The DNA-damage response in human biology and disease

Construction of a novel prognostic model based on lncRNAs-related to DNA damage repair for predicting the prognosis of clear cell renal cell carcinoma

BACKGROUND

CcRCC has the characteristics of high aggression, high metastasis, high mortality, wide tumour heterogeneity and variable clinical course. The purpose of this study was to explore the potential value of lncRNAs-related to DNA damage repair (DDR) in predicting the prognosis of ccRCC by construction and verification a novel prognostic model.

METHODS

RNA-seq data and clinical data of ccRCC were downloaded from public databases. Subsequently, Pearson correlation analysis and differential expression analysis were performed to identify DElncRNAs-related to DDR. Then, through univariate Cox analysis and LASSO analysis, the DElncRNAs-related to DDR associated with prognosis were screened for the construction of novel risk score prognostic model. In addition, functional annotation, tumour mutation burden, immune correlation and drug sensitivity analyses were performed based on risk score to assess the characteristics of patients in different risk score groups.

RESULTS

Based on univariate Cox analysis and LASSO analysis, four best DElncRNAs-related to DDR were selected. Subsequently, a novel risk score prognostic model based on these four DElncRNAs was constructed through LASSO. Multivariate Cox analysis showed that risk score and age were independent prognostic factors for ccRCC (p < 0.05). Functional enrichment analysis showed that DDR-related biological processes were mainly enriched in the high risk group. The highly mutated genes in the high and low risk groups were the same (VHL, PBRM1 and TTN), but they also had their own unique mutated genes. Pearson correlation analysis showed that the risk score was significantly (p < 0.05) positively correlated with the infiltration degree of CD8 T cells evaluated by six algorithms. In addition, it was found that the high and low risk groups had different sensitivities to the drugs Etoposide, Imatinib, Sorafenib, Bosutinib and Sunitinib.

CONCLUSION

A novel prognostic model was constructed based on four DElncRNAs-related to DDR. The model has satisfactory accuracy in predicting survival of ccRCC patients.

Medicinal chemistry breakthroughs on ATM, ATR, and DNA-PK inhibitors as prospective cancer therapeutics

This review discusses the critical roles of Ataxia Telangiectasia Mutated Kinase (ATM), ATM and Rad3-related Kinase (ATR), and DNA-dependent protein kinase (DNA-PK) in the DNA damage response (DDR) and their implications in cancer. Emphasis is placed on the intricate interplay between these kinases, highlighting their collaborative and distinct roles in maintaining genomic integrity and promoting tumour development under dysregulated conditions. Furthermore, the review covers ongoing clinical trials, patent literature, and medicinal chemistry campaigns on ATM/ATR/DNA-PK inhibitors as antitumor agents. Notably, the medicinal chemistry campaigns employed robust drug design strategies and aimed at assembling new structural templates with amplified DDR kinase inhibitory ability, as well as outwitting the pharmacokinetic liabilities of the existing DDR kinase inhibitors. Given the success attained through such endeavours, the clinical pipeline of DNA repair kinase inhibitors is anticipated to be supplemented by a reasonable number of tractable entries (DDR kinase inhibitors) soon.

Expanded insights into the mechanisms of RNA-binding protein regulation of circRNA generation and function in cancer biology and therapy

RNA-binding proteins (RBPs) regulate the generation of circular RNAs (circRNAs) by participating in the reverse splicing of circRNA and thereby influencing circRNA function in cells and diseases, including cancer. Increasing evidence has demonstrated that the circRNA-RBP network plays a complex and multifaceted role in tumor progression. Thus, a better understanding of this network may provide new insights for the discovery of cancer drugs. In this review, we discuss the characteristics of RBPs and circRNAs and how the circRNA-RBP network regulates tumor cell phenotypes such as proliferation, metastasis, apoptosis, metabolism, immunity, drug resistance, and the tumor environment. Moreover, we investigate the factors that influence circRNA-RBP interactions and the regulation of downstream pathways related to tumor development, such as the tumor microenvironment and N6-methyladenosine modification. Furthermore, we discuss new ideas for targeting circRNA-RBP interactions using various RNA technologies.

Prognostic and Potential Therapeutic Roles of PRKDC Expression in Lung Cancer

PRKDC is a key factor involved in the ligation step of the non-homologous end joining pathway. Its dysfunction has proven to be a biomarker for radiosensitivity of cancer cells. However, the prognostic value of PRKDC and its underlying mechanisms have not been clarified yet. In this study, we found that PRKDC overexpressed in lung adenocarcinoma (LUAD) and is significantly related to unfavorable survival, while downregulation of PRKDC is link to inflamed tumor immune signature. Our further in vitro results also showed a potent antitumor efficacy of PRKDC inhibitors alone or combined with cisplatin in human lung cancer cells. This study demonstrated that PRKDC is a potential prognostic biomarker, immunotherapy target, and promising combination candidate for chemotherapy for lung cancer, and highlighted the potential of PRKDC-targeted inhibitors for the treatment of lung cancer.

DDX37 and DDX50 Maintain Genome Stability by Preventing Transcription-dependent R-loop Formation

R-loops consist of an RNA-DNA hybrid and a displaced single-stranded DNA strand that play a central role in several biological processes. However, as the presence of aberrant R-loops forms a significant threat to genome stability, R-loop formation and resolution is strictly controlled by RNAse H and helicases. In a screening for RNA helicases, previously described as RNA-DNA hybrid interactors, that control genome integrity, we identified for the first time DDX37 and DDX50. Depletion of DDX37 and DDX50 promotes DNA damage, as demonstrated by H2AX phosphorylation and increased comet tail length. In addition, knock down of these RNA helicases decreases the DNA replication track length and leads to RPA focus formation, results that are indicative of replication stress. Downregulation of DDX37 and DDX50 triggers an increase in RNA-DNA hybrids, that can be reverted by the overexpression of RNase H1. Interestingly, inhibition of transcription prevented the increased RNA-DNA hybrid formation and DNA damage upon DDX37 or DDX50 depletion. Together these results demonstrate that DDX37 and DDX50 are important for resolving RNA-DNA hybrids appearing during transcription and thereby preventing DNA damage by replication stress.

VCP's nuclear journey: Initiated by interacting with KPNB1 to repair DNA damage

DNA damage repair (DDR) is essential for cancer cell survival and treatment resistance, making it a critical target for tumor therapy. The eukaryotic AAA+ adenosine triphosphatase valosin-containing protein (VCP), which is transported from the cytoplasm into the nucleus, plays a critical role in the DDR process. However, the nuclear translocation and molecular mechanism of VCP for DDR remain elusive. Here, we define VCP as a KPNB1 interacting protein through a combination of chemical and immunoprecipitation mass spectrometry approaches. Further biochemical studies elucidate that KPNB1 directly transports VCP into the nucleus. We also identify withaferin A (WA) as a small molecule that can retard VCP nuclear localization via covalent binding to CYS 158 of KPNB1. Further studies verify WA as an effective antitumor drug candidate via blocking VCP nuclear localization to impact on the DDR pathway in vivo. Our findings underly the unclear VCP's role in DDR in a KPNB1-dependent manner and provide an important theoretical basis for developing small-molecule inhibitors targeting this process.

ESSENTIAL MEIOTIC ENDONUCLEASE 1 is required for chloroplast development and DNA repair in rice

Chloroplast development is fundamental to photosynthesis and plant growth but is sensitive to environmental stress. Chloroplast development and division require genome stability and DNA repair, but the underlying mechanisms have been unclear. Using a forward genetic approach, we identified the striped-leaf mutant k48 in the rice (Oryza sativa L. japonica) cultivar KY131 background. k48 displayed defects in chloroplast development and photosynthesis, especially under high-light conditions. Genetic and complementation studies revealed that the loss of ESSENTIAL MEIOTIC ENDONUCLEASE 1 (EME1) is responsible for the defects in k48. Transcriptomic analysis showed that OsEME1 globally regulates the expression of genes involved in photosynthesis and DNA repair. Furthermore, mutations in OsEME1 led to cell cycle arrest and a DNA damage response. An in vitro endonuclease activity assay indicated that OsEME1 directly binds to and cleaves DNA substrates with a specific structure and that four conserved amino acids are required for its activity. Notably, OsEME1 targeted DNA fragments of rice GOLDEN-LIKE 1 (GLK1) and GLK2. We also demonstrated that OsEME1 interacts with the structure-specific endonuclease methyl methanesulfonate (MMS) and UV-SENSITIVE PROTEIN 81 (MUS81). This study highlights the role of OsEME1 in regulating chloroplast development by modulating homologous recombination repair in response to damage to double-stranded DNA.

