Comparative proteomic analysis of human amniotic fluid supernatants with Down syndrome using mass spectrometry

Down syndrome (DS) is an abnormality of the 21st chromosome that commonly occurs in children born to advanced age women. Amniotic fluid (AF) is usually collected from such women for prenatal diagnosis. This study analyzed human AF supernatants (AFS) by mass spectrometric (MS) approach to search for candidate biomarkers of DS pregnancy. AFS were collected from advanced age pregnant women at 16-18th weeks of gestation by amniocentesis for cytogenetic analysis. AFS from pregnancies carrying DS (n=4) or chromosomally normal (n=6) fetuses, as revealed by cytogenetic analysis, were then subjected to global protein profiling by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Affinity chromatography was applied prior to LC-ESI-MS/MS to minimize the masking effect of highly abundant albumin and immunoglobulin and thereby, increased the diversity of identified proteins. Hereby, at least 30 AFS proteins were newly identified and 44 AFS proteins were found to be differentially expressed between DS and normal cases. Six of these proteins were unique to DS cases while 11 proteins were unique to chromosomally normal cases. In addition, 19 AFS proteins were down-regulated and 8 were up-regulated in DS cases with varying fold changes. A western blot analysis confirmed the LC-ESI-MS/MS data that combined detection of Apolipoprotein A-II (apo A-II) and alpha-fetoprotein (AFP) could be a potential tool for diagnosing DS cases.