Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 775 records · Page 43Linked to original sources

bioRxiv2025

Modulating Hydrogel Stiffness Through Light-Based 3D Printing to Mimic Cardiac Fibrosis and Cardiomyocyte Dysfunction Using hiPSC-Derived Cells

The human hearts limited regenerative capacity is a significant barrier to addressing cardiovascular disease (CVD). This is particularly true for cardiac fibrosis, a form of CVD wherein the wound healing process has gone awry. In cardiac fibrosis, excessive scar tissue formation due to dysregulated remodeling of the hearts extracellular matrix (ECM) results in increased stiffness that reduces cardiac output and can lead to heart failure. This dysregulated ECM deposition is driven by activated cardiac fibroblasts, where cell substrate stiffness is known to play a role in cardiac fibroblast activation. New preclinical models that accurately recapitulate the behavior of activated cardiac fibroblasts are needed to better understand and treat cardiac fibrosis. To this end, we describe a model wherein human induced pluripotent stem cell (hiPSC)-derived cardiac fibroblasts (HCFs) are cultured on 3D printed hydrogels of tunable stiffness, fabricated using dosage controlled digital light processing (DLP). We demonstrate that our model can induce HCF activation in the absence of TGF{beta}, a key mediator of fibroblast activation, surpassing the activation levels seen with HCFs activated with TGF{beta} on protein-coated tissue culture plates. Furthermore, combining stiffer hydrogels with TGF{beta} recapitulates fibroblast activation similar to what is observed in native cardiac tissue. Lastly, by indirectly coculturing HCFs seeded and activated on these stiff hydrogels with hiPSC-derived cardiomyocytes, we demonstrate that the activated HCFs in our cardiac fibrosis model can impair cardiomyocyte function, mimicking the deleterious effects of cardiac fibrosis.

bioengineering↗

bioRxiv2025

Fat-rich diet reprograms intrapulmonary neutrophils to boost tissue-specific antitumor immunity

Neutrophils adapt to tissue-specific signals and exert innate defense functions against infections and malignancies. Fat-rich diet (FRD), such as high-fat diet (HFD) and ketogenic diet (KD), has complex impacts on immunity. However, whether and how FRD shapes tissue-specific functions of neutrophils remain unclear. Here we show that both isocaloric HFD- and KD-fed mice demonstrate enhanced neutrophil-mediated pulmonary tumor resistance than chow diet-fed mice. Intrapulmonary but not systemic neutrophils in FRD-fed mice bear enhanced potential of reactive oxygen species (ROS) production and ROS-dependent tumor cytotoxicity. Mechanistically, FRD-induced increased serum saturated fatty acids and cholesterol stimulate lung vascular endothelial cells (LVECs), which reprogram intrapulmonary neutrophils via contact- and intercellular adhesion molecule-1 (ICAM-1)-dependent mechanisms. Analysis on human lung single-cell RNA sequencing data showed that intensified cell adhesion and priming signals from human LVECs are associated with enhanced antitumor functions in intrapulmonary neutrophils. Our findings highlight the roles of dietary fats in shaping neutrophil functions in a tissue-specific manner. Dietary intervention targeting tissue-specific reprogramming of neutrophils therefore represents a potential strategy against malignancies in the lungs.

immunology↗

bioRxiv2025

Comparative proteomic analysis of skin wound healing responses to biomaterial treatments identifies key pathways which govern differential regenerative outcomes

