Biology subjects

Russo, M.

Publications and source records attributed to Russo, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Flexible predictive control in human interception under visual occlusion and altered gravity

Interception of moving objects requires the nervous system to compensate for sensory delays and uncertainty, yet how behavior is controlled remains debated. Key questions concern whether predictive processes play any role at all and, if so, whether they rely on simple motion extrapolation or incorporate internalized physical priors, such as gravity. Another open question is whether observers adopt a single control strategy or flexibly switch between predictive and reactive control - or between different predictive strategies - depending on task demands. To address these questions, we developed a virtual interception task in which participants intercepted moving targets under systematically varied conditions. We manipulated gravity (1g vs. 0g), visual availability (occluded vs. non-occluded), target velocity, and the initial spatial configuration of the ball and paddle (same vs. opposite side). Results indicate that interception is supported by predictive mechanisms across conditions. Behavioral patterns during occluded 0g trials suggest that participants extrapolate target motion using expectations consistent with gravity. Target velocity, visual occlusion, and task geometry modulated movement strategies, indicating that predictive control is flexibly adapted to task demands. These findings support the view that interception relies on predictive internal models incorporating structured physical priors while revealing flexible, context-dependent adaptations to sensory and task constraints.

neuroscience↗

bioRxiv2026

Legacy Effects of Early β-Adrenergic Stimulation Program Adipose Plasticity and Confer Metabolic Resilience in Obesity

Pathologic white adipose tissue (WAT) remodeling, characterized by fibrosis, inflammation, and adipocyte dysfunction, is a hallmark and driver of metabolic disease in obesity1. Here, we show that legacy effects of early physiological or pharmacological interventions driving adaptive adipose remodeling can mitigate maladaptive WAT remodeling and metabolic dysfunction when developing obesity later in life. Cold exposure or {beta}3-adrenergic receptor ({beta}3AR) agonism (CL316,243) induced thermogenic remodeling of WAT in male mice. After a prolonged recovery at room temperature, trained epididymal WAT reverted to an energy-storing state but retained a population of adipocytes resembling "metabolically flexible" visceral adipocytes found in human metabolically healthy obesity. The legacy of the antecedent treatment conferred lasting protection against glucose intolerance when later developing high fat diet (HFD)-induced obesity, with insulin sensitivity persisting for at least 20 weeks of overnutrition. This metabolic resilience was accompanied by healthy epididymal WAT expansion with reduced fibrosis and inflammation. Our findings demonstrate that short-term interventions, without genetic manipulation, can "train" adipose tissue, enhancing its long-term plasticity and conferring durable protection against future obesity-associated insulin resistance.

physiology↗

bioRxiv2026

Phenotypic reversion and target prioritization for cellular inflammation via representation learning with foundation models

The identification of genetic perturbations that can reverse disease-associated cellular phenotypes toward a healthy state is a central challenge in early drug discovery. We present a proof-of-concept framework leveraging single-cell foundation models (scFMs) and a large-scale Perturb-seq dataset to prioritize targets for phenotypic reversion of cellular inflammation. We incorporated both basal and proinflammatory signaling conditions, specifically stimulation with interleukin-1 beta (IL-1{beta}) and tumor necrosis factor alpha (TNF-), to assess whether atherosclerotic disease-relevant stimulation improved identification of genes and pathways critical to disease progression. Our dataset comprised 864,115 endothelial cells subjected to 1,740 unique genetic perturbations. Through having both conditions, we identified targets that exhibited differential effects on gene expression dependent on cellular state. Using scFMs, we embedded single-cell transcriptomes into high-dimensional latent spaces and ranked perturbations by their ability to shift the inflammatory transcriptomic profile toward that of untreated controls. Benchmarking against both annotated gene sets and expert-curated targets, we found robust enrichment for known regulators of inflammation and biologically relevant targets, despite these models having no prior information about these targets. Importantly, including both basal and proinflammatory conditions improved identification of inflammation-associated targets compared to using just the basal condition. This underscored the value of incorporating disease-relevant stimulations in perturbation experiments. Our results highlight the utility of scFMs for data-driven target nomination, emphasize the role of cellular state in regulatory responses, and provide a scalable, model-agnostic approach for ML-guided target discovery. This work offers a valuable community resource for advancing biological understanding of inflammatory-associated disease.

