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Renal Cell Carcinoma Deep Sequencing: Recent Developments

  • Genitourinary Cancers (E Jonasch, Section Editor)
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Abstract

Renal cell carcinoma (RCC) is the most common type of renal cancer in adults. RCC is notoriously resistant to current therapies suggesting the need to improve our knowledge and create more effective therapies. The molecular genetic defects that occur in RCC are extensive and complex ranging from single DNA changes, to large chromosomal defects, to signature disruptions in the transcription of hundreds of genes. These changes are often shared within each histological RCC subtype, illustrating their significance to the disease phenotype. This review presents an overview of the genetic abnormalities that occur within the most common subtypes of RCC. We discuss the recent molecular findings that have advanced our understanding of the somatic architecture of renal tumors and their impact on disease therapeutics.

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References

Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

  1. Jemal A, Siegel R, Ward E, et al. Cancer statistics, 2009. CA Cancer J Clin. 2009;59:225–49.

    Article  PubMed  Google Scholar 

  2. Maher ER, Kaelin Jr WG. von Hippel-Lindau disease. Med (Baltimore). 1997;76:381–91.

    Article  CAS  Google Scholar 

  3. Latif F, Tory K, Gnarra J, et al. Identification of the von Hippel-Lindau disease tumor suppressor gene. Science. 1993;260(5112):1317–20.

    Article  PubMed  CAS  Google Scholar 

  4. Nickerson ML, Jaeger E, Shi Y, et al. Improved identification of von Hippel-Lindau gene alterations in clear cell renal tumors. Clin Cancer Res. 2008;14(15):4726–34.

    Article  PubMed  CAS  Google Scholar 

  5. Beroukhim R, Brunet JP, Di Napoli A, et al. Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney. Cancer Res. 2009;69(11):4674–81.

    Article  PubMed  CAS  Google Scholar 

  6. Young AP, Schlisio S, Minamishima YA, et al. VHL loss actuates a HIF-independent senescence programme mediated by Rb and p400. Nat Cell Biol. 2008;10:361–9.

    Article  PubMed  CAS  Google Scholar 

  7. Young AP, Kaelin Jr WG. Senescence triggered by the loss of the VHL tumor suppressor. Cell Cycle. 2008;7(12):1709–12.

    Article  PubMed  CAS  Google Scholar 

  8. •• Varela I, Tarpey P, Raine K, et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature. 2011;469(7331):539–42. This study identified the most promising cancer gene associated with ccRCC since VHL as a prognostic and predictive marker.

    Article  PubMed  CAS  Google Scholar 

  9. van Haaften G, Dalgliesh GL, Davies H, et al. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nat Genet. 2009;41(5):521–3.

    Article  PubMed  CAS  Google Scholar 

  10. Dalgliesh GL, Furge K, Greenman C, et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature. 2010;463(7279):360–3.

    Article  PubMed  CAS  Google Scholar 

  11. Wiegand KC, Shah SP, Al-Agha OM, et al. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010;363(16):1532–43.

    Article  PubMed  CAS  Google Scholar 

  12. Jones S, Wang TL, Shih IeM, et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science. 2010;330(6001):228–31.

    Article  PubMed  CAS  Google Scholar 

  13. Wang X, Nagl Jr NG, Flowers S, et al. Expression of p270 (ARID1A), a component of human SWI/SNF complexes, in human tumors. Int J Cancer. 2004;112(4):636.

    Article  PubMed  CAS  Google Scholar 

  14. Orlovsky K, Kalinkovich A, Rozovskaia T, et al. Down-regulation of homeobox genes MEIS1 and HOXA in MLL-rearranged acute leukemia impairs engraftment and reduces proliferation. Proc Natl Acad Sci U S A. 2011;108(19):7956–61.

    Article  PubMed  CAS  Google Scholar 

  15. Niu X, Zhang T, Liao L, et al. The von Hippel-Lindau tumor suppressor protein regulates gene expression and tumor growth through histone demethylase JARID1C. Oncogene. 2011 Jul 4

  16. Abidi FE, Holloway L, Moore CA, et al. Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia. J Med Genet. 2008;45(12):787–93.

