Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and YTHDF2 KD human umbilical cord blood CD34+ cell Transcriptomes
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE107956 | GEO | 2018/08/17
REPOSITORIES: GEO
Similar Datasets
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and YTHDF2 KD human umbilical cord blood CD34+ cell Transcriptomes
| PRJNA422166 | ENA
Project description:Human umbilical cord blood cells (UCB) is an important alternative resource for the hematopoietic stem cells in treatment of leukemia and other non-malignant diseases. The failure of hematopoiesis reconstruction by the UCB is known to be associated with several clinicopathological features of host patients. There are very few reports available, however, seeking for the association with the quality of umbilical cord blood cells (UCB) themselves. Here we try to address the quality of UCBs by transfusion to the lethally irradiated immunocompromized mice. The cryopreserved CD34+ UCBs cells from twelve different single human donors were transplanted to the irradiated NOD/shi-scid Jic mice. In parallel, total RNAs of the UCBs were subjected to the gene expression profiling with oligonucleotide microarrays. The UCBs from three donors failed to establish the engraftment in the host mice whereas other 9 UCBs succeeded to various extents. Oligonucleotide microarray analysis indicated that 71 genes, including HOXB4 and ETS2, were specifically overexpressed and 23 genes were suppressed more than 2 fold in the successful UCBs comparing with the failed ones (p<0.005, Student’s t-test). Functional annotation analyses revealed that the genes mediated cell growth and cell cycle regulations were enriched in successful UCBs comparing with the failed ones. Our results suggest that the hematopoiesis reconstitution ability may vary among the cryopreserved UCBs and the quality can be distinguished with certain sets of gene expression.
2010-07-15 | GSE19835 | GEO
Project description:The characteristics of global gene expression patterns during umbilical cord blood (UCB)-CD34+ stem cell-derived erythropoiesis are not clearly elucidated. In this study, UCB-stem cells were grown in liquid culture as a model for this process. We observed a high proliferative capacity of UCB-stem cells producing over 10 billion viable cells in culture. Normal erythroid maturation was confirmed by increased expression of CD71 and CD235a biomarkers. Furthermore, the gamma- to beta-globin gene switch was observed around day 45 indicating extended gamma-globin gene expression in fetal erythroid cells. To study global gene expression patterns, microarray analysis was performed on days 21, 42, 49 and 56. Forty-five transcription factors were silenced during the culture period (Profile-1) including CUX1 and HES5 among others. Conversely, 30 transcription factors were activated by day 56 (Profile-2) such as KLF1, GATA1, and MAFB. Both datasets were analyzed further using the MIMI Cytoscape platform which defined transcription factor networks around KLF4 and GATA2 from Profile-1 genes and KLF1 and GATA1 for Profile-2 genes. The characteristics of UCB-CD34+ stem cells including high proliferative capacity and prolonged gamma-globin expression combined with novel transcription factor networks suggest novel mechanisms of fetal UCB-stem cell-derived erythropoiesis.
2013-08-02 | GSE49438 | GEO
Project description:Introduction Fetal microchimerism could be involved in the regulation of breast cancer oncogenesis. CD34+ cells could be of a particular interest as up to 12% of the CD34+ population in maternal blood are of fetal origin. The aim of this research was to analyze the impact of umbilical cord blood (UCB) CD34+ on MCF-7 and MDA-MB-231 breast cancer cell lines. Material and Methods UCB CD34+ cells were obtained from healthy women at full-term delivery. Direct and indirect cultures were grown with MCF-7 and MDA-MB-231 cells. Proliferation, migration, invasion, and transcriptomic analysis of breast cancer cell lines were compared between cultures exposed and non-exposed to UCB CD34+ cells. Interactions between UCB CD34+ and breast cancer cells were analyzed under fluorescent microscopy. Functional analyses were generated with QIAGEN’s Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA). Results Direct contact between UCB CD34+ and breast cancer cell lines induced a reduction in the proliferative capacities of MCF-7 and MDA-MB-231 and diminished the migration abilities of MDA-MB-231 cells. In 3D co-culture, UCB CD34+ cells were attracted by tumor spheroids and incorporated into tumor cells. These cell-to-cell interactions were responsible for transcriptome modifications coherent with observed functional modifications. Among the cytokines secreted by UCB CD34+, INF- was identified as a potential upstream regulator responsible for the molecular modifications observed in transcriptomic analysis of MCF-7 breast cancer cells exposed to UCB CD34+ cells, as was IL-17A in MDA-MB-231 cells. Conclusion Direct cell-to-cell contact induces functional modifications in breast cancer cells. Interactions between UCB CD34+ and breast cancer cells could induce cell fusion and signal transmission via cytokines. Further analysis of direct cell-to-cell interactions should be performed at a molecular level to further understand the potential role of fetal CD34+ cells in breast cancer.
