Biology subjects

An, C.

Publications and source records attributed to An, C..

11 recordsLinked to original sources

bioRxiv2026

Mechanochemically-reprogrammed stem cell exosomes reconcile the biogenesis internalization trade-off for pulmonary fibrosis therapy

Matrix stiffness serves as a pivotal biophysical cue that profoundly dictates exosome biogenesis and cellular internalization, yet often creates a functional trade-off that impedes clinical translation. Herein, we developed a mechano-chemo-transductive strategy to engineer mesenchymal stem cell (MSC) exosomes endowed with robust biogenesis and superior delivery potency. Specifically, we revealed that MSCs cultured on soft matrices secreted a significantly elevated exosome yield and demonstrated enhanced competence to drive macrophage towards anti-inflammatory M2 polarization. Conversely, stiff matrices upregulated ATP-binding cassette transporter A1 (ABCA1) expression, enriching exosomal membrane cholesterol and facilitating cellular internalization by recipient cells. By taking advantages of these unique mechano-responses, we engineered MSCs via substrate softening combined with ABCA1 modulation to generate mechanochemically reprogrammed exosomes with concurrently enhanced yield and internalization efficiency. In a murine model of pulmonary fibrosis characterized by restrictive biological barriers, inhaled mechanochemically reprogrammed exosomes treatment demonstrated superior lung retention and deep tissue penetration. Furthermore, they effectively orchestrated immune homeostasis by repolarizing alveolar macrophages to reverse fibrotic remodeling and restore lung function. Collectively, by reconciling the intrinsic trade-off between biogenesis and cellular uptake, this strategy represents a paradigm shift in exosome engineering and paves the way for next-generation therapeutics against refractory fibrotic diseases.

bioengineering↗

bioRxiv2026

Interpretable AI driven materiomics to decode microenvironmental cues for stem cell immunomodulation

Hydrogels that mimic the extracellular matrix create microenvironments containing diverse physicochemical cues that regulate stem cell fate, particularly their immunomodulatory and pro-regenerative functions. However, elucidating how microenvironmental cues regulate cell fate remains challenging because of complex multi-parameter interactions and nonlinear relationships, thereby requiring large numbers of samples and substantial experimental effort. Here, we present a materiomics platform that integrates a large-scale systematic dataset with artificial intelligence (AI) to evaluate and predict optimal stem cell niche features for enhancing the immunomodulatory functions of mesenchymal stem cells (MSCs). Specifically, binary hydrogels composed of methacrylated alginate and gelatin (AMGM) were used to construct a comprehensive materiomics database incorporating seven critical physicochemical cues associated with MSC-mediated regulation of macrophage polarization. Machine learning models trained on this materiomics database successfully predicted hydrogel formulations that enhanced MSC immunomodulatory efficacy and further identified matrix stiffness as the physicochemical cue with the greatest contribution to MSC-mediated immunomodulation within the AMGM hydrogel system. In summary, this study demonstrates the utility of AI for evaluating the relative contributions of microenvironmental cues and establishes a data-driven research framework for investigating microenvironmental regulation of stem cell function.

bioengineering↗

bioRxiv2024

Tunable, self-contained gene dosage control via proteolytic cleavage of CRISPR-Cas systems

The ability to modulate gene expression through modular and universal genetic tools like CRISPR-Cas has greatly advanced gene therapy for therapeutics and basic science. Yet, the inherent stochasticity of delivery methods cause variation in target gene expression at the single-cell level, limiting their applicability in systems that require more precise expression. Thus, we implement a modular incoherent feedforward loop based on proteolytic cleavage of Cas to reduce gene expression variability against the variability of vector delivery. We target a genome-integrated marker and demonstrate dosage control of gene activation and repression, post-delivery tuning, and RNA-based compatibility of the system. To illustrate therapeutic relevance, we target the gene RAI1, the haploinsufficiency and triplosensitivity of which cause two autism-related syndromes. We demonstrate dosage-controlled gene activation for both human and mouse Rai1 via viral delivery to patient-derived cell lines and mouse cortical neurons. Overall, we established a robust dosage control circuit for uniform gene expression, beneficial for basic and translational research.