    Article  PubMed  CAS  Google Scholar 

  17. Adegbola A, Gao H, Sommer S, Browning M. A novel mutation in JARID1C/SMCX in a patient with autism spectrum disorder (ASD). Am J Med Genet A. 2008;146A(4):505–11.

    Article  PubMed  CAS  Google Scholar 

  18. Santos-Rebouças CB, Fintelman-Rodrigues N, Jensen LR, et al. A novel nonsense mutation in KDM5C/JARID1C gene causing intellectual disability, short stature and speech delay. Neurosci Lett. 2011;498(1):67–71.

    Article  PubMed  CAS  Google Scholar 

  19. Edmunds JW, Mahadevan LC, Clayton AL. Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J. 2008;27(2):406–20.

    Article  PubMed  CAS  Google Scholar 

  20. Duns G, van den Berg E, van Duivenbode I, et al. Histone methyltransferase gene SETD2 is a novel tumor suppressor gene in clear cell renal cell carcinoma. Cancer Res. 2010;70(11):4287–91.

    Article  PubMed  CAS  Google Scholar 

  21. Guo G, Gui Y, Gao S, Tang A, et al. Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet. 2012;44(1):17–9.

    Article  CAS  Google Scholar 

  22. Elfving P, Mandahl N, Lundgren R, et al. Prognostic implications of cytogenetic findings in kidney cancer. Br J Urol. 1997;80(5):698–706.

    Article  PubMed  CAS  Google Scholar 

  23. Schullerus D, Herbers J, Chudek J, Kanamaru H, Kovacs G. Loss of heterozygosity at chromosomes 8p, 9p, and 14q is associated with stage and grade of non-papillary renal cell carcinomas. J Pathol. 1997;183(2):151–5.

    Article  PubMed  CAS  Google Scholar 

  24. Herbers J, Schullerus D, Müller H, et al. Significance of chromosome arm 14q loss in nonpapillary renal cell carcinomas. Gene Chromosome Canc. 1997;19(1):29–35.

    Article  CAS  Google Scholar 

  25. Alimov A, Sundelin B, Wang N, Larsson C, Bergerheim U. Loss of 14q31-q32.2 in renal cell carcinoma is associated with high malignancy grade and poor survival. Int J Oncol. 2004;25(1):179–85.

    PubMed  CAS  Google Scholar 

  26. Shen C, Beroukhim R, Schumacher SE, et al. Genetic and functional studies implicate HIF1α as a 14q kidney cancer suppressor gene. Canc Discov. 2011;1:222–35.

    Article  CAS  Google Scholar 

  27. • Dondeti VR, Wubbenhorst B, Lal P, et al. Integrative genomic analyses of sporadic clear cell renal cell carcinoma define disease subtypes and potential new therapeutic targets. Cancer Res. 2012;72(1):112–21. This study advances our understanding ccRCCs by identifying two potential chromosome 5q oncogenes.

    Article  PubMed  CAS  Google Scholar 

  28. • Purdue MP, Johansson M, Zelenika D, et al. Genome-wide association study of renal cell carcinoma identifies two susceptibility loci on 2p21 and 11q13.3. Nat Genet. 2011;43(1):60–5. This study directly implicates mutations in the HIF to RCC tumorigenesis.

    Article  PubMed  CAS  Google Scholar 

  29. Han SS, Yeager M, Moore LE, et al. The chromosome 2p21 region harbors a complex genetic architecture for association with risk for renal cell carcinoma. Hum Mol Genet. 2011, Dec 20

  30. Duesberg P, Stindl R, Li R, et al. Aneuploidy verses gene mutations as cause of cancer. Curr Sci. 2001;81:490–500.

    Google Scholar 

  31. Kovacs G, Akhtar M, Beckwith BJ, et al. The Heidelberg classification of renal cell tumours. J Pathol. 1997;183(2):131–3.

    Article  PubMed  CAS  Google Scholar 

  32. Klatte T, Pantuck AJ, Said JW, et al. Cytogenetic and molecular tumor profiling for type 1 and type 2 papillary renal cell carcinoma. Clin Cancer Res. 2009;15(4):1162–9.

    Article  PubMed  CAS  Google Scholar 

  33. Toma MI, Grosser M, Herr A, et al. Loss of heterozygosity and copy number abnormality in clear cell renal cell carcinoma discovered by high-density affymetrix 10 K single nucleotide polymorphism mapping array. Neoplasia. 2008;10(7):634–42.

