Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic analysis reveals HDAC1 regulates clinically relevant transcriptional programs in Pancreatic cancer

ABSTRACT: Genomic analysis reveals HDAC1 regulates clinically relevant transcriptional programs in Pancreatic cancer

PROVIDER: PRJNA862896 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Genomic analysis reveals HDAC1 regulates clinically relevant transcriptional programs in Pancreatic cancer

Project description:We performed ChIP-seq analysis on H3K27ac in MIA PaCa-2 cells with HDAC1 overexpression using the antibody Abcam H3K27ac (Abcam, ab4729), a non-targeting scrableled sgRNA control, and two replicates for each.

2023-05-31 | GSE209895 | GEO

Genomic analysis reveals HDAC1 regulates clinically relevant transcriptional programs in Pancreatic cancer.

Project description:Novel strategies are needed to combat multidrug resistance in pancreatic ductal adenocarcinoma (PDAC). We applied genomic approaches to understand mechanisms of resistance in order to better inform treatment and precision medicine. Altered function of chromatin remodeling complexes contribute to chemoresistance. Our study generates and analyzes genomic and biochemical data from PDAC cells overexpressing HDAC1, a histone deacetylase involved in several chromatin remodeling complexes. We characterized the impact of overexpression on drug response, gene expression, HDAC1 binding, and chromatin structure using RNA-sequencing and ChIP-sequencing for HDAC1 and H3K27 acetylation. Integrative genomic analysis shows that HDAC1 overexpression promotes activation of key resistance pathways including epithelial to mesenchymal transition, cell cycle, and apoptosis through global chromatin remodeling. Target genes are similarly altered in patient tissues and show correlation with patient survival. We also demonstrate that direct targets of HDAC1 that also show altered chromatin are enriched near genes associated with altered GTPase activity. HDAC1 target genes identified using in vitro methods and observed in patient tissues were used to develop a clinically relevant nine-transcript signature associated with patient prognosis. Integration of multiple genomic and biochemical data types enables understanding of multidrug resistance and tumorigenesis in PDAC, a disease in desperate need of novel treatment strategies.

| S-EPMC10666341 | biostudies-literature

10 Intellectual Disability samples for clinically relevant CNV detection

Project description:10 patients with Intellectual Disability diagnosed with a clinically relevant copy number change, selected to assess the dection performance of alternative platforms.

2013-08-01 | GSE46060 | GEO

10 Intellectual Disability samples for clinically relevant CNV detection

Project description:10 patients with Intellectual Disability diagnosed with a clinically relevant copy number change, selected to assess the dection performance of alternative platforms. 10 Affymetrix arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

2013-08-01 | E-GEOD-46060 | biostudies-arrayexpress

Uncovering the hidden threat: single-organoid analysis reveals clinically relevant treatment-resistant and invasive subclones in pancreatic cancer

Project description:Uncovering the hidden threat: single-organoid analysis reveals clinically relevant treatment-resistant and invasive subclones in pancreatic cancer

| PRJNA986451 | ENA

Advancing a Clinically Relevant Perspective of the Clonal Nature of Cancer

Project description:We used DNA content-based flow cytometry to distinguish and isolate nuclei from clonal populations in primary tissues from three disparate cancers with variable clinical histories. We then developed a methodology to adapt flow cytometrically purified nuclei samples for use with whole genome technologies including aCGH and next generation sequencing (NGS). Our results demonstrate that selected aberrations in the genomes of distinct clonal populations in each patient create clinically relevant contexts at least with respect to the cancer types profiled in this study. We applied DNA content based flow sorting to isolate the nuclei of clonal populations from tumor biopsies. Genomic DNA from each sorted population was amplified with phi29 polymerase. A 1ug aliquot of each amplified sample was digested with DNAse 1 then labeled with Cy5 using a Klenow-based commercial kit (Invitrogen). Each sample was hybridized with a pooled normal (46,XX) reference (Promega) to Agilent 244k CGH arrays. The use of highly purified objectively defined flow sorted populations provides high definition genomic profiles of clonal populations from pancreatic adenocarcinomas (PA), adrenal cortical carcinomas (ACC), and prostate adenocarcinomas (PC).

2011-07-04 | E-GEOD-21660 | biostudies-arrayexpress

Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture [Repli-Chip]

Project description:Human B-lineage precursor acute lymphoid leukemias (BCP-ALLs) comprise a group of genetically and clinically distinct disease entities with features of differentiation arrest at known stages of normal B-lineage differentiation. We previously showed BCP-ALL cells display unique and clonally heritable DNA-replication timing (RT) programs; i.e., programs describing the variable order of replication and sub-nuclear 3D architecture of megabase-scale chromosomal units of DNA in different cell types. To determine the extent to which BCP-ALL RT programs mirror or deviate from specific stages of normal human B-cell differentiation, we transplanted immunodeficient mice with quiescent normal human CD34+ cord blood cells and obtained RT signatures of the regenerating B-lineage populations. We then compared these with RT signatures for leukemic cells from a large cohort of BCP-ALL patients of varied genetic subtype and outcome. The results identify BCP-ALL subtype-specific features that resemble specific stages of B-cell differentiation and features that appear associated with relapse. These results suggest the genesis of BCP-ALL involves alterations in RT that reflect biologically significant and clinically relevant leukemia-specific epigenetic changes that have potential as a novel genre of prognostic biomarkers.

2019-12-27 | GSE130372 | GEO

Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture [Repli-Seq]

2019-12-27 | GSE130373 | GEO

Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment

Project description:Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment

| PRJNA362226 | ENA

Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups

Project description:Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups

| PRJNA259766 | ENA