Single Cell Multiomics Identifies Cells and Genetic Networks Underlying Alveolar Capillary Dysplasia

Authors

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
Jeffrey A Whitsett

Publication Date

9-15-2023

Journal

American Journal of Respiratory and Critical Care Medicine

DOI

10.1164/rccm.202210-2015OC

PMID

37463497

PMCID

PMC10515568

PubMedCentral® Posted Date

6-18-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

RNA, Vascular Endothelial Growth Factor A, Infant, Newborn, Lung, Humans, Persistent Fetal Circulation Syndrome, Endothelial Cells, Pulmonary Alveoli, Forkhead Transcription Factors, Gene Regulatory Networks, Multiomics, alveolar capillary dysplasia, FOXF1, pulmonary microvasculature

Abstract

Rationale

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal developmental disorder of lung morphogenesis caused by insufficiency of FOXF1 (forkhead box F1) 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 assay for transposase-accessible chromatin 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 copy-number variant 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 a paucity of pulmonary microvasculature. Single-nucleus RNA and assay for transposase-accessible chromatin 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 the differentiation or survival of capillary 2 ECs and cell–cell interactions necessary for both pulmonary vasculogenesis and alveolar type 1 cell differentiation. Loss of the pulmonary microvasculature was associated with increased VEGFA (vascular endothelial growth factor A) signaling and marked expansion of systemic bronchial ECs expressing COL15A1 (collagen type XV α 1 chain).

Conclusions

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