Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors

Qualitative Assessment of Contrast-Enhanced Ultrasound in Differentiating Clear Cell Renal Cell Carcinoma and Oncocytoma

BACKGROUND

We aimed to assess whether clear cell renal cell carcinoma (ccRCC) can be differentiated from renal oncocytoma (RO) on a contrast-enhanced ultrasound (CEUS).

METHODS

Between January 2021 and October 2022, we retrospectively queried and analyzed our prospectively maintained dataset. Renal mass features were scrutinized with conventional ultrasound imaging (CUS) and CEUS. All lesions were confirmed by histopathologic diagnoses after nephron-sparing surgery (NSS). A multivariable analysis was performed to identify the potential predictors of ccRCC. The area under the curve (AUC) was depicted in order to assess the diagnostic accuracy of the multivariable model.

RESULTS

A total of 126 renal masses, including 103 (81.7%) ccRCC and 23 (18.3%) RO, matched our inclusion criteria. Among these two groups, we found significant differences in terms of enhancement (homogeneous vs. heterogeneous) (p < 0.001), wash-in (fast vs. synchronous/slow) (p = 0.004), wash-out (fast vs. synchronous/slow) (p = 0.001), and rim-like enhancement (p < 0.001). On the multivariate logistic regression, heterogeneous enhancement (OR: 19.37; p = <0.001) and rim-like enhancement (OR: 3.73; p = 0.049) were independent predictors of ccRCC. Finally, these two variables had an AUC of 82.5% and 75.3%, respectively.

CONCLUSIONS

Diagnostic imaging for presurgical planning is crucial in the choice of either conservative or radical management. CEUS, with its unique features, revealed its usefulness in differentiating ccRCC from RO.

In-utero exposure to zidovudine-containing antiretroviral therapy and clonal hematopoiesis in HIV-exposed uninfected newborns

OBJECTIVE

Zidovudine (ZDV) has been extensively used in pregnant women to prevent vertical transmission of HIV but few studies have evaluated potential mutagenic effects of ZDV during fetal development.

DESIGN

Our study investigated clonal hematopoiesis in HIV-exposed uninfected (HEU) newborns, 94 of whom were ZDV-exposed and 91 antiretroviral therapy (ART)-unexposed and matched for potential confounding factors.

METHODS

Utilizing high depth sequencing and genotyping arrays, we comprehensively examined blood samples collected during the first week after birth for potential clonal hematopoiesis associated with fetal ZDV exposure, including clonal single nucleotide variants (SNVs), small insertions and deletions (indels), and large structural copy number or copy neutral alterations.

RESULTS

We observed no statistically significant difference in the number of SNVs and indels per person in ZDV-exposed children (adjusted ratio [95% confidence interval, CI] for expected number of mutations = 0.79 [0.50--1.22], P = 0.3), and no difference in the number of large structural alterations. Mutations in common clonal hematopoiesis driver genes were not found in the study population. Mutational signature analyses on SNVs detected no novel signatures unique to the ZDV-exposed children and the mutational profiles were similar between the two groups.

CONCLUSION

Our results suggest that clonal hematopoiesis at levels detectable in our study is not strongly influenced by in-utero ZDV exposure; however, additional follow-up studies are needed to further evaluate the safety and potential long-term impacts of in-utero ZDV exposure in HEU children as well as better investigate genomic aberrations occurring late in pregnancy.

