Biology subjects

Kim, S.-Y.

Publications and source records attributed to Kim, S.-Y..

At least 19 recordsLinked to original sources

bioRxiv2026

A Multiclass Mechanistic Model of Vaccine-Induced Humoral Response

Vaccine-induced humoral immunity emerges from complex interactions among competing B-cell populations and antibody production in response to antigen exposure, yet the mechanisms governing these interactions remain only partially understood. We developed a mechanistic mathematical model that integrates vaccine regimen features, immunogen kinetics, multiclass B-cell dynamics, and germinal center processes. The model was calibrated to data from the G001 HIV vaccine trial evaluating eOD-GT8, a germline-targeting immunogen designed to activate VRC01-class precursor B cells capable of developing into broadly neutralizing antibody-producing cells. The model reproduced key features of the observed B-cell and antibody responses, enabled estimation of class-specific activation and competition parameters, and supported investigation of the identifiability of competition parameters. Activation rates varied across B-cell classes, with memory B cells exhibiting substantially higher activation rates than naive B cells. Importantly, competition was stronger within than between classes, with the strongest competition occurring among VRC01-class B cells. These findings suggest that class-specific differences in activation and competition shape the magnitude and composition of vaccine-induced humoral response and may influence the expansion of broadly neutralizing antibody precursors. More broadly, the model provides a quantitative framework for dissecting multiclass B-cell competition and antibody responses, and for evaluating how vaccination strategies shape humoral immunity.

immunology↗

bioRxiv2026

AnimalTA: A simple yet flexible tool for video tracking and manual corrections.

O_LIVideo-tracking programs have now become an essential tool for researchers measuring animal behavior across biological fields. The panel of available programs is growing rapidly, providing researchers with numerous specific tools that will match their precise needs. However, their proliferation may complicate post-tracking data processing, and some programs do not even provide tools for correcting tracking errors or analysing tracking data. In the case of commercial software, the loss of access to a program due to budget limitations or researchers mobility from one institution to another could prevent them from accessing and visualizing their tracking data. C_LIO_LIThere is therefore a growing need for an accessible and flexible tool to handle post-tracking processes such as the correction and analysis of tracking data obtained across different video-tracking programs. C_LIO_LIWe present here the latest update of the video tracking and analysis program AnimalTA. With this new release, we propose to solve the above-mentioned problems by providing the scientific community with a program that will allow for data importation from other video-tracking programs. Like in its previous versions, AnimalTA remains a free, open-source, and highly user-friendly program, ensuring that it will always be accessible without restriction. Now, with this new importation option, users who performed their tracking with other programs can benefit from AnimalTAs complete toolset of data visualization, correction, and analysis. C_LIO_LIFinally, this article gives an overview of the other main improvements associated with this new release. The program is now faster in both video importation and tracking, proposes an amplified toolset for data visualization and correction, and features new options for data analysis. C_LI

animal behavior and cognition↗

bioRxiv2026

Terminal Schwann Cells Regulate Presynaptic Vesicle Homeostasis but Not Neuromuscular Junction Integrity in Mice

Terminal Schwann cells (tSCs) are specialized glial cells persistently residing at the neuromuscular junction (NMJ), where they are widely postulated to participate in synaptic transmission and maintenance. However, elucidating their precise in vivo roles has been hindered by a lack of tSC-specific genetic models, as conventional tools simultaneously targeted axonal Schwann cells. Here, we identify Col20a1 as a highly specific marker for tSCs through single-cell transcriptomic analysis and establish a novel Col20a1-CreERT2 knock-in mouse model. Utilizing this model, we achieved highly specific systemic labeling and ablation of tSCs during the postnatal maturation window. Surprisingly, systemic tSC loss disrupted neither gross NMJ architecture nor overall motor behavior. Instead, electrophysiological and ultrastructural analyses revealed profound pre-synaptic defects, characterized by increased spontaneous miniature endplate potentials (mEPPs), accelerated synaptic depression during high-frequency stimulation, and significant physical depletion of pre-synaptic vesicles. Furthermore, long-term analysis revealed a robust glial repopulation that sustained prolonged neuromuscular integrity. Together, our findings establish Col20a1 as a definitive genetic handle for tSC research, delineating that while tSCs are dispensable for macroscopic synaptic structure, they serve a precise and critical role in regulating pre-synaptic vesicle homeostasis.

