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Lin, J.

Publications and source records attributed to Lin, J..

At least 109 records · Page 6Linked to original sources

Identification and characterization of a novel exo-glycosidase activity of NGLY1 on ENGase-digested N-GlcNAc proteins in vitro

N-Glycanase 1 (NGLY1) is known for its activity to completely remove conjugated N-glycans from glycoproteins. Early studies illustrated that NGLY1 defects were associated with a rare disease named NGLY1-related congenital disorder of deglycosylation (NGLY1-CDDG). Although extensive research has been conducted over the past decade on the biological impact of NGLY1s endo-(N-)glycanase activity in cells and on disease, whether NGLY1 also exhibits an exo-(N-)glycanase activity remains open. In this study, an exo-(N-)glycanase activity of NGLY1 on the N-GlcNAc proteins was firstly reported and characterized in vitro. To distinguish for the conventional endo-(N-)glycanase activity and the newly reported exo-(N-)glycanase activity of NGLY1, the active sites of exo-NGLY1 were predicted and compared with those of endo-NGLY1. In addition, the correlation between NGLY1s exo-(N-)glycanase activity in vitro and NGLY1-CDDGs clinical characterization was investigated and discussed. The observation of NGLY1s novel exo-(N-)glycanase activity expanded the functional repertoire of NGLY1 beyond canonical endo-(N-)glycanase-mediated deglycosylation, and may provide a new framework to explain the clinical heterogeneity of NGLY1-CDDG.

biochemistry↗

Interpretable spatial multi-omics data integration and dimension reduction with SpaMV

Spatial multi-omics technologies have revolutionized our understanding of biological systems by providing spatially resolved molecular profiles from multiple perspectives. Existing spatial multi-omics integration methods often assume that data from different modalities share a common underlying distribution, aiming to project them into a single unified latent space. This assumption, however, can obscure the unique insights offered by each modality, thereby limiting the full potential of multi-omics analyses. To address this limitation, we present the Spatial Multi-View (SpaMV) representation learning algorithm, which captures both the shared information across modalities and the distinct, modality-specific information, enabling a more comprehensive and interpretable representation of spatial multi-omics data. Through extensive evaluation on both simulated and real-world datasets, SpaMV demonstrates superior spatial domain clustering performance and provides users with more interpretable dimension reduction for downstream analysis. Moreover, SpaMV effectively annotates cell types within clusters of a mouse thymus dataset, highlighting its effectiveness in interpretable dimensionality reduction.

bioinformatics↗

Innate Immune Remodeling Drives Therapy Resistance via Macrophage-NK Cell Crosstalk.

The dynamic evolution of the immune tumor microenvironment (TME) during targeted therapy is a critical yet poorly understood determinant of treatment response and resistance. While most studies compare immune states before and after treatment, temporal immune changes during therapy remain largely uncharacterized, limiting development of effective combination strategies. Here, we investigated immune dynamics throughout targeted therapy using mouse melanoma models that recapitulate human therapeutic responses. Single-cell RNA sequencing (scRNA-seq) identified a previously unrecognized inflection point where the inflamed TME during tumor regression, characterized by robust NK cell infiltration, transitions to an immune-excluded state upon onset of drug-tolerant residual disease. We uncovered a unique macrophage subset (F4/80hiCCL5MHCIICD63) that orchestrates NK cell recruitment through CCR2/5 signaling during regression. Depletion of these macrophages using LysM-cre;iDTR mice significantly reduced NK cell infiltration. Specifically during residual disease, pharmacological inhibition of Ptpn22, a phosphatase that negatively regulates immune activation, reprogrammed macrophages, restored NK cell recruitment and enhanced therapeutic efficacy. Extending these findings to human cancer, longitudinal scRNA-seq analysis of melanoma and lung cancer patient samples revealed dynamic NK cell infiltration during targeted therapy, establishing a direct link between innate immune remodeling and treatment outcome. Unlike prior prognostic studies assessing immune states at single time points, our results provide mechanistic evidence of a temporal relationship between NK cell infiltration and therapeutic efficacy. Together, these findings position immune evolution as a driver of acquired resistance and identify macrophage-NK cell crosstalk as a therapeutically actionable axis to overcome immune exclusion and improve targeted therapy across multiple cancer types. One Sentence SummaryCancer therapy resistance emerges from a dynamic evolution of the tumor microenvironment, characterized by macrophage-driven NK cell infiltration during initial tumor regression, followed by exclusion of NK cells during residual disease, highlighting macrophage-NK cell interactions as a promising therapeutic target to improve clinical outcomes.

