DEVOLUTION-A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data.

Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers and high-risk adult cancer. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on data from 56 pediatric tumors comprising 253 tumor biopsies and show a robust performance on simulations of bulk genotyping data. We also benchmark DEVOLUTION to similar bioinformatic tools using an external dataset. DEVOLUTION holds the potential to facilitate insights into the development, progression, and response to treatment, particularly in tumors with high burden of chromosomal copy number alterations.

Dataset for the reporting of nephrectomy specimens for Wilms' tumour treated with preoperative chemotherapy: recommendations from the International Society of Paediatric Oncology Renal Tumour Study Group.

Datasets for histopathological reporting of many cancer types are developed by the International Collaboration on Cancer Reporting (ICCR), and are used in order to ensure standardised and uniformly accepted reporting as one of the essential requirements for comparison across patient populations in evaluating and validating pathological prognostic and predictive factors. Wilms' tumours are rare, and international reporting guidelines have not yet been published by the ICCR. The assessment of Wilms' tumours differs according to the treatment approach. The Children's Oncology Group, whose approach is followed mainly in North America, advocates primary surgery, and the International Society of Paediatric Oncology Renal Tumour Study Group (SIOP-RTSG), whose approach is followed in most countries around the world, uses preoperative chemotherapy as a first step, resulting in different subclassifications, staging criteria, and histopathological prognostic factors. This dataset is developed for the countries and institutions following the SIOP-RTSG approach, and it contains core (required) and non-core (recommended) elements, based on the results of the previous SIOP-RTSG studies, which are incorporated in the latest SIOP-RTSG UMBRELLA 2016 Study protocol. The core elements include clinical information, additional specimen submitted, macroscopic tumour site and appearance, tumour focality, tumour dimensions, macroscopic extent of invasion, block identification key, histological tumour type, histological tumour grade and risk group assessment, microscopic extent of invasion, lymphovascular invasion, resection margin status, regional lymph node status, histologically confirmed distant metastases, and pathological staging (SIOP staging system). The dataset should improve communication for patient care and prognostic determination of the old and new histopathological features.

Clinically and biologically relevant subgroups of Wilms tumour defined by genomic and epigenomic analyses.

BACKGROUND: Although cure rates for Wilms tumours (WT) are high, many patients receive therapy with attendant long-term complications. Our goal was to stratify WT using genome-wide analyses to identify candidate molecular features for patients who would benefit from a reduction in therapy. METHODS: We generated DNA methylation and exome sequencing data on WT-kidney pairs (n = 57) and unpaired tumours (n = 27) collected either at our centre or by the Children's Oncology Group. Samples were divided into a discovery set (n = 32) and validation set (n = 52). RESULTS: Analysis of DNA methylation revealed two subgroups of WT with distinct features. Subgroup A has a similar DNA methylation profile to mature kidney, while Subgroup B has genome-wide dysregulation of DNA methylation. The rate of non-synonymous missense mutations and segmental chromosomal aberrations was higher in Subgroup B tumours, suggesting that this group has genome instability related to its epigenetic state. Subgroup A had a higher proportion of cases of bilateral disease. Tumours with high-risk histology or from patients who relapsed were only found in Subgroup B. CONCLUSION: We have identified subgroup-specific molecular events that could inform future work supporting more targeted therapeutic approaches and patient stratification. We propose a novel developmental tumour model based on these findings.

The prognosis of prechemotherapy blastemal predominant histology subtype in Wilms tumor: A retrospective study in China.

PURPOSE: This study aimed to retrospectively analyze survival outcomes for Chinese patients with prechemotherapy blastemal predominant histology type Wilms tumors (WTs). METHODS: We collected and analyzed clinical data concerning patients aged <15 years with favorable histology (FH) WTs treated at the Sun Yat-Sen University Cancer Center from December 2005 to May 2016, based on the Children's Oncology Group protocol. Pathological specimens were collected through biopsy or surgical resection before initiation of chemotherapy. We analyzed survival outcomes involving different prechemotherapy histology subtypes. RESULTS: We enrolled 97 patients with FH WTs (median follow-up, 71.5 months; range, 22.2-170.7). The total recurrence rate was 17.5%, and the subtype recurrence rates were as follows: blastemal predominant (45.5%), mixed (7.5%), epithelial (14.3%), and mesenchymal (9.5%) (P = .010). Five-year event-free survival (EFS) and overall survival (OS) rates were 84.9% and 81.4%, respectively. Respective 5-year EFS and OS rates for subtypes were as follows: blastemal predominant (54.5% and 68.2%), mixed (90.0% and 88.9%), epithelial (85.7% and 85.1%), and mesenchymal (90.5% and 94.7%). Multivariate survival analyses showed that the blastemal predominant subtype was an independent prognostic factor of EFS (P = .001) and OS (P = .017). CONCLUSIONS: Our findings showed that prechemotherapy blastemal predominant WTs had higher recurrence and lower EFS and OS rates. Our findings suggested that, albeit with some deficiencies, blastemal predominant histology WT-diagnosed prechemotherapy may have prognostic relevance. Further research into other potential confounding variables are required to determine whether such patients warrant altered risk-stratified therapy.