neuroscience↗

bioRxiv2026

Inhibition of oogenic JNK preserves fertility and ovarian hormones during DNA-damaging cancer therapy

Primary ovarian insufficiency (POI) and related infertility, early menopause, and endocrine disorders due to hormonal deficiency are major side effects in young female cancer patients undergoing cancer therapy. Current strategies preserving the fertility and hormonal functions of the ovary remain imperfect due to concerns of feasibility, efficacy, or safety. Herein, we identified c-Jun N-terminal kinase (JNK) as a pivotal regulator of the DNA damage response (DDR) signaling in oocytes of primordial follicles in response to DNA-damaging cancer therapy. Using pharmacological JNK inhibition and a genetically modified mouse model with oocyte-specific JNK deletion, together with histological, bioinformatic, and molecular approaches, we demonstrated that JNK inhibition prevented chemotherapy-induced oocyte apoptosis and POI, and preserved long-term reproductive cycles and fertility. Mechanistically, JNK was activated in response to chemotherapy-induced DNA damage in oocytes of primordial follicles, causing activation of transcription factor TAp63 and subsequent oocyte apoptosis, ultimately resulting in diminished ovarian reserve and POI. A more clinically relevant breast cancer-bearing mouse model revealed that JNK inhibition preserved the ovarian reserve without compromising anti-cancer efficacy of chemotherapy. Together, our study identifies oocyte-intrinsic JNK as a promising target for developing ovarian protectants and safeguarding reproductive health and fertility in young female cancer survivors.

pharmacology and toxicology↗

bioRxiv2026

HAETAE: A highly accurate and efficient epigenome transformer for tissue-specific histone modification prediction

While genomic models trained on four bases often fail to capture cell-type specificity, we introduce HAETAE, which integrates 5-methylcytosine from long-read sequencing into a 5-base framework. By explicitly modeling epigenetic context, HAETAE achieves state-of-the-art accuracy (>0.95) with orders of magnitude fewer parameters, challenging the prevailing scaling-law paradigm. Furthermore, HAETAE deciphers tissue-specific regulatory logic, as demonstrated by revealing the distinct, context-dependent functional impact of the TERT promoter mutation across diverse tissues.

bioinformatics↗

bioRxiv2026

Fixative eXchange (FX)-seq: Scalable Single-nucleus RNA Sequencing Analysis of PFA-fixed or FFPE Tissue

Single-nucleus RNA sequencing (snRNA-seq) of clinical formalin-fixed, paraffin-embedded (FFPE) samples has long been a challenge due to low reverse transcription (RT) yields. Here, we present Fixative-eXchange (FX)-seq, a highly scalable snRNA-seq method for heavily paraformaldehyde (PFA)-fixed and/or FFPE samples. We employ an organocatalyst to facilitate the removal of PFA crosslinks to increase RT yield and additional regiospecific Pt(II)-based crosslinking of RNA molecules to prevent leakage. FX-seq reveals cellular heterogeneity across multiple fixed samples by analyzing 321,710 nuclei, including PFA-fixed tissue, FFPE blocks, thin FFPE and hematoxylin and eosin (H&E)-stained sections from mouse brain and human cancer specimens such as gastrointestinal stromal tumor and colorectal cancer. FX-seq enables integrated analysis with pathologist annotation to label tumor and non-tumor regions of H&E-stained sections. FX-seq can also be applied to PFA-perfusion-based animal studies, large human cohort studies, and personalized drug treatment through precision medicine.

genomics↗

bioRxiv2025

Non-selective beta blockers reduce bystander CD8+ T cell activation in decompensated liver cirrhosis

