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Series GSE59455 Query DataSets for GSE59455
Status Public on Dec 31, 2016
Title Whole genome expression data from formalin-fixed parrafin embedded (FFPE) primary and metastatic melanomas
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The dominant genetic signature found in melanoma is C to T mutations due to UV radiation. Nucleotide excision repair (NER) recognises and repairs UV-induced DNA damage. We aimed to determine the effect of high UV exposure on the melanoma transcriptome and key NER transcripts in melanoma tumours in association with clinical and genetic features of the disease. 196 primary or metastatic melanomas were utilised for this study. Solar elastosis and transcriptome data was collected. mRNA transcript levels of NER components XPC, DDB1 and DDB2 were quantified and compared to clinical parameters. Solar elastosis negatively correlated with Breslow thickness (-0.251, p=0.017) and was significantly lower in BRAFV600E melanomas. Lower XPC expression was associated with BRAFV600E and NRASQ61R mutations, earlier age of diagnosis and poorer survival. Transcriptome profiling identified an over-representation of DNA repair processes in high vs low solar elastosis. Further analysis revealed DNA repair and kinase activity related transcripts in the low XPC melanomas. XPC deficiency is associated with the presence of kinase mutations and an aggressive disease phenotype, both of which result from the hypermutability of melanoma.
Overall design Formalin fixed paraffin embedded (FFPE) primary and metastatic melanoma tumours; collected for diagnostic purposes at the Hunter Area Pathology Service, NSW, Australia between 2004 and 2009; were used for this study. The Hunter New England Area Health Service Human Ethics Committee approved the study. 196 tumours were identified with sufficient tissue (>2mm width and length) and clinical information for the study. Departmental records where searched for melanoma cases reported between 2005 to 2009. The need to access sufficient tumour tissue to allow matching genomic sequencing, gene expression and immunohistochemical analysis required that cases with a thin primary melanoma (Breslow thickness less than 2mm) with only a small volume of metastatic disease (locoregional or distant metastases) were excluded from the study. All cases utilised had stage 2 or greater disease as either metastatic lymph nodes or primary melanomas greater than 2mm were used. RNA and DNA was successfully extracted from 157 of the 196 tumours (80%).
Contributor(s) Bowden NA, Vilain RE, Ashton KA
Citation(s) 27487145
Submission date Jul 16, 2014
Last update date Apr 10, 2018
Contact name Nikola Bowden
Organization name University of Newcastle
Department School of Medicine and Public Health
Lab DNA Repair
Street address University Dr
City Callaghan
State/province NSW
ZIP/Postal code 2308
Country Australia
Platforms (1)
GPL8432 Illumina HumanRef-8 WG-DASL v3.0
Samples (141)
GSM1437254 4531335087_A
GSM1437255 4531335087_B
GSM1437256 4531335087_C
BioProject PRJNA255368

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
GSE59455_RAW.tar 9.7 Mb (http)(custom) TAR
GSE59455_non_normalized.txt.gz 22.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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