The wound healing cascade is characterized by the steady progression of distinct stages. Though biomaterials are used clinically to enhance wound closure rate and quality of healed tissue, their mechanisms of action are less understood. Here we use proteomic analysis to characterize changes in the wound healing response across three biomaterial treatments: a clinically used collagen hydrogel, and two synthetic biomaterials that are characterized by an increased regenerative response either through decreased fibrosis or through an activation of adaptive immunity. We identified close to 5,000 proteins shared across the biomaterial treatment groups, sampled at timepoints representing the inflammation, proliferation, and resolution phases of wound healing. The collagen hydrogel maintains an enrichment of immune-related pathways throughout the healing process. The fibrosis-suppressing material enriches gene ontology (GO) terms related to increased epidermis development pathways, collagen synthesis, and collagen fibril organization. In contrast, the adaptive immunity-activating biomaterial shows an early enrichment of GO terms related to broad immunity and inflammation. Later, this same material promotes keratinization, muscle and lipid oxidation GO pathways. Taken together, this work determines the key temporal pathways (immunity, keratinization, muscle system process, and ECM organization) mediated by three biomaterials, which result in varying healed tissue structure.

bioengineering↗

bioRxiv2025

Molecular Basis of Sodium Channel Inactivation

Voltage-gated sodium channels initiate action potentials and control electrical signaling throughout the animal kingdom. Fast inactivation is an essential auto-inhibitory mechanism and requisite component of sodium channel physiology. Recent structural and electrophysiological results are inconsistent with the canonical "ball and chain" model of fast inactivation thus necessitating an updated theoretical framework. Here, we use encoded fluorescence spectroscopy and high-resolution electrophysiology to capture key steps in the fast inactivation mechanism, from voltage-sensor activation to pore occlusion, an ultra-fast process which occurs in less than 2 milliseconds. Upon depolarization, activation of the domain IV voltage sensor initiates cytoplasmic DIII_DIV linker movement and quickly repositions the IFM motif into a hydrophobic pocket adjacent to the pore. This triggers a structural rearrangement of the pocket. The phenylalanine of the IFM motif contacts the pore-forming helices via a hydrophobic interaction with S6 of DIV and an aromatic/hydrophobic interaction with S6 of DIIII. These two interactions occur only after both S6 segments rotate, thus exposing the hydrophobic gate into the pore producing the fast inactivation. Based on the current results, we propose an alternative "lock and key" model to explain the molecular mechanism of fast inactivation.

biophysics↗

bioRxiv2025

Guided Co-clustering Transfer Across Unpaired and Paired Single-cell Multi-omics Data

Single-cell multi-omics technologies enable the simultaneous profiling of gene expression and chromatin accessibility, providing complementary insights into cellular identity and gene regulatory mechanisms. However, integrating paired scRNA-seq and scATAC-seq data remains challenging due to inherent sparsity, technical noise, and the limited availability of high-quality paired measurements. In contrast, large-scale unpaired scRNA-seq datasets often exhibit robust and biologically meaningful cell cluster structures. We introduce Guided Co-clustering Transfer (GuidedCoC), a novel unsupervised framework that transfers structural knowledge from unpaired scRNA-seq source data to improve both cell clustering and feature alignment in paired scRNA-seq/scATAC-seq target data. GuidedCoC jointly co-clusters cells and features across modalities and domains via a unified information-theoretic objective, aligning gene expression modules with regulatory elements while implicitly performing cross-modal dimensionality reduction to reduce noise. Additionally, it automatically aligns cell types across unpaired and paired datasets without requiring explicit annotations. Extensive experiments on multiple benchmark datasets demonstrate that GuidedCoC achieves superior clustering accuracy and biological interpretability compared to existing methods. These results highlight the promise of structure-guided, unsupervised transfer learning for robust, scalable, and interpretable integration of single-cell multi-omics data. Code is available at https://github.com/No-AgCl/GuidedCoC.

