Application of systems theory in longitudinal studies on the origin and progression of Alzheimer's disease

Systems Biology of Alzheimer's Disease

Volumn , Issue , 2015, Pages 49-67

  Lista, Simone ^a   Khachaturian, Zaven S ^b   Rujescu, Dan ^a   Garaci, Francesco ^c,d,f   Dubois, Bruno ^e   Hampel, Harald ^e  

^a MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^b Campaign to Prevent Alzheimer's Disease by 2020 (PAD2020)   (United States)

^c UNIVERSITY OF ROME TOR VERGATA   (Italy)

^d IRCCS SAN RAFFAELE PISANA   (Italy)

^e PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

^f Department of Imaging   (Italy)

Author keywords

Biological markers; Early onset Alzheimer's disease; Late onset alzheimer's disease; Lipidomics; Longitudinal studies; Metabolomics; Proteomics; Sporadic alzheimer's disease; Systems biology; Transcriptomics

Indexed keywords

ALZHEIMER DISEASE; DISEASE COURSE; GENETICS; HUMAN; LONGITUDINAL STUDY; METABOLISM; PATHOLOGY; PROCEDURES; PROTEOMICS; SYSTEMS BIOLOGY;

ALZHEIMER DISEASE; DISEASE PROGRESSION; HUMANS; LONGITUDINAL STUDIES; PROTEOMICS; SYSTEMS BIOLOGY;

EID: 84958642042     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4939-2627-5_2     Document Type: Chapter

References (120)

