In vivo dexamethasone-induced gene expression in pediatric acute lymphoblastic leukemia patient-derived xenografts
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ABSTRACT:
ORGANISM(S): Mus musculus Homo sapiens
PROVIDER: GSE57795 | GEO | 2014/05/20
SECONDARY ACCESSION(S): PRJNA248171
REPOSITORIES: GEO
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Project description:Glucocorticoids are critical components of combination chemotherapy regimens in pediatric acute lymphoblastic leukemia (ALL). The pro-apoptotic BIM protein is an important mediator of glucocorticoid-induced apoptosis in normal and malignant lymphocytes, while the anti-apoptotic BCL2 confers resistance. The signaling pathways regulating BIM and BCL2 expression in glucocorticoid-treated lymphoid cells remain unclear. In this study, pediatric ALL patient-derived xenografts (PDXs) inherently sensitive or resistant to glucocorticoids were exposed to dexamethasone in vivo. In order to understand the basis for differential in vivo glucocorticoid sensitivity of PDXs, microarray analysis of gene expression was carried out on 5 each of dexamethasone-sensitive and resistant PDXs . This provided a global understanding of dexamethasone-induced signaling cascades in ALL cells in vivo, and especialy identified the genes that are involved in transducing the apoptotic signal, upstream of BIM/BCL2 dynamic interactions. ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly. When >70% %huCD45+ engraftment in the peripheral blood was apparent, which occurred 8-10 weeks post-transplantation, mice were treated with either dexamethasone (15 mg/kg) or vehicle control by intra-peritoneal (IP) injection, and culled at 8 hours following the treatment. Cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation. RNA was extracted using the RNeasy Mini Kit (QIAGEN, Valencia, CA, USA), and RNA samples with integrity number (RIN) > 8.0 were amplified and hybridized onto Illumina HumanWG-6 v3 Expression BeadChips (6 samples/chip). All chips (with associated reagents) were purchased from Illumina, and scanned on the Illumina BeadArray Reader according to the manufacturer’s instructions. Microarray data were analyzed using the online modules in GenePattern. 10 xenografts were derived from patients of 5 dexamethasone-good responder and 5 dexamethasone-poor responder. Each xenograft was innoculated into 5-6 mice, and treated with dexamethasone (15 mg/kg) or vehicle control. In total spleen-harvest xenograft samples from 58 mice were analyzed using microarray.
2014-05-20 | E-GEOD-57795 | biostudies-arrayexpress
Project description:Glucocorticoids are critical components of combination chemotherapy regimens in pediatric acute lymphoblastic leukemia (ALL). However, the signaling pathways regulating apoptosis in glucocorticoid-treated lymphoid cells remain unclear. In this study, pediatric ALL patient-derived xenograft inherently sensitive to glucocorticoids were exposed to dexamethasone in vivo. Whole-genome GR binding sites and histone acetylation status were detected using chromatin immunoprecipitation sequencing analyses. This provided a global understanding of dexamethasone-induced DNA modulations in ALL cells in vivo, which is likely to be important in the understanding of mechanisms of glucocorticoid response in lymphoid malignancies. One xenograft (ALL-54) was derived from a patient of dexamethasone-good responder. The xenograft was innoculated into 2 NOD/SCID mice, and treated with dexamethasone (15 mg/kg) or vehicle control. Binding of glucocorticoid receptor (GR), histone acetylation and IgG control in spleen-harvest xenograft samples were detected using ChIP-seq.
2014-12-18 | E-GEOD-58266 | biostudies-arrayexpress
Project description:Glucocorticoids are critical components of combination chemotherapy regimens in pediatric acute lymphoblastic leukemia (ALL). However, the signaling pathways regulating apoptosis in glucocorticoid-treated lymphoid cells remain unclear. In this study, pediatric ALL patient-derived xenograft inherently sensitive to glucocorticoids were exposed to dexamethasone in vivo. Whole-genome GR binding sites and histone acetylation status were detected using chromatin immunoprecipitation sequencing analyses. This provided a global understanding of dexamethasone-induced DNA modulations in ALL cells in vivo, which is likely to be important in the understanding of mechanisms of glucocorticoid response in lymphoid malignancies.
2014-12-18 | GSE58266 | GEO
Project description:Glucocorticoids are an essential part of many multi-agent treatment regimens for lymphoid malignancies where the emergence of glucocorticoid resistance is a significant barrier to a cure. We have previously identified that aberrant chromatin accessibility, at lymphocyte-specific glucocorticoid-response elements (GREs), is associated with drug resistance in acute lymphoblastic leukaemia (ALL). To gain a deeper understanding of regulatory mechanisms leading to these epigenetic alterations, we conducted a multi-omics study, to examine changes in chromatin conformation, following the in-vivo treatment of patient-derived xenografts (PDXs) with glucocorticoid i.e., dexamethasone (DEX). We found that glucocorticoid treatment led to distinct patterns of topological associated domains (TADs) in DEX sensitive and resistant ALLs. Pre-treatment, these TADs were primed by a development-related pioneer transcription factor PU.1, which also occupied GREs in glucocorticoid sensitive but not resistant ALLs. PU.1 binding was associated with lymphocyte-specific activation of GREs and GRE-interacting super-enhancers within the TADs. Furthermore, the PU.1-associated TADs modulated epigenetics and promoted expression of multiple genes, including BIM, ZBTB16, RASA1 and other genes mediating glucocorticoid-induced apoptosis in ALL. The inhibition of PU.1 enhanced sensitivity of ALL cells to glucocorticoid treatment. Overall, this study illustrated a link between the lineage-specific efficiency of glucocorticoids and the developmental epigenetic modulators and provides insights into the role of fundamental epigenetics in clinical practice.
