Renal oncocytoma with a translocation t(9;11)(p23;q13)

Report From the International Society of Urological Pathology (ISUP) Consultation Conference on Molecular Pathology of Urogenital Cancers: III: Molecular Pathology of Kidney Cancer

Renal cell carcinoma (RCC) subtypes are increasingly being discerned via their molecular underpinnings. Frequently this can be correlated to histologic and immunohistochemical surrogates, such that only simple targeted molecular assays, or none at all, are needed for diagnostic confirmation. In clear cell RCC, VHL mutation and 3p loss are well known; however, other genes with emerging important roles include SETD2, BAP1, and PBRM1, among others. Papillary RCC type 2 is now known to include likely several different molecular entities, such as fumarate hydratase (FH) deficient RCC. In MIT family translocation RCC, an increasing number of gene fusions are now described. Some TFE3 fusion partners, such as NONO, GRIPAP1, RBMX, and RBM10 may show a deceptive fluorescence in situ hybridization result due to the proximity of the genes on the same chromosome. FH and succinate dehydrogenase deficient RCC have implications for patient counseling due to heritable syndromes and the aggressiveness of FH-deficient RCC. Immunohistochemistry is increasingly available and helpful for recognizing both. Emerging tumor types with strong evidence for distinct diagnostic entities include eosinophilic solid and cystic RCC and TFEB/VEGFA/6p21 amplified RCC. Other emerging entities that are less clearly understood include TCEB1 mutated RCC, RCC with ALK rearrangement, renal neoplasms with mutations of TSC2 or MTOR, and RCC with fibromuscular stroma. In metastatic RCC, the role of molecular studies is not entirely defined at present, although there may be an increasing role for genomic analysis related to specific therapy pathways, such as for tyrosine kinase or MTOR inhibitors.

Molecular Genetics of Renal Cell Tumors: A Practical Diagnostic Approach

Renal epithelial cell tumors are composed of a heterogeneous group of tumors with variable morphologic, immunohistochemical, and molecular features. A "histo-molecular" approach is now an integral part of defining renal tumors, aiming to be clinically and therapeutically pertinent. Most renal epithelial tumors including the new and emerging entities have distinct molecular and genetic features which can be detected using various methods. Most renal epithelial tumors can be diagnosed easily based on pure histologic findings with or without immunohistochemical examination. Furthermore, molecular-genetic testing can be utilized to assist in arriving at an accurate diagnosis. In this review, we presented the most current knowledge concerning molecular-genetic aspects of renal epithelial neoplasms, which potentially can be used in daily diagnostic practice.

Molecular pathology of renal oncocytoma: a review

Differentiating renal oncocytoma from its renal cell carcinoma (RCC) mimics, particularly chromophobe RCC, can be difficult, especially when limited tissue is available for evaluation and requires sophisticated microscopic, ultrastructural and immunohistochemical evaluation. In this review, the relevant literature has been reviewed, and supporting data obtained by applying modern microarray-based technologies are discussed with a focus on molecular pathology of renal oncocytoma. The high resolution whole-genome DNA-microarray based analyses excluded with all certainty the occurrence of small specific alterations. Renal oncocytomas are characterized by variable chromosomal patterns. The number of genes selected by global gene expression analyses and their usefulness in the diagnostic pathology based on immunohistochemical evaluation is far below the expectations. The conflicting staining patterns, together with the poor specificity of proposed antibodies, leads us to believe that these candidate immunomarkers might not help in the separation of these tumors. Applying DNA based tools might help in the diagnosis of renal oncocytoma with uncertain histology. However, only the combination of all available techniques could give reliable information.

A new translocation between chromosomes 6 and 9 helps to establish diagnosis of renal oncocytoma

Renal oncocytomas are benign epithelial tumors of the kidney. Histologically, they resemble certain malignant renal tumors, such as chromophobe renal cell carcinoma and the eosinophilic or granular form of clear cell renal carcinoma. It is, therefore, important to be able to differentiate among these tumors. Cytogenetic analysis is an important adjunct to the diagnosis of renal tumors, as the various subtypes have specific acquired chromosome abnormalities. Oncocytomas present either with loss of chromosome 1 and a sex chromosome, or with recurring translocations involving chromosome 11. We describe 2 patients with renal oncocytoma and a new translocation between chromosomes 6 and 9. The tumors in both patients were histologically virtually identical. The t(6;9)(p21;p23) may be a new translocation associated with renal oncocytomas.

