Gene expression analysis of Pax5-/- proB cells transduced with control or EBF retrovirus.
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE9878 | GEO | 2007/12/15
SECONDARY ACCESSION(S): PRJNA103869
REPOSITORIES: GEO
Similar Datasets
Project description:We have determined that sustained expression of EBF suppresses alternate lineage genes independently of Pax5. Experiment Overall Design: Pax5-/- pro-B cells transduced with control or EBF retrovirus. Transduced cells were FACS sorted based on GFP expression and total RNA was isolated. RNA isolated from control or EBF transduced cells was analyzed using the Affymetrix Rat 230A microarrays.
2008-06-16 | E-GEOD-9878 | biostudies-arrayexpress
Project description:In order to investigate how transcription factor dose impacts B-lymphocyte development, we generated mice carrying transheterozygous mutations in the Pax5 and Ebf1 genes. While combined reduction of Pax5 and Ebf1 dose had minimal impact on the development of the earliest CD19+ progenitors, these cells displayed an increased T-cell potential in vivo and in vitro. Alteration in lineage fate depended on a Notch1 mediated conversion process while no signs of de-differentiation could be detected. The differences in functional response to Notch signaling in Wt and Pax5+/-Ebf1+/- pro-B cells was reflected in the transcriptional response because even though cells of both genotypes responded by the generation of intracellular Notch1 and activation of a set of target genes, only the Pax5+/-Ebf1+/- pro-B cells down-regulated genes central for the preservation of stable B-cell identity. This report stresses the importance of transcription factor dose in lymphocyte development and suggests that Pax5 and Ebf1 collaborate to modulate the transcriptional response to Notch signaling after the generation of activated intracellular Notch1. This provides an insight to how transcription factors like Ebf1 and Pax5 preserve cellular identity during differentiation. EBF-1 ChIP-seq: Cultivated CD43+IgM- cells (ProB) cells from Wt, EBF-1 +/-, PAX-5 +/- and EBF-1 +/- PAX-5 +/- (TH) were assessed for EBF-1 binding by ChIP-seq. Replicate Ebf1 ChIP-seq runs on each genotype (Wt, TH, Ebf1+/- and Pax5+/-) and corresponding inputs were pooled into one dataset and analyzed as one combined sample per genotype. RNA-seq no treatment: Briefly, ProB-cells from C57BL/6J Ebf1+/-Pax5+/- (n=4), WT (n=4), Ebf1+/- (n=2) and Pax5+/- (n=2) were sorted and RNA extracted with Qiagen RNeasy Micro Kit. RNA was sent to UCLA Microarray Core for library preparation and were subsequently for 50 cycles of HiSeq 2000 SBS sequencing generating 20-30 million reads/sample. Data analysis was performed with Arraystar® (DNASTAR)). RNA-seq 1 day on OP9DL1 and OP9: In short, in vitro expanded ProB-cells from C57BL/6J Ebf1+/-Pax5+/- (n=4) and WT (n=4) were exposed either on OP9 or OP9-DL1 stromal cells for 24 hours and RNA extracted with Qiagen RNeasy Micro Kit. Due to low reads, two Wt and Ebf1+/-Pax5+/- were sequenced twice. Libraries were constructed using Nugen's Ovation Ultralow Library systems and were subsequently for 50 cycles of NextSeq500 sequencing generating 20-30 million reads/sample. Data analysis was performed with Arraystar® (DNASTAR)).
2015-05-27 | E-GEOD-69227 | biostudies-arrayexpress
Project description:EBF1 and PAX5 are crucial factors for B-cell development. Knock down of either factor leads to an arrest in differentiation. RNA-seq data of WT, Ebf1-/- and Pax5-/- FL-ProB cells allowed for identification of activated and repressed target genes. ATAC-seq data of corresponding cell populations could connect gene activity and chromatin accessibility. This finding provided an explanation to the lineage instability observed in early B-cell progenitors. Taken together, the reported data provide an increased insight into mechanisms governing regulation of stage- and lineage specific transcription in early B-lymphocyte development.
