MALDI imaging and in-source decay for top-down characterization of glioblastoma

Proteomics

Volumn 14, Issue 10, 2014, Pages 1290-1301

  Ait Belkacem, Rima ^a   Berenguer, Caroline ^a   Villard, Claude ^a   Ouafik, L'Houcine ^a,b   Figarella Branger, Dominique ^a,c   Chinot, Olivier ^a,c   Lafitte, Daniel ^a  

^a University of the Mediterranean Aix Marseille II   (France)

^b HÔPITAL NORD   (France)

^c TIMONE HOSPITAL   (France)

Author keywords

Biomarkers; Biomedicine; Glioblastoma multiforme; MALDI imaging MS; MALDI in source decay; Top down

Indexed keywords

BRAIN PROTEIN; CALCYCLIN; GLIAL FIBRILLARY ACIDIC PROTEIN; HEMOGLOBIN ALPHA CHAIN; MYELIN BASIC PROTEIN; THYMOSIN BETA4; MYELIN; MYOSIN; MYOSIN REGULATORY LIGHT CHAIN 12A FRAGMENT; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CANCER GRADING; CANCER PROGNOSIS; CANCER STAGING; CONTROLLED STUDY; FEMALE; GLIOBLASTOMA; HUMAN; HUMAN CELL; MALE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; TISSUE SECTION; TUMOR DIAGNOSIS; TUMOR LOCALIZATION; ANIMAL CELL; BLEEDING; BRAIN REGION; BRAIN TISSUE; CARCINOGENESIS; HISTOLOGY; MASS SPECTROMETRY; MOLECULAR IMAGING; MOLECULAR PATHOLOGY; PROTEIN STRUCTURE; TUMOR NECROSIS; ANIMAL; BRAIN; BRAIN TUMOR; IMAGE PROCESSING; NUDE MOUSE; PATHOLOGY; PROCEDURES; TUMOR CELL LINE;

ANIMALS; BRAIN; BRAIN NEOPLASMS; CELL LINE, TUMOR; FEMALE; GLIOBLASTOMA; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MALE; MICE; MICE, NUDE; MOLECULAR IMAGING; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84899857309     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300329     Document Type: Article

References (66)

