Biology subjects

Min, H.

Publications and source records attributed to Min, H..

17 recordsLinked to original sources

bioRxiv2026

Systematic Functional Interrogation of Neurodevelopmental Disorder Risk Variants

Neurodevelopmental disorders (NDDs) are highly polygenic, yet the functional consequences of most associated non-coding variants remain unclear. We used a massively parallel reporter assay (MPRA) to test 727 NDD-associated non-coding variants in human neural progenitors, identifying 38 expression-modulating variants (emVars) with regulatory activity. These emVars were predicted to alter transcription factor binding motifs linked to neurodevelopmental signaling and cellular metabolism. We mapped emVars to candidate target genes using expression quantitative trait loci and activity-by-contact (ABC) models. We then used CRISPR droplet sequencing (CROP-seq) in human pluripotent stem cell-derived neurons to identify endogenous target genes and characterize their downstream transcriptional effects. CROP-seq preferentially supported ABC predictions, identified additional regulatory relationships, and revealed convergence on developmentally regulated programs involving neuronal connectivity, synaptic function, and mitochondrial biology. Together, these results connect NDD risk variants to endogenous target genes and shared neurodevelopmental transcriptional programs.

genomics↗

bioRxiv2026

Type-I IFNs in EAE drive synaptic transcriptional responses in neurons and astrocytes in the brain

Neuronal pathology plays a prominent role in the cognitive and neuropathic symptoms of multiple sclerosis; however, little is known about these pathological signals to neurons in the brain and their consequences on cognition. Here, using a transgenic reporter of IFN signaling with spatial RNA-sequencing, we determined myelin-specific autoimmune T cells enter the brain parenchyma through the interface between the fimbria and third ventricle. Here, astrocytes and microglia express high levels of MHC-II-associated transcripts. Using this reporter, we also showed microglia within the brain are not direct responders of IFNs, but express transcripts associated with synaptic pruning, potentially contributing to pathological remodeling of neuronal circuits. Moreover, both type-I and type-II IFNs are required for T cells to infiltrate the brain and initiate an IFN response associated with synaptic and metabolic programs in neurons and astrocytes in the cortex and hippocampus. In summary, this study elucidates multiple steps of the pathogenesis of EAE pathology within the brain independent of the spinal cord.

neuroscience↗

bioRxiv2026

Polygenic hierarchies of macroscale brain structural organisation

Different Magnetic Resonance Imaging-derived cortical, subcortical, and white matter measures are presumed to reflect different developmental and cellular processes, but how their genetic architecture is organised and the underlying cellular and developmental processes is unclear. We conducted genome-wide association studies of 2,326 imaging-derived phenotypes (IDPs) spanning twelve structural measures across the cortex, subcortex, ventricles, and white matter tracts in the UK Biobank (Nmax = 53,751), replicated in ABCD (Nmax = 5,119), identifying 14,176 experiment-wide significant loci and prioritizing 848 genes. We found that IDPs primarily cluster by measure into six families: brain size, cortical thickness, curvature, microstructural coherence, microstructural diffusivity, and orientation dispersion. This structure was preserved across prioritized genes, cell types, and developmental timing; brain size implicates first-trimester radial glia programs, while white matter coherence implicates adolescent astrocyte and oligodendrocyte lineages. Within individual measures, genetic effects were further organised along broad spatial gradients, with a principal gradient reflecting allometric scaling for most measures and secondary gradients showing correspondence with the sensory-association topographic axis across several measures. We identified 79 genes with spatially restricted effects along the cortex, with many aligning with these dominant gradients while a substantial subset showed additional spatial patterns. Together, these findings reveal a hierarchical organisation of the genetic architecture of macroscale human brain structure, spanning phenotype families, broad spatial gradients, and regionally restricted developmental programmes.

genomics↗

bioRxiv2026

Perturbation of genes linked to common schizophrenia risk variants identifies cilia programs

