Targeting the DNA Damage Response in Cancer

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.

Rational design, synthesis, and molecular modelling insights of dual DNA binders/DHFR inhibitors bearing arylidene-hydrazinyl-1,3-thiazole scaffold with apoptotic and anti-migratory potential in breast MCF-7 cancer cells

In light of searching for new breast cancer therapies, DNA-targeted small molecules were rationally designed to simultaneously bind DNA and inhibit human dihydrofolate reductase (hDHFR). Fourteen new arylidene-hydrazinyl-1,3-thiazoles (5-18) were synthesised and their dual DNA groove binding potential and in vitro hDHFR inhibition were performed. Two compounds, 5 and 11, proved their dual efficacy. Molecular docking and molecular dynamics simulations were performed for those active derivatives to explore their mode of binding and stability of interactions inside DHFR active site. Anti-breast cancer activity was assessed for 5 and 11 on MCF-7 cells using MTX as reference. IC50 measurements revealed that both compounds were more potent and selective than MTX. Cytotoxicity was examined against normal skin fibroblasts to examine safety and selectivity Moreover, mechanistic studies including apoptosis induction and wound healing were performed. Further in silico ADMET assessment was conducted to determine their eligibility as drug leads suitable for future optimisation and development.

Comparative in vivo toxicology of ATR inhibitors ceralasertib, elimusertib, and berzosertib alone and in combination with ionizing radiation

Ionizing radiation (IR) induces damage in the form of DNA strand breaks. As an apical initiator of the DNA damage response, Ataxia telangiectasia and Rad3-related (ATR) mitigates DNA damage, limiting therapeutic efficacy. Small molecule ATR inhibitors (ATRi) restrict this effect and sensitize cancer cells to radiation-induced damage. However, the impact of ATR inhibition in non-malignant tissues following IR is currently unknown. Here, we document the impact of ATRi on murine toxicity profiles following total body irradiation (TBI). Mice were stratified to receive single-dose ATRi (ceralasertib, elimusertib, or berzosertib), 6 Gy TBI, or the combination. Mice were euthanized 48 h post TBI. Blood and tissues were collected for analysis of complete blood counts and histopathology. To further distinguish toxicity profiles, IC50 values were compared between ATRi. Pharmacokinetics (PK) and pharmacodynamics (PD) were considered as potential explanatory factors of differences in toxicity profiles. Elimusertib was determined to be the most potent ATRi, and ceralasertib the least. We observed neutrophilia with all ATRi. We found that ATRi did not exacerbate any TBI-induced toxicities in mice. Berzosertib presented a unique profile among all ATRi across several toxicity endpoints, including modest amelioration of TBI-associated effects on spleen and lymphocyte and white blood cell counts. Cardiotoxicity was observed following single-dose ceralasertib, but no other ATRi, possibly due to high unbound plasma drug concentrations. Our results further support and guide clinical development of ATRi in clinic.

Synergistic enhancement of PARP inhibition via small molecule UNI66-mediated suppression of BRD4-dependent transcription of RAD51 and CtIP

Targeted therapy leveraging synthetic lethality in homologous recombination (HR)-defective tumors, particularly in BRCA-mutated tumors through poly(ADP-ribose) polymerase (PARP)-dependent repair inhibition, has shown success. However, the challenge lies in the ability of the tumors to reactivate HR via diverse mechanisms, leading to resistance against PARP-dependent repair inhibition. Addressing this issue, the down-regulation of HR activity has been explored as a potential strategy to overcome PARP inhibitor-resistant tumors. Yet, the intricate modulation of HR gene expression in mammalian cells is still not fully understood. In this study, we used a small molecule, UNI66, identified from high-throughput screening, to investigate regulatory mechanisms of HR. UNI66 was observed to induce synthetic lethality in PARP1-deficient cells and enhanced the sensitivity of multiple cancer cells to PARP inhibitors, suggesting a role in HR down-regulation. Mechanistically, UNI66 was found to interact with and inhibit BRD4 protein binding to the promoters of CtIP and RAD51 genes, resulting in the down-regulation of their transcription. This decrease in CtIP and RAD51 expression was associated with reduced HR activity, thereby increasing the sensitivity of tumors to PARP inhibitors. These findings indicate that BRD4-mediated transcriptional regulation of CtIP and RAD51 influences HR activity, which may have implications for overcoming resistance to PARP inhibitors.

Optimal bevacizumab treatment strategy in advanced ovarian cancer: A review

Bevacizumab was the first targeted therapy developed for newly diagnosed and recurrent advanced ovarian cancer (AOC). Although bevacizumab has been approved for the treatment of AOC for several years, identifying patients who may benefit most from this treatment is still debated. Bevacizumab has been associated with improved progression-free survival (PFS) regardless of clinical risk, but in some countries the use of bevacizumab in the treatment of newly diagnosed AOC has been restricted to higher-risk patients (stage III inoperable or suboptimally debulked disease, or stage IV disease); this is primarily due to the findings of exploratory subgroup analyses from phase III trials that suggest only higher-risk patients derive an overall survival (OS) advantage with bevacizumab. Recently reported post hoc analyses from the PAOLA-1 trial of maintenance olaparib plus bevacizumab versus bevacizumab alone for patients with newly diagnosed AOC and homologous recombination deficiency-positive tumors suggested PFS and OS benefit was achieved in both lower-risk (with stage III disease who had undergone upfront surgery and had complete resection) and higher-risk (with stage III disease who had undergone upfront surgery and had residual disease or who had received neoadjuvant chemotherapy, or with stage IV disease) patients, prompting reassessment of the role of bevacizumab in lower-risk patients. This review examines the role of bevacizumab in the AOC treatment pathway by discussing its efficacy and safety in the first-line, maintenance and recurrent settings, and evaluates the clinical implications of bevacizumab use across risk groups and lines of therapy.

Pharmacological, computational, and mechanistic insights into triptolide's role in targeting drug-resistant cancers

As a promising candidate for tackling drug-resistant cancers, triptolide, a diterpenoid derived from the Chinese medicinal plant Tripterygium wilfordii, has been developed. This review summarizes potential antitumor activities, including the suppression of RNA polymerase II, the suppression of heat shock proteins (HSP70 and HSP90), and the blockade of NF-kB signalling. Triptolide is the first known compound to target cancer cells specifically but spare normal cells, and it has success in treating cancers that are difficult to treat, including pancreatic, breast, and lung cancers. It acts against the tolerance mechanisms, including efflux pump upregulation, epithelial-mesenchymal transition, and cancer stem cells. Triptolide modulates important cascades, including PI3K/AKT/mTOR, enhancing the efficacy of conventional therapies. Nonetheless, its clinical application is constrained by toxicity and bioavailability challenges. Emerging drug delivery systems, such as nanoparticles and micellar formulations, are being developed to address these limitations. It has strong interactions with key anticancer targets, like PARP, as determined in preclinical and computational studies consistent with its mechanism of action. Early-phase clinical trials of Minnelide, a water-soluble derivative of triptolide, are promising, but additional work is necessary to optimize dosing, delivery, and safety. This comprehensive analysis demonstrates that triptolide may constitute a repurposed precision medicine tool to overcome tolerance in cancer therapy.

Advances in Targeted Therapy for Metastatic Prostate Cancer

OPINION STATEMENT

Over the past few years, treatment for advanced prostate cancer has begun shifting away from a one-size-fits-all approach toward biomarker-based therapies for select groups of patients. This review highlights the role of poly-ADP-ribose-polymerase (PARP) inhibitors in metastatic prostate cancer, emerging strategies to target the androgen receptor (AR), and innovative therapies aimed at cell surface proteins, including radioligand therapies, bispecific T cell engagers, and antibody-drug conjugates. For patients with homologous recombination repair (HRR)-mutated metastatic castration-resistant prostate cancer (CRPC), we favor combining a PARP inhibitor (PARPi) with an AR pathway inhibitor (ARPI), provided they can tolerate a more aggressive treatment strategy. In our opinion, patients with BRCA1 or BRCA2 mutations who are unable to handle combination therapy benefit from PARPi monotherapy. We are enthusiastic about the potential of ongoing clinical trials for new AR-directed therapies, such as AR ligand-directed degraders and CYP11A1 inhibitors, in metastatic CRPC. These treatments are expected to be most beneficial for patients whose cancer continues to rely on AR pathway signaling, suggesting they might also be effective in earlier stages of the disease. Progress in drug development and understanding of protein structures has led to new therapies that target cell surface proteins predominantly found in prostate cancer. We use 177Lu-PSMA-617 for patients with PSMA avid metastatic CRPC who have progressed on an ARPI and a taxane chemotherapy. Additionally, we see promising potential in bispecific T-cell engagers (e.g., STEAP1-CD3 and PSMA-CD3) and novel radioligand therapies, including those utilizing actinium, to target these proteins. These advances show great promise in further enhancing survival for patients with metastatic prostate cancer.

