Skip to main content

Proteomics of Human Malignant Lymphoma

  • Chapter
  • First Online:
Molecular Pathology of Hematolymphoid Diseases

Part of the book series: Molecular Pathology Library ((MPLB,volume 4))

  • 1289 Accesses

Abstract

The proteome represents the total complement of proteins present in a complex, an organelle, a cell, tissue, or an organism. Proteomics encompass the multifaceted study of protein expression, interactions, posttranslational modification, and function at the cellular level. Mass spectrometry offers significant opportunities for the analysis of single proteins and the unbiased large-scale analysis of proteins in complex mixtures. The ability to conduct large-scale investigation of proteins in an unbiased fashion dramatically improves the opportunities for biological discovery and is relevant for the elucidation of novel biological insights into physiology and disease. In this regard, mass spectrometry is considered a key technology that will drive the achievement of several milestones in the identification of key proteins involved in disease detection and treatment. This chapter provides a synopsis of the principles of the techniques employed in the current state-of-the art proteomics and the opportunities that this suite of technologies offers in biological discovery as it relates to human lymphomas. Advances in mass spectrometry-based proteomics have shifted the paradigm of translational cancer research (for a review of background on proteomics and mass spectrometry see). The achievement of the ultimate goals of identifying biomarkers for diagnosis and prognosis and the development of novel agents for therapy will require significant effort in understanding the basic protein building blocks and the global proteomic circuitry.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 279.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Blackstock WP, Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol. 1999;17(3):121–127.

    Article  CAS  PubMed  Google Scholar 

  2. Lim MS, Elenitoba-Johnson KS. Proteomics in pathology research. Lab Invest. 2004;84(10):1227–1244.

    Article  CAS  PubMed  Google Scholar 

  3. Mirza SP, Olivier M. Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry. Physiol Genomics. 2008;33(1):3–11.

    CAS  PubMed  Google Scholar 

  4. Qian WJ, Jacobs JM, Liu T, Camp DG II, Smith RD. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics. 2006;5(10):1727–1744.

    CAS  PubMed  Google Scholar 

  5. Ahram M, Flaig MJ, Gillespie JW, et al. Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications. Proteomics. 2003;3(4):413–421.

    Article  CAS  PubMed  Google Scholar 

  6. Crockett DK, Lin Z, Vaughn CP, Lim MS, Elenitoba-Johnson KS. Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. Lab Invest J Tech Methods Pathol. 2005;85(11):1405–1415.

    CAS  Google Scholar 

  7. Hood BL, Darfler MM, Guiel TG, et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics. 2005;4(11):1741–1753.

    CAS  PubMed  Google Scholar 

  8. Li C, Hong Y, Tan YX, et al. Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mol Cell Proteomics. 2004;3(4):399–409.

    CAS  PubMed  Google Scholar 

  9. Nishizuka S, Charboneau L, Young L, et al. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci USA. 2003;100(24):14229–14234.

    Article  CAS  PubMed  Google Scholar 

  10. Yates JR III, Eng JK, McCormack AL, Schieltz D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem. 1995;67(8):1426–1436.

    Article  CAS  PubMed  Google Scholar 

  11. MacCoss MJ, McDonald WH, Saraf A, et al. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci USA. 2002;99(12):7900–7905.

    Article  CAS  PubMed  Google Scholar 

  12. Orenes-Pinero E, Corton M, Gonzalez-Peramato P, et al. Searching urinary tumor markers for bladder cancer using a two-dimensional differential gel electrophoresis (2D-DIGE) approach. J Proteome Res. 2007;6(11):4440–4448.

    Article  CAS  PubMed  Google Scholar 

  13. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999;17(10):994–999.

    Article  CAS  PubMed  Google Scholar 

  14. DeSouza L, Diehl G, Rodrigues MJ, et al. Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J Proteome Res. 2005;4(2):377–386.

    Article  CAS  PubMed  Google Scholar 

  15. Ong SE, Foster LJ, Mann M. Mass spectrometric-based approaches in quantitative proteomics. Methods. 2003;29(2):124–130.

