Mutational signatures are jointly shaped by DNA damage and repair

AbstractCells possess an armamentarium of DNA repair pathways to counter DNA damage and prevent mutation. Here we use C. elegans whole genome sequencing to systematically quantify the contributions of these factors to mutational signatures. We analyse 2,717 genomes from wild-type and 53 DNA repair defective backgrounds, exposed to 11 genotoxins, including UV-B and ionizing radiation, alkylating compounds, aristolochic acid, aflatoxin B1, and cisplatin. Combined genotoxic exposure and DNA repair deficiency alters mutation rates or signatures in 41% of experiments, revealing how different DNA alterations induced by the same genotoxin are mended by separate repair pathways. Error-prone translesion synthesis causes the majority of genotoxin-induced base substitutions, but averts larger deletions. Nucleotide excision repair prevents up to 99% of point mutations, almost uniformly across the mutation spectrum. Our data show that mutational signatures are joint products of DNA damage and repair and suggest that multiple factors underlie signatures observed in cancer genomes.

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Mutational signatures are jointly shaped by DNA damage and repair

10.1101/686295 ◽

2019 ◽

Cited By ~ 2

Author(s):

Nadezda V Volkova ◽

Bettina Meier ◽

Víctor González-Huici ◽

Simone Bertolini ◽

Santiago Gonzalez ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Excision Repair ◽

Dna Lesions ◽

Single Nucleotide Variants ◽

Mutational Signatures ◽

Experimental Conditions ◽

Repair Deficiency ◽

Dna Repair Deficiency ◽

Mutation Spectra

AbstractMutations arise when DNA lesions escape DNA repair. To delineate the contributions of DNA damage and DNA repair deficiency to mutagenesis we sequenced 2,717 genomes of wild-type and 53 DNA repair defective C. elegans strains propagated through several generations or exposed to 11 genotoxins at multiple doses. Combining genotoxin exposure and DNA repair deficiency alters mutation rates or leads to unexpected mutation spectra in nearly 40% of all experimental conditions involving 9/11 of genotoxins tested and 32/53 genotypes. For 8/11 genotoxins, signatures change in response to more than one DNA repair deficiency, indicating that multiple genes and pathways are involved in repairing DNA lesions induced by one genotoxin. For many genotoxins, the majority of observed single nucleotide variants results from error-prone translesion synthesis, rather than primary mutagenicity of altered nucleotides. Nucleotide excision repair mends the vast majority of genotoxic lesions, preventing up to 99% of mutations. Analogous mutagenic DNA damage-repair interactions can also be found in cancers, but, except for rare cases, effects are weak owing to the unknown histories of genotoxic exposures and DNA repair status. Overall, our data underscore that mutation spectra are joint products of DNA damage and DNA repair and imply that mutational signatures computationally derived from cancer genomes are more variable than currently anticipated.

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Systematic analysis of mutational spectra associated with DNA repair deficiency in C. elegans

10.1101/2020.06.04.133306 ◽

2020 ◽

Cited By ~ 1

Author(s):

B Meier ◽

NV Volkova ◽

Y Hong ◽

S Bertolini ◽

V González-Huici ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Excision Repair ◽

Structural Variants ◽

Systematic Analysis ◽

C Elegans ◽

Mutational Spectra ◽

Base Substitutions ◽

Repair Pathways ◽

Complex Structural

AbstractGenome integrity is particularly important in germ cells to faithfully preserve genetic information across generations. As yet little is known about the contribution of various DNA repair pathways to prevent mutagenesis. Using the C. elegans model we analyse mutational spectra that arise in wild-type and 61 DNA repair and DNA damage response mutants cultivated over multiple generations. Overall, 44% of lines show >2-fold increased mutagenesis with a broad spectrum of mutational outcomes including changes in single or multiple types of base substitutions induced by defects in base excision or nucleotide excision repair, or elevated levels of 50-400 bp deletions in translesion polymerase mutants rev-3(pol ζ) and polh-1(pol η). Mutational signatures associated with defective homologous recombination fall into two classes: 1) mutants lacking brc-1/BRCA1 or rad-51/RAD51 paralogs show elevated base substitutions, indels and structural variants, while 2) deficiency for MUS-81/MUS81 and SLX-1/SLX1 nucleases, and HIM-6/BLM, HELQ-1/HELQ and RTEL-1/RTEL1 helicases primarily cause structural variants. Genome-wide investigation of mutagenesis patterns identified elevated rates of tandem duplications often associated with inverted repeats in helq-1 mutants, and a unique pattern of ‘translocation’ events involving homeologous sequences in rip-1 paralog mutants. atm-1/ATM DNA damage checkpoint mutants harboured complex structural variants enriched in subtelomeric regions, and chromosome end-to-end fusions. Finally, while inactivation of the p53-like gene cep-1 did not affect mutagenesis, combined brc-1 cep-1 deficiency displayed increased, locally clustered mutagenesis. In summary, we provide a global view of how DNA repair pathways prevent germ cell mutagenesis.

