23 research outputs found
Large scale RNAi screen reveals that the inhibitor of DNA binding 2 (ID2) protein is repressed by p53 family member p63 and functions in human keratinocyte differentiation
No full textThe inhibitor of DNA binding 2, dominant negative helix-loop-helix protein, ID2, acts as an oncogene and elevated levels of ID2 have been reported in several malignancies. Whereas some inducers of the ID2 gene have been characterized, little is known regarding the proteins capable to repress its expression. We developed siRNA microarrays to perform a large scale loss-of-function screen in human adult keratinocytes engineered to express GFP under the control of the upstream region of ID2 gene. We screened the effect of siRNA-dependent inhibition of 220 cancer-associated genes on the expression of the ID2::GFP reporter construct. Three genes NBN, RAD21, and p63 lead to a repression of ID2 promoter activity. Strikingly NBN and RAD21 are playing on major role in cell cycle progression and mitosis arrest. These results underline the pregnant need to silence ID2 expression at transcript level to promote cell cycle exit. Central to this inhibitory mechanism we find p63, a key transcription factor in epithelial development and differentiation, which binds specific cis-acting sequence within the ID2 gene promoter both in vitro and in vivo. P63 would not suppress ID2 expression, but would rather prevent excessive expression of that protein to enable the onset of keratinocyte differentiation
Acquired abnormalities of chromosome 21 in acute lymphoblastic leukaemia
No full textThe intrachromosomal amplification of chromosome 21 (iAMP21) was identifiedas a novel and prognositically important acquired chromosomal abnormality inchildhood acute lymphoblastic leukaemia (ALL). It is defined by multiple copiesof the RUNX1 gene, as seen by fluorescence in situ hybridisation (FISH), localisedto a single abnormal duplicated chromosome 21 [dup(21)]. The morphologicalform of this chromosome is highly variable between patients and currently theonly reliable method of detection is FISH with probes to RUNX1. Studies of 48iAMP21 patients using detailed FISH techniques and array-based comparativegenomic hybridisation highlighted an extensive region of chromosome 21involvement. A minimum common region of amplification, between 33.19 and39.80Mb, including RUNX1 was identified, together with a minimum commonregion of deletion, between 46.54 and 46.92Mb, in 100% and 77% of patients,respectively. This study established that there were unique patterns of imbalance,with evidence of deletions, inversions and amplification, displayed on thedup(21), between individual patients. This provided evidence of an abnormalitythat may have arisen from a breakage-fusion-bridge mechanism, possibly initiatedby loss of a telomere. Results indicated that iAMP21 represents a distinct geneticsubgroup of childhood ALL and is not secondary to a cryptic abnormality ofchromosome 21. Two possible variant cases were identified both involvingchromosome 15. The abnormality can be distinguished from other numericalabnormalities of chromosome 21 by exploiting the unique pattern of gain,amplification and deletion seen in these patients. This allowed for thedevelopment of diagnostic tests based on copy number using either FISH ormultiplex ligation dependent probe amplification (MLPA), both of whichsuccessfully identified iAMP21 patients
RNAi–mediated knockdown of ATR, ETV1, or TERT induces senescence and prolongs G2/M preferentially in p53− cells.
