br Few singleton tumors were also uncovered
Few singleton tumors were also uncovered, with highly enriched tumor-specific terms. These included CESC, where human leukocyte antigen (HLA) genes of the “Antigen processing and presentation” term populated 26 KEGG pathway terms; SKCM, where the correlations between weakly expressed genes and mu-tations mentioned in section 3.2.2 were enriched in olfactory re-ceptor genes; and BRCA, enriched in genes associated with the “Protein processing in the endoplasmic reticulum” term (Fig. 5C). We also conducted the gene enrichment analysis for the 270 genes (in each tumor type), whose expression was most negatively correlated with mutations, but did not find any enriched term. Similarly, only one term with a Benjamini-corrected P-value of 0.02 was found when 270 genes with no significant correlation with mutations were selected for each tumor. Therefore, our correlation analysis of gene expression versus mutation loads identified pathways that are commonly altered in different types of cancer.
We found it counterintuitive that for some enriched gene pathways, such as DNA repair, there were positive correlations between gene expression and mutations, since we expected weak DNA repair to increase mutations. In LUAD, although not in KICH and PRAD, the main pathways for the repair of Disuccinimidyl Suberate mismatch and base lesions, i.e. BER, MMR and NER, contained at least one gene that displayed negative correlation between expression and mu-
In this study we addressed the contribution of two distinct mechanisms to the induction of somatic mutations in cancer: the formation of G4 DNA structures and tumor-specific changes in gene transcriptional profiles. Translocation breakpoints were enriched at sequences with the potential to form G4 DNA structures in tumor samples that were characterized by elevated genetic instability and frequent mutations in tumor suppressor genes, such as TP53. SVA and L1 elements contribute thousands of identical G4 DNA-forming motifs in the genome, although translocations were readily found at motifs present in the former but not in the latter classes of ret-rotransposons. Transcription of hundreds of genes correlated strongly with somatic mutation loads in some cancer types but not in others. Most genes with the strongest correlations were not listed as “cancer-genes”, although their expression shows strong predictive power of survival in Kaplan-Meier plots. Genes whose expression is positively correlated with mutations were enriched in selected KEGG terms in more than one cancer type, which provides a platform for addressing the contribution of specific pathways to somatic mutation in cancer.
4.1. G4 DNA induces translocations
We assigned the puncta detected in cell nuclei to G4 DNA structures bound to the 1H6 murine monoclonal antibody, which is thought to recognize G4 structures raised from DNA oligonucleo-tides assembling into parallel-stranded G4 conformations (Henderson et al., 2014). This antibody shows selectivity for inter-and intramolecular structures mostly localized to heterochromatin (Hoffmann et al., 2016); however, the use of other probes supports G4 structure-formation throughout nucleoli (Zhang et al., 2018a,b), in mitochondrial DNA (Huang et al., 2015) and in the cytoplasm by RNA (Biffi et al., 2014; Laguerre et al., 2015). Hence, given that >350,000 G4 DNA-forming repeats are present in the human genome and that ~80% of the genome is transcribed (ENCODE
Fig. 5. Mutations are linked to defects in DNA repair gene expression. Panels A - C, bar graphs of P-values adjusted for multiple testing (Benjamini correction) for genes enriched in KEGG pathways from the pool of top 270 genes (for each tumor type) that displayed positive correlation between mRNA levels (expression) and cancer somatic mutations. Panels A and B group tumors that displayed common terms, whereas panel C shows singletons of tumor-specific KEGG pathway enrichment. Panel D, graph of regression coefficients (y axis) for DNA repair genes (x axis) displaying P-values <1 10 5 for the correlations between gene expression and cancer mutation loads in patients with LUAD; shaded areas highlight genes in the same pathway; BER, base excision repair; MMR, mismatch repair; NER, nucleotide excision repair; HR, homologous recombination; FA, Fanconi anemia.
Please cite this article as: Bacolla, A et al., Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction, Progress in Biophysics and Molecular Biology, https://doi.org/10.1016/j.pbiomolbio.2019.03.004
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Consortium, 2012), the potential for G4 structures comprising DNA, RNA, and perhaps DNA:RNA hybrids in cells is remarkably high and therefore constitutes sites where DNA structure is likely to impact outcomes to cellular stress in cancer.