Biology subjects

Kim, H. K.

Publications and source records attributed to Kim, H. K..

17 recordsLinked to original sources

bioRxiv2026

Visual experience-driven switch in endothelial metabolic transporters is essential for cerebrovascular maturation

Angiogenesis and blood-brain barrier (BBB) maturation are tightly regulated by coordinated interactions among neuronal, glial, and endothelial cells. Although neuronal activity is essential for postnatal cerebrovascular development, how it is translated into endothelial programs that coordinate vascular maturation remains unknown. Here, we show that visual experience drives metabolic reprogramming in brain endothelial cells by decreasing the lactate transporter MCT1 while increasing the glucose transporter GLUT1, a switch that is essential for proper vascular development. Sustained endothelial expression of MCT1 impaired vascular development and BBB maturation, resulting in vascular leakage. Mechanistically, the developmental decline in TGF-beta signaling drives the endothelial MCT1-to-GLUT1 transition. Endothelial-derived TGF-beta1 further reinforces the immature angiogenic state through a lactate-dependent autocrine positive feedback loop, whereas sensory experience promotes astrocyte maturation, which attenuates endothelial TGF-beta signaling, potentially by altering the perivascular environment. Together, our findings identify a neuron-astrocyte-endothelial metabolic signaling axis that links sensory experience to endothelial metabolic reprogramming and coordinates the transition from angiogenesis to BBB maturation.

neuroscience↗

bioRxiv2026

Biotin-operated ligand trapping enables dynamic spatial redistribution of protein and organelle in living cells

Controlling protein localization through chemical biology tools is essential for mechanistic interrogations, functional perturbations, and therapeutic development. While existing tools cover a wide range of applications, no single approach simultaneously enables inducible trapping, controlled release, and visualization of a protein of interest (POI). To address this gap, we developed Biotin-Operated Ligand Trapping (BOLT), which combines a HaloTag-fused POI with a streptavidin trap. Desthiobiotin-conjugated Janelia Fluor HaloTag ligands enable POI visualization, trapping, and biotin-operated release. We demonstrate BOLT's capacity in synchronized secretory cargo release, microtubule-directed organelle movement and hitchhiking, and ectopically localizing nuclear transcription factor. Importantly, pulse-chase BOLT further reveals bidirectional endoplasmic reticulum-Golgi trafficking of an endogenous Golgi enzyme and distinguishes recycled from newly synthesized enzyme populations using distinct HTLs. Altogether, BOLT provides an all-in-one platform to interrogate how subcellular localization regulates protein function across HaloTag-compatible systems.

synthetic biology↗

bioRxiv2026

A custom two-in-one HIST and line-scanning confocal excitation module

Fluorescence microscopy applications often require specialized instruments that are optimized for different experimental goals. Here, we present a reconfigurable microscopy module that integrates highly inclined swept tile (HIST) illumination for high-sensitivity single-molecule imaging and line-scanning confocal microscopy for rapid and optically sectioned volumetric acquisition. The system shares major hardware components, including lasers, scanning optics, and detection hardware, while employing unique beam shaping pathways to enable rapid switching between modalities without realignment. We characterize the module performance by measuring the excitation beam profiles, the point spread functions (PSF), and the optical transfer functions (OTF) across 40x, 60x, and 100x magnifications and demonstrate imaging applications including diffraction-limited fixed and live-cell volumetric imaging, fluorescence recovery after photobleaching, and super-resolution DNA-PAINT and single particle tracking (SPT). We also demonstrate the capability to execute multimodal imaging workflows by performing confocal imaging for chromatin density classification correlated with SPT data of nuclear proteins with diverse functions. Together, these results demonstrate a versatile imaging platform capable of supporting complementary fluorescence imaging modalities within a single instrument.

