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Distinct transcriptional signatures in mIDH leukemia cells as compared to wild type

ABSTRACT: Distinct transcriptional signatures in mIDH leukemia cells as compared to wild type

PROVIDER: PRJNA775975 | ENA |

REPOSITORIES: ENA

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Distinct transcriptional signatures in mIDH leukemia cells as compared to wild type

Project description:We report the results of bulk RNA sequencing on both parental and mIDH2R140Q TF-1 cell lines. We obtained 1 million cells of each cell line and extracted RNA to generate libraries. Our sequencing was performed with Novogene assistance. Differentially expressed genes (DEGs) were analyzed using DEseq2. Ultimately, we compared the expression of NF-κB targets and our results indicated upregulation of IL-1, IFNα and IFNγ in the mIDH2 cell line as compared to parental. Additionally using GSEA software, we noted increased expression of upstream and downstream constituents of the NF-κB pathway. This component of our study indicates the broad transcriptional changes induced by mIDH2R140Q mutation and demonstrates the upregulation of NF-κB specifically.

2021-10-30 | GSE186759 | GEO

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Nonconverters exhibit differential transcriptional signatures compared to converters.

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Distinct cell type-specific protein signatures in GRN and MAPT genetic subtypes of frontotemporal dementia

Project description:INTRODUCTION: Frontotemporal dementia (FTD) is characterized by progressive atrophy of frontal and/or temporal cortices and considerable clinical, pathological, and genetic heterogeneity. METHODS: Frontal and temporal cortex tissues from FTD-GRN (n=9), FTD-MAPT (n=13), and non-demented controls (n=11) were analysed with quantitative proteomics (DIA). Expression-weighted cell type enrichment deduced the role of major brain cell types and gene ontology analysis identified distinct biological processes. FTD-MAPT data was also compared to an AD (n=10) protein signature. RESULTS: We identified brain region-specific FTD protein expression signatures. In frontal cortex of FTD-GRN, we observed immune processes in endothelial cells and mitochondrial dysregulation in neurons. In temporal cortex of FTD-MAPT, we observed dysregulated RNA processing, oligodendrocyte dysfunction, and axonal impairment. Comparison with AD indicated that alterations in RNA processing and oligodendrocyte function are distinct for FTD-MAPT. DISCUSSION: Our results indicate cell type-specific biological processes distinctive for genetic FTD subtypes. These findings may aid the development of FTD subtype-specific treatment strategies.

2022-08-12 | PXD031419 | Pride

Robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures.

Project description:Microarray gene expression (MAGE) signatures allow insights into the transcriptional processes of leukemias and may evolve as a molecular diagnostic test. Introduction of MAGE into clinical practice of leukemia diagnosis will require comprehensive assessment of variation due to the methodologies. For the first time, we present a study focused on analyzing the impact of different RNA preparation procedures on gene expression data for different subtypes of pediatric acute leukemias. Keywords: comparison of various total RNA preparation procedures

2007-05-31 | GSE7757 | GEO

Single-cell transcriptomics reveals distinct microglia signatures under inflammation

Project description:Single-cell transcriptomics reveals distinct microglia signatures under inflammation

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MicroRNA profiling of patients with acute myeloid leukemia to identify microRNA signatures associated with cytogenetics and prognosis

Project description:MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia

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Sera-induced transcriptional signatures in human leukemia cell lines

Project description:Inflammation is common to many disorders and responsible for tissue and organ damage. However, the associated peripheral cytokine milieu is frequently dilute and difficult to measure, necessitating development of more sensitive and informative biomarkers for mechanistic studies, earlier diagnosis, and monitoring therapeutic interventions. Previously, we have shown that sera from type 1 diabetes (T1D) patients induces a unique disease-specific pro-inflammatory transcriptional profile in fresh peripheral blood mononuclear cells (PBMCs) compared to sera of healthy controls. To address the potential variance introduced by heterogeneity in responsiveness of PBMCs from different donors, we evaluated human leukemia cell lines as surrogates for fresh PBMCs. Expression signatures of 7 different cell lines were 1) tested in their power to differentiate sera of T1D patients from healthy controls; and 2) compared to the signature obtained with fresh PBMCs.

2010-09-16 | GSE24147 | GEO

Acute lymphoblastic leukemia displays a distinct highly methylated genome

Project description:Acute lymphoblastic leukemia displays a distinct highly methylated genome

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Distinct chromatin signatures in plant male germline cells - RNA-seq

Project description:Distinct chromatin signatures in plant male germline cells - RNA-seq

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