Single cell multiomics identifies cells and genetic networks underlying alveolar capillary dysplasia

Minzhe Guo, Kathryn A. Wikenheiser-Brokamp, Joseph A. Kitzmiller, Cheng Jiang, Guolun Wang, Allen Wang, Sebastian Preissl, Xiaomeng Hou, Justin Buchanan, Justyna A. Karolak, Yifei Miao, David B. Frank, William J. Zacharias, Xin Sun, Yan Xu, Mingxia Gu, Pawel Stankiewicz, Vladimir V. Kalinichenko, Jennifer A. Wambach, Jeffery A. Whitsett


Rationale: Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV) is a lethal developmental disorder of lung morphogenesis caused by insufficiency of FOXF1 transcription factor function. The cellular and transcriptional mechanisms by which FOXF1 deficiency disrupts human lung formation are unknown.

Objectives: To identify cell types, gene networks, and cell-cell interactions underlying the pathogenesis of ACDMPV. Methods: We used single nucleus RNA and ATAC sequencing, immunofluorescence confocal microscopy, and RNA in situ hybridization to identify cell types and molecular networks influenced by FOXF1 in ACDMPV lungs.

Measurements and Main Results: Pathogenic single nucleotide variants and CNV deletions involving the FOXF1 gene locus in all subjects with ACDMPV (n=6) were accompanied by marked changes in lung structure, including deficient alveolar development and paucity of pulmonary microvasculature. Single nucleus RNA and ATAC sequencing identified alterations in cell number and gene expression in endothelial cells (ECs), pericytes, fibroblasts, and epithelial cells in ACDMPV lungs. Distinct cell-autonomous roles for FOXF1 in capillary ECs and pericytes were identified. Pathogenic variants involving the FOXF1 gene locus disrupt gene expression in EC progenitors, inhibiting differentiation or survival of CAP2 ECs and cell-cell interactions necessary for both pulmonary vasculogenesis and AT1 cell differentiation. Loss of the pulmonary microvasculature was associated with increased VEGFA signalling and marked expansion of systemic bronchial ECs expressing COL15A1.

Conclusions: Distinct FOXF1 gene regulatory networks were identified in subsets of pulmonary endothelial and fibroblast progenitors, providing both cellular and molecular targets for development of therapies for ACDMPV and other diffuse lung diseases of infancy.


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