New Study Reveals How Non-Coding FOXF1 Gene Deletions Lead to Fatal Lung Disease in Newborns

Mutations in the FOXF1 gene, which is important for lung blood vessel development, cause Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins, a deadly lung disease in newborns and infants.

A new study published in June online in Nature Communications, looked to show how frequent non-coding FOXF1 gene deletions that interfere with important DNA regulatory regions can lead to a rare, lethal, genetic lung disease which causes respiratory failure in many newborns and infants.

The research was conducted by a collaboration between doctors at the Phoenix Children’s Research Institute at the University of Arizona College of Medicine and the Cincinnati Children’s Hospital Medical Center, and revealed how these enhancers could ultimately lead to Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV).

The study team, led by Vlad Kalinichenko, MD, PhD, director of the Phoenix Children’s Research Institute at the University of Arizona College of Medicine—Phoenix, explained that finding new regulatory elements that control FOXF1 is crucial to understanding why common non-coding deletions of this gene are associated with the disease.

In the study, the researchers utilized advanced RNA and ATAC sequencing techniques on mouse and human patient lungs to identify four key FOXF1 enhancers in endothelial and mesenchymal cells.

“We show that FOXF1 enhancers in endothelial cells activate themselves, while those in mesenchymal cells are controlled by EBF1 and GLI1,” Kalinichenko said. “We confirm the cell-specific function of these enhancers by disrupting them in mouse embryonic stem cells using CRISPR/Cpf1 and tracing the altered cells in mouse embryos.”

By doing so, the research explains why deletions in non-coding regions of FOXF1 that affect these enhancers can cause the disease.

Kalinichenko explained that the FOXF1 protein plays a crucial role in pulmonary vascular development, as it is specifically responsible for the extension and branching of airways and blood vessels in the developing lung.

“Prior to this study, we knew deletions and mutations in the FOXF1 gene locus can result in ACDMPV, so our goal was to identify FOXF1 enhancers associated with the disease so we can diagnose it more precisely in newborn babies,” he said.

In the study, the researchers identified four upstream enhancers in the FOXF1 gene locus — FOXF1 Expression in the Lung 1, 2, 3 and 4, and revealed that the quartet of elements stimulate cell-specific FOXF1 expression in pulmonary endothelium and stromal cells, including fibroblasts and pericytes.

“Pulmonary endothelial cells are essential to the development of alveoli, the tiny branches of air tubes in the lungs responsible for the exchange of oxygen and carbon dioxide in the bloodstream,” Kalinichenko said. “Likewise, pulmonary stromal cells are also important to lung development and are a crucial component of overall lung structure.”

Going forward, the identifications of mutations in the FOXF1 gene locus will be critical for accurate genetic diagnosis of this severe congenital disease.

“As we continue to gain additional insight into how genes work, it will improve our capabilities to implement effective therapeutic interventions in more common pulmonary disorders of newborns and infants, such as bronchopulmonary dysplasia and congenital diaphragmatic hernia,” Kalinichenko said.