cancer biology↗

Myocyte Enhancer Factor 2A Orchestrates Vascular Redox Homeostasis via Direct Transcriptional Activation of SIRT1

Myocyte enhancer factor 2A (MEF2A), a transcription factor implicated in coronary artery disease, remains unexplored in vascular redox regulation. To address this gap and overcome limitations of current antioxidant therapies, we investigated MEF2As role in oxidative defense using human umbilical vein endothelial cells (HUVECs) and murine models. Adenoviral vectors encoding MEF2A-specific shRNA or mRNA were employed to silence or overexpress MEF2A in HUVECs. For in vivo validation, endothelial-targeted MEF2A knockdown was achieved via AAV1-shRNA delivery in mice fed a high-fat diet. Systemic redox status was assessed by measuring reactive oxygen species (ROS), glutathione homeostasis (GSH/GSSG ratio), NADH/NAD+ balance, mitochondrial membrane potential ({Delta}{Psi}m), and 8-hydroxy-2'-deoxyguanosine (8-OHdG). Mechanistic insights were derived from immunofluorescence, qPCR, western blotting, and dual-luciferase reporter assays. MEF2A silencing induced redox imbalance, characterized by elevated ROS, reduced GSH/GSSG ratio, and {Delta}{Psi}m collapse. Conversely, MEF2A overexpression synergized with SIRT1 to restore glutathione pools, maintain NAD+ homeostasis, and suppress ROS under oxidative stress. Chromatin immunoprecipitation confirmed direct MEF2A binding to two cis-elements in the SIRT1 promoter, driving transcriptional activation. In vivo, MEF2A-deficient mice exhibited amplified vascular oxidative damage, including elevated DNA damage marker (8-OHdG) and ROS levels. Downregulation of SIRT1/PGC-1 in MEF2A silenced cells was verified in vivo. Our findings establish MEF2A as a master regulator of endothelial redox defense via the SIRT1-PGC-1 axis, offering a mechanistic foundation for targeting oxidative cardiovascular disorders. This work suggests pharmacological MEF2A activation as a novel strategy for precision antioxidant therapy in vascular medicine.

molecular biology↗

mRNABench: A curated benchmark for mature mRNA property and function prediction

Messenger RNA (mRNA) is central in gene expression, and its half-life, localization, and translation efficiency drive phenotypic diversity in eukaryotic cells. While supervised learning has widely been used to study the mRNA regulatory code, self-supervised foundation models support a wider range of transfer learning tasks. However, the dearth and homogeneity of standardized benchmarks limit efforts to pinpoint the strengths of various models. Here, we present O_SCPLOWMC_SCPLOWRNABO_SCPLOWENCHC_SCPLOW, a comprehensive benchmarking suite for mature mRNA biology that evaluates the representational quality of mature mRNA embeddings from self-supervised nucleotide foundation models. We curate ten datasets and 59 prediction tasks that broadly capture salient properties of mature mRNA, and assess the performance of 18 families of nucleotide foundation models for a total of 135K experiments. Using these experiments, we study parameter scaling, compositional generalization from learned biological features, and correlations between sequence compressibility and performance. We identify synergies between two self-supervised learning objectives, and pre-train a new Mamba-based model that achieves state-of-the-art performance using 700x fewer parameters. O_SCPLOWMC_SCPLOWRNABO_SCPLOWENCHC_SCPLOW can be found at: https://github.com/morrislab/mRNABench.

genomics↗

Coupling of habitat-preference barriers leads to reproductive isolation in sympatric speciation

