Biology subjects

Min, S.

Publications and source records attributed to Min, S..

17 recordsLinked to original sources

bioRxiv2026

Ultrastructural and Proteomic Signatures of Mechanoadaptive Fibroblast Remodeling across Microphysiological and Mesoscale Shear Platforms

Mechanobiological cues in the tissue microenvironment increasingly drive pathological fibroblast activation in inflammatory bowel disease (IBD), yet engineered platforms modeling this transition remain limited. Here, a microfluidic gut-on-a-chip microphysiological system and a mesofluidic rotary shaker are used to demonstrate that sustained fluid shear stress alone is necessary and sufficient to drive an irreversible, profibrotic phenotypic switch in primary normal human intestinal fibroblasts. Across both platforms, normal fibroblasts from small and large intestine reproducibly self-organize into three-dimensional (3D) multicellular aggregates within 72 h, independent of shear delivery format, indicating that the transition is governed by mechanical dose rather than device geometry. The resulting aggregates acquire robust -smooth muscle actin (-SMA) expression with aligned stress fibers, contrasting with the -SMA-negative parental population. Scanning electron microscopy (SEM) resolves densely packed cellular microarchitecture embedded in a microfibrillar extracellular network, while ultrastructural serial block-face 3D EM reveals expansive intercellular spaces, stochastic fibrillar extrusions, and electron-dense cytoplasmic material at cell boundaries. Proteomic profiling confirms enrichment of core matrisome components, including collagen subtypes and matrix metalloproteinases. Together, these results establish fluid shear stress as a platform-independent, sufficient mechanical trigger for fibroblast-to-mechanoadaptive transition, positioning microphysiological shear platforms as tractable tools for modeling and targeting early fibrogenesis in IBD.

bioengineering↗

bioRxiv2026

A Centimeter-Scale, Peristaltic Human Intestinal Organoid with Integrated Neuro-Immune-Vascular Systems Recapitulates Enteritis and Orthotopic Colorectal Cancer

Human pluripotent stem cell-derived intestinal organoids hold great promise for disease modeling, drug screening, and regenerative medicine. However, conventional intestinal organoids are predominantly epithelial, small in scale, and lack the multicellular complexity required to recapitulate the pathophysiology of intestinal disorders such as inflammatory bowel disease (IBD) and colorectal cancer (CRC). Here, we report the development of Centimeter-Scale, purely 3D self-organized human intestinal organoids (IOs) from induced pluripotent stem cells (iPSCs) that encompass multiple tissue lineages, including epithelium, mesenchyme, smooth muscle, neurons, immune cells, and vasculature. These organoids achieve functional maturation by day 100+, exhibiting rhythmic peristaltic-like contractions, and by day 147 they display histological structures including lumens, crypt-like architecture, goblet cells, and smooth muscle. Importantly, for the first time, the neuro-muscle lineages arise spontaneously and autonomously in a purely 3D culture system, without any external stimulation (e.g., electrical, chemical, or mechanical), and mature to form functional neuromuscular junctions, driving macroscopically visible peristaltic-like contractions that mimic intestinal motility entirely through in vitro culture, without any xenotransplantation. Single-cell RNA sequencing at day 115 identified 12 cell subtypes across four major lineages, recapitulating the cellular diversity of the developing human intestine. Using this platform, we established an LPS/IFN-{gamma}-induced IBD model that recapitulated key pathological features, including epithelial disruption, immune cell infiltration, and IL-6 elevation. Transcriptomic analysis confirmed activation of the NF-{kappa}B and JAK2-STAT3 pathways, multi-modal cell death, and immune recruitment machinery, all consistent with clinical IBD pathology. Furthermore, we developed intestinal cancer models at 7 and 21 days showing abnormal hyperplasia, and a probiotic co-culture system demonstrating anti-inflammatory efficacy. Together, these results establish Centimeter-Scale intestinal organoids as a physiologically relevant, multicellular platform for modeling intestinal diseases and evaluating therapeutic interventions.