2024-02-08 | GSE224410 | GEO
Project description:Human umbilical cord blood cells (UCB) is an important alternative resource for the hematopoietic stem cells in treatment of leukemia and other non-malignant diseases. The failure of hematopoiesis reconstruction by the UCB is known to be associated with several clinicopathological features of host patients. There are very few reports available, however, seeking for the association with the quality of umbilical cord blood cells (UCB) themselves. Here we try to address the quality of UCBs by transfusion to the lethally irradiated immunocompromized mice. The cryopreserved CD34+ UCBs cells from twelve different single human donors were transplanted to the irradiated NOD/shi-scid Jic mice. In parallel, total RNAs of the UCBs were subjected to the gene expression profiling with oligonucleotide microarrays. The UCBs from three donors failed to establish the engraftment in the host mice whereas other 9 UCBs succeeded to various extents. Oligonucleotide microarray analysis indicated that 71 genes, including HOXB4 and ETS2, were specifically overexpressed and 23 genes were suppressed more than 2 fold in the successful UCBs comparing with the failed ones (p<0.005, Student’s t-test). Functional annotation analyses revealed that the genes mediated cell growth and cell cycle regulations were enriched in successful UCBs comparing with the failed ones. Our results suggest that the hematopoiesis reconstitution ability may vary among the cryopreserved UCBs and the quality can be distinguished with certain sets of gene expression. The gene expression in human umbilical cord blood cells (UCBs) was measured before transplantation to the lethally irradiated immunocompromized mice. UCBs from 12 individuals were examined.
2010-07-15 | E-GEOD-19835 | biostudies-arrayexpress
Project description:The characteristics of global gene expression patterns during umbilical cord blood (UCB)-CD34+ stem cell-derived erythropoiesis are not clearly elucidated. In this study, UCB-stem cells were grown in liquid culture as a model for this process. We observed a high proliferative capacity of UCB-stem cells producing over 10 billion viable cells in culture. Normal erythroid maturation was confirmed by increased expression of CD71 and CD235a biomarkers. Furthermore, the gamma- to beta-globin gene switch was observed around day 45 indicating extended gamma-globin gene expression in fetal erythroid cells. To study global gene expression patterns, microarray analysis was performed on days 21, 42, 49 and 56. Forty-five transcription factors were silenced during the culture period (Profile-1) including CUX1 and HES5 among others. Conversely, 30 transcription factors were activated by day 56 (Profile-2) such as KLF1, GATA1, and MAFB. Both datasets were analyzed further using the MIMI Cytoscape platform which defined transcription factor networks around KLF4 and GATA2 from Profile-1 genes and KLF1 and GATA1 for Profile-2 genes. The characteristics of UCB-CD34+ stem cells including high proliferative capacity and prolonged gamma-globin expression combined with novel transcription factor networks suggest novel mechanisms of fetal UCB-stem cell-derived erythropoiesis. Cd34 cell from umbilical cord blood were grown in three independent cultures using the one-phase protocol. Cells were cultured in aMEM containing 30% fetal bovine serum, 1% deionized BSA with penicillin (100 U/mL) and streptomycin (0.1 mg/mL) at 37°C and 5% CO2. The following growth factors were added on day 0: stem cell factor (50 ng/mL), interleukin-3 (10 ng/mL) and erythropoietin (4 U/mL). Approximately 1.5 million cells were harvested from each culture (triplicate samples) on day 21, 42, 49 and 56 for microarray analysis on the whole-genome Illumina HumanWG-12 V4 Expression BeadChip.
2013-08-02 | E-GEOD-49438 | biostudies-arrayexpress
Project description:We found that the experssion of STAT5A was upregulated when the YTHDF2 was knocked down. To identify the function of STAT5A protein as a Transcription factor in YTHDF2 kockdown(KD) and wildtype(WT) cells in Multiple Myeloma. CHIP-seq was conducted to analyze changes in related signaling pathways and gene expression in Multiple Myeloma cells when YTHDF2 was knocked down.
2022-06-30 | GSE163138 | GEO
Project description:Umbilical cord blood (UCB) is a valuable source of hematopoietic stem cells (HSCs) for use in allogeneic transplantation. Key advantages of UCB are rapid availability and less stringent requirements for HLA matching. However, UCB contains an inherently limited HSC count, which is associated with delayed time to engraftment, high graft failure rates and early mortality. 16,16 dimethyl prostaglandin E2 (dmPGE2) was previously identified to be a critical regulator of HSC homeostasis and we hypothesized that a brief ex vivo modulation could improve patient outcomes by increasing the “effective dose” of HSCs. Molecular profiling with Affymetrix GeneChips were used to determine the optimal ex vivo modulation conditions (e.g., temperature and media) for use in a clinical setting by measured pathway induced expression changes. Isolated human CD34+ from umbilical cord blood were incubated ex vivo in Stem Span (SS) media evaluating three treatment temperatures (4 deg C, 25 deg C, and 37 deg C) with 10uM 16,16-dmPGE2 or Vehicle (DMSO) for 2 hours. To evaluate optimal media, similar CD34+ cells were incubated ex vivo in either Stem Span-SFEM (SS) media or 8% Low Molecular Weigh Dextran 40/5% HSA solution (LMD/HSA) with 10uM 16,16-dmPGE2 or Vehicle (DMSO) for 2 hours at 37 deg C. Total RNA was isolated post incubation and analyzed on Affymetrix microarrays for pathway activation.
2013-09-12 | E-GEOD-46569 | biostudies-arrayexpress
Project description:Evidence for the epigenetic regulation of hematopoietic stem cells (HSCs) is growing, but the genome-wide epigenetic signature of HSCs and its functional significance remain unclear. In this study, we used high-resolition (Agilent, CpG Island ChIP-on-chip) platforms for genome-wide comparison of CpG methylation in human CD34+ and CD34- cells.
2009-08-29 | GSE17833 | GEO
Project description:YTHDF2 kockdown(KD) and wildtype(WT) cells in Multiple Myeloma
| PRJNA685044 | ENA