E-GEOD-27187
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA142055PRJNA142067PRJNA137173
PROVIDER: E-GEOD-27187 | ExpressionAtlas | 2015-09-16
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:To understand the pathogenesis of DNMT3A in acute monocytic leukemia (AML-M5), we identified genes that are expressed differently in leukemia cells from AML-M5 patients collected at diagnosis with DNMT3A mutations (6 cases) compared to those without the mutations (4 cases). Differences of expression level were observed in 889 out of 20,723 (4.3%) annotated genes by using Affymetrix microarray with 469 genes upregulated and 420 genes downregulated. Leukemia cells in bone marrow of acute monocytic leukemia patients were collected at diagnosis for RNA extraction and hybridization on Affymetrix microarrays. 6 cases of AML-M5 samples with DNMT3A mutations and 4 cases of AML-M5 samples wihtout DNMT3A mutations were used.
2011-02-12 | E-GEOD-27187 | biostudies-arrayexpress
Project description:The pretreatment karyotype of leukemic blasts is currently the key determinant in therapy decision-making in acute myeloid leukemia (AML). However, approximately fifty percent of AML patients, often carrying a normal karyotype, are currently unclassifiable based these established methods. Gene expression profiling has proven to be valuable for risk stratification of AML. The gene expression profiles of AML samples of two independent cohorts (n=247 and n=214) were determined using Affymetrix U133Plus2.0 GeneChips: all Samples (starting with 'amlrrays 2') below 4000 are in the training cohort; all Samples higher than 4000 are in the validation cohort. Data analyses were carried out to discover and predict prognostically relevant subtypes in AML (<60 years) based on their gene expression signatures. Statistical analyses were performed to determine the prognostic significance of cases of AML with specific molecular signatures. Unsupervised cluster analyses of the gene expression signatures of both independent cohorts of AML patients confirmed that chromosomal lesions and mutations, often resulting in aberrant transcription factors, induce discriminatory patterns of gene expression. In contrast, however, mutations in signalling molecules do not establish strong molecular signatures. Consequently, prognostically important subtypes, which express mutated trancription factors were predicted with high accuracy using minimal sets of genes. We identified several novel clusters, some consisting of patients with normal karyotypes. Gene expression profiling allows classification of AML subtypes characterized by the expression of abnormal transcription factors, however, prediction of clinically relevant mutations affecting signalling molecules is impossible and thus still requires addition molecular methods. Experiment Overall Design: 461 blood or bone marrow samples of acute myeloid leukemia patients were hybridized to Affymetrix HG-U133 plus 2 GeneChips.
2008-04-05 | E-GEOD-6891 | biostudies-arrayexpress
Project description:Acute Myeloid Leukemia (AML) is the most common and aggressive form of acute leukemia, with a 5-year survival rate of just 24%. Over a third of all AML patients harbor activating mutations in kinases, such as the receptor tyrosine kinases FLT3 and KIT. FLT3 and KIT mutations are associated with poor clinical outcomes and lower remission rates in response to standard-of-care chemotherapy. We have recently identified that the core kinase of the non-homologous end joining DNA repair pathway, DNA-PK, is activated downstream of FLT3; and targeting DNA-PK sensitized FLT3-mutant AML cells to standard-of-care therapies. Herein, we investigated DNA-PK as a possible therapeutic vulnerability in KIT mutant AML, using isogenic FDC-P1 myeloid progenitor cell lines transduced with an empty vector or oncogenic mutant KIT (V560G, D816V). Targeted quantitative phosphoproteomic profiling identified phosphorylation of DNA-PK at threonine 2599 in KIT mutant cells, indicative of DNA-PK activation. Accordingly, proliferation assays revealed that KIT mutant FDC-P1 cells were more sensitive to the DNA-PK inhibitors M3814 or NU7441, compared to empty vector controls. DNA-PK inhibition combined with inhibition of KIT signaling via using the kinase inhibitors dasatinib or ibrutinib, or the protein phosphatase 2A activators FTY720 or AAL(S), led to synergistic cell death. Discovery phosphoproteomic analysis of KIT-D816V cells revealed that dasatinib single-agent treatment inhibited ERK1 activity, and M3814 single-agent treatment inhibited Akt/mTOR activity. The combination of dasatinib and M3814 treatment inhibited both ERK/MAPK and Akt/mTOR activity, and induced synergistic inhibition of phosphorylation of transcription regulators including MYC and MYB. This study provides insight into the oncogenic pathways regulated by DNA-PK beyond its canonical role in DNA repair, and demonstrates that DNA-PK is a promising novel therapeutic target for KIT mutant cancers.