Schizophrenia (SCZ) is a common psychiatric disorder characterized by psychosis, emotional withdrawal, and cognitive deficits. Most SCZ risk variants reside in non-coding regions of the genome and are thought to influence disease risk by modulating gene regulation. However, the target genes, biological pathways, and cell types through which these variants exert their effects remain poorly understood. To address this gap, we employed in vivo CRISPR droplet sequencing (CROP-seq) in the postnatal mouse neocortex. We perturbed 12 SCZ risk genes previously linked to functionally validated risk variants, followed by single-cell RNA sequencing. We identified 3,031 differentially expressed genes (DEGs) that recapitulate transcriptional alterations observed in postmortem SCZ brains. Integrative analysis using DEG clustering, factor analysis, and gene regulatory network inference uncovered convergent gene programs with distinct biological functions and cell type specificity. Notably, ciliary transcriptional programs consistently emerged across analytical frameworks. The primary cilium is a neurocircuit modulating signaling organelle in neurons and glia that remains understudied in SCZ. Perturbation of key contributors to the ciliary transcriptional programs led to significant alterations in ciliary structure, suggesting that SCZ genetic risk factors may influence how brain cells sense and transduce extracellular signals through synapse-independent mechanisms. Together, this study provides the first in vivo characterization of the functional consequence of common variant architecture in SCZ and implicates ciliary dysfunction as a convergent downstream mechanism.

neuroscience↗

bioRxiv2026

Caffeine extends lifespan by enhancing lysosomal lipolysis in Caenorhabditis elegans

Caffeine is a globally consumed stimulant that has beneficial effects on biological processes including metabolism and aging, but its causal role in physiology remains incompletely understood. By using the roundworm Caenorhabditis elegans, here we show that caffeine extends lifespan by eliciting transcriptional remodeling that enhances lysosomal lipolysis. We found that transcriptomes of aged, caffeine-fed animals shifted toward youthful states. By comparing with three longevity-promoting regimens, including reduced insulin/insulin-like growth factor 1 (IGF-1) signaling, mild reductions in mitochondrial function, and dietary restriction (DR), we showed that caffeine induced a DR-like transcriptional program. Comparison with eat-2 mutants (a genetic DR model) identified lysosomal lipases lipl-1 and lipl-2 as commonly upregulated genes. The induction of lipl-1 and lipl-2 was required for increased lifespan and reduced neutral lipid accumulation by caffeine intake. Together, these findings indicate that caffeine promotes longevity in a DR-like metabolic reprogramming by enhancing lysosome-driven lipolysis.

genetics↗

bioRxiv2025

Anti-vitronectin single-chain variable fragment targeting the hemopexin-like domain decreases age-related macular degeneration indicators in ex vivo models of the retinal pigment epithelium

Vitronectin is a prominent constituent of the extracelluar matrix (ECM) that plays a key role in inflammation by regulating cell adhesion, migration, and complement activation. Together with other inflammatory biomarkers, lipids, and hydroxyapatite, an ECM component, vitronectin, accumulates in abnormal deposits and drusen associated with age-related macular degeneration (AMD). Using an engineered polypeptide (VnHX) containing the hexmopexin-like domain (HX) of vitronectin, we found that the HX domain directly promotes hydroxyapatite (HAP) accumulation. Next, we screened humanized single-chain variable fragments (scFvs) against vitronectin that inhibit the interaction between VnHX and HAP, leveraging the binding of VnHX to HAP. We then tested these scFvs for their ability to block Vn-containg deposits secreted by stem cell-derived retinal pigment epithelium (RPE). In this in vitro drusen model, treatment with the anti-vitronectin antibodies decreased vitronectin accumulation. Furthermore, the antibody treatment led to decreased accumulation of C5b-9 and clusterin, indicating alterations in the complement pathway and cellular stress. These results support that vitronectin has a functional role drusen accumulation and possibly in AMD progression. Vitronectin would be a novel, promising therapeutic target for AMD.

cell biology↗

bioRxiv2024

Clathrins are involved in the endocytosis of host cytosol in the malaria parasite

