Table of Contents Author Guidelines Submit a Manuscript
Journal of Immunology Research
Volume 2015, Article ID 737168, 10 pages
http://dx.doi.org/10.1155/2015/737168
Review Article

Computational Modelling Approaches on Epigenetic Factors in Neurodegenerative and Autoimmune Diseases and Their Mechanistic Analysis

1Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754 Sankt Augustin, Germany
2Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany

Received 31 July 2015; Revised 19 October 2015; Accepted 20 October 2015

Academic Editor: Francesco Pappalardo

Copyright © 2015 Afroza Khanam Irin et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. C. H. Waddington, “The epigenotype. 1942,” International Journal of Epidemiology, vol. 41, no. 1, pp. 10–13, 2012. View at Publisher · View at Google Scholar · View at Scopus
  2. G. Egger, G. Liang, A. Aparicio, and P. A. Jones, “Epigenetics in human disease and prospects for epigenetic therapy,” Nature, vol. 429, no. 6990, pp. 457–463, 2004. View at Publisher · View at Google Scholar · View at Scopus
  3. K. S. Gill, “Epigenetics of the promorphology of the egg in Drosophila Melanogaster,” Journal of Experimental Zoology, vol. 155, no. 1, pp. 91–104, 1964. View at Publisher · View at Google Scholar · View at Scopus
  4. R. Tsanev and B. Sendov, “An epigenetic mechanism for carcinogenesis,” Zeitschrift für Krebsforschung und Klinische Onkologie, vol. 76, no. 4, pp. 299–319, 1971. View at Publisher · View at Google Scholar · View at Scopus
  5. R. Holliday, “The inheritance of epigenetic defects,” Science, vol. 238, no. 4824, pp. 163–170, 1987. View at Publisher · View at Google Scholar · View at Scopus
  6. F. Song, S. Mahmood, S. Ghosh et al., “Tissue specific differentially methylated regions (TDMR): changes in DNA methylation during development,” Genomics, vol. 93, no. 2, pp. 130–139, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. M. Chen and L. Zhang, “Epigenetic mechanisms in developmental programming of adult disease,” Drug Discovery Today, vol. 16, no. 23-24, pp. 1007–1018, 2011. View at Publisher · View at Google Scholar · View at Scopus
  8. K. L. Saban, H. L. Mathews, H. A. de Von, and L. W. Janusek, “Epigenetics and social context: implications for disparity in cardiovascular disease,” Aging and Disease, vol. 5, no. 5, pp. 346–355, 2014. View at Publisher · View at Google Scholar · View at Scopus
  9. F. Prattichizzo, A. Giuliani, A. Ceka et al., “Epigenetic mechanisms of endothelial dysfunction in type 2 diabetes,” Clinical Epigenetics, vol. 7, article 56, 2015. View at Publisher · View at Google Scholar
  10. N. Duru, R. Gernapudi, G. Eades, R. Eckert, and Q. Zhou, “Epigenetic regulation of miRNAs and breast cancer stem cells,” Current Pharmacology Reports, vol. 1, no. 3, pp. 161–169, 2015. View at Publisher · View at Google Scholar
  11. S. J. Van Dijk, P. L. Molloy, H. Varinli et al., “Epigenetics and human obesity,” International Journal of Obesity, vol. 39, no. 1, pp. 85–97, 2015. View at Publisher · View at Google Scholar · View at Scopus
  12. P. Cordero, J. Li, and J. A. Oben, “Epigenetics of obesity: beyond the genome sequence,” Current Opinion in Clinical Nutrition & Metabolic Care, vol. 18, no. 4, pp. 361–366, 2015. View at Publisher · View at Google Scholar
  13. T. Palomo, T. Archer, R. J. Beninger, and R. M. Kostrzewa, “Gene-environment interplay in neurogenesis and neurodegeneration,” Neurotoxicity Research, vol. 6, no. 6, pp. 415–434, 2004. View at Publisher · View at Google Scholar · View at Scopus
  14. T. L. Spires and A. J. Hannan, “Nature, nurture and neurology: gene-environment interactions in neurodegenerative disease. FEBS Anniversary Prize Lecture delivered on 27 June 2004 at the 29th FEBS Congress in Warsaw,” FEBS Journal, vol. 272, no. 10, pp. 2347–2361, 2005. View at Publisher · View at Google Scholar
  15. F. Coppedè, M. Mancuso, G. Siciliano, L. Migliore, and L. Murri, “Genes and the environment in neurodegeneration,” Bioscience Reports, vol. 26, no. 5, pp. 341–367, 2006. View at Publisher · View at Google Scholar · View at Scopus