Analysis of differentially expressed mitochondrial proteins in chromophobe renal cell carcinomas and renal oncocytomas by 2-D gel electrophoresis

Renal oncocytomas (RO) and chromophobe renal cell carcinomas (RCC) display morphological and functional alterations of the mitochondria. Previous studies showed that accumulation of mitochondria in ROs is associated with somatic mutations of mitochondrial DNA (mtDNA) resulting in decreased activity of the respiratory chain complex I, whereas in chromophobe RCC only heteroplasmic mtDNA mutations were found. To identify proteins associated with these changes, for the first time we have compared the mitochondrial proteomes of mitochondria isolated from ROs and chromophobe RCCs as well as from normal kidney tissues by two-dimensional polyacrylamide gel electrophoresis. The proteome profiles were reproducible within the same group of tissues in subsequent experiments. The expression patterns within each group of samples were compared and 81 in-gel digested spots were subjected to nanoLC-MS/MS-based identification of proteins. Although the list of mitochondrial proteins identified in this study is incomplete, we identified the downregulation of NDUFS3 from complex I of the respiratory chain and upregulation of COX5A, COX5B, and ATP5H from complex IV and V in ROs. In chromophobe RCCs downregulation of ATP5A1, the alpha subunit of complex V, has been observed, but no changes in expression of other complexes of the respiratory chain were detected. To confirm the role of respiratory chain complex alterations in the morphological and/or functional changes in chromophobe RCCs and ROs, further studies will be necessary.

High-resolution DNA copy number and gene expression analyses distinguish chromophobe renal cell carcinomas and renal oncocytomas

Background

The diagnosis of benign renal oncocytomas (RO) and chromophobe renal cell carcinomas (RCC) based on their morphology remains uncertain in several cases.

Methods

We have applied Affymetrix GeneChip Mapping 250 K NspI high-density oligoarrays to identify small genomic alterations, which may occur beyond the specific losses of entire chromosomes, and also Affymetrix GeneChip HG-U133 Plus2.0 oligoarrays for gene expression profiling.

Results

By analysing of DNA extracted from 30 chRCCs and 42 ROs, we have confirmed the high specificity of monosomies of chromosomes 1, 2, 6, 10, 13, 17 and 21 in 70–93% of the chRCCs, while ROs displayed loss of chromosome 1 and 14 in 24% and 5% of the cases, respectively. We demonstrated that chromosomal gene expression biases might correlate with chromosomal abnormalities found in chromophobe RCCs and ROs. The vast majority genes downregulated in chromophobe RCC were mapped to chromosomes 2, 6, 10, 13 and 17. However, most of the genes overexpressed in chromophobe RCCs were located to chromosomes without any copy number changes indicating a transcriptional regulation as a main event.

Conclusion

The SNP-array analysis failed to detect recurrent small deletions, which may mark loci of genes involved in the tumor development. However, we have identified loss of chromosome 2, 10, 13, 17 and 21 as discriminating alteration between chromophobe RCCs and ROs. Therefore, detection of these chromosomal changes can be used for the accurate diagnosis in routine histology.

Losses of 1p and chromosome 14 in renal oncocytomas

We performed cytogenetic analyses of 8 renal oncocytomas to identify chromosomal regions involved in the tumorigenesis of oncocytomas. All cases showed chromosomal findings corresponding to established cytogenetic subsets of renal oncocytomas: 3 cases with normal karyotypes, 1 case with rearrangement of 11q, and 4 cases with losses of chromosome 14. In the latter cytogenetic subgroup, monosomy 14 was additionally accompanied by either monosomy 1 in 2 cases or loss of 1p in a third case, providing insights in the cytogenetic evolution of this subgroup.