bioengineering↗

bioRxiv2026

Cellular origin and therapeutic potential of SERPINA3N in ischemic stroke

Murine serine protease inhibitor clade A member 3N (SERPINA3N) and its human homolog SERPINA3 are injury-associated molecules induced in virtually all neurological conditions including ischemic stroke. Clinically, SERPINA3 is elevated in stroke patients, correlating with severe brain pathology and worse neurological outcomes. Yet, the exact cellular sources and therapeutic value of SERPINA3N/SERPINA3 in the ischemic brain remain elusive. Here, we report that oligodendrocytes are the major sources of SERPINA3/SERPINA3N and that SERPINA3N exerts neurotoxic effects in experimental cerebral ischemia. Given SERPINA3Ns secretory nature, we used knock-in Serpina3n-tdTom reporter mice to define its temporospatial evolution. The tdTom signal was barely detectable by day1 but gradually increased from day 3 through day 7 following cerebral ischemia. The majority of tdTom+ cells were identified as oligodendrocytes and astrocytes with fewer found in neurons or microglia. This cellular identity was corroborated by meta-analysis of single-cell transcriptomics datasets and human ischemic stroke brain data. Antagonizing SERPINA3N attenuated blood-brain barrier disruption, neuroinflammation, and neuronal damage and improved neurological function in a mouse model of cerebral ischemia. These findings resolve a longstanding debate regarding the cellular origins of SERPINA3N, identifying oligodendrocytes as its major source. Our studies highlight SERPINA3N antagonism as a possible therapeutic intervention for ischemic stroke, providing new insights for precision therapies that target oligodendroglia- or astroglia-specific SERPINA3N.

neuroscience↗

bioRxiv2026

Powassan Virus LB Neurovirulence and Lethality is Determined by Envelope Protein Domain III Residues

Powassan Viruses (POWV) are tick-borne Flaviviruses that cause lethal encephalitis and long-term neurologic sequelae. POWVs are divided into two lineages that share 86% genetic identity. POWV-LB (Lin I) was isolated from a fatal case of encephalitis, while POWV-LI9 (Lin II) is a tick-derived isolate that causes age-dependent lethality in mice. Domain III of Flavivirus envelope proteins (EDIII) directs cell attachment, and determines murine neuropathology and lethality. Here we developed POWV LB reverse genetics, analyzed the CNS of LB and recLB mutant infected mice, and assessed the role of EDIII residues in LB pathogenesis. LB infection of 50-week-old B6 mice focally activated microglia in the midbrain and cerebellum discrete from, and independent of, the location of envelope protein in the cerebral cortex, hippocampus and thalamus. Reverse genetic analysis of LB EDIII residues revealed that mutating D308N only partially reduced LB neuropathology and lethality. However, mutating D308N along with an adjacent EDIII residue, A310T, completely abolished LB-D308N/A310T neurovirulence, neuroinvasion and lethality, yet elicited neutralizing antibody responses that protected mice from a lethal WT LB challenge. Signifying changes in neurotropism, LB-D308N/A310T failed to activate microglia or yield detectable POWV RNA and antigen in the CNS. Overall, recombinant LB-D308N/A310T mutants fail to induce neurologic symptoms or neuropathology while eliciting a protective immune response. These findings reveal that EDIII residues determine the neurovirulence and lethality of lineage I POWVs and that genetically modifying EDIII provides a mechanism for POWV attenuation and vaccine development. ImportancePowassan virus causes lethal encephalitis and long-term neurological sequalae in survivors; however, there are currently no licensed POWV vaccines or therapeutics. POWVs are comprised of two genetic lineages (LB-Lin I; LI9 Lin II) that are derived from discrete ticks and small mammal hosts. Flavivirus envelope proteins determine cell attachment, viral tropism, and neurovirulent spread and lethality in mice. Here we created a POWV LB reverse genetics system and assessed mutations that determine LB neurovirulence in 50 wk old mice. Studies reveal novel LB neuropathology with divergent patterns of gliosis and POWV antigen expression within the CNS. Mice infected with an LB-D308N/A310T envelope mutant elicited responses that protect mice from a lethal LB challenge and failed to enter the CNS, cause neurologic symptoms, CNS pathology or lethality. LB reverse genetics permits defining determinants of LB neurovirulence that are required for rational vaccine development.

