Imaging mass spectrometry in biomarker discovery and validation

Journal of Proteomics

Volumn 75, Issue 16, 2012, Pages 4990-4998

  Schwamborn, Kristina ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Biomarker; Imaging; Mass spectrometry

Indexed keywords

BIOLOGICAL MARKER; CYSTEINE RICH INTESTINAL PROTEIN 1; CYTOCHROME C; DEFENSIN 1; DIAZEPAM BINDING INHIBITOR; HISTONE H2B; HISTONE H3; HISTONE H4; MACROPHAGE MIGRATION INHIBITION FACTOR; PHOSPHOPROTEIN; PROTEIN; THYMOSIN BETA10; THYMOSIN BETA4; UBIQUITIN; UNCLASSIFIED DRUG;

BIOINFORMATICS; CANCER DIAGNOSIS; CANCER INVASION; CANCER PROGNOSIS; CANCER RECURRENCE; CANCER RELAPSE; CANCER STAGING; CANCER SURVIVAL; CANCER TISSUE; DISEASE COURSE; FALSE POSITIVE RESULT; GASTROSCOPY; GENETIC ALGORITHM; HIGH RISK POPULATION; HISTOLOGY; HUMAN; IMMUNOHISTOCHEMISTRY; LASER CAPTURE MICRODISSECTION; LIQUID CHROMATOGRAPHY; LUNG CANCER; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MEDICAL RESEARCH; MELANOMA; METASTASIS; OVARY CANCER; PERSONALIZED MEDICINE; PRIORITY JOURNAL; PROSTATE CANCER; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEOMICS; REPRODUCIBILITY; REVIEW; SENSITIVITY AND SPECIFICITY; STOMACH CANCER; TREATMENT RESPONSE; VALIDATION PROCESS; WESTERN BLOTTING;

ANIMALS; BIOLOGICAL MARKERS; DIAGNOSTIC IMAGING; GENETIC ASSOCIATION STUDIES; HISTOLOGICAL TECHNIQUES; HUMANS; MASS SPECTROMETRY; MODELS, BIOLOGICAL; PROTEOMICS; VALIDATION STUDIES AS TOPIC;

EID: 84865168916     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.06.015     Document Type: Review

References (78)

