Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome

Abstract

BackgroundDown 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.ResultsChromosomally 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.ConclusionsThe 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.

Preliminary study of protein changes in trisomy 21 fetus by proteomics analysis in amniocyte

“…Among them, most have focused on T21 because it is the most common aneuploidy worldwide . Cho's research revealed that over 900 proteins were dysregulated in amniocytes with T21, and their most significant finding was the upregulation of Cu, Zn superoxide dismutase and the down regulation of nestin downregulated in amniocytes with T21 . In this study, 2DE and MALDI‐TOF MS were used to identify candidate biomarker proteins in T21 amniocytes, and 6 proteins were found to be upregulated and no significant changes of expressions of Cu, Zn superoxide dismutase or nestin in our study.…”

“…10 Cho's research revealed that over 900 proteins were dysregulated in amniocytes with T21, and their most significant finding was the upregulation of Cu, Zn superoxide dismutase and the down regulation of nestin downregulated in amniocytes with T21. 11 In this study, 2DE and MALDI-TOF MS were used to identify candidate biomarker proteins in T21 amniocytes, and 6 proteins were found to be upregu- Calumenin, which is encoded by a gene located in chrome 7 called CALU, is a 48-kDa Ca 2+ -dependent protein. It is a member of Ca2 +binding family, which has Cab45, 12 reticulocalbin, 13 ERC-55, 14 and crocalbin.…”

Multi-omics biomarker pipeline reveals elevated levels of protein-glutamine gamma-glutamyltransferase 4 in seminal plasma of prostate cancer patients

“…Reviewer account details (http://www.ebi.ac.uk/pride/archive/login): Username: ****** Password: ****** Development of SRM assays for the verification phase. SRM assays were developed as previously described 23,44,48,74,76 . Briefly, the Peptide Atlas (www.peptideatlas.org) was used to select top 5-7 peptides (charge +2 and +3) for each of 148 candidate proteins and 11 control proteins (representing other six glands or cell types in the male urogenital system).…”

Mapping Isoform Abundance and Interactome of the Endogenous TMPRSS2-ERG Fusion Protein with Orthogonal Immunoprecipitation-Mass Spectrometry Assays

“…4,5 The most promising biomarkers are also explored for the molecular mechanisms of their differential expression or regulation. [6][7][8] Recent genomic studies on the primary prostate adenocarcinoma revealed major subtypes defined by the gene fusions of E26 transformation-specific (ETS) transcription factors, and mutations in SPOP, FOXA1, and IDH1 genes. 9,10 The most common genomic subtype of primary prostate cancer was represented by the fusion of the androgen-responsive gene TMPRSS2 with the transcription factor ERG (~50% of all cases).…”