Exploring the double-edged role of cellular senescence in chronic liver disease for new treatment approaches

Cellular senescence is a fundamental yet complex defense mechanism that restricts excessive proliferation, maintains cellular homeostasis under various stress conditions-such as oncogenic activation and inflammation-and serves as a dynamic stress response program involved in development, aging, and immunity. Its reversibility depends on essential maintenance components. Cellular senescence is a "double-edged sword": on one hand, it limits the malignant proliferation of damaged cells, thereby preventing tumor development. However, by retaining secretory functions, senescent cells can also induce persistent changes in the microenvironment and disrupt homeostasis, leading to tissue inflammation, fibrosis, and carcinogenesis. Senescence plays a critical role in the pathogenesis of various chronic liver diseases, including chronic viral hepatitis, liver fibrosis, and hepatocellular carcinoma. It exerts a dual influence by facilitating immune evasion and inflammation in chronic viral hepatitis, modulating hepatic stellate cell activity in fibrosis, and reshaping the tumor microenvironment to accelerate hepatocarcinogenesis. This article reviews the characteristics of cellular senescence and its role in the pathogenesis of these chronic liver diseases while exploring potential treatment and prevention strategies. The aim is to provide a comprehensive reference for future clinical and research investigations into chronic liver disease.

WDR11-DT enhances radiosensitivity via promoting PARP1 degradation and homologous recombination deficiency

Radiotherapy is an important management for non-small cell lung cancer (NSCLC). Although long non-coding RNAs (lncRNAs) have been reported to be involved in modulating radiosensitivity, the underlying mechanisms are still largely unclear. Here, we found that tumor suppressor WDR11-DT is a novel radiation-induced lncRNA, which is transcriptionally regulated by SPDEF, in NSCLC. In contrast to normal tissues, WDR11-DT is down-regulated in NSCLC specimens and its low expression was associated with poor prognosis of patient receiving radiotherapy. Importantly, WDR11-DT can markedly enhance NSCLC cells' radiosensitivity in vitro and in vivo. WDR11-DT functions through distinct mechanisms via binding different proteins. WDR11-DT facilitates interactions between PARP1 and its E3 ligase TRIP12, promotes PARP1 protein degradation and suppresses PARP1-controlled Single-strand breaks (SSBs) repair. Additionally, WDR11-DT binds RNA-bind protein HNRNPK, represses its functions in improving RNA stability of homologous recombination (HR) genes, decreases expression of BRCA1, ATM, BLM and RAD50, and suppresses radiotherapy-triggered HR repair. WDR11-DT-induced dual restraints of PARP1 and the HR pathway lead to the accumulation of double-strand breaks as well as synthetic lethal effects of malignant cells, which, thereby, enhances radiosensitivity and inhibits progression of lung cancer. These results extend our current knowledge of radio-biology and elucidate that WDR11-DT may be a new target for boosting cancer radiotherapy.

Phospho-TRIM21 orchestrates RPA2 ubiquitination switch to promote homologous recombination and tumor radio/chemo-resistance

RPA2, a key component of the RPA complex, is essential for single-stranded DNA (ssDNA) binding and DNA repair. However, the regulation of RPA2-ssDNA interaction and the recruitment of repair proteins following DNA damage remain incompletely understood. Our study uncovers a novel mechanism by which phosphorylated TRIM21 (Phospho-TRIM21) regulates RPA2 ubiquitination, thereby modulating homologous recombination and tumor radio/chemo-resistance. In the absence of DNA damage, TRIM21 mediates K63-linked ubiquitination of RPA2, countering K6-linked ubiquitination. Upon DNA damage, ubiquitination-modified RPA2 binds ssDNA, stabilizing the DNA structure and facilitating ATRIP/ATR recruitment. ATR subsequently phosphorylates TRIM21 at Ser41, leading to the dissociation of the TRIM21-RPA2 complex and a shift in RPA2 ubiquitination from K63 to K6 linkage. This shift maintains RPA2 ubiquitination homeostasis and stabilizes the RPA2-ATRIP complex, which is crucial for efficient homologous recombination (HR) repair and enhanced tumor radio/chemo-resistance. We also demonstrate that TRIM21 is frequently upregulated in cancers, and its depletion sensitizes cancer cells to radio/chemotherapy, suggesting its potential as a therapeutic target. This study provides novel insights into TRIM21's role in the DNA damage response and its implications for cancer treatment.

Human papilloma virus (HPV) mediated cancers: an insightful update

Human papillomavirus (HPV), a DNA virus, is a well-documented causative agent of several cancers, including cervical, vulvar, vaginal, penile, anal, and head & neck cancers. Major factors contributing to HPV-related cancers include persistent infection and the oncogenic potential of particular HPV genotypes. High-risk HPV strains, particularly HPV-16 and HPV-18, are responsible for over 70% of cervical cancer cases worldwide, as well as a significant proportion of other genital and head and neck cancers. At the molecular level, the oncogenic activity of these viruses is driven by the overexpression of E6 and E7 oncoproteins. These oncoproteins dysregulate the cell cycle, inhibit apoptosis, and promote the accumulation of DNA damage, ultimately transforming normal cells into cancerous ones. This review aims to provide a comprehensive overview of the recent advances in HPV-related cancer biology and epidemiology. The review highlights the molecular pathways of HPV-driven carcinogenesis, focusing on the role of viral oncoproteins in altering host cell targets and disrupting cellular signalling pathways. The review explores the therapeutic potential of these viral proteins, and discusses current diagnostic and treatment strategies for HPV-associated cancers. Furthermore, the review highlights the critical role of HPV in the development of various malignancies, emphasizing the persistent challenges in combating these cancers despite advancements in vaccination and therapeutic strategies. We also emphasize recent breakthroughs in utilizing biomarkers to monitor cancer therapy responses, such as mRNAs, miRNAs, lncRNAs, proteins, and genetic markers. We hope this review will serve as a valuable resource for researchers working on HPV, providing insights that can guide future investigations into this complex virus, which continues to be a major contributor to global morbidity and mortality.

HPV-mediated PARP1 regulation and drug sensitization in head and neck cancer

INTRODUCTION

Human Papillomavirus (HPV)-positive Head and Neck (HNC) cancer responds better to radiotherapy and platinum-based chemotherapy than HPV-negative HNC, likely due to impaired DNA damage repair. Inhibiting PARP1 enhances the effects of radiation and chemotherapy in tumours with defective DNA repair, such as HPV-positive cancers. In this study we investigated the role of HPV in the upregulation of PARP1, determining HNC cell sensitivity to both olaparib and cisplatin.

MATERIALS AND METHODS

PARP1 expression was assessed in HPV-positive and HPV-negative HNC using TCGA data, HNC cell lines and frozen tumour tissue samples from HNC patients. HPV16 expression was modulated by E6/E7 transduction in Human Primary keratinocytes (HK). Sensitivity to the PARP inhibitor olaparib and cisplatin, alone and in combination, was assessed in HNC cell lines.

RESULTS

HPV-positive tumours and cell lines showed upregulated PARP1 expression and activity, mediated by HPV16 oncoproteins. HPV-positive cell lines were more sensitive to olaparib or cisplatin treatment than HPV-negative ones. Combining cisplatin with olaparib synergistically inhibited cell viability in all HNC cell lines tested, regardless of HPV status.

CONCLUSION

Our study demonstrates that PARP1 is upregulated in HPV-positive HN tumours and cell lines, compared to HPV-negative. Despite the higher sensitivity of HPV-positive HNC cell lines to olaparib and cisplatin compared to HPV-negative cells, the combination of cisplatin with olaparib synergistically inhibits cell viability across all HNC cell lines tested, regardless of HPV status. This combination may allow for reduced drug concentrations, potentially decreasing side effects and enhancing therapeutic efficacy in HN tumours.