1. Blennow K, de Leon MJ, Zetterberg H (2006) Alzheimer's disease. Lancet 368:387-403.
2. Bertram L, Lill CM, Tanzi RE (2010) The genetics of Alzheimer disease: back to the future. Neuron 68:270-281.
3. Bertram L, Tanzi RE (2012) The genetics of Alzheimer's disease. Prog Mol Biol Transl Sci 107:79-100.
4. Van Deerlin VM, Wood EM, Moore P et al (2007) Clinical, genetic, and pathologic characteristics of patients with frontotemporal dementia and progranulin mutations. Arch Neurol 64:1148-1153.
5. Huey ED, Grafman J, Wassermann EM et al (2006) Characteristics of frontotemporal dementia patients with a Progranulin mutation. Ann Neurol 60:374-380.
6. Perry DC, Lehmann M, Yokoyama JS et al (2013) Progranulin mutations as risk factors for Alzheimer disease. JAMA Neurol 70:774-778.
7. Jin SC, Pastor P, Cooper B et al (2012) Pooled-DNA sequencing identifies novel causative variants in PSEN1, GRN and MAPT in a clinical early-onset and familial Alzheimer's disease Ibero-American cohort. Alzheimers Res Ther 4:34.
8. Kelley BJ, Haidar W, Boeve BF et al (2010) Alzheimer disease-like phenotype associated with the c.154delA mutation in progranulin. Arch Neurol 67:171-177.
9. Finch N, Baker M, Crook R et al (2009) Plasma progranulin levels predict progranulin mutation status in frontotemporal dementia patients and asymptomatic family members. Brain 132:583-591.
10. Brouwers N, Nuytemans K, van der Zee J et al (2007) Alzheimer and Parkinson diagnoses in progranulin null mutation carriers in an extended founder family. Arch Neurol 64:1436-1446.
11. Strittmatter WJ, Saunders AM, Schmechel D et al (1993) Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. Proc Natl Acad Sci U S A 90:1977-1981.
12. Bertram L, McQueen MB, Mullin K et al (2007) Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet 39:17-23.
13. Harold D, Abraham R, Hollingworth P et al (2009) Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nat Genet 41:1088-1093.
14. Lambert JC, Heath S, Even G et al (2009) Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease. Nat Genet 41:1094-1099.
15. Seshadri S, Fitzpatrick AL, Ikram MA et al (2010) Genome-wide analysis of genetic loci associated with Alzheimer disease. JAMA 303:1832-1840.
16. Hollingworth P, Harold D, Sims R et al (2011) Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat Genet 43:429-435.
17. Naj AC, Jun G, Beecham GW et al (2011) Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet 43:436-441.
18. Zetzsche T, Rujescu D, Hardy J et al (2010) Advances and perspectives from genetic research: development of biological markers in Alzheimer's disease. Expert Rev Mol Diagn 10:667-690.
19. Jones L, Holmans PA, Hamshere ML et al (2010) Genetic evidence implicates the immune system and cholesterol metabolism in the etiology of Alzheimer's disease. PLoS One 5:e13950.
20. Lambert JC, Ibrahim-Verbaas CA, Harold D et al (2013) Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat Genet 45:1452-1458.
21. Jonsson T, Stefansson H, Steinberg S et al (2013) Variant of TREM2 associated with the risk of Alzheimer's disease. N Engl J Med 368:107-116.
22. Guerreiro R, Wojtas A, Bras J et al (2013) TREM2 variants in Alzheimer's disease. N Engl J Med 368:117-127.
23. Neumann H, Daly MJ (2013) Variant TREM2 as risk factor for Alzheimer's disease. N Engl J Med 368:182-184.
24. Chinn S (1989) Longitudinal studies: design and analysis. Rev Epidemiol Sante Publique 37:431-441.
25. Gibbons RD (2008) Design and analysis of longitudinal studies. Psychiatr Ann 38:758-761.
26. Liu C, Cripe TP, Kim MO (2010) Statistical issues in longitudinal data analysis for treatment efficacy studies in the biomedical sciences. Mol Ther 18:1724-1730.
27. Hampel H, Lista S (2012) Alzheimer disease:from inherited to sporadic AD-crossing the biomarker bridge. Nat Rev Neurol 8:598-600.
28. Hampel H, Lista S, Khachaturian ZS (2012) Development of biomarkers to chart all Alzheimer's disease stages: the royal road to cutting the therapeutic Gordian Knot. Alzheimers Dement 8:312-336.
29. Hampel H, Lista S (2013) Use of biomarkers and imaging to assess pathophysiology, mechanisms of action and target engagement. J Nutr Health Aging 17:54-63.
30. Rosén C, Hansson O, Blennow K et al (2013) Fluid biomarkers in Alzheimer's disease - current concepts. Mol Neurodegener 8:20.
31. Carrillo MC, Blennow K, Soares H et al (2013) Global standardization measurement of cerebral spinal fluid for Alzheimer's disease:an update from the Alzheimer's Association Global Biomarkers Consortium. Alzheimers Dement 9:137-140.
