Biology subjects

Xie, A.

Publications and source records attributed to Xie, A..

16 recordsLinked to original sources

bioRxiv2026

Structural divergence in protein evolution of a photoreceptor family undetected by AlphaFold is observed by high sensitivity FT-IR spectroscopy

A universal mechanism in molecular evolution is functional and structural divergence of members of a protein family. The ability of AlphaFold to predict atomic-resolution protein structures promises to accelerate insights into this process. We study the interplay of changes in sequence, structure, and function in photoactive yellow protein (PYP), a family of bacterial blue light photoreceptors. Halorhodospira halophila contains two PYP homologs that diverged to 60% sequence identity, differ 100-fold in the lifetime ({tau}pB) of their pB signaling intermediate, and display altered peak wavelengths ({lambda}max) for color sensing. We resurrected ancestral PYPs and determined these properties along the resulting recapitulating evolutionary divergence. The resurrected ancestral PYP is functionally similar to PYP1, indicating divergence on the path to PYP2. AlphaFold predictions for PYP2 and these ancestral proteins revealed the absence of structural changes compared to the crystal structure of PYP1. To experimentally validate these predictions, we optimized second-derivative Fourier transform infrared (FTIR) spectroscopy. The FTIR spectra of PYP1 and 2 and their resurrected ancestral proteins demonstrated clear differences in their secondary structure. These results demonstrate an important limitation of AlphaFold and show how ancestral sequence reconstruction combined with spectroscopic approaches yields insights into divergence in a protein family.

biophysics↗

bioRxiv2026

GYS2 Promotes the Progression of Aortic Dissection and Aortic Aneurysm via C5a/NF-κB-Mediated Pro-Inflammatory Macrophage Polarization

BackgroundAortic aneurysm and aortic dissection (AAD) are lethal cardiovascular emergencies characterized by sudden onset and extremely high early mortality. The pro-inflammatory polarization of macrophages is one of the core factors driving the pathogenesis of AAD, but its underlying mechanism remains unclear. This study focuses on the aberrant expression of glycogen synthase 2 (GYS2) in the AAD microenvironment and its role in driving macrophage polarization toward the pro-inflammatory M1 phenotype. MethodsProteomic analysis was conducted to identify protein heterogeneity associated with AAD. Clinical and animal samples were used to evaluate the correlation between GYS2 expression and AAD progression. Whole-body GYS2 knockout mice and adeno-associated virus (AAV)-mediated macrophage-specific gain- and loss-of-function models were utilized to investigate the regulatory role of GYS2 in macrophage polarization and complement activation. Downstream molecular pathways were identified and validated through in vitro stimulation and in vivo exogenous C5a rescue experiments. ResultsGYS2 expression was significantly upregulated in AAD tissues and primarily localized in macrophages. Activation of GYS2 by LiCl or macrophage-specific overexpression of GYS2 exacerbated aortic dilation and extracellular matrix degradation, and increased mortality in AAD mice. Conversely, whole-body GYS2 knockout or macrophage-specific GYS2 knockdown suppressed inflammatory factors, significantly reduced the incidence of AAD, and attenuated vascular injury. Mechanistically, excessive GYS2 in macrophages specifically triggered the complement-coagulation cascade, promoting the generation of the potent anaphylatoxin C5a. C5a further bound to its receptor C5AR1, activating the downstream PLC{beta}3/NF-{kappa}B signaling pathway, thereby inducing M1 macrophage polarization and matrix metalloproteinase-mediated extracellular matrix degradation. In vivo exogenous C5a rescue completely reversed the vascular protective effects conferred by GYS2 deficiency. ConclusionsThis study demonstrates that highly expressed GYS2 regulates the pro-inflammatory polarization of macrophages and extracellular matrix degradation via the complement C5a/PLC{beta}3/NF-{kappa}B signaling axis, which is a key mechanism driving AAD progression. Specific inhibition of macrophage GYS2 can effectively alleviate aortic vascular inflammation and prevent AAD progression, providing a promising novel strategy for the clinical conservative treatment of AAD.

