Homologous recombination in DNA repair and DNA damage tolerance

Organelle-oriented nanomedicines in tumor therapy: Targeting, escaping, or collaborating?

Precise tumor therapy is essential for improving treatment specificity, enhancing efficacy, and minimizing side effects. Targeting organelles is a key strategy for achieving this goal and is a frontier research area attracting a considerable amount of attention. The concept of organelle targeting has a significant effect on the structural design of the nanodrugs employed. Most notably, the intricate interactions among different organelles in a tumor cell essentially create a unified system. Unfortunately, this aspect might have been somewhat overlooked when existing organelle-targeting nanodrugs were designed. In this review, we underscore the synergistic relationship among the various organelles and advocate for a holistic view of organelle-targeting design. Through the integration of biology and material science, recent advancements in organelle targeting, escaping, and collaborating are consolidated to offer fresh perspectives for the development of antitumor nanomedicines.

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.

Stronger preference of human tumor suppressor protein BRCA1 for an open-planar Holliday junction: Insights from a combined spectroscopic and computational study

BRCA1 is a complex tumor suppressor protein involved in multiple critical cellular processes, e.g., DNA double-strand break repair, cell cycle checkpoint, etc. BRCA1-depleted cells show decreased homologous recombination (HR) and promote error-prone non-homologous end joining for DNA damage repair. Holliday junction (HJ) is an essential intermediate of DNA damage repair mechanism through HR. BRCA1 protein has high affinity for HJ and recruits several proteins to DNA damage site. Nonetheless, questions remain regarding the binding of BRCA1 protein with HJ. Does BRCA1 protein show preference for isomers of HJ? Why do specific mutations in BRCA1 protein lead to impaired DNA damage repair? Do those amino acids play any role in BRCA1-HJ interactions? Using single-molecule Fluorescence Correlation Spectroscopy, we showed that BRCA1 prefers an open-planar conformation of HJ and has a 10-fold lesser affinity for stacked HJ. The preference for an open-planar structure is independent of the nucleotide sequence at the branch point. Molecular docking and all-atom molecular dynamics simulation unraveled that primarily charged and polar residues in the DNA binding region from exon 11 of BRCA1 participated in the interaction. Most of those amino acids are places for missense changes. Further computational studies revealed that mutating these residues disrupted the interaction.

Rational Design of UvsX Recombinase Variants for Enhanced Performance in Recombinase Polymerase Amplification Applications

Homologous recombination is a vital biological process for DNA repair, genomic stability, and genetic diversity, driven by the RecA/Rad51 recombinase family. However, as a T4 bacteriophage recombinase homologous to RecA/Rad51, UvsX has limited in vitro performance during recombinase polymerase amplification (RPA) due to ATP utilization and DNA affinity. In this study, UvsX was rationally engineered to enhance these properties through homology modeling, virtual saturation mutations, and consensus mutation strategies. Targeted mutagenesis produced UvsX variants (E198N, E198R, E198K, and K35G) with a 16 ± 4% to 39 ± 6% improvement in RPA activity, while the double mutant K35G/E198R showed an increase of up to 43 ± 4%. Structural analysis revealed that the K35G/E198R mutation enlarged ATP-binding pockets and increased the positive surface potential of DNA-binding sites, resulting in a 12 ± 4% improvement in ATP utilization and more ADP and less AMP generated, a 10 ± 2% enhancement in DNA interaction compared to the wild-type, and better inhibitor tolerance. These findings establish a foundation for the rational optimization of recombinases in nucleic acid amplification and promote their potential for industrial RPA applications.

Mechanisms of radioresistance and radiosensitization strategies for Triple Negative Breast Cancer

Breast cancer is one of the most common malignant tumors in women. Triple-negative breast cancer (TNBC) is a molecular subtype of breast cancer that is characterized by a high risk of recurrence and poor prognosis. With the increasingly prominent role of radiotherapy in TNBC treatment, patient resistance to radiotherapy is an attractive area of clinical research. Gene expression changes induced by multiple mechanisms can affect the radiosensitivity of TNBC cells to radiotherapy through a variety of ways, and the enhancement of radioresistance is an important factor in the malignant progression of TNBC. The above pathways mainly include DNA damage repair, programmed cell death, cancer stem cells (CSC), antioxidant function, tumor microenvironment, and epithelial-mesenchymal transition (EMT) pathway. Tumor cells can reduce the damage of radiotherapy to themselves through the above ways, resulting in radioresistance. Therefore, in this review, we aim to summarize the strategies for immunotherapy combined with radiotherapy, targeted therapy combined with radiotherapy, and epigenetic therapy combined with radiotherapy to identify the best treatment for TNBC and improve the cure and survival rates of patients with TNBC. This review will provide important guidance and inspiration for the clinical practice of radiotherapy for TNBC, which will help deepen our understanding of this field and promote its development.

Germline-Somatic Interactions in BRCA-Associated Cancers: Unique Molecular Profiles and Clinical Outcomes Linking ATM to TP53 Synthetic Essentiality

PURPOSE

Germline alterations in homologous recombination repair (gHRR) genes affect the pathogenesis, treatment options, and survival of patients with cancer. However, distinct gHRR gene alterations may differentially affect treatment response and oncogenic signaling. In this study, we interrogated genomic and transcriptomic data and assessed clinical outcomes of patients with gHRR mutations across four BRCA-associated cancers (breast, ovarian, pancreatic, and prostate cancers) to identify therapeutic vulnerabilities.

EXPERIMENTAL DESIGN

We assessed 24,309 patients undergoing matched tumor/normal next-generation DNA and RNA sequencing. Annotated gHRR gene variants [germline BRCA1, germline BRCA2, germline PALB2, germline ATM (gATM), and germline CHEK2] were analyzed. HRs were used to assess survival outcomes comparing germline versus sporadic groups. Somatic alterations and their frequencies were compared across gHRR-altered groups. Differential gene expression and gene set enrichment analysis were used to compare transcriptomic profiles.

RESULTS

Somatic TP53 mutations were depleted in gATM carriers (P < 0.05) across all four BRCA-associated cancers by up to 2.5-fold. Tumors with germline BRCA1/2 mutations were associated with improved survival in patients with ovarian cancer and had consistent enrichment of TP53 mutations in all four cancers. gATM mutations displayed elevated p53 transcriptional activity in all four cancers, with significance reached in breast and prostate cancers (P < 0.01). In breast, ovarian, and prostate cancers, gATM tumors demonstrated significantly increased inflammatory pathways (P < 0.001). Finally, using gene dependency data, we found that cell lines that were highly dependent on ATM were co-dependent on canonical p53 function.

CONCLUSIONS

gATM-associated cancers seem to require intact p53 activity and this synthetic essentiality may be used to guide targeted therapies that perturb canonical TP53 function.

PARP Inhibitors in the Neoadjuvant Setting; A Comprehensive Overview of the Rationale for their Use, Past and Ongoing Clinical Trials

PURPOSEOF REVIEW

Poly (ADP-ribose) polymerases (PARPs) are enzymes essential for detecting and repairing DNA damage through poly-ADP-ribosylation. In cancer, cells with deficiencies in homologous recombination repair mechanisms often become more dependent on PARP-mediated repair mechanisms to effectively repair dsDNA breaks. As such, PARP inhibitors (PARPis) were introduced into clinical practice, serving as a key targeted therapy option through synthetic lethality in the treatment of cancers with homologous recombination repair deficiency (HRD). Though PARPis are currently approved in the adjuvant setting for several cancer types such as ovarian, breast, prostate and pancreatic cancer, their potential role in the neoadjuvant setting remains under investigation. This review outlines the rationale for using PARPi in the neoadjuvant setting and evaluates findings from early and ongoing clinical trials.

