A comprehensive profile and inter-individual variations analysis of the human normal amniotic fluid proteome

Abstract Amniotic fluid contains large amounts of proteins produced by amnion epithelial cells, fetal tissues, fetal excretions and placental tissues; thus, it is an important potential source of biomarkers for identifying fetal pathologies. In this study, a pooled AF sample from 7 healthy volunteers was used to provide a comprehensive profile of normal human AF proteome using immunoaffinity depletion of 14 high-abundance proteins. Each individual AF sample was used to analyze inter-individual variations with iTRAQ method. As a result, a total of 2881 non-redundant proteins were identified, and 1624 proteins were quantified based on the peak intensity-based semi-quantification (iBAQ) method. Gene Ontology (GO) analysis showed that the AF proteome was enriched in extracellular region and extracellular matrix. Further function annotation showed that the top canonical pathway was axonal guidance signaling. The inter-individual variation analysis of 7 individual AF samples showed that the median inter-individual CV (Coefficient of variation) was 0.22. iBAQ quantification analysis revealed that the inter-individual variations were not correlated with protein abundance. GO analysis indicated that intracellular proteins tended to have higher CVs, and extracellular proteins tended to have lower CVs. These data will contribute to a better understanding of amniotic fluid proteomic analysis and biomarker discovery. Significance Amniotic fluid is an important potential source of biomarkers for identifying fetal pathologies. This study provided a large database for the normal human amniotic fluid proteome and analysis of inter-individual variations in amniotic fluid proteomes, which will offer a baseline reference for further AF proteomic analysis and pregnancy-related disease biomarker discovery.