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Cited by 20DNA and Nucleic Acid ChemistryCancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

G-quadruplex-mediated genomic instability drives SNVs in cancer

Open access
Richl, Tilmann, Kuper, Jochen, Kisker, Caroline·2024·Nucleic Acids Research
DOI 10.1093/nar/gkae098PMC PMC10954472
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Abstract

G-quadruplex (G4s) DNA structures have been implicated in inducing genomic instability and contributing to cancer development. However, the relationship between G4s and cancer-related single nucleotide variants (cSNVs) in clinical settings remains unclear. In this large-scale study, we integrated experimentally validated G4s with genomic cSNVs from 13480 cancer patients to investigate the spatial association of G4s with the cellular cSNV landscape. Our findings demonstrate an increase in local genomic instability with increasing local G4 content in cancer patients, suggesting a potential role for G4s in driving cSNVs. Notably, we observed distinct spatial patterns of cSNVs and common single nucleotide variants (dbSNVs) in relation to G4s, implying different mechanisms for their generation and accumulation. We further demonstrate large, cancer-specific differences in the relationship of G4s and cSNVs, which could have important implications for a new class of G4-stabilizing cancer therapeutics. Moreover, we show that high G4-content can serve as a prognostic marker for local cSNV density and patient survival rates. Our findings underscore the importance of considering G4s in cancer research and highlight the need for further investigation into the underlying molecular mechanisms of G4-mediated genomic instability, especially in the context of cancer.

AI snapshot

Written from the paper’s full text.

TL;DR

Integrating experimentally validated G-quadruplexes (G4s) with cancer single nucleotide variants (cSNVs) from 13,480 patients, this study finds that local G4 content is associated with increased local cSNV density and genomic instability. The authors also report cancer-type-specific G4–cSNV relationships and show that a patient’s global G4-average is associated with cancer-related mortality.

Key findings

  • cSNVs showed a stronger spatial correlation with G4s than common dbSNVs: Pearson’s r = 0.194 for cSNVs vs 0.082 for dbSNVs, with cSNVs predominantly downstream of G4s (95% CI 63–391 bp) and dbSNVs predominantly upstream (95% CI –2143 to –447 bp); the cSNV Gaussian fit was 5.2-fold compressed compared with dbSNVs.
  • In 5 kb genomic windows, windows without G4s had a mean of 6.5 cSNVs, windows with at least one G4 had 10.8 cSNVs, and windows with ≥10 G4s had 49.5 cSNVs—a 7.6-fold increase over windows without G4s (ind. t-test = –89.601, P < 0.001).
  • Cancer genes contained higher G4 levels than non-cancer genes: median 15 G4s per gene (mean 27) vs median 6 (mean 15), a 2.8-fold increase.
  • Incomplete categorical bootstrapping yielded an r² of 0.96 for the linear relationship between cSNVs and G4s; in 3416 patients, the G4-average was a significant prognostic marker (P < 0.005) with a relative hazard coefficient of 0.38, corresponding to a 38% increase in hazard of cancer-related death per one-unit increase in G4-average.

Methods

  • The study integrated experimentally validated G4s with cSNVs from the NCI GDC Data Portal: 14,932 whole-exome sequencing experiments initially yielded 3,454,377 cSNVs from 13,480 patients across 154 cancer types; after removing germline mutations by intersecting with common dbSNVs and excluding cancer types with fewer than 10 samples, 2,847,440 cSNVs remained.
  • G4 locations were obtained from Balasubramanian et al. and lifted to hg38, yielding 716,310 G4s; 15,175,044 dbSNVs from UCSC and 50 million random G4-like sequences in human exons were used for comparison.
  • Analyses included distance-to-nearest-G4 calculations, parametric Gaussian fitting, 5 kb fixed-end and sliding genomic window analyses, linear regression with incomplete categorical bootstrapping, GC normalization and partial correlation, and Cox proportional hazards modeling.

Limitations

  • The authors state that the study is correlative and cannot establish causality or directionality between G4s and cSNVs; they also note that they correlated local potential quadruplex-forming sequences (PQSs) rather than formed G4s with cSNVs.
  • The authors state that extending the analyses to individual patients was beyond the scope, and that the survival model’s relatively low concordance likely stems from heterogeneous training data; they call for cancer-specific models and rigorous validation before clinical use.
  • Evident from the text: the analysis is based on whole-exome cSNV data and bulk patient cohorts rather than patient-specific chromatin-mapped G4s, and the reported associations may be influenced by cancer-type heterogeneity and selection pressures in cancer cells.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1093/nar/gkae098

Cites

94 of 94 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

41 of 48 cited sources checked · 8 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    Deregulated G4 formation is a major driver of genomic instability.

