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Transcriptome Signatures of Sezary Cells from Patients and Cultured Hut 78, Hut 102 and Jurkat Cells

ABSTRACT: Comparative transcriptome profiles of patient-derived Sezary cells and cultured Sezary cell line (Hut78) mycosis fungoides cell line (Hut 102) and non-Sezary T cell leukemia cell line (Jurkat) relative to benign CD4+ T cells from individuals with no T cell malignancy. There are three goals. The first and primary goal is to establish a list of genes with differential expression between Sezary cells and the benign CD4+ T cell counter part from individuals without Sezary syndrome. A secondary goal is to examine if these differentially expresses genes in clinical samples of Sezary cells are preserved in Hut78 and Hut102 cells, which are the two most frequently used experimental cell models of Sezary cells in the research community. The third goal is to examine if these Sezary cell specific genes are also present in a non-Sezary T cell malignancy, such as Jurkat cells, which is derived from a non-Sezary cell T cell leukemia patient. Two color experiment, 6 biological replicates (6 unique patients) with Sezary syndrome, 1 Hut78 cell,1 Hut102 cell and 1 Jurkat cell lines as the experimental samples, each compared with a distinct individual with no T cell malignancy of the skin or the blood.

ORGANISM(S): Homo sapiens

SUBMITTER: Youwen Zhou

PROVIDER: E-GEOD-23113 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome Signatures of Sezary Cells from Patients and Cultured Hut 78, Hut 102 and Jurkat Cells

Project description:Comparative transcriptome profiles of patient-derived Sezary cells and cultured Sezary cell line (Hut78) mycosis fungoides cell line (Hut 102) and non-Sezary T cell leukemia cell line (Jurkat) relative to benign CD4+ T cells from individuals with no T cell malignancy. There are three goals. The first and primary goal is to establish a list of genes with differential expression between Sezary cells and the benign CD4+ T cell counter part from individuals without Sezary syndrome. A secondary goal is to examine if these differentially expresses genes in clinical samples of Sezary cells are preserved in Hut78 and Hut102 cells, which are the two most frequently used experimental cell models of Sezary cells in the research community. The third goal is to examine if these Sezary cell specific genes are also present in a non-Sezary T cell malignancy, such as Jurkat cells, which is derived from a non-Sezary cell T cell leukemia patient.

2010-12-31 | GSE23113 | GEO

Transcriptome of SATB1 transduced Hut78 cells

Project description:Hut78 cell line was used as Sezary syndrome cell model. Comparative transcriptome profiles of SATB1 transduced Hut78 cells (Hut78-SATB1) relative to empty MIG vector transduced control Hut78 cells (Hut78-MIG) were analyzed. The primary goal is to establish a list of genes with differential expression between SATB1 transduced Hut78 cells and control Hut78 cells to identify the gene expression regulation effect of SATB1 expression in Sezary cells.

2011-12-01 | GSE24951 | GEO

Transcriptome of SATB1 transduced Hut78 cells

2011-12-01 | E-GEOD-24951 | biostudies-arrayexpress

Epigenetic inhibitors

Project description:The project aims to looks at differential gene targets in the human Sezary syndrome HuT78 cell line when treated with epigenetic inhibitors romidepsin, F5446, and chaetocin compared to the vehicle treated cells (DMSO) for 72hrs.

2022-10-26 | GSE159963 | GEO

Gene expression profiling of resting and stimulated CD4+CD45RO+ T cells from Sezary syndrome patients and normal donors

Project description:Sezary syndrome is an aggressive cutaneous T cell lymphoma with pruritic skin inflammation and immune dysfunction, driven by neoplastic, clonal memory T cells in both peripheral blood and skin. To gain insight into how abnormal gene expression in Sezary syndrome promotes T cell dysfunction, lymphoproliferation and transformation, we first compared functional transcriptomic profiles of both resting and activated memory T cells from Sezary syndrome patients and normal donors. To differentiate gene expression associated with malignancy vs. benign inflammation and proliferation, we performed a within-platform meta-analysis of our data for Sezary syndrome and a GEO data set (GSE12079) for lymphocytic variant hypereosinophilic syndrome (L-HES). L-HES is a benign lymphoproliferation of clonal memory T cells that produces skin symptoms very similar to Sezary syndrome. This approach revealed gene expression changes unique to either Sezary syndrome or L-HES, and a subset of genes dysregulated in both SS and L-HES. L-HES patient 1 progressed to peripheral T cell lymphoma, and acquired Sezary-like gene expression during progression, suggesting that these genes contribute to neoplastic transformation.

