Multi-omics in COVID-19: Seeing the unseen but overlooked in the clinic

Tian, Li; Wang, Yingrui; Guo, Tiannan

doi:10.1016/j.xcrm.2022.100580

Cited by 11 publications

(11 citation statements)

References 15 publications

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“…In principle, MS analysis provides a holistic proteomic view of SARS‐CoV‐2 infected samples (Che et al, 2004 ; S.‐J. Cho et al, 2011 ; Kammila et al, 2008 ; Van Puyvelde et al, 2021 ) that complements RT‐PCR methods for the diagnosis of COVID‐19 (Lu et al, 2022 ; Overmyer et al, 2021 ; Wandernoth et al, 2020 ; Wörner et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Proteomics‐based mass spectrometry profiling of SARS‐CoV‐2 infection from human nasopharyngeal samples

Chatterjee

Zaia

2022

Mass Spectrometry Reviews

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Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is the cause of the on‐going global pandemic of coronavirus disease 2019 (COVID‐19) that continues to pose a significant threat to public health worldwide. SARS‐CoV‐2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin‐converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high‐throughput technique. Alternate strategies such as proteomics and glycoproteomics‐based mass spectrometry enable a more detailed and holistic view of the viral proteins and host–pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS‐CoV‐2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS‐CoV‐2 from biological complex matrices to identify potential COVID‐19 markers.

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Section: Introductionmentioning

confidence: 99%

Proteomics‐based mass spectrometry profiling of SARS‐CoV‐2 infection from human nasopharyngeal samples

Chatterjee

Zaia

2022

Mass Spectrometry Reviews

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“…Multi-omics approaches have recently been applied to understand host responses to SARS-CoV-2, thus accelerating drug development and drug repositioning against COVID-19 (Kamel et al, 2021, Lu et al, 2022, Chu et al, 2021, Ho et al, 2021, Klann et al, 2020). For instance, phosphoproteomic analysis of SARS-CoV-2-infected cells has revealed the activation of growth factor receptor (GFR) and its downstream pathways including the RAF/MEK/ERK MAPK signaling and PI3K/AKT/mTOR signaling in SARS-CoV-2-infected cells (Klann et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Transcription regulation of SARS-CoV-2 receptor ACE2 by Sp1: a potential therapeutic target

Han

Luo

Long

et al. 2023

Preprint

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Angiotensin-converting enzyme 2 (ACE2) is a major cell entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Induction of ACE2 expression may represent an effective tactic employed by SARS-CoV-2 to facilitate its own propagation. However, the regulatory mechanisms of ACE2 expression after viral infection remain largely unknown. By employing an array of 45 different luciferase reporters, we identify that the transcription factor Sp1 positively and HNF4α negatively regulate the expression of ACE2 at the transcriptional levels in HPAEpiC cells, a human lung epithelial cell line. SARS-CoV-2 infection promotes and inhibits the transcription activity of Sp1 and HNF4α, respectively. The PI3K/AKT signaling pathway, which is activated by SARS-CoV-2 infection, is a crucial node for induction of ACE2 expression by increasing Sp1 phosphorylation, an indicator of its activity, and reducing HNF4α nuclear location. Furthermore, we show that colchicine could inhibit the PI3K/AKT signaling pathway, thereby suppressing ACE2 expression. Inhibition of Sp1 by either its inhibitor mithramycin A or colchicine reduces viral replication and tissue injury in Syrian hamsters infected with SARS-CoV-2. In summary, our study uncovers a novel function of Sp1 in regulating ACE2 expression and suggests that Sp1 is a potential target to reduce SARS-CoV-2 infection.

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Section: Introductionmentioning

confidence: 99%

“…Some existing reviews summarized the development of different omics for understanding COVID-19 [ [42] , [43] , [44] , [45] , [46] ]. Lu et al [ 42 ] focused on the limitation of current multi-omics analysis for COVID-19 clinical applications. Lin et al [ 43 ] and Yang et al [ 44 ] summarized the application of genomics, proteomics, transcriptomics, and metabolomics in understanding the COVID-19 molecular mechanism.…”

Section: Introductionmentioning

confidence: 99%