In eukaryotic cells, clathrins interact with adaptor protein complexes to regulate key intracellular trafficking events. Specifically, they are associated with the adaptor protein (AP) complex-2 (AP2) to facilitate endocytosis and AP1 to mediate secretion and trafficking between endosome and Golgi. In Plasmodium falciparum, recent studies revealed that the Kelch domain-containing protein 13 and AP2 participate in hemoglobin uptake via cytostomes. However, clathrins appear not to be involved in this process because they primarily associate with AP1. To investigate the roles of clathrins in P. falciparum, we characterized the clathrin heavy chain (PfCHC), the clathrin light chain (PfCLC), and the AP1 {gamma} subunit (PfAP1 {gamma}). Extensive interactome analyses confirmed the major association of clathrins with AP1 components alongside proteins involved in cytostome formation. Live-cell imaging and protein colocalization studies showed that PfCHC, PfCLC, and PfAP1 {gamma} are localized in the parasite cytoplasm, predominantly at the parasite periphery and near the cis-Golgi. Ultrastructural studies using ascorbate peroxidase 2- based electron microscopy confirmed their presence at coated vesicle-like structures at the parasite periphery and, unexpectedly, at the collars of cytostomes. Consistent with these observations, the knockdown of PfCHC led to the formation of abnormally long cytostome tubes and impaired hemoglobin digestion. This study demonstrates that clathrins are essential for proper cytostome formation in P. falciparum, highlighting their critical role in the parasites hemoglobin uptake and digestion processes. IMPORTANCEMalaria is still one of the most severe public health problems worldwide and understanding how malaria parasites obtain hemoglobin from their host cells, red blood cells (RBCs), is critical for identifying targets for antimalarials. In this study, affinity purification revealed that clathrins (PfCHC and PfCLC) were not only mainly associated with AP1 complex but also marginally interacted with proteins that participated in hemoglobin uptake. Localization analysis demonstrated that clathrins and AP1 coated the clusters of vesicles at the parasite periphery and at the neck of the cytostome, an organelle for hemoglobin uptake. Consistently, the knockdown of PfCHC caused the formation of abnormally long cytostome tubes and reduced hemoglobin digestion. Collectively, this study demonstrates that clathrins play a critical role in the parasites hemoglobin uptake.

microbiology↗

bioRxiv2024

Cold induces brain region-selective neuronal activity-dependent lipid metabolism

It has been well documented that cold is an enhancer of lipid metabolism in peripheral tissues, yet its effect on central nervous system lipid dynamics is underexplored. It is well recognized that cold acclimations enhance adipocyte functions, including white adipose tissue (WAT) lipid lipolysis and beiging, and brown adipose tissue (BAT) thermogenesis in mammals. However, it remains unclear whether and how lipid metabolism in the brain is also under the control of cold acclimations. Here, we show that cold exposure predominantly increases the expressions of the lipid lipolysis genes and proteins within the paraventricular nucleus of the hypothalamus (PVH). Mechanistically, we find that cold activates cells within the PVH and pharmacological inactivation of cells blunts cold-induced effects on lipid peroxidation, accumulation of lipid droplets (LDs), and lipolysis in the PVH. Together, these findings suggest that PVH lipid metabolism is cold sensitive and integral to cold-induced broader regulatory responses.

neuroscience↗

bioRxiv2024

Inositol polyphosphate multikinase regulates Th1 and Th17 cell differentiation by controlling Akt-mTOR signaling

Activated proinflammatory T helper (Th) cells, such as Th1 and Th17 cells, mediate immune responses against intra- and extra-cellular pathogens as well as cause the development of various autoimmune diseases. Inositol polyphosphate multikinase (IPMK) is a key enzyme essential for inositol phosphate and phosphoinositide metabolism, which is known to control major biological events such as growth; however, its role in the function of Th cells remains unclear. Here we show that the expression of IPMK is highly induced in distinct Th1 and Th17 subsets. Further, while conditional deletion of IPMK in CD4+ T cells is dispensable for Th2-dependent immune responses, both Th1- and Th17-mediated immune responses are markedly diminished when this enzyme is absent resulting in reduced resistance to Leishmania major infection and attenuation of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. In addition, IPMK-deficient naive CD4+ T cells display aberrant T cell activation and impaired differentiation into Th17 cells, which is associated with reduced activation of Akt, mechanistic target of rapamycin (mTOR), and STAT3. Mechanistically, IPMK as a phosphatidylinositol 3-kinase (PI3-kinase) controls the production of phosphatidylinositol (3,4,5)-trisphosphate, thereby promoting T cell activation, differentiation, and effector functions. Our findings suggest that IPMK acts as a critical regulator of Th1 and Th17 differentiation, highlighting the physiological importance of IPMK in Th1- and Th17-mediated immune homeostasis.