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.

Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 single-cell transcriptomes of human renal tumors and normal tissue from fetal, pediatric, and adult kidneys. We matched childhood Wilms tumor with specific fetal cell types, thus providing evidence for the hypothesis that Wilms tumor cells are aberrant fetal cells. In adult renal cell carcinoma, we identified a canonical cancer transcriptome that matched a little-known subtype of proximal convoluted tubular cell. Analyses of the tumor composition defined cancer-associated normal cells and delineated a complex vascular endothelial growth factor (VEGF) signaling circuit. Our findings reveal the precise cellular identities and compositions of human kidney tumors.

Diagnostic utility of Wilms' tumour-1 protein (WT-1) immunostaining in paediatric renal tumours.

BACKGROUND & OBJECTIVES: Renal tumours constitute about 7 per cent of all neoplasms in children. It is important to differentiate Wilms' tumour (commonest tumour) from non-Wilms' tumours. The aim of this study was to evaluate the immunoexpression and diagnostic role of Wilms' tumour-1 protein (WT1) in paediatric renal tumours. METHODS: A total of 53 cases of renal tumours in children (below 18 yr) who underwent total nephrectomy were included in this retrospective study. WT1 immunostaining was done using mouse monoclonal WT1 antibody (clone: 6F-H2). RESULTS: Of the 53 cases, 38 (72%) were of Wilms' tumour. Non-Wilms' group (15) included six cases of mesoblastic nephroma (MN), two each of clear cell sarcoma (CCSK), renal cell carcinoma (RCC) and peripheral neuroectodermal tumour (PNET) and one each of angiomyolipoma (AML), rhabdomyosarcoma (RMS) and malignant rhabdoid tumour (MRT). Proportion of WT1 positivity in Wilms' tumour was 100 per cent in contrast to 26.7 per cent in non-Wilms' tumours ( P<0.001). Epithelial and blastemal components of Wilms' tumour showed moderate (2+) nuclear and cytoplasmic staining in 80 (24/30) and 75 per cent (24/32) cases, respectively. MN, PNET, CCSK and AML were negative for WT1. RMS, RCC and MRT showed cytoplasmic staining, strongest in RMS. No significant association was seen between WT1 expression and NWTSG (National Wilms' Tumor Study Group) stage. INTERPRETATION & CONCLUSIONS: WT1 helps to differentiate Wilms' tumour from other paediatric renal tumours. It may help in differentiating the two subgroups of Wilms' tumour which have distinct molecular pathogenesis and biological behaviour, however, further prospective studies are required for validation of this hypothesis.

A multi-Gaussian model for apparent diffusion coefficient histogram analysis of Wilms' tumour subtype and response to chemotherapy.

Wilms' tumours (WTs) are large heterogeneous tumours, which typically consist of a mixture of histological cell types, together with regions of chemotherapy-induced regressive change and necrosis. The predominant cell type in a WT is assessed histologically following nephrectomy, and used to assess the tumour subtype and potential risk. The purpose of this study was to develop a mathematical model to identify subregions within WTs with distinct cellular environments in vivo, determined using apparent diffusion coefficient (ADC) values from diffusion-weighted imaging (DWI). We recorded the WT subtype from the histopathology of 32 tumours resected in patients who received DWI prior to surgery after pre-operative chemotherapy had been administered. In 23 of these tumours, DWI data were also available prior to chemotherapy. Histograms of ADC values were analysed using a multi-Gaussian model fitting procedure, which identified 'subpopulations' with distinct cellular environments within the tumour volume. The mean and lower quartile ADC values of the predominant viable tissue subpopulation (ADC(1MEAN), ADC(1LQ)), together with the same parameters from the entire tumour volume (ADC(0MEAN), ADC(0LQ)), were tested as predictors of WT subtype. ADC(1LQ) from the multi-Gaussian model was the most effective parameter for the stratification of WT subtype, with significantly lower values observed in high-risk blastemal-type WTs compared with intermediate-risk stromal, regressive and mixed-type WTs (p < 0.05). No significant difference in ADC(1LQ) was found between blastemal-type and intermediate-risk epithelial-type WTs. The predominant viable tissue subpopulation in every stromal-type WT underwent a positive shift in ADC(1MEAN) after chemotherapy. Our results suggest that our multi-Gaussian model is a useful tool for differentiating distinct cellular regions within WTs, which helps to identify the predominant histological cell type in the tumour in vivo. This shows potential for improving the risk-based stratification of patients at an early stage, and for guiding biopsies to target the most malignant part of the tumour.