RECENT FINDINGS

Our analysis indicates that numerous studies have explored PARPi as a neoadjuvant treatment for HRD-related cancers. The majority of neoadjuvant PARPi trials have been performed in breast and ovarian cancer, while phase II/III evidence supporting efficacy in prostate and pancreatic cancers remains limited. Studies are investigating PARPi in the neoadjuvant setting of HRD-related cancers. Future research should prioritize combination strategies with immune checkpoint inhibitors and expand outcome measures to include patient satisfaction and quality-of-life metrics.

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.

High-LET Proton Irradiation Significantly Alters the Clonogenic and Tumorigenic Potential of Human Breast Cancer Cell Lines In Vitro and In Vivo

BACKGROUND

The implementation of proton beam irradiation (PBI) for breast cancer (BC) treatment is rapidly advancing due to its enhanced target coverage and reduced toxicities to organs at risk. However, the effects of PBI can vary depending on the cell type. This study aimed to explore the effects of PBI on two BC cell lines, MCF7 and MDA-MB-231.

METHODS

The relative biological effectiveness (RBE) of PBI was assessed using a clonogenic assay. DNA double-strand break (DSB) repair, epithelial-mesenchymal transition (EMT), and filamentous actin (F-actin) were evaluated using immunofluorescence analysis. The extent of entosis and the senescence-associated β-galactosidase (SA-β-gal) activity were estimated by cytochemistry analysis. The influence of the extracellular matrix was evaluated by cultivating cells in both adherent two-dimensional (2D) environments and within 3D fibrin gels of varying stiffness. The metastatic propensity of cells was investigated using migration tests and the cell encapsulation of carboxylate-modified fluorescent nanoparticles. The comparative tumorigenic potential of cells was investigated using an in vivo model of the chick embryo chorioallantoic membrane (CAM).

RESULTS

PBI demonstrated superior efficacy in eliminating MCF7 and MDA-MB-231 cells with RBE 1.7 and 1.75, respectively. Following PBI, MDA-MB-231 cells exhibited significantly lower clonogenic survival compared to MCF7, which was accompanied by the accumulation of phosphorylated histone H2AX (γH2AX), p53-binding protein 1 (53BP1) and Rad51 foci of DNA DSBs repair proteins. After surviving 7 days post-PBI, MCF7 cells exhibited 2.5-fold higher levels of the senescence phenotype and entosis compared to the MDA-MB-231 offspring. Both PBI-survived cell lines had greater capability for 2D collective migration, but their metastatic potential was significantly reduced. A significant influence of extracellular matrix stiffness on the correlation between F-actin expression in PBI-survived cells-an indicator of cell stiffness-and their ability to uptake nanoparticles, a trait associated with metastatic potential, was observed. PBI-survived MDA-MB-231RP subline exhibited a hybrid EMT phenotype and a 70% reduction in tumor growth in the in vivo model of the chick embryo CAM. In contrast, PBI-survived MCF7RP cells exhibit mesenchymal-to-epithelial transition (MET)-like features, and their in vivo tumor growth increased by 66% compared to parental cells.

CONCLUSIONS

PBI triggers various cellular responses in different BC cell lines, influencing tumor growth through mechanisms like DNA damage repair, stress-induced premature senescence (SIPS), and alterations in the stiffness of tumor cell membranes. Our insights into entosis and the effect of extracellular matrix stiffness on metastatic propensity (nanoparticle uptake) enhance the understanding of the role of PBI in BC cells, emphasizing the need for more research to optimize its therapeutic application.

Maternal exposure to Aristolochic Acid I affects meiotic I progression by impairing DNA damage repair in fetal oocytes

Aristolochic acid I (AAI), the predominant compound in Aristolochiaceae plants and Asarum species, is a widespread environmental contaminant capable of accumulating in soil, contaminating water and crops, ultimately entering the human body. Its nephrotoxic, carcinogenic, and reproductive toxic effects pose significant health concerns. This study investigates the impact of maternal AAI exposure on meiotic prophase I (MPI) during early fetal oogenesis. Pregnant mice were orally administered AAI at doses of 0.03125, 0.125, and 1 mg/kg from 14.5 to 16.5 dpc, with fetal ovaries collected at 17.5 dpc. AAI exposure induced meiotic defects in fetal oocytes, including delayed progression of MPI, increased DNA damage, and impaired homologous recombination. Furthermore, AAI induced oxidative stress, reduced mitochondrial membrane potential and triggered apoptosis, leading to a diminished ovarian reserve in neonatal ovaries. Mechanistically, these defects were mediated by heat shock proteins which altered protein-protein interactions crucial for DNA repair. Given the pivotal role of early oogenesis in determining female fertility and ensuring the health of offspring, these findings underscore the potential reproductive risks of AAI exposure during pregnancy. This study highlights the urgent need for greater awareness of foodborne contaminants and the implementation of preventative measures to mitigate maternal AAI exposure, thereby safeguarding offspring fertility and health.

Role of MRE11 in DNA damage repair pathway dynamics and its diagnostic and prognostic significance in hereditary breast and ovarian cancer

BACKGROUND

DNA damage repair pathway genes are key components for maintaining genomic stability and are mainly associated with hereditary breast and ovarian cancer.

METHODS

The present study aimed to investigate the gene expression profile of DNA damage repair pathway genes, including BRCA1, BRCA2, ATM, TP53, CHEK2, MRE11, RAD50, BARD1, PALB2, and NBN, in hereditary breast and ovarian cancer patients using quantitative real-time PCR.

RESULTS

The study showed significant upregulation of most DNA damage repair genes in HBOC patients compared to controls, except MRE11, which was downregulated. Receiver operating characteristic (ROC) curve analysis revealed that MRE11 (p < 0.001), BRCA1 (p < 0.001), BRCA2 (p < 0.001), and PALB2 (p < 0.001) can be used as potential diagnostic biomarkers for hereditary breast and ovarian cancer. Spearman correlation analysis showed that RAD50 was significantly associated with the BRCA1/2 mutation status (p = 0.05). Furthermore, bivariate analysis revealed a strong positive correlation between BARD1 gene expression and the expression of BRCA1, PALB2, and NBN genes. Kaplan-Meier survival analysis showed that reduces expression of the MRE11 gene was associated with better overall survival.

CONCLUSIONS

The study findings may lead to a better understanding of the molecular mechanisms underlying hereditary breast and ovarian cancer, suggesting its role as a potential diagnostic and prognostic marker.

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.

Nanoparticle-mediated enhancement of DNA Vaccines: Revolutionizing immunization strategies

DNA vaccines are a novel form of vaccination that aims to harness genetic material to produce targeted immune responses. Nevertheless, their therapeutic application is hampered by low transfection efficacy, immunogenicity, and instability. Nanoparticle (NP) - based delivery systems are beneficial in enhancing DNA stability, increasing DNA uptake by antigen-presenting cells (APCs), and controlling antigen release. Some key progress includes the polymeric, lipid-based, and hybrid NPs and biocompatible carriers with inherent adjuvant effects. These systems have helped to enhance the antigen cross-presentation and T-cell activation significantly. In addition, biocompatible hybrid nanocarriers, antigen cross-presentation strategies, and next-generation sequencing (NGS) technologies are speeding up the identification of new antigens, while AI and machine learning are facilitating the development of efficient delivery systems. This review aims to assess how NPs have contributed to improving the effectiveness of DNA vaccines for treating diseases, cancer, and emerging diseases, as well as advancing the next generation of DNA vaccines.

