Biology subjects

Fan, X.

Publications and source records attributed to Fan, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatiotemporal proteomic profiling of genome editing-associated microenvironment

Genome editing outcomes are influenced by local genomic context, yet the dynamic protein assemblies that form around genome editing sites remain poorly characterized. Here, we developed a Cas9-TurboID proximity labeling platform that combines programmable genomic targeting with rapid and minimally perturbative protein labeling, enabling spatiotemporal mapping of dynamic protein assemblies associated with distinct genome editing processes. Dynamic comparative profiling identified ACTL6A and H2A.Z as candidate regulators of genome editing, and Cas9 fusion with either ACTL6A or H2A.Z enhanced editing efficiency and improved editing outcomes in heterochromatic regions, which are generally refractory to genome editing due to limited DNA accessibility. We further extended the platform to prime editing and identified WRN as a functional regulator. Together, this study provides a strategy for systematically decoding editor-associated protein microenvironments, establishing a framework for understanding genome editing mechanisms and guiding the rational engineering of genome editors.

cell biology↗

bioRxiv2026

PPARγ brakes cytosolic DNA-induced macrophage inflammation by super-enhancer metabolic reprogramming

Cytoplasmic DNA sensing triggers intense innate immune responses that require tight regulation. PPAR{gamma} is a master metabolic regulator in macrophages, but its role in cytoplasmic DNA immunity remains unclear. Using poly(dA:dT) to mimic cytoplasmic DNA stimulation, we combined transcriptomics, epigenomics (PPAR{gamma}/H3K27ac ChIP-seq), and functional assays. Poly(dA:dT) induced a cytokine storm with MAPK activation and apoptosis/necrosis. PPAR{gamma} activation by rosiglitazone (RGZ) antagonized this response, reducing cell death and transcriptionally inhibiting MAPK genes (e.g., DUSP4/10). Mechanistically, PPAR{gamma} bound promoters/enhancers via PPRE motifs and distal intergenic regions, remodeling H3K27ac (reduced at inflammatory loci, increased at metabolic genes). RGZ induced de novo super-enhancers coupling PPAR metabolic programs (e.g., CPT2) with immune suppression by targeting TLR4, CEBPB, and PIM3. Thus, PPAR{gamma} acts as a brake in cytoplasmic DNA immunity, integrating metabolic reprogramming and inflammation suppression through a multi-level genomic/epigenetic program. This study highlights PPAR{gamma} as a key immune-metabolic integrator and therapeutic target for diseases driven by excessive cytoplasmic DNA sensing.

immunology↗

bioRxiv2026

A lactate-HIF1-VDR positive feedback loop drives protective SPP1+ macrophage differentiation to inhibit schistosomiasis induced liver fibrosis

Hepatic fibrosis remains a major cause of morbidity and mortality in patients with schistosomiasis without effective therapy. Here we show that vitamin D receptor (VDR) signaling in macrophages is essential for limiting fibrosis, acting through a previously unrecognized metabolic epigenetic circuit. Hepatic macrophages exhibit the highest VDR expression among liver resident cells, and pharmacological VDR activation with paricalcitol selectively expands a protective SPP1+ macrophage subset derived from circulating monocytes. Myeloid specific VDR knockout exacerbates fibrosis and abrogates paricalcitol's hepatoprotective effects, whereas SPP1+ macrophage depletion worsens disease. Mechanistically, VDR activation synergizes with hypoxia and lactate to drive SPP1 expression via glycolytic reprogramming. Moreover, lactate and HIF1alpha cooperatively induce VDR transcription by binding to the Vdr promoter and enhancing histone lactylation, forming a positive feedback loop that amplifies the antifibrotic response. Our findings establish the lactate-HIF1alpha-VDR-SPP1 axis as an endogenous defense mechanism and identify macrophage VDR as a promising therapeutic target for fibrotic liver diseases.

