Nucleotide excision repair (NER) is the key pathway for the removal of DNA damage induced by UV irradiation and chemotherapeutic reagents. Protein-protein interactions are crucial for the dynamic and coordinated assembly of the proteins involved in DNA lesions. Here we focus on the role of interactions between the multi-subunit helicase/translocase complex TFIIH and the 3' endonuclease XPG. We show that XPG interacts with the p62 and XPD subunits of TFIIH through its long spacer region bridging its split active site. We show that interactions between three acidic regions of XPG and the Pleckstrin homology (PH) domain of p62 are of moderate importance for NER, while defects in the interactions with XPD fail to pull-down TFIIH and strongly reduce NER activity. These p62 and XPD interface mutations additively reduce NER activity. Unexpectedly, we show that these interactions did not impair the recruitment of XPG but instead were defective in the formation of a catalytically competent NER complex and in triggering the incision 5' to the lesion by ERCC1-XPF. Our studies provide fundamental insights into how interactions between TFIIH and XPG contribute to the NER pathway and, more generally, how modular protein-protein interactions control each step along the NER reaction coordinate.

Molecular mechanism underlying radiation resistance in esophageal squamous cell carcinoma.

AimCircular RNAs (circRNAs) have been identified as key regulators in inflammatory diseases, yet their function in pulpitis is unclear. This study investigates their potential role in the progression of pulpitis.MethodologyMicroarray and single-cell RNA sequencing were applied to assess DNA damage responses (DDR) in inflammatory pulp and its derived stem cells, respectively. qRT-PCR and Western blot were employed to detect the DNA double-strand break (DSB) marker γ-H2AX and inflammatory cytokines in pulp tissue. Bioinformatics analysis was used to identify upregulated circRNAs in inflamed DPSCs. Functional assays were performed to assess the impact of circ_0042103 on LPS-driven cellular damage and inflammation in DPSCs. The interaction between circ_0042103 and TAF15 was investigated using RNA FISH, pulldown, and nuclear-cytoplasmic fractionation assays. Transfection with circ_0042103/TAF15-siRNA in DPSCs was carried out to evaluate activation of the nucleotide excision repair (NER) pathway and its regulatory effects on DNA damage and inflammation.ResultsDDR was activated in both pulpitis and inflamed DPSCs. DNA damage showed a positive correlation with inflammation in pulpitis. In vitro, circ_0042103 upregulation amplified LPS-stimulated DDR and inflammatory signaling, whereas its knockdown alleviated both effects. Mechanistically, circ_0042103 bound TAF15, leading to decreased levels of the NER-related proteins (ERCC1 and PCNA) and increased DNA damage and inflammation.ConclusionBy interacting with TAF15, circ_0042103 reduces the levels of the NER-related proteins ERCC1 and PCNA, leading to increased DNA damage and inflammation in hDPSCs, thereby defining a circ_0042103/TAF15/NER axis in pulpitis progression.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13287-025-04817-1.

206 Background: Patients with refractory microsatellite-stable metastatic colorectal cancer (MSS mCRC), representing the vast majority of mCRC cases, derive minimal benefit from immune checkpoint inhibitor (ICI) monotherapy. Combining anti-angiogenic tyrosine kinase inhibitors (TKIs) with ICIs has emerged as a promising strategy to overcome resistance. Methods: This multicenter retrospective study compared the efficacy and safety of anlotinib plus tislelizumab (n=65) versus anlotinib monotherapy (n=59) in patients with refractory MSS mCRC. Integrative whole-exome sequencing (WES), RNA sequencing, and multiplex immunohistochemistry (mIHC) were performed on pre-treatment tumor samples (n=29 from the combination group) to identify biomarkers of response. Immunotherapy response was defined as complete response (CR), partial response (PR), or stable disease (SD) lasting ≥6 months. Results: Combination therapy significantly improved median progression-free survival (196 vs 122 days, P =0.028) and median overall survival (453 vs 245 days, P <0.001) versus monotherapy. Genomic analysis linked TP53 pathway ( P =0.0022) and FLG2 ( P =0.0421) mutations to non-response, and identified mutations in the nucleotide excision repair (NER) ( P =0.0169) sub-pathway of DNA damage response (DDR) showed a trend toward association with response to combination therapy. RNA sequencing suggested that increased immune and metabolic pathways correlated with a better response. Crucially, responders exhibited significantly higher pre-treatment intratumoral infiltration of plasma cells (CD138+) ( P = 0.0237), while CD8+ T-cell infiltration did not differ. A predictive model integrating TP53/NER pathway status, FLG2 mutation, and plasma cell signatures achieved an AUC of 0.962 for response prediction. Conclusions: Anlotinib-tislelizumab combination therapy demonstrates modest antitumor efficacy in refractory MSS mCRC. NER pathway mutations, alongside plasma cell infiltration and TP53-pathway/FLG2 mutations, constitute a novel multi-omics biomarker framework for predicting therapeutic response, supporting contribution to the development of immune combination therapy and the prediction of its efficacy. Clinical trial information: NCT06573424 .