Global demethylation in loss of imprinting subtype of Wilms tumor.

Epigenetic abnormalities at the IGF2/H19 locus play a key role in the onset of Wilms tumor. These tumors can be classified into three molecular subtypes depending on the events occurring at this locus: loss of imprinting (LOI), loss of heterozygosity (LOH), or retention of imprinting (ROI). As IGF2 LOI is a consequence of aberrant methylation, we hypothesized that this subtype of Wilms tumors might display global abnormalities of methylation. We therefore analyzed the methylation status of satellite DNA, as a surrogate for global methylation in 50 Wilms tumor patients. Satellite methylation was quantified by a methylation-sensitive quantitative PCR. We confirmed hypomethylation of both satellite α (Sat α) and satellite 2 (Sat 2) DNA in Wilms tumor samples compared with normal kidney. In addition, we found that LOI tumors, unlike ROI or LOH ones, showed concordant hypomethylation of both Sat α and Sat 2 DNA. This would suggest that the LOI subtype of Wilms tumor, which unlike other subtypes results from an epimutation, has a global deregulation of methylation mechanisms.

Factors associated with relapse and survival in Wilms tumor: a multivariate analysis.

PURPOSE: Lymph node metastasis and anaplasia predict relapse-free survival in Wilms tumor. We performed a multivariate analysis of our institutional database to identify factors independently associated with relapse-free and overall survival. METHODS: We retrospectively reviewed cases of confirmed Wilms tumor diagnosed between 1990 and 2010 and treated at our institution. The log-rank test was used to screen variables for consideration in the proportional hazards model. RESULTS: A total of 95 patients were treated at our institution during the study period, with a median follow-up of 3.3 years. Factors correlated with overall survival in the univariate analysis were local disease, metastasis, tumor size, anaplasia, renal vein tumor thrombus, inferior vena cava tumor thrombus, lymph node positivity, and tumor rupture. On multivariate analysis, factors associated with increased risk of death were lymph node positivity and anaplasia. Factors correlated with probability of relapse in the univariate analysis were lymph node positivity, anaplasia, and female sex. All 3 of these factors were also independently significant on multivariate analysis. CONCLUSION: Lymph node involvement and anaplasia are significantly correlated with probability of relapse and overall survival, reemphasizing the strong recommendation to sample regional lymph nodes during Wilms tumor resection.

Stratification of Wilms tumor by genetic and epigenetic analysis.

Somatic defects at five loci, WT1, CTNNB1, WTX, TP53 and the imprinted 11p15 region, are implicated in Wilms tumor, the commonest childhood kidney cancer. In this study we analysed all five loci in 120 Wilms tumors. We identified epigenetic 11p15 abnormalities in 69% of tumors, 37% were H19 epimutations and 32% were paternal uniparental disomy (pUPD). We identified mutations of WTX in 32%, CTNNB1 in 15%, WT1 in 12% and TP53 in 5% of tumors. We identified several significant associations: between 11p15 and WTX (P=0.007), between WT1 and CTNNB1 (P less than 0.001), between WT1 and pUPD 11p15 (P=0.01), and a strong negative association between WT1 and H19 epimutation (P less than 0.001). We next used these data to stratify Wilms tumor into three molecular Groups, based on the status at 11p15 and WT1. Group 1 tumors (63%) were defined as 11p15-mutant and WT1-normal; a third also had WTX mutations. Group 2 tumors (13%) were WT1-mutant. They either had 11p15 pUPD or were 11p15-normal. Almost all had CTNNB1 mutations but none had H19 epimutation. Group 3 tumors (25%) were defined as 11p15-normal and WT1-normal and were typically normal at all five loci (P less than 0.001). We also identified a novel clinical association between H19 epimutation and bilateral disease (P less than 0.001). These data provide new insights into the pattern, order, interactions and clinical associations of molecular events in Wilms tumor.

Heterogeneity of disease classified as stage III in Wilms tumor: a report from the Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP).