immunology↗

bioRxiv2026

The common evolution of fungicide persistence in cryptococcosis patients

Fungicide persistence, the ability of dormant fungal cells to survive lethal drug exposure, undermines treatment efficacy, yet its clinical evolution remains largely unexplored. We assembled a nationwide collection of clinical Cryptococcus neoformans isolates from China and revealed extensive inter strain variation in amphotericin B (AmB) persistence. This variation can arise from common evolutionary events in patients, generating previously undescribed high persistence cryptococcal variants refractory to AmB clearance. Genome wide fitness landscape analysis shows that persistence associated mutations generally impose minimal fitness costs, facilitating persistence evolution even in fungistatic resistant and hypervirulent genetic backgrounds. Machine learning identified deficient ACO2 expression as a key predictor of high persistence clinical isolates. ACO2 deficiency reproduces the high persistence phenotype by promoting POPC accumulation, which competes with AmB for its target. Moreover, the clinical stage antifungal T-2307 effectively eliminates high persistence strains across diverse genetic backgrounds. Collectively, our findings unveil common evolution of fungicide persistence in cryptococcosis patients, representing a previously overlooked clinical concern.

microbiology↗

bioRxiv2026

Orthoflaviviruses use diverse binding modes to engage LDLR family receptors

Orthoflaviviruses are major human pathogens that cause substantial morbidity and mortality worldwide. The viral envelope (E) mediates entry of orthoflaviviruses into host cells by interacting with cellular receptors, including members of the low-density lipoprotein receptor (LDLR) family. Here, we determined cryo-electron microscopy (cryo-EM) structures of yellow fever virus (YFV) E bound to low-density lipoprotein receptor-related protein 4 (LRP4) and LRP8, and of tick-borne encephalitis virus (TBEV) E bound to LRP8. Structural and functional studies reveal that YFV engages two low-density lipoprotein receptor class A (LA) repeats of LRP4 and LRP8 primarily through domain III (DIII) and the DI-DIII linker of its E protein, with each LA repeat making distinct contacts. In contrast, TBEV relies on a distinct surface on domain II (DII) of its E protein to interact with LRP8. Despite these differences, both viruses require engagement of two sequential receptor LA repeats for binding. Our findings identify key determinants of receptor specificity for these two orthoflaviviruses, with implications for vaccine development and therapeutic antibody targeting.

microbiology↗

bioRxiv2026

"Transcriptional and isoform-level regulation of lipid-candidate genes in preeclamptic placentas"

Preeclampsia (PE) is a hypertensive pregnancy-specific disorder and a leading cause of maternal and fetal mortality. A common feature of PE placentas and maternal plasma is dyslipidemia, or abnormal lipid levels, which can increase oxidative stress and endothelial dysfunction. However, the precise transcriptional, post-transcriptional, and epigenetic mechanisms underlying these abnormalities remain poorly characterized. Identifying such changes may clarify disease mechanisms and identify lipid-related PE biomarkers. We conducted a large-scale meta-analysis integrating public placental datasets from NCBI GEO, comprising four DNA methylation (DNAm) datasets (n = 172), three RNA-sequencing datasets (n = 92), and an independent RNA microarray validation cohort (n =146). We evaluated differential DNAm (limma), gene expression (DESeq2), transcript-level shifts (Swish), and alternative splicing (rMATS) in PE versus control placentas, with all analyses stratified by fetal sex via an interaction term model. We also performed placental cell-type deconvolution to quantify PE-associated cell-type proportion changes. Our results demonstrated that lipid-related regulation changes in PE placentas occur primarily at the gene and transcript level, with DNAm showing no changes. We also identified significant isoform switching in PE that were undetected by differential gene expression analysis, and primarily driven by alternative transcription initiation and termination sites rather than alternative splicing. A subset of these isoform switches mapped to pathways dysregulated in PE and were predicted to cause functional protein changes. An interaction term model identified several sex-specific differentially expressed genes (DEGs) in PE, including a subset of male-specific downregulated genes involved in oxidative metabolism. However, many of the remaining sex-specific DEGs across both sexes were previously uncharacterized in the literature. These findings suggest that transcriptional and isoform-level regulation play a role in PE-associated dyslipidemia, with certain regulatory pathways displaying fetal sex-specific patterns. Highlights- Preeclampsia-associated dyslipidemia manifests at the gene and transcript level - Reciprocal isoform switches were missed by standard gene-level analyses - Alternative transcript initiation and termination drove isoform switching - Sex-interaction modeling identified sex-specific transcriptional shifts in PE

genomics↗

bioRxiv2026

Virtual-cell verification enables self-auditing AI discovery for immune rejuvenation