    “there is strong evidence that deregulated G4-formation is a major driver of genomic instability”
    Quote in the paperSubstantial claim6 of 7 sources checked
    • cites [26] Rodriguez, 2012, Small-molecule-induced DNA damage identifies alternative DNA structures in human genes, Nat. Chem. Biol. source

      The Results section (‘Transcription- and replication-dependent DNA damage’; page unavailable) shows that pyridostatin, a G-quadruplex-binding drug, induces DNA damage in treated cells. That supports a link between targeting G-quadruplexes and DNA damage, but it does not establish that deregulated G4 formation is a major driver of genomic instability generally. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [27] De Magis, 2019, DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells, Proc. Nat. Acad. Sci. U.S.A. source

      The Abstract says that stabilization of G4s by specific ligands or genetic defects can lead to genome instability. The Discussion reports an R-loop-dependent mechanism in human cancer cells treated with the studied G4 ligands. These passages support a link, but do not establish that deregulated G4 formation is a major driver of genomic instability generally. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [28] Salvati, 2007, Telomere damage induced by the G-quadruplex ligand RHPS4 has an antitumor effect, J. Clin. Invest. source

      The ‘RHPS4 induces damage foci at telomeres’ section reports a strong DNA-damage response at telomeres after treatment with a G4-binding ligand. The Discussion links this response to stabilized telomeric G4 DNA, but treats the mechanism as speculative. These passages do not establish that deregulated G4 formation is a major driver of genomic instability generally. Page numbers are unavailable in our copy. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [29] Rodriguez, 2008, A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres, J. Am. Chem. Soc. source

      In the paper’s main text (page unavailable), compound-induced stabilization of telomeric G-quadruplexes is linked to POT1 uncapping and a DNA-damage response in a human cancer cell line. That supports a specific route by which altered G4 formation can provoke damage signaling, but not the broader assertion that deregulated G4 formation is a major driver of genomic instability. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [34] Paeschke, 2011, DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase, Cell source

      The Introduction reports that unresolved G4 structures can impede replication and cause chromosome breakage in Pif1-deficient yeast. The Results also show elevated recombination at G4 motifs in pif1Δ cells. These findings support a link to genomic instability under those conditions, but do not establish deregulated G4 formation as a major driver of genomic instability generally. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [35] Wu, 2008, FANCJ helicase defective in Fanconia anemia and breast cancer unwinds G-quadruplex DNA to defend genomic stability, Mol. Cell. Biol. source
    • cites [36] Wang, 2019, G-quadruplex DNA drives genomic instability and represents a targetable molecular abnormality in ATRX-deficient malignant glioma, Nat. Commun. source

      The Introduction reports that ATRX loss increased G4 formation, replication stress, and DNA damage in astrocyte and glioma stem-cell models. The Discussion links G4-mediated damage to genomic alterations in ATRX-deficient glioma, but says G4s contribute “at least in part”; it does not establish deregulated G4 formation as a major driver of genomic instability generally. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Premisecitation

    One well-documented mechanism for G4-mediated genomic instability involves G4-enhanced formation of R-loops that can spread into adjacent regions containing G4s.

    “While not exclusively resulting in point-mutations, one well-documented mechanism for G4-mediated genomic instability involves G4-enhanced formation of R-loops, that can spread into adjacent regions containing G4s (27).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [27] De Magis, 2019, DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells, Proc. Nat. Acad. Sci. U.S.A. source
  • Premisecitation

    Recent genome-wide investigations underscore that these effects are not confined to promotors, but are rather observed across the genome.

    “Recent genome-wide investigations underscore that these effects are not confined to promotors, but are rather observed across the genome (68–70).”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites [68] Bruno, 2020, The primary mechanism of cytotoxicity of the chemotherapeutic agent CX-5461 is topoisomerase II poisoning, Proc. Nat. Acad. Sci. U.S.A. source

      The Significance and Data sections describe CX-5461’s mechanism and analyses across cell lines, not where effects occur within the genome. Searches for promoters and effects across the genome found no passage establishing that the effects extend beyond promoters. (LLM, conf=0.74)

      Experimental — accuracy not yet measured
    • cites [69] Olivieri, 2020, A genetic map of the response to DNA damage in human cells, Cell source

      The Results (‘Global view of the screens’; page unavailable) describe genome-wide screens for genes affecting the response to DNA damage. Our copy does not say that the effects invoked by the citing sentence occur outside promoters or across genomic locations; a search for promoters and genomic distribution found no such passage. (LLM, conf=0.74)

      Experimental — accuracy not yet measured
    • cites [70] Bossaert, 2021, Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands, eLife source

      The Introduction (page unavailable) says G-quadruplexes are present throughout the human genome and reports genome-wide associations with RNA polymerase pausing and R-loop-forming regions. The paper also describes G4-ligand effects at transcribed genomic regions, but the passages do not establish that those effects were observed across the genome rather than at promoters alone. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
  • Premisecitation

    More serious DNA damages, such as double-strand breaks associated with non-B DNA structures like G4s, and the subsequent DNA repair can be mutagenic.

