Biology subjects

Lee, S.

Publications and source records attributed to Lee, S..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

Ultrasound imaging of in situ transcriptional activity in opaque tissue

Ultrasound imaging and acoustic reporter genes provide unique capabilities for in vivo biological imaging by leveraging ultrasounds ability to visualize opaque tissues with high spatiotemporal resolution. But until now, the expression of acoustic reporter genes - based on gas vesicle (GV) proteins - has been limited to ex vivo-modified cells due to the complexity of the GV gene cluster, precluding valuable in situ applications. Here, we develop a system capable of introducing GV genes directly into native tissues via stoichiometric multi-AAV delivery. We validate this system in the mouse brain, demonstrating well-tolerated in situ gene expression and repeated ultrasound imaging over more than a month in the same animal. Furthermore, by placing GV genes under the control of immediate early gene promoters, we demonstrate the ability to track in vivo gene expression changes arising from elevated neural activity during epileptic seizures. This work connects ultrasound to in situ transcriptional dynamics happening inside the opaque tissues of living creatures.

bioengineering↗

bioRxiv2025

Hypoosmolarity inhibits archaeal ammonia oxidation

Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity on them remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and lake environments, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels ([~]120 S/cm), comparable to values commonly found in pristine terrestrial and aquatic environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by Nitrosomonas oligotropha, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by "Ca. Nitrosotenuis" of the Nitrosopumilaceae family, was stimulated by high salinity ([~]760 S/cm). In ammonium-fed lake microcosms, the abundance of AOB, dominated by N. oligotropha, significantly increased under both low ([~]170 S/cm) and high salinity ([~]850 S/cm) conditions. In the presence of allylthiourea, a bacterial nitrification inhibitor, AOA were sensitive to low salinity in both soil and lake microcosms. Consistently, pure culture studies revealed marked growth inhibition of AOA, especially members of Nitrosopumilaceae, under hypoosmolarity, unlike AOB and complete ammonia oxidizer (comammox) strains. Comparative genomic analyses with AOB and comammox, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress was possibly due to a lack of sophisticated osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study highlights hypoosmolarity as a key factor shaping the ecological niches and distribution of ammonia oxidizers, as well as nitrification activities, in terrestrial and aquatic environments that are increasingly affected by intensified water cycles due to climate change.

microbiology↗

bioRxiv2025

PathCLAST: Pathway-Augmented Contrastive Learning with Attention for Spatial Transcriptomics

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSSpatial transcriptomics provides high-resolution insights into tissue architecture and disease progression. While recent computational methods have advanced spatial domain identification, many focus primarily on gene expression alone, which may limit biological interpretability and underexploit complementary data such as histological images and known gene-pathway associations. ResultsWe present PathCLAST (Pathway-Augmented Contrastive Learning with Attention for Spatial Transcriptomics), a novel framework that integrates gene expression, histopathological image features, and curated pathway graphs through a contrastive learning strategy. By embedding gene expression within biologically grounded pathway-level graphs and aligning them with histological features, PathCLAST enhances spatial domain resolution and provides interpretable attention scores over functional pathways. Across three benchmark datasets, PathCLAST consistently outperforms existing methods in clustering accuracy-achieving a 37% improvement over STAGATE on the IDC dataset and uncovers domain-specific signaling programs and spatial heterogeneity. Additional analyses of spatial autocorrelation and inter-domain crosstalk demonstrate its potential to reveal localized biological processes and tumor microenvironmental dynamics. Our code is available at the following link: https://github.com/sslim-aidrug/PathCLAST.

bioinformatics↗

bioRxiv2025

Orthorexia is associated with a paradoxical appetitive gastric response to unhealthy foods

Orthorexia involves an obsessive tendency towards "healthy" foods. It is a risk factor for eating disorders (anorexia nervosa and the proposed "orthorexia nervosa") and psychological distress, but its biological mechanism remains unknown. We hypothesised that this mechanism operates through the stomach: increased gastric power differentiates appetising from unappetising foods, vagal stimulation reduces food liking, and gastric proto-nausea can be evoked by disgust; all contributors to disordered eating. We used electrogastrography alongside high-density facial landmark tracking to gauge responses to minimally processed ("healthy"), highly processed ("unhealthy"), and culturally unaccepted ("disgusting") foods in a non-clinical sample (N=77). Trait orthorexia was associated with increased self-reported desire to eat healthy foods. Moreover, we found that higher orthorexia was associated with increasing disgust-related facial responses to unhealthy and disgusting foods. We then identified a relationship between food-healthiness ratings and gastric power: those who generally assigned lower healthiness ratings to foods showed higher gastric power for unhealthy than healthy foods, whereas those who expressed higher healthiness ratings showed higher gastric power for healthy over unhealthy foods. This suggests that the stomach tracks individual differences in eating preferences. Crucially, and contrary to our expectations, higher trait orthorexia was associated with a paradoxical increase in gastric power to unhealthy foods. One explanation is that higher gastric power for unhealthy foods reflects increased appetite for self-denied foods. Alternatively, orthorexia itself could be an adaptive response to exert stronger cognitive control over a pre-existing gastric appetite for unhealthy foods.

