Screening for submicroscopic chromosomal rearrangements in Wilms tumor using whole-genome microarrays

A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.

Submicroscopic chromosomal imbalances contribute to early abortion

Background

Chromosomal abnormalities are one of the genetic mechanisms associated with abortion. However, the roles of submicroscopic chromosomal imbalances in early abortion are still unclear. This study aims to find out whether submicroscopic chromosomal imbalances contribute to early abortion.

Methods

A total of 78 chorionic villus specimens from early spontaneous abortion patients with no obvious abnormality are collected after miccroassay analysis (the case group). At the same time, 60 chorionic villus specimens from induced abortion patients with no obvious abnormality are selected as the control group. The submicroscopic structures of chromosomes from two groups are analyzed using an array-based comparative genomic hybridization (aCGH).

Results

In the case group, 15 specimens show submicroscopic chromosomal abnormalities including 14 micro-deletion/micro-duplication in chromosomes 2, 4, 5, 6, 7, 8, 9, 12, 15, 16, 18, and 22, and 1 uniparental disomy (UPD) in chromosome 19. Moreover, no pathogenic copy number variations are found in the control group. The results between these two groups exhibit significantly statistical difference.

Conclusion

Submicroscopic chromosomal imbalances may be one of the main reasons for early abortion.

Acquired Genetic and Epigenetic Variation in Human Pluripotent Stem Cells

Human pluripotent stem cells (hPSCs) can acquire non-random genomic variation during culture. Some of these changes are common in tumours and confer a selective growth advantage in culture. Additionally, there is evidence that reprogramming of human induced pluripotent stem cells (hiPSCs) introduces mutations. This poses a challenge to both the safety of clinical applications and the reliability of basic research using hPSCs carrying genomic variation. A number of methods are available for monitoring the genomic integrity of hPSCs, and a balance between practicality and sensitivity must be considered in choosing the appropriate methods for each use of hPSCs. Adjusting protocols by which hPSCs are derived and cultured is an evolving process that is important in minimising acquired genomic variation. Assessing genetic variation for its potential impact is becoming increasingly important as techniques to detect genome-wide variation improve.

Array CGH Analysis of Paired Blood and Tumor Samples from Patients with Sporadic Wilms Tumor

Wilms tumor (WT), the most common cancer of the kidney in infants and children, has a complex etiology that is still poorly understood. Identification of genomic copy number variants (CNV) in tumor genomes provides a better understanding of cancer development which may be useful for diagnosis and therapeutic targets. In paired blood and tumor DNA samples from 14 patients with sporadic WT, analyzed by aCGH, 22% of chromosome abnormalities were novel. All constitutional alterations identified in blood were segmental (in 28.6% of patients) and were also present in the paired tumor samples. Two segmental gains (2p21 and 20q13.3) and one loss (19q13.31) present in blood had not been previously described in WT. We also describe, for the first time, a small, constitutive partial gain of 3p22.1 comprising 2 exons of CTNNB1, a gene associated to WT. Among somatic alterations, novel structural chromosomal abnormalities were found, like gain of 19p13.3 and 20p12.3, and losses of 2p16.1-p15, 4q32.5-q35.1, 4q35.2-q28.1 and 19p13.3. Candidate genes included in these regions might be constitutively (SIX3, SALL4) or somatically (NEK1, PIAS4, BMP2) operational in the development and progression of WT. To our knowledge this is the first report of CNV in paired blood and tumor samples in sporadic WT.

Retrospective analysis of FFPE based Wilms' Tumor samples through copy number and somatic mutation related Molecular Inversion Probe Based Array