Molecular Biology↗

bioRxiv2026

Tracing the Evolutionary Origin of Interferon to Basal Chordates and Unveiling Its Antiviral Functionality in Jawless Vertebrates

Interferons (IFNs) are essential mediators of antiviral defense in vertebrates, having gradually replaced the RNA interference (RNAi) antiviral mechanism that predominates in invertebrates and plants. To date, IFNs have been identified exclusively in jawed vertebrates, leaving the origin of IFN-based antiviral mechanisms largely mysterious. In this study, by conducting a genome-wide screening of IFN homologs accross various species, we successfully identified seveal IFN homologs from agnatha and lancelet, but not other invertebrates. Notably, both agnatha and lancelet IFN homologs have ability to induce a set of interferon-stimulated genes (ISGs)-like genes, thus tracing the origin of IFN to basal chordate. Using VSV infected peripheral blood mononuclear cells (PBMCs) of Japanese lampreys, we found that lamprey IFNs have antiviral functionality by inducing the expression of hundreds of ISGs through interacting with a heterodimeric complex composed of CRFB7 and CRFB14. In addition to robustly mediating antiviral responses in monocytes, lamprey IFNs exert their effects on variable lymphocyte receptor B (VLRB)+ cells by remodeling the cytokine/chemokine networks to orchestrate antiviral innate and adaptive immunity. Furthermore, cross-species functional comparison of Dicer revealed that changes in residues essential for dsRNA processing occurred concurrently with the evolution of the IFN system. Collectively, these findings uncover the evolutionary origin of IFN and underscore its ancient roles in antiviral response and immune regulation, especially in the takeover of the RNAi antiviral mechanism during the early evolution of vertebrates. Significance StatementInterferons (IFNs) represent a hallmark of vertebrate antiviral immunity, yet their origin has remained elusive. Here, we reported bona fide IFN ligands and cognate receptors in both lamprey and lancelet, two key species placed at the transition from invertebrates to vertebrates. Using the VSV infection model, we further demonstrated the roles of lamprey IFN in antiviral defense and immune regulation. We also found that substitutions in residues essential for Dicer mediated dsRNA processing coincided with the emergence of the IFN system. Collectively, our findings provide key insights into the evolutionary origin of IFN-based immunity and its gradual replacement of RNAi as the dominant antiviral strategy in vertebrates.

evolutionary biology↗

bioRxiv2026

Stool Metabolomics Reveals Catecholamine and Tryptophan-NAD+ Pathway Alterations in Autism Spectrum Disorder

Gut-brain axis dysregulation and microbiome-linked metabolic disturbances have been implicated in autism spectrum disorder (ASD), yet gut-derived neuroactive metabolites remain incompletely characterized. We applied targeted liquid chromatography-tandem mass spectrometry in a cross-sectional case-control study to quantify 18 stool metabolites related to catecholamine synthesis, GABAergic signaling, and tryptophan (Trp) and NAD+ metabolism in 59 participants (32 ASD, 27 non-ASD controls). Group differences were evaluated using log2 fold change and covariate-adjusted linear models. Random forest classifiers with five-fold cross-validation assessed multivariate discriminative performance, and within-group Spearman correlations examined metabolic network organization. Norepinephrine exhibited the largest elevation in ASD, while dopamine and tetrahydrobiopterin showed nominal group effects consistent with altered BH4-dependent catecholamine metabolism. Among individual metabolites, tetrahydrobiopterin, GABA, and kynurenine were the most informative, and their combination achieved an area under the receiver operating characteristic curve of 0.737 (95% confidence interval, 0.603 to 0.871). Correlation analyses revealed conserved lithocholic acid-deoxycholic acid coupling in both groups. In controls, Trp correlated with kynurenine, whereas ASD showed expanded Trp associations with GABA, norepinephrine, anandamide, and nicotinic acid, consistent with reorganization of Trp-NAD+ precursor pathways. These findings identify coordinated, gut-linked metabolic differences in ASD and define a metabolite signature reflecting altered catecholaminergic and Trp-related network structure. ImportanceAutism spectrum disorder is currently diagnosed using behavioral assessments, and objective biological measures are limited. The gut microbiome produces many small molecules that can influence brain development and function, but the specific metabolites involved in ASD remain unclear. Using targeted analysis of stool samples, we identified changes in metabolites related to neurotransmitter synthesis and tryptophan metabolism and showed that their relationships form distinct metabolic networks in individuals with ASD. A small panel of metabolites provided moderate ability to distinguish ASD from controls. These results suggest that gut-derived metabolites capture biologically meaningful variation in ASD and may help guide future studies aimed at understanding gut-brain communication and developing noninvasive biomarkers.

