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Transcription profiling of human fibroblasts from patients with HGPS compared to age matched controls treated both control and HGPS fibroblasts with a protein farnesyltransferase inhibitor (FTI)

ABSTRACT: We analyzed and compared global gene expression changes in fibroblasts from human subjects with HGPS compared to age matched controls. We then treated both control and HGPS fibroblasts with a protein farnesyltransferase inhibitor (FTI), a medication currently used in clinical trials to treat HGPS, to look for a reversal of the gene defects present in HGPS fibroblasts.

ORGANISM(S): Homo sapiens

DISEASE(S): Hutchinson Gilford Progeria Syndrome

SUBMITTER: Venkata Satagopam

PROVIDER: E-MEXP-2597 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of human Hutchinson-Gilord progeria syndrome fibroblast cell lines with dominant mutation in the LMNA gene and age-matched normal controls

Project description:Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease with widespread phenotypic features resembling premature aging. HGPS was recently shown to be caused by dominant mutations in the LMNA gene, resulting in the in-frame deletion of 50 amino acids near the carboxyl terminus of the encoded lamin A protein. Children with this disease typically succumb to myocardial infarction or stroke caused by severe atherosclerosis at an average age of 13 years. To elucidate further the molecular; pathogenesis of this disease, we compared the gene expression patterns of three HGPS fibroblast cell lines heterozygous for the LMNA mutation with three normal, age-matched cell lines. We defined a set of 361 genes (1.1% of the approximately 33 000 genes analyzed) that showed at least a 2-fold, statistically significant change. The most prominent categories encode transcription factors and extracellular matrix proteins, many of which are known to function in the tissues severely affected in HGPS. The most affected gene, MEOX2/GAX, is a homeobox transcription factor implicated as a negative regulator of mesodermal tissue proliferation. Thus, at the gene expression level, HGPS shows the hallmarks of a developmental disorder affecting mesodermal and mesenchymal cell lineages. The identification of a large number of genes implicated in atherosclerosis is especially valuable, because it provides clues to pathological processes that can now be investigated in HGPS patients or animal models. Experiment Overall Design: Three fibroblast cell lines derived from HGPS patients were compared to three control fibroblast cell lines using Affymetrix HG-U133A and HG-133B probe arrays. Triplicates were used for each cell line. Total RNA was used in the analysis. Quantitation was done by MAS 5.0 software (Affymetrix).

2007-12-12 | E-GEOD-3860 | biostudies-arrayexpress

SILAC pulse labeling in HGPS fibroblasts - HGPS samples

Project description:Premature aging disorders provide a lens through which to study the drivers of aging. In Hutchinson-Gilford progeria syndrome (HGPS) a mutant form of the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins. We used stable isotope labeling and quantitative mass spectrometry to investigate nuclear protein homeostasis in primary HGPS-derived cells.

2017-07-07 | PXD006016 | Pride

Project description:Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor site in exon 11, and leads to an in-frame deletion within the prelamin A mRNA and the production of a dominant negative lamin A protein, known as progerin. Here we show that HGPS cells experience genome-wide alterations in patterns of H3K27me3 deposition, changes in the associations of genomic loci with nuclear lamin A/C, and, at late passages, genome-wide loss of spatial compartmentalization of active and inactive chromatin domains that characterizes chromosome folding in normal cells. We further demonstrate that the H3K27me3 changes associate with gene expression alterations in HGPS cells. Our results support a model that the accumulation of progerin in the nuclear lamina leads to altered H3K27me3 marks in heterochromatin, possibly through the down-regulation of EZH2, and disrupts heterochromatin-lamina interactions. These changes may then lead to the genomic disorganization and changes in transcriptional regulation we observe in HGPS fibroblasts. ChIP-Seq was performed for H3K27me3 and lamin A/C in the human genome in three primary fibroblast cell lines: an HGPS patient (HGPS), normal cells from the father of the HGPS patient (Father), and age-matched normal cells (Age Control). Two biological replicates were performed.