cell biology↗

bioRxiv2026

Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer

Single-cell proteomics (SCP) has emerged as a powerful approach for understanding cellular heterogeneity and biological processes at unprecedented resolution. However, the extremely limited protein content of individual cells (femtogram to picogram levels) pushes current mass spectrometry instrumentation to its sensitivity limits, creating a critical analytical bottleneck. While selected reaction monitoring (SRM) using triple quadrupole (QqQ) instruments offers advantages in sensitivity and reproducibility for targeted proteomics quantification, SRM still struggles with sensitivity for quantification of moderate- or low-abundance proteins from single-cell sample amounts. Here, we report the development and systematic evaluation of a dual ion funnel interface designed to address the sensitivity limitation by significantly enhancing ion transmission efficiency in commercial QqQ mass spectrometers. The dual ion funnel interface, composed of a curved S-funnel followed by a conventional ion funnel, improves ion transmission efficiency while reducing chemical noise through selective ion focusing. The performance of the dual ion funnel interface was systematically compared to standard interface on a TSQ Vantage platform across samples with different levels of complexity. The dual funnel interface demonstrated to provide up to 25-fold improvement in sensitivity across a wide range of protein concentrations in different biological matrices (low complex mouse macrophage and high complex human cells). Critically, enhanced sensitivity was accompanied by increased analytical reproducibility with lower coefficient of variations. Most importantly, the dual funnel interface enabled reliable quantification of low-abundance proteins that were barely detectable or not detected by the standard interface, extending analysis to single-cell equivalent amounts while maintaining excellent reproducibility. These results demonstrate that the dual funnel interface addresses the critical bottleneck in quantitative targeted proteomics, providing a technological foundation for ultrasensitive targeted SCP that requires both high sensitivity and robust quantitative performance.

biochemistry↗

bioRxiv2025

Vagal volume receptors in the heart compensate for blood loss and posture change

Cranial nerves densely innervate the heart and vasculature, with sensory neurons reporting on blood pressure, respiratory gases, and tissue damage1. The roles of arterial baroreceptors in systemic physiology are well appreciated2, but the functions of vagal cardiac mechanoreceptors have been more difficult to parse, in part due to the closed-loop structure of the cardiovascular system. Here, we use genetic tools for isolated study of vagal mechanoreceptors in the heart, finding that they are acutely sensitive to circulating blood volume and play key roles in compensating for decreased filling of the heart that occurs in an upright posture and during hemorrhage. Vagal PIEZO2 neurons form characteristic end-net endings in the heart and display blood volume-dependent responses with every heartbeat that are timelocked to atrial and ventricular systole. Vagal PIEZO2 knockout eliminates heartbeatcoupled nerve activity, and compromises carotid blood pressure when mice on a tilttable are rotated to an upright position. Vagal PIEZO2 knockout mice also display a lethal failure to sustain blood pressure during trauma-induced blood loss. Together, these findings demonstrate an essential function for vagal cardiac mechanoreceptors in sustaining the constancy of blood circulation.

neuroscience↗

bioRxiv2025

piRNAs safeguard splicing and RNA fidelity during heat shock

Piwi-interacting RNAs (piRNAs) silence transposons and foreign sequences; yet, for poorly understood reasons, they also extensively target endogenous mRNAs. Here, we demonstrate that this targeting preserves transcript isoform fidelity by regulating pre-mRNA splicing in C. elegans. Using the heat shock response to provoke rapid transcriptional changes, we found that piRNAs and PIWI/PRG-1 direct the production of endogenous antisense 22G-RNAs from newly induced transcripts. These endo-siRNAs associate with RNA Polymerase II, spliceosome protein MOG-7/C2orf3/Ntr2, and nascent RNAs to delay splice completion and regulate splice-site selection. Long-read transcriptome sequencing revealed that loss of piRNAs accelerates splice completion but compromises accurate splice-site selection, increasing the production of aberrant transcript isoforms that are normally eliminated by alternative splicing coupled to nonsense-mediated decay (AS-NMD). Consequently, piRNA pathway mutants are profoundly reliant on NMD for embryonic survival, development, and proteostasis maintenance. Together, our findings identify a previously unrecognized role for the piRNA pathway in coordinating splicing with RNA quality control to preserve proteome integrity. We propose that this unexpected role for the piRNA pathway may have evolved from its ancestral function in recognizing transposable elements, which frequently introduce cryptic splice sites and undergo exonization, to generate novel transcripts that require elimination by NMD.

cell biology↗

bioRxiv2025

Mechanostimulatory cues determine intestinal fibroblast fate and profibrotic remodeling in a physiodynamic human gut-on-a-chip

