Nucleotide Excision Repair Research Articles

Constructing mRNA-meth-miRNA single-sample networks to reveal the molecular interaction patterns induced by lunar orbital stressors in rice (Oryzasativa).

To explore the bio-effects during Moon exploration missions, we utilized the Chang'E 5 probe to carry the seeds of Oryza. Sativa L., which were later returned to Earth after 23 days in lunar orbit and planted in an artificial climate chamber. Compared to the control group, rice seeds that underwent spaceflight showed inhibited growth and development when planted on the ground. Then we collected samples and employed RNA sequencing (RNA-Seq) and whole-genome bisulfite sequencing (WGBS) in the tillering and heading stages of rice. To gain a comprehensive understanding of the dysregulation in molecular interaction patterns during Moon exploration, a bioinformatics pipeline based on mRNA-meth-miRNA Single-Sample Networks (SSNs) was developed. Specifically, we constructed four SSNs for each sample at the mRNA, DNA methylation (promoter and gene bodies), and miRNA levels. By combining with the Protein-Protein Interaction (PPI) network, SSNs can character individual-specific gene interaction patterns. Under spaceflight conditions, distinct interaction patterns emerge across various omics levels. However, the molecules driving changes at each omics level predominantly regulate consistent biological functions, such as metabolic processes, DNA damage and repair, cell cycle, developmental processes, etc. In the tillering stage, pathways such as ubiquitin mediated proteolysis, nucleotide excision repair, and nucleotide metabolism are significantly enriched. Moreover, we identified 18 genes that played key/hub roles in the dysregulation of multi-omics molecular interaction patterns, and observed their involvement in regulating the above biological processes. As aforementioned, our multi-omics SSNs method can reveal the molecular interaction patterns under deep space exploration.

STK19: A critical factor coordinating transcription-coupled DNA repair

STK19: A critical factor coordinating transcription-coupled DNA repair

An Oxidative Stress Nanoamplifier to Enhance the Efficacy of Cisplatin in Head and Neck Cancer

Cisplatin (CP) is a first‐line platinum‐based drug used for the treatment of head and neck cancer. However, tumor cells can diminish the therapeutic effects of CP through the detoxification system mediated by glutathione (GSH) and the nucleotide excision repair (NER) pathway. Herein, we present a light‐activable and pH‐responsive oxidative stress nanoamplifier (FPLC@IR OSNA), comprising an amphiphilic compound (FPLC) with Fmoc‐lysine acting as a connector between a nitroimidazole derivative and a pH‐responsive cinnamaldehyde (CA) derivative, loaded with photosensitizer IR780. The acidic microenvironment of lysosome can trigger the release of CA to produce H2O2, which breaks down into oxygen, further improving the phototherapy efficacy mediated by IR780 irradiation. The consumption of oxygen during the phototherapy process induces hypoxia, prompting the reduction of nitroimidazole to aminoimidazole and leading to reduced GSH synthesis, enhancing tumor cell death induced by CP. Meanwhile, the accumulation of intracellular reactive oxygen species (ROS) during phototherapy attenuates the nuclear NER pathway, further augmenting the therapy effect of CP. This strategy, by combining FPLC@IR OSNA with laser and CP, significantly promotes the therapeutic effect in vitro, and notably inhibits tumor growth in both Cal27 cell line‐derived xenograft models and patient‐derived xenograft models.

An Oxidative Stress Nanoamplifier toEnhance the Efficacy of Cisplatin in Head and Neck Cancer.

