Open Access Research article

Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma

Min-Han Tan1234*, Chin Fong Wong5, Hwei Ling Tan2, Ximing J Yang6, Jonathon Ditlev1, Daisuke Matsuda1, Sok Kean Khoo1, Jun Sugimura1, Tomoaki Fujioka7, Kyle A Furge8, Eric Kort19, Sophie Giraud10, Sophie Ferlicot11, Philippe Vielh12, Delphine Amsellem-Ouazana13, Bernard Debré19, Thierry Flam13, Nicolas Thiounn14, Marc Zerbib13, Gérard Benoît15, Stéphane Droupy15, Vincent Molinié16, Annick Vieillefond17, Puay Hoon Tan5, Stéphane Richard1819 and Bin Tean Teh12*

Author Affiliations

1 Laboratory of Cancer Genetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA

2 NCCS-VARI Translational Cancer Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, 169610 Singapore

3 Department of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, 169610 Singapore

4 Department of Epidemiology and Public Health, National University of Singapore, 16 Medical Drive, 117597 Singapore

5 Department of Pathology, Singapore General Hospital, Outram Road, 169608 Singapore

6 Northwestern University Feinberg School of Medicine, 251 E. Huron, Chicago, IL, 60611, USA

7 Department of Urology, Iwate Medical University School of Medicine, 19-1, Uchimaru, Marioka, 020-8505 Japan

8 Laboratory of Computational Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA

9 Laboratory of Molecular Epidemiology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA

10 Laboratoire de Génétique, Hôpital Herriot, Batiment 7, Place d'Arsonval, 69437 Lyon Cedex 03, France

11 Laboratoire d’Anatomie Pathologique, Hôpital de Bicêtre, AP-HP, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre Cedex, France

12 Department of Biology and Pathology, Institut de Cancérologie Gustave Roussy, 39 rue Camile Desmoulins, 94805 Villejuif, France

13 Department of Urology, Hôpital Cochin, 27 rue du Faubourg Saint-Jacques, 75679 Paris Cedex 14, France

14 Service d'Urologie, Hôpital Necker, AP-HP, 149, rue de Sevres, 75743 Paris, France

15 Service d’Urologie, Hôpital de Bicêtre, AP-HP, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France

16 Service d'Anatomie Pathologique, Hôpital Saint Joseph, 185 rue Raymond Losserand, 75674 Paris Cedex, France

17 Laboratoire d'Anatomie Pathologique, Hôpital Cochin, 27 rue du Faubourg Saint-Jacques, 75679 Paris Cedex 14, France

18 Consultation d'Oncogénétique Spécialisée, Service d'Urologie, Hôpital de Bicêtre, 78 rue du General Leclerc, 94275 Le Kremlin-Bicêtre, France

19 Génétique Oncologique EPHE-INSERM U753 and Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, and Institut de Cancérologie Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif, France

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BMC Cancer 2010, 10:196  doi:10.1186/1471-2407-10-196

Published: 12 May 2010

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.