ArticleMolecular genetics & genomic medicine2019
Integrative genomic analysis identifies associations of molecular alterations to APOBEC and BRCA1/2 mutational signatures in breast cancer.
Article in Molecular genetics & genomic medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 7 citations in OpenAlex.
- The Roles of MicroRNAs, Oncogenes, and Tumor Suppressor Gene Molecular Subtypes of Breast Cancer: Therapeutic Potential of Pharmaceutical and Natural Products.International journal of breast cancer · 2026Review
- KIF4A in disease pathogenesis and therapeutics: from molecular mechanisms to clinical translation.Biology direct · 2025Review
- Roles and regulatory mechanisms of KIN17 in cancers (Review).Oncology letters · 2023Review
- Fixing the GAP: The role of RhoGAPs in cancer.European journal of cell biology · 2022Review
- Mitotic chromosomes.Seminars in cell & developmental biology · 2021Review
- APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival.International journal of molecular sciences · 2019Article
- Integrative genomic analysis identifies associations of molecular alterations to APOBEC and BRCA1/2 mutational signatures in breast cancer.Molecular genetics & genomic medicine · 2019Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe observed mutations in cancer are the result of ~30 mutational processes, which stamp particular mutational signatures (MS). Nevertheless, it is still not clear which genomic alterations correlate to several MS. Here, a method to analyze associations of genomic data with MS is presented and applied to The Cancer Genome Atlas breast cancer data revealing promising associations.
methodsThe MS were discretized into clusters whose extremes were statistically associated with mutations, copy number, and gene expression data.
resultsKnown associations for apolipoprotein B editing complex (APOBEC) and for BRCA1 and BRCA2 support the proposal. For BRCA1/2, mutations in ARAP3, three focal deletions, and one amplification were detected. Around 50 mutated genes for the two APOBEC signatures were identified including three kinesins (KIF13A, KIF1B, KIF4A), three ubiquitins (USP45, UBR4, UBR1), and two demethylases (KDM5B, KDM5C) among other genes also connected to DNA damage pathways. The results suggest novel roles for other genes currently not involved in DNA repair. The altered expression program was very high for the BRCA1/2 signature, high for APOBEC signature 13 clearly associated to immune response, and low for APOBEC signature 2. The remaining signatures show scarce associations.
conclusionSpecific genetic alterations can be associated with particular MS.
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