bioinformatics↗

bioRxiv2025

A vesicle-based platform for high-efficiency, high-viability CRISPR/Cas9 knockout in primary human myeloid cells

Myeloid cells, including monocytes, macrophages, and dendritic cells, are central to host defence, inflammation, and antigen presentation. However, functional genetics studies in corresponding primary cells remain limited due to inefficient delivery methods. Here we report a vesicle-based CRISPR/Cas9 platform for effective genome editing in primary human myeloid cells using engineered virus-like particles (VLPs) and extracellular vesicles (EVs) to deliver Cas9-gRNA ribonucleoproteins (RNPs). Targeting primary CD14+ monocytes enables rapid generation of robust polyclonal knockouts while preserving cell viability and subsequent differentiation into macrophages and dendritic cells. Because our workflow relies on standard cell-culture handling rather than electroporation instrumentation, it is inexpensive, highly scalable and readily transferable across laboratories. Edited cells remain compatible with diverse downstream assays and functional readouts, enabling scalable loss-of-function studies and mechanistic dissection of primary human myeloid cell biology in health and disease. Vesicle-mediated RNP delivery thus provides a broadly applicable route to genetic perturbation in primary human myeloid lineages. SummaryFiori and colleagues describe a vesicle-based platform for efficient CRISPR/Cas9 knockout in primary human myeloid cells. This approach preserves cell viability, enables near-complete gene disruption, and supports functional studies of innate immunity, antigen presentation, and HIV-1 infection.

immunology↗

bioRxiv2025

Integrated proteogenomics uncovers ancestry-specific and shared molecular drivers in localized prostate cancer

Our integrative proteogenomics (genome, proteome and phosphoproteome) of localized prostate cancer (PCa) in an equal-access Military Health System patient cohort (57 Black and 55 White) revealed significant ancestry-associated differences. Somatic and germline regulatory differences converged on androgen, metabolic, PI3K/AKT/mTOR, and DNA damage response (DDR) pathways, with ancestry-specific immune- and stromal-associated signals. Black patients displayed greater genomic variability, enhanced androgen response, fatty-acid metabolism, and epithelial-mesenchymal transition, while White patients showed prevalent DDRG alterations, activated oncogenic signaling (MYC, E2F, mTORC1), and cell cycle regulation. Phosphoproteomics highlighted distinct kinase activities and candidate druggable dependencies. Multiomics integration revealed three exploratory tumor subtypes whose distinct biological programs were reproducibly validated. Ancestry-associated eQTLs supported inherited regulation of the proteome independent of CNAs. Ancestry-specific CNA and protein panels improved progression risk prediction beyond PSA and pathology models. These findings provide a framework for ancestry-informed prognostic models and generate testable hypotheses for precision therapies to reduce outcome disparities.

cancer biology↗

bioRxiv2025

skNAC is a Key Driver of Cardiomyocyte Integrity Against Pathological Cardiac Hypertrophy and Heart Failure