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Immune checkpoint inhibitor sensitivity of DNA repair deficient tumors

Immunotherapy ◽

10.2217/imt-2021-0024 ◽

2021 ◽

Vol 13 (14) ◽

pp. 1205-1213

Author(s):

Pauline Rochefort ◽

Françoise Desseigne ◽

Valérie Bonadona ◽

Sophie Dussart ◽

Clélia Coutzac ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Immune Checkpoint ◽

Genome Stability ◽

Immune Checkpoint Inhibitor ◽

Checkpoint Inhibitor ◽

Excision Repair ◽

Checkpoint Inhibitors ◽

Repair Deficiency ◽

Dna Repair Deficiency

Faithful DNA replication is necessary to maintain genome stability and implicates a complex network with several pathways depending on DNA damage type: homologous repair, nonhomologous end joining, base excision repair, nucleotide excision repair and mismatch repair. Alteration in components of DNA repair machinery led to DNA damage accumulation and potentially carcinogenesis. Preclinical data suggest sensitivity to immune checkpoint inhibitors in tumors with DNA repair deficiency. Here, we review clinical studies that explored the use of immune checkpoint inhibitor in patient harboring tumor with DNA repair deficiency.

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DNA Repair Biosensor-Identified DNA Damage Activities of Endophyte Extracts from Garcinia cowa

Biomolecules ◽

10.3390/biom10121680 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1680

Author(s):

Tassanee Lerksuthirat ◽

Rakkreat Wikiniyadhanee ◽

Sermsiri Chitphuk ◽

Wasana Stitchantrakul ◽

Somponnat Sampattavanich ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Fluorescent Proteins ◽

Strand Break ◽

Control Group ◽

Focus Formation ◽

Dna Damage And Repair ◽

Biological Compounds ◽

Repair Pathways ◽

Garcinia Cowa

Recent developments in chemotherapy focus on target-specific mechanisms, which occur only in cancer cells and minimize the effects on normal cells. DNA damage and repair pathways are a promising target in the treatment of cancer. In order to identify novel compounds targeting DNA repair pathways, two key proteins, 53BP1 and RAD54L, were tagged with fluorescent proteins as indicators for two major double strand break (DSB) repair pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). The engineered biosensor cells exhibited the same DNA repair properties as the wild type. The biosensor cells were further used to investigate the DNA repair activities of natural biological compounds. An extract from Phyllosticta sp., the endophyte isolated from the medicinal plant Garcinia cowa Roxb. ex Choisy, was tested. The results showed that the crude extract induced DSB, as demonstrated by the increase in the DNA DSB marker γH2AX. The damaged DNA appeared to be repaired through NHEJ, as the 53BP1 focus formation in the treated fraction was higher than in the control group. In conclusion, DNA repair-based biosensors are useful for the preliminary screening of crude extracts and biological compounds for the identification of potential targeted therapeutic drugs.