Biomechanical cues, including shear stress and mechanical strain, are key regulators of intestinal cellular behavior, yet their mechanostimulatory impact on fibroblasts responses during early fibrotic remodeling remains poorly understood. Using a bioengineered gut-on-a-chip model, we independently modulated flow and mechanical strain to assess fibroblast dynamics under intact or impaired epithelial barriers. Inflammation-associated fibroblasts resisted biomechanical stress, exhibiting myofibroblast-like phenotypes with hypertrophy and elevated -smooth muscle actin aligned with stress fibers. In contrast, normal fibroblasts were highly susceptible to shear stress, undergoing matrix metalloproteinase-dependent apoptotic injury, while mechanical strain alone had minimal effect. Notably, an intact epithelial barrier was both necessary and sufficient to protect fibroblasts from shear-induced damage, suggesting that "good fences make good neighbors". Under barrier dysfunction, prolonged exposure to shear stress induced the formation of stiff fibroblast aggregates composed of mechanoadaptive myofibroblast-like cells. These findings identify mechanostimulatory cues, particularly shear stress, as critical drivers of early fibrotic remodeling in inflammatory bowel disease and underscore epithelial barrier integrity as an essential biomechanical safeguard against pathological fibroblast dysregulation.

bioengineering↗

bioRxiv2024

A FRET-Based FLIM Method to Probe Membrane-Induced Alpha-Synuclein Aggregation in Neurons

1Parkinsons disease (PD) involves the aggregation of the protein alpha-synuclein, a process promoted by interactions with intracellular membranes. To study this phenomenon in neurons for the first time, we developed a fluorescence lifetime imaging (FLIM) method using Forster resonance energy transfer and self-quenching reporters, analyzed with a custom-built FLIM microscope. This method offers insights into aggregate formation in PD and can be broadly applied to probe protein-membrane interactions in neurons.

neuroscience↗

bioRxiv2024

Mechanisms of Alpha-Synuclein Seeded Aggregation in Neurons Revealed by Fluorescence Lifetime Imaging

1The brains of Parkinsons disease (PD) patients are characterized by the presence of Lewy body inclusions enriched with fibrillar forms of the presynaptic protein alpha-synuclein (aSyn). Despite related evidence that Lewy pathology spreads across different brain regions as the disease progresses, the underlying mechanism hence the fundamental cause of PD progression is unknown. The propagation of aSyn pathology is thought to potentially occur through the release of aSyn aggregates from diseased neurons, their uptake by neighboring healthy neurons via endocytosis, and subsequent seeding of native aSyn aggregation in the cytosol. A critical aspect of this process is believed to involve the escape of internalized ag-gregates from the endolysosomal compartment, though direct evidence of this mechanism in cultured neuron models remains lacking. In this study, we utilize a custom-built, time-gated fluorescence lifetime imaging microscope (FLIM) to investigate the progression of seeded ag-gregation over time in live cortical neurons. By establishing fluorescence lifetime sensitivity to aSyn aggregation level, we are able to monitor the proteins aggregation state. Through a FLIM analysis of neurons expressing aSyn-mVenus and exposed to aSyn preformed fibrils labeled with the acid-responsive dye pHrodo, we reveal the proteins aggregation state in both the cytosol and the endolysosomal compartment. The results indicate that aSyn seeds undergo partial disassembly prior to escaping the endocytic pathway, and that this escape is closely linked to the aggregation of cytosolic aSyn. In certain neurons, monomeric aSyn is found to translocate from the cytosol into the endolysosomal compartment, where it appar-ently forms aggregates in proximity to retained seeds. Additional analyses reveals zones of neuritic aSyn aggregates that overlaps with regions of microtubule disruption. Collectively, these findings enhance our understanding of aSyn pathology propagation in PD and other synucleinopathies, motivate additional experiments along these lines, and offer a path to guide the development of disease-modifying therapies.

neuroscience↗

bioRxiv2023

Effects of Neighboring Phosphorylation Events on the Affinities of pT181-Tau Antibodies

A tau variant phosphorylated on threonine 181 (pT181-tau) has been widely investigated as a potential Alzheimers disease (AD) biomarker in cerebrospinal fluid (CSF) and blood. pT181-tau is present in neurofibrillary tangles (NFTs) of AD brains, and CSF levels of pT181-tau correlate with overall NFT burden. Various immuno-based analytical methods, including Western blotting and ELISA, have been used to quantify pT181-tau in human biofluids. The reliability of these methods depends on the affinity and binding specificity of the antibodies used to measure pT181-tau levels. Although both of these properties could in principle be affected by phosphorylation within or near the antibodys cognate antigen, such effects have not been extensively studied. Here, we developed a biolayer interferometry assay to determine the degree to which the affinity of pT181-tau antibodies is altered by the phosphorylation of serine or threonine residues near the target epitope. Our results revealed that phosphorylation near T181 negatively affected the binding of pT181-tau antibodies to their cognate antigen to varying degrees. In particular, two of three antibodies tested showed a complete loss of affinity for the pT181 target when S184 or S185 was phosphorylated. These findings highlight the importance of selecting antibodies that have been thoroughly characterized in terms of affinity and binding specificity, addressing the potential disruptive effects of post-translational modifications in the epitope region, to ensure accurate biomarker quantitation.

