Detergent fractionation with subsequent subtractive suppression hybridization as a tool for identifying genes coding for plasma membrane proteins

Experimental Dermatology

Volumn 18, Issue 6, 2009, Pages 527-535

  Lange, Andreas ^a,b   Kistler, Claudia ^a,b   Jutzi, Tanja B ^a,b   Bazhin, Alexandr V ^a,b   Klemke, Claus Detlev ^b   Schadendorf, Dirk ^a,b   Eichmüller, Stefan B ^a,b  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Cutaneous T cell lymphoma; Digitonin treatment; Membrane proteins; Subtractive suppression hybridization; Tumor associated antigens

Indexed keywords

DETERGENT; DIGITONIN; G PROTEIN COUPLED RECEPTOR 137B; HEAT SHOCK PROTEIN 90; INTERLEUKIN 1 RECEPTOR ASSOCIATED KINASE; MEMBRANE PROTEIN; MESSENGER RNA; PROTEIN ARC; PROTEIN CLIF; PROTEIN FAM 62A; PROTEIN IBP2; PROTEIN NOMO1; PROTEIN SLIT1; TUMOR ANTIGEN; UNCLASSIFIED DRUG;

ARTICLE; BLOOD SAMPLING; CANCER CELL CULTURE; CASE REPORT; CELL FRACTIONATION; CELL MEMBRANE; CONTROLLED STUDY; CUTANEOUS T CELL LYMPHOMA; ENDOPLASMIC RETICULUM; GENE IDENTIFICATION; GENE OVEREXPRESSION; GENE SEQUENCE; GENETIC CODE; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOHISTOLOGY; MONOCYTE; PERIPHERAL BLOOD MONONUCLEAR CELL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEIN SECRETION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; WESTERN BLOTTING;

CELL FRACTIONATION; CELL LINE, TUMOR; DETERGENTS; DIGITONIN; ENDOPLASMIC RETICULUM, ROUGH; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; KERATINOCYTES; LYMPHOMA, T-CELL, CUTANEOUS; MEMBRANE PROTEINS; MITOCHONDRIA; NEOPLASM PROTEINS; ORGAN SPECIFICITY; POLYRIBOSOMES; RIBOSOMAL PROTEINS; RNA, MESSENGER; RNA, NEOPLASM; SKIN NEOPLASMS; SUBCELLULAR FRACTIONS; SUBTRACTION TECHNIQUE; SWEAT GLANDS;

EID: 66149139271     PISSN: 09066705     EISSN: 16000625     Source Type: Journal    
DOI: 10.1111/j.1600-0625.2008.00821.x     Document Type: Article

References (73)

