Prediction of metabolic gene biomarkers for neurodegenerative disease by an integrated network-based approach

BioMed Research International

Volumn 2015, Issue , 2015, Pages

  Ni, Qi ^a   Su, Xianming ^b   Chen, Jingqi ^a   Tian, Weidong ^a  

^a FUDAN UNIVERSITY   (China)

^b XI'AN JIAOTONG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; ENZYME;

ARTICLE; BIOACCUMULATION; CALCULATION; DEGENERATIVE DISEASE; GENE EXPRESSION PROFILING; GENE EXPRESSION SYSTEM; GENE FUNCTION; GENE IDENTIFICATION; GENETIC DATABASE; HUMAN; HUNTINGTON CHOREA; MARKER GENE; MATHEMATICAL ANALYSIS; METABOLISM; MICROARRAY ANALYSIS; PARKINSON DISEASE; PREDICTION; GENE EXPRESSION REGULATION; GENETICS; META ANALYSIS; PATHOPHYSIOLOGY;

BIOMARKERS; GENE EXPRESSION REGULATION; HUMANS; HUNTINGTON DISEASE; METABOLIC NETWORKS AND PATHWAYS; MICROARRAY ANALYSIS; PARKINSON DISEASE;

EID: 84929646304     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2015/432012     Document Type: Article

References (40)