Weaponizing CRISPR/Cas9 for selective elimination of cells with an aberrant genome

The CRISPR/Cas9 technology is a powerful and versatile tool to disrupt genes' functions by introducing sequence-specific DNA double-strand breaks (DSBs). Here, we repurpose this technology to eradicate aberrant cells by specifically targeting silent and non-functional genomic sequences present only in target cells to be eliminated. Indeed, an intrinsic challenge of most current therapies against cancer and viral infections is the non-specific toxicity that they can induce in normal tissues because of their impact on important cellular mechanisms shared, to different extents, between unhealthy and healthy cells. The CRISPR/Cas9 technology has potential to overcome this limitation; however, so far effectiveness of these approaches was made dependent on the targeting and inactivation of a functional gene product. Here, we generate proof-of-principle evidence by engineering HeLa and RKO cells with a promoterless Green Fluorescent Protein (GFP) construct. The integration of this construct simulates either a genomic alteration, as in cancer cells, or a silent proviral genome. Cas9-mediated DSBs in the GFP sequence activate the DNA damage response (DDR), reduce cell viability and increase mortality. This is associated with increased cell size, multinucleation, cGAS-positive micronuclei accumulation and the activation of an inflammatory response. Pharmacological inhibition of the DNA repair factor DNA-PK enhances cell death. These results demonstrate the therapeutic potential of the CRISPR/Cas9 system in eliminating cells with an aberrant genome, regardless of the expression or the function of the target DNA sequence.

REV7 functions with REV3 as a checkpoint protein delaying mitotic entry until DNA replication is completed

REV7, also named MAD2B or MAD2L2, is a subunit of the DNA translesion polymerase zeta and also part of the 53BP1-shieldin complex, which is present at sites of DNA double-strand breaks. REV7 has high sequence similarity to the MAD2 spindle assembly checkpoint protein, prompting us to examine whether REV7 has a checkpoint function. We observed that, in chicken and human cells exposed to agents that induce DNA replication stress, REV7 inhibits mitotic entry; this effect is most evident when the canonical DNA replication stress checkpoint, mediated by ATR, is inhibited. Similar to MAD2, REV7 undergoes conformational changes upon ligand binding, and its checkpoint function depends on its ability to homodimerize and bind its ligands. Notably, even in unchallenged cells, deletion of the REV7 gene leads to premature mitotic entry, raising the possibility that the REV7 checkpoint monitors ongoing DNA replication.

USP1 inhibition: A journey from target discovery to clinical translation

Ubiquitin-specific protease 1 (USP1) is a deubiquitinating enzyme involved in the DNA damage response. Upon DNA damage, USP1 stabilizes replication forks by removing monoubiquitin from PCNA and FANCD2-FANCI, thereby catalyzing critical final steps in translesion synthesis and interstrand crosslink (ICL) repair. This function is particularly crucial in BRCA1 mutant cancers, where the homologous recombination pathway is compromised, leading tumors to rely on USP1 for effective repair. USP1 is also overexpressed in BRCA1 mutant cancers, as well as other tumor types. Preclinical studies have demonstrated that knockout of USP1 is synthetically lethal in tumors with biallelic BRCA1 mutations, and this relationship is enhanced by combination with PARP inhibitors. Newly developed USP1 inhibitors have confirmed this synthetic lethality in BRCA1-deficient tumor cells. Moreover, these drugs have the potential for resensitizing platinum-resistant tumors. Currently, potent and specific USP1 inhibitors are undergoing evaluation in phase I clinical trials. RO7623066 (KSQ-4279) reported an acceptable safety profile during a phase I dose escalation study, with anemia being the most common side effect, and demonstrated robust pharmacokinetic, pharmacodynamic, and clinical activity. Other USP1 inhibitors, including SIM0501, XL309-101, and HSK39775, are currently in early clinical development. In this review, we provide an overview of the molecular function of USP1 and its importance as a therapeutic target in oncology, before focusing on the current state of preclinical and clinical development of USP1 inhibitors.

The Impact of Uncommon HRR Alterations as Predictors of Efficacy of PARP Inhibitors in Metastatic Castration-Resistant Prostate Cancer: A Meta-Analysis of Randomized Controlled Trials

BACKGROUND

Metastatic castration-resistant prostate cancer (mCRPC) patients with BRCA1/2 mutations show significant responses to poly-ADP ribose polymerase inhibitors (PARPi), while the efficacy of these agents in patients with homologous recombination repair (HRR) gene alterations other than BRCA remains unclear.

OBJECTIVE

This meta-analysis aimed at assessing the efficacy of PARPi in mCRPC harboring alterations in four rare HRR genes (i.e. CDK12, PALB2, ATM, and CHEK2).

PATIENTS AND METHODS

Five randomised phase III trials (PROfound, PROpel, MAGNITUDE, TALAPRO-2, TRITON3) were selected through searching the Medline/PubMed, Cochrane Library, and ASCO Meeting abstracts. Data extraction followed the PRISMA statement. The primary endpoints, radiographic progression-free survival (rPFS) and overall survival (OS) with the relative 95% CI, were calculated using fixed- or random-effects methods, depending on the studies' heterogeneity. RevMan software for meta-analysis (v.5.2.3) was used.

RESULTS

PARPi significantly improved rPFS in mCRPC patients with CDK12 alterations (hazard ratio (HR) = 0.65; p = 0.02) without OS benefit. In patients with ATM, CHEK2, or PALB2 alterations, no significant benefit was observed in rPFS or OS. Due to the low incidence of these rare mutations, we grouped them into gene panels, revealing a significant rPFS advantage when CDK12+PALB2 (HR = 0.63; p = 0.009) were combined, and a similar benefit when including CHEK2 in the gene panel (HR = 0.69; p = 0.01).

CONCLUSION

CDK12 alterations could be considered as a predictive biomarker of rPFS benefit with PARPi. A gene panel grouping CDK12 and PALB2 with or without CHEK2 mutations could also enable prediction of rPFS benefit with PARPi.

Recent Progress and Potential of G4 Ligands in Cancer Immunotherapy

G-quadruplex (G4) structures are non-canonical nucleic acid conformations that play crucial roles in gene regulation, DNA replication, and telomere maintenance. Recent studies have highlighted G4 ligands as promising anticancer agents due to their ability to modulate oncogene expression and induce DNA damage. By stabilizing G4 structures, these ligands affect tumor progression. Additionally, they have been implicated in tumor immunity modulation, particularly through the activation and immunogenic cell death induction of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway. Moreover, their disruption of telomere maintenance and regulation of key oncogenes, such as c-MYC and KRAS, position them as candidates for immune-based therapeutic interventions. Despite their therapeutic potential, challenges remain in optimizing their clinical applications, particularly in patient stratification and elucidating their immunomodulatory effects. This review provides a comprehensive overview of the mechanisms through which G4 ligands influence tumor progression and immune regulation, highlighting their potential role in future cancer immunotherapy strategies.

Stained DNA Dot Detection (SD3): An automated tool for quantifying fluorescent features along single stretched DNA molecules

The main information in DNA is its four-letter sequence that builds up the genetic information and that is traditionally read using sequencing methodologies. DNA can, however, also carry other important information, such as epigenetic marks and DNA damage. This information has recently been visualized along single DNA molecules using fluorescent labels. Quantifying fluorescent labels along DNA is done by counting the number of "dots" per length of each DNA molecule on DNA stretched on a glass surface. So far, a major challenge has been the lack of standardized data analysis tools. Focusing on DNA damage, we here present a Matlab-based automated software, Stained DNA Dot Detection (SD3), which uses a robust method for finding DNA molecules and estimating the number of dots along each molecule. We have validated SD3 by comparing the outcome to manual analysis using DNA extracted from cells exposed to H2O2 as a model system. Our results show that SD3 achieves high accuracy and reduced analysis time relative to manual counting. SD3 allows the user to define specific parameters regarding the DNA molecule and the location of dots to include during analysis via a user-friendly interface. We foresee that our open-source software can have broad use in the analysis of single DNA molecules and their modifications in research and in diagnostics.

Comprehensive pan-cancer analysis of PPP1R3G reveals its diagnostic, prognostic, and immunotherapeutic implications

BACKGROUND

PPP1R3G, a regulatory subunit of protein phosphatase 1, plays a critical role in glycogen metabolism and has been implicated in various cancers. This study provides a comprehensive pan-cancer analysis of PPP1R3G, evaluating its expression, diagnostic and prognostic significance, and potential as a therapeutic target.

METHODS

We performed an extensive pan-cancer analysis of PPP1R3G using several databases to assess its expression and investigate its correlations with clinical outcomes. Our investigation included assessing PPP1R3G's impact on survival, its correlation with immune checkpoints and tumor stemness scores, and its prognostic significance. We also explored its relationship with immunomodulators, genomic profiles, and immunological characteristics, as well as its response to immunotherapy and involvement in various biological pathways.

RESULTS

PPP1R3G expression varied significantly across different cancers and correlated with both diagnostic and prognostic outcomes. Moreover, PPP1R3G was significantly linked to immune checkpoints, immunomodulators, prognosis, immunoregulatory genes, tumor stemness, cellular function, and immune infiltration across numerous cancer types. Further analysis of PPP1R3G-related gene enrichment, mutation profiles, RNA modifications, and genomic heterogeneity revealed that missense mutations were the predominant alteration affecting PPP1R3G.

