Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of genome-wide gene expression in wild-type and swd2.2delta fission yeast cells

ABSTRACT: Swd2.2 is associated with the Cleavage and Polyadenylation Factor (CPF) in fission yeast. The CPF is required for the 3'end processing of RNAs. To establish the contribution of Swd2.2 to gene expression, we used single-strand tiling array hybridization. The results show that 47 genes are significantly down-regulated (FCM-bM-^IM-$1,9, p<0,01) and 14 are up-regulated (FCM-bM-^IM-%1,9, p<0,01) when Swd2.2 is missing. To establish the contribution of Swd2.2 to transcription termination, we also used these data as follows: for every gene in the genome whose 3'UTR was annotated (4727 genes), the average RNA signal intensity observed in the 3'UTR of the gene was compared to the average signal intensity observed in the ORF of the gene. This ratio was named "UTR ratio". This UTR ratio was calculated for every gene, in swd2.2+ or swd2.2delta cells. The UTR ratio observed in swd2.2delta cells was then compared to the UTR ratio observed in swd2.2+ cells. When this ratio is superior to 1.5, it means that there was proportionnally a 50% increase of the RNA signal in the 3'UTR of this gene when Swd2.2 was missing. We interpreted this observation as a transcription termination defect. We detected 780 genes (out of 4727) for which this was the case. This list is highy enriched for convergent, overlapping genes. RNA extracted from swd2.2+ and swd2.2delta cells were retrotranscribed and labelled. These were then hybridized on an Affymetrix S. pombe Tiling 1.0FR Array (accession GPL7715). The data were established in triplicates.

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Vincent Vanoosthuyse

PROVIDER: E-GEOD-38005 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background. Flow cytometry (FCM) identifies leukemic blasts in cerebrospinal fluid (CSF) in approximately 30% of children with acute lymphoblastic leukemia (ALL), whereas conventional cytospin preparations frequently miss such involvement. <br>Procedure. To explore biological properties of leukemic cells that migrate into central nervous system (CNS), we compared gene expression profiles of leukemic cells from 26 patients with CNS involvement and 138 patients without CNS leukemia as determined by FCM and/or cytospin preparations. Results were validated by real-time quantitative PCR (qPCR). <br>Results. We found the cysteine endopeptidase legumain (LGMN) that plays a role in hydrolysis of proteins and small molecules to be significantly differentially expressed between FCM+ and FCM- B-cell precursor (BCP) ALL patients. When LGMN expression was validated by qPCR it stayed differentially expressed between FCM+ and FCM- BCP-ALL patients (P=0.006), and also between FCM+ and cytospin-negative BCP-ALL patients (P=0.01). In multivariate regression analysis including sex, age and WBC, LGMN expression levels above population median were associated with an odds ratio of 9.1 for CNS involvement as determined by FCM compared with expression less than the median (95% CI, 1.26 to 65.50; P=0.03). Conclusions. The use of more sensitive methods for detecting and quantifying CNS involvement, such as FCM, may facilitate detection of markers of leukemia biology, such as LGMN, which could have therapeutical implications for future CNS-directed therapy.<br>FCM+: Patients had leukemic cells in the cerebrospinal fluid (CSF) detected by flow cytometry and no blood contamination. FCM-: Patients had no leukemic cells in the CSF detected by flow cytometry with or without blood contamination.<br>CNS1: No leukemic cells in CSF detected by cytospin examination with or without blood contamination and no other clinical signs of central nervous system (CNS) leukaemia. CNS2: CSF leukocyte count <5 x106/ÂµL with blasts on cytospin examination and no blood contamination. CNS3: CSF leukocyte count >5 x106/ÂµL with blasts on cytospin examination and no blood contamination, and/or cranial nerve palsy, and/or CNS leukaemia by neuroimaging.

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Comparison of genome-wide gene expression in wild-type and swd2.2delta fission yeast cells

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