Objective: Trisomy 21 (T21), resulting in Down Syndrome, is the most common chromosomal abnormality worldwide. This multisystem disorder is associated with several developmental defects, including numerous lung anomalies. We have observed that prenatal T21 lungs have abnormal dilatation of the distal airways and acini accompanied by what appears to be a defect in cell adhesion, likely from compromised intercellular junctions. This study aimed to interrogate transcriptional changes across epithelial lineages in the human prenatal T21 lung and assess their potential impact on epithelial structure and development. Hypothesis: We hypothesized that signaling alterations in T21 lungs disrupt epithelial cell adhesion programs in a stage- and lineage-specific manner. Methods: We analyzed single nucleus (sn)RNA-seq data from 23 prenatal lung samples (14 Trisomy 21 and 9 Disomic 21; 13-20 post-conception weeks). After SoupX decontamination, stringent QC, and consensus doublet removal, data were normalized with SCTransform, integrated with RPCA, and clustered in Seurat. Epithelial nuclei were then subsetted, reprocessed, and subclustered (resolution 0.5), and annotated using ToppGene-derived markers. Differential expression was performed using NEBULA, modeling raw counts with karyotype, age, and sex as fixed effects and subject as a random effect. Pathway analyses included over-representation tests (GO/KEGG/Reactome) and GSEA on full ranked gene lists. Results: T21 exhibited developmentally dynamic and lineage-specific disruptions in epithelial adhesion pathways. In the early developmental window (< 15 weeks), T21 epithelium showed disruption of the cell-cell junction organization pathway, consistent with reduced expression of the tight-junction component, OCLN. These disruptions were confirmed by electron microscopy. By mid-gestation (16-20 weeks), T21 displayed a coordinated upregulation of junctional and integrin-ECM adhesion programs. Across epithelial subpopulations, we observed increased expression of adhesion-related genes, including: TJP1, VMP1, CDH2, CDH19, TIAM1, VCL, TLN2, ITGA6, ITGAV, ITGB1, FN1, COL3A1, and NPNT, with individual genes enriched in distinct clusters such as AT1, AT2, airway progenitor, and neuroendocrine. These gene sets enriched for “cell junction assembly”, “cell junction organization”, and “cell-matrix adhesion”, indicating continued disruption and a possible compensatory effect of cell-cell and cell-matrix adhesion programs in mid-gestation T21 lungs. The pulmonary neuroendocrine cluster displayed a distinct increase in neuronal Ig-domain adhesion molecules (CADM1, IGSF11, TENM3, NLGN4X, LRRC4C), suggesting aberrant stabilization of neuroepithelial bodies in T21. Conclusions: Our findings suggest that adhesion dysregulation is an important feature of prenatal T21 lung epithelium. A pattern of early tight-junction loss followed by later enhancement of junctional, integrin, and ECM pathways supports a model in which altered adhesion programs contribute to disrupted epithelial maturation, altered epithelial-matrix interactions, and aberrant neuroepithelial body stabilization in T21 lung development. Funding: NIH/NHLBI Office of The Director, National Institutes of Health (OD) R01HL155104; NIH/NHLBI R01HL141856; and NIH/NICHD R24HD000836. This abstract was presented at the American Physiology Summit 2026 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.
Shinde et al. (Fri,) studied this question.