title: Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma.
abstract: BACKGROUND
  Chromophobe renal cell carcinoma (chRCC) and renal oncocytoma are two distinct but closely related entities with strong morphologic and genetic similarities. While chRCC is a malignant tumor, oncocytoma is usually regarded as a benign entity. The overlapping characteristics are best explained by a common cellular origin, and the biologic differences between chRCC and oncocytoma are therefore of considerable interest in terms of carcinogenesis, diagnosis and clinical management. Previous studies have been relatively limited in terms of examining the differences between oncocytoma and chromophobe RCC.
  
  
  METHODS
  Gene expression profiling using the Affymetrix HGU133Plus2 platform was applied on chRCC (n = 15) and oncocytoma specimens (n = 15). Supervised analysis was applied to identify a discriminatory gene signature, as well as differentially expressed genes. High throughput single-nucleotide polymorphism (SNP) genotyping was performed on independent samples (n = 14) using Affymetrix GeneChip Mapping 100 K arrays to assess correlation between expression and gene copy number. Immunohistochemical validation was performed in an independent set of tumors.
  
  
  RESULTS
  A novel 14 probe-set signature was developed to classify the tumors internally with 93% accuracy, and this was successfully validated on an external data-set with 94% accuracy. Pathway analysis highlighted clinically relevant dysregulated pathways of c-erbB2 and mammalian target of rapamycin (mTOR) signaling in chRCC, but no significant differences in p-AKT or extracellular HER2 expression was identified on immunohistochemistry. Loss of chromosome 1p, reflected in both cytogenetic and expression analysis, is common to both entities, implying this may be an early event in histogenesis. Multiple regional areas of cytogenetic alterations and corresponding expression biases differentiating the two entities were identified. Parafibromin, aquaporin 6, and synaptogyrin 3 were novel immunohistochemical markers effectively discriminating the two pathologic entities.
  
  
  CONCLUSIONS
  Gene expression profiles, high-throughput SNP genotyping, and pathway analysis effectively distinguish chRCC from oncocytoma. We have generated a novel transcript predictor that is able to discriminate between the two entities accurately, and which has been validated both in an internal and an independent data-set, implying generalizability. A cytogenetic alteration, loss of chromosome 1p, common to renal oncocytoma and chRCC has been identified, providing the opportunities for identifying novel tumor suppressor genes and we have identified a series of immunohistochemical markers that are clinically useful in discriminating chRCC and oncocytoma.
authors.affiliation: Laboratory of Cancer Genetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA. tan.min.han@nccs.com.sg
authors.forename: Min-Han
authors.initials: MH
authors.lastname: Tan
authors.forename: Chin Fong
authors.initials: CF
authors.lastname: Wong
authors.forename: Hwei Ling
authors.initials: HL
authors.lastname: Tan
authors.forename: Ximing J
authors.initials: XJ
authors.lastname: Yang
authors.forename: Jonathon
authors.initials: J
authors.lastname: Ditlev
authors.forename: Daisuke
authors.initials: D
authors.lastname: Matsuda
authors.forename: Sok Kean
authors.initials: SK
authors.lastname: Khoo
authors.forename: Jun
authors.initials: J
authors.lastname: Sugimura
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Fujioka
authors.forename: Kyle A
authors.initials: KA
authors.lastname: Furge
authors.forename: Eric
authors.initials: E
authors.lastname: Kort
authors.forename: Sophie
authors.initials: S
authors.lastname: Giraud
authors.forename: Sophie
authors.initials: S
authors.lastname: Ferlicot
authors.forename: Philippe
authors.initials: P
authors.lastname: Vielh
authors.forename: Delphine
authors.initials: D
authors.lastname: Amsellem-Ouazana
authors.forename: Bernard
authors.initials: B
authors.lastname: Debré
authors.forename: Thierry
authors.initials: T
authors.lastname: Flam
authors.forename: Nicolas
authors.initials: N
authors.lastname: Thiounn
authors.forename: Marc
authors.initials: M
authors.lastname: Zerbib
authors.forename: Gérard
authors.initials: G
authors.lastname: Benoît
authors.forename: Stéphane
authors.initials: S
authors.lastname: Droupy
authors.forename: Vincent
authors.initials: V
authors.lastname: Molinié
authors.forename: Annick
authors.initials: A
authors.lastname: Vieillefond
authors.forename: Puay Hoon
authors.initials: PH
authors.lastname: Tan
authors.forename: Stéphane
authors.initials: S
authors.lastname: Richard
authors.forename: Bin Tean
authors.initials: BT
authors.lastname: Teh
mesh_terms: D018249:Adenoma, Oxyphilic / Q000737:chemistry / Q000175:diagnosis / Q000235:genetics*; D051403:Aquaporin 6 / Q000032:analysis; D014408:Biomarkers, Tumor / Q000032:analysis / Q000235:genetics*; D002292:Carcinoma, Renal Cell / Q000737:chemistry / Q000175:diagnosis / Q000235:genetics*; D002878:Chromosomes, Human, Pair 1; D020732:Cytogenetic Analysis; D003937:Diagnosis, Differential; D018628:Gene Dosage; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D007150:Immunohistochemistry; D007680:Kidney Neoplasms / Q000737:chemistry / Q000175:diagnosis / Q000235:genetics*; D008565:Membrane Proteins / Q000032:analysis; D009419:Nerve Tissue Proteins / Q000032:analysis; D016017:Odds Ratio; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D011237:Predictive Value of Tests; D015203:Reproducibility of Results; D062805:Synaptogyrins; D025521:Tumor Suppressor Proteins / Q000032:analysis
chemical_list: C102226:AQP6 protein, human; D051403:Aquaporin 6; D014408:Biomarkers, Tumor; C454900:CDC73 protein, human; D008565:Membrane Proteins; D009419:Nerve Tissue Proteins; C540370:SYNGR3 protein, human; D062805:Synaptogyrins; D025521:Tumor Suppressor Proteins
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