Cisplatin (CP) is a first-line platinum-based drug used for the treatment of head and neck cancer. However, tumor cells can diminish the therapeutic effects of CP through the detoxification system mediated by glutathione (GSH) and the nucleotide excision repair (NER) pathway. Herein, we present a light-activable and pH-responsive oxidative stress nanoamplifier (FPLC@IR OSNA), comprising an amphiphilic compound (FPLC) with Fmoc-lysine acting as a connector between a nitroimidazole derivative and a pH-responsive cinnamaldehyde (CA) derivative, loaded with photosensitizer IR780. The acidic microenvironment of lysosome can trigger the release of CA to produce H2O2, which breaks down into oxygen, further improving the phototherapy efficacy mediated by IR780 irradiation. The consumption of oxygen during the phototherapy process induces hypoxia, prompting the reduction of nitroimidazole to aminoimidazole and leading to reduced GSH synthesis, enhancing tumor cell death induced by CP. Meanwhile, the accumulation of intracellular reactive oxygen species (ROS) during phototherapy attenuates the nuclear NER pathway, further augmenting the therapy effect of CP. This strategy, by combining FPLC@IR OSNA with laser and CP, significantly promotes the therapeutic effect in vitro, and notably inhibits tumor growth in both Cal27 cell line-derived xenograft models and patient-derived xenograft models.

P-1835. Evolution of Antibiotic Resistance Patterns in Acinetobacter baumannii Clinical Isolates in Response to Bleach Exposure

Abstract Background Acinetobacter baumannii (Ab) is a common cause of drug-resistant infections. Ab rapidly acquires antibiotic resistance and can survive exposure to numerous antiseptics such as bleach. Prior research has demonstrated increased antibiotic resistance in Ab following exposure to antiseptics, likely due to increased expression of efflux pumps, but the relationship between antiseptic resistance and antibiotic resistance is not well known. In this study, we describe the evolution of antibiotic resistance in two Ab isolates following exposure to bleach.Table 1:Antibiotic Susceptibilities for Evolved Strains of ACB3 Antibiotic susceptibilities for the evolved strains of ACB3 are depicted. For each strain, antibiotic susceptibilities were determined based on Clinical & Laboratory Standards Institute (CLSI) reference standards, and were classified as susceptible (S) or non-susceptible (NS). Non-susceptible values were those that were determined to be either intermediate or resistant. ACB3 was initially susceptible to most antibiotics at G0, and developed increased resistance to all antibiotic classes by G450. Methods Two Ab clinical isolates, ACB3 and ACB9, were exposed to sublethal (0.01%) concentrations of bleach and grown in triplicate, with strains selected at baseline (G0), the 450th generation (G450), and the 1000th generation (G1000) for further analysis. Antibiotic susceptibility profiles for each strain were established by determining minimum inhibitory concentration (MIC) values against 24 standard-of-care antibiotics using broth microdilution assays. Whole genome sequencing (WGS) of each strain was performed to evaluate for the emergence of new alleles to affecting antibiotic resistance.Table 2:Antibiotic Susceptibilities for Evolved Strains of ACB9 Antibiotic susceptibilities for the evolved strains of ACB9 are depicted. For each strain, antibiotic susceptibilities were determined based on Clinical & Laboratory Standards Institute (CLSI) reference standards, and were classified as susceptible (S) or non-susceptible (NS). Non-susceptible values were those that were determined to be either intermediate or resistant. NS* denotes strains with MIC values that were decreased, but not enough to be classified as susceptible. ACB9 was initially PDR at G0 but developed increased susceptibility to all aminoglycoside and tetracycline drugs by G1000. Results The ACB3 line was susceptible to most antibiotics at G0, but developed increased resistance to various antibiotics by G450, particularly against aminoglycoside and beta-lactam drugs (Table 1). Conversely, the ACB9 line was pan-drug resistant (PDR) at G0 but developed increased susceptibility to all aminoglycoside and tetracycline drugs by G1000 (Tables 2, 3). WGS of ACB9 G1000 demonstrated mutations in uvrA and uvrB, which encode nucleotide excision repair proteins, with concomitant mutations in the ABC transporter TssG, and type IV secretion system (T4SS) proteins TssC and VgrG. Mutations were observed in numerous other unidentified genes with close homology to ABC transporters, MFS efflux pumps, and OprD porins.Table 3:Minimum Inhibitor Concentration (MIC) Values for Aminoglycoside and Tetracycline Drugs Against Evolved Strains of ACB9 MIC values for aminoglycoside and tetracycline drugs against evolved strains of ACB9 are depicted. All three triplicates of ACB9 were initially resistant to all aminoglycoside and tetracycline drugs tested at G0. By G1000, all three triplicates demonstrated increased susceptibility to all aminoglycoside and tetracycline drugs, as indicated by decreased MIC values. Conclusion We describe the evolution of antibiotic resistance in Ab after exposure to bleach. ACB3 was initially susceptible to most antibiotics but developed increased resistance. ACB9 was initially PDR but developed increased susceptibility to aminoglycoside and tetracycline drugs, likely due to mutations in hypermutators uvrA and uvrB, enabling mutations in genes which may confer resistance to these drugs. Disclosures All Authors: No reported disclosures

