Biology subjects

Shin, J.

Publications and source records attributed to Shin, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

High-variance phenome database reveals important roles of WD40 proteins in the plant pathogenic fungus Fusarium graminearum

WD40 is a highly conserved protein domain in eukaryotes, playing a critical role in various cellular process. We conducted genome-wide functional analysis of WD40 genes in Fusarium graminearum-a phytopathogenic fungus that causes severe yield loss and mycotoxin contamination in major cereal crops. Comprehensive phenome analysis of 119 WD40 gene deletion mutants across 22 distinct phenotypic traits revealed phenotypic divergence within the phenome, establishing a strong correlation between virulence and sexual reproduction. Notably, 21 core WD40 genes were identified, offering valuable insights into divergent biological processes. Pilot interactome studies of Fgwd101 and Fgwd133 provided further insights into their potential pathobiological functions. Our investigation contributes to broadening our knowledge of the biological mechanisms underlying fungal pathogenesis and may assist in the identification of targets for antifungal agents.

molecular biology↗

bioRxiv2026

Co-regulatory changes in Homo sapiens prefrontal cortex shape RNA-chromatin interactions

Noncoding RNAs (ncRNAs) regulate gene expression through RNA-chromatin interactions, yet their role in human brain evolution remains unclear. To map these interactions, we integrated FANTOM6 neurogenic data with a comprehensive atlas of regulatory regions active during early cortical development. This integration effort linked ncRNAs and transcription factors (TFs) to their genomic targets, revealing functional interactions captured by RNA-DNA contact mapping, yet largely missed by chromatin conformation data. Overlaying these interactions with nearly fixed variants in Homo sapiens relative to extinct hominins uncovered widespread rewiring of TF binding, affecting genes implicated in progenitor proliferation and neuronal differentiation. Gene regulatory network reconstruction identified TEAD2 and ONECUT2 as key regulators of intermediate progenitors and migrating neurons. Functional perturbation followed by Cut&Tag and ATAC-seq linked the two TFs to disease- and evolutionarily- relevant pathways. Together, these results show how ncRNA-TF cooperation and selective cis-regulatory rewiring contributed to sapiens-specific features of cortical development.

molecular biology↗

bioRxiv2026

Infant gut microbiomes contribute to metabolic states that impact brain function

Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.

microbiology↗

bioRxiv2026

Transient activation of potent progenitor cells is required for spinal cord regeneration

Adult zebrafish exhibit full recovery following spinal cord injury. Transient expansion of stem cell-like progenitors is thought to underlie their regenerative capacity. Yet, our understanding of the identities and contributions of the crucial stem cell populations that direct spontaneous neural repair remains limited. Moreover, while most neural regeneration research is centered on promoting proliferative repair, the regulatory mechanisms that reinstate quiescence post-repair are unknown. Here, we determined the molecular identities and cellular contributions of sox2+ progenitors during spinal cord repair. Genetic lineage tracing shows zebrafish spinal progenitors, while quiescent in uninjured tissues, self-renew and differentiate into neurons and glia after injury. By single-cell sequencing, sox2+ cells are heterogeneous and biased towards neuronal or glial fates in both homeostatic and regenerating tissues. By screening for transcription factors that are differentially expressed in acute versus chronic spinal cord injury, we find the Bach1 transcription factors control transient progenitor cell activation by acting as dual activators and repressors of sox2 expression. This study elucidates the molecular diversity and contributions of sox2 expressing cells during spinal cord repair and identifies a transcriptional regulatory switch by which progenitor cells expand after injury and restore quiescence after regeneration is completed.

neuroscience↗

bioRxiv2026

Accurate somatic variant detection from formalin fixed, paraffin embedded tissue (FFPE) derived WES and WGS by DeepOmicsFFPE-PLUS, a sequence context-based transformer