BRCA1 and BRCA2 in DNA damage and replication stress response: Insights into their functions, mechanisms, and implications for cancer treatment

Genomic stability is a cornerstone of cellular survival and proliferation. To counter the constant threat posed by endogenous and exogenous DNA-damaging agents, cells rely on a network of intricate mechanisms to safeguard DNA integrity and ensure accurate replication. Among these, the BRCA1 and BRCA2 tumor suppressor proteins play pivotal roles. While traditionally recognized for their involvement in homologous recombination repair and cell cycle checkpoints, emerging evidence highlights their essential functions in protecting stalled replication forks during replication stress. Mutations in BRCA1 or BRCA2 disrupt these critical functions, leading to compromised genome stability and an increased susceptibility to various cancers, particularly breast and ovarian cancers. This review provides a comprehensive analysis of the multifaceted roles of BRCA1 and BRCA2, focusing on their contributions to DNA damage responses and replication stress management. By elucidating the molecular pathways through which BRCA1 and BRCA2 operate, we aim to provide insights into their pivotal roles in maintaining genomic integrity and their implications for cancer treatment.

Proteomic Characterization of Extracellular Vesicles from Human Neural Precursor Cells: A Promising Advanced Therapy for Neurodegenerative Diseases

Background

The therapeutic effect of stem cells is attributed to their direct maturation into somatic cells and their paracrine effects, which influence the extracellular environment. One such component released is extracellular vesicles containing proteins and genetic materials with immunomodulatory functions and facilitating cell-to-cell communication.

Purpose

The study's main objective was to characterize extracellular vesicles (EVs) from Human Neural Precursor Cells (hNPCs).

Methods

Wharton's Jelly mesenchymal stem cells (WJ-MSCs) were isolated by explant technique and characterized by flow cytometry and trilineage differentiation. The hNPCs obtained from neurospheres were produced by seeding WJ-MSCs on a natural functional biopolymer matrix. EVs derived from WJ-MSCs and hNPCs were isolated by precipitation methodology and characterized by flow cytometry, nanoparticle tracking analysis (NTA), scanning electron microscopy (TEM), and proteomic.

Results

hNPCs expressed proteins and genes characteristic of neural precursor cells. The EVs were characterized by flow cytometry and showed varied expression for the markers CD63, CD9, and CD81, indicating different subpopulations based on their origin of formation. NTA and TEM of the EVs exhibited characteristic size, shape, and structural integrity consistent with the criteria established by the International Society for Extracellular Vesicles (ISEV). EV-hNPCs function enrichment analysis of the proteomic results showed that these vesicles presented abundant proteins directly involved in neuronal biological processes such as plasticity, transduction, postsynaptic density, and overall brain development.

Discussion

The results indicate that EVs derived from hNPCs maintain key neural precursor characteristics and exhibit marker variability, suggesting distinct subpopulations. Their structural integrity aligns with ISEV standards, supporting their potential as reliable biological entities. The proteomic analysis highlights their role in neuronal functions, reinforcing their applicability in neurodegenerative research and therapeutic strategies.

Conclusion

The EVs were successfully isolated from hNPCs with abundant proteins involved in neuronal processes, making them attractive for acellular therapies to treat neurodegenerative diseases.

The Electronic Properties of Cordycepin in the Adenine Nucleoside Landscape: A Theoretical Approach

The anticancer activity of 3'-deoxyadenosine (Cordycepin, or dCor) is known to be linked to the inhibition of the MAPK/ERK signalling and Hedgehog pathways, as well as the termination of primer elongation by primase in DNA lagging-strand synthesis. In this study, the electronic properties of dCor, 7,8-dihydro-8-oxo-3'-deoxyadenosine (OXOdCor), and 8-hydroxy-3'deoxyadenosie (HOdCor), together with their spin densities, charge distributions, and global reactive descriptors, have been taken into consideration at the M06-2x/6-31++G** level of theory in the aqueous phase. It was found that dCor predominantly adopts a 3'-endo,anti conformation, while OXOdCor and HOdCor adopt a 2'-endo,syn conformation. Also, the keto form of oxidised dCor was found to be energetically preferred to its enolic form. The adiabatic ionisation potentials (AIPs) were noted as follows (in eV): 6.29 for dCor, 6.21 for OXOdCor, and 6.17 for HOdCor. The lowest adiabatic electron affinity among all the discussed adenine nucleosides analogues was assigned for OXOdCor at 1.12 eV. A thorough analysis of the spin density distribution of the adiabatic radical cation reveals that it has a higher accumulation at N6 > C5 > C8 > 3 of dCor, C5 > N6 > N7 > O8 of OXOdCor, and N6 > C5 > C8 > C2 of HOdCor. The results suggest that Cordycepin is more easily converted to OXOdCor and HOdCor than canonical adenine nucleosides. Much like typical drugs, after its administration and release, Cordycepin is exposed to various physiological factors and can be exposed to ionisation radiation during combined therapy. These factors can influence the therapeutic potential of Cordycepin. Therefore, further studies on its stability are of utmost importance.

Investigation of mRNA expression levels of DNA damage response genes in Merkel Cell Polyomavirus-positive Merkel Cell Carcinoma: a pilot study

Merkel Cell Polyomavirus (MCPyV) is recognized as the major aetiological agent of Merkel Cell Carcinoma (MCC), an aggressive skin tumor. MCPyV-mediated oncogenesis is strictly dependent on viral integration and the expression of a truncated form of the Large T Antigen (LT). Moreover, like other oncogenic DNA viruses, MCPyV may interfere with the DNA damage response (DDR) machinery, thus promoting genomic instability and tumorigenesis. Therefore, the objective of this study was to characterize MCPyV infection in 7 MCC patients and to elucidate the plausible role of the virus in the DDR pathway. MCPyV DNA was detected in 3/7 MCC patients and, as expected, viral integration and LT truncation were observed in virus-positive MCCs, along with the expression of early genes only. Over-expression of DDR genes such as ATM, ATR and their downstream kinases Chk1 and Chk2 was reported in MCPyV-positive MCCs supporting the potential role of the virus in interfering with DDR. Our findings support the established viral aetiology of MCC, and describe, for the first time, an over-expression of DDR components in MCPyV-positive MCC, laying the basis for future studies aimed at investigating the contribution of this pathway to MCPyV-mediated carcinogenesis and exploring the plausible clinical implications of host DDR factors for the treatment of MCC.

Exploring the Potential of Homologous Recombination Protein PALB2 in Synthetic Lethal Combinations

Cells with defective homologous recombination (HR) are highly sensitive to poly(ADP-ribose) polymerase (PARP) inhibition. Current therapeutic approaches leverage this vulnerability by using PARP inhibitors in cells with genetically compromised HR. However, if HR factors in cancer cells could be inhibited or degraded pharmacologically, it might reveal other opportunities for synergistic combinations. In this study, we developed a model system that recapitulates PARP/HR synthetic lethality by integrating a small-molecule responsive zinc-finger degron into the HR factor Partner and Localizer of BRCA2 (PALB2). We further tested a series of peptide ligands for PALB2 based on its natural binding partners, which led to the discovery of a high affinity peptide that will support future work on PALB2 and HR. Together, our findings validate PALB2 as a promising drug target and provide the tools and starting points for developing molecules with therapeutic applications.