Abstract A011: Activity of antibody-drug conjugates with radiation in preclinical bladder cancer models

Abstract Antibody-drug conjugates (ADCs) are transforming the treatment landscape in metastatic bladder cancer, but the role of ADCs in localized disease is uncertain. Radiation is a central component of trimodality therapy (TMT), a curative-intent treatment approach for muscle-invasive bladder cancer (MIBC) that includes concurrent radiation and cytotoxic chemotherapy. We investigated the safety and efficacy of combining novel ADCs with radiation in preclinical bladder cancer models. We observed additive cytotoxicity in vitro, and the combination of ADCs with conformal fractionated radiation was well-tolerated and resulted in improved tumor control compared to either agent alone in vivo. We also assessed the impact of DNA repair pathway alterations commonly observed in bladder tumors on sensitivity to ADCs alone and in combination with radiation and DNA repair targeted agents. Homologous recombination (HR) deficiency modestly sensitized bladder cancer cells to MMAE, the payload of the ADC enfortumab vedotin (EV), and potently sensitized cells to govitecan, the payload of the ADC sacitumuzab govitecan (SG). Conversely, nucleotide excision repair (NER) deficiency did not sensitize cells to either MMAE or govitecan. The combination of govitecan and PARP inhibition resulted in synergistic cell killing independent of HR or NER status. Together these data provide preclincal support for clinical efforts to combine ADCs with radiation in MIBC and identify rationale combination therapy approaches. Citation Format: Yuzhen Zhou, Surish Shanmugam, Vincent D'Andrea, Isabella Stelter, Dag Stormoen, Rea Chroneos, Timothy Hanlon, Ilana Epstein, Raie Bekele, William Anderson, Zoltan Szallasi, Joaquim Bellmunt, Kent Mouw. Activity of antibody-drug conjugates with radiation in preclinical bladder cancer models. [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Targeted Therapies in Combination with Radiotherapy; 2025 Jan 26-29; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(2_Suppl):Abstract nr A011.

DNA Repair Capacity and Clinicopathological Characteristics in Puerto Rican Hispanic/Latino Patients with Metastatic Castration-Resistant Prostate Cancer.