Formalin-fixed paraffin-embedded (FFPE) tissues represent a vast archival resource for genomic studies, yet their utility remains constrained by fixation-induced DNA damage and subsequent sequencing artifacts. To comprehensively characterize and address this challenge, we analyzed matched FFPE and fresh-frozen tumor samples from two institutions, spanning different storage durations, DNA qualities, sequencing platforms (WES and WGS), exome capture kits, and somatic variant callers. We found that FFPE-induced artifacts exhibit strong batch- and age-specific patterns, with a predominance of C:G>T:A substitutions, which particularly complicate the accurate identification of low allele frequency true variants. Enzymatic repair methods partially alleviated these artifacts but remained insufficient. To overcome these limitations, we developed DeepOmicsFFPE-PLUS(https://github.com/Theragen-Bio/DeepOmicsFFPE-PLUS), an advanced AI-based tool to accurately distinguish true somatic variants from FFPE-specific artifacts. DeepOmicsFFPE-PLUS demonstrated consistently superior performance across diverse conditions, achieving high sensitivity and specificity--even for low-frequency variants--outperforming existing tools. Application of our model to WGS data further enabled recovery of biologically relevant mutational signatures, including restoration of microsatellite instability (MSI)-associated signatures initially obscured by FFPE artifacts. Our findings underscore the necessity of artifact-aware variant calling in FFPE genomics and establish DeepOmicsFFPE-PLUS as a robust tool for artifact removal, enabling high-fidelity downstream analyses and personalized therapeutic target discovery.

cancer biology↗

bioRxiv2026

NetCrafter: Ontology-derived gene network modeling and interpretation

Understanding the complex nature of multi-functional interactions among genes is crucial for interpreting omics data. We developed NetCrafter, an ontology-driven platform for constructing de novo gene networks that are specific to each input gene list and quantitatively defined by ontology-weighted similarity. By incorporating the probabilistic association of ontology or curated gene sets into a weighted Tanimoto similarity metric, NetCrafter transforms enrichment results into quantitative semantic similarity scores between genes, enabling the creation of context-specific statistical networks. These networks can be further decomposed into optimal sub-networks, facilitating multi-functional interpretation and the identification of gene interaction hotspots. NetCrafter also supports the integration of heterogeneous omics-derived gene lists through consensus ontology scoring. Importantly, this list-specific, quantitative framework reveals functional hotspots and target-biomarker relationships - even in cases where ontology terms alone are not predictive of node-level attributes such as CRISPR efficacy. NetCrafter provides an interactive platform for constructing and interpreting dynamic, context-specific gene networks, leveraging ontology-based functional associations to uncover underlying mechanisms and identify key nodes. It is freely available at https://netcrafter.sookmyung.ac.kr and integrated into Q-omics platform (https://qomics.ai) to enhance the utility of cancer omics data.

bioinformatics↗

bioRxiv2026

Gonadal and sex chromosomal contributions to sex differences in mammalian brain organization

Sex differences in brain development may contribute to well-known sex differences in behavior and neuropsychiatric risk - making it important to comprehensively map and mechanistically annotate normative sex differences in brain organization. Most sex differences in mammalian brain organization have previously been attributed to differential effects of gonadal hormones based on outcomes from rodent endocrine manipulations at canonical subcortical foci of male-biased brain volume. However, a systematic quantification of both gonadal and sex chromosome dosage (SCD) contributions across all regions of sex-biased brain volume has been lacking. Here, using structural neuroimaging scans from wild-type (n=670) and transgenic mice that dissociate gonadal, X-, and Y-chromosome effects (n=181), we show that: many more brain regions are volumetrically sex-biased than previously recognized; gonadal effects dominate throughout this expanded map of sex differences; several regions also show prominent SCD contributions to anatomical sex differences, which can both reinforce or counteract gonadal effects in a regionally specific manner. Targeted single nucleus RNA sequencing at a region of female-biased cerebellar volume reveals that combined gonadal and SCD effects also drive sex-biased cellular gene expression. These findings revise our understanding of the spatial distribution and causal basis of sex-differences in the mammalian brain, illuminating a key axis of biological variation in health and disease.