2019-11-16 | GSE131738 | GEO

RNA-seq analysis of two common T cell models, HUT78 and JURKAT E6.1: Project 5 of Open Targets - Epigenomes of Cell Lines

Project description:The aim of this experiment was to characterize the gene expression of two common immortalized T cell lines (HUT78 and JURKAT E6.1) with and without activating stimuli. Two independent cultures were carried out for each of the cell lines. Cells were cultured according to supplier recommendations and either left untreated or stimulated with Dynabeads human T-activator CD4/CD28 beads (Invitrogen, UK) at a ratio of 1 bead:3 cells for 48 hours. This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalised cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.

2018-06-11 | E-MTAB-6869 | biostudies-arrayexpress

Genomic Analysis of Mycosis Fungoides and Sézary Syndrome

Project description:<p>Mycosis Fungoides (MF) and Sézary Syndrome (Sz) comprise the majority of Cutaneous T-Cell Lymphoma (CTCL) cases and are characterized by clinical heterogeneity. This array of symptoms includes skin patches, plaques and tumors as well as blood involvement and erythroderma. Because the genetic basis of CTCL is still poorly understood, we performed whole-exome sequencing on 11 MF/Sz samples and their matched, normal control DNA. Upon analyzing this data, we distilled a list of an additional 494 genes to be sequenced at depth. The majority of these 494 genes were sequenced in the exons alone, however, for a small subset of these genes we sequenced the entire genomic locus in search of structural variation events. This 494 gene targeted resequencing effort was performed upon 72 patients with MF/Sz and their matched, normal control DNA. An additional 5 MF/Sz and matched, normal DNA samples underwent whole genome amplification (WGA) prior to library preparation, which appears to have introduced mutations into these samples, however we also include them here. We additionally include 10 MF/Sz samples without a matched, normal control samples, 1 of which underwent WGA. In addition to primary disease samples, we also performed targeted resequencing on 4 CTCL cell lines (HH, MyLa, SeAx and Hut78) as well as on H9 cells (a subclone of Hut78 cells) and Jurkat cells, a T-ALL derived cell line that was used as an experimental system for our work. In sum, this data deposition includes exome and/or targeted resequencing from 92 individuals with 192 samples submitted.</p>

| phs000913 | dbGaP

Methyltransferase Inhibitors Restore SATB1 Protective Activity Against Cutaneous T cell Lymphoma

Project description:We report Chromatin Immunoprecipitation for the histone modifications H3K27ac, H3K27m3 and H3K9m3 in human leukemia and lymphoma cell lines HuT78, Jurkat, K562, and RAJI to ascertain the regulatory landscape of in regards to transcriptional repression and activation.

2022-10-26 | GSE159962 | GEO

Oncogenic role of TOX in CTCL

Project description:TOX is a nuclear factor essential for the development of CD4+ T cells in the thymus. TOX is found to be aberrantly up-regulated in the skin biopsies and in the blood CD4+ T cells of cutaneous T cell lymphoma. The goal of this study is to identify potential transcriptional targets of TOX in CTCL by comparison between TOX shRNA transfected CTCL cells (Hut78 and HH) and control CTCL cells. Two color experiment. Lentivirus transduced control vector vs. TOX shRNA vectors on Hut78 and HH cell lines. Biological replicates: 3 control replicates, 3 shRNA tansduced replicates for each cell line.

2014-04-29 | E-GEOD-57122 | biostudies-arrayexpress

Gene expression changes induced by the pan-PIM inhibitor ETP-39010 in 4 peripheral T cell lymphoma cell lines

Project description:Peripheral T cell lymphoma (PTCL) is a very aggressive disease which currently lacks efficient targeted therapy. New therapeutic strategies are needed to improve the very poor outcome of these patients. In these study we hypothesized that PIM kinases could be of therapeutic value in PTCL because we found an overexpression of PIM1 and PIM2, but not PIM3, in PTCL cases, cell lines and primary tumoral T cells from Sezary Syndrome patients, compared with reactive lymph nodes and normal T cells from healthy donors, respectively. In order to understand the mechanism of action of this pan-PIM inhibitor in PTCL, 4 cell lines (DERL7, HuT78, SR786 and MyLa) were treated with 10 Î¼M of ETP-39010 for 0, 2, 4, 6, 10 and 24 h, and gene expression profiling was performed. 4 PTCL cell lines (DERL7, HuT78, SR786 and MyLa) were treated with DMSO and 10 Î¼M of the pan-PIM inhibitor ETP-39010, and hybridized using the Universal Human Reference RNA (Stratagene, La Jolla, CA) as the reference sample.

2014-11-14 | E-GEOD-42595 | biostudies-arrayexpress

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