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Towards a proteome signature for invasive ductal breast carcinoma derived from label-free nanoscale LC-MS protein expression profiling of tumorous and glandular tissue

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Abstract

As more and more alternative treatments become available for breast carcinoma, there is a need to stratify patients and individual molecular information seems to be suitable for this purpose. In this study, we applied label-free protein quantitation by nanoscale LC-MS and investigated whether this approach could be used for defining a proteome signature for invasive ductal breast carcinoma. Tissue samples from healthy breast and tumor were collected from three patients. Protein identifications were based on LC-MS peptide fragmentation data which were obtained simultaneously to the quantitative information. Hereby, an invasive ductal breast carcinoma proteome signature was generated which contains 60 protein entries. The on-column concentrations for osteoinductive factor, vimentin, GAP-DH, and NDKA are provided as examples. These proteins represent distinctive gene ontology groups of differentially expressed proteins and are discussed as risk markers for primary tumor pathogenesis. The developed methodology has been found well applicable in a clinical environment in which standard operating procedures can be kept; a prerequisite for the definition of molecular parameter sets that shall be capable for stratification of patients.

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Abbreviations

ATP:

Adenosine triphosphate

EGFR:

Epidermal growth factor receptor

EMT:

Epithelial-mesenchymal transition

G:

Gland

GAP-DH:

Glyceraldehyde-3-phosphate dehydrogenase

HER-1/2:

Human epidermal growth factor receptor 1/2

IAA:

Iodoacetamide

mTOR:

Mammalian targets of rapamycin

NDKA/B:

Nucleoside diphosphate kinase A/B

OIF:

Osteoinductive factor

PC:

Principle component

Q-Tof:

Quadrupole time of flight

RF:

Radio frequency

RMS:

Root mean square

SVM:

Support vector machine algorithm

T:

Tumor

tRNA:

Transfer ribonucleic acid

TXNDC5:

Thioredoxin domain-containing protein 5

VEGF-A:

Vascular endothelial growth factor A

References

  1. Croce CM (2008) Oncogenes and cancer. N Engl J Med 358:502–511

    Article  CAS  Google Scholar 

  2. Adjei AA, Hidalgo M (2005) Intracellular signal transduction pathway proteins as targets for cancer therapy. J Clin Oncol 23:5386–5403

    Article  CAS  Google Scholar 

  3. Gerber B, Krause A, Markmann S, Reimer T, Fietkau R, Müller H (2001) Effectiveness of trastuzumab (Herceptin) in a patient with locally recurrent breast cancer after cardiac failure caused by severe cytotoxic pretreatment. Oncology 61:271–274

    Article  CAS  Google Scholar 

  4. Baselga J, Perez EA, Pienkowski T, Belld R (2006) Adjuvant trastuzumab: a milestone in the treatment of HER-2-positive early breast cancer. Oncologist 11:4–12

    Article  CAS  Google Scholar 

  5. Petrelli F, Cabiddu M, Cazzaniga ME, Cremonesi M, Barni S (2008) Targeted therapies for the treatment of breast cancer in the post-trastuzumab era. Oncologist 13:373–381

    Article  CAS  Google Scholar 

  6. Lin NU, Winer EP (2004) New targets for therapy in breast cancer: small molecule tyrosine kinase inhibitors. Breast Cancer Res 6:204–210

    Article  CAS  Google Scholar 

  7. Payne DJ (2008) Microbiology. Desperately seeking new antibiotics. Science 321:1644–1645

    Article  CAS  Google Scholar 

  8. Steeg PS, Horak CE, Miller KD (2008) Clinical-translational approaches to the Nm23-H1 metastasis suppressor. Clin Cancer Res 14:5006–5012

    Article  CAS  Google Scholar 

  9. Kuramitsu Y, Kazuyuki N (2006) Proteomic analysis of cancer tissues: shedding light on carcinogenesis and possible biomarkers. Proteomics 6:5650–5661

