Biology subjects

Lin, L.

Publications and source records attributed to Lin, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Proximal Pulmonary Artery Stiffening as a Biomarker of Cardiopulmonary Aging

The geroscience hypothesis suggests that understanding underlying ageing mechanisms will enable us to delay aging and lessen age-related disability and diseases. While hallmarks of ageing list multiple contributing factors, role of mechanics has only been recently recognized and increasingly appreciated. Here, we use mouse models of ageing to investigate changes in mechanics of the proximal pulmonary artery, lung and right ventricle function in ageing. We found an age-related decline in the capacity to store energy and increased circumferential stiffness of the proximal pulmonary artery with age that associated with a reorientation of collagen towards the circumferential direction, decreased exercise ability, and decreased function of the lung and right ventricle. The observed compromised mechanics in proximal pulmonary artery is consistent across multiple mouse models of accelerated ageing. Further, transcriptional changes in proximal pulmonary artery indicate that aging is associated with senescence of perivascular macrophages, adventitial fibroblasts, and medial smooth muscle cells. Older pulmonary arteries increase expression of genes associated with ECM turnover (including genes in the TGF{beta} pathway) and increased intercellular signaling amongst perivascular macrophages, fibroblasts and smooth muscle cells. Our results provide promising biomarkers of ageing for diagnosis and potential pathways and molecular targets for targeting anti-ageing therapies.

physiology↗

bioRxiv2025

Functional rescue of a fatal ERAD mutation via alternative splicing

Endoplasmic reticulum (ER)-associated degradation (ERAD) is essential for cellular proteostasis, with the SEL1L-HRD1 protein complex targeting misfolded proteins in the ER for proteasomal degradation. Disruption of this pathway underlies a recently identified infant-onset neurodevelopmental disorder (ENDI syndrome), characterized by profound developmental delay, microcephaly, and immune deficiency. Its most severe form, ENDI with agammaglobulinemia (ENDI-A), is driven by a bi-allelic SEL1L Cys141Tyr (C141Y) mutation within the fibronectin II (FNII) domain, for which no treatment currently exists. Here, we serendipitously uncover a striking mechanism of intrinsic rescue in knock-in mouse models of the C141Y mutation: enhanced usage of an alternative splice donor site within exon 4 bypasses the mutant FNII-encoding region, restoring ERAD activity and rescuing key disease phenotypes including perinatal lethality, growth retardation, B cell deficiency, and neurodevelopmental defects. Building on this discovery, we demonstrate that antisense oligonucleotide (ASO)-mediated exon skipping in patient-derived fibroblasts generates a truncated yet functional SEL1L protein, fully rescuing ERAD function and ER proteostasis. These results establish RNA splicing modulation as a viable therapeutic strategy for ERAD deficiency and extend the clinical potential of exon-skipping therapy to diseases of protein misfolding. ONE-SENTENCE SUMMARYThis study reports the discovery of using antisense oligonucleotides (ASOs) to rescue the biallelic SEL1L C141Y variant, offering a potential therapeutic strategy.

cell biology↗

bioRxiv2025

Self-amplifying mRNA expression is governed by mitochondrial machinery and ACSL4

RNA-based vaccines offer a superior efficacious and economic approach over traditional vaccines. However, current dose requirement and short half-life of conventional modified mRNA (modRNA) may hinder the development of more effective vaccines. Self-amplifying mRNA (saRNA) is a modality that has the potential to address these limitations by reducing delivery dosage and enhancing the duration of expression over modRNA. Despite marked success in preclinical studies, saRNA vaccines have thus far underperformed in most clinical trials. We hypothesized that non-optimal human cellular context limits saRNA expression, and that elucidating the factors underlying saRNA expression would be key in developing saRNA as a viable therapeutic modality. To identify factors involved in the regulation of saRNA, we performed a quasi-genome-wide CRISPR knockout screen, which revealed that saRNA expression in human cells is linked to mitochondrial function and governed by ACSL4. We validated these findings through pharmacological intervention and single gene editing, demonstrating that ACSL4-mediated regulation is unique to saRNA and does not impact modRNA. Moreover, we show that modulating ACSL4 leads to improved saRNA expression across multiple cell types. We demonstrate for the first time that mitochondrial function and ACSL4 play key roles in saRNA expression, providing insight for the development and implementation of saRNA as a therapeutic modality.