Artificial-intelligence agents propose drug-discovery hypotheses faster than experiments can test them, yet their conclusions are rarely verified, against the underlying biology, the predicted perturbation, or the agent's own scoring logic. We close this verification gap with an agentic framework built on three verifiers. First, PACE, a phenotype verifier, resolves immune aging into ten directionally scored, cell-type-resolved gene-set modules, selected for cross-cohort stability across four PBMC cohorts, and outperforms five established aging clocks in an independent in-house aging cohort of 434 elderly donors. Second, CellQ, a virtual-cell verifier built with multi-modal LLM, compresses each single-cell transcriptome into eight discrete tokens aligned to a language model's vocabulary through residual vector quantization; it attains state-of-the-art perturbation prediction and uniquely resolves the weak, module-level shifts that differential-expression recovery misses. Third, an Analyzer-Planner-Auditor agent verifies its own scoring logic: screening 110 compounds in primary human PBMCs, it found aged-down modules more reversible than aged-up modules and revised its objective from an equal-weight mean to a balance-constrained minimum, a self-correction that generalized to an independent 13-compound T-cell assay. By verifying its predictions and its own objective against experiment, the framework points beyond hypothesis-generating AI toward self-correcting AI scientists whose objectives could continuously evolve.

bioinformatics↗

bioRxiv2026

MetaAMI: A Novel Meta-Learning Approach for Predicting In-Hospital Mortality in Acute Myocardial Infarction

Acute myocardial infarction (AMI) is one of the leading cardiovascular diseases worldwide and remains a major cause of mortality. Early risk prediction can help clinicians identify high risk patients shortly after admission and support timely monitoring and individualized treatment. Previous AMI risk assessment approaches predominantly rely on a single model structure or fixed feature representation, which may limit their ability to capture diverse risk related patterns and reduce predictive performance. To address these challenges, we propose MetaAMI, a random projection based meta-learning framework for AMI outcome prediction. Specifically, patients were selected based on ICD-9 and ICD-10 diagnostic codes for AMI from the Medical Information Mart for Intensive Care IV (MIMIC-IV) v3.1 database. Features were transformed through multiple random projections, with each random projection generating a distinct lower dimensional feature representation. Subsequently, baseline classifiers were trained on each lower dimension representation to predict in-hospital mortality among AMI patients. The predictions were aggregated to construct an integrated feature representation, which was used as input to a meta-learner architecture. By effectively integrating complementary information from diverse baseline models, the meta-learner refined the decision boundary and enhanced overall predictive performance. Survival analysis and SHapley Additive exPlanations (SHAP) analysis were further performed to evaluate clinical utility and interpret the model predictions. Benchmarking results based on MIMIC-IV dataset suggested that our MetaAMI consistently outperformed all the baseline classifiers across seven evaluation metrics including Accuracy, Area Under the Curve (AUC), F1 Score, G-Measure, Jaccard Index, Youden J, and Matthews Correlation Coefficient (MCC). In addition, feature importance analysis showed clinically relevant predictors of in-hospital mortality. In summary, MetaAMI provides an effective and robust solution for machine learning based AMI risk prediction. We anticipate that the application of MetaAMI will have a positive impact on clinical risk stratification and personalized treatment strategies for AMI.

bioinformatics↗

bioRxiv2026

Molecular basis for chikungunya virus recognition of a mosquito-specific receptor