microbiology↗

bioRxiv2026

CASTLE: Cell-type Aware SpaTial domain detection via contrastive Learning Embedding

With advances in spatially resolved transcriptomics across platforms and resolutions, it is now possible to measure gene-expression profiles while preserving the tissue microenvironment. Spatial clustering is central to these analyses, and recent graph neural network (GNN)-based approaches have greatly improved their accuracy. Nevertheless, precisely delineating spatial domain boundaries remains a significant challenge. Here we present a novel method CASTLE (Cell-type Aware SpaTial domain detection via contrastive Learning Embedding) by leveraging cell type information for improved spatial domain detection. CASTLE first integrates spatial proximity to construct a spatial graph, refined from cell-type similarity or expression similarity when cell type information is unavailable. Then, a self-supervised, local-context contrastive objective aligns embeddings with their immediate microenvironments. Evaluated across multiple tissues and technology resolutions, CASTLE outperforms state-of-the-art methods and detects more accurate and stable spatial domains. In downstream analyses, it resolves fine-grained tissue structures and differentiates functional subtypes, supporting more nuanced biological interpretation.

bioinformatics↗

bioRxiv2025

gnSPADE: a reference-free deconvolution method incorporating gene network structures in spatial transcriptomics

Spatial transcriptomics (ST) technologies have offered unprecedented insights into the spatial organization of gene expression, allowing for the study of tissue architecture, domain boundaries, and cell-cell interactions. However, most ST data generated so far are at multicellular resolution, where each spot captures transcripts from a mixture of diverse cells of different cell types. While reference-based deconvolution approaches offer robust solutions, they rely heavily on the availability and quality of external single-cell reference data, which may be incomplete, unavailable, or poorly matched to the spatial data. Moreover, even when such references are available, they often represent only broad cell types, potentially obscuring finer subpopulation structures and masking intra-type heterogeneity. To overcome these limitations, we introduce gnSPADE, a reference-free spatial deconvolution method that incorporates gene network structures via a Markov random field within a latent Dirichlet allocation (LDA) modeling framework. gnSPADE jointly infers cell type-specific transcriptional profiles and spatial compositions without external references. Applied to synthetic and real ST datasets, gnSPADE achieves improved accuracy, spatial resolution, and biological interpretability compared to other methods, highlighting the power of reference-free deconvolution in resolving complex tissues.

bioinformatics↗

bioRxiv2025

Human iPSC derived alveolar macrophages reveal macrophage subtype specific functions of itaconate in M. tuberculosis host defense

Mycobacterium tuberculosis (Mtb) must survive within multiple macrophage populations during infection, including alveolar macrophages (AM) and recruited inflammatory macrophages. In mice, itaconate, produced in macrophages by ACOD1 mediated decarboxylation of aconitate, has direct antimicrobial activity, modulates inflammatory cytokines, and is required for resistance to M. tuberculosis (Mtb) infection. The role of itaconate in human macrophages is less clear and whether itaconate mediates distinct effects in macrophage subtypes is unknown. Here, we investigated the role of itaconate in human iPSC-derived macrophages, either induced by GM-CSF to resemble alveolar macrophages (AM-Like cells), or treated with M-CSF to generate control macrophages (MCDM cells). Both types of human macrophages produce substantially less itaconate than mouse macrophages and AM-Ls produced 4-fold less itaconate than MCDMs. Surprisingly, ACOD1 deficient AM-L macrophages, but not MCDM macrophages, were permissive for Mtb growth. Moreover, itaconate functioned to dampen the Mtb induced inflammatory response in MCDMs, but not AM-L macrophages, affecting both the Type I IFN and TNF pathways. These results indicate that itaconate is involved in human macrophage responses to TB, with distinct roles in different macrophage subsets. These results also show that genetically tractable hiPSC-derived macrophages are a robust and versatile model to dissect cellular host pathogen interactions.

