Biology subjects

Kim, B.

Publications and source records attributed to Kim, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

HIV-1 infection does not confer intrinsic resistance to cell death induced by cytotoxic T lymphocytes

To eliminate the persistent reservoir of cells harboring intact HIV-1 proviruses in people living with HIV-1 (PLWH), cure strategies like the Shock-and-Kill approach rely on effector functions of cytolytic T lymphocytes (CTL). CTL are involved in the initial control of HIV-1 viremia and target productively infected cells throughout the course of infection. However, selective killing of susceptible cells could generate a reservoir dominated by cells with dysregulated cell death pathways or other features conferring resistance to killing. Here, we use CTL-engaging single-chain diabodies to assess the rate of lysis of uninfected and HIV-1-infected primary CD4+ T cells under identical CTL pressure in the settings of both latent and active infection. Our findings indicate that with this mode of CTL triggering, infected and uninfected CD4+ T cells from PLWH on ART are generally lysed at identical rates, and that an apparent survival advantage for actively infected CD4+ T cells primarily reflects the reduced surface antigen availability through previously described Nef-dependent downregulation of MHC class I molecules. No survival advantage is observed when the CTL response is directed through diabodies to the stably expressed non-classical MHC class I molecule HLA-E, indicating equal susceptibility to cell death.

immunology↗

bioRxiv2026

Dynamic remodeling of chromatin during human mucosal-associated invariant T cell development

T cell development in the thymus is a tightly regulated process where epigenetic modifications, such as histone 3 lysine 27 acetylation (H3K27ac), play a crucial role in controlling the activation of genes. The epigenetic regulation of human mucosal-associated invariant T (MAIT) cell development is unknown; we mapped the regulatory chromatin landscape in the three developmental stages of thymic MAIT cells to identify the regulatory elements and enhancer activity involved in thymic maturation and analysed whether these chromatin dynamics are associated with the acquisition of effector programs in developing MAIT cells. Utilising cleavage under target and tagmentation (CUT&Tag), genome-wide H3K27ac profiles were generated and combined with transcriptome data from thymic MAIT cells, which revealed how developmental shifts in enhancer activity correspond to changes in gene expression. In total, 41,958 genomic regions with H3K27ac signal were identified in MAIT cells across the three development stages, of which 1,200 regions showed acetylation changes during differentiation from stage 1 to stage 3. At dynamic regions, the greatest differences were observed between stage 1 and stage 3, highlighting a progressive gain or loss of H3K27ac during MAIT cell development. Overall, MAIT cell maturation was associated with the gradual accumulation of H3K27ac at promoters and enhancers, which closely correlated with gene expression changes during development. Stage-specific enrichment of H3K27ac was observed at key transcription factor gene loci involved in MAIT cell development, including ZBTB16 (PLZF), EOMES, RUNX3, NFATC2, FOXO1, TGIF1, IRF1, and MAF genes. Epigenetic remodelling was also observed at cytokine and cytokine receptors (IL7R, IL18R1, IL23R, IFNG), chemokines and chemokine receptors (CCL4, CCL5, CCR5, CCR9, CXCR4, CXCR6), as well as several surface molecules with known immunological function. Our work reveals a previously uncharacterised epigenetic profile of human MAIT cells that regulates and inuences their development.

immunology↗

bioRxiv2026

Age-dependent pathogenicity of two severe fever with thrombocytopenia syndrome viruses in a ferret model

