genomics↗

bioRxiv2025

VISTA-induced tumor suppression by a four amino acid intracellular motif

VISTA is a key immune checkpoint receptor under investigation for cancer immunotherapy; however, its signaling mechanisms remain unclear. Here we identify a conserved four amino acid (NPGF) intracellular motif in VISTA that suppresses cell proliferation by constraining cell-intrinsic growth receptor signaling. The NPGF motif binds to the adapter protein NUMB and recruits Rab11 endosomal recycling machinery. We identify and characterize a class of triple-negative breast cancers with high VISTA expression and low proliferative index. In tumor cells with high VISTA levels, the NPGF motif sequesters NUMB at endosomes, which interferes with epidermal growth factor receptor (EGFR) trafficking and signaling to suppress tumor growth. These effects do not require canonical VISTA ligands, nor a functioning immune system. As a consequence of VISTA expression, EGFR receptor remains abnormally phosphorylated and cannot propagate ligand-induced signaling. Mutation of the VISTA NPGF domain reverts VISTA-induced growth suppression in multiple breast cancer mouse models. These results define a mechanism by which VISTA represses NUMB to control malignant epithelial cell growth and signaling. They also define distinct intracellular residues that are critical for VISTA-induced cell-intrinsic signaling that could be exploited to improve immunotherapy.

cancer biology↗

bioRxiv2024

Deep homology of a brachyury regulatory syntax and origin of the notochord

The brachyury gene encodes a T-box transcription factor (TF) that is crucial for the development of the notochord, a novel trait of chordates1. Brachyury expression in axial mesodermal cells (notochord progenitors) is regarded as a chordate innovation2, yet it remains unclear how the chordate ancestor acquired this expression domain. By examining the sequences of previously identified notochord enhancers of several chordate brachyury genes3-5, we uncovered a regulatory syntax consisting of binding sites for four TFs (Su(H), Foxh1, Zic, and Ets) with a strict order and orientation. We also identified this syntax, here named SFZE, in potential cis-regulatory modules (CRMs) of brachyury orthologs in various non-chordate animals and even in Capsaspora, a close unicellular relative to animals. Reporter assays demonstrated that SFZE-containing CRMs from non-chordate organisms exhibited regulatory activity in the zebrafish notochord, and mutagenesis of the TF sites reduced the activity. Furthermore, the SFZE syntax in sea urchin confers its endoderm activity, with the TF sites functionally decoupled during gastrulation. These findings indicate that the association of the SFZE syntax with brachyury is ancient, likely predating the origin of animals. The emergence of axial brachyury expression is therefore probably not the result of a newly acquired notochord enhancer, but is instead likely attributed to co-option of upstream signals acting on the conserved SFZE syntax, which facilitates the origin of the notochord from rudimentary endodermal cells.

evolutionary biology↗

bioRxiv2024

Novel murine model of human astrovirus infection reveals a cardiovascular tropism

Astroviruses are a common cause of gastrointestinal disease in humans and have been recognized to cause fatal cases of encephalitis. A major barrier to the study of human-infecting astroviruses is the lack of an in vivo model, as previous attempts failed to identify a suitable host that supports viral replication. We describe a novel murine model of infection using astrovirus VA1/HMO-C (VA1), an astrovirus with high seroprevalence in humans that is a causative agent of encephalitis. VA1 RNA levels peak in heart tissue at day 7 post-inoculation. The cardiotropism was observed in multiple different murine genetic backgrounds evidenced by high VA1 RNA loads in heart tissue of A/J, C57BL/6, C3H/HeJ, Balb/c, and J:ARC mice. Infectious VA1 particles could be recovered from heart tissue 3 and 5 days post-inoculation. Intracellular viral capsid was present in tissue sections based on immunofluorescent staining and viral RNA was detected in cardiac myocytes, endocardium, and endothelial cells based on fluorescent in situ hybridization and confocal microscopy. Histologically, we identified inflammatory infiltrates consistent with myocarditis in some mice, with viral RNA co-localizing with the infiltrates. These foci contained CD3+ T cells and CD68+ macrophages. Viral RNA levels increased by > 10-fold in heart tissue or serum samples from Rag1 or Stat1 knockout mice, demonstrating the role of both adaptive and innate immunity in the response to VA1 infection. Based on the in vivo tropisms, we also tested cardiac-derived primary cells and determined that VA1 can replicate in human cardiac microvascular and coronary artery endothelial cells, suggesting a novel cardiovascular tropism in human cells. This novel in vivo model of a human-infecting astrovirus enables further characterization of viral pathogenesis and reveals a new cardiovascular tropism of astroviruses. Author SummaryAstroviruses typically cause viral diarrhea in humans but can also cause serious infections of the brain. Previously, the methods available to study how these viruses lead to invasive infections were limited. Here, we describe the first system to study human-infecting astroviruses using mice. We demonstrate that mice are susceptible to astrovirus VA1, a strain that commonly infects humans and has been linked to fatal brain infections. The virus infected heart tissue and was associated with inflammation. When mice with impaired immune systems were infected with VA1, they were found to have higher amounts of virus in their hearts and blood. Linking back to human health, we also found that VA1 can infect cells derived from human blood vessels of the heart. This model will enable us to better understand how astroviruses cause disease and how the immune system responds to infection. Our findings also suggest that astroviruses could be linked to cardiovascular diseases, including in humans. In the future, we can develop interventions that will prevent and treat astrovirus infections in humans.

microbiology↗