physiology↗

bioRxiv2025

γ-Amino Carboxylic Acid Modification Enhances the Efficacy of PNAs Targeting miR-221-3p in A549 Cells

Peptide nucleic acids (PNAs) are versatile tools for diagnostic and therapeutic applications, including gene regulation and miRNA targeting. However, their therapeutic potential is often limited by challenges such as biological efficacy. To address this, PNAs offer a key advantage over other nucleic acids--their ease of modification, which allows for enhanced properties. In this study, we introduced a novel{gamma} -amino carboxylic acid ({gamma}-ACA) modification to PNAs targeting miR-221-3p, a key miRNA implicated in various pathological processes. The modified PNAs showed significantly improved binding affinity to their targets and more efficient inhibition of miR-221-3p expression compared to unmodified PNAs in A549 cells, leading to effective regulation of downstream gene and protein expression. These results highlight the potential of{gamma} -modified PNAs as a platform for developing miRNA-targeted therapeutics.

molecular biology↗

bioRxiv2025

Sono-uncaging for Spatiotemporal Control of Chemical Reactivity

Photo-uncaging - the use of light to reveal the active part of a chemical compound by photolysis of a protecting group - has long been used to study and actuate biochemical processes. However, light scattering limits the applications of photo-uncaging in opaque specimens or tissues. Here, we introduce sono-uncaging, a process in which a chemical functional group becomes exposed upon the application of ultrasound, which can be applied and focused in optically opaque materials. We engineered gas vesicles (GVs), air-filled protein nanostructures sensitive to ultrasound, to contain cysteines on their concealed inner surface, hypothesizing that the application of ultrasound would collapse the GV shell and reveal the cysteines. The resulting SonoCage construct reacted with monobromobimane (mBBr), a fluorogenic, thiol-reactive molecule, only after treatment with ultrasound, establishing the sono-uncaging proof of concept. We then demonstrated the spatial patterning capability of sono-uncaging by embedding the SonoCages in an mBBr-containing hydrogel and creating fluorescent patterns with phased array ultrasound. This patterning could be accomplished using a diagnostic imaging transducer. This work establishes sono-uncaging as a method for spatiotemporal control over chemical reactivity using widely available ultrasound technology.

bioengineering↗

bioRxiv2025

Patch deconvolution for Fourier light-field microscopy

Imaging flow cytometry using Fourier light-field microscopy enables high-throughput three-dimensional cellular imaging, capable of capturing thousands of events per second. However, volumetric reconstruction speed remains orders of magnitude slower than the acquisition speed. The current state of art uses Richardson-Lucy algorithm, restricted to just 5-10 reconstructed per second with GPU acceleration. This limitation hinders real-time applications such as cell sorting and thus has bottlenecked the widespread adoption of 3D imaging flow cytometry. We introduce patch deconvolution, an optimisation compatible with the Richardson-Lucy framework that significantly accelerates convergence, achieving over 100-200 reconstructions per second on standard GPUs, a 20-40 fold improvement over Richardson-Lucy. Validated on both simulated and experimental datasets, patch deconvolution achieves reconstruction quality comparable to Richardson-Lucy in both static and flow data. This supports rapid cell sorting based on spatial features and enables advanced applications, such as detecting rare spatial events in large cell populations, which would otherwise be indistinguishable in traditional flow cytometry.

biophysics↗

bioRxiv2025

Identification of reactive CpGs and RNA expression in early COVID-19 through cis-eQTM analysis reflecting disease severity and recovery