1. Hanash S. Disease proteomics. Nature 2003, 422:226-232.
2. Celis J.E., Gromov P. Proteomics in translational cancer research: toward an integrated approach. Cancer Cell 2003, 3:9-15.
3. Petricoin E.F., Liotta L.A. Proteomic approaches in cancer risk and response assessment. Trends Mol Med 2004, 10:59-64.
4. Ludwig J.A., Weinstein J.N. Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 2005, 5:845-856.
5. Banks R.E., Dunn M.J., Hochstrasser D.F., Sanchez J.C., Blackstock W., Pappin D.J., et al. Proteomics: new perspectives, new biomedical opportunities. Lancet 2000, 356:1749-1756.
6. Pastwa E., Somiari S.B., Czyz M., Somiari R.I. Proteomics in human cancer research. Proteomics Clin Appl 2007, 1:4-17.
7. Chen G., Gharib T.G., Huang C.-C., Thomas D.G., Shedden K.A., Taylor J.M.G., et al. Proteomic analysis of lung adenocarcinoma. Clin Cancer Res 2002, 8:2298-2305.
8. Anderson L., Seilhamer J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 1997, 18:533-537.
9. Domon B., Aebersold R. Mass spectrometry and protein analysis. Science 2006, 312:212-217.
10. Anderson N.L. The roles of multiple proteomic platforms in a pipeline for new diagnostics. Mol Cell Proteomics 2005, 4:1441-1444.
11. Kulasingam V., Pavlou M.P., Diamandis E.P. Integrating high-throughput technologies in the quest for effective biomarkers for ovarian cancer. Nat Rev Cancer 2010, 10:371-378.
12. Issaq H.J., Waybright T.J., Veenstra T.D. Cancer biomarker discovery: opportunities and pitfalls in analytical methods. Electrophoresis 2011, 32:967-975.
13. Yang J., Caprioli R.M. Matrix sublimation/recrystallization for imaging proteins by mass spectrometry at high spatial resolution. Anal Chem 2011, 83:5728-5734.
14. Angel P.M., Spraggins J.M., Baldwin H.S., Caprioli R. Enhanced sensitivity for high spatial resolution lipid analysis by negative ion mode matrix assisted laser desorption ionization imaging mass spectrometry. Anal Chem 2012, 84:1557-1564.
15. Chaurand P., Cornett D.S., Angel P.M., Caprioli R.M. From whole-body sections down to cellular level, multiscale imaging of phospholipids by MALDI mass spectrometry. Mol Cell Proteomics 2011, 10. O110 004259.
16. Caprioli R.M., Farmer T.B., Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal Chem 1997, 69:4751-4760.
17. Chaurand P., Schwartz S.A., Billheimer D., Xu B.J., Crecelius A., Caprioli R.M. Integrating histology and imaging mass spectrometry. Anal Chem 2004, 76:1145-1155.
18. Seeley E.H., Caprioli R.M. Molecular imaging of proteins in tissues by mass spectrometry. Proc Natl Acad Sci U S A 2008, 105:18126-18131.
19. Schwamborn K., Caprioli R.M. Molecular imaging by mass spectrometry-looking beyond classical histology. Nat Rev Cancer 2010, 10:639-646.
20. Cornett D.S., Reyzer M.L., Chaurand P., Caprioli R.M. MALDI imaging mass spectrometry: molecular snapshots of biochemical systems. Nat Methods 2007, 4:828-833.
21. Chaurand P., Schwartz S.A., Reyzer M.L., Caprioli R.M. Imaging mass spectrometry: principles and potentials. Toxicol Pathol 2005, 33:92-101.
22. Schwamborn K., Caprioli R.M. MALDI imaging mass spectrometry-painting molecular pictures. Mol Oncol 2010, 4:529-538.
23. Emmert-Buck M.R., Bonner R.F., Smith P.D., Chuaqui R.F., Zhuang Z., Goldstein S.R., et al. Laser capture microdissection. Science 1996, 274:998-1001.
24. Cornett D.S., Mobley J.A., Dias E.C., Andersson M., Arteaga C.L., Sanders M.E., et al. A novel histology-directed strategy for MALDI-MS tissue profiling that improves throughput and cellular specificity in human breast cancer. Mol Cell Proteomics 2006, 5:1975-1983.
25. Aerni H.R., Cornett D.S., Caprioli R.M. Automated acoustic matrix deposition for MALDI sample preparation. Anal Chem 2006, 78:827-834.
26. Caprioli R.M. Deciphering protein molecular signatures in cancer tissues to aid in diagnosis, prognosis, and therapy. Cancer Res 2005, 65:10642-10645.
27. Schwartz S.A., Weil R.J., Thompson R.C., Shyr Y., Moore J.H., Toms S.A., 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.
28. Rauser S., Marquardt C., Balluff B., Deininger S.O., Albers C., Belau E., et al. Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry. J Proteome Res 2010, 9:1854-1863.
29. Bauer J.A., Chakravarthy A.B., Rosenbluth J.M., Mi D., Seeley E.H., De Matos Granja-Ingram N., et al. Identification of markers of taxane sensitivity using proteomic and genomic analyses of breast tumors from patients receiving neoadjuvant paclitaxel and radiation. Clin Cancer Res 2010, 16:681-690.
