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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Dexamethasone and lenalidomide have distinct functional effects on erythropoiesis

ABSTRACT: We explored the effects of dexamethasone and lenalidomide, individually and in combination, on the differentiation of primary human bone marrow progenitor cells in vitro. Both agents promote erythropoiesis, increasing the absolute number of erythroid cells produced from normal CD34+ cells and from CD34+ cells with the types of ribosome dysfunction found in DBA and del(5q) MDS. However, the drugs had distinct effects on the production of erythroid progenitor colonies; dexamethasone selectively increased the number burst-forming units-erythroid (BFU-E), while lenalidomide specifically increased colony-forming units-erythroid (CFU-E). Use of the drugs in combination demonstrates that their effects are not redundant. Human CD34+ cells were cultured for 48 hours in the erythroid differentiation media described above with the addition of 40 ng/mL of FMS-like tyrosine kinase 3 (flt-3; Miltenyi Biotech) and 15 ng/mL of Granulocyte colony-stimulating factor (G-CSF; Amgen). Cells were cultured in the presence of the drugs of interest for 24 hours. RNA was purified using Trizol (Invitrogen). RNA was amplified and labeled by in vitro transcription and hybridized to the Affymetrix HT Human Genome U133A Array. Three replicates per condition.

ORGANISM(S): Homo sapiens

SUBMITTER: Fatima Al-Shahrour

PROVIDER: E-GEOD-28896 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dexamethasone and lenalidomide have distinct functional effects on erythropoiesis

Project description:We explored the effects of dexamethasone and lenalidomide, individually and in combination, on the differentiation of primary human bone marrow progenitor cells in vitro. Both agents promote erythropoiesis, increasing the absolute number of erythroid cells produced from normal CD34+ cells and from CD34+ cells with the types of ribosome dysfunction found in DBA and del(5q) MDS. However, the drugs had distinct effects on the production of erythroid progenitor colonies; dexamethasone selectively increased the number burst-forming units-erythroid (BFU-E), while lenalidomide specifically increased colony-forming units-erythroid (CFU-E). Use of the drugs in combination demonstrates that their effects are not redundant.

2011-04-28 | GSE28896 | GEO

p57Kip2 alterations in adult CFU-E contribute to steroid resistance in Diamond Blackfan anemia

Project description:Ashley R, Yan H, Wang N, Hale J, Dulmovits BM, Papoin J, Olive ME, Udeshi ND, Carr SA, Vlachosa A, Lipton JM, Da Costa L, Hillyer C, Kinet S, Taylor N, Mohandas N, Narla A, Blanc L. 2019. Despite the effective clinical use of steroids for the treatment of Diamond Blackfan anemia (DBA), the mechanistic bases via which glucocorticoids regulate human erythropoiesis remain poorly understood. Here, we report that the sensitivity of erythroid differentiation to dexamethasone (Dex) is dependent on the developmental origin of human CD34+ progenitor cells, specifically increasing the expansion of CD34+ progenitors from peripheral blood (PB) but not cord blood (CB). Dexamethasone treatment of erythroid-differentiated PB, but not CB, CD34+ progenitors resulted in the expansion of a novel CD34+CD36+CD71hiCD105med immature colony-forming unit-erythroid (CFU-E) population. Furthermore, proteomics analyses revealed the induction of distinct proteins in dexamethasone-treated PB and CB erythroid progenitors. Dexamethasone treatment of PB progenitors resulted in the specific upregulation of p57Kip2, a Cip/Kip cyclin-dependent kinase inhibitor, and we identified this induction as critical; shRNA-mediated downregulation of p57Kip2, but not the related p27Kip1, significantly attenuated the impact of dexamethasone on erythroid differentiation and inhibited the expansion of the immature CFU-E subset. Notably, in the context of DBA, we found that steroid resistance was associated with a dysregulated p57Kip2 expression. Altogether, these data identify a novel glucocorticoid-responsive human erythroid progenitor and provide new insights into glucocorticoid-based therapeutic strategies for the treatment of patients with DBA.

