NEW YORK – An international team led by investigators in the UK has characterized the cellular changes that accompany harm to the lung known as "diffuse alveolar damage" (DAD) in individuals with severe forms of COVID-19. Their research uncovered altered cellular processes and interactions during early and late phases of damage to the lung's alveoli.
"Our study allowed us to build a more thorough picture of how our lungs respond to the SARS-CoV-2 virus," co-first author Jimmy Tsz Hang Lee, a postdoctoral researcher at the Wellcome Sanger Institute, said in a statement, noting that the new findings "provide a more detailed understanding about a disease that affects people worldwide."
For their study, published in Nature Communications on Monday, members of the UK Coronavirus Immunology Consortium (UK-CIC) used 10x Genomics-based single-cell RNA sequencing, spatial transcriptomics, and imaging mass cytometry to assess gene expression, cellular interactions, and lung features in histologically characterized postmortem lung samples from individuals with or without COVID-19.
Based on single-cell RNA-seq or single-nucleus RNA-seq data spanning nearly 514,800 cells from postmortem lung samples of 77 organ donors and 51 COVID-19 patients, the team uncovered nearly three dozen expression-based clusters representing distinct cell types, subtypes, or cell states. The data also provided a look at transcriptomic shifts found in samples from COVID-19 patients with early-stage or late-stage DAD.
Using a NanoString whole transcriptome assay, meanwhile, the investigators profiled samples from 33 individuals between the ages of 22 and 98 years who died of severe COVID-19 during the first or second pandemic waves, tracking spatial transcriptomic changes associated with COVID-19-related alveolar damage detected by histopathology.
In the process, the team uncovered genes, pathways, and cellular interactions contributing to different stages of lung damage in individuals with severe COVID-19. These ranged from an uptick in the expression of protective inflammatory and toxic metal protection-related genes in early-stage DAD to late-stage DAD shifts in macrophage immune cells, lung fibrosis markers, and fibrosis-related collagen deposition.
"We identified a group of new cell types that change between early and late stages of lung damage," Lee explained. "We also identified subgroups of immune cells, called macrophages, that start to accumulate in very early stages of infection, and how they shift to different groups as the disease worsens."
While lung fibrosis markers associated with lung tissue scarring and rigidity ticked up in samples from individuals with late-stage DAD, the investigators detected enhanced expression of interleukin-, interferon-alpha and interferon-gamma-, cell checkpoint-, and metallothionein-related genes in early-stage DAD.
"Taken together, these data present biomarkers to stratify alveolar damage stages and highlight molecular pathways underlying the progression of an inflammatory phenotype in early damage to a profibrotic phenotype observed histologically in late damage," the authors reported.
During the transition from early- to late-stage DAD, the team saw macrophage immune cell changes, together with declining representation by epithelial and endothelial cell populations and a shift in the expression of SERPINE1, which regulates a blood clot breakdown process in blood vessels known as fibrinolysis.
In particular, the investigators explained, SERPINE1 expression appeared to be dramatically increased during early-stage DAD but dipped during late-stage disease. This happened apparently due to interactions with endothelial cells and macrophage cell populations that express the osteopontin (OPN)-coding inflammatory signaling gene SPP1.
When they explored such interactions further in human umbilical vein endothelial cell line experiments, the team saw an uptick in SERPINE1 expression when they exposed the cells to several concentrations of recombinant human osteopontin, consistent with their suggestion that osteoponin has a regulatory role in severe COVID-19 responses in the lung.
"Taken together, our study provides a unique resource to investigate the cellular and molecular landscape of alveolar damage progression within COVID-19 lung tissue at single-cell and spatial resolution," the researchers wrote, adding that the work "provides mechanistic inferences and a baseline to explore novel putative therapeutic targets for early and late stages of alveolar damage."