    PubMed  CAS  Google Scholar 

  34. Brunelli M, Eccher A, Gobbo S, et al. Loss of chromosome 9p is an independent prognostic factor in patients with clear cell renal cell carcinoma. Mod Pathol. 2008;21(1):1–6.

    Article  PubMed  CAS  Google Scholar 

  35. Hagenkord JM, Parwani AV, Lyons-Weiler MA, et al. Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors. Diagn Pathol. 2008;3:44.

    Article  PubMed  CAS  Google Scholar 

  36. Cohen AJ, Li FP, Berg S, et al. Hereditary renal-cell carcinoma associated with a chromosomal translocation. N Engl J Med. 1979;301(11):592–5.

    Article  PubMed  CAS  Google Scholar 

  37. Zbar B, Brauch H, Talmadge C, Linehan M. Loss of alleles of loci on the short arm of chromosome 3 in renal cell carcinoma. Nature. 1987;327(6124):721–4.

    Article  PubMed  CAS  Google Scholar 

  38. Kovacs G, Brusa P. Recurrent genomic rearrangements are not at the fragile sites on chromosomes 3 and 5 in human renal cell carcinomas. Hum Genet. 1988;80:99–101.

    Article  PubMed  CAS  Google Scholar 

  39. Glover TW, Coyle-Morris JF, Li FP, et al. Translocation t(3;8)(p14.2;q24.1) in renal cell carcinoma affects expression of the common fragile site at 3p14(FRA3B) in lymphocytes. Canc Genet Cytogenet. 1988;31(1):69–73.

    Article  CAS  Google Scholar 

  40. Tajara EH, Berger CS, Hecht BK, et al. Loss of common 3p14 fragile site expression in renal cell carcinoma with deletion breakpoint at 3p14. Canc Genet Cytogenet. 1988;31(1):75–82.

    Article  CAS  Google Scholar 

  41. Shridhar V, Rivard S, Shridhar R, et al. A gene from human chromosomal band 3p21.1 encodes a highly conserved arginine-rich protein and is mutated in renal cell carcinomas. Oncogene. 1996;12(9):1931–9.

    PubMed  CAS  Google Scholar 

  42. Gunawan B, Huber W, Holtrup M, et al. Prognostic impacts of cytogenetic findings in clear cell renal cell carcinoma: gain of 5q31-qter predicts a distinct clinical phenotype with favorable prognosis. Cancer Res. 2001;61:7731–8.

    PubMed  CAS  Google Scholar 

  43. Monzon FA, Alvarez K, Peterson L, et al. Chromosome 14q loss defines a molecular subtype of clear-cell renal cell carcinoma associated with poor prognosis. Mod Pathol. 2011;24:1470–9.

    Article  PubMed  CAS  Google Scholar 

  44. Moch H, Presti Jr JC, Sauter G, et al. Genetic aberrations detected by comparative genomic hybridization are associated with clinical outcome in renal cell carcinoma. Cancer Res. 1996;56(1):27–30.

    PubMed  CAS  Google Scholar 

  45. Nagao K, Yamaguchi S, Matsuyama H, et al. Allelic loss of 3p25 associated with alterations of 5q22.3 approximately q23.2 may affect the prognosis of conventional renal cell carcinoma. Canc Genet Cytogenet. 2005;160(1):43–8.

    Article  CAS  Google Scholar 

  46. Junker K, Moravek P, Podhola M, et al. Genetic alterations in metastatic renal cell carcinoma detected by comparative genomic hybridization: correlation with clinical and histological data. Int J Oncol. 2000;17(5):903–8.

    PubMed  CAS  Google Scholar 

  47. Amin MB, Corless CL, Renshaw AA, Tickoo SK, Kubus J, Schultz DS. Papillary (chromophil) renal cell carcinoma: histomorphologic characteristics and evaluation of conventional pathologic prognostic parameters in 62 cases. Am J Surg Pathol. 1997;21(6):621–35.

    Article  PubMed  CAS  Google Scholar 

  48. Jiang F, Richter J, Schraml P, et al. Chromosomal imbalances in papillary renal cell carcinoma: genetic differences between histological subtypes. Am J Pathol. 1998;153(5):1467–73.