Prostate cancer (PCa) accounts for 22% of the new cases diagnosed in Hispanic/Latino (H/L) men in the US. PCa has the highest incidence (38.3%) and mortality (16.4%) among all types of cancer diagnosed in Puerto Rico. We previously showed that PCa patients (n = 41) have a significant reduction of 59% in their levels of DNA repair capacity (DRC) when compared to controls (n = 14). This study aimed to evaluate DRC levels through the nucleotide excision repair (NER) pathway for the first time in 16 Puerto Rican H/L men with metastatic castration-resistant PCa (mCRPCa) while establishing comparisons with controls and PCa patients with indolent and aggressive disease. Blood samples and clinicopathological data from PCa cases (n = 71) and controls (n = 25) were evaluated. PCa cases were stratified into mCRPCa (n = 16), aggressive (n = 31), and indolent (n = 24). DRC levels through NER were measured in lymphocytes with the CometChip assay. The stratification by Gleason score (GS) was GS6 (n = 7), GS7 (n = 23), GS ≥ 8 (n = 20), and mCRPCa patients (n = 16). Significant statistical differences were found when comparing the DRC values of the controls with any other of the four PCa patient groups. mCRPCa patients had the lowest mean DRC level of all four patient groups studied. The mean DRC level of mCRPCa patients was 6.65%, and compared to the controls, this represented a statistically significant reduction of 62% (p < 0.0001). Further analysis was performed to evaluate the contributions of age, anthropometric measurements, and prostate-specific antigen (PSA) levels to the DRC. Kaplan-Meier curves of mCRPCa revealed that survival probability decreased by approximately 50% by 30 months. This pilot study uses a blood-based phenotypic assay to present the first report of mCRPCa in Puerto Rican men and at a global level of DRC levels of mCRPCa patients. This study evaluated DRC levels through the NER pathway for the first time in 16 Puerto Rican H/L men with mCRPCa. Significant differences in DRC values were found between the controls and the three PCa patient groups. Kaplan-Meier curves revealed that survival probability decreased by approximately 50% by 30 months, and only 20% of the cohort was alive at 50 months, confirming the lethality of mCRPCa in this H/L population. This pilot study represents the first report of metastatic PCa in Puerto Rican men at a global level of DRC levels of mCRPCa patients using a blood-based phenotypic assay.

Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex.

Altered DNA dynamics at lesion sites are implicated in how DNA repair proteins sense damage within genomic DNA. Using laser temperature-jump (T-jump) spectroscopy combined with cytosine-analog FörsterResonance Energy Transfer (FRET) probes that sense local DNA conformations, we measured the intrinsic dynamics of DNA containing 3 base-pair mismatches recognized in vitro by Rad4 (yeast ortholog of XPC). Rad4/XPC recognizes diverse lesions from environmental mutagens and initiates nucleotide excision repair. T-jump measurements, together with a novel and rigorous comparison with equilibrium FRET, uncovered conformational dynamics spanning multiple timescales and revealed key differences between Rad4-specific and non-specific DNA. AT-rich non-specific sites (matched or mismatched) exhibited dynamics primarily within the T-jump observation window, albeit with some amplitude in 'missing' fast (<20 μs) kinetics. These fast-kinetics amplitudes were dramatically larger for specific sites (CCC/CCC and TTT/TTT), which also exhibited 'missing' slow (>50 ms) kinetics at elevated temperatures, unseen in non-specific sites. We posit that the rapid (μs-ms) intrinsic DNA fluctuations help stall a diffusing protein at AT-rich/damaged sites and that the>50-ms kinetics in specific DNA reflect a propensity to adopt unwound/bent conformations resembling Rad4-bound DNA structures. These studies provide compelling evidence for sequence/structure-dependent intrinsic DNA dynamics and deformability that likely govern damage sensing by Rad4.

Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency.

Cyclobutane pyrimidine dimers (CPDs) are formed in DNA following exposure to ultraviolet (UV) light and are mutagenic unless repaired by nucleotide excision repair (NER). It is known that CPD repair rates vary in different genome regions owing to transcription-coupled NER and differences in chromatin accessibility; however, the impact of regional chromatin organization on CPD formation remains unclear. Furthermore, nucleosomes are known to modulate UV damage and repair activity, but how these damage and repair patterns are affected by the overarching chromatin domains in which these nucleosomes are located is not understood. Here, we generated a new CPD damage map in Drosophila S2 cells using CPD-seq and analyzed it alongside existing excision repair-sequencing (XR-seq) data to compare CPD damage formation and repair rates across five previously established chromatin types in Drosophila This analysis revealed that repair activity varies substantially across different chromatin types, whereas CPD formation is relatively unaffected. Moreover, we observe distinct patterns of repair activity in nucleosomes located in different chromatin types, which we show is owing to domain-specific differences in nucleosome repeat length (NRL). These findings indicate that NRL is altered in different chromatin types in Drosophila and that changes in NRL modulate the repair of UV lesions.

