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ABSTRACT: Whole-exome sequencing of large to giant congenital melanocytic naevi

PROVIDER: PRJNA832532 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18935408_1.fastq.gz	Fastqsanger.gz
	SRR18935408_2.fastq.gz	Fastqsanger.gz
	SRR18935409_1.fastq.gz	Fastqsanger.gz
	SRR18935409_2.fastq.gz	Fastqsanger.gz
	SRR18935410_1.fastq.gz	Fastqsanger.gz

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Project description:Large Congenital Melanocytic Naevi have a higher propensity to malignant transformation compared to acquired naevi. They thus represent a good model for studying initial steps of melanocarcinogenesis. We have performed genotypic (karyotype, FISH and mutational analyses) and differential expression studies on a large cohort of medium (n=3) and large (n=24) congenital melanocytic naevi. Unlike malignant melanoma, chromosomal abnormalities were rare and single, a feature probably reflecting the benignity of these lesions. Mutational screening showed a high frequency of NRAS mutations in our series, while BRAF mutations were less common. Differential expression study between tumoral and normal melanocytes did not show significant alterations of cellular processes such as cell proliferation, cell migration/invasion, angiogenesis, apoptosis, and immune/inflammatory responses. However, significant down-regulation of genes involved in pigmentation and up-regulation of genes playing a role in DNA protection were observed. Lastly, our micro-arrays displayed up-regulation of genes mediating chemoresistance in cancer. As alteration of pigmentation mechanisms can trigger oxidative damage, increased expression of genes involved in maintenance of DNA integrity might reflect the ability of naevocytic cells to self protection against cellular stress. Furthermore, the observed alterations linked to chemoresistance might partially account for the well known inefficacy of chemotherapy in malignant melanoma. Keywords: cell type comparison

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Project description:Large and giant congenital melanocytic nevi (CMN) are rare melanocytic lesions mostly caused by post-zygotic acquisition of NRAS alteration. However, large/giant CMN may exhibit phenotypic differences among distinct areas patients and in addition, patients differ in features such as presence of multiple CMN or Spilus-like lesions. Overall, 50 fresh-frozen biopsies corresponding to 37 phenotypically characterized areas of large/giant CMNs, 9 satellite lesions, 1 acquired nevus and 3 healthy skin biopsies were analyzed by a multigene panel and RNA sequencing (RNA-seq). Mutational screening showed mutations in 76.2% of large/giant CMN. NRAS mutation was found in 57.1% of cases, and mutations in other genes such as BRAF, KRAS, APC and MET were detected in 14.3% of patients. RNA-seq revealed the fusion transcript ZEB2-ALK and SOX5-RAF1 in large/giant CMN from two patients without point mutations. Both alterations were not detected in unaffected skin and were detected in different affected skin. These findings suggest that large/giant CMN may result from distinct molecular events in addition to NRAS mutations including point mutations and fusions transcripts.

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Project description:Among children with multiple congenital melanocytic naevi (CMN), 25% have no established genetic cause. Here, we study 169 CMN patients, 38 of whom were double wild-type for NRAS/BRAF mutations. Nineteen of these 38 patients had sufficient tissue to undergo RNAseq, which revealed mosaic BRAF fusions in 11/19 patients and mosaic RAF1 fusions in 1/19. These findings offer a genetic diagnosis to an additional group of patients opening the possibility for treatment options.

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