    Article  PubMed  CAS  Google Scholar 

  49. Delahunt B, Furge K, Greenman C, et al. Morphologic typing of papillary renal cell carcinoma: comparison of growth kinetics and patient survival in 66 cases. Hum Pathol. 2001;32(6):590–5.

    Article  PubMed  CAS  Google Scholar 

  50. Pignot G, Elie C, Conquy S, et al. Survival analysis of 130 patients with papillary renal cell carcinoma: prognostic utility of type 1 and type 2 subclassification. Urology. 2007;69(2):230–5.

    Article  PubMed  Google Scholar 

  51. Gunawan B, von Heydebreck A, Fritsch T, et al. Cytogenetic and morphologic typing of 58 papillary renal cell carcinomas: evidence for a cytogenetic evolution of type 2 from type 1 tumors. Cancer Res. 2003;63(19):6200–5.

    PubMed  CAS  Google Scholar 

  52. Waldert M, Haitel A, Marberger M, et al. Comparison of type I and II papillary renal cell carcinoma (RCC) and clear cell RCC. BJU Int. 2008;102(10):1381–4.

    PubMed  Google Scholar 

  53. Yang XJ, Tan MH, Kim HL, et al. A molecular classification of papillary renal cell carcinoma. Cancer Res. 2005;65(13):5628–37.

    Article  PubMed  CAS  Google Scholar 

  54. Furge KA, Tan MH, Dykema K, et al. Identification of deregulated oncogenic pathways in renal cell carcinoma: an integrated oncogenomic approach based on gene expression profiling. Oncogene. 2007;26(9):1346–50.

    Article  PubMed  CAS  Google Scholar 

  55. Schmidt L, Duh FM, Chen F, et al. Germline and somatic mutations in the tyrosine kinase domain of the MET proto-oncogene in papillary renal carcinomas. Nat Genet. 1997;16(1):68–73.

    Article  PubMed  CAS  Google Scholar 

  56. Schmidt L, Junker K, Nakaigawa N, et al. Novel mutations of the MET proto-oncogene in papillary renal carcinomas. Oncogene. 1999;18(14):2343–50.

    Article  PubMed  CAS  Google Scholar 

  57. Lubensky IA, Schmidt L, Zhuang Z, et al. Hereditary and sporadic papillary renal carcinomas with c-met mutations share a distinct morphological phenotype. Am J Pathol. 1999;155(2):517–26.

    Article  PubMed  CAS  Google Scholar 

  58. Bellon SF, Kaplan-Lefko P, Yang Y, et al. c-Met inhibitors with novel binding mode show activity against several hereditary papillary renal cell carcinoma-related mutations. J Biol Chem. 2008;283(5):2675–83.

    Article  PubMed  CAS  Google Scholar 

  59. Koski TA, Lehtonen HJ, Jee KJ, et al. Array comparative genomic hybridization identifies a distinct DNA copy number profile in renal cell cancer associated with hereditary leiomyomatosis and renal cell cancer. Gene Chromosome Canc. 2009;48(7):544–51.

    Article  CAS  Google Scholar 

  60. Looyenga BD, Furge KA, Dykema KJ, et al. Chromosomal amplification of leucine-rich repeat kinase-2 (LRRK2) is required for oncogenic MET signaling in papillary renal and thyroid carcinomas. Proc Natl Acad Sci U S A. 2011;108(4):1439–44.

    Article  PubMed  Google Scholar 

  61. Tomlinson IP, Alam NA, Rowan AJ, et al. Germline mutations in FH predispose to dominantly inherited uterine fibroids, skin leiomyomata and papillary renal cell cancer. Nat Genet. 2002;30(4):406–10.

    Article  PubMed  CAS  Google Scholar 

  62. Toro JR, Nickerson ML, Wei MH, et al. Mutations in the fumarate hydratase gene cause hereditary leiomyomatosis and renal cell cancer in families in North America. Am J Hum Genet. 2003;73(1):95–106.

    Article  PubMed  CAS  Google Scholar 

  63. Lehtonen HJ, Kiuru M, Ylisaukko-Oja SK, et al. Increased risk of cancer in patients with fumarate hydratase germline mutation. J Med Genet. 2006;43(6):523–6.