    “Lastly, more serious DNA damages, such as double-strand breaks associated with non-B DNA structures like G4s, and the subsequent DNA repair can be mutagenic (7,27).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [7] Spiegel, 2020, The structure and function of DNA G-quadruplexes, Trends Chem. source

      The G4 Detection and Mapping section reports double-strand breaks predominantly at predicted G4 regions after treatment with a G4-stabilising ligand. The Intervention and Therapeutics section says G4 ligands cause double-strand breaks and activate DNA repair pathways, but does not say that the subsequent repair is mutagenic. The break evidence is also specifically tied to ligand treatment, a condition the claim omits. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [27] De Magis, 2019, DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells, Proc. Nat. Acad. Sci. U.S.A. source

      The Results (page not available) report that G4 ligands induce double-strand breaks and that PDS-induced breaks can lead to micronuclei, a hallmark of genome instability. The paper does not show that subsequent DNA repair is mutagenic; it instead links micronuclei to breaks that fail to be properly repaired. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Premisecitation

    The prevalence of G4s is significantly increased in immortalized cells compared to primary human cells.

    “Furthermore, the prevalence of G4s was found to be significantly increased in immortalized cells as compared to primary human cells (13).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [13] Hänsel-Hertsch, 2016, G-quadruplex structures mark human regulatory chromatin, Nat. Genet. source

      The comparison on p. 5 reports 10,560 G4 ChIP-seq peaks in immortalized HaCaT cells versus 1,496 in normal human epidermal keratinocytes; the Figure 3 caption calls the increase significant. The source supports this specific cell-type comparison, but not a general increase across immortalized cells compared with primary human cells. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim. 20
  • May combine two claims. 31

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    G4s were reported to cluster in functional regions and are enriched in genes involved in cancer formation.

    “Given that G4s were reported to cluster in functional regions and are enriched in genes involved in cancer formation (59), we hypothesized that cancer-specific genes might contain higher G4-levels, thus explaining the observed exclusive correlation in cancer patients.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [59] Hui, 2021, Single-cell mapping of DNA G-quadruplex structures in human cancer cells, Sci. Rep. source

      The Results and discussion section (no page available) reports G4s at gene promoters, supporting their presence in functional regions. It also reports that 28% of the top 50 differentially enriched promoter G4 peaks in MCF7 cells were associated with genes showing increased copy number. It does not establish that G4s are enriched in genes involved in cancer formation. (LLM, conf=0.85)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    An increased frequency of SNVs can disrupt the normal function and regulation of genes, potentially leading to the development and progression of cancer.

    “In this context, we considered local cSNV or dbSNV enrichment as marker for local genomic instability, as an increased frequency of SNVs can disrupt the normal function and regulation of genes, potentially leading to the development and progression of cancer (58).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [58] Lemmens, 2015, Mutagenic consequences of a single G-quadruplex demonstrate mitotic inheritance of DNA replication fork barriers, Nat. Commun. source

      The Abstract reports G-quadruplex-induced deletions, and the Discussion compares more extensive rearrangements with those found in cancer cells. Neither passage addresses whether an increased frequency of SNVs disrupts gene function or regulation and contributes to cancer development or progression; searches for SNVs, point mutations, and those cancer effects found no such passage in our copy. (LLM, conf=0.74)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    Recent studies have demonstrated the involvement of G4s in inducing or aggravating genomic damage, such as copy number alterations, deletions or translocations.

    “Recent studies have demonstrated the involvement of G4s in inducing or aggravating genomic damage, such as copy number alterations, deletions or translocations (65).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [65] Sauer, 2017, G-quadruplex unwinding helicases and their function in vivo, Biochem. Soc. Trans. source

      The passages labeled Abstract contain bibliographic metadata and a ‘GENOME INSTABILITY’ keyword, but no discussion of G4s causing genomic damage. Searches for copy-number alterations, deletions, translocations, and chromosome rearrangements returned no substantive passage, so our copy cannot verify the claim. (LLM, conf=0.70)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    Deregulated or ligand-induced G4-formation is associated with the activation of DNA-damage responses, implying that aberrant G4-formation triggers similar pathways as DNA-damage.