Cirrhosis is characterized by immune dysfunction in which activated CD8 T cells fuel systemic inflammation and disease progression. Non-selective beta-blockers (NSBB), widely prescribed for portal hypertension, have incompletely understood immunomodulatory effects. Here we show that CD8 T cells express {beta}2-adrenergic receptors, enriched in bystander relative to antigen-specific subsets. In vitro, the NSBB propranolol selectively suppressed cytokine-driven bystander activation, reducing CD69CXCR6 and NKG2D populations and pro-inflammatory cytokines, while preserving antigen-specific responses. Transcriptomic profiling after NSBB treatment revealed downregulation of interferon signaling pathway via STAT1. In paired blood and ascites samples from patients with decompensated cirrhosis (n = 31), NSBB therapy was associated with reduced bystander-activated CD8 T cells. In a retrospective cohort (n = 624), NSBB therapy correlated with lower systemic and intrahepatic inflammation. These findings identify {beta}-adrenergic blockade as a mechanism that restrains bystander CD8 T cell responses without impairing antigen-specific immunity, supporting NSBB therapy as a strategy to mitigate inflammation and improve outcomes in cirrhosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/688703v1_ufig1.gif" ALT="Figure 1000"> View larger version (29K): org.highwire.dtl.DTLVardef@191c6dcorg.highwire.dtl.DTLVardef@196aef0org.highwire.dtl.DTLVardef@1b73c83org.highwire.dtl.DTLVardef@e5d6fb_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer

Dysregulation of Polycomb Repressive Complex 2 (PRC2) is established to contribute to cancer. Of its catalytic subunits, EZH1 and EZH2, EZH2 mutations in cancer have been extensively identified and studied, but the role of EZH1 in cancer remains largely unexplored. The recurrent presence of the EZH1Q571R mutation in follicular thyroid cancer suggests its involvement in tumor progression. Using EZH1 ChIP-seq, ATAC-seq, and H3K27me3 CUT&Tag, we demonstrated that EZH1Q571R enhances chromatin binding and compaction and stimulates PRC2-EZH1 catalytic activity, leading to increased H3K27me3 levels and repression of tumor suppressor genes. Purified PRC2-EZH1Q571R demonstrated a significant increase in histone methyltransferase activity compared to PRC2-EZH1WT via enhanced nucleosome binding and DNA compaction. Notably, this effect is particularly observed with EZH1Q571R but only to a lesser extent with the corresponding EZH2Q570R mutation, highlighting it as an EZH1-specific mechanism. We additionally demonstrated PRC2-EZH1Q571R to efficiently methylate H3K27 in pre-existing H3K36me2/3 nucleosomes, disrupting chromatin homeostasis. Our findings provide key insights into the molecular pathogenesis of EZH1Q571R-driven follicular thyroid cancer.

molecular biology↗

bioRxiv2025

TCR signaling via NFATc1 constrains IL-15-induced NK-like activation of human memory CD8+ T cells

Here we investigated the regulatory mechanisms of TCR-independent bystander activation and NK-like cytotoxicity of human memory CD8+ T cells. We found that TCR signals suppressed characteristic features of IL-15-induced CD8+ T-cell activation, including increased NKG2D expression and upregulation of genes related to NK cytotoxicity and IFN response. Moreover, ionomycin suppressed IL-15-induced bystander activation and NK-like cytotoxicity, indicating that Ca2+-calcineurin signaling is responsible for TCR-mediated suppression of IL-15-induced bystander activation. In detail, NFATc1 suppressed IL-15-induced bystander activation via binding to AP-1 that is necessary for the IL-15-induced upregulation of NK cytotoxicity-related genes. Consistent with these results, calcineurin inhibitors enhanced IL-15-induced NKG2D expression in the presence of TCR signals. Additionally, we defined genes upregulated by IL-15 and downregulated by concurrent TCR signals as an IL-15-induced bystander activation gene set, and found that this gene signature was upregulated in bystander CD8+ T cells from patients with hepatitis A virus infection. This study paves the way for further investigation of bystander CD8+ T-cell activation in various pathological conditions, and its regulation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/632884v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1e6c320org.highwire.dtl.DTLVardef@114a23eorg.highwire.dtl.DTLVardef@1a7b9edorg.highwire.dtl.DTLVardef@9faccc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITCR signaling downregulates IL-15-induced transcriptomic features related to NK-like bystander activation of human memory CD8+ T cells via the Ca2+-calcineurin pathway. C_LIO_LINFATc1 suppresses IL-15-induced bystander activation via binding to AP-1, which is responsible for IL-15-induced NK-like cytotoxic activity. C_LIO_LICalcineurin inhibitors cannot suppress IL-15-induced bystander CD8+ T-cell activation, and paradoxically increase IL-15-induced NKG2D expression in the presence of TCR signals. C_LIO_LIGenes upregulated by IL-15 and downregulated by concurrent TCR signals define the gene set of bystander CD8+ T-cell activation, which was validated in disease contexts. C_LI