1. Zafir-Lavie I, Michaeli Y, Reiter Y. Novel antibodies as anticancer agents. Oncogene 2007: 26: 3714-3733.
2. Willemze R, Jaffe E S, Burg G et al. WHO-EORTC classification for cutaneous lymphomas. Blood 2005: 105: 3768-3785.
3. Dummer R. Future perspectives in the treatment of cutaneous T-cell lymphoma (CTCL). Semin Oncol 2006: 33: S33-S36.
4. Klemke C D, Goerdt S, Schrama D, Becker J C. New insights into the molecular biology and targeted therapy of cutaneous T-cell lymphomas. J Dtsch Dermatol Ges 2006: 4: 395-406.
5. Pichardo D A, Querfeld C, Guitart J, Kuzel T M, Rosen S T. Cutaneous T-cell lymphoma: A paradigm for biological therapies. Leuk Lymphoma 2004: 45: 1755-1765.
6. Winter D, Fiebiger E, Meraner P et al. Definition of TCR Epitopes for CTL-Mediated Attack of Cutaneous T Cell Lymphoma. J Immunol 2003: 171: 2714-2724.
7. Zeng J, Müller-Berghaus J, Nguyen X D et al. Identification of HLA class I dependent immunogenic peptides from clonotypic TCR expressed in cutaneous T cell lymphoma. Int J Cancer 2006: 119: 2476-2480.
8. Hartmann T B, Mattern E, Wiedemann N et al. Differentially expressed genes in cutaneous T-cell lymphoma. Exp Dermatol 2008: 17: 324-334.
9. Hartmann T B, Thiel D, Dummer R, Schadendorf D, Eichmüller S. SEREX identification of new tumour-associated antigens in cutaneous T-cell lymphoma. Br J Dermatol 2004: 150: 252-258.
10. Eichmüller S, Usener D, Thiel D, Schadendorf D. Tumor-specific antigens in cutaneous T-cell lymphoma: Expression and sero-reactivity. Int J Cancer 2003: 104: 482-487.
11. Eichmüller S, Usener D, Dummer R, Stein A, Thiel D, Schadendorf D. Serological detection of cutaneous T-cell lymphoma-associated antigens. Proc Natl Acad Sci U S A 2001: 98: 629-634.
12. Usener D, Schadendorf D, Koch J, Dubel S, Eichmüller S. cTAGE: A cutaneous T cell lymphoma associated antigen family with tumor-specific splicing. J Invest Dermatol 2003: 121: 198-206.
13. Poszepczynska-Guigne E, Schiavon V, D'Incan M et al. CD158k/KIR3DL2 is a new phenotypic marker of Sezary cells: Relevance for the diagnosis and follow-up of Sezary syndrome. J Invest Dermatol 2004: 122: 820-823.
14. Lee M, Kistler C, Hartmann T B et al. Immunoscreening of a cutaneous T-cell lymphoma library for plasma membrane proteins. Cancer Immunol Immunother 2007: 56: 783-795.
15. Lerner R S, Seiser R M, Zheng T et al. Partitioning and translation of mRNAs encoding soluble proteins on membrane-bound ribosomes. RNA 2003: 9: 1123-1137.
16. Maemura K, de la Monte S M, Chin M T et al. CLIF, a novel cycle-like factor, regulates the circadian oscillation of plasminogen activator inhibitor-1 gene expression. J Biol Chem 2000: 275: 36847-36851.
17. Castello R, Estelles A, Vazquez C et al. Quantitative real-time reverse transcription-PCR assay for urokinase plasminogen activator, plasminogen activator inhibitor type 1, and tissue metalloproteinase inhibitor type 1 gene expressions in primary breast cancer. Clin Chem 2002: 48: 1288-1295.
18. Diatchenko L, Lau Y F, Campbell A P et al. Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A 1996: 93: 6025-6030.
19. Spangenberg C, Winterpacht A, Zabel B U, Lobbert R W. Cloning and characterization of a novel gene (TM7SF1) encoding a putative seven-pass transmembrane protein that is upregulated during kidney development. Genomics 1998: 48: 178-185.
20. Morris N J, Ross S A, Neveu J M, Lane W S, Lienhard G E. Cloning and preliminary characterization of a 121kDa protein with multiple predicted C2 domains. Biochim Biophys Acta 1999: 1431: 525-530.
21. Haffner C, Frauli M, Topp S et al. Nicalin and its binding partner Nomo are novel Nodal signaling antagonists. EMBO J 2004: 23: 3041-3050.
22. Eustace B K, Sakurai T, Stewart J K et al. Functional proteomic screens reveal an essential extracellular role for hsp90 alpha in cancer cell invasiveness. Nat Cell Biol 2004: 6: 507-514.
23. Wong K, Park H T, Wu J Y, Rao Y. Slit proteins: Molecular guidance cues for cells ranging from neurons to leukocytes. Curr Opin Genet Dev 2002: 12: 583-591.
24. Nakada M, Miyamori H, Yamashita J, Sato H. Testican 2 abrogates inhibition of membrane-type matrix metalloproteinases by other testican family proteins. Cancer Res 2003: 63: 3364-3369.
