Chromosomal abnormalities in non-neoplastic renal tissue

Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease

BACKGROUND

Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and chronic kidney disease.

RESULTS

The likelihood of a cell having LOY varies depending on its location in the nephron. Cortical epithelial cell types have a greater proportion of LOY than medullary or glomerular cell types, which may reflect their proliferative history. Proximal tubule cells are the most abundant cell type in the cortex and are susceptible to hypoxic injury. A subset of these cells acquires a pro-inflammatory transcription and chromatin accessibility profile associated with expression of HAVCR1, VCAM1, and PROM1. These injured epithelial cells have the greatest proportion of LOY and their presence predicts future kidney function decline. Moreover, proximal tubule cells with LOY are more likely to harbor additional large chromosomal gains and express pro-survival pathways. Spatial transcriptomics localizes injured proximal tubule cells to a pro-fibrotic microenvironment where they adopt a secretory phenotype and likely communicate with infiltrating immune cells.

CONCLUSIONS

We hypothesize that LOY is an indicator of increased DNA damage and potential marker of cellular senescence that can be applied to single-cell datasets in other tissues.

Y-chromosome loss is frequent in male renal tumors

Background

Loss of the Y-chromosome is a common event in different tumor types but its prevalence and clinical relevance in renal cell tumors is still not understood.

Methods

It was the aim of this study to estimate the frequency and clinical relevance of Y-loss in kidney neoplasms. A cohort of 1,252 male renal tumors was analyzed in a tissue microarray format by fluorescence in-situ hybridization (FISH).

Results

Y-loss was found in 47% of tumors. The frequency of this alteration varied markedly between kidney tumor subtypes. Y-loss was most prevalent in papillary renal cell carcinoma (RCC) (77%) followed by chromophobe RCC (60%), oncocytoma (51%), clear cell RCC (39%) and clear cell (tubulo)papillary RCC (19%). Y-loss was linked to higher patient age and smaller tumor size at diagnosis. Mean age (95% CI) was 65 (64–66) years in patients with Y-loss in their tumor compared to 60 (58–61) years in patients without Y-loss (P<0.0001). Significant correlations between Y-loss and tumor phenotype were found only for papillary carcinomas (P=0.002), especially for type 1 (P=0.03).

Conclusions

Y-loss is present in different histologic subtypes of renal neoplasm. The highest frequency is in papillary RCC, where it may represent a potentially relevant prognostic biomarker suggesting favorable disease outcome.

"Atrophic Kidney"-like Lesion: Clinicopathologic Series of 8 Cases Supporting a Benign Entity Distinct From Thyroid-like Follicular Carcinoma

Renal mass lesions with a follicular architecture resembling atrophic kidney have been described, but their distinction from thyroid-like follicular carcinoma of the kidney remains controversial. We collected 8 cases of this purported "atrophic kidney"-like lesion to fully describe their clinical and histologic spectrum, their possible etiology, and to discuss their distinction from other renal neoplasms. Eight total cases were identified with patient ages ranging from 9 to 48 years (mean: 29 y; median: 28.5 y). Four patients were female and 4 were male. The tumors were unifocal and size ranged from 1.6 to 4.9 cm (mean: 3.4 cm; median: 3.4 cm). All 8 tumors had a remarkably similar histology. Each was enveloped by a smooth muscle rich capsule and had an overall low power "follicular" architecture. The luminal spaces of the "follicles" (or cysts) contained eosinophilic secretions and the lining epithelium was often flattened and atrophic, but some had more rounded cells with a distinctive hobnail arrangement. Many cysts contained discohesive round cells floating within the eosinophilic material, and some contained small intraluminal tufts with features of markedly atrophic glomeruli. Periodic acid-Schiff stains highlighted basement membrane material extending into these glomerular-like tufts, and some contained small distinct capillaries surrounded by endothelial cells, interspersed mesangial-like cells, and rare surrounding podocyte-like cells, providing additional evidence for glomerulocystic structures. Scattered calcifications were present within cysts (or within cyst walls) in varying numbers and were characterized by 2 types: psammoma body-like or more amorphous deposits. The tissue between cystic glomeruli contained predominantly small atrophic tubular structures, but collagenized stroma and smaller collapsed glomeruli were also present. The 2 tumors from the oldest 2 patients (48 and 39 y) had a more striking degree of stromal hyalinization. Immunohistochemically, the cyst lining cells had a predominant WT-positive/PAX-8 negative/CK7-negative phenotype, while tubules were typically WT-1 negative/PAX-8 positive/CK7-positive. Upon comparison to a control group of 10 kidneys containing incidental non-mass-forming glomerulocystic change, the morphologic features and immunophenotype were identical. To date, no patient has had any recurrence or aggressive clinical behavior based on follow status in 7 of 8 cases (follow-up range: 9 to 168 mo; median: 24 mo; mean: 40 mo). In summary, we describe the clinicopathologic features of 8 unique, benign "atrophic kidney"-like lesions that may simply represent a non-neoplastic form of organizing tubular atrophy and glomerulocystic change, and emphasize their distinction from thyroid-like follicular carcinoma of the kidney.

