Novel Genes Associated with Malignant Melanoma but not Benign Melanocytic Lesions

Abstract

Purpose: Cutaneous melanoma is a common, aggressive cancer with increasing incidence. The identification of melanoma-specific deregulated genes could provide molecular markers for lymph node staging assays and further insight into melanoma tumorigenesis. Experimental Design:Total RNA isolated from 45 primary melanoma,18 benign skin nevi, and 7 normal skin tissue specimens were analyzed on an Affymetrix Hu133A microarray containing 22,000 probe sets. Results: Hierarchical clustering revealed a distinct separation of the melanoma samples from the benign and normal specimens. Novel genes associated with malignant melanoma were identified. Differential gene expression of two melanoma-specific genes, PLAB and L1CAM, were tested by a one-step quantitative reverse transcription-PCR assay on primary malignant melanoma, benign nevi, and normal skin samples, as well as on malignant melanoma lymph node metastasis and melanoma-free lymph nodes. The performance of the markers was compared with conventional melanoma markers such as tyrosinase, gp100, and MART1. Conclusion: Our study systematically identified novel melanoma-specific genes and showed the feasibility of using a combination of PLAB and L1CAM in a reverse transcription-PCR assay to differentiate clinically relevant samples containing benign or malignant melanocytes.

Molecular classification of melanomas and nevi using gene expression microarray signatures and formalin-fixed and paraffin-embedded tissue

“…The L1CAM homolog gene expression pattern in our study was inconsistent with a previous study of melanomas and nevi that used frozen tissue on DNA microarray and reported increased L1CAM expression in melanoma compared to nevi. 12 The discrepancy may relate to our study of a L1CAM homolog, rather than the L1CAM examined in the prior study. Previous studies reported relatively similar expression levels of HLA (MHC class I) genes in melanoma and nevi 11 whereas we found higher expression of HLA-A and HLA-B (MHC class I) genes in melanoma relative to nevi (Figure 3a).…”

“…Previous DNA microarray studies of melanocytic lesions used frozen tissue and did not employ laser capture microdissection. [9][10][11][12][13]16 In this study, arrays were processed in two groups; the initial 120 cases and a 'blind' group of 45. As slight variations in array data between different lots can artificially bias the results of an unsupervised clustering study, tissues from primary cutaneous melanomas and nevi from the first 86-sample subset were subjected to unsupervised hierarchical clustering which identified two separate and distinctive groups of lesions.…”

“…Additional studies, using DNA microarrays prepared from frozen tissues have also reported that melanomas, nevi, and normal melanocytes have separate gene profiles. [11][12][13] Studies of cell lines and fresh frozen tissues suggest that it will be possible to distinguish the molecular changes associated with melanoma cells from those seen in nevocytes and melanocytes. Molecular classifiers may also be able to predict metastatic potential and clinical outcome.…”

Impact of chemotactic factors and receptors on the cancer immune infiltrate: a bioinformatics study revealing homogeneity and heterogeneity among patient cohorts

“…Five different datasets were included for several major cancer types, in particular breast carcinoma (TCGA consortium), 31–34 colorectal carcinoma (http://www.intgen.org or TCGA consortium), 35,36 non-small cell lung carcinoma (TCGA consortium) 37–40 and melanoma, 41–45 to study the correlation between the expression level of metagenes indicating the presence of immune cell types and a variety of chemotactic factors and receptors. An extra dataset concerning breast carcinoma 46 was used for studying expression variability and treatment response.…”

Differential gene expression profiling of primary cutaneous melanoma and sentinel lymph node metastases

“…Others, using cell lines or tissue samples, have studied DNA expression profiling of normal melanocytes, nevi, primary melanomas, and regional and distant metastases. [7][8][9][10][11][12][13][14][15][16][17][18][19] Conway et al 19 used the cDNA-mediated annealing, selection, extension, and ligation assay to evaluate formalin-fixed, paraffin-embedded archival primary melanoma specimens, and reported osteopontin overexpression as a potential prognostic biomarker. Rangel et al, 20 using immunohistochemistry, had previously shown that overexpression of osteopontin, correlated with the likelihood of sentinel lymph node metastasis.…”