An EWS/ERG fusion with a truncated N-terminal domain of EWS in a Ewing's tumor

Establishment of multiplex RT-PCR to detect fusion genes for the diagnosis of Ewing sarcoma

Background

Detection of the tumor-specific EWSR1/FUS-ETS fusion gene is essential to diagnose Ewing sarcoma. Reverse transcription–polymerase chain reaction (RT–PCR) and fluorescence in situ hybridization are commonly used to detect the fusion gene, and assays using next-generation sequencing have recently been reported. However, at least 28 fusion transcript variants have been reported, making rapid and accurate detection difficult.

Methods

We constructed two sets of multiplex PCR assays and evaluated their utility using cell lines and clinical samples.

Results

EWSR1/FUS-ETS was detected in five of six tumors by the first set, and in all six tumors by the second set. The fusion gene detected only by the latter was EWSR1-ERG, which completely lacked exon 7 of EWSR1. The fusion had a short N-terminal region of EWSR1 and showed pathologically atypical features.

Conclusions

We developed multiplex RT–PCR assays to detect EWSR1-ETS and FUS-ETS simultaneously. These assays will aid the rapid and accurate diagnosis of Ewing sarcoma. In addition, variants of EWSR1/FUS-ETS with a short N-terminal region that may have been previously missed can be easily detected.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13000-021-01164-6.

Regulation of endothelial homeostasis, vascular development and angiogenesis by the transcription factor ERG

Over the last few years, the ETS transcription factor ERG has emerged as a major regulator of endothelial function. Multiple studies have shown that ERG plays a crucial role in promoting angiogenesis and vascular stability during development and after birth. In the mature vasculature ERG also functions to maintain endothelial homeostasis, by transactivating genes involved in key endothelial functions, while repressing expression of pro-inflammatory genes. Its homeostatic role is lineage-specific, since ectopic expression of ERG in non-endothelial tissues such as prostate is detrimental and contributes to oncogenesis. This review summarises the main roles and pathways controlled by ERG in the vascular endothelium, its transcriptional targets and its functional partners and the emerging evidence on the pathways regulating ERG's activity and expression.

Directly targeting transcriptional dysregulation in cancer

Drugs that target intracellular signalling pathways have markedly improved progression-free survival of patients with cancers who were previously regarded as untreatable. However, the rapid emergence of therapeutic resistance, as a result of bypass signalling or downstream mutation within kinase-mediated signalling cascades, has curtailed the benefit gained from these therapies. Such resistance mechanisms are facilitated by the linearity and redundancy of kinase signalling pathways. We argue that, in each cancer, the dysregulation of key transcriptional regulators not only defines the cancer phenotype but is essential for its development and maintenance. Furthermore, we propose that, as therapeutic targets, these transcriptional regulators are less prone to bypass by alternative mutational events or clonal heterogeneity, and therefore we must rekindle our efforts to directly target transcriptional regulation across a broad range of cancers.

Ewing's sarcoma of bone

Ewing's sarcoma of bone is a primary bone sarcoma found predominantly in patients during their second decade of life. It is a high-grade aggressive small round blue cell tumor that is part of the Ewing's family of tumors. Its exact eitiology is unknown but it commonly demonstrates reproducible staining of CD99 and translocations of the EWS gene. Historically, this diagnosis was associated with near certain metastasis and subsequent mortality. However, current management consists of extensive chemotherapy in addition to local control with surgical resection and/or radiation. As a result, survival has improved to the 55-75% range in those patients who present without known metastases. Current research aims to continue this improvement by looking further into the associated gene abnormalities and possibly targeted therapies.

Progress in the molecular biology of ewing tumors

Purpose/results/discussion. Rearrangement of the EWS gene with an ETS oncogene by chromosomal translocation is a hallmark of the Ewing family of tumors (EFT). Detectability, incidence, tumor specificity and variability of this aberration have been matters of intense investigation in recent years. A number of related alterations have also been found in other malignancies. The common consequence of these gene rearrangements is the generation of an aberrant transcription factor. In EFT, the ETS partner is responsible for target recognition. However, synergistic and possibly tissue-restricted transcription factors interacting with either the EWS or the ETS portion may influence target selection. Minimal domains of both fusion partners were defined that have proved necessary for the in vitro transformation of murine fibroblasts. These functional studies suggest a role for aberrant transcriptional regulation of transforming target genes by the chimeric transcription factors. Also, fusion of the two unrelated protein domains may affect overall protein conformation and consequently DNA binding specificity. Recent evidence suggests that EWS, when fused to a transcription factor, interacts with different partners than germ-line EWS. Variability in EWS–ETS gene fusions has recently been demonstrated to correlate with clinical outcome. This finding may reflect functional differences of the individual chimeric transcription factors. Alternatively, type and availability of specific recombinases at different time-points of stem cell development or in different stem cell lineages may determine fusion type. Studies on EFT cell lines using EWS–ETS antagonists do suggest a rate-limiting essential role for the gene rearrangement in the self-renewal capacity of EFT cells. The presence of additional aberrations varying in number and type that may account for immortalization and full transformation is postulated. Knowledge about such secondary alterations may provide valuable prognostic markers that could be used for treatment stratification.