No full text<p>(A) Senescence-associated β-galactosidase assay in p53+ and p53− HCT116 cells expressing a NS shRNA or one of two unrelated TERT shRNAs. Senescence-associated β-galactosidase activity was normalized to that obtained using a NS shRNA, which was set to 1. Error bars represent SD. (B) Senescence-associated β-galactosidase assay in p53+ and p53− HCT116 cells expressing a NS, ATR or ETV1 shRNA. Senescence-associated β-galactosidase activity was normalized to the level obtained using a NS shRNA, which was set to 1. Error bars represent SD. (C) Table showing the percentage of cells in G1, S and G2/M in p53+ and p53− HCT116 cells expressing a NS shRNA or one of two unrelated TERT shRNAs. (D) Table showing the percentage of cells in G1, S and G2/M in p53+ and p53− HCT116 cells expressing a NS shRNA or one of two unrelated ATR or ETV1 shRNAs. (E) Proliferation of p53+ and p53− HCT116 cells transfected with a control (LMNA), ATR or ETV1 siRNA and stably expressing TERT, or as a control GFP, was determined by an Alamar Blue fluorescence assay. Cell proliferation was normalized to that obtained using a LMNA siRNA, which was set to 1. Error bars represent SD.</p
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
No full textHere we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein–protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group
Additional file 6: of Transcriptomic and epigenetic profiling of ‘diffuse midline gliomas, H3 K27M-mutant’ discriminate two subgroups based on the type of histone H3 mutated and not supratentorial or infratentorial location
No full textFigure S3. A-C. Metaplots showing average signal accumulation in reads of all the regions bound by H3K27me3 in at least one sample (A, n = 16,979) or H3K27me3 occupied regions with or without overlapping genes (B, n = 11,003 and C, n = 5976 respectively) in both H3.1- and H3.3-K27M GSC cells. Each plot is centered on the summit of the average occupancy and extended 10 kb upstream and downstream (− 10 kb and + 10 kb, respectively). Below the metaplots, heatmaps illustrating average H3K27me3 levels in the 20 kb genomic intervals centered on the summit of the peak in each subgroup are presented. D. Violin plot displaying transcript expression level of RNA-seq data in tpm in H3.1- and H3.3-K27M subgroups. Boxplots represent the 5th,25th,75th and 95th percentiles and the median of the transcript distribution, The distributions were divided in 4 categories: non expressed genes ( 10 tpm). (PDF 2819 kb
EZHIP is a specific diagnostic biomarker for posterior fossa ependymomas, group PFA and diffuse midline gliomas H3-WT with EZHIP overexpression
No full textInternational audienc
An integrative radiological, histopathological and molecular analysis of pediatric pontine histone-wildtype glioma with MYCN amplification (HGG-MYCN)
No full textInternational audienc
Histone H3 wild-type DIPG/DMG overexpressing EZHIP extend the spectrum diffuse midline gliomas with PRC2 inhibition beyond H3-K27M mutation
No full textInternational audienc
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
No full textHere we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1\%) protein-coding and 642 (1.9\%) non-protein-coding loci; 858 (2.5\%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group
Diffuse intrinsic pontine gliomas (DIPG) at recurrence: is there a window to test new therapies in some patients?
No full textIF 2.980International audienceChildren with diffuse intrinsic pontine glioma (DIPG) need new and more efficient treatments. They can be developed at relapse or at diagnosis, but therefore they must be combined with radiotherapy. Survival of children after recurrence and its predictors were studied to inform the possibility to design early phase clinical trials for DIPG at this stage. Among 142 DIPG patients treated between 1998 and 2014, 114 had biopsy-proven DIPG with histone H3 status available for 83. We defined as long survivors' patients who survived more than 3 months after relapse which corresponds to the minimal life expectancy requested for phase I/II trials. Factors influencing post-relapse survival were accordingly compared between short and long-term survivors after relapse. Fifty-seven percent of patients were considered long survivors and 70% of them had a Lansky Play Scale (LPS) above 50% at relapse. Patients who became steroids-independent after initial treatment for at least 2 months had better survival after relapse (3.7 versus 2.6 months, p = 0.001). LPS above 50% at relapse was correlated with better survival after relapse (3.8 versus 1.8 months, p < 0.001). Patients with H3.1 mutation survived longer after relapse (4.9 versus 2.7 months, p = 0.007). Patients who received a second radiotherapy at the time of relapse had an improved survival (7.5 versus 4 months, p = 0.001). In the two-way ANOVA analysis, steroid-independence and LPS predicted survival best and the type of histone H3 (H3.1 or H3.3) mutated did not improve prediction. Survival of many DIPG patients after relapse over 3 months would make possible to propose specific trials for this condition. Steroid-independence, H3 mutation status and LPS should be considered to predict eligibility