immunology↗

bioRxiv2024

Identification of neuron-glia signaling feedback in human schizophrenia using patient-derived, mix-and-match forebrain assembloids

Although abnormal activities across multiple cell types are believed to contribute to the development of various neurodevelopmental disorders, current brain organoid technologies fall short in accurately modeling the dynamic cellular interactions in the human brain. Recently, we developed a cellular reconstitution technology to create human forebrain assembloids with enhanced cellular diversity, representing dynamic interactions between neurons and glial cells. Here, we created patient-derived, mix-and-match forebrain assembloids, in which neurons, astrocytes, and microglia from both healthy individuals and schizophrenia patients were reconstituted in a combinatorial manner, and identified aberrant cellular interactions between neurons and glial cells in human schizophrenia. At the early stage, schizophrenia forebrain assembloids showed premature neurogenesis induced by the abnormal proliferation and differentiation of neural progenitor cells. Integrated modular analysis of gene expression in post-mortem schizophrenia brain tissue and brain assembloids found increased expression of tumor protein p53 (TP53) and nuclear factor of activated T-cells 4 (NFATC4), which functioned as master transcriptional regulators to epigenetically reprogram the transcriptome involved in the cellular dynamics of neuronal progenitor cells, leading to premature neurogenesis. At the later stage, we observed weakened structures of laminar organization of the cortical layers in forebrain assembloids and identified the neuron-dependent transcriptional plasticity of glial cells and their altered signaling feedback with neurons, in which neuronal urocortin (UCN) and protein tyrosine phosphatase receptor type F (PTPRF) elicited the expression of Wnt family member 11 (WNT11) and thrombospondin 4 (THBS4) in astrocytes and microglia, respectively. These aberrant signaling axes altered the neuronal transcriptome associated with neuronal response to various stimuli and synthetic processes of biomolecules, resulting in reduced synapse connectivity. Thus, we elucidated developmental stage-specific, multifactorial mechanisms by which dynamic cellular interplay among neural progenitor cells, neurons, and glial cells contribute to the development of the human schizophrenia brain. Our study further demonstrated the potential and applicability of patient-derived forebrain assembloid technology to advance our understanding of the pathogenesis of various neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

A bacterial site 2 protease contributes to RNA phage resistance by targeting phage lysis protein

Lytic phages culminate their lifecycle by causing lysis of the infected host cell. Despite extensive research on the molecular mechanisms of phage lysis, our understanding of anti-phage resistance mechanisms during the lysis stage remains less understood. Here, we demonstrated that MucP, a site 2 protease of Pseudomonas aeruginosa (PA), mitigates the activity of the RNA phage PP7 lysis protein (LP), which contains a transmembrane (TM) helix, suggesting that MucP act as a resistance mechanism against PP7-induced lysis. We identified an LP variant (LP*) having enhanced helical propensity due to P26L and S40L mutations, which was unaffected by MucP and exhibited killing activity against PA strains that are resistant to the wild type LP, with an inverse correlation between MucP activity and LP susceptibility. A PP7 mutant with LP* exhibited MucP-escaper phenotype such as discernable plaque formation on MucP-expressing cells. These results suggest that MucP targets the RNA phage LP at the TM helix in certain strains, providing a resistance function compromising phage lysis by utilizing an existing bacterial enzyme in PA. IMPORTANCEDespite the importance of cell lysis as the last stage of phage lifecycle, the factors influencing coordinated lysis remain elusive in the context of phage-bacteria interactions. Our study identifies MucP, a membrane protease in Pseudomonas aeruginosa (PA), as a resistance factor against the RNA phage PP7 by destabilizing its lysis protein (LP), with lower helical tendency at transmembrane (TM) domain. An LP variant with higher helical tendency exhibits strong killing activity against PA isolates, revealing an inverse correlation between MucP activity and LP susceptibility. Since MucP is a conserved protease in mucoid conversion of PA, we propose that MucP offers an intrinsic or passive defense or resistance mechanism against the RNA phage, whose activities vary among the diverse PA isolates.