    “deregulated or ligand-induced G4-formation is associated with the activation of DNA-damage responses, implying that aberrant G4-formation triggers similar pathways as DNA-damage (83).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [83] Miglietta, 2022, Ligands stimulating antitumour immunity as the next G-quadruplex challenge, Mol. Cancer source

  • Classified as probably not a substantial claim.

    Premisecitation

    DNA polymerase errors during replication or repair processes at G4 loci contribute to elevated mutagenesis due to steric, G4 mediated inhibition.

    “One possibility is that DNA polymerase errors during replication or repair processes at G4 loci contribute to elevated mutagenesis due to steric, G4 mediated inhibition (78).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [78] Stein, 2022, Variation in G-quadruplex sequence and topology differentially impacts human DNA polymerase fidelity, DNA Repair (Amst.) source

  • May combine two claims.

    Premisecitation

    The application of G4-stabilizing ligands has been observed to activate DDRs and arrest cells in G2-phase, hinting at an increase in genomic instability due to aberrant G4 formation.

    “Moreover, the application of G4-stabilizing ligands has been observed to activate DDRs and arrest cells in G2-phase, hinting at an increase in genomic instability due to aberrant G4 formation (30).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [30] Lerner, 2019, Replication of G quadruplex DNA, Genes source

      Section 4.2 reports genetic instability in budding yeast treated with a G4-stabilising ligand and interrupted DNA synthesis when G4s are stabilised with ligands in wild-type cells. It does not report that the ligands activate DNA damage responses or arrest cells in G2 phase (searched: DNA damage response, DDR, and G2-phase). The genomic-instability implication is supported, but those specific observed effects are not. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    G-rich sequences, like G4 motifs, are prone to oxidative DNA damage, which can lead to mutations if not repaired properly.

    “Additionally, G-rich sequences, like G4 motifs, are prone to oxidative DNA damage, which can lead to mutations if not repaired properly (76).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [76] Biffi, 2014, Elevated levels of G-quadruplex formation in human stomach and liver cancer tissues, PLoS One source

      The Introduction (page unavailable) says G-quadruplexes form from guanine-rich sequences and that stabilizing them with a small molecule can induce DNA damage. It does not say G-rich sequences are especially prone to oxidative DNA damage or that unrepaired oxidative damage leads to mutations; searches for oxidative damage and 8-oxoG found no such passage. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    Further reports demonstrated that G4s cause replication-dependent DNA-damage or change the overall chromatin structure.

    “Further reports demonstrated that G4s cause replication-dependent DNA-damage or change the overall chromatin structure (66,67).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [66] Sato, 2021, Multistep mechanism of G-quadruplex resolution during DNA replication, Sci. Adv. source

      The Introduction reports that DNA damage induced by G4-stabilizing ligands is replication dependent. The Discussion links G4-related polymerase stalling to possible replication-associated breaks, but also says that G4 structures do not directly cause an accumulation of DNA damage under unperturbed conditions. The claim omits those conditions and presents the damage link more categorically than this paper does. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [67] Valton, 2016, G-Quadruplexes in DNA replication: a problem or a necessity, Trends Genet. source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    G4s have been predominantly associated with the promoters of oncogenes such as MYC, KIT or KRAS, where their stabilization is associated with suppressed oncogene expression.

    “While G4s have been predominantly associated with the promoters of oncogenes such as MYC, KIT or KRAS (23–25), where their stabilization is associated with suppressed oncogene expression”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites [23] Eilers, 2008, Myc's broad reach, Genes Dev. source

      The passages from “Transcriptional regulation by Myc” and “In and out of the E-box?” discuss Myc’s effects on gene expression and its binding to promoter sequences, but not G-quadruplexes. Searches for G4s in MYC, KIT, or KRAS promoters and for suppression of oncogene expression through G4 stabilization found no passage addressing the claim. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
    • cites [24] Lutz, 2002, Contributions of Myc to tumorigenesis, Biochim. Biophys. Acta source
    • cites [25] Meyer, 2008, Reflecting on 25 years with MYC, Nat. Rev. Cancer source

  • May combine two claims.

    Premisecitation

    G4s are highly susceptible to oxidative damage, as G-rich sequences have a low redox-potential and thus can act as ROS-sinks.

