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| Status |
Public on Jul 01, 2015 |
| Title |
Gene expression profiling of primary human retinoblastoma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Background
Retinoblastoma is a pediatric eye cancer associated with RB1 loss or MYCN amplification (RB1+/+MYCNA). There are controversies concerning the existence of molecular subtypes within RB1-/- retinoblastoma. To test whether these molecular subtypes exist, we performed molecular profiling.
Methods
Genome-wide mRNA expression profiling was performed on 76 primary human retinoblastomas. Expression profiling was complemented by genome-wide DNA profiling and clinical, histopathological, and ex vivo drug sensitivity data.
Findings
RNA and DNA profiling identified major variability between retinoblastomas. While gene expression differences between RB1+/+MYCNA and RB1-/- tumors seemed more dichotomous, differences within the RB1-/- tumors were gradual. Tumors with high expression of a photoreceptor gene signature were highly differentiated, smaller in volume and diagnosed at younger age compared to tumors with low photoreceptor signature expression. Tumors with lower photoreceptor expression showed increased expression of genes involved in M-phase and mRNA and ribosome synthesis and increased frequencies of somatic copy number alterations.
Interpretation
Molecular, clinical and histopathological differences between RB1-/- tumors are best explained by tumor progression, reflected by a gradual loss of differentiation and photoreceptor expression signature. Since copy number alterations were more frequent in tumors with less photoreceptorness, genomic alterations might be drivers of tumor progression.
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| Overall design |
Fresh frozen material from 76 primary human retinoblastoma samples were profiled with Affymetrix human genome u133 plus 2.0 PM microarray
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| Web link |
http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/26288838
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| Contributor(s) |
Kooi IE, Mol BM, Moll AC, van der Valk P, de Jong MC, de Graaf P, Schouten-van Meeteren AY, Meijers-Heijboer H, Kaspers GJ, te Riele H, Cloos J, Dorsman JC |
| Citation(s) |
26288838 |
| Submission date |
Jul 31, 2014 |
| Last update date |
Apr 20, 2018 |
| Contact name |
Irsan Kooi |
| E-mail(s) |
ei.kooi@vumc.nl
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| Phone |
0031204448425
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| Organization name |
VU university medical centre
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| Department |
Clininical Genetics
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| Lab |
Oncogenetics
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| Street address |
van der Boechorstraat 7
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| City |
Amsterdam |
| State/province |
Noord-Holland |
| ZIP/Postal code |
1081 BT |
| Country |
Netherlands |
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| Platforms (1) |
| GPL13158 |
[HT_HG-U133_Plus_PM] Affymetrix HT HG-U133+ PM Array Plate |
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| Samples (76)
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| Relations |
| BioProject |
PRJNA257212 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE59983_RAW.tar |
149.3 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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