SFTSV is an emerging tick-borne pathogen associated with high case fatality rates, particularly in elderly patients. While severe pathogenicity has been reported in aged ferrets, lethal or clinically significant infection in younger animals and genotype-dependent differences in pathogenicity remain insufficiently defined. In this study, we established a ferret infection model using two Korean clinical isolates representing genotypes B and F and systematically compared disease progression between one-year-old and three-year-old ferrets. Three-year-old ferrets exhibited rapid fever onset, marked body weight loss, early clinical deterioration, severe thrombocytopenia and leukopenia, significant elevations in AST and ALT levels, and earlier peak viremia with higher tissue viral loads, indicating impaired early viral control and accelerated systemic dissemination. Notably, one-year-old ferrets also developed measurable pathogenic manifestations, including febrile responses, progressive weight loss, detectable viremia, and multiorgan viral distribution, although disease progression was delayed and less severe compared with older animals. Within the same age group, differences in pathogenicity between genotypes B and F were limited. These findings demonstrate that host age is a major determinant of SFTSV disease severity and support the use of an age-stratified ferret model for preclinical evaluation of vaccines and antiviral therapeutics. ImportanceSFTS is an emerging tick-borne disease that can cause high fever, thrombocytopenia, and multi-organ failure, with particularly severe outcomes in older adults. Currently, no approved vaccines or specific antiviral treatments are available. Reliable animal models that recapitulate human disease are therefore essential for the development of effective countermeasures. Ferrets have recently been proposed as a useful model for SFTS, especially in aged animals, but the susceptibility of younger ferrets and the impact of viral strain differences remain unclear. Here we show that host age strongly determines disease severity in ferrets infected with two genetically distinct SFTS virus strains, establishing a flexible animal model for evaluating vaccines and antiviral therapies.

microbiology↗

bioRxiv2026

Beyond the skin barrier: optical clearing enables non-invasive cortex-wide optical coherence angiography in mice in-vivo

Non-invasive, high-resolution visualization of mouse brain vasculature remains challenging due to significant light scattering and absorption by mammalian tissues, hence many optical imaging protocols require scalp and/or skull excision. Here we present a fully reversible tartrazine-based optical clearing strategy that enables cortex-wide optical coherence tomography angiography (OCTA) through intact scalp and skull. We characterized tartrazine properties in the near infrared (NIR)-II band of the 1.3 {micro}m swept-source OCTA system, confirming minimal absorption across 1.25-1.35 {micro}m wavelength range and an effectively constant refractive index, suggesting negligible OCTA distortions. Spatially selective agent application showed that intracranial vessels emerge selectively within the treated region of interest (ROI), whereas untreated regions retain strong interference by the scalp vascular features. Depth-encoded projections and cross-sectional OCTA demonstrated an increased signal recovery at depth and an extended vessel-detection range after clearing. Vessel-map changes were quantified using intersection-over-union and Dice coefficients, yielding high similarity outside the ROI and reduced similarity within the ROI, consistent with a transition from scalp to brain vasculature. Reproducibility was confirmed in three independent 11-week-old mice and validated against scalp-removed reference OCTA. Screening tartrazine in the 0.3-0.8 Molar concentration range (7-min application) identified 0.6 M as optimal for whole-cortex scanning, balancing clearing efficacy and solution handling. Finally, the protocol generalized across mice aged 5-18 weeks. This approach provides a practical route to non-invasive structural cerebrovascular mapping with OCTA.

bioengineering↗

bioRxiv2026

Temporal Coding rather than Circuit Wiring allows Hippocampal CA3 Neurons to Dynamically Distinguish Different Cortical Inputs

Memory relies on associating and indexing multimodal information. How does this occur within single neurons? The hippocampus integrates multisensory information from medial (MEC) and lateral (LEC) entorhinal cortices to form environmental representations1-6, yet their synaptic dynamics, circuit organization, and integrative functions remain elusive. Contrary to canonical models emphasizing anatomical and functional segregation, our dual-color optogenetic7 circuit mapping revealed that both MEC and LEC inputs converge on virtually every CA3 pyramidal neuron and exhibit similar input-output functions and modulation via GABAergic microcircuitry. Divergence occurs in their frequency-dependent short-term plasticity. With increasing frequencies, facilitating LEC-evoked responses undergo synaptic depression, whereas MEC-evoked responses continue facilitating. In vivo, MEC-originating dentate spikes fire CA3 more than LEC, likely due to their distinct temporal relationship with oscillatory activity. Our findings support that hippocampal area CA3 processes region-specific information from MEC and LEC via temporal coding, rather than hard-wired circuit organization, at both single-neuron and network levels.

