Reprogramming of Human Fibroblasts into Hematopoietic Progenitors by Fusion With Human Fetal Liver CD34+ Cells (HuGene-1_0-st)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Vladislav Sandler
PROVIDER: E-GEOD-23413 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2016-07-06 | GSE73683 | GEO
Project description:Histone variants are important epigenetic regulators known to play a role in governing the processes of self-renewal and lineage specific differentiation . Phosphorylation of the histone variant H2A.X (γH2A.X) has historically been associated with DNA damage response, but more recent investigations have further demonstrated it’s role in cell cycle, aging and early development. Through both genetic and chemical targeting approaches, we now reveal a direct involvement of γH2A.X in hPSC self-renewal and differentiation decisions in vitro and in vivo. Namely, reduction of γH2A.X levels enhance hPSC differentiation toward mesodermal derivatives with concomitant inhibition of ectodermal derivatives. In contrast, ectopic expression of a constitutively phosphorylated mimic of γH2A.X enhanced hPSCs differentiation toward ectodermal fate while mesodermal differentiation was hindered. These phenotypic observations were associated with γH2A.X occupancy in the promoter regions of key regulatory genes associated with pluripotency and lineage choice. Our study suggests γH2A.X is a functional epigenetic pluripotency marker and novel target for guiding cell-fate commitment during differentiation.
2021-12-06 | GSE92643 | GEO
Project description:Short interfering RNAs (siRNA) are widely used as tool for gene inactivation in basic research and therapeutic applications. One of the major shortcomings of siRNA experiments are sequence-specific Off-target effects. Such effects are largely unpredictable because siRNAs can affect partially complementary sequences and function like microRNAs (miRNAs), which inhibit gene expression on mRNA stability or translational levels. Here we demonstrate that novel, enzymatically generated siRNA pools - referred to as siPools - containing up to 60 accurately defined siRNAs eliminate Off-target effects. This is achieved by the low concentration of each individual siRNA diluting sequence-specific Off-target effects below detection limits. In fact, whole transcriptome analyses reveal that single siRNA transfections can severely affect global gene expression. However, when complex siRNA pools are transfected, almost no transcriptome alterations are observed. Taken together, we present enzymatically-produced complex but accurately defined siRNA pools with potent On-target silencing but without detectable Off-target effects. To demonstrate the reduction of Off-target gene deregulation by use of complex siRNA pools (siPools), a single siRNA targeting human SCYL1 was transfected alone or in combination with 14 or 59 other siRNAs at a total siRNA concentration of 3 nM in human Hela cells. Mock transfected cells served as negative control. Every sample was tested in biological triplicates. Total RNA was extract 48h after transfection for affimetrix expression analysis.
2014-05-15 | E-GEOD-57667 | biostudies-arrayexpress
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2016-07-06 | E-GEOD-73683 | biostudies-arrayexpress
Project description:This is one of expressional parts of the study. These data were correlated to epigenetic marks and CG density of genes in analyzed cells. The whole study has a following summary: To elucidate possible roles of DNA methylation and chromatin marks in transcription, we performed epigenetic profiling of chromosome 19 in human bronchial epithelial cells (HBEC) and in the colorectal cancer cell line HCT116 as well as its counterpart with double knockout of DNMT1 and DNMT3B (HCT116-DKO). We found that H3K9me3 forms intragenic chromatin blocks along genes with low CpG density in the gene body. Analysis of H3K36me3 profiles indicated that this mark associates either with active genes with low CpG density and H3K9me3 in the gene body or with active genes with high CpG density and DNA hypermethylation in the gene body. In HCT116 cells with double knockout of DNMT1 and DNMT3B, transcription of genes with low CpG density in the gene body was highly elevated and associated with promoter DNA demethylation and rearrangement of H3K9me3 and H3K36me3 occupation. Our finding suggests that similar to DNA methylation, H3K9me3 may play a role in intragenic gene regulation. Further, we observed that a combination of low CpG density in gene bodies together with H3K9me3 and H3K36me3 marking is a specific epigenetic feature of zinc finger (ZNF) genes, which comprise 90% of all genes carrying both histone marks on chromosome 19. For high CpG density genes, transcription and H3K36me3 occupancy were not changed in condition of partial or intensive loss of DNA methylation in gene bodies in the HCT116-DKO cell line. siRNA experiments with SETD2 knockdown in both HBEC and HCT116-DKO cell lines failed to reduce DNA methylation in gene bodies under conditions of H3K36me3 depletion. Our study suggests that the H3K36me3 and DNA methylation marks in gene bodies are established independently from each other and points to similar functional roles of intragenic DNA methylation and intragenic H3K9me3 for CpG-rich and CpG-poor genes, respectively.
2011-03-31 | GSE26019 | GEO
Project description:Background: Ameloblast differentiation is the most critical stepwise process in amelogenesis and controlled by a precisely molecules synergistically. To better understand the molecular events defining cell differentiation between preameloblasts and secretory ameloblasts during amelogenesis, a more precise identification of molecules and signaling networks would shed light on the mechanisms governing enamel formation and help lay a foundation for enamel regeneration. Results: Gene expression profiles of human preameloblast and secretory ameloblast cells were obtained using human genome microarrays. From a total of 28,869 analyzed transcripts, 923 differentially expressed genes (DEGs) with FDR<0.01 and Fold-change > 2 were obtained. Among them, more than twice DEGs were found enriched in PAB (n = 647) compared with SAB (n = 276). Notably, 38 genes were identified significantly differentially expressed between PAB and SAB (Fold Change > 8). Comparison of transcriptional profiles of PAB and SAB together with KEGG pathway analysis revealed genes enrichment in PAB were chiefly involved in cell cycle control, DNA damage repair and apoptosis, while genes related to cell adhesion and extracellular matrix had elevated expression level in SAB. Two co-expression modules were further identified significantly associated with the ameloblast differentiation process by weighted gene co-expression network analysis (WGCNA).These gene networks seem to contribute to cell adhesion, tissue development, cell signaling and division. Furthermore, the co-expression associations of RunX2 and BMP8A were also observed in these modules. Conclusions: In this study, we uncovered that the differentiation from PAB to SAB may rely on a highly regulated network of interactions between conserved signal transduction pathways, including members of BMP/TGF-β, Notch, MAPK pathways to coordinate all aspects of ameloblast in intracellular processes and their social contexts. Specifically, expression of genes associated with cell cycle control, DNA damage repair, and apoptosis pathways regulates pre-ameloblast maturation during tooth development. And the SAB cells are regulated by several signaling pathways controlling enamel matrix proteins secretion and cell adhesion, which are critical for enamel formation and cell-cell interactions. Apart from showing the transcriptional patterns of PAB and SAB, the application of bioinformatic analysis also explored the potential key genes and gene-associations in ameloblast differentiation. These findings will aid in the design of new strategies to promote ameloblast functional differentiation in the regeneration and tissue engineering of teeth. Human tooth buds (18-22 weeks) were obtained from fetal cadaver tissue within 3 hours after legal abortion. Teeth were dissected from the mandibles under a laminar flow hood, embedded in OCT compound, and cryosectioned at 10-μm thickness. These sections were used for laser capture microdissection (LCM). In total of 3 pre-ameloblasts and 3 secretory ameloblasts pooled samples were used for RNA extraction and hybridization on Affymetrix microarray.
2014-10-01 | E-GEOD-59214 | biostudies-arrayexpress
Project description:Reprogramming of the human fibroblast genome into the state of the hematopoietic progenitors One sample analyzed.
2011-08-04 | E-GEOD-23415 | biostudies-arrayexpress