Airspace Macrophages and Monocytes Exist in Transcriptionally Distinct Subsets in Healthy Adults

Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution

“…All BALF and PBMC cohorts were obtained from separate prior studies (Arunachalam et al, 2020;Lee et al, 2020;Liao et al, 2020;Schulte-Schrepping et al, 2020;Wilk et al, 2020). A BALF cross-control cohort was created by merging data from two additional studies (Morse et al, 2019;Mould et al, 2021). Detailed information on datasets and clinical characteristics of patient donors are available in Table 1.…”

“…The sample sizes and clinical status of human subjects analyzed in this study are given in Table 1. The age, sex or gender, and other demographic data for these subjects are available in the source publications (Arunachalam et al, 2020;Lee et al, 2020;Liao et al, 2020;Morse et al, 2019;Mould et al, 2021;Schulte-Schrepping et al, 2020;Wilk et al, 2020).…”

“…To set up a more comprehensive analysis and mitigate confounders in our investigation that could arise from batch effects, we incorporated 4 cohorts consisting of COVID-19 patients and healthy controls when provided (Arunachalam et al, 2020;Schulte-Schrepping et al, 2020;Wauters et al, 2021;Wilk et al, 2020) as well as an additional cohort for cross-control assembled from 2 studies containing healthy BALF donors (Morse et al, 2019;Mould et al, 2021). These additional BALF and PBMC cohorts, shown in Table 1, were used to provide additional granularity and increase the number of possible BALF-PBMC comparisons to be made.…”

Signs of self-sustained inflammatory circuits in severe COVID pneumonia

“…Intriguingly, the authors found that the immune cells from people who had COVID-19 contained a greater proportion of T cells and monocytes, compared with the immune-cell population of people whose pneumonia arose from a different cause. T cells and monocytes are relatively rare in healthy lungs 3 , so the assumption is that these immune cells were recruited to the air sacs by locally produced chemo attractant proteins. Importantly, these differences in inflammatory cell types in people with COVID-19 could not be explained by other clinical factors, such as the phase of their illness or a co-infection with other disease-causing agents.…”

“…Although the process of loop extrusion was hypothesized decades ago [2][3][4][5] , only in the past few years has it become clear that it is a universal mechanism that organizes DNA in organisms from bacteria to humans. In 2016, computational models showed that extrusion can compact DNA, turning a hairball of chromatin into detangled yet tightly packed chromosomes 6 .…”