Genetic signatures of ERCC1 and ERCC2 expression, along with SNPs variants, unveil favorable prognosis in SCLC patients undergoing platinum-based chemotherapy.

Platinum chemotherapy (CT) remains the backbone of systemic therapy for patients with small-cell lung cancer (SCLC). The nucleotide excision repair (NER) pathway plays a central role in the repair of the DNA damage exerted by platinum agents. Alteration in this repair mechanism may affect patients' survival. We conducted a retrospective analysis of data from 38 patients with extensive disease (ED)-SCLC who underwent platinum-CT at the Clinical Oncology Unit, Careggi University Hospital, Florence (Italy), from 2015 to 2020. mRNA expression analysis and single nucleotide polymorphism (SNP) characterization of three NER pathway genes-namely ERCC1, ERCC2, and ERCC5-were performed on patient tumor samples. Overall, elevated expression of ERCC genes was observed in SCLC patients compared to healthy controls. Patients with low ERCC1 and ERCC5 expression levels exhibited a better median progression-free survival (mPFS = 7.1 vs. 4.9 months, p = 0.39 for ERCC1 and mPFS = 6.9 vs. 4.8 months, p = 0.093 for ERCC5) and overall survival (mOS = 8.7 vs. 6.0 months, p = 0.4 for ERCC1 and mOS = 7.2 vs. 6.2 months, p = 0.13 for ERCC5). Genotyping analysis of five SNPs of ERCC genes showed a longer survival in patients harboring the wild-type genotype or the heterozygous variant of the ERCC1 rs11615 SNP (p = 0.24 for PFS and p = 0.14 for OS) and of the rs13181 and rs1799793 ERCC2 SNPs (p = 0.43 and p = 0.26 for PFS and p = 0.21 and p = 0.16 for OS, respectively) compared to patients with homozygous mutant genotypes. The comprehensive analysis of ERCC gene expression and SNP variants appears to identify patients who derive greater survival benefits from platinum-CT.

Comparative Studies on Bulky DNA Damage Binding by Nucleotide Excision Repair Proteins Using Surface Plasmon Resonance, Differential Scanning Fluorometry, and DNase I Footprinting.

Nucleotide excision repair is a crucial cellular mechanism that ensures genomic stability, thereby preventing mutations that can lead to cancer. The human XPC and its yeast ortholog Rad4 protein complexes are central to this process and were the focus of the study. We used surface plasmon resonance and differential scanning fluorimetry to study the binding characteristics of XPC and Rad4 when bound to the bulky cluster di-FAAF-containing 55-mer duplex DNA. Our findings revealed that XPC binds 10 times more significant affinity to control and di-FAAF-modified DNA than Rad4 with greater protein-DNA interactions. Differential scanning fluorimetry indicates that Rad4 causes comparatively more significant conformational changes upon complexation with the damaged DNA. We conducted DNase I footprinting of the Rad4/DNA complex for the first time by determining the regions protected from DNase I digestion. The DNA at the lesion is entirely resistant to digestion by DNase I in the absence of Rad4 several nucleotides to the 3'-side of the first FAAF lesion. The lack of DNase I cleavage at the lesions did not change upon adding Rad4. However, in the presence of Rad4, a footprint is observed on the 7-nucleotide region (5'-TGGTGAT-3') of the complementary strand to the 3' side of the lesion.

