PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function

Why some and not others? Understanding vascular phenotypes in genetic developmental lung diseases

PURPOSE OF REVIEW

Pulmonary vascular disease is more common in certain genetic developmental lung disorders. This review synthesizes clinical descriptions, molecular analyses, and single-cell transcriptional data to build a conceptual framework to help understand why some variants affect the vasculature while others primarily manifest with parenchymal disease.

RECENT FINDINGS

Genes predominantly expressed in endothelial and mesenchymal compartments ( TBX4 , FGF10 , FOXF1 , KDR ) commonly present with both parenchymal and pulmonary vascular disease, while epithelial-restricted genes ( SFTPC , ABCA3 , NKX2.1 ) typically manifest as parenchymal disease. Single-cell analyses reveal that compartment-specific expression patterns correlate with clinical phenotypes. Phenotypic variability, even among individuals sharing identical variants, suggests complex interactions between genetic modifiers, epigenetic factors, and developmental processes that remain poorly understood.

SUMMARY

Compartment-specific gene expression patterns fundamentally underlie the differential presence of vascular phenotypes in DEVLDs. Genetic advances and single cell technologies have revolutionized our understanding of these disorders, but we are in the early stages of translating this knowledge into meaningful clinical advances. Future efforts must bridge this gap to transform clinical care from supportive to targeted, disease-modifying treatment based on cell-specific molecular mechanisms.

The Homeobox Transcription Factor CUX1 Coordinates Postnatal Epithelial Developmental Timing but Is Dispensable for Lung Organogenesis and Regeneration

Lung epithelial progenitors use a complex network of known and predicted transcriptional regulators to influence early lung development. In this study, we evaluated the function of one predicted regulator, CUX1, that we identified from transcriptional regulatory analysis of the SOX9+ distal lung progenitor network. We generated a new Cux1-floxed mouse model and created an epithelium-specific knockout of CUX1 using Shh-Cre (Cux1ShhCre-LOF). Postnatal Cux1ShhCre-LOF animals recapitulated key skin phenotypic features found in prior constitutive CUX1 knockout animals, confirming the functionality of our new floxed model. Postnatal Cux1ShhCre-LOF mice displayed subtle alveolar simplification and a transient delay in alveologenesis and alveolar type 1 cell development without persistent lung phenotypes. Cux1ShhCre-LOF mice developed failure to thrive in their second and third weeks of life because of delayed ileal maturation, which similarly resolves by Postnatal Day 35. Finally, we challenged Cux1ShhCre-LOF with influenza-mediated lung injury to demonstrate that Cux1ShhCre-LOF mice undergo productive alveolar regeneration that is indistinguishable from that in wild-type animals. Together, these findings indicate that epithelium-specific loss of CUX1 leads to transient developmental delays in the skin, lung, and intestine without defects in definitive organogenesis. We conclude that CUX1 function is required for temporal optimization of developmental maturation in multiple organs with implications for susceptibility windows in developmental disease pathogenesis.

Heparan sulfate regulates myofibroblast heterogeneity and function to mediate niche homeostasis during alveolar morphogenesis

Postnatal respiration requires bulk formation of alveoli that produces extensive surface area for gas diffusion from epithelium to the circulatory system. Alveolar morphogenesis initiates at late gestation or postnatal stage during mammalian development and is mediated by coordination among multiple cell types. Here we show that fibroblast-derived Heparan Sulfate Glycosaminoglycan (HS-GAG) is essential for maintaining a niche that supports alveolar formation by modulating both biophysical and biochemical cues. Gli1-CreER mediated deletion of HS synthase gene Ext1 in lung fibroblasts results in enlarged and simplified alveolar structures. Ablation of HS results in loss of a subset of PDGFRαhi αSMA+ alveolar myofibroblasts residing in the distal alveolar region, which exhibit contractile properties and maintain WNT signaling activity to support normal proliferation and differentiation of alveolar epithelial cells. HS is essential for proliferation while preventing precocious apoptosis of alveolar myofibroblasts. We show that these processes are dependent upon FGF/MAPK signaling and forced activation of MAPK/ERK signaling partially corrected alveolar simplification and restored alveolar myofibroblast number and AT2 cell proliferation in HS deficient mice. These data reveal HS-dependent myofibroblast heterogeneity and function as an essential orchestrator for developing alveolar niche critical for the generation of gas exchange units.

A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis

The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and showed that STAG2 is uniquely tumor-suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. STAG2 inactivation elicits changes in gene expression, chromatin accessibility, and 3D genome conformation that impact the cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relate STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin-mediated mechanisms of lung tumor suppression.