TY - JOUR
T1 - A comprehensive genome-wide analysis of melanoma Breslow thickness identifies interaction between CDC42 and SCIN genetic variants
AU - Vaysse, Amaury
AU - Fang, Shenying
AU - Brossard, Myriam
AU - Wei, Qingyi
AU - Chen, Wei V.
AU - Mohamdi, Hamida
AU - Vincent-Fetita, Lynda
AU - Margaritte-Jeannin, Patricia
AU - Lavielle, Nolwenn
AU - Maubec, Eve
AU - Lathrop, Mark
AU - Avril, Marie Françoise
AU - Amos, Christopher I.
AU - Lee, Jeffrey E.
AU - Demenais, Florence
N1 - Publisher Copyright:
© 2016 UICC
PY - 2016/11/1
Y1 - 2016/11/1
N2 - Breslow thickness (BT) is a major prognostic factor of cutaneous melanoma (CM), the most fatal skin cancer. The genetic component of BT has only been explored by candidate gene studies with inconsistent results. Our objective was to uncover the genetic factors underlying BT using an hypothesis-free genome-wide approach. Our analysis strategy integrated a genome-wide association study (GWAS) of single nucleotide polymorphisms (SNPs) for BT followed by pathway analysis of GWAS outcomes using the gene-set enrichment analysis (GSEA) method and epistasis analysis within BT-associated pathways. This strategy was applied to two large CM datasets with Hapmap3-imputed SNP data: the French MELARISK study for discovery (966 cases) and the MD Anderson Cancer Center study (1,546 cases) for replication. While no marginal effect of individual SNPs was revealed through GWAS, three pathways, defined by gene ontology (GO) categories were significantly enriched in genes associated with BT (false discovery rate ≤5% in both studies): hormone activity, cytokine activity and myeloid cell differentiation. Epistasis analysis, within each significant GO, identified a statistically significant interaction between CDC42 and SCIN SNPs (pmeta-int =2.2 × 10−6, which met the overall multiple-testing corrected threshold of 2.5 × 10−6). These two SNPs (and proxies) are strongly associated with CDC42 and SCIN gene expression levels and map to regulatory elements in skin cells. This interaction has important biological relevance since CDC42 and SCIN proteins have opposite effects in actin cytoskeleton organization and dynamics, a key mechanism underlying melanoma cell migration and invasion.
AB - Breslow thickness (BT) is a major prognostic factor of cutaneous melanoma (CM), the most fatal skin cancer. The genetic component of BT has only been explored by candidate gene studies with inconsistent results. Our objective was to uncover the genetic factors underlying BT using an hypothesis-free genome-wide approach. Our analysis strategy integrated a genome-wide association study (GWAS) of single nucleotide polymorphisms (SNPs) for BT followed by pathway analysis of GWAS outcomes using the gene-set enrichment analysis (GSEA) method and epistasis analysis within BT-associated pathways. This strategy was applied to two large CM datasets with Hapmap3-imputed SNP data: the French MELARISK study for discovery (966 cases) and the MD Anderson Cancer Center study (1,546 cases) for replication. While no marginal effect of individual SNPs was revealed through GWAS, three pathways, defined by gene ontology (GO) categories were significantly enriched in genes associated with BT (false discovery rate ≤5% in both studies): hormone activity, cytokine activity and myeloid cell differentiation. Epistasis analysis, within each significant GO, identified a statistically significant interaction between CDC42 and SCIN SNPs (pmeta-int =2.2 × 10−6, which met the overall multiple-testing corrected threshold of 2.5 × 10−6). These two SNPs (and proxies) are strongly associated with CDC42 and SCIN gene expression levels and map to regulatory elements in skin cells. This interaction has important biological relevance since CDC42 and SCIN proteins have opposite effects in actin cytoskeleton organization and dynamics, a key mechanism underlying melanoma cell migration and invasion.
KW - Breslow thickness
KW - gene-gene interaction
KW - genome-wide association studies
KW - melanoma
KW - pathway analysis
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U2 - 10.1002/ijc.30245
DO - 10.1002/ijc.30245
M3 - Article
C2 - 27347659
AN - SCOPUS:84983086281
SN - 0020-7136
VL - 139
SP - 2012
EP - 2020
JO - International journal of cancer
JF - International journal of cancer
IS - 9
ER -