Chronic pressure overload induces cardiac hypertrophy and heart failure through coordinated alterations in proteome homeostasis, metabolism and sarcomere organisation. The muscle-specific -isoform of the nascent polypeptide-associated complex (skNAC) is essential for sarcomere assembly during development, but its role in adult hearts remains largely unknown. Here, we show that skNAC expression is reduced in hypertrophic cardiomyocytes, mouse models of pressure overload, and human hypertrophic hearts, in association with disease severity. Cardiomyocyte-specific skNAC deletion results in basal hypertrophy, systolic dysfunction, and premature death, and exacerbates pressure overload-induced heart failure. At the molecular level, skNAC associates with ribosomes and is required for sarcomere organisation maintenance, while its loss induces autophagy and ultrastructural defects. Integrated transcriptomic and proteomic analyses reveal early downregulation of metabolic gene expression despite increased abundance of corresponding proteins, indicating compensatory metabolic responses. Gain-of-function studies confirm a protective role against hypertrophy. Together, these data establish skNAC as a key regulator of cardiac proteome homeostasis and metabolic adaptation during pathological remodelling.

physiology↗

bioRxiv2025

Glucocorticoids unleash immune-dependent melanoma control through inhibition of the GARP/TGF-β axis

Half of advanced melanoma patients fail to benefit from immune checkpoint blockade and novel treatments are urgently required. Testing topical medications used in other skin diseases for anti-cancer activity in an immunotherapy-resistant murine melanoma model, we counterintuitively found that glucocorticoids elicit rapid cytotoxic T lymphocyte (CTL)-dependent tumor control. Genetic ablation of the glucocorticoid receptor in different cellular compartments revealed glucocorticoids acted not on immune cells but directly on tumor cells to downregulate expression of GARP (glycoprotein A repetitions predominant). This inhibited TGF-{beta} signaling and unleashed CTL killing. In agreement, glucocorticoids stimulated tumor control in multiple cancer models, but only if the tumors also responded to pharmacological inhibition of TGF-{beta} signaling. Furthermore, melanoma patients with high glucocorticoid receptor expression or signaling showed improved prognosis and lower TGF-{beta} signaling in tumor-infiltrating CTLs. Additionally, elevated GARP expression correlated with reduced survival, including in immunotherapy-treated patients. Thus, the GARP/TGF-{beta} axis emerges as a glucocorticoid-sensitive cancer cell-intrinsic immune evasive mechanism. SignificanceScreening widely used topical treatments in a melanoma model, this study uncovers a surprising role for glucocorticoids in triggering CD8+ T cell-dependent tumor control through downregulation of GARP and thus TGF-{beta} signaling. Melanoma patient sample analysis supported these findings suggesting GARP/TGF-{beta} activity functions as a tumor cell-intrinsic immune evasive mechanism, and GARP expression may serve as both a biomarker of poor antitumor immunity and a therapeutic target to improve the response to immunotherapy.

cancer biology↗

bioRxiv2025

Immune cells regulate circulating adipocyte extracellular vesicle levels in response to metabolic shifts

Extracellular vesicles (EVs) are now recognized as potent mediators of intercellular and inter-organ signaling and implicated in the pathogenesis of obesity and its associated comorbidities such as diabetes, cancer, cardiovascular disease, and neurodegeneration. Despite a surge of new functional information about EVs, we still lack a basic understanding of how endogenous EV levels are controlled to regulate inter-organ signaling. New flow cytometry technology has allowed us to study the regulation of circulating, endogenous EVs from metabolically relevant cell types like adipocytes. From this, we provide evidence for a paradigm of EV regulation where tissue resident immune cells, predominantly macrophages, clear EVs released by local tissue cells or EVs entering the tissue from circulation, an activity that determines circulating EV levels. In obesity, EV uptake by adipose tissue immune cells is reduced, concomitant with increased circulating adipocyte-specific EVs (adipoEVs) and reduced EV clearance rates. AdipoEVs are significantly elevated in mouse circulation from one day to 20 weeks of high-fat feeding. In humans we found that adipocyte EV levels negatively correlate with whole-body and liver insulin sensitivity and are not associated with adipose mass. This work suggests that tissue resident immune cells act as a gatekeeper for tissue EV entry into circulation and are thereby a major regulator of inter-organ EV signaling.

physiology↗

bioRxiv2024

Changes in Muscle Synergy Structure and Activation Patterns Underlie Force Field Adaptation, Retention, and Generalization