microbiology↗

bioRxiv2024

Neuron-derived Prox1 suppresses injury-induced reprogramming of Muller glia to proliferative retinal progenitor cells

Individuals with retinal degenerative diseases face significant obstacles in restoring normal vision due to the inability to regenerate degenerated retinal cells. While retinal neurons can be regenerated from Muller glia (MG) in cold-blooded vertebrates, this regenerative ability is lacking in mammals, indicating the limited competence of mammalian MG for retinal regeneration. In this study, we elucidate the role of prospero-related homeobox 1 (Prox1) in rendering the mammalian retina incompetent for MG-derived regeneration. Prox1 accumulates in MG in the degenerating human and mouse retinas but not in those in the regenerating zebrafish retina. Strikingly, Prox1 in mouse MG originated from neighboring retinal neurons through intercellular protein transfer. Consequently, inhibition of Prox1 transfer to MG enables the reprogramming of MG into proliferative retinal progenitor cells in injured mouse retinas. Furthermore, we succeeded in regenerating retinal neurons and delaying vision loss in retinitis pigmentosa disease model in mice by adenoassociated viral gene delivery of an anti-Prox1 antibody that sequesters extracellular Prox1 in the mouse retina. Taken together, our findings highlight the therapeutic potential of anti-Prox1 therapy in restoring the regenerative potential of the mammalian retina.

developmental biology↗

bioRxiv2024

Quantitative Analysis of Roles of Direct and Indirect Pathways for Action Selection in The Basal Ganglia

We are concerned about action selection in the basal ganglia (BG). We quantitatively analyze functions of direct pathway (DP) and indirect pathway (IP) for action selection in a spiking neural network with 3 competing channels. For such quantitative analysis, in each channel, we obtain the competition degree [C]d, given by the ratio of strength of DP ([S]DP) to strength of IP ([S]IP) (i.e., [C]d = [S]DP /[S]IP). Then, a desired action is selected in the channel with the largest [C]d. Desired action selection is made mainly due to strong focused inhibitory projection to the output nucleus, SNr (substantia nigra pars reticulata) via the DP in the corresponding channel. Unlike the case of DP, there are two types of IPs; intra-channel IP and inter-channel IP, due to widespread diffusive excitation from the STN (subthalamic nucleus). The intra-channel IP serves a function of brake to suppress the desired action selection. In contrast, the inter-channel IP to the SNr in the neighboring channels suppresses competing actions, leading to highlight the desired action selection. In this way, function of the inter-channel IP is opposite to that of the intra-channel IP. However, to the best of our knowledge, no quantitative analysis for such functions of the DP and the two IPs was made. Here, through direct calculations of the DP and the intra- and the inter-channel IP presynaptic currents into the SNr in each channel, we obtain the competition degree of each channel to determine a desired action, and then functions of the DP and the intra- and inter-channel IPs are quantitatively made clear. PACS numbers87.19.lj, 87.19.lu, 87.19.rs

neuroscience↗

bioRxiv2023

Break-up and Recovery of Harmony between Direct and Indirect Pathways in The Basal Ganglia; Huntington's Disease and Treatment

