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RNA-seq of CD34+ CML CP cells transduced with pL-CELF2

ABSTRACT: RNA-seq of CD34+ CML CP cells transduced with pL-CELF2

PROVIDER: PRJEB72798 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12721600_1.fastq.gz	Fastqsanger.gz
	ERR12721600_2.fastq.gz	Fastqsanger.gz
	ERR12721601_1.fastq.gz	Fastqsanger.gz
	ERR12721601_2.fastq.gz	Fastqsanger.gz
	ERR12721602_1.fastq.gz	Fastqsanger.gz

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RNA-seq of CD34+ CML CP or healthy donor cells

Project description:RNA-seq of CD34+ CML CP or healthy donor cells

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Gene expression profile at single cell level of LMPP (lymphoid-primed multipotent progenitor) cells from CP-CML and BC-CML patients.

Project description:LMPPs comprise of heterogeneous populations which are progenitors of lymphocytes and myeloid cells. We aim to identify the difference of distribution of the diverse populations from CP-CML versus BC-CML patients.

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Gene expression profile at single cell level of Lin-Sca-1+c-Kit+ cells (LSKs) from miR-142 WT CML mice (CP LSC) and of LSKs from miR-142 KO CML mice (BC LSC). [scRNA-Seq]

Project description:To assess how the miR-142 deficit affected the BM LSC-enriched LSK landscape, we conducted a single cell RNA-seq analysis of BM miR-142+/+ BCR-ABL (CP CML) and miR-142−/− BCR-ABL (BC CML) LSKs which were harvested from the respective mice, 2 weeks after BCR-ABL induction.

2022-11-02 | GSE217076 | GEO

Gene profiling changes in BM Lin-Sca-1+c-Kit+ cells (LSKs) from miR-142-/- (KO), miR-142+/+ (WT), miR-142-/- BCR-ABL (BC CML) and miR-142+/+ BCR-ABL (CP CML) mice. [bulk RNA-Seq]

Project description:To gain insight into how miR-142 deficit drives a BC-like transformation, we performed RNA-seq on bone marrow (BM) Lin-Sca-1+c-Kit+ cells (LSKs) harvested from normal miR-142+/+ (wt) and miR-142−/− (miR-142 KO) mice, as well as from leukemic miR-142+/+ BCR-ABL (CP CML) and miR-142−/− BCR-ABL (BC CML) mice, two weeks after BCR-ABL induction. We then performed gene expression profiling analysis using data obtained from RNA-seq of 24 samples of LSK cells from 4 mouse strains (KO vs WT, KO CML vs CML).

2022-11-01 | GSE216794 | GEO

Bone marrow CD34+/lin- cells of patients with Chronic Phase- Chronic Myeloid Leukemia (CP-CML) after 12 months of nilotinib treatment exhibit a different expression signature compared to the diagnosis and the same cells from healthy subjects

Project description:Chronic Phase-Chronic Myeloid Leukemia (CP-CML) is defined by the presence of BCR-ABL1 fusione gene, which encodes a tyrosine kinase protein that drives the uncontrolled proliferation and survival of leukemic stem cells (LSCs). Nilotinib, a tyrosine kinase inhibitor, targets the activity of BCR-ABL1 by reducing aberrant signalling pathways which drive the regeneration of LSCs. Despite nilotinib’s action, a population of resilient LSCs persist in the bone marrow (BM) and can indeed drives relapse and progression in CML patients. Our study investigated the gene expression profiling (GEP) of BM CD34+/lin- cells from 79 CP-CML patients at diagnosis compared to the BM CD34+/lin- cells from the same patients after 12 months of nilotinib treatment, and to the normal cell counterpart from 10 donors (CTRLs). GEP analyses identified 3012 significantly differentially expressed genes. Among these, we focused on certain genes involved in crucial KEGG pathways: CML, cell cycle, JAK-STAT, PI3K-Akt, MAPK, Ras, NF-kB, and ABC transporters. We demonstrated the upregulation of several genes at diagnosis compared to both 12 months of nilotinib treatment and the CTRLs. We highlighted that certain transcriptome features characterizing the diagnosis persist after 12 months of nilotinib treatment compared to CTRLs, potentially influencing the self-renewal and survival properties of LSCs.