1Humans can adapt their motor commands in response to errors when they perform reaching movements in new dynamic conditions, a process called motor adaptation. They acquire knowledge about the new dynamics, which they can use when they are re-exposed and, limitedly, generalize to untrained reaching directions. While force field adaptation, retention, and generalization have been thoroughly investigated at a kinematic and kinetic task level, the underlying coordination at a muscular level remains unclear. Many studies propose that the central nervous system uses low- dimensional control, i.e., coordinates muscles in functional groups: so-called muscle synergies. Accordingly, we hypothesized that changes in muscle synergy structure and activation patterns represent the acquired knowledge underlying force field adaptation, retention, and generalization. To test this, 36 male humans practiced reaching to a single target in a viscous force field and were tested for retention and generalization to new directions, while we simultaneously measured muscle activity from 13 upper-body muscles. We found that muscle synergies used for unperturbed reaching cannot explain the muscle patterns when adapted. Instead, muscle synergies specific to this adapted state were necessary, alongside a novel four-phasic pattern of muscle synergy activation. Furthermore, these structural changes and patterns were also evident during retention and generalization. Our results suggest that reaching in an environment with altered dynamics requires structural changes to muscle synergies compared to unperturbed reaching, and that these changes facilitate retention and generalization. These findings provide new insights into how the central nervous system coordinates the muscles underlying motor adaptation, retention, and generalization. 2 Significance StatementHumans can adapt their reaching movements to new dynamic conditions. They acquire knowledge about the new dynamics and can use it not only when re-exposed to these conditions but also, in part, to generalize unpracticed reaching directions. While adaptation, retention, and generalization in a force field with new dynamics have been thoroughly investigated at a kinematic and kinetic task level, coordination of the underlying muscles remains elusive. Our results show how muscle synergies - functional groupings of co-activated muscles - underlie adaptation, retention, and generalization. In particular, we observed structural changes in the muscle synergies after adaptation compared to unperturbed reaching. These changes facilitate retention and spatial generalization. Thus, muscle synergies provide new insights into human motor adaptation.

neuroscience↗

bioRxiv2024

The chemopreventive effects of Curcumin against oxidative stress induced by Cadmium or H2O2 are mediated by Nrf2/ARE signaling and protective autophagy in myeloid cells

The evidence linking high levels of environmental pollutants to chronic degenerative diseases is alarming, with heavy metals (HM) identified as a key factor. Research suggests that certain phytochemicals in the diet can reduce HM levels and mitigate their adverse health effects.Curcumin (Cur), a natural polyphenol, is particularly effective in protecting against Cadmium (Cd) toxicity. The present study demonstrates that preincubation with low doses of Cur (1 M) in differentiated HL-60 and K-562 human myeloid cells can significantly protect against cytotoxicity induced by Cd and or H2O2. Cur reduced the increased levels of reactive oxygen species (ROS) generated by Cd or H2O2 by inducing a protective form of autophagy. Cur activated mild oxidative stress that triggers the expression of Nrf2-dependent transcripts, such as HO and NQO1. The potential chemopreventive effects of Cur against redox stress have been strengthened by the observation that free and unmetabolized Cur is detectable inside the cells after 5 minutes of treatment, and its presence parallels with increased levels of intracellular GSH. These findings suggest that supplementation with Cur in the form of nutraceuticals may represent a promising way to protect people living in highly polluted areas against the adverse effects of HM contaminants.

cell biology↗

bioRxiv2024

Dissecting the ocular impact of SARS-CoV-2 variants: Analysis of eye globe and retina in animal models

