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Subungual melanoma and atypical lentiginous melanocytic proliferations: New insights for the use of molecular analyses

ABSTRACT: In the study, researchers investigated acral melanomas, particularly subungual melanomas (SUM), which are primarily characterized by whole genome copy number variations (CNV) such as amplifications, gains, and losses. Previous research has utilized various cytogenetic or molecular analyses ranging from targeted methods focused on specific genes to comprehensive whole genome and whole transcriptome sequencing techniques. To differentiate between malignant and benign lesions, fluorescence in situ hybridization (FISH) methods have been commonly employed, utilizing probes targeting genes like CCND1, RREB1, MYB, CDKN2A, or MYC either individually or in combination.In this study a Comparative Genomic Hybridization on array (array-CGH) was performed to detect whole genome CNV. This approach aimed to improve the classification of malignant and benign lesions in a cohort consisting of 31 SUM cases and 8 subungual lentiginous melanocytic proliferations with or without atypia.

ORGANISM(S): Homo sapiens

PROVIDER: GSE262724 | GEO | 2024/05/31

REPOSITORIES: GEO

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Project description:Background. Although gene expression arrays have been used to generate molecular predictors of relapse and drug sensitivity in breast cancer, no large study describes genes and exons differentially expressed between breast cancer and benign lesions. Methods. One hundred and sixty-five tumour samples were obtained by fine needle aspiration (FNA). cDNA were hybridized on Splice ArrayTM. A nearest centroid prediction rule was developed to classify lesions as malignant or benign on a training set, and its performance evaluated on an independent validation set. A two-way ANOVA model was used to identify probesets that present a differential expression between cancer and benign lesions while adjusting for scan dates. P-values were adjusted for False Discovery Rate. Findings. Overall 120 breast cancers and 45 benign lesions were included in the study. A 1228-probeset molecular classifier for breast cancer diagnosis was generated from the training set (n=94). This signature accurately classified all samples (100% accuracy, 95% exact CI: 96-100%). In the validation set (n=71), the molecular predictor accurately classified 68 out of 71 tumours (96%, 95% CI: 88-99%). When the 165 samples were taken into account, 37 858 exon-probesets (5.4%) and 3733 genes (20%) were found to be differentially expressed between malignant and benign conditions (adjusted p-value<0.05). Pathway analyses showed that genes involved in spliceosome assembly were significantly enriched in malignant condition (permutation p=0.002). In the same population of 165 samples, 956 exon-probesets presented both a higher intensity and higher splice index in breast cancer, although located on unchanged genes. Interpretation. The present study provides a thorough description of differentially expressed exons between breast cancer and benign lesions, and emphasizes the contribution of spliceosome and alternative transcripts to the molecular portrait of breast malignancy. This allowed the development of a molecular classifier for breast cancer diagnosis using FNA.

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Subungual melanoma and atypical lentiginous melanocytic proliferations: New insights for the use of molecular analyses

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