Alphaviruses are arthropod-borne viruses that recognize cellular receptors in both vertebrate hosts and mosquito vectors to complete their transmission cycle, yet how they maintain recognition of receptors across evolutionarily divergent host species remains unresolved. Among alphaviruses, chikungunya virus (CHIKV), which is primarily vectored in urban settings by Aedes species mosquitoes, is the most widespread, and causes explosive outbreaks that can involve hundreds of thousands to millions of cases annually. The cell adhesion protein Lachesin is a mosquito-specific cellular receptor for CHIKV and multiple other arthritogenic alphaviruses. The envelope E2-E1 glycoproteins of these alphaviruses broadly recognize Lachesin orthologs from diverse mosquito species, but not other insects or arachnids. Lachesin genetic manipulation to prevent mosquito virus infection without interfering with endogenous receptor function could have a major impact for CHIKV control. Here, we determined high-resolution cryo-electron microscopy (cryo-EM) structures of alphaviruses bound to Aedes albopictus Lachesin. Comparative analysis of Lachesin-bound CHIKV, Semliki Forest virus (SFV), and Middelburg virus (MIDV) revealed that these three genetically divergent viruses use a similar surface to recognize Lachesin domain 1, but with reorganized E2-E1 glycoprotein contact residues. We show that a soluble Ae. albopictus Lachesin receptor decoy protein blocks the E2-E1-mediated entry of CHIKV and other arthritogenic alphaviruses into mammalian cells with greater breadth than a vertebrate receptor MXRA8 decoy and protects against lethal SFV challenge and CHIKV pathogenesis in murine models. Additionally, we identified a naturally occurring single residue Lachesin polymorphism that is found in some Anopheles (malaria vector) mosquitoes, and fully ablates CHIKV E2-E1 recognition, informing strategies for mosquito-targeted genetic interventions that could prevent mosquito vector infection and virus transmission. These findings define distinct determinants of receptor binding in mosquitoes and humans for arthritogenic alphaviruses, with implications for countermeasure development and outbreak preparedness.

microbiology↗

bioRxiv2026

Lachesin is a mosquito receptor for multiple arthritogenic alphaviruses

Arthritogenic alphaviruses cause acute febrile illnesses associated with rash and arthritis when they are transmitted to humans through the bite of infected mosquitoes. Among these, chikungunya virus (CHIKV), transmitted primarily through the bite of infected Aedes aegypti and Aedes albopictus mosquitoes, causes explosive outbreaks involving hundreds of thousands to millions of cases, with recent re-emergence in several global regions. While several cellular receptors that mediate alphavirus entry into mammalian cells have been identified, their mosquito counterparts remained unknown, largely due to a lack of functional genomics tools for these invertebrate species. Here, we established a CRISPR-based genetic screening platform in Aedes albopictus cells and used it to identify Lachesin, a conserved invertebrate cell adhesion molecule, as a receptor for CHIKV and multiple related alphaviruses including Semliki Forest virus (SFV), onyong-nyong virus (ONNV), Mayaro virus (MAYV), and Ross River virus (RRV). Lachesin depletion using RNA interference, anti-Lachesin antibody treatment, and soluble forms of Lachesin blocked CHIKV and SFV E2-E1 glycoprotein-mediated infection of mosquito cells. We show that alphavirus E2-E1 glycoproteins bind the first immunoglobulin domain of Lachesin, facilitating attachment and internalization of virus-like particles. Orthologs from divergent mosquito genera, but not from arachnids or other arthropods, also serve as alphavirus receptors, suggesting that cellular receptor binding is not the main obstacle to arthritogenic alphavirus vector host expansion. Our findings enhance understanding of the mechanisms of alphavirus emergence and vector competence and could aid in the development of broadly active, entry-targeted therapeutics against multiple alphaviruses that threaten public health.

microbiology↗

bioRxiv2026

Effects of Tempo, Dynamics, and String on Physical Exposure in Professional Violinists

1.This study examined how tempo, dynamics, and string influence upper-extremity physical exposure in professional violinists and how exposure variability is distributed among musical characteristics, between-subject differences, and residual variability. Twelve violinists performed seven standardized scales while bilateral upper-arm and wrist kinematics and shoulder and forearm muscle activity were recorded. Linear mixed-effects models showed that faster tempo increased right upper-arm velocity and bilateral forearm activity while reducing right upper-arm and wrist ranges of motion. Louder dynamics increased bilateral forearm and right trapezius activity and right-wrist ranges of motion. Higher-posture strings increased right upper-arm elevation and right shoulder muscle activity. Variance analysis identified exposures predominantly related to musical characteristics, jointly related to musical characteristics and between-subject differences, predominantly related to between-subject differences, or mainly unexplained. These findings support future exposure prediction from musical characteristics and targeted prevention through repertoire-based workload management, structured recovery, and individualized technique-focused strategies. 2. HighlightsO_LITempo, dynamics, and string produced distinct upper-extremity exposures. C_LIO_LIFaster tempo and louder dynamics increased bilateral forearm muscle activity. C_LIO_LIHigher-posture strings increased right upper-arm elevation and shoulder activity. C_LIO_LIDistinct musical, between-subject, and residual variance patterns were identified. C_LIO_LIFindings support repertoire-based and individualized PRMSD prevention. C_LI

bioengineering↗

bioRxiv2026

Hepatitis B virus protein X promotes hepatocyte plasticity and survival in a differentiated human liver organoid system