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Functional Characterization of Excision Repair and RecA-Dependent Recombinational DNA Repair in Campylobacter jejuni

Journal of Bacteriology ◽

10.1128/jb.01817-08 ◽

2009 ◽

Vol 191 (12) ◽

pp. 3785-3793 ◽

Cited By ~ 25

Author(s):

Esther J. Gaasbeek ◽

Fimme J. van der Wal ◽

Jos P. M. van Putten ◽

Paulo de Boer ◽

Linda van der Graaf-van Bloois ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Campylobacter Jejuni ◽

Uv Irradiation ◽

Excision Repair ◽

Spontaneous Mutation ◽

Functional Characterization ◽

Point Mutations ◽

Phase Variable ◽

Repair Mechanisms

ABSTRACT The presence and functionality of DNA repair mechanisms in Campylobacter jejuni are largely unknown. In silico analysis of the complete translated genome of C. jejuni NCTC 11168 suggests the presence of genes involved in methyl-directed mismatch repair (MMR), nucleotide excision repair, base excision repair (BER), and recombinational repair. To assess the functionality of these putative repair mechanisms in C. jejuni, mutS, uvrB, ung, and recA knockout mutants were constructed and analyzed for their ability to repair spontaneous point mutations, UV irradiation-induced DNA damage, and nicked DNA. Inactivation of the different putative DNA repair genes did not alter the spontaneous mutation frequency. Disruption of the UvrB and RecA orthologues, but not the putative MutS or Ung proteins, resulted in a significant reduction in viability after exposure to UV irradiation. Assays performed with uracil-containing plasmid DNA showed that the putative uracil-DNA glycosylase (Ung) protein, important for initiation of the BER pathway, is also functional in C. jejuni. Inactivation of recA also resulted in a loss of natural transformation. Overall, the data indicate that C. jejuni has multiple functional DNA repair systems that may protect against DNA damage and limit the generation of genetic diversity. On the other hand, the apparent absence of a functional MMR pathway may enhance the frequency of on-and-off switching of phase variable genes typical for C. jejuni and may contribute to the genetic heterogeneity of the C. jejuni population.

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Characteristics of mutational signatures of unknown etiology

NAR Cancer ◽

10.1093/narcan/zcaa026 ◽

2020 ◽

Vol 2 (3) ◽

Author(s):

Xiaoju Hu ◽

Zhuxuan Xu ◽

Subhajyoti De

Keyword(s):

Dna Damage ◽

Point Mutations ◽

Gc Content ◽

Unknown Origin ◽

Unknown Etiology ◽

Mutational Signatures ◽

Dna Damage And Repair ◽

Disease Etiology ◽

Repair Processes ◽

A Genome

Abstract Although not all somatic mutations are cancer drivers, their mutational signatures, i.e. the patterns of genomic alterations at a genome-wide scale, provide insights into past exposure to mutagens, DNA damage and repair processes. Computational deconvolution of somatic mutation patterns and expert curation pan-cancer studies have identified a number of mutational signatures associated with point mutations, dinucleotide substitutions, insertions and deletions, and rearrangements, and have established etiologies for a subset of these signatures. However, the mechanisms underlying nearly one-third of all mutational signatures are not yet understood. The signatures with established etiology and those with hitherto unknown origin appear to have some differences in strand bias, GC content and nucleotide context diversity. It is possible that some of the hitherto ‘unknown’ signatures predominantly occur outside gene regions. While nucleotide contexts might be adequate to establish etiologies of some mutational signatures, in other cases additional features, such as broader (epi)genomic contexts, including chromatin, replication timing, processivity and local mutational patterns, may help fully understand the underlying DNA damage and repair processes. Nonetheless, remarkable progress in characterization of mutational signatures has provided fundamental insights into the biology of cancer, informed disease etiology and opened up new opportunities for cancer prevention, risk management, and therapeutic decision making.

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RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer

10.1101/2020.11.21.392878 ◽

2020 ◽

Author(s):