2019-11-23 | MSV000084614 | MassIVE

Isolation and Transcriptome Analyses of Human Erythroid Progenitors: BFU-E and CFU-E

Project description:Burst-forming unit-erythroid (BFU-E) and colony-forming unit-erythroid (CFU-E) cells are erythroid progenitors traditionally defined by colony assays. We developed a flow cytometry-based strategy for isolating human BFU-E and CFU-E cells based on the changes in expression of cell surface markers during in vitro erythroid cell culture. BFU-E and CFU-E are characterized by CD45+GPA-IL-3R-CD34+CD36-CD71low and CD45+GPA-IL-3R-CD34-CD36+CD71high phenotypes, respectively. Colony assays validated phenotypic assignment giving rise to BFU-E and CFU-E colonies, both at a purity ~90%. The BFU-E colony forming ability of CD45+GPA-IL-3R-CD34+CD36-CD71low cells required SCF and erythropoietin, while the CFU-E colony forming ability of CD45+GPA-IL-3R-CD34-CD36+CD71high cells required only erythropoietin. Bioinformatic analysis of the RNA-seq data revealed unique transcriptomes in each differentiation stage. The sorting strategy was validated in uncultured primary cells isolated from bone marrow and peripheral blood, indicating that marker expression is not an artifact of in vitro cell culture, but represents an in vivo characteristic of erythroid progenitor populations. The ability to isolate highly pure human BFU-E and CFU-E progenitors will enable detailed cellular and molecular characterization of these distinct progenitor populations and define their contribution to disordered erythropoiesis in inherited and acquired hematological disease. Our data provide important resource for future studies. Transcription profiles of Human erythroid progenitors at distinct developmental stages were generated by deep sequencing, in triplicate, using IlluminaHiSeq 2000. The complete dataset comprises 4 sample types: CD34, BFU, CFU, and Pro (reanalysis of GSM1304777-GSM1304779).

2014-10-30 | E-GEOD-61566 | biostudies-arrayexpress

Isolation and Transcriptome Analyses of Human Erythroid Progenitors: BFU-E and CFU-E

2014-10-30 | GSE61566 | GEO

Cereblon expression is required for the anti-myeloma activity of lenalidomide and pomalidomide [expression profiling]

Project description:The precise molecular mechanism of action and targets through which thalidomide and related immunomodulatory drugs (IMiDs) exert their anti-tumor effects remains unclear. We investigated the role of cereblon (CRBN), a primary teratogenic target of thalidomide, in the anti-myeloma activity of IMiDs. CRBN depletion is initially cytotoxic to human myeloma cells but surviving cells with stable CRBN depletion become highly resistant to both lenalidomide and pomalidomide, but not to the unrelated drugs bortezomib, dexamethasone and melphalan. Acquired deletion of CRBN was found to be the primary genetic event differentiating isogenic MM1.S cell lines cultured to be sensitive or resistant to lenalidomide and pomalidomide. Gene expression changes induced by lenalidomide were dramatically suppressed in the presence of CRBN depletion further demonstrating that CRBN is required for lenalidomide activity. Downstream targets of CRBN include interferon regulatory factor 4 (IRF4) previously reported to also be a target of lenalidomide. Patients exposed to and putatively resistant to lenalidomide had lower CRBN levels in paired samples before and after therapy. In summary, CRBN is an essential requirement for IMiD activity, and a possible biomarker for the clinical assessment of anti-myeloma efficacy. We included 15 samples from multiple myeloma cell lines.

2011-09-30 | E-GEOD-31421 | biostudies-arrayexpress

Single cell RNA sequencing of primary-isolated erythroid progenitors [BFUE, CFUE, intermediates]

Project description:Single cell RNA sequencing of freshly isolated mouse burst forming unit-erythroid (BFU-E) , colony forming unit-erythroid (CFU-E), and intermediate stages of erythroid development cells.