immunology↗

bioRxiv2023

56Fe ion exposure increases the incidence of lung and brain tumors at a similar rate in male and female mice

The main deterrent to long-term space travel is the risk of Radiation Exposure Induced Death (REID). The National Aeronautics and Space Administration (NASA) has adopted Permissible Exposure Levels (PELs) to limit the probability of REID to 3% for the risk of death due to radiation-induced carcinogenesis. The most significant contributor to current REID estimates for astronauts is the risk of lung cancer. Recently updated lung cancer estimates from Japans atomic bomb survivors showed that the excess relative risk of lung cancer by age 70 is roughly four-fold higher in females compared to males. However, whether sex differences may impact the risk of lung cancer due to exposure to high charge and energy (HZE) radiation is not well studied. Thus, to evaluate the impact of sex differences on the risk of solid cancer development post-HZE radiation exposure, we irradiated Rbfl/fl; Trp53fl/+ male and female mice infected with Adeno-Cre with various doses of 320 kVp X-rays or 600 MeV/n 56Fe ions and monitored them for any radiation-induced malignancies. We observed that lung adenomas/carcinomas and esthesioneuroblastomas (ENBs) were the most common primary malignancies in X-ray and 56Fe ion-exposed mice, respectively. In addition, 1 Gy 56Fe ion exposure compared to X-rays led to a significantly higher incidence of lung adenomas/carcinomas (p=0.02) and ENBs (p<0.0001). However, we did not find a significantly higher incidence of any solid malignancies in female mice as compared to male mice, regardless of radiation quality. Furthermore, gene expression analysis of ENBs suggested a distinct gene expression pattern with similar hallmark pathways altered, such as MYC targets and MTORC1 signaling, in X-ray and 56Fe ion-induced ENBs. Thus, our data revealed that 56Fe ion exposure significantly accelerated the development of lung adenomas/carcinomas and ENBs compared to X-rays, but the rate of solid malignancies was similar between male and female mice, regardless of radiation quality.

cancer biology↗

bioRxiv2023

A burns and COVID-19 shared stress responding gene network deciphers CD1C-CD141- DCs as the key cellular components in septic prognosis

Differential body responses to various stresses, infectious or noninfectious, govern clinical outcomes ranging from asymptoma to death. However, the common molecular and cellular nature of the stress responsome across different stimuli is not described. In this study, we compared the expression behaviors between burns and COVID-19 infection by choosing the transcriptome of peripheral blood from related patients as the analytic target since the blood cells reflect the systemic landscape of immune homeostasis. We identified an immune co-stimulator (CD86)-centered network, named stress-response core (SRC), which coordinated multiple immune processes and was robust in membership and highly related to the clinical traits in both burns and COVID-19. An independent whole blood single-cell RNA sequencing of COVID-19 patients demonstrated that the monocyte-dendritic cell (Mono-DC) wing was the major cellular source of the SRC, among which the higher expression of the SRC in the monocyte was associated with the asymptomatic COVID-19 patients, while the quantity-restricted and function-defected CD1C-CD141-DCs were recognized as the key signature which linked to bad consequences in COVID-19. Specifically, the proportion of the CD1C-CD141-DCs and their SRC expression levels were step-wise reduced along with worse clinic conditions while the sub-cluster of CD1C-CD141-DCs of the critical COVID-19 patients was characterized of IFN signaling quiescence, high mitochondrial metabolism and immune-communication inactivation. Thus, our study identified an expression-synchronized and function-focused gene network which was decreased under burns and COVID-19 stress and argued the CD1C-CD141-DC as the prognosis-related cell population which might serve as a new target of diagnosis and therapy.

