Conservation of gene expression patterns between the amniotic epithelium at birth and a newborn's nasal epithelium

Background: Amniotic epithelial cells are foetal-derived stem cells, capable of differentiating into all three germ layers, including mature epithelial cell populations. However, the conservation between amniotic epithelium and other epithelial tissues has not been sufficiently explored. We hypothesised that the amniotic epithelium might serve as a surrogate tissue source for investigating transcriptional profiles in the respiratory epithelium of the newborn. We compared gene expression profiles and weighted gene co-expression network structure in paired amniotic and newborn nasal epithelial samples from 85 participants in the Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) birth cohort. Results: In total, 11,867 genes (79.7%) were commonly expressed in both amniotic and nasal epithelium, with uniquely expressed genes (2,563 and 458, respectively) enriched for biological functions related to each tissue's specialist functions (e.g. developmental programs and ciliated cells, respectively). We observed a strong overlap in weighted gene co-expression network structure between both tissues, with ten co-expression modules identified in consensus network analysis. Genes commonly expressed in both tissues and/or found in the consensus network modules were enriched for biologically relevant gene signatures and pathway terms related to airway function. We also observed significant overlap in gene expression and network structure between the amniotic epithelium and published datasets of epithelial samples from the lower airway and other epithelial tissues including skin and oesophagus, suggesting a global epithelial signature. Conclusions: Overall, we observed significant overlap in gene expression and network structure between paired amniotic and nasal epithelial samples, supporting the potential of the amnion as a non-invasive and abundant tissue surrogate. Observed differences between tissues were related to each tissue's specialist functions, which remains an important consideration when assessing their overlap. Future studies aimed at investigating amnion-based biomarkers for respiratory exposures in utero and disease outcomes in childhood are needed to extend these results towards clinical translation.