immunology↗

bioRxiv2025

Meiotic prophase I disruption as a strategy for non-hormonal male contraception using small-molecule inhibitor JQ1

Long-acting non-hormonal male contraceptives are urgently needed but developing strategies that are both effective and reversible presents significant challenges. Here, we investigated the potential of meiotic prophase I blockade as a promising and potentially reversible approach to male contraception. To do this, we utilized (+)-JQ1, a small-molecule inhibitor of the testis-specific protein, BRDT. Daily injections of (+)-JQ1 for three weeks resulted in disrupted spermatogenesis resulting in loss of spermatozoa and an inability to sire pups. While spermatogenic cells repopulated the testis within six weeks post drug cessation, full fertility restoration required a longer recovery period. We attribute this delay in full recovery to persistent issues with the pachytene transcriptional program, which is crucial for meiotic progression and spermatid development. These findings underscore the potential of pharmacological approaches to disrupt meiotic prophase I as a targeted, reversible male contraceptive strategy, providing new insights into developing effective non-hormonal contraceptive approaches.

cell biology↗

bioRxiv2025

PAX3-FOXO1 drives targetable cell state-dependent metabolic vulnerabilities in rhabdomyosarcoma

PAX3-FOXO1, an oncogenic transcription factor, drives a particularly aggressive subtype of rhabdomyosarcoma (RMS) by enforcing gene expression programs that support malignant cell states. Here we show that PAX3-FOXO1+ RMS cells exhibit altered pyrimidine metabolism and increased dependence on enzymes involved in de novo pyrimidine synthesis, including dihydrofolate reductase (DHFR). Consequently, PAX3-FOXO1+ cells display increased sensitivity to inhibition of DHFR by the chemotherapeutic drug methotrexate, and this dependence is rescued by provision of pyrimidine nucleotides. Methotrexate treatment mimics the metabolic and transcriptional impact of PAX3-FOXO1 silencing, reducing expression of genes related to PAX3-FOXO1-driven malignant cell states. Accordingly, methotrexate treatment slows growth of multiple PAX3-FOXO1+ tumor xenograft models, but not fusion-negative counterparts. Taken together, these data demonstrate that PAX3-FOXO1 induces cell states characterized by altered pyrimidine dependence and nominate methotrexate as an addition to the current therapeutic arsenal for treatment of these malignant pediatric tumors.

cancer biology↗

bioRxiv2024

p53 enables phospholipid headgroup scavenging

Changes in cell state are often accompanied by altered metabolic demands, and homeostasis depends on cells adapting to their changing needs. One major cell state change is senescence, which is associated with dramatic changes in cell metabolism, including increases in lipid metabolism, but how cells accommodate such alterations is poorly understood. Here, we show that the transcription factor p53 enables recycling of the lipid headgroups required to meet the increased demand for membrane phospholipids during senescence. p53 activation increases supply of phosphoethanolamine (PEtn), an intermediate in the Kennedy pathway for de novo synthesis of phosphatidylethanolamine (PE), by transactivating genes involved in autophagy and lysosomal catabolism that enable membrane turnover. Disruption of PEtn conversion to PE is well-tolerated in the absence of p53 but results in dramatic organelle remodeling and perturbs growth and gene expression following p53 activation. Consistently, CRISPR-Cas9-based genetic screens reveal that p53-activated cells preferentially depend on genes involved in lipid metabolism. Together, these results reveal lipid headgroup recycling to be a homeostatic function of p53 that confers a cell-state specific metabolic vulnerability.

