A novel EWS-ERG rearrangement generating two hybrid mRNAs in a peripheral primitive neuroectodermal tumour (pPNET) with a t(15;22) translocation

Functional characterization of FgERG3 and FgERG5 associated with ergosterol biosynthesis, vegetative differentiation and virulence of Fusarium graminearum

The ergosterol biosynthesis pathway is well characterized in Saccharomyces cerevisiae, while little is known about the pathway in filamentous fungi. In this study, we isolated and genetically documented biological functions of FgErg3 and FgErg5, which are located upstream of FgErg4, the enzyme catalyzing the final step of ergosterol synthesis in Fusarium graminearum. Our results demonstrated that F. graminearum contains two paralogous FgERG3 and two FgERG5 genes. FgErg3, but not FgErg5, is involved in ergosterol biosynthesis. Double deletion mutants of FgERG3 alleles or the double deletion mutants of FgERG5 alleles showed decreased conidiation and produced abnormal conidia. Fungicide susceptibility tests revealed that FgERG3 and FgERG5 mutants have increased resistance towards triadimefon. However, FgERG3 mutants exhibited increased susceptibility to tebuconazole as well as increased susceptibility to oxidative stress, paraquat and to Mg(2+). Pathogenicity tests showed that the FgERG3 and FgERG5 double deletion mutant displayed dramatically attenuated virulence although they were able to successfully colonize flowering wheat head. In addition, complementation of FgERG3 and FgERG5 genes into S. cerevisiae partially rescued the susceptibility of S. cerevisiae ERG3 and ERG5 deletion mutants towards hydroxyurea and caffeine. Taken together, our results indicate that FgERG3 and FgERG5 play a crucial role in vegetative differentiation, resistance to fungicides and virulence in F. graminearum. FgErg3 alleles, but not FgErg5 alleles, are required for ergosterol biosynthesis in the filamentous fungus F. graminearum.

Multiple splice variants of EWSR1-ETS fusion transcripts co-existing in the Ewing sarcoma family of tumors

PURPOSE

The Ewing sarcoma family of tumors (EFT) is characterized by fusions of the EWSR1 gene on chromosome 22q12 with either one of the genes encoding members of the ETS family of transcription factors, in the majority of cases FLI1 or ERG. Many alternative EWSR1-ETS gene fusions have been encountered, due to variations in the locations of the EWSR1 and ETS genomic breakpoints. The resulting heterogeneity in EWSR1-ETS fusion transcripts may further be increased by the occurrence of multiple splice variants within the same tumor. Here we present a retrospective study designed to detect all of the EWSR1-FLI1 and EWSR1-ERG fusion transcripts in a series of 23 fresh frozen EFT tissues.

METHODS

RT-PCR and nested fluorescent multiplex PCR were used to amplify EWSR1-FLI1 and EWSR1-ERG transcripts from EFT tissues. Fusion transcripts were identified by laser-induced fluorescent capillary electrophoresis and confirmed by sequence analysis.

RESULTS

Nine different EWSR1-FLI1 fusion transcripts and one EWSR1-ERG fusion transcript were identified in 21 out of 23 fresh frozen EFT tissue samples. In five cases multiple fusion transcripts were found to coexist in the same tumor sample. We additionally reviewed previous reports on twelve cases with multiple EWSR1-ETS fusion transcripts.

CONCLUSIONS

Alternative splicing may frequently affect the process of EFT-associated fusion gene transcription and, as such, may significantly contribute to the pathogenic role of EFT-associated chromosome translocations. In a considerable number of cases this may result in multiple splice variants within the same tumor.

Molecular detection and targeting of EWSR1 fusion transcripts in soft tissue tumors

Soft tissue tumors are a heterogeneous group of tumors, traditionally classified according to morphology and histogenesis. Molecular classification divides sarcomas into two main categories: (a) sarcomas with specific genetic alterations and (b) sarcomas showing multiple complex karyotypic abnormalities without any specific pattern. Most chromosomal alterations are represented by translocations which are increasingly detected. The identification of fusion transcripts, in fact, not only support the diagnosis but also provides the basis for the development of new therapeutic strategies aimed at blocking aberrant activity of the chimeric proteins. One of the genes most susceptible to breakage/translocation in soft tissue tumors is represented by Ewing sarcoma breakpoint region 1 (EWSR1). This gene has a large number of fusion partners, mainly associated with the pathogenesis of Ewing's sarcoma but with other soft tissue tumors too. In this review, we illustrate the characteristics of this gene/protein, both in normal cellular physiology and in carcinogenesis. We describe the different fusion partners of EWSR1, the molecular pathways in which is involved and the main molecular biology techniques for the identification of fusion transcripts and for their inhibition.

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.