synthetic biology↗

bioRxiv2024

The barley MLA13-AVRA13 heterodimer reveals principles for immunoreceptor recognition of RNase-like powdery mildew effectors

Co-evolution between cereals and pathogenic grass powdery mildew fungi is exemplified by sequence diversification of an allelic series of barley resistance genes encoding Mildew Locus A (MLA) nucleotide-binding leucine-rich repeat (NLR) immunoreceptors with a N-terminal coiled-coil domain (CNLs). Each immunoreceptor recognises a matching, strain-specific powdery mildew effector encoded by an avirulence gene (AVRa). We present here the cryo-EM structure of barley MLA13 in complex with its cognate effector AVRA13-1. The effector adopts an RNase-like fold when bound to MLA13 in planta, similar to crystal structures of other RNase-like AVRA effectors purified from E. coli. AVRA13-1 interacts via its basal loops with MLA13 C-terminal leucine rich repeats (LRRs) and the central winged helix domain (WHD). Co-expression of structure-guided MLA13 and AVRA13-1 substitution variants show that the receptor-effector interface plays an essential role in mediating immunity-associated plant cell death. Furthermore, by combining structural information from the MLA13-AVRA13-1 heterocomplex with sequence alignments of other MLA receptors, we designed a single amino acid substitution in MLA7 that enables expanded effector detection of AVRA13-1 and the virulent variant AVRA13-V2. In contrast to the pentameric conformation of previously reported effector-activated CNL resistosomes, MLA13 was purified and resolved as a stable heterodimer from an in planta expression system. Our study suggests that the MLA13-AVRA13-1 heterodimer might represent a CNL output distinct from CNL resistosomes and highlights opportunities for the development of designer gain-of-function NLRs.

plant biology↗

bioRxiv2023

CLIPB4 is a central node in the protease network that regulates humoral immunity in Anopheles gambiae mosquitoes

Insect humoral immune responses are regulated in part by protease cascades, whose components circulate as zymogens in the hemolymph. In mosquitoes, these cascades consist of clip domain serine proteases (cSPs) and/or their non-catalytic homologs (cSPHs), which form a complex network, whose molecular make-up is not fully understood. Using a systems biology approach, based on a co-expression network of gene family members that function in melanization and co-immunoprecipitation using the serine protease inhibitor (SRPN)2, a key negative regulator of the melanization response in mosquitoes, we identify the cSP CLIPB4 from the African malaria mosquito Anopheles gambiae as a central node in this protease network. CLIPB4 is tightly co-expressed with SRPN2 and forms protein complexes with SRPN2 in the hemolymph of immune-challenged female mosquitoes. Genetic and biochemical approaches validate our network analysis and show that CLIPB4 is required for melanization and antibacterial immunity, acting as a prophenoloxidase (proPO)-activating protease, which is inhibited by SRPN2. In addition, we provide novel insight into the structural organization of the cSP network in An. gambiae, by demonstrating that CLIPB4 is able to activate proCLIPB8, a cSP upstream of the proPO-activating protease CLIPB9. These data provide the first evidence that, in mosquitoes, cSPs provide branching points in immune protease networks and deliver positive reinforcement in proPO activation cascades.

immunology↗

bioRxiv2023

Histone deacetylase 3 plays a critical role in hypertension-induced kidney inflammation and fibrosis

