Network Analysis Identifies SOD2 mRNA as a Potential Biomarker for Parkinson's Disease

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Santiago, Jose A ^a   Scherzer, Clemens R ^b   Potashkin, Judith A ^a  

^a ROSALIND FRANKLIN UNIVERSITY OF MEDICINE AND SCIENCE   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID PRECURSOR PROTEIN; BRAIN DERIVED NEUROTROPHIC FACTOR; COPPER ZINC SUPEROXIDE DISMUTASE; FAS ANTIGEN; GAMMA INTERFERON; GUANOSINE TRIPHOSPHATE CYCLOHYDROLASE I; HEME OXYGENASE 1; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; INDUCIBLE NITRIC OXIDE SYNTHASE; INTERLEUKIN 6; MANGANESE SUPEROXIDE DISMUTASE; MESSENGER RNA; PROTEIN GLUTAMINE GAMMA GLUTAMYLTRANSFERASE 2; PROTEIN P53; SOMATOMEDIN C; TUMOR NECROSIS FACTOR; BIOLOGICAL MARKER; SUPEROXIDE DISMUTASE;

ABCC8 GENE; ADULT; AGED; AKT1 GENE; ALGORITHM; APP GENE; AREA UNDER THE CURVE; ARTICLE; BDNF GENE; CONTROLLED STUDY; CYP17A1 GENE; FAS GENE; FEMALE; GCH1 GENE; GENE; GENE IDENTIFICATION; GENE REGULATORY NETWORK; HMOX1 GENE; HNF4A GENE; HUMAN; IFNG GENE; IGF1 GENE; IL6 GENE; MAJOR CLINICAL STUDY; MALE; MT ND1 GENE; NON INSULIN DEPENDENT DIABETES MELLITUS; NOS2 GENE; PARKINSON DISEASE; PDX1 GENE; PTGS2 GENE; QUANTITATIVE ANALYSIS; RANDOM WALK ALGORITHM WITH RESTART; RECEIVER OPERATING CHARACTERISTIC; SLC2A4 GENE; SOD1 GENE; SOD2 GENE; TGM2 GENE; TNF GENE; TP53 GENE; UCHL1 GENE; UPREGULATION; GENETIC DATABASE; GENETICS; MIDDLE AGED;

AGED; ALGORITHMS; BIOMARKERS; DATABASES, GENETIC; DIABETES MELLITUS, TYPE 2; GENE REGULATORY NETWORKS; HUMANS; MALE; MIDDLE AGED; PARKINSON DISEASE; RNA, MESSENGER; SUPEROXIDE DISMUTASE; UP-REGULATION;

EID: 84915744886     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0109042     Document Type: Article

References (61)