Neoadjuvant PARP inhibitor scheduling in BRCA1 and BRCA2 related breast cancer: PARTNER, a randomized phase II/III trial

Poly (ADP-ribose) polymerase inhibitors (PARPi) exploit DNA repair deficiency in germline BRCA1 and BRCA2 pathogenic variant (gBRCAm) cancers. Haematological toxicity limits chemotherapy-PARPi treatment combinations. In preclinical models we identified a schedule combining olaparib and carboplatin that avoids enhanced toxicity but maintains anti-tumour activity. We investigated this schedule in a neoadjuvant, phase II-III, randomised controlled trial for gBRCAm breast cancers (ClinicalTrials.gov ID:NCT03150576; PARTNER). The research arm included carboplatin (Area Under the Curve 5, 3-weekly); paclitaxel (80 mg/m2, weekly) day 1, plus olaparib (150 mg twice daily) day 3-14 (4 cycles), followed by anthracycline-containing chemotherapy (3 cycles); control arm gave chemotherapy alone. The primary endpoint, pathological complete response rate, showed no statistical difference between research 64.1% (25/39); control 69.8% (30/43) (p = 0.59). However, estimated survival outcomes at 36-months demonstrated improved event-free survival: research 96.4%, control 80.1% (p = 0.04); overall survival: research 100%, control 88.2% (p = 0.04) and breast cancer specific survival: research 100%, control 88.2% (p = 0.04). There were no statistical differences in relapse-free survival and distant disease-free survival, both were: research 96.4%, control 87.9% (p = 0.20). Similarly, local recurrence-free survival and time to second cancer were both: research 96.4%, control 87.8% (p = 0.20). The PARTNER trial identified a safe, tolerable schedule combining neoadjuvant chemotherapy with olaparib. This combination demonstrated schedule-dependent overall survival benefit in early-stage gBRCAm breast cancer. This result needs confirmation in larger trials.

Bibliometric analysis of research trends on the combination of radiotherapy and PARP inhibitors in solid tumors

Introduction

Radiotherapy has served as a cornerstone in cancer treatment for over a century. However, the efficacy of radiotherapy is often compromised by the intrinsic and acquired radioresistance of tumors, which can lead to treatment failure and disease recurrence. Recent advancements in preclinical and clinical research have highlighted the potential synergistic efficacy of combining radiotherapy with poly-ADP-ribose polymerase inhibitors (PARPi), offering promising therapeutic avenues for solid tumors. This study employs bibliometric analysis to systematically evaluate the evolution, trends, and intellectual landscape of research on the combination of radiotherapy and PARPi in solid tumors.

Methods

Publications addressing the combination of radiotherapy and PARPi for solid tumors between 2005 and 2024 were retrieved from the Web of Science Core Collection (WOSCC) database. Bibliometric assessments were conducted using VOSviewer and CiteSpace to analyze publication trends, collaborative networks, and research foci.

Results

A total of 901 articles were included. The United States dominated research output, with the University of Texas MD Anderson Cancer Center identified as the most productive institution. Hannah Farmer emerged as the most frequently cited author. Keywords co-occurrence analysis revealed a thematic shift from foundational studies on molecular mechanisms, such as DNA damage response and mechanism of action of PARPi, toward clinical investigations evaluating combination therapy efficacy and safety in trials.

Conclusion

This bibliometric analysis underscores the rapid growth of research on radiotherapy and PARPi combination therapy, with the United States maintaining a leading role due to its extensive scientific infrastructure and collaborative networks. The field has transitioned from mechanistic explorations to translational and clinical applications, reflecting progress toward therapeutic optimization. These findings provide a comprehensive overview of the knowledge structure within this domain and serve as a strategic reference for guiding future research priorities and clinical implementations.

Identification and validation of hub genes in uterine corpus endometrioid carcinoma: An observational study from TCGA and GEO

Uterine corpus endometrioid carcinoma (UCEC) is a prevalent malignant tumor of the female reproductive system. Despite advancements in molecular biology and treatment strategies, the underlying molecular mechanisms of UCEC tumorigenesis remain incompletely understood. This study aimed to identify differentially expressed genes (DEGs) associated with UCEC pathogenesis, and to determine potential prognostic biomarkers and immunotherapy targets for UCEC. RNA expression datasets and clinical data from UCEC patients were collected from the UCSC Xena database and The Cancer Genome Atlas database. Principal component analysis and LIMMA methods were employed to screen 177 UCEC tissues and 24 normal endometrial tissues. Gene ontology enrichment analysis revealed that up-regulated DEGs were primarily involved in tissue development, cell cycle regulation, and epithelial development. Subsequently, weighted gene co-expression network analysis (WGCNA) identified DEGs in the blue modules that were significantly positively correlated with UCEC, while DEGs in the black modules were significantly negatively correlated with UCEC. Among the identified DEGs through WGCNA, 16 genes were selected, and further Kaplan-Meier analysis demonstrated that 5 of these genes (AURKA, CCNE1, IQGAP3, TTK, and UBE2C) were significantly negatively correlated with overall survival (OS) and considered as hub genes. The expression of these hub genes was validated using GEO datasets and immunohistochemistry (IHC) analysis from the human protein atlas. Additionally, the calculation of immune scores for immune infiltration, immune cell infiltration, and immune cell regulation across the 5 hub genes revealed potential immunotherapeutic targets and strategies. This comprehensive investigation provides insights into the molecular mechanisms underlying UCEC development, identifies 5 promising prognostic biomarkers and immunotherapy targets, and offers guidance for UCEC treatment approaches.

Interleukin-24: A Multidimensional Therapeutic for Treatment of Human Diseases

The field of targeted therapy exploits the selective expression of therapeutic genes or proteins in diseased cells. While this area is gaining attraction in the context of cardiovascular diseases, diabetes, and other major health disorders, it has been most extensively explored in the realm of cancer. Targeted therapy has gained significance in the cancer field for its potential to address the limitations of conventional treatments and enhance patient survival. Interleukin-24 (IL-24), a versatile cytokine, has been evaluated as a cancer therapeutic in various preclinical cancer models and clinical trials, and has yielded promising results. Consequently, multiple studies highlight IL-24 as a viable "anti-cancer" therapeutic, with successful outcomes observed in combination therapies involving small molecule inhibitors, chemotherapeutic drugs, and radiation. Despite the evidence validating the tumor-suppressing properties of IL-24 in cancer models, there is a dearth of information regarding its role in other human diseases. The objective of this review is to offer a synopsis of the potential role of IL-24 in diverse human diseases. Additionally, it provides a comprehensive review of the progress in cancer therapy utilizing IL-24. Finally, from the author's standpoint, the review also addresses some of the limitations that impede the translational potential of IL-24-based therapy in clinical settings. It offers arguments in favor of incorporating IL-24-based targeted therapy as an effective and safer alternative for current treatment modalities, thereby highlighting its potential to revolutionize the field of therapeutics.

Gold nanoparticles-based targeted delivery of rapamycin and Olaparib to breast cancer: An in vitro and in vivo approach

Triple negative form of breast cancer (abbreviated as TNBC) is considered as the most aggressive form causing high mortality worldwide. Different treatment modalities such as chemotherapy, surgery, hormonal therapy and radiation therapy are employed for eliminating breast cancer, which are associated with many limitations. Therefore, considering the significance of metal nanoparticles in the biomedical sector, especially gold nanoparticles, in the current manuscript, we have designed and developed a combinatorial approach for synthesizing two types of gold (Au) nanoformulations (Au-Dex-MUA-Rapa, Au-Dex-MUA-Ola) using 11-mercaptoundecanoic acid (MUA), dexamethasone (Dex) (glucocorticoid receptor targeted molecule) along with rapamycin (Rapa: inhibitor of mTOR) or olaparib (Ola: inhibitor of PARP) against TNBC. These gold nanoformulations were characterized thoroughly using several analytical techniques such as TEM, spectroscopy, DLS, HPLC and ICPOES. The in vitro MTT assays (normal cells: HEK-293 and CHO) and ex vivo CAM assay displays the biocompatible properties of the conjugated gold nanoformulations. Further, the anticancer properties of the conjugated gold nanoformulations in TNBC cells (MDA-MB-231) were evaluated through several in vitro experiments along with plausible mechanism of action. The intraperitoneal administration of gold nanoformulations into the breast tumor bearing BALB/c mice inhibits the tumor growth and increases their survivability. Additionally, we have investigated the plausible mechanistic studies behind the anticancer properties of the conjugated gold nanoformulations. Finally, we have found the non-toxic nature of these nanoformulations at therapeutic dose. Considering the above results, the conjugated gold nanoformulations could be used as an alternative therapeutic strategy for the treatment of breast carcinoma in near future.