Habitat preference is a widely recognized mechanism of reproductive isolation, yet its role in initiating premating barriers and coupling with other barrier mechanisms to establish robust and irreversible reproductive isolation (RI) in sympatric speciation remains unclear. In this study, we developed mathematical models and computer applications to investigate one- and two-allele models of habitat-preference barriers in sympatric populations under disruptive ecological selection. We examined two spatial arrangements: an open-space model inspired by sympatric cichlid fishes that meet in open water with niche habitats that are small relative to lake size, and a no-open-space model inspired by sympatric hawthorn and apple maggot flies that move directly between trees without lingering in midair. Next, we examined coupling between habitat-preference barriers and a two-allele mating-bias barrier developed in a prior study to analyze how their invasion and coupling dynamics could lead to stronger RI. Our findings confirm that habitat preference is an independent mechanism capable of establishing initial premating barriers in sympatric speciation. Moreover, it can couple with additional barriers, such as those based on mating-trait discrimination, to enhance overall RI. Because habitat preference is an adaptive barrier mechanism, its invasion and coupling are driven by selection pressures arising from maladaptive hybrid loss, and it is readily reversed when disruptive ecological selection weakens. The one-allele model is easier to evolve than the two-allele model because it is immune to recombination by gene flow. Habitat-preference barriers can facilitate the emergence of mating-bias barriers. Open-space systems provide fewer opportunities for inter-niche encounters and tend to result in stronger RI compared to no-open-space systems. By elucidating the habitat-preference mechanism, our study reinforces the important role of habitat-preference barriers in sympatric speciation. It also provides insights into a wide range of premating isolating mechanisms--temporal, behavioral, and mechanical--that function similarly by reducing mating encounters.

evolutionary biology↗

Buffer Valency Engineering Enables High-concentration and Shelf-stable DNA Transfection Particles for Viral Vector Production

Cost-effective and scalable production is critical for advancing the clinical translation of adeno-associated virus (AAV)-mediated gene therapy. The widely used transient transfection method using plasmid DNA (pDNA)-loaded transfection particles for AAV production faces technical challenges due to instability of the particles and the concentration limits for particle preparation, hindering reproducibility and scalability. Here, we report a streamlined and scalable strategy to generate shelf-stable, highly concentrated pDNA/poly(ethylenimine) (PEI) transfection particles. By incorporating trivalent citrate ions in the dilution buffers, we kinetically modulate electrostatic complexation to achieve uniform nanoparticle assembly and prevent aggregation at high concentrations. This enables a tenfold increase in pDNA concentration in stabilized transfection particles from a typical range of 10-20 g/mL to 200 g/mL, while reducing the required dosing volume from 5-10% to 0.5% of the cell culture medium. The particle assembly process is robust to changes in mixing scale and timing and is compatible with standard workflows. We demonstrate equivalent AAV production efficiencies to standard methods and consistent performance in various production scales, which confirms the practical utility of this assembly method in developing robust, scalable, and cost-effective AAV manufacturing processes.

biochemistry↗

Discovery of oxyacanthine dihydrochloride monohydrate polymorphs from obfuscated samples by MicroED

It is estimated that more than 50% of marketed pharmaceuticals are derived from natural products. Structural characterization of natural products and their drug formulations is essential for the pharmaceutical industry. Here we report the use of microcrystal electron diffraction (MicroED), to identify two polymorphic crystal structures of oxyacanthine dihydrochloride monohydrate from obfuscated samples that were mislabeled as "berbamine dihydrochloride". The two polymorphs display primary conformational differences in one of the tetrahydroisoquinoline rings: one polymorph exhibits an intermediate conformation between half-chair and half-boat, while the other adopts a distinct half-boat conformation. Analysis of their structures, energies and crystal packing diagrams indicates a thermodynamic preference for a transformation into the latter. This study highlights the value of integrating MicroED into pharmaceutical pipelines as an efficient tool for structural analysis and quality control.

biochemistry↗

Hollow condensates emerge from gelation-induced spinodal decomposition

Recent studies have identified diverse hollow biomolecular condensates, characterized by biomolecule-depleted interiors surrounded by biomolecule-rich shells. Although several formation mechanisms have been proposed, a general thermodynamic driving force remains elusive. Here, we investigate a well-defined system in which the human transcription factor p53 and non-specific double-stranded DNA (dsDNA) form biomolecule-rich condensates. Introduction of dsDNA containing p53-binding motifs induces a morphological transition to hollow structures, accompanied by a material state transition from liquid-like to gel-like. In vitro assays indicate that the formation of hollow condensates is driven by p21 DNA-induced localized gelation at the condensate periphery. Guided by these findings, we developed a three-component phase-field model that quantitatively recapitulates the formation of hollow condensates. Simulations show that peripheral gelation leads to gradual depletion of protein and Random DNA from the condensate core, triggering spinodal decomposition and lumen formation inside condensates. Together, these results offer mechanistic insights into multi-component hollow condensates.