    Article  CAS  PubMed  Google Scholar 

  16. Dent AL, Doherty TM, Paul WE, Sher A, Staudt LM. BCL-6-deficient mice reveal an IL-4-independent, STAT6-dependent pathway that controls susceptibility to infection by Leishmania major. J Immunol. 1999;163(4):2098–2103.

    CAS  PubMed  Google Scholar 

  17. Shaffer AL, Yu X, He Y, Boldrick J, Chan EP, Staudt LM. BCL-6 represses genes that function in lymphocyte differentiation, inflammation, and cell cycle control. Immunity. 2000;13(2):199–212.

    Article  CAS  PubMed  Google Scholar 

  18. Ye BH, Cattoretti G, Shen Q, et al. The BCL-6 proto-oncogene controls germinal-centre formation and Th2-type inflammation. Nat Genet. 1997;16(2):161–170.

    Article  CAS  PubMed  Google Scholar 

  19. Chang CC, Ye BH, Chaganti RS, Dalla-Favera R. BCL-6, a POZ/zinc-finger protein, is a sequence-specific transcriptional repressor. Proc Natl Acad Sci USA. 1996;93(14):6947–6952.

    Article  CAS  PubMed  Google Scholar 

  20. Lemercier C, Brocard MP, Puvion-Dutilleul F, Kao HY, Albagli O, Khochbin S. Class II histone deacetylases are directly recruited by BCL6 transcriptional repressor. J Biol Chem. 2002;277(24):22045–22052.

    Article  CAS  PubMed  Google Scholar 

  21. Dhordain P, Albagli O, Ansieau S, et al. The BTB/POZ domain targets the LAZ3/BCL6 oncoprotein to nuclear dots and mediates homomerisation in vivo. Oncogene. 1995;11(12):2689–2697.

    CAS  PubMed  Google Scholar 

  22. Miles RR, Crockett DK, Lim MS, Elenitoba-Johnson KS. Analysis of BCL6-interacting proteins by tandem mass spectrometry. Mol Cell Proteomics. 2005;4(12):1898–1909.

    CAS  PubMed  Google Scholar 

  23. Lin Z, Jenson SD, Lim MS, Elenitoba-Johnson KS. Application of SELDI-TOF mass spectrometry for the identification of differentially expressed proteins in transformed follicular lymphoma. Mod Pathol. 2004;17(6):670–678.

    Article  CAS  PubMed  Google Scholar 

  24. Kaufmann SH, Gores GJ. Apoptosis in cancer: cause and cure. Bioessays. 2000;22(11):1007–1017.

    Article  CAS  PubMed  Google Scholar 

  25. Lee JM, Bernstein A. Apoptosis, cancer and the p53 tumour suppressor gene. Cancer Metastasis Rev. 1995;14(2):149–161.

    Article  CAS  PubMed  Google Scholar 

  26. Reed JC. Mechanisms of apoptosis avoidance in cancer. Curr Opin Oncol. 1999;11(1):68–75.

    Article  CAS  PubMed  Google Scholar 

  27. Elenitoba-Johnson KS, Jenson SD, Abbott RT, et al. Involvement of multiple signaling pathways in follicular lymphoma transformation: p38-mitogen-activated protein kinase as a target for therapy. Proc Natl Acad Sci USA. 2003;100(12):7259–7264.

    Article  CAS  PubMed  Google Scholar 

  28. Lin Z, Crockett DK, Jenson SD, Lim MS, Elenitoba-Johnson KS. Quantitative proteomic and transcriptional analysis of the response to the p38 mitogen-activated protein kinase inhibitor SB203580 in transformed follicular lymphoma cells. Mol Cell Proteomics. 2004;3(8):820–833.

    CAS  PubMed  Google Scholar 

  29. Cairo MS, Raetz E, Perkins SL. Non-Hodgkin lymphoma in children. In: Kufe DWP RR, Weichselbaum RR, Bast RC Jr, Gansler TS, Holland JF, Frei E III, ed. Cancer Medicine. 7th ed. Hamilton, London: BC Decker, Inc; 2006:1962–1975

    Google Scholar 

  30. Henrich S, Cordwell SJ, Crossett B, Baker MS, Christopherson RI. The nuclear proteome and DNA-binding fraction of human Raji lymphoma cells. Biochim Biophys Acta. 2007;1774(4):413–432.

