Epigenetic Landscapes of Single-Cell Chromatin Accessibility and Transcriptomic Immune Profiles of T Cells in COVID-19 Patients

Abstract

T cells play a critical role in coronavirus diseases. How they do so in COVID-19 may be revealed by analyzing the epigenetic chromatin accessibility of cis- and trans-regulatory elements and creating transcriptomic immune profiles. We performed single-cell assay for transposase-accessible chromatin (scATAC) and single-cell RNA (scRNA) sequencing (seq) on the peripheral blood mononuclear cells (PBMCs) of severely ill/critical patients (SCPs) infected with COVID-19, moderate patients (MPs), and healthy volunteer controls (HCs). About 76,570 and 107,862 single cells were used, respectively, for analyzing the characteristics of chromatin accessibility and transcriptomic immune profiles by the application of scATAC-seq (nine cases) and scRNA-seq (15 cases). The scATAC-seq detected 28,535 different peaks in the three groups; among these peaks, 41.6 and 10.7% were located in the promoter and enhancer regions, respectively. Compared to HCs, among the peak-located genes in the total T cells and its subsets, CD4+ T and CD8+ T cells, from SCPs and MPs were enriched with inflammatory pathways, such as mitogen-activated protein kinase (MAPK) signaling pathway and tumor necrosis factor (TNF) signaling pathway. The motifs of TBX21 were less accessible in the CD4+ T cells of SCPs compared with those in MPs. Furthermore, the scRNA-seq showed that the proportion of T cells, especially the CD4+ T cells, was decreased in SCPs and MPs compared with those in HCs. Transcriptomic results revealed that histone-related genes, and inflammatory genes, such as NFKBIA, S100A9, and PIK3R1, were highly expressed in the total T cells, CD4+ T and CD8+ T cells, both in the cases of SCPs and MPs. In the CD4+ T cells, decreased T helper-1 (Th1) cells were observed in SCPs and MPs. In the CD8+T cells, activation markers, such as CD69 and HLA class II genes (HLA-DRA, HLA-DRB1, and HLA-DRB5), were significantly upregulated in SCPs. An integrated analysis of the data from scATAC-seq and scRNA-seq showed some consistency between the approaches. Cumulatively, we have generated a landscape of chromatin epigenetic status and transcriptomic immune profiles of T cells in patients with COVID-19. This has provided a deeper dissection of the characteristics of the T cells involved at a higher resolution than from previously obtained data merely by the scRNA-seq analysis. Our data led us to suggest that the T-cell inflammatory states accompanied with defective functions in the CD4+ T cells of SCPs may be the key factors for determining the pathogenesis of and recovery from COVID-19.

Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion

“…The fact that these signals are robust even in a small cohort of subjects with subtle differences in disease severity (WHO OS 1 vs 2) suggests the potential power of epigenetic approaches to classify subsets of SARS-CoV-2 infection. This study complements previous work that identi ed signatures of accessible chromatin in severe or convalescing COVID-19 [19][20][21][22] The data show that transcription factor motifs enriched in peaks accessible prior to seroconversion had the highest occupancy in cells from the myeloid lineage, speci cally CD14+ monocytes, dendritic cells, and CD16+ monocytes. KLF and CREB transcription factor families, which are known to regulate monocyte-macrophage polarization, have elevated motif accessibility in subjects with mild or moderate symptoms, suggesting an epigenetic priming mechanism controlling cell fate 23,24 .…”

Differential Co-Expression Network Analysis Reveals Key Hub-High Traffic Genes as Potential Therapeutic Targets for COVID-19 Pandemic

“…Given the importance of NK cells and their genes/proteins in antiviral activity, as well as their reduction in COVID-19 patients, development of treatment strategies to restore NK cells may control infection in the early stages of COVID-19 ( 303 ). Moreover, other genes in the lightyellow module, e.g., ERBB2 ( 151 ) and ADRB2 ( 275 , 304 ), as well as TBX21 ( 305 – 307 ) hub-high traffic TF, have critical roles during SARS-CoV-2 infection. For instance, in addition to the IRAK3 hub-high traffic gene (described in the lightgreen module section), increased ADRB2 hub-high traffic gene expression during SARS-CoV-2 infection also increased the risk of asthma in COVID-19 patients ( 275 ).…”

Transcriptome and DNA methylome analysis of peripheral blood samples reveals incomplete restoration and transposable element activation after 3-month recovery of COVID-19

“…Majority of the COVID-19-related DMRs are near the gene promoter regions and were hypo-methylated even though the global methylation level remains similar between healthy control and COVID-19 patients (Balnis et al, 2021). However, currently reported results on DNA methylome of COVID-19 patients (Balnis et al, 2021; Bernardes et al, 2020; Li et al, 2021) all depended on 450K or 850K methylation array which covered only a small percent of CpG sites (1% to 3 %) and couldn’t be used to obtain DNA methylation information of transposable elements. Our WGBS data produced nearly whole-genome CpG sites coverage (coverages of all samples are around 80%) which is valuable for genome-wide identification of differentially methylated regions, especially for transposable elements.…”