Comparative scRNA-seq Analysis of Peripheral Blood Mononuclear Cells from Patients with COVID-19 and Idiopathic Pulmonary Fibrosis Demonstrates Dissimilar Cell Shifts and Gene Expression Profiles

Abstract

Rationale: Similar to other human coronaviruses like MERS and SARS, severe manifestations of COVID-19 are associated with acute lung injury and sustained pulmonary dysfunction. A recent single-cell study of lung tissue from severe COVID-19 and idiopathic pulmonary fibrosis (IPF) patients suggested these diseases share common pro-fibrotic molecular pathways. To determine whether similar changes can be detected in the blood, we compared single-cell RNA-seq profiles of peripheral blood mononuclear cells (PBMCs) from patients with IPF or COVID-19, using influenza and healthy individuals as controls. Methods: 25 IPF, 18 COVID-19, and 13 healthy control PBMC samples were sequenced in our lab using 10X Genomics 5' single-cell technology. This data was processed using CellRanger and integrated with publicly available datasets of Covid-19, influenza, and healthy PBMC samples, yielding ∼300,000 single cells. Severe COVID-19 patients were treated in the ICU and succumbed to the disease, while severe IPF had transplant-free survival of fewer than three years. Downstream analysis was performed with the R package Seurat. The Louvain clustering algorithm generated 28 distinct cell clusters. Wilcoxon rank-sum test was used to determine significant cell type proportion differences and differentially expressed genes (DEGs). Significantly enriched pathways were found using EnrichR and Gene Set Enrichment Analysis (GSEA). Results: We report significantly increased platelets as a proportion of total cells in patients with severe COVID-19 (p = 0.0047) and severe IPF (p = 0.05) compared to healthy patients. Stable IPF and severe COVID-19 shared similar cell proportions of platelets (p=0.15) and monocytes (p=0.42). Across most cell types, COVID-19 and influenza patients had gene expression changes consistent with type I interferon activation while IPF patients exhibited changes in ribosomal upregulation and pro-fibrotic pathways relative to healthy controls. Using a composite pro-fibrotic score of TGFB1 targets and effectors, hierarchical clustering markedly differentiates between IPF and controls versus COVID-19 and influenza, perhaps distinctly highlighting mechanisms of disease. Within monocytes, we did not observe a significant pro-fibrotic phenotype (SPP1, MMP9, CHI3L1, PLA2G7) in samples of patients with any disease;hierarchical clustering of these genes again segregated IPF and controls from COVID-19 and influenza. Conclusions: Pro-fibrotic gene expression patterns could not be seen in PBMCs from patients with acute severe COVID-19 infection. More studies are needed in distinct COVID-19 patient populations, such as those with prolonged respiratory failure or with sustained respiratory dysfunction after recovery.