    CAS  PubMed  Google Scholar 

  31. Ma Y, Visser L, Roelofsen H, et al. Proteomics analysis of Hodgkin lymphoma: identification of new players involved in the cross-talk between HRS cells and infiltrating lymphocytes. Blood. 2008;111(4):2339–2346.

    Article  CAS  PubMed  Google Scholar 

  32. Wallentine JC, Kim KK, Seiler CE III, et al. Comprehensive identification of proteins in Hodgkin lymphoma-derived Reed-Sternberg cells by LC-MS/MS. Lab Invest. 2007;87(11):1113–1124.

    Article  CAS  PubMed  Google Scholar 

  33. Zhang X, Wang B, Zhang XS, Li ZM, Guan ZZ, Jiang WQ. Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning. BMC Cancer. 2007;7:235.

    Article  PubMed  Google Scholar 

  34. Roy S, Josephson SA, Fridlyand J, et al. Protein biomarker identification in the CSF of patients with CNS lymphoma. J Clin Oncol. 2008;26(1):96–105.

    Article  CAS  PubMed  Google Scholar 

  35. Vaughn CP, Crockett DK, Lin Z, Lim MS, Elenitoba-Johnson KS. Identification of proteins released by follicular lymphoma-derived cells using a mass spectrometry-based approach. Proteomics. 2006;6(10):3223–3230.

    Article  CAS  PubMed  Google Scholar 

  36. van Kempen LC, van den Oord JJ, van Muijen GN, Weidle UH, Bloemers HP, Swart GW. Activated leukocyte cell adhesion molecule/CD166, a marker of tumor progression in primary malignant melanoma of the skin. Am J Pathol. 2000;156(3):769–774.

    PubMed  Google Scholar 

  37. Kristiansen G, Pilarsky C, Wissmann C, et al. ALCAM/CD166 is up-regulated in low-grade prostate cancer and progressively lost in high-grade lesions. Prostate. 2003;54(1):34–43.

    Article  PubMed  Google Scholar 

  38. Weichert W, Knosel T, Bellach J, Dietel M, Kristiansen G. ALCAM/CD166 is overexpressed in colorectal carcinoma and correlates with shortened patient survival. J Clin Pathol. 2004;57(11):1160–1164.

    Article  CAS  PubMed  Google Scholar 

  39. Ueda K, Nakanishi T, Shimizu A, Takubo T, Matsuura N. Identification of L-plastin autoantibody in plasma of patients with non-Hodgkin’s lymphoma using a proteomics-based analysis. Ann Clin Biochem. 2008;45(Pt 1):65–69.

    Article  CAS  PubMed  Google Scholar 

  40. Iwahara T, Fujimoto J, Wen D, et al. Molecular characterization of ALK, a receptor tyrosine kinase expressed specifically in the nervous system. Oncogene. 1997;14(4):439–449.

    Article  CAS  PubMed  Google Scholar 

  41. Morris SW, Naeve C, Mathew P, et al. ALK, the chromosome 2 gene locus altered by the t(2;5) in non-Hodgkin’s lymphoma, encodes a novel neural receptor tyrosine kinase that is highly related to leukocyte tyrosine kinase (LTK) [published erratum appears in Oncogene 1997 Dec 4;15(23):2883]. Oncogene. 1997;14(18):2175–2188.

    Article  CAS  PubMed  Google Scholar 

  42. Souttou B, Carvalho NB, Raulais D, Vigny M. Activation of anaplastic lymphoma kinase receptor tyrosine kinase induces neuronal differentiation through the mitogen-activated protein kinase pathway. J Biol Chem. 2001;276(12):9526–9531.

    Article  CAS  PubMed  Google Scholar 

  43. Motegi A, Fujimoto J, Kotani M, Sakuraba H, Yamamoto T. ALK receptor tyrosine kinase promotes cell growth and neurite outgrowth. J Cell Sci. 2004;117(Pt 15):3319–3329.

