Whole transcriptome analysis of sinonasal sarcoma with translocation t(2;4)(q37.1;q31.3)
ABSTRACT: Conventioal cytogenetic on 2 sinonasal sarcoma (SNS) cases showed t(2;4)(q37.1;q31.3) translocation previously. The aim of this whole transcriptome analysis is to determine potential candidate genes involved in this translocation. Total RNA extracted from frozen cultured primary tumor cells from a SNS characterized at the cytogenetics level was subjected to Illumina whole transcriptome RNA-sequencing anslysis.
Project description:Analyses of gene expression profiling in sinonasal sarcoma (SNS) harboring PAX3-MAML3 fusion gene or PAX3 rearrangement and other types of tumors without having such fusion or rearrangement. The results provide important information for further investigations of the PAX3-MAML3 fusion functions in SNS. Total RNA was obtained from FFPE tissues of 41 tumors including 8 SNS (6 with PAX3-MAML3 fusion and 2 with PAX3 rearrangement only) and 33 cases from other 10 different types of tumors. Gene expression profiling of fusion group including 8 SNA vs.non-fusion group including 33 control tumors were analyszed.
Project description:Comparative analysis of gene expression in murine sinonasal mucosa in wild-type and CC10-knockout littermates with allergic eosinophilic chronic rhinosinusitis. The data provide a comprehensive overview of genes expressed in the mouse sinonasal mucosa and show that the expression of several known and unidentified genes is modified by disruption of the CC10 gene. Overall design: Total RNA isolated from sinonasal mucosae of 6- to 8-week-old mice, C57BL/6 strain, was used for this comparison. Three groups: wild-type control, wild-type with allergic eosinophilic chronic rhinosinusitis, and CC10-knockout with allergic eosinophilic chronic rhinosinusitis.
Project description:Transcriptional profiling of ethmoïd tumors samples comparing normal samples from the controlateral sinus. RNA were extracted from biopsies. Sinonasal adenocarcinomas are uncommon tumors developping in ethmoid sinus after wood dust exposure. Although the etiology of these tumors is well defined very little is known regarding the molecular basis of these tumors. In an attempt to identify genes involved in this disease we proceed to a gene expression profiling using cancer-dedicated microarrays, on matched samples of nine sinonasal adenocarcinomas and non-tumoral sinusal tissue. Among the genes with significant differential expression we selected: LGALS4, ACS5, CLU, BAX, PDGFRa, SRI and CCT5 for further exploration by quantitative real-time reverse-transcription-PCR on a larger set of tumors and confirmed the microarray data. Protein expression alterations were shown for LGALS4, ACS5, and CLU by immunohistochemistry. Our results suggest that two genes might be involved in the pathogenesis of these tumors: LGALS4 highly up-regulated, particularly in the most differentiated tumors, and CLU, whose expression was lost. After further evaluation these genes could be used as markers for a better characterization of these tumors and will potentially help to an earlier detection of cancer in woodworkers, who have high risk of developing sinonasal adenocarcinomas. Overall design: Two-condition experiment tumor samples from frozen section vs normal samples. There were two arrays by sample when it was possible.
Project description:SnowShoes-FTD, a fusion transcript discovery tool, was used to identify fusions in breast cancer cell lines using the RNA-Seq data Total RNA extracted from cell lines. The total RNA was used for construction of RNA-Seq library for RNA-Sequencing.
Project description:Comparative analysis of gene expression in murine sinonasal mucosa in wild-type and CC10-knockout littermates with allergic eosinophilic chronic rhinosinusitis. The data provide a comprehensive overview of genes expressed in the mouse sinonasal mucosa and show that the expression of several known and unidentified genes is modified by disruption of the CC10 gene. Total RNA isolated from sinonasal mucosae of 6- to 8-week-old mice, C57BL/6 strain, was used for this comparison. Three groups: wild-type control, wild-type with allergic eosinophilic chronic rhinosinusitis, and CC10-knockout with allergic eosinophilic chronic rhinosinusitis.