  16. S. C. Marques, C. R. Oliveira, C. M. Pereira, and T. F. Outeiro, “Epigenetics in neurodegeneration: a new layer of complexity,” Progress in Neuro-Psychopharmacology & Biological Psychiatry, vol. 35, no. 2, pp. 348–355, 2011. View at Publisher · View at Google Scholar
  17. F. Coppedè, “Genetics and epigenetics of Parkinson's disease,” The Scientific World Journal, vol. 2012, Article ID 489830, 12 pages, 2012. View at Publisher · View at Google Scholar · View at Scopus
  18. J. M. Greer and P. A. McCombe, “The role of epigenetic mechanisms and processes in autoimmune disorders,” Biologics, vol. 6, pp. 307–327, 2012. View at Publisher · View at Google Scholar · View at Scopus
  19. G. Ravaglia, P. Forti, F. Maioli et al., “Homocysteine and folate as risk factors for dementia and Alzheimer disease,” The American Journal of Clinical Nutrition, vol. 82, no. 3, pp. 636–643, 2005. View at Google Scholar · View at Scopus
  20. J. Wu, M. R. Basha, B. Brock et al., “Alzheimer's disease (AD)-like pathology in aged monkeys after infantile exposure to environmental metal lead (Pb): evidence for a developmental origin and environmental link for AD,” The Journal of Neuroscience, vol. 28, no. 1, pp. 3–9, 2008. View at Publisher · View at Google Scholar · View at Scopus
  21. A. Baccarelli and V. Bollati, “Epigenetics and environmental chemicals,” Current Opinion in Pediatrics, vol. 21, no. 2, pp. 243–251, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. I. A. Qureshi and M. F. Mehler, “Advances in epigenetics and epigenomics for neurodegenerative diseases,” Current Neurology and Neuroscience Reports, vol. 11, no. 5, pp. 464–473, 2011. View at Publisher · View at Google Scholar · View at Scopus
  23. P. Kaliman, M. J. Álvarez-López, M. Cosín-Tomás, M. A. Rosenkranz, A. Lutz, and R. J. Davidson, “Rapid changes in histone deacetylases and inflammatory gene expression in expert meditators,” Psychoneuroendocrinology, vol. 40, no. 1, pp. 96–107, 2014. View at Publisher · View at Google Scholar · View at Scopus
  24. V. Nicolia, M. Lucarelli, and A. Fuso, “Environment, epigenetics and neurodegeneration: focus on nutrition in Alzheimer's disease,” Experimental Gerontology, vol. 68, pp. 8–12, 2015. View at Publisher · View at Google Scholar
  25. D. Mastroeni, A. Grover, E. Delvaux, C. Whiteside, P. D. Coleman, and J. Rogers, “Epigenetic changes in Alzheimer's disease: decrements in DNA methylation,” Neurobiology of Aging, vol. 31, no. 12, pp. 2025–2037, 2010. View at Publisher · View at Google Scholar · View at Scopus
  26. Y. I. Francis, M. Fà, H. Ashraf et al., “Dysregulation of histone acetylation in the APP/PS1 mouse model of Alzheimer's disease,” Journal of Alzheimer's Disease, vol. 18, no. 1, pp. 131–139, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. E. Martí, L. Pantano, M. Bañez-Coronel et al., “A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing,” Nucleic Acids Research, vol. 38, no. 20, pp. 7219–7235, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. D. M. Mintzer, S. N. Billet, and L. Chmielewski, “Drug-induced hematologic syndromes,” Advances in Hematology, vol. 2009, Article ID 495863, 11 pages, 2009. View at Publisher · View at Google Scholar · View at Scopus
  29. T. Uhlig, K. B. Hagen, and T. K. Kvien, “Current tobacco smoking, formal education, and the risk of rheumatoid arthritis,” Journal of Rheumatology, vol. 26, no. 1, pp. 47–54, 1999. View at Google Scholar · View at Scopus
  30. A. Kuhn and S. Beissert, “Photosensitivity in lupus erythematosus,” Autoimmunity, vol. 38, no. 7, pp. 519–529, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. M. N. Artyomov, A. Meissner, and A. K. Chakraborty, “A model for genetic and epigenetic regulatory networks identifies rare pathways for transcription factor induced pluripotency,” PLoS Computational Biology, vol. 6, no. 5, Article ID e1000785, 2010. View at Publisher · View at Google Scholar · View at Scopus