biophysics↗

Substrate properties and actin polymerization speed dictate universal modes of cell migration: gripping, slipping, and stick-slip

Understanding how cells sense mechanical cues and regulate migration is crucial in the development, fibrosis, and oncogenesis processes. However, a comprehensive physical picture of cell migration remains lacking, given the diverse environmental properties and cell physiologies. Here, we generalize the motor-clutch model to the whole-cell level and systematically investigate the effects of substrate stiffness, friction, and actin polymerization speed on cell migration. We unveil three distinct migration modes: gripping, slipping, and stick-slip. Notably, stiffness sensing occurs exclusively in the stick-slip mode, which requires a low substrate stiffness and a minimum actin polymerization speed as necessary conditions. Intriguingly, the optimal substrate stiffness that maximizes the migration speed is inversely proportional to the actin polymerization speed. Moreover, the maximal speed only depends on the nature of the clutch molecules, independent of substrate properties. We reveal the boundary criteria between the three migration modes and demonstrate that fast- and slow-migrating cells can coexist in an isogenic cell population without the need for biochemical feedback loops.

biophysics↗

Resolving synaptic events using subsynaptically targeted GCaMP8 variants

While genetically encoded Ca2+ indicators are valuable for visualizing neural activity, their speed and sensitivity have had limited performance when compared to chemical dyes and electrophysiology, particularly at synaptic compartments. We addressed these limitations by engineering a suite of next-generation GCaMP8-based indicators, targeted to presynaptic boutons, active zones, and postsynaptic compartments at the Drosophila neuromuscular junction. We first validated these sensors to be superior to previous versions and synthetic dyes. Next, we developed a Python-based analysis program, CaFire, which enables the automated quantification of evoked and spontaneous Ca{superscript 2} signals. Using CaFire, we show a ratiometric presynaptic GCaMP8m sensor accurately captures physiologically-relevant presynaptic Ca2+ changes with superior sensitivity and similar kinetics compared to chemical dyes. Moreover, we test the ability of an active zone-targeted, ratiometric GCaMP8m sensor to report differences in Ca{superscript 2} between release sites. Finally, a newly engineered postsynaptic GCaMP8m, positioned near glutamate receptors, detects quantal events with temporal and signal resolution comparable to electrophysiological recordings. These next generation indicators and analytical methods demonstrate that GCaMP8 sensors, targeted to synaptic compartments, can now achieve the speed and sensitivity necessary to resolve Ca2+ dynamics at levels previously only attainable with chemical dyes or electrophysiology.

neuroscience↗

Human placental stem cells induce a novel multiple myeloid cell-driven immunosuppressive program that ameliorates proinflammatory CNS pathology

Despite a growing interest in Amniotic Epithelial Cell (AEC)-based therapies, the immune responses triggered by AEC transplantation in vivo remain poorly characterized. In particular, how direct exposure to AECs within the central nervous system (CNS) shapes the local immune environment is currently unknown. Herein we describe a novel CNS- specific immunoregulatory pathway induced by intracisternal delivery of human AECs. Local immune responses induced by AECs in the brain led to recruitment of immunosuppressive Arginase 1+ (ARG1+) macrophages and a novel population of myeloid-derived suppressor cells with eosinophilic characteristics, which we term Eo- MDSCs. We further demonstrate that Eo-MDSCs produce Maresin 2 (MaR2), a specialized pro-resolving mediator (SPM) involved in the resolution of inflammation. In a mouse model of Multiple Sclerosis (MS), treatment of established disease with AECs induced immunological responses that resulted in reduced numbers of pathogenic macrophages and T helper (TH)17 cells, increased anti-inflammatory T cell subsets, and enhanced myelin phagocytosis, all of which led to functional recovery. These findings suggest that AEC therapy has the potential to target CNS-intrinsic inflammatory processes in MS, providing a strong rationale for translation into the clinic.

neuroscience↗

Controlling Payload Heterogeneity in Lipid Nanoparticles for RNA-Based Therapeutics