CONCLUSIONS

Overall, the expression of PPP1R3G is closely associated with various cancers and may serve as a potential biomarker for cancer detection.

Ivosidenib Confers BRCAness Phenotype and Synthetic Lethality to Poly (ADP-Ribose) Polymerase Inhibition in BRCA1/2-Proficient Cancer Cells

Background/Objectives: PARP inhibitors (PARPi) are pivotal to treating homologous recombination repair-deficient (HRD) cancers, particularly BRCA1/2-mutated ovarian and breast cancers. However, most ovarian and breast cancers harbor wild-type (WT) BRCA1/2, limiting PARPi eligibility. This study aims to identify an approved drug that could induce a BRCAness phenotype, thereby sensitizing WT BRCA cancers to PARPi. Methods: Ovarian and breast cancer cell lines with WT BRCA1/2 were treated with ivosidenib. HR repair efficiency was assessed via RAD51 foci formation and reporter assays. Synthetic lethality with PARPi was evaluated using viability and colony formation assays. Mechanistic studies included RNA-binding protein pulldown, co-immunoprecipitation, and functional analyses of DNA repair pathways. YTHDC2's role in HR was investigated through siRNA knockdown and rescue experiments. Results: Ivosidenib significantly reduced HR repair efficiency and sensitized cells to PARPi, inducing synthetic lethality. Mechanistically, ivosidenib directly bound YTHDC2, an m6A reader critical for HR. This interaction disrupted YTHDC2's ability to promote DNA double-strand break repair via HR, evidenced by impaired recruitment of repair proteins (e.g., BRCA1, RAD51) and accumulation of DNA damage (γH2AX foci). YTHDC2 knockdown phenocopied ivosidenib effects, while overexpression rescued HR defects. Conclusions: Ivosidenib induces BRCAness in WT BRCA ovarian and breast cancers by targeting YTHDC2, thereby suppressing HR repair and enhancing PARPi sensitivity. This uncovers a novel, metabolism-independent mechanism of ivosidenib, repositioning it as a therapeutic agent for HRD tumors. These findings propose a strategy to expand PARPi eligibility to WT BRCA cancers, addressing a critical unmet need in oncology.

NK Cell Senescence in Cancer: From Molecular Mechanisms to Therapeutic Opportunities

P Natural killer (NK) cells function as crucial effectors in the innate immune response against tumors. Nevertheless, NK cell senescence, characterized by phenotypic and functional changes, substantially compromises their antitumor immune response. This review provides a comprehensive summary of the molecular mechanisms governing NK cell senescence and its implications for cancer immunotherapy. We propose a refined definition of NK cell senescence based on distinct biomarkers, including elevated CD57 expression, reduced cytotoxicity, and altered cytokine secretion. Moreover, we investigate the complex interactions between the tumor microenvironment (TME) and NK cell senescence, highlighting the influence of chronic inflammation, immunosuppressive cytokines, and persistent tumor antigenic stimulation. Additionally, this review underscores the potential utility of senescent NK cells as biomarkers for assessing antitumor efficacy and examines the adverse effects of NK cell senescence on cancer immunotherapy. Lastly, we summarize current approaches to mitigate NK cell senescence, such as gene editing techniques and cytokine modulation, which may enhance the efficacy of NK cell-based immunotherapies. By establishing a comprehensive framework for understanding NK cell senescence within the TME, this review aims to guide future research and the development of innovative therapeutic strategies targeting senescent NK cells to improve cancer immunotherapy outcomes.

Mechanistic insights into LdCen1-LdDRP interaction facilitating UV-induced DNA damage repair in Leishmania donovani

Leishmania donovani is the causative agent of the fatal visceral leishmaniasis (VL) disease in humans in the tropical regions, mainly the Indian Subcontinent and Africa. We have previously described centrin1, a basal body associated cell division specific protein in this parasite important for the parasite's host intracellular stage. In this study, we identified a novel centrin1-binding protein called LdDRP through pull-down and MS/MS analysis, which is a homolog of the XPC protein of humans involved in DNA damage. The protein interaction with LdCen1 was also confirmed through peptide spectrum analysis against the UniProt database. Immunofluorescence analysis confirms that LdDRP is localized within the nucleus, suggesting the protein's possible role in DNA interaction. The overexpression of three LdDRP forms in the parasite, each fused with HA-tag (LdDRPF [full length] LdDRPN [only N-terminal], and LdDRPC [only C-terminal]), revealed that only LdDRPF and LdDRPC were able to support the retention of the parasite's shape and promote rapid division following the UV-damage recovery period. This was also correlated to the elevated expression level of both LdDRPC and LdCen1, by Western blot analysis soon after UV-C exposure in the parasites compared to control. The study emphasizes the role of the LdDRP, and its crucial domains involved in the DNA binding process, DNA damage response, and interaction with centrin, particularly in response to UV-C light-induced DNA damage.

Utilization of natural products in diverse pathogeneses of diseases associated with single or double DNA strand damage repair

The appearance of DNA damage often involves the participation of related enzymes, which can affect the onset and development of various diseases. Several natural active compounds have been found to efficiently adjust the activity of crucial enzymes associated with single or double-strand DNA damage, thus demonstrating their promise in treating diseases. This paper provides an in-depth examination and summary of these modulation mechanisms, leading to a thorough review of the subject. The connection between natural active compounds and disease development is explored through an analysis of the structural characteristics of these compounds. By reviewing how different scholarly sources describe identical structures using varied terminology, this study also delves into their effects on enzyme regulation. This review offers an in-depth examination of how natural active compounds can potentially be used therapeutically to influence key enzyme activities or expression levels, which in turn can affect the process of DNA damage repair (DDR). These natural compounds have been shown to not only reduce the occurrence of DNA damage but also boost the efficiency of repair processes, presenting new therapeutic opportunities for conditions such as cancer and other disease pathologies. Future research should focus on clarifying the exact mechanisms of these compounds to maximize their clinical utility and support the creation of novel approaches for disease prevention and treatment.

Expression of REV7 has prognostic significance in cervical cancer treated with intensity-modulated radiation therapy

BACKGROUND

Human cervical cancer is the fourth most common malignancies among females worldwide. Radiotherapy is crucial in the treatment of cervical cancer. REV7 is associated with the radiosensitivity of cancer cells. We aimed to investigate the relationship between the REV7 expression and the clinical outcome for patients with cervical cancer who received radiation therapy and identify new markers for studying radiosensitivity in cervical cancer.

MATERIAL AND METHODS

The expression of REV7 in 71 cases of cervical squamous cell carcinoma (CSCC) tissues, 20 paracancerous tissues and 20 normal cervical epithelia tissues were analyzed by qRT-PCR and immunohistochemistry (IHC). Among them, 60 patients who underwent intensity-modulated radiation therapy (IMRT) and met the inclusion and exclusion criteria were divided into groups based on the REV7 IHC score: high-expression and low-expression. The relationship between REV7 expression level and short-term efficacy, recurrence and metastasis was investigated. Meanwhile, univariate, multivariate, and Kaplan-Meier analyses were used to analyze the association of REV7 expression with disease-free survival (DFS) and overall survival (OS).

RESULTS

The expression of REV7 is upregulated in CSCC tissues. There was a higher likelihood of progression (pelvic recurrence or distant metastasis) in the group with high REV7 expression (P = 0.024). Moreover, the REV7-high expression patients showed a shorter DFS than the REV7-low expression group (P = 0.011).

CONCLUSIONS

The higher expression level of REV7 indicates an unfavorable prognosis in cervical cancer patients undergoing IMRT treatment. REV7 could potentially serve as a novel biomarker and therapeutic target for investigating the radiosensitivity of cervical cancer.

Senescence, NK cells, and cancer: navigating the crossroads of aging and disease

Cellular senescence, a state of stable cell cycle arrest, acts as a double-edged sword in cancer biology. In young organisms, it acts as a barrier against tumorigenesis, but in the aging population, it may facilitate tumor growth and metastasis through the senescence-associated secretory phenotype (SASP). Natural killer (NK) cells play a critical role in the immune system, particularly in the surveillance, targeting, and elimination of malignant and senescent cells. However, age-related immunosenescence is characterized by declining NK cell function resulting in diminished ability to fight infection, eliminate senescent cells and suppress tumor development. This implies that preserving or augmenting NK cell function may be central to defense against age-related degenerative and malignant diseases. This review explores the underlying mechanisms behind these interactions, focusing on how aging influences the battle between the immune system and cancer, the implications of senescent NK cells in disease progression, and the potential of adoptive NK cell therapy as a countermeasure to these age-related immunological challenges.