30. Schwamborn K., Krieg R.C., Reska M., Jakse G., Knuechel R., Wellmann A. Identifying prostate carcinoma by MALDI-Imaging. Int J Mol Med 2007, 20:155-159.
31. Groseclose M.R., Massion P.P., Chaurand P., Caprioli R.M. High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry. Proteomics 2008, 8:3715-3724.
32. Oppenheimer S.R., Mi D., Sanders M.E., Caprioli R.M. Molecular analysis of tumor margins by MALDI mass spectrometry in renal carcinoma. J Proteome Res 2010, 9:2182-2190.
33. Cazares L.H., Troyer D., Mendrinos S., Lance R.A., Nyalwidhe J.O., Beydoun H.A., et al. Imaging mass spectrometry of a specific fragment of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase kinase 2 discriminates cancer from uninvolved prostate tissue. Clin Cancer Res 2009, 15:5541-5551.
34. Willems S.M., van Remoortere A., van Zeijl R., Deelder A.M., McDonnell L.A., Hogendoorn P.C. Imaging mass spectrometry of myxoid sarcomas identifies proteins and lipids specific to tumour type and grade, and reveals biochemical intratumour heterogeneity. J Pathol 2010, 222:400-409.
35. Djidja M.C., Claude E., Snel M.F., Scriven P., Francese S., Carolan V., et al. MALDI-ion mobility separation-mass spectrometry imaging of glucose-regulated protein 78kDa (Grp78) in human formalin-fixed, paraffin-embedded pancreatic adenocarcinoma tissue sections. J Proteome Res 2009, 8:4876-4884.
36. Makawita S., Diamandis E.P. The bottleneck in the cancer biomarker pipeline and protein quantification through mass spectrometry-based approaches: current strategies for candidate verification. Clin Chem 2010, 56:212-222.
37. Kulasingam V., Diamandis E.P. Strategies for discovering novel cancer biomarkers through utilization of emerging technologies. Nat Clin Pract Oncol 2008, 5:588-599.
38. Baker S.G., Kramer B.S., McIntosh M., Patterson B.H., Shyr Y., Skates S. Evaluating markers for the early detection of cancer: overview of study designs and methods. Clin Trials 2006, 3:43-56.
39. Lilienfeld A.M. Some limitations and problems of screening for cancer. Cancer 1974, 33:1720-1724.
40. Lilja H., Ulmert D., Vickers A.J. Prostate-specific antigen and prostate cancer: prediction, detection and monitoring. Nat Rev Cancer 2008, 8:268-278.
41. Esserman L., Shieh Y., Thompson I. Rethinking screening for breast cancer and prostate cancer. JAMA 2009, 302:1685-1692.
42. Stears R.L., Martinsky T., Schena M. Trends in microarray analysis. Nat Med 2003, 9:140-145.
43. Ransohoff D.F. Cancer. Developing molecular biomarkers for cancer. Science 2003, 299:1679-1680.
44. Ransohoff D.F. The process to discover and develop biomarkers for cancer: a work in progress. J Natl Cancer Inst 2008, 100:1419-1420.
45. Poste G. Bring on the biomarkers. Nature 2011, 469:156-157.
46. Petricoin E.F., Ardekani A.M., Hitt B.A., Levine P.J., Fusaro V.A., Steinberg S.M., et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359:572-577.
47. Baggerly K.A., Morris J.S., Edmonson S.R., Coombes K.R. Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst 2005, 97:307-309.
48. Rifai N., Gillette M.A., Carr S.A. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 2006, 24:971-983.
49. Pepe M.S., Etzioni R., Feng Z., Potter J.D., Thompson M.L., Thornquist M., et al. Phases of biomarker development for early detection of cancer. J Natl Cancer Inst 2001, 93:1054-1061.
50. Hulley S.B. Designing clinical research: an epidemiologic approach 2001, Lippincott Williams & Wilkins, Philadelphia. 2nd ed.
51. Baker S.G., Kramer B.S., Srivastava S. Markers for early detection of cancer: statistical guidelines for nested case-control studies. BMC Med Res Methodol 2002, 2:4.
52. Lawton K.A., Berger A., Mitchell M., Milgram K.E., Evans A.M., Guo L., et al. Analysis of the adult human plasma metabolome. Pharmacogenomics 2008, 9:383-397.
53. Braakhuis B.J., Tabor M.P., Kummer J.A., Leemans C.R., Brakenhoff R.H. A genetic explanation of Slaughter's concept of field cancerization: evidence and clinical implications. Cancer Res 2003, 63:1727-1730.
54. Espina V., Mueller C., Edmiston K., Sciro M., Petricoin E.F., Liotta L.A. Tissue is alive: new technologies are needed to address the problems of protein biomarker pre-analytical variability. Proteomics Clin Appl 2009, 3:874-882.