Single-center study: the diagnostic performance of contrast-enhanced ultrasound (CEUS) for assessing renal oncocytoma

Purpose: The aim of the present retrospective single-center study is to evaluate the diagnostic performance of contrast-enhanced ultrasound (CEUS) in the evaluation of renal oncocytoma.Method: Thirteen patients with histopathologically confirmed renal oncocytoma and 26 patients with histopathologically confirmed renal cell carcinoma were included in this retrospective single-center study on whom CEUS was performed between 2005 and 2015. The applied contrast agent was a second-generation blood pool agent. CEUS examinations were performed and interpreted by a single radiologist with more than 15 years of experience (EFSUMB Level 3).Results: CEUS examinations were successfully performed in all included patients without any adverse effects. Renal oncocytomas showed varying echogenicity (46% hypoechoic, 23% hyperechoic, 8% iso-/hyperechoic, 8% isoechoic). In two cases renal oncocytoma only demarcated upon i.v. application of contrast medium. In bilateral oncocytosis, lesions presented as hyperechoic. Only 23% of renal oncocytomas showed slight vascularization using Color Doppler. No oncocytoma-specific pattern of microperfusion could be elucidated: 85% of the oncocytomas presented hyperenhancing, of whom 50% also showed delayed venous wash-out; 8% of renal oncocytomas showed venous wash-out without early arterial hyperenhancement.Conclusions: Within the frame of the present study and in line with the recent state of knowledge, no specific sonomorphological feature - including CEUS - could be detected allowing for adequate discrimination between oncocytoma and renal cell carcinoma.

Comprehensive genetic diagnosis of acute myeloid leukemia by next-generation sequencing

Differential induction therapy of all subtypes of acute myeloid leukemia other than acute promyelocytic leukemia is impeded by the long time required to complete complex and diverse cytogenetic and molecular genetic analyses for risk stratification or targeted treatment decisions. Here, we describe a reliable, rapid and sensitive diagnostic approach that combines karyotyping and mutational screening in a single, integrated, next-generation sequencing assay. Numerical karyotyping was performed by low coverage whole genome sequencing followed by copy number variation analysis using a novel algorithm based on in silico-generated reference karyotypes. Translocations and DNA variants were examined by targeted resequencing of fusion transcripts and mutational hotspot regions using commercially available kits and analysis pipelines. For the identification of FLT3 internal tandem duplications and KMT2A partial tandem duplications, we adapted previously described tools. In a validation cohort including 22 primary patients’ samples, 9/9 numerically normal karyotypes were classified correctly and 30/31 (97%) copy number variations reported by classical cytogenetics and fluorescence in situ hybridization analysis were uncovered by our next-generation sequencing karyotyping approach. Predesigned fusion and mutation panels were validated exemplarily on leukemia cell lines and a subset of patients’ samples and identified all expected genomic alterations. Finally, blinded analysis of eight additional patients’ samples using our comprehensive assay accurately reproduced reference results. Therefore, calculated karyotyping by low coverage whole genome sequencing enables fast and reliable detection of numerical chromosomal changes and, in combination with panel-based fusion-and mutation screening, will greatly facilitate implementation of subtype-specific induction therapies in acute myeloid leukemia.

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.

An update of human mesenchymal stem cell biology and their clinical uses

In the past decade, an increasing urge to develop new and novel methods for the treatment of degenerative diseases where there is currently no effective therapy has lead to the emerging of the cell therapy or cellular therapeutics approach for the management of those conditions where organ functions are restored through transplantation of healthy and functional cells. Stem cells, because of their nature, are currently considered among the most suitable cell types for cell therapy. There are an increasing number of studies that have tested the stromal stem cell functionality both in vitro and in vivo. Consequently, stromal (mesenchymal) stem cells (MSCs) are being introduced into many clinical trials due to their ease of isolation and efficacy in treating a number of disease conditions in animal preclinical disease models. The aim of this review is to revise MSC biology, their potential translation in therapy, and the challenges facing their adaptation in clinical practice.

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.