1. Louis, D. N., Ohgaki, H., Wiestler, O. D., Cavenee, W. K. et al., The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol. 2007, 114, 97-109.
2. Dolecek, T. A., Propp, J. M., Stroup, N. E., Kruchko, C., CBTRUS Statistical Report: Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2005-2009. Neuro. Oncol. 2012, 14(suppl. 5).
3. Allen, N. J., Barres, B. A., Neuroscience: glia-more than just brain glue. Nature 2009, 457, 675-677.
4. Liang, S., Shen, G. in: Garami, M. (Ed.), Molecular Targets of CNS Tumors, InTech, Croatia 2011, pp. 325-342.
5. Meyer, M. A., Malignant gliomas in adults. N Engl. J. Med. 2008, 359, 492-507.
6. Brat, D. J., Prayson, R. A., Ryken, T. C., Olson, J. J., Diagnosis of malignant glioma: role of neuropathology. J. Neurooncol. 2008, 89, 287-311.
7. Pan, E., Prados, M. D., in: Kufe, D. W., Pollock, R. E., Weichselbaum, R. R., et al. (Eds), Holland-Frei Cancer Medicine. Decker, Canada 2003, Part VI, Section 23, Chapter 83.
8. Eberlin, L. S., Norton, I., Dill, A. L., Golby, A. J. et al., Classifying human brain tumors by lipid imaging with mass spectrometry. Cancer Res. 2012, 72, 645-654.
9. Van den Bent, M. J., Interobserver variation of the histopathological diagnosis in clinical trials on glioma: a clinician's perspective. Acta Neuropathol. 2010, 120, 297-304.
10. Buchwalow, I., Samoilova, V., Boecker, W., Tiemann, M., Non-specific binding of antibodies in immunohistochemistry: fallacies and facts. Sci. Rep. 2011, 1, 28.
11. Kalinina, J., Peng, J., Ritchie, J. C., Van Meir, E. G., Proteomics of gliomas: initial biomarker discovery and evolution of technology. Neurooncology 2011, 13, 926-942.
12. Nutt, C. L., Betensky, R. A., Brower, M. A., Batchelor, T. T. et al., YKL-40 is a differential diagnostic marker for histologic subtypes of high-grade gliomas. Clin. Cancer Res. 2005, 11, 2258-2264.
13. Pelloski, C. E., Mahajan, A., Maor, M., Chang, E. L. et al., YKL-40 expression is associated with poorer response to radiation and shorter overall survival in glioblastoma. Clin. Cancer Res. 2005, 11, 3326-3334.
14. Hegi, M. E., Diserens, A.-C., Gorlia, T., Hamou, M.-F. et al., MGMT gene silencing and benefit from temozolomide in glioblastoma. N. Engl. J. Med. 2005, 352, 997-1003.
15. Figarella-Branger, D., Bouvier, C., de Paula, A. M. et al., Molecular genetics of adult grade II gliomas: towards a comprehensive tumor classification system. J. Neurooncol. 2012, 110, 205-213.
16. Theeler, B. J., Yung, W. K. A., Fuller, G. N., De Groot, J. F., Moving toward molecular classification of diffuse gliomas in adults. Neurology 2012, 79, 1917-1926.
17. Maier, S. K., Hahne, H., Moghaddas Gholami, A., Balluff, B. et al., Comprehensive identification of proteins from MALDI imaging. Mol Cell. Proteomics 2013, 12, 2901-2910.
18. Bouchal, P., Dvorakova, M., Scherl, A., Garbis, S. D. et al., Intact protein profiling in breast cancer biomarker discovery: protein identification issue and the solutions based on 3D protein separation, bottom-up and top-down mass spectrometry. Proteomics 2013, 13, 1053-1058.
19. Bonnel, D., Longuespee, R., Franck, J., Roudbaraki, M. et al., Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: application to prostate cancer. Anal. Bioanal. Chem. 2011, 401, 149-165.
20. Switzar, L., Giera, M., Niessen, W. M. A., Protein digestion: an overview of the available techniques and recent developments. J. Proteome Res. 2013, 12, 1067-1077.
21. Lobas, A. A., Verenchikov, A. N., Goloborodko, A. A., Levitsky, L. I., Gorshkov, M. V, Combination of Edman degradation of peptides with liquid chromatography/mass spectrometry workflow for peptide identification in bottom-up proteomics. Rapid Commun. Mass Spectrom. 2013, 27, 391-400.
22. Couto, N., Barber, J., Gaskell, S. J., Matrix-assisted laser desorption/ionisation mass spectrometric response factors of peptides generated using different proteolytic enzymes. J. Mass Spectrom. 2011, 46, 1233-1240.