2019-03-01 | GSE117228 | GEO

Cereblon expression is required for the anti-myeloma activity of lenalidomide and pomalidomide [aCGH]

2011-09-30 | E-GEOD-31451 | biostudies-arrayexpress

Transcription profiling of human CD34+ hematopoietic cells grown in suspension culture or in a collegen I matrix

Project description:CD34+ hematopoietic stem/progenitor cells (HSC) reside in the bone marrow in close vicinity to the endosteal bone surface, surrounded by osteoblasts, stromal cells and various extracellular matrix molecules. We utilized a bioartificial matrix containing fibrillar collagen I, the major matrix component of bone, as scaffold for ex vivo expansion of HSCs. CD34+ HSCs were isolated from umbilical cord blood and cultivated within reconstituted collagen I fibrils in presence of FLT3-ligand, SCF and IL-3. After seven days of culture cell number, colony-forming units and gene expression profile of the cultured cells were assessed. Although the total expansion factor of CD34+ cells was slightly lower when cells were cultivated in the collagen I gel, the frequency of colony-forming units (CFU-C) increased compared to control suspension cultures. Gene expression analysis with microarray chip technology revealed the upregulation of more than 50 genes in presence of collagen I. Among them, genes for several growth factors, cytokines and chemokines (e.g. interleukin 8, MIP1-Î±) could be confirmed by quantitative PCR. Furthermore, increased expression of the negative cell-cycle regulator BTG2/TIS21 and an inhibitor of MAP kinase pathway, DUSP2, underline the regulatory role of the extracellular matrix. Together, these data show that the expansion of CD34+ cord blood cells in a culture system containing a three-dimensional collagen I matrix induces a qualitative change in the gene expression profile of cultivated HSCs. Experiment Overall Design: Gene expression profiling of CD34+ hematopoietic cells expanded in a collagen I matrix

2007-12-12 | E-GEOD-3003 | biostudies-arrayexpress

Single cell RNA sequencing of primary-isolated erythroid progenitors [BFUE & CFUE]

Project description:single cell RNA sequencing of freshly isolated mouse burst forming unit-erythroid (BFU-E) and colony forming unit-erythroid (CFU-E).

2019-03-01 | GSE117225 | GEO

Gene expression profiling of CD34+ hematopoietic cells expanded in a collagen I matrix

Project description:CD34+ hematopoietic stem/progenitor cells (HSC) reside in the bone marrow in close vicinity to the endosteal bone surface, surrounded by osteoblasts, stromal cells and various extracellular matrix molecules. We utilized a bioartificial matrix containing fibrillar collagen I, the major matrix component of bone, as scaffold for ex vivo expansion of HSCs. CD34+ HSCs were isolated from umbilical cord blood and cultivated within reconstituted collagen I fibrils in presence of FLT3-ligand, SCF and IL-3. After seven days of culture cell number, colony-forming units and gene expression profile of the cultured cells were assessed. Although the total expansion factor of CD34+ cells was slightly lower when cells were cultivated in the collagen I gel, the frequency of colony-forming units (CFU-C) increased compared to control suspension cultures. Gene expression analysis with microarray chip technology revealed the upregulation of more than 50 genes in presence of collagen I. Among them, genes for several growth factors, cytokines and chemokines (e.g. interleukin 8, MIP1-α) could be confirmed by quantitative PCR. Furthermore, increased expression of the negative cell-cycle regulator BTG2/TIS21 and an inhibitor of MAP kinase pathway, DUSP2, underline the regulatory role of the extracellular matrix. Together, these data show that the expansion of CD34+ cord blood cells in a culture system containing a three-dimensional collagen I matrix induces a qualitative change in the gene expression profile of cultivated HSCs. Keywords: hematopoietic stem/progenitor cells, collagen I, gene expression

2005-09-21 | GSE3003 | GEO

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