neuroscience↗

bioRxiv2026

Reactive Astrocytes Drive Extracellular Acidification to Mediate α-Synuclein Neurodegeneration

Astrocytes are increasingly recognized as key players in neurodegeneration1-3, yet the molecular mechanisms by which they drive disease remain elusive. Here, we uncover a fundamental pathway in which reactive astrocytes fuel neurodegeneration in -synucleinopathies--including Dementia with Lewy bodies and Parkinsons disease dementia--by acidifying the brains extracellular environment. We demonstrate that both human patient tissue and a gut-to-brain -synuclein mouse model exhibit accumulation of reactive astrocytes and extracellular acidosis. Mechanistically, we show that astrocytic lysosomal exocytosis releases acidic contents, driving a drop in pH that activates neuronal acid-sensing ion channel 1a (ASIC1a), resulting in neuronal loss and behavioral decline. Blocking this pathway--either by inhibiting astrocytic lysosomal exocytosis or genetically or pharmacologically targeting neuronal ASIC1a--mitigates pathology and rescues neurodegenerative phenotypes in vivo. These findings provide a conceptual advance by establishing a mechanistic link between glial inflammation, acid-base homeostasis, and neuronal vulnerability, and suggest that targeting astrocyte-driven acidification or ASIC1a signaling could offer new avenues for disease modification in -synucleinopathies.

neuroscience↗

bioRxiv2025

Sleep-Wake Transitions Are Impaired in the AppNL-G-FMouse Model of Early Onset Alzheimers Disease

Poor sleep quality and reduced sleep duration are associated with Alzheimers disease (AD)-related {beta}-amyloid (A{beta}) pathologies. We conducted two studies of sleep/wake, activity and body temperature in AppNL-G-F mice, a strain that exhibits three mutations in the human App gene associated with elevated risk for early onset AD. First, AppNL-G-F mice were compared to wildtype (WT) littermates at 14-18 and 18-22 months of age and, at both ages, were found to exhibit more Wake and less NREM and REM sleep than WT littermates. This long wake/short sleep phenotype was evident during the dark phase at 14-18 months but occurred in both the light and dark phases at 18-22 months. AppNL-G-F mice had fewer short (<60 sec) and more long (>260 sec) Wake bouts and were hyperactive at 18-22 months, which undoubtedly contributed to the increased Wake/reduced sleep. Despite this reduced sleep phenotype, AppNL-G-F mice were no sleepier than WT mice and the sleep homeostat was functional in both strains. In the second study, sex differences in these parameters were assessed at 18-24 months. Reduced sleep was evident in both sexes of AppNL-G-F mice but was clearly more evident in females. Wake and REM sleep bout durations were longer in both sexes of AppNL-G-F mice than in WT littermates. EEG spectral power during NREM sleep was reduced in female AppNL-G-F mice between 4.88-10.50 Hz compared to WT mice whereas, during REM sleep, both male and female AppNL-G-F mice exhibited reduced spectral power in the theta range. These results suggest that A{beta} deposition may impair state transition mechanism(s) in AppNL-G-F mice and demonstrate that, as in human AD patients, the long wake/short sleep phenotype was more evident in female AppNL-G-F mice, thus supporting the use of this strain as a model to investigate interventions that mitigate AD burden during early disease stages.

neuroscience↗

bioRxiv2025

Mitochondrial control of fuel switching via carnitine biosynthesis

Environmental adaptation often involves a shift in energy utilization toward mitochondrial fatty acid oxidation, which requires carnitine. Besides dietary sources of animal origin, carnitine biosynthesis from trimethyllysine (TML) is essential, particularly for those who consume plant-based diets; however, its molecular regulation and physiological role remain elusive. Here, we identify SLC25A45 as a mitochondrial TML carrier that controls carnitine biosynthesis and fuel switching. SLC25A45 deficiency decreased the carnitine pool and impaired mitochondrial fatty acid oxidation, shifting reliance to carbohydrate metabolism. Slc25a45-deficient mice were cold-intolerant and resistant to lipid mobilization by GLP1 receptor agonist (GLP-1RA), rendering them resistant to adipose tissue loss. Our study suggests that mitochondria serve as a regulatory checkpoint in fuel switching, with implications for metabolic adaptation and the efficacy of GLP-1RA-based anti-obesity therapy.

