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| Status |
Public on Nov 22, 2011 |
| Title |
Diagnostic microRNA profiling in cutaneous T-cell lymphoma (CTCL) |
| Platform organisms |
Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; human gammaherpesvirus 4; JC polyomavirus; Human immunodeficiency virus 1; Murid gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus hominis; Betapolyomavirus macacae |
| Sample organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
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.
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| Overall design |
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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| Contributor(s) |
Ralfkiaer U, Hagedorn PH, Bangsgaard N, Løvendorf MB, Ahler CB, Svensson L, Kopp K, Vennegaard MT, Lauenborg B, Zibert J, Krejsgaard T, Bonefeld CM, Gjerdrum L, Labuda T, Mathiesen A, Grønbæk K, Wasik MA, Litman T, Sokolowska-Wojdylo M, Queille-Roussel C, Gniadecki R, Ralfkiaer E, Søkilde R, Geisler C, Woetmann A, Glue C, Røpke MA, Skov L, Odum N |
| Citation(s) |
21865341 |
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| Submission date |
Aug 16, 2011 |
| Last update date |
Apr 10, 2012 |
| Contact name |
Rolf Søkilde |
| E-mail(s) |
rolf.soekilde@gmail.com
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| Organization name |
Lund University, Sweden
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| Department |
Department of Oncology
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| Street address |
Scheelevägen 2
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| City |
Lund |
| ZIP/Postal code |
221 85 |
| Country |
Sweden |
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| Platforms (1) |
| GPL14149 |
miRCURY LNA microRNA Array, 5th generation [Human miRBase 17] |
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| Samples (148)
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| Relations |
| BioProject |
PRJNA145737 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31408_RAW.tar |
130.5 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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