Particulate matter air pollution as a cause of lung cancer: epidemiological and experimental evidence

Air pollution has a significant global impact on human health. Epidemiological evidence strongly suggests that airborne particulate matter (PM), the dust components of polluted air, is associated with increased incidence and mortality of lung cancer. PM2.5 (PM less than 2.5 µm) from various sources carries different toxic substances, such as sulfates, organic compounds, polycyclic aromatic hydrocarbons, and heavy metals, which are considered major carcinogens that increase lung cancer risk. The incidence and mortality of lung cancer caused by PM2.5 exposure may be due to significant geographical differences, and can be influenced by various factors, including local sources of air pollution, socioeconomic conditions, and public health measures. This review aims to provide comprehensive insights into the health implications of air pollution and to inform strategies for lung cancer prevention, by summarising the relationship between exposure to PM2.5 and lung cancer development. We explore the different sources of PM2.5 and relevant carcinogenic mechanisms in the context of epidemiological studies on the development of lung cancer from various geographical regions worldwide.

Role of the nucleotide excision repair function of CETN2 in the inhibition of the sensitivity of hepatocellular carcinoma cells to oxaliplatin

Resistance to platinum-based chemotherapy agents like oxaliplatin (OXA) poses significant challenges in the treatment of cancers such as hepatocellular carcinoma (HCC). Centrin 2 (CETN2), which functions in nucleotide excision repair (NER) of DNA damage, is overexpressed in HCC. We investigated the potential role of CETN2 in modulating the sensitivity of HCC cells to OXA. CETN2 expression correlated with decreased OXA sensitivity in Huh7 and Hep3B HCC cell lines. CETN2 forms a complex with XPC, which is crucial for the initial DNA damage recognition in NER, thereby enhancing NER and reducing the efficacy of OXA. siRNA-mediated knockdown of CETN2 increased OXA-induced cytotoxicity and apoptosis, confirming its role in chemoresistance. Moreover, overexpression of CETN2 inhibited OXA-induced DNA damage, an effect partially reversed by XPC knockdown. Our findings highlight CETN2 as a potential biomarker and therapeutic target in overcoming OXA resistance in HCC and suggest the possibility for CETN2 inhibitors in enhancing chemotherapeutic efficacy in the treatment of HCC.

The association of rs25487 of the XRCC1 gene and rs13181 of the ERCC2 gene polymorphisms with the ovarian cancer risk

Ovarian cancer (OC) is the most lethal gynecological cancer worldwide. DNA damage plays an important role in cancer development, and the proteins encoded by XRCC1 and ERCC2 are important components of the DNA repair system. This study aimed to examine the relationship between the rs25487 XRCC1 and rs13181 ERCC2 polymorphisms and the risk of OC development in women from the Moscow region. DNA was isolated from the blood of 129 healthy donors and tissues and blood samples from 125 patients with OC and studied using real-time PCR. An increase in odds ratios (OR) was obtained for OC tissue and blood for both T (OR = 1.46, 95% confidence interval [CI] = 1.22-1.76, P = 0.00005), and for T/T of rs25487 XRCC1. The most significant OR values were found for the T/T genotype using the codominant model (OR = 2.11, 95% CI = 1.44-3.07, P = 0.00006) and dominant model (OR = 3.13, 95% CI = 1.44-6.79, P = 0.0025) for the pooled blood and tissue groups. For rs13181 ERCC2, differences were observed for the T/G genotype in OC tissues (OR = 0.69, 95% CI = 0.51-0.92, P = 0.011) in the codominant model. In this study, the association of allele T and genotypes of rs25487 XRCC1 and T/G of rs13181 ERCC2 with OC was shown. Our results indicate that these polymorphisms may be involved in the pathogenesis of OC and are promising for further studies on therapeutic applications in OC.

20 years of histone lysine demethylases: From discovery to the clinic and beyond

Twenty years ago, histone lysine demethylases (KDMs) were discovered. Since their discovery, they have been increasingly studied and shown to be important across species, development, and diseases. Considerable advances have been made toward understanding their (1) enzymology, (2) role as critical components of biological complexes, (3) role in normal cellular processes and functions, (4) implications in pathological conditions, and (5) therapeutic potential. This Review covers these key relationships related to the KDM field with the awareness that numerous laboratories have contributed to this field. The current knowledge coupled with future insights will shape our understanding about cell function, development, and disease onset and progression, which will allow for novel biomarkers to be identified and for optimal therapeutic options to be developed for KDM-related diseases in the years ahead.

The kinase ATM delays Arabidopsis leaf senescence by stabilizing the phosphatase MKP2 in a phosphorylation-dependent manner

Arabidopsis thaliana (Arabidopsis) Ataxia Telangiectasia Mutated (ATM) kinase plays a vital role in orchestrating leaf senescence; however, the precise mechanisms remain elusive. Here, our study demonstrates that ATM kinase activity is essential for mitigating age- and reactive oxygen species-induced senescence, as restoration of wild-type ATM reverses premature senescence in the atm mutant, while a kinase-dead ATM variant is ineffective. ATM physically interacts with and phosphorylates Mitogen-Activated Protein Kinase Phosphatase 2 (MKP2) to enhance stability under oxidative stress. Mutations in putative phosphorylation sites S15/154 on MKP2 disrupt its phosphorylation, stability, and senescence-delaying function. Moreover, mutation of mitogen-activated protein kinase 6, a downstream target of MKP2, alleviates the premature senescence phenotype of the atm mutant. Notably, the dual-specificity protein phosphatase 19 (HsDUSP19), a predicted human counter protein of MPK2, interacts with both ATM and HsATM and extends leaf longevity in Arabidopsis when overexpressed. These findings elucidate the molecular mechanisms underlying the role of ATM in leaf senescence and suggest that the ATM-MKP2 module is likely evolutionarily conserved in regulating the aging process across eukaryotes.

Cellular senescence and glaucoma

Cellular senescence, a characteristic feature of the aging process, is induced by diverse stressors. In recent years, glaucoma has emerged as a blinding ocular disease intricately linked to cellular senescence. The principal pathways implicated are oxidative stress, mitochondrial dysfunction, DNA damage, autophagy impairment, and the secretion of various senescence- associated secretory phenotype factors. Research on glaucoma-associated cellular senescence predominantly centers around the increased resistance of the aqueous humor outflow pathway, which is attributed to the senescence of the trabecular meshwork and Schlemm's canal. Additionally, it focuses on the mechanisms underlying retinal ganglion cell senescence in glaucoma and the corresponding intervention measures. Given that cell senescence represents an irreversible phase preceding cell death, an in-depth investigation into its mechanisms in the pathogenesis and progression of glaucoma, particularly by specifically blocking the signal transduction of cell senescence, holds the potential to decrease the outflow resistance of aqueous humor. This, in turn, could provide a novel avenue for safeguarding the optic nerve in glaucoma.

Mechanisms of cisplatin sensitivity and resistance in testicular germ cell tumors and potential therapeutic agents (Review)

Testicular germ cell tumors (TGCTs) are the most common tumors in men aged 20-40 years and are primarily treated with cisplatin-based drugs. Although TGCTs are highly sensitive to DNA damage induced by cisplatin and show a hypersensitive apoptotic response, cisplatin resistance still exists. Emerging evidence shows that cisplatin resistance in TGCTs is mainly related to the inhibition of apoptotic pathways such as MDM2/p53, OCT4/NOXA, PDGFR/PI3K/AKT, inhibition of cell cycle checkpoints, increased methylation or neddylation and DNA repair balance. In this review, recent advances regarding the mechanisms of TGCTs' sensitivity and resistance to cisplatin were summarized and potential therapeutic agents for cisplatin-resistant TGCTs were presented, providing a new therapeutic strategy for drug-resistant TGCTs.

Oxygen/siRNA-carrying fluoro-nanosensitizers for radio-immunotherapy sensitization

The anti-tumor efficacy of radiotherapy (RT) is limited by the hypoxic and immunosuppressive tumor microenvironment (TME), which leads to RT resistance and failure in eradicating distant metastatic lesions. Herein, we developed a fluorinated nanosensitizer that could deliver both oxygen (O2) and ADAR1 siRNA into tumor cells to reinforce RT by alleviating hypoxia and immunosuppression. Fluorinated poly(β-amino ester) (fPBAE) was designed to complex ADAR1 siRNA (siADAR1) via electrostatic attraction and load O2 due to the O2-dissolving capacity of fluoroalkyls. The formed nanocomplexes (NCs) facilitated robust cytosolic delivery into cancer cells after intratumoral injection, enabling efficient ADAR1 silencing to promote IFN-β release and enhance DC maturation and T cell infiltration. At the meantime, O2 was released to alleviate tumoral hypoxia. As thus, NCs significantly enhanced the anti-tumor efficacy of RT and when further coupled with programmed death ligand-1 antibody, they effectively restrained the growth of both treated primary tumors and untreated distant tumors by eliciting robust systemic immune response. This study therefore reports an enlightened strategy for remodeling the immunosuppressive TME and sensitizing radio-immunotherapy. STATEMENT OF SIGNIFICANCE: The hypoxic and immunosuppressive tumor microenvironment (TME) greatly limits the anti-tumor efficacy of radiotherapy (RT). To address this critical issue, a nano-sensitizer based on fluorinated poly(β-amino ester) (fPBAE) is herein developed to mediate efficient co-delivery of oxygen (O₂) and ADAR1 siRNA into tumor cells. ADAR1 silencing promotes DC maturation and T cell infiltration to reverse immunosuppression while the released O₂ alleviates hypoxia to sensitize RT. Thus, the nano-sensitizer remarkably enhances the anti-tumor efficacy of RT and elicits robust systemic immune response to eradicate primary and distant tumors when further coupled with PD-L1 antibody. This study provides a promising approach for RT sensitization and radio-immunotherapy.

Punicalagin as an Artemis inhibitor synergizes with photodynamic therapy in tumor suppression

Photodynamic therapy (PDT) is a minimally invasive treatment that utilizes a photosensitizer, specific light wavelengths, and oxygen to generate reactive oxygen species (ROS), causing oxidative damage and tumor cell death. However, the effectiveness of PDT can be reduced by the intrinsic antioxidant and DNA repair mechanisms of tumor cells. Artemis (SNM1C/DCLRE1C) is an endonuclease essential for repairing DNA double-strand breaks (DSBs) via non-homologous end-joining (NHEJ). Herein, we conducted a high-throughput small-molecule screening and identified Punicalagin (PUG), a natural polyphenol from pomegranate, as a novel Artemis inhibitor with an IC50 value of 296.1 nM. We also investigated the effects of PUG combined with PDT in tumor treatment, using the pentalysine β-carbonylphthalocyanine zinc (ZnPc5K) as the photosensitizer. In HeLa cells, ZnPc5K-based PDT induced significant DSBs, which could be repaired by the intrinsic DNA repair mechanisms within 12 h. Co-treatment with PUG compromised DNA repair, promoted cell apoptosis, inhibited cell invasion, and suppressed the growth of various tumor cells. Furthermore, in a mouse xenograft model, the combination of PUG and ZnPc5K-PDT effectively inhibited tumor growth with minimal side effects. These findings suggest that PUG, as an Artemis inhibitor, can enhance the therapeutic efficacy of PDT in tumor suppression by impairing DNA repair through the NHEJ pathway.

Transcription-coupled repair of DNA-protein crosslinks

DNA-protein crosslinks (DPCs) are highly toxic DNA lesions that are relevant to multiple human diseases. They are caused by various endogenous and environmental agents, and from the actions of enzymes such as topoisomerases. DPCs impede DNA polymerases, triggering replication-coupled DPC repair. Until recently the consequences of DPC blockade of RNA polymerases remained unclear. New methodologies for studying DPC repair have enabled the discovery of a transcription-coupled (TC) DPC repair pathway. Briefly, RNA polymerase II (RNAPII) stalling initiates TC-DPC repair, leading to sequential engagement of Cockayne syndrome (CS) proteins CSB and CSA, and to proteasomal degradation of the DPC. Deficient TC-DPC repair caused by loss of CSA or CSB function may help to explain the complex clinical presentation of CS patients.

Comprehensive interrogation of synthetic lethality in the DNA damage response

The DNA damage response (DDR) is a multifaceted network of pathways that preserves genome stability1,2. Unravelling the complementary interplay between these pathways remains a challenge3,4. Here we used CRISPR interference (CRISPRi) screening to comprehensively map the genetic interactions required for survival during normal human cell homeostasis across all core DDR genes. We captured known interactions and discovered myriad new connections that are available online. We defined the molecular mechanism of two of the strongest interactions. First, we found that WDR48 works with USP1 to restrain PCNA degradation in FEN1/LIG1-deficient cells. Second, we found that SMARCAL1 and FANCM directly unwind TA-rich DNA cruciforms, preventing catastrophic chromosome breakage by the ERCC1-ERCC4 complex. Our data yield fundamental insights into genome maintenance, provide a springboard for mechanistic investigations into new connections between DDR factors and pinpoint synthetic vulnerabilities that could be exploited in cancer therapy.

Insights into the behaviour of phosphorylated DNA breaks from molecular dynamic simulations

Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity-understanding how DNA sensor proteins recognize certain SSB types is crucial for studies of the DNA repair pathways. During repair of damaged DNA the final SSB that is to be ligated contains a 5'-phosphorylated end. The present work employed molecular simulation (MD) of DNA with a phosphorylated break in solution to address multiple questions regarding the dynamics of the break site. How does the 5'-phosphate group behave before it initiates a connection with other biomolecules? What is the conformation of the SSB site when it is likely to be recognized by DNA repair factors once the DNA repair response is triggered? And how is the structure and dynamics of DNA affected by the presence of a break? For this purpose, a series of MD simulations of 20 base pair DNAs, each with either a pyrimidine-based or purine-based break, were completed at a combined length of over 20,000 ns simulation time and compared with intact DNA of the same sequence. An analysis of the DNA forms, translational and orientational helical parameters, local break site stiffness, bending angles, 5'-phosphate group orientation dynamics, and the effects of the protonation state of the break site phosphate group provides insights into the mechanism for the break site recognition.

DNA Damage Response and Repair Genes and Anthracycline-Induced Cardiomyopathy in Childhood Cancer Survivors: A Report From the Children's Oncology Group and the Childhood Cancer Survivor Study

BACKGROUND

Anthracyclines induce cardiotoxicity via DNA double-strand breaks and reactive oxygen species formation, resulting in cardiomyocyte dysfunction. The role of DNA damage response/repair (DDR) genes in anthracycline-induced cardiomyopathy remains unstudied.

METHODS

We conducted a gene-based and pathway-based analysis to examine the main effect and gene-anthracycline interaction effect between DDR genes and anthracycline-induced cardiomyopathy. A discovery analysis performed with a matched case-control set of anthracycline-exposed non-Hispanic White childhood cancer survivors from Children's Oncology Group-ALTE03N1 (113 cases; 226 controls) was replicated using a cohort of anthracycline-exposed non-Hispanic White childhood cancer survivors from the Childhood Cancer Survivor Study cohort (n=1658; 97 cases). Functional analyses were performed by examining the response to doxorubicin of human-induced pluripotent stem cell-derived cardiomyocytes with CRISPR/Cas9-mediated knockout of prioritized genes.

RESULTS

Successfully replicated DDR genes demonstrating main-effect association included FANCC (P=0.037) and XRCC5 (P=0.001) and demonstrated gene-anthracycline interaction included MGMT (P=0.041). Knockouts of FANCC and MGMT in human-induced pluripotent stem cell-derived cardiomyocytes demonstrated significant resistance to doxorubicin, suggesting that these genes play a role in anthracycline-induced cardiotoxicity. Successfully replicated DDR pathways demonstrating main-effect association included base excision repair (P=2.7×10-4); role of BRCA1 in DDR (P=9.2×10-5); p53 signaling (P<1×10-16); role of checkpoint kinases proteins in cell cycle checkpoint control (P<1×10-16); mismatch repair (P<10-16); and double-strand break repair by homologous recombination (P<1×10-16). Successfully replicated DDR pathways demonstrating significant interaction effects included role of BRCA1 in DDR (P=1.4×10-4); p53 signaling (P<1×10-16); the role of checkpoint kinases proteins in cell cycle checkpoint control (P<1×10-16); mismatch repair (P<1×10-16); cell cycle: G2/M DNA damage checkpoint regulation (P=0.002); double-strand break repair by homologous recombination (P=0.009); GADD45 signaling (P=4.8×10-4); and cell cycle control of chromosomal replication (P=4.5×10-4).

CONCLUSIONS

These findings provide evidence for the role of DDR genes and pathways in anthracycline-induced cardiomyopathy and provide a framework for targeted therapeutic interventions.