neuroscience↗

bioRxiv2026

Springtail-inspired compliant hinge enables terrain-adaptable takeoff in insect-scale robots

Springtails execute millisecond-scale escape jumps with a single appendage, the furca, on soil, snow, leaf litter, and water. Across 15 taxonomic families (n=552 individuals), relative furca length is bimodal. High-speed video and confocal imaging show that in some long-furca springtails, the resilin-rich manubrium-dens joint behaves as a compliant hinge. It bends during push-off to prolong contact, suppress pitch, and bias takeoff forward, whereas rigid joints drive backward launches with rapid body rotation. We translate this mechanism to a 20-mm, 84-mg jumping robot with an elastic robo-furca hinge. This flexible hinge reduces body rotation by [~] 90% on flat ground compared to rigid-hinge designs, while maintaining takeoff speed on gravel, springboards, leaves, and pine needles, enabling passive, terrain-adaptable launches for power-limited insect-scale robots without onboard sensing or active control.

animal behavior and cognition↗

bioRxiv2026

Intranasal Replicating Adenovirus type 4-SARS-CoV-2 Recombinants Induce Superior Immune Response Durability and Efficacy in Preclinical Testing Compared to Standard Intramuscular Vaccines

The portfolio of next generation COVID-19 vaccines would benefit from candidates that induce durable systemic and mucosal immune responses that would lessen person-to-person transmission. We constructed an intranasal (IN) replication-competent adenovirus type 4 recombinant platform to express SARS-CoV-2 Spike variants (Ad4-S) and assessed immunogenicity and efficacy in the Syrian hamster model. Although both IN Ad4-S and intramuscular (IM) vaccines (Ad26.CoV2.S and mRNA-1273) induced serum binding antibodies, only Ad4-S induced a robust mucosal response in the nasal cavity. IN Ad4-S vaccination induced serum neutralizing titers equivalent to or greater than IM vaccination but more durable up to 6 months. Upon challenge, IN immunization also resulted in less weight loss, greater breadth and durability of restriction of viral replication, and less lung pathology than IM immunization up to 268 days after immunization. These data support the potential of the IN Ad4 vaccine platform to reduce transmission of SARS-CoV-2 and other respiratory viruses with pandemic potential.

immunology↗

bioRxiv2026

A Preoptic Neurocircuit That Modulates Metabolic Flexibility

Precise, dynamic control of metabolic fuel usage in response to environmental challenges such as altered food availability or temperature change is essential for animal survival. In mammals, metabolic flexibility--the capacity to shift cellular metabolism between carbohydrate and fatty acid oxidation--is understood to be largely regulated by circulating hormones such as insulin and glucagon. However, the role of the central nervous system in coordinating fuel selection and tissue metabolic tuning remains underexplored. Here, we investigated the mechanisms that mediate metabolic reprogramming following the acute activation of torpor-associated glutamatergic Adcyap1+ torpor-regulating neurons in the anteroventral preoptic area (avPOAVglut2/PACAP). The activation of these neurons rapidly shifts whole-body fuel use from glucose to fatty acids, irrespective of fuel/food availability. This shift is associated with reduced glucose utilization stemming from the transient induction of selective insulin resistance in skeletal muscle. We find that this reduction in skeletal muscle glucose metabolism does not require direct muscle innervation but is rather mediated in part via corticosterone. In contrast to their activation, avPOAVglut2/PACAP neuronal silencing results in improved glucose tolerance, demonstrating powerful bidirectional control of tissue-specific glucose metabolism, whole-body glucose levels, and fuel usage. Together, our findings uncover a novel POA -skeletal muscle pathway that dynamically controls glucose utilization and metabolic flexibility.

