Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease

Genome Medicine

Volumn 6, Issue 12, 2014, Pages

  Malhotra, Ashutosh ^a,b   Younesi, Erfan ^a   Bagewadi, Shweta ^a,b   Hofmann Apitius, Martin ^a,b  

^a FRAUNHOFER INSTITUTE FOR ALGORITHMS AND SCIENTIFIC COMPUTING SCAI   (Germany)

^b UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALZHEIMER DISEASE; ARTICLE; ATTITUDE TO ILLNESS; CHOLESTEROL METABOLISM; CHOLINERGIC NERVE CELL; DISEASE COURSE; DISEASE MARKER; GENE EXPRESSION; GENE EXPRESSION REGULATION; HUMAN; INFORMATION RETRIEVAL; MOLECULAR INTERACTION; NONHUMAN; PATHOPHYSIOLOGY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION;

EID: 84927948818     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-014-0097-z     Document Type: Article

References (41)

1. Hampel H, Prvilovic D, Teipel S, Jessen F, Luckhaus C, Frolich L, Riepe MW, Dodel R, Leyhe L, Bertam L, Hoffmann W, Faltraco F. The future of Alzheimer's disease: the next 10 years. Prog Neurobiol 2011, 95:718-728. 10.1016/j.pneurobio.2011.11.008, 22137045.
2. Blennow K, Hampel H, Weiner M, Zetterberg H. Cerebrospinal fluid and plasma biomarkers in Alzheimer disease. Nat Rev Neurol 2010, 6:131-144. 10.1038/nrneurol.2010.4, 20157306.
3. The Alzheimer association.., http://www.alz.org/research/science/earlier_alzheimers_diagnosis.asp
4. Hampel H, Frank R, Broich K, Teipel S, Katz RG, Hardy J, Herholz K, Bokde AL, Jessen F, Hoessler YC, Sanhai WR, Zetterberg H, Woodcock J, Blennow K. Biomarkers for Alzheimer's disease: academic, industry and regulatory perspectives. Nat Rev Drug Discov 2010, 9:560-574. 10.1038/nrd3115, 20592748.
5. Lehmann S, Delaby C, Touchon J, Hirtz C, Gabelle A. Biomarkers of Alzheimer's disease: The present and the future. Rev Neurol 2013, 169:719-723. 10.1016/j.neurol.2013.07.012, 24021316.
6. Moghekar A, Goh J, Li J, Albert M, O'Brien RJ. Cerebrospinal fluid Aβ and tau level fluctuation in an older clinical cohort. Arch Neurol 2012, 69:246-250. 10.1001/archneurol.2011.732, 22332192.
7. Herrup K, Varrilo MC, Schenk D, Cacace A, DeSanti S, Fremeau R, Bhat R, Glicksman M, May P, Swerdlow R, Van Eldik L, Bain LJ, Budd S. Beyond amyloid: Getting real about nonamyloid targets in Alzheimer's disease. Alzheimers Dement 2013, 9:452-458. 10.1016/j.jalz.2013.01.017, 23809366.
8. Greco I, Day N, Contreras JR, Reed J, Soininen H, Kloszewska I, Tsolaki M, Vellas B, Spenger C, Mecocci P, Wahlund L, Simmons A, Barnes J, Lovestone S. Alzheimer's disease biomarker discovery using in silico literature mining and clinical validation. J Transl Med 2012, 10:217. 10.1186/1479-5876-10-217, 23113945.
9. Malhotra A, Younesi E, Gurulingappa H, Hofmann-Apitius M. 'HypothesisFinder':A strategy for the detection of speculative statements in scientific text. PLoS Comput Biol 2013, 9:e1003117. 10.1371/journal.pcbi.1003117, 23935466.
10. Younesi E, Hofmann-Apitius M. From integrative disease modeling to predictive, preventive, personalized and participatory (P4) medicine. EPMA J 2013, 4:23. 10.1186/1878-5085-4-23, 24195840.