Karyotyping of human chondrocytes in scaffold-assisted cartilage tissue engineering

Scaffold-assisted autologous chondrocyte implantation (ACI) is an effective clinical procedure for cartilage repair. The aim of our study was to evaluate the chromosomal stability of human chondrocytes subjected to typical cell culture procedures needed for regenerative approaches in polymer-scaffold-assisted cartilage repair. Chondrocytes derived from post mortem donors and from donors scheduled for ACI were expanded, cryopreserved and re-arranged in polyglycolic acid (PGA)-fibrin scaffolds for tissue culture. Chondrocyte redifferentiation was analyzed by electron microscopy, histology and gene expression analysis. Karyotyping was performed using GTG banding and fluorescence in situ hybridization on a single cell basis. Chondrocytes showed de- and redifferentiation accompanied by the formation of extracellular matrix and induction of typical chondrocyte marker genes like type II collagen in PGA-fibrin scaffolds. Post mortem chondrocytes showed up to 1.7% structural and high numbers of numerical (up to 26.7%) chromosomal aberrations, while chondrocytes from living donors scheduled for ACI showed up to 1.8% structural and up to 1.3% numerical alterations. Cytogenetically, cell culture procedures and PGA-fibrin scaffolds did not significantly alter chromosomal integrity of the chondrocyte genome. Human chondrocytes derived from living donors subjected to regenerative medicine cell culture procedures like cell expansion, cryopreservation and culture in resorbable polymer-based scaffolds show normal chromosomal integrity and normal karyotypes.

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.

Novel karyotypes in giant cell-rich lesions of bone

Giant cell-rich lesions of bone, including giant cell tumor of bone, giant cell reparative granuloma (GCRG), and aneurysmal bone cyst (ABC), may have overlapping clinical, radiologic, and histopathologic features. In fact, GCRG and solid ABC are currently differentiated solely based on skeletal location. Prior cytogenetic studies have reported that telomeric associations are present in the majority of giant cell tumors of bone, whereas translocations involving 16q22 and/or 17p13 are characteristic of ABCs. There is only one previously published karyotype of a GCRG, which revealed a reciprocal translocation, t(X;4)(q22;q31.3). We report 3 cases of giant cell-rich bone lesions with novel karyotypes: one lesion located in the first metacarpal, a typical location for GCRG, was histologically consistent with a giant cell tumor and showed the following karyotype [46,XX,inv(2)(p13q21),t(inv2;11)(q21;q13)]; the second lesion, also a giant cell tumor of bone, in the sacrum showed the following karyotype [46,XX,r(9)(p24q34)[cp7]/46,idem,?r(16)(p13.3q24)[cp10]/46,XX]. The third lesion, a hard palate mass, had the histopathologic features of a GCRG and a karyotype showing a reciprocal translocation, 46,XY,t(2;10)(q23;q24). These findings suggest that at least a subset of GCRGs may be neoplastic and that these lesions differ cytogenetically from classic giant cell tumors of bone or solid ABC, although the latter entity is otherwise indistinguishable from reparative granuloma. Further cytogenetic characterization of giant cell-rich bone lesions may improve the utility of karyotyping as a tool in their differential diagnosis and may shed light on the pathogenetic relationship between these lesions.