Neurological and ocular manifestations were reported in COVID-19 patients and in SARS-CoV-2 infected animal models. However, the effects of SARS-CoV-2 variants of concern (VoC) on the eyes and the retina remain unclear. Here, we investigate the cellular and molecular consequences of SARS-CoV-2 VoC infection on the eye and retina in mice and hamsters. Infection with the ancestral SARS-CoV-2 and the Gamma VoC induced a subtle increase in the eye volume of K18-hAce2 mice, but no morphological alteration was observed in hamsters eyes. Evaluation of the ocular tropism revealed that distinct SARS-CoV-2 VoC reached the eye globe, but not the retina of K18-hAce2 mice. In contrast, SARS-CoV-2 variants are detected in the hamsters retina during both acute infection and after disease recovery. Despite the presence of viral RNA, no inflammation was observed in the hamster retina, as evidenced by unchanged microglial cell density and unaltered gene expression of several immune mediators. Altogether, these findings indicate a limited impact of SARS-CoV-2 variants on the eye and retina.

neuroscience↗

bioRxiv2024

Human Foot Force Informs Balance Control Strategies when Standing on a Narrow Beam

Despite the abundance of studies on the control of standing balance, insights about the roles of biomechanics and neural control have been limited. Previous work introduced an analysis combining the direction and orientation of ground reaction forces. The "intersection point" of the lines of actions of these forces exhibited a consistent pattern across healthy, young subjects when computed for different frequency components of the center of pressure signal. To investigate the control strategy of quiet stance, we applied this intersection point analysis to experimental data of 15 healthy, young subjects balancing in tandem stance on a narrow beam and on the ground. Data from the sagittal and frontal planes were analyzed separately. The task was modeled as a double-inverted pendulum controlled by an optimal controller with torque-actuated ankle and hip joints and additive white noise. To test our prediction that the controller that minimized overall joint effort would yield the best fit across the tested conditions and planes of analyses, experimental results were compared to simulation outcomes. The controller that minimized overall effort produced the best fit in both balance conditions and planes of analyses. For some conditions, the relative penalty on the hip and ankle joints varied in a way relevant to the balance condition or to the plane of analysis. These results suggest that unimpaired quiet balance in a challenging environment can be best described by a controller that maintains minimal effort through the adjustment of relative ankle and hip joint torques. NEW & NOTEWORTHYThis study explored balance control in humans during a challenging task using the novel intersection point analysis, based on ground reaction force direction and point of application. Experimental data of subjects standing on a narrow beam in tandem stance were compared with modeling results of a double-inverted pendulum. The analysis showed that individuals minimized effort by adjusting ankle and hip torques, shedding light on the interplay of biomechanics and neural control in maintaining balance.

physiology↗

bioRxiv2024

Dorsal horn dendrite polarization during Spinal Cord Stimulation (SCS) predicted using the quasi-uniform-mirror assumption.

While the mechanisms of Spinal Cord Stimulation are traditionally assumed to follow pacing of dorsal columns axons, the development of sub-paresthesia SCS and new waveforms has encouraged consideration of different cellular targets. Given their relative proximity to the stimulation electrodes and role in pain processing (e.g., synaptic processing and gate control theory), spinal cord dorsal horn interneurons may be direct targets of stimulation. We developed a novel computational modeling pipeline termed quasi-uniform-mirror assumption and apply it to predict polarization of dorsal horn inter-neuron cell types (Islet type, Central type, Stellate/Radial, Vertical-like) to SCS. The quasi-uniform-mirror assumption allows prediction, for each cell type and location in the dorsal horn, the peak and axis of dendritic polarization as well as the impact of stimulation pulse width. For long pulse (dc), the peak polarization per mA of SCS with a bipolar montage were: Islet type 3.5 mV, Central type 2 mV, Stellate/Radial 1.4 mV, Vertical-like 2.5 mV. For Stellate/Radial the peak dendritic polarization was dorsal-ventral, and for Islet type Central peak dendrite polarization was in the rostral-caudal axis. For Islet type and Central type cells peak dendrite polarization was between stimulation electrodes, while for Stellate/Radial and Vertical-like peak dendrite polarization was under stimulation electrodes. The impact of pulse width depended on cell membrane time constants, which in the quasi-uniform-mirror assumption are uniform first-order. Assuming 1 ms time constant, for a 1 ms or 100 us pulse width, the peak dendrite polarization decreases (from the dc values) by [~]33% and [~]88%. These results suggest, for the conditions modeled, maximum polarization is of islet-cells in the superficial dorsal horn at locations between electrodes; applying 2 mA 1 ms pulse SCS, the peak islet-cell dendrite polarization is [~]4.7 mV. Polarizations of a few mV have been shown to modulate synaptic processing through sub-threshold mechanisms.

