High-dimensional comparison of monocytes and T cells in post-COVID and idiopathic pulmonary fibrosis

Up to 30% of hospitalized COVID-19 patients experience persistent sequelae, including pulmonary fibrosis (PF). We examined COVID-19 survivors with impaired lung function and imaging worrisome for developing PF and found within six months, symptoms, restriction and PF improved in some (Early-Resolving COVID-PF), but persisted in others (Late-Resolving COVID-PF). To evaluate immune mechanisms associated with recovery versus persistent PF, we performed single-cell RNA-sequencing and multiplex immunostaining on peripheral blood mononuclear cells from patients with Early- and Late-Resolving COVID-PF and compared them to age-matched controls without respiratory disease. Our analysis showed circulating monocytes were significantly reduced in Late-Resolving COVID-PF patients compared to Early-Resolving COVID-PF and non-diseased controls. Monocyte abundance correlated with pulmonary function forced vital capacity and diffusion capacity. Differential expression analysis revealed MHC-II class molecules were upregulated on the CD8 T cells of Late-Resolving COVID-PF patients but downregulated in monocytes. To determine whether these immune signatures resembled other interstitial lung diseases, we analyzed samples from Idiopathic Pulmonary Fibrosis (IPF) patients. IPF patients had a similar marked decrease in monocyte HLA-DR protein expression compared to Late-Resolving COVID-PF patients. Our findings indicate decreased circulating monocytes is associates with decreased lung function and uniquely distinguishes Late-Resolving COVID-PF from Early-Resolving COVID-PF, IPF, and non-diseased controls. Patients with IPF donated peripheral blood mononuclear cells (PBMCs) in the outpatient setting while in a stable clinical state. Three control PBMC samples from age-matched patients with no known pulmonary disease were prepared and sequenced at the Mayo Clinic (IRB #:19-012187). We recruited a subset of patients from the University of Virginia COVID-19 survivor clinic (IRB #:13166) with restrictive lung physiology on pulmonary function tests (PFTs) and features consistent with pulmonary fibrosis on chest CT performed at the associated visit. Radiographic features indicative of possible development of pulmonary fibrosis included bilateral reticulation, traction bronchiectasis, and/or honeycomb change in peripheral and basilar distribution, similar to the presently recognized progressive pulmonary fibrosis clinical radiologic phenotype, and similar to previously defined COVID-19 pulmonary fibrosis characteristics. PFT and chest imaging was performed in association with the patient's first visit to the outpatient COVID-19 survivor clinic. Early- and Late-Resolvers were identified by comparing chest imaging and PFT values from the patient's first and subsequent visit. Patients with COVID-19 associated pulmonary fibrosis (COVID PF) were followed for 6 months or until the patient clinically improved. COVID PF patients were age-matched to IPF patients to control for age-related differences in peripheral immune signatures.