Background & AimsHepatitis B virus (HBV) drives hepatocellular carcinoma in part through the activity of its X protein (HBx), yet the mechanisms by which HBx alters hepatocyte function remain incompletely understood. Progress has been limited by the lack of relevant human models that support controlled HBx expression in mature hepatocytes. Here, we use an improved hepatocyte-like organoid (HLO) platform that supports enhanced hepatocyte maturation to investigate HBx function in a differentiated hepatocyte context. MethodsAdult stem cell-derived HLOs were differentiated using an optimized protocol to generate hepatocyte-like cells with enhanced maturation and transcriptional similarity to primary liver tissue. HBx function was interrogated using both cognate promoter-driven expression and doxycycline-inducible systems across multiple donor-derived organoid lines. Transcriptomic, pathway, and single-cell imaging analyses were performed to assess the impact of HBx expression on hepatocytes. ResultsHBx expression consistently suppressed apoptosis-associated transcripts and reduced expression of core hepatocyte identity genes, including CYP3A4. Pathway analysis revealed downregulation of liver-specific functions, including metabolism, detoxification, complement, and coagulation. At the single-cell level, higher HBx expression was associated with reduced caspase 3/7 activation following apoptotic challenge and decreased hepatocyte marker expression. Functionally, HBx expression increased resistance to apoptosis and enhanced the ability of differentiated hepatocyte-like cells to revert to a proliferative, less differentiated state. ConclusionsHBx expression in differentiated human liver organoids reduces apoptosis and impairs hepatocyte identity, consistently across donors and expression systems. These findings support a model in which HBx promotes a survival-permissive less differentiated state that may contribute to early HBV-driven tumorigenesis. This HLO platform provides a relevant system to dissect HBV-host interactions and reveals a mechanism by which HBV may prime the liver for malignant transformation. Impact and implicationsUnderstanding how HBV promotes hepatocellular carcinoma remains a critical challenge, partly due to the lack of physiologically relevant human derived model systems to study HBx function. Using a differentiated adult human liver organoid system, we show that HBx simultaneously suppresses apoptosis and disrupts hepatocyte identity, providing a mechanistic framework for how HBV may prime hepatocytes for malignant transformation. These findings are particularly relevant for researchers studying HBV pathogenesis and liver cancer, as well as for clinicians aiming to better understand early disease progression. While further validation in more complex multicellular systems is needed, this platform can support the identification of HBx-targeted therapeutic strategies and guide the development of improved adult human derived models for virus-host interaction studies.

cell biology↗

bioRxiv2026

Singlet-states-mediated highly efficient two-photon fluorescence in organic dyes

This study reports a brand-new continuous-wave-excited (CW-excited) two-photon fluorescence emission mechanism in indocyanine green (ICG), an organic fluorescent dye widely used in clinical practice. This mechanism is based on the excited state absorption (ESA) process of the first singlet excited state. Intramolecular electrons sequentially absorb two photons to reach a high-energy singlet excited state, followed by direct radiative transition to the ground state to generate fluorescence. The entire process is exclusively mediated by singlet states. We further summarize the essential requirements for organic dyes to realize this luminescence mechanism. First, the dye must possess at least two well-separated singlet excited states with distinct energies, corresponding to two absorption peaks at different wavelengths in the absorption spectrum. The wavelength of the high-energy singlet excited state is about half that of the first singlet excited state. Second, the peak in the absorption spectrum corresponding to the transition from the ground state to the first singlet excited state has a sufficiently large molar extinction coefficient. Third, the first singlet excited state exhibits the capability of ESA. Fourth, electrons at the high-energy singlet excited state can directly transit to the ground state and emit fluorescence. We validated this mechanism in a variety of organic dyes satisfying the above conditions, confirming its universality. Using CW laser as the excitation source, we achieved two-photon fluorescence imaging of mouse cerebral blood vessels at a depth of 400 m, which clearly resolves three-dimensional vascular networks with high resolution. We also performed two-photon fluorescence imaging on human gastric cancer tissue samples at a depth of around 150 m, which provides a low-cost strategy for clinicians to rapidly acquire high-contrast tumor tissue images.