23. Franck, J., Ayed, M. El, Wisztorski, M., Salzet, M., Fournier, I., on tissue protein identification improvement by N-terminal peptide derivatization. Methods Mol. Biol. 2010, 656, 323-338.
24. Schey, K. L., Anderson, D. M., Rose, K. L., Spatially-directed protein identification from tissue sections by top-down LC-MS/MS with electron transfer dissociation. Anal. Chem. 2013, 85, 6767-6774.
25. Calligaris, D., Villard, C., Lafitte, D., Advances in top-down proteomics for disease biomarker discovery. J. Proteomics 2011, 74, 920-934.
26. Debois, D., Smargiasso, N., Demeure, K., Asakawa, D. et al., MALDI in-source decay, from sequencing to imaging. Top. Curr. Chem. 2013, 331, 117-141.
27. Ait-Belkacem, R., Calligaris, D., Sellami, L., Villard, C. et al., Tubulin isoforms identified in the brain by MALDI in-source decay. J. Proteomics 2013, 79, 172-179.
28. Ait-Belkacem, R., Sellami, L., Villard, C., DePauw, E. et al., Mass spectrometry imaging is moving toward drug protein co-localization. Trends Biotechnol. 2012, 30, 466-474.
29. Enthaler, B., Pruns, J. K., Wessel, S., Rapp, C. et al., Improved sample preparation for MALDI-MSI of endogenous compounds in skin tissue sections and mapping of exogenous active compounds subsequent to ex-vivo skin penetration. Anal. Bioanal. Chem. 2012, 402, 1159-1167.
30. Seeley, E. H., Caprioli, R. M., Molecular imaging of proteins in tissues by mass spectrometry. Proc. Natl. Acad. Sci. USA 2008, 105, 18126-18131.
31. Trim, P. J., Francese, S., Clench, M. R., Imaging mass spectrometry for the assessment of drugs and metabolites in tissue. Bioanalysis 2009, 1, 309-319.
32. Zaima, N., Hayasaka, T., Goto-Inoue, N., Setou, M., Imaging of metabolites by MALDI mass spectrometry. J. Oleo Sci. 2009, 58, 415-419.
33. Lagarrigue, M., Becker, M., Lavigne, R., Deininger, S.-O. et al., Revisiting rat spermatogenesis with MALDI imaging at 20-microm resolution. Mol. Cell. Proteomics 2011, 10, M110.005991.
34. Chaurand, P., Fouchécourt, S., DaGue, B. B., Xu, B. J. et al., Profiling and imaging proteins in the mouse epididymis by imaging mass spectrometry. Proteomics 2003, 3, 2221-2239.
35. Chaurand, P., Caprioli, R. M., Direct profiling and imaging of peptides and proteins from mammalian cells and tissue sections by mass spectrometry. Electrophoresis 2002, 23, 3125-3135.
36. Hsieh, Y., Chen, J., Korfmacher, W. A., Mapping pharmaceuticals in tissues using MALDI imaging mass spectrometry. J. Pharmacol. Toxicol. Methods n.d., 2007, 55, 193-200.
37. Reyzer, M. L., Chaurand, P., Angel, P. M., Caprioli, R. M., Direct molecular analysis of whole-body animal tissue sections by MALDI imaging mass spectrometry. Methods Mol. Biol. 2010, 656, 285-301.
38. Stoeckli, M., Staab, D., Schweitzer, A., Gardiner, J., Seebach, D., Imaging of a beta-peptide distribution in whole-body mice sections by MALDI mass spectrometry. J. Am. Soc. Mass Spectrom. 2007, 18, 1921-1924.
39. Nilsson, A., Fehniger, T. E., Gustavsson, L., Andersson, M. et al., Fine mapping the spatial distribution and concentration of unlabeled drugs within tissue micro-compartments using imaging mass spectrometry. PloS ONE 2010, 5, e11411.
40. Yang, J., Caprioli, R. M., Matrix sublimation/recrystallization for imaging proteins by mass spectrometry at high spatial resolution. Anal. Chem. 2011, 83, 5728-5734.
41. Paxinos, G., Franklin, K. B. J., The mouse brain in stereotaxic coordinates, 4th Edn, Elsevier Academic Press, USA 2012.
42. Meier, S., Bräuer, A. U., Heimrich, B., Nitsch, R., Savaskan, N. E., Myelination in the hippocampus during development and following lesion. Cell. Mol. Life Sci. 2004, 61, 1082-1094.
43. Collet, B., Guitton, N., Saïkali, S., Avril, T. et al., Differential analysis of glioblastoma multiforme proteome by a 2D-DIGE approach. Proteome Sci. 2011, 9, 16.
44. Khalil, A. A., James, P., Biomarker discovery: a proteomic approach for brain cancer profiling. Cancer Sci. 2007, 98, 201-213.
45. Vogel, T. W., Zhuang, Z., Li, J., Okamoto, H. et al., Proteins and protein pattern differences between glioma cell lines and glioblastoma multiforme. Clin. Cancer Res. 2005, 11, 3624-3632.
