Amniotic fluid proteome analysis from Down syndrome pregnancies for biomarker discovery

Down syndrome (DS) is an anomaly caused by an extra chromosome 21, and it affects 1 in 750 live births. Phenotypes include cognitive impairment, congenital defects, and increased risk for several diseases such as Alzheimer's disease and leukemia. Current DS-screening tests subject many women to invasive procedures for accurate diagnosis due to insufficient specificity. Since amniotic fluid (AF) surrounds the developing fetus, understanding the changes in AF composition in the presence of DS may provide insights into genotype-phenotype associations, and aid in discovery of novel biomarkers for better screening. On the basis of our previous study, in which we reported an extensive proteome of AF, we performed two-dimensional liquid chromatography followed by MS/MS to analyze triplicates of pooled AF of chromosomally normal and DS-affected pregnancies (10 samples per pool). A total of 542 proteins were identified from the two sets of triplicate analyses by the LTQ-Orbitrap mass spectrometer and data were compared semiquantitatively by spectral counting. Candidate biomarkers were selected based on the spectral count differences between the two conditions after normalization. Comparison between the two groups revealed 60 candidates that showed greater than 2-fold increase or decrease in concentration in the presence of DS. Among these candidates, amyloid precursor protein and tenascin-C were verified by ELISA, and both showed a 2-fold increase, on average, in DS-AF samples compared to controls. All proteins that showed significant differences between the two conditions were bioinformatically analyzed to preliminarily understand their biological implications in DS.