microbiology↗

bioRxiv2026

Injury-transduced SerpinOLs modulate neuroinflammation and glial activation in the diseased and non-diseased CNS

Oligodendroglial dysfunction is common in CNS diseases and injuries, but the molecular and functional responses of oligodendroglia to CNS pathologies remain poorly defined. Here, we report that oligodendrocytes (OLs) respond to demyelinating diseases by dysregulating serine protease inhibitor clade A member 3N (SERPINA3N). Homeostatic OLs transition to Serpina3n-expressing OLs (SerpinOLs) under other diseased conditions including stroke, endotoxicity, neurodegeneration, neurotrauma, and non-diseased healthy aging conditions. Mechanistically, general neuroinflammation or inflammatory mediators is insufficient for SerpinOL transition. Instead, oligodendrocyte damage/injury, even in the absence of neuroinflammation or glial activation, is sufficient for the transition. Phenotypically, SerpinOLs are characterized by molecular signatures of inflammatory and immune regulation and STAT3 signaling activation. Functionally, SerpinOLs exacerbate neuroinflammation and promote glial activation toward pro-inflammatory and neurodegenerative states. Together, our findings suggest SerpinOLs are a common population of injury-transduced OLs that amplify neuroinflammation and glial activation in the diseased and non-diseased CNS through SERPINA3N secretion. Our findings provide new insights into myelination-independent role of OLs in regulating CNS pathophysiology.

neuroscience↗

bioRxiv2025

Deciphering Tumor Microenvironment Dynamics in Tumorigenesis and Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma using Single-Cell RNA Sequencing

Esophageal squamous cell carcinoma (ESCC) exhibits profound inter-tissue heterogeneity, yet how immune and stromal ecosystems diverge between primary tumors and metastatic lymph nodes remains poorly understood. Here, we generated a single-cell atlas of 344,790 cells and paired T cell receptor profiles from primary tumor mucosa, adjacent mucosa, non-metastatic lymph nodes, and metastatic lymph nodes from 18 patients with treatment-naive ESCC. We identify compartment-specific immune and stromal architectures that shape distinct antitumor responses and suppressive programs. Primary tumors were characterized by marked enrichment of regulatory T cells (TREG) and activated dendritic cells coordinated through CTLA4-associated circuits, accompanied by accelerated CD8+ T cell differentiation toward intermediate and terminal exhaustion with loss of cytotoxicity. In contrast, metastatic lymph nodes preserved substantial pools of pre-exhausted CD8+ T cells with retained effector potential and strong clonal connectivity to the primary tumor, suggesting sustained antigen-driven trafficking. However, these reinvigoration-competent populations were embedded within a niche dominated by TREM2high macrophages that delivered SPP1-dependent suppressive signals to exhausted and regulatory T cells. Stromal lineages also displayed niche-specific specialization: tumor mucosa contained chemokine-rich inflammatory fibroblasts, whereas metastatic lymph nodes upregulated extracellular matrix remodeling programs. Together, our findings demonstrate that ESCC progression is governed by anatomically distinct exhaustion trajectories, clonal behaviors, stromal states, and suppressive circuits. This framework provides mechanistic insight into why lymph node response is a key determinant of clinical outcome and highlights the need for site-tailored immunomodulation strategies that target TREG-mediated suppression in primary tumors and TREM2high macrophage programs in metastatic nodes.

cancer biology↗

bioRxiv2024

Unveiling the influence of tumor and immune signatures on immune checkpoint therapy in advanced lung cancer

