Gene expression profiling predicts pathways and genes associated with Parkinson’s disease

Neurological Sciences

Volumn 37, Issue 1, 2016, Pages 73-79

  Liu, Shuang ^a   Zhang, Yong ^a   Bian, Hong ^a   Li, Xiaohong ^a  

^a JINAN CENTRAL HOSPITAL AFFILIATED TO SHANDONG UNIVERSITY   (China)

Author keywords

Differentially expressed genes; Hub protein; Parkinson s disease; Pathway enrichment analysis; Protein protein interaction network

Indexed keywords

DROSOPHILA HOMOLOG ASSOCIATED PROTEIN 3; ELAV LIKE PROTEIN 2; EVEN SKIPPED HOMEOBOX 1; GLUTAMATE RECEPTOR; IONOTROPIC RECEPTOR; N METHYL DEXTRO ASPARTIC ACID; N METHYL DEXTRO ASPARTIC ACID 1; N METHYL DEXTRO ASPARTIC ACID 2 D; SYNAPSIN I; SYNAPSIN II; UNCLASSIFIED DRUG;

ARTICLE; CALCIUM SIGNALING; CONTROLLED STUDY; DISEASE COURSE; DOWN REGULATION; ERYTHROCYTE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENETIC ASSOCIATION; HUMAN; MOLECULAR PATHOLOGY; NONHUMAN; PARKINSON DISEASE; PREDICTIVE VALUE; PROTEIN PROTEIN INTERACTION; UPREGULATION; CLUSTER ANALYSIS; GENETICS; METABOLISM; MICROARRAY ANALYSIS; PHYSIOLOGY; PRINCIPAL COMPONENT ANALYSIS; PROCEDURES; SIGNAL TRANSDUCTION;

CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; HUMANS; MICROARRAY ANALYSIS; PARKINSON DISEASE; PRINCIPAL COMPONENT ANALYSIS; SIGNAL TRANSDUCTION;

EID: 84955758470     PISSN: 15901874     EISSN: 15903478     Source Type: Journal    
DOI: 10.1007/s10072-015-2360-5     Document Type: Article

References (43)

