High-resolution array CGH of metanephric adenomas: lack of DNA copy number changes

Key Renal Neoplasms With a Female Predominance

Renal neoplasms largely favor male patients; however, there is a growing list of tumors that are more frequently diagnosed in females. These tumors include metanephric adenoma, mixed epithelial and stromal tumor, juxtaglomerular cell tumor, mucinous tubular and spindle cell carcinoma, Xp11.2 (TFE3) translocation-associated renal cell carcinoma, and tuberous sclerosis complex (somatic or germline) associated renal neoplasms. The latter category is a heterogenous group with entities still being delineated. Eosinophilic solid and cystic renal cell carcinoma is the best-described entity, whereas, eosinophilic vacuolated tumor is a proposed entity, and the remaining tumors are currently grouped together under the umbrella of tuberous sclerosis complex/mammalian target of rapamycin-related renal neoplasms. The entities described in this review are often diagnostic considerations when evaluating renal mass tissue on biopsy or resection. For example, Xp11.2 translocation renal cell carcinoma is in the differential when a tumor has clear cell cytology and papillary architecture and occurs in a young or middle-aged patient. In contrast, tuberous sclerosis complex-related neoplasms often enter the differential for tumors with eosinophilic cytology. This review provides an overview of the clinical, gross, microscopic, immunohistochemical, genetic, and molecular alterations in key renal neoplasms occurring more commonly in females; differential diagnoses are also discussed regardless of sex predilection.

Pediatric Renal Tumors: Updates in the Molecular Era

Molecular characterization has led to advances in the understanding of pediatric renal tumors, including the association of pediatric cystic nephromas with DICER1 tumor syndrome, the metanephric family of tumors with somatic BRAF mutations, the characterization of ETV6-NTRK3-negative congenital mesoblastic nephromas, the expanded spectrum of gene fusions in translocation renal cell carcinoma, the relationship of clear cell sarcoma of the kidney with other BCOR-altered tumors, and the pathways affected by SMARCB1 alterations in rhabdoid tumors of the kidney. These advances have implications for diagnosis, classification, and treatment of pediatric renal tumors.

Genetic and Chromosomal Aberrations and Their Clinical Significance in Renal Neoplasms

The most common form of malignant renal neoplasms is renal cell carcinoma (RCC), which is classified into several different subtypes based on the histomorphological features. However, overlaps in these characteristics may present difficulties in the accurate diagnosis of these subtypes, which have different clinical outcomes. Genomic and molecular studies have revealed unique genetic aberrations in each subtype. Knowledge of these genetic changes in hereditary and sporadic renal neoplasms has given an insight into the various proteins and signalling pathways involved in tumour formation and progression. In this review, the genetic aberrations characteristic to each renal neoplasm subtype are evaluated along with the associated protein products and affected pathways. The potential applications of these genetic aberrations and proteins as diagnostic tools, prognostic markers, or therapeutic targets are also assessed.

BRAF mutations in pediatric metanephric tumors

Metanephric neoplasms of the kidney are uncommon, and some cases are associated with papillary carcinoma. Most cases of metanephric adenoma occur in adults, with fewer than 25 cases reported in children, and metanephric adenofibroma is even less common. The few metanephric tumors studied at the genetic level have not shown the gains of chromosomes 7 and 17 commonly seen in renal cell carcinoma, suggesting that the carcinoma arising in this setting has a separate genetic origin from the adenoma. However, the assumption that this carcinoma has the same chromosome gains as sporadic renal cell carcinoma has never been validated. We studied 4 cases of metanephric tumors in children, including 1 metanephric adenofibroma with papillary carcinoma. The composite tumor was studied by single nucleotide polymorphism array and fluorescence in situ hybridization, with the adenoma and carcinoma components analyzed separately. No copy number alterations were detected in either component. A BRAF V600E mutation has been reported in most cases of metanephric adenoma in adults. We performed BRAF V600E immunostaining and sequencing in our 4 pediatric cases. Three cases had a BRAF V600E mutation including the composite tumor, with both the adenoma and carcinoma components showing the same mutation. This finding provides the first genetic evidence that these 2 tumors are biologically linked. Ten cases each of pediatric renal cell carcinoma and Wilms tumor were immunonegative. Thus, BRAF V600E immunostaining is a helpful marker for pediatric metanephric adenoma, and additional research is required on the possible role of this mutation in the development of renal carcinoma.