Automated Scoring to Assess RAD51-Mediated Homologous Recombination in Ovarian Patient-Derived Tumor Organoids

Poly(ADP-ribose) polymerase inhibitors (PARPi) have been shown to improve progression-free survival, particularly in homologous recombination-deficient ovarian cancers. Identifying patients eligible for PARPi is currently based on next-generation sequencing, but the persistence of genomic scars in tumors after restoration of homologous recombination (HR) or epigenetic changes can be a limitation. Functional assays could thus be used to improve this profiling and faithfully identify homologous recombination-deficient tumors. The repair capacity (RECAP) test assesses the formation of RAD51 foci in proliferating cells after irradiation and can be used on tumors as well as on patient-derived tumor organoids (PDTO). However, RAD51 foci scoring is often performed manually without standardization. The purpose of this translational study was to develop an automated tool for scoring RAD51-mediated HR based on whole slide imaging of ovarian PDTO. To that end, we quantified Cyclin A2 and RAD51 immunofluorescence on 9 PDTO models derived from 8 ovarian cancer patients, and next, we compared the RECAP test results to genome instability score and to the patient clinical response. We therefore developed a standardized and automatized quantitative histoimaging tool allowing a comparative RAD51 foci evaluation and thus to define the HR status in PDTO. Our RECAP-based classification was correlated to the genome instability score, offering a new opportunity for standardization of HR assessment in PDTO. This new automated tool to score HR status, which remains to be validated on a large cohort of patients, may thus be used as a complement to next-generation sequencing-based tests in order to improve the identification of the number of patients eligible for PARPi.

Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA

Single-stranded DNA-binding proteins (SSBs) are essential for genome stability, facilitating replication, repair, and recombination by binding ssDNA, recruiting other proteins, and dynamically relocating in response to cellular demands. Using single-molecule fluorescence resonance energy transfer (smFRET) assays, we elucidated the mechanisms underlying direct strand transfer from one locale to another, protein exchange, and RNA interactions at high resolution. Both bacterial SSB and eukaryotic replication protein A (RPA) exhibited direct strand transfer to competing ssDNA, with rates strongly influenced by ssDNA length. Strand transfer proceeded through multiple failed attempts before a successful transfer, forming a ternary intermediate complex with transient interactions, supporting a direct transfer mechanism. Both proteins efficiently exchanged DNA-bound counterparts with freely diffusing molecules, while hetero-protein exchange revealed that SSB and RPA could replace each other on ssDNA in a length-dependent manner, indicating that protein exchange does not require specific protein-protein interactions. Additionally, both proteins bound RNA and underwent strand transfer to competing RNA, with RPA demonstrating faster RNA transfer kinetics. Competitive binding assays confirmed a strong preference for DNA over RNA. These findings provide critical insights into the dynamic behavior of SSB and RPA in nucleic acid interactions, advancing our understanding of their essential roles in genome stability, regulating RNA metabolism, and orchestrating nucleic acid processes.

The Complex Interactions Between HIV-1 and Human Host Cell Genome: From Molecular Mechanisms to Clinical Practice

Antiretroviral therapy (ART) has significantly improved the prognosis of human immunodeficiency virus type 1 (HIV-1) infection. Although ART can suppress plasma viremia below detectable levels, it cannot eradicate the HIV-1 DNA (provirus) integrated into the host cell genome. This integration often results in unrepaired DNA damage due to the HIV-1-induced inhibition of DNA repair pathways. Furthermore, HIV-1 infection causes telomere attrition in host chromosomes, a critical factor contributing to CD4+ T cell senescence and apoptosis. HIV-1 proteins can induce DNA damage, block DNA replication, and activate DNA damage responses across various organs. In this review, we explore multiple aspects of the intricate interactions between HIV-1 and the host genome involved in CD4+ T cell depletion, inflammaging, the clonal expansion of infected cells in long-term-treated patients, and viral latency. We discuss the molecular mechanisms of DNA damage that contribute to comorbidities in HIV-1-infected individuals and highlight emerging therapeutic strategies targeting the integrated HIV-1 provirus.

BRCA1 and BRCA2 as prognostic markers in oral squamous cell carcinoma: a minireview

Oral squamous cell carcinoma (OSCC), a subset of head and neck cancers, primarily originates in the epithelial tissues of the oral cavity. Despite advancements in treatment, the mortality rate for OSCC remains around 50%, underscoring the urgent need for improved prognostic markers. This review explores the role of the BRCA1 and BRCA2 genes-traditionally associated with breast and ovarian cancers-in the context of OSCC. We discuss the molecular pathways involving BRCA genes, their potential as diagnostics and prognostic biomarkers, and their implications for personalized treatment strategies, including addressing chemotherapy resistance. Furthermore, this review emphasizes the significance of genome stability in cancer progression and examines both current and emerging methodologies for detecting BRCA mutations in OSCC patients. Despite limited prevalence of BRCA mutations in OSCC compared to other cancers, their role in DNA repair and therapeutic response underscores their potential as clinical biomarkers. However, standardized, multicenter studies are still needed to validate their utility in OSCC management. A better understanding of the role of BRCA genes in OSCC could pave the way for more effective therapeutic approaches and improved patient outcomes.

Poly (ADP-ribose) polymerase inhibitors in cancer therapy

ABSTRACT

Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) have emerged as critical agents for cancer therapy. By inhibiting the catalytic activity of PARP enzymes and trapping them in the DNA, PARPis disrupt DNA repair, ultimately leading to cell death, particularly in cancer cells with homologous recombination repair deficiencies, such as those harboring BRCA mutations. This review delves into the mechanisms of action of PARPis in anticancer treatments, including the inhibition of DNA repair, synthetic lethality, and replication stress. Furthermore, the clinical applications of PARPis in various cancers and their adverse effects as well as their combinations with other therapies and the mechanisms underlying resistance are summarized. This review provides comprehensive insights into the role and mechanisms of PARP and PARPis in DNA repair, with a particular focus on the potential of PARPi-based therapies in precision medicine for cancer treatment.

Lipoylation inhibition enhances radiation control of lung cancer by suppressing homologous recombination DNA damage repair

Lung cancer exhibits altered metabolism, influencing its response to radiation. To investigate the metabolic regulation of radiation response, we conducted a comprehensive, metabolic-wide CRISPR-Cas9 loss-of-function screen using radiation as selection pressure in human non-small cell lung cancer. Lipoylation emerged as a key metabolic target for radiosensitization, with lipoyltransferase 1 (LIPT1) identified as a top hit. LIPT1 covalently conjugates mitochondrial 2-ketoacid dehydrogenases with lipoic acid, facilitating enzymatic functions involved in the tricarboxylic acid cycle. Inhibiting lipoylation, either through genetic LIPT1 knockout or a lipoylation inhibitor (CPI-613), enhanced tumor control by radiation. Mechanistically, lipoylation inhibition increased 2-hydroxyglutarate, leading to H3K9 trimethylation, disrupting TIP60 recruitment and ataxia telangiectasia mutated (ATM)-mediated DNA damage repair signaling, impairing homologous recombination repair. In summary, our findings reveal a critical role of LIPT1 in regulating DNA damage and chromosome stability and may suggest a means to enhance therapeutic outcomes with DNA-damaging agents.