Objective: Hypertension is a major cause of chronic kidney disease. The molecular mechanisms how hypertension causes kidney disease are not fully understood. In this study, we examined the functional role of histone deacetylase 3 (HDAC3) in the pathogenesis of hypertensive kidney disease. Approach and Results: Myeloid HDAC3 knockout mice were generated by crossing HDAC3f/f mice with LysM-Cre+/- mice. Both LysM-Cre-/-HDAC3f/f (HDAC3CON) mice and LysM-Cre+/+HDAC3f/f (HDAC3MKO) mice were subjected to uninephrectomy and treated with angiotensin II at 1.5 ug/kg/min or vehicle for 28 days. Blood pressure increased comparably in both HDAC3CON and HDAC3MKO mice following angiotensin II treatment. Compared with HDAC3CON mice, HDAC3MKO mice were protected from angiotensin II-induced kidney dysfunction and pathological injury and developed less proteinuria. Myeloid HDAC3 deficiency markedly attenuated the protein levels of fibronectin, collagen I, and ?-SMA in the kidney following angiotensin II treatment. Furthermore, HDAC3MKO mice accumulated significantly fewer myeloid fibroblasts and macrophages in the kidney after angiotensin II treatment. Myeloid HDAC3 deficiency significantly reduced the mRNA expression of proinflammatory molecules in the kidney following angiotensin II treatment. In cultured macrophages, knockdown of HDAC3 with shRNA suppressed proinflammatory molecule expression. Furthermore, knockdown of HDAC3 inhibited NF-kB p65 enrichment to IL-6 promoter. Conclusion: Our study identifies a critical role of myeloid HDAC3 in the regulation of hypertension-induced kidney inflammation and fibrosis. Targeting HDAC3 may represent a novel therapeutic strategy for hypertensive kidney disease.

pathology↗

bioRxiv2020

High-resolution architecture of human epiphysis formation

Human limb skeletal system consists of both bone and cartilage which originated from fetal cartilage. However, the roadmap of chondrocyte divergent differentiation to bone and articular cartilage has yet to be established. Epiphysis possesses articular cartilage, growth plate and the secondary ossification center (SOC), making it an ideal model to uncover the trajectory of chondrocyte divergent differentiation. Here, we mapped differentiation trajectory of human chondrocyte during postnatal finger epiphysis development by using single-cell RNA sequencing. Our results uncovered that chondroprogenitors have two differentiation pathways to hypertrophic chondrocytes during ossification, and one pathway to articular chondrocytes for formation of cartilages. Interestingly, we found that, as an addition to the known typical endochondral ossification path from resting, proliferative to hypertrophic chondrocytes, there was a bypass by which chondroprogenitors differentiate into hypertrophic chondrocytes without proliferative stage. Furthermore, our results revealed two new chondrocyte subpopulations (bypass chondrocytes as it appeared in the ossification bypass, and ID1+ chondroblasts in articular chondrocyte path) during postnatal epiphysis development in addition to six well-known subpopulations. Overall, our study provides a comprehensive roadmap of chondrocyte differentiation in human epiphysis thereby expanding the knowledge of bone and articular cartilage, which could be utilized to design biotherapeutics for bone and articular cartilage regeneration.

developmental biology↗

bioRxiv2019

t-SNE transformation: a normalization method for local features of single-cell RNA-seq data

Single-cell RNA sequencing has been widely used by biology researchers. There are many analysis tools developed accordingly. However, almost all of them use log transformation in the process of normalization, which may result in system bias on global features of datasets. It is considered that they may not be suitable for researchers who expect local and detailed features of datasets, such as rare cell population and independent expressed genes. In this study, we developed a method called t-SNE transformation to replace log transformation. We found that it can well respond to some specific bio-markers in real datasets. When the cluster number was changed, t-SNE transformation was steadier than log transformation. Further study showed that clustering after t-SNE transformation detected the residual cells more accurately after majority cells of one type were removed manually. It was also sensitive to a highly-variated independent gene added artificially. In conclusion, t-SNE transformation is an alternative normalization for detecting local features, especially interests arouse in cell types with rare populations or highly-variated but independently expressed genes.