biochemistry↗

bioRxiv2025

Mitochondria-derived PEP licenses glycerolipid synthesis via SLC25A35

Mitochondria provide a variety of metabolites, in addition to ATP, to meet cell-specific needs. One such metabolite is phosphoenolpyruvate (PEP), which contains a higher-energy phosphate bond than ATP and has diverse biological functions. However, how mitochondria-generated PEP is delivered to the cytosol and fulfills cell-specific requirements remains elusive. Here, we show that SLC25A35 regulates mitochondrial PEP efflux and glyceroneogenesis in lipogenic cells that utilize the pyruvate-to-PEP bypass. Reconstitution and structural studies demonstrated PEP transport by SLC25A35 in a pH gradient-dependent manner. Loss of SLC25A35 in adipocytes impaired the conversion of mitochondrial PEP into glycerol-3-phosphate, thereby reducing glycerolipid synthesis. Significantly, hepatic inhibition of SLC25A35 in obese mice alleviated steatosis and improved systemic glucose homeostasis. Together, these results suggest that mitochondria facilitate glycerolipid synthesis by providing PEP via SLC25A35, offering lipogenic mitochondria as a target to limit glycerolipid synthesis, a pivotal step in the pathogenesis of hepatic steatosis and Type 2 diabetes.

cell biology↗

bioRxiv2025

Relative contribution of gonads and sex chromosomes to sex differences in cell-type gene expression in the mouse medial septum and sex-biased disease risk

BackgroundWhile sex differences in the brain have traditionally been attributed to gonadal hormones, emerging evidence points to regulation by sex chromosomes. This study aims to differentiate the influence of gonads versus sex chromosomes on cellular gene expression in the mouse medial septum (MS), a critically understudied brain region. MethodsUsing single nucleus RNA-sequencing and the Sex Chromosome Trisomy mouse model, we (1) quantified sex differences in cellular gene expression and (2) isolated sex-biasing effects by identifying perturbed cell types, differentially expressed genes, biological pathways, and gene networks, which were integrated with GWAS data to explore links with sex-biased human phenotypes. ResultsOur analysis revealed that volumetric sex differences in the MS are mirrored by widespread transcriptomic changes across cell types. Critically, genetic effects displayed elevated relevance compared to sex hormones in driving sex-biased gene expression. These effects converge to regulate synaptic/neuronal development, transcriptional regulation, and cellular metabolism. Sex chromosome-associated DEGs were enriched for various human disorders, suggesting a cellular and mechanistic basis for their sex-biased patterns. ConclusionsOur findings challenge the classical gonad-centric views of sexual differentiation, as the MS displays sex-biased transcriptional regulation driven by sex chromosome-associated effects that are highly relevant for human health.

neuroscience↗

bioRxiv2025

Primary Cilia Dysfunction in Brown Fat Results in Fatal Thermogenesis Failure in Neonatal Mice

Primary cilium, microtubule-based sensory organelle that has emerged as a central player in coordinating numerous signaling pathways. Although primary cilia are known to regulate cellular signaling and energy metabolism, the relationship between these roles in the context of ciliopathies and brown adipose tissue (BAT) dysfunction remains poorly understood. To elucidate the role of primary cilia in BAT, we generated Ucp1-Cre;Ift88flox/flox mice with BAT-specific ciliary loss. There were no significant differences in body size, weight, or BAT weight relative to body weight between P0 Ucp1-Cre;Ift88flox/flox and P0 Ucp1-Cre;Ift88+/+ pups. Embryos examined at E14.5 and E18.5 also showed no discernible differences in size, morphology, or histology. However, P0 Ucp1-Cre;Ift88flox/flox pups exhibited neonatal lethality caused by defective thermogenesis, despite preserved Ucp1 expression. These mice displayed markedly reduced ketone body levels in both BAT and serum, accompanied by downregulation of Hmgcs2, a key enzyme in ketogenesis. Loss of primary cilia in BAT suppressed ketogenesis and increased ROS production through HMGCS2 downregulation, ultimately impairing non-shivering thermogenesis. Remarkably, neonatal lethality of Ucp1-Cre;Ift88flox/flox pups was completely rescued by thermoneutral housing or {beta}-hydroxybutyrate supplementation. Our findings identified a previously unrecognized mechanism by which primary cilia regulate non-shivering, UCP1-independent thermogenesis via ketogenesis.