Damian Wojtowicz ◽

Jan Hoinka ◽

Bayarbaatar Amgalan ◽

Yoo-Ah Kim ◽

Teresa M. Przytycka

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Mutational Signatures ◽

Dna Damage And Repair ◽

Therapeutic Implications ◽

Mutational Landscape ◽

Repair Processes ◽

Cancer Genomes ◽

Current Paradigm ◽

Mutational Processes

AbstractMany mutagenic processes leave characteristic imprints on cancer genomes known as mutational signatures. These signatures have been of recent interest regarding their applicability in studying processes shaping the mutational landscape of cancer. In particular, pinpointing the presence of altered DNA repair pathways can have important therapeutic implications. However, mutational signatures of DNA repair deficiencies are often hard to infer. This challenge emerges as a result of deficient DNA repair processes acting by modifying the outcome of other mutagens. Thus, they exhibit non-additive effects that are not depicted by the current paradigm for modeling mutational processes as independent signatures. To close this gap, we present RepairSig, a method that accounts for interactions between DNA damage and repair and is able to uncover unbiased signatures of deficient DNA repair processes. In particular, RepairSig was able to replace three MMR deficiency signatures previously proposed to be active in breast cancer, with just one signature strikingly similar to the experimentally derived signature. As the first method to model interactions between mutagenic processes, RepairSig is an important step towards biologically more realistic modeling of mutational processes in cancer. The source code for RepairSig is publicly available at https://github.com/ncbi/RepairSig.

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Potentiation of Melphalan-Induced Cytotoxicity through Targeting of the Base Excision Repair Pathway in Multiple Myeloma.

Blood ◽

10.1182/blood.v110.11.4799.4799 ◽

2007 ◽

Vol 110 (11) ◽

pp. 4799-4799

Author(s):

April M. Reed ◽

Melissa L. Fishel ◽

Mark R. Kelley ◽

Rafat Abonour

Keyword(s):

Multiple Myeloma ◽

Dna Damage ◽

Dna Repair ◽

Side Effects ◽

Small Molecule ◽

Base Excision Repair ◽

Excision Repair ◽

Chemotherapeutic Agents ◽

Repair Pathways ◽

Base Excision

Abstract Melphalan (M) is an active agent against multiple myeloma (MM). One of the obstacles with M treatment is the patient’s ability to tolerate side effects such as mucositis and pancytopenia. This is especially true for those patients >70 years of age. We hypothesize that potentiation of M-induced cytotoxicity is possible in MM with agents that target, and therefore further imbalance, multiple DNA repair pathways. A key protein in the Base Excision Repair (BER) pathway, Apurinic/apyrimidinic endonuclease/ redox factor (APE1/Ref-1 or APE1) plays a major role in the repair of damage caused by chemotherapeutic agents including M and Temozolomide (TMZ), interacts with a number of transcription factors (HIF1-a, p53, AP1, NFkB, etc) to regulate their function through oxidation/reduction (redox) signaling, and is overexpressed in refractory/relapsed MM cells. Furthermore, a reduction in APE1 protein sensitizes MM cells to melphalan indicating that inhibition of this protein may have therapeutic potential in MM. In order to decipher the importance of APE1’s redox and repair functions in MM cells’ response to DNA damage via melphalan and TMZ, we have available to us small molecule APE1 inhibitors that affect only the repair activity or only the redox activity of APE1. The mechanism of action of MLP is primarily via monoadduct leading to DNA interstrand cross-link (ICL) formation which is processed by the Nucleotide Excision Repair (NER) pathway. MLP also causes N7methyl-G and N3methyl-A adduct formation which are repaired by the BER pathway. For these studies, we treated RPMI 8226 cells with several chemotherapeutic agents: M; TMZ, which creates primarily N7methyl-G and N3methyl-A adducts; Methoxyamine (MX), which has been shown to inhibit further processing by the BER pathway; and a small molecule which blocks the redox function of APE1. Our purpose was to overwhelm the DNA repair pathways by causing the accumulation of DNA repair intermediates and inducing apoptosis. M-induced cytotoxicity is enhanced by TMZ (CI=0.08), MX (CI=0.89), and E3330 (CI=0.06), and this effect was synergistic as determined by CalcuSyn software which generates median effect and combinational index (CI) values, with CI<1 indicative of synergy. Using MX to inhibit APE1 in combination with TMZ results in an increase in DNA damage and an increase in apoptosis in 8226 cells. Furthermore, the combination of the redox inhibitor + MX which blocks both functions of APE1 also results in an increase in apoptosis in the MM cells. Further studies include the addition of M to these combinations that are demonstrating an increase in efficacy in MM cells. These results indicate that using these DNA repair-targeted agents in addition to MLP may be a feasible way to increase the effect of the M on MM cells. The potential advantages to patients would be that they would be able to tolerate more treatments and that the combination treatments would be more effective than treatment with M alone. We anticipate that effective modulation of M and/or TMZ will overcome resistance without compromising efficacy and help to alleviate some of the side effects patients have to endure with melphalan treatment. This may be particularly advantageous to the more elderly patients.