molecular biology↗

bioRxiv2025

GABA-independent activation of GABAB receptor by mechanical forces

The heterodimeric GABAB receptor, composed of GB1 and GB2 subunits, is a metabotropic G protein-coupled receptor (GPCR) activated by the neurotransmitter GABA. GABA binds to the extracellular domain of GB1 to activate G proteins through GB2. Here we show that GABAB receptors can be activated by mechanical forces, such as traction force and shear stress, in a GABA-independent manner. This GABA-independent mechano-activation of GABAB receptor is mediated by a direct interaction between integrins and the extracellular domain of GB1, indicating that GABAB receptor and integrin form a novel type of mechano-transduction complex. Mechanistically, shear stress promotes the binding of integrin to GB1 and induces an allosteric re-arrangement of GABAB receptor transmembrane domains towards an active conformation, culminating in receptor activation. Furthermore, we demonstrate that shear stress-induced GABAB receptor activation plays a crucial role in astrocyte remodeling. These findings reveal a previously unrecognized function of GABAB receptor in mechano-transduction, uncovering a novel ligand-independent activation mechanism for GPCRs.

neuroscience↗

bioRxiv2025

ROMO1 loss in cholinergic neurons induces mitochondrial ultrastructural damage and ALS-like neuromuscular degeneration

Mitochondrial dysfunction is strongly associated with the pathogenesis of amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder characterized by progressive motor neuron degeneration. However, it remains obscure whether mitochondrial abnormities are sufficient to drive ALS development. Here, we show that selective depletion of reactive oxygen species modulator 1 (ROMO1), an inner mitochondrial membrane-delimited protein, in cholinergic neurons leads to adult-onset, progressive locomotor deficits in mice that closely resemble ALS pathology. ROMO1 ablation in cholinergic neurons induces ALS-like neuromuscular degeneration, as evidenced by age-dependent motor neuron loss, axon degeneration, disrupted cholinergic transmission, neuromuscular junction denervation, and the resultant muscle atrophy. Notably, ROMO1 loss induces early and progressive mitochondrial cristae deformation in motor neurons, preceding the onset of ALS-like syndromes. Our findings support that mitochondrial impairment in vulnerable motor neurons is a sufficient contributor to ALS etiology, positioning mitochondria as a potential therapeutic target.

neuroscience↗

bioRxiv2025

IL-17A-driven Macrophage Disorder Promotes Plaque Instability in Psoriatic Atherosclerosis

Psoriasis is a common chronic inflammatory skin disease that predisposes individuals to cardiovascular diseases such as atherosclerosis. However, the underlying mechanisms linking these conditions have not yet been fully elucidated. Recent studies have indicated that the inflammatory cytokine IL-17A plays a significant role in both diseases. The aim of this study was to investigate how psoriasis affects the stability of atherosclerotic plaques via the IL-17A/IL-17RA pathway. We performed single-cell sequencing on patients with both psoriasis and atherosclerosis to analyze changes in the immune microenvironment within their carotid plaques and psoriatic lesions. We found that IL-17A significantly upregulated the expression of pro-inflammatory factors (e.g., CXCL8) in macrophages of psoriatic atherosclerosis patients, leading to weakening of the fibrous cap structure of plaques. Additionally, IL-17A further exacerbated plaque instability by interfering with macrophage lipid metabolism, particularly sphingolipid metabolism. Finally, using in vitro experiments and animal models, we demonstrated that IL-17A enhances pro-inflammatory and metabolic abnormalities in macrophages by downregulating PPAR{gamma}. Therapeutic strategies targeting IL-17A may contribute to the simultaneous mitigation of psoriasis and atherosclerosis-associated cardiovascular risk, providing new directions for clinical intervention.

cell biology↗

bioRxiv2025

Mapping satellite glial cell heterogeneity reveals distinct spatial organization and signifies functional diversity in the dorsal root ganglion

Satellite glial cells (SGCs) envelop the somata, axon hillock, and initial axon segment of sensory neurons in the dorsal root ganglia (DRG), playing a critical role in regulating the neuronal microenvironment. While DRG neurons have been extensively studied and classified based on size, molecular markers, and functional characteristics, very little is still known about SGC heterogeneity and its potential implications on sensory processing in the DRG. Single cell transcriptional analyses have proposed the existence of SGC subtypes, yet in situ validation, spatial distribution, and potential functional implications of such subtypes are still largely unexplored. Here, we present the first comprehensive in situ characterization of SGC heterogeneity within the mouse DRG. By integrating single-cell RNA sequencing with immunohistochemistry, in situ hybridization, and advanced imaging techniques, distinct SGC subclusters were identified, validated, and spatially mapped within their native anatomical context. We visually identify four distinct subpopulations: 1) a predominant population of perisomatic SGC sheaths defined by the expression of marker proteins traditionally used to characterize the entire SGC population, including FABP7, KIR4.1, GS, and CX43. 2) OCT6+ SGCs occasionally being found in mosaic perisomatic sheaths, and consistently associated with axonal glomeruli, primarily ensheathing initial segment axon. 3) SCN7A+ SGCs, exhibiting no/low expression of traditional SGC markers and forming specialized homogenous sheaths around non-peptidergic neuron subtypes, implicating their potential role in pruritic (itch-related) conditions. 4) Interferon response gene-expressing SGCs, responding to Herpes Simplex Virus infection, suggesting potential involvement in antiviral protection. Finally, we investigate human DRG and find an inner perisomatic SGC layer surrounded by an outer SGC layer, with traditional and novel markers distinctively distributed between the two layers. Our results provide novel insight into SGC heterogeneity in the DRG and suggests distinct functional properties for such subtypes of relevance for the neuronal microenvironment.

neuroscience↗

bioRxiv2025

eSPred: Explainable scRNA-seq Prediction via Customized Foundation Models and Pathway-Aware Fine-tuning

Single-cell RNA sequencing (scRNA-seq) has been widely used for studying cellular heterogeneity, but its use for subject-level prediction and clinical applications is still limited. We introduce eSPred, a customized foundation model designed for predictive analysis of scRNA-seq. It integrates cell-type information through a grouping strategy during pre-training and leverages pathway information to guide network flow during fine-tuning. Across multiple datasets, eSPred improves prediction accuracy and highlights pathways linked to disease mechanisms. These results suggest that eSPred can help bridge the gap between single-cell data and subject-level clinical insights, supporting more precise diagnosis and better-informed treatment decisions.

bioinformatics↗

bioRxiv2025

Metabolic modulation of intratumoral cholesterol with gut microbiota for the treatment of colorectal cancer

Excess cholesterol is positively correlated with colorectal cancer (CRC). Current therapeutic strategies for modulating cholesterol levels in CRC are limited and often come with complications. Here, we demonstrated that microbiome shunting of intestinal cholesterol to anticancer metabolites is a safe and applicable therapeutic approach for CRC. By screening major microbial metabolic products of cholesterol, we found that 4-cholesten-3-one (4-C-3) was selectively depleted in fecal samples and tumor tissues of patients with CRC. 4-C-3 exhibits strong antitumor effects on human CRC cell lines, patient-derived organoids, and patient-derived xenograft (PDX) models. Mechanistically, 4-C-3 suppresses CRC tumorigenesis by dually targeting the epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homologue (KRAS). 4-C-3 directly binds to EGFR, blocking its signal transduction by inhibiting the binding of EGFR ligands. Additionally, 4-C-3 inhibits oncogenic KRAS variants, such as KRASG12D, by suppressing nucleotide exchange activity and effector engagement. By targeting both EGFR and KRAS, 4-C-3 reduces primary resistance to anti-EGFR therapies caused by KRAS mutations in CRC. As a proof-of-concept study, we showed that delivery of 4-C-3 by Oscillibacter ruminantium, a 4-C-3- producing commensal bacterium that is reduced in CRC patients, or a nonpathogenic Escherichia coli strain engineered to specifically convert intestinal cholesterol into 4-C-3, removed intratumoral cholesterol and led to rapid tumor regression in multiple models of CRC. These results suggest that microbial therapies for restoring intestinal cholesterol homeostasis represent a new therapeutic avenue for CRC.

cancer biology↗

bioRxiv2025

cytoGPNet: Enhancing Clinical Outcome Prediction Accuracy Using Longitudinal Cytometry Data in Small Cohort Studies

Cytometry data, including flow cytometry and mass cytometry, are now standard in numerous immunological studies, such as cancer immunotherapy and vaccine trials. These data enable the monitoring of an individuals peripheral immune status over time, providing detailed insights into immune cells and their role in clinical outcomes. However, traditional analyses relying on summary statistics, such as cell subset proportions and mean fluorescence intensity, may overlook critical single-cell information. To address this limitation, we introduce cytoGPNet, a novel approach that harnesses extensive cytometry data to predict individual-level outcomes. cytoGPNet is designed to address four key challenges: (1) accommodating varying numbers of cells per sample; (2) analyzing the longitudinal cytometry data to understand temporal relationships; (3) maintaining robustness under the constraints of limited individual samples in immunological studies; and (4) ensuring interpretability to facilitate biomarker identification. We apply cytoGPNet to data from multiple diverse studies, each with unique characteristics. Despite these differences, cytoGPNet consistently outperforms other popular methods in terms of prediction accuracy. Moreover, cytoGPNet provides interpretable results at multiple levels, offering valuable insights. Our findings underscore the effectiveness and versatility of cytoGPNet in enhancing the analysis of cytometry data and its potential to advance immunological research.

bioinformatics↗

bioRxiv2025

VARS-fUSI: Variable Sampling for Fast and Efficient Functional Ultrasound Imaging using Neural Operators

Functional ultrasound imaging (fUSI) is a promising neuroimaging method that infers neural activity by detecting cerebral blood volume changes. It offers high sensitivity and spatial resolution relative to fMRI and is an epidural alternative to electrophysiology for medical and neuroscience applications, including brain-computer interfaces. However, current fUSI methods require hundreds of compounded images and ultrasound pulse emissions, leading to high computational costs, memory demands, and potential probe heating. We propose VARiable Sampling fUSI (VARS-fUSI), the first deep learning fUSI method to allow for different sampling durations and rates during training and inference by using neural operators. VARS-fUSI reconstructs high-quality fUSI images using 10 - 15% of the time or sampling rate needed per image while preserving decodable behavior-correlated signals. Additionally, VARS-fUSI offers efficient finetuning for generalization to new animals and humans. Demonstrated across mouse, monkey, and human data, VARS-fUSI achieves state-of-the-art performance, enhancing imaging efficiency by significantly reducing storage and processing needs.

bioengineering↗

bioRxiv2025

SCARF: Single Cell ATAC-seq and RNA-seq Foundation model

Recent advances in single-cell multi-omics have provided unprecedented insights into gene regulation by jointly profiling transcriptomic (scRNA-seq) and chromatin accessibility (scATAC-seq) landscapes. However, the inherent heterogeneity and high dimensionality of these multimodal data present significant challenges for effective integration and downstream analysis. Foundation models have demonstrated strong representation learning capabilities for scRNA-seq or scATAC-seq data. So far, however, no model has been specifically developed for the integrative analysis of these two modalities. Here, we introduce SCARF, a single cell ATAC-seq and RNA-seq foundation model. SCARF is pre-trained on X-Omics, the largest curated collection of single-cell multi-omics data to date, comprising over 2.7 million cells across multiple tissues and species. The model utilizes a Mamba architecture for efficiently capturing long-context relationships between genes and between accessible regions. Modality-specific and shared features are learned by the model through self-supervised learning and contrastive learning, respectively. SCARF achieves state-of-the-art performance on multiple downstream tasks, including cell representation, cell matching, and cross-omics translation. Furthermore, SCARF enables few-shot cell type annotation, demonstrating strong generalizability across previously unseen datasets. These results highlight the power of foundation models for advancing integrative analysis of single cell multi-omics data, with broad applications in important tasks including cellular characterization, gene or genomic perturbation analysis, and regulation network analysis.