Altered expression of nucleotide excision repair genes ERCC2 and ERCC5 in prostate cancer tissues.

Exploring the interaction between nucleotide excision repair pathways and Huntington disease: Implications for neurodegeneration and phenotypic overlap.

Design, synthesis and biological evaluation of magnolol-sulforaphane hybrid analogues as potential therapeutics of triple-negative breast cancer.

CRISPR/Cas9-mediated editing of XPA in induced pluripotent stem cells: A model for investigating Xeroderma Pigmentosum and NER dysfunction.

Ultraviolet (UV)-induced DNA lesions threaten genomic stability and are associated with skin carcinogenesis. These lesions are primarily repaired by the nucleotide excision repair (NER) pathway. However, alternative repair mechanisms and regulators are emerging as critical contributors to managing UV lesions. Here, we used a click chemistry-based proteomic approach to identify DEK and NUMA1 as novel regulators of UV-induced DNA lesion repair. Depletion of DEK or NUMA1 resulted in delayed UV lesion repair and increased cellular UV sensitivity. This was accompanied by delayed recruitment of XPF to UV-damaged sites. Notably, abnormal accumulation of proliferating cell nuclear antigen (PCNA) at UV lesions was observed in DEK- or NUMA1-depleted cells. This PCNA accumulation was not entirely dependent on NER, as it also involved contributions from apurinic/apyrimidinic endonuclease 1 (APE1), a key protein in base excision repair (BER). Co-depletion experiments revealed an epistatic relationship between DEK or NUMA1 and APE1, but not with XPA, suggesting an impaired BER in DEK- or NUMA1-depleted cells, possibly due to excessive PCNA accumulation. Our findings suggest that DEK and NUMA1 facilitate efficient UV lesion removal by promoting proper NER activity and regulating APE1-mediated long-patch BER, highlighting the collaborative roles of NER and BER in UV lesion repair.

RNA polymerase II (Pol II)-mediated gene transcription is frequently disrupted by DNA damage from various sources. Transcription-blocking DNA lesions hinder the progression of elongating Pol II, leading to transcription stress that, if unresolved, causes cellular dysfunction, neurodegeneration and ageing. In this Review, we discuss how different types of lesion are recognized by obstructing Pol II and removed by the intricate transcription-coupled nucleotide excision repair (TC-NER) pathway, emphasizing recent structural findings that reveal key aspects of the TC-NER mechanism. We also discuss the mechanisms proposed for processing lesion-stalled Pol II, which is crucial to facilitate TC-NER, and focus on how Pol II ubiquitylation orchestrates repair-complex assembly and Pol II degradation. In addition, we discuss the alternative mechanism of transcription-coupled DNA-protein crosslink repair, which was recently identified to be important for resolving DNA-protein crosslinks in active genes. Finally, we describe how these insights elucidate the different pathological causes of hereditary TC-NER deficiencies, namely of the mild cutaneous ultraviolet-sensitive syndrome and the severe progeroid Cockayne syndrome.

Xeroderma pigmentosum as a germline predisposition syndrome for haematological malignancies

Integrative clinical and molecular analysis of outcome in elderly African ancestry Acute Myeloid Leukemia

Inhibition of Mycobacterium tuberculosis UvrB by small molecules: Potent NER disruption and structural insights into dimer conformation.

The nucleotide excision repair (NER) pathway is the primary mechanism for removing UVB-induced photoproducts in mammals. While early steps of NER are well defined, the later step of gap-filling DNA synthesis remains incompletely understood. Here, we report And-1, a DNA replication and repair factor, as a critical regulator of this process. And-1 localizes to UV lesions, directly interacts with the catalytic subunit of DNA polymerase δ (p125), and promotes its recruitment to facilitate repair synthesis. In vitro, And-1 enhances p125 polymerase activity. Importantly, And-1 function in NER requires phosphorylation at T826, which strengthens its binding to both damaged DNA and p125. To evaluate its physiological relevance, we generated phosphorylation-deficient And-1 knock-in mice. These mice exhibited impaired NER and developed keratoacanthomas upon chronic UVB exposure. Collectively, our findings uncover And-1 as a pivotal factor in NER-mediated DNA repair and highlight its role in skin tumorigenesis.