Lipid nanoparticles (LNPs) are a leading platform for nucleic acid delivery, yet conventional assembly by mixing lipids with RNA yields particles with heterogeneous, bimodal payload distribution. Our transfection experiments demonstrate that heterogeneous siRNA distribution within LNPs significantly reduces gene knockdown efficiency. To systematically investigate the origin and extent of payload heterogeneity, we integrate coarse-grained molecular dynamics and kinetic Monte Carlo simulations with single-particle characterization via cylindrical illumination confocal spectroscopy and machine learning analysis. We find that the balance between RNA diffusion kinetics and lipid self-assembly dynamics is the dominant driver of payload heterogeneity. Leveraging this mechanistic insight, we show that (i) finely controlled turbulent mixing minimizes payload variance and increases the uniformity of RNA distribution without altering LNP size, and (ii) systematic adjustment of salt concentration and PEG-lipid content tunes RNA loading in a volume-dependent manner. Together, these results elucidate the self-assembly landscape of RNA-LNPs and provide actionable design principles for crafting more uniform, potent, and safer LNP-based nucleic acid therapies.

bioengineering↗

G1 and G2 ApolipoproteinL1 modulate macrophage inflammation and lipid accumulation through the polyamine pathway

The G1 and G2 variants of the gene encoding Apolipoprotein L1 (APOL1) increase risk for kidney disease and cardiometabolic traits. While previous studies have elucidated key mechanisms by which G1 and G2 APOL1 cause cellular inflammation and cytotoxicity, it remains unclear whether these mechanisms drive inflammation in G1 and G2 macrophages. In this study, we used mouse bone-marrow-derived macrophages and human induced pluripotent stem cell-derived macrophages to identify altered immune signaling and inflammatory activation caused by G1 and G2 APOL1. We demonstrated that G1 and G2 APOL1 increased lipid accumulation, pro-inflammatory cytokine expression, and inflammasome signaling; this inflammatory response was sustained when treated with anti-inflammatory cytokines IL-4 and IL-10. Additionally, in G1 and G2 macrophages we observed increased mitochondrial size and elongation, oxidative phosphorylation, and glycolysis. Finally, we used unbiased metabolite analysis to identify an accumulation of polyamine spermidine and the enrichment of the spermidine synthesis pathway in G1 and G2 macrophages. When treated with polyamine inhibitor -difluoromethylornithine (DFMO), lipid accumulation and inflammasome gene expression decreased in G1 and G2 macrophages. Together, these findings establish the pro-inflammatory effects of G1 and G2 APOL1 in macrophages and identify a novel pathway which ameliorates G1 and G2 effects on cellular inflammation.

cell biology↗

Disentangling the cost of gene expression

Gene expression is essential for biological functions but also incurs a fitness cost. Although the fitness cost can be experimentally measured as the relative reduction in growth rate, it remains unclear how the cost quantitatively depends on different limiting factors. In this work, we establish a resource competition model and disentangle the fitness cost into components arising from limiting resources, including ribosomes, RNA polymerases, and transcription factors. Comparing our model predictions with experimental data for Saccharomyces cerevisiae, we demonstrate that ribosome competition dominates the translation cost, and that transcription factor competition dominates the transcription cost. Our model reveals that the fitness costs originate from the processes of transcription and translation, rather than from the products. The model also systematically connects the fitness cost to genetic and environmental properties, making quantitative predictions consistent with various experimental observations. Our work establishes a systematic framework for gene expression cost, guiding synthetic biology to optimize genetic design.

systems biology↗

Social experience alters behaviors by reprogramming the Fruitless pathway and circadian state in Drosophila

