Promoter methylation data from ALL diagnosis and relapse pediatric acute lymphoblastic leukemia cases
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE28461 | GEO | 2011/09/23
SECONDARY ACCESSION(S): PRJNA143231
REPOSITORIES: GEO
Similar Datasets
Project description:Relapse samples have high methylation level than dianosis samples Promoter mehtylation level was measured and compared between relapse and diagnosis samples
2011-09-22 | E-GEOD-28461 | biostudies-arrayexpress
Project description:There is a distinct signature of differentially expressed probes from diagnosis to relapse Gene expression profiles of pediatric patients with B-precursor ALL were compared to at 2 time points, diagnosis and relapse. The overall design was a comparison of gene expression at diagnosis and relapse within individual patients. A subset analysis (comparing diagnosis to relapse expression within individuals), was done for early relapse (less than 36 months) cases only and late relapse (greater than 36 months) cases only.
2011-09-23 | E-GEOD-28460 | biostudies-arrayexpress
Project description:There is a distinct signature of differentially expressed probes from diagnosis to relapse
2011-09-23 | GSE28460 | GEO
Project description:Despite high survival rates in pediatric acute lymphoblastic leukemia (ALL), relapse remains a leading cause of cancer-related death in children. Many patients suffer from adverse drug effects during treatment and other complications later in life, and would benefit from improved relapse prediction at diagnosis. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients with pediatric ALL. Somatic mutations were called using individually matched remission samples as controls, and allelic expression of the mutations in the ALL cells was assessed using RNA-sequencing. These analyses identified 29 previously known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, and 20 mutated driver genes occurred in individual samples. We detected putative non-coding mutations in regulatory regions of seven additional genes that have not been described previously in ALL. We observed an increased burden of somatic mutations at relapse. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression. In an “ancestral clone trajectory”, the major cell clone at relapse originated from a founder clone that was not detectable at diagnosis. In a “rising diagnostic clone trajectory”, a minor cell clone at diagnosis expanded to form the major cell clone at relapse. In a “persistent diagnostic clone trajectory”, the major cell clone at diagnosis persisted during treatment until relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.
2021-08-11 | GSE163634 | GEO
Project description:The mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.
| S-EPMC8346595 | biostudies-literature
Project description:If relapses occur in only 20% of T-ALL children, 70% will have a dismal outcome, justifying the need for new therapeutic options. Transcriptomic plasticity is a property of leukemic cells to adapt their functions and resist to treatments. The project aims at analyzing, at a single cell resolution, the variations of the gene expression, between diagnostic and relapse. This will allow identification of relapse-associated genes as potential new targets for future innovative treatments.
2024-05-17 | GSE262271 | GEO
Project description:Pediatric acute myeloid leukemia (AML) bone marrow (BM) samples from diagnosis (Dx), end of induction (EOI), and relapse timepoints were analyzed by single-cell RNA sequencing (scRNA-seq). Analysis of matched Dx, EOI scRNA-seq datasets and TARGET AML RNA-seq datasets revealed a novel AML blasts-associated 7-gene signature (CLEC11A, PRAME, AZU1, NREP, ARMH1, C1QBP, TRH) that was validated in two independent datasets. Distinct clusters of relapse- and continuous complete remission (CCR)-associated AML-blasts were observed at Dx, with differential expression of genes associated with survival. At Dx, relapse-associated samples had more exhausted T cells while CCR-associated samples had more inflammatory M1 macrophages. Post-therapy EOI residual blasts overexpressed fatty acid oxidation, tumor growth, and stemness genes. Also, a post-therapy T-cells cluster present in relapse-associated samples exhibited downregulation of MHC Class I and T-cell regulatory genes. Altogether, this study deeply characterizes pediatric AML relapse- and CCR-associated samples to provide novel insights into BM microenvironment landscape.
2023-09-05 | GSE235923 | GEO
Project description:Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia
| PRJNA686976 | ENA
Project description:The development of a clinically relevant xenograft model of pediatric acute lymphoblastic leukemia, using a 4-drug treatment regimen designed to mimic pediatric remission induction therapy. Relapse and acquired drug resistance in T-cell acute lymphoblastic leukemia (T-ALL) remains a significant clinical problem. This study was designed to establish a preclinical model of resistance to induction therapy in childhood T-ALL to examine the emergence of drug resistance and identify novel therapies. We performed transcription profiling by array of human CD45-positive human lymphocytes from patients with acute pediatric lymphoblastic leukemia, and from xenografted NOD/SCID mice treated with vincristine, daunorubicin, dexamethasone and L-asparagine. Several different treatment regimes were used in this study (VLXD, VLXDR, VLXD2, VXL and VLXD2-ALL31) and are summarised in the protocols associated with this submission.
2013-11-01 | E-MEXP-3916 | biostudies-arrayexpress
Project description:We surveyed the DNA methylation levels of 435,941 CpG sites in samples from 764 children at diagnosis of ALL and from 27 children at relapse. This survey uncovered four characteristic methylation signatures. First, compared with control blood cells, the methylomes of ALL cells shared 9,406 predominantly hypermethylated CpG sites, independent of cytogenetic background. Second, each cytogenetic subtype of ALL displayed a unique set of hyper- and hypomethylated CpG sites. The CpG sites that constituted these two signatures differed in their functional genomic enrichment to regions with marks of active or repressed chromatin. Third, we identified subtype-specific differential methylation in promoter and enhancer regions that were strongly correlated with gene expression. Fourth, a set of 6,612 CpG sites was predominantly hypermethylated in ALL cells at relapse, compared with matched samples at diagnosis. Analysis of relapse-free survival identified CpG sites with subtype-specific differential methylation that divided the patients into different risk groups, depending on their methylation status. The DNA methylation levels of primary pediatric ALL samples taken at diagnosis (n= 764), remission(n=86), first relapse (n=27), second relapse (n=5), fractionated blood cells from healthy blood donors (n=51), and methylation +/- controls (n=11) were analyzed with the Illumina Infinium HumanMethylation 450k BeadChips. One ALL sample was run in duplicate (technical replicate).
2013-09-18 | E-GEOD-49031 | biostudies-arrayexpress