Multi-omics analyses of severe COVID-19 cases are crucial in deciphering the complex interplay between genetic and epigenetic factors. Here, we present an analysis of Expression Quantitative Trait Methylation (eQTM) to investigate the complex interplay of methylation and gene expression pattern during the acute phase of severe COVID-19. We identified 16 differentially expressed genes and 30 nearby differentially methylated CpG sites. Six key genes--SRXN1, FURIN, IL18RAP, FOXO3, GCNT4, and FKBP5--were either up-regulated or down-regulated near hypomethylated CpG sites. These genes are associated with viral infiltration, immune activation, lung damage, and oxidative stress-related multi-organ failure, which are the hallmarks of severe COVID-19. Interestingly, during the recovery phase, methylation and gene expression levels returned to baseline, underscoring the rapid and reversible nature of these molecular changes. These findings provide insight into the dynamics of epigenetic and transcriptomic shifts according to the infectious stage, supporting potential prognostic and therapeutic approaches for severe COVID-19.

bioinformatics↗

bioRxiv2025

The longevity effects of reduced IGF-1 signaling depend on the stability of the mitochondrial genome

Suppression of insulin-like growth factor-1 (IGF-1) signaling extends mammalian lifespan and protects against a range of age-related diseases. Surprisingly though, we found that reduced IGF-1 signaling fails to extend the lifespan of mitochondrial mutator mice. Accordingly, most of the longevity pathways that are normally initiated by IGF-1 suppression were either blocked or blunted in the mutator mice. These observations suggest that the pro-longevity effects of IGF-1 suppression critically depend on the integrity of the mitochondrial genome and that mitochondrial mutations may impose a hard limit on mammalian lifespan. Together, these findings deepen our understanding of the interactions between the hallmarks of aging and underscore the need for interventions that preserve the integrity of the mitochondrial genome.

molecular biology↗

bioRxiv2025

Synthetic Serum Markers Enable Noninvasive Monitoring of Gene Expression in Primate Brains

We demonstrate a noninvasive approach to measure transgene expression in the brain of nonhuman primates using blood tests with engineered reporters called Released Markers of Activity (RMAs). RMAs can exit the brain and enter the bloodstream via reverse-transcytosis across the blood-brain barrier. We demonstrate that these reporters can be used to repeatedly monitor expression of multiple transgenes in cortical and subcortical brain regions simultaneously over a period of three months. RMAs are also sensitive enough to detect circuit-specific Cre-dependent AAV expression. Through this study, the RMA platform provides a cost-efficient, noninvasive tool for neuroscience study of large animals, enabling sensitive, multiplexed, and repeatable measurements of gene expression in the brain with a blood test.

neuroscience↗

bioRxiv2025

Noninvasive Control of Seizure Threshold with Acoustically Targeted Chemogenetics

Many neurological and psychiatric diseases are characterized by pathological neuronal activity. Current treatments involve drugs, surgeries, and implantable devices to modulate or remove the affected region. However, none of these methods can be simultaneously non-invasive and possess site- and cell type specificity. Here, we apply a non-invasive neuromodulation approach called Acoustically-Targeted Chemogenetics, or ATAC, to increase the seizure threshold. Here, the ATAC approach used a multi-point focused ultrasound to transiently open the blood-brain barrier of the whole hippocampus and transduce pyramidal neurons with engineered G-protein-coupled receptors to inhibit their activity. To express the engineered receptors in the mouse hippo-campus, we used a recently engineered viral vector optimized for ultrasound-based gene delivery to the brain, AAV.FUS.3. In a mouse flurothyl seizure model, we showed successful gene delivery throughout the hippocampus, a significant neuronal activity inhibition as evidence by an increase in seizure threshold. Finally, we benchmarked these effects against a clinically prescribed drug that acts without spatial precision.

bioengineering↗

bioRxiv2025

Enhancing Wnt signaling lowers fracture incidence in a severe mouse model of Osteogenesis Imperfecta

Increased risk of fracture is a hallmark feature in the skeletal disorder Osteogenesis Imperfecta (OI). One therapy in clinical trials for OI is an antibody that neutralizes sclerostin (a Wnt signaling inhibitor) that is already FDA approved for patients with osteoporosis. In addition to increasing bone mass and lowering incident fractures in patients with osteoporosis, anti-sclerostin antibody increased bone mass and skeletal strength (measured ex vivo) in several preclinical models of OI. Because in vivo fracture incidence is the primary outcome measure in human OI trials, we examined the effect of enhancing Wnt signaling in a preclinical mouse model of moderate-severe, autosomal dominant OI (the Col1a1Aga2/+ mouse). We genetically enhanced Wnt signaling using the Lrp5A214V allele, which makes the Wnt co-receptor LRP5 resistant to inhibition by sclerostin. By crossing Col1a1Aga2/+ sires with Lrp5A214V/+ dams, we generated pups with OI alone and OI with enhanced Wnt signaling. We radiographically examined these animals for fracture at 5, 9, and 13 weeks of age. We observed that enhanced Wnt signaling significantly reduced the number of fractures in this model by 30% at all 3 ages (e.g., 5.4 {+/-} 1.7 fractures compared to 7.8 {+/-} 1.8 fractures at 5-weeks-old, p < 0.001). These data indicate enhancing Wnt signaling lowers incident fractures in a pre-clinical model of OI and suggest lower fracture incidence should achieved by giving anti-sclerostin antibody to patients with OI. These data also suggest that bone mass could be used as a surrogate marker for lowering fracture risk in patients with OI.