PURPOSE: We analyzed whether the prognosis can differ among Wilms tumors (WT) labeled as Stage III according to currently adopted classification systems. METHODS AND MATERIALS: Patients with nonanaplastic Stage III WT consecutively registered in two Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP) trials (CNR-92, TW-2003) were the subjects in the present analysis. The steady mainstay of therapy was primary nephrectomy, followed by three-drug chemotherapy with vincristine, dactinomycin, doxorubicin, and abdominal radiotherapy (RT). RESULTS: Ninety-nine WT patients met the criteria for classification as Stage III according to a revised version of the National Wilms Tumor Study-3 staging system (51 patients in CNR-92, 48 patients in TW-2003). Regional lymph nodes (LN) were not biopsied in 16 patients. After a median follow-up of 66 months, the 4-year disease-free survival (DFS) and overall survival (OS) rates were 85% ± 4% and 92% ± 3%, respectively, for the whole group. For 38 children with positive LN, the 4-year DFS rate was 73% ± 7%, as opposed to 98% ± 2% for the 45 children with Stage III WT according to the other criteria but with negative biopsied LN (p = 0.001). The subgroup with the worst prognosis consisted of children more than 2 years old with positive LN (DFS 67% ± 8%). A delay between surgery and RT > 30 days had an adverse impact on the abdominal tumor relapse rate. CONCLUSIONS: This study provides further evidence that Stage III tumors with LN metastases might be distinguished from WTs meeting the other criteria for classification as Stage III. The worse outcome of the former may warrant a prospective study on the effects of intensified therapy. A subclassification of Stage III tumors is discussed.

Teratoid Wilms' tumor: case report of a rare variant that can mimic aggressive biology during chemotherapy.

Teratoid Wilms' tumor is considered by some as a variant of Wilms' tumor containing at least 50% heterologous differentiated tissue. Fewer than 30 cases have been described. We report a 9-month-old boy with bilateral Wilms' tumors who did not respond to multiagent chemotherapy and underwent right nephrectomy that showed a teratoid Wilms' tumor. The patient continued to survive despite cessation of treatment. The overall predominance of differentiated stromal elements in this subtype of Wilms' tumor might explain the poor response to chemotherapy yet generally favorable outcome. Recognition of this subtype on biopsy might justify earlier surgical intervention that, for bilateral tumors, might allow for greater nephron sparing.

The use of computer image analyses in the assessment of chosen histoclinical features of nephroblastoma cells in children.

The goal of the research was to assess the nuclear morphometric discriminant function (MV(f)) in the analyzed group of nephroblastomas and to evaluate its potential prognostic value. We found a statistically important correlation between favourable histology of Wilms' tumours (according to SIOP 93-01 and SIOP 2001 classifications of kidney tumours of childhood) and low values of MV(f) discriminant function, which was also associated with the best prognosis for the patients. We believe that MV(f) assessment may be a helpful tool in making prognosis in doubtful cases of nephroblastomas in children.

Nephron-sparing surgery for bilateral Wilms' tumours: a single-centre experience with 23 cases.

INTRODUCTION: The challenge of management with bilateral Wilms' tumours is the eradication of the neoplasm, while at the same time preserving renal function. Surgical management with a variety of nephron-sparing techniques, combined with chemotherapy and occasionally supplemented by transplantation has evolved over the last 30 years to achieve remarkable success. We document the experience of a single centre in a developing country. MATERIAL AND METHODS: Twenty-three bilateral Wilms' tumours were seen in our service between 1981 and 2007. Treatment was, in most cases, according to National Wilms' Tumour Study Group protocols, with initial bilateral biopsy, neoadjuvant chemotherapy, and tumourectomy. Technique of nephrectomy included full mobilization of the tumour-involved kidney, topical cooling with slush ice, vascular exclusion, tumour resection and reconstruction of the remnant kidney. RESULTS: Twelve patients are alive and free of disease one to 15 years after treatment, all with well-preserved renal function (lowest glomerular filtration rate was 65 ml/min per (1.73 m 2 ). None of the survivors have hypertension. Eleven have died (two of unrelated disease) including six of the seven with spread outside the kidney. All three with unfavourable histology are alive. Four of the five metachronous presentations are alive, as are eight of 12 patients with synchronous bilateral tumours who presented since 2000. CONCLUSIONS: Appropriate chemotherapy and nephron-sparing surgery can achieve good results with preservation of adequate renal function in nearly all cases. Unfavourable histology did not have a reduced survival in our series. Metastatic spread outside the kidney had a poor prognosis.

Metanephric adenofibroma: robotic partial nephrectomy of a large Wilms' tumor variant.