2018-06-08 | GSE92434 | GEO
Project description:we have investigated molecular and functional properties in early B-lineage cells from Pax-5 deficient animals crossed to a B-lineage restricted reporter mouse. Gene expression analysis of ex vivo isolated progenitor cells revealed that Pax-5 deficiency has a minor impact on Bcell specification.By comparison of gene expression patterns in ex vivo isolated Pax-5 and Ebf-1 deficient progenitors, it was possible to identify a set of B-cell restricted genes dependent of Ebf-1 but not Pax-5, supporting the idea that B-cell specification and commitment is controlled by distinct regulatory networks.
2012-07-23 | GSE39554 | GEO
Project description:we have investigated molecular and functional properties in early B-lineage cells from Pax-5 deficient animals crossed to a B-lineage restricted reporter mouse. Gene expression analysis of ex vivo isolated progenitor cells revealed that Pax-5 deficiency has a minor impact on Bcell specification.By comparison of gene expression patterns in ex vivo isolated Pax-5 and Ebf-1 deficient progenitors, it was possible to identify a set of B-cell restricted genes dependent of Ebf-1 but not Pax-5, supporting the idea that B-cell specification and commitment is controlled by distinct regulatory networks. wt ?5 reporter+ and Pax5ko ?5reporter+ fetal liver from d15 embryos isolated and transplanted into sublethaly irradiated mice. After 4 weeks B220+?5+ cells were sorted out from the bone marrow of the mice and subjected to microarray analyses
2012-07-22 | E-GEOD-39554 | biostudies-arrayexpress
Project description:Pax5 controls B-cell commitment, development and immunity by repressing B-lineage-inappropriate genes and activating B-cell-specific genes. In addition to the N-terminal DNA-binding paired domain, Pax5 contains a conserved octapeptide, partial homeodomain and C-terminal sequences with transactivating and inhibitory potential. To understand how the C-terminal domains of Pax5 contribute to the repression and activation function of Pax5, we performed Pax5 pulldown combined with mass spectrometry to identify coactivator or corepressor complexes that bind to the C-terminal regions of Pax5.
2023-08-24 | PXD040424 | Pride
Project description:B lymphopoiesis is a key developmental event orchestrated by a complex combinatorial action of lineage-specific transcription factors. In early B cell progenitors, lineage commitment is directly mediated by the master regulator PAX5, whose deficiency is commonly associated with B cell Acute Lymphoblastic Leukemia (B-ALL). Despite its essential role in mammalian immunity, the regulatory mechanisms that control PAX5 function remain largely unknown. Here we show that NAD+-dependent enzyme SIRT7 coordinates B cell development progression through PAX5. We have identified a SIRT7-dependent regulatory switch based on dynamic deacetylation of a single PAX5 residue, which controls its activity and thereby B cell fate. While a PAX5K198 acetylated mimic is incapable of inducing both B cell development and identity due to reduced protein stability and impaired binding to chromatin, deacetylation of this residue boosts PAX5 activity, leading to massive gene repression and in vivo restoration of B cell commitment but not differentiation. These findings suggest an unexpected uncoupling of hematopoietic differentiation and lineage commitment. Further supporting the functional relevance of the SIRT7-PAX5 axis, the interplay between both factors is conserved in human B-ALL, where high SIRT7 expression is an independent good prognostic factor. Our findings unveil a crucial mechanism in the regulation of B cell production based on the control of PAX5 function and underscore the key role of Sirtuins in the regulation of the immune system.