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Tumor suppressive role of CELF2 in skin tumorignesis

Project description:To investigate the function of CELF2 in non-melanoma skin cancer, we performed immunofluorescence staining studies and found lower CELF2 expression in human squamous cell carcinoma (SCC) tumors than in adjacent normal skin. CELF2 expression was also downregulated during both ultraviolet light- and chemical-induced skin tumorigenesis in mice, suggesting that CELF2 loss might promote skin cancer development. By using shRNA-mediated knockdown (KD) of CELF2 expression, we showed that CELF2 deficiency significantly increased SCC cell proliferation and colony growth in vitro and increased SCC tumor growth in a xenograft mouse model. Although control SCC cells were sensitive to anticancer drugs such as doxorubicin, CELF2-KD SCC cells were resistant to drug-induced tumor growth retardation. Through RNA-seq analysis, we identified that CELF2 loss led to activation of KRT80 and GDF15, which could confer growth and survival advantages to CELF2-deficient SCC cells.

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The hematopoietic stem cell in chronic phase CML is characterized by a transcriptional profile resembling normal myeloid progenitor cells and reflecting loss of quiescence

Project description:We found that composition of cell subsets within the CD34+ cell population is markedly altered in chronic phase (CP) chronic myeloid leukemia (CML). Specifically, proportions and absolute cell counts of common myeloid progenitors (CMP) and megakaryocyte-erythrocyte progenitors (MEP) are significantly greater in comparison to normal bone marrow whereas absolute numbers of hematopoietic stem cells (HSC) are equal. To understand the basis for this, we performed gene expression profiling (Affymetrix HU-133A 2.0) of the distinct CD34+ cell subsets from six patients with CP CML and five healthy donors. Euclidean distance analysis revealed a remarkable transcriptional similarity between the CML patients' HSC and normal progenitors, especially CMP. CP CML HSC were transcriptionally more similar to their progeny than normal HSC to theirs, suggesting a more mature phenotype. Hence, the greatest differences between CP CML patients and normal donors were apparent in HSC including downregulation of genes encoding adhesion molecules, transcription factors, regulators of stem-cell fate and inhibitors of cell proliferation in CP CML. Impaired adhesive and migratory capacities were functionally corroborated by fibronectin detachment analysis and transwell assays, respectively. Based on our findings we propose a loss of quiescence of the CML HSC on detachment from the niche leading to expansion of myeloid progenitors.

2008-12-01 | GSE11889 | GEO

Transcription profiling of human indolent and aggressive forms of Chronic Myeloid Leukaemia (CML)

Project description:Title: Gene expression analysis of indolent and aggressive forms of Chronic Myeloid Leukaemia (CML). Description: Chronic Myeloid Leukaemia presents in chronic phase (CP) and terminates in 'blast crisis'. Despite a common abnormality, the duration of CP is variable. The aim is to compare the gene expression profiles of the indolent and aggressive forms of CML. All samples were taken within 3 months of first diagnosis. Indolent patients were defined by chronic phase CML, duration minimum 7 years. Aggressive patients were defined by chronic phase, duration maximum 3 years.

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CELF2 CLIP-seq in human JSL1 T cells

Project description:In this study, CLIP-seq was used to identify sites of CELF2-mRNA interactions in JSL1 T cells. (SRA study SRP059226, BioProject accession PRJNA285907)

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H3K27 tri-methylation signature in CML CD34+ cells

Project description:This study compares the epigenetic signatures of CD34+ cells from chronic phase chronic myeloid leukemia (CML) samples and blast phase CML samples v.s. normal CD34+ cells from cord blood and adult bone marrow samples. H3K27me3 genomic loci were detected by ChIP-seq.

2021-11-08 | GSE188241 | GEO

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