Oncocytic renal neoplasms: diagnostic considerations

Advances in our understanding of renal neoplasia have resulted in recognition of numerous tumors that are composed predominantly of cells with abundant eosinophilic cytoplasm. This article discusses the features of renal oncocytoma (including oncocytosis), chromophobe renal cell carcinoma (RCC), and clear cell RCC; explores the relationship between renal oncocytoma and chromophobe RCC; briefly discusses other tumors with abundant eosinophilic cytoplasm; and emphasizes the differential diagnosis of such tumors.

Microsatellite allelotyping differentiates chromophobe renal cell carcinomas from renal oncocytomas and identifies new genetic changes

AIMS

The diagnosis of renal oncocytomas (ROs) and chromophobe renal cell carcinomas (RCCs) based on histological features is often uncertain. To assess the value of genetic analysis in their differential diagnosis we analysed 27 ROs and 21 chromophobe RCCs by microsatellite allelotyping.

METHODS AND RESULTS

Markers at the short and long arms of chromosomes specifically involved in the genetic changes of the four main types of renal cancers were selected. Allelic changes were identified by automated sequencing. Allelic changes at chromosome 1p occurred in 8/26 (31%) and at chromosome 14q in 4/27 (15%) ROs. Loss of heterozygosity (LOH) at chromosomes 1, 2, 6, 10, 13, 17 and 21 were seen in 90%, 90%, 96%, 86%, 85%, 90% and 72% of the chromophobe RCCs, respectively. Alterations of at least three of these chromosomal sites were detected in each chromophobe RCC. In addition, we found recurrent LOH at chromosomes 9p23 (43%), 18q22 (30%), 5q22 (28%) and 8p (28%) in chromophobe RCCs.

CONCLUSIONS

Chromophobe RCCs can be differentiated from ROs by analysing specific chromosomal regions with microsatellites.

Renal oncocytomas with 11q13 rearrangements: cytogenetic, molecular, and immunohistochemical analysis of cyclin D1

Two groups of renal oncocytomas have been cytogenetically defined by the loss of one or both of chromosomes Y and 1 or by structural rearrangement involving 11q12~q13. We report five renal oncocytomas with structural chromosomal rearrangements involving 11q13 with previously unreported partner chromosomes (namely, 1, 6, and 7). For two of the five cases, a t(6;11)(p21;q13) translocation was revealed; the others had t(1;11)(p13;q13), t(7;11)(q11.2;q13), and t(5;11)(q35; q13). Fluorescence in situ hybridization confirmed translocation of CCND1 at 11q13 to partner chromosomes 5, 6, and 7. Overexpression of cyclin D1, the protein product of CCND1, was detected in three of the five cases (60%) by means of immunohistochemical staining of formalin-fixed, paraffin-embedded tumor sections. In three cases for which fresh tissue was available, Southern blot analysis using the MDL-5 probe for the BCL1 breakpoint did not reveal rearrangement of BCL1. In addition, six consecutive renal oncocytomas diagnosed at our institution between 1999 and 2002 whose karyotypes did not show 11q13 translocations were all negative for cyclin D1 overexpression under immunohistochemical analysis. The findings of CCND1 rearrangement with FISH and correlation with cyclin D1 overexpression under immunohistochemical analysis suggest that cyclin D1 alterations play a role in the subset of renal oncocytomas with 11q translocations, although other genes may also be involved.

Renal oncocytomas with rearrangements involving 11q13 contain breakpoints near CCND1

Oncocytomas are typically benign epithelial tumors whose predominant feature is a massive accumulation of mitochondria in the cytoplasm. With the goal of identifying genes controlling mitochondrial proliferation, we studied three oncocytomas belonging to the cytogenetic subgroup with 11q13 rearrangements. Fluorescence in situ hybridization using bacterial artificial chromosome (BAC) clones showed that the 11q13 breakpoints in all three tumors were near the CCND1 (previously BCL1) gene and did not disrupt any other known gene. The rearrangement in one tumor consisted of a segmental duplication that included 11q13, suggesting that known mitochondrially targeted genes immediately distal to CCND1 may be involved in oncocytic proliferation.

