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Series GSE84976 Query DataSets for GSE84976
Status Public on Aug 07, 2016
Title Upregulation of HLA expression in primary Uveal Melanoma by infiltrating leukocytes
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Uveal melanoma (UM) with an inflammatory phenotype, characterized by infiltrating leukocytes and increased human leukocyte antigen (HLA) expression, carry an increased risk of death due to metastases. These tumors shoud be ideal for T-cell based therapies, yet it is not clear why prognostically-infaust tumors have a high HLA expression. We set out to determine whether the level of HLA molecules in UM is associated with other genetic factors, HLA transcriptional regulators, or microenvironmental factors. 28 enucleated UM were used to study HLA class I and II expression, and several regulators of HLA by immunohistochemistry, PCR microarray, qPCR and chromosome SNP-array. Fresh tumor samples of eight primary UM and four metastases were compared to their corresponding xenograft in SCID mice, using a PCR microarray and SNP array. Increased expression levels of HLA class I and II showed no dosage effect of chromosome 6p, but, as expected, were associated with monosomy of chromosome 3. Increased HLA class I and II protein levels were positively associated with their gene expression and with raised levels of the peptide-loading gene TAP1, and HLA transcriptional regulators IRF1, IRF8, CIITA, and NLRC5, revealing a higher transcriptional activity in prognostically-bad tumors. Implantation of fresh human tumor samples into SCID mice led to a loss of infiltrating leukocytes, and to a decreased expression of HLA class I and II genes , and their regulators. Our data provides evidence for a proper functioning HLA regulatory system in UM, offering a target for T-cell based therapies. NB: Here we show the PCR microarray (Illumina array).
 
Overall design Total RNA was isolated from (malignant) uveal melanoma cells is from stored tissue of surgically removed specimen.
 
Contributor(s) van Essen T, van Pelt S
Citation(s) 27764126
Submission date Jul 29, 2016
Last update date Aug 13, 2018
Contact name Theodorus Huibertus van Essen
E-mail(s) t.h.van_essen@lumc.nl
Organization name Leiden University Medical Center
Street address Albinusdreef 2
City Leiden
ZIP/Postal code 2333ZA
Country Netherlands
 
Platforms (1)
GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Samples (28)
GSM2254877 UM_01
GSM2254878 UM_02
GSM2254879 UM_03
Relations
BioProject PRJNA335794

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE84976_RAW.tar 26.2 Mb (http)(custom) TAR
GSE84976_non-normalized.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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