Chromothripsis
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27541 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genomic rearrangements typically occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving chromosome shattering and reshuffling ('chromothripsis'), for which no genetic basis has yet been described. Whole-genome sequencing of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome) revealed massive, complex rearrangements resulting from chromothripsis. Integrating TP53 status with genomic rearrangement data in additional medulloblastomas revealed a striking association between TP53 mutation and chromothripsis in SHH-MBs. Unexpectedly, five seemingly sporadic SHH-MB patients with chromothripsis harbored TP53 germline mutations – findings relevant for clinical management. Analysis of additional tumor entities substantiated a link between TP53 mutation and chromothripsis, beyond general genomic instability. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings implicate p53 in the initiation of, or cellular reaction to, chromothripsis – a novel role for the 'guardian of the genome'.
2012-01-20 | GSE34258 | GEO
Project description:Genomic rearrangements typically occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving chromosome shattering and reshuffling ('chromothripsis'), for which no genetic basis has yet been described. Whole-genome sequencing of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome) revealed massive, complex rearrangements resulting from chromothripsis. Integrating TP53 status with genomic rearrangement data in additional medulloblastomas revealed a striking association between TP53 mutation and chromothripsis in SHH-MBs. Unexpectedly, five seemingly sporadic SHH-MB patients with chromothripsis harbored TP53 germline mutations – findings relevant for clinical management. Analysis of additional tumor entities substantiated a link between TP53 mutation and chromothripsis, beyond general genomic instability. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings implicate p53 in the initiation of, or cellular reaction to, chromothripsis – a novel role for the 'guardian of the genome'. The DNA copy-number profiles of 11 primary medulloblastoma samples were analyzed on the Affymetrix Mapping250K Nsp array, together with data from 70 primary samples taken from GSE21140. Data from diploid reference samples were taken from GSE9222. Additionally, DNA copy-number profiles for 19 additional medulloblastoma samples were generated on the Affymetrix SNP6 platform with matched blood samples.
2012-01-20 | E-GEOD-34258 | biostudies-arrayexpress
Project description:Breast cancer in Spain remains the first leading cause of cancer-related death in women from all age, and in younger women breast tumors often exhibit more aggressive phenotypes, worse prognosis and more frequently germline mutation in BRCA1/2 genes. Chromothripsis, a massive genome rearrangement, has been recently described but its etiology and effect on cancer cells remain unknown. Chromothripsis in breast cancer has been poorly studied and prevalence rates vary between 11-61%. We have studied chromothripsis-like patterns (CTLPs) in 58 DNA extracted from formalin-fixed paraffin-embedded (FFPE) breast cancer tissues from patients below 40 years old. Chromothripsis was confirmed with website tool CTLPScanner in 10/58 (17%) and most frequently involved chromosomal segment was 17q12-q21 (5/10 cases, 50%). We have also find that chromothripsis was related to low recurrence rates and familial history of breast cancer. In summary, we have analyzed chromothripsis in early-onset breast cancer for the first time and could have a prognostic value for this patients
2021-03-31 | GSE128583 | GEO
Project description:Breast cancer in Spain remains the first leading cause of cancer-related death in women from all age, and in younger women breast tumors often exhibit more aggressive phenotypes, worse prognosis and more frequently germline mutation in BRCA1/2 genes. Chromothripsis, a massive genome rearrangement, has been recently described but its etiology and effect on cancer cells remain unknown. Chromothripsis in breast cancer has been poorly studied and prevalence rates vary between 11-61%. We have studied chromothripsis-like patterns (CTLPs) in 58 DNA extracted from formalin-fixed paraffin-embedded (FFPE) breast cancer tissues from patients below 40 years old. Chromothripsis was confirmed with website tool CTLPScanner in 10/58 (17%) and most frequently involved chromosomal segment was 17q12-q21 (5/10 cases, 50%). We have also find that chromothripsis was related to low recurrence rates and familial history of breast cancer. In summary, we have analyzed chromothripsis in early-onset breast cancer for the first time and could have a prognostic value for this patients
2021-03-31 | GSE128586 | GEO
Project description:Breast cancer in Spain remains the first leading cause of cancer-related death in women from all age, and in younger women breast tumors often exhibit more aggressive phenotypes, worse prognosis and more frequently germline mutation in BRCA1/2 genes. Chromothripsis, a massive genome rearrangement, has been recently described but its etiology and effect on cancer cells remain unknown. Chromothripsis in breast cancer has been poorly studied and prevalence rates vary between 11-61%. We have studied chromothripsis-like patterns (CTLPs) in 58 DNA extracted from formalin-fixed paraffin-embedded (FFPE) breast cancer tissues from patients below 40 years old. Chromothripsis was confirmed with website tool CTLPScanner in 10/58 (17%) and most frequently involved chromosomal segment was 17q12-q21 (5/10 cases, 50%). We have also find that chromothripsis was related to low recurrence rates and familial history of breast cancer. In summary, we have analyzed chromothripsis in early-onset breast cancer for the first time and could have a prognostic value for this patients
2021-03-31 | GSE128584 | GEO
Project description:Mutations in the TMEM260 gene cause structural heart defects and renal anomalies syndrome (SHDRA), but the function of the encoded protein remains unknown. We report that TMEM260 is an ER-located protein O-mannosyltransferase that selectively glycosylates defined extracellular immunoglobulin, plexin, transcription factor (IPT) domains of the hepatocyte growth factor receptor (cMET), macrophage-stimulating protein receptor (RON), and plexin receptors. We demonstrate that disease-causing TMEM260 mutations impair O-mannosylation of IPT domains and that TMEM260 knock out in cells results in receptor maturation defects and abnormal growth of 3D cell models. Thus, our study identifies a new, receptor-specific O-mannosylation pathway that serves critical functions during e.g. epithelial morphogenesis.
