Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies vesicular transport and cell junction proteins as differentially expressed genes

Clinical Cancer Research

Volumn 12, Issue 23, 2006, Pages 6937-6945

  Rohan, Stephen ^a   Tu, Jiangling J ^a   Kao, Jean ^a   Mukherjee, Piali ^a   Campagne, Fabien ^a   Zhou, Xi K ^a   Hyjek, Elizabeth ^a   Alonso, Miguel A ^b   Chen, Yao Tseng ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CLAUDIN; GENE PRODUCT; PROTEIN MAL2; VESICULAR TRANSPORT PROTEIN;

ARTICLE; CELL JUNCTION; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION; GENE IDENTIFICATION; HISTOGENESIS; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; KIDNEY CARCINOMA; KIDNEY DISTAL TUBULE; NUCLEOTIDE SEQUENCE; ONCOCYTOMA; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TIGHT JUNCTION; UNINDEXED SEQUENCE;

ADAPTOR PROTEIN COMPLEX 1; ADAPTOR PROTEIN COMPLEX MU SUBUNITS; ADENOMA, OXYPHILIC; CARCINOMA, RENAL CELL; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; HUMANS; INTERCELLULAR JUNCTIONS; KIDNEY NEOPLASMS; MEMBRANE GLYCOPROTEINS; MEMBRANE PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOLIPIDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; RNA-BINDING PROTEINS; SERINE ENDOPEPTIDASES; THYROID NEOPLASMS; TRANSPORT VESICLES; VESICULAR TRANSPORT PROTEINS;

EID: 33845734138     PISSN: 10780432     EISSN: None     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-06-1268     Document Type: Article

References (30)