2023-01-26 | PXD030214 | panorama
Project description:The caudal-related homeobox transcription factor CDX2 is ectopically expressed in the majority of patients with acute myeloid leukemia (AML). We generated an inducible transgenic mouse model whereby Cdx2 was specifically activated in HSCs . Cdx2 mice developed myelodysplastic syndrome (MDS) with progression to acute leukemia associated with stepwise acquisition of additional driver mutations.
2019-09-30 | GSE133680 | GEO
Project description:The caudal-related homeobox transcription factor CDX2 is ectopically expressed in the majority of patients with acute myeloid leukemia (AML). We generated an inducible transgenic mouse model whereby Cdx2 was specifically activated in HSCs. Cdx2 mice developed myelodysplastic syndrome (MDS) with progression to acute leukemia associated with stepwise acquisition of additional driver mutations.
2020-03-09 | GSE146598 | GEO
Project description:The caudal-related homeobox transcription factor CDX2 is ectopically expressed in the majority of patients with acute myeloid leukemia (AML). We generated an inducible transgenic mouse model whereby Cdx2 was specifically activated in HSCs . Cdx2 mice developed myelodysplastic syndrome (MDS) with progression to acute leukemia associated with stepwise acquisition of additional driver mutations.
2019-09-30 | GSE133828 | GEO
Project description:The caudal-related homeobox transcription factor CDX2 is ectopically expressed in the majority of patients with acute myeloid leukemia (AML). We generated an inducible transgenic mouse model whereby Cdx2 was specifically activated in HSCs. Cdx2 mice developed myelodysplastic syndrome (MDS) with progression to acute leukemia associated with stepwise acquisition of additional driver mutations.
2019-09-30 | GSE133679 | GEO
Project description:Acute myeloid leukemia (AML) is a heterogeneous disease in respect of molecular aberrations and prognosis. We used gene expression profiling of 562 patients treated in the German AMLCG 1999 trial to develop a gene signature that predicts survival in AML. Analysis of 562 samples (140 HGU-133plus2; 422 HGU-133A; 422 HGU-133B) from adult patients with acute myeloid leukemia (AML).
2013-02-07 | E-GEOD-37642 | biostudies-arrayexpress
Project description:We hypothesized that DNA methylation distributes into specific patterns in cancer cells, which reflect critical biological differences. We therefore examined the methylation profiles of 344 patients with acute myeloid leukemia (AML). Clustering of these patients by methylation data segregated patients into 16 groups. Five of these groups defined new AML subtypes that shared no other known feature. In addition, DNA methylation profiles segregated patients with CEBPA aberrations from other subtypes of leukemia, defined four epigenetically distinct forms of AML with NPM1 mutations, and showed that established AML1-ETO, CBFb-MYH11 and PML-RARA leukemia entities are associated with specific methylation profiles. We report a 15-gene methylation classifier predictive of overall survival in an independent patient cohort (p<0.001, adjusted for known covariates). Keywords: DNA methylation profiling DNA methylation profiling of a cohort of 344 AML patients from Erasmus Medical Center and enrolled in clinical trials from the Dutch-German cooperative group HOVON. Additionally, a control group consisting of 8 CD34+ bone marrow samples from healthy donors was also studied.
2010-01-12 | E-GEOD-18700 | biostudies-arrayexpress
Project description:The pretreatment karyotype of leukemic blasts is currently the key determinant in therapy decision-making in acute myeloid leukemia (AML). However, approximately fifty percent of AML patients, often carrying a normal karyotype, are currently unclassifiable based these established methods. Gene expression profiling has proven to be valuable for risk stratification of AML. The gene expression profiles of AML samples of two independent cohorts (n=247 and n=214) were determined using Affymetrix U133Plus2.0 GeneChips: all Samples below 4000 are in the training cohort; all Samples higher than 4000 are in the validation cohort. Data analyses were carried out to discover and predict prognostically relevant subtypes in AML (<60 years) based on their gene expression signatures. Statistical analyses were performed to determine the prognostic significance of cases of AML with specific molecular signatures. Unsupervised cluster analyses of the gene expression signatures of both independent cohorts of AML patients confirmed that chromosomal lesions and mutations, often resulting in aberrant transcription factors, induce discriminatory patterns of gene expression. In contrast, however, mutations in signalling molecules do not establish strong molecular signatures. Consequently, prognostically important subtypes, which express mutated trancription factors were predicted with high accuracy using minimal sets of genes. We identified several novel clusters, some consisting of patients with normal karyotypes. Gene expression profiling allows classification of AML subtypes characterized by the expression of abnormal transcription factors, however, prediction of clinically relevant mutations affecting signalling molecules is impossible and thus still requires addition molecular methods. Keywords: acute myeloid leukemia, patient blood or bone marrow samples
2008-03-12 | GSE6891 | GEO