  32. K. Raghavan, H. J. Ruskin, D. Perrin, F. Goasmat, and J. Burns, “Computational micromodel for epigenetic mechanisms,” PLoS ONE, vol. 5, no. 11, Article ID e14031, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. L. Y. Wang, P. Wang, M. J. Li et al., “EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans,” Epigenetics, vol. 6, no. 12, pp. 1505–1512, 2011. View at Publisher · View at Google Scholar · View at Scopus
  34. S. Althammer, A. Pagès, and E. Eyras, “Predictive models of gene regulation from high-throughput epigenomics data,” Comparative and Functional Genomics, vol. 2012, Article ID 284786, 13 pages, 2012. View at Publisher · View at Google Scholar · View at Scopus
  35. A. P. Turner, M. A. Lones, L. A. Fuente, S. Stepney, L. S. D. Caves, and A. M. Tyrrell, “The incorporation of epigenetics in artificial gene regulatory networks,” BioSystems, vol. 112, no. 2, pp. 56–62, 2013. View at Publisher · View at Google Scholar · View at Scopus
  36. K.-E. Lee and H.-S. Park, “A review of three different studies on hidden markov models for epigenetic problems: a computational perspective,” Genomics & Informatics, vol. 12, no. 4, pp. 145–150, 2014. View at Publisher · View at Google Scholar
  37. K. K.-H. Farh, A. Marson, J. Zhu et al., “Genetic and epigenetic fine mapping of causal autoimmune disease variants,” Nature, vol. 518, no. 7539, pp. 337–343, 2015. View at Publisher · View at Google Scholar
  38. A. T. Kodamullil, E. Younesi, M. Naz, S. Bagewadi, and M. Hofmann-Apitius, “Computable cause-and-effect models of healthy and Alzheimer's disease states and their mechanistic differential analysis,” Alzheimer's & Dementia, 2015. View at Publisher · View at Google Scholar
  39. N. L. Catlett, A. J. Bargnesi, S. Ungerer et al., “Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data,” BMC Bioinformatics, vol. 14, article 340, 2013. View at Publisher · View at Google Scholar · View at Scopus
  40. F. Martin, T. M. Thomson, A. Sewer et al., “Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks,” BMC Systems Biology, vol. 6, article 54, 2012. View at Publisher · View at Google Scholar · View at Scopus
  41. D. Laifenfeld, D. A. Drubin, N. L. Catlett et al., “Early patient stratification and predictive biomarkers in drug discovery and development: a case study of ulcerative colitis anti-TNF therapy,” Advances in Experimental Medicine and Biology, vol. 736, pp. 645–653, 2012. View at Publisher · View at Google Scholar · View at Scopus
  42. D. A. Fryburg, D. H. Song, and D. De Graaf, “Early patient stratification is critical to enable effective and personalised drug discovery and development,” Drug Discovery World, vol. 12, no. 3, pp. 47–56, 2011. View at Google Scholar · View at Scopus
  43. B. Thomas and M. F. Beal, “Molecular insights into Parkinson's disease,” F1000 Medicine Reports, vol. 3, article 7, 2011. View at Publisher · View at Google Scholar
  44. A. Jowaed, I. Schmitt, O. Kaut, and U. Wüllner, “Methylation regulates alpha-synuclein expression and is decreased in Parkinson's disease patients' brains,” The Journal of Neuroscience, vol. 30, no. 18, pp. 6355–6359, 2010. View at Publisher · View at Google Scholar · View at Scopus
  45. L. Matsumoto, H. Takuma, A. Tamaoka et al., “CpG demethylation enhances alpha-synuclein expression and affects the pathogenesis of Parkinson's disease,” PLoS ONE, vol. 5, no. 11, Article ID e15522, 2010. View at Publisher · View at Google Scholar · View at Scopus
  46. A. G. Riedl, P. M. Watts, P. Jenner, and C. D. Marsden, “P450 enzymes and Parkinson's disease: the story so far,” Movement Disorders, vol. 13, no. 2, pp. 212–220, 1998. View at Publisher · View at Google Scholar · View at Scopus
  47. Y. Feng, J. Jankovic, and Y.-C. Wu, “Epigenetic mechanisms in Parkinson's disease,” Journal of the Neurological Sciences, vol. 349, no. 1-2, pp. 3–9, 2015. View at Publisher · View at Google Scholar
  48. O. W. Wan and K. K. K. Chung, “The role of alpha-synuclein oligomerization and aggregation in cellular and animal models of Parkinson's disease,” PLoS ONE, vol. 7, no. 6, Article ID e38545, 2012. View at Publisher · View at Google Scholar · View at Scopus
