Use of Gene Expression Microarray To Discriminate Conventional Melanoma, Nevoid Melanoma and Benign Atypical Nevi
RR Huang, G P Sarantopoulos, B Bernaba, XM Li, J Zhou, S Binder, A J Cochran. Geffen-UCLA School of Medicine, Los Angeles, CA
Background: Nevoid melanoma (NM) is a form of malignant melanoma (MM) which mimics atypical nevi (AN). Histological features of NM are subtle and there is a high risk of misdiagnosis and delay of treatment. No molecular tests currently differentiate AN from NM. We sought to distinguish NM from AN and MM using gene microarray technology.
Design: Tissue from 8 MM, 7 NM and 10 AN was cut into 8 µm sections and dissected by LCM. Total mRNA was labeled with Nu-GEN WT-Ovation FFPE RNA Amplification System and FL-Ovation cDNA Biotin Module V2 kit, hybridized to the Affymetrix U133 Plus 2.0 Array. Differentially expressed genes were selected at 2-fold expression difference and FDR p<1.00E-2. Clustering and PCA were performed with Partek Genomics Suite v.6.4. Selected genes were validated by qRT PCR.
Results: Clustering analysis compared MM to AN and showed three distinct gene expression patterns for MM, NM and AN (Fig 1). Principle component analysis (PCA) of the 504 differentially expressed genes showed 3 phenotypes into 3 groups in 3 dimensional space that correlated with histopathology. One AN gene expression profile lay in NM territory (Fig 2).
In normalized gene signal intensity, gene PXT1 was more highly expressed in NM, as were HIF3a in AN and cREM in MM, compared to the other 2 groups respectively.
Fig. 1: Clustering Analysis
Fig. 2: PCA
Down-regulated FOXO3 and up-regulated CTLA4, PTPLA and MCHR1 genes in NM vs. AN were validated by qRT-PCR with average-fold changes of 0.64, 75.80, 2.71 and 45.31, respectively. Validation studies are on-going.
Conclusions: These results offer leads for novel molecular tests. Although commonality exists between NM and MM the overall discrete clustering of genes expressed in NM compared to AN and MM suggests a distinct molecular pathobiology for NM. Further study of genes expressed in NM may lead to novel tests which may distinguish these diagnostically challenging lesions.
Wednesday, March 21, 2012 1:00 PM
Poster Session VI # 108, Wednesday Afternoon