1. Eble JN, Togashi K, Pisani P, et al. Renal cell carcinoma. In: Eble JN, Sauter G, Epstein Jl, Sesterhenn IA, editors. WHO classification of tumours: pathology and genetics of tumours of the urinary system and male genital organs. Lyon: IARC Press; 2004. p. 10-32.
2. Amin MB, Tamboli P, Javidan J, et al. Prognostic impact of histologic subtyping of adult renal epithelial neoplasms: an experience of 405 cases. Am J Surg Pathol 2002;26:281-91.
3. Storkel S, Steart PV, Drenckhahn D, et al. The human chromophobe cell renal carcinoma: its probable relation to intercalated cells of the collecting duct. Virchows Arch B Cell Pathol Incl Mol Pathol 1989; 56:237-45.
4. Schuetz AN, Yin-Goen Q, Amin MB, et al. Molecular classification of renal tumors by gene expression profiling. J Mol Diagn 2005;7:206-18.
5. Takahashi M, Yang XJ, Sugimura J, et al. Molecular subclassification of kidney tumors and the discovery of new diagnostic markers. Oncogene 2003;22: 6810-8.
6. Young AN, Amin MB, Moreno CS, et al. Expression profiling of renal epithelial neoplasms: a method for tumor classification and discovery of diagnostic molecular markers. Am J Pathol 2001;158:1639-51.
7. Higgins JP, Shinghal R, Gill H, et al. Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarray. Am J Pathol 2003;162: 925-32.
8. Boer JM, Huber WK, Sultmann H, et al. Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31, 500-element cDNA array. Genome Res 2001;11:1861-70.
9. Speicher MR, Schoell B, du Manoir S, et al. Specific loss of chromosomes 1, 2, 6, 10, 13, 17, and 21 in chromophobe renal cell carcinomas revealed by comparative genomic hybridization. Am J Pathol 1994;145: 356-64.
10. Iqbal MA, Akhtar M, Ali MA. Cytogenetic findings in renal cell carcinoma. Hum Pathol 1996;27: 949-54.
11. Brunelli M, Eble JN, Zhang S, Martignoni G, Delahunt B, Cheng L. Eosinophilic and classic chromophobe renal cell carcinoma have similar frequent losses of multiple chromosomes from among chromosomes 1, 2, 6, 10, and 17, and this pattern of genetic abnormality is not present in renal oncocytoma. Mod Pathol 2005;18:161-9.
12. Brown JA, Takahashi S, Alcaraz A, et al. Fluorescence in situ hybridization analysis of renal oncocytoma reveals frequent loss of chromosomes Y and 1. J Urol 1996;156:31-5.
13. Mazal PR, Exner M, Haitel A, et al. Expression of kidney-specific cadherin distinguishes chromophobe renal cell carcinoma from renal oncocytoma. Hum Pathol 2005;36:22-8.
14. Shen SS, Krishna B, Chirala R, Amato RJ, Truong LD. Kidney-specific cadherin, a specific marker for the distal portion of the nephron and related renal neoplasms. Mod Pathol 2005;18:933-40.
15. Wu SL, Kothari P, Wheeler TM, Reese T, Connelly JH. Cytokeratins 7 and 20 immunoreactivity in chromophobe renal cell carcinomas and renal oncocytomas. Mod Pathol 2002;15:712-7.
16. Abrahams NA, MacLennan GT, Khoury JD, et al. Chromophobe renal cell carcinoma: a comparative study of histological, immunohistochemical and ultrastructural features using high throughput tissue microarray. Histopathology 2004;45:593-602.
17. Young AN, de Oliveira Salles PG, Lim SD, et al. β Defensin-1, parvalbumin, and vimentin: a panel of diagnostic immunohistochemical markers for renal tumors derived from gene expression profiling studies using cDNA microarrays. Am J Surg Pathol 2003;27: 199-205.
18. Lin F, Yang W, Betten M, The BT, Yang XJ. The French Kidney Cancer Study Group. Expression of S100 protein in renal cell neoplasms. Hum Pathol 2006;37: 462-70.
19. Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonudeotide array probe level data. Biostatistics 2003;4: 249-64.
20. Benjamini Y, Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B Met 1995;57:289-300.
21. Cortes C, Vapnik V. Support-Vector Networks. Machine Learning 1995;20:273-97.
22. Pavlidis P, Wapinski I, Noble WS. Support vector machine classification on the web. Bioinformatics 2004;20:586-7.
23. Joachims T. Learning to classify text using support vector machines. Dordrecht: Kluwer Academic Publishers; 2001. p. 35-45.
24. Mukherjee S, Tamayo P, Roger S, et al. Estimating data set size requirements for classifying DNA microarray data. J Comput Biol 2003;10:119-42.
25. Chen YT, Tu JJ, Kao J, Zhou XK, Mazumdar M. Messenger RNA expression ratios among four genes predict subtypes of renal cell carcinoma and distinguish oncocytoma from carcinoma. Clin Cancer Res 2005; 11:6558-66.
26. de Marco MC, Martin-Belmonte F, Kremer L, et al. MAL2, a novel raft protein of the MAL family, is an essential component of the machinery for transcytosis in hepatoma HepG2 cells. J Cell Biol 2002;159:37-44.
27. Marazuela M, Acevedo A, Garcia-Lopez MA, Adrados M, de Marco MC, Alonso MA. Expression of MAL2, an integral protein component of the machinery for basolateral-to-apical transcytosis, in human epithelia. J Histochem Cytochem 2004;52: 243-52.
28. Dennis G, Jr., Sherman BT, Hosack DA, et al. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 2003;4:P3.
29. Marazuela M, Martin-Belmonte F, Garcia-Lopez MA, Aranda JF, de Marco MC, Alonso MA. Expression and distribution of MAL2, an essential element of the machinery for basolateral-to-apical transcytosis, in human thyroid epithelial cells. Endocrinology 2004;145:1011-6.
30. Pavlovich CP, Walther MM, Eyler RA, et al. Renal tumors in the Birt-Hogg-Dube syndrome. Am J Surg Pathol 2002;26:1542-52.