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Biomedical subjects

D Brett

Publications and source records attributed to D Brett.

13 recordsLinked to original sources
PubMed2001

A rapid bioinformatic method identifies novel genes with direct clinical relevance to colon cancer.

Identifying genes whose differential expression affect the survival of patients after primary tumor surgery is a major aim of clinical cancer research. To address this issue we combined rapid bioinformatic search algorithms with quantitative RT-PCR in a panel of clearly defined cases of colorectal carcinomas with detailed patient histories. Search algorithms were written that identified Expressed Sequence Tags (ESTs) from the Unigene EST collection of putative open reading frames (ORFs). Expression ratios of healthy to cancerous tissue of each Unigene ORF were calculated. The first 35 candidates arising from bioinformatic searches were examined for mRNA expression in a panel of 20 well documented cases of colon cancer. Four of these 35 genes showed significant correlations with histopathological parameters. Therefore, their expression was further analysed by quantitative RT-PCR in a larger patient cohort. Kaplan-Meier/log rank statistical tests of up to 49 patients in three of the four genes demonstrated significant association of gene expression with poor survival. All four genes demonstrated a strong association with metastatic tumor progression. Expression of the genes was localized to epithelial cells by in-situ hybridization.

Algorithms↗
PubMed2000

EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.

Expressed sequence tag (EST) databases represent a large volume of information on expressed genes including tissue type, expression profile and exon structure. In this study we create an extensive data set of human alternative splicing. We report the analysis of 7867 non-redundant mRNAs, 3011 of which contained alternative splice forms (38% of all mRNAs analysed). From a total of 12572 ESTs 4560 different possible alternative splice forms were detected. Interestingly, 70% of the alternative splice forms correspond to exon deletion events with only 30% exonic insertions. We experimentally verified 19 different splice forms from 16 genes in a total subset of 20 studied; all of the respective genes are of medical relevance.

Alternative Splicing↗
PubMed1999

Molecular cloning, expression and evolutionary analysis of the avian tyrosine kinase JAK1.

The Janus protein tyrosine kinases (JAK) constitute a protein family that plays a pivotal role in signalling of a large number of cytokine receptors. The cDNA of the chicken homologue of JAK1 was cloned and its nucleotide sequence determined. Chicken JAK1 protein comprises 1150 amino acids as deduced from its cDNA sequence with a calculated molecular mass of 133kDa. The overall structure of JAK proteins exemplified by the JAK homology domains JH1-JH7 is also preserved in chicken JAK1. Additionally, phylogenetic analysis demonstrates that chicken JAK1 is more closely related to mammalian JAK1 than to those of fish, exhibiting 80%, 79% and 63% identity in amino acid sequence to human, mouse and zebrafish JAK1, respectively. JAK1 proteins were found to be most conserved in the kinase (JH1) and pseudokinase (JH2) domains. This data is supported by Southern hybridization studies of ZOO blots. Chicken JAK1 shows a ubiquitous expression pattern and is transcribed as a 5.5kb mRNA in various tissues and cell types. JAK1 expression was particularly high in lymphoid cells.

Amino Acid Sequence↗
PubMed1999

Functional domains of the SYT and SYT-SSX synovial sarcoma translocation proteins and co-localization with the SNF protein BRM in the nucleus.

The t(X;18)(p11.2;q11.2) chromosomal translocation commonly found in synovial sarcomas fuses the SYT gene on chromosome 18 to either of two similar genes, SSX1 or SSX2, on the X chromosome. The SYT protein appears to act as a transcriptional co-activator and the SSX proteins as co-repressors. Here we have investigated the functional domains of the proteins. The SYT protein has a novel conserved 54 amino acid domain at the N-terminus of the protein (the SNH domain) which is found in proteins from a wide variety of species, and a C-terminal domain, rich in glutamine, proline, glycine and tyrosine (the QPGY domain), which contains the transcriptional activator sequences. Deletion of the SNH domain results in a more active transcriptional activator, suggesting that this domain acts as an inhibitor of the activation domain. The C-terminal SSX domain present in SYT-SSX translocation protein contributes a transcriptional repressor domain to the protein. Thus, the fusion protein has transcriptional activating and repressing domains. We demonstrate that the human homologue of the SNF2/Brahama protein BRM co-localizes with SYT and SYT-SSX in nuclear speckles, and also interacts with SYT and SYT-SSX proteins in vitro. This interaction may provide an explanation of how the SYT protein activates gene transcription.

Amino Acid Sequence↗
PubMed1997

The SYT protein involved in the t(X;18) synovial sarcoma translocation is a transcriptional activator localised in nuclear bodies.

The t(X;18)(p11.2;q11.2) translocation found in synovial sarcomas results in the fusion of the SYT gene on chromosome 18 to either of two closely related genes SSX1 and SSX2 on chromosome X. The resulting chimaeric genes express SYT-SSX1 or SYT-SSX2 fusion proteins in which the C-terminal amino acids of SYT are replaced by amino acids from the C-terminus of the SSX proteins. Using green fluorescent protein fusions we demonstrate that the SYT, SSX and the SYT-SSX proteins are nuclear proteins. We demonstrate that whilst the SSX1 protein has a uniform nuclear distribution the SYT protein has a speckled distribution in the cell nucleus, and this distribution is retained with the SYT-SSX2 fusion protein. Since the SYT speckles do not co-localise with PML-containing bodies (PODs) or spliceosomes it is possible that they represent a novel nuclear structure. Transfection of constructs expressing GAL4 fusion proteins demonstrate that the SYT domains present in the SYT-SSX fusion proteins can activate transcription of a luciferase reporter. It is proposed that the t(X;18) translocation results in the generation of an SYT-SSX transcriptional co-activator in which the addition of the C-terminal SSX domain to SYT provides a new interacting domain that redirects the SYT activation domain to different target promoters.

Cell Nucleus↗
PubMed1994

Sinonasal hemangiopericytoma.

Sino-nasal hemangiopericytomas are rare indolent mesenchymal tumors which slowly invade local tissue. Electronmicroscopy and immunohistochemical techniques may be necessary to differentiate hemangiopericytomas from other sarcomatous tumors. Differentiation between malignant and benign tumors poses a difficult task, therefore clinical correlation as well histological confirmation is necessary to establish a diagnosis. Due to the low incidence of distant metastasis and low mortality, surgery consisting of wide local excision is usually curative.

Aged↗