25. Hoeflich A, Reisinger R, Lahm H et al. Insulin-like growth factor-binding protein 2 in tumorigenesis: Protector or promoter? Cancer Res 2001: 61: 8601-8610.
26. Falvella F S, Pascale R M, Gariboldi M et al. Stearoyl-CoA desaturase 1 (Scd1) gene overexpression is associated with genetic predisposition to hepatocarcinogenesis in mice and rats. Carcinogenesis 2002: 23: 1933-1936.
27. Kikuchi K, Ishii N, Asao H, Sugamura K. Identification of AMSH-LP containing a Jab1/MPN domain metalloenzyme motif. Biochem Biophys Res Commun 2003: 306: 637-643.
28. Janssens S, Beyaert R. Functional diversity and regulation of different interleukin-1 receptor-associated kinase (IRAK) family members. Mol Cell 2003: 11: 293-302.
29. Stoss O, Schwaiger F W, Cooper T A, Stamm S. Alternative splicing determines the intracellular localization of the novel nuclear protein Nop30 and its interaction with the splicing factor SRp30c. J Biol Chem 1999: 274: 10951-10962.
30. Muller J, Ory S, Copeland T, Piwnica-Worms H, Morrison D K. C-TAK1 regulates Ras signaling by phosphorylating the MAPK scaffold, KSR1. Mol Cell 2001: 8: 983-993.
31. Chen J, Liu B, Liu Y et al. A novel gene IC53 stimulates ECV304 cell proliferation and is upregulated in failing heart. Biochem Biophys Res Commun 2002: 294: 161-166.
32. Nika J, Erickson F L, Hannig E M. Ribosomal protein L9 is the product of GRC5, a homolog of the putative tumor suppressor QM in S. cerevisiae. Yeast 1997: 13: 1155-1166.
33. Song D, Sakamoto S, Taniguchi T. Inhibition of poly(ADP-ribose) polymerase activity by Bcl-2 in association with the ribosomal protein S3a. Biochemistry 2002: 41: 929-934.
34. Vega F, Medeiros L J, Leventaki V et al. Activation of mammalian target of rapamycin signaling pathway contributes to tumor cell survival in anaplastic lymphoma kinase-positive anaplastic large cell lymphoma. Cancer Res 2006: 66: 6589-6597.
35. Barnard G F, Staniunas R J, Bao S et al. Increased expression of human ribosomal phosphoprotein P0 messenger RNA in hepatocellular carcinoma and colon carcinoma. Cancer Res 1992: 52: 3067-3072.
36. Kim J H, You K R, Kim I H, Cho B H, Kim C Y, Kim D G. Over-expression of the ribosomal protein L36a gene is associated with cellular proliferation in hepatocellular carcinoma. Hepatology 2004: 39: 129-138.
37. Zhu Y, Lin H, Li Z, Wang M, Luo J. Modulation of expression of ribosomal protein L7a (rpL7a) by ethanol in human breast cancer cells. Breast Cancer Res Treat 2001: 69: 29-38.
38. Mambo E, Chatterjee A, Xing M et al. Tumor-specific changes in mtDNA content in human cancer. Int J Cancer 2005: 116: 920-924.
39. Melendez B, Martinez-Delgado B, Cuadros M, Fernandez V, Diaz-Uriarte R, Benitez J. Identification of amplified and highly expressed genes in amplicons of the T-cell line huT78 detected by cDNA microarray CGH. Mol Cancer 2005: 4: 5.
40. Valbuena J R, Rassidakis G Z, Lin P et al. Expression of heat-shock protein-90 in non-Hodgkin's lymphomas. Mod Pathol 2005: 18: 1343-1349.
41. Watarai H, Inagaki Y, Kubota N et al. Proteomic approach to the identification of cell membrane proteins. Electrophoresis 2000: 21: 460-464.
42. Nomiyama H, Egami K, Wada N et al. Identification of genes differentially expressed in osteoclast-like cells. J Interferon Cytokine Res 2005: 25: 227-231.
43. Schier A F. Nodal signaling in vertebrate development. Annu Rev Cell Dev Biol 2003: 19: 589-621.
44. Minchiotti G. Nodal-dependant Cripto signaling in ES cells: From stem cells to tumor biology. Oncogene 2005: 24: 5668-5675.
45. Picard D. Hsp90 invades the outside. Nat Cell Biol 2004: 6: 479-480.
46. Didelot C, Schmitt E, Brunet M, Maingret L, Parcellier A, Garrido C. Heat shock proteins: Endogenous modulators of apoptotic cell death. Handb Exp Pharmacol 2006: 172: 171-198.
47. Sharp S, Workman P. Inhibitors of the HSP90 molecular chaperone: Current status. Adv Cancer Res 2006: 95: 323-348.
48. Wu J Y, Feng L, Park H T et al. The neuronal repellent Slit inhibits leukocyte chemotaxis induced by chemotactic factors. Nature 2001: 410: 948-952.
49. Fujiwara M, Ghazizadeh M, Kawanami O. Potential role of the Slit/Robo signal pathway in angiogenesis. Vasc Med 2006: 11: 115-121.
50. Stevens A, Jacobs J R. Integrins regulate responsiveness to slit repellent signals. J Neurosci 2002: 22: 4448-4455.