46. Grzendowski, M., Wolter, M., Riemenschneider, M. J., Knobbe, C. B. et al., Differential proteome analysis of human gliomas stratified for loss of heterozygosity on chromosomal arms 1p and 19q. Neurooncology 2010, 12, 243-256.
47. Chaurand, P., Schwartz, S. A., Reyzer, M. L., Caprioli, R. M., Imaging mass spectrometry: principles and potentials. Toxicol. Pathol. 2005, 33, 92-101.
48. Schwartz, S. A., Weil, R. J., Thompson, R. C., Shyr, Y. et al., Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry. Cancer Res. 2005, 65, 7674-7681.
49. El Ayed, M., Bonnel, D., Longuespée, R., Castelier, C. et al., MALDI imaging mass spectrometry in ovarian cancer for tracking, identifying, and validating biomarkers. Med. Sci. Monit. 2010, 16, BR233-BR245.
50. Stauber, J., MacAleese, L., Franck, J., Claude, E. et al., On-tissue protein identification and imaging by MALDI-ion mobility mass spectrometry. J. Am. Soc. Mass Spectrom. 2010, 21, 338-347.
51. Lemaire, R., Desmons, A., Tabet, J. C., Day, R. et al., Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections. J. Proteome Res. 2007, 6, 1295-1305.
52. Debois, D., Bertrand, V., Quinton, L., De Pauw-Gillet, M.-C., De Pauw, E., MALDI-in source decay applied to mass spectrometry imaging: a new tool for protein identification. Anal. Chem. 2010, 82, 4036-4045.
53. Calligaris, D., Villard, C., Terras, L., Braguer, D. et al., MALDI in-source decay of high mass protein isoforms: application to alpha- and beta-tubulin variants. Anal. Chem. 2010, 82, 6176-6184.
54. McLendon, R. E., Rich, J. N., Glioblastoma stem cells: a neuropathologist's view. J. Oncol. 2011, 2011, 397195.
55. Miller, C. R., Perry, A., Glioblastoma. Arch. Pathol. Lab. Med. 2007, 131, 397-406.
56. Demeure, K., Gabelica, V., De Pauw, E. A., New advances in the understanding of the in-source decay fragmentation of peptides in MALDI-TOF-MS. J. Am. Soc. Mass Spectrom. 2010, 21, 1906-1917.
57. Gunnersen, J. M., Spirkoska, V., Smith, P. E., Danks, R. A., Tan, S. S., Growth and migration markers of rat C6 glioma cells identified by serial analysis of gene expression. Glia 2000, 32, 146-154.
58. Xiong, Y., Zhang, Y., Mahmood, A., Meng, Y. et al., Neuroprotective and neurorestorative effects of thymosin β4 treatment initiated 6 hours after traumatic brain injury in rats. J. Neurosurg. 2012, 116, 1081-1092.
59. Camby, I., Nagy, N., Lopes, M. B., Schäfer, B. W. et al., Supratentorial pilocytic astrocytomas, astrocytomas, anaplastic astrocytomas and glioblastomas are characterized by a differential expression of S100 proteins. Brain Pathol. 1999, 9, 1-19.
60. Restrepo, A., Smith, C. A., Agnihotri, S., Shekarforoush, M. et al., Epigenetic regulation of glial fibrillary acidic protein by DNA methylation in human malignant gliomas. Neurooncology 2011, 13, 42-50.
61. Jung, C. S., Foerch, C., Schänzer, A., Heck, A. et al., Serum GFAP is a diagnostic marker for glioblastoma multiforme. Brain J. Neurol. 2007, 130, 3336-3341.
62. Beadle, C., Assanah, M. C., Monzo, P., Vallee, R. et al., The role of myosin II in glioma invasion of the brain. Mol. Biol. Cell 2008, 19, 3357-3368.
63. Lunsford, L. D., Martinez, A. J., Latchaw, R. E., Magnetic resonance imaging does not define tumor boundaries. Acta Radiol. Suppl. 1986, 369, 154-156.
64. Lilja, A., Bergström, K., Spännare, B., Olsson, Y., Reliability of computed tomography in assessing histopathological features of malignant supratentorial gliomas. J. Comput. Assist. Tomogr. 1981, 5, 625-636.
65. Eberlin, L. S., Norton, I., Orringer, D., Dunn, I. F. et al., Ambient mass spectrometry for the intraoperative molecular diagnosis of human brain tumors. Proc. Natl. Acad. Sci. USA 2013, 110, 1611-1616.
66. Thiery-Lavenant, G., Zavalin, A. I., Caprioli, R. M., Targeted multiplex imaging mass spectrometry in transmission geometry for subcellular spatial resolution. J. Am. Soc. Mass Spectrom. 2013, 24, 609-614.