bioinformatics↗

bioRxiv2025

Quantifying ecosystem degradation via energetic deficits

Ecosystem degradation is accelerating, threatening biodiversity and human economies. Quantifying this degradation relative to a reference baseline remains a key challenge. Yet, this quantification is essential to provide the necessary resources to regenerate ecosystems. We address this challenge by studying the energetics of population dynamics, where energy inputs such as sunlight and rainfall are transformed into other forms of energy embodied as biomass. This approach provides a unifying framework to quantify degradation across diverse ecosystems via the energetic ecodeficit: the extra energy supply the degraded ecosystem would require to regenerate to a reference state. This energetic deficit can then be translated into a monetary ecodeficit, representing the economic cost of regeneration, considering the local cost of embodied energy. Our analysis reveals nonlinear relationships between biomass loss and energetic ecodeficit, including points of no return beyond which restoration becomes economically infeasible. We showcase our methodology using the current mammal deficits across the African savanna, finding that the monetary ecodefict is about 100 times larger than current estimates. Our work demonstrates how integrating energetic principles into conservation planning can transform ecosystem valuation globally, linking ecosystems and economies sustainably.

ecology↗

bioRxiv2025

Tomosyn-2 Regulates Postnatal β-Cell Expansion and Insulin Secretion to Maintain Glucose Homeostasis.

The transition from proliferative to functionally mature {beta}-cells is a critical developmental process, yet the molecular mechanisms that coordinate this shift remain poorly understood. Here, we identify Tomosyn-2 as a key regulator of {beta}-cell maturation. Tomosyn-2 expression declines with age in mouse islets, coinciding with enhanced biphasic glucose-stimulated insulin secretion (GSIS) and reduced {beta}-cell proliferation. Genetic deletion of Tomosyn-2 improves glucose tolerance, elevates plasma insulin levels, and augments islet insulin secretion, without altering systemic insulin sensitivity. Mechanistically, Tomosyn-2 interacts with syntaxin-1A (Stx1A) to inhibit insulin granule exocytosis by limiting SNARE complex formation. Transcriptomic and network analyses reveal that Tomosyn-2 loss reprograms gene expression to strengthen the coupling between insulin secretion and proliferative pathways. Its deletion also reduces {beta}-cell proliferation and mass expansion, suppresses cell cycle and Akt1 signaling, and promotes {beta}-cell identity, maturation, and altered islet architecture. These findings identify Tomosyn-2 as a crucial molecular switch that orchestrates the balance between proliferation and functional maturation during postnatal {beta}-cell development.

cell biology↗

bioRxiv2025

Molecular mechanisms regulating PDE11A4 age-related liquid-liquid phase separation (LLPS) and its reversal by selective, potent and orally-available PDE11A4 small molecule inhibitors both in vitro and in vivo

PDE11A is a little-studied phosphodiesterase family that breaks down cAMP and cGMP, with the PDE11A4 isoform enriched in the memory-related hippocampus. Age-related increases in hippocampal PDE11A expression occur in human and rodents, causing age-related cognitive decline of social memories. Interestingly, this age-related increase triggers PDE11A4 liquid-liquid phase separation (LLPS), causing the enzyme to accumulate in the brain in filamentous structures termed "ghost axons". Here we sought to identify molecular mechanisms regulating PDE11A4 LLPS and therapeutic approaches capable of reversing it. PDE11A4 LLPS was reduced by phosphorylation of PDE11A4-S163 or-S239 and the D355A mutation that blocks the effect of cGMP binding the PDE11A4 GAF-A domain. PDE11A4 LLPS was increased by inhibiting kinases with staurosporine or stimulating packaging/repacking via the trans-Golgi network by overexpressing TGN38 or RhoB. 8 PDE11 inhibitors (MLG-122, MLG-185, MLG-199, SMQ-02-57, SMQ-03-30, SMQ-03-20, tadalafil, and BC11-38) across 3 scaffolds reverse overexpression-related PDE11A4 LLPS in HT22 mouse hippocampal neuronal cells. This effect of PDE11A4 inhibitors occurs within minutes, is reversed upon washout of lower but not higher concentrations, and occurs in part by reducing PDE11A4 homodimerization. PDE11A4 inhibitors also rescued exacerbated PDE11A4 LLPS triggered by aging-like S117D/S124D phosphomimic mutations, staurosporine, or TGN38/RhoB overexpression. In vivo, orally-administered 30mg/kg SMQ-03-20 reversed age-related increases in PDE11A4 ghost axons and neuroinflammation in old mice. Thus, PDE11A inhibitors that reverse age-related PDE11A4 LLPS in HT22 hippocampal cells also reduce PDE11A4 ghost axons and neuroinflammation in the aged mouse brain, indicating therapeutical potential.

