ABSTRACT
BACKGROUND: Understanding the host genetic architecture and viral immunity contributes to the development of effective vaccines and therapeutics for controlling the COVID-19 pandemic. Alterations of immune responses in peripheral blood mononuclear cells play a crucial role in the detrimental progression of COVID-19. However, the effects of host genetic factors on immune responses for severe COVID-19 remain largely unknown. METHODS: We constructed a computational framework to characterize the host genetics that influence immune cell subpopulations for severe COVID-19 by integrating GWAS summary statistics (N = 969,689 samples) with four independent scRNA-seq datasets containing healthy controls and patients with mild, moderate, and severe symptom (N = 606,534 cells). We collected 10 predefined gene sets including inflammatory and cytokine genes to calculate cell state score for evaluating the immunological features of individual immune cells. RESULTS: We found that 34 risk genes were significantly associated with severe COVID-19, and the number of highly expressed genes increased with the severity of COVID-19. Three cell subtypes that are CD16+monocytes, megakaryocytes, and memory CD8+T cells were significantly enriched by COVID-19-related genetic association signals. Notably, three causal risk genes of CCR1, CXCR6, and ABO were highly expressed in these three cell types, respectively. CCR1+CD16+monocytes and ABO+ megakaryocytes with significantly up-regulated genes, including S100A12, S100A8, S100A9, and IFITM1, confer higher risk to the dysregulated immune response among severe patients. CXCR6+ memory CD8+ T cells exhibit a notable polyfunctionality including elevation of proliferation, migration, and chemotaxis. Moreover, we observed an increase in cell-cell interactions of both CCR1+ CD16+monocytes and CXCR6+ memory CD8+T cells in severe patients compared to normal controls among both PBMCs and lung tissues. The enhanced interactions of CXCR6+ memory CD8+T cells with epithelial cells facilitate the recruitment of this specific population of T cells to airways, promoting CD8+T cell-mediated immunity against COVID-19 infection. CONCLUSIONS: We uncover a major genetics-modulated immunological shift between mild and severe infection, including an elevated expression of genetics-risk genes, increase in inflammatory cytokines, and of functional immune cell subsets aggravating disease severity, which provides novel insights into parsing the host genetic determinants that influence peripheral immune cells in severe COVID-19.
Subject(s)
CD8-Positive T-Lymphocytes/virology , COVID-19/genetics , COVID-19/pathology , Monocytes/virology , Single-Cell Analysis/methods , COVID-19/immunology , Computational Biology/methods , GPI-Linked Proteins/metabolism , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Megakaryocyte Progenitor Cells/immunology , Megakaryocyte Progenitor Cells/virology , Monocytes/metabolism , Quantitative Trait Loci , Receptors, CCR1/immunology , Receptors, CCR1/metabolism , Receptors, CXCR6/immunology , Receptors, CXCR6/metabolism , Receptors, IgG/metabolism , Sequence Analysis, RNA , Severity of Illness IndexABSTRACT
OBJECTIVE: To explore the suppression effect of human cytomegalovirus (HCMV) on megakaryocytes and their precursors and study the antiviral effect of antisense phosphorothioate deoxyoligonucleotide (ASON) against HCMV. METHODS: CD34(+) cells were induced to proliferate and differentiate committedly to megakaryocytes in a semi-solid CFU-MK culture system. Cultured cells and ASON pretreated CD34(+) cells were infected by HCMV of AD169 strain. HCMV immediate early protein (IEP) DNA and mRNA and UL36 mRNA were detected by PCR and reverse transcription-polymerase chain reaction (RT-PCR). Cytotoxicity was evaluated by MTT assay. RESULTS: HCMV AD169 suppressed the proliferation of megakaryocytes significantly. Compared with the mock group, the CFU-MK yields were decreased by 21.6%, 33.8%, and 46.3%, respectively, in 3 different titers of virus infected groups (P < 0.05). The suppression was virus titer dependent. HCMV IEP DNA, HCMV IEP mRNA and UL36 mRNA were detected in the colony cells of viral infection group. Compared with the infected group by HCMV AD169, UL36Anti treatment at 0.08 micromol/L could recover the CFU-MK yields significantly (P < 0.05). In the infected MK, which was pretreated with UL36Anti at 0.08 micromol/L, HCMV UL36 mRNA was undetectable by RT-PCR. The oligonucleotide MM(1) containing a G-to-C substitution in UL36Anti was inactive at 0.08 micromol/L but active at 0.40 micromol/L. The concentration of UL36Anti necessary to significantly affect cell growth was 90.00 micromol/L. CONCLUSIONS: HCMV AD169 infection inhibits the proliferation and differentiation of megakaryocytes and their precursors. There are early transcriptions of HCMV IE and UL36 protein in infected CFU-MK. The specific ASON has a definite anti-HCMV activity.