    Article  PubMed  CAS  Google Scholar 

  64. Refae MA, Wong N, Patenaude F, et al. Hereditary leiomyomatosis and renal cell cancer: an unusual and aggressive form of hereditary renal carcinoma. Nat Clin Pract Oncol. 2007;4(4):256–61.

    Article  PubMed  CAS  Google Scholar 

  65. Toro JR, Wei MH, Glenn GM, et al. BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dube syndrome: a new series of 50 families and a review of published reports. J Med Genet. 2008;45(6):321–31.

    Article  PubMed  CAS  Google Scholar 

  66. Wei MH, Toure O, Glenn GM, et al. Novel mutations in FH and expansion of the spectrum of phenotypes expressed in families with hereditary leiomyomatosis and renal cell cancer. J Med Genet. 2006;43(1):18–27.

    Article  PubMed  CAS  Google Scholar 

  67. Lehtonen HJ, Blanco I, Piulats JM, et al. Conventional renal cancer in a patient with fumarate hydratase mutation. Hum Pathol. 2007;38(5):793–6.

    Article  PubMed  CAS  Google Scholar 

  68. Adam J, Hatipoglu E, O’Flaherty L, et al. Renal cyst formation in Fh1-deficient mice is independent of the Hif/Phd pathways: roles for fumarate in KEAP1 succination and Nrf2 signaling. Canc Cell. 2011;20:524–37.

    Article  CAS  Google Scholar 

  69. Ooi A, Wong JC, Petillo D, et al. An antioxidant response phenotype shared between hereditary and sporadic type 2 papillary renal cell carcinoma. Canc Cell. 2011;20:511–23.

    Article  CAS  Google Scholar 

  70. Delahunt B, Eble JN. Papillary renal cell carcinoma: a clinicopathologic and immunohistochemical study of 105 tumors. Mod Pathol. 1997;10(6):537–44.

    PubMed  CAS  Google Scholar 

  71. Schuetz AN, Yin-Goen Q, Amin MB, et al. Molecular classification of renal tumors by gene expression profiling. J Mol Diagn. 2005;7(2):206–18.

    Article  PubMed  CAS  Google Scholar 

  72. Mayr JA, Meierhofer D, Zimmermann F, et al. Loss of complex I due to mitochondrial DNA mutations in renal oncocytoma. Clin Cancer Res. 2008;14(8):2270–5.

    Article  PubMed  CAS  Google Scholar 

  73. Gasparre G, Hervouet E, de Laplanche E, et al. Clonal expansion of mutated mitochondrial DNA is associated with tumor formation and complex I deficiency in the benign renal oncocytoma. Hum Mol Genet. 2008;17(7):986–95.

    Article  PubMed  CAS  Google Scholar 

  74. Kovacs A, Storkel S, Thoenes W, Kovacs G. Mitochondrial and chromosomal DNA alterations in human chromophobe renal cell carcinomas. J Pathol. 1992;167(3):273–7.

    Article  PubMed  CAS  Google Scholar 

  75. Welter C, Kovacs G, Seitz G, Blin N. Alteration of mitochondrial DNA in human oncocytomas. Gene Chromosome Canc. 1989;1(1):79–82.

    Article  CAS  Google Scholar 

  76. Brunelli M, Eble JN, Zhang S, et al. Eosinophilic and classic chromophobe renal cell carcinomas 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(2):161–9.

    Article  PubMed  CAS  Google Scholar 

  77. Takahashi M, Yang XJ, Sugimura J, et al. Molecular sub-classification of kidney cancer and the discovery of new diagnostic markers. Oncogene. 2003;22:6810–8.

    Article  PubMed  CAS  Google Scholar 

  78. 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(3):925–32.

    Article  PubMed  CAS  Google Scholar 

  79. Brown JA, Takahashi S, Alcaraz A, et al. Fluorescence in situ hybriziation analysis of renal oncocytoma reveals frequent loss of chromosomes Y and 1. J Urol. 1996;156:31–5.

    Article  PubMed  CAS  Google Scholar 

  80. Paner GP, Lindgren V, Jacobson K, et al. High incidence of chromosome 1 abnormalities in a series of 27 renal oncocytomas: cytogenetic and fluorescence in situ hybridzation studies. Arch Pathol Lab Med. 2006;131:81–5.