neuroscience↗

bioRxiv2025

AF3Score: A Score-Only Adaptation of AlphaFold3 for Biomolecular Structure Evaluation

Scoring biomolecular complexes remains central to structural modeling efforts. Recent studies suggest that AlphaFold (AF) - a revolutionary deep learning model for biomolecular structure prediction - has implicitly learned an approximate biophysical energy function. While many researchers highly rely on AF-derived scores for structure evaluation, existing AlphaFold2-based implementations require iterative refinement of the input structure, leading to biased scoring. To address this limitation, we adapted AlphaFold3 into a score-only model, AF3Score, by directly feeding input coordinates into the confidence head while bypassing the diffusion-based structure module. AF3Score demonstrates robust performance in structural quality assessment across diverse systems including monomeric proteins, protein-protein complexes, de novo designed binders, and fold-switching proteins. In benchmarking designed binder screening, AF3Score outperformed state-of-the-art methods for 8 out of 10 targets. Moreover, combining AF3Score with AlphaFold2-derived methods significantly improved the enrichment of experimentally validated binders, increasing the success rate from 15.2% to 31.6%. Additionally, AF3Score effectively identified stable conformations in fold-switching proteins, whereas AlphaFold predominantly predicted only the dominant fold. These findings highlight the broad applicability of AF3Score, from high-throughput screening in de novo binder design to filtering docking-generated poses and molecular dynamics (MD) trajectories.

bioinformatics↗

bioRxiv2025

Isoform-Specific Roles of NTRK2 in Pulmonary Vascular Regeneration

Bronchopulmonary dysplasia (BPD) is a chronic lung disease in premature infants with no curative therapy, characterized by impaired alveologenesis and capillary formation. However, the molecular mechanisms underlying endothelial dysfunction, a key driver of BPD pathogenesis in human, remain poorly understood. Here, through multiomic profiling of vascular endothelial cells isolated from control and BPD patient lungs, we uncovered an expansion of general capillary endothelial cells (gCap) with aberrant expression of the neurotrophic receptor tyrosine kinase 2 (NTRK2) in BPD. Importantly, we identified a pathological NTRK2 isoform switch that dictates the regenerative capacity of gCap cells. Full-length NTRK2 (NTRK2-FL) promoted gCap regeneration in response to hyperoxic injury, whereas RBFOX2-mediated splicing of NTRK2-FL into a truncated isoform (NTRK2-T1) contributed to maladaptive responses and irreversible alveolar simplification in severe BPD cases. Restoring NTRK2-FL using lipid nanoparticle-delivered mRNA promoted angiogenesis and reversed alveolar simplification in vessel organoids and BPD-like mice. These findings identified NTRK2 isoform imbalance as a key driver of endothelial dysfunction and support isoform-specific RNA therapy as a promising strategy for vascular regeneration and repair. HIGHLIGHTS* Multiomic and spatial profiling reveal abnormal gCap subtype in human BPD lungs * NTRK2 isoform switch dictates endothelial regeneration in response to hyperoxic injury * RBFOX2 mediates splicing from NTRK2-FL to NTRK2-T1, driving irreversible alveolar damage * NTRK2-FL mRNA therapy restores vascular regeneration after injury

developmental biology↗

bioRxiv2025

TidyMass2: Advancing LC-MS Untargeted Metabolomics Through Metabolite Origin Inference and Metabolic Feature-based Functional Module Analysis