bioengineering↗

bioRxiv2023

An organic extract from ascidian Ciona robusta induces cytotoxic autophagy in human malignant cell lines

The last decades have seen an increase in the isolation and characterization of anticancer compounds derived from marine organisms, especially invertebrates, and their use in clinical trials. In this regard, ascidians, which are included in the subphylum Tunicata, represent successful examples with two drugs, Aplidine(C) and Yondelis(C), that reached the market as orphan drugs against several malignancies. Here, we report that an organic extract prepared from homogenized tissues of the Mediterranean ascidian Ciona robusta inhibited cell proliferation in HT-29, Hep G2, and U2 OS human cells with the former resulting as the most sensitive to the extract (EC50 = 250 {micro}g/ml). We demonstrated that the ascidian organic extract was not cytotoxic on HT-29 cells induced to differentiate with sodium butyrate, suggesting a preference for the mixture for the malignant phenotype. Finally, we reported that the cell death induced by the organic extract was mediated by the activation of a process of cytotoxic autophagy as a result of the increased expression of the LC3-II marker and the number of autophagic vacuoles, which almost doubled in treated HT-29 cells. In summary, although the detailed chemical composition of the Ciona robusta extract is still undetermined, our data suggest the presence in it of bioactive compounds possessing anticancer activity.

pharmacology and toxicology↗

bioRxiv2023

MTOR modulation induces selective perturbations in histone methylation which influence the anti-proliferative effects of mTOR inhibitors

Emerging data suggest a significant cross-talk between metabolic and epigenetic programs. However, the relationship between the mechanistic target of rapamycin (mTOR) which is a pivotal regulator of cellular metabolism, and epigenetic modifications remains poorly understood. We thus explored the impact of modulating mTOR signaling on histone methylation, a well-known epigenetic modification. Our results showed that mTORC1 activation caused by abrogation of TSC2 increased H3K27me3 but not H3K4me3 or H3K9me3. This appeared to be mediated via the induction of EZH2 protein synthesis, downstream of 4EBPs. Surprisingly, mTOR inhibition also induced H3K27me3 independently of TSC2. This coincided with reduced EZH2 and increased EZH1 protein levels. Notably, the ability of mTOR inhibitors to induce H3K27me3 levels was positively correlated with their anti-proliferative effects. Collectively, our findings demonstrate that both activation and inhibition of mTOR selectively increase H3K27me3 by distinct mechanisms, whereby the ability of mTOR inhibitors to induce H3K27me3 influences their anti-proliferative effects. HighlightsO_LIParadoxically, both mTOR activation and inhibition induce H3K27me3. C_LIO_LIThe effect of mTOR inhibitors on H3K27me3 are not secondary to cell cycle arrest. C_LIO_LIH3K27me3 triggered by mTOR suppression coincides with perturbations in EZH1/2 ratio. C_LIO_LIH3K27me3 impacts on the anti-proliferative effects of mTOR inhibitors. C_LI

molecular biology↗

bioRxiv2023

Chrysin directing an enhanced solubility through the formation of a supramolecular cyclodextrin-calixarene drug delivery system: a potential strategy in antifibrotic diabetes therapeutics