Project description:We report on two novel t(15;21) alterations [t(15;21)(q24;q22) and t(15;21)(q21;q22)], which led to concurrent disruption of RUNX1 and two translocation partner genes encoding for transcription factors (SIN3A, TCF12) Examination of four different patients with myeloid disorders. 2 out of 4 have been analyzed by means RNAseq
Project description:Mutations of TCF4, which encodes a basic helix-loop-helix transcription factor, cause Pitt-Hopkins syndrome (PTHS) via multiple genetic mechanisms. TCF4 is a complex locus expressing multiple transcripts by alternative splicing and use of multiple promoters. We report a three-generation family segregating mild intellectual disability with an apparently balanced chromosomal translocation t(14;18)(q23.3;q21.2) that we characterized as a complex unbalanced karyotype 46,XY,der(14)del(14)(q23.3q23.3)t(14;18)(q23.3;q21.2)del(18)(q21.2q21.2) del(18)(q21.2q21.2)inv(18)(q21.2q21.2),der(18)t(14 ;18)(q23.3;q21.2) disrupting TCF4. Using whole genome sequencing, transcriptome sequencing, qRT-PCR and nCounter analysis, we characterized the breakpoint junctions from derivative chromosomes and gene expression at the TCF4 locus. Our analyses revealed that family members segregating mild intellectual disability with the complex chromosome aberration had normal expression of genes along chromosomes 14 or 18 and no marked changes in expression of genes other than TCF4. Affected individuals had 12-33 fold higher mRNA levels of TCF4 than did unaffected controls or individuals with PTHS. Increased levels of TCF4 transcript variants originating distal to the translocation breakpoint, not the fusion transcript generated by the derivative chromosome, contributed to this increased. Although validation in additional patients is required, our findings suggest that the dysmorphic features and severe intellectual disability characteristic of PTHS is partially rescued by overexpression of short TCF4 transcripts encoding a nuclear localization signal, a transcription activation domain, and the basic helix-loop-helix domain. Examination of TCF4 Isoform expression comparison between mutant and control skin fibroblast tissues
Project description:We developed a new approach called antibody detection of translocations (ADOT) which combines a transcriptional microarray-based approach with a novel antibody-based detection method to detect translocations in cancer. ADOT allows for the accurate and sensitive identification of translocations and provides exon-level information about the fusion transcript. ADOT can detect translocations in poor quality unprocessed total RNA. We demonstrate the feasibility of ADOT by examples in which both known and unknown Ewing sarcoma translocations are identified from cell lines, tumor xenografts, and FFPE primary tumors. These results demonstrate that ADOT may be an effective approach for translocation analysis in clinical specimens with significant RNA degradation and may offer a novel diagnostic tool for translocation-based cancers. We designed oligonucleotide probes for each possible exon-exon combination between potential fusion partners and printed the DNA oligonucleotides on custom-designed microarrays. Total RNA from tumor cells or tissues was hybridized on the array. Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion,and detected with Cy3-labeled anti-mouse IgG.
Project description:Escherichia coli is the most widely used bacterial model organism and is the most commonly used host for the expression of recombinant proteins. Here we describe an unexpected protein translocation phenomenon in E. coli, whereby over-expression of recombinant proteins leads to high-level lysis-independent, mechanosensitive channel (MscL) dependent release of recombinant protein into the periplasmic space. Protein accumulation in the periplasm leads to protein release into the extracellular environment, independent of outer membrane vesicle formation. The translocated proteins retain their corresponding biological activity, and can be isolated directly from the extracellular medium with high purity and yield. Condition-specific metabolomic and proteomic analyses combined with statistical enrichment analysis indicate a role of both osmotic and translational stress responses in the regulation of the MscL-dependent translocation phenomenon. We suggest a model coupling translational stress to the regulation of MscL via the action of both osmotic stress and the Alternative ribosome-rescue factor A (ArfA) to explain this potentially very useful phenomenon.