Eva Stejskalova

Cytogenetic and array comparative genomic hybridization analysis of a series of hepatoblastomas.

Hepatoblastoma is the most common primary hepatic tumor in children, and only a limited number of detailed karyotypic analyses have been reported to date. In the present study, cytogenetic abnormalities were identified in nine cases of hepatoblastoma from a single institution. Among characteristic chromosomal changes detected were simple numerical aberrations, structural alterations of chromosomes 1, 2, and 8, and the recurrent unbalanced rearrangements der(4)t(1;4)(q25.2;q35.1) and der(6)t(1;6)(q21;q26). Array comparative genomic hybridization was applied in four of the cases. The combined cytogenetic, molecular cytogenetic, and histopathologic analyses are presented here, together with clinical data. The results substantially confirm previous findings of aberrations involving chromosomal loci on 1q, 2 or 2q, 4q, 6q, 8 or 8q, and 20 as significant in the development and clinical course of this disease.

Malignant peripheral primitive neuroectodermal tumor of the kidney.

Ewing family of tumors is a group of highly aggressive neoplasias that occur most commonly in the first two decades of life. These tumors are most frequently localized in bones, less frequently in soft tissues. They usually appear as undifferentiated small round-cell tumors. With current treatment regiments, 5-year disease-free survival rates exceed 60% in patients with a localized disease. Patients with metastatic disease at the time of their first presentation have a poor prognosis. We describe a rare case of visceral primitive neuroectodermal tumor with the involvement of the kidney in a 9-year-old girl. The tumor was studied with immunohistochemistry, cytogenetics, and molecular biology methods. Strong expression of protein MIC(2) by immunochemistry (antibody HBA 71) with subsequent demonstration of a translocation consistent with t(11;22)(q24;q12) using cytogenetic and reverse transcriptase polymerase chain reaction (RT-PCR) confirmed the histopathological diagnosis of peripheral primitive neuroectodermal tumor. We detected minimal residual disease in bone marrow using RT-PCR.

The splicing factor U1-70K interacts with the SMN complex and is required for nuclear gem integrity.

ABSTRACT The nuclear SMN complex localizes to specific structures called nuclear gems. The loss of gems is a cellular marker for several neurodegenerative diseases. Here, we identify that the U1-snRNP-specific protein U1-70K localizes to nuclear gems, and we show that U1-70K is necessary for gem integrity. Furthermore, we show that the interaction between U1-70K and the SMN complex is RNA independent, and we map the SMN complex binding site to the unstructured N-terminal tail of U1-70K. Consistent with these results, the expression of the U1-70K N-terminal tail rescues gem formation. These findings show that U1-70K is an SMN-complex-associating protein, and they suggest a new function for U1-70K in the formation of nuclear gems.

A Novel Variant of Syt-ssx1 Fusion Gene in a Case of Spindle Cell Synovial Sarcoma

Synovial sarcoma (SS) is a rare soft-tissue tumor that affects children and young adults. It is characterized by chromosomal translocation t(X;18)(p11.2;q11.2), which results in the fusion of the gene SYT on chromosome 18 with SSX genes on chromosome X. Heterogeneity within SS fusion junctions is rare. We report a case of a 9-year-old boy with a high-grade spindle cell sarcoma. Reverse transcriptase-polymerase chain reaction revealed a characteristic translocation of SSs. However, this sarcoma showed a longer-than-expected PCR product after gel electrophoresis. Direct sequencing of the product disclosed a novel SYT/SSX1 fusion transcript. Detection of fusion transcripts is useful for diagnostics of SS. In each case, when considering this diagnosis on the morphologic grounds an attempt to analyze the translocation using PCR should be made, including the recognition of its uncommon variants.

Teratoma in an Adolescent With Malignant Transformation into Embryonal Rhabdomyosarcoma: Case Report

Background The somatic type tumors are occasionally found in nonseminomatous germ cell tumors in men. These malignancies are presumed to arise from malignant transformation (MT) of teratoma or by differentiation of totipotential germ cell. Observation A case of MT of germ cell tumor in 17-year-old male into embryonal rhabdomyosarcoma is described. The histopathologic diagnosis was that of embryonal rhabdomyosarcoma in which no germ cell elements were found. The germ cell origin of transformed histology is supported by cytogenetic analysis (isochromosome 12p), and elevated α1-fetoprotein. Despite intensive therapy the patient died. Conclusions MT of teratoma is rare entity with poor prognosis.

A t(4;19) pediatric undifferentiated sarcoma with a novel variant of the CIC-DUX4 fusion transcript

We report cytogenetic and molecular genetic analysis of a pediatric tumor positive for the CIC-DUX4 fusion. The tumor belongs to a rare, diagnostically challenging subgroup of undifferentiated small round cell sarcomas. A balanced t(4;19)(q35;q13.1-2) was identified by G-banding, as a sole cytogenetic finding. The translocation was also identified by the M-FISH technique. After RT-PCR, the tumor sample was positive for the CIC-DUX4 fusion. The PCR product contains a novel, so far unreported variant of the CIC-DUX4 fusion transcript, with a fusion of the exon 20 from the CIC gene and the exon 1 from the DUX4 gene.

PUF60-activated exons uncover altered 3 ' splice-site selection by germline missense mutations in a single RRM

Abstract PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.