2023-05-05 | PXD032328 | Pride
Project description:Purpose: profiling the differential transcripts usage in wild type and Plxnd1 knockout condition of brain Methods: transcriptome analysis by the RNA-seq through the mRNA pull-down Results: We performed RNA-seq analysis from neonatal mouse striatum and found that the repulsive Semaphorin 3E (Sema3E)-Plexin-D1 guidance signaling transcriptionally upregulates Mtss1 in striatonigral projecting neurons of basal ganglia circuitry Conclusions: our findings demonstrate a molecular mechanism in which repulsive guidance cues activate an autoregulatory program enabling growing axons to perform both avoiding repellants and continuing axonal extension in the navigation to their target
2022-12-31 | GSE196558 | GEO
Project description:Comment on published article "Massive genomic rearrangement acquired in a single catastrophic event during cancer development." by Stephens, P.J., Greenman, C.D., Beiyuan, F., Yang, F., Bignell, G.R., Mudie, L.J., Pleasance, E.D., Lau, K.W., Beare, D., Stebbings, L.A., et al. (2011). Cell 144, 27-40. [PMID: 21215367]
2011-06-06 | GSE27560 | GEO
Project description:[Aim] To characterize the transcriptomic changes in skin lesions of lepromatous leprosy patients before and after multidrug therapy (MDT). Likewise, not all patients improve their bacillary index after MDT. Thus, the further analysis aims to compare patients who responded or did not to MDT and identify underlying modulated genes. [Design] Lepromatous patients were treated for 12 months with multidrug therapy. Skin biopsy samples were collected before (BT) and after treatment (AT). At the end of 12 months of MDT, those who decreased their bacillary index by at least one log10 unit were considered responders (R) and otherwise non-responders (NR). RNA was isolated, poly-A captured, and sequenced. Comparisons both within-patient and between-patients were done. [Results] At the end of MDT, genes involved with lipid metabolism, innate and adaptive immunity, extracellular matrix, and epidermis development were all differentially expressed. Comparisons between responders and non-responders to MDT identified differentially expressed genes involved with lipid metabolism, semaphorin-plexin signaling pathway, epidermis development, and vasculogenesis. This study identified gene expression signatures modulated after 12 months of MDT. Also, a subset of patients with poor bacterial clearance has dysregulated pathways relative to responders.
2022-04-10 | E-MTAB-11605 | biostudies-arrayexpress
Project description:Non-coding sense and antisense germline transcription within the immunoglobulin heavy chain locus precedes V(D)J recombination and has been proposed to be associated with Igh locus accessibility, although its precise role remains elusive. However, no global analysis of germline transcription throughout the Igh locus has been done. Therefore, we performed directional RNAseq, demonstrating the locations and extent of both sense and antisense transcription throughout the Igh locus. Surprisingly, the majority of antisense transcripts are localized around two PAIR elements in the distal IghV region. Importantly, long-distance loops measured by 3C are observed between these two active PAIR promoters and EM-NM-<, the start site of IM-NM-< germline transcription, in a lineage- and stage-specific manner, even though this antisense transcription is EM-NM-<-independent. YY1-/- pro-B cells are greatly impaired in distal VH gene rearrangement and Igh locus compaction, and we demonstrate that YY1 deficiency greatly reduces antisense transcription and PAIR-EM-NM-< interactions. ChIP-seq shows high level YY1 binding only at EM-NM-<, but low levels near some antisense promoters. PAIR-EM-NM-< interactions are not disrupted by DRB, which blocks transcription elongation without disrupting transcription factories once they are established, but the looping is reduced after heat shock treatment, which disrupts transcription factories. We propose that transcription-mediated interactions, most likely at transcription factories, initially compact the Igh locus, bringing distal VH genes close to the DJH rearrangement, which is adjacent to EM-NM-<. Therefore, we hypothesize that one key role of non-coding germline transcription is to facilitate locus compaction, allowing distal VH genes to undergo efficient rearrangement. ChIP Seq YY1 vs. input control
2012-10-18 | E-GEOD-40822 | biostudies-arrayexpress