    Google Scholar 

  81. Fuzesi L, Gunawan B, Braun S, et al. Cytogenetic analysis of 11 renal oncocytomas: further evidence of structural rearrangments of 11q13 as a characteristics of chromosomal anomaly. Canc Genet Cytogenet. 1999;107:1–6.

    Article  Google Scholar 

  82. Takahashi M, Rhodes DR, Furge KA, et al. Gene expression profiling of clear cell renal cell carcinoma: gene identification and prognostic classification. Proc Natl Acad Sci U S A. 2001;98(17):9754–9.

    Article  PubMed  CAS  Google Scholar 

  83. Gieseg MA, Cody T, Man MZ, et al. Expression profiling of human renal carcinomas with functional taxonomic analysis. BMC Bioinforma. 2002;3:26.

    Article  Google Scholar 

  84. Boer JM, Huber WK, Sültmann 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(11):1861–70.

    PubMed  CAS  Google Scholar 

  85. Jones J, Otu H, Spentzos D, et al. Gene signatures of progression and metastasis in renal cell cancer. Clin Cancer Res. 2005;11(16):5730–9.

    Article  PubMed  CAS  Google Scholar 

  86. Liou LS, Shi T, Duan ZH, et al. Microarray gene expression profiling and analysis in renal cell carcinoma. BMC Urol. 2004;4:9.

    Article  PubMed  Google Scholar 

  87. Yamazaki K, Sakamoto M, Ohta T, et al. Overexpression of KIT in chromophobe renal cell carcinoma. Oncogene. 2003;22(6):847–52.

    Article  PubMed  CAS  Google Scholar 

  88. Skubitz KM, Skubitz AP. Differential gene expression in renal-cell cancer. J Lab Clin Med. 2002;140(1):52–64.

    Article  PubMed  CAS  Google Scholar 

  89. Skubitz KM, Zimmermann W, Kammerer R, et al. Differential gene expression identifies subgroups of renal cell carcinoma. J Lab Clin Med. 2006;147(5):250–67.

    Article  PubMed  CAS  Google Scholar 

  90. Furge KA, Dykema K, Petillo D, et al. Combining differential expression, chromosomal and pathway analyses for the molecular characterization of renal cell carcinoma. Can Urol Assoc J. 2007;1(2 Suppl):S21–7.

    PubMed  Google Scholar 

  91. Zhou M, Kort E, Hoekstra P, et al. Adult cystic nephroma and mixed epithelial and stromal tumor of the kidney are the same disease entity: molecular and histologic evidence. Am J Surg Pathol. 2009;33(1):72–80.

    Article  PubMed  Google Scholar 

  92. Moch H, Schraml P, Bubendorf L, et al. High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma. Am J Pathol. 1999;154(4):981–6.

    Article  PubMed  CAS  Google Scholar 

  93. Li G, Barthelemy A, Feng G, et al. S100A1: a powerful marker to differentiate chromophobe renal cell carcinoma from renal oncocytoma. Histopathology. 2007;50(5):642–7.

    Article  PubMed  CAS  Google Scholar 

  94. Lin F, Yang W, Betten M, et al. Expression of S-100 protein in renal cell neoplasms. Hum Pathol. 2006;37(4):462–70.

    Article  PubMed  CAS  Google Scholar 

  95. Rocca PC, Brunelli M, Gobbo S, et al. Diagnostic utility of S100A1 expression in renal cell neoplasms: an immunohistochemical and quantitative RT-PCR study. Mod Pathol. 2007;20(7):722–8.

    Article  PubMed  CAS  Google Scholar 

  96. Yao M, Huang Y, Shioi K, et al. Expression of adipose differentiation-related protein: a predictor of cancer-specific survival in clear cell renal carcinoma. Clin Cancer Res. 2007;13(1):152–60.

    Article  PubMed  CAS  Google Scholar 

  97. Kosari F, Parker AS, Kube DM, et al. Clear cell renal cell carcinoma: gene expression analyses identify a potential signature for tumor aggressiveness. Clin Cancer Res. 2005;11(14):5128–39.