11. Malhotra A, Younesi E, Gündel M, Müller B, Heneka MT, Hofmann-Apitius M. ADO: A disease ontology representing the domain knowledge specific to Alzheimer's disease. Alzheimers Dement 2014, 10:238-246. 10.1016/j.jalz.2013.02.009, 23830913.
12. SCAIView tool. []., www.scaiview.com
13. Hofmann-Apitius M, Fluck J, Furlong L, Fornes O, Kolářik C, Hanser S, Boecker M, Schultz S, Sanz F, Klinger R, Mevissen T, Gatterneyer T, Oliva B, Friedrich C. Knowledge environments representing molecular entities for the virtual physiological human. Philos Transact A Math Phys Eng Sci 2008, 366:3091-3110. 10.1098/rsta.2008.0099.
14. Gurulingappa H, Müller B, Klinger R, Mevissen T, Hofmann-Apitius M, Fluck J, Friedrich C. Patent Retrieval in Chemistry based on semantically tagged Named Entities. The Eighteenth Text RETrieval Conference (TREC 2009) Proceedings 2009, National Institute of Standards and Technology, Gaithersburg, MD.
15. Gurulingappa H, Mueller B, Hofmann-Apitius M, Fluck J. A Semantic Platform for Information Retrieval for E-Health Records. Notebook Proceeding of Twentieth Text Retrieval Conference Medical Records Track, Gaithersburg, USA 2011, National Institute of Standards and Technology, Gaithersburg, MD.
16. Younesi E, Toldo L, Müller B, Friedrich CM, Novac N, Scheer A, Fluck J. Mining biomarker information in biomedical literature. BMC Med Inform Decis Mak 2012, 12:148. 10.1186/1472-6947-12-148, 23249606.
17. Bobić T, Klinger R, Thomas P, Hofmann-Apitius M. Improving Distantly Supervised Extraction of Drug-Drug and Protein-Protein Interactions. Proceedings of the Joint Workshop on Unsupervised and Semi-Supervised Learning in NLP 2012, 35-43. Association for Computational Linguistics, Avignon.
18. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 10.1101/gr.1239303, 14597658.
19. Mouse genome database. []., http://www.informatics.jax.org
20. Biological expression language. []., http://www.openbel.org/
21. Cytoscape tool. []., https://github.com/OpenBEL/Cytoscape-Plugins
22. Gene Expression Omnibus database. []., http://www.ncbi.nlm.nih.gov/geo/
23. Array express database. []., https://www.ebi.ac.uk/arrayexpress/
24. Statistical data language R. []., http://www.r-project.org
25. Irizarry R, Hobbs B, Collin F, Beaze-Barclay Y, Antonellis K, Scherf U, Speed T. Exploration, normalization, and summaries of high density oligoneucleotide array probe level data. Biostatistics 2003, 4:249. 10.1093/biostatistics/4.2.249, 12925520.
26. Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:3.
27. Medline. []., http://www.ncbi.nlm.nih.gov/pubmed
28. SCAI downloads. []., http://www.scai.fraunhofer.de/de/geschaeftsfelder/bioinformatik/downloads.html
29. Fleisher AS, Chen K, Quiroz YT, Jakimovich LJ, Gomez MG, Langois CM, Langbaum J, Ayutyanont N, Roontiva A, Thiyyagura P, Lee W, Mo H, Lopez L, Moreno S, Baena N, Giraldo M, Garcia G, Reiman R, Huentelman M, Kosik K, Tariot P. Florbetapir PET analysis of amyloid-β deposition in the presenilin 1 E280A autosomal dominant Alzheimer's disease kindred: a cross-sectional study. Lancet Neurol 2012, 11:1057-1065. 10.1016/S1474-4422(12)70227-2, 23137949.