    “Furthermore, G4s are highly susceptible to oxidative damage, as G-rich sequences have a low redox-potential and thus can act as ROS-sinks (84).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [84] Wu, 2023, Crosstalk between G-quadruplex and ROS, Cell Death. Dis. source

      The Introduction says guanine has a low redox potential, and the “ROS and G4S” section says G4s are highly susceptible to ROS-mediated oxidative damage because they are G-rich. The paper suggests that greater G4 stability may increase the antioxidant capacity of telomeres, but it does not establish that G4s generally act as ROS sinks. (LLM, conf=0.82)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    G4s can be detected in patient-derived tissues using immunohistochemistry, with a significantly elevated number of G4-positive nuclei observed in human cancers of the liver and stomach compared to non-neoplastic tissue.

    “recent studies have shown that G4s can be detected in patient-derived tissues using immunohistochemistry, with a significantly elevated number of G4-positive nuclei observed in human cancers of the liver and stomach compared to non-neoplastic tissue (76).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [76] Biffi, 2014, Elevated levels of G-quadruplex formation in human stomach and liver cancer tissues, PLoS One source

  • May combine two claims.

    Interpretationcitation

    Elevated G-quadruplex formation might be a characteristic of some cancers and G4s could contribute to genomic instability in cancer patients.

    “This suggests that elevated G-quadruplex formation might be a characteristic of some cancers and supports the hypothesis that G4s could contribute to genomic instability in cancer patients (76).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [76] Biffi, 2014, Elevated levels of G-quadruplex formation in human stomach and liver cancer tissues, PLoS One source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    G4s hold various regulatory functions in transcription and translation.

    “However, G4s hold various regulatory functions in transcription and translation (20)”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [20] Lago, 2021, Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome, Nat. Commun. source

      The Introduction and Results describe several ways G4s may regulate transcription, including effects on RNA polymerase, transcription-factor binding, and gene expression. The passages do not establish a regulatory role in translation; the Results discuss 5′UTRs in relation to transcription, not protein synthesis. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    Error-prone polymerases might be engaged at slowed or stalled replication forks to ensure complete G4 replication, as specialized polymerases like eta, kappa, and Rev1 are essential for G4 stability, further increasing the density of localized genomic damages.

    “Error-prone polymerases might be engaged at slowed or stalled replication forks to ensure complete G4 replication, as specialized polymerases like eta, kappa, and Rev1 are essential for G4 stability – further increasing the density of localized genomic damages (26,78–80).”
    Quote in the paperSubstantial claim4 of 4 sources checked
    • cites [26] Rodriguez, 2012, Small-molecule-induced DNA damage identifies alternative DNA structures in human genes, Nat. Chem. Biol. source

      Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites [78] Stein, 2022, Variation in G-quadruplex sequence and topology differentially impacts human DNA polymerase fidelity, DNA Repair (Amst.) source

      Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites [79] Fleming, 2020, Interplay of guanine oxidation and G-quadruplex folding in gene promoters, J. Am. Chem. Soc. source

      Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites [80] Estep, 2019, G4-interacting DNA helicases and polymerases: potential therapeutic targets, Curr. Med. Chem. source

      Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Cellular treatment with G4 ligands, such as PDS or 20A, is linked to anti-tumorigenic effects and G2/M cell cycle arrest.

    “One study has linked cellular treatment with G4 ligands, such as PDS or 20A, to anti-tumorigenic effects and G2/M cell cycle arrest (71).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [71] Beauvarlet, 2019, Modulation of the ATM/autophagy pathway by a G-quadruplex ligand tips the balance between senescence and apoptosis in cancer cells, Nucleic Acids Res. source

      The Discussion reports that the G4 ligand 20A inhibits cancer-cell growth in vitro and in vivo, supporting the anti-tumorigenic part of the claim. The Results describe growth arrest through senescence and apoptosis, but do not identify it as G2/M arrest; the passages found also do not establish the claimed effect for PDS (searched: G2/M, PDS/pyridostatin, and cell-cycle arrest). (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    G4-associated intratumor heterogeneity exists in breast cancer patient-derived tumor xenografts beyond current classifications.

    “as a recent study revealed G4-associated intratumor heterogeneity in breast cancer patient-derived tumor xenografts beyond current classifications (90).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [90] Hänsel-Hertsch, 2020, Landscape of G-quadruplex DNA structural regions in breast cancer, Nat. Genet. source

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    Cancer cells are often characterized by increased replication stress, altered DNA repair mechanisms or changes in chromatin structure.