Untargeted metabolomics provides a direct window into biochemical activities but faces critical challenges in determining metabolite origins and interpreting unannotated metabolic features. Here, we present TidyMass2, an enhanced computational framework for Liquid Chromatography-Mass Spectrometry (LC-MS) untargeted metabolomics that addresses these limitations. TidyMass2 introduces three major innovations compared its predecessor, TidyMass: (1) a comprehensive metabolite origin inference capability that traces metabolites to human, microbial, dietary, pharmaceutical, and environmental sources through integration of 11 metabolite databases containing 532,488 metabolites with source information; (2) a metabolic feature-based functional module analysis approach that bypasses the annotation bottleneck by leveraging metabolic network topology to extract biological insights from unannotated metabolic features; and (3) an intuitive graphical interface that makes advanced metabolomics analyses accessible to researchers without programming expertise. Applied to longitudinal urine metabolomics data from human pregnancy, TidyMass2 identified diverse metabolites originating from human, microbiome, and environment, and uncovered 27 dysregulated metabolic modules. It increased the proportion of biologically interpretable metabolic features from 5.8% to 58.8%, revealing coordinated changes in steroid hormone biosynthesis, carbohydrate metabolism, and amino acid processing. By expanding biological interpretation beyond conventionally MS2 spectra-based annotated metabolites, TidyMass2 enables more comprehensive metabolic phenotyping while upholding strict open-source principles of reproducibility, traceability, and transparency.

bioinformatics↗

bioRxiv2025

Lactate metabolism antagonizes antiviral innate immunity bypromoting VDAC1-lactylation-mediated mtDNA release

Foot-and-mouth disease (FMD) is an acute, highly contagious disease caused by the foot-and-mouth disease virus (FMDV). Due to its zoonotic nature, this disease not only significantly impacts livestock productivity but also poses a serious threat to human health. FMDV exhibits distinct host specificity, mainly infecting cloven-hoofed animals such as cattle, sheep, pigs, and deer, while perissodactyl animals like horses and donkeys show natural resistance. Elucidating the interspecies differences in response to FMDV infection is essential for understanding the pathogenesis of the virus. In this study, we report that FMDV infection in horse epithelial cells induces the production of lactate, which modulates the function of VDAC1 protein through lactylation, facilitating the release of mtDNA from mitochondria into the cytoplasm. This process activates the cGAS-STING signaling pathway, which stimulates interferon-{beta} expression and suppresses FMDV replication. Our findings provide new insights into the mechanism behind horse resistance to FMDV and lay a theoretical foundation for further research concerning the differential pathogenesis of FMDV infection across species.

cell biology↗

bioRxiv2025

VAMP5 is a novel target for selective inhibition of gliomas with high NDRG4 expression via downregulating PLK1 and beyond

BackgroundSNAREs participate in cancers progression or stress resistance. But the current conclusions on their involvement in cancers are generally unsystematic and even contradictory on one SNAREs roles in different types of cancer. Its necessary to find universal mechanisms of SNAREs participation in cancers possessing generalizability within appropriate range for application of targeted therapy. MethodsOur study initiated with database analysis on clinical information and bulk RNA-seq data to locate potential effective target for certain cancer type. Then experiment validations/explorations were performed on clinical human sections, cell lines and xenograft models. Lentivirus (LV) were applied for gene KD, overexpression and microRNAs sponge; Bulk RNA-seq, microRNA-seq and DIA proteomics for identification, quantification, genesets/target analysis; WB, single-IF, TSA (Tyramide signal amplification) multi-IF, IHC for proteins detection using antibodies; QPCR for artificial microRNA-sponge sequences test; Other reagents/instruments applied for corresponding purposes. ResultsVAMP5 is a therapeutic target for gliomas with expression selectivity. Gliomas could be divided into 2 types according to effects after VAMP5 KD. In VAMP5-KD sensitive type, PLK1, a classical gene vital for tumor growth/survival, is universally protein-level down-regulated that mediated partly via decrease of several up-reg microRNAs like mir-1301-3p and mir-12135, causing growth inhibition. While among insensitive type that VAMP5-KD is invalid for growth inhibition, PLK1 is not altered consistently, which serves as an evaluation marker for inhibition effectiveness. NDRG4 is a prediction marker for VAMP5-KD sensitivity that sensitive gliomas express higher NDRG4 than insensitive type on RNA level. Moreover, NDRG4 overexpression converts VAMP5-KD insensitive gliomas into sensitive type and additionally cause protein-level downregulation of VCAM1 and especially TNKS which also benefit the growth inhibition and PLK1 reduction partly. Except for results above, LGALS1 correlated and colocalized with VAMP5 possessing broader consistency than other membrane proteins so indicates the immune-enhancing potential of down-reg LGALS1 via KD VAMP5. ConclusionsThese discoveries elucidated the mechanism of VAMP5 KD on gliomas inhibition preliminarily. New sights for glioma therapies including selective therapeutic target, prediction marker, evaluation marker, enhancing strategy and correlated immuno-checkpoint markers were concluded with further development potentials.