neuroscience↗

bioRxiv2026

NFATc3 enhances DREAM complex-driven tumorigenesis

The nuclear factor of activated T cells (NFAT) transcription factors, activated by calcium-calcineurin signaling, regulate various cellular processes, including cell differentiation, angiogenesis, and immune cell activation. Nonetheless, their roles in tumor cells remain largely undefined. The dimerization partner, RB-like, E2F, and multi-vulval class B (DREAM) complex orchestrates cell quiescence and proliferation. Pharmacological mimicry of DREAM-activated transcriptional signatures identified two calcium signaling inhibitors that suppressed lung adenocarcinoma (LUAD) cell proliferation. Among the five NFAT members, NFATc3/NFAT4 was predominantly expressed in LUAD cells and required for both LUAD cell proliferation and DREAM target gene transactivation. NFATc3 was enriched at DREAM target promoters and associated with the DREAM complex, possibly via LIN9, a scaffolding protein of the Multi-Vulva class B (MuvB) core proteins. These findings reveal an unexpected role for NFATc3 in promoting DREAM target gene transactivation and suggest the calcium-NFATc3 axis as a molecular target in LUAD, enriched by DREAM complex activation.

molecular biology↗

bioRxiv2025

Emergence of a new material through ligation of DNA nanostar hydrogels

DNA nanostar hydrogels hold great promise as biomaterials, but their mechanical properties and nuclease susceptibility limit their use. Here, we propose ligation of nanostar sticky ends as a strategy to fundamentally transform the mechanical and dynamic properties of DNA nanostar hydrogels and enhance their nuclease resistance. Ligation eliminates free ends of DNA nanostars, conferring strong exonuclease resistance; suppresses strand rearrangement, converting liquid-like into gel-like assemblies; and prevents macroscopic reversibility despite preserving microscopic motif hybridization. Ligation also stiffens the material, enabling facile handling and 3D printing, and markedly slows digestion in serum-supplemented medium. In the presence of low concentrations of the DNase I inhibitor actin, ligated hydrogels remain stable for at least two weeks. As a proof-of-concept application, we captured and maintained cells within ligated hydrogels for one week in culture. By overcoming the limitations of DNA nanostar hydrogels, this work enables their use as programmable biomaterials that fully leverage the DNA nanotechnology toolbox.

bioengineering↗

bioRxiv2025

Quantitative trait locus mapping of root exudate metabolome in a Solanum lycopersicum Moneymaker x S. pimpinellifolium RIL population and their putative links to rhizosphere microbiome

Crop resilience to abiotic and biotic stresses is vital for sustainable agriculture and global food security. The root exudates (RE)--a complex mixture of metabolites exuded by the plant roots--plays a central role in this resilience by mediating interactions with organisms around the roots, including soil microorganisms. These interactions influence nutrient cycling, the recruitment of beneficial microbes, and ultimately plant health. Although host genotype is known to affect the RE composition, the specific metabolites and underlying genetic mechanisms remain poorly understood. Here, we employed untargeted metabolomics to analyse the tomato RE composition and mapped individual metabolic features to the tomato genome using quantitative trait locus (QTL) analysis in a recombinant inbred line population derived from Solanum lycopersicum and Solanum pimpinellifolium. Our results shed light on the intricate chemical composition of the tomato RE, and reveal domestication-driven shifts in the RE composition and genetic loci associated with the abundance of specific metabolites. Notably, we identify overlap between metabolic and earlier published microbial QTLs, supportive of a link between RE composition and microbiome assembly, and providing a basis for further unravelling of the plant-microbe chemical interaction.

plant biology↗

bioRxiv2025

TOE1 influences canonical Wnt signalling in myeloid leukaemia cells through LEF-1 modulation and regulates the proliferation of haematopoietic cells through PAK2.