2012-10-30 | E-GEOD-41757 | biostudies-arrayexpress

DNA methylation of fibroblasts from one HGPS patient

Project description:DNAm profiling of fibroblasts from one HGPS patient (6 years; 3 replicates assessed) and two healthy controls (12 and 15 years, each assessed in 2 replicates)

2023-10-26 | GSE196148 | GEO

Expression data from transformed WT and HGPS cell lines, including HGPS cells after knock-down of BRD4

Project description:Primary skin fibroblasts from a HGPS patient and an age-matched control wild-type individual were challenged in a standard transformation assay by retroviral introduction of TERT (T), V12-HRAS (R) and SV40 large and small T antigens (S). Knock-down of BRD4 in this TRS-HGPS cell line (TRS-HGPS-shBRD4) was achieved by retroviral introduction of independent shRNAs (shBRD4-1 to -3) Abstract: Advanced age and DNA damage accumulation are strong risk factors for cancer. The premature-aging disorder Hutchinson Gilford Progeria Syndrome (HGPS) provides a unique opportunity to study the interplay between DNA damage and aging-associated tumor mechanisms, since HGPS patients do not develop tumors despite elevated levels of DNA damage. Here, we have used HGPS patient cells to identify a protective mechanism to oncogenesis. We find that HGPS cells are resistant to neo-plastic transformation. This resistance is mediated by the bromodomain protein BRD4, which exhibits altered genome-wide binding patterns in transformation-resistant cells leading to inhibition of oncogenic de-differentiation. BRD4 also in-hibits, albeit to a lower extent, the tumorigenic potential of transformed cells from healthy individuals and BRD4-mediated tumor protection is clinically relevant, since a BRD4 gene signature predicts positive clinical outcome in breast and lung cancer. Our results demonstrate a protective function for BRD4 and suggest tissue-specific functions for BRD4 in tumorigenesis. 2 biological replicates are included for TRS-WT and TRS-HGPS cell lines. 3 biological replicates are included for TRS-HGPS-shBRD4 (derived from 3 independent shRNAs against BRD4)

2014-10-02 | E-GEOD-60519 | biostudies-arrayexpress

Expression data from transformed WT and HGPS cell lines, including HGPS cells after knock-down of BRD4

2014-10-02 | GSE60519 | GEO

RNA seq of HGPS treated cells

Project description:Evaluation of transcript levels in HGPS cells upon treatment with proteasome inhibitor

2017-06-18 | E-MTAB-5807 | biostudies-arrayexpress

DNA methylation of fibroblasts from one HGPS patient

Project description:DNA methylation of fibroblasts from one HGPS patient

| PRJNA803475 | ENA

SILAC pulse labeling in HGPS fibroblasts - WT samples

2017-07-07 | PXD006015 | Pride

Project description:Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease that is frequently caused by a de novo point mutation at position 1824 in LMNA. This mutation activates a cryptic splice donor site in exon 11, and leads to an in-frame deletion within the prelamin A mRNA and the production of a dominant negative lamin A protein, known as progerin. Here we show that HGPS cells experience genome-wide alterations in patterns of H3K27me3 deposition, changes in the associations of genomic loci with nuclear lamin A/C, and, at late passages, genome-wide loss of spatial compartmentalization of active and inactive chromatin domains that characterizes chromosome folding in normal cells. We further demonstrate that the H3K27me3 changes associate with gene expression alterations in HGPS cells. Our results support a model that the accumulation of progerin in the nuclear lamina leads to altered H3K27me3 marks in heterochromatin, possibly through the down-regulation of EZH2, and disrupts heterochromatin-lamina interactions. These changes may then lead to the genomic disorganization and changes in transcriptional regulation we observe in HGPS fibroblasts. Hi-C was performed on three primary fibroblast cell lines: an HGPS patient (passage 17 and 19; HGPS), normal cells from the father of the HGPS patient (passage 18; Father), and age-matched normal cells (passage 20; Age Control).

2012-10-30 | E-GEOD-41763 | biostudies-arrayexpress

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