High quality genomic copy number data from archival formalin-fixed paraffin-embedded leiomyosarcoma: optimisation of universal linkage system labelling

Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment.

BRAF mutations in metanephric adenoma of the kidney

BACKGROUND

Metanephric adenoma (MA) of the kidney is a rare, indolent tumor that may be difficult to differentiate from other small renal masses (SRMs). Genetic alterations associated with MA remain largely unknown.

OBJECTIVE

We aimed at defining genetic events in MA of the kidney and determining their influence in the management of this disease.

DESIGN, SETTING, AND PARTICIPANTS

Multiplexed mass spectrometric genotyping was performed on 29 MA cases after tumor DNA extraction. We also conducted a mutational screen in an additional 129 renal neoplasms. Immunohistochemistry was performed on the MA cases to assess molecular markers of signaling pathway activation. Patients' baseline characteristics, as well as follow-up data, were captured.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

We used descriptive statistics for baseline clinical characteristics and incidence of mutations. The Wilcoxon rank-sum test was used to correlate patient characteristics with mutational status.

RESULTS AND LIMITATIONS

We identified the v-raf murine sarcoma viral oncogene homolog B1 (BRAF) V600E mutation in 26 of 29 MA cases. These results were validated in all cases using the commercially available BRAF Pyro Kit (QIAGEN). In contrast, BRAF mutations were rare in the other 129 non-MA renal neoplasms that were screened. We detected a BRAF mutation (V600E) in only one papillary renal cell carcinoma case. In all MA tumors, we documented expression of phosphorylated mitogen-activated protein kinase and phosphorylated extracellular signal-regulated kinase, accompanied by immunoreactivity for p16 (INK4a). All patients were treated with a partial or radical nephrectomy, and after a median follow-up of 26.5 mo, there were no local or distant recurrences. Limitations include the retrospective nature of this study.

CONCLUSIONS

BRAF V600E mutations are present in approximately 90% of all MA cases, serving as a potential valuable diagnostic tool in the differential diagnosis of SRMs undergoing a percutaneous biopsy. The presence of BRAF V600E and mitogen-activated protein kinase activation in a largely benign tumor supports the necessity for secondary events (e.g., p16 loss) in BRAF-driven oncogenesis.

Detection of chromosome copy number alterations in metanephric adenomas by array comparative genomic hybridization

Metanephric adenoma is a rare benign renal tumor typically found in adults. Previous cytogenetic analyses, including karyotyping, fluorescence in situ hybridization (FISH), and comparative genomic hybridization, have yielded conflicting results regarding the somatic genetic aberrations of these tumors. In this study, we investigated the genomic profile of nine cases of metanephric adenoma using array comparative genomic hybridization. Two cases revealed multiple chromosomal gains and losses. Three cases showed sporadic chromosomal imbalances involving no more than three chromosomes. Four cases showed normal chromosome copy numbers. The gain of chromosome 19 was the most common finding (five cases), and FISH using 19p and 19q telomeric probes further confirmed this finding. We did not observe consistent gains of chromosomes 7 and 17, which are common in papillary renal cell carcinoma, neither did we find chromosomal alterations frequently present in Wilms' tumors, including chromosome gains of 1q, 7q, and 12, and losses of 11p and 16q. Our series demonstrates that the genetic profile of metanephric adenoma is fundamentally distinct from those of papillary renal cell carcinoma and Wilms' tumor.