bioinformatics↗

bioRxiv2018

Diagnosis of Osteoarthritis Subtypes with Blood Biomarkers

ObjectiveTo identity osteoarthritis(OA) subtypes with gene expression of peripheral blood mononuclear cells.\n\nMethodsGene expression data (GSE48556) of Genetics osteoARthritis and Progression (GARP) study was downloaded from Gene Expression Omnibus. Principal component analysis and unsupervised clustering were analyzed to identify subtypes of OA and compare major KEGG pathways and cell type enrichment using GSEA and xCell. Classification of subtypes were explored by the utilization of support vector machine.\n\nResultsUnsupervised clustering identified two distinct OA subtypes: Group A comprised of 60 patients (56.6%) and Group B had 46 patients (43.3%). A classifier including nine genes and CD4+ T cell and Regulatory T cell flow cytometry could accurately distinguish patients from each group (area under the curve of 0.99 with gene expression). Group A is typical degenerative OA with glycosaminoglycan biosynthesis and apoptosis. Group B is related to Graft versus host disease and antigen processing and presentation, which indicated OA has a new type of \"Antigen processing and presentation\" similarly as that of RA.\n\nConclusionOA can be clearly classified into two distinguished subtypes with blood transcriptome, which have important significance on the development of precise OA therapeutics.

bioinformatics↗

bioRxiv2018

High resolution profile of body wide pathological changes induced by abnormal elastin metabolism in Loxl1 knockout mice

Abnormal ECM caused serious body wide diseases and elastin is one of the important ECM components. But its systemic function still has not yet been thoroughly illustrated due to limitations related to novel research technologies. To uncover the functions of elastin, a new method for body-wide organ transcriptome profiling, combined with single-cell mass cytometry of the blood, was developed. A body-wide organ transcriptomic (BOT) map was created by performing RNA-seq of 17 organs from both Loxl1 knockout (KO) and wide type (WT) mice. The BOT results showed a systematic up-regulation of genes related to immune response and proliferation process in multiple tissues of the KO mice; histological and immune staining also confirmed the hyperplasia and infiltration of local immune cells in the vagina, small intestine, and liver tissues of KO mice. Furthermore, using 32 markers, CYTOF mass cytometry analysis of the immune cell subpopulations from the peripheral blood revealed apparent systemic immune changes in the KO mice; data showed an activated NK cells and T cells with a higher expression of CD44 and CD38, and a suppressed B cells, macrophages and neutrophils with lower expressions of CD62L, CD44 and IL6. More interestingly, these findings also correlated well with the data obtained from cancer patient databases; tumor patients had higher mutation frequency of Loxl1, and the Loxl1-mutant tumor patients had up-regulated immune process, cell proliferation and decreased survival rate. Thus, this research provided a powerful strategy to screen body-wide organ functions of a particular gene; the findings also illustrated the important biological roles of elastin on multiple organ cells and systemic immunity. These strategy and discoveries are both of important value for the understanding of ECM biology and multi-organ cancer pathology.

cancer biology↗

bioRxiv2018

Cell atlas of human uterus

The human uterus is a highly dynamic tissue that undergoes repeated damage repair and regeneration during the menstrual cycle, which make it ideal model to study tissue regeneration and pathological process. Stem/progenitors were speculated to be involved in the regeneration of endometrial epithelial and pathogenesis of endometriosis. But the identity, microenvironment and regulatory mechanisms of the uterus epithelial stem/progenitors in vivo remain unclear. Here, we dissected the cell heterogeneities of the full-thickness human uterus epithelial cells (11 clusters), stroma cells (6 clusters), endothelial cells (5 clusters), smooth muscle cells (2 clusters), myofibroblasts (2 clusters) and immune cells (6 clusters) from 2735 single cell by single cell RNA-seq. Further analysis identified a unique ciliated epithelial cell cluster showing characteristics of stem/progenitors with properties of epithelial-mesenchymal transition (EMT) that mainly localized in the upper functionalis of the endometrium. Ordering the cell subpopulations along the pseudo-space revealed cell clusters possess cellular states of stress, inflammation and apoptosis in the upper functionalis cellular ecosystem of the endometrium. Connectivity map between the human uterus subpopulations revealed potential inflammatory (cytokines and chemokines) and developmental (WNT, FGF, VEGF) signals within the upper functionalis cellular ecosystem of the endometrium, especially from other epithelial clusters, regulating cell plasticity of the EMT-epithelial clusters. This study reconstructed the heterogeneities, space-specific distribution and connectivity map of human uterus atlas, which would provide insight in the regeneration of uterus endometria and reference for the pathogenesis of uterus.

cell biology↗