Activation of the mTOR pathway in sporadic angiomyolipomas and other perivascular epithelioid cell neoplasms

Angiomyolipoma (AML) belong to a family of tumors known as perivascular epithelioid cell tumors (PEComas) that share a common immunophenotypic profile of muscle and melanocytic differentiation. These tumors are clonal in nature and have a strong association with tuberous sclerosis. Genetic analyses have reported allelic imbalance at the TSC2 locus on 16p13. In the context of non-tuberous sclerosis complex (TSC), non-lymphangioleiomyomatosis-associated AMLs, and non-renal PEComas, the functional status of the TSC2 signaling pathway has not been reported. Studies over the last several years have uncovered a critical role of the TSC1/2 genes in negatively regulating the Rheb/mTOR/p70S6K cascade. Here, we examined the activity of this pathway in sporadic AMLs and PEComas using immunohistochemical and biochemical analyses. We found increased levels of phospho-p70S6K, a marker of mTOR activity, in 15 of 15 non-TSC AMLs. This was accompanied by reduced phospho-AKT expression, a pattern that is consistent with the disruption of TSC1/2 function. Western blot analysis confirmed mTOR activation concurrent with the loss of TSC2 and not TSC1 in sporadic AMLs. Similarly, elevated phospho-p70S6K and reduced phospho-AKT expression was detected in 14 of 15 cases of extrarenal PEComas. These observations provide the first functional evidence that mTOR activation is common to sporadic, non-TSC-related AMLs and PEComas. This suggests the possibility that mTOR inhibitors such as rapamycin may be therapeutic for this class of disease.

High Incidence of Chromosome 1 Abnormalities in a Series of 27 Renal Oncocytomas: Cytogenetic and Fluorescence In Situ Hybridization Studies

Context.—It has recently been shown by cytogenetics that there is a high incidence of chromosome 1 abnormalities in renal oncocytomas.

Objective.—To confirm the cytogenetic results by fluorescence in situ hybridization (FISH) analysis.

Design.—Nine additional cytogenetic analyses were added to those reported in our recent study, with a total of 27 tumors studied, which makes it the largest series of renal oncocytomas studied to date by cytogenetics and/or FISH. We used the LSI 1p36/LSI 1q25 Dual Color Probe Set to make the analyses.

Results.—In this study, combined cytogenetics and FISH showed loss of chromosome arm 1p1 in 48% of renal oncocytomas. By FISH, deletion of 1p36.3 was observed in 59% of renal oncocytomas, whereas by cytogenetics, abnormality in chromosome 1 was seen in 32% of tumors. However, the incidence of chromosome 1 abnormalities among 9 bilateral tumors was much higher than in single tumors (88% vs 28%, respectively). Loss of only the 1p36.3 site occurred in 2 renal oncocytomas with translocation of chromosome 1, as shown by cytogenetics. Concordance between the 2 techniques, when they were used simultaneously to detect chromosome 1p1 abnormality, was 82%.

Conclusions.—This study further confirmed our prior results demonstrating the widespread occurrence of chromosome 1 abnormalities in renal oncocytomas. Although no abnormalities in chromosome 1 in tumors with normal karyotypes were detected by FISH using the current set of probes, a much higher incidence of such abnormalities was found in bilateral tumors, suggesting that genetic alterations related to the development of renal oncocytoma reside in this region.

Translocation (10;17)(q22;p13): a recurring translocation in clear cell sarcoma of kidney

A clear cell sarcoma from the kidney of a 12-month-old male child manifested a balanced translocation, t(10;17)(q22;p13). This is the second report of this cytogenetic abnormality in renal clear cell sarcoma.

Cytogenetic Analysis of a Series of 13 Renal Oncocytomas

PURPOSE

Only about 50 renal oncocytomas have been studied cytogenetically. They fall into 3 categories, namely 1-normal karyotype, 2-monosomy 1, often with Y chromosome loss, and 3-structural abnormalities of 11q13. Additional abnormalities may occur with transformation to chromophobe renal cell carcinoma, although exactly which one is unclear. We expanded the oncocytoma data base to shed light on changes that characterize transformation.

MATERIALS AND METHODS

A total of 14 oncocytomas from 12 patients were collected in 2(1/2) years. One tumor failed to grow but 13 were successfully karyotyped.

RESULTS

Seven tumors (53.8%), including 2 from 1 kidney, had normal karyotypes or abnormalities characteristic of normal kidney tissue. A total of 6 tumors from 5 individuals (46.2%) had chromosome 1 abnormalities. Monosomy 1 was detected in 2 single tumors and in both tumors in a bilateral case. Structural anomalies resulting in loss of the short arm of chromosome 1 were found in an additional 2 patients. Other abnormalities, including Y chromosome loss and monosomy 14, were observed but no abnormalities of 11q13 were seen.