2024-10-08 | GSE236085 | GEO
Project description:Gamma-secretase inhibitors (GSIs), which block the activation of NOTCH receptors, are being tested in the treatment of T-cell acute lymphoblastic leukemia (T-ALL). Thus far, limited antileukemic cytotoxicity and severe gastrointestinal toxicity have restricted the clinical application of these targeted drugs. Here we show that combination therapy with GSIs plus glucocorticoids can improve the antileukemic effects of GSIs and reduce their gut toxicity in vivo. Inhibition of NOTCH1 signaling in glucocorticoid-resistant T-ALL restored glucocorticoid receptor auto-up-regulation and induced apoptotic cell death through induction of BIM expression. Additionally, cotreatment with glucocorticoids induced Ccnd2 upregulation in the gut which protected mice from the intestinal secretory metaplasia typically induced by loss of NOTCH signaling. These results support a role for glucocorticoids plus GSIs in the treatment of glucocorticoid-resistant T-ALL. Experiment Overall Design: Experiments analyzing the interacition of dexamethasone and the gamma-secretase inhibitor DBZ were carried out in 6-week-old C57/Black6 female mice (Jackson Laboratory). In these studies we treated mice with vehicle (DMSO) (n=2), dexamethasone (15 mg/kg) (n=2), DBZ (10 micromol/kg) (n=2) and dexamethasone (15 mg/kg) plus DBZ (10 micromol/kg) (n=2) daily by intraperitoneal injection for 5 days. At the end of the treatment, animals were euthanized and segments of the small intestine were collected and processed for RNA extraction, histological and immunohistochemical analysis.
2009-04-10 | E-GEOD-11184 | biostudies-arrayexpress
Project description:LC-MS data and DIA-NN search files relating to: PU.1 Eviction at Lymphocyte-Specific Chromatin Domains Mediates Glucocorticoid Response in Acute Lymphoblastic Leukemia.
Abstract: The epigenetic landscape plays a critical role in the onset and evolution of various malignancies, but its therapeutic utility remains underutilized. Glucocorticoids are an essential part of many multi-agent treatment regimens for lymphoid malignancies. However, the emergence of glucocorticoid resistance is a significant barrier to cure, which is in part due to epigenetic alterations, including aberrant chromatin accessibility and hypermethylation at lymphocyte-specific glucocorticoid-response elements (GREs). To gain a deeper understanding of regulatory mechanisms leading to these epigenetic alterations, we conducted a multi-omics study, including chromosome conformation capture sequencing (HiC), to examine changes in the 3D genome structure following the in vivo treatment of acute lymphoblastic leukemia (ALL) patient-derived xenografts (PDXs) with glucocorticoid. We found that glucocorticoid treatment led to distinct patterns of topologically associated domains (TADs) in glucocorticoid sensitive compared to resistant PDXs. Furthermore, we show that these TADs were primed by the development-related pioneer transcription factor PU.1, which extensively interacts with the glucocorticoid receptor (GR) exclusively in glucocorticoid-sensitive ALL PDXs. An integrative analysis of rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) and ChIP-seq revealed that PU.1 binding was associated with lymphocyte-specific activation of GREs and GRE-interacting super-enhancers. The PU.1-associated TADs modulated epigenetic marks, and particularly the eviction of PU.1 promoted GR binding and the expression of signature genes, including BIM, ZBTB16 and RASA1, mediating glucocorticoid-induced apoptosis in ALL. These findings were phenocopied using a PU.1 inhibitor DB2313 to restore glucocorticoid sensitivity in ALL. Taken together, this study identified a new epigenetic pathway integrating PU.1 priming and PU.1-GR interaction which ultimately leads to PU.1 eviction in ALL. This pathway provides the first link between the activity of a lineage-specific transcription factor and epigenetic modulators mediating the response to glucocorticoids and thus offers a new avenue to translate fundamental epigenetic research into the clinic.
2024-10-03 | MSV000096019 | MassIVE
Project description:Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types. This submission represents the WGBS component of the study.
2019-11-08 | GSE109948 | GEO
Project description:Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types. This submission represents the RNAseq component of the study.
2019-11-08 | GSE109947 | GEO
Project description:Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types. This submission represents the ChIPseq component of the study.
2019-11-08 | GSE109946 | GEO
Project description:Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types. This submission represents the ATACseq component of the study.
2019-11-08 | GSE109945 | GEO