ArticleBMC medical genomics2020
Somatic synonymous mutations in regulatory elements contribute to the genetic aetiology of melanoma.
Article in BMC medical genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 34 citations in OpenAlex.
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- A Targeted Next-Generation Sequencing Panel to Genotype Gliomas.Life (Basel, Switzerland) · 2022Article
- A seven-gene prognostic signature predicts overall survival of patients with lung adenocarcinoma (LUAD).Cancer cell international · 2021Article
- Synonymous mutations that regulate translation speed might play a non-negligible role in liver cancer development.BMC cancer · 2021Article
- Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population.GigaScience · 2021Article
- Globally learning gene regulatory networks based on hidden atomic regulators from transcriptomic big data.BMC genomics · 2020Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNon-synonymous mutations altering tumor suppressor genes and oncogenes are widely studied. However, synonymous mutations, which do not alter the protein sequence, are rarely investigated in melanoma genome studies.
methodsWe explored the role of somatic synonymous mutations in melanoma samples from TCGA (The Cancer Genome Atlas). The pathogenic synonymous mutation and neutral synonymous mutation data were used to assess the significance of pathogenic synonymous mutations in melanoma likely to affect genetic regulatory elements using Fisher's exact test. Poisson distribution probabilities of each gene were used to mine the genes with multiple potential functional synonymous mutations affecting regulatory elements.
resultsConcentrating on five types of genetic regulatory functions, we found that the mutational patterns of pathogenic synonymous mutations are mostly involved in exonic splicing regulators in near-splicing sites or inside DNase I hypersensitivity sites or non-optimal codon. Moreover, the sites of miRNA binding alteration exhibit a significantly lower rate of evolution than other sites. Finally, 12 genes were hit by recurrent potentially functional synonymous mutations, which showed statistical significance in the pathogenic mutations. Among them, nine genes (DNAH5, ADCY8, GRIN2A, KSR2, TECTA, RIMS2, XKR6, MYH1, SCN10A) have been reported to be mutated in melanoma, and other three genes (SLC9A2, CASR, SLC8A3) have a great potential to impact melanoma.
conclusionThese findings confirm the functional consequences of somatic synonymous mutations in melanoma, emphasizing the significance of research in future studies.
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