Renal cell neoplasms contain shared tumor type-specific copy number variations

Copy number variant (CNV) analysis was performed on renal cell carcinoma (RCC) specimens (chromophobe, clear cell, oncocytoma, papillary type 1, and papillary type 2) using high-resolution arrays (1.85 million probes). The RCC samples exhibited diverse genomic changes within and across tumor types, ranging from 106 to 2238 CNV segments in a clear-cell specimen and in a papillary type 2 specimen, respectively. Despite this heterogeneity, distinct CNV segments were common within each tumor classification: chromophobe (seven segments), clear cell (three segments), oncocytoma (nine segments), and papillary type 2 (two segments). Shared segments ranged from a 6.1-kb deletion (oncocytomas) to a 208.3-kb deletion (chromophobes). Among common tumor type-specific variations, chromophobes, clear-cell tumors, and oncocytomas were composed exclusively of noncoding DNA. No CNV regions were common to papillary type 1 specimens, although there were 12 amplifications and 12 deletions in five of six samples. Three microRNAs and 12 mRNA genes had a ≥98% coding region contained within CNV regions, including multiple gene families (chromophobe: amylases 1A, 1B, and 1C; oncocytoma: general transcription factors 2H2, 2B, 2C, and 2D). Gene deletions involved in histone modification and chromatin remodeling affected individual subtypes (clear cell: SFMBT and SETD2; papillary type 2: BAZ1A) and the collective RCC group (KDM4C). The genomic amplifications/deletions identified herein represent potential diagnostic and/or prognostic biomarkers.

Clear cell renal cell carcinoma: multiphasic multidetector CT imaging features help predict genetic karyotypes

PURPOSE

To determine whether imaging characteristics at multiphasic multidetector computed tomography (CT) correlate with common karyotypic abnormalities in patients with clear cell renal cell carcinomas (ccRCCs).

MATERIALS AND METHODS

Institutional review board approval was obtained, and informed consent was waived for this HIPAA-compliant retrospective study. From January 2000 through September 2007, the prenephrectomy multiphasic (corticomedullary, nephrographic, and excretory phases), multidetector helical CT images of 58 histologically proved and karyotyped ccRCCs were reviewed by two readers with experience in abdominal imaging. Imaging features assessed included degree of attenuation, contour, and presence of calcifications and neovascularity. These features were independently correlated with specific karyotypic abnormalities on the resected specimens. Degree of attenuation data were analyzed with logistic regression for significance (P < .05), and morphologic characteristics were analyzed with odds ratios for assessing their diagnostic power.

RESULTS

On unenhanced scans, 7% (two of 28) of ccRCCs with the loss of chromosome 3p were calcified, whereas 37% (11 of 30) of lesions without this anomaly were calcified (odds ratio, 0.13). During the corticomedullary phase, ccRCCs with the loss of chromosome Y enhanced more than those without this anomaly (130.0 vs 102.5 HU, P = .04), and ccRCCs with trisomy 7 enhanced less than those without this anomaly (105.8 vs 139.3 HU, P = .04). During the excretory phase, ccRCCs with trisomy 5 enhanced more than those without this anomaly (115.5 vs 83.4 HU, P = .03).

CONCLUSION

The genetic makeup of ccRCCs affects their imaging features at multidetector CT examinations. Multidetector CT imaging characteristics may help suggest differences at the cytogenetic level among ccRCCs.

Clinical genomics of renal epithelial tumors

Kidney and upper urinary tract cancers account for approximately 54,000 cases every year in the United States, and represent about 3.7% of adult malignancies, with more than 13,000 annual deaths. Classification of renal tumors is typically based on histomorphologic characteristics but, on occasion, morphologic characteristics are not sufficient. Each of the most common histologic subtypes harbors specific recurrent genetic abnormalities, such as deletion of 3p in conventional clear cell carcinoma, trisomy 7 and 17 in papillary renal cell carcinoma, multiple monosomies in chromophobe renal cell carcinoma, and a nearly diploid genome in benign oncocytomas. Knowledge of this information can provide diagnostic support and prognostic refinement in renal epithelial tumors. Identification of the specific subtype of a renal tumor is critical in guiding surveillance for recurrence and the appropriate use of targeted therapies. Cytogenomic arrays are increasingly being used as a clinical tool for genome-wide assessment of copy number and loss of heterozygosity in renal tumors. In addition, the improved understanding of the hereditary causes of renal tumors and their role in sporadic malignancies has led to the development of more effective targeted therapies. This review summarizes the genetic and genomic changes in the most common types of renal epithelial tumors and highlights the clinical implications of these aberrations.

