Integrative Imaging Reveals SARS-CoV-2 Induced Reshaping of Subcellular Morphologies

Cortese, Mirko; Lee, Ji-Young; Cerikan, Berati; Neufeldt, Christopher J; Oorschot, Viola; Köhrer, Sebastian; Hennies, Julian; Schieber, Nicole L.; Ronchi, Paolo; Mizzon, Giulia; Brey, Inés Romero; Santarella-Mellwig, Rachel; Schorb, Martin; Boermel, Mandy; Mocaer, Karel; Beckwith, Marianne Sandvold; Templin, Rachel; Gross, Viktoriia; Frankish, Jamie; Horvat, Natalie K.; Laketa, Vibor; Stanifer, Megan L.; Boulant, Steeve; Ruggieri, Alessia; Chatel‐Chaix, Laurent; Schwab, Yannick; Bartenschlager, Ralf

doi:10.2139/ssrn.3668344

Cited by 27 publications

(55 citation statements)

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“…In the case of SARS-CoV-2, we first compared replication kinetics between Huh7-Lunet/T7 and A549 cells, each stably expressing ACE2 (Huh7-Lunet/T7/ACE2 and A549/ACE2, respectively) (Cortese et al, 2020). As shown in Figure S1B, both cell pools supported robust infection and replication as revealed by production of infectious progeny viruses.…”

Section: Resultsmentioning

confidence: 99%

“…By the end of July 2021, SARS-CoV-2 had caused around 205 million infections worldwide with more than 4 million deaths as a result of coronavirus disease 2019 (COVID-19) (World Health Organization, 2021). As in the case of HCV, DMVs induced by SARS-CoV-2 are derived from the ER (Cortese et al, 2020;Snijder et al, 2020) (Figure 1B). Moreover, DMVlike structures can be induced by the sole expression of viral polyprotein fragments, which comprise nonstructural protein 3-4A-4B-5A-5B (NS3-5B) in the case of HCV and nsp3-4 in the case of SARS-CoV and Middle Eastern respiratory syndrome (MERS)-CoV (Oudshoorn et al, 2017;Romero-Brey et al, 2012Wolff et al, 2020).…”

Section: Introductionmentioning

confidence: 92%

“…(B) Tomographic slices and 3D renderings of DMVs induced in HCV-and SARS-CoV-2-infected cells. Figure modified according to Romero-Brey et al (2012) and Cortese et al (2020), respectively, with permission of the publishers. (C) CRISPR-Cas-9-based KO of ATG5 and ATG16L1 in Huh7-Lunet/T7 cells was confirmed using western blotting with ATG5 and ATG16L1 antibodies, respectively.…”

Section: Introductionmentioning

confidence: 99%

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Contribution of autophagy machinery factors to HCV and SARS-CoV-2 replication organelle formation

et al. 2021

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Positive-strand RNA viruses replicate in close association with rearranged intracellular membranes. For hepatitis C virus (HCV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), these rearrangements comprise endoplasmic reticulum (ER)-derived double membrane vesicles (DMVs) serving as RNA replication sites. Cellular factors involved in DMV biogenesis are poorly defined. Here, we show that despite structural similarity of viral DMVs with autophagosomes, conventional macroautophagy is dispensable for HCV and SARS-CoV-2 replication. However, both viruses exploit factors involved in autophagosome formation, most notably class III phosphatidylinositol 3-kinase (PI3K). As revealed with a biosensor, PI3K is activated in cells infected with either virus to produce phosphatidylinositol 3-phosphate (PI3P) while kinase complex inhibition or depletion profoundly reduces replication and viral DMV formation. The PI3P-binding protein DFCP1, recruited to omegasomes in early steps of autophagosome formation, participates in replication and DMV formation of both viruses. These results indicate that phylogenetically unrelated HCV and SARS-CoV-2 exploit similar components of the autophagy machinery to create their replication organelles.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Contribution of autophagy machinery factors to HCV and SARS-CoV-2 replication organelle formation

et al. 2021

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“…Enlarged late endosomal compartments were previously observed using EM [53,60], but have remained underappreciated in the absence of a more comprehensive overview of MVB morphology throughout infected cells. Whereas some viruses use MVBs to exit cells [61,62], recent work reported that viral egress was unaffected by treatments aimed at blocking MVB fusion with the plasma membrane [27].…”