genetics↗

bioRxiv2025

Identification of α-azacyclic acetamide-based inhibitors of P. falciparum Na+ pump (PfATP4) with fast-killing asexual blood-stage antimalarial activity by phenotypic screening

Malaria treatments are compromised by drug resistance, creating an urgent need to discover new drugs. We used a phenotypic high-throughput screening (HTS) platform to identify new antimalarials, uncovering three related pyrrole-, indole-, and indoline-based series with a shared -azacyclic acetamide core. These compounds showed fast-killing activity on asexual blood-stage Plasmodium falciparum parasites, were not cytotoxic, and disrupted parasite intracellular pH and Na+ regulation similarly to cipargamin (KAE609), a clinically advanced inhibitor of the P. falciparum Na+ pump (PfATP4). PfATP4 is localized to the parasite plasma membrane and is essential for maintaining a low cytosolic Na+ concentration. Resistance selections on P. falciparum parasites with two -azacyclic acetamide analogs identified mutations in PfATP4, and cross-resistance was observed across the -azacyclic acetamides and KAE609, confirming PfATP4 as the target. PfATP4 is a well-established antimalarial target, and identification of additional PfATP4 inhibitors provides alternative avenues to disrupt its function.

microbiology↗

bioRxiv2025

Single-Cell RNA Sequencing and Inferred Protein Activity Analysis Reveal a Distinct Tumor Phenotype in Early-Onset Colorectal Cancer Patients

Colorectal cancer (CRC) diagnosed before age 50 years (early-onset CRC, EO-CRC) is rising at an alarming rate, yet its molecular and microenvironmental drivers remain poorly understood. EO-CRC is highly heterogeneous, and while subtle differences from late-onset CRC (LO-CRC) have been reported, their full extent remains unresolved due to the limited scope of previous studies. Here, we integrate public data with in-house clinical samples profiled by single-cell RNA sequencing (scRNA-seq) and multiplex immunofluorescence (mIF) to compare EO-CRC and LO-CRC. Additionally, we employ gene regulatory network-based protein activity inference (VIPER), enabling a more precise characterization of key regulatory proteins driving tumor-stroma interactions. Our analysis reveals that EO-CRC and LO-CRC have a largely similar immune composition, challenging previous reports of an "immune-cold" phenotype in EO-CRC. However, we identify distinct stromal differences, including a significant enrichment of fibroblasts in EO-CRC. Notably, we define a previously unrecognized epithelial subpopulation in EO-CRC, marked by high expression of toll-like receptor 4 (TLR4) and C-C chemokine receptor type 5 (CCR5)--key mediators of inflammation-driven tumor progression and fibroblast recruitment. These findings suggest that EO-CRC may be driven by a tumor-intrinsic inflammatory phenotype with enhanced stromagenesis, providing new insights into potential mechanisms underlying its increasing incidence in young adults.

cancer biology↗

bioRxiv2025

Aberrant Fibro-Adipogenic Progenitor Subpopulations Drive Volumetric Muscle Loss-Induced Fibrosis

Volumetric muscle loss (VML) injuries result in chronic fibrosis, inflammation, and persistent functional deficits. Fibro-adipogenic progenitor (FAP) cells are a heterogeneous, muscle-resident stromal cell population that play a crucial role in muscle regeneration, but also contribute to fibrosis in muscle disease. The role of FAPs in VML is not well established and may be critical target to ensure functional muscle regeneration after VML. We utilized a VML model in the mouse quadriceps to study the location, secretome, surface marker distribution, gene expression, and single-cell transcriptional profile of FAPs after VML. After VML, a subpopulation of FAPs highly expressed {beta}1-integrin and were elevated in the post-VML muscle tissue; these FAPs had increased fibrotic gene expression and increased myofibroblast differentiation potential. Transforming growth factor-{beta}1 (TGF-{beta}1) and tissue inhibitor of matrix metalloproteinase 1 (TIMP1) were identified as secreted proteins from VML derived FAPs that produced both pro-fibrotic and anti-myogenic signaling. These data establish an aberrant FAP sub-population that are elevated in VML injury and provides novel targets for future scarless muscle regeneration in VML.