Deciphering the structural consequences of R83 and R152 methylation on DNA polymerase β using molecular modeling

DNA polymerase β, a member of the X-family of DNA polymerases, undergoes complex regulations both in vitro and in vivo through various posttranslational modifications, including phosphorylation and methylation. The impact of these modifications varies depending on the specific amino acid undergoing alterations. In vitro, methylation of DNA polymerase β with the enzyme protein arginine methyltransferase 6 (PRMT6) at R83 and R152 enhances polymerase activity by improving DNA binding and processivity. Although these studies have shown that methylation improves DNA binding, the underlying mechanism of enhancement of polymerase activity in terms of structure and dynamics remains poorly understood. To address this gap, we modeled the methylated enzyme/DNA complex and conducted a microsecond-long simulation in the presence of Mg ions. Our results revealed significant structural changes induced by methylating both R83 and R152 sites in the enzyme. Specifically, these changes caused the DNA fragment to move closer to the C- and N-subdomains, forming additional hydrogen bonds. Furthermore, the cross-correlation map demonstrated that methylation enhanced long-range correlations within the domains/subdomains of DNA polymerase β, along with an increase in the linear mutual information value between the domains/subdomains and DNA fragments. The graph connectivity network also illustrated that methylation modulates the information pathway and identifies residues exhibiting long-distance coupling with the methylated sites. Our results provide an atomic-level understanding of the structural transition induced by methylation, shedding light on the mechanisms underlying the methylation-induced enhancement of activity in DNA polymerase β.

Genome-wide mapping and quantification of DNA damage induced by catechol estrogens using Click-Probe-Seq and LC-MS2

Genotoxic estrogen metabolites generate various DNA lesions; however, their target genes and carcinogenic mechanisms remain unexplored. Here, genome-wide sequencing using click probe enrichment coupled with liquid chromatography-tandem mass spectrometry (Click-Probe-Seq/LC-MS2) is developed to identify damaged genes and characterize the released and stable adducts induced by 4-hydroxy-17β-estradiol (4OHE2) in MCF-7 cell chromatin. The data reveal that guanine nucleobases in the GC-rich transcription-relevant domain are the main target sites. Moreover, the damage abundance positively correlates with DNase hypersensitive sites, suggesting that 4OHE2 preferentially attacks accessible chromatin regions beyond the estrogen receptor (ER) binding sites. Cell-based studies indicate that accumulated 4OHE2 suppresses gene transcription, causes ineffective damage repair, and decreases cell viability, differing from the uncontrolled cell growth caused by extensive ER signaling. The Click-Probe-Seq/LC-MS2 approach reveals the first chromatin damage map induced by an endogenous metabolite, exposing a previously unexplored landscape in cancer research that is applicable to other genotoxic species.

The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range

Microorganisms endure novel challenges for which other microorganisms in other biomes may have already evolved solutions. This is the case of nosocomial bacteria under antibiotic therapy because antibiotics are of ancient natural origin and resistances to them have previously emerged in environmental bacteria. In such cases, the rate of adaptation crucially depends on the acquisition of genes by horizontal transfer of plasmids from distantly related bacteria in different biomes. We hypothesized that such processes should be driven by plasmids among the most mobile and evolvable. We confirmed these predictions by showing that plasmid species encoding antibiotic resistance are very mobile, have broad host ranges, while showing higher rates of homologous recombination and faster turnover of gene repertoires than the other plasmids. These characteristics remain outstanding when we remove resistance plasmids from our dataset, suggesting that antibiotic resistance genes are preferentially acquired and carried by plasmid species that are intrinsically very mobile and plastic. Evolvability and mobility facilitate the transfer of antibiotic resistance, and presumably of other phenotypes, across distant taxonomic groups and biomes. Hence, plasmid species, and possibly those of other mobile genetic elements, have differentiated and predictable roles in the spread of novel traits.

DNA Damaging Agents Induce RNA Structural and Transcriptional Changes for Genes Associated with Redox Homeostasis in Arabidopsis thaliana

Living organisms are constantly exposed to various DNA damaging agents. While the mechanisms of DNA damage and DNA repair are well understood, the impact of these agents on RNA secondary structure and subsequent function remains elusive. In this study, we explore the effects of DNA damaging reagent methyl methanesulfonate (MMS) on arabidopsis gene expression and RNA secondary structure using the dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq) method. Our analyses reveal that changes in transcriptional levels and mRNA structure are key factors in response to DNA damaging agents. MMS treatment leads to the up-regulation of arabidopsis RBOHs (respiratory burst oxidase homologues) and alteration in the RNA secondary structure of GSTF9 and GSTF10, thereby enhancing mRNA translation efficiency. Redox homeostasis manipulated by RBOHs and GSTFs plays a crucial role in MMS-induced primary root growth inhibition. In conclusion, our findings shed light on the effects of DNA damaging agents on RNA structure and potential mRNA translation, which provide a new insight to understand the mechanism of DNA damage.

Molecular mechanisms of extrachromosomal circular DNA formation

Recent research reveals that eukaryotic genomes form circular DNA from all parts of their genome, some large enough to carry whole genes. In organisms like yeast and in human cancers, it is often observed that extrachromosomal circular DNA (eccDNA) benefits the individual cell by providing resources for rapid cellular growth. However, our comprehension of eccDNA remains incomplete, primarily due to their transient nature. Early studies suggest they arise when DNA breaks and is subsequently repaired incorrectly. In this review, we provide an overview of the evidence for molecular mechanisms that lead to eccDNA formation in human cancers and yeast, focusing on nonhomologous end joining, alternative end joining, and homologous recombination repair pathways. Furthermore, we present hypotheses in the form of molecular eccDNA formation models and consider cellular conditions which may affect eccDNA generation. Finally, we discuss the framework for future experimental evidence.

Genome-wide KAS-Seq mapping of leukocytes in ischemia-reperfusion model reveals IL7R as a potential therapeutic target for ischemia-reperfusion injury

Ischemia-reperfusion injury (IRI) is one of the leading causes of mortality and disability worldwide. Owing to its complex pathogenesis, there is still a lack of effective therapeutic targets in clinical practice, and exploring the mechanism and targets of IRI is still a major clinical challenge. This study aimed to explore the genetic alterations in leukocytes in peripheral blood after ischemia-reperfusion, aiming to discover new biomarkers and potential therapeutic targets. KAS-Seq (Kethoxal-assisted single-strand DNA sequencing) was used to obtain gene expression profiles of circulating leukocytes in a porcine ischemia-reperfusion model at 24, 48, and 72 h post-ischemia‒reperfusion. This method integrated genes that exhibited regular changes over time. In this study, we thoroughly analyzed the dynamic changes in gene expression post-IRI, revealing significant enrichment in key signaling pathways that regulate immune responses and T-cell activation over time. Our identification of the interleukin-7 receptor (IL7R) was particularly striking, as it plays a crucial molecular role in IRI. Additionally, using database mining technology, we confirmed the close relationship between IL7R and IRI, explored the interaction between interferon-γ (IFNG) and IL7R in T-cell activation, and clarified their joint influence on ischemia-reperfusion injury. Using KAS-Seq analysis of leukocytes from peripheral blood, we successfully delineated the temporal patterns of gene expression and changes in signal transduction pathways in porcine models of ischemia-reperfusion. Subsequent in-depth analysis identified IL7R as a potential novel therapeutic target for IRI. The pivotal role of this gene in modulating immune responses provides innovative avenues for the development of IRI treatments.