1. Scheele C, Nielsen AR, Walden TB, Sewell DA, Fischer CP, et al. (2007) Altered regulation of the PINK1 locus: A link between type 2 diabetes and neurodegeneration? FASEB journal: Official publication of the Federation of American Societies for Experimental Biology 21: 3653-3665.
2. Cereda E, Barichella M, Pedrolli C, Klersy C, Cassani E, et al. (2011) Diabetes and risk of Parkinson's disease: A systematic review and meta-analysis. Diabetes care 34: 2614-2623.
3. Cereda E, Barichella M, Pedrolli C, Klersy C, Cassani E, et al. (2013) Diabetes and risk of Parkinson's disease. Movement disorders: Official journal of the Movement Disorder Society 28: 257.
4. Santiago JA, Potashkin JA (2013) Shared dysregulated pathways lead to Parkinson's disease and diabetes. Trends in molecular medicine 19: 176-186.
5. Santiago JA, Potashkin JA (2014) System-based approaches to decode the molecular links in Parkinson's disease and diabetes. Neurobiology of disease.
6. D'Amelio M, Ragonese P, Callari G, Di Benedetto N, Palmeri B, et al. (2009) Diabetes preceding Parkinson's disease onset. A case-control study. Parkinsonism & related disorders 15: 660-664.
7. Lu L, Fu DL, Li HQ, Liu AJ, Li JH, et al. (2014) Diabetes and risk of Parkinson's disease: An updated meta-analysis of case-control studies. PloS one 9: E85781.
8. Palacios N, Gao X, McCullough ML, Jacobs EJ, Patel AV, et al. (2011) Obesity, diabetes, and risk of Parkinson's disease. Movement disorders: Official journal of the Movement Disorder Society 26: 2253-2259.
9. Noyce AJ, Bestwick JP, Silveira-Moriyama L, Hawkes CH, Giovannoni G, et al. (2012) Meta-analysis of early nonmotor features and risk factors for Parkinson disease. Annals of neurology 72: 893-901.
10. Kotagal V, Albin RL, Muller ML, Koeppe RA, Frey KA, et al. (2013) Diabetes is associated with postural instability and gait difficulty in Parkinson disease. Parkinsonism & related disorders 19: 522-526.
11. Bosco D, Plastino M, Cristiano D, Colica C, Ermio C, et al. (2012) Dementia is associated with Insulin Resistance in patients with Parkinson's disease. Journal of the neurological sciences 315: 39-43.
12. Aviles-Olmos I, Limousin P, Lees A, Foltynie T (2013) Parkinson's disease, insulin resistance and novel agents of neuroprotection. Brain: A journal of neurology 136: 374-384.
13. Wang L, Zhai YQ, Xu LL, Qiao C, Sun XL, et al. (2014) Metabolic inflammation exacerbates dopaminergic neuronal degeneration in response to acute MPTP challenge in type 2 diabetes mice. Experimental neurology 251: 22-29.
14. Santos RX, Correia SC, Alves MG, Oliveira PF, Cardoso S, et al. (2014) Mitochondrial quality control systems sustain brain mitochondrial bioenergetics in early stages of type 2 diabetes. Molecular and cellular biochemistry.
15. Santiago JA, Potashkin JA (2013) Integrative network analysis unveils convergent molecular pathways in Parkinson's disease and diabetes. PloS one 8: E83940.
16. Santiago JA, Potashkin JA (2014) A network approach to diagnostic biomarkers in progressive supranuclear palsy. Movement disorders: Official journal of the Movement Disorder Society 29: 550-555.
17. Bauer-Mehren A, Bundschus M, Rautschka M, Mayer MA, Sanz F, et al. (2011) Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases. PloS one 6: E20284.
18. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome research 13: 2498-2504.
19. Peng K, Xu W, Zheng J, Huang K, Wang H, et al. (2013) The Disease and Gene Annotations (DGA): An annotation resource for human disease. Nucleic acids research 41: D553-560.
20. Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, et al. (2009) Exploring the human genome with functional maps. Genome research 19: 1093-1106.
21. Wang L, Khankhanian P, Baranzini SE, Mousavi P (2011) iCTNet: A Cytoscape plugin to produce and analyze integrative complex traits networks. BMC bioinformatics 12: 380.
22. Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, et al. (2010) GeneMANIA Cytoscape plugin: Fast gene function predictions on the desktop. Bioinformatics 26: 2927-2928.
23. Le DH, Kwon YK (2012) GPEC: A Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection. Computational biology and chemistry 37: 17-23.
24. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102: 15545-15550.
25. Gao L, Zhao G, Fang JS, Yuan TY, Liu AL, et al. (2013) Discovery of the neuroprotective effects of alvespimycin by computational prioritization of potential anti-parkinson agents. The FEBS journal.
26. Ding H, Sarokhan AK, Roderick SS, Bakshi R, Maher NE, et al. (2011) Association of SNCA with Parkinson: Replication in the Harvard NeuroDiscovery Center Biomarker Study. Movement disorders: Official journal of the Movement Disorder Society 26: 2283-2286.
27. Potashkin JA, Santiago JA, Ravina BM, Watts A, Leontovich AA (2012) Biosignatures for Parkinson's disease and atypical parkinsonian disorders patients. PloS one 7: E43595.
28. Scherzer CR, Eklund AC, Morse LJ, Liao Z, Locascio JJ, et al. (2007) Molecular markers of early Parkinson's disease based on gene expression in blood. Proceedings of the National Academy of Sciences of the United States of America 104: 955-960.
29. Adler CH, Beach TG, Hentz JG, Shill HA, Caviness JN, et al. (2014) Low clinical diagnostic accuracy of early vs advanced Parkinson disease: Clinicopathologic study. Neurology.
30. Rajput AH, Rajput A (2014) Accuracy of Parkinson disease diagnosis unchanged in 2 decades. Neurology.
31. Kohler S, Bauer S, Horn D, Robinson PN (2008) Walking the interactome for prioritization of candidate disease genes. American journal of human genetics 82: 949-958.
32. Bragina EY, Tiys ES, Freidin MB, Koneva LA, Demenkov PS, et al. (2014) Insights into pathophysiology of dystropy through the analysis of gene networks: An example of bronchial asthma and tuberculosis. Immunogenetics 66: 457-465.
33. Gupta A, Mohanty P, Bhatnagar S (2014) Integrative analysis of ocular complications in atherosclerosis unveils pathway convergence and crosstalk. Journal of receptor and signal transduction research: 1-16.
34. Altshuler D, Hirschhorn JN, Klannemark M, Lindgren CM, Vohl MC, et al. (2000) The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nature genetics 26: 76-80.
35. Novelli G, Ciccacci C, Borgiani P, Papaluca Amati M, Abadie E (2008) Genetic tests and genomic biomarkers: Regulation, qualification and validation. Clinical cases in mineral and bone metabolism: The official journal of the Italian Society of Osteoporosis, Mineral Metabolism, and Skeletal Diseases 5: 149-154.
36. Dzamko N, Chua G, Ranola M, Rowe DB, Halliday GM (2013) Measurement of LRRK2 and Ser910/935 phosphorylated LRRK2 in peripheral blood mononuclear cells from idiopathic Parkinson's disease patients. Journal of Parkinson's disease 3: 145-152.
37. Lin X, Cook TJ, Zabetian CP, Leverenz JB, Peskind ER, et al. (2012) DJ-1 isoforms in whole blood as potential biomarkers of Parkinson disease. Scientific reports 2: 954.
38. Levine AJ, Feng Z, Mak TW, You H, Jin S (2006) Coordination and communication between the p53 and IGF-1-AKT-TOR signal transduction pathways. Genes & development 20: 267-275.
39. Maddocks OD, Vousden KH (2011) Metabolic regulation by p53. Journal of molecular medicine 89: 237-245.
40. Dunn L, Allen GF, Mamais A, Ling H, Li A, et al. (2014) Dysregulation of glucose metabolism is an early event in sporadic Parkinson's disease. Neurobiology of aging 35: 1111-1115.
41. Przedborski S (2010) Inflammation and Parkinson's disease pathogenesis. Movement disorders: Official journal of the Movement Disorder Society 25 Suppl 1: S55-57.
42. Nolan YM, Sullivan AM, Toulouse A (2013) Parkinson's disease in the nuclear age of neuroinflammation. Trends in molecular medicine 19: 187-196.
43. Marcil V, Seidman E, Sinnett D, Boudreau F, Gendron FP, et al. (2010) Modification in oxidative stress, inflammation, and lipoprotein assembly in response to hepatocyte nuclear factor 4alpha knockdown in intestinal epithelial cells. The Journal of biological chemistry 285: 40448-40460.
