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First Author: Ana Dominguez Andres, Yongmei Feng, Alexandre Rosa Campos, Jun Yin 

Journal/preprint name: bioRxiv 

Tags: Proteomics, TranscriptomicsImmunology, Virology 

Summary 

This study characterised the SARS-CoV-2 ORF9c protein as a highly unstable protein and showed it can interact with membrane-associated proteins distributed throughout the membrane compartments in A549 cells. Cells expressing only SARS-CoV-2 ORF9c protein had altered proteome and transcriptome, including induced IL-6 signaling, downregulated interferon signaling, complement signaling, and antigen presentation. Remarkably, the transcriptome and ubiquitinome changes upon ORF9c protein expression resemble the full viral infection reported previously. Moreover, Inhibition of ERAD/proteasome could partially restore the cellular changes caused by ORF9c protein expression. This study indicates that ORFs encoding “accessory” proteins could be of importance in affecting host cell response. 

Research Highlights 

  1. SARS-CoV-2 ORF9c is identified as the first human coronavirus protein with a putative transmembrane domain and is highly unstable, undergoing proteasome-dependent  degradation.   

  1. A549 cells transfected with only SARS-CoV-2 ORF9c protein showed induced IL-6 signaling and downregulated interferon signaling, complement, and antigen presentation-associated pathways. 

  1. The transcriptome and ubiquitinome changes upon SARS-CoV-2 ORF9c protein expression showed similarity with those upon full viral infection reported previously. 

Impact for COVID-19 research:  

  • Does this research alter our view of the disease? 

This study is focused on a less well-studied viral protein and provided important insights into how SARS-CoV-2 ORF9c contributes to host cell responses. 

  • Could this research benefit clinicians (disease management etc.)? 

This research doesn’t have direct translatability, but provides new directions for therapeutics development if the effects of ORF9c protein are further validated in primary lung cells or animal models. 

Methodologies: 

  • Study Type:  in vitro 

  • Important cell lines/viral models used: A549 cells 

  • Key Techniques: liquid chromatography tandem mass spectrometry (LC-MS/MS)label free quantification (LFQ) and tandem mass tag (TMT) mass spectrometry analysisRNA-seq analysisPathway and network analysis 

Limitations: 

  • The study is mainly conducted in A549 cells. Further validation in primary human lung cells or animal models is needed to strengthen the conclusions in this paper. 

  • The function of proteasome-dependent degradation of ORF9c protein in regulating the host cell responses is not yet clear and therefore more mechanistic studies is needed to support their inhibitor experiments.