    Article  CAS  PubMed  Google Scholar 

  44. Powers C, Aigner A, Stoica GE, McDonnell K, Wellstein A. Pleiotrophin signaling through anaplastic lymphoma kinase is rate-limiting for glioblastoma growth. J Biol Chem. 2002;277(16):14153–14158.

    Article  CAS  PubMed  Google Scholar 

  45. Stoica GE, Kuo A, Powers C, et al. Midkine binds to anaplastic lymphoma kinase (ALK) and acts as a growth factor for different cell types. J Biol Chem. 2002;277(39):35990–35998.

    Article  CAS  PubMed  Google Scholar 

  46. Bischof D, Pulford K, Mason DY, Morris SW. Role of the nucleophosmin (NPM) portion of the non-Hodgkin’s lymphoma-associated NPM-anaplastic lymphoma kinase fusion protein in oncogenesis. Mol Cell Biol. 1997;17(4):2312–2325.

    CAS  PubMed  Google Scholar 

  47. Shiota M, Mori S. Anaplastic large cell lymphomas expressing the novel chimeric protein p80NPM/ALK: a distinct clinicopathologic entity. Leukemia. 1997;11(Suppl 3):538–540.

    PubMed  Google Scholar 

  48. Bai RY, Dieter P, Peschel C, Morris SW, Duyster J. Nucleophosmin-anaplastic lymphoma kinase of large-cell anaplastic lymphoma is a constitutively active tyrosine kinase that utilizes phospholipase C-gamma to mediate its mitogenicity. Mol Cell Biol. 1998;18:6951–6961.

    CAS  PubMed  Google Scholar 

  49. Slupianek A, Nieborowska-Skorska M, Hoser G, et al. Role of phosphatidylinositol 3-kinase-Akt pathway in nucleophosmin/anaplastic lymphoma kinase-mediated lymphomagenesis. Cancer Res. 2001;61(5):2194–2199.

    CAS  PubMed  Google Scholar 

  50. Bai RY, Ouyang T, Miething C, Morris SW, Peschel C, Duyster J. Nucleophosmin-anaplastic lymphoma kinase associated with anaplastic large-cell lymphoma activates the phosphatidylinositol 3-kinase/Akt antiapoptotic signaling pathway. Blood 2000;96:4319–4327

    CAS  PubMed  Google Scholar 

  51. Amin HM, Medeiros LJ, Ma Y, et al. Inhibition of JAK3 induces apoptosis and decreases anaplastic lymphoma kinase activity in anaplastic large cell lymphoma. Oncogene. 2003;22(35):5399–5407.

    Article  CAS  PubMed  Google Scholar 

  52. Zamo A, Chiarle R, Piva R, et al. Anaplastic lymphoma kinase (ALK) activates Stat3 and protects hematopoietic cells from cell death. Oncogene. 2002;21(7):1038–1047.

    Article  CAS  PubMed  Google Scholar 

  53. Cussac D, Greenland C, Roche S, et al. Nucleophosmin-anaplastic lymphoma kinase of anaplastic large-cell lymphoma recruits, activates, and uses pp 60c-src to mediate its mitogenicity. Blood. 2004;103(4):1464–1471.

    Article  CAS  PubMed  Google Scholar 

  54. Piva R, Pellegrino E, Inghirami G. Identification and validation of the anaplastic large cell lymphoma signature. Adv Exp Med Biol. 2007;604:129–136.

    Article  PubMed  Google Scholar 

  55. Sjostrom C, Seiler C, Crockett DK, Tripp SR, Elenitoba Johnson KS, Lim MS. Global proteome profiling of NPM/ALK-positive anaplastic large cell lymphoma. Exp Hematol. 2007;35(8):1240–1248.

    Article  CAS  PubMed  Google Scholar 

  56. Zeeberg BR, Feng W, Wang G, et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 2003;4(4):R28.

    Article  PubMed  Google Scholar 

  57. Cussac D, Pichereaux C, Colomba A, et al. Proteomic analysis of anaplastic lymphoma cell lines: identification of potential tumour markers. Proteomics 2006;6(10):3210–3222.