bioinformatics↗

bioRxiv2025

Cytokine-driven cellular polarization in preeclampsia revealed through the "Dictionary of immune responses"

BackgroundPreeclampsia (PE) is a pregnancy-related hypertensive disorder and a leading cause of maternal and perinatal mortality. Current treatments focus primarily on symptom management, as delivery remains the only definitive cure. This underscores the urgent need for innovative therapeutic strategies. Cytokines released by placental immune cells may contribute to the progression of PE and represent promising therapeutic targets. MethodsWe conducted single-cell sequencing on placental tissues obtained via cesarean section from patients with severe PE and cases of non-infectious preterm birth. Machine learning was applied to identify critical immune cells. Immune Response Enrichment Analysis was performed on these key cells to evaluate their polarization states and cytokine responses associated with PE. Additionally, we investigated cell-cell communications, key genes, and their related functions ResultsWe identified cell type-specific alterations in PE, including an increased proportion of CD4+ T cells polarized towards an IL-1- and IL-1{beta} enriched T4-c state. Altered SPP1 signaling between macrophages and CD4+ T cells was observed, indicating immune response dysregulation. Additionally, machine learning algorithms identified four hub genes, and six small-molecule drugs were predicted to hold therapeutic potential for PE. ConclusionsThis study emphasizes the importance of further understanding CD4+ T cell dynamics in preeclampsia, providing potential insights into the principles of placental immunity and contributing to the exploration of immunotherapeutic strategies

bioinformatics↗

bioRxiv2025

A bioprinting approach for high-throughput production of micropatterned neuroepithelial tissues and modeling TSC2-deficient brain malformations

In vitro human pluripotent stem cell-derived models have been crucial in advancing our understanding of the mechanisms underlying neurodevelopment, though knowledge of the earliest stages of brain formation is lacking. Micropatterning of cell populations as they transition from pluripotency through the process of neurulation can produce self-assembled neuroepithelial tissues (NETs) with precise spatio-temporal control, enhancing the fidelity of hPSC models to the early developing human brain and their use in phenotypic assessments. Here, we introduce an accessible, customizable and scalable method to produce self-assembled NETs using bioprinting to rapidly deposit reproducibly sized extracellular matrix droplets. Matrix addition to the media provides a scaffold that promotes 3D tissue folding, reflecting neural tube development. We demonstrate that these scaffolded NETs (scNETs) exhibit key architectural and biological features of the human brain during normal and abnormal development, notably hyperproliferation and structural malformations induced by TSC2-deficiency, and provide a robust drug screening tool.

neuroscience↗

bioRxiv2025

Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms

Polyethylene, one of the most widely used synthetic polymers, presents significant environmental challenges due to its resistance to biodegradation. Its surface offers a unique ecological niche for microbial colonization and serves as a primary habitat for degrading microorganisms. Despite the pivotal role microbial communities play in plastic degradation, there has been limited research on constructing stable, interacting microbial consortia. In this study, we explored the potential of evolving bacterial biofilm communities to enhance polyethylene degradation. Through long-term experimental evolution, six microbial populations underwent 40 selection cycles using polyethylene as their sole carbon source. The resulting evolved communities formed robust, multi-species biofilms with enhanced degradation capabilities, outperforming their ancestral populations in biofilm production. Pseudomonas stutzeri emerged as the dominant species, orchestrating a synergistic interaction with two other isolates through metabolic division of labor. (Meta)-transcriptomics analysis revealed that Pseudomonas primarily contributed to the expression of enzymes involved in microbe-mediated degradation of polyethylene, whereas the other community members were responsible for secreting extracellular polysaccharides, improving biofilm formation. This study highlights the potential of experimentally evolved microbial consortia to synergistically accelerate plastic biodegradation, offering promising strategies for environmental bioremediation.

