Detection of chromosomal aberrations in renal tumors: a comparative study of conventional cytogenetics and virtual karyotyping with single-nucleotide polymorphism microarrays

Clinical utility of concurrent single-nucleotide polymorphism microarray on fresh tissue as a supplementary test in the diagnosis of renal epithelial neoplasms

OBJECTIVES

The histologic and immunohistochemical variability of renal epithelial tumors makes classification difficult; with significant clinical implications, efforts to make the proper diagnoses are necessary. Single-nucleotide polymorphism (SNP) microarray analysis has been proposed as a supplementary study for the classification of renal epithelial neoplasms; however, its practical use in the routine clinical setting has not been explored.

METHODS

Surgical pathology cases that were classified histologically as renal epithelial tumor subtypes and had concurrent SNP microarray were retrospectively reviewed to correlate tumor morphology and SNP microarray results.

RESULTS

Of the 99 cases reviewed, 88 (89%) had concordant histologic and microarray results. Four (4%) cases were unclassifiable by microarray due to uncharacteristic chromosomal abnormalities. Seven (7%) of the 99 cases had discordant microarray and histologic diagnoses, and following review of the histology, the diagnoses in two of these cases were subsequently changed.

CONCLUSIONS

For most cases, concurrent SNP microarray confirmed the histologic diagnosis. However, discrepant microarray results prompted review of morphology and further ancillary studies, resulting in amendment of the final diagnosis in 29% of discrepant cases. SNP microarray analysis can be used to assist with the diagnosis of renal epithelial tumors, particularly those with atypical morphologic features.

Juxtaglomerular cell tumor: a morphological, immunohistochemical and genetic study of six cases

Juxtaglomerular cell tumors (JGCTs) are rare tumors characterized by renin synthesis, hyperaldosteronism and hypertension. A curious immunohistochemical overlap between JGCT and gastrointestinal stromal tumor (GIST) including the expression of vimentin, CD34, CD117, α-smooth muscle actin was previously reported, prompting us to further investigate JGCT and its phenotypic and molecular genetic characteristics. Virtual karyotyping showed gain of chromosomes 3, 4, 10, 13, 17 and 18 in one JGCT, and fluorescence in situ hybridization (FISH) study confirmed this multiple gain pattern. Additionally, loss of chromosome 9 was observed in four of six cases analyzed with FISH. A whole genome expression analysis revealed 415 up-regulated (including renin, and CD117) and 325 down-regulated genes between the 2 cases. The study confirmed earlier reports on the gain of chromosomes 4 and 10, and provided further evidence of up-regulation of the genes located on these 2 chromosomes. For the first time our study indicated the importance of the loss of chromosome 9 and loss of expression of several tumor suppressor genes located on this chromosome as possible pathogenetic events important in development of JGCT.

Integrative genomic analyses of sporadic clear cell renal cell carcinoma define disease subtypes and potential new therapeutic targets

Sporadic clear cell renal cell carcinoma (ccRCC), the most common type of adult kidney cancer, is often associated with genomic copy number aberrations on chromosomes 3p and 5q. Aberrations on chromosome 3p are associated with inactivation of the tumor suppressor gene von-Hippel Lindau (VHL), which activates the hypoxia-inducible factors HIF1α and HIF2α. In contrast, ccRCC genes on chromosome 5q remain to be defined. In this study, we conducted an integrated analysis of high-density copy number and gene expression data for 54 sporadic ccRCC tumors that identified the secreted glycoprotein STC2 (stanniocalcin 2) and the proteoglycan VCAN (versican) as potential 5q oncogenes in ccRCCs. In functional assays, STC2 and VCAN each promoted tumorigenesis by inhibiting cell death. Using the same approach, we also investigated the two VHL-deficient subtypes of ccRCC, which express both HIF1α and HIF2α (H1H2) or only HIF2α (H2). This analysis revealed a distinct pattern of genomic aberrations in each group, with the H1H2 group displaying, on average, a more aberrant genome than the H2 group. Together our findings provide a significant advance in understanding ccRCCs by offering a molecular definition of two subtypes with distinct characteristics as well as two potential chromosome 5q oncogenes, the overexpression of which is sufficient to promote tumorigenesis by limiting cell death.