30. Sagare AP, Deane R, Zetterberg H, Wallin A, Blennow K, Zlokovic BV. Impaired lipoprotein receptor-mediated peripheral binding of plasma amyloid-β is an early biomarker for mild cognitive impairment preceding Alzheimer's disease. J Alzheimers Dis 2011, 24:25-34. 21157031.
31. Durakoglugil MS, Chen Y, White C, Kavalali ET, Herz J. Reelin signaling antagonizes β-amyloid at the synapse. Proc Natl Acad Sci 2009, 106:15938-15943. 10.1073/pnas.0908176106, 19805234.
32. Tsai VW, Scott HL, Lewis RJ, Dodd PR. The role of group I metabotropic glutamate receptors in neuronal excitotoxicity in Alzheimer's disease. Neurotox Res 2005, 7:125-141. 10.1007/BF03033782, 15639804.
33. Lee J-H, Cheon YH, Woo RD, Song DY, Moon C, Baik TK. Evidence of early involvement of apoptosis inducing factor-induced neuronal death in Alzheimer brain. Anatomy Cell Biol 2012, 45:26-37. 10.5115/acb.2012.45.1.26.
34. Hook V, Funkelstein L, Wegrzyn J, Bark S, Kindy M, Hook G. Cysteine Cathepsins in the secretory vesicle produce active peptides: Cathepsin L generates peptide neurotransmitters and cathepsin B produces beta-amyloid of Alzheimer's disease. Biochimica et Biophysica Acta (BBA)-Proteins Proteomics 2012, 1824:89-104. 10.1016/j.bbapap.2011.08.015.
35. Sundelöf J, Sundstrom J, Hansson O, Jonhagen ME, Giedraitis V, Larsson A, Gunnarsson MD, Ingelsson M, Minthon L, Blennow K, Kilander L, Basun H, Lannfelt L. Higher cathepsin B levels in plasma in Alzheimer's disease compared to healthy controls. J Alzheimers Dis 2010, 22:1223-1230. 20930303.
36. Klein DM, Felsenstein KM, Brenneman DE. Cathepsins B and L differentially regulate amyloid precursor protein processing. J Pharmacol Exp Ther 2009, 328:813-821. 10.1124/jpet.108.147082, 19064719.
37. Basak JM, Verghese PB, Yoon H, Kim J, Holtzman DM. Low-density lipoprotein receptor represents an apolipoprotein E-independent pathway of Aβ uptake and degradation by astrocytes. J Biol Chem 2012, 287:13959-13971. 10.1074/jbc.M111.288746, 22383525.
38. Pani A, Dessi S, Diaz G, Colla P, Abete C, Mulas C, Angius F, Cannas M, Orru CD, Cocco PL, Mandas A, Putzu P, Laurenzana A, Cellai C, Costanza AM, Bavazzano A, Mocali A, Paoletti F. Altered cholesterol ester cycle in skin fibroblasts from patients with Alzheimer's disease. J Alzheimers Dis 2009, 18:829-841. 19749436.
39. Castellano JM, Deane R, Gottesdiener AJ, Verghese PB, Stewart FR, West T, Paoletti AC, Kasper TR, Demattos RB, Zlokovic BV, Holtzman DM. Low-density lipoprotein receptor overexpression enhances the rate of brain-to-blood Aβ clearance in a mouse model of β-amyloidosis. Proc Natl Acad Sci 2012, 109:15502-15507. 10.1073/pnas.1206446109, 22927427.
40. Abisambra JF, Fiorelli T, Padmanabhan J, Neame P, Wefes I, Potter H. LDLR expression and localization are altered in mouse and human cell culture models of Alzheimer's disease. PLoS One 2010, 5:e8556. 10.1371/journal.pone.0008556, 20049331.
41. Braskie MN, Ringman JM, Thompson PM. Neuroimaging measures as endophenotypes in Alzheimer's disease. Int J Alzheimers Dis 2011, 2011:490140. 10.4061/2011/490140, 21547229.