DNA replication initiation drives focal mutagenesis and rearrangements in human cancers

AbstractThe rate and pattern of mutagenesis in cancer genomes is significantly influenced by DNA accessibility and active biological processes. Here we show that efficient sites of replication initiation drive and modulate specific mutational processes in cancer. Sites of replication initiation impede nucleotide excision repair in melanoma and are off-targets for activation-induced deaminase (AICDA) activity in lymphomas. Using ductal pancreatic adenocarcinoma as a cancer model, we demonstrate that the initiation of DNA synthesis is error-prone at G-quadruplex-forming sequences in tumours displaying markers of replication stress, resulting in a previously recognised but uncharacterised mutational signature. Finally, we demonstrate that replication origins serve as hotspots for genomic rearrangements, including structural and copy number variations. These findings reveal replication origins as functional determinants of tumour biology and demonstrate that replication initiation both passively and actively drives focal mutagenesis in cancer genomes.

SPRTN metalloprotease participates in repair of ROS-mediated DNA-protein crosslinks

Exposure to reactive oxygen species (ROS) can induce DNA-protein crosslinks (DPCs), unusually bulky DNA lesions that block replication and transcription and play a role in aging, cancer, cardiovascular disease, and neurodegenerative disorders. Repair of DPCs depends on the coordinated efforts of proteases and DNA repair enzymes to cleave the protein component of the lesion to smaller DNA-peptide crosslinks which can be processed by tyrosyl-DNA phosphodiesterases 1 and 2, nucleotide excision and homologous recombination repair pathways. DNA-dependent metalloprotease SPRTN plays a role in DPC repair, and SPRTN-deficient mice exhibit an accelerated aging phenotype and develop liver cancer early in life. We investigated the role of the SPRTN enzyme in the repair of DPCs produced by a free radical mechanism. Sprtn-deficient MEF cells treated with ionizing radiation had higher levels of total DPCs and exhibited greater sensitivity upon exposure to hydrogen peroxide and other crosslinking agents including cisplatin, phosphoramide mustard, and 1,2,3,4-diepoxybutane. Using a sensitive and accurate nanoLC-ESI+-MS/MS assay, we specifically measured the radical-induced crosslinking of thymidine in DNA crosslinking of thymidine in DNA to tyrosine in proteins (dT-Tyr) in the tissues of SPRTN hypomorphic (SprtnH/H) and wild type mice. Genomic DNA isolated from the tissues of SPRTN hypomorphic (SprtnH/H) mice exhibited higher levels of dT-Tyr in the liver, brain, heart, and kidney than wild-type animals. Overall, our results are consistent with the understanding that SPRTN has a role in maintaining genomic integrity upon exposure to ionizing radiation and endogenous reactive oxygen species.

Generation and characterization of CRISPR-Cas9-mediated XPC gene knockout in human skin cells

Xeroderma pigmentosum group C (XPC) is a versatile protein crucial for sensing DNA damage in the global genome nucleotide excision repair (GG-NER) pathway. This pathway is vital for mammalian cells, acting as their essential approach for repairing DNA lesions stemming from interactions with environmental factors, such as exposure to ultraviolet (UV) radiation from the sun. Loss-of-function mutations in the XPC gene confer a photosensitive phenotype in XP-C patients, resulting in the accumulation of unrepaired UV-induced DNA damage. This remarkable increase in DNA damage tends to elevate by 10,000-fold the risk of developing melanoma and non-melanoma skin cancers. To date, creating accurate and reproducible models to study human XP-C disease has been an important challenge. To tackle this, we used CRISPR-Cas9 technology in order to knockout the XPC gene in various human skin cells (keratinocytes, fibroblasts, and melanocytes). After validation of the knockout in these edited skin cells, we showed that they recapitulate the major phenotypes of XPC mutations: photosensitivity and the impairment of UV-induced DNA damage repair. Moreover, these knockout cells demonstrated a reduced proliferative capacity compared to their respective controls. Finally, to better mimic the disease environment, we built a 3D reconstructed skin using these XPC knockout skin cells. This model exhibited an abnormal behavior, showing an extensive remodeling of its extracellular matrix compared to normal skin. Analyzing the composition of the fibroblast secretome revealed a significant augmented shift in the inflammatory response following XPC knockout. Our innovative “disease on a dish” approach can provide valuable insights into the molecular mechanisms underlying XP-C disease, paving the way to design novel preventive and therapeutic strategies to alleviate the disease phenotype. Also, given the high risk of skin cancer onset in XP-C disease, our new approach can serve as a link to draw novel insights into this elusive field.