55. Lim M.D., Dickherber A., Compton C.C. Before you analyze a human specimen, think quality, variability, and bias. Anal Chem 2011, 83:8-13.
56. Espina V., Edmiston K.H., Heiby M., Pierobon M., Sciro M., Merritt B., et al. A portrait of tissue phosphoprotein stability in the clinical tissue procurement process. Mol Cell Proteomics 2008, 7:1998-2018.
57. Spruessel A., Steimann G., Jung M., Lee S.A., Carr T., Fentz A.K., et al. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. Biotechniques 2004, 36:1030-1037.
58. Goodwin R.J., Dungworth J.C., Cobb S.R., Pitt A.R. Time-dependent evolution of tissue markers by MALDI-MS imaging. Proteomics 2008, 8:3801-3808.
59. Goodwin R.J., Iverson S.L., Andren P.E. The significance of ambient-temperature on pharmaceutical and endogenous compound abundance and distribution in tissues sections when analyzed by matrix-assisted laser desorption/ionization mass spectrometry imaging. Rapid Commun Mass Spectrom 2012, 26:494-498.
60. Ransohoff D.F. Rules of evidence for cancer molecular-marker discovery and validation. Nat Rev Cancer 2004, 4:309-314.
61. Harrell F.E. Regression modeling strategies: with applications to linear models, logistic regression, and survival analysis 2001, Springer, New York.
62. Michiels S., Koscielny S., Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005, 365:488-492.
63. Steyerberg E.W., Harrell F.E., Borsboom G.J., Eijkemans M.J., Vergouwe Y., Habbema J.D. Internal validation of predictive models: efficiency of some procedures for logistic regression analysis. J Clin Epidemiol 2001, 54:774-781.
64. Efron B. 1977 Rietz Lecture - bootstrap methods - another look at the Jackknife. Annu Stat 1979, 7:1-26.
65. Baser O., Crown W.H., Pollicino C. Guidelines for selecting among different types of bootstraps. Curr Med Res Opin 2006, 22:799-808.
66. van der Merwe D.E., Oikonomopoulou K., Marshall J., Diamandis E.P. Mass spectrometry: uncovering the cancer proteome for diagnostics. Adv Cancer Res 2007, 96:23-50.
67. Alaiya A., Al-Mohanna M., Linder S. Clinical cancer proteomics: promises and pitfalls. J Proteome Res 2005, 4:1213-1222.
68. Hardesty W.M., Kelley M.C., Mi D., Low R.L., Caprioli R.M. Protein signatures for survival and recurrence in metastatic melanoma. J Proteomics 2011, 74:1002-1014.
69. Hannappel E. Thymosin beta4 and its posttranslational modifications. Ann N Y Acad Sci 2010, 1194:27-35.
70. Eadie J.S., Kim S.W., Allen P.G., Hutchinson L.M., Kantor J.D., Zetter B.R. C-terminal variations in beta-thymosin family members specify functional differences in actin-binding properties. J Cell Biochem 2000, 77:277-287.
71. Balluff B., Rauser S., Meding S., Elsner M., Schone C., Feuchtinger A., et al. MALDI imaging identifies prognostic seven-protein signature of novel tissue markers in intestinal-type gastric cancer. Am J Pathol 2011.
72. Kim H.K., Reyzer M.L., Choi I.J., Kim C.G., Kim H.S., Oshima A., et al. Gastric cancer-specific protein profile identified using endoscopic biopsy samples via MALDI mass spectrometry. J Proteome Res 2010, 9:4123-4130.
73. Mohri Y., Mohri T., Wei W., Qi Y.J., Martin A., Miki C., et al. Identification of macrophage migration inhibitory factor and human neutrophil peptides 1-3 as potential biomarkers for gastric cancer. Br J Cancer 2009, 101:295-302.
74. Rahman S.M., Gonzalez A.L., Li M., Seeley E.H., Zimmerman L.J., Zhang X.J., et al. Lung cancer diagnosis from proteomic analysis of preinvasive lesions. Cancer Res 2011, 71:3009-3017.
75. Rahman S.M., Shyr Y., Yildiz P.B., Gonzalez A.L., Li H., Zhang X., et al. Proteomic patterns of preinvasive bronchial lesions. Am J Respir Crit Care Med 2005, 172:1556-1562.
76. Yanagisawa K., Shyr Y., Xu B.J., Massion P.P., Larsen P.H., White B.C., et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 2003, 362:433-439.
77. Lemaire R., Menguellet S.A., Stauber J., Marchaudon V., Lucot J.P., Collinet P., et al. Specific MALDI imaging and profiling for biomarker hunting and validation: fragment of the 11S proteasome activator complex, Reg alpha fragment, is a new potential ovary cancer biomarker. J Proteome Res 2007, 6:4127-4134.
78. Lazova R., Seeley E.H., Keenan M., Gueorguieva R., Caprioli R.M. Imaging mass spectrometry-a new and promising method to differentiate spitz nevi from spitzoid malignant melanomas. Am J Dermatopathol 2012, 34:82-90.