PURPOSE: A case of the rare, benign, Wilms' tumor (WT) variant, metanephric adenofibroma (MAF), is presented. MATERIALS AND METHODS: The patient is a 21-year-old female with an incidentally discovered enhancing renal mass. The diagnosis, workup and treatment are outlined. RESULTS: The 19 cm renal mass was ultimately resected via robot-assisted partial nephrectomy. Pathologic diagnosis at our institution was confirmed as a MAF by the National Wilms' Tumor Study Group (NWTSG). CONCLUSION: Difficult to differentiate from WT, it is imperative that MAF be recognized and appropriately diagnosed because unlike adult WT, the natural history of MAF is indolent and adjuvant chemo/radiation therapy is rarely necessary. This case reinforces the importance of review of potential WT variants by the NWTSG.

Subtype-specific FBXW7 mutation and MYCN copy number gain in Wilms' tumor.

PURPOSE: Wilms' tumor (WT), the most common pediatric renal malignancy, is associated with mutations in several well-characterized genes, most notably WT1, CTNNB1, WTX, and TP53. However, the majority of cases do not harbor mutations in these genes. We hypothesized that additional drivers of tumor behavior would be contained within areas of consistent genomic copy number change, especially those associated with the WT risk groups defined by the International Society of Paediatric Oncology (SIOP). EXPERIMENTAL DESIGN: We analyzed high-resolution (Affymetrix 250K single nucleotide polymorphism array) genomic copy number profiles of over 100 tumors from selected risk groups treated under the SIOP protocols, further characterizing genes of interest by sequencing, Multiplex Ligation-dependent Probe Amplification, or fluorescence in situ hybridization. RESULTS: We identified FBXW7, an E3 ubiquitin ligase component, as a novel Wilms' tumor gene, mutated or deleted in approximately 4% of tumors examined. Strikingly, 3 of 14 (21%) of tumors with epithelial type histology after neoadjuvant chemotherapy had FBXW7 aberrations, whereas a fourth WT patient had germline mutations in both FBXW7 and WT1. We also showed that MYCN copy number gain, detected in 9 of 104 (8.7%) of cases, is relatively common in WT and significantly more so in tumors of the high risk diffuse anaplastic subtype (6 of 19, 32%). CONCLUSIONS: Because MYCN is itself a target of FBXW7-mediated ubiquitination and degradation, these results suggest that a common pathway is dysregulated by different mechanisms in various WT subtypes. Emerging therapies that target MYCN, which is amplified in several other pediatric cancers, may therefore be of value in high risk Wilms' tumor.

Histoclinical study of nephroblastoma in relation to current and previous SIOP Classification of Renal Tumors of Childhood.

Histological classifications are essential for prognosis in children malignancies. Currently, the histological type of tumor is one of the main prognostic factors in this group. We investigated histoclinical features of nephroblastoma in relation to SIOP 93-01 and SIOP 2001 Classifications of Renal Tumors of Childhood. We examined all the routinely available histological features and histological nephroblastoma types and investigated their influence on patients' survival with the use of log-rank test and Kaplan-Meier method. The results of statistical analysis indicated that SIOP 93-01 more precisely separated nephroblastoma types according to their biology and malignant potential. We also observed that epithelial type of nephroblastoma showed a mixture of results typical for both intermediate and high risk tumors. What is more, we noticed statistically important correlations between developmental defects found in patients with nephroblastoma and tumor volume and the course of disease.

Nonviable tumor tissue should not upstage Wilms' tumor from stage I to stage II: a report from the SIOP 93-01 nephroblastoma trial and study.

In SIOP trials, Wilms' tumors were labeled as stage II by the presence of nonviable and/or viable tumor in the renal sinus and/or perirenal fat. The aim of this study was to determine if this approach was justified. Stage II Wilms' tumors were reviewed to establish whether staging was due to viable or nonviable tumor, and this was related to clinical outcome. One hundred sixty-nine patients were included: 40 had stage II due to the presence of nonviable tumor and 129 due to viable tumor. Postoperatively, 29 patients were undertreated: 7 with nonviable and 22 with viable stage II tumors. No undertreated patient with nonviable stage II relapsed or died (event-free survival [EFS] and overall survival [OS] 100%), whereas 3 of 22 with viable stage II relapsed, and 2 of them died (EFS 86%, OS 91%). Of 140 correctly treated patients, only 1 of 33 nonviable stage II patients relapsed and died (EFS and OS 97%); 8 of 107 patients with viable stage II relapsed (EFS 92%), and 3 of them died (OS 97%). The presence of nonviable tumor in the renal sinus and/or perirenal fat does not predict an adverse outcome in Wilms' tumors, and alone it does not warrant designation to stage II.