In this report, retrospectively, we analyzed fifteen histo-pathologically characterized FFPE based Wilms' Tumor (WT) samples following an integrative approach of copy number (CN) and loss of heterozygosity (LOH) imbalances. The isolated-DNA was tested on CN and somatic-mutation related Molecular-Inversion-Probe based-Oncoscan Array™ and was analyzed through Nexus-Express OncoScan-3.0 and 7.0 software. We identified gain of 3p13.0-q29, 4p16.3-14.0, 7, 12p13.33-q24.33, and losses of 1p36.11-q44, 11p15.5-q25, 21q 22.2-22.3 and 22q11.21-13.2 in six samples (W1-6) and validated them in nine more samples (W7-9, W12-15, W17-18). Some observed that discrete deletions (1p, 1q, 10p, 10q, 13q, 20p) were specific to our samples. Maximum-LOH was observed in Ch11 as reported in previous studies. However, LOH was also observed in different regions of Ch7 including some cancer genes. The identified LOH-regions (1q21.2-q21.3, 2p24.1-23.3, 2p24.3-24.3, 3p21.3-21.1, 4p16.3, 7p11.2-p11.1, 7q31.2-31.32, 7q34-q35 and Ch 8) in W1-W6 were also validated in W7-9, W12-15 and W18. In addition, previously reported LOH of 1p and 16q region was also observed in our cases. The proven and novel onco (OG)- and tumor-suppressor genes (TSGs) involved in the CNV regions affected the major pathways like Chromatin Modification, RAS, PI3K; RAS in 14/15 cases, NOTCH/TGF-β and Cell Cycle Apoptosis in 10/15 cases, APC in 9/15 cases and Transcriptional Regulation in 7/15 cases, PI3K and genome maintenance in 6/15 cases. This exhaustive profiling of OG and TG may help in prognosis and diagnosis of the disease after validation of all the relevant results, especially the novel ones, obtained in this research in a larger number of samples.

Gain of 1q is associated with inferior event-free and overall survival in patients with favorable histology Wilms tumor: a report from the Children's Oncology Group

BACKGROUND

Wilms tumor is the most common childhood renal tumor. Although the majority of patients with favorable histology Wilms tumor (FHWT) have good outcomes, some patients still experience disease recurrence and death from disease. The goal of the current study was to determine whether tumor-specific chromosome 1q gain is associated with event-free survival (EFS) and overall survival (OS) in patients with FHWT.

METHODS

Unilateral FHWT samples were obtained from patients enrolled on National Wilms Tumor Study-4 and Pediatric Oncology Group Wilms Biology Study (POG 9046). 1q gain, 1p loss, and 16q loss were determined using multiplex ligation-dependent probe amplification.

RESULTS

The 8-year EFS rate was 87% (95% confidence interval [95% CI], 82%-91%) for the entire cohort of 212 patients. Tumors from 58 of 212 patients (27%) displayed 1q gain. A strong relationship between 1q gain and 1p/16q loss was observed. The 8-year EFS rate was 76% (95% CI, 63%-85%) for patients with 1q gain and 93% (95% CI, 87%-96%) for those lacking 1q gain (P = .0024). The 8-year OS rate was 89% (95% CI, 78%-95%) for those with 1q gain and 98% (95% CI, 94%-99%) for those lacking 1q gain (P = .0075). Gain of 1q was not found to correlate with disease stage (P = .16). After stratification for stage of disease, 1q gain was associated with a significantly increased risk of disease recurrence (risk ratio estimate: 2.72; P = .0089).

CONCLUSIONS

Gain of 1q may provide a valuable prognostic marker with which to stratify therapy for patients with FHWT. A confirmatory study is necessary before this biomarker is incorporated into the risk stratification schema of future therapeutic studies.

Comparative genomic hybridization of Wilms' tumor

Cytogenetic analysis of solid tumors including Wilms' tumor is challenging due to poor chromosome morphology, complexity of abnormalities, and to the possibility of stromal cell overgrowth in tissue culture. Molecular cytogenetic techniques such as chromosomal comparative genomic hybridization (CGH) have improved the diagnosis of chromosomal aberrations in Wilms' tumor since they can provide results based on the analysis of DNA from nondividing cells. However, chromosomal CGH provides only a limited resolution across the whole genome, which is not different than routine cytogenetic analysis (gains or losses of less than one chromosome band or 10 Mb are not detectable by routine cytogenetics or chromosomal CGH). More recently, the development of genomic arrays opened the possibility of assessing the whole genome at a much higher resolution at a sub-microscopic or sub-band level. Based on the principle of chromosomal CGH, this approach, frequently termed array-CGH, opens the possibility to find invisible changes at the whole genome level not only in abnormal but also in normal tumor karyotypes. Here, we discuss the main technical features, benefits, and limitations of the above three techniques as applied to Wilms' tumor and summarize the main advances in our knowledge about the genetic changes of Wilms' tumor and their clinical relevance.