    Article  CAS  Google Scholar 

  10. Pastwa E, Somiari SB, Czyz M, Somiari RI (2007) Proteomics in human cancer research. Proteomics Clin Appl 1:4–17

    Article  CAS  Google Scholar 

  11. Callesen AK, Vach W, Jørgensen PE, Cold S, Mogensen O, Kruse TA, Jensen ON, Madsen JS (2008) Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies: a systematic review. J Proteome Res 7:1395–1402

    Article  CAS  Google Scholar 

  12. Hondermarck H, Tastet C, El Yazidi-Belkoura I, Toillon R-A, Le Bourhis X (2008) Proteomics of breast cancer: the quest for markers and therapeutic targets. J Proteome Res 7:1403–1411

    Article  CAS  Google Scholar 

  13. Hawkins OE, VanGundy RS, Eckerd AM, Bardet W, Buchli R, Weidanz JA, Hildebrand WH (2008) Identification of breast cancer peptide epitopes presented by HLA-A*0201. J Proteome Res 7:1445–1457

    Article  CAS  Google Scholar 

  14. Abbott KL, Aoki K, Lim J-M, Porterfield M, Johnson R, O’Regan RM, Wells L, Tiemeyer M, Michael P (2008) Targeted glycoproteomic identification of biomarkers for human breast carcinoma. J Proteome Res 7:1470–1480

    Article  CAS  Google Scholar 

  15. Chen S-T, Pan T-L, Juan H-F, Chen T-Y, Lin Y-S, Huang C-M (2008) Breast tumor microenvironment: proteomics highlights the treatments targeting secretome. J Proteome Res 7:1379–1387

    Article  Google Scholar 

  16. Lu H, Goodell V, Disis ML (2008) Humoral immunity directed against tumor-associated antigens as potential biomarkers for the early diagnosis of cancer. J Proteome Res 7:1388–1394

    Article  CAS  Google Scholar 

  17. Ou K, Yu K, Kesuma D, Hooi M, Huang N, Chen W, Lee SY, Pei Goh X, Lk T, Liu J, Soon SY, Rashid SBA, Putti TC, Jikuya H, Ichikawa T, Nishimura O, Salto-Tellez M, Tan P (2008) Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping. J Proteome Res 7:1518–1528

    Article  CAS  Google Scholar 

  18. Sanders ME, Dias EC, Xu BJ, Mobley JA, Billheimer D, Roder H, Grigorieva J, Dowsett M, Arteaga CL, Caprioli RM (2008) Differentiating proteomic biomarkers in breast cancer by laser capture microdissection and MALDI MS. J Proteome Res 7:1500–1507

    Article  CAS  Google Scholar 

  19. Pucci-Minafra I, Cancemi P, Marabeti MR, Albanese NN, Di Cara G, Taomina P, Marrazzo A (2007) Proteomic profiling of 13 paired ductal infiltrating breast carcinomas and non-tumoral adjacent counterparts. Proteomics Clin Appl 1:118–129

    Article  CAS  Google Scholar 

  20. Seike M, Kondo T, Fujii K, Yamada T, Gemma A, Kudoh S, Hirohashi S (2004) Proteomic signature of human cancer cells. Proteomics 4:2776–2788

    Article  CAS  Google Scholar 

  21. Yamada M, Fujii K, Koyama K, Hirohashi S, Kondo T (2009) The proteomic profile of pancreatic cancer cell lines corresponding to carcinogenesis and metastasis. J Proteomics Bioinform 2:001–018

    Article  CAS  Google Scholar 

  22. Wang M, You J, Bemis KG, Tegeler TJ, Brown DPG (2008) Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. Brief Funct Genomic Proteomic 7:329–339

    Article  CAS  Google Scholar 

  23. Alldridge L, Metodieva G, Greenwood C, Al-Janabi K, Thwaites L, Sauven P, Metodiev M (2008) Proteome profiling of breast tumors by gel electrophoresis and nanoscale electrospray ionization mass spectrometry. J Proteome Res 7:1458–1469