Section: Discussionmentioning

confidence: 98%

Optical nanoscopy reveals SARS-CoV-2-induced remodeling of human airway cells

Nijenhuis

Damstra

Grinsven

et al. 2021

Preprint

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A better understanding of host cell remodeling by the coronavirus SARS-CoV-2 is urgently needed to understand viral pathogenesis and guide drug development. Expression profiling and electron microscopy have frequently been used to study virus-host interactions, but these techniques do not readily enable spatial, sub-cellular and molecular analysis of specific cellular compartments. Here, we use diffraction-unlimited fluorescence microscopy to analyze how SARS-CoV-2 infection exploits and repurposes the subcellular architecture of primary human airway cells. Using STED nanoscopy, we detect viral entry factors along the motile cilia of ciliated cells and visualize key aspects of the viral life cycle. Using Tenfold Robust Expansion (TREx) microscopy, we analyze the extensively remodeled three-dimensional ultrastructure of SARS-CoV-2-infected ciliated cells and uncover Golgi fragmentation, emergence of large and atypical multivesicular bodies enclosing viral proteins, ciliary clustering, and remodeling of the apical surface. These results demonstrate a broadly applicable strategy to study how viruses reorganize host cells with spatial and molecular specificity and provide new insights into SARS-CoV-2 infection in primary human cell models.

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“…In addition to endosomes, other organelles such as endoplasmic reticulum, lysosomes, mitochondria and lipid droplets have been implicated in the pathogenesis [68][69][70][71]. Importantly, SARS-CoV-2-induced cytopathic effects have been shown to cause remodelling of membrane and cytoskeleton elements, as well as extensive morphological alterations of organelles to meet their biosynthetic needs, such as fragmentation of the Golgi apparatus, perturbation of the mitochondrial network, increased biogenesis of lipid droplets and peroxisome recruitment to viral replication organelles [71,72]. Additional studies will further define role of pH and ionic balance in different organelles, as well as structural reorganizations and inter-organelle communication, in the pathogenesis of COVID-19, with functional and potentially translational implications.…”

Section: Translational Insights With Learning Opportunitiesmentioning

confidence: 99%

Protons to Patients: targeting endosomal Na⁺/H⁺ exchangers against COVID‐19 and other viral diseases

Prasad

2021

The FEBS Journal

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While there is undeniable evidence to link endosomal acid-base homeostasis to viral pathogenesis, the lack of druggable molecular targets has hindered translation from bench to bedside. The recent identification of variants in the interferon-inducible endosomal Na + /H + exchanger 9 associated with severe coronavirus disease-19 (COVID-19) has brought a shift in the way we envision aberrant endosomal acidification. Is it linked to an increased susceptibility to viral infection or a propensity to develop critical illness? This review summarizes the genetic and cellular evidence linking endosomal Na + /H + exchangers and viral diseases to suggest how they can act as a broad-spectrum modulator of viral infection and downstream pathophysiology. The review also presents novel insights supporting the complex role of endosomal acid-base homeostasis in viral pathogenesis and discusses the potential causes for negative outcomes of clinical trials utilizing alkalinizing drugs as therapies for COVID-19. These findings lead to a pathogenic model of viral disease that predicts that nonspecific targeting of endosomal pH might fail, even if administered early on, and suggests that endosomal Na + /H + exchangers may regulate key host antiviral defence mechanisms and mediators that act to drive inflammatory organ injury.Abbreviations APOE4, apolipoprotein 4 allele; COVID-19, coronavirus disease 19; CTD, C-terminal cytoplasmic domain; EBOV, Ebolavirus; eNHE, endosomal Na + /H + exchanger; EV, extracellular vesicles; GP, glycoproteins; GWAS, genome-wide association studies; HA, haemagglutinin; HCV, hepatitis C virus; IFNAR2, interferon alpha and beta receptor subunit 2; IFN, interferon b; NHE6, Na + /H + exchanger 6; NHE7, Na + /H + exchanger 7; NHE9, Na + /H + exchanger 9; NHP, nonhuman primate; N-Ras, neuroblastoma RAS viral oncogene homolog; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; TM, transmembrane segment; V-ATPase, vacuolar-type ATPase; VPS10, vacuolar protein sorting 10; WNV, West Nile virus.

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Integrative Imaging Reveals SARS-CoV-2 Induced Reshaping of Subcellular Morphologies

Cited by 27 publications

References 0 publications

Contribution of autophagy machinery factors to HCV and SARS-CoV-2 replication organelle formation

Contribution of autophagy machinery factors to HCV and SARS-CoV-2 replication organelle formation

Optical nanoscopy reveals SARS-CoV-2-induced remodeling of human airway cells

Protons to Patients: targeting endosomal Na⁺/H⁺ exchangers against COVID‐19 and other viral diseases

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Integrative Imaging Reveals SARS-CoV-2 Induced Reshaping of Subcellular Morphologies

Cited by 27 publications

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Contribution of autophagy machinery factors to HCV and SARS-CoV-2 replication organelle formation

Contribution of autophagy machinery factors to HCV and SARS-CoV-2 replication organelle formation

Optical nanoscopy reveals SARS-CoV-2-induced remodeling of human airway cells

Protons to Patients: targeting endosomal Na+/H+ exchangers against COVID‐19 and other viral diseases

Contact Info

Product

Resources

About

Protons to Patients: targeting endosomal Na⁺/H⁺ exchangers against COVID‐19 and other viral diseases