  49. O. Kaut, I. Schmitt, and U. Wüllner, “Genome-scale methylation analysis of Parkinson's disease patients' brains reveals DNA hypomethylation and increased mRNA expression of cytochrome P450 2E1,” Neurogenetics, vol. 13, no. 1, pp. 87–91, 2012. View at Publisher · View at Google Scholar · View at Scopus
  50. M. J. Devine and P. A. Lewis, “Emerging pathways in genetic Parkinson's disease: tangles, Lewy bodies and LRRK2,” The FEBS Journal, vol. 275, no. 23, pp. 5748–5757, 2008. View at Publisher · View at Google Scholar · View at Scopus
  51. C. Hague, M. A. Uberti, Z. Chen et al., “Olfactory receptor surface expression is driven by association with the beta2-adrenergic receptor,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 37, pp. 13672–13676, 2004. View at Publisher · View at Google Scholar · View at Scopus
  52. E.-Y. Lee, P. J. Eslinger, G. Du, L. Kong, M. M. Lewis, and X. Huang, “Olfactory-related cortical atrophy is associated with olfactory dysfunction in Parkinson's disease,” Movement Disorders, vol. 29, no. 9, pp. 1205–1208, 2014. View at Publisher · View at Google Scholar · View at Scopus
  53. P. Desplats, B. Spencer, E. Coffee et al., “Alpha-synuclein sequesters Dnmt1 from the nucleus: a novel mechanism for epigenetic alterations in Lewy body diseases,” The Journal of Biological Chemistry, vol. 286, no. 11, pp. 9031–9037, 2011. View at Publisher · View at Google Scholar · View at Scopus
  54. P. Viitala, K. Posti, A. Lindfors, O. Pelkonen, and H. Raunio, “cAMP mediated upregulation of CYP2A5 in mouse hepatocytes,” Biochemical and Biophysical Research Communications, vol. 280, no. 3, pp. 761–767, 2001. View at Publisher · View at Google Scholar · View at Scopus
  55. Y. Fujii, N. Osaki, T. Hase, and A. Shimotoyodome, “Ingestion of coffee polyphenols increases postprandial release of the active glucagon-like peptide-1 (GLP-1(7–36)) amide in C57BL/6J mice,” Journal of Nutritional Science, vol. 4, article e9, 9 pages, 2015. View at Publisher · View at Google Scholar
  56. Y. Li, T. Perry, M. S. Kindy et al., “GLP-1 receptor stimulation preserves primary cortical and dopaminergic neurons in cellular and rodent models of stroke and Parkinsonism,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 4, pp. 1285–1290, 2009. View at Publisher · View at Google Scholar · View at Scopus
  57. P. Prasad, A. K. Tiwari, K. M. P. Kumar et al., “Association analysis of ADPRT1, AKR1B1, RAGE, GFPT2 and PAI-1 gene polymorphisms with chronic renal insufficiency among Asian Indians with type-2 diabetes,” BMC Medical Genetics, vol. 11, article 52, 2010. View at Publisher · View at Google Scholar · View at Scopus
  58. E. Masliah, W. Dumaop, D. Galasko, and P. Desplats, “Distinctive patterns of DNA methylation associated with Parkinson disease: identification of concordant epigenetic changes in brain and peripheral blood leukocytes,” Epigenetics, vol. 8, no. 10, pp. 1030–1038, 2013. View at Publisher · View at Google Scholar · View at Scopus
  59. C. Song, A. Kanthasamy, V. Anantharam, F. Sun, and A. G. Kanthasamy, “Environmental neurotoxic pesticide increases histone acetylation to promote apoptosis in dopaminergic neuronal cells: relevance to epigenetic mechanisms of neurodegeneration,” Molecular Pharmacology, vol. 77, no. 4, pp. 621–632, 2010. View at Publisher · View at Google Scholar · View at Scopus
  60. I. F. Harrison and D. T. Dexter, “Epigenetic targeting of histone deacetylase: therapeutic potential in Parkinson's disease?” Pharmacology and Therapeutics, vol. 140, no. 1, pp. 34–52, 2013. View at Publisher · View at Google Scholar · View at Scopus
  61. D. Qu, J. Rashidian, M. P. Mount et al., “Role of Cdk5-Mediated Phosphorylation of Prx2 in MPTP Toxicity and Parkinson's Disease,” Neuron, vol. 55, no. 1, pp. 37–52, 2007. View at Publisher · View at Google Scholar · View at Scopus
  62. E. Miñones-Moyano, S. Porta, G. Escaramís et al., “MicroRNA profiling of Parkinson's disease brains identifies early downregulation of miR-34b/c which modulate mitochondrial function,” Human Molecular Genetics, vol. 20, no. 15, pp. 3067–3078, 2011. View at Publisher · View at Google Scholar · View at Scopus