This study investigates the variability among patients with non-small cell lung cancer (NSCLC) in their responses to immune checkpoint inhibitors (ICI). Recognizing that patients with advanced-stage NSCLC rarely qualify for surgical interventions, it becomes crucial to identify biomarkers that influence responses to ICI therapy. We conducted an analysis of single-cell transcriptomes from 33 lung cancer biopsy samples, with a particular focus on 14 core samples taken before the initiation of palliative ICI treatment. Our objective was to link tumor and immune cell profiles with patient responses to ICI. We discovered that ICI non-responders exhibited a higher presence of CD4+ regulatory T cells, resident memory T cells, and TH17 cells. This contrasts with the diverse activated CD8+ T cells found in responders. Furthermore, tumor cells in non-responders frequently showed heightened transcriptional activity in the NF-kB and STAT3 pathways, suggesting a potential inherent resistance to ICI therapy. Through the integration of immune cell profiles and tumor molecular signatures, we achieved an discriminative power (AUC) exceeding 95% in identifying patient responses to ICI treatment. These results underscore the crucial importance of the interplay between tumor and immune microenvironment, including within metastatic sites, in affecting the effectiveness of ICIs in NSCLC.

bioinformatics↗

bioRxiv2023

Age-dependent Powassan Virus Lethality is Directed by Glial Cell Activation and Divergent Neuroinflammatory Cytokine Responses in a Murine Model

Powassan virus (POWV) is an emergent tick-borne flavivirus that causes fatal encephalitis in the elderly and long-term neurologic sequelae in survivors. How age contributes to severe POWV encephalitis remains an enigma and there are currently no animal models that reflect age-dependent POWV neuropathology. Inoculating C57BL/6 mice with a POWV strain (LI9) currently circulating in Ixodes ticks, resulted in age-dependent POWV lethality with overt spongiform brain damage 10-15 dpi. Infection of 50 week old mice resulted in 82% lethality 10-15 dpi that was sequentially reduced by age to 7.1% in 10 week old mice. LI9 encephalitis resulted in early neuronal depletion, with severe CNS damage, persistent inflammatory gliosis and long-term spongiform pathology in survivors (30 dpi). In all mice POWV LI9 was neuroinvasive and reached maximum POWV loads in the CNS 10 dpi. Coincident with murine lethality, in 50 week old mice maximum POWV CNS levels persisted 15 dpi, while instead decreasing by 2-4 logs in 10-30 week old mice. Although glial cells were highly activated in all POWV infected mice, differences in age-dependent CNS cytokine responses were striking 15 dpi. In 50 week old mice POWV induced Th1-type cytokines (IFN{gamma}, IL-2, IL-12, IL-4, TNF, IL-6), suggesting a pro-inflammatory M1 microglial activation cascade. In contrast, POWV induced Th2-type cytokines (IL-10, TGF{beta}, IL-4) in 10 week old mice consistent with a neuroprotective M2 microglial phenotype. These findings reflect differences in neurodegenerative versus neuroprotective glial cell responses that correlate with divergent CNS viral clearance and age-dependent POWV LI9 lethality. Discrete age-dependent CNS cytokine responses suggest neuroinflammatory targets as potential POWV therapeutics. These studies establish a highly lethal POWV murine model and reveal a hyperinflammatory mechanism of age-dependent POWV lethality that mirrors human POWV severity and long-term CNS sequelae in the elderly. ImportancePowassan virus is an emerging tick-borne flavivirus causing lethal encephalitis in aged individuals. We reveal an age-dependent POWV murine model that mirrors human POWV encephalitis and long-term CNS damage in the elderly. Findings demonstrate that POWV load and discrete glial cell cytokine responses in the CNS are critical determinants of age-dependent POWV lethality. POWV age-independently activates microglia and astrocytes, but directs neuroprotective Th2 cytokine responses in 10 week old mice and distinct pro-inflammatory Th1 cytokine responses in the CNS of 50 week old mice. This reveals roles for a hyperinflammatory CNS cytokine cascade in age-dependent POWV lethality, and protective anti-inflammatory cytokines in murine survival. Notably, results define potential therapeutic targets and rationalize approaches for preventing severe POWV encephalitis that may be broadly applicable to neurodegenerative diseases. This age-dependent murine POWV model permits analysis of vaccines, and therapeutics that prevent POWV neuroinvasion or resolve severe POWV encephalitis in the elderly.