    Article  CAS  PubMed  Google Scholar 

  58. Crockett DK, Lin Z, Elenitoba-Johnson KS, Lim MS. Identification of NPM-ALK interacting proteins by tandem mass spectrometry. Oncogene. 2004;23(15):2617–2629.

    Article  CAS  PubMed  Google Scholar 

  59. Ruchatz H, Coluccia AM, Stano P, Marchesi E, Gambacorti-Passerini C. Constitutive activation of Jak2 contributes to proliferation and resistance to apoptosis in NPM/ALK-transformed cells. Exp Hematol. 2003;31(4):309–315.

    Article  CAS  PubMed  Google Scholar 

  60. Zhang Q, Raghunath PN, Xue L, et al. Multilevel dysregulation of STAT3 activation in anaplastic lymphoma kinase-positive T/null-cell lymphoma. J Immunol. 2002;168(1):466–474.

    CAS  PubMed  Google Scholar 

  61. Bassermann F, von Klitzing C, Munch S, et al. NIPA defines an SCF-type mammalian E3 ligase that regulates mitotic entry. Cell. 2005;122(1):45–57.

    Article  CAS  PubMed  Google Scholar 

  62. Chiarle R, Simmons WJ, Cai H, et al. Stat3 is required for ALK-mediated lymphomagenesis and provides a possible therapeutic target. Nat Med. 2005;11(6):623–629.

    Article  CAS  PubMed  Google Scholar 

  63. Voena C, Conte C, Ambrogio C, et al. The tyrosine phosphatase Shp2 interacts with NPM-ALK and regulates anaplastic lymphoma cell growth and migration. Cancer Res. 2007;67(9):4278–4286.

    Article  CAS  PubMed  Google Scholar 

  64. Ambrogio C, Voena C, Manazza AD, et al. p130Cas mediates the transforming properties of the anaplastic lymphoma kinase. Blood. 2005;106(12):3907–3916.

    Article  CAS  PubMed  Google Scholar 

  65. Neckers L, Mimnaugh E, Schulte TW. Hsp90 as an anti-cancer target. Drug Resist Updat. 1999;2(3):165–172.

    Article  CAS  PubMed  Google Scholar 

  66. Bonvini P, Gastaldi T, Falini B, Rosolen A. Nucleophosmin-anaplastic lymphoma kinase (NPM-ALK), a novel Hsp90-client tyrosine kinase: down-regulation of NPM-ALK expression and tyrosine phosphorylation in ALK(+) CD30(+) lymphoma cells by the Hsp90 antagonist 17-allylamin0,17-demethoxygeldanamycin. Cancer Res. 2002;62(5):1559–1566.

    CAS  PubMed  Google Scholar 

  67. Bonvini P, Dalla Rosa H, Vignes N, Rosolen A. Ubiquitination and proteasomal degradation of nucleophosmin-anaplastic lymphoma kinase induced by 17-allylamino-demethoxygeldanamycin: role of the co-chaperone carboxyl heat shock protein 70-interacting protein. Cancer Res. 2004;64(9):3256–3264.

    Article  CAS  PubMed  Google Scholar 

  68. Picard D. Heat-shock protein 90, a chaperone for folding and regulation. Cell Mol Life Sci. 2002;59(10):1640–1648.

    Article  CAS  PubMed  Google Scholar 

  69. Caplan AJ, Jackson S, Smith D. Hsp90 reaches new heights. Conference on the Hsp90 chaperone machine. EMBO Rep. 2003;4(2):126–130.

    Article  CAS  PubMed  Google Scholar 

  70. Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat Med. 2001;7(4):493–496.

    Article  CAS  PubMed  Google Scholar 

  71. Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics. 2006;5(4):573–588.

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Lim, M.S., Miles, R.R., Elenitoba-Johnson, K.S.J. (2010). Proteomics of Human Malignant Lymphoma. In: Dunphy, C. (eds) Molecular Pathology of Hematolymphoid Diseases. Molecular Pathology Library, vol 4. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-5698-9_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-4419-5698-9_14

  • Published:

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4419-5697-2

  • Online ISBN: 978-1-4419-5698-9

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics