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Enhancement of direct reprogramming from fibroblasts to epithelial lineages by OVOL2-induced mesenchymal-to-epithelial transition [ATAC-seq]

ABSTRACT: Mesenchymal-to-epithelial transition (MET) is an important step in cell reprogramming from fibroblast, a most frequently used cell type for this purpose, to various epithelial cell types. However, how MET can be induced in fibroblast has not been fully studied. In this study, we sought for transcription factors (TFs) that can efficiently induce MET in dermal fibroblasts and identified OVOL2 as a potent inducer of key epithelial genes. In addition, OVOL2 cooperatively enhanced MET induced by HNF1A, TP63 and KLF4, known reprogramming TFs to epithelial lineages. In TP63/KLF4-induced fibroblast-keratinocyte cell reprogramming, OVOL2 greatly facilitated activation of epithelial genes as well as keratinocyte-specific genes. This enhancement of epithelial gene expression program was accompanied by enhanced changes in chromatin accessibility across the genome. Mechanistically, motif enrichment analysis revealed that target loci of KLF4 and TP63 become accessible upon reprogramming while OVOL2 target loci become inaccessible, indicating that KLF4 and TP63 positively regulate their targets while OVOL2 primarily induces closed chromatin state at its target loci. Thus, OVOL2 and tissue-specific reprogramming factors cooperatively facilitate cell reprogramming of fibroblast into epithelial lineages through distinct mechanisms.

ORGANISM(S): Homo sapiens

PROVIDER: GSE122035 | GEO | 2019/05/17

REPOSITORIES: GEO

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Enhancement of direct reprogramming from fibroblasts to epithelial lineages by OVOL2-induced mesenchymal-to-epithelial transition [CAGE]

Project description:Mesenchymal-to-epithelial transition (MET) is an important step in cell reprogramming from fibroblast, a most frequently used cell type for this purpose, to various epithelial cell types. However, how MET can be induced in fibroblast has not been fully studied. In this study, we sought for transcription factors (TFs) that can efficiently induce MET in dermal fibroblasts and identified OVOL2 as a potent inducer of key epithelial genes. In addition, OVOL2 cooperatively enhanced MET induced by HNF1A, TP63 and KLF4, known reprogramming TFs to epithelial lineages. In TP63/KLF4-induced fibroblast-keratinocyte cell reprogramming, OVOL2 greatly facilitated activation of epithelial genes as well as keratinocyte-specific genes. This enhancement of epithelial gene expression program was accompanied by enhanced changes in chromatin accessibility across the genome. Mechanistically, motif enrichment analysis revealed that target loci of KLF4 and TP63 become accessible upon reprogramming while OVOL2 target loci become inaccessible, indicating that KLF4 and TP63 positively regulate their targets while OVOL2 primarily induces closed chromatin state at its target loci. Thus, OVOL2 and tissue-specific reprogramming factors cooperatively facilitate cell reprogramming of fibroblast into epithelial lineages through distinct mechanisms.

2019-05-17 | GSE122034 | GEO

Transcription factors OVOL1 and OVOL2 induce the mesenchymal to epithelial transition in human cancer

Project description:This paper shows, for the first time, a novel function of the OVO-like proteins (OVOL1and OVOL2) as critical inducers of mesenchymal to epithelial transition (MET) in human cancer. Examination of the effects of OVOL1 and OVOL2 overexpression in a prostate cancer model.

2013-08-01 | E-GEOD-48230 | biostudies-arrayexpress

Gene expression changes by exogenous expression of epithelial-to-mesenchymal (EMT)-inducing transcription factors (Snail and Zeb1) and mesenchymal-to-epithelial transition (MET)-inducing transcription factor (Ovol2) in MCF10A cells

Project description:Multiple EMT-promoting/inhibiting transcription factors have been identified including Snail, Zeb1 and Ovol2. To understand differential roles of these factors, we performed gene expression profiling by RNA-seq upon Snail-/Zeb1-induced EMT or Ovol2-induced MET in human mammary epithelial MCF10A cells.

2019-07-01 | GSE70551 | GEO

Expression profile of early stage in OKS mediated reprogramming regulated by Sox2 and Klf4

Project description:Klf4 and Sox2 are among the core reprogramming factor, and have different function in reprogramming. Klf4 is supposed to trigger MET in the early stage of reprogramming ,Sox2 is well known plutipotent relative gene. Klf4 and Sox2 play important role in induced reprogramming. We performed this experiment to identify the targets regulated by Sox2 and Klf4 respectively.

