BACKGROUND: Down syndrome (DS), caused by an extra copy of chromosome 21, 
affects 1 in 750 live births and is characterized by cognitive impairment and a 
constellation of congenital defects. Currently, little is known about the 
molecular pathogenesis and no direct genotype-phenotype relationship has yet 
been confirmed. Since DS amniocytes are expected to have a distinct biological 
behaviour compared to normal amniocytes, we hypothesize that relative 
quantification of proteins produced from trisomy and euploid (chromosomally 
normal) amniocytes will reveal dysregulated molecular pathways.
RESULTS: Chromosomally normal- and Trisomy 21-amniocytes were quantitatively 
analyzed by using Stable Isotope Labeling of Amino acids in Cell culture and 
tandem mass spectrometry. A total of 4919 unique proteins were identified from 
the supernatant and cell lysate proteome. More specifically, 4548 unique 
proteins were identified from the lysate, and 91% of these proteins were 
quantified based on MS/MS spectra ratios of peptides containing isotope-labeled 
amino acids. A total of 904 proteins showed significant differential expression 
and were involved in 25 molecular pathways, each containing a minimum of 16 
proteins. Sixty of these proteins consistently showed aberrant expression from 
trisomy 21 affected amniocytes, indicating their potential role in DS 
pathogenesis. Nine proteins were analyzed with a multiplex selected reaction 
monitoring assay in an independent set of Trisomy 21-amniocyte samples and two 
of them (SOD1 and NES) showed a consistent differential expression.
CONCLUSIONS: The most extensive proteome of amniocytes and amniotic fluid has 
been generated and differentially expressed proteins from amniocytes with 
Trisomy 21 revealed molecular pathways that seem to be most significantly 
affected by the presence of an extra copy of chromosome 21.