The basal ganglia (BG) in the brain exhibit diverse functions for motor, cognition, and emotion. Such BG functions could be made via competitive harmony between the two competing pathways, direct pathway (DP) (facilitating movement) and indirect pathway (IP) (suppressing movement). As a result of break-up of harmony between DP and IP, there appear pathological states with disorder for movement, cognition, and psychiatry. In this paper, we are concerned about the Huntingtons disease (HD), which is a genetic neurodegenerative disorder causing involuntary movement and severe cognitive and psychiatric symptoms. For the HD, the number of D2 SPNs (ND2) is decreased due to degenerative loss, and hence, by decreasing xD2 (fraction of ND2), we investigate break-up of harmony between DP and IP in terms of their competition degree[C] d, given by the ratio of strength of DP ([S]DP) to strength of IP (([S]IP) (i.e.,[C] d = ([S]DP /([S]IP). In the case of HD, the IP is under-active, in contrast to the case of Parkinsons disease with over-active IP, which results in increase in[C] d (from the normal value). Thus, hyperkinetic dyskinesia such as chorea (involuntary jerky movement) occurs. We also investigate treatment of HD, based on optogenetics and GP ablation, by increasing strength of IP, resulting in recovery of harmony between DP and IP. Finally, we study effect of loss of healthy synapses of all the BG cells on HD. Due to loss of healthy synapses, disharmony between DP and IP increases, leading to worsen symptoms of the HD.

biophysics↗

bioRxiv2023

Depletion of SMN Protein in Mesenchymal Progenitors Impairs the Development of Bone and Neuromuscular Junction in Spinal Muscular Atrophy

Spinal Muscular Atrophy (SMA) is a neuromuscular disorder characterized by the deficiency of the survival motor neuron (SMN) protein, which leads to motor neuron dysfunction and muscle atrophy. In addition to the requirement for SMN in motor neurons, recent studies suggest that SMN deficiency in peripheral tissues plays a key role in the pathogenesis of SMA. Using limb mesenchymal progenitor cells (MPCs)-specific SMN-depleted mouse models, we reveal that SMN reduction in chondrocytes and fibro-adipogenic progenitors (FAPs) derived from limb MPCs causes defects in the development of bone and neuromuscular junction (NMJ), respectively. We showed that impaired growth plate homeostasis, which causes skeletal growth defects in SMA, is due to reduced IGF signaling from chondrocytes rather than the liver. Furthermore, the reduction of SMN in FAPs resulted in abnormal NMJ maturation, altered release of neurotransmitters, and NMJ morphological defects. Transplantation of healthy FAPs rescued the morphological deterioration. Our findings highlight the significance of mesenchymal SMN in neuromusculoskeletal pathogenesis in SMA and provide insights into potential therapeutic strategies targeting mesenchymal cells for the treatment of SMA.

neuroscience↗

bioRxiv2023

Ying-Yang Competitive Harmony between Direct and Indirect Pathways in A Spiking Neural Network of The Basal Ganglia

The basal ganglia (BG) show a variety of functions for motor and cognition. There are two competitive pathways in the BG; direct pathway (DP) which facilitates movement and indirect pathway (IP) which suppresses movement. It is well known that diverse functions of the BG may be made through "balance" between DP and IP. But, to the best of our knowledge, so far no quantitative analysis for such balance was done. In this paper, as a first time, we introduce the competition degree [C]d between DP and IP. Then, by employing [C]d, we quantify their competitive harmony (i.e., competition and cooperative interplay), which could lead to improving our understanding of the traditional "balance" so clearly and quantitatively. We first consider the case of normal dopamine (DA) level of {phi}* = 0.3. In the case of phasic cortical input (10 Hz), a healthy state with [Formula] (i.e., DP is 2.82 times stronger than IP) appears. In this case, normal movement occurs via harmony between DP and IP. Next, we consider the case of decreased DA level,{phi} ={phi} *(= 0.3) xDA (1 > xDA [≥] 0). With decreasing xDA from 1, the competition degree [C]d between DP and IP decreases monotonically from[Formula], which results in appearance of a pathological Parkinsonian state with reduced [C]d. In this Parkinsonian state, strength of IP is much increased than that in the case of normal healthy state, leading to disharmony between DP and IP. Due to such break-up of harmony between DP and IP, impaired movement occurs. Finally, we also study treatment of the pathological Parkinsonian state via recovery of harmony between DP and IP. PACS numbers87.19.lj, 87.19.lu, 87.19.rs

neuroscience↗

bioRxiv2023

KoNA: Korean Nucleotide Archive as a New Data Repository for Nucleotide Sequence Data

