Expression data from CTCL patient skin lesion [Agilent]
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ABSTRACT:
PROVIDER: PRJNA417498 | ENA |
REPOSITORIES: ENA
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Project description:Expression data from CTCL patient skin lesion
| PRJNA417497 | ENA
Project description:Expression data from CTCL patient skin lesion [Affymetrix]
| PRJNA417499 | ENA
Project description:Cutaneous T cell lymphoma (CTCL) can have clinical and histological features resembling benign inflammatory dermatosis (BID) and can be difficult to diagnose especially at the early stage of CTCL. We used microarrays to detail the global alteration of miRNA transcriptome and generate a diagnosis and prognosis signature.
2017-11-08 | GSE106645 | GEO
Project description:Cutaneous T cell lymphoma (CTCL) can have clinical and histological features resembling benign inflammatory dermatosis (BID) and can be difficult to diagnose especially at the early stage of CTCL. We used microarrays to detail the global alteration of miRNA transcriptome and generate a diagnosis and prognosis signature.
2017-11-08 | GSE106644 | GEO
Project description:Cutaneous T-cell lymphomas (CTCL) are the most frequent primary skin lymphomas. Nevertheless, diagnosis of early disease has proven difficult due to a clinical and histological resemblance to benign inflammatory skin diseases. To address if microRNA (miRNA) profiling can discriminate CTCL from benign inflammation, we study miRNA expression in 199 patients with CTCL, peripheral T-cell lymphoma (PTL), and benign skin diseases (psoriasis and dermatitis). Using microarrays we show that the most induced- (miR-326, miR-663b, miR-711) and repressed- (miR-203, miR-205) miRNAs distinguish CTCL from benign skin diseases with > 90% accuracy in a training set of 90 samples and a test set of 58 blinded samples. These miRNAs also distinguish malignant and benign lesions in an independent set of 50 patients with PTL and skin inflammation and in experimental human xenograft mouse models of psoriasis and CTCL. Q-RT-PCR analysis of 104 patients with CTCL and benign skin disorders validates differential expression of 4 out of the 5 miRNAs and confirms previous reports on miR-155 in CTCL. A q-RT-PCR-based classifier consisting of miR-155, miR-203, and miR-205 distinguishes CTCL from benign disorders with high specificity, sensitivity, and a classification accuracy of 95% indicating that miRNAs have a high diagnostic potential in CTCL. miRNA microarray. From each sample 100 ng of total RNA was labeled with Hy3 fluorescent dye using the miRCURY LNA Array power labeling kit (Exiqon, Denmark). All samples were labeled the same day with the same master mix, in order to minimize technical variation. The Hy3-labelled samples were hybridized to miRCURY LNA arrays (v11.0) (Exiqon, Denmark), containing capture probes targeting all human miRNAs registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed overnight at 56°C according to manufacturer specifications using a Tecan HS4800 hybridization station (Tecan, Austria). Since it was not possible to hybridize all arrays in one go, samples were randomly split into 5 batches as to minimize day to day variation in the hybridization process. After hybridization the microarray slides were scanned using an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) at 5µm resolution, and the resulting TIFF images were analyzed using the ImaGene 8.0 software on standard settings (BioDiscovery, Inc., USA).
2011-11-22 | E-GEOD-31408 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2017-11-08 | GSE106646 | GEO
Project description:Cutaneous T-cell lymphomas (CTCL) are the most frequent primary skin lymphomas. Nevertheless, diagnosis of early disease has proven difficult due to a clinical and histological resemblance to benign inflammatory skin diseases. To address if microRNA (miRNA) profiling can discriminate CTCL from benign inflammation, we study miRNA expression in 199 patients with CTCL, peripheral T-cell lymphoma (PTL), and benign skin diseases (psoriasis and dermatitis). Using microarrays we show that the most induced- (miR-326, miR-663b, miR-711) and repressed- (miR-203, miR-205) miRNAs distinguish CTCL from benign skin diseases with > 90% accuracy in a training set of 90 samples and a test set of 58 blinded samples. These miRNAs also distinguish malignant and benign lesions in an independent set of 50 patients with PTL and skin inflammation and in experimental human xenograft mouse models of psoriasis and CTCL. Q-RT-PCR analysis of 104 patients with CTCL and benign skin disorders validates differential expression of 4 out of the 5 miRNAs and confirms previous reports on miR-155 in CTCL. A q-RT-PCR-based classifier consisting of miR-155, miR-203, and miR-205 distinguishes CTCL from benign disorders with high specificity, sensitivity, and a classification accuracy of 95% indicating that miRNAs have a high diagnostic potential in CTCL.
2011-11-22 | GSE31408 | GEO
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.
2014-04-29 | GSE57122 | GEO
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
Project description:It is unknown why cutaneous T cell lymphoma (CTCL) progress from a relative indolent skin condition to severe cancer with a poor prognosis. Staphylococcus aureus (SA) has been suspected to play a role, because antibiotics have an inhibitory effect on the tumor burden in some patients. As these patients often display skin colonization by SA, it was hypothesized, but never proven, that SA generate a pro-oncogenic milieu in lesional skin. Here, we study the effect of short-term aggressive antibiotic treatment on tumor cells, the microenvironment, and disease activity in treatment-refractory, advanced stage CTCL. We report that advanced stage CTCL patients experienced significant decrease in clinical and patient-self-reported symptoms in response to aggressive 4-week antibiotic therapy, which eradicated SA. Notably, the clinical improvement lasted for more than 8 months in some patients. Global mRNA expression and cell-signaling pathway analysis indicated a decrease in IL-2 signaling, inflammation, and mitosis in skin lesions after antibiotic therapy. In accordance, IL-2 receptor chain (IL2R-) expression, STAT3 activation, and mitotic activity were decreased in lesional skin following antibiotic treatment. Conversely, SA toxins triggered IL2R- expression, STAT3 activation, and enhanced proliferation ex vivo in primary malignant T cells derived from untreated patients. In conclusion, we demonstrate that transient, aggressive antibiotic treatment inhibits tumor cells, partly normalizes the microenvironment, and decreases disease activity in lesional skin. Thus, we provide a first mechanistic link between antibiotics, skin inflammation, and tumor burden and therefore a novel rationale for treatment of SA in advanced CTCL.
2020-04-13 | GSE122934 | GEO