Wilms' tumor in patients with 9q22.3 microdeletion syndrome suggests a role for PTCH1 in nephroblastomas

Nephroblastoma (Wilms' tumor; WT) is the most common renal tumor of childhood. To date, several genetic abnormalities predisposing to WT have been identified in rare overgrowth syndromes. Among them, abnormal methylation of the 11p15 region, GPC3 and DIS3L2 mutations, which are responsible for Beckwith-Wiedemann, Simpson-Golabi-Behmel and Perlman syndromes, respectively. However, the underlying cause of WT remains unknown in the majority of cases. We report three unrelated patients who presented with WT in addition to a constitutional 9q22.3 microdeletion and dysmorphic/overgrowth syndrome. The size of the deletions was variable (ie, from 1.7 to 8.9 Mb) but invariably encompassed the PTCH1 gene. Subsequently, we identified a somatic PTCH1 nonsense mutation in the renal tumor of one patient. In addition, by array comparative genomic hybridization method, we analyzed the DNA extracted from the blood samples of nine patients with overgrowth syndrome and WT, but did not identify any deleterious chromosomal imbalances in these patients. These findings strongly suggest that patients with constitutional 9q22.3 microdeletion have an increased risk of WT, and that PTCH1 have a role in the pathogenesis of nephroblastomas.

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.

Pathology, genetics and cytogenetics of Wilms' tumour

Wilms' tumour (WT) is an embryonal cancer of childhood and is thought to be derived from embryonic kidney precursor cells. The Knudson two hit model was initially thought to occur in WT, but findings emerging from genetic and cytogenetic studies in the past two decades have implicated several genetic events. Recent techniques in genetic analysis have improved our ability to characterise changes in genes involved in WT which include WT1, CTNNB1, IGF2 and WTX. These genetic events have not only provided insight into the pathobiology of this malignancy, but the recognition of these candidate genes may offer potential targets for novel therapies. In this review, we will provide an overview of the pathological, genetic and cytogenetic characteristics of WT.

Wilms tumor incidence in children with 2q terminal deletions: a cohort study

Three individuals with chromosome 2q terminal deletions have been reported in the medical literature to have developed Wilms tumor. By looking at a UK national cohort, we aimed to ascertain the chance of an individual with a 2q terminal deletion developing a Wilms tumor. The objective was to clarify screening recommendations. All individuals over a 40-year period with chromosome 2q terminal deletions were ascertained from the Chromosome Abnormality Database. The names and dates of birth of these individuals were obtained from the Regional Cytogenetic Departments where the original chromosome analyses were performed. These data were collated and compared with the National Registry of Childhood Tumors. One hundred twenty-nine subjects were identified over a 40-year study period. Only a single individual in our national cohort was affected by Wilms tumor. This individual had an add(2)(q35) karyotype. We conclude that the incidence of Wilms tumor in the majority of individuals with a 2q terminal deletion is low, and is below the recommended threshold for surveillance for tumor development.

Cytogenetic findings in Wilms' tumour: a single institute study

AIMS

Cytogenetic abnormalities of Wilms' tumour (WT) treated in a single institution in Western Australia were reviewed. Correlation with histologic subtypes, stage, presence of nephrogenic rests and age of the patient at diagnosis were also evaluated.

METHODS

53 WT specimens were encountered between 1995 and 2009. Tissue culture was obtained in 49 (92%) specimens. Reports documenting histopathological features of the tumour, stage and outcome were also retrieved.