microbiology↗

bioRxiv2023

Live Malassezia strains isolated from the mucosa of patients with ulcerative colitis

The human gut is inhabited by a complex ecosystem of diverse microorganisms. While most studies on the gut microbiota have focused on bacteria, accumulating evidence has underscored the role of the mycobiota in inflammatory bowel disease (IBD). This study is the first to isolate and characterize live Malassezia globosa strains from the intestinal mucosa of patients with ulcerative colitis. Malassezia species primarily inhabit the human skin. We therefore compared the M. globosa gut isolates with the M. globosa skin isolates and noted a striking disparity between them. The gut isolates led to a greater exacerbation of colitis in mice. Transcriptome analysis revealed that the gut isolates were more sensitive to normoxia than the skin isolates, suggesting adaptation to hypoxia prevalent in the intestinal environment. These findings provide novel insights into the potential impact of M. globosa on the pathogenesis of IBD and the influence of niche-specific adaptations on its virulence.

microbiology↗

bioRxiv2023

Age-dependent Powassan Virus Lethality and Neuropathogenesis in Mice

Powassan viruses (POWV) are emergent tick-borne flaviviruses that cause severe neurologic disease in humans. Subcutaneous inoculation of C57BL/6 mice with POWV (strain LI9) resulted in overt brain damage resembling spongiform encephalitis. Noting higher POWV lethality in older mice, we assessed neurovirulence as a function of age. We found that POWV LI9 inoculation was lethal in 80% of 50 wk old mice, 10-15 dpi, and that lethality was sequentially reduced in 40, 30, 20, 10 wk old mice to <10%. Lethality was conferred by 2-20 POWV FFUs, and POWV neuropathology was evident as early as 5 dpi, with lethal disease 10-15 dpi correlated with sustained POWV RNA levels in brains of aged mice. Histology of POWV infected 50 wk old murine brains revealed severe spongiform neuronal necrosis, microgliosis, and inflammation with increased brainstem and cerebellar damage. These findings delineate an age-dependent murine model of lethal POWV infection that mirrors human POWV disease and permits analysis of age-dependent neurovirulence determinants. SignificanceOur findings establish a novel age-dependent lethal animal model to study encephalitic POWV disease in vivo. These initial findings demonstrate that following peripheral inoculation, non-neuroadapted POWV LI9 is neuroinvasive and enters the brains of young and aged mice. However, POWV LI9 lethality is strictly age-dependent and correlated with increased viral load in the brains of aged mice. POWV rapidly directs neuronal loss and spongiform lesions, microglial activation and causes prolonged inflammation that fails to clear POWV from the brains of aged mice. Our results provide a lethal murine model of POWV neurovirulence that mirrors the prevalence of severe human POWV encephalitis in the elderly. This lethal murine POWV model provides mechanisms for defining POWV protective responses of the young, revealing determinants of age-dependent POWV lethality and evaluating potential POWV therapeutics. SUMMARYPowassan virus is an emerging tick-borne flavivirus linked to severe neurologic disease in aged individuals. Here we describe an age-dependent mouse model of POWV pathogenesis. SUBJECTSPowassan virus, flavivirus, neurovirulence, neuroinvasion, neurotropic, spongiform encephalopathy, microgliosis, neuroinflammation

microbiology↗

bioRxiv2023

Establishment of a CPER Reverse Genetics System for Powassan Virus Defines Attenuating NS1 Glycosylation Sites and an Infectious NS1-GFP11 Reporter Virus

