ArticleProgress in biophysics and molecular biology2019
Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction.
Article in Progress in biophysics and molecular biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 52 citations in OpenAlex.
- The SMARCA4 subunit of the SWI/SNF complex prevents genome instability at G quadruplexes.Genome biology · 2026Article
- Non-B DNA structures and their contributions to genetic diversity, aging, and disease.Nucleic acids research · 2026Review
- RNA sculpting by the primordial Helix-clasp-Helix-Strand-Loop (HcH-SL) motif enforces chemical recognition enabling diverse KH domain functions.The Journal of biological chemistry · 2025Review
- ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences.Briefings in bioinformatics · 2025Article
- Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome.Nucleic acids research · 2025Article
- Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.Cell genomics · 2025Article
- Beyond sequence: A physics-informed machine learning framework for predicting DNA mutations.Computational and structural biotechnology journal · 2025Article
- Non-B DNA-informed mutation burden as a marker of treatment response and outcome in cancer.British journal of cancer · 2024Article
- Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.bioRxiv : the preprint server for biology · 2024Article
- A prismatic view of the epigenetic-metabolic regulatory axis in breast cancer therapy resistance.Oncogene · 2024Review
- G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients.International journal of molecular sciences · 2024Article
- A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions.Frontiers in molecular biosciences · 2024Article
- Replication-induced DNA secondary structures drive fork uncoupling and breakage.The EMBO journal · 2023Article
- Novobiocin blocks nucleic acid binding to Polθ and inhibits stimulation of its ATPase activity.Nucleic acids research · 2023Article
- NBBC: a non-B DNA burden explorer in cancer.Nucleic acids research · 2023Article
- G4-interacting proteins endangering genomic stability at G4 DNA-forming sites.Biochemical Society transactions · 2023Article
- Noncanonical DNA structures are drivers of genome evolution.Trends in genetics : TIG · 2023Review
- Immunogenic chemotherapy: great potential for improving response rates.Frontiers in oncology · 2023Review
- Variation in G-quadruplex sequence and topology differentially impacts human DNA polymerase fidelity.DNA repair · 2022Article
- Creation and resolution of non-B-DNA structural impediments during replication.Critical reviews in biochemistry and molecular biology · 2022Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
A hallmark of cancer is genomic instability, which can enable cancer cells to evade therapeutic strategies. Here we employed a computational approach to uncover mechanisms underlying cancer mutational burden by focusing upon relationships between 1) translocation breakpoints and the thousands of G4 DNA-forming sequences within retrotransposons impacting transcription and exemplifying probable non-B DNA structures and 2) transcriptome profiling and cancer mutations. We determined the location and number of G4 DNA-forming sequences in the Genome Reference Consortium Human Build 38 and found a total of 358,605 covering ∼13.4 million bases. By analyzing >97,000 unique translocation breakpoints from the Catalogue Of Somatic Mutations In Cancer (COSMIC), we found that breakpoints are overrepresented at G4 DNA-forming sequences within hominid-specific SVA retrotransposons, and generally occur in tumors with mutations in tumor suppressor genes, such as TP53. Furthermore, correlation analyses between mRNA levels and exome mutational loads from The Cancer Genome Atlas (TCGA) encompassing >450,000 gene-mutation regressions revealed strong positive and negative associations, which depended upon tissue of origin. The strongest positive correlations originated from genes not listed as cancer genes in COSMIC; yet, these show strong predictive power for survival in most tumor types by Kaplan-Meier estimation. Thus, correlation analyses of DNA structure and gene expression with mutation loads complement and extend more traditional approaches to elucidate processes shaping genomic instability in cancer. The combined results point to G4 DNA, activation of cell cycle/DNA repair pathways, and mitochondrial dysfunction as three major factors driving the accumulation of somatic mutations in cancer cells.
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