bioengineering↗

bioRxiv2026

Host genetic regulation of fermentation-related cecal microbial taxa is associated with loin muscle deposition in meat rabbits

Loin muscle weight is an important indicator of carcass yield in meat rabbit production, but the host genetic and intestinal microbial factors associated with its variation remain poorly understood. Because the cecum is the primary site of hindgut fermentation in rabbits, we integrated whole-genome resequencing, cecal transcriptome profiling, and cecal and rectal 16S rRNA sequencing data from 321 Kangda meat rabbits, with rectal microbiome data used as a downstream comparative reference. Compared with the rectum, the cecum contained a richer microbial community, with more ASVs and genera and significantly higher microbial diversity, whereas predicted metabolic functions were largely conserved between the two segments. Loin muscle weight showed moderate SNP-based heritability (h{superscript 2} = 0.39), and the cecal microbiome explained a smaller but detectable proportion of phenotypic variation (m{superscript 2} = 0.13). Multi-strategy microbial screening identified 19 candidate cecal genera associated with loin muscle weight, with Methanosphaera showing the strongest negative association. Host GWAS prioritized candidate loci near MEX3C and TCF4 on chromosome 10, and integration of cecal cis-eQTL and GWAS summary statistics further prioritized GJB3 as a candidate gene associated with loin muscle weight. Consistent with the cecum-centered model, host genetic relatedness was weakly but significantly correlated with cecal microbial similarity, whereas no such global association was observed for the rectal microbiome. Microbial GWAS and SMR analyses further prioritized a cecal MRAP2-Methanobrevibacter association as the main host-regulated microbial signal, while rectal analyses identified distinct segment-specific signals, including SULF1-Roseburia. These findings suggest that host genetic variation may be linked to loin muscle deposition partly through cecal gene expression and fermentation-related cecal microbial taxa, with the rectal microbiome providing comparative evidence for hindgut segment specificity. This study provides candidate host and microbial targets for future functional validation and microbiome-informed nutritional strategies to improve carcass traits in meat rabbits.

genetics↗

bioRxiv2026

Spatiotemporal Cascade of AP1/CCA1-TOC1 Module Gates Stem Development

Stem development is crucial in plant vertical architecture and overall crop improvement. The molecular mechanisms underlying the initiation and circadian growth of stem remain still enigmatic. Here, we demonstrate that APETALA1 (AP1) spatially initiates circadian stem growth through a noncell-autonomous role of TIMING OF CAB EXPRESSION1 (TOC1) emanating from the floral meristem to inflorescence meristem in Arabidopsis thaliana. Mechanistically, AP1 interacts with and recruits CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) to associate TOC1. Dynamic formation of the AP1-CCA1 complex is crucial for maintaining the circadian rhythmicity and expression of TOC1. Tissue-specific expression of TOC1 in floral meristems rescues the developmental defects of toc1 mutants at both functional and transcriptional levels. Furthermore, TOC1 directly activates the circadian expression of pectin methylesterase gene family, which is critical for its role in stem development. AP1 homologs regulate circadian stem elongation and plant height in wheat and rice, underscoring the conserved mechanism across flowering plants. Our findings uncovered a spatiotemporal regulatory cascade gating stem development and identified candidate genes for crop improvement.

plant biology↗

bioRxiv2026

Super-resolved spatial organization of the nucleolar transcriptome

AbstractsMembraneless organelles (MLOs) often exhibit internal architecture, yet whether the local transcriptome differentially partitions across MLO subdomains remains largely uncharacterized. Here we combine super-resolution imaging with in situ reverse transcription-based sequencing to profile transcriptomes within MLO subdomains. Using the human tripartite nucleolus as a model system, we identify distinct RNA populations in the fibrillar center (FC), dense fibrillar component (DFC), and granular component (GC). Pre-rRNA processing intermediates demonstrate a layered progression across nucleolar subdomains, reflecting the temporal order of the processing steps. Processing steps involved in large-small subunit separation show increased retention in the DFC in highly differentiated cells. Mature small nucleolar RNAs (snoRNAs) are preferentially enriched in the DFC and spatially segregated from their precursor transcripts. Many non-snoRNA-related transcripts, often derived from nucleolus-proximal genes, show modest enrichment in the GC. These results illustrate functional RNA organization across nucleolar subdomains and provide a framework for nanoscale transcriptome mapping of biomolecular condensates.