During the last decade, generation and accumulation of petabase-scale high-throughput sequencing data have resulted in ethical and technical challenges, including access to human data, and transfer, storage, and sharing of enormous amount of data. To promote data-driven research in biology, the Korean government announced that all the biological data generated from government-funded research projects should be deposited in the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. We introduce the Korean Nucleotide Archive (KoNA), a repository for nucleotide sequence data. As of July 2022, the Korean Read Archive in KoNA has collected over 477 TB of raw next generation sequencing data from several national genome projects. To ensure data quality and prepare for international alignment, a standard operating procedure (SOP) was adopted, which is similar to the International Nucleotide Sequence Database Collaboration. The SOP includes quality control processes for submitted data and metadata using an automated pipeline followed by manual examination. To ensure fast and stable data transfer, a high-speed transmission system called GBox is used in KoNA. Furthermore, the data uploaded to or downloaded from KoNA through GBox can be readily processed in a cloud-computing service for genomic data analysis called Bio-Express. This seamless coupling of KoNA, GBox, and Bio-Express enhances data experience including submission, access, and analysis of raw nucleotide sequences. KoNA not only satisfies the unmet needs for a national sequence repository in Korea, but also provides datasets to researchers globally and contribute to advances in genomics. KoNA is available at https://www.kobic.re.kr/kona/.

genomics↗

bioRxiv2023

Development of an in situ cell-type specific proteome analysis method using antibody-mediated biotinylation

Since proteins are essential molecules exerting cellular functions, decoding proteome changes is the key to understanding the normal physiology and pathogenesis mechanism of various diseases. However, conventional proteomic studies are often conducted on tissue lumps, in which multiple cell types are entangled, presenting challenges in interpreting the biological dynamics among diverse cell types. While recent cell-specific proteome analysis techniques, like BONCAT, TurboID, and APEX, have emerged, their necessity for genetic modifications limits their usage. The alternative, laser capture microdissection (LCM), although it does not require genetic alterations, is labor-intensive, time-consuming, and requires specialized expertise, making it less suitable for large-scale studies. In this study, we develop the method for in situ cell-type specific proteome analysis using antibody-mediated biotinylation (iCAB), in which we combined immunohistochemistry (IHC) with the biotin-tyramide signal amplification approach. Poly-horseradish peroxidase (HRP) conjugated to the secondary antibody will be localized at a target cell type via a primary antibody specific to the target cell type and biotin-tyramide activated by HRP will biotinylate the nearby proteins. Therefore, the iCAB method can be applied to any tissues that can be used for IHC. As a proof-of-concept, we employed iCAB for mouse brain tissue enriching proteins for neuronal cell bodies, astrocytes, and microglia, followed by identifying the enriched proteins using 16-plex TMT-based proteomics. In total, we identified [~]8,400 and [~]6,200 proteins from enriched and non-enriched samples. Most proteins from the enriched samples showed differential expressions when we compared different cell type data, while there were no differentially expressed proteins from non-enriched samples. The cell type enrichment analysis with the increased proteins in respective cell types using Azimuth showed that neuronal cell bodies, astrocytes, and microglia data exhibited Glutamatergic Neuron, Astrocyte and Microglia/Perivascular Macrophage as the representative cell types, respectively. The proteome data of the enriched proteins showed similar subcellular distribution as non-enriched proteins, indicating that the iCAB-proteome is not biased toward any subcellular compartment. To our best knowledge, this study represents the first implementation of a cell-type-specific proteome analysis method using an antibody-mediated biotinylation approach. This development paves the way for the routine and widespread use of cell-type-specific proteome analysis. Ultimately, this could accelerate our understanding of biological and pathological phenomena.

systems biology↗