Cancer sequencing gets a little more personal

In this Perspective, we discuss a paper in this issue of Science Translational Medicine, in which Leary and colleagues present a new method based on massive, parallel, and near-complete sequencing of individual tumor genomes. Their findings support the notion that cancer genomes house a spectrum of genetic alterations, many of which are unique to the individual tumor. More validation and a reduction in cost are required for this approach to become common in clinics.

Complex rearrangement of chromosomes 19, 21, and 22 in Ewing sarcoma involving a novel reciprocal inversion-insertion mechanism of EWS-ERG fusion gene formation: a case analysis and literature review

EWS-ERG Ewing sarcoma (ES) gene fusions often result from complex chromosomal rearrangements. We report an unusually aggressive case of ES with an EWS-ERG fusion gene that appeared to be a result of a simple balanced and reciprocal translocation, t(19;22)(q13.2;q12.2). Subsequent molecular investigation of the primary tumor, the metastasis, and a cell line generated from this ES permitted reconstruction of each genomic step in the evolution of this complex EWS-ERG fusion. We elucidated a new mechanism of reciprocal insertion inversion between chromosome 21 and 22, involving cryptic alterations to both the ERG and EWS genes. Molecular cytogenetic investigation, using systematic analysis with locus-specific probes, identified the cognate genomic breakpoints within chromosome 21 and 22, mandatory for the excision and exchange of both 3'ERG and 3'EWS, resulting in the formation of the EWS-ERG fusion gene present on the der(22). Array comparative genomic hybridization and fluorescence in situ hybridization studies of the ES cell line derived from this tumor identified additional acquired chromosomal and genomic abnormalities, likely associated with establishment and adaptation to in vitro growth. Notably, the cell line had lost one copy of the RB1 gene within the 13q13.1 approximately q14.2 region, and also had a near-tetraploid karyotype. The significance of these findings and their relationship to other reports of variant and complex ES translocations involving the ERG gene are reviewed.

Ploidy and karyotype complexity are powerful prognostic indicators in the Ewing's sarcoma family of tumors: a study by the United Kingdom Cancer Cytogenetics and the Children's Cancer and Leukaemia Group

Ewing's sarcoma family tumors (ESFT) are characterized by the presence of EWSR1-ETS fusion genes. Secondary chromosome changes are frequently described, although their clinical significance is not clear. In this study, we have collected and reviewed abnormal karyotypes from 88 patients with primary ESFT and a rearrangement of 22q12. Secondary changes were identified in 80% (70/88) of tumors at diagnosis. Multivariate analysis showed a worse overall and relapse free survival (RFS) for those with a complex karyotype (overall survival, P = 0.005; RFS, P = 0.04), independent of metastatic disease. Univariate survival analysis showed that a chromosome number above 50 or a complex karyotype was associated with a worse overall survival (>50 chromosomes, P = 0.05; complex karyotype, P = 0.04). There was no association between type of cytogenetic abnormality and the presence of metastatic disease at diagnosis. Univariate and multivariate survival analysis of a small subgroup with trisomy 20 indicated that trisomy 20 was associated with a worse overall and RFS. There was no difference in outcome associated with other recurrent trisomies (2, 5, 7, 8, or 12) or the common recurrent secondary structural rearrangements (deletions of 1p36, 9p12, 17p13, and 16q, and gain of 1q), although numbers were small. These data demonstrate the continued value of cytogenetics as a genome-wide screen in ESFT and illustrates the potential importance of secondary chromosome changes for stratification of patients for risk. Specifically, karyotype complexity appears to be a powerful predictor of prognosis, and the presence of trisomy 20 may be a marker of a more aggressive subset of this group.

