Toponomics and neurotoponomics: A new way to medical systems biology

Expert Review of Proteomics

Volumn 5, Issue 2, 2008, Pages 361-369

  Schubert, Walter ^a   Bode, Marcus ^a   Hillert, Reyk ^a   Krusche, Andreas ^a   Friedenberger, Manuela ^a  

^a OTTO VON GUERICKE UNIVERSITY   (Germany)

Author keywords

CNS; Hippocampus; Medical systems biology; MELC; Spinal cord; Synapses; Synaptic toponome; TIS; Toponome

Indexed keywords

EPITOPE;

CELL FUNCTION; CELL POLARITY; COMPUTER PROGRAM; DYNAMICS; FLUORESCENCE; GENOMICS; HIPPOCAMPUS; HUMAN; IMAGING; MEDICAL TECHNOLOGY; NONHUMAN; PROTEIN DEGRADATION; PROTEOMICS; REVIEW; ROBOTICS; SPINAL CORD; SYNAPSE; SYSTEMS BIOLOGY;

ANIMALS; HUMANS; NERVE TISSUE PROTEINS; ORGANELLES; PROTEOMICS; SYSTEMS BIOLOGY;

EID: 43449120439     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.5.2.361     Document Type: Review

References (44)

1. Schubert W. Cytomics in characterizing toponomes: towards the biological code of the cell. Cytometry A 69, 209-211 (2006).
2. Schubert W. Breaking the biological code. Cytometry A 71, 771-772 (2007).
3. Schubert W. Topological proteomics, Toponomics, MELK Technology. Adv. Biochem. Eng. Biotechnol. 83, 189-209 (2003).
4. Schubert W, Bonnekoh B, Pommer AJ et al. Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nat. Biotechnol. 24, 1270-1278 (2006). •• Describes toponome technology comprehensively and gives several biologically and medically relevant examples for its use, including 3D toponome images of synaptic protein networks.
5. Friedenberger M, Bode M, Krusche A, Schubert W. Fluorescence detection of protein clusters in individual cells and tissue sections by using toponome imaging system: sample preparation and measuring procedures. Nat. Protoc. 2, 2285-2294 (2007). • Gives detailed protocols essential for protein cluster detection by toponomics.
6. Murphy RF. Putting proteins on a map. Nat. Biotechnol. 24, 1223-1224 (2006). • Outlines the importance of systems biology approaches to understanding protein function, with special reference to toponomics.
7. Zipf GK. Human Behavior and the Principle of Least Effort. Addison-Wesley, Cambridge, MS, USA (1949).
8. Schubert W. Multiple antigen - mapping microscopy of human tissue. In: Advances in Analytical Cellular Pathology. Burger G, Oberholzer M, Vooijs GP (Eds). Elsevier, Amsterdam 97-98 (1990).
9. Schubert W. Antigenic determinants of T Iymphocyte α/β receptor and other leukocyte surface proteins as differential markers of skeletal muscle regeneration: detection of spatially and timely restricted patterns by MAM microscopy. Eur. J. Cell Biol. 58, 395-410 (1992). • First to study vascular cells as a source of myogenic stem cells in human skeletal muscle cells using toponomics.
10. Schubert W. Exploring molecular networks directly in the cell. Cytometry A 69, 109-112 (2006).
11. Schubert W. A three symbol code for organized proteomes based on cyclical imaging of protein locations. Cytometry A 71, 352-360 (2007).
12. Ecker RC, Rogojanu B, Streit M, Osterreicher K, Steiner GE. An improved method for discrimination of cell populations in tissue sections using microscopy-based multicolcor tissue cytometry. Cytometry A 69(3), 119-123 (2006).
13. Ecker RC, Tarnok A. Cytomics goes 3D: toward tissomics. Cytometry A 65(1), 1-3 (2005).
14. Mittag A, Lenz D, Gerstner AO, Tarnok A. Hyperchromatic cytometry principles for cytomics using slide based cytometry. Cytometry A 69(7), 691-703 (2006).
15. Laffers W, Mittag A, Lenz D, Tarnok A, Gerstner AO. Iterative restaining as a privotal tool for n-color immunophenotyping by slide-based cytometry. Cytometry A 69(3), 127-130 (2006). • Demonstration that restaining is feasible for immnunophenotyping.
16. Bedner E, Du L, Traganos F, Darzynkiewicz Z. Caffeine dissociates complexes between DNA and intercalating dyes: application for bleaching fluorochrome-stained cells for their subsequent restaining and analysis by laser scanning cytometry. Cytometry 43(1), 38 (2001).
17. De Angelis L, Berghella L, Coletta M et al. Skeletal muscle progenitors originating from embryonic dorsal aorta coexpress endothelial and myogenic markers and contribute to postnatal muscle growth and regeneration. J. Cell Biol. 147, 869-878 (1999).