Contributing factors to the oxidation-induced mutational landscape in human cells.

8-oxoguanine (8-oxoG) is a common oxidative DNA lesion that causes G > T substitutions. Determinants of local and regional differences in 8-oxoG-induced mutability across genomes are currently unknown. Here, we show DNA oxidation induces G > T substitutions and insertion/deletion (INDEL) mutations in human cells and cancers. Potassium bromate (KBrO3)-induced 8-oxoGs occur with similar sequence preferences as their derived substitutions, indicating that the reactivity of specific oxidants dictates mutation sequence specificity. While 8-oxoG occurs uniformly across chromatin, 8-oxoG-induced mutations are elevated in compact genomic regions, within nucleosomes, and at inward facing guanines within strongly positioned nucleosomes. Cryo-electron microscopy structures of OGG1-nucleosome complexes indicate that these effects originate from OGG1's ability to flip outward positioned 8-oxoG lesions into the catalytic pocket while inward facing lesions are occluded by the histone octamer. Mutation spectra from human cells with DNA repair deficiencies reveals contributions of a DNA repair network limiting 8-oxoG mutagenesis, where OGG1- and MUTYH-mediated base excision repair is supplemented by the replication-associated factors Pol η and HMCES. Transcriptional asymmetry of KBrO3-induced mutations in OGG1- and Pol η-deficient cells also demonstrates transcription-coupled repair can prevent 8-oxoG-induced mutation. Thus, oxidant chemistry, chromatin structures, and DNA repair processes combine to dictate the oxidative mutational landscape in human genomes.

Multiple DNA repair pathways prevent acetaldehyde-induced mutagenesis in yeast.

Acetaldehyde is the primary metabolite of alcohol and is present in many environmental sources including tobacco smoke. Acetaldehyde is genotoxic, whereby it can form DNA adducts and lead to mutagenesis. Individuals with defects in acetaldehyde clearance pathways have increased susceptibility to alcohol-associated cancers. Moreover, a mutation signature specific to acetaldehyde exposure is widespread in alcohol and smoking-associated cancers. However, the pathways that repair acetaldehyde-induced DNA damage and thus prevent mutagenesis are vaguely understood. Here, we used Saccharomyces cerevisiae to delete genes in each of the major DNA repair pathways to identify those that alter acetaldehyde-induced mutagenesis. We observed that loss of functional nucleotide excision repair (NER) had the largest effect on acetaldehyde mutagenesis. In addition, base excision repair (BER), as well as DNA protein crosslink (DPC) repair pathways were involved in modulating acetaldehyde mutagenesis, while mismatch repair (MMR), homologous recombination (HR) and post replication repair are dispensable for acetaldehyde mutagenesis. Acetaldehyde-induced mutations in an NER-deficient (Δrad1) background were dependent on translesion synthesis as well as DNA inter-strand crosslink (ICL) repair. Moreover, whole genome sequencing of the mutated isolates demonstrated an increase in C→A changes coupled with an enrichment of gCn→A changes which is diagnostic of acetaldehyde exposure in yeast and in human cancers. Finally, downregulation of the leading strand replicative polymerase Pol epsilon, but not the lagging strand polymerase, resulted in increased acetaldehyde mutagenesis, indicating that lesions are likely formed on the leading strand. Our findings demonstrate that multiple DNA repair pathways coordinate to prevent acetaldehyde-induced mutagenesis.

Transcription-coupled repair - mechanisms of action, regulation, and associated human disorders.