Differentiating Ewing's sarcoma from other round blue cell tumors using a RT-PCR translocation panel on formalin-fixed paraffin-embedded tissues

Ewing's sarcoma is a common malignancy of bone and soft tissue that occurs most often in children and young adults. Differentiating Ewing's sarcoma from other round blue cell tumors can be a diagnostic challenge because of their similarity in histology and clinical presentation. Thus, ancillary molecular tests for detecting disease-defining translocations are important for confirming the diagnosis. We analyzed 65 round blue cell tumors, including 53 Ewing's sarcoma samples from 50 unique cases. Samples were processed for RNA from archived formalin-fixed paraffin-embedded tissue blocks. Real-time RT-PCR assays specific for Ewing's sarcoma (EWS-FLI1, EWS-ERG, EWS-ETV1, EWS-ETV4, and EWS-FEV), synovial sarcoma (SYT-SSX1 and SYT-SSX2), and rhabdomyosarcoma (PAX3-FKHR and PAX7-FKHR) were tested across the samples. The translocation panel had a sensitivity of 81% (43 out of 53 samples) for diagnosing Ewing's sarcoma when using the histological criteria as the 'gold' standard. None of the Ewing's specific translocations were found in the non-Ewing's samples (100% specificity). Of the 43 samples with translocations detected, 26 (60%) had an EWS-FLI1 type 1 translocation, 13 (30%) had an EWS-FLI1 type 2 translocation, 3 (7%) had an EWS-ERG translocation, 1 had an EWS-ETV1 translocation, and 1 sample had both an EWS-FLI1 type 1 and type 2 translocation. Our real-time RT-PCR assay for detecting sarcoma translocations has high sensitivity and specificity for Ewing's sarcoma and has clinical utility in differentiating small round blue cell tumors in the clinical lab.

EWS–ETS oncoproteins: The linchpins of Ewing tumors

Ewing tumors, which comprise Ewing's sarcoma and peripheral primitive neuroectodermal tumors, are highly aggressive and mostly affect children and adolescents. Their molecular signature is a chromosomal translocation leading to the generation of EWS-ETS (or very rarely FUS-ETS) fusion proteins that are capable of transforming cells. These oncoproteins act as aberrant transcription factors due to the fusion of an ETS DNA binding domain to a highly potent EWS (or FUS) transactivation domain. Accordingly, many EWS-ETS target genes have been identified whose dysregulation could contribute to the development of tumor formation. Furthermore, EWS-ETS oncoproteins may impact on RNA splicing or affect other proteins through disturbing their ability to form functional complexes. The molecular knowledge gained so far from studying EWS-ETS oncoproteins has not only broadened our understanding of Ewing tumors but also improved the diagnosis of these highly undifferentiated tumors. In addition, several potential prognostic markers have been uncovered and novel therapies are suggested that may improve the still dismal survival rate of Ewing tumor patients.

Saccharomyces cerevisiae as a model system to define the chromosomal instability phenotype

Translocations, deletions, and chromosome fusions are frequent events seen in cancers with genome instability. Here we analyzed 358 genome rearrangements generated in Saccharomyces cerevisiae selected by the loss of the nonessential terminal segment of chromosome V. The rearrangements appeared to be generated by both nonhomologous end joining and homologous recombination and targeted all chromosomes. Fifteen percent of the rearrangements occurred independently more than once. High levels of specific classes of rearrangements were isolated from strains with specific mutations: translocations to Ty elements were increased in telomerase-defective mutants, potential dicentric translocations and dicentric isochromosomes were associated with cell cycle checkpoint defects, chromosome fusions were frequent in strains with both telomerase and cell cycle checkpoint defects, and translocations to homolog genes were seen in strains with defects allowing homoeologous recombination. An analysis of human cancer-associated rearrangements revealed parallels to the effects that strain genotypes have on classes of rearrangement in S. cerevisiae.

Profiling and functional annotation of mRNA gene expression in pediatric rhabdomyosarcoma and Ewing's sarcoma

Using Affymetrix oligonucleotide microarrays, we analyzed mRNA gene expression patterns of 12 primary pediatric rhabdomyosarcomas (RMS) and 11 Ewing's sarcomas (EWS), which belong to the small round blue cell tumors (SRBCTs). Diagnostic classification of these cancers is frequently complicated by the highly similar appearance in routine histology, and additional molecular markers could significantly improve tumor classification. A combination of three independent statistical approaches (t-test, SAM, k-nearest neighborhood analysis) resulted in 101 highly significant probe sets that clearly discriminate between EWS and RMS. We identified novel marker transcripts that have not been previously associated with either RMS or EWS yet, including CITED2, glypican 3 (GPC3), and cyclin D1 (CCND1). Expression levels for selected candidate genes were validated by quantitative real-time reverse-transcription PCR. Furthermore, to identify biologically meaningful trends, functional annotations were assigned to 946 genes differentially expressed between EWS and RMS (t-test). Genes involved in protein biosynthesis (n = 28) and complex assembly (n = 9), lipid metabolism (n = 23), energy generation (n = 22), and mRNA processing (n = 11) were expressed significantly higher in EWS. Thus, functional annotation of tumor-specific genes reveals detailed insights into tumor biology and differentiation-specific expression patterns and gives important clues related to the possible cellular origin of these pediatric tumors. Supplementary material for this article is available at the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat/index.html.