cancer biology↗

bioRxiv2025

Transcriptional Subtypes on Immune Microenvironment and Predicting Postoperative Recurrence and Metastasis in Pheochromocytoma and Paraganglioma

Pheochromocytomas and paragangliomas (PPGLs) exhibit substantial molecular and immune heterogeneity, complicating risk assessment and treatment. Here, we define three distinct transcriptional subtypes (C1, C2, C3) through integrative transcriptomic and immunogenomic profiling. C1 is characterized by hypoxia-driven pathways and an immunosuppressive microenvironment, correlating with poor prognosis. C2 exhibits a highly inflamed immune landscape with robust CD8+ T cell infiltration, suggesting potential sensitivity to immunotherapy. C3 is enriched in metabolic reprogramming pathways and displays intermediate clinical outcomes. Genetic analysis reveals subtype-specific mutational patterns, with pseudohypoxic driver mutations (SDHB, VHL, SDHA, SDHD) predominant in C1 and C3, while kinase pathway alterations (NF1, RET) define C2. Single-nucleus RNA sequencing further delineates immune ecosystem diversity. Notably, we identify ANGPT2, PCSK1N, and GPX3 as key subtype-specific biomarkers, with ANGPT2 driving tumor progression in C1 and emerging as a potential therapeutic target. Our findings provide a refined molecular classification integrating immune and genomic features, offering a framework for improved prognostication and precision therapies in PPGLs.

cancer biology↗

bioRxiv2025

Neural organoids protect engineered heart tissues from glucolipotoxicity by transferring versican in a co-culture system

Metabolic disorders could cause dysregulated glucose and lipid at the systemic level, but how inter-tissue/organ communications contribute to glucolipotoxicity is difficult to dissect in animal models. To solve this problem, myocardium and nerve tissues were modeled by 3D engineered heart tissues (EHTs) and neural organoids (NOs), which were co-cultured in a generalized medium with normal or elevated glucose/fatty acid contents. Morphology, gene expression, cell death and functional assessments detected no apparent alterations of EHTs and NOs in co-culture under normal conditions. By contrast, NOs significantly ameliorated glucolipotoxicity in EHTs. Transcriptomic and protein secretion assays identified the extracellular matrix protein versican as a key molecule that was transferred from NOs into EHTs in the high-glucose/fatty acid condition. Recombinant versican protein treatment was sufficient to reduce glucolipotoxicity in EHTs. Adeno-associated virus-delivered versican overexpression was sufficient to ameliorate cardiac dysfunction in a murine model of diabetic cardiomyopathy. These data provide the proof-of-concept evidence that inter-tissue/organ communications exist in the co-culture of engineered tissues and organoids, which could be systemically studied to explore potential pathological mechanisms and therapeutic strategies for multi-organ diseases in vitro.