Olaparib Monotherapy or in Combination with Abiraterone for the Treatment of Patients with Metastatic Castration-Resistant Prostate Cancer (mCRPC) and a BRCA Mutation

Treatment strategies to improve outcomes in patients with metastatic castration-resistant prostate cancer (mCRPC) are evolving. Of particular interest are therapies that target DNA damage responses in tumor cells by inhibiting poly(ADP-ribose) polymerase (PARP) activity. Several PARP inhibitors have recently received regulatory approval for the treatment of patients with mCRPC, of which olaparib was the first for prostate cancer. Olaparib received approval as a monotherapy following the PROfound study (NCT02987543) and in combination with abiraterone following the PROpel study (NCT03732820) for mCRPC. Both PROfound (homologous recombination repair mutation biomarker-selected) and PROpel (biomarker unselected) patients demonstrated statistically significant longer radiographic progression-free survival (rPFS) with olaparib versus their respective control arms in the intention-to-treat population. In both studies, the greatest clinical benefit with olaparib was seen in patients with BRCA1 and/or BRCA2 mutations (BRCAm): PROfound rPFS hazard ratio (HR) 0.22 (95% confidence interval [CI] 0.15-0.32); PROpel rPFS HR 0.23 (95% CI 0.12-0.43). Clinical benefit was also observed in terms of overall survival: PROfound HR 0.63 (95% CI 0.42-0.95); PROpel HR 0.29 (95% CI 0.14-0.56). We provide a comprehensive overview of the utility of olaparib for patients with mCRPC harboring a BRCAm. Key clinical and safety data in BRCAm subgroup populations are discussed, predominantly based on findings from PROfound and PROpel, as well as investigator-initiated studies, to help inform treatment decision-making in this patient population. We also discuss the importance of genetic testing to identify patients who may optimally benefit from treatment with olaparib, either as a monotherapy or in combination with abiraterone.

A novel lncRNA YIL163C enhances genomic stability and antifungal resistance via the DNA damage response in Saccharomyces cerevisiae

Introduction

Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators in cellular processes, including the DNA damage response (DDR). In Saccharomyces cerevisiae, DDR is critical for maintaining genomic integrity under stress, mediated by proteins like Mec1 and Rad53. However, the involvement of lncRNAs in DDR pathways, remains largely unexplored. This study investigates the function of a novel lncRNA, YIL163C, in promoting cell survival and genomic stability under DNA damage conditions.

Methods

Genetic suppressor screening was employed to assess the role of YIL163C in rescuing lethality in mec1Δ sml1Δ and rad53Δ sml1Δ exposed to DNA damage. Proteomic and phosphoproteomic analyses were conducted to evaluate changes in protein abundance and phosphorylation states. The impact of YIL163C on DDR and antifungal drug tolerance, specifically to 5-fluorocytosine, was also examined.

Results

Overexpression of YIL163C was found to rescue lethality in mec1Δ sml1Δ and rad53Δ sml1Δ under DNA damage conditions. Proteomic analyses revealed that YIL163C modulates pathways related to DNA replication, ER stress response, and ribosome biogenesis, enhancing cellular resilience to HU-induced stress. Additionally, YIL163C reduced sensitivity to 5-fluorocytosine, indicating a role in antifungal drug tolerance. Phosphoproteomic data suggested YIL163C influences phosphorylation states, potentially acting downstream of the Mec1-Rad53 signaling pathway.

Conclusion

This study provides new insights into the regulatory mechanisms of lncRNAs in DDR, with broader implications for antifungal therapy and genomic stability research, emphasizing the role of lncRNAs in stress responses beyond traditional protein-centric mechanisms.

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.

Maintenance olaparib monotherapy in patients with platinum-sensitive relapsed ovarian cancer without a germline BRCA1 and/or BRCA2 mutation: Final overall survival results from the OPINION trial

OBJECTIVE

Maintenance olaparib demonstrated clinical activity for progression-free survival in patients without a germline BRCA1 and/or BRCA2 mutation (non-gBRCAm) who had platinum-sensitive relapsed ovarian cancer in the phase IIIb, open-label, single-arm, non-comparator, international OPINION trial (NCT03402841). We report final overall survival (OS; secondary endpoint), prespecified secondary endpoint updates and ad hoc OS analysis by homologous recombination deficiency (HRD) and somatic BRCAm (sBRCAm) status.

METHODS

Patients with non-gBRCAm platinum-sensitive relapsed ovarian cancer, ≥2 prior lines of platinum-based chemotherapy, and in response following their last platinum-based chemotherapy received 300 mg olaparib tablets twice daily until disease progression or unacceptable toxicity.

RESULTS

279 patients were enrolled and treated. With a median follow-up in patients censored for OS of 33.1 months (data cut-off September 17, 2021), median OS was 32.7 months (95 % CI 29.5-35.3); the 24-month OS rate was 65.8 %. In ad hoc subgroup analyses, OS rates tended to be higher in patients with HRD-positive tumors; 24-month OS rates were 81.5 %, 74.2 %, 72.0 % and 55.8 % in the sBRCAm, HRD-positive including sBRCAm, HRD-positive excluding sBRCAm, and HRD-negative subgroups, respectively. Grade ≥ 3 treatment-emergent adverse events were reported in 82 patients (29.4 %), most commonly anemia (13.6 %). Overall, two cases of myelodysplastic syndrome were reported (no new cases since the primary analysis).

CONCLUSION

These data provide additional evidence of olaparib as maintenance therapy in patients with non-gBRCAm platinum-sensitive relapsed ovarian cancer, with longer OS observed in those with HRD-positive tumors. The safety profile was consistent with the primary analysis and known safety profile of olaparib, with no new safety findings.

SOX5 inhibition overcomes PARP inhibitor resistance in BRCA-mutated breast and ovarian cancer

Poly (ADP-ribose) polymerase (PARP) inhibitors are effective in cells with homologous recombination (HR) deficiency, including BRCA1/2 mutation. However, PARP inhibitors remain a therapeutic challenge in breast and ovarian cancer due to inevitably acquired resistance in most cases. Therefore, strategies to overcome PARP inhibitor resistance are unmet clinical need. SRY-box transcription factor 5 (SOX5) plays a crucial role in development of various cancers but the role of SOX5 in PARP inhibitor resistance is poorly understood. This study identified SOX5 as a potential biomarker associated with PARP inhibitor resistance and addressed potential treatment strategies to overcome PARP inhibitor resistance using the olaparib-resistant preclinical model. We observed that SOX5 was significantly upregulated in olaparib-resistant cells and contributed to PARP inhibitor resistance by upregulating DNA repair pathway genes. Ectopic SOX5 overexpression contributed to PARP inhibitor resistance by suppressing DNA double-strand breaks (DSBs) in BRCA-mutated breast and ovarian cancer. SOX5 small interfering RNA combined with olaparib sensitized olaparib-resistant cells and suppressed the growth of olaparib-resistant xenografts in mice via increased DSBs represented by ɣH2AX formation. Mechanistically, SOX5 directly interacted with yes-associated protein 1 (YAP1) and promoted its nuclear translocation by suppressing the Hippo pathway. YAP1, in association with TEA domain family members (TEAD), upregulated HR-related gene expression and conferred PARP inhibitor resistance. Furthermore, the clinical relevance of SOX5 as a therapeutic target was supported by a significant association between SOX5 overexpression and poor prognosis in ovarian cancer on public mRNA microarray data sets. Therefore, we propose SOX5 as a promising therapeutic target for overcoming PARP inhibitor resistance in BRCA1/2-mutated breast and ovarian cancer.

Discovery of Naphthyridinone Derivatives as Selective and Potent PKMYT1 Inhibitors with Antitumor Efficacy

PKMYT1 is a crucial regulator of the cell cycle, particularly involved in the G2/M transition through the inhibitory phosphorylation of CDK1, and is a promising therapeutic target for cancer therapy. Data mining in the Roche kinome screen database identified a hit characterized by 100% PKMYT1 inhibitory activity at a 10 μM concentration, which was further validated with a PKMYT1 enzymatic assay showing double-digit nanomolar potency. The hit featured a quinolinone central core and a phenol headgroup. The replacement of the problematic phenol headgroup with an indazole moiety induced a flip in the kinase hinge cysteine and glycine residues, resulting in a series of derivatives with enhanced potency, superior kinome selectivity, and no GSH flag. Further structural fine-tuning led to the discovery of compound 36, a novel, selective, and potent PKMYT1 inhibitor with favorable oral pharmacokinetic profiles and promising in vivo antitumor efficacy.

