Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma.
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.
Tan
Min-Han
MH
Laboratory of Cancer Genetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA. tan.min.han@nccs.com.sg
Wong
Chin Fong
CF
Tan
Hwei Ling
HL
Yang
Ximing J
XJ
Ditlev
Jonathon
J
Matsuda
Daisuke
D
Khoo
Sok Kean
SK
Sugimura
Jun
J
Fujioka
Tomoaki
T
Furge
Kyle A
KA
Kort
Eric
E
Giraud
Sophie
S
Ferlicot
Sophie
S
Vielh
Philippe
P
Amsellem-Ouazana
Delphine
D
Debré
Bernard
B
Flam
Thierry
T
Thiounn
Nicolas
N
Zerbib
Marc
M
Benoît
Gérard
G
Droupy
Stéphane
S
Molinié
Vincent
V
Vieillefond
Annick
A
Tan
Puay Hoon
PH
Richard
Stéphane
S
Teh
Bin Tean
BT
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
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
Oncogene. 2001 Aug 23;20(37):5239-42
11526515
J Comp Neurol. 2004 Mar 8;470(3):266-81
14755516
Cell. 2006 Apr 21;125(2):327-41
16630820
Proc Natl Acad Sci U S A. 2002 May 14;99(10):6567-72
12011421
Genome Biol. 2004;5(10):R80
15461798
Am J Clin Pathol. 2008 Mar;129(3):377-82
18285259
Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21
11309499
Oncogene. 2007 May 17;26(23):3440-9
17130827
Clin Cancer Res. 2004 Sep 15;10(18 Pt 2):6315S-21S
15448024
Cancer Res. 2004 May 1;64(9):3060-71
15126342
Clin Cancer Res. 2006 Dec 1;12(23):6937-45
17145811
Cancer Res. 2005 Jul 1;65(13):5628-37
15994935
Cancer Cell. 2002 Aug;2(2):157-64
12204536
J Mol Diagn. 2005 May;7(2):206-18
15858144
J Clin Endocrinol Metab. 2004 Feb;89(2):994-1005
14764826
Int J Cancer. 2000 Aug 1;87(3):349-59
10897039
Am J Surg Pathol. 2003 May;27(5):612-24
12717246
Am J Surg Pathol. 1998 Apr;22(4):419-24
9537468
Hum Genet. 1996 Jun;97(6):770-6
8641695
Oncogene. 2003 Oct 2;22(43):6810-8
14555994
Clin Cancer Res. 2004 Oct 1;10(19):6629-37
15475453
Hum Mol Genet. 2008 Apr 1;17(7):986-95
18156159
Cancer Res. 2004 Jun 15;64(12):4117-21
15205321
J Clin Pathol. 2008 Jan;61(1):64-7
17468290
Am J Pathol. 1996 Dec;149(6):2081-8
8952540
N Engl J Med. 2007 May 31;356(22):2271-81
17538086
Proc Natl Acad Sci U S A. 1999 May 11;96(10):5808-13
10318966
J Clin Pathol. 2007 Jun;60(6):720-2
17557872
Virchows Arch B Cell Pathol Incl Mol Pathol. 1989;56(4):237-45
2565618