neuroscience↗

bioRxiv2022

Sniper2L, a high-fidelity Cas9 variant with high activity

Although several high-fidelity SpCas9 variants that have reduced activities at mismatched target sequences have been reported, it has been observed that this increased specificity is associated with reduced on-target activity, limiting the applications of the high-fidelity variants when efficient genome editing is required. Here, we developed an improved version of Sniper-Cas9, Sniper2L, which represents an exception to this trade-off trend as it showed higher specificity with retained high activity. We evaluated Sniper2L activities at a large number of target sequences, and developed DeepSniper, a deep-learning model that can predict the activity of Sniper2L. We also confirmed that Sniper2L can induce highly efficient and specific editing at a large number of target sequences when it is delivered as a ribonucleoprotein complex. Mechanically, the high specificity of Sniper2L originates from its superior ability to avoid unwinding a target DNA containing even a single mismatch. We envision that Sniper2L will be useful when efficient and specific genome editing is required.

bioengineering↗

bioRxiv2022

Magneto-acoustic protein nanostructures for non-invasive imaging of tissue mechanics in vivo

Measuring cellular and tissue mechanics inside intact living organisms is essential for interrogating the roles of force in physiological and disease processes, and is a major goal in the field of mechanobiology. However, existing biosensors for 3D tissue mechanics, primarily based on fluorescent emissions and deformable materials, are limited for in vivo measurement due to the limited light penetration and poor material stability inside intact, living organisms. While magneto-motive ultrasound (MMUS), which uses superparamagnetic nanoparticles as imaging contrast agents, has emerged as a promising modality for real-time in vivo imaging of tissue mechanics, it has poor sensitivity and spatiotemporal resolution. To overcome these limitations, we introduce magneto-gas vesicles (MGVs), a unique class of protein nanostructures based on gas vesicles and magnetic nanoparticles that produces differential ultrasound signals in response to varying mechanical properties of surrounding tissues. These hybrid protein nanostructures significantly improve signal strength and detection sensitivity. Furthermore, MGVs enable non-invasive, long-term, and quantitative measurement of mechanical properties within 3D tissues and organs in vivo. We demonstrated the performance of MGV-based mechano-sensors in vitro, in fibrosis models of organoids, and in vivo in mouse liver fibrosis models.

biochemistry↗

bioRxiv2022

Genomic analysis of population structure, antimicrobial resistance, and virulent factors of methicillin-resistant Macrococcus caseolyticus in global lineages

Macrococcus caseolyticus is an opportunistic pathogen frequently detected in dairy products as well as veterinary infections. The present study examined the population structure, antimicrobial resistance, and virulent factors of methicillin-resistant M. caseolyticus isolates in retail meat from Shanghai (n=10) and global isolates from GenBank (n=87). All strains were divided into five lineages that distributed in Europe (82.4%, n = 80), Asia (11.3%, n = 11), North America (4.1%, n = 4), Oceania (1%, n = 1) and Africa (1%, n = 1). MLST typing revealed novel alleles in Chinese M. caseolyticus strains. Furthermore, a total of 24 AMR genes associated with 10 classes of antimicrobial agents were identified in the isolates from global lineages, carried by dominant plasmids such as rep7a, rep22 and repUS56. Comparing to other lineages, genomes from the Chinese lineage carried significantly more AMR genes (p<0.005) and less virulent factors (p<0.001), which may be explained by the local evolution of M. caseolyticus in China. Finally, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were enrolled for morphology comparison between M. caseolyticus and S. aureus, showing that M. caseolyticus has a larger diameter and thicker cell wall. The present study showed geographical variation with regards to MLST profiles, antimicrobial resistance, and virulent factors in global M. caseolyticus lineages. This study suggests that such local evolution of foodborne or livestock origin M. caseolyticus may serve as vehicles for domestic transmission of methicillin resistance in retail meat in China. HighlightsO_LIGlobal M. caseolyticus strains were divided into five lineages from A to E. C_LIO_LIMLST typing revealed novel alleles in Chinese M. caseolyticus strains. C_LIO_LIChinese lineage carried significantly more AMR genes and less virulent factors. C_LIO_LIMacrococcus caseolyticus has a larger diameter and thicker cell wall compared with S.aureus. C_LIO_LIMacrococcus caseolyticus may enhance the domestic transmission of methicillin resistance in China. C_LI

microbiology↗

bioRxiv2021

Nerve-mediated amputation-induced stem cell activation primes distant appendages for future regeneration events in axolotl

