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

Clinical Proteomics

Eleftherios P Diamandis²  Apostolos Dimitromanolakis¹  Shawn Dason²  Eduardo Martínez-Morillo¹  George S Karagiannis¹  Andrei P Drabovich¹  Chan-Kyung J Cho² 

[1] Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada;Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada

关键词: Quantitative proteomics;    Amniotic fluid cells;    Amniocyte;    Trisomy 21;    Down syndrome;   

Others  :  1026348
DOI  :  10.1186/1559-0275-10-2

 received in 2012-11-15, accepted in 2013-01-18,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Cho et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Amano K, Sago H, Uchikawa C, Suzuki T, Kotliarova SE, Nukina N, Epstein CJ, Yamakawa K: Dosage-dependent over-expression of genes in the trisomic region of Ts1Cje mouse model for down syndrome. Hum Mol Genet 2004, 13:1333-1340.
• [2]Kahlem P, Sultan M, Herwig R, Steinfath M, Balzereit D, Eppens B, Saran NG, Pletcher MT, South ST, Stetten G, Lehrach H, Reeves RH, Yaspo ML: Transcript level alterations reflect gene dosage effects across multiple tissues in a mouse model of down syndrome. Genome Res 2004, 14:1258-1267.
• [3]Lyle R, Gehrig C, Neergaard-Henrichsen C, Deutsch S, Antonarakis SE: Gene expression from the aneuploid chromosome in a trisomy mouse model of down syndrome. Genome Res 2004, 14:1268-1274.
• [4]Mao R, Wang X, Spitznagel EL Jr, Frelin LP, Ting JC, Ding H, Kim JW, Ruczinski I, Downey TJ, Pevsner J: Primary and secondary transcriptional effects in the developing human down syndrome brain and heart. Genome Biol 2005, 6:R107. BioMed Central Full Text
• [5]Saran NG, Pletcher MT, Natale JE, Cheng Y, Reeves RH: Global disruption of the cerebellar transcriptome in a down syndrome mouse model. Hum Mol Genet 2003, 12:2013-2019.
• [6]Cho CK, Smith CR, Diamandis EP: Amniotic fluid proteome analysis from down syndrome pregnancies for biomarker discovery. J Proteome Res 2010, 9:3574-3582.
• [7]Buhimschi IA, Christner R, Buhimschi CS: Proteomic biomarker analysis of amniotic fluid for identification of intra-amniotic inflammation. BJOG 2005, 112:173-181.
• [8]Cho CK, Shan SJ, Winsor EJ, Diamandis EP: Proteomics analysis of human amniotic fluid. Mol Cell Proteomics 2007, 6:1406-1415.
• [9]Underwood MA, Gilbert WM, Sherman MP: Amniotic fluid: not just fetal urine anymore. J Perinatol 2005, 25:341-348.
• [10]Kim J, Lee Y, Kim H, Hwang KJ, Kwon HC, Kim SK, Cho DJ, Kang SG, You J: Human amniotic fluid-derived stem cells have characteristics of multipotent stem cells. Cell Prolif 2007, 40:75-90.
• [11]Milunsky A: Amniotic fluid cell culture. In Genetic disorder and the fetus. Edited by Milunsky A. New York: Plenum Press; 1979:75-84.
• [12]De Coppi P, Bartsch G Jr, Siddiqui MM, Xu T, Santos CC, Perin L, Mostoslavsky G, Serre AC, Snyder EY, Yoo JJ, Furth ME, Soker S, Bartsch A: Isolation of amniotic stem cell lines with potential for therapy. Nat Biotechnol 2007, 25:100-106.
• [13]Drabovich AP, Jarvi K, Diamandis EP: Verification of male infertility biomarkers in seminal plasma by multiplex selected reaction monitoring assay. Mol Cell Proteomics 2012, 10:M110 004127.
• [14]Mann M: Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 2006, 7:952-958.
• [15]Cho CK, Drabovich AP, Batruch I, Diamandis EP: Verification of a biomarker discovery approach for detection of down syndrome in amniotic fluid via multiplex selected reaction monitoring (SRM) assay. J Proteomics 2011, 74:2052-2059.
• [16]Lee EJ, Seo SR, Um JW, Park J, Oh Y, Chung KC: NF-kappaB-inducing kinase phosphorylates and blocks the degradation of down syndrome candidate region 1. J Biol Chem 2008, 283:3392-3400.
• [17]Arron JR, Winslow MM, Polleri A, Chang CP, Wu H, Gao X, Neilson JR, Chen L, Heit JJ, Kim SK, Yamasaki N, Miyakawa T, Francke U, Graef IA, Crabtree GR: NFAT dysregulation by increased dosage of DSCR1 and DYRK1A on chromosome 21. Nature 2006, 441:595-600.
• [18]Yankner BA, Lu T: Amyloid beta-protein toxicity and the pathogenesis of Alzheimer disease. J Biol Chem 2009, 284:4755-4759.
• [19]Iwatsubo T, Mann DM, Odaka A, Suzuki N, Ihara Y: Amyloid beta protein (a beta) deposition: a beta 42(43) precedes a beta 40 in down syndrome. Ann Neurol 1995, 37:294-299.
• [20]Kwak YD, Brannen CL, Qu T, Kim HM, Dong X, Soba P, Majumdar A, Kaplan A, Beyreuther K, Sugaya K: Amyloid precursor protein regulates differentiation of human neural stem cells. Stem Cells Dev 2006, 15:381-389.
• [21]Kong J, Xu Z: Massive mitochondrial degeneration in motor neurons triggers the onset of amyotrophic lateral sclerosis in mice expressing a mutant SOD1. J Neurosci 1998, 18:3241-3250.
• [22]Harris-Cerruti C, Kamsler A, Kaplan B, Lamb B, Segal M, Groner Y: Functional and morphological alterations in compound transgenic mice overexpressing Cu/Zn superoxide dismutase and amyloid precursor protein [correction]. Eur J Neurosci 2004, 19:1174-1190.
• [23]Kurnit DM: Down syndrome: gene dosage at the transcriptional level in skin fibroblasts. Proc Natl Acad Sci USA 1979, 76:2372-2375.
• [24]Chung IH, Lee SH, Lee KW, Park SH, Cha KY, Kim NS, Yoo HS, Kim YS, Lee S: Gene expression analysis of cultured amniotic fluid cell with down syndrome by DNA microarray. J Korean Med Sci 2005, 20:82-87.
• [25]Lockstone HE, Harris LW, Swatton JE, Wayland MT, Holland AJ, Bahn S: Gene expression profiling in the adult down syndrome brain. Genomics 2007, 90:647-660.
• [26]Olson LE, Roper RJ, Baxter LL, Carlson EJ, Epstein CJ, Reeves RH: Down syndrome mouse models Ts65Dn, Ts1Cje, and Ms1Cje/Ts65Dn exhibit variable severity of cerebellar phenotypes. Dev Dyn 2004, 230:581-589.
• [27]Yaworsky PJ, Kappen C: Heterogeneity of neural progenitor cells revealed by enhancers in the nestin gene. Dev Biol 1999, 205:309-321.
• [28]Drabovich AP, Diamandis EP: Combinatorial peptide libraries facilitate development of multiple reaction monitoring assays for low-abundance proteins. J Proteome Res 2010, 9:1236-1245.