    Article  CAS  Google Scholar 

  24. Zhang X, Li L, Wei D, Yap Y, Chen F (2007) Moving cancer diagnostics from bench to bedside. Trends Biotechnol 25:166–173

    Article  Google Scholar 

  25. Kondo T (2008) Tissue proteomics for cancer biomarker development: laser microdissection and 2D-DIGE. BMB Rep 41:626–634

    CAS  Google Scholar 

  26. Silva JC, Denny R, Dorschel CA, Gorenstein MV, Kass IJ, Li G-Z, McKenna T, Nold MJ, Richardson K, Young P, Geromanos SJ (2005) Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem 77:2187–2200

    Article  CAS  Google Scholar 

  27. Geromanos SJ, Silva JC, Vissers JPC, Dorschel CA, Li G-Z, Gorenstein MV, Bateman RH, Langridge JI (2009) The detection, correlation and comparison of peptide precursor and products ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 9:1683–1695

    Article  CAS  Google Scholar 

  28. Remmele W, Stegner HE (1987) Recommendation for uniform definition of an immunoreactive score (IRS) for immunohistochemical estrogen receptor detection (ER-ICA) in breast cancer tissue. Pathologe 8:138–140

    CAS  Google Scholar 

  29. Just T, Gafumbegete E, Gramberg J, Prüfer I, Mikkat S, Ringel B, Pau HW, Glocker MO (2006) Differential proteome analysis of tonsils from children with chronic tonsillitis or with hyperplasia reveals disease-associated protein expression differences. Anal Bioanal Chem 384:1134–1144

    Article  CAS  Google Scholar 

  30. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    Article  CAS  Google Scholar 

  31. Lorenz P, Bantscheff M, Ibrahim SM, Thiesen H-J, Glocker MO (2003) Proteome analysis of diseased joints from mice suffering from collagen-induced arthritis. Clin Chem Lab Med 41:1622–1632

    Article  CAS  Google Scholar 

  32. Yu Y-Q, Gilar M, Lee PJ, Bouvier ESP, Gebler JC (2003) Enzyme-friendly, mass spectrometry-compatible surfactant for in-solution enzymatic digestion of proteins. Anal Chem 75:6023–6028

    Article  CAS  Google Scholar 

  33. Li G-Z, Vissers JPC, Silva JC, Golick D, Gorenstein MV, Geromanos SJ (2009) Database searching and accounting of data independent acquired precursor and products ions from simple and complex peptide mixtures. Proteomics 9:1696–1719

    Article  CAS  Google Scholar 

  34. Vissers JPC, Langridge JI, Aerts JMFG (2007) Analysis and quantification of diagnostic serum markers and protein signatures for gaucher disease. Mol Cell Proteomics 6:755–766

    Article  CAS  Google Scholar 

  35. Jollife JT (1986) Principal component analysis. Springer, New York

    Google Scholar 

  36. Schölkopf B, Smola AJ (2002) Learning with kernels. MIT Press, Cambridge, MA

    Google Scholar 

  37. Cawley GC (2000) School of information systems. University of East Anglia, Norwich, Norfolk, UK

    Google Scholar 

  38. Tukey JW (1977) Exploratory data analysis. Addison Wesley, UK

    Google Scholar 

  39. Elston CW (2005) Classification and grading of invasive breast carcinoma. Verh Dtsch Ges Pathol 89:35–44

    CAS  Google Scholar 

  40. Chambery A, Vissers JPC, Langridge JI, Lonardo E, Minchiotti G, Ruvo M, Parente A (2009) Qualitative and quantitative proteomic profiling of cripto−/− embryonic stem cells by means of accurate mass LC-MS analysis. J Proteome Res 8:1047–1058