1. Mutez E, Larvor L, Leprêtre F, Mouroux V, Hamalek D, Kerckaert J-P, Pérez-Tur J, Waucquier N, Vanbesien-Mailliot C, Duflot A (2011) Transcriptional profile of Parkinson blood mononuclear cells with LRRK2 mutation. Neurobiol Aging 32(10):1839–1848
2. Valente EM, Abou-Sleiman PM, Caputo V, Muqit MM, Harvey K, Gispert S, Ali Z, Del Turco D, Bentivoglio AR, Healy DG (2004) Hereditary early-onset Parkinson’s disease caused by mutations in PINK1. Science 304(5674):1158–1160
3. Starkstein SE, Mayberg HS, Leiguarda R, Preziosi TJ, Robinson RG (1992) A prospective longitudinal study of depression, cognitive decline, and physical impairments in patients with Parkinson’s disease. J Neurol Neurosurg Psychiatry 55(5):377–382
4. Dorsey E, Constantinescu R, Thompson J, Biglan K, Holloway R, Kieburtz K, Marshall F, Ravina B, Schifitto G, Siderowf A (2007) Projected number of people with Parkinson disease in the most populous nations, 2005 through 2030. Neurology 68(5):384–386
5. Greenamyre JT, Hastings TG (2004) Parkinson’s: divergent causes, convergent mechanisms. Science 304(5674):1120–1122
6. Azzouz M, Martin-Rendon E, Barber RD, Mitrophanous KA, Carter EE, Rohll JB, Kingsman SM, Kingsman AJ, Mazarakis ND (2002) Multicistronic lentiviral vector-mediated striatal gene transfer of aromatic L-amino acid decarboxylase, tyrosine hydroxylase, and GTP cyclohydrolase I induces sustained transgene expression, dopamine production, and functional improvement in a rat model of Parkinson’s disease. J Neurosci 22(23):10302–10312
7. Dauer W, Przedborski S (2003) Parkinson’s disease: mechanisms and models. Neuron 39(6):889–909
8. Dawson TM, Dawson VL (2003) Molecular pathways of neurodegeneration in Parkinson’s disease. Science 302(5646):819–822
9. Zahurak M, Parmigiani G, Yu W, Scharpf RB, Berman D, Schaeffer E, Shabbeer S, Cope L (2007) Pre-processing Agilent microarray data. BMC Bioinformatics 8(1):142
10. Cai JJ, Smith DK, Xia X, K-y Yuen (2005) MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics 6(1):64
11. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57(1):289–300
12. Kaufman L, Rousseeuw PJ (2009) Finding groups in data: an introduction to cluster analysis[M]. Wiley, New Jersey
13. Abdi H, Williams LJ (2010) Principal component analysis. Wiley Interdiscip Rev Comput Stat 2(4):433–459
14. Kamburov A, Wierling C, Lehrach H, Herwig R (2009) ConsensusPathDB—a database for integrating human functional interaction networks. Nucleic Acids Res 37(suppl 1):D623–D628
15. Von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 31(1):258–261
16. Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27(3):431–432
17. Nepusz T, Yu H, Paccanaro A (2012) Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods 9(5):471–472
18. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2(10):2366–2382
19. Schrag A (2007) Epidemiology nf movement disorders. Parkinsons Dis Mov Disord 50
20. Braak H, Tredici KD, Rüb U, de Vos RA, Jansen Steur EN, Braak E (2003) Staging of brain pathology related to sporadic Parkinson’s disease. Neurobiol Aging 24(2):197–211
21. Huttner W, Schiebler W, Greengard P, De Camilli P (1983) Synapsin I (protein I), a nerve terminal-specific phosphoprotein. III. Its association with synaptic vesicles studied in a highly purified synaptic vesicle preparation. J Cell Biol 96(5):1374–1388
22. Cesca F, Baldelli P, Valtorta F, Benfenati F (2010) The synapsins: key actors of synapse function and plasticity. Prog Neurobiol 91(4):313–348
23. Qin S, Hu X-Y, Xu H, Zhou J-N (2004) Regional alteration of synapsin I in the hippocampal formation of Alzheimer’s disease patients. Acta Neuropathol 107(3):209–215
24. Lachman HM, Stopkova P, Rafael MA, Saito T (2005) Association of schizophrenia in African Americans to polymorphism in synapsin III gene. Psychiatr Genet 15(2):127–132
25. Lachman HM, Stopkova P, Papolos DF, Pedrosa E, Margolis B, Aghalar MR, Saito T (2006) Analysis of synapsin III–196 promoter mutation in schizophrenia and bipolar disorder. Neuropsychobiology 53(2):57–62
26. Mundo E, Tharmalingham S, Neves-Pereira M, Dalton E, Macciardi F, Parikh S, Bolonna A, Kerwin R, Arranz M, Makoff A (2003) Evidence that the N-methyl-d-aspartate subunit 1 receptor gene (GRIN1) confers susceptibility to bipolar disorder. Mol Psychiatry 8(2):241–245
27. Makino C, Shibata H, Ninomiya H, Tashiro N, Fukumaki Y (2005) Identification of single-nucleotide polymorphisms in the human N-methyl-d-aspartate receptor subunit NR2D gene, GRIN2D, and association study with schizophrenia. Psychiatr Genet 15(3):215–221
28. Wu S-L, Wang W-F, Shyu H-Y, Ho Y-J, Shieh J-C, Fu Y-P, Wu S-T, Cheng C-W (2010) Association analysis of GRIN1 and GRIN2B polymorphisms and Parkinson’s disease in a hospital-based case–control study. Neurosci Lett 478(2):61–65
29. Kalsi G, Whiting P, Bourdelles BL, Callen D, Barnard EA, Gurling H (1998) Localization of the human NMDAR2D receptor subunit gene (GRIN2D) to 19q13. 1–qter, the NMDAR2A subunit gene to 16p13. 2 (GRIN2A), and the NMDAR2C subunit gene (GRIN2C) to 17q24–q25 using somatic cell hybrid and radiation hybrid mapping panels. Genomics 47(3):423–425
30. Markowitz AJ, White MG, Kolson DL, Jordan-Sciutto KL (2007) Cellular interplay between neurons and glia: toward a comprehensive mechanism for excitotoxic neuronal loss in neurodegeneration. Cellscience 4(1):111
31. Cuomo D, Martella G, Barabino E, Platania P, Vita D, Madeo G, Selvam C, Goudet C, Oueslati N, Pin JP (2009) Metabotropic glutamate receptor subtype 4 selectively modulates both glutamate and GABA transmission in the striatum: implications for Parkinson’s disease treatment. J Neurochem 109(4):1096–1105
32. Meldrum B (1993) Amino acids as dietary excitotoxins: a contribution to understanding neurodegenerative disorders. Brain Res Rev 18(3):293–314
33. Toescu EC, Verkhratsky A (2007) The importance of being subtle: small changes in calcium homeostasis control cognitive decline in normal aging. Aging Cell 6(3):267–273
34. Nicotera P, Leist M, Manzo L (1999) Neuronal cell death: a demise with different shapes. Trends Pharmacol Sci 20(2):46–51
35. Becker C, Jick SS, Meier CR (2008) Use of antihypertensives and the risk of Parkinson disease. Neurology 70((16 Part 2)):1438–1444
36. Chen M, Wan Y, Ade K, Ting J, Feng G, Calakos N (2011) Sapap3 deletion anomalously activates short-term endocannabinoid-mediated synaptic plasticity. J Neurosci 31(26):9563–9573
37. Wan Y, Feng G, Calakos N (2011) Sapap3 deletion causes mGluR5-dependent silencing of AMPAR synapses. J Neurosci 31(46):16685–16691
38. Penzes P, Cahill ME, Jones KA, VanLeeuwen J-E, Woolfrey KM (2011) Dendritic spine pathology in neuropsychiatric disorders. Nat Neurosci 14(3):285–293
39. van Spronsen M, Hoogenraad CC (2010) Synapse pathology in psychiatric and neurologic disease. Curr Neurol Neurosci Rep 10(3):207–214
40. Li J-M, Lu C-L, Cheng M-C, Luu S-U, Hsu S-H, Chen C-H (2013) Exonic resequencing of the DLGAP3 gene as a candidate gene for schizophrenia. Psychiatry Res 208(1):84–87
41. Boardman L, van der Merwe L, Lochner C, Kinnear CJ, Seedat S, Stein DJ, Moolman-Smook JC, Hemmings SM (2011) Investigating SAPAP3 variants in the etiology of obsessive-compulsive disorder and trichotillomania in the South African white population. Compr Psychiatry 52(2):181–187
42. Mallet L, Mesnage V, Houeto J-L, Pelissolo A, Yelnik J, Behar C, Gargiulo M, Welter M-L, Bonnet A-M, Pillon B (2002) Compulsions, Parkinson’s disease, and stimulation. Lancet 360(9342):1302–1304
43. Alegret M, Junque C, Valldeoriola F, Vendrell P, Marti M, Tolosa E (2001) Obsessive-compulsive symptoms in Parkinson’s disease. J Neurol Neurosurg Psychiatry 70(3):394–396