cell biology↗

bioRxiv2022

Assessment of urinary exosome NHE3 as a biomarker of acute kidney injury

The diagnosis of acute kidney injury (AKI) traditionally depends on the serum creatinine (SCr) and urine output, which lack sufficient sensitivity and specificity. Urinary exosome as a biomarker has unique advantages. To assessed whether urinary exosome Na+/H+ exchanger isoform 3 (NHE3) protein as a nonivasive diagnostic biomarker of AKI, we constructed 4 AKI rat models: cisplatin (7.5mg/kg) injection intraperitoneally (IP), furosemide (20mg/kg, IP) with low NaCl (0.03%) diet, low NaCl (0.03%) diet with candesartan (1mg/kg, IP) and bilaterally ischemia and reperfusion(I/R) injury for 40 minutes. Besides, we assessed 6 sepsis associated AKI patients and 6 healthy volunteers. Urinary exosomes were extracted by ultra-centrifugation and NHE3 protein abundance was tested by immunoblotting in all AKI rats and human subjects. The isolated cup-shape particles with an average diameter of 70nm and enrichment in CD63 were identified as exosomes. NHE3 abundance was 6 times higher in exosome than in original urine. In cisplatin induced AKI rats, urinary exosome NHE3 was increased at day 2, 1 day earlier than the increases of serum creatinine creatinine (SCr) and blood urea nitrogen (BUN). In additional rats, urinary exosome NHE3 decreased along with the decline of SCr after EPO pretreatment. In volume depletion AKI induced by furosemide injection with low NaCl diet, urinary exosome NHE3 expression was higher than control. In low NaCl diet with candesartan related AKI, urinary exosome NHE3 was elevated at day 5, 2 days earlier than SCr. In I/R injury AKI, urinary exosome NHE3 was also raised compared with control. In humans, the urinary exosome NHE3 level was also elevated in sepsis associated AKI patients in comparison with the healthy volunteers. Then urinary exosome NHE3 protein may be used as a noninvasive diagnostic biomarker of AKI. Impact StatementThe high non-recognition acute kidney injury (AKI) is due to lacking of alarming symptoms or specific early biomarkers. Urinary exosome as a biomarker has unique advantages. In our study, we detected urinary exosome NHE3 protein abundance in 4 different cause of AKI rat model. Urinary exosome NHE3 was increased in all 4 AKI, and even elevated earlier than SCr in some cases. Another novel point was we established a new AKI model of low NaCl diet with candesartan injection, which was common in patients with hypertension or proteinuria clinically. The detailed methods and mechanisms of this new AKI model were presented in another article being submitted. Third, we are not limited to animals, but also selected sepsis associated AKI patients to study. The conclusion that urinary exosome NHE3 may be used as a diagnosis biomarker of AKI has important clinical application value.

molecular biology↗

bioRxiv2020

Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila

Recognition of environmental cues is essential for the survival of all organisms. Precise transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes of Drosophila olfactory receptor neurons (ORNs), thermosensory and hygrosensory neurons from the third antennal segment at an early developmental and adult stage. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using these receptors and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuronal types across multiple developmental stages. Cell-type-specific transcriptomes, in part, reflected axon trajectory choices in early development and sensory modality in adults. Our analysis also uncovered type-specific and broadly expressed genes that could modulate adult sensory responses. Collectively, our data reveal important transcriptomic features of sensory neuron biology and provides a resource for future studies of their development and physiology.

neuroscience↗

bioRxiv2020

Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons

Neurons undergo substantial morphological and functional changes during development to form precise synaptic connections and acquire specific physiological features. What are the underlying transcriptomic bases? Here, we obtained the single-cell transcriptomes of Drosophila olfactory projection neurons (PNs) at four developmental stages. We decoded the identity of 21 transcriptomic clusters corresponding to 20 PN types and developed methods to match transcriptomic clusters representing the same PN type across development. We discovered that PN transcriptomes reflect unique biological processes unfolding at each stage--neurite growth and pruning during metamorphosis at an early pupal stage; peaked transcriptomic diversity during olfactory circuit assembly at mid-pupal stages; and neuronal signaling in adults. At early developmental stages, PN types with adjacent birth order share similar transcriptomes. Together, our work reveals principles of cellular diversity during brain development and provides a resource for future studies of neural development in PNs and other neuronal types.