32. Villemagne VL, Burnham S, Bourgeat P et al (2013) Amyloid β deposition, neurodegeneration, and cognitive decline in sporadic Alzheimer's disease: a prospective cohort study. Lancet Neurol 12:357-367.
33. Bateman RJ, Xiong C, Benzinger TL et al (2012) Clinical and biomarker changes in dominantly inherited Alzheimer's disease. N Engl J Med 367:795-804.
34. Noorbakhsh F, Overall CM, Power C (2009) Deciphering complex mechanisms in neurodegenerative diseases: the advent of systems biology. Trends Neurosci 32:88-100.
35. Tyers M, Mann M (2003) From genomics to proteomics. Nature 422:193-197.
36. Dong Z, Chen Y (2013) Transcriptomics:advances and approaches. Sci China Life Sci 56:960-967.
37. Wang Z, Gerstein M, Snyder M (2009) RNASeq:a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63.
38. Liang WS, Dunckley T, Beach TG et al (2008) Altered neuronal gene expression in brain regions differentially affected by Alzheimer's disease: a reference data set. Physiol Genomics 33:240-256.
39. Tan MG, Chua WT, Esiri MM et al (2010) Genome wide profiling of altered gene expression in the neocortex of Alzheimer's disease. J Neurosci Res 88:1157-1169.
40. Maes OC, Xu S, Yu B et al (2007) Transcriptional profiling of Alzheimer blood mononuclear cells by microarray. Neurobiol Aging 28:1795-1809.
41. Colangelo V, Schurr J, Ball MJ et al (2002) Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: transcription and neurotrophic factor down-regulation and upregulation of apoptotic and proinflammatory signaling. J Neurosci Res 70:462-473.
42. Blalock EM, Geddes JW, Chen KC et al (2004) Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses. Proc Natl Acad Sci U S A 101:2173-2178.
43. Yao PJ, Zhu M, Pyun EI et al (2003) Defects in expression of genes related to synaptic vesicle trafficking in frontal cortex of Alzheimer's disease. Neurobiol Dis 12:97-109.
44. Fehlbaum-Beurdeley P, Jarrige-Le Prado AC, Pallares D et al (2010) Toward an Alzheimer's disease diagnosis via high-resolution blood gene expression. Alzheimers Dement 6:25-38.
45. Chen KD, Chang PT, Ping YH et al (2011) Gene expression profiling of peripheral blood leukocytes identifies and validates ABCB1 as a novel biomarker for Alzheimer's disease. Neurobiol Dis 43:698-705.
46. Booij BB, Lindahl T, Wetterberg P et al (2011) A gene expression pattern in blood for the early detection of Alzheimer's disease. J Alzheimers Dis 23:109-119.
47. Fehlbaum-Beurdeley P, Sol O, Désiré L et al (2012) Validation of AclarusDx™, a bloodbased transcriptomic signature for the diagnosis of Alzheimer's disease. J Alzheimers Dis 32:169-181.
48. Han G, Wang J, Zeng F et al (2013) Characteristic transformation of blood transcriptome in Alzheimer's disease. J Alzheimers Dis 35:373-386.
49. Wasinger VC, Cordwell SJ, Cerpa-Poljak A et al (1995) Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16:1090-1094.
50. Tambor V, Fucíková A, Lenco J et al (2010) Application of proteomics in biomarker discovery:a primer for the clinician. Physiol Res 59:471-497.
51. Thambisetty M, Lovestone S (2010) Bloodbased biomarkers of Alzheimer's disease:challenging but feasible. Biomark Med 4:65-79.
52. Becker M, Schindler J, Nothwang HG (2006) Neuroproteomics - the tasks lying ahead. Electrophoresis 27:2819-2829.
53. Hamacher M, Meyer HE (2005) HUPO Brain Proteome Project: aims and needs in proteomics. Exp Rev Proteomics 2:1-3.
54. Rifai N, Gillette MA, Carr SA et al (2006) Protein biomarker discovery and validation:the long and uncertain path to clinical utility. Nat Biotechnol 24:971-983.
55. Portelius E, Gustavsson MK, Zetterberg H et al (2012) Evaluation of the performance of novel Aβ isoforms as theragnostic markers in Alzheimer's disease: from the cell to the patient. Neurodegener Dis 10:138-140.
56. Portelius E, Price E, Brinkmalm G et al (2011) A novel pathway for amyloid precursor protein processing. Neurobiol Aging 32:1090-1098.
57. Perrin RJ, Craig-Schapiro R, Malone JP et al (2011) Identification and validation of novel cerebrospinal fluid biomarkers for staging early Alzheimer's disease. PLoS One 6:e16032.
58. Craig-Schapiro R, Kuhn M, Xiong C et al (2011) Multiplexed immunoassay panel identifies novel CSF biomarkers for Alzheimer's disease diagnosis and prognosis. PLoS One 6:e18850.
59. Craig-Schapiro R, Perrin RJ, Roe CM et al (2010) YKL-40: a novel prognostic fluid biomarker for preclinical Alzheimer's disease. Biol Psychiatry 68:903-912.