microbiology↗

bioRxiv2025

scBiopsy-seq: a platform for temporal single-cell RNA-seq analysis

The development of temporal single-cell RNA-seq (scRNA-seq) assay enabled us to systemically investigate the effects of various types of perturbations in a time course with single-cell resolution. However, the existing temporal scRNA-seq technologies have certain limitations in reliability, detection efficacy and detection diversity. In the current study, we develop scBiopsy-seq assay, which combines a synergistic electroosmosis-electrophoresis extraction method for efficient RNA extraction and digital microfluidics with contamination-isolated hydrophobic interface for high-performance sample processing. scBiopsy-seq extracts the cytoplasm at well-controlled volume to detect >10K genes per extraction with 90% successful rate. Functional enrichment analysis revealed that the genes robustly detected by scBiopsy-seq were associated to diverse biological processes, demonstrating its superb diversity of detection. scBiopsy-seq can perform the sequential extraction of the cytoplasm from the same cell multiple times, which allows us to associate the cell phenotypic responses with its transcriptional dynamics. We employed scBiopsy-seq to analyze the temporal response to a BRD4 degrader induced transcriptional suppression, which identified the key roles of fatty acid beta oxidation in this biological process. scBiopsy-seq with similar data quality as scRNA-seq will dramatically expand the application of temporal scRNA-seq towards a broader spectrum of cell biology research.

bioengineering↗

bioRxiv2025

China Autism Brain Imaging Consortium: Charting Brain Growth in Chinese Children with Autism

Autism Spectrum Disorder (ASD) is a lifelong neurodevelopmental condition characterized by atypical brain growth. While advances in neuroimaging and openly sharing large-sample datasets such as the Autism Brain Imaging Data Exchange (ABIDE) have improved understanding of ASD, most studies focus on adolescents and adults, with early brain development-critical for diagnosis and intervention-remaining underexplored. Existing research predominantly involves Western samples, offering limited insight and generalizability into non-Caucasian populations. We introduce the China Autism Brain Imaging Consortium (CABIC) (https://php.bdnilab.com/resources/), a grassroots effort by researchers across the country to aggregate previously collected multi-site structural MRI datasets and phenotypic information from 1,451 autistic children and 1,119 typically developing children, covering an age range from early childhood to school age (1.0 - 12.92 years). Here, we present this resource and depict brain growth charts to push forward a more comprehensive understanding of the brain development in Chinese autism children. We constructed brain growth charts that reveal a developmental shift in autistic children, transitioning from early overgrowth to delayed maturation. Regional analyses identified distinct atypical trajectories across specific brain regions. Individual deviation scores quantified inter-subject variability, characterizing the heterogeneity of brain development in ASD. Comparative analyses between CABIC and ABIDE highlighted differences potentially attributable to ethnicity and culture, advancing our understanding of cross-population neurodevelopmental diversity. CABIC MRI datasets will be shared publicly to foster investigation of the potential neural mechanisms underlying ASD in non-Western populations and support efforts toward precision medicine for autistic individuals across diverse backgrounds.

neuroscience↗

bioRxiv2025

Structural elucidation of the haptoglobin-hemoglobin clearance mechanism by macrophage scavenger receptor CD163

Intravascular hemolysis releases hemoglobin into the bloodstream, which can damage vascular and renal tissues due to its oxidative nature. Circulating haptoglobin acts as a primary defense by binding to free hemoglobin, forming a haptoglobin-hemoglobin (HpHb) complex that is then recognized and cleared by the CD163 scavenger receptor on macrophages. While the function and structure of HpHb complex are mostly well-defined, the molecular mechanism underlying its interaction with CD163 remains unclear. Here we report the cryo-electron microscopy structures of CD163 in its unliganded state and in its complex with HpHb. These structures reveal that CD163 functions as a trimer, forming a composite binding site at its center for one protomer of the dimeric HpHb, resulting in a 3:1 binding stoichiometry. In the unliganded state, CD163 can also form a trimer, but in an autoinhibitory configuration that occludes the ligand binding site. Widespread electrostatic interactions mediated by calcium ions are pivotal in both pre-ligand and ligand-bound receptor assemblies. This calcium-dependent mechanism enables CD163/HpHb complexes to assemble and, once internalized, disassemble into individual components upon reaching the endosome, where low calcium and lower pH conditions prevail. Collectively, this study elucidates the molecular mechanism by which CD163-mediated endocytosis efficiently clears different isoforms of HpHb.

biophysics↗