51. Dickinson R E, Dallol A, Bieche I et al. Epigenetic inactivation of SLIT3 and SLIT1 genes in human cancers. Br J Cancer 2004: 91: 2071-2078.
52. Latil A, Chene L, Cochant-Priollet B et al. Quantification of expression of netrins, slits and their receptors in human prostate tumors. Int J Cancer 2003: 103: 306-315.
53. Rossi M R, Huntoon K, Cowell J K. Differential expression of the LGI and SLIT families of genes in human cancer cells. Gene 2005: 356: 85-90.
54. Katoh Y, Katoh M. Comparative genomics on SLIT1, SLIT2, and SLIT3 orthologs. Oncol Rep 2005: 14: 1351-1355.
55. Yang F, Zeng Q, Yu G, Li S, Wang C Y. Wnt/beta-catenin signaling inhibits death receptor-mediated apoptosis and promotes invasive growth of HNSCC. Cell Signal 2006: 18: 679-687.
56. Hettmer S, Dannecker L, Foell J, Elmlinger M W, Dannecker G E. Effects of insulin-like growth factors and insulin-like growth factor binding protein-2 on the in vitro proliferation of peripheral blood mononuclear cells. Hum Immunol 2005: 66: 95-103.
57. Wang G K, Hu L, Fuller G N, Zhang W. An interaction between insulin-like growth factor-binding protein 2 (IGFBP2) and integrin alpha5 is essential for IGFBP2-induced cell mobility. J Biol Chem 2006: 281: 14085-14091.
58. Miyake H, Hara I, Yamanaka K, Muramaki M, Gleave M, Eto H. Introduction of insulin-like growth factor binding protein-2 gene into human bladder cancer cells enhances their metastatic potential. Oncol Rep 2005: 13: 341-345.
59. Zhang H, Chung D, Yang Y C et al. Identification of new biomarkers for clinical trials of Hsp90 inhibitors. Mol Cancer Ther 2006: 5: 1256-1264.
60. Yeh C T, Lu S C, Tseng I C et al. Antisense overexpression of BMAL2 enhances cell proliferation. Oncogene 2003: 22: 5306-5314.
61. Koseki T, Inohara N, Chen S, Nunez G. ARC, an inhibitor of apoptosis expressed in skeletal muscle and heart that interacts selectively with caspases. Proc Natl Acad Sci U S A 1998: 95: 5156-5160.
62. Braun F K, Fecker L F, Schwarz C et al. Blockade of death receptor-mediated pathways early in the signaling cascade coincides with distinct apoptosis resistance in cutaneous T-cell lymphoma cells. J Invest Dermatol 2007: 127: 2425-2473.
63. Mercier I, Vuolo M, Madan R et al. ARC, an apoptosis suppressor limited to terminally differentiated cells, is induced in human breast cancer and confers chemo- and radiation-resistance. Cell Death Differ 2005: 12: 682-686.
64. Wang M, Qanungo S, Crow M T, Watanabe M, Nieminen A L. Apoptosis repressor with caspase recruitment domain (ARC) is expressed in cancer cells and localizes to nuclei. FEBS Lett 2005: 579: 2411-2415.
65. Sors A, Jean-Louis F, Pellet C et al. Down-regulating constitutive activation of the NF-kappaB canonical pathway overcomes the resistance of cutaneous T-cell lymphoma to apoptosis. Blood 2006: 107: 2354-2363.
66. Sims J E. IL-1 and IL-18 receptors, and their extended family. Curr Opin Immunol 2002: 14: 117-122.
67. Naora H, Takai I, Adachi M, Naora H. Altered cellular responses by varying expression of a ribosomal protein gene: Sequential coordination of enhancement and suppression of ribosomal protein S3a gene expression induces apoptosis. J Cell Biol 1998: 141: 741-753.
68. Goodin J L, Rutherford C L. Characterization of human ribosomal S3a gene expression during adenosine 3′:5′ cyclic monophosphate induced neuroendocrine differentiation of LNCaP cells. Regulation of S3a gene expression in LNCaP. Mol Biol Rep 2002: 29: 301-316.
69. Hu Z B, Minden M D, McCulloch E A, Stahl J. Regulation of drug sensitivity by ribosomal protein S3a. Blood 2000: 95: 1047-1055.
70. van Doorn R, van Kester M S, Dijkman R et al. Oncogenomic analysis of mycosis fungoides reveals major differences with Sezary syndrome. Blood 2008: Oct 1. [Epub ahead of print].
71. Vermeer M H, van Doorn R, Dijkman R et al. Novel and highly recurrent chromosomal alterations in Sezary syndrome. Cancer Res 2008: 68: 2689-2698.
72. Klemke C D, Fritzsching B, Franz B et al. Paucity of FOXP3(+) cells in skin and peripheral blood distinguishes Sezary syndrome from other cutaneous T-cell lymphomas. Leukemia 2006: 20: 1123-1129.
73. Booken N, Gratchev A, Utikal J et al. Sezary syndrome is a unique cutaneous T-cell lymphoma as identified by an expanded gene signature including diagnostic marker molecules CDO1 and DNM3. Leukemia 2008: 22: 393-399.