Causes and consequences of DNA double-stranded breaks in cardiovascular disease

The genome, whose stability is essential for survival, is incessantly exposed to internal and external stressors, which introduce an estimated 104 to 105 lesions, such as oxidation, in the nuclear genome of each mammalian cell each day. A delicate homeostatic balance between the generation and repair of DNA lesions maintains genomic stability. To initiate transcription, DNA strands unwind to form a transcription bubble and provide a template for the RNA polymerase II (RNAPII) complex to synthesize nascent RNA. The process generates DNA supercoils and introduces torsional stress. To enable RNAPII processing, the supercoils are released by topoisomerases by introducing strand breaks, including double-stranded breaks (DSBs). Thus, DSBs are intrinsic genomic features of gene expression. The breaks are quickly repaired upon processing of the transcription. DNA lesions and damaged proteins involved in transcription could impede the integrity and efficiency of RNAPII processing. The impediment, which is referred to as transcription stress, not only could lead to the generation of aberrant RNA species but also the accumulation of DSBs. The latter is particularly the case when topoisomerase processing and/or the repair mechanisms are compromised. The DSBs activate the DNA damage response (DDR) pathways to repair the damaged DNA and/or impose cell cycle arrest and cell death. In addition, the release of DSBs into the cytosol activates the cytosolic DNA-sensing proteins (CDSPs), which along with the nuclear DDR pathways induce the expression of senescence-associated secretory phenotype (SASP), cell cycle arrest, senescence, cell death, inflammation, and aging. The primary stimulus in hereditary cardiomyopathies is a mutation(s) in genes encoding the protein constituents of cardiac myocytes; however, the phenotype is the consequence of intertwined complex interactions among numerous stressors and the causal mutation(s). Increased internal DNA stressors, such as oxidation, alkylation, and cross-linking, are expected to be common in pathological conditions, including in hereditary cardiomyopathies. In addition, dysregulation of gene expression also imposes transcriptional stress and collectively with other stressors provokes the generation of DSBs. In addition, the depletion of nicotinamide adenine dinucleotide (NAD), which occurs in pathological conditions, impairs the repair mechanism and further facilitates the accumulation of DSBs. Because DSBs activate the DDR pathways, they are expected to contribute to the pathogenesis of cardiomyopathies. Thus, interventions to reduce the generation of DSBs, enhance their repair, and block the deleterious DDR pathways would be expected to impart salubrious effects not only in pathological states, as in hereditary cardiomyopathies but also aging.

Young bone marrow transplantation delays bone aging in old mice

Recent discoveries have shown that systemic manipulations, such as parabiosis, blood exchange, and young plasma transfer, can counteract many hallmarks of aging. This rejuvenation effect has been attributed to circulatory factors produced by cells from both hematopoietic and non-hematopoietic lineages. However, the specific involvement of bone marrow (BM) or hematopoietic cells in producing such factors and their effects on aging is still unclear. We developed a model of aged mice with transplanted young or old BM cells and assessed the impact on the aging process, specifically on energy metabolism and bone remodeling parameters. The donor BM cell engraftment in the aged mice was confirmed by flow cytometry using a transplanted cell-specific marker (green fluorescent protein). Energy metabolism was assessed using Oxymax indirect calorimetry system after 3 months of transplantation. Tibiae and L3-L4 vertebrae were analyzed using micro-CT, a three-point bending test and bone histomorphometry. Moreover, bone marrow proteome was assessed using proteomics, and blood serum/plasma was collected and analyzed using the Luminex assay. Our results showed that while the effect on energy metabolism was insignificant, rejuvenating the BM through young bone marrow transplantation reversed age-associated low bone mass traits in old mice. Specifically, young bone marrow transplantation improved bone trabecular microarchitecture both in tibiae and vertebrae of old mice and increased the number of osteoblasts and osteoclasts compared to old bone marrow transplantation. In conclusion, young bone marrow cells may represent a future therapeutic strategy for age-related diseases such as osteoporosis. The findings of this study provide important insights into our understanding of aging.

HUWE1-Mediated Degradation of MUTYH Facilitates DNA Damage and Mitochondrial Dysfunction to Promote Acute Kidney Injury

The role of MUTYH, a DNA repair glycosylase in the pathogenesis of acute kidney injury (AKI) is unclear. In this study, it is found that MUTYH protein levels are significantly decreased in the kidneys of cisplatin- or folic acid (FA)-induced mouse AKI models and patients with AKI. MUTYH deficiency aggravates renal dysfunction and tubular injury following cisplatin and FA treatment, along with the accumulation of 7, 8-dihydro-8-oxoguanine (8-oxoG) and impairs mitochondrial function. Importantly, the overexpression of type 2 MUTYH (nuclear) significantly ameliorates cisplatin-induced apoptosis, oxidative stress, mitochondrial dysfunction, and DNA damage in vivo and in vitro. In contrast, overexpression of type 1 MUTYH (mitochondrial) shows a marginal effect against cisplatin-induced injury, indicating the chief role of type 2 MUTYH in antagonizing AKI. Interestingly, the results also indicate that the upregulation of the E3 ligase HUWE1 causes the ubiquitination and degradation of MUTYH in tubular epithelial cells. HUWE1 knockout or treatment with the HUWE1 inhibitor BI8622 significantly protect against cisplatin-induced AKI. Taken together, these results suggest that the ubiquitin E3 ligase HUWE1-mediates ubiquitination and degradation of MUTYH can aggravate DNA damage in the nucleus and mitochondria and promote AKI. Targeting the HUWE1/MUTYH pathway may be a potential strategy for AKI treatment.

ALDH1A3 Regulates Cellular Senescence and Senescence-Associated Secretome in Prostate Cancer

Background: Radiotherapy is a key treatment for cancer, effectively controlling local tumor growth through DNA damage that induces senescence or apoptosis in cancer cells. However, radiotherapy can trigger complex cellular reactions, such as cell senescence, which is characterized by irreversible cell cycle arrest and the secretion of pro-inflammatory factors known as the senescent-associated secretory phenotype (SASP). Methods: This study investigates the regulatory role of ALDH1A3, a key enzyme implicated in cancer cell metabolism and radiotherapy resistance, in the induction of senescence and SASP. Using in vitro models, we demonstrate that ALDH1A3 knockdown accelerates cellular senescent-like phenotype while regulating the SASP through the cGAS-STING immune response pathway. Results: Our results indicate that while ALDH1A3 knockdown promotes senescence, it reduces the secretion of pro-inflammatory factors via inhibition of the cGAS-STING pathway, potentially mitigating SASP-related tumor progression. Conclusions: These findings provide insights into the molecular mechanisms underlying prostate cancer cell senescence and suggest that ALDH1A3 could be a potential therapeutic target to enhance the efficacy of radiotherapy while controlling the adverse effects of SASP.

Could the inhibition of systemic NLRP3 inflammasome mediate central redox effects of yerba mate? An in silico and pre-clinical translational approach

ETHNOPHARMACOLOGICAL RELEVANCE

Empirically, Ilex paraguariensis A. St. Hil, or yerba-mate, has been used by natives of South America as a stimulant. Nowadays, this plant has gained popularity due to its neuroprotective effects. However, there are few studies on the biochemical-molecular mechanisms of action involved in its effect.

AIM OF THE STUDY

Chemically characterize an aqueous extract of yerba mate (YME) and evaluate if it could suppress the aberrant inflammatory response related to neurodegeneration.

MATERIALS AND METHODS

Macrophages and microglia cells were exposed to lipopolysaccharide (LPS; 100 ng/mL) plus nigericin (100 μM) or quinolinic acid (QA; 5 mM). Cellular viability, oxidative, and inflammatory markers were evaluated. Chemical matrix (HPLC - DAD), antioxidant activity, safety profile in vitro and in vivo, and an in silico docking of main targets were also assessed.

RESULTS

Pre-treatment with YME (15 μg/mL) prevented impairments in redox metabolism and inflammatory markers in BV-2 cells. In macrophages, YME showed similar results to MCC950, an inflammasome inhibitor. YME presented 282.88 mg EAG/g total phenolic content and a redox capacity of 32.94 ± 1.30 μg/mL (IC50), and its major compounds were chlorogenic acid > rutin > ferulic acid > catechin > sinapic acid. Chlorogenic acid and rutin presented a high affinity to the MCC950 region. Additionally, YME did not cause genotoxicity and was safe in vivo.

CONCLUSION

YME has significantly affected macrophages and microglia by regulating the NLRP3 inflammatory pathway.

