Expressed fusion transcripts in rare bone tumours
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-ERAD-276 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:mRNA-Seq on total RNA from primary osteoblastomas and phosphaturic mesenchymal tumours, focussing on fusion transcript expression
| EGAS00001000763 | EGA
Project description:mRNA-Seq on total RNA from primary osteoblastomas and phosphaturic mesenchymal tumours, focussing on fusion transcript expression
| EGAD00001000990 | EGA
Project description:Identification of novel fusion transcripts in neuroblastoma
| PRJNA605944 | ENA
Project description:BACKGROUND: Epstein-Barr Virus (EBV) associated lymphoproliferative disorders are encountered in immunodeficiency states. Amongst these, primary CNS lymphoma in HIV/AIDS patients is relatively rare and represents a therapeutic challenge. MATERIALS AND METHODS: This report was generated from patient's medical records throughout hospitalizations and outpatient visits. RESULTS: A 20-year-old female with congenitally acquired HIV and poor medication compliance presented with severe headaches and mild cranial nerve deficits. HIV viral load at presentation was 89,976/ml with CD4 count of 4/uL. Head MRI revealed 3-cm thick-walled ring-enhancing lesion in right basal ganglia. Serum titers for toxoplasmosis were negative. EBV DNA was detected by PCR in CSF without peripheral viremia. Imaging with thallium scan and MRI findings in combination with EBV PCR positive CSF allowed for the presumptive diagnosis of EBV-associated primary CNS lymphoma. Highly active anti-retroviral therapy (HAART) was reinitiated. Karnofsky score was 90%, thus chemotherapy was offered to optimize chance of cure. Agents of choice were high-dose Methotrexate for CNS penetration/anti-lymphoma activity and Rituximab. Within the next 5 months she received 8 cycles of alternating Methotrexate (4000 mg/m2/dose on Day 1) and Rituximab (375 mg/m2/dose on Day 8). Supportive care included leucovorin rescue and urine alkalinization. Therapy was tolerated well without sepsis episodes during neutropenia. Her headaches and neurological deficits resolved after the first cycle of therapy. Serial imaging demonstrated substantial and continuous regression of the lymphoma lesion. No adjunctive radiotherapy was administered. Patient remains in remission 18 months after diagnosis, despite fluctuating viral loads and CD4 counts due to the poor HAART compliance. No chronic hypogammaglobulinemia resulted from therapy to date. CONCLUSION: Given the observed results and acceptable toxicity profile, methotrexate and rituximab combination may be effective and should be considered in addition to HAART for treating EBV-associated CNS lymphoma in young patients with minimal comorbidities and underlying HIV/AIDS. INTRODUCTION: Pediatric pineal parenchymal tumors of intermediate differentiation (PPTID, WHO grade II or III) are extremely uncommon. Appropriate therapy has not been defined. We present three new cases of pediatric PPTID and 8 cases in patients under age 45 identified in a literature review. METHODS: This study utilized the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) (http://www.prisma-statement.org.). RESULTS: We diagnosed two children (female age 5 y, male age 14 y) with PPTID in the pineal region and negative work-up for metastases. Both underwent gross total resection (GTR). Pathologic evaluation was consistent with PPTID grade II in each. Both were treated with local radiation therapy via protons to 50.4 CGE. The first patient (case 1) is now 4 years since diagnosis with no evidence of disease (NED) and the second (case 2) is 8 months after surgery and NED. Our third case (male age 15 y) was diagnosed with PPTID grade III with drop metastases in the thecal sac (case 3). He was treated with craniospinal and boost radiation and multiagent chemotherapy but relapsed with leptomeningeal disease near the conus 2 years after diagnosis. Our literature review identified 8 cases of PPTID in patients under age 45, described in Table 1 (cases 4-11). There were broad treatment strategies from GTR only to craniospinal radiation and multiagent chemotherapy. While the therapy varied, the outcome for those with non-metastatic grade II tumors was good. Grade III tumors were associated with metastatic disease and a worse outcome. DISCUSSION: With very few cases, definitive recommendations for therapy are impossible. For PPTID grade II, GTR alone may be sufficient. PPTID grade III should be considered for more aggressive therapy.
| S-EPMC4046297 | biostudies-literature
Project description:Characterisation of epithelial and mesenchymal cells in murine pancreatic tumours
| PRJNA660217 | ENA
Project description:A novel oligonucleotide microarray design is described whereby one can screen for all known oncogenic fusion transcripts by one microarray hybridization. Measurements of chimeric transcript junctions are combined with exon-wise measurements of individual fusion partners. Keywords: Nimblegen custom-design The pilot data included a design with 68,861 oligonucleotide probes covering all combinations of chimeric exon-exon junctions from 275 pairs of fusion genes, as well as sets of oligos internal to all the exons of the fusion partners. Proof of principle was demonstrated by detection of known fusion genes (such as TCF3:PBX1, ETV6:RUNX1, and TMPRSS2:ERG) from six positive controls consisting of leukemia cell lines and prostate cancer biopsies.
2010-05-06 | E-GEOD-14435 | biostudies-arrayexpress
Project description:Soft-tissue tumours are derived from mesenchymal cells such as fibroblasts, muscle cells, or adipocytes, but for many such tumours the histogenesis is controversial. We aimed to start molecular characterisation of these rare neoplasms and to do a genome-wide search for new diagnostic markers. We analysed gene-expression patterns of 41 soft-tissue tumours with spotted cDNA microarrays. After removal of errors introduced by use of different microarray batches, the expression patterns of 5520 genes that were well defined were used to separate tumours into discrete groups by hierarchical clustering and singular value decomposition. Synovial sarcomas, gastrointestinal stromal tumours, neural tumours, and a subset of the leiomyosarcomas, showed strikingly distinct gene-expression patterns. Other tumour categories--malignant fibrous histiocytoma, liposarcoma, and the remaining leiomyosarcomas--shared molecular profiles that were not predicted by histological features or immunohistochemistry. Strong expression of known genes, such as KIT in gastrointestinal stromal tumours, was noted within gene sets that distinguished the different sarcomas. However, many uncharacterised genes also contributed to the distinction between tumour types. These results suggest a new method for classification of soft-tissue tumours, which could improve on the method based on histological findings. Large numbers of uncharacterised genes contributed to distinctions between the tumours, and some of these could be useful markers for diagnosis, have prognostic significance, or prove possible targets for treatment. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design
2005-10-13 | GSE3443 | GEO
Project description:We performed RNA-seq analysis on YFP+EpCAM+ and YFP+EpCAM- cell populations freshly isolated from three Pdx1-Cre;KrasLSL-G12D;Trp53fl/fl;Rosa26LSL-YFP (KPCY) murine pancreatic tumours. We compared the transcriptome between these two populations with the aim to understand their molecular interactions that could underlie epithelial-mesenchymal plasticity and tumour heterogeneity.
2022-04-08 | GSE157134 | GEO
Project description:The HMGA2 gene is frequently deranged by translocation and/or amplification in mesenchymal tumours, generally leading to over-expression of shorted transcripts and a truncated protein. In this experiment we have over-expressed wild type and truncated HMGA2 protein in an immortalized mesenchymal stem-like cell line and investigated their effects on gene expression patterns.
2010-06-26 | E-MEXP-2647 | biostudies-arrayexpress