Calixarene 0118 (OTX008) and chrysin (CHR) are promising molecules for the treatment of fibrosis and diabetes complications but require an effective delivery system to overcome their low solubility and bioavailability. Sulfobutylated {beta}-cyclodextrin (SBECD) was evaluated for its ability to increase the solubility of CHR by forming a ternary complex with OTX008. The resulting increase in solubility and the mechanisms of complex formation were identified through phase-solubility studies, while dynamic light-scattering assessed the molecular associations within the CHR-OTX008-SBECD system. Nuclear magnetic resonance, differential scanning calorimetry, and computational studies elucidated the interactions at the molecular level, and cellular assays confirmed the systems biocompatibility. Combining SBECD with OTX008 enhances CHR solubility more than using SBECD alone, by forming water-soluble molecular associates in a ternary complex. This aids in the solubilization and delivery of CHR and OTX008. Structural investigations revealed non-covalent interactions essential to complex formation, which showed no cytotoxicity in hyperglycemic in vitro conditions. A new ternary complex has been formulated to deliver promising antifibrotic agents for diabetic complications, featuring OTX008 as a key structural and pharmacological component.

pharmacology and toxicology↗

bioRxiv2022

Specialized Tfh cell subsets driving type-1 and type-2 humoral responses in lymphoid tissue

Effective antibody responses are essential to generate protective humoral immunity. Different inflammatory signals polarize T cells towards an appropriate effector phenotype during an infection or immunization. Th1 and Th2 cells have been associated with the polarization of humoral responses for several decades. However, it is now established that T follicular helper cells (Tfh) have a unique ability to access the B cell follicle and support the Germinal Centre (GCs) responses by providing help to B cells. We investigated the specialization of Tfh cells induced under type-1 and type-2 conditions. We first studied homogenous Tfh cell populations generated by adoptively transferred TCR-transgenic T cells in mice immunized with type-1 and type-2 adjuvants. Using a machine learning approach, we established a gene expression signature that discriminates Tfh cells polarized towards type-1 and type-2 response, defined as Tfh1 and Tfh2 cells. The Tfh1 and Tfh2 distinct signature was validated against datasets of Tfh cells induced following LCMV or helminth infection. Using single-cell transcriptomics, we also dissected the heterogeneity of Tfh cells from the two immunizing conditions. Our results show that Tfh cells acquire a specialized function under distinct types of immune responses, but with the coexistence of a small population of Tfh cells of the alternative type. Furthermore, the specific molecular hallmarks of Tfh1 and Tfh2 cells identified herein offer putative new targets for tuning humoral responses.

immunology↗

bioRxiv2021

Genome-scale CRISPR Screens Identify Host Factors that Promote Human Coronavirus Infection

The COVID-19 pandemic has resulted in 153 million infections and 3.2 million deaths as of May 2021. While effective vaccines are being administered globally, there is still a great need for antiviral therapies as potentially antigenically distinct SARS-CoV-2 variants continue to emerge across the globe. Viruses require host factors at every step in their life cycle, representing a rich pool of candidate targets for antiviral drug design. To identify host factors that promote SARS-CoV-2 infection with potential for broad-spectrum activity across the coronavirus family, we performed genome-scale CRISPR knockout screens in two cell lines (Vero E6 and HEK293T ectopically expressing ACE2) with SARS-CoV-2 and the common cold-causing human coronavirus OC43. While we identified multiple genes and functional pathways that have been previously reported to promote human coronavirus replication, we also identified a substantial number of novel genes and pathways. Of note, host factors involved in cell cycle regulation were enriched in our screens as were several key components of the programmed mRNA decay pathway. Finally, we identified novel candidate antiviral compounds targeting a number of factors revealed by our screens. Overall, our studies substantiate and expand the growing body of literature focused on understanding key human coronavirus-host cell interactions and exploit that knowledge for rational antiviral drug development. One Sentence SummaryGenome-wide CRISPR screens identified host factors that promote human coronavirus infection, revealing novel antiviral drug targets.

microbiology↗