Apelin/APJ: Another Player in the Cancer Biology Network

The apelinergic system exerts multiple biological activities in human pathologies, including cancer. Overactivation of apelin/APJ, which has been detected in many malignant tumors, and the strong correlation with progression-free and overall survival, suggested the role of an oncogene for the apelin gene. Emerging evidence sheds new light on the effects of apelin on cellular functions and homeostasis in cancer cells and supports a direct role for this pathway on different hallmarks of cancer: "sustaining proliferative signaling", "resisting cell death", "activating invasion and metastasis", "inducing/accessing vasculature", "reprogramming cellular metabolism", "avoiding immune destruction" and "tumor-promoting inflammation", and "enabling replicative immortality". This article reviews the currently available literature on the intracellular processes regulated by apelin/APJ, focusing on those pathways correlated with tumor development and progression. Furthermore, the association between the activity of the apelinergic axis and the resistance of cancer cells to oncologic treatments (chemotherapy, immunotherapy, radiation) suggests apelin/APJ as a possible target to potentiate traditional therapies, as well as to develop diagnostic and prognostic applications. This issue will be also covered in the review.

Wdr5-mediated H3K4 methylation facilitates HSPC development via maintenance of genomic stability in zebrafish

During fetal stage, hematopoietic stem and progenitor cells (HSPCs) undergo rapid proliferation with a tight control of genomic stability. Although histone H3 lysine 4 (H3K4) methylation has been reported to stabilize the genome in proliferating cells, its specific role in HSPC development remains elusive. In this study, we demonstrated that tryptophan-aspartic acid (WD) repeat protein 5 (Wdr5)-mediated H3K4 methylation is crucial for maintaining genomic stability of proliferating HSPCs in zebrafish embryos. Loss of wdr5 led to a severe reduction of HSPC pool in the caudal hematopoietic tissue, accompanied with attenuated H3K4 methylation level and evident p53-dependent apoptosis in the HSPCs. Mechanistically, Wdr5-mediated H3K4 methylation maintains genomic stability by inhibiting the formation of abnormal R-loops in the HSPCs, whereas accumulation of R-loops exacerbates DNA damage. Moreover, the absence of H3K4 trimethylation leads to an inactivated DNA damage response (DDR) pathway, which is deleterious to DNA damage repair and genomic stability. Subsequently, we found that DDR-associated genes, mutL homolog 1 and breast and ovarian cancer interacting helicase 1, are important to ensure HSPC survival, likely by stabilizing their genome. In summary, these findings reveal that Wdr5-mediated H3K4 methylation is essential for HSPC development through tight control of R-loop accumulation and DDR-associated program to ensure genomic stability and survival of proliferating HSPCs.

Transport of DNA repair proteins to the cell nucleus by the classical nuclear importin pathway - a structural overview

DNA repair is a crucial biological process necessary to address damage caused by both endogenous and exogenous agents, with at least five major pathways recognized as central to this process. In several cancer types and other diseases, including neurodegenerative disorders, DNA repair mechanisms are often disrupted or dysregulated. Despite the diversity of these proteins and their roles, they all share the common requirement of being imported into the cell nucleus to perform their functions. Therefore, understanding the nuclear import of these proteins is essential for comprehending their roles in cellular processes. The first and best-characterized nuclear targeting signal is the classical nuclear localization sequence (NLS), recognized by importin-α (Impα). Several structural and affinity studies have been conducted on complexes formed between Impα and NLSs from DNA repair proteins, although these represent only a fraction of all known DNA repair proteins. These studies have significantly advanced our understanding of the nuclear import process of DNA repair proteins, often revealing unexpected results that challenge existing literature and computational predictions. Despite advances in computational, biochemical, and cellular assays, structural methods - particularly crystallography and in-solution biophysical approaches - continue to play a critical role in providing insights into molecular events operating in biological pathways. In this review, we aim to summarize experimental structural and affinity studies involving Impα and NLSs from DNA repair proteins, with the goal of furthering our understanding of the function of these essential proteins.

Seneca Valley virus infection exploits DNA damage response to facilitate viral replication

Seneca Valley virus (SVV) is an emerging pathogen that causes severe vesicular diseases in swine, posing a significant threat to the global pork industry. DNA and RNA viruses manipulate the host DNA damage response (DDR) to modulate cellular machinery and facilitate their life cycles. However, the interaction between the host DDR and SVV infection remains unexplored. Here, we aimed to comprehensively investigate the DDR and DNA repair signaling pathways during SVV infection. We found that SVV infection causes DNA damage and triggers distinct DDR signaling pathways, including ataxia telangiectasia-mutated (ATM) kinase, ATM-Rad3-related kinase, and DNA-dependent protein kinase. However, it failed to induce the formation of γH2AX and 53BP1 foci, resulting in unrepaired DNA damage. Furthermore, we found that SVV 2B and 2C proteins can activate DDR signaling pathways and impair DNA repair. SVV-induced DDR triggered NF-κB signaling accompanied by upregulation of pro-inflammatory cytokines, as evidenced by the inhibition of ATM kinase, abolished SVV-induced NF-κB activation. Inhibition of the ATM pathway attenuated SVV replication. These findings expand our understanding of host DDR manipulation during viral infection and provide crucial insights into a novel mechanism exploited by SVV to regulate the inflammatory response for efficient replication.IMPORTANCEDDR is a cellular machinery that senses and repairs host DNA lesions to maintain genome integrity. Viruses have evolved diverse strategies to manipulate host DDR for replicative efficiency. SVV is an emerging virus that causes vesicular diseases in pigs and severely threatens the swine industry. However, the interaction between SVV and DDR remains unclear. Here, we found that SVV modulates host DDR pathways to facilitate viral replication. Our results demonstrated that SVV infection causes DNA damage, activates ATM-mediated DNA double-strand break response, and impedes DNA repair. SVV 2B and 2C proteins induced DNA damage and activated the DDR pathway while impairing repair mechanisms. This study revealed a fine-tuned molecular mechanism of SVV-modulated DDR that contributes to viral replication, facilitating deeper insight into SVV replication.

γ-tubulin mediates DNA double-strand break repair

Double-strand breaks (DSBs) in DNA pose a critical threat to genomic integrity, potentially leading to the onset and progression of various diseases, including cancer. Cellular responses to such lesions entail sophisticated repair mechanisms primarily mediated by non-homologous end joining (NHEJ) and homologous recombination (HR). Interestingly, the efficient recruitment of repair proteins and completion of DSB repair likely involve complex, inter-organelle communication and coordination of cellular components. In this study, we report a role of γ-tubulin in DSB repair. γ-tubulin is a major microtubule nucleation factor governing microtubule dynamics. We show that γ-tubulin is recruited to the site of DNA damage and is required for efficient DSB repair via both NHEJ and HR. Suppression of γ-tubulin impedes DNA repair and exacerbates DNA damage accumulation. Furthermore, γ-tubulin mediates the mobilization and formation of DNA damage foci, which serve as repair centers, thereby facilitating the recruitment of HR and NHEJ repair proteins on damaged chromatin. Finally, pharmacological inhibition of γ-tubulin enhances the cytotoxic effect of DNA-damaging agents, consistent with the DNA repair function of γ-tubulin, and underscoring the potential of its therapeutic intervention in cancer therapy.

The Impact of Radiation Therapy on Intrathecal Drug Delivery System Functioning and Safety

PURPOSE OF REVIEW

Intrathecal drug delivery systems (IDDS) are integral to managing chronic pain and spasticity, especially in oncology patients who may also require radiation therapy (RT). Concerns regarding the potential effects of ionizing radiation on IDDS functionality have been raised, with limited but growing evidence on device resilience. This review summarizes the current literature on radiation-induced IDDS malfunctions, identifies key risk factors, and discusses mitigation strategies.

RECENT FINDINGS

Although most IDDS remain functional during RT, isolated cases of radiation-induced pump failure have been reported. Factors such as radiation dose, proximity to the treatment field, and shielding methods influence device susceptibility to failure. Case studies and retrospective reviews have suggested that cumulative doses above 10 Gy may increase malfunction risks, though some devices have withstood doses as high as 36 Gy without failure. Advances in RT, including proton therapy and stereotactic techniques, may reduce exposure to IDDS. Current recommendations emphasize preemptive planning, shielding strategies, and close post-radiation monitoring to mitigate these potential risks. RT presents unique challenges for patients with IDDS, requiring a multidisciplinary approach to balance cancer treatment efficacy with device integrity. While modern IDDS demonstrate resilience to radiation exposure, careful consideration of radiation dose thresholds, device placement, and shielding is needed. Given the lack of standardized guidelines, more research is needed to establish evidence-based protocols to optimize patient safety and device performance during RT.