60. Portelius E, Dean RA, Gustavsson MK et al (2010) A novel Abeta isoform pattern in CSF reflects gamma-secretase inhibition in Alzheimer disease. Alzheimers Res Ther 2:7.
61. Albertini V, Bruno A, Paterlini A et al (2010) Optimization protocol for amyloid-β peptides detection in human cerebrospinal fluid using SELDI TOF MS. Proteomics Clin Appl 4:352-357.
62. Portelius E, Brinkmalm G, Tran AJ et al (2009) Identification of novel APP/Abeta isoforms in human cerebrospinal fluid. Neurodegener Dis 6:87-94.
63. Simonsen AH, McGuire J, Podust VN et al (2008) Identification of a novel panel of cerebrospinal fluid biomarkers for Alzheimer's disease. Neurobiol Aging 29:961-968.
64. Simonsen AH, McGuire J, Hansson O et al (2007) Novel panel of cerebrospinal fluid biomarkers for the prediction of progression to Alzheimer dementia in patients with mild cognitive impairment. Arch Neurol 64:366-370.
65. Simonsen AH, McGuire J, Podust VN et al (2007) A novel panel of cerebrospinal fluid biomarkers for the differential diagnosis of Alzheimer's disease versus normal aging and frontotemporal dementia. Dement Geriatr Cogn Disord 24:434-440.
66. Finehout EJ, Franck Z, Choe LH et al (2007) Cerebrospinal fluid proteomic biomarkers for Alzheimer's disease. Ann Neurol 61:120-129.
67. Portelius E, Tran AJ, Andreasson U et al (2007) Characterization of amyloid beta peptides in cerebrospinal fluid by an automated immunoprecipitation procedure followed by mass spectrometry. J Proteome Res 6:4433-4439.
68. Portelius E, Zetterberg H, Andreasson U et al (2006) An Alzheimer's disease-specific beta amyloid fragment signature in cerebrospinal fluid. Neurosci Lett 409:215-219.
69. Portelius E, Westman-Brinkmalm A, Zetterberg H et al (2006) Determination of beta-amyloid peptide signatures in cerebrospinal fluid using immunoprecipitation-mass spectrometry. J Proteome Res 5:1010-1016.
70. Carrette O, Demalte I, Scherl A et al (2003) A panel of cerebrospinal fluid potential biomarkers for the diagnosis of Alzheimer's disease. Proteomics 3:1486-1494.
71. Guo LH, Alexopoulos P, Wagenpfeil S (2013) Plasma proteomics for the identification of Alzheimer disease. Alzheimer Dis Assoc Disord. doi: 10.1097/WAD.0b013e31827b60d2.
72. Doecke JD, Laws SM, Faux NG et al (2012) Blood-based protein biomarkers for diagnosis of Alzheimer disease. Arch Neurol 69:1318-1325.
73. Hu WT, Holtzman DM, Fagan AM et al (2012) Plasma multianalyte profiling in mild cognitive impairment and Alzheimer disease. Neurology 79:897-905.
74. Soares HD, Potter WZ, Pickering E et al (2012) Plasma biomarkers associated with the apolipoprotein E genotype and Alzheimer disease. Arch Neurol 69:1310-1317.
75. Johnstone D, Milward EA, Berretta R et al (2012) Multivariate protein signatures of preclinical Alzheimer's disease in the Alzheimer's disease neuroimaging initiative (ADNI) plasma proteome dataset. PLoS One 7:e34341.
76. O'Bryant SE, Xiao G, Barber R et al (2011) A blood-based algorithm for the detection of Alzheimer's disease. Dement Geriatr Cogn Disord 32:55-62.
77. O'Bryant SE, Xiao G, Barber R et al (2011) A blood-based screening tool for Alzheimer's disease that spans serum and plasma: findings from TARC and ADNI. PLoS One 6:e28092.
78. O'Bryant SE, Xiao G, Barber R et al (2010) A serum protein-based algorithm for the detection of Alzheimer disease. Arch Neurol 67:1077-1081.
79. Ray S, Britschgi M, Herbert C et al (2007) Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins. Nat Med 13:1359-1362.
80. Hye A, Lynham S, Thambisetty M et al (2006) Proteome-based plasma biomarkers for Alzheimer's disease. Brain 129:3042-3050.
81. Henriksen K, O'Bryant SE, Hampel H et al (2013) The future of blood-based biomarkers for Alzheimer's disease. Alzheimers Dement. doi: 10.1016/j.jalz.2013.01.013.
82. Gupta VB, Sundaram R, Martins RN (2013) Multiplex biomarkers in blood. Alzheimers Res Ther 5:31.
83. Lista S, Faltraco F, Prvulovic D et al (2013) Blood and plasma-based proteomic biomarker research in Alzheimer's disease. Prog Neurobiol 101-102:1-17.
84. Blennow K, Hampel H, Weiner M et al (2010) Cerebrospinal fluid and plasma biomarkers in Alzheimer disease. Nat Rev Neurol 6:131-144.
85. Portelius E, Zetterberg H, Gobom J et al (2008) Targeted proteomics in Alzheimer's disease: focus on amyloid-beta. Expert Rev Proteomics 5:225-237.
86. Davidsson P, Sjogren M (2005) The use of proteomics in biomarker discovery in neurodegenerative diseases. Dis Markers 21:81-92.
87. Irizarry MC (2004) Biomarkers of Alzheimer disease in plasma. NeuroRx 1:226-234.
