Molecular characterization of mucosal melanomas
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ABSTRACT:
PROVIDER: PRJNA470997 | ENA |
REPOSITORIES: ENA
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Project description:Molecular characterization of mucosal melanomas
| PRJNA470998 | ENA
Project description:Cutaneous, ocular and mucosal melanomas are histologically indistinguishable tumors that are driven by different spectrum of genetic alterations. With current methods, identification of the site of origin of a melanoma metastasis is challenging, in particular when the metastasis is the first tumor manifestation. Genome wide DNA methylation profiling has shown promise for the identification of the site of tumor origin in various settings. Here we explore the DNA methylation landscape of melanomas from different sites and analyze if different melanoma origins can be distinguished by their epigenetic profile. We performed DNA methylation analysis, next generation DNA panel sequencing and copy number analysis of 82 non-cutaneous and 25 cutaneous melanoma samples. We further analyzed eight normal melanocyte cell culture preparations by DNA methylation profiling. DNA methylation analysis clearly separated uveal melanomas from melanomas of other primary sites while mucosal, conjunctival and cutaneous melanomas were epigenetically almost identical. Still, we observed DNA methylation differences in cancer-related genes, such as low frequencies of RARB and CDKN2A promoter methylation in mucosal melanomas, while conjunctival melanomas frequently harbored APC promoter methylation. Furthermore, all investigated melanomas of the paranasal sinus showed loss of PTEN expression, mainly caused by promoter methylation. This was less frequently seen in melanomas of other sites. Copy number analysis revealed recurrent amplifications in mucosal melanomas, including chromosome 4q, 5p, 11q and 12q. Most melanomas of the oral cavity showed gains of chromosome 5p with TERT amplification while 11q amplifications were enriched in melanomas of the nasal cavity. Mucosal, conjunctival and cutaneous melanomas show a surprisingly similar DNA methylation profile and identification of the site of origin by DNA methylation testing is likely not feasible. Still, our study shows that there are DNA methylation differences on the gene level in known tumor drivers, related to the anatomical primary site.
2021-09-21 | GSE178416 | GEO
Project description:Although identified as the key environmental driver of common cutaneous melanoma, the role of ultraviolet radiation (UVR)-induced DNA damage in mucosal melanoma is poorly defined. We present the largest cohort of mucosal melanomas of conjunctival origin to be analyzed by whole genome sequencing and show a predominance of UVR-associated single base substitution signature 7 (SBS7) in the majority of the samples. Our data shows mucosal melanomas with SBS7 dominance have similar genomic patterns to cutaneous melanomas and therefore this subset could benefit from treatments currently used for common cutaneous melanoma.
| EGAS00001004697 | EGA
Project description:NanoString data on 12 conjunctival melanomas and mucosal melanoma The objective was to compare conjunctival melanoma with other mucosal melanomas at the RNA level using NanoString expression analysis of FFPE material.
2020-01-21 | GSE143952 | GEO
Project description:<p>Mucosal melanoma is a deadly disease that carries the worst prognosis amongst subtypes of melanoma. Like all melanomas, mucosal melanomas are frequently driven by activating mutations in the MAPK and/or PI3K pathways; however, unlike melanomas that arise on sun-exposed skin, mucosal melanomas harbor few point mutations. Instead, most somatic alterations involve structural alterations, which appear early during tumor progression. Molecular studies in mucosal melanoma generally only profile point mutations without interrogating copy number alterations, and pathogenic mutations are only found in 30% of cases. We sequenced 38 mucosal melanomas, and in addition to profiling point mutations, we looked for copy number alterations that amplify oncogenes or delete tumor suppressors.</p>
| phs001594 | dbGaP
Project description:We conducted whole genome sequencing of 5 mucosal melanomas and their matched DNA from blood. We conducted whole exome sequencing of a further 5 mucosal melanomas and their matched DNA from blood.
| EGAS00001000474 | EGA
Project description:Molecular characterization of DLBCL
| PRJNA605794 | ENA
Project description:Mucosal Melanomas (MM) are highly aggressive neoplasms arising from mucosal melanocytes. Current treatments offer a limited survival benefit for patients with advanced MM; moreover, the lack of pre-clinical cellular systems has significantly limited the understanding of their immunobiology. By morphology, ultrastructure and phenotype analysis, this study reports the validation and functional characterization of five cell lines obtained from human melanomas arising from the sino-nasal mucosa and designated as SN-MM1-5. Compared to the normal counterpart, the proteomic profile of SN-MM is consistent with transformed melanocytes showing a heterogeneous degree of melanocytic differentiation and activation of cancer-related pathways. All SN-MM cell lines resulted tumorigenic in vivo in NOD/SCID mice. Of relevance, the microscopic analysis of the corresponding xenotransplants allowed the identification of clusters of MITF-/CDH1-/CDH2+/ZEB1+/CD271+ cells, supporting the existence of melanoma initiating cells also in MM, as confirmed on clinical samples. The proteomic analysis of SN-MM cell lines revealed that RICTOR, a subunit of mTORC2 complex, is the most significantly activated upstream regulator, suggesting a relevant role for the PI3K-Akt-mTOR pathway in these neoplasms. Accordingly, Akt activation, as measured by pAkt(Ser473) and pAkt(Thr308), was observed in all SN-MM and resulted constitutive and sustained by PTEN loss in SN-MM2 and SN-MM3 . A functional role for PI3K-Akt-mTOR pathway was confirmed by PI3K chemical inhibitor LY294002 which significantly impaired SN-MM cell lines viability. Overall, these novel and unique cellular systems represent relevant experimental tools for a better understanding of the immunobiology of these neoplasms and, as extension, to MM from other sites.
2024-01-26 | PXD037551 | Pride
Project description:Molecular mechanisms of intestinal mucosal injury induced by lipopolysaccharide challenge in broiler chickens
2024-03-04 | PXD050298 |
Project description:Molecular characterization of acral melanoma
| PRJNA471577 | ENA