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Genetic Interactions of DNA Repair Pathways in the Pathogen Neisseria meningitidis

Journal of Bacteriology ◽

10.1128/jb.00161-07 ◽

2007 ◽

Vol 189 (15) ◽

pp. 5728-5737 ◽

Cited By ~ 27

Author(s):

Tonje Davidsen ◽

Hanne K. Tuven ◽

Magnar Bjørås ◽

Einar A. Rødland ◽

Tone Tønjum

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Neisseria Meningitidis ◽

Excision Repair ◽

Spontaneous Mutation ◽

Recombinational Repair ◽

Major Pathway ◽

Current Increase ◽

E Coli ◽

Repair Pathways

ABSTRACT The current increase in the incidence and severity of infectious diseases mandates improved understanding of the basic biology and DNA repair profiles of virulent microbes. In our studies of the major pathogen and model organism Neisseria meningitidis, we constructed a panel of mutants inactivating genes involved in base excision repair, mismatch repair, nucleotide excision repair (NER), translesion synthesis, and recombinational repair pathways. The highest spontaneous mutation frequency among the N. meningitidis single mutants was found in the MutY-deficient strain as opposed to mutS mutants in Escherichia coli, indicating a role for meningococcal MutY in antibiotic resistance development. Recombinational repair was recognized as a major pathway counteracting methyl methanesulfonate-induced alkylation damage in the N. meningitidis. In contrast to what has been shown in other species, meningococcal NER did not contribute significantly to repair of alkylation-induced DNA damage, and meningococcal recombinational repair may thus be one of the main pathways for removal of abasic (apurinic/apyrimidinic) sites and strand breaks in DNA. Conversely, NER was identified as the main meningococcal defense pathway against UV-induced DNA damage. N. meningitidis RecA single mutants exhibited only a moderate decrease in survival after UV exposure as opposed to E. coli recA strains, which are extremely UV sensitive, possibly reflecting the lack of a meningococcal SOS response. In conclusion, distinct differences between N. meningitidis and established DNA repair characteristics in E. coli and other species were identified.

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Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation

PLoS ONE ◽

10.1371/journal.pone.0250291 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0250291

Author(s):

Bettina Meier ◽

Nadezda V. Volkova ◽

Ye Hong ◽

Simone Bertolini ◽

Víctor González-Huici ◽

...

Keyword(s):

Dna Repair ◽

Germ Cell ◽

Excision Repair ◽

Base Substitution ◽

Structural Variants ◽

C Elegans ◽

Repair Deficiency ◽

Repair Pathways ◽

Cell Genome ◽

Dna Repair Mutants

Maintaining genome integrity is particularly important in germ cells to ensure faithful transmission of genetic information across generations. Here we systematically describe germ cell mutagenesis in wild-type and 61 DNA repair mutants cultivated over multiple generations. ~44% of the DNA repair mutants analysed showed a >2-fold increased mutagenesis with a broad spectrum of mutational outcomes. Nucleotide excision repair deficiency led to higher base substitution rates, whereaspolh-1(Polη) andrev-3(Polζ) translesion synthesis polymerase mutants resulted in 50–400 bp deletions. Signatures associated with defective homologous recombination fall into two classes: 1)brc-1/BRCA1andrad-51/RAD51 paralog mutants showed increased mutations across all mutation classes, 2)mus-81/MUS81andslx-1/SLX1nuclease, andhim-6/BLM,helq-1/HELQorrtel-1/RTEL1helicase mutants primarily accumulated structural variants. Repetitive and G-quadruplex sequence-containing loci were more frequently mutated in specific DNA repair backgrounds. Tandem duplications embedded in inverted repeats were observed inhelq-1helicase mutants, and a unique pattern of ‘translocations’ involving homeologous sequences occurred inrip-1recombination mutants.atm-1/ATM checkpoint mutants harboured structural variants specifically enriched in subtelomeric regions. Interestingly, locally clustered mutagenesis was only observed for combinedbrc-1andcep-1/p53 deficiency. Our study provides a global view of how different DNA repair pathways contribute to prevent germ cell mutagenesis.

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