Performing discovery-driven neonatal research by transcriptomic analysis of routinely discarded biofluids

Abstract

Objective: To perform discovery-driven research on the neonatal salivary and cord blood transcriptomes.

Methods: Two separate cohorts of infants were enrolled in this study. In one, cord blood (n = 10) and in the other, saliva samples (n = 10) were collected at term gestation. Total RNA was extracted, amplified and hybridized onto Affymetrix HG U133a gene expression microarrays. Following normalization, genes expressed in the highest quintile (≥ 80%) across all subjects in each biofluid were analyzed with Ingenuity Pathway Analysis. Over-represented pathways relating to organ specific development and physiological functions in the newborn were explored.

Results: There were 303 genes in neonatal saliva and 282 genes in umbilical cord blood that met statistical criteria. Of these, 114 were common to both biofluids. Pathway analyses revealed the important roles of redox balance, cellular proliferation, and smooth muscle relaxation. In blood, hematopoiesis and immune response pathways predominated. In saliva, pathways associated with the gastrointestinal system were highlighted.

Conclusions: Neonatal cord blood and saliva provide a wealth of transcriptomic information. These normally discarded biofluids should be considered an important source of real-time gene expression data that may elucidate key pathways in neonatal physiology and pathology.

Figure 1

Venn diagram depicting gene expression in whole blood and whole saliva. In our analysis, we considered the highest quintile of genes expressed in cord blood (dashed lines) and saliva (dots), as well as those genes that were shared (n = 114) and unique to cord blood (n = 168) and saliva (n = 189).