Powassan virus (POWV) is an emerging tick-borne Flavivirus that causes lethal encephalitis and long term neurologic damage. Currently there are no POWV therapeutics, licensed vaccines or reverse genetics systems for producing infectious POWVs from recombinant DNA. Here we used a circular polymerase extension reaction (CPER) approach to generate recombinant LI9 (recLI9) POWVs with attenuating NS1 protein mutations and a recLI9-split-eGFP reporter virus. Flavivirus NS1 proteins are highly conserved glycoproteins that regulate replication, spread and neurovirulence. POWV NS1 proteins contain three putative N-linked glycosylation sites that we modified individually in infectious recLI9 mutants (N85Q, N208Q, N224Q). NS1 glycosylation site mutations reduced replication kinetics and were attenuated with a 1-2 log decrease in infectious titers. The severely attenuated recLI9-N224Q mutant exhibited a 2-3 day delay in focal cell-to-cell spread and reduced NS1 secretion. Like WT LI9, the recLI9-N224Q mutant was lethal when intracranially inoculated into suckling mice. However, footpad inoculation of recLI9-N224Q resulted in the survival of 80% of mice and demonstrated that NS1-N224Q mutations attenuate POWV neuroinvasion in vivo. To monitor NS1 trafficking, we CPER fused a split GFP11-tag to the NS1 C-terminus and generated an infectious reporter virus, recLI9-NS1-GFP11. Cells infected with recLI9-NS1-GFP11 revealed NS1 trafficking in live cells and the novel formation of large NS1 lined intracellular vesicles. An infectious recLI9-NS1-GFP11 reporter virus permits real-time analysis of NS1 functions in POWV replication, assembly and secretion, and provides a platform for evaluating antiviral compounds. Collectively, our robust POWV reverse genetics system permits analysis of viral spread and neurovirulence determinants in vitro and in vivo, and enables the rational genetic design of live attenuated POWV vaccines.

microbiology↗

bioRxiv2021

Powassan Viruses Spread Cell to Cell During Direct Isolation from IxodesTicks and Persistently Infect Human Brain Endothelial Cells and Pericytes

Powassan viruses (POWVs) are neurovirulent tick-borne flaviviruses emerging in the Northeastern U.S., with a 2% prevalence in Long Island (LI) deer ticks (Ixodes scapularis). POWVs are transmitted in as little as 15 minutes of a tick bite, and enter the CNS to cause encephalitis (10% fatal) and long-term neuronal damage. POWV-LI9 and POWV-LI41 present in LI Ixodes ticks were isolated by directly inoculating VeroE6 cells with tick homogenates and detecting POWV infected cells by immunoperoxidase staining. Inoculated POWV-LI9 and LI41 were exclusively present in infected cell foci, indicative of spread cell to cell, despite growth in liquid culture without an overlay. Cloning and sequencing establish POWV-LI9 as a phylogenetically distinct lineage II POWV strain circulating in LI deer ticks. Primary human brain microvascular endothelial cells (hBMECs) and pericytes form a neurovascular complex that restricts entry into the CNS. We found that POWV-LI9, -LI41 and Lineage I POWV-LB, productively infect hBMECs and pericytes and that POWVs were basolaterally transmitted from hBMECs to lower chamber pericytes without permeabilizing polarized hBMECs. Synchronous POWV-LI9 infection of hBMECs and pericytes induced proinflammatory chemokines, interferon-{beta} (IFN{beta}) and IFN-stimulated genes, with delayed IFN{beta} secretion by infected pericytes. IFN inhibited POWV infection, but despite IFN secretion a subset of POWV infected hBMECs and pericytes remained persistently infected. These findings suggest a potential mechanism for POWVs (LI9/LI41 and LB) to infect hBMECs, spread basolaterally to pericytes and enter the CNS. hBMEC and pericyte responses to POWV infection suggest a role for immunopathology in POWV neurovirulence and potential therapeutic targets for preventing POWV spread to neuronal compartments. ImportanceWe isolated POWVs from LI deer ticks (I. scapularis) directly in VeroE6 cells and sequencing revealed POWV-LI9 as a distinct lineage II POWV strain. Remarkably, inoculating VeroE6 cells with POWV containing tick homogenates resulted in infected cell foci in liquid culture, consistent with cell to cell spread. POWV-LI9, -LI41, and Lineage I POWV-LB strains infected hBMECs and pericytes that comprise neurovascular complexes. POWVs were nonlytically transmitted basolaterally from infected hBMECs to lower chamber pericytes, suggesting a mechanism for POWV transmission across BBB. POWV-LI9 elicited inflammatory responses from infected hBMEC and pericytes that may contribute to immune cell recruitment and neuropathogenesis. This study reveals a potential mechanism for POWVs to enter the CNS by infecting hBMECs and spreading basolaterally to abluminal pericytes. Our findings reveal that POWV-LI9 persists in cells that form a neurovascular complex spanning the BBB, and suggest potential therapeutic targets for preventing POWV spread to neuronal compartments.