    “One possible explanation for the observed difference between cSNVs and dbSNVs could be system-wide alterations in cancer cells, which are often characterized by increased replication stress, altered DNA repair mechanisms or changes in chromatin structure (85,86).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [85] Cairns, 2011, Regulation of cancer cell metabolism, Nat. Rev. Cancer source
    • cites [86] Li, 2020, DNA repair pathways in cancer therapy and resistance, Front. Pharmacol. source

      The ‘Role of DNA Repair Pathways in Cancer Biology’ section (page unavailable) describes defects and downregulation of DNA repair pathways in cancers, supporting the altered-repair part of the claim. The passages found do not establish that cancer cells are often characterized by increased replication stress or changes in chromatin structure; searches for those terms did not find support for those parts. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    There is a significant correlation of G4s and cSNVs in the absence of GC-content (P-value: 0), with only a slight decrease in Pearson's r from 0.173 to 0.158.

    “Our results show a significant correlation of G4s and cSNVs in the absence of GC-content (P-value: 0), with only a slight decrease in Pearson's r from 0.173 to 0.158.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In the MYC gene, most cSNVs are located in the second coding exon, which is also the only coding exon to contain G4s.

    “Similarly, in the MYC gene, most cSNVs are located in the second coding exon, which is also the only coding exon to contain G4s.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Length-normalized cancer genes contain a median average of 15 G4s per gene (mean: 27), while non-cancer genes contain a median average of 6 G4s per gene (mean: 15).

    “Comparing the average number of G4s in cancer or non-cancer genes, we found length-normalized cancer genes to contain a median average of 15 G4s per gene (mean: 27), while non-cancer genes contained a median average of 6 G4s per gene (mean: 15).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The difference in dbSNV-levels for varying G4-levels is less pronounced and not significant in both cancer- and non-cancer genes.

    “However, consistent with earlier results, the difference in dbSNV-levels for varying G4-levels is less pronounced and not significant in both cancer- and non-cancer genes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The relationship between G4s and cSNVs differs across cancer and tissue types (large cancer-specific differences / variations in the strength of the correlation).

    “We further demonstrate large, cancer-specific differences in the relationship of G4s and cSNVs”
    • Also stated in: § Introduction · plain
      “we observed variations in the strength of this correlation among different cancer- and tissue types”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In 736 hallmark cancer genes, the normalized density distributions of cSNVs and G4s were frequently corresponding and equally clustered in similar exons, with a significant positive correlation (Pearson's r = 0.243, P < 0.001).

    “We found that the normalized density distributions of cSNVs and G4s were frequently corresponding and equally clustered in similar exons of these genes, with a significant positive correlation (Pearson's r = 0.243, P < 0.001).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Higher G4-content in cancer genes is excluded as the origin of the observed effect, as the observation prevailed after normalizing the data to cancer genes.

    “However, our results exclude the higher G4-content in cancer genes as origin of this effect, as this observation prevailed even after normalizing the data to cancer genes.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    Genomic windows with more than 15 G4s were excluded due to statistically insufficient window quantities to ensure reliability of G4 data.

    “To ensure the reliability of the G4 data, we excluded genomic windows with more than 15 G4s due to statistically insufficient window quantities.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    There is a strong spatial correlation between cSNVs and G4s in cancer patients, and a weaker but still significant correlation between dbSNVs and G4s.

    “Overall, our analysis suggests a strong spatial correlation between cSNVs and G4s in cancer patients, as well as a weaker but still significant correlation between dbSNVs and G4s.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Linear regression models were tested with data randomly split into 70% training and 30% test data.

    “Wherever we tested the linear regression models, data were randomly split into 70% training data and 30% test data.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Partial correlation between G4s and cSNVs per window was calculated controlling for GC-content as a fraction of base pairs.

    “Partial correlation between the number of G4s per window and the number of cSNVs per window was calculated using the pingouin package in python (Version 0.5.3) and controlling for the GC-content as a fraction of base pairs in each genomic window.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    96% of the variance in the dataset can be explained by the linear relationship between cSNVs and G4s, demonstrating a strong correlation between G4s and cSNVs in cancer patients.

    “This value indicates that 96% of the variance in the dataset can be explained by the linear relationship between cSNVs and G4s and demonstrated the strong correlation between G4s and cSNVs in cancer patients.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    High G4 content can serve as a prognostic marker for local cSNV density and patient survival rates.

    “we show that high G4-content can serve as a prognostic marker for local cSNV density and patient survival rates”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductreasoning

    Known germline mutations were removed by intersecting cSNVs with common SNVs, and cancer types with fewer than 10 samples were excluded, to ensure statistical reliability.