18. Zheng B, Cao B, Crisan M et al. Prospective identification of myogenic endothelial cells in human skeletal muscle. Nat. Biotechnol. 25, 1025-1034 (2007). • Demonstrates that myogenic endothelial cells of the type detected in [9] by toponomics effectively regenerate muscle tissue in an animal model.
19. Sampaolesi M Blot S, D'Antona G, Granger N et al. Mesangioblast stem cells ameliorate muscle function in dystrophic dogs. Nature 444, 552-553 (2006).
20. + stem cells in Duchenne patients. Cell Transplant. 16, 563-577 (2007).
21. Conrad C, Boyman O, Tonel G et al. α1β1 integrin is crucial for accumulation of epidermal T cells and the development of psoriasis. Nat. Med. 13, 836-842 (2007).
22. Nattkemper T, Ritter H, Schubert W. A neural classifyer enabling high-throughput topological analysis of Iymphocytes in tissue sections. IEEE Trans. Inf. Techn. Biomed. 5, 138-149 (2001).
23. Nattkemper TW, Twellmann T, Schubert W, Ritter H. Human vs. machine: evaluation of fluorescence micrographs. Comput. Biol. Med. 33, 31-43 (2003).
24. Dress A, Lokot T, Pustyl'nikov LD, Schubert W. Poisson numbers and poisson distributions in subset surprisology. Ann. Combinatorics 8, 473-485 (2004).
25. Schubert W, Friedenberger M, Haars R, Nattkemper T, Ritter H. Automatic recognition of muscle invasive T cells expressing dipeptidyl-peptidase IV (CD26), and analysis of the associated cell surface phenotypes. J. Theoret. Med. 4, 67-74 (2002).
26. Dress A, Lokot T, Schubert W, Serocka P. Two theorems about similarity maps. Ann. Combinatorics. (2008) (In Press).
27. Schubert W. Method of blocking cytotoxic activity in patients with amyotrophic lateral sclerosis using antibodies to FcγRIII. US patent No. 6,638,506 (first published as international patent application WO 99/29731) (1999).
28. Mohamed HA, Mosier DR, Zou LL et al. Immunoglobulin Fcgamma receptor promotes immunoglobulin uptake, immunoglobulin-mediated calcium release, and neurotransmitter release in motor neurons. J. Neurosci. Res. 69, 110-116 (2002).
29. Schubert W, Masters CL, Beyreuther K. APP+ T Iymphocytes selectively sorted to endomysial tubes in polymyositis displace NCAM-expressing muscle fibers. Eur. J. Cell Biol. 62, 333-342 (1992).
30. Haars R, Schneider A, Bode M, Schubert W. Secretion and differential localization of the proteolytic cleavage products Aβ40 and Aβ42 of the Alzheimer amyloid precursor protein in human fetal myogenic cells. Eur. J. Cell Biol. 79, 400-406 (2000).
31. Schubert W. Polymositis, topological proteomics technology and paradigm for cell invasion dynamics. J. Theoret. Med. 4, 67-74 (2002).
32. + cells analogous to intestinal intraepithelial Iymphocytes infiltrate the pancreas in chronic pancreatitis. Clin. Exp. Immunol. 112, 21-26 (1998).
33. + cells by multi-epitope imaging. Am. J. Gastroenterol. 11, 2141-2147 (1998).
34. Schubert W, Zimmermann K, Cramer K, Starzinski-Powitz A. Lymphocyte antigen Leul9 as a molecular marker of regeneration in human skeletal muscle. Proc. Natl Acad. Sci. USA 86, 307-311 (1989).
35. Blitzer RD, Iyengar R, Landau EM. Postsynaptic signaling networks: cellular crogwheels underlying long-term plasticity. Biol. Psychiatry 57, 113-119 (2005).
36. Malenka RC, Nicoll RA. Long-term potentiation - a decade of progress ? Science 285, 1870-1874 (1999).
37. Lismann J. Long-term potentiation: outstanding questions and attempted synthesis. Philos. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 358, 829-842 (2003).
38. Greengard P. The neurobiology of slow synaptic transmission. Science 294, 1024-1030 (2001).
39. Kandal ER. The molecular biology of memory storage: a dialogue between genes and synapses. Science 294, 1030-1038 (2001).
40. Bennett GJ, Yie YK. A peripheral mononeuropathy in rat that produces disorders of pain sensation like those seen in man. Pain 33, 87-107 (1988).
41. Garry EM, Moss A, Delaney A et al. Neuropathic sensitisation of behavioral reflexes and spinal NMDA receptor/CaM kinase II interactions are disrupted in PSD-95 mutant mice. Curr. Biol. 13, 321-328 (2003).
42. Bode M, Irmler M, Friedenberger. M, et al. Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in murine hippocampus. Proteomics 8(6), 1170-1178 (2008).
43. Bode M, Krusche A. Toponome Imaging System (TIS): imaging the proteome with functional resolution. Application note. Nat. Methods 4, iii-iv (2007).
44. ToposNomos Ltd: an innovative provider and consultant partner for applications of toponomics in the life sciences www.toposnomos.com