cell biology↗

bioRxiv2026

Tripeptidyl peptidase II is essential for maintaining cerebrovascular homeostasis of female mice and represents a novel therapeutic target for vascular dementia

Although cerebrovascular impairment is a known common driver of both Vascular dementia (VaD) and Alzheimers disease (AD), the underlying mechanisms remain poorly defined. Substantial evidence has demonstrated that brain-derived estrogen is essential for cerebrovascular health and neuroprotection. Consequently, therapeutic strategies that can replicate the beneficial effects of estrogen replacement therapy (ERT) in the brain while avoiding its peripheral risks are being actively pursued. Here, we demonstrate that tripeptidyl peptidase II (TPP2) is essential for cerebrovascular homeostasis in adult female mice by orchestrating intracellular Ca{superscript 2} distribution and local estrogen biosynthesis. Specifically, TPP2 deficiency triggers a vicious cycle of Ca{superscript 2} imbalance and estrogen deficiency, thereby disrupting the anticipatory unfolded protein response (UPR). This disruption consequently drives aberrant pexophagic flux and ultimately depletes ether-linked phosphatidylcholine (PC-O)--the essential building block of endothelial cell (EC) membranes. In addition, we identified PC-O as a key facilitator of choline uptake through FLVCR2 and therefore its deficiency causes subsequent choline depletion as well as significantly decreased acetylcholine (ACh). Consistent with the fact that choline is a building block of PC and that ACh is a primary driver of vascular dilation, TPP2 depletion leads to significant cerebrovascular degeneration characterized by narrowed lumens, decreased EC number, and abnormal aggregation of ECs within the blood vessel. Additionally, AAV-mediated specific expression of Far1 in ECs to promote ether-PC biosynthesis significantly increases cerebrovascular volume and diameter in hippocampi of adult female TPP2 knockout (T2KO) mice. Importantly, ectopic expression of Far1 in ECs not only significantly ameliorates memory impairment in global and conditional TPP2-depleted female mice, but also significantly improves memory performance of naturally aged female mice. In total, our findings establish TPP2 as a key determinant of cerebrovascular homeostasis in adult female mice, positioning it as a novel therapeutic candidate for the treatment of VaD and AD.

neuroscience↗

bioRxiv2026

A Perturb-seq screen guided by species divergence uncovers pathways for collateral artery formation

Collateral arteries are natural bypasses that can reroute blood flow around arterial blockages, limiting tissue injury during stroke and coronary artery disease. Despite their clinical effectiveness, therapeutic strategies to stimulate collateral artery growth remain unavailable due to our limited understanding of their developmental mechanisms. Remarkably, guinea pigs display exceptionally dense collateral artery networks across various organs, resulting in complete resistance to ischemic damage in the brain and heart. In this study, we compared single-cell RNA sequencing (scRNA-seq) from guinea pig and mouse tissues to identify endothelial cell (EC) gene expression patterns associated with extensive collateral artery development. We then developed an in vivo Perturb-seq platform in mice to test whether genes differentially expressed in guinea pigs influence artery EC specification. This pipeline identified artery repressors that were downregulated in guinea pigs and increased pial collateral abundance when inhibited in mice. Downstream analysis suggests that artery repressors, including WNT and hypoxia response genes, function in two capillary EC subsets--Esm1+ pre-artery and Apln+ angiogenic tip cells. Reduced activity of these repressors allows more ECs to acquire arterial identity, potentiating collateral artery formation. Collectively, our study establishes a strategy for discovering the genes underlying species-specific traits, suggests that guinea pigs have collaterals due to decreased activity of artery inhibitor pathways and hypoxia responses, and identifies novel targets for stimulating collateral artery formation (Graphical abstract). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/721711v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@18b36cdorg.highwire.dtl.DTLVardef@bafbaforg.highwire.dtl.DTLVardef@1e1a6bdorg.highwire.dtl.DTLVardef@189f585_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