microbiology↗

bioRxiv2021

Integrative annotation of genomic features reveal functional elements and epigenetic landscapes in the developing zebrafish

Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish developmental functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and reanalysed published genomics data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements in development, including novel classes with distinct features dependent on their activity in time and space. We delineated the distinction between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of how they relate to each other. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals.

developmental biology↗

bioRxiv2021

A Protein A based Staphylococcus aureus vaccine with improved safety

Exposure to Staphylococcus aureus does not lead to immunity as evidenced by the persistent colonization of one third of the human population. S. aureus immune escape is mediated by factors that preempt complement activation, destroy phagocytes, and modify B and T cell responses. One such factor, Staphylococcal protein A (SpA) encompasses five Immunoglobulin binding domains (IgBDs) that associate with the Fc{gamma} domain to block phagocytosis. IgBDs also associate with the Fab domain of VH3-idiotypic IgM which activates B cells with the resulting secretion of antibodies that cannot bind determinants of S. aureus. SpA crosslinking of VH3-idiotypic IgG and IgE receptors of mast cells and basophils promotes histamine release and anaphylaxis. Previous work demonstrated the safety, immunogenicity, and protective efficacy of SpAKKAA, a variant partially defective for VH3-idiotypic Ig cross-linking, in murine models of S. aureus. Compared to mice (10%), humans produce significantly more VH3-idiotypic B cells (50%), prompting a search for safer SpA variants that may be suitably developed as clinical-grade vaccines for efficacy testing in humans. Here, we report the identification of such variants.

microbiology↗

bioRxiv2020

Generation of tonsil organoids as an ex vivo model for SARS-CoV-2 infection

Palatine tonsil (hereinafter referred to as "tonsil") plays role in the immune systems first line of defense against foreign pathogens. Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic since the infection was first reported in China in December 2019. The aim of this study was to establish tonsil epithelial cell-derived organoids and to examine their feasibility as an ex vivo model for SARS-CoV-2 infection. Using an optimized protocol, we achieved 3D tonsil organoid culture from human tonsil tissue that reflects the distinctive characteristics of the tonsil epithelium, such as its cellular composition, histologic properties, and molecular biological features. Notably, we verified that SARS-CoV-2 can infect tonsil organoids with a robust replication efficiency. Furthermore, treatment with remdesivir, an antiviral agent, effectively protected them from viral infection. Therefore, tonsil organoids could be available for investigation of SARS-CoV-2 infection-mediated pathology and for preclinical screening of novel antiviral drug candidates. One-sentence SummaryThis study established tonsil epithelial cell-derived organoids and demonstrated their feasibility as an ex vivo model for SARS-CoV-2 infection.

microbiology↗

bioRxiv2019

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

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

genetics↗