Gene expression profiling of mouse HSPCs retrovirally transduced with Plzf
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE84771 | GEO | 2017/04/26
SECONDARY ACCESSION(S): PRJNA331123
REPOSITORIES: GEO
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Project description:To uncover gene programs that are regulated by PLZF in the early hematopoietic compartment, we performed micro array-based gene expression analysis of wild-type (WT) or PLZF-mutant (Zbtb16lu/lu) KSLs. DNA-microarrays were used to define and compare the transcriptional profiles of KSL cells isolated from Zbtb16lu/lu mice and WT mice (n=4).
2016-06-29 | E-MTAB-3682 | biostudies-arrayexpress
Project description:Natural killer (NKT) T cells exhibit tissue distribution, surface phenotype, and functional responses that are strikingly different from those of conventional T cells. The transcription factor PLZF is responsible for most of these properties, as its ectopic expression in conventional T cells is sufficient to confer to them an NKT-like phenotype. The molecular program downstream of PLZF, however, is largely unexplored. Here we report that PLZF regulates the expression of a surprisingly small set of genes, many with known immune functions. This includes several established components of the NKT cell developmental program. Transcriptional program downstream of PLZF in gammadelta NKT cells was analyzed by comparing wt, heterozygous and PLZF-deficient gammadelta NKT cells
2012-11-09 | E-GEOD-42168 | biostudies-arrayexpress
Project description:Natural killer (NKT) T cells exhibit tissue distribution, surface phenotype, and functional responses that are strikingly different from those of conventional T cells. The transcription factor PLZF is responsible for most of these properties, as its ectopic expression in conventional T cells is sufficient to confer to them an NKT-like phenotype. The molecular program downstream of PLZF, however, is largely unexplored. Here we report that PLZF regulates the expression of a surprisingly small set of genes, many with known immune functions. This includes several established components of the NKT cell developmental program.
2012-11-09 | GSE42168 | GEO
Project description:The PLZF-RARa fusion oncoprotein is overexpressed in the t(11;17) subtype of acute promyelocytic leukemia. Gene expression microarrays were used to identify genes involved in leukemic transformation. We used microarray to detect gene expression changes induced by the PLZF-RARa fusion oncoprotein in the U937 cell line Experiment Overall Design: The U937T:PLZF-RARa cell line was engineered to express PLZF-RARa upon tetracycline removal. PLZF-RARa was induced for 48hr and RNA was extracted and hybridized to Affymetrix HGU133Plus2.0 Chips
2009-12-05 | E-GEOD-18476 | biostudies-arrayexpress
Project description:The transcription factor PLZF (promyelocytic leukemia zinc finger) is encoded by the BTB domain-containing 16 (Zbtb16) gene. Its repressor function regulates specific transcriptional programs. During the development of invariant natural killer T (NKT) cells, PLZF is expressed and directs their effector program but the detailed mechanisms underlying PLZF regulation of multi-stage NKT cell developmental program are not well understood. This study investigated the role of acetylation-induced PLZF activation on NKT cell development by analyzing mice expressing a mutant form of PLZF mimicking constitutive acetylation (PLZFON mice). NKT populations in PLZFON mice were reduced in proportion and numbers of cells, and the cells present were blocked at the transition from developmental stage 1 to stage 2. NKT cell subset differentiation was also altered, with T-bet+ NKT1 and RORt+ NKT17 subsets dramatically reduced, and the emergence of a T-bet-RORt- NKT cell subset with features of cells in early developmental stages rather than mature NKT2 cells. Preliminary analysis of DNA methylation patterns suggested that activated PLZF acts on the DNA methylation signature to regulate NKT cells’ entry into the early stages of development, while repressing maturation. In wild-type NKT cells, deacetylation of PLZF is possible, allowing subsequent NKT cell differentiation. Interestingly, development of other innate lymphoid and myeloid cells, that are dependent on PLZF for their generation, is not altered in PLZFON mice highlighting lineage specific regulation. Overall, we propose that specific epigenetic control of PLZF through acetylation levels is required to regulate normal NKT cell differentiation. Key points: Constitutive acetylation of PLZF (PLZFON) blocks NKT cell development. PLZFON might act on the DNA methylation signature to control gene expression. PLZF acetylation levels regulate normal NKT cell differentiation.