immunology↗

bioRxiv2022

Neurodegeneration Risk Factor, EIF2AK3 (PERK), Influences Tau Protein Aggregation

Tauopathies are neurodegenerative diseases caused by pathologic misfolded tau protein aggregation in the nervous system. Population studies implicate EIF2AK3 (eukaryotic translation initiation factor 2 alpha kinase 3), better known as PERK (protein kinase R-like endoplasmic reticulum kinase), as a genetic risk factor in several tauopathies. PERK is a key regulator of intracellular proteostatic mechanisms - Unfolded Protein Response (UPR) and Integrated Stress Response (ISR). Previous studies found that tauopathy-associated PERK variants encoded functional hypomorphs with reduced signaling in vitro. But, it remained unclear how altered PERK activity led to tauopathy. Here, we chemically or genetically modulated PERK signaling in cell culture models of tau aggregation and found that PERK pathway activation prevented tau aggregation while inhibition exacerbated tau aggregation. In primary tauopathy patient brain tissues, we found that reduced PERK signaling correlated with increased tau neuropathology. We found that tauopathy-associated PERK variants targeted the ER luminal domain; and two of these variants damaged hydrogen bond formation. Our studies support that PERK activity protects against tau aggregation and pathology. This may explain why people carrying hypomorphic PERK variants have increased risk for developing tauopathies. Finally, our studies identify small molecule augmentation of PERK signaling as an attractive therapeutic strategy to treat tauopathies by preventing tau pathology.

neuroscience↗

bioRxiv2021

Label-free three-dimensional analyses of live cells with deep-learning-based segmentation exploiting refractive index distributions

Visualisations and analyses of cellular and subcellular organelles in biological cells is crucial for the study of cell biology. However, existing imaging methods require the use of exogenous labelling agents, which prevents the long-time assessments of live cells in their native states. Here we propose and experimentally demonstrate three-dimensional segmentation of subcellular organelles in unlabelled live cells, exploiting a 3D U-Net-based architecture. We present the high-precision three-dimensional segmentation of cell membrane, nucleus membrane, nucleoli, and lipid droplets of various cell types. Time-lapse analyses of dynamics of activated immune cells are also analysed using label-free segmentation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/445351v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@b92093org.highwire.dtl.DTLVardef@9caa8org.highwire.dtl.DTLVardef@d81408org.highwire.dtl.DTLVardef@b3c87_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2021

A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum

The histone acetyltransferase GCN5-associated SAGA complex is evolutionarily conserved from yeast to human and functions as a general transcription co-activator in global gene regulation. In this study, we identified a divergent GCN5 complex in Plasmodium falciparum, which contains two plant homeodomain (PHD) proteins (PfPHD1 and PfPHD2) and a plant apetela2 (AP2)-domain transcription factor (PfAP2-LT). To dissect the functions of the PfGCN5 complex, we generated parasites with the bromodomain deletion in PfGCN5 and the PHD domain deletion in PfPHD1. The two deletion mutants closely phenocopied each other, exhibiting significantly reduced merozoite invasion of erythrocytes and elevated sexual conversion. These domain deletions caused dramatic decreases not only in histone H3K9 acetylation but also in H3K4 trimethylation, indicating synergistic crosstalk between the two euchromatin marks. Domain deletion in either PfGCN5 or PfPHD1 profoundly disturbed the global transcription pattern, causing altered expression of more than 60% of the genes. At the schizont stage, these domain deletions were linked to specific downregulation of merozoite genes involved in erythrocyte invasion, many of which harbor the DNA-binding motifs for AP2-LT and/or AP2-I, suggesting targeted recruitment of the PfGCN5 complex to the invasion genes by these specific transcription factors. Conversely, at the ring stage, PfGCN5 or PfPHD1 domain deletions disrupted the mutually exclusive expression pattern of the entire var gene family, which encodes the virulent factor PfEMP1. Correlation analysis between the chromatin state and alteration of gene expression demonstrated that up- and down-regulated genes in these mutants are highly correlated with the silenct and active chromatin states in the wild-type parasite, respectively. Collectively, the PfGCN5 complex represents a novel HAT complex with a unique subunit composition including the AP2 transcription factor, which signifies a new paradigm for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist. Author SummaryEpigenetic regulation of gene expression plays essential roles in orchestrating the general and parasite-specific cellular pathways in the malaria parasite Plasmodium falciparum. Using tandem affinity purification and proteomic characterization, we identified a divergent transcription co-activator - the histone acetyltransferase GCN5-associated complex in P. falciparum, which contains nine core components, including two PHD domain proteins (PfPHD1 and PfPHD2) and a plant apetela2-domain transcription factor. To understand the functions of the PfGCN5 complex, we performed gene disruption in two subunits of this complex, PfGCN5 and PfPHD1. We found that the two deletion mutants displayed very similar growth phenotypes, including significantly reduced merozoite invasion rates and elevated sexual conversion. These two mutants were associated with dramatic decreases in histone H3K9 acetylation and H3K4 trimethylation, which led to global changes in chromatin states and gene expression. Genes significantly affected by the PfGCN5 and PfPHD1 gene disruption include those participating in parasite-specific pathways such as invasion, virulence, and sexual development. In conclusion, this study presents a new model of the PfGCN5 complex for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist.