RESULTS

A total of 53 tumour specimens from 42 patients/cases were examined and staged in accordance with the National Wilms' Tumor Study (NWTS). Thirty-eight cases were unilateral (34 unifocal, 4 multifocal) and four were bilateral (2 multifocal). Fifty tumours showed favourable histology WT. One tumour was a cystic partially differentiated nephroblastoma (CPDN). Two tumours showed diffuse anaplasia. Eighteen specimens had nephrogenic rests, seven with perilobar rests, 10 with intralobar rests and one with both types of nephrogenic rests. Twelve WTs were assigned as stage 1, 22 as stage 2, 16 as stage 3, and two each for stages 4 and 5. For chromosomal analysis, 92% of the specimens yielded results, of which 70% showed abnormal karyotype and 22% displayed normal karyotypic findings. Hyperdiploidy was more common than hypodiploidy. The most common chromosomal gain involved chromosome 12. Low stage tumours tended to have abnormal karyotypes with hyperdiploidy and hypodiploidy being more common. There was no statistical correlation between abnormal karyotype and stage or abnormal karyotype and age group or abnormal karyotype and non-blastemal WT. Eleven (58%) tumours harbouring nephrogenic rests displayed an abnormal karyotype. 16q loss or der(16)t(1;16) were more common in younger patients but no association was made between this chromosomal abnormality and stage. Monosomy 22 and gain of 1q were more common in older patients. Furthermore, monosomy 22 tended to occur in tumours of earlier stage. No correlation between 11p deletions and age or stage was seen.

CONCLUSIONS

WTs are karyotypically heterogeneous tumours. Conventional cytogenetic analysis of WTs still remains a useful technique to assist in the understanding of these tumours.

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.

Deletions of 16q in Wilms tumors localize to blastemal-anaplastic cells and are associated with reduced expression of the IRXB renal tubulogenesis gene cluster

Wilms tumor is the most common pediatric renal neoplasm, but few molecular prognostic markers have been identified for this tumor. Somatic deletion in the long arm of chromosome 16 (16q) is known to predict a less favorable outcome in Wilms tumor, but the underlying molecular mechanisms are not known. We show that 16q deletions are typically confined to immature anaplastic-blastic tumor elements, while deletions are absent in maturing tumor components. The smallest region of deletion overlap mapped to a 1.8-Mb segment containing the IRXB gene cluster including IRX3, IRX5, and IRX6, of which IRX3 is a recently identified regulator of tubular maturation during nephrogenesis. Tumors with 16q deletion showed a lower overall mRNA expression of IRXB genes, and 16q-deleted tumor cells failed to express IRX3 while it was expressed in differentiating tubular tumor elements with intact 16q. Consistent with a role for IRX3 in tubular differentiation, gene sets linked to Notch signaling, Rho signaling, and ion channel activity were enriched in tumors with high IRX3 expression, while WTs with low expression were enriched for gene sets linked to cell cycle progression. Low mRNA levels of IRXB genes were associated with diffuse anaplasia, high-stage disease, and death. A disturbed balance between tubular differentiation and self-renewal of anaplastic-blastic elements may thus be one mechanism linking 16q deletion to adverse outcome in Wilms tumor.

Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562

PURPOSE

Wilms' tumor is a childhood cancer of the kidney with an incidence of approximately 1 in 10,000. Cooccurrence of Wilms' tumor with 2q37 deletion syndrome, an uncommon constitutional chromosome abnormality, has been reported previously in three children. Given these are independently rare clinical entities, we hypothesized that 2q37 harbors a tumor suppressor gene important in Wilms' tumor pathogenesis.

EXPERIMENTAL DESIGN

To test this, we performed loss of heterozygosity analysis in a panel of 226 sporadic Wilms' tumor samples and mutation analysis of candidate genes.

RESULTS

Loss of heterozygosity was present in at least 4% of cases. Two tumors harbored homozygous deletions at 2q37.1, supporting the presence of a tumor suppressor gene that follows a classic two-hit model. However, no other evidence of second mutations was found, suggesting that heterozygous deletion alone may be sufficient to promote tumorigenesis in concert with other genomic abnormalities. We show that miR-562, a microRNA within the candidate region, is expressed only in kidney and colon and regulates EYA1, a critical gene for renal development. miR-562 expression is reduced in Wilms' tumor and may contribute to tumorigenesis by deregulating EYA1. Two other candidate regions were localized at 2q37.3 and 2qter, but available data from patients with constitutional deletions suggest that these probably do not confer a high risk for Wilms' tumor.

CONCLUSIONS

Our data support the presence of a tumor suppressor gene at 2q37.1 and suggest that, in individuals with constitutional 2q37 deletions, any increased risk for developing Wilms' tumor likely correlates with deletions encompassing 2q37.1.