Genomic aberrations in salivary duct carcinoma arising in Warthin tumor of parotid gland: DNA microarray and HER2 fluorescence in situ hybridization

Carcinoma arising from Warthin tumor is extremely rare. A 79-year-old man was admitted for a firm, well-defined, 5-cm left infra-auricular mass. Aspiration cytology showed many lymphohistiocytes and oncocytes in a proteinaceous background, compatible with Warthin tumor. A left superficial parotidectomy showed a solid mass around the cyst wall. The tumor cells of the solid area were arranged as infiltrative ducts with a few foci of malignant transformation. Virtual karyotyping disclosed a complex pattern of genetic aberrations with a focal amplification in 12q14-q21.2. This chromosomal region contains the MDM2 (murine double minute) gene, which regulates p53 inactivation. HER2 fluorescence in situ hybridization showed a focal amplification. Subsequently, the patient underwent total parotidectomy and ipsilateral neck dissection for a recurrence. To our knowledge, this is the first case of salivary duct carcinoma arising from Warthin tumor. The essential molecular pathway has not been reported, we presume an important role of MDM2 amplification- P53 inactivation.

Renal medullary carcinomas: histopathologic phenotype associated with diverse genotypes

Chromosomal abnormalities and gene mutations have become major determinants in the classification of kidney carcinomas. Most renal medullary carcinomas develop in patients with hereditary sickle cell disease, but sporadic cases unassociated with sickle cell disease have also been described, for which underlying genetic abnormality is unknown. We evaluated 3 patients with renal medullary carcinoma (1 patient with sickle cell disease and 2 patients without sickle cell disease) for germ line and somatic mutations in genes commonly involved in pathogenesis of renal carcinomas using denaturing high-performance liquid chromatography and direct sequencing. Chromosomal abnormalities were studied by the conventional cytogenetic and SNP arrays analysis. Expression of hypoxia-inducible factor 1α was examined using immunohistochemistry. Two new mutations in the gene for fumarate hydratase were identified in 1 case of medullary renal carcinoma without sickle cell disease: a germ line mutation in exon 6 (R233H) and an acquired (somatic) mutation in exon 8 (P374S). No fumarate hydratase mutations were identified in the other 2 patients. The second sporadic case of renal medullary carcinoma harbored double somatic mutations in von Hippel-Lindau gene, and renal medullary carcinoma in the patient with sickle cell disease showed von Hippel-Lindau gene promoter methylation (epigenetic silencing). No consistent pattern of chromosomal abnormalities was found between 2 cases tested. All 3 cases showed increased hypoxia-inducible factor 1α expression. Medullary renal carcinomas from patients with or without sickle cell disease show involvement of genes important in hypoxia-induced signaling pathways. Generalized cellular hypoxia (in sickle cell disease) or pseudohypoxia (in tumors with fumarate hydratase and von Hippel-Lindau mutations or epigenetic silencing) may act alone or in concert at the level of medullary tubular epithelium to promote development of this rare type of renal carcinoma, which could then be genetically reclassified as either fumarate hydratase-associated renal carcinomas or high-grade clear cell renal cell carcinomas.

Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffin-embedded tissues

BACKGROUND

Chromosomal imbalances are commonly seen in cancer and inherited genetic diseases. These imbalances may assist in the diagnosis, prognosis, and/or therapeutic management of certain neoplasms. Several methods for detecting chromosomal imbalances, such as, fluorescent in situ hybridization, array comparative genomic hybridization, and single nucleotide polymorphism (SNP) arrays have proven useful in formalin-fixed paraffin-embedded (FFPE) tissues. Here, we report the performance and reproducibility of virtual karyotyping of FFPE tissues with Affymetrix SNP arrays.

METHODS

Virtual karyotypes from 442 FFPE tumor samples were generated using the Affymetrix GeneChip Mapping 10K Xba 2.0 and/or 250K Nsp SNP mapping arrays. Samples ranged from a few weeks to 17 years in archival storage. Virtual karyotypes were assessed for copy number changes, loss of heterozygosity, and acquired uniparental disomy.

RESULTS

Overall, 75.3% of samples produced interpretable virtual karyotypes with the 10K arrays and 76.7% in the 250K arrays. Parameters for the selection of samples for hybridization were determined, which increased the success rate in both platforms to 81.3 and 92.6%, respectively. FFPE virtual karyotypes generated with both 10K Xba 2.0 and 250K Nsp arrays showed 100% concordance in intralaboratory and interlaboratory reproducibility studies. Samples older than 7 years showed decreased performance.

CONCLUSIONS

SNP arrays are a reliable, reproducible, and robust platform for the virtual karyotyping of FFPE tumor tissues with performance characteristics adequate for clinical application. Parameters that most significantly affected sample performance were sample age and storage conditions.