IHCH9033, a novel class I HDAC inhibitor, synergizes with FLT3 inhibitor and rescues quizartinib resistance in FLT3-ITD AML via enhancing DNA damage response

BACKGROUND

Despite initial success with FLT3 inhibitors (FLT3is), outcomes for FLT3-ITD acute myeloid leukemia (AML) patients remain unsatisfactory, underscoring the need for more effective treatment options. Epigenetic modifications, such as histone acetylation, contribute to AML's onset and persistence, advocating the potential for epigenetic therapies. However, the poor specificity of pan-histone deacetylase inhibitors (HDACis) leads to undesirable adverse effects, prompting the need for isoform-specific HDACis. This study aims to explore the antileukemic activities and mechanisms of IHCH9033, a novel class I HDACi, alone or combined with FLT3i in FLT3-ITD AML.

METHODS

The viability of AML cell lines and primary AML cells treated with HDACis alone or in combination with FLT3i was detected by MTT or CCK8 assay. Flow cytometry was utilized to examine cell apoptosis, cell cycle progression and ROS production. RNA sequencing analysis, RT-qPCR, western blotting, and co-immunoprecipitation assays were employed to elucidate the molecule mechanisms. The in vivo anti-leukemia efficacy was tested in xenografted mice models derived from FLT3-ITD cell lines and primary AML patients.

RESULTS

Here, we identified IHCH9033, a novel selective class I HDACi, which exhibited an increased antitumor effect in FLT3-ITD AML through effectively eliminating leukemia burden and overcoming resistance to FLT3i. Mechanically, IHCH9033 selectively inhibited DNA repair in FLT3-ITD AML cells, leading to the accumulation of DNA damage that eventually resulted in cell cycle arrest and apoptosis. Additionally, IHCH9033 induced HSP90 acetylation, FLT3 ubiquitination, and proteasomal degradation of FLT3, thereby inhibiting FLT3 downstream signaling. Notably, IHCH9033 maintained its potency in both FLT3i-resistant AML cell lines and primary-resistant patient samples, and exerted strong synergy with the FLT3i quizartinib, leading to tumor regression in FLT3-ITD/TKD AML xenografts. In patient-derived xenografts, the treatment with IHCH9033, both alone and in combination, led to nearly complete eradication of the AML burden, without significant adverse effects.

CONCLUSIONS

Our study shows that IHCH9033, a novel class I HDACi with a desirable pharmacological profile, is a promising drug candidate for FLT3-ITD AML, and suggests a strategy of combining class I HDACis and FLT3is in AML clinical trials to increase efficacy and overcome resistance, thus potentially providing a curative treatment option.

Association between DNA damage repair alterations and outcomes to 177Lu-PSMA-617 in advanced prostate cancer

BACKGROUND

177Lu-prostate-specific membrane antigen (PSMA)-617 (LuPSMA) is a radionuclide therapy approved for patients with PSMA-avid metastatic castrate-resistant prostate cancer (mCRPC). We evaluated whether alterations in the DNA damage repair (DDR) pathway were associated with outcomes to LuPSMA.

PATIENTS AND METHODS

We identified an institutional cohort of men (n = 134) treated with ≥2 cycles of LuPSMA who had panel-based germline and/or tumor genomic sequencing. Mutations or two-copy losses in any of BRCA1, BRCA2, ATM, CDK12, PALB2, RAD51, and MSH2 were considered DDR defects. The primary outcome was a ≥50% reduction in the prostate-specific antigen (PSA) level during LuPSMA therapy (PSA50); secondary outcomes were PSA progression-free survival (PSA-PFS) and overall survival (OS). Models were adjusted for age, number of prior systemic therapies, sites of metastasis, and log-transformed PSA at cycle 1.

RESULTS

Thirty-four patients (25%) harbored DDR alterations, most commonly in BRCA2 and ATM (both n = 13). The presence of a DDR defect was not associated with PSA50 [adjusted odds ratio 0.48 (0.20-1.09), P = 0.08], PSA-PFS [adjusted hazard ratio (HR) 1.29 (0.79-2.10), P = 0.30], or OS [adjusted HR 1.42 (0.74-2.72), P = 0.29], with a non-significant trend toward poorer outcomes among DDR-altered patients.

CONCLUSIONS

DDR alterations were not associated with outcomes following LuPSMA. This has implications for treatment sequencing in mCRPC, particularly in patients with DDR alterations.

Particulate hexavalent chromium exposure induces DNA double-strand breaks and inhibits homologous recombination repair in rat and human lung tissues

Lung cancer is an important human health concern because of its high mortality rate, with many cases caused by environmental chemicals other than tobacco. Particulate hexavalent chromium [Cr(VI)] is a well-established human lung carcinogen, but how Cr(VI) induces lung cancer is poorly understood. Chromosome instability, a hallmark of lung cancer, is considered a major driving factor in Cr(VI)-induced lung cancer. Our previous studies in cultured human lung cells showed that particulate Cr(VI) induces DNA double-strand breaks during the late S and G2 phases of the cell cycle, which are repaired by homologous recombination, one of the main repair pathways of DNA double-strand breaks. Our previous data showed that prolonged exposure to Cr(VI) inhibits homologous recombination repair by targeting RAD51, a key protein that mediates homologous recombination. Therefore, particulate Cr(VI)-induced DNA damage combined with failure of DNA repair can lead to chromosome instability. In this study we translated these results to rat lung tissue and lung tumor tissue from Cr(VI)-exposed workers. Wistar rats were exposed to zinc chromate in a saline solution or saline alone by oropharyngeal aspiration with a single dose repeated weekly for 90 days. We observed DNA double-strand breaks increased in a concentration-dependent manner, but homologous recombination repair decreased in rat lungs after 90 days of exposure. Notably, these effects were more pronounced in bronchioles than alveoli. We also considered these effects in Cr(VI)-associated human lung tumors and observed increased DNA double-strand breaks and reduced RAD51 levels in lung tumor tissue compared with adjacent normal lung tissue. Thus, Cr(VI)-induced induction of DNA double-strand breaks, and inhibition of homologous recombination repair translates from cultured cells to experimental animals, normal lung tissue adjacent to the tumor, and Cr(VI)-associated human lung tumors.

Lactylation: The metabolic accomplice shaping cancer's response to radiotherapy and immunotherapy

Protein lactylation, an emerging post-translational modification, is providing new insights into tumor biology and challenging our current understanding of cancer mechanisms. Our review illuminates the intricate roles of lactylation in carcinogenesis, tumor progression, and therapeutic responses, positioning it as a critical linchpin connecting metabolic reprogramming, epigenetic modulation, and treatment outcomes. We provide an in-depth analysis of lactylation's molecular mechanisms and its far-reaching impact on cell cycle regulation, immune evasion strategies, and therapeutic resistance within the complex tumor microenvironment. Notably, this review dissects the paradoxical nature of lactylation in cancer immunotherapy and radiotherapy. While heightened lactylation can foster immune suppression and radioresistance, strategically targeting lactylation cascades opens innovative avenues for amplifying the efficacy of current treatment paradigms. We critically evaluate lactylation's potential as a robust diagnostic and prognostic biomarker and explore frontier therapeutic approaches targeting lactylation. The synergistic integration of multi-omics data and artificial intelligence in lactylation research is catalyzing significant strides towards personalized cancer management. This review not only consolidates current knowledge but also charts a course for future investigations. Key research imperatives include deciphering tumor-specific lactylation signatures, optimizing synergistic strategies combining lactylation modulation with immune checkpoint inhibitors and radiotherapy, and comprehensively assessing the long-term physiological implications of lactylation intervention. As our understanding of lactylation's pivotal role in tumor biology continues to evolve, this burgeoning field promises to usher in transformative advancements in cancer diagnosis, treatment modalitie.

