Project description:We sequenced mRNA from both cell lines and primary samples to investigate transcriptomic profiles of human AML cell lines and primary samples. We then performed gene expression profiling analysis using data obtained from RNA-seq of AML cell lines and primary samples that have sphingolipidomic characterization to identify transcriptional differences between two distinct sphingolipidomic subtypes in AML samples.
Project description:In vitro study with AML cell lines that are treated with different concentrations of cytarabine (nucleoside analog). 8 AML cell lines were incubated for 24hr with 0uM, 1uM and 10uM ara-C. After 24hr the cells were washed and pellets were stored in -80°C for genomic and metabolomic analysis.
Project description:In vitro study with AML cell lines that are treated with different concentrations of cytarabine (nucleoside analog). 8 AML cell lines were incubated for 24hr with 0uM, 1uM and 10uM ara-C. After 24hr the cells were washed and pellets were stored in -80°C for genomic and metabolomic analysis.
Project description:Genome-wide DNA methylation profiling of primary AML samples treated with 100nM decitabine (DAC), cytarabine (AraC), or DMSO. Eight distinct AML samples were grown using an in vitro stromal co-culture system for 4 days and then treated with either DAC, Ara-C or DMSO for 3 days. DNA was prepared for genome-wide methylation analysis with the Illumina Infinium 450k Human DNA methylation BeadChip. DNA from each sample/treatment was analyzed on duplicate arrays.
Project description:Kinase hyperactivity is a common driver of acute myeloid leukemia (AML) and serves as a therapeutic target. The most frequent genetic aberration leading to hyperactive kinase signaling and poor prognosis is internal tandem duplication (ITD) of the FMS-tyrosine-like Kinase 3-gene (FLT3). FLT3-ITD induces ligand independent activation of FLT3 and downstream pathways leading to proliferation, decreased apoptosis and partial differentiation block. Combined with chemotherapy, FLT3-Tyrosine Kinase Inhibitor (FLT3-TKI) midostaurin improves overall survival (OS) of newly diagnosed FLT3-mutated AML patients, whereas single agent gilteritinib proved superior to chemotherapy in relapsed/refractory FLT3-mutated AML patients . As the primary targets of currently approved FLT3-TKIs are tyrosine (Y) kinases, we hypothesized that direct evaluation of tyrosine phosphorylation status could reveal pY phosphorylation profiles associated with FLT3-TKI response. Therefore, we used label-free pTyr-based phosphoproteomics in 35 primary AML samples (18 FLT3-WT, 17 FLT3-ITD), to identify differentially phosphorylated proteins underlying response to the FLT3-TKIs gilteritinib and midostaurin. We identified a total of 3024 unique phosphosites (median 1299 per sample, range 286 – 1612, pS:pT:pY 11.9%:9.5%:78.6%). Due to low number of identified phosphosites, we excluded two samples from further analyses. On the remaining 33 samples, we additionally performed IMAC global phosphoproteomics and on 17 samples protein expression analysis.
Project description:As part of a clinical trial of the MDM2 inhibitor DS-3032b, 41 primary tumor samples were obtained before treatment from 38 patients newly diagnosed with AML, or relapsed or refractory to standard induction chemotherapy Gene expression features of pretreatment samples, along with TP53 mutation status, were found to correlate with clinical response to DS-3032b (manuscript under review).
Project description:Analysis of gene expression profiles of human AML patient samples. The hypothesis tested was that AML patient samples showing a higher sensitivity to subsequent telomerase inhibition would already harbour a telomerase deficiency gene expression signature before treatment that may be useful to predict therapeutic efficacy. The results provide a clear separation of AML patient samples based on a telomerase deficiency gene signature that is correlated with subsequent sensitivity to pharmacologic telomerase inhibition assessed in a xenograft transplantation system in vivo.