Gene expression in cutaneous T cell lymphoma (CTCL), dermatitis (D), and healthy subjects (HS)
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ABSTRACT:
PROVIDER: PRJNA600263 | ENA |
REPOSITORIES: ENA
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Project description:FFPE skin biopsy samples from patients with CTCL, dermatitis, or healthy controls were profiled by NanoString gene expression analysis A classifier was constructed that was able to identify mycosis fungoides (MF) samples from dermatitis and healthy controls.
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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: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).
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Project description:Leukemic cutaneous T-cell lymphomas (L-CTCL) are lymphoproliferative disorders of skin-homing mature T-cells causing chronic inflammation, tissue destruction, severe infections and sepsis, all linked to poor quality of life and high mortality. Despite numerous sequencing efforts in L-CTCL, recurrent driver mutations have not been identified, but chromosomal losses and gains are frequent and dominant. We integrated genomic landscape analysis with innovative pharmacologic interference studies to identify key vulnerable nodes in L-CTCL. In order to examine IQDMA-specific effects in an unbiased and dose-dependent manner without limiting the analysis to only kinases, we carried out global proteomics profiling in SeAx cells after 24 h treatment with 1, 2.5 and 10 µM IQDMA. The differential proteins affected in response to increasing IQDMA concentrations were found to be related to multiple cellular processes in metabolism, ribosomal RNA processing/modification, protein translation, and surprisingly keratinization.. Dual inhibition of STAT3/5 using small molecule degraders abolished L-CTCL cell growth in vitro. Furthermore, upstream broad range kinase targeting through IQDMA, a newly classified multi-kinase inhibitor, revealed a pharmacologic opportunity to alternatively block the STAT3/5 pathway by inhibiting the PAK2 serine/threonine kinase, which was very effective in patient cells carrying STAT3/5 copy number gains and in vivo in reducing tumor growth and disease dissemination in an intradermal xenograft mouse model. In summary, we conclude that STAT3/5 and PAK2 are new therapy targets to be further explored in L-CTCL.
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Project description:Leukemic cutaneous T-cell lymphomas (L-CTCL) are lymphoproliferative disorders of skin-homing mature T-cells causing chronic inflammation, tissue destruction, severe infections and sepsis, all linked to poor quality of life and high mortality. Despite numerous sequencing efforts in L-CTCL, recurrent driver mutations have not been identified, but chromosomal losses and gains are frequent and dominant. We integrated genomic landscape analysis with innovative pharmacologic interference studies to identify key vulnerable nodes in L-CTCL. In order to examine IQDMA-specific effects in an unbiased and dose-dependent manner without limiting the analysis to only kinases, we carried out global proteomics profiling in SeAx cells after 24 h treatment with 1, 2.5 and 10 µM IQDMA. The differential proteins affected in response to increasing IQDMA concentrations were found to be related to multiple cellular processes in metabolism, ribosomal RNA processing/modification, protein translation, and surprisingly keratinization.. Dual inhibition of STAT3/5 using small molecule degraders abolished L-CTCL cell growth in vitro. Furthermore, upstream broad range kinase targeting through IQDMA, a newly classified multi-kinase inhibitor, revealed a pharmacologic opportunity to alternatively block the STAT3/5 pathway by inhibiting the PAK2 serine/threonine kinase, which was very effective in patient cells carrying STAT3/5 copy number gains and in vivo in reducing tumor growth and disease dissemination in an intradermal xenograft mouse model. In summary, we conclude that STAT3/5 and PAK2 are new therapy targets to be further explored in L-CTCL.
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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.
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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.
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