The genetic basis of renal cell carcinoma

The recognition of hereditary forms of renal cancer and the development of high-throughput genetic analysis have led to the identification of genes responsible for familial renal epithelial tumors of differing histologies and cytogenetic features. Some of these genes (VHL) are known to have an important role in sporadic renal neoplasia. This article describes the various epithelial renal tumors most commonly encountered by the urologist, the molecular and cytogenetic distinctions between them, and the hereditary syndromes that predispose to these tumors. Consideration of these syndromes is important for proper treatment when one encounters patients with multiple renal tumors, tumors at an early age of onset, or patients with a positive family history of renal cell carcinoma.

Translocation t(9;22) (p23;q11) in atypical chronic myeloid leukemia (aCML) presenting osteolytic lesions

A 58-year-old man with a 4-month history of atypical chronic myeloid leukemia (aCML), treated with INF-alpha and hydroxyurea, presented with severe localized bone pain with involvement of upper limbs on July 17, 2000. Cytogenetic analysis of peripheral blood cells showed 46,XY,t(9;22)(p23;q11) and no BCR-ABL fusion gene was detected by fluorescence in situ hybridization (FISH). On October 30,2000, x-rays revealed extended destruction of the bilateral proximal upper limbs; pain in the femoral bones appeared in December, and the patient couldn't walk. Roentgenograms taken on January 4, 2001, showed diffuse lytic changes in bilateral femoral bones. On January 23, 2001, fixation of pending fractures in the bilateral femoral bones with an intramedullary rod had produced good results. The infiltration of immature myeloid cells was diagnosed by the histological findings of a bone specimen from the right femur. Because the serum levels of parathyroid hormone (PTH), PTH related protein, and calcitonin were normal, we considered that the bone destruction was caused by the invasion of immature myeloid cells. Four months later, the patient showed a marked increase in peripheral immature granulocytes. A bone marrow specimen showed blastic marrow, and he died of a brain hemorrhage. This report suggests that aCML might cause destructive bone lesions prior to the disease progression. To our knowledge, this is the first published case of aCML in which the chromosomal abnormality t(9;22)(p23;ql 1) was detected.

Renal cancer: cytogenetic and molecular genetic aspects

To date, much progress has been made in the fields of cytogenetics and molecular genetics of renal tumors. The previous and recent findings have delineated the characteristics of the various tumors, particularly the cytogenetic and molecular differences that exist between papillary and nonpapillary clear cell renal cell carcinomas (RCCs). At the same time, new cytogenetic subtypes have emerged [e.g., t(X;1)] in subtypes of RCC, while in others (e.g., Wilms tumors) several new cytogenetic abnormalities and consequent molecular involvement have been found. In addition to Wilms tumor, papillary RCC, and clear-cell RCC, cytogenetic and fluorescence in situ hybridization analyses have been performed on several other tumors of the kidney, including chromophobic carcinoma, metanephric adenoma, collecting duct carcinoma, transitional cell carcinoma, congenital mesoblastic nephroma, and malignant rhabdoid tumors of the kidney. This review is therefore intended to present a concise update on the cytogenetic and molecular data on renal tumors, focusing mainly on the clinical usefulness of the findings reported in the literature.

A distinctive pediatric renal neoplasm characterized by epithelioid morphology, basement membrane production, focal HMB45 immunoreactivity, and t(6;11)(p21.1;q12) chromosome translocation

We report two cases of a hitherto undescribed pediatric renal neoplasm that is distinctive at the morphological, immunohistochemical, ultrastructural, and cytogenetic levels. On light microscopy, the tumors are composed of nests of polygonal, clear to eosinophilic cells associated with a subpopulation of smaller cells that surround hyaline material. Despite their epithelioid morphology, these tumors do not label immunohistochemically for epithelial markers but instead label focally for melanocytic markers HMB45 and Melan A. The hyaline material is positive with periodic acid-Schiff and methenamine-silver histochemical stains, and labels immunohistochemically for type 4 collagen. Ultrastructural examination confirms that it represents basement membrane material. Cytogenetic analysis reveals the identical t(6;11)(p21.1;q12) chromosome translocation as the sole abnormality in these two tumors, confirming their identity and distinctive nature.