    “To ensure statistical reliability, we removed known germline mutations by intersecting cSNVs with common SNVs and excluded cancer types with less than 10 samples.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The observed correlation between cSNVs and G4s is present both genome-wide and on an intragenic level.

    “These findings suggest that the observed correlation between cSNVs and G4s is present both genome-wide and on an intragenic level.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    Experimentally validated G4s were used to ensure a high level of confidence in the results.

    “We used experimentally validated G4s in our study to ensure a high level of confidence in our results.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Balasubramanian et al. [10]

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationown data

    For each one-unit increase in G4-average, the hazard of cancer-related death increases by 38%, associating high G4-averages with a worse prognosis.

    “This implies that for each one-unit increase in G4-average, the hazard of cancer-related death increases by 38%, associating high G4-averages with a worse prognosis (Figure 3F).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The proportional hazards assumption of the Cox proportional hazards model holds for the G4-average survival analysis.
    • Rests on an assumption: The survival status and cause of death recorded in the metadata are accurate.

  • May combine two claims.

    Interpretationreasoning

    G4s might be drivers of local cSNV formation in cancer patients, while having a lesser effect on SNVs outside of cancer.

    “Thus, our results indicate that G4s might be drivers of local cSNV formation in cancer patients, while having a lesser effect on SNVs outside of cancer.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    The study correlated local PQS rather than formed G4s with cSNVs, so it cannot establish causality or directionality between G4s and cSNVs.

    “An important limitation of our study is that we correlated local PQS rather than formed G4s with cSNVs – thus, we cannot establish causality between G4s and cSNVs.”
    • Also stated in: § Discussion · plain
      “It is important to note that our correlative study design has a significant limitation: We cannot make a definitive assumption about the directionality of the correlation, i. e. whether cSNVs correlate with G4s (with G4s as drivers of nucleotide variation) or G4s correlate with cSNVs (with cSNVs providing more permissive conditions for the formation of G4-sequences).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    These mechanisms predominantly substantiate the presence of SNVs within PQS or their immediate adjacent regions and do not directly account for the observed elevation in cSNV-frequencies in G4-rich multi-kilobase pair windows.

    “Nevertheless, while these mechanisms could explain how G4s drive genome plasticity through nucleotide variation, they predominantly substantiate the presence of SNVs within PQS or their immediate adjacent regions. They do not directly account for our observed elevation in cSNV-frequencies in G4-rich multi-kilobase pair windows.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    If other G4s are within sufficient distance, R-loops might extend and open the chromatin, allowing additional R-loop formation in adjacent G4s and further extension of single-stranded DNA regions, which would not be possible for solitary G4s.

    “If other G4s are within sufficient distance, R-loops might extend and open the chromatin, allowing additional R-loop formation in the adjacent G4s and further extension of single-stranded DNA regions. This would not be possible for solitary G4s.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    Clustered G4s could lead to clusters of single-stranded R-loops in the flanking region of G4s that would be more susceptible to DNA damage.

    “As G4s often occur clustered, this could lead to clusters of single-stranded R-loops in the flanking region of G4s that would be more susceptible to DNA damage.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: G4s often occur clustered.

  • May combine two claims.

    Interpretationreasoning

    Taken together, these findings point to a scenario in which G4s pre-exist and potentially function as initiators for the occurrence of cSNVs.

    “Taken together, these findings point to a scenario in which G4s pre-exist and potentially function as initiators for the occurrence of cSNVs.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    There is a distinct cSNV landscape in cancer patients compared to dbSNVs, which could partly originate from their similar pathogenetic backgrounds.

    “This suggests that there is a distinct cSNV landscape in cancer patients compared to dbSNVs, which could partly originate from their similar pathogenetic backgrounds.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    This R-loop mechanism could explain why cSNVs tend to accumulate in the immediate vicinity of G4s rather than within the G4 motif itself.

    “This observation could explain why cSNVs tend to accumulate in the immediate vicinity of G4s rather than within the G4 motif itself.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationnone given

    The model's relatively low concordance likely originates from the heterogeneous training data.

    “The model's relatively low concordance likely originates from the heterogeneous training data, which could be improved by focusing on patients with similar diagnoses.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationreasoning

    The patients investigated in this study probably experienced other forms of G4-mediated DNA damage, including insertions, deletions and double-strand breaks.

    “While our study focused on the detection of SNVs in relation to G4s, it is highly probable that the patients we investigated experienced other forms of G4-mediated DNA damage, including insertions, deletions and double-strand breaks - as G4-mediated genomic instability is not limited to a specific type of DNA damage but rather has been observed to contribute to various types of DNA damage.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: G4-mediated genomic instability is not limited to a specific type of DNA damage but contributes to various types of DNA damage.
44 of 44

  • The paper relies on this without support.

