Cell type-specific immune dysregulation in severely ill COVID-19 patients

Yao, Changfu; Bora, Stephanie A.; Parimon, Tanyalak; Zaman, Tanzira; Friedman, Oren A.; Palatinus, Joseph A.; Surapaneni, Nirmala S.; Matusov, Yuri P.; Chiang, Giuliana Cerro; Kassar, Alexander G.; Patel, Nayan; Green, Chelsi ER.; Aziz, Adam W.; Suri, Harshpreet; Suda, Jo; Lopez, Andres A.; Martins, Gislâine A.; Stripp, Barry R.; Gharib, Sina A.; Goodridge, Helen S.; Chen, Peter

Recent studies have demonstrated immunologic dysfunction in severely ill COVID-19 patients. We use single-cell RNA sequencing (scRNA-seq) to analyze the transcriptome of peripheral blood mononuclear cells (PBMC) from healthy (n=3) and COVID-19 patients with moderate disease (n = 5), acute respiratory distress syndrome (ARDS, n = 6), or recovering from ARDS (n = 6). Our data reveal transcriptomic profiles indicative of defective antigen presentation and interferon responsiveness in monocytes from ARDS patients, which contrasts with higher responsiveness to interferon signaling in lymphocytes. Furthermore, genes involved in cytotoxic activity are suppressed in both NK and CD8 lymphocytes, and B cell activation is deficient, which is consistent with delayed viral clearance in severely ill COVID-19 patients. Our study demonstrates that COVID-19 patients with ARDS have a state of immune imbalance in which dysregulation of both the innate and adaptive immune responses may be contributing to a more severe disease course.