Osteoid osteomas with chromosome alterations involving 22q

Cytogenetic analysis was performed in two osteoid osteomas. In both, the modal chromosome number was 46. One of the cases presented a del(22)(q13.1) as the sole clonal chromosome alteration. The other had clonal monosomies of chromosomes 3, 6, 9, 17, 19, and 21, as well as a +del(22)(q13.1) was detected as a non-clonal chromosome alteration. There is only one osteoid osteoma reported so far showing clonal karyotypic alterations. The cytogenetic behavior of osteoid osteomas described here was different from that of the osteoid osteoma of the literature. Numerical alterations of chromosomes 3, 6, 9, 17, 19, 21 and 22 have been described in several neoplasias including bone tumors. The breakpoint of chromosome 22 involves a region where important genes for the regulation of the cell cycle have been mapped.

Cytogenetic analysis of 11 renal oncocytomas: further evidence of structural rearrangements of 11q13 as a characteristic chromosomal anomaly

We carried out cytogenetic analysis on 11 renal oncotytomas by using G-banding and DAPI-banding techniques. Four of our tumors exhibited structural rearrangements affecting chromosome 11 at band q13. Together with another case previously described by us, our tumors constitute the largest series of renal oncocytomas displaying translocations involving 11q13. A review of the literature disclosed only 6 similar oncocytomas, 1 tumor with a t(9;11)(p23;q12), 2 tumors with a nearly identical t(9;11)(p23;q13), and 3 tumors with a t(5;11)(q35;q13). Therefore, our findings provide further cytogenetic evidence that genes located on 11q12-13 may be involved in the tumorigenesis of renal oncocytomas.

Familial renal oncocytoma: clinicopathological study of 5 families

PURPOSE

We analyzed familial renal oncocytoma to provide a foundation for studies aimed at defining genes involved in the pathogenesis of renal oncocytoma.

MATERIALS AND METHODS

We describe 5 families with multiple members affected with renal oncocytoma. Tumors were analyzed pathologically, and affected and nonaffected members were screened clinically and genetically.

RESULTS

We identified 12 affected male and 3 affected female (ratio 4:1) individuals in the 5 families. In affected family members renal oncocytomas were often multiple and bilateral. No metastatic disease was observed. Most renal oncocytomas were detected incidentally in asymptomatic individuals or during screening of asymptomatic members of renal oncocytoma families. One identical twin pair was affected with bilateral multiple renal oncocytomas.

CONCLUSIONS

Renal oncocytoma may be inherited in some families.

Lack of genetic changes at specific genomic sites separates renal oncocytomas from renal cell carcinomas

Morphological similarities between renal oncocytomas and 'oncocytic' renal cell carcinomas (RCCs) make a differential diagnosis in many cases difficult. A series of 41 renal oncocytomas has been analysed by microsatellite markers from chromosomes 1, 2, 3p, 6q, 8p, 9, 10, 13q, 14q, 17, and 21, alterations of which are known to be involved specifically in non-papillary and chromophobe RCCs. Only eight of the 41 renal oncocytomas showed loss of heterozygosity (LOH). LOH at chromosomes 1 and 14 occurred in four tumours each and at chromosomes 2, 8, and 9 in one tumour each. Combined LOH at chromosomes 1, 9, and 14 and also at chromosomes 1 and 14 occurred in one case each. No LOH was seen at any other genomic sites. The lack of combination of LOH at specific chromosomal sites differentiates renal oncocytomas from other renal cell tumours with overlapping phenotypes. Applying the microsatellite assay described here, the diagnosis can be established within 2 days, from fresh as well as from paraffin-embedded material.