DNA damage response deficiency enhances neuroblastoma progression and sensitivity to combination PARP and ATR inhibition

Sequencing of neuroblastoma (NB) tumors has revealed genetic alterations in genes involved in DNA damage response (DDR) pathways. However, roles for specific alterations of DDR genes in pediatric solid tumors remain poorly understood. To address this, mutations in the DDR pathway including Brca2, Atm, and Palb2 were incorporated into an established zebrafish MYCN transgenic model (Tg(dbh:EGFP-MYCN)). These mutations enhance NB formation and metastasis and result in upregulation of cell-cycle checkpoint and DNA damage repair signatures, revealing molecular vulnerabilities in DDR-deficient NB. DDR gene knockdown in zebrafish and human NB cells increases sensitivity to the poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, and this effect is enhanced by inhibition of the ataxia telangiectasia and rad3-related (ATR) kinase. This work provides in vivo evidence demonstrating that alterations in certain DDR-pathway genes promote aggressive NB and supports combination PARP + ATR inhibitor therapy for NB patients with tumors harboring specific genetic alterations in DDR.

Nuclear accumulation of YTHDF1 regulates mRNA splicing in the DNA damage response

YTH domain-containing family protein 1 (YTHDF1), a reader of N6-methyladenosine (m6A), has been implicated in regulating RNA metabolism in the cytosol. Here, we report a role of YTHDF1 within the nucleus in response to genotoxic stress. Upon radiation, YTHDF1 is phosphorylated at serine-182 in an ataxia telangiectasia and Rad3-related-dependent manner. This phosphorylation inhibits exportin 1-mediated nuclear export of YTHDF1, resulting in its accumulation within the nucleus. Nuclear YTHDF1 enhances the binding capacity of serine- and arginine-rich splicing factor 2 to a group of m6A-modified exons, leading to increased exon inclusion. Specifically, YTHDF1 promotes splicing and expression of DNA repair genes, such as BRCA1 and TP53BP1, thereby mitigating excessive DNA damage. Depletion of YTHDF1 sensitizes cancer cells to radiation treatment. Together, our study reveals a crucial role of YTHDF1 in m6A-mediated messenger RNA splicing in the DNA damage response, proposing it as a potential target for radiation therapy.

Steroid-Modulated Transcription Synergistically Forms DNA Double-Strand Breaks With Topoisomerase II Inhibitor

The synergistic effects of drug combinations have emerged as a promising approach for achieving efficient cancer treatment. Through our exploration of drug combinations, we found that medroxyprogesterone acetate (MPA), a steroid, induced a synergistic antitumor effect in combination with the topoisomerase II inhibitor etoposide (ETP). In this study, we investigated the mechanisms underlying this synergistic effect for potential clinical applications. To elucidate the relevant mechanisms, we performed a cell viability assay, cell cycle analysis, DNA repair assays, detection of DNA double-strand breaks (DSBs) and the nuclear localization of topoisomerase II (Top2), and genome-wide detection of DSBs. MPA synergistically increased ETP-induced DSBs, resulting in cell cycle arrest in the G2/M phase. Interestingly, this effect was not due to the inhibition of DSB repair but to a specific increase in the Top2-DNA covalent complex formed by ETP. A genome-wide search for DSB locations revealed that DSB formation was promoted near promoter regions, suggesting the involvement of MPA transcriptional modulation in this mechanism. We also found that various steroids promoted DSB formation when combined with ETP, strongly supporting our synergistic model. Therefore, this synergistic effect is based on an innovative mechanism that differs from conventional strategies targeting the DNA damage response and is expected to contribute toward novel therapeutic options.

Therapeutic Targeting of Oncogene-induced Transcription-Replication Conflicts in Pancreatic Ductal Adenocarcinoma

BACKGROUND AND AIMS

Transcription-replication conflicts (TRCs) are a key source of replication stress in cancer, with pancreatic ductal adenocarcinoma (PDAC) showing uniquely high levels. This study investigated the mechanism, oncogene dependency, subtype specificity, and preclinical activity of the TRC-targeting molecule AOH1996 in PDAC models. Initial clinical evidence of AOH1996 activity in patients with PDAC is also provided.

METHODS

The oncogene-dependent toxicity of AOH1996 was studied in KRAS(G12D)-inducible systems. Its effects on replication fork progression, TRCs, DNA damage, cell cycle, and apoptosis were assessed in PDAC cell lines. Subtype-specific responses were tested in organoids, and in vivo efficacy was evaluated using murine and patient-derived xenografts. Clinical activity was measured through radiographic response and progression-free survival in patients.

RESULTS

AOH1996 exhibited dose-dependent cytotoxicity reliant on KRAS(G12D) induction (average half maximal inhibitory concentration: 0.93 μM). It inhibited replication fork progression and induced TRCs by enhancing interactions between RNA Polymerase II and proliferating cell nuclear antigen, causing transcription-dependent DNA damage and transcription shutdown. Organoids with high replication stress were most sensitive (half maximal inhibitory concentration: 406 nM-2 μM). In mouse models, AOH1996 reduced tumor growth, induced tumor-selective DNA damage, and prolonged survival (median 14 vs 21 days, P = .04) without toxicity. Two patients with chemotherapy-refractory PDAC treated with AOH1996 showed up to 49% tumor shrinkage in hepatic metastases.

CONCLUSIONS

AOH1996 safely and effectively targets TRCs in preclinical PDAC models, with initial clinical evidence supporting its potential for treating chemotherapy-refractory PDAC. Further clinical development is warranted.

Simulations probe the role of space in the interplay between drug-sensitive and drug-resistant cancer cells

The interplay between drug-sensitive and drug-resistant cancer cells has been observed to impact cell-to-cell interactions in experimental settings. However, the role that space plays in these interactions remains unclear. In this study, we develop mathematical models to investigate how spatial factors affect cell-to-cell competition between drug-sensitive and drug-resistant cancer cells in silico. We develop two baseline models to study cells from the epithelial FaDu cell line subjected to two drugs, specifically the ATR inhibitor ceralasertib and the PARP inhibitor olaparib, that target DNA damage response pathways. Our baseline models are: (1) a temporally resolved ordinary differential equation (ODE) model, and (2) a spatio-temporally resolved agent-based model (ABM). The models simulate cells in well-mixed and spatially structured cell systems, respectively. The ODE model is calibrated against in vitro data and is thereafter mapped onto the baseline ABM which, in turn, is extended to enable a simulation-based investigation on how spatial factors impact cell-to-cell competition. Simulation results from the extended ABMs demonstrate that the in silico treatment responses are simultaneously affected by: (i) the initial spatial cell configurations, (ii) the initial fraction of drug-resistant cells, (iii) the drugs to which cells express resistance, (iv) drug combinations, (v) drug doses, and (vi) the doubling time of drug-resistant cells compared to the doubling time of drug-sensitive cells. These results reveal that spatial structures of the simulated cancer cells affect both cell-to-cell interactions, and the impact that these interactions have on the ensuing population dynamics. This leads us to suggest that the role that space plays in cell-to-cell interactions should be further investigated and quantified in experimental settings.

Pancreatic Cancer: Pathogenesis and Clinical Studies

Pancreatic cancer (PC) is a highly lethal malignancy, with pancreatic ductal adenocarcinoma (PDAC) being the most common and aggressive subtype, characterized by late diagnosis, aggressive progression, and resistance to conventional therapies. Despite advances in understanding its pathogenesis, including the identification of common genetic mutations (e.g., KRAS, TP53, CDKN2A, SMAD4) and dysregulated signaling pathways (e.g., KRAS-MAPK, PI3K-AKT, and TGF-β pathways), effective therapeutic strategies remain limited. Current treatment modalities including chemotherapy, targeted therapy, immunotherapy, radiotherapy, and emerging therapies such as antibody-drug conjugates (ADCs), chimeric antigen receptor T (CAR-T) cells, oncolytic viruses (OVs), cancer vaccines, and bispecific antibodies (BsAbs), face significant challenges. This review comprehensively summarizes these treatment approaches, emphasizing their mechanisms, limitations, and potential solutions, to overcome these bottlenecks. By integrating recent advancements and outlining critical challenges, this review aims to provide insights into future directions and guide the development of more effective treatment strategies for PC, with a specific focus on PDAC. Our work underscores the urgency of addressing the unmet needs in PDAC therapy and highlights promising areas for innovation in this field.

