TY - JOUR
T1 - Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes
AU - Jain, Ruchi
AU - Ramaswamy, Sathishkumar
AU - Harilal, Divinlal
AU - Uddin, Mohammed
AU - Loney, Tom
AU - Nowotny, Norbert
AU - Alsuwaidi, Hanan
AU - Varghese, Rupa
AU - Deesi, Zulfa
AU - Alkhajeh, Abdulmajeed
AU - Khansaheb, Hamda
AU - Alsheikh-Ali, Alawi
AU - Abou Tayoun, Ahmad
N1 - Publisher Copyright:
© 2020 The Author(s)
PY - 2021/1
Y1 - 2021/1
N2 - Characterizing key molecular and cellular pathways involved in COVID-19 is essential for disease prognosis and management. We perform shotgun transcriptome sequencing of human RNA obtained from nasopharyngeal swabs of patients with COVID-19, and identify a molecular signature associated with disease severity. Specifically, we identify globally dysregulated immune related pathways, such as cytokine-cytokine receptor signaling, complement and coagulation cascades, JAK-STAT, and TGF- β signaling pathways in all, though to a higher extent in patients with severe symptoms. The excessive release of cytokines and chemokines such as CCL2, CCL22, CXCL9 and CXCL12 and certain interferons and interleukins related genes like IFIH1, IFI44, IFIT1 and IL10 were significantly higher in patients with severe clinical presentation compared to mild and moderate presentations. Differential gene expression analysis identified a small set of regulatory genes that might act as strong predictors of patient outcome. Our data suggest that rapid transcriptome analysis of nasopharyngeal swabs can be a powerful approach to quantify host molecular response and may provide valuable insights into COVID-19 pathophysiology.
AB - Characterizing key molecular and cellular pathways involved in COVID-19 is essential for disease prognosis and management. We perform shotgun transcriptome sequencing of human RNA obtained from nasopharyngeal swabs of patients with COVID-19, and identify a molecular signature associated with disease severity. Specifically, we identify globally dysregulated immune related pathways, such as cytokine-cytokine receptor signaling, complement and coagulation cascades, JAK-STAT, and TGF- β signaling pathways in all, though to a higher extent in patients with severe symptoms. The excessive release of cytokines and chemokines such as CCL2, CCL22, CXCL9 and CXCL12 and certain interferons and interleukins related genes like IFIH1, IFI44, IFIT1 and IL10 were significantly higher in patients with severe clinical presentation compared to mild and moderate presentations. Differential gene expression analysis identified a small set of regulatory genes that might act as strong predictors of patient outcome. Our data suggest that rapid transcriptome analysis of nasopharyngeal swabs can be a powerful approach to quantify host molecular response and may provide valuable insights into COVID-19 pathophysiology.
KW - COVID-19
KW - Disease severity
KW - Expression signature
KW - Nasopharyngeal swabs
KW - Transcriptome sequencing
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U2 - 10.1016/j.csbj.2020.12.016
DO - 10.1016/j.csbj.2020.12.016
M3 - Article
C2 - 33425248
AN - SCOPUS:85099203549
SN - 2001-0370
VL - 19
SP - 153
EP - 160
JO - Computational and Structural Biotechnology Journal
JF - Computational and Structural Biotechnology Journal
ER -