Fine mapping of the human renal oncocytoma-associated translocation (5;11)(q35;q13) breakpoint

Recent cytogenetic analysis of a series of human renal oncocytomas revealed the presence of a recurring chromosomal translocation (5;11)(q35;q13) as sole anomaly in a subset of the tumors. The molecular characterization of this translocation was initiated using two primary t(5;11)-positive renal oncocytomas and a panel of somatic cell hybrids derived from one of these tumors, in conjunction with fluorescence in situ hybridization (FISH) and Southern blot analysis. The breakpoint in chromosome band 11q13 could be located within a genomic interval of at maximum 400 Kb immediately centromeric to the BCL1 locus.

Involvement of the chromosomal region 11q13 in renal oncocytoma: case report and literature review

Renal oncocytomas comprise a cytogenetically heterogeneous group of tumors consisting potentially of cytogenetic distinguishable subgroups. Review of the literature revealed loss of chromosome 1 and Y as a possible anomaly for at least one subset oncocytomas. The frequent finding of rearrangements involving chromosome 11 band q13 characterizes another subset of oncocytomas. We report the cytogenetic and pathological features of a renal oncocytoma diagnosed in a 72-year-old woman and found a t(9;11)(p23;q13) as a consistent abnormality. This supports the idea that translocations involving 11q13 define a further subset of oncocytoma.

Renal oncocytoma: a reappraisal of morphologic features with clinicopathologic findings in 80 cases

Renal oncocytoma has several features that overlap with other renal neoplasms with a preponderance of granular cytoplasm, such as chromophobe, granular, and papillary renal cell carcinomas. Lack of knowledge of this entire spectrum of eosinophilic renal cell neoplasms has led to several misconceptions in the literature regarding renal oncocytoma. These include the "grading of oncocytomas," "metastatic oncocytomas," and the impression that renal oncocytoma is usually low grade and lacks prominent nucleoli. In order to further characterize the histologic features and embelLish diagnostic criteria, we evaluated 93 tumors from 80 patients. Four tumors were bilateral and two were multifocal. The mean age was 67.2 years (32-89 years), men were more commonly affected (3.1:1), and 82.7% tumors were incidental findings. Grossly, the tumors were mahogany brown, lacked necrosis, and averaged 4.4 cm in size (range 0.6-15 cm). Histologically, renal oncocytoma was composed of an exclusive or predominant component of acidophilic cells with three architectural patterns of disposition: (a) The "classic" pattern (57.5%), composed of a characteristic nested or organoid arrangement of cells, each surrounded by a distinct reticulin framework; (b) a "tubulocystic pattern" (6.3%) with numerous closely packed cystically dilated tubular structures; and (c) "mixed pattern" (36.2%), which had both the organoid and tubulocystic patterns. A gross or microscopic scar was noted in 53.8% cases, and histologically a distinctive myxoid and/or hyalinized stroma separated nests of cells. Generally, the nuclei of renal oncocytoma were round with uniform nuclear contours. Nearly half of the tumors had prominent nucleoli (42.5% had prominent nucleoli equivalent to Fuhrman's grade III or IV). Pleomorphism was absent in 50% of cases but was conspicuous in 12.5% of cases including foci of bizarre cells. Other atypical features included perinephric fat involvement (11.3%), renal parenchymal invasion not associated with desmoplasia (10%), and hemorrhage (31.3%). Renal oncocytoma by definition lacks areas of clear cell carcinoma, significant lesional necrosis, or conspicuous papillary formations. Ancillary features noted included normal-appearing renal tubules within the lesion (15%), intranuclear holes (20%), psammoma bodies (7.5%), and foam cells (7.5%). 15% of tumors were locally excised, and 85% resulted in radical nephrectomy. Mean follow-up of 7.6 years (range 15-200 months) showed no evidence of recurrence, metastasis, or death due to tumor. In conclusion, renal oncocytoma, herein described, is a benign neoplasm and therefore does not merit a nuclear grading scheme. It has unique histologic features including an organoid and tubulocystic architecture, myxoid or hyalinized stroma, and occasionally some atypical findings including nuclear pleomorphism, prominent nucleoli, and adjacent renal parenchymal and perinephric fat involvement.