    The relationship between G4s and cancer-related single nucleotide variants (cSNVs) in clinical settings remains unclear.

    “However, the relationship between G4s and cancer-related single nucleotide variants (cSNVs) in clinical settings remains unclear.”

  • The paper relies on this without support.

    G4 formation frequently occurs in cancer tissue.

    “Given the frequent occurrence of G4 formation in cancer tissue and recent evidence linking G4s to mutation hotspots in lymphoma cells (56), we investigated the genome-wide spatial correlation of SNVs with G4s.”

  • The paper relies on this without support.

    The association between G4 content and cSNVs is not due to unmeasured confounding factors other than GC content.

    “Taken together, these results further indicate that the increase in cSNVs is largely driven by the presence of G4s rather than GC content.”

  • The paper relies on this without support.

    The proportional hazards assumption of the Cox proportional hazards model holds for the G4-average survival analysis.

    “We calculated the global G4-average for each patient in genomic 5 kb windows containing cSNVs and utilized these data to fit Cox's proportional hazards model—a well-established model to investigate the association between the survival time of patients and predictor variables (60,61).”

  • The paper relies on this without support.

    The survival status and cause of death recorded in the metadata are accurate.

    “Based on the associated metadata, we selected 3416 patients that either had died due to their primary cancer diagnosis or remained alive throughout the data collection period. Patients with incomplete survival data or survival status, as well as patients who had died from causes unrelated to cancer were excluded.”

  • The paper relies on this without support.

    Current knowledge regarding the effects of G4s on cancer development in a clinical context is limited.

    “Consistently, current knowledge regarding the effects of G4s on cancer development in a clinical context is limited.”

  • The paper relies on this without support.

    Most studies investigating the potential role of G4s as drivers of genomic instability remain confined to cellular models.

    “while there is a substantial number of studies investigating the potential role of G4s as drivers of genomic instability, most of these studies remain confined to cellular models.”

  • The paper relies on this without support.

    G4s have not yet been suggested as global drivers of cSNVs in cancer patients.

    “However, G4s have not yet been suggested as global drivers of cSNVs in cancer patients.”

  • The paper relies on this without support.

    G4s often occur clustered.

    “As G4s often occur clustered”

  • The paper relies on this without support.

    G4-mediated genomic instability is not limited to a specific type of DNA damage but contributes to various types of DNA damage.

    “as G4-mediated genomic instability is not limited to a specific type of DNA damage but rather has been observed to contribute to various types of DNA damage.”

  • The paper relies on this without support.

    G4s are predominantly located in functional regions and cancer genes.

    “As G4s are predominantly located in functional regions and cancer-genes, cellular changes resulting in the genome-wide stabilization of G4s could result in genomic instability in genomic regions which most likely confer growth advantages.”
11 of 11

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Normalized G4-average exceeds its defined maximum

    Major

    Dividing the mean G4 count across selected windows by the sum across those same windows yields one divided by the number of windows, which cannot exceed 1. The reported normalized G4-average of 7.3 is therefore incompatible with the stated definition.

  • Absolute distances are reported as negative

    Minor

    An absolute distance cannot be negative, but the reported confidence interval includes negative distances. The stated absolute-distance calculation also cannot, on its own, distinguish upstream from downstream.

  • Nearest-neighbor search reverses direction between Methods and Results

    Minor

    The Methods describe finding the nearest G4 for each SNV, whereas the Results describe finding the nearest SNV for each G4. These searches need not produce the same set of distances.

3 of 3

Cites

Flagged first, then by citations

1 of the 95 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Related

Authors
Richl, T., Kuper, J., & Kisker, C.
Affiliations
University of Würzburg (DE)
Corresponding author
Kuper, Jochen
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2024-02-26
Volume
52
Issue
5
Pages
2198-2211
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkae098
PMC
PMC10954472
OpenAlex
W4392157064
Cited by
20
References
95
Citations by year
2026: 10 · 2025: 6 · 2024: 4
FWCI
2.31
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Online Publication Service of Würzburg University (Würzburg University) (submittedVersion, cc-by)
Funders
University of Wuerzburg
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Keywords
G-quadruplex, genomic instability, single nucleotide variants, cancer, prognostic factors, patient survival
MeSH terms
DNA, Humans, Neoplasms, Nucleotides, Polymorphism, Genetic, Genomic Instability, G-Quadruplexes

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-20.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-20.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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