    Article  CAS  Google Scholar 

  41. Silva JC, Gorenstein MV, Li G-Z, Vissers JPC, Geromanos SJ (2006) Absolute quantification of proteins by LCMSE-A virtue of parallel MS acquisition. Mol Cell Proteomics 5:144–156

    CAS  Google Scholar 

  42. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    Article  CAS  Google Scholar 

  43. Ciocca DR, Calderwood SK (2005) Heat shock proteins in cancer: diagnostic, prognostic, predictive, and treatment implications. Cell Stress Chaperones 10:86–103

    Article  CAS  Google Scholar 

  44. Ciocca DR, Frayssinet P, Cuello-Carrión FD (2007) A pilot study with a therapeutic vaccine based on hydroxyapatite ceramic particles and self-antigens in cancer patients. Cell Stress Chaperones 12:33–43

    Article  CAS  Google Scholar 

  45. Shadidi M, Sørensen D, Dybwad A, Furset G, Sioud M (2008) Mucosal vaccination with phage-displayed tumour antigens identified through proteomics-based strategy inhibits the growth and metastasis of 4T1 breast adenocarcinoma. Int J Oncol 32:241–247

    CAS  Google Scholar 

  46. Petrak J, Ivanek R, Toman O, Cmejla R, Cmejlova J, Vyoral D, Zivny J, Vulpe CD (2008) Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins. Proteomics 8:1744–1749

    Article  CAS  Google Scholar 

  47. Wang P, Bouwman FG, Mariman ECM (2009) Generally detected proteins in comparative proteomics—a matter of cellular stress response? Proteomics 9:2955–2966

    Article  CAS  Google Scholar 

  48. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 389:1017–1031

    Article  CAS  Google Scholar 

  49. Glocker MO, Guthke R, Kekow J, Thiesen H-J (2006) Rheumatoid arthritis, a complex multifactorial disease: on the way toward individualized medicine. Med Res Rev 26:63–87

    Article  CAS  Google Scholar 

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Acknowledgment

We thank Annika Kasten, Stefanie Haase, Katharina Dreschler, Paul Witt, Michael Kreutzer, and Manuela Sieb for excellent technical assistance. We like to express our thanks to Dr. Falk Pommerenke from the Institute of Pathology of the Südstadt Clinical Center, Rostock, for supplying project relevant pathological information and evaluating immunohistochemical staining on the individual samples. The valuable contributions of James I. Langridge, Timothy Riley, and Leonhard Pollack with the LC-MS experiments are also kindly acknowledged.

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Authors and Affiliations

  1. Proteome Center Rostock, University of Rostock, 18055, Rostock, Germany

    Claudia Röwer, Cornelia Koy & Michael O. Glocker

  2. Waters Corporation, M22 5PP, Manchester, UK

    Johannes P. C. Vissers & Marc Kipping

  3. Institute of Immunology, University of Rostock, 18055, Rostock, Germany

    Michael Hecker & Hans-Jürgen Thiesen

  4. IndyMed GmbH, 18055, Rostock, Germany

    Michael Hecker & Hans-Jürgen Thiesen

  5. Department of Obstetrics and Gynecology, University of Rostock, 18055, Rostock, Germany

    Toralf Reimer & Bernd Gerber

  6. Proteome Center Rostock, Department for Proteome Research, Institute of Immunology, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, P.O. Box 100 888, 18055, Rostock, Germany

    Michael O. Glocker

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  1. Claudia Röwer
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  2. Johannes P. C. Vissers
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  9. Michael O. Glocker
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Correspondence to Michael O. Glocker.

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Röwer, C., Vissers, J.P.C., Koy, C. et al. Towards a proteome signature for invasive ductal breast carcinoma derived from label-free nanoscale LC-MS protein expression profiling of tumorous and glandular tissue. Anal Bioanal Chem 395, 2443–2456 (2009). https://doi.org/10.1007/s00216-009-3187-9

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