1. C. A. Ross andM. A. Poirier, "Protein aggregation and neurodegenerative disease, " Nature Medicine, vol. 10, pp. S10-S17, 2004.
2. National Collaborating Centre for Chronic Conditions, Parkinson's Disease: National Clinical Guideline for Diagnosis and Management in Primary and Secondary Care, Royal College of Physicians, London, UK, 2006.
3. M. J. Baptista, M. R. Cookson, and K. Gwinn-Hardy, "Parkinson's Disease: Insights from Genetic Causes, " in Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, pp. 1359-1360, Springer, Berlin, Germany, 2006.
4. F. O. Walker, "Huntington's disease, " The Lancet, vol. 369, no. 9557, pp. 218-228, 2007.
5. S. Wieczorek and J. T. Epplen, "Huntington's disease, " in Encyclopedic Reference of Genomics and Proteomics inMolecular Medicine, pp. 832-835, Springer, Berlin, Germany, 2006.
6. Z. T. Kincses and L. Vecsei, "Pharmacological therapy in Parkinson's disease: focus on neuroprotection, " CNS Neuroscience and Therapeutics, vol. 17, no. 5, pp. 345-367, 2011.
7. E.-J. Bae, H.-J. Lee, Y.-H. Jang et al., "PhospholipaseD1 regulates autophagic flux and clearance of α-synuclein aggregates, " Cell Death & Differentiation, vol. 21, no. 7, pp. 1132-1141, 2014.
8. N. Exner, A. K. Lutz, C. Haass, and K. F. Winklhofer, "Mitochondrial dysfunction in Parkinsonαs disease: molecular mechanisms and pathophysiological consequences, "TheEMBO Journal, vol. 31, no. 14, pp. 3038-3062, 2012.
9. A. Campbell, "Inflammation, neurodegenerative diseases, and environmental exposures, " Annals of the New York Academy of Sciences, vol. 1035, pp. 117-132, 2004.
10. H. Ischiropoulos and J. S. Beckman, "Oxidative stress and nitration in neurodegeneration: cause, effect, or association?" The Journal of Clinical Investigation, vol. 111, no. 2, pp. 163-169, 2003.
11. S. Grimm, A. Hoehn, K. J. Davies, and T. Grune, "Protein oxidativemodifications in the ageing brain: consequence for the onset of neurodegenerative disease, " Free Radical Research, vol. 45, no. 1, pp. 73-88, 2011.
12. A. H. V. Schapira, C. W. Olanow, J. T. Greenamyre, and E. Bezard, "Slowing of neurodegeneration in Parkinson's disease and Huntington's disease: future therapeutic perspectives, " The Lancet, vol. 9942, no. 384, pp. 545-555, 2014.
13. K. Jomova, D. Vondrakova, M. Lawson, andM. Valko, "Metals, oxidative stress and neurodegenerative disorders, " Molecular and Cellular Biochemistry, vol. 345, no. 1-2, pp. 91-104, 2010.
14. J. Chen, M. Ma, N. Shen, J. J. Xi, and W. Tian, "Integration of cancer gene co-expression network and metabolic network to uncover potential cancer drug targets, " Journal of Proteome Research, vol. 12, no. 6, pp. 2354-2364, 2013.
15. A. Alexeyenko, T. Schmitt, A. Tjärnberg, D. Guala, O. Frings, and E. L. L. Sonnhammer, "Comparative interactomics with Funcoup 2. 0, " Nucleic Acids Research, vol. 40, no. 1, pp. D821-D828, 2012.
16. E. W. Dijkstra, "A note on two problems in connexion with graphs, " Numerische Mathematik, vol. 1, pp. 269-271, 1959.
17. H. A. Lashuel, C. R. Overk, A. Oueslati, and E. Masliah, "The many faces of α-synuclein: from structure and toxicity to therapeutic target, " Nature Reviews Neuroscience, vol. 14, no. 1, pp. 38-48, 2013.
18. S. Hands, M. U. Sajjad, M. J. Newton, and A. Wyttenbach, "In vitro and in vivo aggregation of a fragment of huntingtin protein directly causes free radical production, "The Journal of Biological Chemistry, vol. 286, no. 52, pp. 44512-44520, 2011.
19. R. Musanti, E. Parati, E. Lamperi, and G. Ghiselli, "Decreased cholesterol biosynthesis in fibroblasts from patients with Parkinson disease, " Biochemical Medicine and Metabolic Biology, vol. 49, no. 2, pp. 133-142, 1993.
20. M. Valenza and E. Cattaneo, "Emerging roles for cholesterol in Huntington's disease, " Trends in Neurosciences, vol. 34, no. 9, pp. 474-486, 2011.
21. D. Heras-Sandoval, J. M. Pérez-Rojas, J. Hernández-Damián, and J. Pedraza-Chaverri, "The role of PI3K/AKT/mTOR pathway in themodulation of autophagy and the clearance of protein aggregates in neurodegeneration, " Cellular Signalling, vol. 26, no. 12, pp. 2694-2701, 2014.
22. T. F. Franke, "PI3K/Akt: getting it right matters, " Oncogene, vol. 27, no. 50, pp. 6473-6488, 2008.
23. S. Humbert, E. A. Bryson, F. P. Cordelières et al. , "The IGF-1/Akt pathway is neuroprotective inHuntington's disease and involves huntingtin phosphorylation by Akt, " Developmental Cell, vol. 2, no. 6, pp. 831-837, 2002.
24. V. Law, C. Knox, Y. Djoumbou et al. , "DrugBank 4. 0: shedding new light on drug metabolism, " Nucleic Acids Research, vol. 42, no. 1, pp. D1091-D1097, 2014.
25. P. D. Stenson, "The human gene mutation database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution, " in Current Protocols in Bioinformatics, unit 1. 13, JohnWiley & Sons, New York, NY, USA, 2012.
26. A. Hamosh, A. F. Scott, J. S. Amberger, C. A. Bocchini, and V. A. McKusick, "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders, " Nucleic Acids Research, vol. 33, pp. D514-D517, 2005.
27. K. G. Becker, K. C. Barnes, T. J. Bright, and S. A. Wang, "The Genetic Association Database[1], " Nature Genetics, vol. 36, no. 5, pp. 431-432, 2004.
28. M. Kanehisa and S. Goto, "KEGG: kyoto encyclopedia of genes and genomes, " Nucleic Acids Research, vol. 28, no. 1, pp. 27-30, 2000.
29. T. M. Michel, L. Käsbauer, W. Gsell et al. , "Aldehyde dehydrogenase 2 in sporadic Parkinson's disease, " Parkinsonism & Related Disorders, vol. 20, no. 1, pp. S68-S72, 2014.
30. C. H. Chen, J. C. B. Ferreira, E. R. Gross, and D. Mochly-Rosen, "Targeting aldehyde dehydrogenase 2: new therapeutic opportunities, " Physiological Reviews, vol. 94, no. 1, pp. 1-34, 2014.
31. J. Dorszewska, J. Florczak, A. Rozycka et al. , "Oxidative DNA damage and level of thiols as related to polymorphisms of MTHFR, MTR, MTHFD1 in Alzheimer's and Parkinson's diseases, " Acta Neurobiologiae Experimentalis, vol. 67, no. 2, pp. 113-129, 2007.
32. J. Jin, G. J. Li, J. Davis et al. , "Identification of novel proteins associated with both α-synuclein and DJ-1, "Molecular & Cellular Proteomics, vol. 6, no. 5, pp. 845-859, 2007.
33. A. A. Dukes, V. S. van Laar, M. Cascio, and T. G. Hastings, "Changes in endoplasmic reticulumstress proteins and aldolase A in cells exposed to dopamine, " Journal of Neurochemistry, vol. 106, no. 1, pp. 333-346, 2008.
34. T. Tatusova, S. Ciufo, B. Fedorov, K. O'Neill, and I. Tolstoy, "RefSeq microbial genomes database: new representation and annotation strategy, " Nucleic Acids Research, vol. 42, no. 1, pp. D553-D559, 2014.
35. N. Szabó, Z. T. Kincses, J. Toldi, and L. Vécsei, "Altered tryptophan metabolism in Parkinson's disease: a possible novel therapeutic approach, " Journal of the Neurological Sciences, vol. 310, no. 1-2, pp. 256-260, 2011.
36. T. W. Stone, C. M. Forrest, N. Stoy, and L. G. Darlington, "Involvement of kynurenines in Huntington's disease and stroke-induced brain damage, " Journal of Neural Transmission, vol. 119, no. 2, pp. 261-274, 2012.
37. M. Ohgami, N. Takahashi, M. Yamasaki, and T. Fukui, "Expression of acetoacetyl-CoA synthetase, a novel cytosolic ketone body-utilizing enzyme, in human brain, " Biochemical Pharmacology, vol. 65, no. 6, pp. 989-994, 2003.
38. S. Hasegawa, H. Kume, S. Iinuma, M. Yamasaki, N. Takahashi, and T. Fukui, "Acetoacetyl-CoA synthetase is essential for normal neuronal development, " Biochemical and Biophysical Research Communications, vol. 427, no. 2, pp. 398-403, 2012.
39. D. Separovic, K. Hanada, M. Y. Awad Maitah et al. , "Sphingomyelin synthase 1 suppresses ceramide production and apoptosis post-photodamage, " Biochemical and Biophysical Research Communications, vol. 358, no. 1, pp. 196-202, 2007.
40. A. McCampbell, D. Truong, D. C. Broomet al. , "Mutant SPTLC1 dominantly inhibits serine palmitoyltransferase activity in vivo and confers an age-dependent neuropathy, " Human Molecular Genetics, vol. 14, no. 22, pp. 3507-3521, 2005.