Angiopoietin-like protein 8 directs DNA damage responses towards apoptosis by stabilizing PARP1-DNA condensates

Upon genotoxic stresses, cells employ various DNA damage responses (DDRs), including DNA damage repair or apoptosis, to safeguard genome integrity. However, the determinants among different DDRs choices are largely unknown. Here, we report angiopoietin-like protein 8 (ANGPTL8), a secreted regulator of lipid metabolism, localizes to the nucleus and acts as a dynamic switch that directs DDRs towards apoptosis rather than DNA repair after genotoxin exposure. ANGPTL8 deficiency alleviates DNA damage and apoptosis in cells exposed to genotoxins, as well as in the liver or kidney of mice injured by hepatic ischemia/reperfusion or cisplatin treatment. Mechanistically, ANGPTL8 physically interacts with Poly (ADP-ribose) polymerase 1 (PARP1), in a PARylation-independent manner, and reduces the fluidity of PARP1-DNA condensates, thereby enhancing the pro-apoptotic accumulation of PARP1 and PAR chains on DNA lesions. However, the transcription of ANGPTL8 is gradually decreased following genotoxin treatment, partly due to downregulation of CCAAT enhancer binding protein alpha (CEBPA), presumably to avoid further cytotoxicity. Together, we provide new insights by which genotoxic stress induced DDRs are channeled to suicidal apoptosis to safeguard genome integrity.

Significance of homologous recombinant deficiency as a biomarker for drug sensitivity in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is a substantial global health concern due to its limited treatment options, especially for oxaliplatin (L-OHP) regimen resistance. This study used organoid-based screening methodologies to evaluate drug responses in CRC while validating the approach with patient-derived CRC organoids and investigating potential biomarkers.

METHODS

Patient-derived organoids were created from CRC surgical specimens, and drug screening were performed. Selected organoids with high and low L-OHP sensitivity underwent next-generation sequencing (NGS), and in vivo experiments using xenotransplantation were used to validate in vitro results. Moreover, the clinical application of homologous recombination deficiency (HRD) as a biomarker was investigated.

RESULTS

Organoid drug screening revealed differences in L-OHP sensitivity among 34 patient-derived CRC organoids, and NGS deemed HRD as a potential biomarker. In vivo experiments validated the correlation between HRD status and L-OHP sensitivity, and clinical data suggested the potential of HRD as a biomarker for recurrence-free survival in patients treated with L-OHP. Additionally, HRD exhibited potential as a biomarker for other platinum agents and poly (ADP-ribose) polymerase inhibitors in CRC.

CONCLUSIONS

The study underscores HRD as a potential biomarker for predicting L-OHP sensitivity, expanding its application to other drugs in CRC. Organoid screening is reliable, providing insights into the intricate association between genetic features and treatment responses.

Benzimidazole scaffold as a potent anticancer agent with different mechanisms of action (2016-2023)

Benzimidazole scaffolds have potent anticancer activity due to their structure similarity to nucleoside. In addition, benzimidazoles could function as hydrogen donors or acceptors and bind to different drug targets that participate in cancer progression. The literature had many anticancer agents containing benzimidazole cores that gained much interest. Provoked by our endless interest in benzimidazoles as anticancer agents, we summarized the successful trials of the benzimidazole scaffolds in this concern. Moreover, we discuss the substantial opportunities in cancer treatment using benzimidazole-based drugs that may direct medicinal chemists for a compelling future design of more active chemotherapeutic agents with potential clinical applications. The uniqueness of this work lies in the highlighted benzimidazole scaffold hybridization with different molecules and benzimidazole-metal complexes, detailed mechanisms of action, and the IC50 of the developed compounds determined by different laboratories after 2015.

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.

The multiple facets of ovarian high grade serous carcinoma: A review on morphological, immunohistochemical and molecular features

High-grade serous ovarian carcinoma (HGSOC) is the most aggressive subtype of epithelial ovarian cancer and a leading cause of mortality among gynecologic malignancies. This review aims to comprehensively analyze the morphological, immunohistochemical, and molecular features of HGSOC, highlighting its pathogenesis and identifying biomarkers with diagnostic, prognostic, and therapeutic significance. Special emphasis is placed on the role of tumor microenvironment (TME) and genomic instability in shaping the tumor's behavior and therapeutic vulnerabilities. Key advancements, such as the identification of TP53 and BRCA mutations, the classification of homologous recombination repair (HRR) deficiencies, and the clinical implications of biomarkers like folate receptor alpha (FRα) and PD-L1 are discussed. These findings reveal actionable insights into targeted therapies, including immune checkpoint inhibitors and PARP inhibitors, which hold promise for improving outcomes in HGSOC. This synthesis of knowledge aims to bridge gaps in understanding HGSOC's multifaceted biology, enhance clinical decision-making, and foster the development of precision therapies.

D-bait: A siDNA for regulation of DNA-protein kinases against DNA damage and its implications in cancer

siDNA fragments, also called Dbait and Pbait, are small DNA oligonucleotides of 30-32 base pairs that cause impairment in DNA repair pathways. Like siRNA and miRNA molecules, which lead to the degradation of mRNA molecules through the Argonaute and Drosha machinery, respectively, Dbait molecules act as false DNA damage signals and trigger and exhaust the DNA repair machinery. In normal cells with no significant DNA damage, the influence of these molecules is negligible. However, in cancer, when there is heavy DNA damage due to replication and anticancer therapies, the cancer cell is heavily dependent on DNA repair proteins to keep the genome intact and limit breaks. This phenomenon primarily occurs during radiation therapy, as significant DNA damage surpasses several DNA repair mechanisms, causing an accumulation of unrepaired lesions and ultimately leading to cell death. This review explores the therapeutic capacity of siDNA molecules in cancer treatment by stimulating the repair mechanisms in cells that depend on DNA repair pathways. For aggressive malignancies such as glioblastoma, prostate cancer, and colorectal cancer, the use of siDNA as a radiosensitizer, especially when combined with other treatments, increases the vulnerability of tumor cells to radiation-induced DNA damage, hence potentially enhancing therapy results.

Targeting NAT10 attenuates homologous recombination via destabilizing DNA:RNA hybrids and overcomes PARP inhibitor resistance in cancers

AIMS

RNA metabolism has been extensively studied in DNA double-strand break (DSB) repair. The RNA acetyltransferase N-acetyltransferase 10 (NAT10)-mediated N4-acetylcytidine (ac4C) modification in DSB repair remains largely elusive. In this study, we aim to decipher the role for ac4C modification by NAT10 in DSB repair in hepatocellular carcinoma (HCC).

METHODS

Laser micro-irradiation and chromatin immunoprecipitation (ChIP) were used to assess the accumulation of ac4C modification and NAT10 at DSB sites. Cryo-electron microscopy (cryo-EM) was used to determine the structures of NAT10 in complex with its inhibitor, remodelin. Hepatocyte-specific deletion of NAT10 mouse models were adopted to detect the effects of NAT10 on HCC progression. Subcutaneous xenograft, human HCC organoid and patient-derived xenograft (PDX) model were exploited to determine the therapy efficiency of the combination of a poly (ADP-ribose) polymerase 1 (PARP1) inhibitor (PARPi) and remodelin.

RESULTS

NAT10 promptly accumulates at DSB sites, where it executes ac4C modification on RNAs at DNA:RNA hybrids dependent on PARP1. This in turn enhances the stability of DNA:RNA hybrids and promotes homologous recombination (HR) repair. The ablation of NAT10 curtails HCC progression. Furthermore, the cryo-EM yields a remarkable 2.9 angstroms resolution structure of NAT10-remodelin, showcasing a C2 symmetric architecture. Remodelin treatment significantly enhanced the sensitivity of HCC cells to a PARPi and targeting NAT10 also restored sensitivity to a PARPi in ovarian and breast cancer cells that had developed resistance.

CONCLUSION

Our study elucidated the mechanism of NAT10-mediated ac4C modification in DSB repair, revealing that targeting NAT10 confers synthetic lethality to PARP inhibition in HCC. Our findings suggest that co-inhibition of NAT10 and PARP1 is an effective novel therapeutic strategy for patients with HCC and have the potential to overcome PARPi resistance.