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.

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.

Molecular pathology of chromophobe renal cell carcinoma: a review

The recognition of chromophobe renal cell carcinoma (RCC) among other distinct types of renal cell tumors (RCT) based on light-microscopic features, such as cytoplasmic and nuclear characteristics, might pose a dilemma in some cases because of morphological pattern overlapping with renal oncocytoma or conventional RCC. The present article reviews chromophobe RCC with focus on aspects of its molecular pathology, which was shown using ancillary modern microarray-based technology that can distinguish it from its mimics and therefore be helpful for its correct diagnosis. Although the high resolution DNA-microarray analyses excluded with all certainty the occurrence of small specific alterations, the loss of entire chromosomes 2, 10, 13, 17 and 21 occurs exclusively in chromophobe RCC and therefore probes localized at these chromosomes might be used to establish the diagnosis of chromophobe RCC in cases with uncertain histology. The usefulness of proposed candidate genes selected by the global gene expression analyses in the diagnostic pathology is far below expectations. The conflicting staining patterns, together with the poor specificity of used antibodies, leads us to believe that these candidate immunomarkers might not help in the separation of chromophobe RCC, with the exception of CD82, which has recently been suggested to be used for routine histological diagnosis.

Papillary renal cell-like carcinoma in a retroperitoneal teratoma

We report a case of somatic type malignancy with papillary renal cell carcinoma differentiation arising in a retroperitoneal mixed germ cell tumor. The patient was a 36-year-old man with a synchronous mediastinal teratoma. The somatic type malignancy in the retroperitoneal tumor was composed of papillary structures covered by atypical epithelial cells with eosinophilic cytoplasm, prominent nucleoli and pseudostratified nuclei. Papillary cores contained numerous aggregates of foamy macrophages, typical of type I papillary renal cell carcinomas. The immunohistochemical profile was consistent with papillary renal cell carcinoma, including positive reactions for cytokeratin 7 and alpha-methyl acyl CoA racemase. There was no somatic type malignancy component in the synchronous mediastinal teratoma. Both the retroperitoneal and the mediastinal tumor showed gains of 12p and chromosome 17 material. There was no c-MET mutation in the somatic type malignancy. To our knowledge, this is the first report of a somatic type malignancy with features of papillary renal cell carcinoma arising in a germ cell tumor. It is important not to confuse such a retroperitoneal tumor with a conventional papillary renal cell carcinoma, because presence of other malignant histologies within the germ cell tumor may warrant different treatment. In such cases, the presence of isochromosome 12p can be helpful to the diagnosis.

Immunohistochemical expression of tumor antigens MAGE-A3/4 and NY-ESO-1 in renal oncocytoma and chromophobe renal cell carcinoma

The distinction between renal oncocytoma (RO) and chromophobe renal cell carcinoma (ChRCC), especially the eosinophilic variant, can often be difficult. Our study has documented for the first time the expression of MAGE-A3/4 and NY-ESO-1 cancer testis antigens (CTAs) in these tumors. A total of 35 patients (17 ROs and 18 ChRCCs) were included in the study. Two antibodies were used for immunohistochemical staining: 57B recognizing multiple MAGE-A and D8.38 recognizing NY-ESO-1 CTAs. Fifteen (88.2%) samples of RO stained positively for both MAGE-A3/4 and NY-ESO-1 antigens. Regarding ChRCC, seven (38.9%) stained positively for MAGE-A3/4 and six (33.3%) for NY-ESO-1 antigens. Median MAGE-A3/4 expression was moderately positive in RO and negative in ChRCC. The difference in MAGE-A3/4 expression between two tumor groups was significant (P=0.0013). Median NY-ESO-1 expression was strongly positive in RO and negative in ChRCC. The difference in NY-ESO-1 expression between two tumor groups was also significant (P=0.0008). Our study has shown that RO had a significantly higher expression of both CTAs. However, additional research is needed to clarify their potential diagnostic implications.