Many species regenerate lost body parts following amputation. Most limb regeneration research has focused on the immediate injury site. Meanwhile, body-wide injury responses remain largely unexplored but may be critical for regeneration. Here, we discovered a role for the sympathetic nervous system in stimulating a body-wide stem cell activation response to amputation that drives enhanced limb regeneration in axolotls. This response is mediated by adrenergic signaling, which coordinates distant cellular activation responses via the 2A-adrenergic receptor, and local regeneration responses via {beta}-adrenergic receptors. Both 2A- and {beta}-adrenergic signaling act upstream of mTOR signaling. Notably, systemically-activated axolotls regenerate limbs faster than naive animals, suggesting a potential selective advantage in environments where injury from cannibalism or predation is common. This work challenges the predominant view that cellular responses underlying regeneration are confined to the injury site and argues instead for body-wide cellular priming as a foundational step that enables localized tissue regrowth.

developmental biology↗

bioRxiv2021

Germline activity of the heat shock factor HSF-1 programs the insulin-receptor daf-2 in C. elegans

The mechanisms by which maternal stress alters offspring phenotypes remain poorly understood. Here we report that the heat shock transcription factor HSF-1, activated in the C. elegans maternal germline upon stress, epigenetically programs the insulin-like receptor daf-2 by increasing repressive H3K9me2 levels throughout the daf-2 gene. This increase occurs by the recruitment of the C. elegans SETDB1 homolog MET-2 by HSF-1. Increased H3K9me2 levels at daf-2 persist in offspring to downregulate daf-2, activate the C. elegans FOXO ortholog DAF-16 and enhance offspring stress resilience. Thus, HSF-1 activity in the mother promotes the early life programming of the insulin/IGF-1 signaling (IIS) pathway and determines the strategy of stress resilience in progeny. One Sentence SummaryHSF-1 recruits MET-2 to silence daf-2 and mediate early life programming of C. elegans upon stress

cell biology↗

bioRxiv2020

Control of feeding by Piezo-mediated gut mechanosensation in Drosophila

Across animal species, meals are terminated after ingestion of large food volumes, yet underlying mechanosensory receptors have so far remained elusive. Here, we identify an essential role for Drosophila Piezo in volume-based control of meal size. We discover a rare population of fly neurons that express Piezo, innervate the anterior gut and crop (a food reservoir organ), and respond to tissue distension in a Piezo-dependent manner. Activating Piezo neurons decreases appetite, while Piezo knockout and Piezo neuron silencing cause gut bloating and increase both food consumption and body weight. These studies reveal that disrupting gut distension receptors changes feeding patterns, and identify a key role for Drosophila Piezo in internal organ mechanosensation.

neuroscience↗

bioRxiv2019

Neural correlates of episodic memory modulated by temporally delayed rewards

When a stimulus is associated with an external reward, its chance of being consolidated into long-term memory is boosted via dopaminergic facilitation of long-term potentiation in the hippocampus. Given that higher temporal distance (TD) has been found to discount the subjective value of a reward, we hypothesized that memory performance associated with a more immediate reward will result in better memory performance. We tested this hypothesis by measuring both behavioral memory performance and brain activation using functional magnetic resonance imaging (fMRI) during memory encoding and retrieval tasks. Contrary to our hypothesis, both behavioral and fMRI results suggest that the TD of rewards might enhance the chance of the associated stimulus being remembered. The fMRI data demonstrate that the lateral prefrontal cortex, which shows encoding-related activation proportional to the TD, is reactivated when searching for regions that show activation proportional to the TD during retrieval. This is not surprising given that this region is not only activated to discriminate between future vs. immediate rewards, it is also a part of the retrieval-success network. These results provide support for the conclusion that the encoding-retrieval overlap provoked as the rewards are more delayed lead to better memory performance of the items associated with the rewards.

neuroscience↗

bioRxiv2019

SpCas9 activity prediction by DeepCas9, a deep learning-based model with unparalleled generalization performance

We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing sgRNA-encoding and target sequence pairs. Deep learning-based training on this large data set of SpCas9-induced indel frequencies led to the development of a SpCas9-activity predicting model named DeepSpCas9. When tested against independently generated data sets (our own and those published by other groups), DeepSpCas9 showed unprecedentedly high generalization performance. DeepSpCas9 is available at http://deepcrispr.info/DeepCas9.

genetics↗