cell biology↗

bioRxiv2025

APOE4-Aβ synergy drives brain network dysfunction and neuronal lysosomal-ER proteostasis dysregulation in preclinical Alzheimer's disease

Amyloid-{beta} (A{beta}) and APOE4 represent two of the strongest pathological and genetic risk factors for Alzheimers disease (AD), but how these co-pathogens interact during preclinical stages remains undefined. We addressed this question by developing a humanized knock-in model expressing physiological, endogenously regulated human A{beta} and APOE4. Aged AppNLF:APOE4 mice displayed incipient amyloidosis with subtle memory-related changes, consistent with preclinical AD. We found largely distinct, non-overlapping APOE4- and A{beta}-driven functional synaptic, sleep, and behavioral alterations. However, at the transcriptomic level, APOE4xA{beta} had a pronounced detrimental interaction in neuronal populations, whereas glial populations were primarily affected by either genotype. We found APOE4xA{beta} molecular interactions in neuronal populations, including excitatory and inhibitory cells, converged on a core lysosomal-ER proteostasis axis. We propose that APOE4xA{beta} interaction produces an early neuronal pathogenic signature, involving the lysosomal-ER proteostasis axis, preceding functional decline and driving disease progression. APOE4xA{beta}-KI models provide a physiologically relevant platform to study early pathogenesis. HighlightsO_LIEarly synergistic APOE4xA{beta} interaction emerges predominantly at the transcriptomic level in neurons, but not in glial cells. C_LIO_LIAPOE4 and A{beta} drive largely non-overlapping physiological changes in preclinical stages of disease, but converge at the level of network hyperexcitability. C_LIO_LIAPOE4xA{beta} neuronal synergy converges on a conserved lysosomal-ER proteostasis axis. C_LIO_LIHumanized APOE4xA{beta} KI mice provide a physiologically relevant model to dissect early AD pathogenesis in preclinical stages C_LI

neuroscience↗

bioRxiv2025

A comprehensive view of somatic mosaicism by single-cell DNA analysis

Single-cell DNA sequencing offers a powerful means of studying somatic mosaicism but requires careful analysis to mitigate DNA amplification-related artifacts. We performed primary template-directed amplification (PTA) and sequencing of 102 nuclei from postmortem lung and colon tissues of a 74-year-old male. Single-cell mutation burdens and spectra were validated by duplex sequencing and revealed heterogeneity across organs and cells, including signatures of APOBEC activity and tobacco exposure. Cells from both tissues exhibited chromosomal aneuploidies, loss of chromosome Y, and chromosomal rearrangements including rearrangements of the T-cell receptor loci indicative of T-cells. Shared embryonic mutations between cells enabled reconstruction of cellular ancestries from the zygote, which were validated by bulk sequencing. Collectively, we demonstrate a comprehensive approach for single-cell genomics that yields an expansive view of diverse somatic mutation types from development through aging across diverse tissues--insights that are obscured in bulk sequencing and only partially captured by other single-cell methods.

genomics↗

bioRxiv2025

Engineering a Biomimetic Multiphasic Suture Anchor System for Enhanced Rotator Cuff Enthesis Regeneration

