Jose Gomez-Arroyo, Arjan C. Houweling, Alex V. Postma, Tushar Ganjawala, Dennis Dooijes, Harm Jan Bogaard, Jurjan Aman, Rob Zwart, Joseph A. Kizmiller, Gabriëla G. Edel, Aleksey Porollo, Lilian J. Meijboom, Nidhy P. Varghese, Philip Hale, Jason Hong, Na Zhu, Carrie L. Welch, Yufeng Shen, Francis X. McCormack, Micheala A. Aldred, Matthew T. Weirauch, Robbert J. Rottier, Pawel Stankiewicz, Stefan Graf, Christopher Rhodes, Wendy K. Chung, Jeffrey A. Whitsett, William J. Zacharias, Lisa J. Martin, Vladimir V. Kalinichenko, William C. Nichols
University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center. University of California San Francisco and Zuckerberg San Francisco General Hospital. Amsterdam University Medical Centers and University of Amsterdam. University Medical Center Utrecht. VU University Medical Center. Erasmus MC-Sophia and Erasmus University Medical Center. Baylor College of Medicine and Texas Children’s Hospital. University of California, Los Angeles. Columbia University Medical Center. oston Children’s Hospital and Harvard Medical School. Indiana University School of Medicine. Cambridge Biomedical Campus and University of Cambridge. Phoenix Children’s Hospital and University of Arizona College of Medicine.
United States, Netherlands and United Kingdom
American Journal of Respiratory and Critical Care Medicine
Am J Respir Crit Care Med 2026;
DOI: 10.1093/ajrccm/aamag550
Abstract
Rationale: Most patients with nonheritable forms of pulmonary arterial hypertension (PAH) lack identifiable pathogenic variants. Increasing evidence suggests that, in addition to high-impact predicted loss-of-function variants, rare missense coding variants may also contribute to disease pathogenesis.
Objectives: We identified ultra-rare missense variants in FOXF1 in two index cases with PAH. FOXF1 encodes a highly conserved transcription factor essential for lung vascular development. We sought to define the frequency of FOXF1 variants, characterize FOXF1 expression, and assess the functional relevance of FOXF1 alterations in PAH.
Methods: Three independent international PAH cohorts were analyzed for predicted deleterious FOXF1 variants. FOXF1 expression was evaluated using bulk and single-cell RNA sequencing and immunofluorescence. Bioinformatic and chromatin-profiling approaches were used to identify potential downstream transcriptional targets, followed by promoter-reporter assays in vitro.
Measurements and main results: Nine novel and one rare missense variants, one start-site variant, and one in-frame deletion in FOXF1 were identified across the three cohorts. FOXF1 expression was reduced in PAH lungs and localized predominantly to the endothelial cell compartment. Histopathological analysis revealed heterogeneous FOXF1 expression, with the lowest levels in phenotypically abnormal endothelial cells within complex vascular lesions. Single-cell analyses confirmed reduced endothelial FOXF1 expression in PAH, whereas broad FOXF1 downregulation across endothelial populations was not observed in other chronic lung diseases. Integration of CUT&Tag and ATAC-seq identified a canonical FOXF1-binding motif within the BMPR2 promoter. Promoter-reporter assays further supported FOXF1-dependent transcriptional regulation of BMPR2 and demonstrated reduced transcriptional activity of PAH-associated FOXF1 variants.
Conclusions: Large-scale genomic and transcriptomic analyses support an association between FOXF1 dysregulation and PAH and identify BMPR2 as a potential downstream transcriptional target.
Category
Class III. Pulmonary Hypertension Associated with Developmental Diseases of the Lung
Genetic Factors Associated with Pulmonary Vascular Disease
Age Focus: Pediatric Pulmonary Vascular Disease or Adult Pulmonary Vascular Disease
Fresh or Filed Publication: Fresh (PHresh). Less than 1-2 years since publication
Article Access
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