CONCLUSIONS

Our series confirms that 1p loss is the most common anomaly in oncocytoma. Additional studies are required to understand the transformation potential of this usually benign tumor, identify the putative 1p tumor suppressor gene and determine whether karyotypically normal tumors have molecular abnormalities of 1p.

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.

Atypical epithelial proliferations in acquired renal cystic disease harbor cytogenetic aberrations

Acquired renal cystic disease (ARCD) complicating end-stage renal failure confers an increased risk for renal cell carcinoma, and atypical epithelial proliferation in the cysts may represent the precursor lesion. In this report we used an interphase cytogenetic technique to analyze the karyotypic features of various forms of atypical epithelial proliferations in a patient with ARCD. Both kidneys harbored numerous simple and atypical cysts. In addition, papillary tufts and a hitherto undescribed cribriform epithelial proliferation were found in the right kidney. The left kidney contained a 10-mm renal cell carcinoma with features indeterminate between clear cell and papillary types. There was gain of chromosome 7 in the papillary tufts; gain of chromosomes 7 and 17 in the cribriform lesion; gain of chromosomes 7, 12, 17, 20, and Y in the atypical cysts; and gain of chromosomes 7, 12, 17, and 20 in the renal cell carcinoma. These chromosomal aberrations suggest that atypical epithelial proliferations in ARCD represent early neoplastic lesions.

Trisomy of chromosome 10 in two cases of ovarian carcinoma

Simple numerical chromosome aberrations have been observed in tumorigenesis and may point to indicative initiating or early events in tumorigenesis. We have identified two cases of ovarian carcinomas with trisomy of chromosome 10 using conventional GTG-banding and fluorescence in situ hybridization. This is, to our knowledge, the first report of trisomy 10 as a simple karyotypic abnormality observed in ovarian carcinoma. These results suggest that further studies investigating whether chromosome 10 genes are associated with the pathogenesis of some ovarian tumors are warranted.

Clonal chromosome aberrations in three of five sporadic angiomyolipomas of the kidney

Clonal chromosomal changes were detected in three of five sporadic angiomyolipomas of the kidney irrespective of a solitary or multifocal appearance of this benign tumor type. No specific chromosomal changes have been identified. Including the cytogenetic data of the four renal angiomyolipomas reported in the literature, trisomy 7 as the single clonal chromosomal abnormality was detected in two angiomyolipomas. Because trisomy 7 has been reported in both neoplastic and nonneoplastic kidney cells, it may be assumed that trisomy 7 is already physiologically resident in renal cells but undergoes positive selection in this tumor type.

Cytogenetic classification of renal cell cancer

Cytogenetic and molecular genetic investigations in cancer are important tools to address problems of oncogenesis and tumor progression, of classification, and of diagnosis of tumors. A combination of advanced molecular genetic, cytogenetic, and (immuno) histopathologic analysis will contribute significantly to the elucidation of the oncogenic steps that lead to immortalization and subsequent malignant behavior. In this review written on the occasion of Dr. Avery Sandberg's 75th anniversary, we will present a model for the pathogenesis of renal cell tumors based on a new cytomorphologic classification and our (cyto)genetic analysis of about 175 renal cell tumors, together with the accumulated data in the literature.

Chromosomal findings and p53-mutation analysis in chromophilic renal-cell carcinomas

The chromosomal pattern of 31 specimens of chromophilic renal-cell cancer (RCC), selected according to the criteria mentioned in the classification of Thoenes and Störkel, is presented. A high male preponderance was found (8.7:1). Cytogenetic analysis revealed a typical pattern of numeric alterations specific for this sub-type in the majority of cases (i.e., --Y,+7, +12, +16, +17, and/or +20), which is different from the chromosomal patterns found in other sub-types of RCC. Gain of chromosome 20, as well as loss of the extra copy of chromosome 17 or loss of 17p, was found to be related to the higher-grade chromophilic carcinomas. None of the 14 cases examined by SSCP analysis revealed mutations of the p53 gene, indicating that other genes at 17(p) might be important in the progression of this sub-type of RCC.