From flies to humans, social experience affects various cognitive and behavioral processes. Previous studies have shown that group housing suppresses many behaviors like courtship, aggression, and feeding in Drosophila melanogaster, in addition to resetting the circadian state. Here, we focus on group housing-induced courtship suppression. To determine the mechanisms by which social experience modulates courtship behaviors, we performed bulk tissue RNAseq and single-cell RNAseq from cells expressing FruitlessM (FruM) and DoublesexM (DsxM), two transcription factors that label interconnected neural circuits for socially driven behaviors, from grouped or isolated male brains. These revealed that social isolation alters fru and dsx levels throughout the brain. Knocking down fruM in different fruM-positive neuron subpopulations in the brains has diverse effects on social experience-dependent changes in courtship. Furthermore, group housing increases the expression of stripe (sr) and Hormone receptor-like in 38 (Hr38) genes encoding neural activity-induced transcription factors in most neurons within social circuits. We found that knocking down sr in fruM-positive neurons effectively eliminates the impact of social experience by increasing courtship in group-housed males. Importantly, social experience also alters the expression of FruM/DsxM putative target genes regulating circadian states throughout the brain. Disrupting the function of multiple circadian genes diminishes the effect of group housing on courtship. Our findings suggest that group housing/social enrichment suppresses courtship by reprogramming the circadian arousal state, whereas courtship-elevating effects of social experience rely on unique influences of FruM expression and function in different neurons within social and clock circuits. These results are significant as they point to modulation of circadian arousal state as a possible central strategy for mediating the pleiotropic effects of social experience on organismal responses.

neuroscience↗

Pyruvate kinase activates SARM1 to exacerbate axonal degeneration in diabetic peripheral neuropathy

Diabetic peripheral neuropathy (DPN) is a prevalent and disabling complication of diabetes, characterized by progressive axonal degeneration. However, the molecular link between hyperglycemia and axon injury remains unclear. Here, we identify pyruvate kinase M (PKM) as a direct metabolic activator of the NADase SARM1 under high-glucose conditions. Proteomic and biochemical analyses reveal that PKM binds the TIR domain of SARM1 via its C-terminal region, allosterically enhancing NADase activity independently of PKMs glycolytic role. In dorsal root ganglion (DRG) neurons, hyperglycemia strengthens the PKM-SARM1 interaction, driving NAD depletion, axonal fragmentation, and sensory dysfunction. Genetic depletion of PKM protects against streptozotocin-induced neuropathy, preserving nerve fiber density, restoring NAD levels, and alleviating mechanical allodynia. Most notably, we developed Pep-SP1, a competitive inhibitory peptide derived from residues 645-655 of the SARM1 TIR domain, which selectively disrupts the PKM-SARM1 interaction without impairing PKM metabolism or SARM1 catalytic activity. Systemic delivery of Pep-SP1 attenuates axonal degeneration and improves sensory outcomes in diabetic mice. By targeting a disease-potentiating interface, we expand therapeutic strategies beyond catalytic and allosteric inhibition, offering a mechanistically distinct avenue for axon protection with broad relevance to metabolic and neurodegenerative disorders.

neuroscience↗

Advanced Age in Mice Exacerbates Sepsis-Induced Inflammation, Vascular Permeability, and Multi-Organ Dysfunction

Sepsis is a life-threatening syndrome marked by a dysregulated immune response to an infection and significant endothelial vascular permeability, often leading to multi-organ failure. Elderly patients are particularly vulnerable to sepsis, with higher morbidity and mortality rates. We hypothesized that advanced age exacerbates sepsis-induced inflammation and endothelial vascular permeability, resulting in a delayed recovery, persistent inflammation, and sustained organ injury. Using a polymicrobial sepsis model in young (3-month-old) and aged (18-month-old) C57BL/6 mice, sepsis was induced via intraperitoneal cecal slurry (CS) injection. Outcomes were assessed during the acute (24-hour; 1.6mg/g CS) and recovery (8-day; 1.0 mg/g CS) phases. During the acute phase, aged mice exhibited worse physiologic dysfunction, higher systemic (plasma TNF-a: young septic 202.1 pg/mL [17.44, 398.9] vs. aged septic 482.6 pg/mL [279.8, 711.7]; p = 0.0352 Mann-Whitney) and organ-specific inflammation, increased endothelial injury and vascular permeability, as well as greater kidney and liver dysfunction compared to young mice. During recovery, aged mice had sustained physiologic dysfunction, prolonged systemic and organ-specific inflammation, and sustained organ injury (kidney tissue NGAL: young septic 291.5 RE [203.7, 373.2] vs. aged septic 821 RE [456, 1258] protein normalized to beta actin; p = 0.0008 Mann-Whitney) compared to young mice. These results support the hypothesis that advanced age worsens sepsis severity and outcomes and delays recovery, emphasizing the need for aged models and multi-organ evaluations to develop effective therapies for this vulnerable population.

physiology↗