88. Fagan AM, Perrin RJ (2012) Upcoming candidate cerebrospinal fluid biomarkers of Alzheimer's disease. Biomark Med 6:455-476.
89. Kaddurah-Daouk R, Kristal BS, Weinshilboum RM (2008) Metabolomics: a global biochemical approach to drug response and disease. Annu Rev Pharmacol Toxicol 48:653-683.
90. Kristal BS, Kaddurah-Daouk R et al (2007) Metabolomics: concept and potential neuroscience application. In: Lajtha A, Gibson G, Dienel G (eds) Handbook of neurochemistry and molecular neurobiology. Brain energetics. Integration of molecular and cellular processes, 3rd edn. Springer, New York, pp 889-912.
91. Sun J, Beger RD, Schnackenberg LK (2013) Metabolomics as a tool for personalizing medicine: 2012 update. Personal Med 10:149-161.
92. Smith CA, Want EJ, O'Maille G et al (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78:779-787.
93. Baker M (2011) Metabolomics: from small molecules to big ideas. Nat Methods 8:117-121.
94. Trushina E, Dutta T, Persson XM et al (2013) Identification of altered metabolic pathways in plasma and CSF in mild cognitive impairment and Alzheimer's disease using metabolomics. PLoS One 8:e63644.
95. Han X, MHoltzman D, McKeel DW Jr (2002) Substantial sulfatide deficiency and ceramide elevation in very early Alzheimer's disease: potential role in disease pathogenesis. J Neurochem 82:809-818.
96. Kaddurah-Daouk R, Krishnan KR (2009) Metabolomics: a global biochemical approach to the study of central nervous system diseases. Neuropsychopharmacology 34:173-186.
97. Dunn WB, Broadhurst D, Begley P et al (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 6:1060-1083.
98. Cottingham K (2008) HUSERMET researchers look to the metabolome for answers. J Proteome Res 7:4213.
99. Han X (2010) Multi-dimensional mass spectrometry- based shotgun lipidomics and the altered lipids at the mild cognitive impairment stage of Alzheimer's disease. Biochim Biophys Acta 1801:774-783.
100. Kaddurah-Daouk R, Zhu H, Sharma S et al (2013) Alterations in metabolic pathways and networks in Alzheimer's disease. Transl Psychiatry 3:e244.
101. Czech C, Berndt P, Busch K et al (2012) Metabolite profiling of Alzheimer's disease cerebrospinal fluid. PLoS One 7:e31501.
102. Kaddurah-Daouk R, Rozen S, Matson W et al (2011) Metabolomic changes in autopsyconfirmed Alzheimer's disease. Alzheimers Dement 7:309-317.
103. Sato Y, Suzuki I, Nakamura T et al (2012) Identification of a new plasma biomarker of Alzheimer's disease using metabolomics technology. J Lipid Res 53:567-576.
104. Orešič M, Hyötyläinen T, Herukka SK et al (2011) Metabolome in progression to Alzheimer's disease. Transl Psychiatry 1:e57.
105. Han X, Rozen S, Boyle SH et al (2011) Metabolomics in early Alzheimer's disease:identification of altered plasma sphingolipidome using shotgun lipidomics. PLoS One 6:e21643.
106. Wenk MR (2010) Lipidomics: new tools and applications. Cell 143:888-895.
107. Astarita G, Piomelli D (2011) Towards a whole-body systems [multi-organ] lipidomics in Alzheimer's disease. Prostaglandins Leukot Essent Fatty Acids 85:197-203.
108. Niemelä PS, Ollila S, Hyvönen MT et al (2007) Assessing the nature of lipid raft membranes. PLoS Comput Biol 3:e34.
109. Yetukuri L, Söderlund S, Koivuniemi A et al (2010) Composition and lipid spatial distribution of HDL particles in subjects with low and high HDL-cholesterol. J Lipid Res 51:2341-2351.
110. Kitano H (2002) Systems biology: a brief overview. Science 295:1662-1664.
111. Horvath S, Dong J (2008) Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol 4:e1000117.
112. Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559.
113. Langfelder P, Horvath S (2007) Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol 1:54.
114. Miller JA, Oldham MC, Geschwind DH (2008) A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci 28:1410-1420.
115. Miller JA, Horvath S, Geschwind DH (2010) Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A 107:12698-12703.
116. Kann MG (2007) Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform 8:333-346.
117. Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5:101-115.
118. Hallock P, Thomas MA (2012) Integrating the Alzheimer's disease proteome and transcriptome:a comprehensive network model of a complex disease. OMICS 16:37-49.
119. Prasad TSK, Goel R, Kandasamy K et al (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37:D767-D772.
120. Orešič M, Lötjönen J, Soininen H (2010) Systems medicine and the integration of bioinformatic tools for the diagnosis of Alzheimer's disease. Genome Med 2:83.