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Transcription factors OVOL1 and OVOL2 induce the mesenchymal to epithelial transition in human cancer

2013-08-01 | GSE48230 | GEO

Gene expression analysis during reprogramming with sequential infecion of Oct4/Klf4/cMyc/Sox2

Project description:To further understand the mechanism of reprogramming, the mouse embryonic fibroblast cells were infected with Oct4, Klf4, c-Myc and Sox2 with special sequence. 1) Oct4 and Klf4 containing retrovirus was delivered on day 0. 2) Oct4, Klf4 and c-Myc were delivered on Day 1.5. 3) c-Myc and Sox-2 were deivered on Day 3. 4) Sox2 were delivered on Day 4.5. 5) Vitamin C containging medium were used from Day 6. The gene expression of Day 0 (MEF), Day 1.5, Day 3, Day 4.5 and Day 6 were analyzed with micro array to indentify the possible underlying mechanism. Especially the factors related to MET/EMT, cell cycle and epigenetic were focused. MEF cells were subjected for reprogramming with special protoocl: 1) Oct4 and Klf4 containing retrovirus were delivered on day 0. 2) Oct4, Klf4 and c-Myc were delivered on Day 1.5. 3) c-Myc and Sox-2 were deivered on Day 3. 4) Sox2 were delivered on Day 4.5. 5) Vitamin C containging medium were used from Day 6. RNA on Day 0 (MEF), Day 1.5, Day 3, Day 4.5 and Day 6 were collected for analysis.

2012-07-11 | E-GEOD-39260 | biostudies-arrayexpress

Gene expression data of fibroblasts transduced with LacZ or p63+KLF4.

Project description:To determine if fibroblasts could be reprogrammed to a keratinocyte phenotype p63+KLF4 or LacZ expressing retroviruses were transduced into primary human neonatal fibroblasts. Global gene expression profiling using U133 plus 2.0 arrays were used to deteremine the extent of reprogramming to a keratinocyte phenoypte upon transduction with p63+KLF4. Fibroblasts transduced with p63+KLF4 were also treated +/- high calcium to determine if treatment with calcium could induce differentiation of these cells. Microarray analysis was also performed on cells treated +/- calcium. For gene expression profiling, cultured human fibroblasts were infected with LacZ or p63+KLF4 expressing retroviruses. p63+KLF4 cells were also treated +/- calcium. Microarray analysis using Affymetrix HG-U133 2.0 plus arrays was performed on duplicate samples.

2013-11-03 | E-GEOD-47746 | biostudies-arrayexpress

Gene expression analysis during reprogramming with sequential infecion of Oct4/Klf4/cMyc/Sox2

2012-07-12 | GSE39260 | GEO

Gene expression data of fibroblasts transduced with LacZ or p63+KLF4.

2013-11-03 | GSE47746 | GEO

Alternative routes to induced pluripotent stem cells revealed by reprogramming of neural lineage

Project description:During the reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells, the activation of pluripotency genes such as Nanog occurs after the mesenchymal to epithelial transition (MET). Here we report that both adult stem cells (neural stem cells- NSCs) and differentiated cells (astrocytes) of the neural lineage can activate Nanog in the absence of cadherin expression during reprogramming. Gene expression analysis revealed that only the Nanog+Ecadherin+ populations expressed stabilization markers and had upregulated several cell cycle genes; and were transgene independent. Inhibition of Dot1L activity, which has previously been shown to increase MET, enhanced both the numbers of Nanog+ and Nanog+E-cadherin+ colonies, suggesting a MET independent pathway for activation of Nanog in NSCs. Expressing Sox2 in MEFs prior to reprogramming does not alter the ratio of Nanog colonies that express E-cadherin obtained. Taken together these results provide a novel pathway for reprogramming taken by cells of the neural lineage. Neural Stem Cells (NSCs) were induced to reprogram by the induction of Oct4, Sox2, c-Myc and Klf4. Reprogramming colonies that expressed either Nanog alone (N+E-) or Nanog and E-cadherin (N+E+) were sorted by flow cytometry and used as input for RNA-sequencing. There are 3 replicates each for the N+E- and N+E+ samples.

2016-02-18 | E-GEOD-76130 | biostudies-arrayexpress

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