Potassium ion channel modulation at cancer-neural interface enhances neuronal excitability in epileptogenic glioblastoma multiforme

The central nervous system (CNS) is increasingly recognized as a critical modulator in the oncogenesis of glioblastoma multiforme (GBM), with interactions between cancer and local neuronal circuits frequently leading to epilepsy; however, the relative contributions of these factors remain unclear. Here, we report a coordinated intratumor shift among distinct cancer subtypes within progenitor-like families of epileptic GBM patients, revealing an accumulation of oligodendrocyte progenitor (OPC)-like subpopulations at the cancer-neuron interface along with heightened electrical signaling activity in the surrounding neuronal networks. The OPC-like cells associated with epilepsy express KCND2, which encodes the voltage-gated K+ channel KV4.2, enhancing neuronal excitability via accumulation of extracellular K+, as demonstrated in patient-derived ex vivo slices, xenografting models, and engineering organoids. Together, we uncovered the essential local circuitry, cellular components, and molecular mechanisms facilitating cancer-neuron interaction at peritumor borders. KCND2 plays a crucial role in mediating nervous system-cancer electrical communication, suggesting potential targets for intervention.

Nanomaterials exert biological effects by influencing the ubiquitin-proteasome system

The ubiquitin-proteasome system (UPS) is an important type of protein post-translational modification that affects the quantity and quality of various proteins and influences cellular processes such as the cell cycle, transcription, oxidative stress, and autophagy. Nanomaterials (NMs), which exhibit excellent physicochemical properties, can directly interact with the UPS and act as molecular-targeted drugs to induce changes in biological processes. This review provides an overview of the influence of NMs on the UPS of misfolded proteins and key proteins, which are related to cancer, neurodegenerative diseases and oxidative stress. This review also summarizes the role of modification processes involved in ubiquitination the biological effects of NMs and the mechanism of such effects of NMs through regulation of the UPS. This review deepens our understanding of the influence of NMs on the protein degradation process and provides new potential therapeutic targets for disease.

Integrative bioinformatics approach identifies novel drug targets for hyperaldosteronism, with a focus on SHMT1 as a promising therapeutic candidate

Primary aldosteronism (PA), characterized by autonomous aldosterone overproduction, is a major cause of secondary hypertension with significant cardiovascular complications. Current treatments mainly focus on symptom management rather than addressing underlying mechanisms. This study aims to discover novel therapeutic targets for PA using integrated bioinformatics and experimental validation approaches. We employed a systematic approach combining: gene identification through transcriptome-wide association studies (TWAS); causal inference using summary data-based Mendelian randomization (SMR) and two-sample Mendelian randomization (MR) analyses; additional analyses included phenome-wide association analysis, enrichment analysis, protein-protein interaction (PPI) networks, drug repurposing, molecular docking and clinical validation through aldosterone-producing adenomas (APAs) tissue. Through systematic screening and prioritization, we identified 163 PA-associated genes, of which seven emerged as potential drug targets: CEP104, HIP1, TONSL, ZNF100, SHMT1, and two long non-coding RNAs (AC006369.2 and MRPL23-AS1). SHMT1 was identified as the most promising target, showing significantly elevated expression in APAs compared to adjacent non-tumorous tissues. Drug repurposing analysis identified four potential SHMT1-targeting compounds (Mimosine, Pemetrexed, Leucovorin, and Irinotecan), supported by molecular docking studies. The integration of multiple bioinformatics methods and experimental validation successfully identified novel drug targets for hyperaldosteronism. SHMT1, in particular, represents a promising candidate for future therapeutic development. These findings provide new opportunities for developing causative treatments for PA, though further clinical validation is warranted.

REV7: a small but mighty regulator of genome maintenance and cancer development

REV7, also known as MAD2B, MAD2L2, and FANCV, is a HORMA-domain family protein crucial to multiple genome stability pathways. REV7's canonical role is as a member of polymerase ζ, a specialized translesion synthesis polymerase essential for DNA damage tolerance. REV7 also ensures accurate cell cycle progression and prevents premature mitotic progression by sequestering an anaphase-promoting complex/cyclosome activator. Additionally, REV7 supports genome integrity by directing double-strand break repair pathway choice as part of the recently characterized mammalian shieldin complex. Given that genome instability is a hallmark of cancer, it is unsurprising that REV7, with its numerous genome maintenance roles, is implicated in multiple malignancies, including ovarian cancer, glioma, breast cancer, malignant melanoma, and small-cell lung cancer. Moreover, high REV7 expression is associated with poor prognoses and treatment resistance in these and other cancers. Promisingly, early studies indicate that REV7 suppression enhances sensitivity to chemotherapeutics, including cisplatin. This review aims to provide a comprehensive overview of REV7's myriad roles in genome maintenance and other functions as well as offer an updated summary of its connections to cancer and treatment resistance.

Homologous Recombination and DNA Intermediates Analyzed by Electron Microscopy

Homologous recombination (HR) is a high-fidelity DNA repair pathway that uses a homologous DNA sequence as a template. Recombinase proteins are the central HR players in the three kingdoms of life. RecA/RadA/Rad51 assemble on ssDNA, generated after the processing of double-strand breaks or stalled replication forks into an active and dynamic presynaptic helical nucleofilament. Presynaptic filament formation is regulated by a series of partners of the recombinase, such as scRad52/hBRCA2 mediators or anti-recombinase proteins, to form an active machinery involved in homology search, pair-matching, and invasion within homologous sequences. During homology search, but also during strand invasion, the multiprotein complexes that form the nucleofilament induce the formation of a variety of DNA intermediate states. Here we present specific approaches to study and characterize the different DNA and DNA-protein intermediates formed during homologous recombination. The combination of powerful electron microscopy and sample preparation methods provides a better understanding of these proteins' molecular activity and their interactions.

The hepatic clock synergizes with HIF-1α to regulate nucleotide availability during liver damage repair

Nucleotide availability is crucial for DNA replication and repair; however, the coordinating mechanisms in vivo remain unclear. Here, we show that the circadian clock in the liver controls the activity of the pentose phosphate pathway (PPP) to support de novo nucleotide biosynthesis for DNA synthesis demands. We demonstrate that disrupting the hepatic clock by genetic manipulation or mistimed feeding impairs PPP activity in male mice, leading to nucleotide imbalance. Such defects not only elicit DNA replication stress to limit liver regeneration after resection but also allow genotoxin-induced hepatocyte senescence and STING signalling-dependent inflammation. Mechanistically, the molecular clock activator BMAL1 synergizes with hypoxia-inducible factor-1α (HIF-1α) to regulate the transcription of the PPP rate-limiting enzyme glucose-6-phosphate dehydrogenase (G6PD), which is enhanced during liver regeneration. Overexpressing G6PD restores the compromised regenerative capacity of the BMAL1- or HIF-1α-deficient liver. Moreover, boosting G6PD expression genetically or through preoperative intermittent fasting potently facilitates liver repair in normal mice. Hence, our findings highlight the physiological importance of the hepatic clock and suggest a promising pro-regenerative strategy.