Purpose DNA damage and repair defects in lens epithelial cells (LECs) contribute to the formation and progression of age-related cataracts (ARC). Ku antigen 80 kDa (Ku80) plays an important role in the non-homologous end-joining (NHEJ) pathway for repairing DNA double-strand breaks, while the Cockayne Syndrome Complementary B (CSB) protein plays a critical role in the nucleotide excision repair pathway. This study evaluates the protective effect of AAV-mediated overexpression of Ku80 in rat LECs and explores its contribution to delaying selenium-induced cataract formation. Methods SD rats (11 days) were randomly divided into three groups: control group (n = 7), AAV-NC group (n = 14), and AAV-Ku80 group (n = 14). The AAV-Ku80 group received adenovirus-mediated overexpression of Ku80, the AAV-NC group received adenoviral vector negative control, and the control group was injected with physiological saline. All injections were performed in the anterior chamber. Except for the control group, the other two groups were subcutaneously injected with sodium selenite solution into the nape of the neck 30 min after the injection. The degree of lens opacity was examined using a slit-lamp, and lenses were harvested to assess antioxidant parameters, including superoxide dismutase (SOD) activity, reduced glutathione (GSH) content, and the oxidative damage marker malondialdehyde (MDA) content. Western blot analysis was performed to examine the upregulation of CSB protein and its association with delayed cataract formation. Results Overexpression of Ku80 significantly enhanced the expression of CSB protein, improved DNA repair capacity, and mitigated the influences of oxidative stress on rat LECs. This resulted in a significant increase in SOD and GSH levels, a significant decrease in MDA levels, and postponed the onset of selenium-induced cataracts, hence preserving lens clarity. Moreover, Ku80 overexpression partially alleviated damage to the corneal endothelium and retina. Conclusion Ku80 overexpression alleviates damage to LECs and postpones the development of selenium-induced cataracts by increasing CSB protein levels and controlling DNA repair processes. This research underscores the significant therapeutic potential of Ku80 in postponing cataract formation and may offer new avenues for gene therapy in the prevention and treatment of cataracts.

In this study, RNA-seq analysis of 36 samples from two varieties at six temperature gradients detected a total of 101,193 expressed transcripts, including 25,809 lncRNAs and 75,384 mRNAs. Using 24 °C, 12 °C, and 5 °C as the cold group and 0 °C, -5 °C, and − 8 °C as the freezing group, 2719 CT_24°C_vs_5°C differentially expressed lncRNAs were detected in the cold group, of which 581 were up-regulated and 2138 were down-regulated, and 2,563 differentially expressed lncRNAs were detected in the freezing group, of which 601 were up-regulated and 1962 were down-regulated. In the group CT_0°C_vs_-8 °C, differentially expressed lncRNAs were 1,415, of which 250 were up-regulated and 1,165 were down-regulated, and in CS_0°C_vs_-8 °C, differentially expressed lncRNAs were 1,301, of which 228 were up-regulated and 1,073 were down-regulated.In the cold-damaged group, the total number of predicted paired lncRNA-mRNA pairs was 1904, of which 1152 pairs were paired by cis, and 752 pairs were paired by tran. In the freezing group, 922 pairs of lncRNA-mRNA pairs were predicted, of which 473 pairs were in the cis mode and 449 pairs were in the tran mode. In the cold group, 656 differential lncRNA target genes intersected with differentially expressed mRNAs in the CT_24℃_vs_5℃ comparison, and 668 in the CS_24℃_vs_5℃ comparison. In the freezing group, 187 differentially expressed mRNAs intersected with differentially expressed lncRNA target genes in the CT_0°C_vs_-8 °C comparison, and 146 in the CS_0°C_vs_-8 °C comparison. GO enrichment analysis indicated significant enrichment in the metabolic process and response to stimulus pathways in both the cold and freezing groups. KEGG enrichment analysis revealed significant enrichment in the Nucleotide excision repair (ko03420) and DNA replication (ko03030) pathways in the cold-damaged group, and in the Ascorbate and aldarate metabolism (ko00053) pathway in the freeze-damaged group. This suggests that the Ascorbate metabolic pathway plays a significant role in the barley response to frost damage.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07403-y.

