ArticleNucleic acids research2020
Prevalence and architecture of posttranscriptionally impaired synonymous mutations in 8,320 genomes across 22 cancer types.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 57 citations in OpenAlex.
- Nucleotide Substitution Biases in Related Cancer Driver Genes.International journal of molecular sciences · 2025Article
- DRP-PSM: Multi-Level Feature Integration Reveals Hierarchical Contributions to Pathogenic Synonymous Mutation Prediction.ACS omega · 2025Article
- The DNA damage sensor ATM kinase interacts with the p53 mRNA and guides the DNA damage response pathway.Molecular cancer · 2024Article
- Comprehensive landscape of integrator complex subunits and their association with prognosis and tumor microenvironment in gastric cancer.Open medicine (Warsaw, Poland) · 2024Article
- Association analysis between Acetyl-Coenzyme A Acyltransferase-1 gene polymorphism and growth traits in Xiangsu pigs.Frontiers in genetics · 2024Article
- Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer.BMC bioinformatics · 2023Article
- Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase.Nucleic acids research · 2023Article
- BDL-SP: A Bio-inspired DL model for the identification of altered Signaling Pathways in Multiple Myeloma using WES data.American journal of cancer research · 2023Article
- Deregulation of ceRNA Networks in Frontal Cortex and Choroid Plexus of Brain during SARS-CoV-2 Infection Aggravates Neurological Manifestations: An Insight from Bulk and Single-Cell Transcriptomic Analyses.Advanced biology · 2022Article
- Genetic association and single-cell transcriptome analyses reveal distinct features connecting autoimmunity with cancers.iScience · 2022Article
- Comprehensive characterization of posttranscriptional impairment-related 3'-UTR mutations in 2413 whole genomes of cancer patients.NPJ genomic medicine · 2022Article
- Article
- Pan-cancer analyses of synonymous mutations based on tissue-specific codon optimality.Computational and structural biotechnology journal · 2022Article
- Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.Genome medicine · 2021Article
- Article
- OncoVar: an integrated database and analysis platform for oncogenic driver variants in cancers.Nucleic acids research · 2021Article
- Transcriptomic signatures and repurposing drugs for COVID-19 patients: findings of bioinformatics analyses.Computational and structural biotechnology journal · 2021Article
- Genomic Variation Prediction: A Summary From Different Views.Frontiers in cell and developmental biology · 2021Review
- AI-Driver: an ensemble method for identifying driver mutations in personal cancer genomes.NAR genomics and bioinformatics · 2020Article
- Alternative Splicing: A New Therapeutic Target for Ovarian Cancer.Technology in cancer research & treatmentArticle
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Somatic synonymous mutations are one of the most frequent genetic variants occurring in the coding region of cancer genomes, while their contributions to cancer development remain largely unknown. To assess whether synonymous mutations involved in post-transcriptional regulation contribute to the genetic etiology of cancers, we collected whole exome data from 8,320 patients across 22 cancer types. By employing our developed algorithm, PIVar, we identified a total of 22,948 posttranscriptionally impaired synonymous SNVs (pisSNVs) spanning 2,042 genes. In addition, 35 RNA binding proteins impacted by these identified pisSNVs were significantly enriched. Remarkably, we discovered markedly elevated ratio of somatic pisSNVs across all 22 cancer types, and a high pisSNV ratio was associated with worse patient survival in five cancer types. Intriguing, several well-established cancer genes, including PTEN, RB1 and PIK3CA, appeared to contribute to tumorigenesis at both protein function and posttranscriptional regulation levels, whereas some pisSNV-hosted genes, including UBR4, EP400 and INTS1, exerted their function during carcinogenesis mainly via posttranscriptional mechanisms. Moreover, we predicted three drugs associated with two pisSNVs, and numerous compounds associated with expression signature of pisSNV-hosted genes. Our study reveals the prevalence and clinical relevance of pisSNVs in cancers, and emphasizes the importance of considering posttranscriptional impaired synonymous mutations in cancer biology.
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