2024-09-20 | PXD046457 | Pride
Project description:Neuroendocrine-like differentiation of castration-resistant prostate cancer is highly aggressive and independent of the androgen receptor signaling for its progression. During such lineage differentiation, adenocarcinoma adopts basal and neuronal characteristics that alter its clinical progression, limiting its therapeutic opportunities. Inadequate understanding of the molecular mechanism for such transformation also restricts its targeted therapies. Using ATAC-Seq, acetylated-histone ChIP-seq, and RNA-seq, we have characterized the early transformation process and identified chromatin occupancy and gene expression differences between adenocarcinoma and neuroendocrine-like cancer cells. By comparing differentially active promoter signatures during lineage-specific transcriptional events, our results indicate that the transcription factor Pax5 plays a major role in the trans-differentiation processes. Using LuCaP PDX tissues and metastatic prostate cancer TMA, in conjunction with patient RNA-expression databases, we validated that Pax5 is selectively expressed only in neuroendocrine like cancer but not in adenocarcinoma. Further analysis reveals that Pax5 expression is involved in neuronal gene expression and critical for imparting therapy resistance. Further, our results indicate that increased hydroxymethylation at the Pax5 promoter leads to recruitment of the homeobox transcription factor Pbx1 for Pax5 transcription. This is in line with our findings that lineage-specific expression of Pbx1/Pax5 is associated with the development of neuroendocrine-like differentiation. Our study suggests, upon continuous exposure to anti-androgen therapeutic stress, chromatin modifications are associated with Pax5-mediated gene expression to adopt neuroendocrine-like characteristics of advanced prostate cancer.
2024-07-25 | GSE210844 | GEO
Project description:Neuroendocrine-like differentiation of castration-resistant prostate cancer is highly aggressive and independent of the androgen receptor signaling for its progression. During such lineage differentiation, adenocarcinoma adopts basal and neuronal characteristics that alter its clinical progression, limiting its therapeutic opportunities. Inadequate understanding of the molecular mechanism for such transformation also restricts its targeted therapies. Using ATAC-Seq, acetylated-histone ChIP-seq, and RNA-seq, we have characterized the early transformation process and identified chromatin occupancy and gene expression differences between adenocarcinoma and neuroendocrine-like cancer cells. By comparing differentially active promoter signatures during lineage-specific transcriptional events, our results indicate that the transcription factor Pax5 plays a major role in the trans-differentiation processes. Using LuCaP PDX tissues and metastatic prostate cancer TMA, in conjunction with patient RNA-expression databases, we validated that Pax5 is selectively expressed only in neuroendocrine like cancer but not in adenocarcinoma. Further analysis reveals that Pax5 expression is involved in neuronal gene expression and critical for imparting therapy resistance. Further, our results indicate that increased hydroxymethylation at the Pax5 promoter leads to recruitment of the homeobox transcription factor Pbx1 for Pax5 transcription. This is in line with our findings that lineage-specific expression of Pbx1/Pax5 is associated with the development of neuroendocrine-like differentiation. Our study suggests, upon continuous exposure to anti-androgen therapeutic stress, chromatin modifications are associated with Pax5-mediated gene expression to adopt neuroendocrine-like characteristics of advanced prostate cancer.
2024-07-25 | GSE210847 | GEO
Project description:Neuroendocrine-like differentiation of castration-resistant prostate cancer is highly aggressive and independent of the androgen receptor signaling for its progression. During such lineage differentiation, adenocarcinoma adopts basal and neuronal characteristics that alter its clinical progression, limiting its therapeutic opportunities. Inadequate understanding of the molecular mechanism for such transformation also restricts its targeted therapies. Using ATAC-Seq, acetylated-histone ChIP-seq, and RNA-seq, we have characterized the early transformation process and identified chromatin occupancy and gene expression differences between adenocarcinoma and neuroendocrine-like cancer cells. By comparing differentially active promoter signatures during lineage-specific transcriptional events, our results indicate that the transcription factor Pax5 plays a major role in the trans-differentiation processes. Using LuCaP PDX tissues and metastatic prostate cancer TMA, in conjunction with patient RNA-expression databases, we validated that Pax5 is selectively expressed only in neuroendocrine like cancer but not in adenocarcinoma. Further analysis reveals that Pax5 expression is involved in neuronal gene expression and critical for imparting therapy resistance. Further, our results indicate that increased hydroxymethylation at the Pax5 promoter leads to recruitment of the homeobox transcription factor Pbx1 for Pax5 transcription. This is in line with our findings that lineage-specific expression of Pbx1/Pax5 is associated with the development of neuroendocrine-like differentiation. Our study suggests, upon continuous exposure to anti-androgen therapeutic stress, chromatin modifications are associated with Pax5-mediated gene expression to adopt neuroendocrine-like characteristics of advanced prostate cancer.
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