Acute myeloid leukaemia (AML) is an aggressive haematological malignancy characterised by the clonal proliferation of myeloid progenitor cells in the bone marrow and peripheral blood. Dysregulation of the Wnt/{beta}-catenin pathway has been implicated in the establishment and maintenance of leukaemic stem cells in AML, where higher expression of {beta}-catenin promotes clonogenic capacity, drug resistance and inferior survival. The finding that low levels of Wnt signalling are necessary to maintain normal haematopoiesis makes {beta}-catenin an attractive therapeutic target; however, drug design has been hampered by a poor understanding of its molecular interactions in leukaemia cells. To address this, we previously characterised the {beta}-catenin interactome in myeloid cells and identified a plethora of novel interacting proteins. One such interactor was Target of EGR1 (TOE1), a member of the Asp-Glu-Asp-Asp (DEDD) family of deadenylases with previously uncharacterised function in haematopoietic cells. The {beta}-catenin:TOE1 interaction was detected in the nuclear and cytosolic compartments of myeloid cell lines and primary AML samples, and {beta}-catenin depletion was found to promote the cytosolic accumulation of TOE1. Furthermore, TOE1 levels were found to be overexpressed in primary AML blasts versus normal cord-blood derived CD34+ haematopoietic stem and progenitor cells (HSPCs), suggesting that TOE1 levels may be dysregulated in leukaemia. TOE1 depletion abrogated Wnt signalling capacity (TCF/LEF activity), potentially via reduced stability/translatability of the Wnt transcription factor lymphoid enhancing factor 1 (LEF-1). TOE1 depletion further suppressed the proliferation and survival of myeloid leukaemia cell lines (HEL and OCI-AML2) and primary human CD34+ HSPC; however, this could not be fully explained through LEF-1 alone, since OCI-AML2 do not express LEF-1. Using tandem mass tag (TMT)-labelling coupled to mass spectrometry analysis in TOE1 deficient HEL and OCI-AML2 cells, we identified and validated p21 (RAC1) activated kinase 2 (PAK2) as a downregulated target that could reduce the proliferation (but not survival) of AML cell lines. Interestingly, ectopic expression of PAK2 was able to partially rescue the proliferation defect in TOE1 depleted myeloid cell lines and primary human CD34+ HSPC. In summary, these data reveal TOE1 as novel interacting partner for {beta}-catenin in haematological cells capable of modulating Wnt signalling output via LEF-1, and as a novel mediator of growth and survival in human HSPC and AML cells partly through PAK2 regulation.

cancer biology↗

bioRxiv2025

A Biologically Grounded Structural Causal Model Enables cfRNA Specific In-Context Learning

Cell-free RNA (cfRNA) in human plasma provides a minimally invasive readout of tissue physiology, yet its extreme sparsity, heavy-tailed abundance distributions, and weak but structured correlation patterns create major challenges for machine learning. Conventional tabular foundation models are typically trained on synthetic datasets that assume generic statistical properties, and as a result, they fail to capture the distinctive characteristics of cfRNA. These limitations become even more pronounced in settings where labeled data are scarce. We introduce cfRNA-ICL, a cfRNA-specific in-context learning model trained entirely on tasks generated from a biologically grounded structural causal model (SCM). The SCM produces realistic cfRNA-like scenarios by incorporating empirical measurements of gene-level dropout, overdispersion, tissue-mixture-driven latent factors, compositional variability, and sequencing noise. This synthetic task universe enables cfRNA-ICL to acquire inductive biases that closely reflect the geometry of real cfRNA data. Across multiple cancer classification benchmarks, cfRNA-ICL demonstrates consistently higher performance than tabular ICL models trained on generic synthetic data. The gains are most sub-stantial in few-shot settings, where the model benefits from its exposure to cfRNA-specific statistical regimes during meta-training. Representation-level analyses further show that cfRNA-ICL organizes samples into biologically coherent manifolds, preserving cancer-type identity without the use of supervised constraints. This finding indicates strong alignment between the synthetic prior and real cfRNA structure. Taken together, these results show that domain-aware generative priors can meaningfully enhance in-context learning for biological tabular data. cfRNA-ICL provides a generalizable framework for cfRNA modeling and establishes a practical path toward foundation-scale models that are intrinsically adapted to the statistical landscape of plasma cfRNA.