neuroscience↗

bioRxiv2019

Cell-Surface Proteomic Profiling in the Fly Brain Uncovers New Wiring Regulators

Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues, and thus govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally-resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed a global down-regulation of wiring molecules and an up-regulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in vivo screen identified 20 new cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally-resolved in situ cell-surface proteomic profiling in discovering new regulators of brain wiring.

neuroscience↗

bioRxiv2019

LARP7 is a BRCA1 ubiquitinase substrate and regulates genome stability and tumorigenesis

Attenuated DNA repair leads to genomic instability and tumorigenesis. BRCA1/BARD1 are the best known tumor suppressors that promote homology recombination (HR) and arrest cell cycle at G2/M checkpoint. As E3 ubiquitin ligases, their ubiquitinase activity has been known to involve in the HR and tumor suppression, but the mechanism remains ambiguous. Here, we demonstrated upon genotoxic stress, BRCA1 together with BARD1 catalyzed the K48 ployubiquitination on LARP7, a 7SK RNA binding protein known to control RNAPII pausing, and thereby degraded it through 26S ubiquitin-proteasome pathway. Depleting LARP7 suppressed the expression of CDK1 complex, arrested cell at G2/M DNA damage checkpoint and reduced BRCA2 phosphorylation which thereby facilitated RAD51 recruitment to damaged DNA to enhance HR. Importantly, LARP7 depletion observed in breast patients lead to the chemoradiotherapy resistance both in vitro and in vivo. Together, this study unveils a mechanism by which BRCA1/BARD1 utilizes their E3 ligase activity to control HR and cell cycle, and highlights LARP7 as a potential target for cancer prevention and therapy.\n\nHighlightsO_LIDNA damage response downregulates LARP7 through BRCA1/BARD1\nC_LIO_LIBRCA1/BARD1 catalyzes the K48 polyubiquitination on LARP7\nC_LIO_LILARP7 promotes G2/M cell cycle transition and tumorigenesis via CDK1 complex\nC_LIO_LILARP7 disputes homology-directed repair that leads to tumor therapy resistance\nC_LI

molecular biology↗

bioRxiv2019

Coordinating Receptor Expression and Wiring Specificity in Olfactory Receptor Neurons

The ultimate function of a neuron is determined by both its physiology and connectivity, but the transcriptional regulatory mechanisms that coordinate these two features are not well understood1-4. The Drosophila Olfactory receptor neurons (ORNs) provide an excellent system to investigate this question. As in mammals5, each Drosophila ORN class is defined by the expression of a single olfactory receptor or a unique combination thereof, which determines their odor responses, and by the single glomerulus to which their axons target, which determines how sensory signals are represented in the brain6-10. In mammals, the coordination of olfactory receptor expression and wiring specificity is accomplished in part by olfactory receptors themselves regulating ORN wiring specificity11-13. However, Drosophila olfactory receptors do not instruct axon targeting6, 14, raising the question as to how receptor expression and wiring specificity are coordinated. Using single-cell RNA-sequencing and genetic analysis, we identified 33 transcriptomic clusters for fly ORNs. We unambiguously mapped 17 to glomerular classes, demonstrating that transcriptomic clusters correspond well with anatomically and physiologically defined ORN classes. We found that each ORN expresses ~150 transcription factors (TFs), and identified a master TF that regulates both olfactory receptor expression and wiring specificity. A second TF plays distinct roles, regulating only receptor expression in one class and only wiring in another. Thus, fly ORNs utilize diverse transcriptional strategies to coordinate physiology and connectivity.

neuroscience↗