Conventional suture anchor methods in rotator cuff repair often fail to replicate the native tendon-to-bone interface, leading to re-tears due to stress concentrations and poor biological integration at anchor sites. To address these challenges, we engineered a biomimetic multiphasic scaffold system (BMS) that integrates with standard suture anchors and deliver spatially organized structural and biological cues to enhance enthesis regeneration. The BMS comprises three distinct phases: aligned nanofibrous decellularized bovine Achilles tendon extracellular matrix (dECM) with stiff methacrylated hyaluronic acid (MeHA) for tendon regeneration; nonaligned nanofibrous dECM with soft MeHA for fibrocartilage formation; and a porous, citrate-based composite scaffold with bioactive glass for bone integration. In vitro, the BMS facilitated zone-specific tenogenic, fibrochondrogenic, and chondrogenic differentiation. Further, in vivo, it promoted successful integrative healing, forming distinct tendon, fibrocartilage, and bone regions at the repair site. This advanced multiphasic scaffold replicates native tissue properties, offering a promising strategy to improve rotator cuff repair. Its integration with conventional suture anchors provides an innovative design that enhances mechanical fixation and guides enthesis healing to reduce re-tear rates. Broadly, this platform offers a versatile solution for biointegrative repair strategies across complex soft-to-hard tissue interfaces.

bioengineering↗

bioRxiv2025

Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of robust CD4+ T cell responses

Chronic infection with hepatitis B virus (HBV), a major global pathogen, often leads to immune-mediated progressive liver injury and liver cancer. While seroclearance of the surface antigen (HBsAg) defines clinical cure and reduces disease-associated risks, HBsAg clearance is rarely observed and remains therapeutically elusive. Here we overcome some of the challenges to studying immune mechanisms of HBsAg clearance in chronic hepatitis B (CHB) using our mouse model of age-dependent HBsAg clearance and persistence, and samples from our BeNEG-DO clinical trial that provided longitudinal PBMCs from patients who either cleared HBsAg or retained stable HBsAg levels after stopping nucleos(t)ide analog therapy. We show that young mice fail to clear HBsAg and have impaired ability to efficiently initiate and sustain HBV-specific CD4+ T cell responses. We also demonstrate a role for CD4+ T cells in hepatic leukocyte organization and cytotoxicity, and in HBV-specific CD8+ T cell cytotoxicity and HBsAg clearance. Upstream of the CD4+ T cell response, we reveal that hepatic dendritic cells, particularly cDC2s, direct effective CD4+ T cell activation and differentiation. Studies in CHB patients identified immune features of HBsAg clearance that overlap with the mouse model, including TH1 and cytotoxic CD4+ T cell activation and CD8+ T cell cytotoxic effector function. These findings identify an essential role for potent CD4+ T cell activation in the clinical cure of CHB and illuminate potential immunotherapeutic targets for enhancing CD4+ T cell responses to achieve greater HBsAg clearance rates. One Sentence SummaryUsing a mouse model of hepatitis B and longitudinal PBMCs from patients with chronic hepatitis B, we identify shared mechanisms of HBsAg seroclearance.

immunology↗

bioRxiv2025

DNA Content and DNA Damage in Raw and Heat-processed Foods

DNA in foods is a source of nucleotides that are salvaged by tissues as building blocks for chromosomal and mitochondrial DNA. A recent study provided preliminary evidence that high-temperature cooking damages the DNA in foods and suggested that certain forms of DNA damage can be taken up as nucleotides via metabolic salvage in cells and animals, directly incorporating genotoxic and mutagenic species into the host DNA. To assess potential risks, we surveyed DNA in 21 food ingredients, including plant- and meat-based foods in raw and roasted form. We find large variation in extractable DNA content, implying widely variable levels of consumption. Cooking resulted in greatly elevated levels of oxidative and deaminated DNA damage in nearly all foods as indicated by 8-oxo-dG and dU nucleotides; with up to 250-fold increases. Studies of human cell lines found that incubation with these damaged nucleosides resulted in cytotoxicity and increased DNA double-strand break levels.

biochemistry↗