genomics↗

bioRxiv2025

Master clock-thalamic-prefrontal circuit controls circadian social priority

Social behaviors arise from complex brain operations that adapt to changing social contexts and internal states. However, how internal states guide the resolution of competing social goals remains unclear. Here, we show that prioritization between competing instincts follows a circadian pattern via a circuit linking the suprachiasmatic nucleus (SCN) to the medial prefrontal cortex (mPFC). Specifically, SCNVIP neurons project to Vipr2-expressing neurons in the nucleus reuniens (RE), which innervate the mPFC to regulate social prioritization. Vipr2 signaling in the RE is essential for circadian modulation of appetitive and consummatory social behaviors, aligning social behaviors with clock-regulated reproductive system. Overall, this SCN-RE-mPFC circuit provides a neural principle through which the master clock coordinates the prefrontal cortex to resolve a conflict of motivated behaviors by referencing an internal state.

neuroscience↗

bioRxiv2025

Antiviral and anti-inflammatory effects of Tabamide A derivative, TA25, against human rhinovirus and multiple zoonotic viruses in vitro and in silico

Human rhinovirus (HRV), first isolated in 1956, belongs to the family Piconaviridae containing a positive-sense, single-stranded RNA genome. HRV causes mild cold and severe respiratory disease, such as asthma, COPD, and pneumonia. To date, no Food and Drug Administration-approved antiviral or anti-inflammatory drugs are available for HRV. TA25 is a phenolic amide derivative extracted from the leaves of Nicotiana tabacum. To investigate the potential candidate for antiviral therapeutics against zoonotic viruses, we evaluated the antiviral potency of TA25 for HRV and multiple zoonotic viruses. The antiviral and anti-inflammatory effects of TA25 were evaluated using RT-qPCR and RNA-seq. Strand-specific RT-qPCR was performed to measure genomic and anti-genomic RNA expression after TA25 treatment. In addition, an AI-based docking test was conducted to investigate the binding affinity of TA25 with viral target proteins. TA25 induced a significant reduction in viral replication and suppressed the expression of pro-inflammatory genes. Inhibition of viral replication by TA25 treatment was confirmed by strand-specific RT-qPCR. TA25 showed broad-spectrum antiviral activity against multiple viruses, including HRV-1A, Zika virus, Dengue virus, Vaccinia virus, and Influenza B virus Victoria. Using an AI-driven structure-based docking analysis, TA25 showed the strongest binding affinity with the HRV 2B protein. This study demonstrates that TA25 confers the broad antiviral and anti-inflammatory activity against HRV and multiple zoonotic viruses. These findings provide valuable insights into antiviral strategies of TA25 for a promising therapeutic candidate in response to emerging RNA and DNA viruses.

microbiology↗

bioRxiv2025

10,239 whole genomes with multiomic and clinical health information as the Korean population multiomic reference dataset

We present Korea10K, the largest genomic dataset of the Korean population, comprising 10,239 high-coverage whole genomes (mean depth 30x) with matched multiomic profiles and phenotype data. Korea10K achieves complete and near-complete discovery of very rare and ultra-rare alleles, respectively, at 9,000 Korean genomes. This dataset provides the high-quality population-specific imputation panel, enabling accurate inference of low-frequency variants. Admixture analyses confirm the genetic homogeneity of the Korean population, despite its diverse Y-chromosomal, mitochondrial, and HLA repertoires. This pattern reflects a long and continuous lineage history characterized by persistent internal admixture and genomic homogenization over thousands of years on the Korean peninsula. We also identified 16.8 million genomic variants that directly modify CG sites by creating or abolishing CG dinucleotides, providing the population-scale evidence of coordinated genomic-epigenomic regulatory mechanism in Koreans.

genomics↗

bioRxiv2025

The Primate Hippocampus Constructs a Temporal Scaffold Anchored to Behavioral Events