cell biology↗

bioRxiv2025

Structural features within precursor microRNA-20a regulate Dicer-TRBP processing

MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression of target messenger (m) RNAs. To maintain proper miRNA expression levels, the enzymatic processing of primary and precursor miRNA elements must be strictly controlled. However, the molecular determinants underlying this strict regulation of miRNA biogenesis are not fully understood. Here, we determined the solution structure of pre-miR-20a, an oncogenic miRNA and component of the oncomiR-1 cluster, using nuclear magnetic spectroscopy (NMR) spectroscopy and small angle X-ray scattering (SAXS). Our structural studies informed on key secondary structure elements of pre-miR-20a which may control its enzymatic processing, namely a flexible apical loop and single-nucleotide bulge near the dicing site. We found that alternative conformations within pre-miR-20as apical loop function to self-regulate its Dicer-TRBP processing, and that a single nucleotide bulge at the -5 position from the 5'-cleavage site is critical for efficient processing. We additionally found that a disease-related single-nucleotide polymorphism in pre-miR-20a, predicted to disrupt the structure near the dicing site, resulted in reduced processing. These results further our structural understanding of the oncomiR-1 cluster and show how transient RNA conformers can function to self-regulate maturation.

biochemistry↗

bioRxiv2025

Measuring neurofilament light in human plasma and cerebrospinal fluid: a comparison of five analytical immunoassays

ObjectivesNeurofilament light (NfL) is an established biofluid marker of neuroaxonal injury for neurological diseases. Several high-throughput and sensitive immunoassays have been developed to quantify NfL in blood and cerebrospinal fluid (CSF), facilitating the use of NfL as a biomarker in research and clinical practice. However, because of the lack of rigorous comparisons of assays, it has been difficult to determine whether data are comparable and whether assay performance differs. Here, we compared the performance of five NfL immunoassays. MethodsTo assess the five NfL immunoassays (Fujirebio, ProteinSimple, Quanterix, Roche and Siemens), we used pooled plasma or pooled CSF, as well as unique samples from 20 healthy controls and 20 individuals with El Escorial defined probable or definite amyotrophic lateral sclerosis (ALS), to evaluate precision, parallelism and/or bias. We also examined correlations between plasma and CSF NfL concentrations within and across assays and evaluated their ability to differentiate healthy controls from individuals with ALS. ResultsFour of the five assays demonstrated exemplary performance based on our analyses of precision and parallelism. Across the five assays, NfL concentrations were lower in plasma than in CSF, although they displayed a high degree of correlation. We noted bias across assays; plasma NfL concentrations were lowest for the Roche assay and highest for the ProteinSimple assay. In addition, all assays reliably distinguished healthy controls from individuals with ALS using plasma or CSF NfL. ConclusionsFour NfL assays demonstrated similar analytic performance. Alongside performance, other factors such as costs, accessibility, useability, footprint, and intended use, should be considered.

neuroscience↗

bioRxiv2025

High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform

We present a multiomics platform comprising Teton, a detection assay system, and AVITI24, a dual-flowcell instrument that performs both cellular imaging and sequencing readout. Teton integrates a compartmentalized flowcell for cell culture with methods to measure morphology, RNA, and protein at subcellular resolution. The platform quantifies morphological features through cell painting of 6 cellular components, RNA expression of up to 350 transcripts via sequencing of oligonucleotides hybridized to mRNA, and protein expression of up to 200 targets using antibody-linked oligonucleotide sequencing. The flow cell accommodates >1 million cells in a 10 cm squared open-well format or can be subdivided into 12 or 48 wells to support experiments with multiple conditions or time points. We describe and validate the detection methods of the platform and showcase its capabilities by co-culturing three cancer cell lines and elucidating the cellular pathways triggered by various drug treatments as a function of time. Using multiple time points enables us to capture the dynamics of cellular processes including receptor activation and signaling cascades. The results demonstrate how different cancer cells evade TNF-induced apoptosis by activating compensatory signaling programs that maintain survival despite pro-apoptotic cues. Our model system replicates previously published results and highlights the versatility of the platform in enabling rapid, high-throughput analysis of complex cellular responses in varied biological contexts.

genomics↗