Protective role of Cockayne Syndrome B (CSB) protein in maintaining genome integrity in human cells under oxidative stress.

Chemoresistance remains an obstacle to effective cancer therapy across multiple tumor types. Damaged DNA-binding protein 2 (DDB2), a key component of the nucleotide excision repair (NER) pathway, contributes to chemoresistance by enhancing DNA repair and inhibiting apoptosis. Although the role of DDB2 in tumor progression is context-dependent, its upregulation has been associated with poor prognosis in various malignancies. In this study, elevated DDB2 levels found in breast, liver, cholangiocarcinoma, and lung cancers correlated with reduced patient survival. DDB2 confers resistance to chemotherapeutic agents. Through structure-based virtual screening and molecular dynamics simulations, lapatinib, an FDA-approved EGFR/HER2 inhibitor, was identified as a compound capable of disrupting the DDB2/DNA complex, which was confirmed by the cellular thermal shift assay and chromatin fractionation. Mechanistically, lapatinib binds to the DNA-binding region of DDB2, thereby reducing its chromatin association and promoting proteasomal degradation. Co-treatment with lapatinib and doxorubicin exhibited synergistic cytotoxicity in both cancer cell lines and patient-derived organoids. These findings reveal a previously unrecognized role for lapatinib in targeting DNA repair machinery, supporting its repurposing as a chemosensitizing agent. Our study highlights DDB2 as a critical mediator of chemoresistance and proposes disruption of DDB2-dependent DNA repair as a novel strategy for chemosensitization.

Background/Objectives: Emerging evidence implicates impaired DNA repair mechanisms in the pathogenesis of Parkinson’s disease (PD), particularly in the context of oxidative stress and environmental exposures. This study investigated the association between five polymorphisms in nucleotide excision repair (NER) pathway genes and PD susceptibility in a northern Mexican mestizo population. Methods: We conducted a case–control study including 137 patients with clinically diagnosed PD and 137 age- and sex-matched controls. Genomic DNA was isolated from peripheral blood, and genotyping of ERCC1 (rs11615), ERCC2 (rs13181), XPA (rs1800975), XPC (rs2228001), and XPF (rs1799801) was performed using TaqMan real-time PCR assays. Associations between genotype frequencies and PD were evaluated using logistic regression models adjusted for age, sex, and pesticide exposure. Results: A significantly higher prevalence of pesticide exposure was observed in PD patients than in controls (OR 2.08, 95% CI 1.18–3.68; p = 0.01). The XPC rs2228001 C/C genotype was independently associated with increased PD risk in males (OR 3.25, 95% CI 1.07–9.85; p = 0.042), even after adjusting for uric acid, pesticide exposure, and cognitive status (MMSE score). No significant associations were found for other NER-related polymorphisms. Male PD patients also exhibited significantly lower serum uric acid levels than controls (p = 0.046), supporting a link between oxidative stress and disease vulnerability. Conclusions: Our findings suggest a sex-specific genetic contribution to PD susceptibility involving the XPC rs2228001 variant, particularly in the context of pesticide exposure. These results underscore the relevance of DNA repair pathways in PD pathogenesis and highlight the importance of integrated models incorporating genetic and environmental risk factors.

Skin carcinogenesis, primarily driven by ultraviolet B (UVB) radiation, affects over two million individuals annually in the United States. Silver nanoparticles (Ag-NPs) have gained prominence due to their multifunctional roles in biomedical applications. This study investigates the photoprotective efficacy of green-synthesized Ag-NPs derived from the aqueous leaf extract of Cudrania tricuspidata (CTAg-NPs) against UVB-induced genotoxicity in HaCaT human keratinocytes. CTAg-NPs exhibited favorable physicochemical properties and efficient intracellular localization within cytoplasmic and nuclear regions. Upon UVB exposure, untreated cells showed elevated DNA damage, increased Bax expression, and reduced Bcl-2 levels, indicative of apoptosis initiation. Pretreatment with CTAg-NPs significantly attenuated these effects, enhancing DNA repair via activation of the nucleotide excision repair (NER) pathway and restoring apoptotic balance. Additionally, antioxidant enzyme activities superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) were markedly increased, contributing to oxidative stress mitigation. These findings highlight the dual protective role of CTAg-NPs in both genetic integrity and cellular resilience under UVB stress. In vivo validation using appropriate animal models or engineered skin equivalents is recommended to substantiate translational relevance and potential for clinical application in skin cancer prevention.