Regulatory and Catalytic Domains of Poly(ADP-ribose) Polymerases Cross-Complement for DNA-Break-Dependent Allosteric Stimulation of Catalytic Activity

Allosteric regulation is achieved by regulatory domains that sense stimuli and induce conformational changes in the functional domain that performs the catalytic activity of the enzyme. Poly-ADP-ribose polymerases (PARPs) are modular enzymes present across all domains of life including Archaea, Bacteria, and Eukarya. A typical domain architecture of PARPs consists of a conserved C-terminal catalytic domain (CAT) associated with multiple distinct N-terminal sensory and/or regulatory domains which together serve as regulatory region (REG). In this study, we investigated whether REG of different orthologs and paralogs of PARPs from mammals (hPARP1 and hPARP2), plants (atPARP2), and bacteria (haPARP) can assemble with CAT of each other to generate functional chimeric assemblies. We have employed qualitative and quantitative enzyme activity assays along with binding studies to examine these in vitro chimeric assemblies. The cis-complemented REG and CAT of hPARP2 exhibited micromolar binding affinity, suggesting that these domains can interact independent of allosteric ligands. Also, our results show that REG and CAT of PARP proteins can assemble in a functionally active conformation in the presence of DNA implying that REG and CAT are not required to be present on a single polypeptide for catalytic activity stimulation. Interestingly, only CAT of atPARP2 displayed functional complementation with REG of the other studied PARPs. Conversely, REG of hPARP1 and atPARP2 failed to cross-complement CAT of other PARPs while REG of hPARP2 showed robust cross-complementation. Our novel studies on chimeric PARP assemblies can be developed as a powerful synthetic biology tool to interrogate and control their activities in living cells. In addition, by co-engineering non-complementing REG and CAT domains of different PARPs, new functional chimeric PARPs can be developed for selective allosteric ligand-dependent regulation of PARP systems. Furthermore, our study can facilitate the understanding of the coevolution of REG and CAT domains in PARP enzymes.

Inhibition of the metalloprotease ADAM19 as a novel senomorphic strategy to ameliorate gut permeability and senescence markers by modulating senescence-associated secretory phenotype (SASP)

Accumulation of DNA damage can accelerate aging through cellular senescence. Previously, we established a Drosophila model to investigate the effects of radiation-induced DNA damage on the intestine. In this model, we examined irradiation-responsive senescence in the fly intestine. Through an unbiased genome-wide association study (GWAS) utilizing 156 strains from the Drosophila Genetic Reference Panel (DGRP), we identified meltrin (the drosophila orthologue of mammalian ADAM19) as a potential modulator of the senescence-associated secretory phenotype (SASP). Knockdown of meltrin resulted in reduced gut permeability, DNA damage, and expression of the senescence marker β-galactosidase (SA-β-gal) in the fly gut following irradiation. Additionally, inhibition of ADAM19 in mice using batimastat-94 reduced gut permeability and inflammation in the gut. Our findings extend to human primary fibroblasts, where ADAM19 knockdown or pharmacological inhibition decreased expression of specific SASP factors and SA-β-gal. Furthermore, proteomics analysis of the secretory factor of senescent cells revealed a significant decrease in SASP factors associated with the ADAM19 cleavage site. These data suggest that ADAM19 inhibition could represent a novel senomorphic strategy.

Senataxin prevents replicative stress induced by the Myc oncogene

Replicative stress (RS) is emerging as a promising therapeutic target in oncology, yet full exploitation of its potential requires a detailed understanding of the mechanisms and genes involved. Here, we investigated the RNA helicase Senataxin (SETX), an enzyme that resolves RNA-DNA hybrids and R-loops, to address its role in preventing RS by oncogenic Myc. Upon Myc activation, silencing of SETX led to selective engagement of the DNA damage response (DDR) and robust cytotoxicity. Pharmacological dissection of the upstream kinases regulating the DDR uncovered a protective role of the ATR pathway, that once inhibited, boosted SETX driven-DDR. While SETX loss did not lead to a genome-wide increase of R-loops, mechanistic analyses revealed enhanced R-loops localized at DDR-foci and newly replicated genomic loci, compatible with a selective role of SETX in resolving RNA-DNA hybrids to alleviate Myc-induced RS. Genome-wide mapping of DNA double-strand breaks confirmed that SETX silencing exacerbated DNA damage at transcription-replication conflict (TRC) regions at early replicated sites. We propose that SETX prevents Myc-induced TRCs by resolving transcription-associated R-loops that encounter the replisome. The identification of SETX as a genetic liability of oncogenic Myc opens up new therapeutic options against aggressive Myc-driven tumors.

Investigating synthetic lethality and PARP inhibitor resistance in pancreatic cancer through enantiomer differential activity

The RAD51-BRCA2 interaction is central to DNA repair through homologous recombination. Emerging evidence indicates RAD51 overexpression and its correlation with chemoresistance in various cancers, suggesting RAD51-BRCA2 inhibition as a compelling avenue for intervention. We previously showed that combining olaparib (a PARP inhibitor (PARPi)) with RS-35d (a BRCA2-RAD51 inhibitor) was efficient in killing pancreatic ductal adenocarcinoma (PDAC) cells. However, RS-35d impaired cell viability even when administered alone, suggesting potential off-target effects. Here, through multiple, integrated orthogonal biological approaches in different 2D and 3D PDAC cultures, we characterised RS-35d enantiomers, in terms of mode of action and single contributions. By differentially inhibiting both RAD51-BRCA2 interaction and sensor kinases ATM, ATR and DNA-PK, RS-35d enantiomers exhibit a 'within-pathway synthetic lethality' profile. To the best of our knowledge, this is the first reported proof-of-concept single small molecule capable of demonstrating this built-in synergism. In addition, RS-35d effect on BRCA2-mutated, olaparib-resistant PDAC cells suggests that this compound may be effective as an anticancer agent possibly capable of overcoming PARPi resistance. Our results demonstrate the potential of synthetic lethality, with its diversified applications, to propose new and concrete opportunities to effectively kill cancer cells while limiting side effects and potentially overcoming emerging drug resistance.

Establishment and genomic profiling of cholangiocarcinoma cells with functional characterization

Cholangiocarcinoma (CCA) is a highly lethal hepatobiliary malignancy, with prognosis is influenced by anatomical subtypes and etiological factors. This study successfully established three CCA cell lines: KKU-097, KKU-466, and KKU-610, from the primary tumors of patients in liver fluke-endemic areas. These cells represent the perihilar CCA (pCCA) and intrahepatic CCA (iCCA) subtypes. Comprehensive analyses, including histopathology, molecular profiling, biomarkers, cancer phenotype characterization, and drug sensitivity testing with standard chemotherapeutics, were conducted. Whole-exome sequencing was performed to explore genetic alterations. All three cell lines exhibited adherent growth with an epithelial morphology and positive expression of the bile duct epithelial markers CK-7 and CK-19. Cytogenetic analysis revealed highly complex hypertriploid karyotypes with multiple chromosomal aberrations. Among the cell lines, KKU-610 demonstrated higher growth and invasion rates, whereas KKU-466 and KKU-097 cells exhibited less aggressive phenotypes. Drug sensitivity testing demonstrated relative resistance to gemcitabine as a monotherapy and in combination with cisplatin in all three cells. Genomic profiling identified targetable mutations, highlighting these new cell lines as valuable models for investigating the pathogenesis of CCA and evaluating therapeutic strategies.

Replication stress promotes cellular transformation in Drosophila epithelium

The accurate control of DNA replication is crucial for the maintenance of genomic stability and cell viability. In this study, we explore the consequences of depleting the replicative DNA Polymerase α (POLA) in the wing disc of Drosophila melanogaster. Our findings reveal that reduced POLA activity induces DNA replication stress and activates the replication checkpoint in vivo. Consistent with this, we demonstrate that dATR, a key component in DNA replication checkpoint signaling, is essential for the maintenance of tissue integrity under conditions of compromised POLA activity. We show that cells within the wing disc exhibiting reduced POLA activity arrest in the G2 phase and undergo p53-dependent apoptosis. We also reveal a critical role for DNA Ligase 4 in sustaining cell viability when POLA function is impaired. Most notably, we report the appearance of oncogenic traits in wing disc cells with diminished POLA activity when apoptosis is suppressed. In this context, the overexpression of the oncogene cdc25/string enhances the oncogenic phenotype. These results indicate that a combination of oncogenic activation, replication stress, and suppression of apoptosis is sufficient to promote the emergence of hallmarks of tumorigenesis, highlighting major implications for cancer development in humans.

4(3H)-Quinazolinone: A Natural Scaffold for Drug and Agrochemical Discovery

4(3H)-quinazolinone is a functional scaffold that exists widely both in natural products and synthetic organic compounds. Its drug-like derivatives have been extensively synthesized with interesting biological features including anticancer, anti-inflammatory, antiviral, antimalarial, antibacterial, antifungal, and herbicidal, etc. In this review, we highlight the medicinal and agrochemical versatility of the 4(3H)-quinazolinone scaffold according to the studies published in the past six years (2019-2024), and comprehensively give a summary of the target recognition, structure-activity relationship, and mechanism of its analogs. The present review is expected to provide valuable guidance for discovering novel lead compounds containing 4(3H)-quinazolinone moiety in both drug and agrochemical research.