The transcription-coupled repair (TCR) pathway resolves transcription-blocking DNA lesions to maintain cellular function and prevent transcriptional arrest. Stalled RNA polymerase II (RNAPII) triggers repair mechanisms, including RNAPII ubiquitination, which recruit UVSSA and TFIIH. Defects in TCR-associated genes cause disorders like Cockayne syndrome, UV-sensitive syndrome, xeroderma pigmentosum, and recently defined AMeDS. TCR safeguards transcription, linking its failure to neurodegeneration and disease phenotypes.

Transcription as a double-edged sword in genome maintenance.

Genome maintenance is essential for the integrity of the genetic blueprint, of which only a small fraction is transcribed in higher eukaryotes. DNA lesions occurring in the transcribed genome trigger transcription pausing and transcription-coupled DNA repair. There are two major transcription-coupled DNA repair pathways. The transcription-coupled nucleotide excision repair (TC-NER) pathway has been well studied for decades, while the transcription-coupled homologous recombination repair (TC-HR) pathway has recently gained attention. Importantly, recent studies have uncovered crucial roles of RNA transcripts in TC-HR, opening exciting directions for future research. Transcription also plays pivotal roles in regulating the stability of highly specialized genomic structures such as telomeres, centromeres, and fragile sites. Despite their positive function in genome maintenance, transcription and RNA transcripts can also be the sources of genomic instability, especially when colliding with DNA replication and forming unscheduled pathological RNA:DNA hybrids (R-loops), respectively. Pathological R-loops can result from transcriptional stress, which may be induced by transcription dysregulation. Future investigation into the interplay between transcription and DNA repair will reveal novel molecular bases for genome maintenance and transcriptional stress-associated genomic instability, providing therapeutic targets for human disease intervention.

Deciphering repair pathways of clustered DNA damage in human TK6 cells: insights from atomic force microscopy direct visualization.

Ionizing radiation induces various types of DNA damage, and the reparability and lethal effects of DNA damage differ depending on its spatial density. Elucidating the structure of radiation-induced clustered DNA damage and its repair processes will enhance our understanding of the lethal impact of ionizing radiation and advance progress toward precise therapeutics. Previously, we developed a method to directly visualize DNA damage using atomic force microscopy (AFM) and classified clustered DNA damage into simple base damage clusters (BDCs), complex BDCs and complex double-strand breaks (DSBs). This study investigated the repair of each type of damage in DNA-repair-deficient human TK6 cells and elucidated the association between each type of clustered DNA damage and the pathway responsible for its repair postirradiation with low linear energy transfer (LET) radiation (X-rays) and high-LET radiation (Fe-ion beams) in cells. We found that base excision repair and, surprisingly, nucleotide excision repair restored simple and complex BDCs. In addition, the number of complex DSBs in wild-type cells increases 1 h postirradiation, which was most likely caused by BDC cleavage initiated with DNA glycosylases. Furthermore, complex DSBs, which are likely associated with lethality, are repaired by homologous recombination with little contribution from nonhomologous-end joining.

Beyond Nucleotide Excision Repair: The Importance of XPF in Base Excision Repair and Its Impact on Cancer, Inflammation, and Aging.

DNA repair involves various intricate pathways that work together to maintain genome integrity. XPF (ERCC4) is a structural endonuclease that forms a heterodimer with ERCC1 that is critical in both single-strand break repair (SSBR) and double-strand break repair (DSBR). Although the mechanistic function of ERCC1/XPF has been established in nucleotide excision repair (NER), its role in long-patch base excision repair (BER) has recently been discovered through the 5'-Gap pathway. This study briefly explores the roles of XPF in different pathways to emphasize the importance of XPF in DNA repair. XPF deficiency manifests in various diseases, including cancer, neurodegeneration, and aging-related disorders; it is also associated with conditions such as Xeroderma pigmentosum and fertility issues. By examining the molecular mechanisms and pathological consequences linked to XPF dysfunction, this study aims to elucidate the crucial role of XPF in genomic stability as a repair protein in BER and provide perspectives regarding its potential as a therapeutic target in related diseases.