A multiplex real-time pcr assay for the detection of gene fusions observed in solid tumors

SUMMARY

Specific gene fusions observed in solid tumors are extremely useful diagnostic markers. We report the development of a method based on real-time PCR which enables the detection upon identical PCR conditions of the different fusions specifically observed in Ewing tumors (ET), alveolar rhabdomyosarcoma (ARMS), synovial sarcoma (SS), small round cell desmoplastic tumors (SRCDT), extraskeletal myxoid chondrosarcoma, malignant melanoma of soft parts, congenital fibrosarcoma, and anaplastic large cell lymphoma. A simple assay, based on multiplexing of primers and probes, is described for the routine genetic diagnosis of small round cell tumors of children. It enables the detection of the five EWS-ETS, the two PAX-FKHR, the three SYT-SSX, and the EWS-WT1 fusions of ET, ARMS, SS, and SRCDT, respectively. The sensitivity of this test is high enough to detect all fusions, including the large EWS-FLI-1 transcripts, with the equivalent of 100 tumor cells as a starting material. This multiplex fluorescent analysis of chromosome translocations (MFACT) was validated in comparison with conventional RT-PCR on a series of 79 tumors. A major advantage of this method is that it completely abolishes the manipulation of PCR-products. It, therefore, considerably lowers the risk of cross-contamination linked to carry-over of RT-PCR products. It also constitutes an important step toward the complete automation of the detection of cancer-specific gene fusions.

Biphenotypic sarcoma with characteristics of both a Ewing sarcoma and a desmoplastic small round cell tumor

BACKGROUND

The EWS gene, a transcription factor of unknown function, is involved in chromosomal translocations associated with a wide variety of tumors, particularly small round blue cell tumors such as Ewing sarcoma. It has previously been reported that desmoplastic small round blue cell tumor (DSRBCT) frequently has an associated t(11;22) abnormality resulting from fusion of the EWS and WT-1 genes.

PROCEDURE

We report a case of a small round blue cell tumor with characteristics of both Ewing sarcoma and DSRBCT with a t(11;22) translocation leading to fusion of the EWS and FLI1genes.

RESULTS

The translocation point and fusion products were confirmed by polymerase chain reaction amplification and restriction fragment mapping of the products.

CONCLUSIONS

The biphenotypic nature of this case and the apparent promiscuity of the EWS gene in tumor-associated translocations coupled with other reports of biphenotypic childhood sarcomas has potential implications for the relationship between small round blue cell tumors and the mechanism of EWS/FLI1 oncogenesis.

The Ewing family of tumors and the search for the Achilles' heel

The ideal cancer therapy would accomodate the specific biology of a tumor and be based upon understanding the mechanisms of malignancy. This vision has been the driving force in cancer research. However, the story of success in clinical cancer management is a story of empirie largely independent from progress in basic research. For the Ewing family of tumors (EFT) comprising Ewing's sarcoma and peripheral primitive neuroectodermal tumor, significant insights into the molecular basis have appeared recently. Some of last year's discoveries may have taken us closer to the identification of the Achilles' heel in this disease. The first clue has been obtained to the mechanism of chromosomal translocation, which constitutes a rate-limiting step in EFT pathogenesis. Also, researchers have progressed in understanding the control of EFT cell proliferation, differentiation, and death. A major role in these processes has been attributed to the EWS-ets gene rearrangement. Specific growth factor circuits appear to be involved in deregulated tumor cell growth. By analogy to heterologous cellular systems, it is possible to postulate an important functional role for CD99(MIC2) as it contributes to the malignant phenotype of EFT. In vitro, as well as the first in vivo, experimental evidence suggests that tumor cell expansion and spread can be counteracted by breaking these physiological pathways. Still, we are far from a tailored biological therapy of EFT. Before this goal may be achieved, we must seek further improvements and diversification of today's standard and intensified treatment regimens.

Molecular genetics in the diagnosis and prognosis of solid pediatric tumors

The field of molecular genetics continues to see an ever increasing number of applications to pediatric tumor analysis. Studies in pediatric tumors have identified novel genes and other genetic changes, a large number of which reflect one of the following mechanisms: (1) activation of proto-oncogenes; (2) loss of tumor suppressor genes; or (3) creation of novel fusion proteins. At least one of these mechanisms is operational in each of the following pediatric tumors: neuroblastoma, Ewing sarcoma and peripheral primitive neuroectodermal tumor (pPNET), intra-abdominal desmoplastic small-cell tumor, rhabdomyosarcoma, synovial sarcoma, and Wilms tumor. Out of this research has come not only an increased understanding of oncogenesis but also, for each of the tumors listed above, diagnostic and/or prognostic markers that can be used by the pathologist and oncologist to improve overall patient management.