Strength of molecular cytogenetic analyses for adjusting the diagnosis of renal cell carcinomas with both clear cells and papillary features: a study of three cases

Histological features are usually sufficient for providing an accurate diagnosis of renal cell carcinomas (RCC). However, the morphological appearance might sometimes be misleading. For instance, RCC with papillary areas and extensive clear cell changes may be difficult to classify either as clear cell renal carcinoma or as papillary renal cell carcinoma (pRCC). We used the combination of immunohistochemistry, conventional cytogenetics, fluorescence in situ hybridization (FISH), bacterial artificial chromosomes comparative genomic hybridization arrays and high-density single nucleotides polymorphism arrays (SNP arrays) to characterize three cases of RCC showing a predominant cytology of cells with clear cytoplasm and variable amounts of papillary areas. In accordance with the 2004 World Health Organization (WHO) classification, we initially assessed the diagnosis of clear cell RCC for one of the cases and unclassified RCC for the two remaining cases. However, because of a strong immunohistochemical labeling for alpha-methylacyl-CoA racemase, as well as the presence of a gain of chromosomes 7 and 17, we concluded that two of these tumors were actually pRCC. As for the third case, because of the presence of both pCCR and ccCCR molecular cytogenetic aberrations, including gains of chromosomes 7 and 17, loss of chromosome Y and whole chromosome 3 loss of heterozyosity (isodisomy), the final diagnosis was hybrid tumor cc-pRCC, so-called "unclassified RCC" according to the WHO classification. Our observations demonstrate the necessity to use immunohistochemical and cytogenetic tools in all cases of RCC showing unusual features. The combination of FISH and SNP arrays is prevailing for characterizing cases with hybrid features.

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

CONTEXT

-Renal epithelial neoplasms have characteristic chromosomal imbalances, and we have shown previously that virtual karyotypes derived from single-nucleotide polymorphism microarrays can be performed on formalin-fixed, paraffin-embedded tissue.

OBJECTIVE

-To perform a direct comparison of virtual and conventional karyotypes to evaluate concordance of results.

DESIGN

-Twenty archival formalin-fixed, paraffin-embedded tumor samples with preexisting, conventional cytogenetic results were analyzed with Affymetrix 10K 2.0 or 250K Nsp single-nucleotide polymorphism microarrays.

RESULTS

-Nineteen samples yielded adequate virtual karyotypes for interpretation. Eight samples showed complete agreement between the 2 techniques, and 8 samples showed partial agreement. The disease-defining lesions (eg, loss of 3p for clear cell carcinoma) were identified in all 19 cases by virtual karyotypes and in 15 cases by conventional karyotypes. Virtual and conventional karyotypic findings were concordant in the identification of these disease-defining lesions in 86% (13 of 15) of cases. In 3 cases, virtual karyotypes identified lesions consistent with the morphologic diagnosis, whereas the conventional karyotypes were unsuccessful because of insufficient tumor representation or stromal overgrowth. Two cases with acquired uniparental disomy were identified by single-nucleotide polymorphism arrays, and 5 cases with translocations were identified by conventional karyotype.

CONCLUSIONS

-Our results show that both techniques are able to identify the characteristic chromosomal abnormality for renal tumor subtypes in most cases. Discrepancies can be explained by inherent limitations of each technique, inadequate tumor sampling, and tumor heterogeneity. We conclude that virtual karyotyping is a robust alternative to conventional cytogenetics for the evaluation of chromosomal anomalies in formalin-fixed, paraffin-embedded tissues from renal epithelial neoplasms.