Meta-Analysis of COVID-19 Bronchoalveolar Lavage scRNA-Seq Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates.

Single-cell RNA-sequencing (scRNA-Seq) of bronchoalveolar lavage (BAL) cells has provided insights into COVID-19. However, reports have been limited by small patient cohorts. We performed a meta-analysis of BAL scRNA-Seq data from healthy controls (n=13) and COVID-19 patients (n=20), sourced from six independent studies (total: 167,280 high-quality cells). Consistent with the source reports, increases in infiltrating leukocyte subtypes were noted, several with type I interferon signatures and unique gene expression signatures associated with transcellular chemokine signaling. Noting dramatic reductions of inferred NKX2-1 and NR4A1 activity in alveolar epithelial type (AT)-II cells, we modeled pseudotemporal AT-II-to-AT-I progression. This revealed changes in inferred AT-II cell metabolic activity, increased transitional cells, and a previously undescribed AT-I state. This cell state was conspicuously marked by induction of genes of the epidermal differentiation complex (EDC), including the cornified envelope protein SPRR3, upregulation of multiple keratin (KRT) genes, inferred mitochondrial dysfunction, and cell death signatures including apoptosis and ferroptosis. Immunohistochemistry of COVID-19 patient lungs confirmed upregulation and co-localization of KRT13 and SPRR3 in the distal airspaces. Forced overexpression of SPRR3 in human alveolar epithelial cells ex vivo did not activate caspase-3 or upregulate KRT13, suggesting that SPRR3 marks an AT-I cornification program in COVID-19 but is not sufficient for phenotypic changes. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).