Lyn kinase regulates egress of flaviviruses in autophagosome-derived organelles

Li, Ming Yuan; Naik, Trupti Shivaprasad; Siu, Lewis; Acuto, Oreste; Spooner, Eric; Wang, Peigang; Yang, Xiaohan; Lin, Yongping; Bruzzone, Roberto; Ashour, Joseph; Evans, Matthew J.; Sanyal, Sumana

doi:10.1038/s41467-020-19028-w

“…LYN codes for a membrane-anchored src tyrosine kinase, localized on the cytoplasmic side of the plasma membrane and is an important regulator of signal transduction 50 . Noteworthy, LYN was shown to regulate inflammatory responses to bacterial infection 51 and to be important for flavivirus egress 52 . Additionally, an scRNA seq study had shown that most of the antiviral genes identified here were expressed in a substantial percentage of epithelial cells from the respiratory epithelium, including ciliated cells and secretory cells, the main targets of SARS-CoV-2 (Fig.…”

Section: Ctrl G1mentioning

confidence: 99%

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs

Goujon¹,

Rebendenne²,

Roy

³

et al. 2021

Preprint

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Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.

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“…LYN codes for a membrane-anchored src tyrosine kinase, localized on the cytoplasmic side of the plasma membrane and is an important regulator of signal transduction (Brodie et al, 2018). Noteworthy, LYN was shown to regulate inflammatory responses to bacterial infection (Li et al, 2014) and to be important for flavivirus egress (Li et al, 2020). Additionally, an scRNA seq study had shown that most of the antiviral genes identified here were expressed in a substantial percentage of epithelial cells from the respiratory epithelium, including ciliated cells and secretory cells, the main targets of SARS-CoV-2 ( Figure S4 , based on (Chua et al, 2020)).…”

Section: Resultsmentioning

confidence: 99%

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal coronaviruses

Rebendenne

¹

,

Roy

²

,

Bonaventure

³

et al. 2021

Preprint

View full text Add to dashboard Cite

Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.

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“…Interestingly, FYN inhibitors repurposed as a COVID-19 treatments 13 , have been also investigated as disease modifying treatments in AD 14 , supporting the convergence of common pathways between SARS-CoV-2 and AD in IFITM3's regulatory network.…”

Section: Sars-cov-2's Relevancy In Ad Pathobiologymentioning

confidence: 95%

FYN, SARS-CoV-2, and IFITM3 in the Neurobiology of Alzheimer’s Disease: A Regulatory Feedback Loop Governing Tau and Aβ Pathology

Vavougios¹,

Breza²,

Nikou³

et al. 2020

Preprint

0

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Introduction IFITM3, an innate immune protein linked to COVID-19 severity, has recently been identified as a novel γ-secretase modulator. Independent research has shown that IFITM3 may facilitate SARS-CoV-2 neurotropism in an ACE2-independent manner. In a previous study, we had detected perturbations in IFITM3 networks in both the CNS and peripheral immune cells donated by AD patients.The purpose of this study is to explore the transcriptomic evidence of the SARS-CoV-2 / IFITM3 / AD interplay, validating previous findings from our group. Methods Exploratory analyses involved meta-analysis of bulk and single cell RNA data for IFITM3 and FYN differential expression. For confirmatory analyses, we performed gene set enrichment analysis (GSEA) on an AD gene signature from AD Consensus transcriptomics; using the Enrichr platform, we scrutinized COVID-19 datasets for significant, overlapping enriched biological networks. Results Bulk RNA data analysis revealed that IFITM3 and FYN were differentially expressed in two CNS regions in AD: the temporal cortex (AD vs. Controls, adj.p-value=1.3e-6) and the parahippocampal cortex (AD vs. controls, adj.p-value=0.012). Correspondingly, single cell RNA analysis of IFITM3 and FYN revealed that it was differentially expressed in neuronal cells donated from AD patients (astrocytes, microglia and oligodendrocyte precursor cells), when compared to controls. Discussion IFITM3 and by extent FYN were found as interactors within biological networks overlapping between AD and SARS-CoV-2 infection. SARS-CoV-2 SARS-CoV-2-mediated IFITM3 induction would mechanistically result in increased Aβ production. FYN recruitment by viral processes results in abrogation of both fusion of IFITM3 vesicles with lysosomes; immunoevasion, by FYN-mediated impairment of autophagy would then serve to promote impaired detoxification from Aβ, while propagating Tau pathology in an IFITM3-independent manner.

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Lyn kinase regulates egress of flaviviruses in autophagosome-derived organelles

Cited by 30 publications

References 62 publications

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal coronaviruses

FYN, SARS-CoV-2, and IFITM3 in the Neurobiology of Alzheimer’s Disease: A Regulatory Feedback Loop Governing Tau and Aβ Pathology

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