pathology↗

bioRxiv2025

Kinetics of de novo Bone and Bone Marrow Niche Formation with Hybrid Click Cryogels

Successful hematopoietic stem cell transplantation (HSCT) critically depends on efficient T cell recovery, which is limited by compromised bone marrow niches following irradiation. While various factors influence the regeneration of bone and bone marrow niches, the dynamics of this process remain elusive. Here, we explore the kinetics of de novo bone and bone marrow development under varying BMP-2 doses, host immune status, and biological sex, using a cryogel of covalently crosslinked alginate and gelatin releasing BMP-2. Bone formation was monitored by ultrasonography and microcomputed tomography (microCT) analysis, while histological analysis provided insights into the relation between mineralized tissue and bone marrow formation. Bone developed within 2-4 weeks, resulting in cortical bone around the cryogels, and a trabecular bone network with hematopoietic tissue within the cryogels. Higher BMP-2 doses significantly accelerated mineralization kinetics and doubled the resident hematopoietic stem cell population. Notably, immunocompromised status delayed niche development by two weeks and reduced hematopoietic stem cells fourfold. We also found that female mice exhibited enhanced niche formation compared to males under the identical conditions. These findings provide insights into the factors that govern the spatiotemporal regulation of bone and bone marrow niche development and establish this hybrid click cryogel system as a promising platform for improving T cell reconstitution in HSCT patients.

bioengineering↗

bioRxiv2025

A High-Dimensional Interfacial Wave Assay for Early Biophysical Profiling of Therapeutic Antibodies

Therapeutic antibody performance depends not only on sequence and structure, but also on how the molecule responds to physico-chemical perturbations encountered in its environment. Whereas sequence and static structure can be inferred under controlled conditions, behaviour is a conditional, multidimensional response to environment, most directly characterised by applying defined perturbations and quantifying the resulting dynamics. Conventional early-stage developability methods capture isolated dimensions of this response under near-equilibrium conditions, deferring integrated behavioural assessment to late-stage characterisation, when the cost of correction is highest. We introduce Variations in Interfacial Behaviour under Excitation (VIBE), an interfacial wave method implemented via Liquid State Intelligence (LSI), a sensing architecture that transduces molecular perturbations at the air-liquid interface into high-dimensional wave patterns. A colloidal liquid substrate operated near a thermodynamic transition couples small molecular perturbations to large dynamical responses, integrating structural flexibility, charge distribution, and surface hydrophobicity into a single behavioural readout from microgram-scale samples. Applied to antibodies previously characterised by industrial benchmarks, the primary behavioural descriptor, VIBE1, functioned as a high-precision triage tool, flagging candidates carrying multiple biophysical liabilities. In a clinical-stage cohort, the proportion of high-VIBE1 antibodies declined progressively from early trials through approval, and high-VIBE1 candidates showed an elevated clinical failure rate. Concordance analysis against estab-lished methods confirmed that VIBE1 captures a composite signal spanning hydrophobicity, polyreactivity, self-interaction, and thermal stability rather than recapitulating any single conventional readout. These findings establish interfacial wave sensing as a low-material modality for early-stage developability assessment, repositioning molecular behaviour from late-stage validation to discovery-phase characterisation.

biophysics↗

bioRxiv2025

Epithelium intrinsic zinc sensor controls immune homeostasis with gut microbes via regulation of Tuft cell lineage

Zinc is an essential micronutrient crucial for cell proliferation, differentiation, and apoptosis, yet its precise role in the constantly renewing intestinal epithelium remains unclear. We generated mice lacking the Zn-dependent transcription factor Metal-responsive Transcription Factor 1(MTF1{Delta}IEC) in intestinal epithelial cells. MTF1{Delta}IEC mice exhibited altered metal homeostasis and acute susceptibility to Zn supplementation. Transcriptional and cellular analyses revealed increased inflammatory immune responses to microbes in MTF1{Delta}IEC mice. Mechanistically MTF1 deletion resulted in the loss of Tuft cell lineages compromising barrier function against commensal microbes and pathogens. Ex vivo experiments demonstrated that at a cellular level, Zn treatment skewed the cellular composition from proliferating to differentiated cells. Specifically, we show that Zn sensing via MTF1 is required for IL-13 dependent induction of Tuft cells. Our findings underscore critical role of Zn in maintaining intestinal immune homeostasis through differentiation of specialized cell lineages, highlighting importance nutrient sensing in the constantly remodeling epithelial barrier.

immunology↗