The hippocampus has been attributed a range of divergent functions, including roles in memory1,2 and navigation3-5, but how its moment-to-moment neuronal activity supports cognition remains poorly understood. The activity of individual hippocampal neurons is correlated with numerous perceptual features and task variables6-14, raising the question of whether these response properties reflect distinct mechanisms or support a single generalized computation. Here, we show that these diverse response properties reflect a unified organizing principle in which the hippocampus segments experience into discrete events, with population activity transitioning between discrete neural states at behaviorally salient moments. Recording from monkeys performing a virtual spatial alternation task, we found that population activity did not evolve smoothly over time but instead shifted abruptly at each relevant event. These discontinuities segmented activity into distinct ensembles, effectively chunking separate task epochs. Notably, many neuronal responses persisted across visually distinct environments, demonstrating that these dynamics reflect abstract task structure rather than specific sensory features. These results reveal that the hippocampus constructs a temporal scaffold anchored to relevant behavioral events, with each neural state tracking a distinct task phase. This organizational principle may explain the diverse neural correlates observed across studies: rather than individually encoding perceptual or behavioral variables, hippocampal neurons collectively signal the current phase of a behavioral sequence. Our findings suggest that the hippocampus parses experience into meaningful elements and tracks "position" within a learned behavioral structure.

neuroscience↗

bioRxiv2025

SAMHD1 promotes SARS-CoV-2 infection by enhancing HNF1-dependent ACE2 expression in lung epithelial cells

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) restricts a board spectrum of viruses through multifaceted mechanisms. It also limits spontaneous- and virus-induced innate immune responses by suppressing proinflammatory cytokine and type-I interferon (IFN-I) production. Some viruses escape SAMHD1 restriction by utilizing SAMHD1-mediated innate immune suppression to establish effective infection through viral antagonism. Our previous studies showed that SAMHD1 is a proviral factor facilitating replication of severe acute respiratory syndrome coronavirus (SARS-CoV-2) in human macrophages, monocytic THP-1 and epithelial-like HEK293T cell lines by suppressing IFN responses. However, it is unclear about the function of SAMHD1 in lung epithelial cells during SARS-CoV-2 infection. Here, we report that SAMHD1 facilitates SARS-CoV-2 replication in lung epithelial Calu-3 cells by enhancing endogenous expression of the viral receptor angiotensin-converting enzyme 2 (ACE2) via hepatocyte nuclear factor 1-alpha (HNF1) and HNF1{beta}. Using pseudotyped SARS-CoV-2 and lentiviral vectors, we found that SARS-CoV-2 spike protein-mediated viral entry was suppressed in Calu-3 cells with SAMHD1 knockout (KO). SAMHD1 KO repressed ACE2 expression in Calu-3 cells at mRNA and protein levels. Functional analyses revealed that HNF1 and HNF1{beta} were crucial for the endogenous ACE2 expression in Calu-3 cells. Additionally, SAMHD1 KO led to a reduction in the expression levels and ACE2-promoting function of HNF1 and HNF1{beta}. Inhibition of IFN antiviral response by baricitinib, a Janus kinase 1 and 2 (JAK 1/2) inhibitor, did not revert the suppression of SARS-CoV-2 in SAMHD1 KO Calu-3 cells. Our findings demonstrate that SAMHD1 facilitates HNF1-mediated ACE2 expression and SARS-CoV-2 replication in Calu-3 cells via a novel mechanism beyond its IFN-suppressive function. Author SummaryDuring viral infection, SAMHD1 acts as a viral restriction factor and a suppressor of the innate immune system, controlling viral replication while also ensuring immune homeostasis. The innate immune suppressive function of SAMHD1 can be proviral for some viruses. SAMHD1 has been shown to facilitate SARS-CoV-2 infection in human macrophages, THP-1 and HEK293T cell lines by promoting IFN antagonism, but its role in lung epithelial cells is unclear. Here, we demonstrated that SAMHD1 promotes SARS-CoV-2 replication in human lung epithelial Calu-3 cells by enhancing expression of the major viral receptor ACE2. We found that SAMHD1 facilitated HNF1-medaited ACE2 expression that was required for spike protein-mediated SARS-CoV-2 entry. However, inhibiting IFN signaling in SAMHD1 KO Calu-3 cells was not sufficient to revert SARS-CoV-2 replication. Our findings shed light on the differential proviral function of SAMHD1 in ACE2 expressing cells and suggest that SAMHD1 can facilitate SARS-CoV-2 infection beyond enhancing IFN antagonism.

microbiology↗