44. Menon R, Farina C (2011) Shared molecular and functional frameworks among five complex human disorders: A comparative study on interactomes linked to susceptibility genes. PloS one 6: E18660.
45. Belluzzi E, Bisaglia M, Lazzarini E, Tabares LC, Beltramini M, et al. (2012) Human SOD2 modification by dopamine quinones affects enzymatic activity by promoting its aggregation: Possible implications for Parkinson's disease. PloS one 7: E38026.
46. Ferrer I, Perez E, Dalfo E, BarraChina M (2007) Abnormal levels of prohibitin and ATP synthase in the substantia nigra and frontal cortex in Parkinson's disease. Neuroscience letters 415: 205-209.
47. Reyna SM, Ghosh S, Tantiwong P, Meka CS, Eagan P, et al. (2008) Elevated toll-like receptor 4 expression and signaling in muscle from insulin-resistant subjects. Diabetes 57: 2595-2602.
48. Schramm F, Kern A, Barthel C, Nadaud S, Meyer N, et al. (2012) Microarray analyses of inflammation response of human dermal fibroblasts to different strains of Borrelia burgdorferi sensu stricto. PloS one 7: E40046.
49. Soderberg JA, Birse RT, Nassel DR (2011) Insulin production and signaling in renal tubules of Drosophila is under control of tachykinin-related peptide and regulates stress resistance. PloS one 6: E19866.
50. Kang L, Dai C, Lustig ME, Bonner JS, Mayes WH, et al. (2014) Heterozygous SOD2 Deletion Impairs Glucose-Stimulated Insulin Secretion, but not Insulin Action in High Fat-Fed Mice. Diabetes.
51. Singh BK, Kumar A, Ahmad I, Kumar V, Patel DK, et al. (2011) Oxidative stress in zinc-induced dopaminergic neurodegeneration: Implications of superoxide dismutase and heme oxygenase-1. Free radical research 45: 1207-1222.
52. Aviles-Olmos I, Dickson J, Kefalopoulou Z, Djamshidian A, Ell P, et al. (2013) Exenatide and the treatment of patients with Parkinson's disease. The Journal of clinical investigation 123: 2730-2736.
53. Wahlqvist ML, Lee MS, Hsu CC, Chuang SY, Lee JT, et al. (2012) Metformininclusive sulfonylurea therapy reduces the risk of Parkinson's disease occurring with Type 2 diabetes in a Taiwanese population cohort. Parkinsonism & related disorders 18: 753-758.
54. Aviles-Olmos I, Dickson J, Kefalopoulou Z, Djamshidian A, Kahan J, et al. (2014) Motor and Cognitive Advantages Persist 12 Months After Exenatide Exposure in Parkinson's Disease. Journal of Parkinson's disease.
55. Kukidome D, Nishikawa T, Sonoda K, Imoto K, Fujisawa K, et al. (2006) Activation of AMP-activated protein kinase reduces hyperglycemia-induced mitochondrial reactive oxygen species production and promotes mitochondrial biogenesis in human umbilical vein endothelial cells. Diabetes 55: 120-127.
56. Lauer B, Tuschl G, Kling M, Mueller SO (2009) Species-specific toxicity of diclofenac and troglitazone in primary human and rat hepatocytes. Chemicobiological interactions 179: 17-24.
57. Ruan H, Pownall HJ, Lodish HF (2003) Troglitazone antagonizes tumor necrosis factor-alpha-induced reprogramming of adipocyte gene expression by inhibiting the transcriptional regulatory functions of NF-kappaB. The Journal of biological chemistry 278: 28181-28192.
58. Onozato ML, Tojo A, Goto A, Fujita T (2004) Radical scavenging effect of gliclazide in diabetic rats fed with a high cholesterol diet. Kidney international 65: 951-960.
59. Doonan F, Wallace DM, O'Driscoll C, Cotter TG (2009) Rosiglitazone acts as a neuroprotectant in retinal cells via up-regulation of sestrin-1 and SOD-2. Journal of neurochemistry 109: 631-643.
60. Santiago JA, Scherzer CR, Potashkin JA (2013) Specific splice variants are associated with Parkinson's disease. Movement disorders: Official journal of the Movement Disorder Society 28: 1724-1727.
61. Stamova BS, Apperson M, Walker WL, Tian Y, Xu H, et al. (2009) Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood. BMC medical genomics 2: 49.