microbiology↗

bioRxiv2020

SRF is a non-histone methylation target of KDM2B and SET7 in the regulation of myogenesis

Demethylation of histone lysines, one of the most important modifications in transcriptional regulation, is associated with various physiological states. KDM2B is a histone H3K4, H3K36, and H3K79 demethylase associated with the repression of transcription. Here, we present a novel mechanism by which KDM2B demethylates serum response factor (SRF) K165 to negatively regulate muscle differentiation, which is counteracted by histone methyltransferase SET7. We show that KDM2B inhibited skeletal muscle differentiation by inhibiting the transcription of SRF-dependent genes. Both KDM2B and SET7 regulated the balance of SRF K165 methylation. SRF K165 methylation was required for the transcriptional activation of SRF and for the promoter occupancy of SRF-dependent genes. SET7 inhibitors blocked muscle cell differentiation. Taken together, these data indicate that SRF is a non-histone target of KDM2B and that the methylation balance of SRF maintained by KDM2B and SET7 plays an important role in muscle cell differentiation.

developmental biology↗

bioRxiv2019

Rapid and label-free identification of individual bacterial pathogens exploiting three-dimensional quantitative phase imaging and deep learning

The healthcare industry is in dire need for rapid microbial identification techniques. Microbial infection is a major healthcare issue with significant prevalence and mortality, which can be treated effectively during the early stages using appropriate antibiotics. However, determining the appropriate antibiotics for the treatment of the early stages of infection remains a challenge, mainly due to the lack of rapid microbial identification techniques. Conventional culture-based identification and matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy are the gold standard methods, but the sample amplification process is extremely time-consuming. Here, we propose an identification framework that can be used to measure minute quantities of microbes by incorporating artificial neural networks with three-dimensional quantitative phase imaging. We aimed to accurately identify the species of bacterial bloodstream infection pathogens based on a single colony-forming unit of the bacteria. The successful distinction between a total of 19 species, with the accuracy of 99.9% when ten bacteria were measured, suggests that our framework can serve as an effective advisory tool for clinicians during the initial antibiotic prescription. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/596486v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@786668org.highwire.dtl.DTLVardef@8b4eb4org.highwire.dtl.DTLVardef@1dc2452org.highwire.dtl.DTLVardef@1d4888c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

Deep-learning based three-dimensional label-free tracking and analysis of immunological synapses of chimeric antigen receptor T cells

We propose and experimentally validate a label-free, volumetric, and automated assessment method of immunological synapse dynamics using a combinational approach of optical diffraction tomography and deep learning-based segmentation. The proposed approach enables automatic and quantitative spatiotemporal analyses of immunological synapse kinetics regarding morphological and biochemical parameters related to the total protein densities of immune cells, thus providing a new perspective for studies in immunology.

immunology↗