Developing filamentous fungal chassis for natural product production

The growing demand for green and sustainable production of high-value chemicals has driven the interest in microbial chassis. Recent advances in synthetic biology and metabolic engineering have reinforced filamentous fungi as promising chassis cells to produce bioactive natural products. Compared to the most used model organisms, Escherichia coli and Saccharomyces cerevisiae, most filamentous fungi are natural producers of secondary metabolites and possess an inherent pre-mRNA splicing system and abundant biosynthetic precursors. In this review, we summarize recent advances in the application of filamentous fungi as chassis cells. Emphasis is placed on strategies for developing a filamentous fungal chassis, including the establishment of mature genetic manipulation and efficient genetic tools, the catalogue of regulatory elements, and the optimization of endogenous metabolism. Furthermore, we provide an outlook on the advanced techniques for further engineering and application of filamentous fungal chassis.

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

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

The human RAD52 complex undergoes phase separation and facilitates bundling and end-to-end tethering of RAD51 presynaptic filaments

Human RAD52 is a prime target for synthetical lethality approaches to treat cancers with deficiency in homologous recombination. Among multiple cellular roles of RAD52, its functions in homologous recombination repair and protection of stalled replication forks appear to substitute those of the tumor suppressor protein BRCA2. However, the mechanistic details of how RAD52 can substitute BRCA2 functions are only beginning to emerge. RAD52 forms an undecameric ring that is enveloped by eleven ~200 residue-long disordered regions, making it a highly multivalent and branched protein complex that potentiates supramolecular assembly. Here, we show that RAD52 exhibits homotypic phase separation capacity, and its condensates recruit key players in homologous recombination such as single-stranded (ss)DNA, RPA, and the RAD51 recombinase. Moreover, we show that RAD52 phase separation is regulated by its interaction partners such as ssDNA and RPA. Using fluorescence microscopy, we show that RAD52 can induce the formation of RAD51-ssDNA fibrillar structures. To probe the fine structure of these fibrils, we utilized single-molecule super-resolution imaging via DNA-PAINT and atomic force microscopy and showed that RAD51 fibrils are bundles of individual RAD51 nucleoprotein filaments. We further show that RAD52 induces end-to-end tethering of RAD51 nucleoprotein filaments. Overall, we demonstrate unique macromolecular organizational features of RAD52 that may underlie its various functions in the cell.

STK39-mediated amplification of γ-H2A.X promotes homologous recombination and contributes to PARP inhibitor resistance

The phosphorylation of histone H2A.X into γH2A.X is a crucial early event in the DNA damage response, marking DNA damage sites and initiating repair processes. While ATM kinase is traditionally recognized as the primary mediator of H2A.X phosphorylation, our study identifies serine/threonine kinase 39 (STK39) as a novel enhancer of this critical signaling pathway. We demonstrate that after DNA damage, STK39 undergoes phosphorylation by the ATM kinase, facilitating its interaction with the Mre11-Rad50-Nbs1 complex and subsequent recruitment to chromatin. This recruitment enables STK39 to further phosphorylate H2A.X, thus amplifying γH2A.X production and promoting homologous recombination repair. Notably, we observe a significant upregulation of STK39 in pancreatic adenocarcinoma (PAAD) tissues, correlating with heightened resistance to PARPi therapy. Furthermore, we demonstrate the synergistic efficacy of combining STK39 inhibition with PARP inhibitors in suppressing and reversing PAAD growth. This study not only provides new insights into the molecular dynamics of H2A.X phosphorylation but also highlights the therapeutic potential of targeting STK39 to enhance PARPi sensitivity in PAAD (created with BioRender).

CRISPR-Cas9-mediated homology-directed repair for precise gene editing

CRISPR-Cas9-mediated homology-directed repair (HDR) is a versatile platform for creating precise site-specific DNA insertions, deletions, and substitutions. These precise edits are made possible through the use of exogenous donor templates that carry the desired sequence. CRISPR-Cas9-mediated HDR can be widely used to study protein functions, disease modeling, and gene therapy. However, HDR is limited by its low efficiency, especially in postmitotic cells. Here, we review CRISPR-Cas9-mediated HDR, with a focus on methodologies for boosting HDR efficiency, and applications of precise editing via HDR. First, we describe two common mechanisms of DNA repair, non-homologous end joining (NHEJ), and HDR, and discuss their impact on CRISPR-Cas9-mediated precise genome editing. Second, we discuss approaches for improving HDR efficiency through inhibition of the NHEJ pathway, activation of the HDR pathway, modification of donor templates, and delivery of Cas9/sgRNA reagents. Third, we summarize the applications of HDR for protein labeling in functional studies, disease modeling, and ex vivo and in vivo gene therapies. Finally, we discuss alternative precise editing platforms and their limitations, and describe potential avenues to improving CRISPR-Cas9-mediated HDR efficiency and fidelity in future research.

Interspecies differences in the transcriptome response of corals to acute heat stress

Rising sea surface temperatures threaten the survival of corals worldwide, with coral bleaching events becoming more commonplace. However, different coral species are known to exhibit variable levels of susceptibility to thermal stress. To elucidate genetic mechanisms that may underlie these differences, we compared the gene repertoire of four coral species, Favites colemani, Montipora digitata, Acropora digitifera, and Seriatopora caliendrum, that were previously demonstrated to have differing responses to acute thermal stress. We found that more tolerant species, like F. colemani and M. digitata, possess a greater abundance of antioxidant protein families and chaperones. Under acute thermal stress conditions, only S. caliendrum showed a significant bleaching response, which was accompanied by activation of the DNA damage response network and drastic upregulation of stress response genes (SRGs). This suggests that differences in SRG orthologs, as well as the mechanisms that control SRG expression response, contribute to the ability of corals to maintain stability of physiological functions required to survive shifts in seawater temperature.

Response and adaptation of Chlorella pyrenoidosa to 6PPD: Physiological and genetic mechanisms

The extensive contamination of the tire antidegradant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) in aquatic environments have raised concerns about its potential threats to aquatic organisms. Here, the responses of green algae Chlorella pyrenoidosa (C. pyrenoidosa) to 6PPD exposure were investigated for the first time. The growth of C. pyrenoidosa experienced three sequential phases, including inhibition, recovery and stimulation. Physiological and transcriptome analysis suggested that the growth inhibition was associated with the suppressed nitrogen assimilation and amino acid biosynthesis pathways, among which nitrate transporter (NRT) 2.1 was a key target of 6PPD. Molecular docking revealed the steadily binding of 6PPD to the substrate entry region of NRT 2.1 via hydrogen bonds and π - cation interaction, blocking the acquisition of extracellular inorganic nitrogen. Along with the removal of 6PPD through abiotic processes and biodegradation, an adaptive metabolic shift in cells not only facilitated growth recovery but also triggered a compensatory stimulation phase. With regard to microalgal adaptation, upregulated DNA replication and repair pathways served to maintain the integrity of the genetic information, enhanced photosynthesis cascades and central carbon metabolism improved carbon flux and energy conversion to microalgal biomass, recovered amino acid biosynthesis produced essential proteins for multiple metabolisms. The results provide new insights into microalgal molecular responses to 6PPD exposure, facilitating a better understanding of ecological consequences of 6PPD in the environment.