Molecular cytogenetic characterization of four previously established and two newly established Ewing sarcoma cell lines

Most Ewing family tumors are identified by the characteristic translocation t(11;22)(q24;q12), resulting in a fusion protein EWS/FLI1 that acts as an aberrant transcription factor. In a minority of cases, the EWS gene is fused to another member of the ETS gene (ERG, ETV1, E1AF, and FEV). Though the oncogenic transforming capability of the EWS/FLI1 protein is highly suggestive, the exact pathway behind remains to be elucidated. The availability of cell lines may help in the understanding of underlying cellular processes. In this study, we have established two new Ewing sarcoma cell lines and characterized them with molecular cytogenetic tools. This technology was also applied on four other previously published Ewing sarcoma cell lines. Our findings in relation to previous data on similar tumors are discussed.

Practical application of molecular genetic testing as an aid to the surgical pathologic diagnosis of sarcomas: a prospective study

The strong correlation of specific reciprocal translocations with individual tumor types and the demonstration that polymerase chain reaction (PCR)-based methods can detect translocations in tissue samples have stimulated interest in the role of molecular genetic testing in diagnostic surgical pathology. To evaluate the clinical utility of PCR-based molecular analysis of soft tissue neoplasms in routine surgical pathology, 131 consecutive soft tissue tumors submitted for molecular genetic testing at a tertiary care teaching hospital were prospectively analyzed over a 36-month period. RT-PCR was used to test tumor RNA for fusion transcripts characteristic of malignant round cell tumors (including Ewing sarcoma/primitive neuroectodermal tumor, desmoplastic small round cell tumor, and alveolar rhabdomyosarcoma), spindle cell tumors (including synovial sarcoma and congenital fibrosarcoma), and fatty tumors (myxoid liposarcoma). DNA sequence analysis was used to confirm the identity of all PCR products, and the PCR results were compared with the histopathologic diagnosis. We found that sufficient RNA for RT-PCR-based testing was recovered from 96% of the 131 cases and the percentage of tumors that tested positive for the associated characteristic fusion transcript was in general agreement with those reported in the literature. DNA sequence analysis of PCR products identified both variant transcripts and spurious PCR products, underscoring the value of product confirmation steps when testing formalin-fixed, paraffin-embedded tissue. Only in rare cases did testing yield a genetic result that was discordant with the histopathologic diagnosis. We conclude that PCR-based testing is a useful adjunct for the diagnosis of malignant small round cell tumors, spindle cell tumors, and other miscellaneous neoplasms in routine surgical pathology practice.

Fine-mapping of cytogenetically undetectable EWS/ERG fusions on DNA fibers of Ewing tumors

In contrast to the EWS/FLI1 fusion which is represented by a t(11;22)(q24;q12), EWS/ERG fusions are frequently cytogenetically not detectable. Three Ewing tumors (ET), two with apparently normal chromosomes 21 and 22, and one ET with a t(2;22)(p25;q12), were studied by FISH on interphase nuclei, metaphase chromosomes and on DNA fibers. EWS/ERG transcripts were detected by RT-PCR in all cases. FISH, using cosmids located proximally (F10, G9) and distally (F7) to the EWS breakpoint region, revealed no detectable separation of these probes in two cases. In contrast, co-hybridization of probe PT1526 containing the ERG breakpoint region with G9 revealed the juxtaposition of two signals per interphase nucleus in all three cases indicating the EWS/ERG fusions. Chromosome preparations displayed the juxtaposed signals on the der(22), and hybridization signals of the probes PT1526 and G9 on the non-rearranged chromosomes 21 and 22 in all cases, respectively. The PT1526 signal on the der(21) was seen only in cases 1 and 2. These results were confirmed by triple-target FISH on tumor DNA fibers. In all three cases, the hybridization pattern F10 - G9 - PT1526 indicates a centromere to telomere orientation. This finding suggests that EWS/ERG fusions in ETs may be generated by an inversion of the ERG gene or a part thereof followed by an insertion into the EWS gene on the der(22). Double-target FISH on interphase nuclei using probes flanking the EWS breakpoint region and probe PT1526 enables the detection of virtually all 22q12 rearrangements in ETs, thus providing a reliable diagnostic assay.

Current aspects of the pathology of soft tissue sarcomas

In soft tissue sarcomas, advances in pathological techniques, including immunohistochemistry, cytogenetics, and molecular genetics, have improved diagnostic accuracy, confirmed or clarified interrelationships between tumor subtypes, and revealed mechanisms of tumorigenesis. Many sarcomas are associated with abnormalities of tumor-suppressor genes, and several types have been found to have specific chromosomal translocations. These data and correlative clinicopathologic studies, although confirming many traditional pathological views, enable refinement or reassessment of terminology and classification of some small round cell, spindle cell, pleomorphic, and lipogenic tumors. New factors are emerging for prediction of tumor behavior, which might ultimately relate to therapy once a wider range of treatment options becomes available. This article reviews these current aspects of sarcoma pathology.