  63. D. A. Umphred, Neurological Rehabilitation, Mosby, St. Louis, Mo, USA, 2001.
  64. M. Iridoy Zulet, L. Pulido Fontes, T. Ayuso Blanco, F. Lacruz Bescos, and M. Mendioroz Iriarte, “Epigenetic changes in neurology: DNA methylation in multiple sclerosis,” Neurología, 2015. View at Publisher · View at Google Scholar
  65. S. Ruhrmann, P. Stridh, L. Kular, and M. Jagodic, “Genomic imprinting: a missing piece of the multiple sclerosis puzzle?” The International Journal of Biochemistry & Cell Biology, vol. 67, pp. 49–57, 2015. View at Publisher · View at Google Scholar
  66. Z. Zhang and R. Zhang, “Epigenetics in autoimmune diseases: pathogenesis and prospects for therapy,” Autoimmunity Reviews, vol. 14, no. 10, pp. 854–863, 2015. View at Publisher · View at Google Scholar
  67. X. Pedre, F. Mastronardi, W. Bruck, G. López-Rodas, T. Kuhlmann, and P. Casaccia, “Changed histone acetylation patterns in normal-appearing white matter and early multiple sclerosis lesions,” The Journal of Neuroscience, vol. 31, no. 9, pp. 3435–3445, 2011. View at Publisher · View at Google Scholar · View at Scopus
  68. A. Keller, P. Leidinger, J. Lange et al., “Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls,” PLoS ONE, vol. 4, no. 10, Article ID e7440, 2009. View at Publisher · View at Google Scholar · View at Scopus
  69. C. İ. Küçükali, M. Kürtüncü, A. Çoban, M. Çebi, and E. Tüzün, “Epigenetics of multiple sclerosis: an updated review,” NeuroMolecular Medicine, vol. 17, no. 2, pp. 83–96, 2015. View at Publisher · View at Google Scholar · View at Scopus
  70. A. Junker, M. Krumbholz, S. Eisele et al., “MicroRNA profiling of multiple sclerosis lesions identifies modulators of the regulatory protein CD47,” Brain, vol. 132, no. 12, pp. 3342–3352, 2009. View at Publisher · View at Google Scholar · View at Scopus
  71. M. Sospedra and R. Martin, “Immunology of multiple sclerosis,” Annual Review of Immunology, vol. 23, pp. 683–747, 2005. View at Publisher · View at Google Scholar · View at Scopus
  72. T. L. Sørensen, M. Tani, J. Jensen et al., “Expression of specific chemokines and chemokine receptors in the central nervous system of multiple sclerosis patients,” Journal of Clinical Investigation, vol. 103, no. 6, pp. 807–815, 1999. View at Publisher · View at Google Scholar · View at Scopus
  73. R. Gandhi, A. Laroni, and H. L. Weiner, “Role of the innate immune system in the pathogenesis of multiple sclerosis,” Journal of Neuroimmunology, vol. 221, no. 1-2, pp. 7–14, 2010. View at Publisher · View at Google Scholar · View at Scopus
  74. Y. C. Q. Zang, S. Li, V. M. Rivera et al., “Increased CD8+ cytotoxic T cell responses to myelin basic protein in multiple sclerosis,” Journal of Immunology, vol. 172, no. 8, pp. 5120–5127, 2004. View at Publisher · View at Google Scholar · View at Scopus