    Article  PubMed  CAS  Google Scholar 

  98. Zhao H, Ljungberg B, Grankvist K, et al. Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med. 2006;3(1):e13.

    Article  PubMed  CAS  Google Scholar 

  99. Tsui KH, Shvarts O, Smith RB, et al. Prognostic indicators for renal cell carcinoma: a multivariate analysis of 643 patients using the revised 1997 TNM staging criteria. J Urol. 2000;163(4):1090–5. quiz 1295.

    Article  PubMed  CAS  Google Scholar 

  100. Gettman MT, Blute ML, Spotts B, et al. Pathologic staging of renal cell carcinoma: significance of tumor classification with the 1997 TNM staging system. Cancer. 2001;91(2):354–61.

    Article  PubMed  CAS  Google Scholar 

  101. Han KR, Bleumer I, Pantuck AJ, et al. Validation of an integrated staging system toward improved prognostication of patients with localized renal cell carcinoma in an international population. J Urol. 2003;170(6 Pt 1):2221–4.

    Article  PubMed  Google Scholar 

  102. Zisman A, Pantuck AJ, Dorey F, et al. Improved prognostication of renal cell carcinoma using an integrated staging system. J Clin Oncol. 2001;19(6):1649–57.

    PubMed  CAS  Google Scholar 

  103. Staller P, Sulitkova J, Lisztwan J, et al. Chemokine receptor CXCR4 downregulated by von Hippel-Lindau tumour suppressor pVHL. Nature. 2003;425(6955):307–11.

    Article  PubMed  CAS  Google Scholar 

  104. Yao M, Tabuchi H, Nagashima Y, et al. Gene expression analysis of renal carcinoma: adipose differentiation-related protein as a potential diagnostic and prognostic biomarker for clear-cell renal carcinoma. J Pathol. 2005;205(3):377–87.

    Article  PubMed  CAS  Google Scholar 

  105. Desai KV, Xiao N, Wang W, et al. Initiating oncogenic event determines gene-expression patterns of human breast cancer models. Proc Natl Acad Sci U S A. 2002;99(10):6967–72.

    Article  PubMed  CAS  Google Scholar 

  106. Ferrando AA, Neuberg DS, Staunton J, et al. Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Canc Cell. 2002;1(1):75–87.

    Article  CAS  Google Scholar 

  107. Huang E, Ishida S, Pittman J, et al. Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet. 2003;34:226–30.

    Article  PubMed  CAS  Google Scholar 

  108. Sweet-Cordero A, Mukherjee S, Subramanian A, et al. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet. 2005;37(1):48–55.

    PubMed  CAS  Google Scholar 

  109. Bild AH, Yao G, Chang JT, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 2006;439:353–7.

    Article  PubMed  CAS  Google Scholar 

  110. Chi JT, Wang Z, Nuyten DS, et al. Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med. 2006;3(3):e47.

    Article  PubMed  CAS  Google Scholar 

  111. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–50.

    Article  PubMed  CAS  Google Scholar 

  112. Kim S, Volsky DJ. PAGE: parametric analysis of gene set enrichment. BMC Bioinforma. 2005;6:144.

    Article  CAS  Google Scholar 

  113. Riss J, Khanna C, Koo S, et al. Cancers as wounds that do not heal: differences and similarities between renal regeneration/repair and renal cell carcinoma. Cancer Res. 2006;66(14):7216–24.

    Article  PubMed  CAS  Google Scholar 

  114. Copland JA, Luxon BA, Ajani L, et al. Genomic profiling identifies alterations in TGFbeta signaling through loss of TGFbeta receptor expression in human renal cell carcinogenesis and progression. Oncogene. 2003;22(39):8053–62.

    Article  PubMed  CAS  Google Scholar 

  115. Furge KA, Chen J, Koeman J, et al. Detection of DNA copy number changes and oncogenic signaling abnormalities from gene expression data reveals MYC activation in high-grade papillary renal cell carcinoma. Cancer Res. 2007;67(7):3171–6.

    Article  PubMed  CAS  Google Scholar 

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Farber, L.J., Furge, K. & Teh, B.T. Renal Cell Carcinoma Deep Sequencing: Recent Developments. Curr Oncol Rep 14, 240–248 (2012). https://doi.org/10.1007/s11912-012-0230-3

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  • DOI: https://doi.org/10.1007/s11912-012-0230-3

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