Genome Editing in Apicomplexan Parasites: Current Status, Challenges, and Future Possibilities

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) technology has revolutionized genome editing across various biological systems, including the Apicomplexa phylum. This review describes the status, challenges, and applications of CRISPR-Cas9 editing technology in apicomplexan parasites, such as Plasmodium, Toxoplasma, Theileria, Babesia, and Cryptosporidium. The discussion encompasses successfully implemented CRISPR-Cas9-based techniques in these parasites, highlighting the achieved milestones, from precise gene modifications to genome-wide screening. In addition, the review addresses the challenges hampering efficient genome editing, including the parasites' complex life cycles, multiple intracellular stages, and the lack of robust genetic tools. It further explores the ethical and policy considerations surrounding genome editing and the future perspectives of CRISPR-Cas applications in apicomplexan parasites.

Role of BRCA1 in glioblastoma etiology

BRCA1 (Breast Cancer 1) is a tumor suppressor gene with a role in DNA repair by Homologous Recombination (HR), and maintenance of genomic stability that is frequently investigated in breast, prostate, and ovarian cancers. BRCA1 mutations or dysregulation in glioblastoma can lead to impaired DNA repair mechanisms, resulting in tumor progression and resistance to standard therapies. Several studies have shown that BRCA1 expression is altered, albeit rarely, in glioblastoma, leading to poor prognosis and increased tumor aggressiveness. In addition, the communication of BRCA1 with other molecular pathways such as p53 and PTEN further complicates its role in glioblastoma pathogenesis. Targeting BRCA1-related pathways in these cases has shown the potential to improve the efficacy of standard treatments, including radiotherapy and chemotherapy. The development of (Poly (ADP-ribose) Polymerase) PARP inhibitors that exploit the lack of HR also offers a therapeutic approach to glioblastoma patients with BRCA1 mutations. Despite these advances, the heterogeneity of glioblastoma and its complex tumor microenvironment make the translation of such approaches into clinical practice still challenging, and there is an "unmet need". This review discusses the current mechanisms of etiology and potential treatment of BRCA1-related glioblastoma.

Employment of a Newly Defined In Vitro Fertilization Protocol to Determine the Cytoskeletal Machinery, DNA Damage, and Subsequent DNA Repair Resulting from Endocrine Disruption by Hexavalent Chromium in Rat Metaphase II Oocytes

These protocols describe a detailed method to determine the DNA damage and F-actin and microtubule defects of metaphase II oocytes caused by hexavalent chromium, Cr(VI), an endocrine disrupting chemical (EDC). The protocol provides systematic steps to determine protein expression encoded by pluripotency proteins such as Oct4, Nanog, and Cdx2 during early embryonic development. Occupational or environmental exposure to EDCs has significantly increased infertility in both men and women. The urinary concentration of the EDC bisphenol A in patients undergoing in vitro fertilization (IVF) is directly related to decreased implantation rates and the number of metaphase II oocytes recovered. This protocol outlines crucial steps in assessing the structure of F-actin and microtubules, DNA damage, and repair mechanisms in metaphase II oocytes as well as pluripotency protein markers of early-stage embryos. IVF techniques to achieve fertility goals in both humans and animals are of paramount importance. The interplay between F-actin and microtubules is crucial for bipolar spindle assembly and correct partitioning of the nuclear genome in mammalian oocyte meiosis. EDCs induce DNA damage and impair DNA repair mechanisms, compromising oocyte quality. In human IVF, this results in failure to implant, early miscarriage, and live births with congenital disorders, thus decreasing success rates and increasing poor outcomes. The application of IVF protocols in rats to understand EDC-mediated defects in the cytoskeletal network of metaphase II oocytes is not well established. We present a newly defined rat IVF protocol and demonstrate outcomes using these protocols to determine the adverse effects of Cr(VI) on metaphase II oocytes. Basic Protocol 1 includes steps to superovulate rats, dissect ampullae, retrieve oocytes/eggs, perform immunofluorescence staining of cytoskeletal machinery (microtubules and F-actin), and assess expression of the DNA double-strand break marker γ-H2AX and the DNA repair protein RAD51 in control and Cr(VI)-exposed rats. Basic Protocol 2 describes methods for detecting the pluripotency proteins Oct4, Nanog, and Cdx2 during early embryonic development in control rats. © 2024 Wiley Periodicals LLC. Basic Protocol 1: In vivo EDC treatment of rats and immunostaining of treated oocytes Basic Protocol 2: In vitro fertilization and immunostaining of early-stage embryos.

Reverse Mutations in Pigmentation Induced by Sodium Azide in the IR64 Rice Variety

Pigmentation in rice is due mainly to the accumulation of anthocyanins. Five color mutant lines, AZ1701, AZ1702, AZ1711, AZ1714, and AZ1715, derived from the sodium azide mutagenesis on the non-pigmented IR64 variety, were applied to study inheritance modes and genes for pigmentation. The mutant line AZ1711, when crossed with IR64, displays pigmentation in various tissues, exhibiting a 3:1 pigmented to non-pigmented ratio in the F2 progeny, indicating a single dominant locus controlling pigmentation. Eighty-four simple sequence repeat (SSR) markers were applied to map the pigment gene using 92 F2 individuals. RM6773, RM5754, RM253, and RM2615 markers are found to be linked to the color phenotype. RM253 explains 78% of the phenotypic variation, implying linkage to the pigmentation gene(s). Three candidate genes, OsC1 (MYB), bHLH, and 3GT, as anthocyanin biosynthesis-related genes, were identified within a 0.83 Mb region tightly linked to RM253. PCR cloning and sequencing revealed 10 bp and 72 bp insertions in the OsC1 and 3GT genes, respectively, restoring pigmentation as in wild rice. The 72 bp insertion is highly homologous to a sequence of Ty1-Copia retrotransposon and shows a particular secondary structure, suggesting that it was derived from the transposition of Ty1-Copia in the IR64 genome.

Integrator complex subunit 6 (INTS-6) mediates DNA damage response in Caenorhabditis elegans

The Caenorhabditis elegans Integrator complex is a set of at least 13 evolutionarily conserved proteins that binds the C-terminal domain of RNA polymerase II to regulate snRNA 3'-end processing and gene expression. Here we show that the Integrator subunit 6 intervenes in the DNA damage response in C. elegans . We find that upon X-ray radiation, INTS-6 is necessary for RAD-51 foci formation. In addition, CDK-1 Tyr-15 phosphorylation depends on the presence of INTS-6 . This work adds a new piece to elucidate the Integrator complex mechanism of action in DNA repair.

Recombination Rate Variation in Social Insects: An Adaptive Perspective

Social insects have the highest rates of meiotic recombination among Metazoa, but there is considerable variation within the Hymenoptera. We synthesize the literature to investigate several hypotheses for these elevated recombination rates. We reexamine the long-standing Red Queen hypothesis, considering how social aspects of immunity could lead to increases in recombination. We examine the possibility of positive feedback between gene duplication and recombination rate in the context of caste specialization. We introduce a novel hypothesis that recombination rate may be driven up by direct selection on recombination activity in response to increases in lifespan. Finally, we find that the role of population size in recombination rate evolution remains opaque, despite the long-standing popularity of this hypothesis. Moreover, our review emphasizes how the varied life histories of social insect species provide an effective framework for advancing a broader understanding of adaptively driven variation in recombination rates.