Revolutionizing prognosis: Introducing cell death index (CDI) as a powerful prognostic tool for CSCC patients

BACKGROUND

Cervical squamous cell carcinoma (CSCC) threatens the body health of women worldwide. This study aimed to foster a new concept of prognostic indicator named cell death index (CDI).

METHODS

RNA-seq and scRNA-seq datasets were downloaded from the GEO and TCGA database as the training and validation cohorts. Programmed cell death (PCD)-related gene signatures were obtained from published research. The construction of prognostic model was performed based on CDI value. Patients with CSCC were divided into high- and low-CDI groups. We explored the differences in overall survival time, immune infiltration, mutation status, and drug sensitivity between high and low CDI groups by R software.

RESULTS

We constructed prognostic model to calculate the CDI value with 23 genes. Patients with high CDI have shorter survival time than those with low CDI. CDI was considered a risk factor compared to other characteristics. The nomogram model estimated overall survival (OS) at 1, 3, and 6 years, with age, Stage, and CDI, indicating the accuracy of the model in predicting 1-, 3-, and 6-year survival rates. CDI values were negatively correlated with most immune checkpoint genes. We measured the significant drug sensitivity of Mitoxantrone, Sabutoclax, Sepantronium bromide, Topotecan, BI-2536, and BMS-754807 between high- and low-CDI groups with significant correlation.

CONCLUSION

This investigation constructed a novel effective prognostic indicator of CDI in patients with CSCC and identified potential genes associated with cell death that could be targeted for prognosis and treatment of CSCC.

Computational Analysis of Non-synonymous SNPs in ATM Kinase: Structural Insights, Functional Implications, and Inhibitor Discovery

Ataxia telangiectasia-mutated (ATM) protein kinase, a key player in cellular integrity regulation, is known for its role in DNA damage response. This study investigates the broader impact of ATM on cellular processes and potential clinical manifestations arising from mutations, aiming to expand our understanding of ATM's diverse functions beyond conventional roles. The research employs a comprehensive set of computational techniques for a thorough analysis of ATM mutations. The mutation data are curated from dbSNP and HuVarBase databases. A meticulous assessment is conducted, considering factors such as deleterious effects, protein stability, oncogenic potential, and biophysical characteristics of the identified mutations. Conservation analysis, utilizing diverse computational tools, provides insights into the evolutionary significance of these mutations. Molecular docking and dynamic simulation analyses are carried out for selected mutations, investigating their interactions with Y2080D, AZD0156, and quercetin inhibitors to gauge potential therapeutic implications. Among the 419 mutations scrutinized, five (V1913C, Y2080D, L2656P, C2770G, and C2930G) are identified as both disease causing and protein destabilizing. The study reveals the oncogenic potential of these mutations, supported by findings from the COSMIC database. Notably, Y2080D is associated with haematopoietic and lymphoid cancers, while C2770G shows a correlation with squamous cell carcinomas. Molecular docking and dynamic simulation analyses highlight strong binding affinities of quercetin for Y2080D and AZD0156 for C2770G, suggesting potential therapeutic options. In summary, this computational analysis provides a comprehensive understanding of ATM mutations, revealing their potential implications in cellular integrity and cancer development. The study underscores the significance of Y2080D and C2770G mutations, offering valuable insights for future precision medicine targeting-specific ATM. Despite informative computational analyses, a significant research gap exists, necessitating essential in vitro and in vivo studies to validate the predicted effects of ATM mutations on protein structure and function.

Pathological modulation of genome maintenance by cancer/testes antigens (CTAs)

The Cancer Testis Antigens (CTAs) are a group of germ cell proteins that are absent from normal somatic cells yet aberrantly expressed in many cancer cells. When mis-expressed in cancer cells, many CTAs promote tumorigenic characteristics including genome instability, DNA damage tolerance and therapy resistance. Here we highlight some of the CTAs for which their roles in genome maintenance in cancer cells are well established. We consider three broad CTA categories: (1) Melanoma Antigens (MAGEs) (2) Mitotic CTAs and (3) CTAs with roles in meiotic homologous recombination. Many cancer cells rely on CTAs to tolerate intrinsic and therapy-induced genotoxic stress. Therefore, CTAs represent molecular vulnerabilities of cancer cells and may provide opportunities for therapy. Owing to their high-level expression in tumors and absence from normal somatic cells, CTA-directed therapies could have a high level of specificity and would likely be devoid of side-effect toxicity.

The Tight Relationship Between the Tumoral Microenvironment and Radium-223

Radium-223 (223Ra) was the first radioactive isotope approved for treating castration-resistant prostate cancer (CRPC) with symptomatic bone metastases without visceral metastatic disease. To better understand the action of 223Ra, its role in the tumor microenvironment represents a crucial aspect. A literature search was conducted using the PubMed/MEDLINE database and studies regarding the relationship between 223Ra and the tumoral microenvironment were considered. The tumoral microenvironment is a complex setting in which complex interactions between cells and molecules occur. Radium-223, as an alpha-emitter, induces double-stranded DNA breaks; to potentiate this effect, it could be used in patients with genetic instability but also in combination with therapies which inhibit DNA repair, modulate the immune response, or control tumor growth. In conclusion, a few studies have taken into consideration the tumoral microenvironment in association with 223Ra. However, its understanding is a priority to better comprehend how to effectively exploit 223Ra and its action mechanism.

Enhanced radiotherapy susceptibility in NSCLC through palbociclib-mediated PP5 inhibition

Radiotherapy remains a cornerstone in the treatment of non-small cell lung cancer (NSCLC), yet radioresistance often limits its efficacy. Identifying molecular targets that enhance radiosensitivity is crucial to offering both curative and palliative benefits for patients with NSCLC. Utilizing bioinformatics analysis, our study revealed significantly higher expression of PP5 in NSCLC tissues compared to normal tissues. Kaplan-Meier survival analysis also showed that high PP5 expression correlates with poorer overall survival, particularly in patients undergoing radiotherapy, suggesting a role for PP5 in radioresistance. We further demonstrated that PP5 is a critical target of palbociclib, distinct from CDK4/6, influencing radiosensitivity in NSCLC. Palbociclib enhanced radiotherapy susceptibility by inducing sustained DNA damage and AMPK activation. The subsequent cellular event is apoptosis rather than autophagy. Furthermore, the enhanced efficacy of combination therapy was counteracted by an AMPK inhibitor and PP5 activator, underscoring the importance of these pathways in mediating the response. Our findings provide compelling evidence that targeting PP5 can significantly enhance the therapeutic outcomes of radiotherapy in NSCLC. This research offers valuable insights into new combination therapy strategies, highlighting the potential of PP5 as a novel therapeutic target to overcome radioresistance.

Real-World Impact of Olaparib Exposure in Advanced Pancreatic Cancer Patients Harboring Germline BRCA1-2 Pathogenic Variants

INTRODUCTION

Pancreatic cancer arising in the context of BRCA predisposition may benefit from poly(ADP-ribose) polymerase inhibitors. We analyzed real-world data on the impact of olaparib on survival in metastatic pancreatic cancer patients harboring germline BRCA mutations in Italy, where olaparib is not reimbursed for this indication.

METHODS

Clinico/pathological data of pancreatic cancer patients with documented BRCA1-2 germline pathogenic variants who had received first-line chemotherapy for metastatic disease were collected from 23 Italian oncology departments and the impact of olaparib exposure on overall survival (OS) was analyzed.

RESULTS

Of 114, 53 BRCA-mutant pancreatic cancer patients had received olaparib for metastatic disease. OS was significantly longer in patients who were exposed to olaparib (hazard ratio [HR] 0.568, 95% confidence interval [CI] 0.351-0.918, log-rank p = 0.02) in any setting/line of treatment; similar results were obtained for patients who received olaparib as maintenance treatment (in any line of treatment), patients who had stage IV disease at diagnosis, and patients who did not experience progressive disease as their best response to first-line chemotherapy. Exposure to olaparib in the first-line maintenance setting after platinum-based chemotherapy, however, did not significantly impact survival. At multivariate analysis, CA19.9 levels at diagnosis and response to first-line chemotherapy were independently prognostic; however, when response to chemotherapy was excluded, any exposure to olaparib was a significant independent predictor of longer OS, together with CA19.9 levels.

CONCLUSION

The real-world data presented here support the use of olaparib for metastatic disease in germline BRCA-mutant pancreatic cancer patients, as it may significantly prolong survival.