2021-05-24 | GSE128558 | GEO
Project description:The transcription factor PLZF (promyelocytic leukemia zinc finger) is encoded by the BTB 42 domain-containing 16 (Zbtb16) gene. Its repressor function regulates specific transcriptional 43 programs. During the development of invariant natural killer T (NKT) cells, PLZF is 44 expressed and directs their effector program but the detailed mechanisms underlying PLZF 45 regulation of multi-stage NKT cell developmental program are not well understood. This 46 study investigated the role of acetylation-induced PLZF activation on NKT cell development 47 by analyzing mice expressing a mutant form of PLZF mimicking constitutive acetylation (PLZFON mice). NKT populations in PLZFON 48 mice were reduced in proportion and numbers 49 of cells, and the cells present were blocked at the transition from developmental stage 1 to stage 2. NKT cell subset differentiation was also altered, with T-bet+ NKT1 and RORJt + 50 NKT17 subsets dramatically reduced, and the emergence of a T-bet - RORJt - 51 NKT cell subset 52 with features of cells in early developmental stages rather than mature NKT2 cells. Analysis 53 of DNA methylation patterns indicated that activated PLZF establishes a unique DNA 54 methylation signature to regulate NKT cells’ entry into the early stages of development, while 55 repressing maturation. In wild-type NKT cells, deacetylation of PLZF alleviates this 56 repression and allows subsequent NKT cell differentiation. Interestingly, development of 57 other innate lymphoid and myeloid cells, that are dependent on PLZF for their generation, is not altered in PLZFON 58 mice highlighting lineage specific regulation. Overall, we propose that 59 specific epigenetic control of PLZF through acetylation levels is required to regulate normal 60 NKT cell differentiation.
2021-04-21 | GSE171984 | GEO
Project description:Diverse populations of natural killer cells, which exert critical early cytolytic functions against virally infected cells, have recently been uncovered, raising issues of lineage relationships. We used expression of the transcription factor PLZF to identify the developmental intermediates of ILC1s, a subset of natural killer-like cells that are particularly abundant in the liver, and demonstrated a distinct precursor but parallel development and partial overlap with established classical NK stages. Using microarray analysis, we defined a set of PLZF-dependent genes that contributed to the lineage divergence between ILC1s and classical NK cells. Liver lymphocytes from pools of PLZF+/+ or PLZF-/- mice were sorted into ILC1s and cNKs for RNA isolation and Illumina expression profiling.
2015-02-13 | E-GEOD-65898 | biostudies-arrayexpress
Project description:This study supports an active role for PLZF and RARα-PLZF in leukemogenesis, identifies upregulation of CRABPI as a novel mechanism contributing to retinoid resistance and reveals the ability of the reciprocal fusion gene products to mediate distinct epigenetic effects contributing to the leukemic phenotype. Keywords: Disease state analysis
2007-08-01 | GSE8510 | GEO
Project description:Sensitivity to Interferon (IFN) is determined by a complex coordination of genetic and environmental factors. A previous experiment using two renal cancer cell lines differing markedly in their response to IFN were analyzed for their ISG profiles in order to determine gene expression changes associated with IFN sensitivity (Holko M, Williams BR. Functional annotation of IFN-alpha-stimulated gene expression profiles from sensitive and resistant renal cell carcinoma cell lines. J Interferon Cytokine Res 2006 Aug;26(8):534-47). Higher and more persistent expression of a subset of ISGs was noted in the IFN-sensitive RCC1 cells when compared with the relatively IFN-insensitive ACHN cells. A subset of Interferon stimulated genes (ISGs) whose sustained expression correlates with heightened IFN sensitivity were analyzed for functional and sequence similarities. This subset predominately contains genes involved in transcription, and most were found to contain in their promoters binding sites for promyleocytic zinc finger factor (PLZF), a transcriptional repressor identified by virtue of its role in the etiology of Acute Promyelocytic Leukemia (APL). Analysis of gene expression in a lymphoid cell line with inducible PLZF expression reveals that increased expression of immune system related genes including ISGs, depends on PLZF expression. Chromatin Immunoprecipitation assays show direct association between PLZF and in silico identified PLZF binding sites in ISG promoters. This study reveals a novel interaction between PLZF and IFN signaling. A time course of IFNa treatment (0, 6, 16, 24 hrs) was performed in tetetracycline induced PLZF overexpressing and control U937T:PLZF45 cells. For the 0 hr time point, PLZF overexpression (Cy5) was compared with control cells (Cy3). For the 6, 16, and 24 hr IFN treated time points, treated RNA was labelled with Cy5 and non-IFN treated RNA with Cy3. Each IFN treatment time point was performed on control and PLZF-overexpressing cells respectively.
2010-05-18 | E-GEOD-16196 | biostudies-arrayexpress
Project description:PLZF (promyelocytic leukemia zinc finger) is a transcription factor acting as a global regulator of hematopoietic commitment. PLZF displays an epigenetic specificity by recruiting chromatin-modifying factors but little is known about its role in remodeling chromatin of cells committed towards a given specific hematopoietic lineage. In murine myeloid progenitors, we decipher a new role for PLZF in restraining active genes and enhancers by targeting acetylated lysine 27 of Histone H3 (H3K27ac). Functional analyses reveal that active enhancers bound by PLZF are involved in biological processes related to metabolism and associated with hematopoietic aging. Comparing the epigenome of young and old myeloid progenitors, we reveal that H3K27ac variation at active enhancers is a hallmark of hematopoietic aging. Taken together, these data suggest that PLZF, associated with active enhancers, appears to restrain their activity as an epigenetic gatekeeper of hematopoietic aging.
2018-12-21 | GSE124190 | GEO